diff --git a/project/json/nmdc_submission_schema.json b/project/json/nmdc_submission_schema.json new file mode 100644 index 00000000..21f95fcf --- /dev/null +++ b/project/json/nmdc_submission_schema.json @@ -0,0 +1,133911 @@ +{ + "name": "nmdc_submission_schema", + "description": "Schema for creating Data Harmonizer interfaces for biosamples based on MIxS and other standards", + "id": "https://example.com/nmdc_submission_schema", + "version": "0.0.0", + "prefixes": { + "UO": { + "prefix_prefix": "UO", + "prefix_reference": "http://purl.obolibrary.org/obo/UO_" + }, + "qud": { + "prefix_prefix": "qud", + "prefix_reference": "http://qudt.org/1.1/schema/qudt#" + }, + "xsd": { + "prefix_prefix": "xsd", + "prefix_reference": "http://www.w3.org/2001/XMLSchema#" + }, + "nmdc_sub_schema": { + "prefix_prefix": "nmdc_sub_schema", + "prefix_reference": "https://example.com/nmdc_sub_schema/" + }, + "linkml": { + "prefix_prefix": "linkml", + "prefix_reference": "https://w3id.org/linkml/" + }, + "shex": { + "prefix_prefix": "shex", + "prefix_reference": "http://www.w3.org/ns/shex#" + }, + "schema": { + "prefix_prefix": "schema", + "prefix_reference": "http://schema.org/" + }, + "CATH": { + "prefix_prefix": "CATH", + "prefix_reference": "https://bioregistry.io/cath:" + }, + "CHEBI": { + "prefix_prefix": "CHEBI", + "prefix_reference": "http://purl.obolibrary.org/obo/CHEBI_" + }, + "CHEMBL.COMPOUND": { + "prefix_prefix": "CHEMBL.COMPOUND", + "prefix_reference": "https://bioregistry.io/chembl.compound:" + }, + "CHMO": { + "prefix_prefix": "CHMO", + "prefix_reference": "http://purl.obolibrary.org/obo/CHMO_" + }, + "Contaminant": { + "prefix_prefix": "Contaminant", + "prefix_reference": "http://example.org/contaminant/" + }, + "DRUGBANK": { + "prefix_prefix": "DRUGBANK", + "prefix_reference": "https://bioregistry.io/drugbank:" + }, + "EC": { + "prefix_prefix": "EC", + "prefix_reference": "https://bioregistry.io/eccode:" + }, + "EFO": { + "prefix_prefix": "EFO", + "prefix_reference": "http://www.ebi.ac.uk/efo/" + }, + "EGGNOG": { + "prefix_prefix": "EGGNOG", + "prefix_reference": "https://bioregistry.io/eggnog:" + }, + "ENVO": { + "prefix_prefix": "ENVO", + "prefix_reference": "http://purl.obolibrary.org/obo/ENVO_" + }, + "FBcv": { + "prefix_prefix": "FBcv", + "prefix_reference": "http://purl.obolibrary.org/obo/FBcv_" + }, + "FMA": { + "prefix_prefix": "FMA", + "prefix_reference": "http://purl.obolibrary.org/obo/FMA_" + }, + "GO": { + "prefix_prefix": "GO", + "prefix_reference": "http://purl.obolibrary.org/obo/GO_" + }, + "HMDB": { + "prefix_prefix": "HMDB", + "prefix_reference": "https://bioregistry.io/hmdb:" + }, + "ISA": { + "prefix_prefix": "ISA", + "prefix_reference": "http://example.org/isa/" + }, + "KEGG.ORTHOLOGY": { + "prefix_prefix": "KEGG.ORTHOLOGY", + "prefix_reference": "https://bioregistry.io/kegg.orthology:" + }, + "MASSIVE": { + "prefix_prefix": "MASSIVE", + "prefix_reference": "https://bioregistry.io/reference/massive:" + }, + "MESH": { + "prefix_prefix": "MESH", + "prefix_reference": "https://bioregistry.io/mesh:" + }, + "MS": { + "prefix_prefix": "MS", + "prefix_reference": "http://purl.obolibrary.org/obo/MS_" + }, + "MetaNetX": { + "prefix_prefix": "MetaNetX", + "prefix_reference": "http://example.org/metanetx/" + }, + "NCBITaxon": { + "prefix_prefix": "NCBITaxon", + "prefix_reference": "http://purl.obolibrary.org/obo/NCBITaxon_" + }, + "NCBI": { + "prefix_prefix": "NCBI", + "prefix_reference": "http://example.com/ncbitaxon/" + }, + "NCIT": { + "prefix_prefix": "NCIT", + "prefix_reference": "http://purl.obolibrary.org/obo/NCIT_" + }, + "OBI": { + "prefix_prefix": "OBI", + "prefix_reference": "http://purl.obolibrary.org/obo/OBI_" + }, + "ORCID": { + "prefix_prefix": "ORCID", + "prefix_reference": "https://orcid.org/" + }, + "PANTHER.FAMILY": { + "prefix_prefix": "PANTHER.FAMILY", + "prefix_reference": "https://bioregistry.io/panther.family:" + }, + "PATO": { + "prefix_prefix": "PATO", + "prefix_reference": "http://purl.obolibrary.org/obo/PATO_" + }, + "PFAM": { + "prefix_prefix": "PFAM", + "prefix_reference": "https://bioregistry.io/pfam:" + }, + "PFAM.CLAN": { + "prefix_prefix": "PFAM.CLAN", + "prefix_reference": "https://bioregistry.io/pfam.clan:" + }, + "PO": { + "prefix_prefix": "PO", + "prefix_reference": "http://purl.obolibrary.org/obo/PO_" + }, + "PR": { + "prefix_prefix": "PR", + "prefix_reference": "http://purl.obolibrary.org/obo/PR_" + }, + "PUBCHEM.COMPOUND": { + "prefix_prefix": "PUBCHEM.COMPOUND", + "prefix_reference": "https://bioregistry.io/pubchem.compound:" + }, + "RO": { + "prefix_prefix": "RO", + "prefix_reference": "http://purl.obolibrary.org/obo/RO_" + }, + "RetroRules": { + "prefix_prefix": "RetroRules", + "prefix_reference": "http://example.org/retrorules/" + }, + "SO": { + "prefix_prefix": "SO", + "prefix_reference": "http://purl.obolibrary.org/obo/SO_" + }, + "SUPFAM": { + "prefix_prefix": "SUPFAM", + "prefix_reference": "https://bioregistry.io/supfam:" + }, + "TIGRFAM": { + "prefix_prefix": "TIGRFAM", + "prefix_reference": "https://bioregistry.io/tigrfam:" + }, + "UBERON": { + "prefix_prefix": "UBERON", + "prefix_reference": "http://purl.obolibrary.org/obo/UBERON_" + }, + "bioproject": { + "prefix_prefix": "bioproject", + "prefix_reference": "https://identifiers.org/bioproject:" + }, + "biosample": { + "prefix_prefix": "biosample", + "prefix_reference": "https://bioregistry.io/biosample:" + }, + "cas": { + "prefix_prefix": "cas", + "prefix_reference": "https://bioregistry.io/cas:" + }, + "doi": { + "prefix_prefix": "doi", + "prefix_reference": "https://bioregistry.io/doi:" + }, + "edam.data": { + "prefix_prefix": "edam.data", + "prefix_reference": "http://edamontology.org/data_" + }, + "emsl.project": { + "prefix_prefix": "emsl.project", + "prefix_reference": "https://bioregistry.io/emsl.project:" + }, + "emsl": { + "prefix_prefix": "emsl", + "prefix_reference": "http://example.org/emsl_in_mongodb/" + }, + "emsl_uuid_like": { + "prefix_prefix": "emsl_uuid_like", + "prefix_reference": "http://example.org/emsl_uuid_like/" + }, + "generic": { + "prefix_prefix": "generic", + "prefix_reference": "https://example.org/generic/" + }, + "gnps.task": { + "prefix_prefix": "gnps.task", + "prefix_reference": "https://bioregistry.io/gnps.task:" + }, + "gtpo": { + "prefix_prefix": "gtpo", + "prefix_reference": "http://example.org/gtpo/" + }, + "igsn": { + "prefix_prefix": "igsn", + "prefix_reference": "https://app.geosamples.org/sample/igsn/" + }, + "img.taxon": { + "prefix_prefix": "img.taxon", + "prefix_reference": "https://bioregistry.io/img.taxon:" + }, + "jgi.analysis": { + "prefix_prefix": "jgi.analysis", + "prefix_reference": "https://data.jgi.doe.gov/search?q=" + }, + "jgi.proposal": { + "prefix_prefix": "jgi.proposal", + "prefix_reference": "https://bioregistry.io/jgi.proposal:" + }, + "jgi": { + "prefix_prefix": "jgi", + "prefix_reference": "http://example.org/jgi/" + }, + "kegg": { + "prefix_prefix": "kegg", + "prefix_reference": "https://bioregistry.io/kegg:" + }, + "KEGG.MODULE": { + "prefix_prefix": "KEGG.MODULE", + "prefix_reference": "https://bioregistry.io/kegg.module:" + }, + "mgnify.proj": { + "prefix_prefix": "mgnify.proj", + "prefix_reference": "https://bioregistry.io/mgnify.proj:" + }, + "my_emsl": { + "prefix_prefix": "my_emsl", + "prefix_reference": "https://release.my.emsl.pnnl.gov/released_data/" + }, + "neon.identifier": { + "prefix_prefix": "neon.identifier", + "prefix_reference": "http://example.org/neon/identifier/" + }, + "neon.schema": { + "prefix_prefix": "neon.schema", + "prefix_reference": "http://example.org/neon/schema/" + }, + "nmdc": { + "prefix_prefix": "nmdc", + "prefix_reference": "https://w3id.org/nmdc/" + }, + "prov": { + "prefix_prefix": "prov", + "prefix_reference": "http://www.w3.org/ns/prov#" + }, + "rdf": { + "prefix_prefix": "rdf", + "prefix_reference": "http://www.w3.org/1999/02/22-rdf-syntax-ns#" + }, + "rdfs": { + "prefix_prefix": "rdfs", + "prefix_reference": "http://www.w3.org/2000/01/rdf-schema#" + }, + "skos": { + "prefix_prefix": "skos", + "prefix_reference": "http://www.w3.org/2004/02/skos/core#" + }, + "wikidata": { + "prefix_prefix": "wikidata", + "prefix_reference": "http://www.wikidata.org/entity/" + }, + "KEGG.COMPOUND": { + "prefix_prefix": "KEGG.COMPOUND", + "prefix_reference": "https://bioregistry.io/kegg.compound:" + }, + "SIO": { + "prefix_prefix": "SIO", + "prefix_reference": "http://semanticscience.org/resource/SIO_" + }, + "UniProtKB": { + "prefix_prefix": "UniProtKB", + "prefix_reference": "https://bioregistry.io/uniprot:" + }, + "biolink": { + "prefix_prefix": "biolink", + "prefix_reference": "https://w3id.org/biolink/vocab/" + }, + "dcterms": { + "prefix_prefix": "dcterms", + "prefix_reference": "http://purl.org/dc/terms/" + }, + "wgs84": { + "prefix_prefix": "wgs84", + "prefix_reference": "http://www.w3.org/2003/01/geo/wgs84_pos#" + }, + "MISO": { + "prefix_prefix": "MISO", + "prefix_reference": "http://purl.obolibrary.org/obo/MISO_" + }, + "COG": { + "prefix_prefix": "COG", + "prefix_reference": "https://bioregistry.io/cog:" + }, + "KEGG.REACTION": { + "prefix_prefix": "KEGG.REACTION", + "prefix_reference": "https://bioregistry.io/kegg.reaction:" + }, + "KEGG_PATHWAY": { + "prefix_prefix": "KEGG_PATHWAY", + "prefix_reference": "https://bioregistry.io/kegg.pathway:" + }, + "MetaCyc": { + "prefix_prefix": "MetaCyc", + "prefix_reference": "https://bioregistry.io/metacyc.compound:" + }, + "RHEA": { + "prefix_prefix": "RHEA", + "prefix_reference": "https://bioregistry.io/rhea:" + }, + "SEED": { + "prefix_prefix": "SEED", + "prefix_reference": "https://bioregistry.io/seed:" + }, + "gold": { + "prefix_prefix": "gold", + "prefix_reference": "https://bioregistry.io/gold:" + }, + "MIXS": { + "prefix_prefix": "MIXS", + "prefix_reference": "https://w3id.org/mixs/" + }, + "MIXS_yaml": { + "prefix_prefix": "MIXS_yaml", + "prefix_reference": "https://raw.githubusercontent.com/microbiomedata/mixs/main/model/schema/" + } + }, + "default_prefix": "nmdc_sub_schema", + "default_range": "string", + "subsets": { + "mixs_environmental_triad": { + "name": "mixs_environmental_triad", + "title": "MIxS Environmental Triad", + "from_schema": "https://example.com/nmdc_submission_schema" + }, + "mixs extension": { + "name": "mixs extension", + "from_schema": "https://example.com/nmdc_submission_schema" + }, + "checklist": { + "name": "checklist", + "description": "A MIxS checklist. These can be combined with packages", + "from_schema": "https://example.com/nmdc_submission_schema" + }, + "package": { + "name": "package", + "description": "A MIxS package. These can be combined with checklists", + "from_schema": "https://example.com/nmdc_submission_schema" + }, + "checklist_package_combination": { + "name": "checklist_package_combination", + "description": "A combination of a checklist and a package", + "from_schema": "https://example.com/nmdc_submission_schema" + }, + "data object subset": { + "name": "data object subset", + "description": "Subset consisting of the data objects that either inputs or outputs of processes or workflows.", + "from_schema": "https://example.com/nmdc_submission_schema" + }, + "data_portal_subset": { + "name": "data_portal_subset", + "description": "Subset consisting of entities that Kitware/nmdc-server use to populate the data portal.", + "comments": [ + "Schema authors are responsible for alerting and supporting Kitware and nmdc-server authors about changes they will have to make if entities labeled with data_portal_subset are modified.", + "Assignment of the data_portal_subset is incomplete in the schema." + ], + "from_schema": "https://example.com/nmdc_submission_schema" + }, + "environment": { + "name": "environment", + "from_schema": "https://example.com/nmdc_submission_schema" + }, + "investigation": { + "name": "investigation", + "from_schema": "https://example.com/nmdc_submission_schema" + }, + "nucleic acid sequence source": { + "name": "nucleic acid sequence source", + "from_schema": "https://example.com/nmdc_submission_schema" + }, + "proteases": { + "name": "proteases", + "from_schema": "https://example.com/nmdc_submission_schema" + }, + "sample subset": { + "name": "sample subset", + "description": "Subset consisting of entities linked to the processing of samples. Currently, this subset consists of study, omics process, and biosample.", + "from_schema": "https://example.com/nmdc_submission_schema" + }, + "sequencing": { + "name": "sequencing", + "from_schema": "https://example.com/nmdc_submission_schema" + }, + "workflow subset": { + "name": "workflow subset", + "description": "Subset consisting of just the workflow execution activities", + "from_schema": "https://example.com/nmdc_submission_schema" + } + }, + "types": { + "unit": { + "name": "unit", + "description": "a string representation of a unit", + "notes": [ + "why isn't this picked up from the nmdc.yaml import?" + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "mappings": [ + "qud:Unit", + "UO:0000000" + ], + "base": "str", + "uri": "xsd:string" + }, + "decimal degree": { + "name": "decimal degree", + "description": "a float representation of a degree of rotation", + "from_schema": "https://example.com/nmdc_submission_schema", + "base": "float", + "uri": "xsd:decimal" + }, + "language code": { + "name": "language code", + "description": "a string representation of a language", + "from_schema": "https://example.com/nmdc_submission_schema", + "base": "str", + "uri": "xsd:language" + }, + "decimal": { + "name": "decimal", + "description": "A real number with arbitrary precision that conforms to the xsd:decimal specification", + "notes": [ + "If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"decimal\"." + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "broad_mappings": [ + "schema:Number" + ], + "base": "Decimal", + "uri": "xsd:decimal" + }, + "double": { + "name": "double", + "description": "A real number that conforms to the xsd:double specification", + "notes": [ + "If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"double\"." + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "close_mappings": [ + "schema:Float" + ], + "base": "float", + "uri": "xsd:double" + }, + "integer": { + "name": "integer", + "description": "An integer", + "notes": [ + "If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"integer\"." + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "exact_mappings": [ + "schema:Integer" + ], + "base": "int", + "uri": "xsd:integer" + }, + "string": { + "name": "string", + "description": "A character string", + "notes": [ + "In RDF serializations, a slot with range of string is treated as a literal or type xsd:string. If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"string\"." + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "exact_mappings": [ + "schema:Text" + ], + "base": "str", + "uri": "xsd:string" + }, + "float": { + "name": "float", + "description": "A real number that conforms to the xsd:float specification", + "notes": [ + "If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"float\"." + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "exact_mappings": [ + "schema:Float" + ], + "base": "float", + "uri": "xsd:float" + }, + "uriorcurie": { + "name": "uriorcurie", + "description": "a URI or a CURIE", + "notes": [ + "If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"uriorcurie\"." + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "base": "URIorCURIE", + "uri": "xsd:anyURI", + "repr": "str" + }, + "boolean": { + "name": "boolean", + "description": "A binary (true or false) value", + "notes": [ + "If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"boolean\"." + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "exact_mappings": [ + "schema:Boolean" + ], + "base": "Bool", + "uri": "xsd:boolean", + "repr": "bool" + }, + "time": { + "name": "time", + "description": "A time object represents a (local) time of day, independent of any particular day", + "notes": [ + "URI is dateTime because OWL reasoners do not work with straight date or time", + "If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"time\"." + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "exact_mappings": [ + "schema:Time" + ], + "base": "XSDTime", + "uri": "xsd:time", + "repr": "str" + }, + "date": { + "name": "date", + "description": "a date (year, month and day) in an idealized calendar", + "notes": [ + "URI is dateTime because OWL reasoners don't work with straight date or time", + "If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"date\"." + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "exact_mappings": [ + "schema:Date" + ], + "base": "XSDDate", + "uri": "xsd:date", + "repr": "str" + }, + "datetime": { + "name": "datetime", + "description": "The combination of a date and time", + "notes": [ + "If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"datetime\"." + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "exact_mappings": [ + "schema:DateTime" + ], + "base": "XSDDateTime", + "uri": "xsd:dateTime", + "repr": "str" + }, + "date_or_datetime": { + "name": "date_or_datetime", + "description": "Either a date or a datetime", + "notes": [ + "If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"date_or_datetime\"." + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "base": "str", + "uri": "linkml:DateOrDatetime", + "repr": "str" + }, + "curie": { + "name": "curie", + "conforms_to": "https://www.w3.org/TR/curie/", + "description": "a compact URI", + "notes": [ + "If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"curie\"." + ], + "comments": [ + "in RDF serializations this MUST be expanded to a URI", + "in non-RDF serializations MAY be serialized as the compact representation" + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "base": "Curie", + "uri": "xsd:string", + "repr": "str" + }, + "uri": { + "name": "uri", + "conforms_to": "https://www.ietf.org/rfc/rfc3987.txt", + "description": "a complete URI", + "notes": [ + "If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"uri\"." + ], + "comments": [ + "in RDF serializations a slot with range of uri is treated as a literal or type xsd:anyURI unless it is an identifier or a reference to an identifier, in which case it is translated directly to a node" + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "close_mappings": [ + "schema:URL" + ], + "base": "URI", + "uri": "xsd:anyURI", + "repr": "str" + }, + "ncname": { + "name": "ncname", + "description": "Prefix part of CURIE", + "notes": [ + "If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"ncname\"." + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "base": "NCName", + "uri": "xsd:string", + "repr": "str" + }, + "objectidentifier": { + "name": "objectidentifier", + "description": "A URI or CURIE that represents an object in the model.", + "notes": [ + "If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"objectidentifier\"." + ], + "comments": [ + "Used for inheritance and type checking" + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "base": "ElementIdentifier", + "uri": "shex:iri", + "repr": "str" + }, + "nodeidentifier": { + "name": "nodeidentifier", + "description": "A URI, CURIE or BNODE that represents a node in a model.", + "notes": [ + "If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"nodeidentifier\"." + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "base": "NodeIdentifier", + "uri": "shex:nonLiteral", + "repr": "str" + }, + "jsonpointer": { + "name": "jsonpointer", + "conforms_to": "https://datatracker.ietf.org/doc/html/rfc6901", + "description": "A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form.", + "notes": [ + "If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"jsonpointer\"." + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "base": "str", + "uri": "xsd:string", + "repr": "str" + }, + "jsonpath": { + "name": "jsonpath", + "conforms_to": "https://www.ietf.org/archive/id/draft-goessner-dispatch-jsonpath-00.html", + "description": "A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form.", + "notes": [ + "If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"jsonpath\"." + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "base": "str", + "uri": "xsd:string", + "repr": "str" + }, + "sparqlpath": { + "name": "sparqlpath", + "conforms_to": "https://www.w3.org/TR/sparql11-query/#propertypaths", + "description": "A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF.", + "notes": [ + "If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"sparqlpath\"." + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "base": "str", + "uri": "xsd:string", + "repr": "str" + } + }, + "enums": { + "BioticRelationshipEnum": { + "name": "BioticRelationshipEnum", + "from_schema": "https://example.com/nmdc_submission_schema", + "permissible_values": { + "commensalism": { + "text": "commensalism", + "annotations": { + "sntc_name": { + "tag": "sntc_name", + "value": "samp_biotic_relationship" + } + }, + "notes": [ + "biotic_relationship_enum: free living", + "parasitism", + "commensalism", + "symbiotic", + "mutualism" + ], + "see_also": [ + "https://genomicsstandardsconsortium.github.io/mixs/biotic_relationship_enum/" + ] + }, + "free living": { + "text": "free living" + }, + "mutualism": { + "text": "mutualism" + }, + "parasitism": { + "text": "parasitism" + }, + "symbiotic": { + "text": "symbiotic" + } + } + }, + "JgiContTypeEnum": { + "name": "JgiContTypeEnum", + "from_schema": "https://example.com/nmdc_submission_schema", + "permissible_values": { + "plate": { + "text": "plate" + }, + "tube": { + "text": "tube" + } + } + }, + "DnaSampleFormatEnum": { + "name": "DnaSampleFormatEnum", + "from_schema": "https://example.com/nmdc_submission_schema", + "permissible_values": { + "10 mM Tris-HCl": { + "text": "10 mM Tris-HCl" + }, + "DNAStable": { + "text": "DNAStable" + }, + "Ethanol": { + "text": "Ethanol" + }, + "Low EDTA TE": { + "text": "Low EDTA TE" + }, + "MDA reaction buffer": { + "text": "MDA reaction buffer" + }, + "PBS": { + "text": "PBS" + }, + "Pellet": { + "text": "Pellet" + }, + "RNAStable": { + "text": "RNAStable" + }, + "TE": { + "text": "TE" + }, + "Water": { + "text": "Water" + } + } + }, + "EnvPackageEnum": { + "name": "EnvPackageEnum", + "from_schema": "https://example.com/nmdc_submission_schema", + "permissible_values": { + "soil": { + "text": "soil", + "notes": [ + "I don't think this is a MIxS term anymore, so it make sense to define it here" + ] + } + } + }, + "GrowthFacilEnum": { + "name": "GrowthFacilEnum", + "from_schema": "https://example.com/nmdc_submission_schema", + "permissible_values": { + "experimental_garden": { + "text": "experimental_garden", + "annotations": { + "sntc_name": { + "tag": "sntc_name", + "value": "growth_facility" + } + }, + "notes": [ + "string range according to MIxS" + ], + "see_also": [ + "https://genomicsstandardsconsortium.github.io/mixs/growth_facil/" + ] + }, + "field": { + "text": "field" + }, + "field_incubation": { + "text": "field_incubation" + }, + "glasshouse": { + "text": "glasshouse" + }, + "greenhouse": { + "text": "greenhouse" + }, + "growth_chamber": { + "text": "growth_chamber" + }, + "lab_incubation": { + "text": "lab_incubation" + }, + "open_top_chamber": { + "text": "open_top_chamber" + }, + "other": { + "text": "other" + } + } + }, + "RelToOxygenEnum": { + "name": "RelToOxygenEnum", + "from_schema": "https://example.com/nmdc_submission_schema", + "permissible_values": { + "aerobe": { + "text": "aerobe", + "annotations": { + "sntc_name": { + "tag": "sntc_name", + "value": "oxygen_relationship" + } + }, + "see_also": [ + "https://genomicsstandardsconsortium.github.io/mixs/rel_to_oxygen_enum/" + ] + }, + "anaerobe": { + "text": "anaerobe" + }, + "facultative": { + "text": "facultative" + }, + "microaerophilic": { + "text": "microaerophilic" + }, + "microanaerobe": { + "text": "microanaerobe" + }, + "obligate aerobe": { + "text": "obligate aerobe" + }, + "obligate anaerobe": { + "text": "obligate anaerobe" + } + } + }, + "RnaSampleFormatEnum": { + "name": "RnaSampleFormatEnum", + "from_schema": "https://example.com/nmdc_submission_schema", + "permissible_values": { + "10 mM Tris-HCl": { + "text": "10 mM Tris-HCl" + }, + "DNAStable": { + "text": "DNAStable" + }, + "Ethanol": { + "text": "Ethanol" + }, + "Low EDTA TE": { + "text": "Low EDTA TE" + }, + "MDA reaction buffer": { + "text": "MDA reaction buffer" + }, + "PBS": { + "text": "PBS" + }, + "Pellet": { + "text": "Pellet" + }, + "RNAStable": { + "text": "RNAStable" + }, + "TE": { + "text": "TE" + }, + "Water": { + "text": "Water" + } + } + }, + "SampleTypeEnum": { + "name": "SampleTypeEnum", + "from_schema": "https://example.com/nmdc_submission_schema", + "permissible_values": { + "soil": { + "text": "soil" + }, + "soil - water extract": { + "text": "soil - water extract" + }, + "plant associated": { + "text": "plant associated" + }, + "sediment": { + "text": "sediment" + }, + "water": { + "text": "water" + } + } + }, + "StoreCondEnum": { + "name": "StoreCondEnum", + "from_schema": "https://example.com/nmdc_submission_schema", + "permissible_values": { + "fresh": { + "text": "fresh", + "annotations": { + "sntc_name": { + "tag": "sntc_name", + "value": "storage_condt" + } + }, + "notes": [ + "see samp_store_dur, samp_store_loc, samp_store_temp and store_cond (which takes a string range according to mixs-source)." + ] + }, + "frozen": { + "text": "frozen" + }, + "lyophilized": { + "text": "lyophilized" + }, + "other": { + "text": "other" + } + } + }, + "YesNoEnum": { + "name": "YesNoEnum", + "description": "replaces DnaDnaseEnum and DnaseRnaEnum", + "from_schema": "https://example.com/nmdc_submission_schema", + "permissible_values": { + "no": { + "text": "no" + }, + "yes": { + "text": "yes" + } + } + }, + "OxyStatSampEnum": { + "name": "OxyStatSampEnum", + "from_schema": "https://example.com/nmdc_submission_schema", + "permissible_values": { + "aerobic": { + "text": "aerobic" + }, + "anaerobic": { + "text": "anaerobic" + }, + "other": { + "text": "other" + } + } + }, + "arch_struc_enum": { + "name": "arch_struc_enum", + "from_schema": "https://example.com/nmdc_submission_schema", + "permissible_values": { + "building": { + "text": "building" + }, + "shed": { + "text": "shed" + }, + "home": { + "text": "home" + } + } + }, + "build_docs_enum": { + "name": "build_docs_enum", + "from_schema": "https://example.com/nmdc_submission_schema", + "permissible_values": { + "building information model": { + "text": "building information model" + }, + "commissioning report": { + "text": "commissioning report" + }, + "complaint logs": { + "text": "complaint logs" + }, + "contract administration": { + "text": "contract administration" + }, + "cost estimate": { + "text": "cost estimate" + }, + "janitorial schedules or logs": { + "text": "janitorial schedules or logs" + }, + "maintenance plans": { + "text": "maintenance plans" + }, + "schedule": { + "text": "schedule" + }, + "sections": { + "text": "sections" + }, + "shop drawings": { + "text": "shop drawings" + }, + "submittals": { + "text": "submittals" + }, + "ventilation system": { + "text": "ventilation system" + }, + "windows": { + "text": "windows" + } + } + }, + "build_occup_type_enum": { + "name": "build_occup_type_enum", + "from_schema": "https://example.com/nmdc_submission_schema", + "permissible_values": { + "office": { + "text": "office" + }, + "market": { + "text": "market" + }, + "restaurant": { + "text": "restaurant" + }, + "residence": { + "text": "residence" + }, + "school": { + "text": "school" + }, + "residential": { + "text": "residential" + }, + "commercial": { + "text": "commercial" + }, + "low rise": { + "text": "low rise" + }, + "high rise": { + "text": "high rise" + }, + "wood framed": { + "text": "wood framed" + }, + "health care": { + "text": "health care" + }, + "airport": { + "text": "airport" + }, + "sports complex": { + "text": "sports complex" + } + } + }, + "building_setting_enum": { + "name": "building_setting_enum", + "from_schema": "https://example.com/nmdc_submission_schema", + "permissible_values": { + "urban": { + "text": "urban" + }, + "suburban": { + "text": "suburban" + }, + "exurban": { + "text": "exurban" + }, + "rural": { + "text": "rural" + } + } + }, + "ceil_cond_enum": { + "name": "ceil_cond_enum", + "from_schema": "https://example.com/nmdc_submission_schema", + "permissible_values": { + "new": { + "text": "new" + }, + "visible wear": { + "text": "visible wear" + }, + "needs repair": { + "text": "needs repair" + }, + "damaged": { + "text": "damaged" + }, + "rupture": { + "text": "rupture" + } + } + }, + "ceil_finish_mat_enum": { + "name": "ceil_finish_mat_enum", + "from_schema": "https://example.com/nmdc_submission_schema", + "permissible_values": { + "drywall": { + "text": "drywall" + }, + "mineral fibre": { + "text": "mineral fibre" + }, + "tiles": { + "text": "tiles" + }, + "PVC": { + "text": "PVC" + }, + "plasterboard": { + "text": "plasterboard" + }, + "metal": { + "text": "metal" + }, + "fiberglass": { + "text": "fiberglass" + }, + "stucco": { + "text": "stucco" + }, + "mineral wool/calcium silicate": { + "text": "mineral wool/calcium silicate" + }, + "wood": { + "text": "wood" + } + } + }, + "ceil_texture_enum": { + "name": "ceil_texture_enum", + "from_schema": "https://example.com/nmdc_submission_schema", + "permissible_values": { + "crows feet": { + "text": "crows feet" + }, + "crows-foot stomp": { + "text": "crows-foot stomp" + }, + "double skip": { + "text": "double skip" + }, + "hawk and trowel": { + "text": "hawk and trowel" + }, + "knockdown": { + "text": "knockdown" + }, + "popcorn": { + "text": "popcorn" + }, + "orange peel": { + "text": "orange peel" + }, + "rosebud stomp": { + "text": "rosebud stomp" + }, + "Santa-Fe texture": { + "text": "Santa-Fe texture" + }, + "skip trowel": { + "text": "skip trowel" + }, + "smooth": { + "text": "smooth" + }, + "stomp knockdown": { + "text": "stomp knockdown" + }, + "swirl": { + "text": "swirl" + } + } + }, + "ceil_type_enum": { + "name": "ceil_type_enum", + "from_schema": "https://example.com/nmdc_submission_schema", + "permissible_values": { + "cathedral": { + "text": "cathedral" + }, + "dropped": { + "text": "dropped" + }, + "concave": { + "text": "concave" + }, + "barrel-shaped": { + "text": "barrel-shaped" + }, + "coffered": { + "text": "coffered" + }, + "cove": { + "text": "cove" + }, + "stretched": { + "text": "stretched" + } + } + }, + "door_comp_type_enum": { + "name": "door_comp_type_enum", + "from_schema": "https://example.com/nmdc_submission_schema", + "permissible_values": { + "metal covered": { + "text": "metal covered" + }, + "revolving": { + "text": "revolving" + }, + "sliding": { + "text": "sliding" + }, + "telescopic": { + "text": "telescopic" + } + } + }, + "door_cond_enum": { + "name": "door_cond_enum", + "from_schema": "https://example.com/nmdc_submission_schema", + "permissible_values": { + "damaged": { + "text": "damaged" + }, + "needs repair": { + "text": "needs repair" + }, + "new": { + "text": "new" + }, + "rupture": { + "text": "rupture" + }, + "visible wear": { + "text": "visible wear" + } + } + }, + "door_direct_enum": { + "name": "door_direct_enum", + "from_schema": "https://example.com/nmdc_submission_schema", + "permissible_values": { + "inward": { + "text": "inward" + }, + "outward": { + "text": "outward" + }, + "sideways": { + "text": "sideways" + } + } + }, + "door_loc_enum": { + "name": "door_loc_enum", + "from_schema": "https://example.com/nmdc_submission_schema", + "permissible_values": { + "north": { + "text": "north" + }, + "south": { + "text": "south" + }, + "east": { + "text": "east" + }, + "west": { + "text": "west" + } + } + }, + "door_mat_enum": { + "name": "door_mat_enum", + "from_schema": "https://example.com/nmdc_submission_schema", + "permissible_values": { + "aluminum": { + "text": "aluminum" + }, + "cellular PVC": { + "text": "cellular PVC" + }, + "engineered plastic": { + "text": "engineered plastic" + }, + "fiberboard": { + "text": "fiberboard" + }, + "fiberglass": { + "text": "fiberglass" + }, + "metal": { + "text": "metal" + }, + "thermoplastic alloy": { + "text": "thermoplastic alloy" + }, + "vinyl": { + "text": "vinyl" + }, + "wood": { + "text": "wood" + }, + "wood/plastic composite": { + "text": "wood/plastic composite" + } + } + }, + "door_move_enum": { + "name": "door_move_enum", + "from_schema": "https://example.com/nmdc_submission_schema", + "permissible_values": { + "collapsible": { + "text": "collapsible" + }, + "folding": { + "text": "folding" + }, + "revolving": { + "text": "revolving" + }, + "rolling shutter": { + "text": "rolling shutter" + }, + "sliding": { + "text": "sliding" + }, + "swinging": { + "text": "swinging" + } + } + }, + "door_type_enum": { + "name": "door_type_enum", + "from_schema": "https://example.com/nmdc_submission_schema", + "permissible_values": { + "composite": { + "text": "composite" + }, + "metal": { + "text": "metal" + }, + "wooden": { + "text": "wooden" + } + } + }, + "door_type_metal_enum": { + "name": "door_type_metal_enum", + "from_schema": "https://example.com/nmdc_submission_schema", + "permissible_values": { + "collapsible": { + "text": "collapsible" + }, + "corrugated steel": { + "text": "corrugated steel" + }, + "hollow": { + "text": "hollow" + }, + "rolling shutters": { + "text": "rolling shutters" + }, + "steel plate": { + "text": "steel plate" + } + } + }, + "door_type_wood_enum": { + "name": "door_type_wood_enum", + "from_schema": "https://example.com/nmdc_submission_schema", + "permissible_values": { + "bettened and ledged": { + "text": "bettened and ledged" + }, + "battened": { + "text": "battened" + }, + "ledged and braced": { + "text": "ledged and braced" + }, + "ledged and framed": { + "text": "ledged and framed" + }, + "ledged, braced and frame": { + "text": "ledged, braced and frame" + }, + "framed and paneled": { + "text": "framed and paneled" + }, + "glashed or sash": { + "text": "glashed or sash" + }, + "flush": { + "text": "flush" + }, + "louvered": { + "text": "louvered" + }, + "wire gauged": { + "text": "wire gauged" + } + } + }, + "drawings_enum": { + "name": "drawings_enum", + "from_schema": "https://example.com/nmdc_submission_schema", + "permissible_values": { + "operation": { + "text": "operation" + }, + "as built": { + "text": "as built" + }, + "construction": { + "text": "construction" + }, + "bid": { + "text": "bid" + }, + "design": { + "text": "design" + }, + "building navigation map": { + "text": "building navigation map" + }, + "diagram": { + "text": "diagram" + }, + "sketch": { + "text": "sketch" + } + } + }, + "ext_wall_orient_enum": { + "name": "ext_wall_orient_enum", + "from_schema": "https://example.com/nmdc_submission_schema", + "permissible_values": { + "north": { + "text": "north" + }, + "south": { + "text": "south" + }, + "east": { + "text": "east" + }, + "west": { + "text": "west" + }, + "northeast": { + "text": "northeast" + }, + "southeast": { + "text": "southeast" + }, + "southwest": { + "text": "southwest" + }, + "northwest": { + "text": "northwest" + } + } + }, + "ext_window_orient_enum": { + "name": "ext_window_orient_enum", + "from_schema": "https://example.com/nmdc_submission_schema", + "permissible_values": { + "north": { + "text": "north" + }, + "south": { + "text": "south" + }, + "east": { + "text": "east" + }, + "west": { + "text": "west" + }, + "northeast": { + "text": "northeast" + }, + "southeast": { + "text": "southeast" + }, + "southwest": { + "text": "southwest" + }, + "northwest": { + "text": "northwest" + } + } + }, + "filter_type_enum": { + "name": "filter_type_enum", + "from_schema": "https://example.com/nmdc_submission_schema", + "permissible_values": { + "particulate air filter": { + "text": "particulate air filter" + }, + "chemical air filter": { + "text": "chemical air filter" + }, + "low-MERV pleated media": { + "text": "low-MERV pleated media" + }, + "HEPA": { + "text": "HEPA" + }, + "electrostatic": { + "text": "electrostatic" + }, + "gas-phase or ultraviolet air treatments": { + "text": "gas-phase or ultraviolet air treatments" + } + } + }, + "floor_cond_enum": { + "name": "floor_cond_enum", + "from_schema": "https://example.com/nmdc_submission_schema", + "permissible_values": { + "new": { + "text": "new" + }, + "visible wear": { + "text": "visible wear" + }, + "needs repair": { + "text": "needs repair" + }, + "damaged": { + "text": "damaged" + }, + "rupture": { + "text": "rupture" + } + } + }, + "floor_finish_mat_enum": { + "name": "floor_finish_mat_enum", + "from_schema": "https://example.com/nmdc_submission_schema", + "permissible_values": { + "tile": { + "text": "tile" + }, + "wood strip or parquet": { + "text": "wood strip or parquet" + }, + "carpet": { + "text": "carpet" + }, + "rug": { + "text": "rug" + }, + "laminate wood": { + "text": "laminate wood" + }, + "lineoleum": { + "text": "lineoleum" + }, + "vinyl composition tile": { + "text": "vinyl composition tile" + }, + "sheet vinyl": { + "text": "sheet vinyl" + }, + "stone": { + "text": "stone" + }, + "bamboo": { + "text": "bamboo" + }, + "cork": { + "text": "cork" + }, + "terrazo": { + "text": "terrazo" + }, + "concrete": { + "text": "concrete" + }, + "none": { + "text": "none" + }, + "sealed": { + "text": "sealed" + }, + "clear finish": { + "text": "clear finish" + }, + "paint": { + "text": "paint" + }, + "none or unfinished": { + "text": "none or unfinished" + } + } + }, + "floor_struc_enum": { + "name": "floor_struc_enum", + "from_schema": "https://example.com/nmdc_submission_schema", + "permissible_values": { + "balcony": { + "text": "balcony" + }, + "floating floor": { + "text": "floating floor" + }, + "glass floor": { + "text": "glass floor" + }, + "raised floor": { + "text": "raised floor" + }, + "sprung floor": { + "text": "sprung floor" + }, + "wood-framed": { + "text": "wood-framed" + }, + "concrete": { + "text": "concrete" + } + } + }, + "floor_water_mold_enum": { + "name": "floor_water_mold_enum", + "from_schema": "https://example.com/nmdc_submission_schema", + "permissible_values": { + "mold odor": { + "text": "mold odor" + }, + "wet floor": { + "text": "wet floor" + }, + "water stains": { + "text": "water stains" + }, + "wall discoloration": { + "text": "wall discoloration" + }, + "floor discoloration": { + "text": "floor discoloration" + }, + "ceiling discoloration": { + "text": "ceiling discoloration" + }, + "peeling paint or wallpaper": { + "text": "peeling paint or wallpaper" + }, + "bulging walls": { + "text": "bulging walls" + }, + "condensation": { + "text": "condensation" + } + } + }, + "furniture_enum": { + "name": "furniture_enum", + "from_schema": "https://example.com/nmdc_submission_schema", + "permissible_values": { + "cabinet": { + "text": "cabinet" + }, + "chair": { + "text": "chair" + }, + "desks": { + "text": "desks" + } + } + }, + "gender_restroom_enum": { + "name": "gender_restroom_enum", + "from_schema": "https://example.com/nmdc_submission_schema", + "permissible_values": { + "all gender": { + "text": "all gender" + }, + "female": { + "text": "female" + }, + "gender neurtral": { + "text": "gender neurtral" + }, + "male": { + "text": "male" + }, + "male and female": { + "text": "male and female" + }, + "unisex": { + "text": "unisex" + } + } + }, + "handidness_enum": { + "name": "handidness_enum", + "from_schema": "https://example.com/nmdc_submission_schema", + "permissible_values": { + "ambidexterity": { + "text": "ambidexterity" + }, + "left handedness": { + "text": "left handedness" + }, + "mixed-handedness": { + "text": "mixed-handedness" + }, + "right handedness": { + "text": "right handedness" + } + } + }, + "heat_cool_type_enum": { + "name": "heat_cool_type_enum", + "from_schema": "https://example.com/nmdc_submission_schema", + "permissible_values": { + "radiant system": { + "text": "radiant system" + }, + "heat pump": { + "text": "heat pump" + }, + "forced air system": { + "text": "forced air system" + }, + "steam forced heat": { + "text": "steam forced heat" + }, + "wood stove": { + "text": "wood stove" + } + } + }, + "heat_deliv_loc_enum": { + "name": "heat_deliv_loc_enum", + "from_schema": "https://example.com/nmdc_submission_schema", + "permissible_values": { + "north": { + "text": "north" + }, + "south": { + "text": "south" + }, + "east": { + "text": "east" + }, + "west": { + "text": "west" + } + } + }, + "indoor_space_enum": { + "name": "indoor_space_enum", + "from_schema": "https://example.com/nmdc_submission_schema", + "permissible_values": { + "bedroom": { + "text": "bedroom" + }, + "office": { + "text": "office" + }, + "bathroom": { + "text": "bathroom" + }, + "foyer": { + "text": "foyer" + }, + "kitchen": { + "text": "kitchen" + }, + "locker room": { + "text": "locker room" + }, + "hallway": { + "text": "hallway" + }, + "elevator": { + "text": "elevator" + } + } + }, + "indoor_surf_enum": { + "name": "indoor_surf_enum", + "from_schema": "https://example.com/nmdc_submission_schema", + "permissible_values": { + "cabinet": { + "text": "cabinet" + }, + "ceiling": { + "text": "ceiling" + }, + "counter top": { + "text": "counter top" + }, + "door": { + "text": "door" + }, + "shelving": { + "text": "shelving" + }, + "vent cover": { + "text": "vent cover" + }, + "window": { + "text": "window" + }, + "wall": { + "text": "wall" + } + } + }, + "int_wall_cond_enum": { + "name": "int_wall_cond_enum", + "from_schema": "https://example.com/nmdc_submission_schema", + "permissible_values": { + "new": { + "text": "new" + }, + "visible wear": { + "text": "visible wear" + }, + "needs repair": { + "text": "needs repair" + }, + "damaged": { + "text": "damaged" + }, + "rupture": { + "text": "rupture" + } + } + }, + "light_type_enum": { + "name": "light_type_enum", + "from_schema": "https://example.com/nmdc_submission_schema", + "permissible_values": { + "natural light": { + "text": "natural light" + }, + "electric light": { + "text": "electric light" + }, + "desk lamp": { + "text": "desk lamp" + }, + "flourescent lights": { + "text": "flourescent lights" + }, + "none": { + "text": "none" + } + } + }, + "mech_struc_enum": { + "name": "mech_struc_enum", + "from_schema": "https://example.com/nmdc_submission_schema", + "permissible_values": { + "subway": { + "text": "subway" + }, + "coach": { + "text": "coach" + }, + "carriage": { + "text": "carriage" + }, + "elevator": { + "text": "elevator" + }, + "escalator": { + "text": "escalator" + }, + "boat": { + "text": "boat" + }, + "train": { + "text": "train" + }, + "car": { + "text": "car" + }, + "bus": { + "text": "bus" + } + } + }, + "occup_document_enum": { + "name": "occup_document_enum", + "from_schema": "https://example.com/nmdc_submission_schema", + "permissible_values": { + "automated count": { + "text": "automated count" + }, + "estimate": { + "text": "estimate" + }, + "manual count": { + "text": "manual count" + }, + "videos": { + "text": "videos" + } + } + }, + "quad_pos_enum": { + "name": "quad_pos_enum", + "from_schema": "https://example.com/nmdc_submission_schema", + "permissible_values": { + "North side": { + "text": "North side" + }, + "West side": { + "text": "West side" + }, + "South side": { + "text": "South side" + }, + "East side": { + "text": "East side" + } + } + }, + "rel_samp_loc_enum": { + "name": "rel_samp_loc_enum", + "from_schema": "https://example.com/nmdc_submission_schema", + "permissible_values": { + "edge of car": { + "text": "edge of car" + }, + "center of car": { + "text": "center of car" + }, + "under a seat": { + "text": "under a seat" + } + } + }, + "room_condt_enum": { + "name": "room_condt_enum", + "from_schema": "https://example.com/nmdc_submission_schema", + "permissible_values": { + "new": { + "text": "new" + }, + "visible wear": { + "text": "visible wear" + }, + "needs repair": { + "text": "needs repair" + }, + "damaged": { + "text": "damaged" + }, + "rupture": { + "text": "rupture" + }, + "visible signs of mold/mildew": { + "text": "visible signs of mold/mildew" + } + } + }, + "room_connected_enum": { + "name": "room_connected_enum", + "from_schema": "https://example.com/nmdc_submission_schema", + "permissible_values": { + "attic": { + "text": "attic" + }, + "bathroom": { + "text": "bathroom" + }, + "closet": { + "text": "closet" + }, + "conference room": { + "text": "conference room" + }, + "elevator": { + "text": "elevator" + }, + "examining room": { + "text": "examining room" + }, + "hallway": { + "text": "hallway" + }, + "kitchen": { + "text": "kitchen" + }, + "mail room": { + "text": "mail room" + }, + "office": { + "text": "office" + }, + "stairwell": { + "text": "stairwell" + } + } + }, + "room_loc_enum": { + "name": "room_loc_enum", + "from_schema": "https://example.com/nmdc_submission_schema", + "permissible_values": { + "corner room": { + "text": "corner room" + }, + "interior room": { + "text": "interior room" + }, + "exterior wall": { + "text": "exterior wall" + } + } + }, + "room_samp_pos_enum": { + "name": "room_samp_pos_enum", + "from_schema": "https://example.com/nmdc_submission_schema", + "permissible_values": { + "north corner": { + "text": "north corner" + }, + "south corner": { + "text": "south corner" + }, + "west corner": { + "text": "west corner" + }, + "east corner": { + "text": "east corner" + }, + "northeast corner": { + "text": "northeast corner" + }, + "northwest corner": { + "text": "northwest corner" + }, + "southeast corner": { + "text": "southeast corner" + }, + "southwest corner": { + "text": "southwest corner" + }, + "center": { + "text": "center" + } + } + }, + "room_type_enum": { + "name": "room_type_enum", + "from_schema": "https://example.com/nmdc_submission_schema", + "permissible_values": { + "attic": { + "text": "attic" + }, + "bathroom": { + "text": "bathroom" + }, + "closet": { + "text": "closet" + }, + "conference room": { + "text": "conference room" + }, + "elevator": { + "text": "elevator" + }, + "examining room": { + "text": "examining room" + }, + "hallway": { + "text": "hallway" + }, + "kitchen": { + "text": "kitchen" + }, + "mail room": { + "text": "mail room" + }, + "private office": { + "text": "private office" + }, + "open office": { + "text": "open office" + }, + "stairwell": { + "text": "stairwell" + }, + ",restroom": { + "text": ",restroom" + }, + "lobby": { + "text": "lobby" + }, + "vestibule": { + "text": "vestibule" + }, + "mechanical or electrical room": { + "text": "mechanical or electrical room" + }, + "data center": { + "text": "data center" + }, + "laboratory_wet": { + "text": "laboratory_wet" + }, + "laboratory_dry": { + "text": "laboratory_dry" + }, + "gymnasium": { + "text": "gymnasium" + }, + "natatorium": { + "text": "natatorium" + }, + "auditorium": { + "text": "auditorium" + }, + "lockers": { + "text": "lockers" + }, + "cafe": { + "text": "cafe" + }, + "warehouse": { + "text": "warehouse" + } + } + }, + "samp_floor_enum": { + "name": "samp_floor_enum", + "from_schema": "https://example.com/nmdc_submission_schema", + "permissible_values": { + "1st floor": { + "text": "1st floor" + }, + "2nd floor": { + "text": "2nd floor" + }, + "basement": { + "text": "basement" + }, + "lobby": { + "text": "lobby" + } + } + }, + "samp_weather_enum": { + "name": "samp_weather_enum", + "from_schema": "https://example.com/nmdc_submission_schema", + "permissible_values": { + "clear sky": { + "text": "clear sky" + }, + "cloudy": { + "text": "cloudy" + }, + "foggy": { + "text": "foggy" + }, + "hail": { + "text": "hail" + }, + "rain": { + "text": "rain" + }, + "snow": { + "text": "snow" + }, + "sleet": { + "text": "sleet" + }, + "sunny": { + "text": "sunny" + }, + "windy": { + "text": "windy" + } + } + }, + "season_use_enum": { + "name": "season_use_enum", + "from_schema": "https://example.com/nmdc_submission_schema", + "permissible_values": { + "Spring": { + "text": "Spring" + }, + "Summer": { + "text": "Summer" + }, + "Fall": { + "text": "Fall" + }, + "Winter": { + "text": "Winter" + } + } + }, + "shading_device_cond_enum": { + "name": "shading_device_cond_enum", + "from_schema": "https://example.com/nmdc_submission_schema", + "permissible_values": { + "damaged": { + "text": "damaged" + }, + "needs repair": { + "text": "needs repair" + }, + "new": { + "text": "new" + }, + "rupture": { + "text": "rupture" + }, + "visible wear": { + "text": "visible wear" + } + } + }, + "shading_device_type_enum": { + "name": "shading_device_type_enum", + "from_schema": "https://example.com/nmdc_submission_schema", + "permissible_values": { + "bahama shutters": { + "text": "bahama shutters" + }, + "exterior roll blind": { + "text": "exterior roll blind" + }, + "gambrel awning": { + "text": "gambrel awning" + }, + "hood awning": { + "text": "hood awning" + }, + "porchroller awning": { + "text": "porchroller awning" + }, + "sarasota shutters": { + "text": "sarasota shutters" + }, + "slatted aluminum": { + "text": "slatted aluminum" + }, + "solid aluminum awning": { + "text": "solid aluminum awning" + }, + "sun screen": { + "text": "sun screen" + }, + "tree": { + "text": "tree" + }, + "trellis": { + "text": "trellis" + }, + "venetian awning": { + "text": "venetian awning" + } + } + }, + "specific_enum": { + "name": "specific_enum", + "from_schema": "https://example.com/nmdc_submission_schema", + "permissible_values": { + "operation": { + "text": "operation" + }, + "as built": { + "text": "as built" + }, + "construction": { + "text": "construction" + }, + "bid": { + "text": "bid" + }, + "design": { + "text": "design" + }, + "photos": { + "text": "photos" + } + } + }, + "substructure_type_enum": { + "name": "substructure_type_enum", + "from_schema": "https://example.com/nmdc_submission_schema", + "permissible_values": { + "crawlspace": { + "text": "crawlspace" + }, + "slab on grade": { + "text": "slab on grade" + }, + "basement": { + "text": "basement" + } + } + }, + "surf_air_cont_enum": { + "name": "surf_air_cont_enum", + "from_schema": "https://example.com/nmdc_submission_schema", + "permissible_values": { + "dust": { + "text": "dust" + }, + "organic matter": { + "text": "organic matter" + }, + "particulate matter": { + "text": "particulate matter" + }, + "volatile organic compounds": { + "text": "volatile organic compounds" + }, + "biological contaminants": { + "text": "biological contaminants" + }, + "radon": { + "text": "radon" + }, + "nutrients": { + "text": "nutrients" + }, + "biocides": { + "text": "biocides" + } + } + }, + "surf_material_enum": { + "name": "surf_material_enum", + "from_schema": "https://example.com/nmdc_submission_schema", + "permissible_values": { + "adobe": { + "text": "adobe" + }, + "carpet": { + "text": "carpet" + }, + "cinder blocks": { + "text": "cinder blocks" + }, + "concrete": { + "text": "concrete" + }, + "hay bales": { + "text": "hay bales" + }, + "glass": { + "text": "glass" + }, + "metal": { + "text": "metal" + }, + "paint": { + "text": "paint" + }, + "plastic": { + "text": "plastic" + }, + "stainless steel": { + "text": "stainless steel" + }, + "stone": { + "text": "stone" + }, + "stucco": { + "text": "stucco" + }, + "tile": { + "text": "tile" + }, + "vinyl": { + "text": "vinyl" + }, + "wood": { + "text": "wood" + } + } + }, + "train_line_enum": { + "name": "train_line_enum", + "from_schema": "https://example.com/nmdc_submission_schema", + "permissible_values": { + "red": { + "text": "red" + }, + "green": { + "text": "green" + }, + "orange": { + "text": "orange" + } + } + }, + "train_stat_loc_enum": { + "name": "train_stat_loc_enum", + "from_schema": "https://example.com/nmdc_submission_schema", + "permissible_values": { + "south station above ground": { + "text": "south station above ground" + }, + "south station underground": { + "text": "south station underground" + }, + "south station amtrak": { + "text": "south station amtrak" + }, + "forest hills": { + "text": "forest hills" + }, + "riverside": { + "text": "riverside" + } + } + }, + "train_stop_loc_enum": { + "name": "train_stop_loc_enum", + "from_schema": "https://example.com/nmdc_submission_schema", + "permissible_values": { + "end": { + "text": "end" + }, + "mid": { + "text": "mid" + }, + "downtown": { + "text": "downtown" + } + } + }, + "vis_media_enum": { + "name": "vis_media_enum", + "from_schema": "https://example.com/nmdc_submission_schema", + "permissible_values": { + "photos": { + "text": "photos" + }, + "videos": { + "text": "videos" + }, + "commonly of the building": { + "text": "commonly of the building" + }, + "site context (adjacent buildings, vegetation, terrain, streets)": { + "text": "site context (adjacent buildings, vegetation, terrain, streets)" + }, + "interiors": { + "text": "interiors" + }, + "equipment": { + "text": "equipment" + }, + "3D scans": { + "text": "3D scans" + } + } + }, + "wall_const_type_enum": { + "name": "wall_const_type_enum", + "from_schema": "https://example.com/nmdc_submission_schema", + "permissible_values": { + "frame construction": { + "text": "frame construction" + }, + "joisted masonry": { + "text": "joisted masonry" + }, + "light noncombustible": { + "text": "light noncombustible" + }, + "masonry noncombustible": { + "text": "masonry noncombustible" + }, + "modified fire resistive": { + "text": "modified fire resistive" + }, + "fire resistive": { + "text": "fire resistive" + } + } + }, + "wall_finish_mat_enum": { + "name": "wall_finish_mat_enum", + "from_schema": "https://example.com/nmdc_submission_schema", + "permissible_values": { + "plaster": { + "text": "plaster" + }, + "gypsum plaster": { + "text": "gypsum plaster" + }, + "veneer plaster": { + "text": "veneer plaster" + }, + "gypsum board": { + "text": "gypsum board" + }, + "tile": { + "text": "tile" + }, + "terrazzo": { + "text": "terrazzo" + }, + "stone facing": { + "text": "stone facing" + }, + "acoustical treatment": { + "text": "acoustical treatment" + }, + "wood": { + "text": "wood" + }, + "metal": { + "text": "metal" + }, + "masonry": { + "text": "masonry" + } + } + }, + "wall_loc_enum": { + "name": "wall_loc_enum", + "from_schema": "https://example.com/nmdc_submission_schema", + "permissible_values": { + "north": { + "text": "north" + }, + "south": { + "text": "south" + }, + "east": { + "text": "east" + }, + "west": { + "text": "west" + } + } + }, + "wall_surf_treatment_enum": { + "name": "wall_surf_treatment_enum", + "from_schema": "https://example.com/nmdc_submission_schema", + "permissible_values": { + "painted": { + "text": "painted" + }, + "wall paper": { + "text": "wall paper" + }, + "no treatment": { + "text": "no treatment" + }, + "paneling": { + "text": "paneling" + }, + "stucco": { + "text": "stucco" + }, + "fabric": { + "text": "fabric" + } + } + }, + "wall_texture_enum": { + "name": "wall_texture_enum", + "from_schema": "https://example.com/nmdc_submission_schema", + "permissible_values": { + "crows feet": { + "text": "crows feet" + }, + "crows-foot stomp": { + "text": "crows-foot stomp" + }, + "": { + "text": "" + }, + "double skip": { + "text": "double skip" + }, + "hawk and trowel": { + "text": "hawk and trowel" + }, + "knockdown": { + "text": "knockdown" + }, + "popcorn": { + "text": "popcorn" + }, + "orange peel": { + "text": "orange peel" + }, + "rosebud stomp": { + "text": "rosebud stomp" + }, + "Santa-Fe texture": { + "text": "Santa-Fe texture" + }, + "skip trowel": { + "text": "skip trowel" + }, + "smooth": { + "text": "smooth" + }, + "stomp knockdown": { + "text": "stomp knockdown" + }, + "swirl": { + "text": "swirl" + } + } + }, + "water_feat_type_enum": { + "name": "water_feat_type_enum", + "from_schema": "https://example.com/nmdc_submission_schema", + "permissible_values": { + "fountain": { + "text": "fountain" + }, + "pool": { + "text": "pool" + }, + "standing feature": { + "text": "standing feature" + }, + "stream": { + "text": "stream" + }, + "waterfall": { + "text": "waterfall" + } + } + }, + "weekday_enum": { + "name": "weekday_enum", + "from_schema": "https://example.com/nmdc_submission_schema", + "permissible_values": { + "Monday": { + "text": "Monday" + }, + "Tuesday": { + "text": "Tuesday" + }, + "Wednesday": { + "text": "Wednesday" + }, + "Thursday": { + "text": "Thursday" + }, + "Friday": { + "text": "Friday" + }, + "Saturday": { + "text": "Saturday" + }, + "Sunday": { + "text": "Sunday" + } + } + }, + "window_cond_enum": { + "name": "window_cond_enum", + "from_schema": "https://example.com/nmdc_submission_schema", + "permissible_values": { + "damaged": { + "text": "damaged" + }, + "needs repair": { + "text": "needs repair" + }, + "new": { + "text": "new" + }, + "rupture": { + "text": "rupture" + }, + "visible wear": { + "text": "visible wear" + } + } + }, + "window_cover_enum": { + "name": "window_cover_enum", + "from_schema": "https://example.com/nmdc_submission_schema", + "permissible_values": { + "blinds": { + "text": "blinds" + }, + "curtains": { + "text": "curtains" + }, + "none": { + "text": "none" + } + } + }, + "window_horiz_pos_enum": { + "name": "window_horiz_pos_enum", + "from_schema": "https://example.com/nmdc_submission_schema", + "permissible_values": { + "left": { + "text": "left" + }, + "middle": { + "text": "middle" + }, + "right": { + "text": "right" + } + } + }, + "window_loc_enum": { + "name": "window_loc_enum", + "from_schema": "https://example.com/nmdc_submission_schema", + "permissible_values": { + "north": { + "text": "north" + }, + "south": { + "text": "south" + }, + "east": { + "text": "east" + }, + "west": { + "text": "west" + } + } + }, + "window_mat_enum": { + "name": "window_mat_enum", + "from_schema": "https://example.com/nmdc_submission_schema", + "permissible_values": { + "clad": { + "text": "clad" + }, + "fiberglass": { + "text": "fiberglass" + }, + "metal": { + "text": "metal" + }, + "vinyl": { + "text": "vinyl" + }, + "wood": { + "text": "wood" + } + } + }, + "window_type_enum": { + "name": "window_type_enum", + "from_schema": "https://example.com/nmdc_submission_schema", + "permissible_values": { + "single-hung sash window": { + "text": "single-hung sash window" + }, + "horizontal sash window": { + "text": "horizontal sash window" + }, + "fixed window": { + "text": "fixed window" + } + } + }, + "window_vert_pos_enum": { + "name": "window_vert_pos_enum", + "from_schema": "https://example.com/nmdc_submission_schema", + "permissible_values": { + "bottom": { + "text": "bottom" + }, + "middle": { + "text": "middle" + }, + "top": { + "text": "top" + }, + "low": { + "text": "low" + }, + "high": { + "text": "high" + } + } + }, + "depos_env_enum": { + "name": "depos_env_enum", + "from_schema": "https://example.com/nmdc_submission_schema", + "permissible_values": { + "Continental - Alluvial": { + "text": "Continental - Alluvial" + }, + "Continental - Aeolian": { + "text": "Continental - Aeolian" + }, + "Continental - Fluvial": { + "text": "Continental - Fluvial" + }, + "Continental - Lacustrine": { + "text": "Continental - Lacustrine" + }, + "Transitional - Deltaic": { + "text": "Transitional - Deltaic" + }, + "Transitional - Tidal": { + "text": "Transitional - Tidal" + }, + "Transitional - Lagoonal": { + "text": "Transitional - Lagoonal" + }, + "Transitional - Beach": { + "text": "Transitional - Beach" + }, + "Transitional - Lake": { + "text": "Transitional - Lake" + }, + "Marine - Shallow": { + "text": "Marine - Shallow" + }, + "Marine - Deep": { + "text": "Marine - Deep" + }, + "Marine - Reef": { + "text": "Marine - Reef" + }, + "Other - Evaporite": { + "text": "Other - Evaporite" + }, + "Other - Glacial": { + "text": "Other - Glacial" + }, + "Other - Volcanic": { + "text": "Other - Volcanic" + }, + "other": { + "text": "other" + } + } + }, + "hc_produced_enum": { + "name": "hc_produced_enum", + "from_schema": "https://example.com/nmdc_submission_schema", + "permissible_values": { + "Oil": { + "text": "Oil" + }, + "Gas-Condensate": { + "text": "Gas-Condensate" + }, + "Gas": { + "text": "Gas" + }, + "Bitumen": { + "text": "Bitumen" + }, + "Coalbed Methane": { + "text": "Coalbed Methane" + }, + "other": { + "text": "other" + } + } + }, + "hcr_enum": { + "name": "hcr_enum", + "from_schema": "https://example.com/nmdc_submission_schema", + "permissible_values": { + "Oil Reservoir": { + "text": "Oil Reservoir" + }, + "Gas Reservoir": { + "text": "Gas Reservoir" + }, + "Oil Sand": { + "text": "Oil Sand" + }, + "Coalbed": { + "text": "Coalbed" + }, + "Shale": { + "text": "Shale" + }, + "Tight Oil Reservoir": { + "text": "Tight Oil Reservoir" + }, + "Tight Gas Reservoir": { + "text": "Tight Gas Reservoir" + }, + "other": { + "text": "other" + } + } + }, + "hcr_geol_age_enum": { + "name": "hcr_geol_age_enum", + "from_schema": "https://example.com/nmdc_submission_schema", + "permissible_values": { + "Archean": { + "text": "Archean" + }, + "Cambrian": { + "text": "Cambrian" + }, + "Carboniferous": { + "text": "Carboniferous" + }, + "Cenozoic": { + "text": "Cenozoic" + }, + "Cretaceous": { + "text": "Cretaceous" + }, + "Devonian": { + "text": "Devonian" + }, + "Jurassic": { + "text": "Jurassic" + }, + "Mesozoic": { + "text": "Mesozoic" + }, + "Neogene": { + "text": "Neogene" + }, + "Ordovician": { + "text": "Ordovician" + }, + "Paleogene": { + "text": "Paleogene" + }, + "Paleozoic": { + "text": "Paleozoic" + }, + "Permian": { + "text": "Permian" + }, + "Precambrian": { + "text": "Precambrian" + }, + "Proterozoic": { + "text": "Proterozoic" + }, + "Silurian": { + "text": "Silurian" + }, + "Triassic": { + "text": "Triassic" + }, + "other": { + "text": "other" + } + } + }, + "lithology_enum": { + "name": "lithology_enum", + "from_schema": "https://example.com/nmdc_submission_schema", + "permissible_values": { + "Basement": { + "text": "Basement" + }, + "Chalk": { + "text": "Chalk" + }, + "Chert": { + "text": "Chert" + }, + "Coal": { + "text": "Coal" + }, + "Conglomerate": { + "text": "Conglomerate" + }, + "Diatomite": { + "text": "Diatomite" + }, + "Dolomite": { + "text": "Dolomite" + }, + "Limestone": { + "text": "Limestone" + }, + "Sandstone": { + "text": "Sandstone" + }, + "Shale": { + "text": "Shale" + }, + "Siltstone": { + "text": "Siltstone" + }, + "Volcanic": { + "text": "Volcanic" + }, + "other": { + "text": "other" + } + } + }, + "oxy_stat_samp_enum": { + "name": "oxy_stat_samp_enum", + "from_schema": "https://example.com/nmdc_submission_schema", + "permissible_values": { + "aerobic": { + "text": "aerobic" + }, + "anaerobic": { + "text": "anaerobic" + }, + "other": { + "text": "other" + } + } + }, + "samp_collect_point_enum": { + "name": "samp_collect_point_enum", + "from_schema": "https://example.com/nmdc_submission_schema", + "permissible_values": { + "well": { + "text": "well" + }, + "test well": { + "text": "test well" + }, + "drilling rig": { + "text": "drilling rig" + }, + "wellhead": { + "text": "wellhead" + }, + "separator": { + "text": "separator" + }, + "storage tank": { + "text": "storage tank" + }, + "other": { + "text": "other" + } + } + }, + "samp_subtype_enum": { + "name": "samp_subtype_enum", + "from_schema": "https://example.com/nmdc_submission_schema", + "permissible_values": { + "oil phase": { + "text": "oil phase" + }, + "water phase": { + "text": "water phase" + }, + "biofilm": { + "text": "biofilm" + }, + "not applicable": { + "text": "not applicable" + }, + "other": { + "text": "other" + } + } + }, + "sr_dep_env_enum": { + "name": "sr_dep_env_enum", + "from_schema": "https://example.com/nmdc_submission_schema", + "permissible_values": { + "Lacustine": { + "text": "Lacustine" + }, + "Fluvioldeltaic": { + "text": "Fluvioldeltaic" + }, + "Fluviomarine": { + "text": "Fluviomarine" + }, + "Marine": { + "text": "Marine" + }, + "other": { + "text": "other" + } + } + }, + "sr_geol_age_enum": { + "name": "sr_geol_age_enum", + "from_schema": "https://example.com/nmdc_submission_schema", + "permissible_values": { + "Archean": { + "text": "Archean" + }, + "Cambrian": { + "text": "Cambrian" + }, + "Carboniferous": { + "text": "Carboniferous" + }, + "Cenozoic": { + "text": "Cenozoic" + }, + "Cretaceous": { + "text": "Cretaceous" + }, + "Devonian": { + "text": "Devonian" + }, + "Jurassic": { + "text": "Jurassic" + }, + "Mesozoic": { + "text": "Mesozoic" + }, + "Neogene": { + "text": "Neogene" + }, + "Ordovician": { + "text": "Ordovician" + }, + "Paleogene": { + "text": "Paleogene" + }, + "Paleozoic": { + "text": "Paleozoic" + }, + "Permian": { + "text": "Permian" + }, + "Precambrian": { + "text": "Precambrian" + }, + "Proterozoic": { + "text": "Proterozoic" + }, + "Silurian": { + "text": "Silurian" + }, + "Triassic": { + "text": "Triassic" + }, + "other": { + "text": "other" + } + } + }, + "sr_kerog_type_enum": { + "name": "sr_kerog_type_enum", + "from_schema": "https://example.com/nmdc_submission_schema", + "permissible_values": { + "Type I": { + "text": "Type I" + }, + "Type II": { + "text": "Type II" + }, + "Type III": { + "text": "Type III" + }, + "Type IV": { + "text": "Type IV" + }, + "other": { + "text": "other" + } + } + }, + "sr_lithology_enum": { + "name": "sr_lithology_enum", + "from_schema": "https://example.com/nmdc_submission_schema", + "permissible_values": { + "Clastic": { + "text": "Clastic" + }, + "Carbonate": { + "text": "Carbonate" + }, + "Coal": { + "text": "Coal" + }, + "Biosilicieous": { + "text": "Biosilicieous" + }, + "other": { + "text": "other" + } + } + }, + "biotic_relationship_enum": { + "name": "biotic_relationship_enum", + "from_schema": "https://example.com/nmdc_submission_schema", + "permissible_values": { + "free living": { + "text": "free living" + }, + "parasite": { + "text": "parasite" + }, + "commensal": { + "text": "commensal" + }, + "symbiont": { + "text": "symbiont" + } + } + }, + "cur_land_use_enum": { + "name": "cur_land_use_enum", + "from_schema": "https://example.com/nmdc_submission_schema", + "permissible_values": { + "badlands": { + "text": "badlands" + }, + "cities": { + "text": "cities" + }, + "conifers": { + "text": "conifers", + "annotations": { + "originally": { + "tag": "originally", + "value": "conifers (e.g. pine,spruce,fir,cypress)" + } + }, + "examples": [ + { + "value": "cypress" + }, + { + "value": "fir" + }, + { + "value": "pine" + }, + { + "value": "spruce" + } + ] + }, + "crop trees": { + "text": "crop trees", + "annotations": { + "originally": { + "tag": "originally", + "value": "crop trees (nuts,fruit,christmas trees,nursery trees)" + } + }, + "examples": [ + { + "value": "christmas trees" + }, + { + "value": "fruit" + }, + { + "value": "nursery trees" + }, + { + "value": "nuts" + } + ] + }, + "farmstead": { + "text": "farmstead" + }, + "gravel": { + "text": "gravel" + }, + "hardwoods": { + "text": "hardwoods", + "annotations": { + "originally": { + "tag": "originally", + "value": "hardwoods (e.g. oak,hickory,elm,aspen)" + } + }, + "examples": [ + { + "value": "aspen" + }, + { + "value": "elm" + }, + { + "value": "hickory" + }, + { + "value": "oak" + } + ] + }, + "hayland": { + "text": "hayland" + }, + "horticultural plants": { + "text": "horticultural plants", + "annotations": { + "originally": { + "tag": "originally", + "value": "horticultural plants (e.g. tulips)" + } + }, + "examples": [ + { + "value": "tulips" + } + ] + }, + "industrial areas": { + "text": "industrial areas" + }, + "intermixed hardwood and conifers": { + "text": "intermixed hardwood and conifers" + }, + "marshlands": { + "text": "marshlands", + "annotations": { + "originally": { + "tag": "originally", + "value": "marshlands (grass,sedges,rushes)" + } + }, + "examples": [ + { + "value": "grass" + }, + { + "value": "rushes" + }, + { + "value": "sedgees" + } + ] + }, + "meadows": { + "text": "meadows", + "annotations": { + "originally": { + "tag": "originally", + "value": "meadows (grasses,alfalfa,fescue,bromegrass,timothy)" + } + }, + "examples": [ + { + "value": "alfalfa" + }, + { + "value": "bromegrass" + }, + { + "value": "fescue" + }, + { + "value": "grasses" + }, + { + "value": "timothy" + } + ] + }, + "mines/quarries": { + "text": "mines/quarries" + }, + "mudflats": { + "text": "mudflats" + }, + "oil waste areas": { + "text": "oil waste areas" + }, + "pastureland": { + "text": "pastureland", + "annotations": { + "originally": { + "tag": "originally", + "value": "pastureland (grasslands used for livestock grazing)" + } + }, + "comments": [ + "grasslands used for livestock grazing" + ] + }, + "permanent snow or ice": { + "text": "permanent snow or ice" + }, + "rainforest": { + "text": "rainforest", + "annotations": { + "originally": { + "tag": "originally", + "value": "rainforest (evergreen forest receiving greater than 406 cm annual rainfall)" + } + }, + "comments": [ + "evergreen forest receiving greater than 406 cm annual rainfall" + ] + }, + "rangeland": { + "text": "rangeland" + }, + "roads/railroads": { + "text": "roads/railroads" + }, + "rock": { + "text": "rock" + }, + "row crops": { + "text": "row crops" + }, + "saline seeps": { + "text": "saline seeps" + }, + "salt flats": { + "text": "salt flats" + }, + "sand": { + "text": "sand" + }, + "shrub crops": { + "text": "shrub crops", + "annotations": { + "originally": { + "tag": "originally", + "value": "shrub crops (blueberries,nursery ornamentals,filberts)" + } + }, + "examples": [ + { + "value": "blueberries" + }, + { + "value": "filberts" + }, + { + "value": "nursery ornamentals" + } + ] + }, + "shrub land": { + "text": "shrub land", + "annotations": { + "originally": { + "tag": "originally", + "value": "shrub land (e.g. mesquite,sage-brush,creosote bush,shrub oak,eucalyptus)" + } + }, + "examples": [ + { + "value": "creosote bush" + }, + { + "value": "eucalyptus" + }, + { + "value": "mesquite" + }, + { + "value": "sage-brush" + }, + { + "value": "shrub oak" + } + ] + }, + "small grains": { + "text": "small grains" + }, + "successional shrub land": { + "text": "successional shrub land", + "annotations": { + "originally": { + "tag": "originally", + "value": "successional shrub land (tree saplings,hazels,sumacs,chokecherry,shrub dogwoods,blackberries)" + } + }, + "examples": [ + { + "value": "blackberries" + }, + { + "value": "chokecherry" + }, + { + "value": "hazels" + }, + { + "value": "shrub dogwoods" + }, + { + "value": "sumacs" + }, + { + "value": "tree saplings" + } + ] + }, + "swamp": { + "text": "swamp", + "annotations": { + "originally": { + "tag": "originally", + "value": "swamp (permanent or semi-permanent water body dominated by woody plants)" + } + }, + "comments": [ + "permanent or semi-permanent water body dominated by woody plants" + ] + }, + "tropical": { + "text": "tropical", + "annotations": { + "originally": { + "tag": "originally", + "value": "tropical (e.g. mangrove,palms)" + } + }, + "examples": [ + { + "value": "mangrove" + }, + { + "value": "palms" + } + ] + }, + "tundra": { + "text": "tundra", + "annotations": { + "originally": { + "tag": "originally", + "value": "tundra (mosses,lichens)" + } + }, + "examples": [ + { + "value": "lichens" + }, + { + "value": "mosses" + } + ] + }, + "vegetable crops": { + "text": "vegetable crops" + }, + "vine crops": { + "text": "vine crops", + "annotations": { + "originally": { + "tag": "originally", + "value": "vine crops (grapes)" + } + }, + "examples": [ + { + "value": "grapes" + } + ] + } + } + }, + "drainage_class_enum": { + "name": "drainage_class_enum", + "from_schema": "https://example.com/nmdc_submission_schema", + "permissible_values": { + "very poorly": { + "text": "very poorly" + }, + "poorly": { + "text": "poorly" + }, + "somewhat poorly": { + "text": "somewhat poorly" + }, + "moderately well": { + "text": "moderately well" + }, + "well": { + "text": "well" + }, + "excessively drained": { + "text": "excessively drained" + } + } + }, + "fao_class_enum": { + "name": "fao_class_enum", + "from_schema": "https://example.com/nmdc_submission_schema", + "permissible_values": { + "Acrisols": { + "text": "Acrisols" + }, + "Andosols": { + "text": "Andosols" + }, + "Arenosols": { + "text": "Arenosols" + }, + "Cambisols": { + "text": "Cambisols" + }, + "Chernozems": { + "text": "Chernozems" + }, + "Ferralsols": { + "text": "Ferralsols" + }, + "Fluvisols": { + "text": "Fluvisols" + }, + "Gleysols": { + "text": "Gleysols" + }, + "Greyzems": { + "text": "Greyzems" + }, + "Gypsisols": { + "text": "Gypsisols" + }, + "Histosols": { + "text": "Histosols" + }, + "Kastanozems": { + "text": "Kastanozems" + }, + "Lithosols": { + "text": "Lithosols" + }, + "Luvisols": { + "text": "Luvisols" + }, + "Nitosols": { + "text": "Nitosols" + }, + "Phaeozems": { + "text": "Phaeozems" + }, + "Planosols": { + "text": "Planosols" + }, + "Podzols": { + "text": "Podzols" + }, + "Podzoluvisols": { + "text": "Podzoluvisols" + }, + "Rankers": { + "text": "Rankers" + }, + "Regosols": { + "text": "Regosols" + }, + "Rendzinas": { + "text": "Rendzinas" + }, + "Solonchaks": { + "text": "Solonchaks" + }, + "Solonetz": { + "text": "Solonetz" + }, + "Vertisols": { + "text": "Vertisols" + }, + "Yermosols": { + "text": "Yermosols" + } + } + }, + "profile_position_enum": { + "name": "profile_position_enum", + "from_schema": "https://example.com/nmdc_submission_schema", + "permissible_values": { + "summit": { + "text": "summit" + }, + "shoulder": { + "text": "shoulder" + }, + "backslope": { + "text": "backslope" + }, + "footslope": { + "text": "footslope" + }, + "toeslope": { + "text": "toeslope" + } + } + }, + "soil_horizon_enum": { + "name": "soil_horizon_enum", + "from_schema": "https://example.com/nmdc_submission_schema", + "permissible_values": { + "O horizon": { + "text": "O horizon" + }, + "A horizon": { + "text": "A horizon" + }, + "E horizon": { + "text": "E horizon" + }, + "B horizon": { + "text": "B horizon" + }, + "C horizon": { + "text": "C horizon" + }, + "R layer": { + "text": "R layer" + }, + "Permafrost": { + "text": "Permafrost" + }, + "M horizon": { + "text": "M horizon" + } + } + }, + "tillage_enum": { + "name": "tillage_enum", + "from_schema": "https://example.com/nmdc_submission_schema", + "permissible_values": { + "drill": { + "text": "drill" + }, + "cutting disc": { + "text": "cutting disc" + }, + "ridge till": { + "text": "ridge till" + }, + "strip tillage": { + "text": "strip tillage" + }, + "zonal tillage": { + "text": "zonal tillage" + }, + "chisel": { + "text": "chisel" + }, + "tined": { + "text": "tined" + }, + "mouldboard": { + "text": "mouldboard" + }, + "disc plough": { + "text": "disc plough" + } + } + }, + "biol_stat_enum": { + "name": "biol_stat_enum", + "from_schema": "https://example.com/nmdc_submission_schema", + "permissible_values": { + "wild": { + "text": "wild" + }, + "natural": { + "text": "natural" + }, + "semi-natural": { + "text": "semi-natural" + }, + "inbred line": { + "text": "inbred line" + }, + "breeder's line": { + "text": "breeder's line" + }, + "hybrid": { + "text": "hybrid" + }, + "clonal selection": { + "text": "clonal selection" + }, + "mutant": { + "text": "mutant" + } + } + }, + "growth_habit_enum": { + "name": "growth_habit_enum", + "from_schema": "https://example.com/nmdc_submission_schema", + "permissible_values": { + "erect": { + "text": "erect" + }, + "semi-erect": { + "text": "semi-erect" + }, + "spreading": { + "text": "spreading" + }, + "prostrate": { + "text": "prostrate" + } + } + }, + "plant_sex_enum": { + "name": "plant_sex_enum", + "from_schema": "https://example.com/nmdc_submission_schema", + "permissible_values": { + "Androdioecious": { + "text": "Androdioecious" + }, + "Androecious": { + "text": "Androecious" + }, + "Androgynous": { + "text": "Androgynous" + }, + "Androgynomonoecious": { + "text": "Androgynomonoecious" + }, + "Andromonoecious": { + "text": "Andromonoecious" + }, + "Bisexual": { + "text": "Bisexual" + }, + "Dichogamous": { + "text": "Dichogamous" + }, + "Diclinous": { + "text": "Diclinous" + }, + "Dioecious": { + "text": "Dioecious" + }, + "Gynodioecious": { + "text": "Gynodioecious" + }, + "Gynoecious": { + "text": "Gynoecious" + }, + "Gynomonoecious": { + "text": "Gynomonoecious" + }, + "Hermaphroditic": { + "text": "Hermaphroditic" + }, + "Imperfect": { + "text": "Imperfect" + }, + "Monoclinous": { + "text": "Monoclinous" + }, + "Monoecious": { + "text": "Monoecious" + }, + "Perfect": { + "text": "Perfect" + }, + "Polygamodioecious": { + "text": "Polygamodioecious" + }, + "Polygamomonoecious": { + "text": "Polygamomonoecious" + }, + "Polygamous": { + "text": "Polygamous" + }, + "Protandrous": { + "text": "Protandrous" + }, + "Protogynous": { + "text": "Protogynous" + }, + "Subandroecious": { + "text": "Subandroecious" + }, + "Subdioecious": { + "text": "Subdioecious" + }, + "Subgynoecious": { + "text": "Subgynoecious" + }, + "Synoecious": { + "text": "Synoecious" + }, + "Trimonoecious": { + "text": "Trimonoecious" + }, + "Trioecious": { + "text": "Trioecious" + }, + "Unisexual": { + "text": "Unisexual" + } + } + }, + "samp_capt_status_enum": { + "name": "samp_capt_status_enum", + "from_schema": "https://example.com/nmdc_submission_schema", + "permissible_values": { + "active surveillance in response to an outbreak": { + "text": "active surveillance in response to an outbreak" + }, + "active surveillance not initiated by an outbreak": { + "text": "active surveillance not initiated by an outbreak" + }, + "farm sample": { + "text": "farm sample" + }, + "market sample": { + "text": "market sample" + }, + "other": { + "text": "other" + } + } + }, + "samp_dis_stage_enum": { + "name": "samp_dis_stage_enum", + "from_schema": "https://example.com/nmdc_submission_schema", + "permissible_values": { + "dissemination": { + "text": "dissemination" + }, + "growth and reproduction": { + "text": "growth and reproduction" + }, + "infection": { + "text": "infection" + }, + "inoculation": { + "text": "inoculation" + }, + "penetration": { + "text": "penetration" + }, + "other": { + "text": "other" + } + } + }, + "sediment_type_enum": { + "name": "sediment_type_enum", + "from_schema": "https://example.com/nmdc_submission_schema", + "permissible_values": { + "biogenous": { + "text": "biogenous" + }, + "cosmogenous": { + "text": "cosmogenous" + }, + "hydrogenous": { + "text": "hydrogenous" + }, + "lithogenous": { + "text": "lithogenous" + } + } + }, + "tidal_stage_enum": { + "name": "tidal_stage_enum", + "from_schema": "https://example.com/nmdc_submission_schema", + "permissible_values": { + "low tide": { + "text": "low tide" + }, + "ebb tide": { + "text": "ebb tide" + }, + "flood tide": { + "text": "flood tide" + }, + "high tide": { + "text": "high tide" + } + } + }, + "host_sex_enum": { + "name": "host_sex_enum", + "from_schema": "https://example.com/nmdc_submission_schema", + "permissible_values": { + "female": { + "text": "female" + }, + "hermaphrodite": { + "text": "hermaphrodite" + }, + "male": { + "text": "male" + }, + "neuter": { + "text": "neuter" + } + } + }, + "AnalysisTypeEnum": { + "name": "AnalysisTypeEnum", + "from_schema": "https://example.com/nmdc_submission_schema", + "permissible_values": { + "metabolomics": { + "text": "metabolomics" + }, + "metagenomics": { + "text": "metagenomics", + "description": "Standard short-read metagenomic sequencing", + "title": "Metagenomics" + }, + "metagenomics_long_read": { + "text": "metagenomics_long_read", + "description": "Long-read metagenomic sequencing", + "title": "Metagenomics (long read)" + }, + "metaproteomics": { + "text": "metaproteomics" + }, + "metatranscriptomics": { + "text": "metatranscriptomics" + }, + "natural organic matter": { + "text": "natural organic matter" + }, + "bulk chemistry": { + "text": "bulk chemistry" + } + } + }, + "DNASampleFormatEnum": { + "name": "DNASampleFormatEnum", + "from_schema": "https://example.com/nmdc_submission_schema", + "permissible_values": { + "10 mM Tris-HCl": { + "text": "10 mM Tris-HCl" + }, + "DNAStable": { + "text": "DNAStable" + }, + "Ethanol": { + "text": "Ethanol" + }, + "Low EDTA TE": { + "text": "Low EDTA TE" + }, + "MDA reaction buffer": { + "text": "MDA reaction buffer" + }, + "PBS": { + "text": "PBS" + }, + "Pellet": { + "text": "Pellet" + }, + "RNAStable": { + "text": "RNAStable" + }, + "TE": { + "text": "TE" + }, + "Water": { + "text": "Water" + }, + "Gentegra-DNA": { + "text": "Gentegra-DNA" + }, + "Gentegra-RNA": { + "text": "Gentegra-RNA" + } + } + }, + "RNASampleFormatEnum": { + "name": "RNASampleFormatEnum", + "from_schema": "https://example.com/nmdc_submission_schema", + "permissible_values": { + "10 mM Tris-HCl": { + "text": "10 mM Tris-HCl" + }, + "DNAStable": { + "text": "DNAStable" + }, + "Ethanol": { + "text": "Ethanol" + }, + "Low EDTA TE": { + "text": "Low EDTA TE" + }, + "MDA reaction buffer": { + "text": "MDA reaction buffer" + }, + "PBS": { + "text": "PBS" + }, + "Pellet": { + "text": "Pellet" + }, + "RNAStable": { + "text": "RNAStable" + }, + "TE": { + "text": "TE" + }, + "Water": { + "text": "Water" + }, + "Gentegra-DNA": { + "text": "Gentegra-DNA" + }, + "Gentegra-RNA": { + "text": "Gentegra-RNA" + } + } + }, + "EcosystemEnum": { + "name": "EcosystemEnum", + "from_schema": "https://example.com/nmdc_submission_schema", + "permissible_values": { + "Engineered": { + "text": "Engineered" + }, + "Environmental": { + "text": "Environmental" + }, + "Host-associated": { + "text": "Host-associated" + } + } + }, + "EcosystemCategoryEnum": { + "name": "EcosystemCategoryEnum", + "from_schema": "https://example.com/nmdc_submission_schema", + "permissible_values": { + "Air": { + "text": "Air" + }, + "Algae": { + "text": "Algae" + }, + "Amoebozoa": { + "text": "Amoebozoa" + }, + "Amphibia": { + "text": "Amphibia" + }, + "Animal feed production": { + "text": "Animal feed production" + }, + "Annelida": { + "text": "Annelida" + }, + "Aquatic": { + "text": "Aquatic" + }, + "Arthropoda: Chelicerates": { + "text": "Arthropoda: Chelicerates" + }, + "Arthropoda: Crustaceans": { + "text": "Arthropoda: Crustaceans" + }, + "Arthropoda: Insects": { + "text": "Arthropoda: Insects" + }, + "Arthropoda: Myriapoda": { + "text": "Arthropoda: Myriapoda" + }, + "Artificial ecosystem": { + "text": "Artificial ecosystem" + }, + "Bioreactor": { + "text": "Bioreactor" + }, + "Bioremediation": { + "text": "Bioremediation" + }, + "Biotransformation": { + "text": "Biotransformation" + }, + "Birds": { + "text": "Birds" + }, + "Bryozoa": { + "text": "Bryozoa" + }, + "Built environment": { + "text": "Built environment" + }, + "Cephalochordata": { + "text": "Cephalochordata" + }, + "Cnidaria": { + "text": "Cnidaria" + }, + "Drugs production": { + "text": "Drugs production" + }, + "Endosymbionts": { + "text": "Endosymbionts" + }, + "Feedstock": { + "text": "Feedstock" + }, + "Fish": { + "text": "Fish" + }, + "Food production": { + "text": "Food production" + }, + "Fungi": { + "text": "Fungi" + }, + "Industrial production": { + "text": "Industrial production" + }, + "Invertebrates": { + "text": "Invertebrates" + }, + "Lab culture": { + "text": "Lab culture" + }, + "Lab enrichment": { + "text": "Lab enrichment" + }, + "Lab synthesis": { + "text": "Lab synthesis" + }, + "Laboratory developed": { + "text": "Laboratory developed" + }, + "Mammals": { + "text": "Mammals" + }, + "Mammals: Human": { + "text": "Mammals: Human" + }, + "Microbial": { + "text": "Microbial" + }, + "Modeled": { + "text": "Modeled" + }, + "Mollusca": { + "text": "Mollusca" + }, + "Paper": { + "text": "Paper" + }, + "Plants": { + "text": "Plants" + }, + "Porifera": { + "text": "Porifera" + }, + "Protists": { + "text": "Protists" + }, + "Protozoa": { + "text": "Protozoa" + }, + "Reptilia": { + "text": "Reptilia" + }, + "Sewage treatment plant": { + "text": "Sewage treatment plant" + }, + "Solid waste": { + "text": "Solid waste" + }, + "Terrestrial": { + "text": "Terrestrial" + }, + "Tunicates": { + "text": "Tunicates" + }, + "Unclassified": { + "text": "Unclassified" + }, + "WWTP": { + "text": "WWTP" + }, + "Wastewater": { + "text": "Wastewater" + } + } + }, + "EcosystemTypeEnum": { + "name": "EcosystemTypeEnum", + "from_schema": "https://example.com/nmdc_submission_schema", + "permissible_values": { + "A/O treatment system": { + "text": "A/O treatment system" + }, + "Abdomen": { + "text": "Abdomen" + }, + "Abdominal cavity": { + "text": "Abdominal cavity" + }, + "Abdominal/Peritoneal cavity": { + "text": "Abdominal/Peritoneal cavity" + }, + "Acidic": { + "text": "Acidic" + }, + "Activated Sludge": { + "text": "Activated Sludge" + }, + "Activated sludge": { + "text": "Activated sludge" + }, + "Aerobic": { + "text": "Aerobic" + }, + "Aerobic digester": { + "text": "Aerobic digester" + }, + "Agricultural field": { + "text": "Agricultural field" + }, + "Agricultural waste": { + "text": "Agricultural waste" + }, + "Amoebozoa": { + "text": "Amoebozoa" + }, + "Anaerobic": { + "text": "Anaerobic" + }, + "Anaerobic digester": { + "text": "Anaerobic digester" + }, + "Anaerobic digestor": { + "text": "Anaerobic digestor" + }, + "Animal cage": { + "text": "Animal cage" + }, + "Animal waste": { + "text": "Animal waste" + }, + "Appressorium": { + "text": "Appressorium" + }, + "Aquaculture": { + "text": "Aquaculture" + }, + "Artesian spring": { + "text": "Artesian spring" + }, + "Ascidians": { + "text": "Ascidians" + }, + "Asphalt lakes": { + "text": "Asphalt lakes" + }, + "Auditory/Hearing system": { + "text": "Auditory/Hearing system" + }, + "Baby formula": { + "text": "Baby formula" + }, + "Bacteria": { + "text": "Bacteria" + }, + "Bacterivore": { + "text": "Bacterivore" + }, + "Bagasse": { + "text": "Bagasse" + }, + "Beans": { + "text": "Beans" + }, + "Benign tumor": { + "text": "Benign tumor" + }, + "Beverages": { + "text": "Beverages" + }, + "Bio- and green waste (BGW)": { + "text": "Bio- and green waste (BGW)" + }, + "Biochar": { + "text": "Biochar" + }, + "Biocrust": { + "text": "Biocrust" + }, + "Bivalves": { + "text": "Bivalves" + }, + "Bread production": { + "text": "Bread production" + }, + "Breviatea": { + "text": "Breviatea" + }, + "Brown Algae": { + "text": "Brown Algae" + }, + "Brown waste": { + "text": "Brown waste" + }, + "Bryophytes": { + "text": "Bryophytes" + }, + "Bryozoans": { + "text": "Bryozoans" + }, + "Building": { + "text": "Building" + }, + "Canal": { + "text": "Canal" + }, + "Cave": { + "text": "Cave" + }, + "Cell Line": { + "text": "Cell Line" + }, + "Cell culture": { + "text": "Cell culture" + }, + "Cellulose associated waste": { + "text": "Cellulose associated waste" + }, + "Cement wall": { + "text": "Cement wall" + }, + "Chemical products": { + "text": "Chemical products" + }, + "Circulatory system": { + "text": "Circulatory system" + }, + "City": { + "text": "City" + }, + "Cnidaria": { + "text": "Cnidaria" + }, + "Coal": { + "text": "Coal" + }, + "Composting": { + "text": "Composting" + }, + "Connective tissue": { + "text": "Connective tissue" + }, + "Continuous culture": { + "text": "Continuous culture" + }, + "Cryptomonads/Cryptophytes": { + "text": "Cryptomonads/Cryptophytes" + }, + "Ctenophora": { + "text": "Ctenophora" + }, + "Culture media": { + "text": "Culture media" + }, + "Currency notes": { + "text": "Currency notes" + }, + "DHS reactor": { + "text": "DHS reactor" + }, + "Dairy processing facility": { + "text": "Dairy processing facility" + }, + "Dairy products": { + "text": "Dairy products" + }, + "Debries": { + "text": "Debries" + }, + "Deep subsurface": { + "text": "Deep subsurface" + }, + "Defined media": { + "text": "Defined media" + }, + "Denitrification": { + "text": "Denitrification" + }, + "Desert": { + "text": "Desert" + }, + "Diatoms": { + "text": "Diatoms" + }, + "Digestive system": { + "text": "Digestive system" + }, + "Dinoflagellata": { + "text": "Dinoflagellata" + }, + "Dinoflagellates": { + "text": "Dinoflagellates" + }, + "Drinking water treatment plant": { + "text": "Drinking water treatment plant" + }, + "Drugs/Supplements": { + "text": "Drugs/Supplements" + }, + "EBPR": { + "text": "EBPR" + }, + "Echinodermata": { + "text": "Echinodermata" + }, + "Effluent": { + "text": "Effluent" + }, + "Egg products": { + "text": "Egg products" + }, + "Embryo": { + "text": "Embryo" + }, + "Endocrine system": { + "text": "Endocrine system" + }, + "Endosphere": { + "text": "Endosphere" + }, + "Engineered product": { + "text": "Engineered product" + }, + "Equipment/Utensils": { + "text": "Equipment/Utensils" + }, + "Excavata": { + "text": "Excavata" + }, + "Excretory system": { + "text": "Excretory system" + }, + "Fat body": { + "text": "Fat body" + }, + "Feedstock": { + "text": "Feedstock" + }, + "Fermentation": { + "text": "Fermentation" + }, + "Fermentation cellar": { + "text": "Fermentation cellar" + }, + "Fermentation pit": { + "text": "Fermentation pit" + }, + "Fermentation starter": { + "text": "Fermentation starter" + }, + "Fermented beverages": { + "text": "Fermented beverages" + }, + "Fermented food": { + "text": "Fermented food" + }, + "Fermented seafood": { + "text": "Fermented seafood" + }, + "Fermented vegetables": { + "text": "Fermented vegetables" + }, + "Fetus": { + "text": "Fetus" + }, + "Fish products": { + "text": "Fish products" + }, + "Floodplain": { + "text": "Floodplain" + }, + "Food sample": { + "text": "Food sample" + }, + "Food waste": { + "text": "Food waste" + }, + "Freshwater": { + "text": "Freshwater" + }, + "Fruiting body": { + "text": "Fruiting body" + }, + "Fungi": { + "text": "Fungi" + }, + "Genetic cross": { + "text": "Genetic cross" + }, + "Genetically modified": { + "text": "Genetically modified" + }, + "Geologic": { + "text": "Geologic" + }, + "Germ tube": { + "text": "Germ tube" + }, + "Gills": { + "text": "Gills" + }, + "Golden Algae": { + "text": "Golden Algae" + }, + "Grains/Grain products": { + "text": "Grains/Grain products" + }, + "Grass": { + "text": "Grass" + }, + "Green algae": { + "text": "Green algae" + }, + "Green waste": { + "text": "Green waste" + }, + "Haptophytes": { + "text": "Haptophytes" + }, + "Head": { + "text": "Head" + }, + "High-salinity/high-pH": { + "text": "High-salinity/high-pH" + }, + "Hospital": { + "text": "Hospital" + }, + "House": { + "text": "House" + }, + "Household waste": { + "text": "Household waste" + }, + "Human waste": { + "text": "Human waste" + }, + "Hydrocarbon": { + "text": "Hydrocarbon" + }, + "Indoor Air": { + "text": "Indoor Air" + }, + "Industrial waste": { + "text": "Industrial waste" + }, + "Industrial wastewater": { + "text": "Industrial wastewater" + }, + "Influent": { + "text": "Influent" + }, + "Integument": { + "text": "Integument" + }, + "Integumentary system": { + "text": "Integumentary system" + }, + "International Space Station": { + "text": "International Space Station" + }, + "Intracellular endosymbionts": { + "text": "Intracellular endosymbionts" + }, + "Landfill": { + "text": "Landfill" + }, + "Larva": { + "text": "Larva" + }, + "Larva: Nauplius": { + "text": "Larva: Nauplius" + }, + "Larva: Zoea": { + "text": "Larva: Zoea" + }, + "Larvae": { + "text": "Larvae" + }, + "Latrine chamber": { + "text": "Latrine chamber" + }, + "Legs and wings": { + "text": "Legs and wings" + }, + "Lichen": { + "text": "Lichen" + }, + "Lymphatic system": { + "text": "Lymphatic system" + }, + "MBR (Membrane bioreactor)": { + "text": "MBR (Membrane bioreactor)" + }, + "Malignant tumor": { + "text": "Malignant tumor" + }, + "Marine": { + "text": "Marine" + }, + "Meat products": { + "text": "Meat products" + }, + "Mesocosm": { + "text": "Mesocosm" + }, + "Metal": { + "text": "Metal" + }, + "Microalgae": { + "text": "Microalgae" + }, + "Microbial enhanced oil recovery": { + "text": "Microbial enhanced oil recovery" + }, + "Microbial fuel cells/MFC": { + "text": "Microbial fuel cells/MFC" + }, + "Microbial solubilization of coal": { + "text": "Microbial solubilization of coal" + }, + "Microcosm": { + "text": "Microcosm" + }, + "Mine": { + "text": "Mine" + }, + "Mixed alcohol bioreactor": { + "text": "Mixed alcohol bioreactor" + }, + "Mixed algae turf": { + "text": "Mixed algae turf" + }, + "Mixed feedstock": { + "text": "Mixed feedstock" + }, + "Mixed liquor": { + "text": "Mixed liquor" + }, + "Mixed parts": { + "text": "Mixed parts" + }, + "Monument": { + "text": "Monument" + }, + "Mud microcosm": { + "text": "Mud microcosm" + }, + "Mud volcano": { + "text": "Mud volcano" + }, + "Multiple systems": { + "text": "Multiple systems" + }, + "Multisystem conditions": { + "text": "Multisystem conditions" + }, + "Municipal landfill": { + "text": "Municipal landfill" + }, + "Muscular system": { + "text": "Muscular system" + }, + "Mushroom farm": { + "text": "Mushroom farm" + }, + "Mycelium": { + "text": "Mycelium" + }, + "Mycorrhiza": { + "text": "Mycorrhiza" + }, + "Nanoflagellates": { + "text": "Nanoflagellates" + }, + "Nematoda": { + "text": "Nematoda" + }, + "Nervous system": { + "text": "Nervous system" + }, + "Nest": { + "text": "Nest" + }, + "Nodule": { + "text": "Nodule" + }, + "Non-marine Saline and Alkaline": { + "text": "Non-marine Saline and Alkaline" + }, + "Nuclear test reactor": { + "text": "Nuclear test reactor" + }, + "Nutrient removal": { + "text": "Nutrient removal" + }, + "Nutrient-poor": { + "text": "Nutrient-poor" + }, + "Nutrient-rich": { + "text": "Nutrient-rich" + }, + "Nuts": { + "text": "Nuts" + }, + "Nymph/Instar": { + "text": "Nymph/Instar" + }, + "Oil refinery": { + "text": "Oil refinery" + }, + "Oil reservoir": { + "text": "Oil reservoir" + }, + "Olfactory system": { + "text": "Olfactory system" + }, + "Oomycetes": { + "text": "Oomycetes" + }, + "Ootheca/Egg mass": { + "text": "Ootheca/Egg mass" + }, + "Outdoor Air": { + "text": "Outdoor Air" + }, + "Oxymonads": { + "text": "Oxymonads" + }, + "Oyster": { + "text": "Oyster" + }, + "Pastry": { + "text": "Pastry" + }, + "Peat moss": { + "text": "Peat moss" + }, + "Percolator": { + "text": "Percolator" + }, + "Persistent organic pollutants (POP)": { + "text": "Persistent organic pollutants (POP)" + }, + "Pessonella": { + "text": "Pessonella" + }, + "Photobioreactor (PBR)": { + "text": "Photobioreactor (PBR)" + }, + "Phyllosphere": { + "text": "Phyllosphere" + }, + "Pipeline": { + "text": "Pipeline" + }, + "Pit lake": { + "text": "Pit lake" + }, + "Pitcher": { + "text": "Pitcher" + }, + "Plant callus": { + "text": "Plant callus" + }, + "Plant growth chamber": { + "text": "Plant growth chamber" + }, + "Plant litter": { + "text": "Plant litter" + }, + "Plant products": { + "text": "Plant products" + }, + "Plastic waste": { + "text": "Plastic waste" + }, + "Platyhelminthes": { + "text": "Platyhelminthes" + }, + "Post-larva": { + "text": "Post-larva" + }, + "Poultry confinement building": { + "text": "Poultry confinement building" + }, + "Prepupa": { + "text": "Prepupa" + }, + "Pupa": { + "text": "Pupa" + }, + "Reclaimed/Recycled wastewater": { + "text": "Reclaimed/Recycled wastewater" + }, + "Red algae": { + "text": "Red algae" + }, + "Remains": { + "text": "Remains" + }, + "Reproductive system": { + "text": "Reproductive system" + }, + "Respiratory system": { + "text": "Respiratory system" + }, + "Rhizoid": { + "text": "Rhizoid" + }, + "Rhizome": { + "text": "Rhizome" + }, + "River": { + "text": "River" + }, + "Rock-dwelling (endoliths)": { + "text": "Rock-dwelling (endoliths)" + }, + "Rock-dwelling (subaerial biofilms)": { + "text": "Rock-dwelling (subaerial biofilms)" + }, + "Roots": { + "text": "Roots" + }, + "SBR-EBPR": { + "text": "SBR-EBPR" + }, + "SSF (Solid state fermentation)": { + "text": "SSF (Solid state fermentation)" + }, + "Salt": { + "text": "Salt" + }, + "Sand microcosm": { + "text": "Sand microcosm" + }, + "Saprolite–Bedrock interface": { + "text": "Saprolite–Bedrock interface" + }, + "Sargassum": { + "text": "Sargassum" + }, + "Sclerotium": { + "text": "Sclerotium" + }, + "Seafood": { + "text": "Seafood" + }, + "Seafood product": { + "text": "Seafood product" + }, + "Seawater microcosm": { + "text": "Seawater microcosm" + }, + "Sediment": { + "text": "Sediment" + }, + "Sediment microcosm": { + "text": "Sediment microcosm" + }, + "Seeds": { + "text": "Seeds" + }, + "Semi-continuous": { + "text": "Semi-continuous" + }, + "Sensory organs": { + "text": "Sensory organs" + }, + "Sewage": { + "text": "Sewage" + }, + "Shell": { + "text": "Shell" + }, + "Silage fermentation": { + "text": "Silage fermentation" + }, + "Simulated communities (DNA mixture)": { + "text": "Simulated communities (DNA mixture)" + }, + "Simulated communities (contig mixture)": { + "text": "Simulated communities (contig mixture)" + }, + "Simulated communities (microbial mixture)": { + "text": "Simulated communities (microbial mixture)" + }, + "Simulated communities (sequence read mixture)": { + "text": "Simulated communities (sequence read mixture)" + }, + "Skeletal system": { + "text": "Skeletal system" + }, + "Slaughterhouse/Abattoir": { + "text": "Slaughterhouse/Abattoir" + }, + "Sludge": { + "text": "Sludge" + }, + "Soil": { + "text": "Soil" + }, + "Soil microcosm": { + "text": "Soil microcosm" + }, + "Soil-bedrock interface": { + "text": "Soil-bedrock interface" + }, + "Solar panel": { + "text": "Solar panel" + }, + "Sourdough": { + "text": "Sourdough" + }, + "Spacecraft Assembly Cleanrooms": { + "text": "Spacecraft Assembly Cleanrooms" + }, + "Spices": { + "text": "Spices" + }, + "Sponge": { + "text": "Sponge" + }, + "Spore": { + "text": "Spore" + }, + "Sporozoa": { + "text": "Sporozoa" + }, + "Stroma": { + "text": "Stroma" + }, + "Subsurface": { + "text": "Subsurface" + }, + "Sulphur Autotrophic Denitrification": { + "text": "Sulphur Autotrophic Denitrification" + }, + "Sweets": { + "text": "Sweets" + }, + "Swim bladder": { + "text": "Swim bladder" + }, + "Swimming pool": { + "text": "Swimming pool" + }, + "Swine confinement building": { + "text": "Swine confinement building" + }, + "Tailings pond": { + "text": "Tailings pond" + }, + "Terephthalate": { + "text": "Terephthalate" + }, + "Tetrachloroethylene and derivatives": { + "text": "Tetrachloroethylene and derivatives" + }, + "Thermal springs": { + "text": "Thermal springs" + }, + "Thiocyanate": { + "text": "Thiocyanate" + }, + "Thiocyanate-remediating": { + "text": "Thiocyanate-remediating" + }, + "Thoracic cavity": { + "text": "Thoracic cavity" + }, + "Thorax": { + "text": "Thorax" + }, + "Tissue": { + "text": "Tissue" + }, + "Train car": { + "text": "Train car" + }, + "Tumor": { + "text": "Tumor" + }, + "UASB (Upflow anaerobic sludge blanket)": { + "text": "UASB (Upflow anaerobic sludge blanket)" + }, + "Unclassified": { + "text": "Unclassified" + }, + "Undefined media": { + "text": "Undefined media" + }, + "Unknown material": { + "text": "Unknown material" + }, + "Unspecified system": { + "text": "Unspecified system" + }, + "Urban waste": { + "text": "Urban waste" + }, + "Urban wastewater": { + "text": "Urban wastewater" + }, + "Urinary system": { + "text": "Urinary system" + }, + "Vegetable": { + "text": "Vegetable" + }, + "Vermicompost": { + "text": "Vermicompost" + }, + "Visual system": { + "text": "Visual system" + }, + "Vivarium": { + "text": "Vivarium" + }, + "Volcanic": { + "text": "Volcanic" + }, + "Wastewater": { + "text": "Wastewater" + }, + "Water microcosm": { + "text": "Water microcosm" + }, + "Water treatment plant": { + "text": "Water treatment plant" + }, + "Whole body": { + "text": "Whole body" + }, + "Whole plant body": { + "text": "Whole plant body" + }, + "Wood": { + "text": "Wood" + }, + "Yellow-green algae": { + "text": "Yellow-green algae" + }, + "Zoo waste": { + "text": "Zoo waste" + } + } + }, + "EcosystemSubtypeEnum": { + "name": "EcosystemSubtypeEnum", + "from_schema": "https://example.com/nmdc_submission_schema", + "permissible_values": { + "A/O bioreactor": { + "text": "A/O bioreactor" + }, + "AGS (Aerobic granular sludge)": { + "text": "AGS (Aerobic granular sludge)" + }, + "Abdomen": { + "text": "Abdomen" + }, + "Abdomen/Pleon": { + "text": "Abdomen/Pleon" + }, + "Abscess": { + "text": "Abscess" + }, + "Abyssopelagic": { + "text": "Abyssopelagic" + }, + "Accessory nidamental gland (ANG)": { + "text": "Accessory nidamental gland (ANG)" + }, + "Acid lake": { + "text": "Acid lake" + }, + "Acid mine drainage": { + "text": "Acid mine drainage" + }, + "Acidic": { + "text": "Acidic" + }, + "Acidic hypersaline lake": { + "text": "Acidic hypersaline lake" + }, + "Acidic lake": { + "text": "Acidic lake" + }, + "Activated sludge": { + "text": "Activated sludge" + }, + "Adenoma": { + "text": "Adenoma" + }, + "Adipose tissue": { + "text": "Adipose tissue" + }, + "Aerial root": { + "text": "Aerial root" + }, + "Aerobic": { + "text": "Aerobic" + }, + "Aerobic media": { + "text": "Aerobic media" + }, + "Agricultural field": { + "text": "Agricultural field" + }, + "Agricultural land": { + "text": "Agricultural land" + }, + "Agricultural wastewater": { + "text": "Agricultural wastewater" + }, + "Air": { + "text": "Air" + }, + "Air sacs": { + "text": "Air sacs" + }, + "Air scrubber": { + "text": "Air scrubber" + }, + "Algae": { + "text": "Algae" + }, + "Algae cultivation tank": { + "text": "Algae cultivation tank" + }, + "Algae raceway pond": { + "text": "Algae raceway pond" + }, + "Alkaline": { + "text": "Alkaline" + }, + "Alligator nest": { + "text": "Alligator nest" + }, + "Alpine": { + "text": "Alpine" + }, + "Amniotic sac": { + "text": "Amniotic sac" + }, + "Anaerobic": { + "text": "Anaerobic" + }, + "Anaerobic media": { + "text": "Anaerobic media" + }, + "Anaerobic-Aerobic": { + "text": "Anaerobic-Aerobic" + }, + "Anode": { + "text": "Anode" + }, + "Antennal/Green glands": { + "text": "Antennal/Green glands" + }, + "Anthosphere": { + "text": "Anthosphere" + }, + "Antlers": { + "text": "Antlers" + }, + "Apocrine sweat glands": { + "text": "Apocrine sweat glands" + }, + "Apoeccrine sweat glands": { + "text": "Apoeccrine sweat glands" + }, + "Aquaculture farm": { + "text": "Aquaculture farm" + }, + "Aquatic biofilm": { + "text": "Aquatic biofilm" + }, + "Aquifer": { + "text": "Aquifer" + }, + "Arable": { + "text": "Arable" + }, + "Archaea": { + "text": "Archaea" + }, + "Archipelago": { + "text": "Archipelago" + }, + "Arterial ulcer": { + "text": "Arterial ulcer" + }, + "Ascites": { + "text": "Ascites" + }, + "Atoll lagoon": { + "text": "Atoll lagoon" + }, + "Autotrophic (ANF)": { + "text": "Autotrophic (ANF)" + }, + "Aviation fuel": { + "text": "Aviation fuel" + }, + "BHK": { + "text": "BHK" + }, + "Bacteria": { + "text": "Bacteria" + }, + "Bark": { + "text": "Bark" + }, + "Bathypelagic": { + "text": "Bathypelagic" + }, + "Beef": { + "text": "Beef" + }, + "Benign tumor tissue": { + "text": "Benign tumor tissue" + }, + "Benthic": { + "text": "Benthic" + }, + "Benthic zone": { + "text": "Benthic zone" + }, + "Benzene": { + "text": "Benzene" + }, + "Biliary tract": { + "text": "Biliary tract" + }, + "Bioanode": { + "text": "Bioanode" + }, + "Biocathode": { + "text": "Biocathode" + }, + "Biochar": { + "text": "Biochar" + }, + "Biocrust": { + "text": "Biocrust" + }, + "Biofilm": { + "text": "Biofilm" + }, + "Biofouling": { + "text": "Biofouling" + }, + "Biogas": { + "text": "Biogas" + }, + "Biological phosphorus removal": { + "text": "Biological phosphorus removal" + }, + "Biomass": { + "text": "Biomass" + }, + "Blade": { + "text": "Blade" + }, + "Blood": { + "text": "Blood" + }, + "Bog lake": { + "text": "Bog lake" + }, + "Bone": { + "text": "Bone" + }, + "Bones": { + "text": "Bones" + }, + "Boreal forest/Taiga": { + "text": "Boreal forest/Taiga" + }, + "Botanical garden": { + "text": "Botanical garden" + }, + "Brain": { + "text": "Brain" + }, + "Bread": { + "text": "Bread" + }, + "Bronchi": { + "text": "Bronchi" + }, + "Buffer": { + "text": "Buffer" + }, + "Bulb": { + "text": "Bulb" + }, + "Bursa of Fabricius": { + "text": "Bursa of Fabricius" + }, + "CHO": { + "text": "CHO" + }, + "CaSki": { + "text": "CaSki" + }, + "Canthus": { + "text": "Canthus" + }, + "Carcinoid": { + "text": "Carcinoid" + }, + "Carcinoma": { + "text": "Carcinoma" + }, + "Carposphere": { + "text": "Carposphere" + }, + "Cartilage": { + "text": "Cartilage" + }, + "Cathode": { + "text": "Cathode" + }, + "Cattle barn": { + "text": "Cattle barn" + }, + "Caulosphere": { + "text": "Caulosphere" + }, + "Cave": { + "text": "Cave" + }, + "Ceca": { + "text": "Ceca" + }, + "Cephalothorax": { + "text": "Cephalothorax" + }, + "Cerebrospinal fluid": { + "text": "Cerebrospinal fluid" + }, + "Ceros": { + "text": "Ceros" + }, + "Ceruminous glands": { + "text": "Ceruminous glands" + }, + "Chaparral": { + "text": "Chaparral" + }, + "Chelicerates nest": { + "text": "Chelicerates nest" + }, + "Chloroethene": { + "text": "Chloroethene" + }, + "Cholesteatoma": { + "text": "Cholesteatoma" + }, + "City park": { + "text": "City park" + }, + "Claws": { + "text": "Claws" + }, + "Claws/Talon": { + "text": "Claws/Talon" + }, + "Clay": { + "text": "Clay" + }, + "Coalbed methane well": { + "text": "Coalbed methane well" + }, + "Coastal": { + "text": "Coastal" + }, + "Coastal area": { + "text": "Coastal area" + }, + "Coastal lagoon": { + "text": "Coastal lagoon" + }, + "Cob": { + "text": "Cob" + }, + "Cocoon": { + "text": "Cocoon" + }, + "Cold seeps": { + "text": "Cold seeps" + }, + "Cold smoked fish": { + "text": "Cold smoked fish" + }, + "Composting": { + "text": "Composting" + }, + "Composting facility": { + "text": "Composting facility" + }, + "Conjunctiva": { + "text": "Conjunctiva" + }, + "Contaminated": { + "text": "Contaminated" + }, + "Contaminated soil": { + "text": "Contaminated soil" + }, + "Continental margin": { + "text": "Continental margin" + }, + "Cooked fish": { + "text": "Cooked fish" + }, + "Cooked meat": { + "text": "Cooked meat" + }, + "Cooling water": { + "text": "Cooling water" + }, + "Coral": { + "text": "Coral" + }, + "Cortex": { + "text": "Cortex" + }, + "Cosmetic products": { + "text": "Cosmetic products" + }, + "Creek": { + "text": "Creek" + }, + "Crop": { + "text": "Crop" + }, + "Crude oil sludge": { + "text": "Crude oil sludge" + }, + "Crustaceans pond": { + "text": "Crustaceans pond" + }, + "Crustaceans raceway": { + "text": "Crustaceans raceway" + }, + "Crustaceans tank": { + "text": "Crustaceans tank" + }, + "Cultivation substrate": { + "text": "Cultivation substrate" + }, + "Cuticle": { + "text": "Cuticle" + }, + "Cyanide/thiocyanate": { + "text": "Cyanide/thiocyanate" + }, + "Dairy farm": { + "text": "Dairy farm" + }, + "Decayed wood": { + "text": "Decayed wood" + }, + "Decomposed body": { + "text": "Decomposed body" + }, + "Deep subsurface": { + "text": "Deep subsurface" + }, + "Deepwater/Brine lake": { + "text": "Deepwater/Brine lake" + }, + "Demersal zone": { + "text": "Demersal zone" + }, + "Dermoid": { + "text": "Dermoid" + }, + "Desert": { + "text": "Desert" + }, + "Desert springs": { + "text": "Desert springs" + }, + "Diabetic foot ulcer (DFU)": { + "text": "Diabetic foot ulcer (DFU)" + }, + "Diaphragm": { + "text": "Diaphragm" + }, + "Digestate": { + "text": "Digestate" + }, + "Digestive system": { + "text": "Digestive system" + }, + "Digestive tube": { + "text": "Digestive tube" + }, + "Dissolved organics (aerobic)": { + "text": "Dissolved organics (aerobic)" + }, + "Dissolved organics (anaerobic)": { + "text": "Dissolved organics (anaerobic)" + }, + "Distilled water": { + "text": "Distilled water" + }, + "Doormat": { + "text": "Doormat" + }, + "Drainage basin": { + "text": "Drainage basin" + }, + "Drainage ditch": { + "text": "Drainage ditch" + }, + "Dried seaweeds": { + "text": "Dried seaweeds" + }, + "Drinking water": { + "text": "Drinking water" + }, + "Drinking water filter": { + "text": "Drinking water filter" + }, + "Drinking water pipeline": { + "text": "Drinking water pipeline" + }, + "Dust": { + "text": "Dust" + }, + "Ear": { + "text": "Ear" + }, + "Eccrine sweat glands": { + "text": "Eccrine sweat glands" + }, + "Ectosymbionts": { + "text": "Ectosymbionts" + }, + "Effluent": { + "text": "Effluent" + }, + "Egg capsule": { + "text": "Egg capsule" + }, + "Eggs": { + "text": "Eggs" + }, + "Embryo": { + "text": "Embryo" + }, + "Endocrine gland": { + "text": "Endocrine gland" + }, + "Endosphere": { + "text": "Endosphere" + }, + "Endosymbionts": { + "text": "Endosymbionts" + }, + "Epidermoid": { + "text": "Epidermoid" + }, + "Epipelagic": { + "text": "Epipelagic" + }, + "Epithelial lining fluid": { + "text": "Epithelial lining fluid" + }, + "Esophagus": { + "text": "Esophagus" + }, + "Evaporite": { + "text": "Evaporite" + }, + "External genitalia": { + "text": "External genitalia" + }, + "External genitalia/Vulva": { + "text": "External genitalia/Vulva" + }, + "External organs": { + "text": "External organs" + }, + "Eye": { + "text": "Eye" + }, + "Eye: Ciliary body": { + "text": "Eye: Ciliary body" + }, + "Eye: Vitreous chamber": { + "text": "Eye: Vitreous chamber" + }, + "Fallopian tubes": { + "text": "Fallopian tubes" + }, + "Fascia": { + "text": "Fascia" + }, + "Feedlot": { + "text": "Feedlot" + }, + "Fermentation": { + "text": "Fermentation" + }, + "Fermented dairy products": { + "text": "Fermented dairy products" + }, + "Fermented fish": { + "text": "Fermented fish" + }, + "Fermented meat products": { + "text": "Fermented meat products" + }, + "Fetal tissue": { + "text": "Fetal tissue" + }, + "Fibroma": { + "text": "Fibroma" + }, + "Filter": { + "text": "Filter" + }, + "Fish pond": { + "text": "Fish pond" + }, + "Fish tank": { + "text": "Fish tank" + }, + "Fjord": { + "text": "Fjord" + }, + "Floodplain": { + "text": "Floodplain" + }, + "Floodplain lake": { + "text": "Floodplain lake" + }, + "Floor": { + "text": "Floor" + }, + "Foregut": { + "text": "Foregut" + }, + "Forest": { + "text": "Forest" + }, + "Fossil": { + "text": "Fossil" + }, + "Fossilized remains": { + "text": "Fossilized remains" + }, + "Fracking water": { + "text": "Fracking water" + }, + "Fresh manure": { + "text": "Fresh manure" + }, + "Freshwater": { + "text": "Freshwater" + }, + "Freshwater RAS": { + "text": "Freshwater RAS" + }, + "Freshwater aquarium": { + "text": "Freshwater aquarium" + }, + "Freshwater debries": { + "text": "Freshwater debries" + }, + "Frozen remains": { + "text": "Frozen remains" + }, + "Frozen seafood": { + "text": "Frozen seafood" + }, + "Fruit processing": { + "text": "Fruit processing" + }, + "Fumaroles": { + "text": "Fumaroles" + }, + "Fungi": { + "text": "Fungi" + }, + "Galls": { + "text": "Galls" + }, + "Ganglion": { + "text": "Ganglion" + }, + "Garden": { + "text": "Garden" + }, + "Geothermal field": { + "text": "Geothermal field" + }, + "Geothermal pool/Hot lake": { + "text": "Geothermal pool/Hot lake" + }, + "Germ cell tumor": { + "text": "Germ cell tumor" + }, + "Gill rakers": { + "text": "Gill rakers" + }, + "Gill/Bronchial chamber": { + "text": "Gill/Bronchial chamber" + }, + "Gills": { + "text": "Gills" + }, + "Glacial till": { + "text": "Glacial till" + }, + "Glacier": { + "text": "Glacier" + }, + "Glands": { + "text": "Glands" + }, + "Gonopore": { + "text": "Gonopore" + }, + "Gowning room": { + "text": "Gowning room" + }, + "Granuloma": { + "text": "Granuloma" + }, + "Grasslands": { + "text": "Grasslands" + }, + "Gravesite": { + "text": "Gravesite" + }, + "Greenhouse": { + "text": "Greenhouse" + }, + "Groundwater": { + "text": "Groundwater" + }, + "Guano": { + "text": "Guano" + }, + "Gulf": { + "text": "Gulf" + }, + "Gut": { + "text": "Gut" + }, + "Gymnolaemates": { + "text": "Gymnolaemates" + }, + "HEK293": { + "text": "HEK293" + }, + "Hadalpelagic": { + "text": "Hadalpelagic" + }, + "Haemal node": { + "text": "Haemal node" + }, + "Hair": { + "text": "Hair" + }, + "Hair/Fur": { + "text": "Hair/Fur" + }, + "Halite": { + "text": "Halite" + }, + "Harbor": { + "text": "Harbor" + }, + "Hay": { + "text": "Hay" + }, + "HeLa": { + "text": "HeLa" + }, + "Head": { + "text": "Head" + }, + "Head/Cephalon": { + "text": "Head/Cephalon" + }, + "Heart": { + "text": "Heart" + }, + "Heart/Dorsal vessel": { + "text": "Heart/Dorsal vessel" + }, + "Hemolymph": { + "text": "Hemolymph" + }, + "Herpetarium": { + "text": "Herpetarium" + }, + "Heterotrophic (HNF)": { + "text": "Heterotrophic (HNF)" + }, + "Hindgut": { + "text": "Hindgut" + }, + "Hoof": { + "text": "Hoof" + }, + "Horn": { + "text": "Horn" + }, + "Hornworts": { + "text": "Hornworts" + }, + "Hospital bedroom": { + "text": "Hospital bedroom" + }, + "Hospital wastewater": { + "text": "Hospital wastewater" + }, + "Hot (42-90C)": { + "text": "Hot (42-90C)" + }, + "Hotel": { + "text": "Hotel" + }, + "HuSC": { + "text": "HuSC" + }, + "Hydroponic media": { + "text": "Hydroponic media" + }, + "Hydrothermal vents": { + "text": "Hydrothermal vents" + }, + "Hyperplastic/Inflammatory polyps": { + "text": "Hyperplastic/Inflammatory polyps" + }, + "Hypersaline": { + "text": "Hypersaline" + }, + "Hypersaline lake": { + "text": "Hypersaline lake" + }, + "Hypersaline soda lake": { + "text": "Hypersaline soda lake" + }, + "Hypoxic zone": { + "text": "Hypoxic zone" + }, + "ICU": { + "text": "ICU" + }, + "ISE6": { + "text": "ISE6" + }, + "Ice": { + "text": "Ice" + }, + "Ice cream": { + "text": "Ice cream" + }, + "Infraorbital sinus": { + "text": "Infraorbital sinus" + }, + "Inlet": { + "text": "Inlet" + }, + "Inner ear": { + "text": "Inner ear" + }, + "Inner tissue": { + "text": "Inner tissue" + }, + "Inoculum": { + "text": "Inoculum" + }, + "Input fracking water": { + "text": "Input fracking water" + }, + "Insectarium": { + "text": "Insectarium" + }, + "Insects nest": { + "text": "Insects nest" + }, + "Interior wall": { + "text": "Interior wall" + }, + "Interstitial water": { + "text": "Interstitial water" + }, + "Intertidal zone": { + "text": "Intertidal zone" + }, + "Intestine": { + "text": "Intestine" + }, + "Intestine: Anterior": { + "text": "Intestine: Anterior" + }, + "Intestine: Mid": { + "text": "Intestine: Mid" + }, + "Intrathoracic space": { + "text": "Intrathoracic space" + }, + "Intromittent organ": { + "text": "Intromittent organ" + }, + "Irrigation canal": { + "text": "Irrigation canal" + }, + "Jakobids": { + "text": "Jakobids" + }, + "Joint capsule": { + "text": "Joint capsule" + }, + "Juice": { + "text": "Juice" + }, + "Kettle hole": { + "text": "Kettle hole" + }, + "Kidney": { + "text": "Kidney" + }, + "Kidneys": { + "text": "Kidneys" + }, + "Lab-grade water": { + "text": "Lab-grade water" + }, + "Lacrimal apparatus": { + "text": "Lacrimal apparatus" + }, + "Lake": { + "text": "Lake" + }, + "Lake water": { + "text": "Lake water" + }, + "Lakeshore": { + "text": "Lakeshore" + }, + "Landfill": { + "text": "Landfill" + }, + "Landfill leachate": { + "text": "Landfill leachate" + }, + "Large intestine": { + "text": "Large intestine" + }, + "Laurel/Subtropical forest": { + "text": "Laurel/Subtropical forest" + }, + "Leachate": { + "text": "Leachate" + }, + "Lentic": { + "text": "Lentic" + }, + "Leptosol": { + "text": "Leptosol" + }, + "Ligament": { + "text": "Ligament" + }, + "Light organ": { + "text": "Light organ" + }, + "Lipoma": { + "text": "Lipoma" + }, + "Litterfall": { + "text": "Litterfall" + }, + "Littoral zone": { + "text": "Littoral zone" + }, + "Liverworts": { + "text": "Liverworts" + }, + "Loam": { + "text": "Loam" + }, + "Lotic": { + "text": "Lotic" + }, + "Lower gastrointestinal tract": { + "text": "Lower gastrointestinal tract" + }, + "Lung": { + "text": "Lung" + }, + "Lymph duct": { + "text": "Lymph duct" + }, + "Lymph nodes": { + "text": "Lymph nodes" + }, + "Lymphoid tissue": { + "text": "Lymphoid tissue" + }, + "Lymphoma": { + "text": "Lymphoma" + }, + "Malignant tumor tissue": { + "text": "Malignant tumor tissue" + }, + "Malpighian tubules": { + "text": "Malpighian tubules" + }, + "Mammary gland": { + "text": "Mammary gland" + }, + "Mangrove soil": { + "text": "Mangrove soil" + }, + "Mantle": { + "text": "Mantle" + }, + "Manure": { + "text": "Manure" + }, + "Manure slurry": { + "text": "Manure slurry" + }, + "Manure-fertilized": { + "text": "Manure-fertilized" + }, + "Marginal Sea": { + "text": "Marginal Sea" + }, + "Marine basin floor": { + "text": "Marine basin floor" + }, + "Marine debries": { + "text": "Marine debries" + }, + "Marine fish farm": { + "text": "Marine fish farm" + }, + "Marine lake": { + "text": "Marine lake" + }, + "Marine media": { + "text": "Marine media" + }, + "Marine sediment inoculum": { + "text": "Marine sediment inoculum" + }, + "Material": { + "text": "Material" + }, + "Maxillary glands": { + "text": "Maxillary glands" + }, + "Meadow": { + "text": "Meadow" + }, + "Meat/Poultry processing plant": { + "text": "Meat/Poultry processing plant" + }, + "Meibomian glands": { + "text": "Meibomian glands" + }, + "Melanoma": { + "text": "Melanoma" + }, + "Mesopelagic": { + "text": "Mesopelagic" + }, + "Metalworking fluids": { + "text": "Metalworking fluids" + }, + "Metasoma": { + "text": "Metasoma" + }, + "Methane": { + "text": "Methane" + }, + "Microbial mats": { + "text": "Microbial mats" + }, + "Microbialites": { + "text": "Microbialites" + }, + "Middle ear": { + "text": "Middle ear" + }, + "Midgut": { + "text": "Midgut" + }, + "Milk glands": { + "text": "Milk glands" + }, + "Mine": { + "text": "Mine" + }, + "Mine pit lake": { + "text": "Mine pit lake" + }, + "Mine pit pond": { + "text": "Mine pit pond" + }, + "Mine water": { + "text": "Mine water" + }, + "Mineral horizon": { + "text": "Mineral horizon" + }, + "Mixed liquor": { + "text": "Mixed liquor" + }, + "Mixed type": { + "text": "Mixed type" + }, + "Mixotrophic (MNF)": { + "text": "Mixotrophic (MNF)" + }, + "Molluscs farm": { + "text": "Molluscs farm" + }, + "Molluscs pond": { + "text": "Molluscs pond" + }, + "Molluscs tank": { + "text": "Molluscs tank" + }, + "Morphine": { + "text": "Morphine" + }, + "Moss": { + "text": "Moss" + }, + "Mouse myeloma": { + "text": "Mouse myeloma" + }, + "Mouth": { + "text": "Mouth" + }, + "Mud": { + "text": "Mud" + }, + "Mud volcano": { + "text": "Mud volcano" + }, + "Multiple organs": { + "text": "Multiple organs" + }, + "Mummified remains": { + "text": "Mummified remains" + }, + "Muscles": { + "text": "Muscles" + }, + "Myeloma": { + "text": "Myeloma" + }, + "Myoma": { + "text": "Myoma" + }, + "Nails": { + "text": "Nails" + }, + "Nasal cavity": { + "text": "Nasal cavity" + }, + "Nature reserve": { + "text": "Nature reserve" + }, + "Near-boiling (>90C)": { + "text": "Near-boiling (>90C)" + }, + "Necrotizing soft tissue infections (NSTI)": { + "text": "Necrotizing soft tissue infections (NSTI)" + }, + "Nephridia": { + "text": "Nephridia" + }, + "Neritic zone/Coastal water": { + "text": "Neritic zone/Coastal water" + }, + "Nevi/Moles": { + "text": "Nevi/Moles" + }, + "Nitrogen removal": { + "text": "Nitrogen removal" + }, + "No head": { + "text": "No head" + }, + "No thorax": { + "text": "No thorax" + }, + "Nodule": { + "text": "Nodule" + }, + "Oak savanna": { + "text": "Oak savanna" + }, + "Ocean trench": { + "text": "Ocean trench" + }, + "Oceanarium": { + "text": "Oceanarium" + }, + "Oceanic": { + "text": "Oceanic" + }, + "Oil": { + "text": "Oil" + }, + "Oil palm": { + "text": "Oil palm" + }, + "Oil sands": { + "text": "Oil sands" + }, + "Oil sands pit lake": { + "text": "Oil sands pit lake" + }, + "Oil seeps": { + "text": "Oil seeps" + }, + "Oil well": { + "text": "Oil well" + }, + "Oil-contaminated sediment": { + "text": "Oil-contaminated sediment" + }, + "Oil/Gas pipeline": { + "text": "Oil/Gas pipeline" + }, + "Olfactory pit": { + "text": "Olfactory pit" + }, + "Optical Instruments": { + "text": "Optical Instruments" + }, + "Oral cavity": { + "text": "Oral cavity" + }, + "Oral/Buccal cavity": { + "text": "Oral/Buccal cavity" + }, + "Orchard": { + "text": "Orchard" + }, + "Organic dairy farm": { + "text": "Organic dairy farm" + }, + "Organic layer": { + "text": "Organic layer" + }, + "Osteoma": { + "text": "Osteoma" + }, + "Outer ear": { + "text": "Outer ear" + }, + "Ovaries": { + "text": "Ovaries" + }, + "Ovicells": { + "text": "Ovicells" + }, + "PCR blank control": { + "text": "PCR blank control" + }, + "Paddy field/soil": { + "text": "Paddy field/soil" + }, + "Palsa": { + "text": "Palsa" + }, + "Pancreas": { + "text": "Pancreas" + }, + "Papillomas": { + "text": "Papillomas" + }, + "Parabasalids": { + "text": "Parabasalids" + }, + "Paranasal sinuses": { + "text": "Paranasal sinuses" + }, + "Park": { + "text": "Park" + }, + "Pasture": { + "text": "Pasture" + }, + "Peat": { + "text": "Peat" + }, + "Pelagic zone": { + "text": "Pelagic zone" + }, + "Periprosthetic joint": { + "text": "Periprosthetic joint" + }, + "Periprosthetic joint: Hip": { + "text": "Periprosthetic joint: Hip" + }, + "Periprosthetic joint: Knee": { + "text": "Periprosthetic joint: Knee" + }, + "Peritoneal fluid": { + "text": "Peritoneal fluid" + }, + "Peritoneum": { + "text": "Peritoneum" + }, + "Permafrost": { + "text": "Permafrost" + }, + "Petiole": { + "text": "Petiole" + }, + "Petrochemical": { + "text": "Petrochemical" + }, + "Petroleum reservoir": { + "text": "Petroleum reservoir" + }, + "Petroleum sludge": { + "text": "Petroleum sludge" + }, + "Peyer's patches": { + "text": "Peyer's patches" + }, + "Pharyngeal glands": { + "text": "Pharyngeal glands" + }, + "Pharynx": { + "text": "Pharynx" + }, + "Pharynx/Throat": { + "text": "Pharynx/Throat" + }, + "Photobioreactor (PBR)": { + "text": "Photobioreactor (PBR)" + }, + "Photophore": { + "text": "Photophore" + }, + "Phycosphere": { + "text": "Phycosphere" + }, + "Phylloplane/Leaf": { + "text": "Phylloplane/Leaf" + }, + "Phylloplane/Leaf surface": { + "text": "Phylloplane/Leaf surface" + }, + "Phytotelma": { + "text": "Phytotelma" + }, + "Pilomatrixoma": { + "text": "Pilomatrixoma" + }, + "Pine litter on sand": { + "text": "Pine litter on sand" + }, + "Pit mud": { + "text": "Pit mud" + }, + "Plant nodule": { + "text": "Plant nodule" + }, + "Pleural cavity": { + "text": "Pleural cavity" + }, + "Pleural space/cavity": { + "text": "Pleural space/cavity" + }, + "Polycyclic aromatic hydrocarbons": { + "text": "Polycyclic aromatic hydrocarbons" + }, + "Polyps": { + "text": "Polyps" + }, + "Pond": { + "text": "Pond" + }, + "Potting soil": { + "text": "Potting soil" + }, + "Poultry farm": { + "text": "Poultry farm" + }, + "Poultry litter": { + "text": "Poultry litter" + }, + "Probiotics": { + "text": "Probiotics" + }, + "Processed milk": { + "text": "Processed milk" + }, + "Produced water": { + "text": "Produced water" + }, + "Proglacial area": { + "text": "Proglacial area" + }, + "Pronghorn": { + "text": "Pronghorn" + }, + "Prostate": { + "text": "Prostate" + }, + "Prothorax": { + "text": "Prothorax" + }, + "Puddle": { + "text": "Puddle" + }, + "Pulp and paper wastewater": { + "text": "Pulp and paper wastewater" + }, + "Pyloric ceca": { + "text": "Pyloric ceca" + }, + "Pyogenic granuloma": { + "text": "Pyogenic granuloma" + }, + "R2A agar": { + "text": "R2A agar" + }, + "Radioactive waste": { + "text": "Radioactive waste" + }, + "Rainwater": { + "text": "Rainwater" + }, + "Ranch": { + "text": "Ranch" + }, + "Rat myeloma": { + "text": "Rat myeloma" + }, + "Raw meat": { + "text": "Raw meat" + }, + "Raw milk": { + "text": "Raw milk" + }, + "Raw wastewater": { + "text": "Raw wastewater" + }, + "Reagent blank": { + "text": "Reagent blank" + }, + "Reptile cage": { + "text": "Reptile cage" + }, + "Reservoir": { + "text": "Reservoir" + }, + "Respiratory tract fluid": { + "text": "Respiratory tract fluid" + }, + "Rhizoplane": { + "text": "Rhizoplane" + }, + "Rhizosphere": { + "text": "Rhizosphere" + }, + "Rice straw": { + "text": "Rice straw" + }, + "Riparian zone": { + "text": "Riparian zone" + }, + "River": { + "text": "River" + }, + "River plume": { + "text": "River plume" + }, + "River water": { + "text": "River water" + }, + "Riverside": { + "text": "Riverside" + }, + "Rock": { + "text": "Rock" + }, + "Rock core/Sediment": { + "text": "Rock core/Sediment" + }, + "Rodent burrow": { + "text": "Rodent burrow" + }, + "Runoff channel": { + "text": "Runoff channel" + }, + "Saline": { + "text": "Saline" + }, + "Saline lake": { + "text": "Saline lake" + }, + "Salt crystallizer ponds": { + "text": "Salt crystallizer ponds" + }, + "Salt flat/Salt pan": { + "text": "Salt flat/Salt pan" + }, + "Salt marsh": { + "text": "Salt marsh" + }, + "Salt mine": { + "text": "Salt mine" + }, + "Salt pan/flat": { + "text": "Salt pan/flat" + }, + "Salted fish": { + "text": "Salted fish" + }, + "Sand": { + "text": "Sand" + }, + "Sand filter": { + "text": "Sand filter" + }, + "Sanger": { + "text": "Sanger" + }, + "Saprolite": { + "text": "Saprolite" + }, + "Sarcoma": { + "text": "Sarcoma" + }, + "Scale": { + "text": "Scale" + }, + "Scales": { + "text": "Scales" + }, + "Sea Star": { + "text": "Sea Star" + }, + "Sea Urchin": { + "text": "Sea Urchin" + }, + "Sea cucumber": { + "text": "Sea cucumber" + }, + "Sea ice": { + "text": "Sea ice" + }, + "Seat surface": { + "text": "Seat surface" + }, + "Seawater": { + "text": "Seawater" + }, + "Seawater RAS": { + "text": "Seawater RAS" + }, + "Seawater aquarium": { + "text": "Seawater aquarium" + }, + "Seaweed": { + "text": "Seaweed" + }, + "Sebaceous glands": { + "text": "Sebaceous glands" + }, + "Sediment": { + "text": "Sediment" + }, + "Seed radicle": { + "text": "Seed radicle" + }, + "Semen/Seminal fluid": { + "text": "Semen/Seminal fluid" + }, + "Seminal glands": { + "text": "Seminal glands" + }, + "Settled granule": { + "text": "Settled granule" + }, + "Settling tank": { + "text": "Settling tank" + }, + "Shale gas reservoir": { + "text": "Shale gas reservoir" + }, + "Shale gas/oil reservoir": { + "text": "Shale gas/oil reservoir" + }, + "Sheath fluid": { + "text": "Sheath fluid" + }, + "Shell": { + "text": "Shell" + }, + "Shipwreck": { + "text": "Shipwreck" + }, + "Shrimp pond": { + "text": "Shrimp pond" + }, + "Shrubland": { + "text": "Shrubland" + }, + "Silt": { + "text": "Silt" + }, + "Simulated rainfall": { + "text": "Simulated rainfall" + }, + "Sink": { + "text": "Sink" + }, + "Sinkhole": { + "text": "Sinkhole" + }, + "Skeletal muscle": { + "text": "Skeletal muscle" + }, + "Skeletonized remains": { + "text": "Skeletonized remains" + }, + "Skin": { + "text": "Skin" + }, + "Skin tag": { + "text": "Skin tag" + }, + "Sludge": { + "text": "Sludge" + }, + "Slums/Informal settlements": { + "text": "Slums/Informal settlements" + }, + "Small intestine": { + "text": "Small intestine" + }, + "Smooth muscle": { + "text": "Smooth muscle" + }, + "Smooth muscles": { + "text": "Smooth muscles" + }, + "Snow": { + "text": "Snow" + }, + "Soda lake": { + "text": "Soda lake" + }, + "Soft tissue": { + "text": "Soft tissue" + }, + "Soft tissues": { + "text": "Soft tissues" + }, + "Soil": { + "text": "Soil" + }, + "Soil crust": { + "text": "Soil crust" + }, + "Solar salt": { + "text": "Solar salt" + }, + "Solar solterns": { + "text": "Solar solterns" + }, + "Soy sauce": { + "text": "Soy sauce" + }, + "Soybean paste": { + "text": "Soybean paste" + }, + "Spacecraft": { + "text": "Spacecraft" + }, + "Spat": { + "text": "Spat" + }, + "Spent mushroom substrate": { + "text": "Spent mushroom substrate" + }, + "Spermathecae": { + "text": "Spermathecae" + }, + "Spinal cord": { + "text": "Spinal cord" + }, + "Spiracles": { + "text": "Spiracles" + }, + "Spleen": { + "text": "Spleen" + }, + "Sporeling": { + "text": "Sporeling" + }, + "Sputum/Phlegm": { + "text": "Sputum/Phlegm" + }, + "Stadium": { + "text": "Stadium" + }, + "Stem": { + "text": "Stem" + }, + "Stem tuber": { + "text": "Stem tuber" + }, + "Sterile water": { + "text": "Sterile water" + }, + "Stomach": { + "text": "Stomach" + }, + "Stone": { + "text": "Stone" + }, + "Storm water": { + "text": "Storm water" + }, + "Strait": { + "text": "Strait" + }, + "Sub-biocrust": { + "text": "Sub-biocrust" + }, + "Sub-saline lake": { + "text": "Sub-saline lake" + }, + "Sub-seafloor": { + "text": "Sub-seafloor" + }, + "Subarachnoid space": { + "text": "Subarachnoid space" + }, + "Subcuticular space": { + "text": "Subcuticular space" + }, + "Subglacial lake": { + "text": "Subglacial lake" + }, + "Subterranean lake": { + "text": "Subterranean lake" + }, + "Subtidal zone": { + "text": "Subtidal zone" + }, + "Subway": { + "text": "Subway" + }, + "Supratidal zone": { + "text": "Supratidal zone" + }, + "Surface": { + "text": "Surface" + }, + "Surface biofilm": { + "text": "Surface biofilm" + }, + "Surface mine": { + "text": "Surface mine" + }, + "Swine waste with corn": { + "text": "Swine waste with corn" + }, + "Tailings": { + "text": "Tailings" + }, + "Tailings pond": { + "text": "Tailings pond" + }, + "Tap water": { + "text": "Tap water" + }, + "Taproot": { + "text": "Taproot" + }, + "Tar": { + "text": "Tar" + }, + "Temperate forest": { + "text": "Temperate forest" + }, + "Tendons": { + "text": "Tendons" + }, + "Tepid (25-34C)": { + "text": "Tepid (25-34C)" + }, + "Terrarium": { + "text": "Terrarium" + }, + "Tertiary lymphoid organ": { + "text": "Tertiary lymphoid organ" + }, + "Testes": { + "text": "Testes" + }, + "Tetrachloroethylene": { + "text": "Tetrachloroethylene" + }, + "Thermophilic digester": { + "text": "Thermophilic digester" + }, + "Thorax": { + "text": "Thorax" + }, + "Thorax/Pereon": { + "text": "Thorax/Pereon" + }, + "Tissue": { + "text": "Tissue" + }, + "Tobacco product": { + "text": "Tobacco product" + }, + "Tonsils": { + "text": "Tonsils" + }, + "Trachea": { + "text": "Trachea" + }, + "Transient pool": { + "text": "Transient pool" + }, + "Tree plantation": { + "text": "Tree plantation" + }, + "Trophosome": { + "text": "Trophosome" + }, + "Tropical forest": { + "text": "Tropical forest" + }, + "Tundra": { + "text": "Tundra" + }, + "Unclassified": { + "text": "Unclassified" + }, + "Unspecified organ": { + "text": "Unspecified organ" + }, + "Urban forest": { + "text": "Urban forest" + }, + "Ureter": { + "text": "Ureter" + }, + "Urethra": { + "text": "Urethra" + }, + "Urinary bladder": { + "text": "Urinary bladder" + }, + "Urine": { + "text": "Urine" + }, + "Uropygial/Preen gland": { + "text": "Uropygial/Preen gland" + }, + "Uterus": { + "text": "Uterus" + }, + "Vaccine": { + "text": "Vaccine" + }, + "Vadose zone": { + "text": "Vadose zone" + }, + "Vagina": { + "text": "Vagina" + }, + "Vas deferens": { + "text": "Vas deferens" + }, + "Venous ulcer": { + "text": "Venous ulcer" + }, + "Verrucas": { + "text": "Verrucas" + }, + "Vinegar": { + "text": "Vinegar" + }, + "Volcanic": { + "text": "Volcanic" + }, + "Wall": { + "text": "Wall" + }, + "Warm (34-42C)": { + "text": "Warm (34-42C)" + }, + "Wart": { + "text": "Wart" + }, + "Wastewater": { + "text": "Wastewater" + }, + "Wastewater effluent": { + "text": "Wastewater effluent" + }, + "Water": { + "text": "Water" + }, + "Water tank": { + "text": "Water tank" + }, + "Water well": { + "text": "Water well" + }, + "Watershed": { + "text": "Watershed" + }, + "Wetland sediment": { + "text": "Wetland sediment" + }, + "Wetland-upland transition": { + "text": "Wetland-upland transition" + }, + "Wetlands": { + "text": "Wetlands" + }, + "Wetsalted hide": { + "text": "Wetsalted hide" + }, + "Whole body": { + "text": "Whole body" + }, + "Wood chips": { + "text": "Wood chips" + }, + "Woodchip Bioreactor (WBR)": { + "text": "Woodchip Bioreactor (WBR)" + }, + "Xylene": { + "text": "Xylene" + } + } + }, + "SpecificEcosystemEnum": { + "name": "SpecificEcosystemEnum", + "from_schema": "https://example.com/nmdc_submission_schema", + "permissible_values": { + "A horizon/Topsoil": { + "text": "A horizon/Topsoil" + }, + "Abdomen": { + "text": "Abdomen" + }, + "Abdomen nodes": { + "text": "Abdomen nodes" + }, + "Abomasum": { + "text": "Abomasum" + }, + "Abscess": { + "text": "Abscess" + }, + "Abscess: Furuncle/Boil": { + "text": "Abscess: Furuncle/Boil" + }, + "Abscess: Pilonidal sinus": { + "text": "Abscess: Pilonidal sinus" + }, + "Abyssal plane": { + "text": "Abyssal plane" + }, + "Abyssopelagic/Abyssal zone": { + "text": "Abyssopelagic/Abyssal zone" + }, + "Acid Mine Drainage": { + "text": "Acid Mine Drainage" + }, + "Acid mine drainage": { + "text": "Acid mine drainage" + }, + "Acid sulfate soil": { + "text": "Acid sulfate soil" + }, + "Acid-saline drainage": { + "text": "Acid-saline drainage" + }, + "Acidic": { + "text": "Acidic" + }, + "Acidic spring": { + "text": "Acidic spring" + }, + "Acne vulgaris": { + "text": "Acne vulgaris" + }, + "Actinic keratosis": { + "text": "Actinic keratosis" + }, + "Activated sludge": { + "text": "Activated sludge" + }, + "Adenoid/Pharyngeal": { + "text": "Adenoid/Pharyngeal" + }, + "Adjacent soil": { + "text": "Adjacent soil" + }, + "Adrenal glands": { + "text": "Adrenal glands" + }, + "Agricultural land": { + "text": "Agricultural land" + }, + "Agricultural soil": { + "text": "Agricultural soil" + }, + "Air sacs": { + "text": "Air sacs" + }, + "Air-breathing organ": { + "text": "Air-breathing organ" + }, + "Algal bloom": { + "text": "Algal bloom" + }, + "Alkaline": { + "text": "Alkaline" + }, + "Alkaline spring": { + "text": "Alkaline spring" + }, + "Alpine": { + "text": "Alpine" + }, + "Alveoli": { + "text": "Alveoli" + }, + "Amniotic fluid": { + "text": "Amniotic fluid" + }, + "Amniotic sac": { + "text": "Amniotic sac" + }, + "Anaerobic": { + "text": "Anaerobic" + }, + "Anal canal": { + "text": "Anal canal" + }, + "Anal canal mucosa": { + "text": "Anal canal mucosa" + }, + "Anammox": { + "text": "Anammox" + }, + "Anorectal abscess": { + "text": "Anorectal abscess" + }, + "Anoxic zone": { + "text": "Anoxic zone" + }, + "Anterior": { + "text": "Anterior" + }, + "Anterior chamber": { + "text": "Anterior chamber" + }, + "Anterior fornix": { + "text": "Anterior fornix" + }, + "Anterior nares": { + "text": "Anterior nares" + }, + "Aphotic zone": { + "text": "Aphotic zone" + }, + "Appendix": { + "text": "Appendix" + }, + "Appendix abscess": { + "text": "Appendix abscess" + }, + "Aquifer": { + "text": "Aquifer" + }, + "Arm nodes": { + "text": "Arm nodes" + }, + "Armpit nodes": { + "text": "Armpit nodes" + }, + "Arterial": { + "text": "Arterial" + }, + "Articular cartilage": { + "text": "Articular cartilage" + }, + "Asbestos": { + "text": "Asbestos" + }, + "Ascending colon": { + "text": "Ascending colon" + }, + "Athalassic": { + "text": "Athalassic" + }, + "Athlete's foot": { + "text": "Athlete's foot" + }, + "Atria": { + "text": "Atria" + }, + "Attached/Keratinized gingiva": { + "text": "Attached/Keratinized gingiva" + }, + "Aural": { + "text": "Aural" + }, + "Auricle/Pinna": { + "text": "Auricle/Pinna" + }, + "Axilla/Armpit": { + "text": "Axilla/Armpit" + }, + "B horizon/Subsoil": { + "text": "B horizon/Subsoil" + }, + "Bark": { + "text": "Bark" + }, + "Bartholin abscess": { + "text": "Bartholin abscess" + }, + "Basal cell carcinoma": { + "text": "Basal cell carcinoma" + }, + "Bathypelagic/Bathyal zone": { + "text": "Bathypelagic/Bathyal zone" + }, + "Beach/Shore": { + "text": "Beach/Shore" + }, + "Beaker's/Popliteal cyst": { + "text": "Beaker's/Popliteal cyst" + }, + "Beef chop": { + "text": "Beef chop" + }, + "Beehive: Brood combs": { + "text": "Beehive: Brood combs" + }, + "Beehive: Cerumen": { + "text": "Beehive: Cerumen" + }, + "Beehive: Honey": { + "text": "Beehive: Honey" + }, + "Beehive: Pollen": { + "text": "Beehive: Pollen" + }, + "Beehive: Royal jelly": { + "text": "Beehive: Royal jelly" + }, + "Bench surface": { + "text": "Bench surface" + }, + "Benthic": { + "text": "Benthic" + }, + "Bile": { + "text": "Bile" + }, + "Bile ducts": { + "text": "Bile ducts" + }, + "Bile ducts: Bile": { + "text": "Bile ducts: Bile" + }, + "Biofilm": { + "text": "Biofilm" + }, + "Biofilter": { + "text": "Biofilter" + }, + "Biofouling": { + "text": "Biofouling" + }, + "Biological": { + "text": "Biological" + }, + "Biomass": { + "text": "Biomass" + }, + "Bioreactor": { + "text": "Bioreactor" + }, + "Black smokers": { + "text": "Black smokers" + }, + "Bladder": { + "text": "Bladder" + }, + "Bladder stones": { + "text": "Bladder stones" + }, + "Bog": { + "text": "Bog" + }, + "Bone": { + "text": "Bone" + }, + "Bone marrow": { + "text": "Bone marrow" + }, + "Boreal forest": { + "text": "Boreal forest" + }, + "Bowens disease/Squamous cell carcinoma in situ": { + "text": "Bowens disease/Squamous cell carcinoma in situ" + }, + "Breast abscess": { + "text": "Breast abscess" + }, + "Breast cancer": { + "text": "Breast cancer" + }, + "Breast cancer: Ductal": { + "text": "Breast cancer: Ductal" + }, + "Breast cancer: Lobular": { + "text": "Breast cancer: Lobular" + }, + "Breast cyst": { + "text": "Breast cyst" + }, + "Brine": { + "text": "Brine" + }, + "Bronchial epithelial cells": { + "text": "Bronchial epithelial cells" + }, + "Bronchioles": { + "text": "Bronchioles" + }, + "Buccal cavity": { + "text": "Buccal cavity" + }, + "Buccal mucosa": { + "text": "Buccal mucosa" + }, + "Buffy coat": { + "text": "Buffy coat" + }, + "Bulk soil": { + "text": "Bulk soil" + }, + "C horizon/Substratum": { + "text": "C horizon/Substratum" + }, + "C1/Glandular saccules": { + "text": "C1/Glandular saccules" + }, + "C2": { + "text": "C2" + }, + "C3": { + "text": "C3" + }, + "Caeca": { + "text": "Caeca" + }, + "Caeca: Bacteriome": { + "text": "Caeca: Bacteriome" + }, + "Carbonate": { + "text": "Carbonate" + }, + "Carcinosarcoma": { + "text": "Carcinosarcoma" + }, + "Cardiac skeleton": { + "text": "Cardiac skeleton" + }, + "Cardiac stomach": { + "text": "Cardiac stomach" + }, + "Cast": { + "text": "Cast" + }, + "Catarrh": { + "text": "Catarrh" + }, + "Cave lake": { + "text": "Cave lake" + }, + "Cave microbial mat": { + "text": "Cave microbial mat" + }, + "Cave pool": { + "text": "Cave pool" + }, + "Cave pool sediment": { + "text": "Cave pool sediment" + }, + "Cave stream": { + "text": "Cave stream" + }, + "Cave stream sediment": { + "text": "Cave stream sediment" + }, + "Cave water": { + "text": "Cave water" + }, + "Ceca": { + "text": "Ceca" + }, + "Cecotropes/Night fecs": { + "text": "Cecotropes/Night fecs" + }, + "Cecum": { + "text": "Cecum" + }, + "Cecum/Intestinal cecum": { + "text": "Cecum/Intestinal cecum" + }, + "Cellulitis": { + "text": "Cellulitis" + }, + "Cerebrospinal fluid": { + "text": "Cerebrospinal fluid" + }, + "Cerumen/Earwax": { + "text": "Cerumen/Earwax" + }, + "Cervical": { + "text": "Cervical" + }, + "Cervical cancer": { + "text": "Cervical cancer" + }, + "Cervical/Neck nodes": { + "text": "Cervical/Neck nodes" + }, + "Cervix": { + "text": "Cervix" + }, + "Cheese": { + "text": "Cheese" + }, + "Chloraminated": { + "text": "Chloraminated" + }, + "Chlorinated": { + "text": "Chlorinated" + }, + "Chorionic villi": { + "text": "Chorionic villi" + }, + "Chyme": { + "text": "Chyme" + }, + "Cibarium/Preoral cavity": { + "text": "Cibarium/Preoral cavity" + }, + "Clasper": { + "text": "Clasper" + }, + "Cloaca": { + "text": "Cloaca" + }, + "Co-culture": { + "text": "Co-culture" + }, + "Coal core": { + "text": "Coal core" + }, + "Coal slurry": { + "text": "Coal slurry" + }, + "Coalbed methane well water": { + "text": "Coalbed methane well water" + }, + "Coalbed water": { + "text": "Coalbed water" + }, + "Cold methane seep": { + "text": "Cold methane seep" + }, + "Colon": { + "text": "Colon" + }, + "Colon cancer": { + "text": "Colon cancer" + }, + "Colon mucosa": { + "text": "Colon mucosa" + }, + "Colonic": { + "text": "Colonic" + }, + "Colorectal polyps": { + "text": "Colorectal polyps" + }, + "Colostrum": { + "text": "Colostrum" + }, + "Commercial compost": { + "text": "Commercial compost" + }, + "Common warts": { + "text": "Common warts" + }, + "Compact bone": { + "text": "Compact bone" + }, + "Concrete surface": { + "text": "Concrete surface" + }, + "Contaminated": { + "text": "Contaminated" + }, + "Cooked blood": { + "text": "Cooked blood" + }, + "Coprolite": { + "text": "Coprolite" + }, + "Coral reef": { + "text": "Coral reef" + }, + "Cornea": { + "text": "Cornea" + }, + "Cover soil": { + "text": "Cover soil" + }, + "Creek": { + "text": "Creek" + }, + "Crop": { + "text": "Crop" + }, + "Crop content": { + "text": "Crop content" + }, + "Crop milk": { + "text": "Crop milk" + }, + "Crustal Fluids": { + "text": "Crustal Fluids" + }, + "Cryoconite": { + "text": "Cryoconite" + }, + "Cryoconite hole": { + "text": "Cryoconite hole" + }, + "Cud": { + "text": "Cud" + }, + "Cutaneous leishmaniasis": { + "text": "Cutaneous leishmaniasis" + }, + "Cuticle": { + "text": "Cuticle" + }, + "Cyanobacterial aggregates": { + "text": "Cyanobacterial aggregates" + }, + "Cyanobacterial bloom": { + "text": "Cyanobacterial bloom" + }, + "Deglaciated soil": { + "text": "Deglaciated soil" + }, + "Delivery networks": { + "text": "Delivery networks" + }, + "Dental abscess": { + "text": "Dental abscess" + }, + "Dental calculus": { + "text": "Dental calculus" + }, + "Dental plaque": { + "text": "Dental plaque" + }, + "Dentin": { + "text": "Dentin" + }, + "Dermal papilla": { + "text": "Dermal papilla" + }, + "Dermatitis": { + "text": "Dermatitis" + }, + "Dermis": { + "text": "Dermis" + }, + "Descending colon": { + "text": "Descending colon" + }, + "Desert": { + "text": "Desert" + }, + "Diabetic foot ulcer (DFU)": { + "text": "Diabetic foot ulcer (DFU)" + }, + "Diffuse flow": { + "text": "Diffuse flow" + }, + "Diffuse large B-cell lymphoma": { + "text": "Diffuse large B-cell lymphoma" + }, + "Digestate": { + "text": "Digestate" + }, + "Digital dermatitis": { + "text": "Digital dermatitis" + }, + "Discharge": { + "text": "Discharge" + }, + "Drainage pipe biofilm": { + "text": "Drainage pipe biofilm" + }, + "Drilled well/Borehole": { + "text": "Drilled well/Borehole" + }, + "Driven well": { + "text": "Driven well" + }, + "Dry permafrost": { + "text": "Dry permafrost" + }, + "Dug well": { + "text": "Dug well" + }, + "Duodenal ulcer": { + "text": "Duodenal ulcer" + }, + "Duodenum": { + "text": "Duodenum" + }, + "E horizon/Subsurface": { + "text": "E horizon/Subsurface" + }, + "Ear canal": { + "text": "Ear canal" + }, + "Ear discharge": { + "text": "Ear discharge" + }, + "Eczema": { + "text": "Eczema" + }, + "Effluent": { + "text": "Effluent" + }, + "Effusion": { + "text": "Effusion" + }, + "Eggs": { + "text": "Eggs" + }, + "Elastic": { + "text": "Elastic" + }, + "Empyema": { + "text": "Empyema" + }, + "Empyema drain": { + "text": "Empyema drain" + }, + "Endometrial/Uterine": { + "text": "Endometrial/Uterine" + }, + "Endometrium": { + "text": "Endometrium" + }, + "Endophytes": { + "text": "Endophytes" + }, + "Endosphere": { + "text": "Endosphere" + }, + "Epibionts": { + "text": "Epibionts" + }, + "Epicuticular wax": { + "text": "Epicuticular wax" + }, + "Epidermal mucus": { + "text": "Epidermal mucus" + }, + "Epidermis": { + "text": "Epidermis" + }, + "Epilimnion": { + "text": "Epilimnion" + }, + "Epilimnion/Euphotic zone": { + "text": "Epilimnion/Euphotic zone" + }, + "Epipelagic/Euphotic zone": { + "text": "Epipelagic/Euphotic zone" + }, + "Epiphytes": { + "text": "Epiphytes" + }, + "Epithelium": { + "text": "Epithelium" + }, + "Erythrocytes": { + "text": "Erythrocytes" + }, + "Esophageal ulcer": { + "text": "Esophageal ulcer" + }, + "Esophagus": { + "text": "Esophagus" + }, + "Estuarine sediment": { + "text": "Estuarine sediment" + }, + "Estuary": { + "text": "Estuary" + }, + "Estuary: Microbial mat": { + "text": "Estuary: Microbial mat" + }, + "Estuary: Sediment": { + "text": "Estuary: Sediment" + }, + "Eustachian tube": { + "text": "Eustachian tube" + }, + "Eutric": { + "text": "Eutric" + }, + "External surfaces": { + "text": "External surfaces" + }, + "Extracellular": { + "text": "Extracellular" + }, + "Extracellular symbionts": { + "text": "Extracellular symbionts" + }, + "Fabric": { + "text": "Fabric" + }, + "Farm": { + "text": "Farm" + }, + "Feathers": { + "text": "Feathers" + }, + "Fecal": { + "text": "Fecal" + }, + "Fen": { + "text": "Fen" + }, + "Fibrocartilage": { + "text": "Fibrocartilage" + }, + "Filiform warts": { + "text": "Filiform warts" + }, + "Filter chamber": { + "text": "Filter chamber" + }, + "Filtered water": { + "text": "Filtered water" + }, + "Fin": { + "text": "Fin" + }, + "Flat warts": { + "text": "Flat warts" + }, + "Floor": { + "text": "Floor" + }, + "Floor sediment": { + "text": "Floor sediment" + }, + "Flow back/Produced fluids": { + "text": "Flow back/Produced fluids" + }, + "Fluvial sediment": { + "text": "Fluvial sediment" + }, + "Forefield soil": { + "text": "Forefield soil" + }, + "Forelegs": { + "text": "Forelegs" + }, + "Forest": { + "text": "Forest" + }, + "Forest Soil": { + "text": "Forest Soil" + }, + "Forest soil": { + "text": "Forest soil" + }, + "Forestomach": { + "text": "Forestomach" + }, + "Formation fluid": { + "text": "Formation fluid" + }, + "Frass": { + "text": "Frass" + }, + "Freshwater": { + "text": "Freshwater" + }, + "Freshwater marsh": { + "text": "Freshwater marsh" + }, + "Frozen shrimp": { + "text": "Frozen shrimp" + }, + "Fungus garden/Fungus gallery": { + "text": "Fungus garden/Fungus gallery" + }, + "Gall bladder": { + "text": "Gall bladder" + }, + "Gallbladder": { + "text": "Gallbladder" + }, + "Gallbladder stones": { + "text": "Gallbladder stones" + }, + "Gallbladder: Bile": { + "text": "Gallbladder: Bile" + }, + "Gametophytes": { + "text": "Gametophytes" + }, + "Gaster": { + "text": "Gaster" + }, + "Gastric caeca": { + "text": "Gastric caeca" + }, + "Gastric carcinoma": { + "text": "Gastric carcinoma" + }, + "Gastric mucosa": { + "text": "Gastric mucosa" + }, + "Gastric ulcer": { + "text": "Gastric ulcer" + }, + "Genital herpes": { + "text": "Genital herpes" + }, + "Genital region": { + "text": "Genital region" + }, + "Genital ulcer": { + "text": "Genital ulcer" + }, + "Genital warts": { + "text": "Genital warts" + }, + "Gibber plain": { + "text": "Gibber plain" + }, + "Gills": { + "text": "Gills" + }, + "Gingiva": { + "text": "Gingiva" + }, + "Gingival crevice/sulcus": { + "text": "Gingival crevice/sulcus" + }, + "Gingival crevicular fluids": { + "text": "Gingival crevicular fluids" + }, + "Gingival sulcus": { + "text": "Gingival sulcus" + }, + "Gizzard": { + "text": "Gizzard" + }, + "Glacial lake": { + "text": "Glacial lake" + }, + "Glacial till/moraine": { + "text": "Glacial till/moraine" + }, + "Glacier": { + "text": "Glacier" + }, + "Glacier forefield": { + "text": "Glacier forefield" + }, + "Glacier meltwater": { + "text": "Glacier meltwater" + }, + "Glacier stream": { + "text": "Glacier stream" + }, + "Glacier terminus": { + "text": "Glacier terminus" + }, + "Glandular stomach": { + "text": "Glandular stomach" + }, + "Gonopodium": { + "text": "Gonopodium" + }, + "Granular sludge": { + "text": "Granular sludge" + }, + "Grasslands": { + "text": "Grasslands" + }, + "Green roof": { + "text": "Green roof" + }, + "Groin": { + "text": "Groin" + }, + "Groin nodes": { + "text": "Groin nodes" + }, + "Hadopelagic zone/Ocean trenches": { + "text": "Hadopelagic zone/Ocean trenches" + }, + "Hair": { + "text": "Hair" + }, + "Hair follicle": { + "text": "Hair follicle" + }, + "Hair roots": { + "text": "Hair roots" + }, + "Hair shaft": { + "text": "Hair shaft" + }, + "Hard palate": { + "text": "Hard palate" + }, + "Head": { + "text": "Head" + }, + "Head nodes": { + "text": "Head nodes" + }, + "Heart valve": { + "text": "Heart valve" + }, + "Heart wall": { + "text": "Heart wall" + }, + "Hepatic caecum": { + "text": "Hepatic caecum" + }, + "Hepatic cysts": { + "text": "Hepatic cysts" + }, + "Hepatic flexure": { + "text": "Hepatic flexure" + }, + "Hepatopancreas": { + "text": "Hepatopancreas" + }, + "Hepatopancreas/Digestive gland/Hepatic cecum": { + "text": "Hepatopancreas/Digestive gland/Hepatic cecum" + }, + "Heroin": { + "text": "Heroin" + }, + "Herpes zoster/Shingles": { + "text": "Herpes zoster/Shingles" + }, + "Hind legs": { + "text": "Hind legs" + }, + "Honeydew": { + "text": "Honeydew" + }, + "Humus": { + "text": "Humus" + }, + "Hyaline": { + "text": "Hyaline" + }, + "Hydrocarbon": { + "text": "Hydrocarbon" + }, + "Hydrothermal plume": { + "text": "Hydrothermal plume" + }, + "Hypodermis/Subcutis": { + "text": "Hypodermis/Subcutis" + }, + "Hypolimnion": { + "text": "Hypolimnion" + }, + "Hypolimnion/Profundal zone": { + "text": "Hypolimnion/Profundal zone" + }, + "Hypophysis/Pituitary gland": { + "text": "Hypophysis/Pituitary gland" + }, + "Ice": { + "text": "Ice" + }, + "Ice accretions": { + "text": "Ice accretions" + }, + "Ice core": { + "text": "Ice core" + }, + "Ileostomy effluent": { + "text": "Ileostomy effluent" + }, + "Ileum": { + "text": "Ileum" + }, + "Ileum-cecum": { + "text": "Ileum-cecum" + }, + "Inferior lobe": { + "text": "Inferior lobe" + }, + "Inner": { + "text": "Inner" + }, + "Insect burrows": { + "text": "Insect burrows" + }, + "Intertidal zone": { + "text": "Intertidal zone" + }, + "Intestinal mucosa": { + "text": "Intestinal mucosa" + }, + "Intestine": { + "text": "Intestine" + }, + "Intestine: Digesta": { + "text": "Intestine: Digesta" + }, + "Intracellular": { + "text": "Intracellular" + }, + "Intraocular fluid/Aqueous humor": { + "text": "Intraocular fluid/Aqueous humor" + }, + "Introitus": { + "text": "Introitus" + }, + "Jejunum": { + "text": "Jejunum" + }, + "Keratoacanthoma": { + "text": "Keratoacanthoma" + }, + "Kidney abscess": { + "text": "Kidney abscess" + }, + "Kidney stones": { + "text": "Kidney stones" + }, + "Kitchen sink": { + "text": "Kitchen sink" + }, + "Lacrimal canaliculus": { + "text": "Lacrimal canaliculus" + }, + "Lacrimal fluids": { + "text": "Lacrimal fluids" + }, + "Lacrimal glands": { + "text": "Lacrimal glands" + }, + "Lacrimal sac": { + "text": "Lacrimal sac" + }, + "Lake biofilm": { + "text": "Lake biofilm" + }, + "Large intestine": { + "text": "Large intestine" + }, + "Large intestine content": { + "text": "Large intestine content" + }, + "Laryngopharyngeal": { + "text": "Laryngopharyngeal" + }, + "Laryngopharynx": { + "text": "Laryngopharynx" + }, + "Lateral fornices": { + "text": "Lateral fornices" + }, + "Leaf lesion": { + "text": "Leaf lesion" + }, + "Leaf nodule": { + "text": "Leaf nodule" + }, + "Leaf surface": { + "text": "Leaf surface" + }, + "Leaf surface biofilm": { + "text": "Leaf surface biofilm" + }, + "Leaves": { + "text": "Leaves" + }, + "Leg nodes": { + "text": "Leg nodes" + }, + "Lens": { + "text": "Lens" + }, + "Lesion": { + "text": "Lesion" + }, + "Lesion site": { + "text": "Lesion site" + }, + "Liftoff microbial mat": { + "text": "Liftoff microbial mat" + }, + "Lignite": { + "text": "Lignite" + }, + "Limnetic zone": { + "text": "Limnetic zone" + }, + "Lingual": { + "text": "Lingual" + }, + "Liquid manure": { + "text": "Liquid manure" + }, + "Littoral zone": { + "text": "Littoral zone" + }, + "Liver": { + "text": "Liver" + }, + "Long bone": { + "text": "Long bone" + }, + "Low gastrointestinal tract": { + "text": "Low gastrointestinal tract" + }, + "Lower digestive tract": { + "text": "Lower digestive tract" + }, + "Lumen": { + "text": "Lumen" + }, + "Lungs": { + "text": "Lungs" + }, + "Lymphoblastic lymphoma": { + "text": "Lymphoblastic lymphoma" + }, + "Lymphoid follicles": { + "text": "Lymphoid follicles" + }, + "Malignant ascites": { + "text": "Malignant ascites" + }, + "Mangrove area": { + "text": "Mangrove area" + }, + "Mangrove sediment": { + "text": "Mangrove sediment" + }, + "Mangrove soil": { + "text": "Mangrove soil" + }, + "Mangrove swamp": { + "text": "Mangrove swamp" + }, + "Mantle fluid": { + "text": "Mantle fluid" + }, + "Marsh": { + "text": "Marsh" + }, + "Mature compost": { + "text": "Mature compost" + }, + "Meadow": { + "text": "Meadow" + }, + "Meat trim": { + "text": "Meat trim" + }, + "Meconium": { + "text": "Meconium" + }, + "Meibum": { + "text": "Meibum" + }, + "Melt pond": { + "text": "Melt pond" + }, + "Meltwater": { + "text": "Meltwater" + }, + "Mesopelagic/Twilight zone": { + "text": "Mesopelagic/Twilight zone" + }, + "Metal surface": { + "text": "Metal surface" + }, + "Metalimnion/Thermocline": { + "text": "Metalimnion/Thermocline" + }, + "Microbial mat": { + "text": "Microbial mat" + }, + "Microbial mats": { + "text": "Microbial mats" + }, + "Microbialites": { + "text": "Microbialites" + }, + "Microfouling/Biofilm": { + "text": "Microfouling/Biofilm" + }, + "Middle lobe": { + "text": "Middle lobe" + }, + "Midpoint": { + "text": "Midpoint" + }, + "Milk": { + "text": "Milk" + }, + "Mine": { + "text": "Mine" + }, + "Mine drainage": { + "text": "Mine drainage" + }, + "Mine pit pond": { + "text": "Mine pit pond" + }, + "Mine water": { + "text": "Mine water" + }, + "Mineral soil": { + "text": "Mineral soil" + }, + "Mineral soil core": { + "text": "Mineral soil core" + }, + "Mire": { + "text": "Mire" + }, + "Mixed segment": { + "text": "Mixed segment" + }, + "Mouth ulcer": { + "text": "Mouth ulcer" + }, + "Mouthparts": { + "text": "Mouthparts" + }, + "Mucilage": { + "text": "Mucilage" + }, + "Mucosa": { + "text": "Mucosa" + }, + "Mucus": { + "text": "Mucus" + }, + "Multiple myeloma": { + "text": "Multiple myeloma" + }, + "Municipal and sewage": { + "text": "Municipal and sewage" + }, + "Muscle abscess": { + "text": "Muscle abscess" + }, + "Muscle tissue": { + "text": "Muscle tissue" + }, + "Mycosis fungoides/Cutaneous T-cell lymphoma": { + "text": "Mycosis fungoides/Cutaneous T-cell lymphoma" + }, + "Myocardial abscess": { + "text": "Myocardial abscess" + }, + "Nasal": { + "text": "Nasal" + }, + "Nasal discharge": { + "text": "Nasal discharge" + }, + "Nasal mucosa": { + "text": "Nasal mucosa" + }, + "Nasolacrimal canal": { + "text": "Nasolacrimal canal" + }, + "Nasopharynx": { + "text": "Nasopharynx" + }, + "Neck": { + "text": "Neck" + }, + "Necrotizing lesion": { + "text": "Necrotizing lesion" + }, + "Nectar": { + "text": "Nectar" + }, + "Neritic zone/Coastal water": { + "text": "Neritic zone/Coastal water" + }, + "Nest dump": { + "text": "Nest dump" + }, + "Neutral": { + "text": "Neutral" + }, + "Nose follicle": { + "text": "Nose follicle" + }, + "O horizen/Organic layer": { + "text": "O horizen/Organic layer" + }, + "O horizon/Organic": { + "text": "O horizon/Organic" + }, + "O horizon/Organic layer": { + "text": "O horizon/Organic layer" + }, + "Oceanic crust": { + "text": "Oceanic crust" + }, + "Ocular surface": { + "text": "Ocular surface" + }, + "Oil sludge": { + "text": "Oil sludge" + }, + "Oil-contaminated": { + "text": "Oil-contaminated" + }, + "Oil-contaminated sediment": { + "text": "Oil-contaminated sediment" + }, + "Olfactory mucosa": { + "text": "Olfactory mucosa" + }, + "Omasum": { + "text": "Omasum" + }, + "Optical Lens": { + "text": "Optical Lens" + }, + "Oral cavity cancer": { + "text": "Oral cavity cancer" + }, + "Oral fluids": { + "text": "Oral fluids" + }, + "Oral herpes": { + "text": "Oral herpes" + }, + "Oral mucosa": { + "text": "Oral mucosa" + }, + "Orchard soil": { + "text": "Orchard soil" + }, + "Organic layer": { + "text": "Organic layer" + }, + "Oropharynx": { + "text": "Oropharynx" + }, + "Osseous tissue": { + "text": "Osseous tissue" + }, + "Outer": { + "text": "Outer" + }, + "Ovarian": { + "text": "Ovarian" + }, + "Ovarian cancer": { + "text": "Ovarian cancer" + }, + "Ovarian cyst": { + "text": "Ovarian cyst" + }, + "P1 segment": { + "text": "P1 segment" + }, + "P3 segment": { + "text": "P3 segment" + }, + "P4 segment": { + "text": "P4 segment" + }, + "P5 segment": { + "text": "P5 segment" + }, + "PBMC": { + "text": "PBMC" + }, + "Palatine/Faucial": { + "text": "Palatine/Faucial" + }, + "Paleofeces": { + "text": "Paleofeces" + }, + "Palsa": { + "text": "Palsa" + }, + "Pancreatic duct": { + "text": "Pancreatic duct" + }, + "Paper": { + "text": "Paper" + }, + "Papillate region": { + "text": "Papillate region" + }, + "Paranasal sinuses": { + "text": "Paranasal sinuses" + }, + "Paranasal sinuses: Catarrh": { + "text": "Paranasal sinuses: Catarrh" + }, + "Paranasal sinuses: Ethmoiddal": { + "text": "Paranasal sinuses: Ethmoiddal" + }, + "Paranasal sinuses: Frontal": { + "text": "Paranasal sinuses: Frontal" + }, + "Paranasal sinuses: Maxillary": { + "text": "Paranasal sinuses: Maxillary" + }, + "Paranasal sinuses: Sphenoidal": { + "text": "Paranasal sinuses: Sphenoidal" + }, + "Parathyroid": { + "text": "Parathyroid" + }, + "Parotid abscess": { + "text": "Parotid abscess" + }, + "Pasture": { + "text": "Pasture" + }, + "Paunch/P3 segment": { + "text": "Paunch/P3 segment" + }, + "Paw pad": { + "text": "Paw pad" + }, + "Peat": { + "text": "Peat" + }, + "Peat permafrost": { + "text": "Peat permafrost" + }, + "Penis": { + "text": "Penis" + }, + "Penis: Glans": { + "text": "Penis: Glans" + }, + "Penis: Urethra opening": { + "text": "Penis: Urethra opening" + }, + "Perineum": { + "text": "Perineum" + }, + "Periodontal pockets": { + "text": "Periodontal pockets" + }, + "Peripheral blood mononuclear cells": { + "text": "Peripheral blood mononuclear cells" + }, + "Periphyton": { + "text": "Periphyton" + }, + "Peritonsillar abscess": { + "text": "Peritonsillar abscess" + }, + "Permafrost": { + "text": "Permafrost" + }, + "Pesticide": { + "text": "Pesticide" + }, + "Petroleum sludge": { + "text": "Petroleum sludge" + }, + "Photic zone": { + "text": "Photic zone" + }, + "Physical": { + "text": "Physical" + }, + "Phytoplankton bloom": { + "text": "Phytoplankton bloom" + }, + "Pineal gland/Epiphysis cerebri": { + "text": "Pineal gland/Epiphysis cerebri" + }, + "Pink": { + "text": "Pink" + }, + "Pitcher": { + "text": "Pitcher" + }, + "Pitcher fluid": { + "text": "Pitcher fluid" + }, + "Placenta": { + "text": "Placenta" + }, + "Plankton": { + "text": "Plankton" + }, + "Plantar warts": { + "text": "Plantar warts" + }, + "Plasma": { + "text": "Plasma" + }, + "Plastic": { + "text": "Plastic" + }, + "Plastic debries": { + "text": "Plastic debries" + }, + "Plastic surface": { + "text": "Plastic surface" + }, + "Pleural effusion": { + "text": "Pleural effusion" + }, + "Pleural fluid": { + "text": "Pleural fluid" + }, + "Podotheca": { + "text": "Podotheca" + }, + "Pollen": { + "text": "Pollen" + }, + "Pond scum": { + "text": "Pond scum" + }, + "Pooled tissues": { + "text": "Pooled tissues" + }, + "Porewater": { + "text": "Porewater" + }, + "Posterior fornix": { + "text": "Posterior fornix" + }, + "Posterior nares": { + "text": "Posterior nares" + }, + "Poultry litter bioaerosol": { + "text": "Poultry litter bioaerosol" + }, + "Poultry processing wastewater": { + "text": "Poultry processing wastewater" + }, + "Primary": { + "text": "Primary" + }, + "Produced water": { + "text": "Produced water" + }, + "Produced water/Flow back": { + "text": "Produced water/Flow back" + }, + "Propleura": { + "text": "Propleura" + }, + "Prostate fluid": { + "text": "Prostate fluid" + }, + "Prothorax": { + "text": "Prothorax" + }, + "Proventriculus": { + "text": "Proventriculus" + }, + "Proventriculus/Gizzard": { + "text": "Proventriculus/Gizzard" + }, + "Proximal colon": { + "text": "Proximal colon" + }, + "Psoriasis lesion": { + "text": "Psoriasis lesion" + }, + "Pulmonary fluid": { + "text": "Pulmonary fluid" + }, + "Pyloric stomach": { + "text": "Pyloric stomach" + }, + "Pyrite containing": { + "text": "Pyrite containing" + }, + "Reclaimed": { + "text": "Reclaimed" + }, + "Rectal mucosa": { + "text": "Rectal mucosa" + }, + "Rectum": { + "text": "Rectum" + }, + "Red": { + "text": "Red" + }, + "Reef zone": { + "text": "Reef zone" + }, + "Regurgitated nectar": { + "text": "Regurgitated nectar" + }, + "Renal cyst": { + "text": "Renal cyst" + }, + "Reticulum": { + "text": "Reticulum" + }, + "Retroauricular crease": { + "text": "Retroauricular crease" + }, + "Retropharyngeal": { + "text": "Retropharyngeal" + }, + "Rhamphotheca": { + "text": "Rhamphotheca" + }, + "Rhinarium": { + "text": "Rhinarium" + }, + "Rhizoids": { + "text": "Rhizoids" + }, + "Right": { + "text": "Right" + }, + "Riparian soil": { + "text": "Riparian soil" + }, + "River biofilm": { + "text": "River biofilm" + }, + "Rock": { + "text": "Rock" + }, + "Rock core/Sediment": { + "text": "Rock core/Sediment" + }, + "Rocks": { + "text": "Rocks" + }, + "Room surface": { + "text": "Room surface" + }, + "Rosacea": { + "text": "Rosacea" + }, + "Royal jelly": { + "text": "Royal jelly" + }, + "Rumen": { + "text": "Rumen" + }, + "Rumen fluid": { + "text": "Rumen fluid" + }, + "Rumen mucosa": { + "text": "Rumen mucosa" + }, + "Rumen: Caudodorsal blind sac": { + "text": "Rumen: Caudodorsal blind sac" + }, + "Rumen: Caudoventral blind sac": { + "text": "Rumen: Caudoventral blind sac" + }, + "Rumen: Cranial sac": { + "text": "Rumen: Cranial sac" + }, + "Rumen: Dorsal sac": { + "text": "Rumen: Dorsal sac" + }, + "Rumen: Ventral sac": { + "text": "Rumen: Ventral sac" + }, + "Runoff": { + "text": "Runoff" + }, + "Sabkha": { + "text": "Sabkha" + }, + "Sabkha sediment": { + "text": "Sabkha sediment" + }, + "Sacciform": { + "text": "Sacciform" + }, + "Saline": { + "text": "Saline" + }, + "Saline spring": { + "text": "Saline spring" + }, + "Saline spring sediment": { + "text": "Saline spring sediment" + }, + "Saline water": { + "text": "Saline water" + }, + "Saliva": { + "text": "Saliva" + }, + "Salivary glands": { + "text": "Salivary glands" + }, + "Salivary glands: Parotid glands": { + "text": "Salivary glands: Parotid glands" + }, + "Salt crust": { + "text": "Salt crust" + }, + "Salt flat/Salt pan": { + "text": "Salt flat/Salt pan" + }, + "Salt flat/Salt pan sediment": { + "text": "Salt flat/Salt pan sediment" + }, + "Salt marsh": { + "text": "Salt marsh" + }, + "Salt marsh sediment": { + "text": "Salt marsh sediment" + }, + "Salt pond": { + "text": "Salt pond" + }, + "Salt pond sediment": { + "text": "Salt pond sediment" + }, + "Sandstone": { + "text": "Sandstone" + }, + "Saprolite": { + "text": "Saprolite" + }, + "Scales": { + "text": "Scales" + }, + "Scalp": { + "text": "Scalp" + }, + "Scalp: Dandruff": { + "text": "Scalp: Dandruff" + }, + "Scalp: Non-dandruff": { + "text": "Scalp: Non-dandruff" + }, + "Scrotum/Scrotal sac": { + "text": "Scrotum/Scrotal sac" + }, + "Scull: Ethmoid": { + "text": "Scull: Ethmoid" + }, + "Sea ice": { + "text": "Sea ice" + }, + "Sea-ice brine": { + "text": "Sea-ice brine" + }, + "Seagrass bed": { + "text": "Seagrass bed" + }, + "Seagrass bed sediment": { + "text": "Seagrass bed sediment" + }, + "Seat surface": { + "text": "Seat surface" + }, + "Sebum": { + "text": "Sebum" + }, + "Secondary": { + "text": "Secondary" + }, + "Sediment": { + "text": "Sediment" + }, + "Sediment core": { + "text": "Sediment core" + }, + "Sediment–water interface": { + "text": "Sediment–water interface" + }, + "Seminal fluid": { + "text": "Seminal fluid" + }, + "Seminal glands fluid": { + "text": "Seminal glands fluid" + }, + "Septum": { + "text": "Septum" + }, + "Serum": { + "text": "Serum" + }, + "Seta": { + "text": "Seta" + }, + "Setae": { + "text": "Setae" + }, + "Shale carbon reservoir": { + "text": "Shale carbon reservoir" + }, + "Shoots": { + "text": "Shoots" + }, + "Short bone": { + "text": "Short bone" + }, + "Shrubland": { + "text": "Shrubland" + }, + "Sieved": { + "text": "Sieved" + }, + "Sigmoid colon": { + "text": "Sigmoid colon" + }, + "Sinus cyst": { + "text": "Sinus cyst" + }, + "Siphon": { + "text": "Siphon" + }, + "Skin": { + "text": "Skin" + }, + "Skin surface": { + "text": "Skin surface" + }, + "Skin tissue": { + "text": "Skin tissue" + }, + "Skull": { + "text": "Skull" + }, + "Sludge": { + "text": "Sludge" + }, + "Small intestine": { + "text": "Small intestine" + }, + "Small intestine content": { + "text": "Small intestine content" + }, + "Small intestine mucosa": { + "text": "Small intestine mucosa" + }, + "Snow": { + "text": "Snow" + }, + "Soft tissues": { + "text": "Soft tissues" + }, + "Soft tissues: Muscles": { + "text": "Soft tissues: Muscles" + }, + "Soil": { + "text": "Soil" + }, + "Solar solterns": { + "text": "Solar solterns" + }, + "Solar solterns sediment": { + "text": "Solar solterns sediment" + }, + "Sonicate fluid": { + "text": "Sonicate fluid" + }, + "Speleothems": { + "text": "Speleothems" + }, + "Sperm": { + "text": "Sperm" + }, + "Spider web": { + "text": "Spider web" + }, + "Splenic aspirate": { + "text": "Splenic aspirate" + }, + "Splenic flexure": { + "text": "Splenic flexure" + }, + "Spongy bone": { + "text": "Spongy bone" + }, + "Sporangium": { + "text": "Sporangium" + }, + "Spores": { + "text": "Spores" + }, + "Sporophytes": { + "text": "Sporophytes" + }, + "Spring": { + "text": "Spring" + }, + "Spring sediment": { + "text": "Spring sediment" + }, + "Squamous cell carcinoma": { + "text": "Squamous cell carcinoma" + }, + "Stolon": { + "text": "Stolon" + }, + "Stomach": { + "text": "Stomach" + }, + "Stomach content": { + "text": "Stomach content" + }, + "Stomach: Cardiac": { + "text": "Stomach: Cardiac" + }, + "Stomach: Fundic": { + "text": "Stomach: Fundic" + }, + "Stomach: Pyloric": { + "text": "Stomach: Pyloric" + }, + "Stone surface": { + "text": "Stone surface" + }, + "Stromatolites": { + "text": "Stromatolites" + }, + "Stye": { + "text": "Stye" + }, + "Subcutaneous fat": { + "text": "Subcutaneous fat" + }, + "Subgingival plaque": { + "text": "Subgingival plaque" + }, + "Subterranean estuary": { + "text": "Subterranean estuary" + }, + "Subtidal zone": { + "text": "Subtidal zone" + }, + "Subtidal zone sediment": { + "text": "Subtidal zone sediment" + }, + "Sugarcane filter cake": { + "text": "Sugarcane filter cake" + }, + "Superior lobe": { + "text": "Superior lobe" + }, + "Supragingival plaque": { + "text": "Supragingival plaque" + }, + "Supratidal zone": { + "text": "Supratidal zone" + }, + "Surface": { + "text": "Surface" + }, + "Swamp": { + "text": "Swamp" + }, + "Sweat": { + "text": "Sweat" + }, + "Synovial fluid": { + "text": "Synovial fluid" + }, + "Synovium": { + "text": "Synovium" + }, + "Synovium/Synovial membrane": { + "text": "Synovium/Synovial membrane" + }, + "Syrinx": { + "text": "Syrinx" + }, + "Tears": { + "text": "Tears" + }, + "Teeth": { + "text": "Teeth" + }, + "Tertiary": { + "text": "Tertiary" + }, + "Testicle/Testes": { + "text": "Testicle/Testes" + }, + "Testicle/Testes: Sperm": { + "text": "Testicle/Testes: Sperm" + }, + "Testicular cancer": { + "text": "Testicular cancer" + }, + "Testicular non-seminoma": { + "text": "Testicular non-seminoma" + }, + "Testicular seminoma": { + "text": "Testicular seminoma" + }, + "Thalassic": { + "text": "Thalassic" + }, + "Thallus/Plant body": { + "text": "Thallus/Plant body" + }, + "Thermokarst pond": { + "text": "Thermokarst pond" + }, + "Thoracic": { + "text": "Thoracic" + }, + "Thoracic segments": { + "text": "Thoracic segments" + }, + "Thorax": { + "text": "Thorax" + }, + "Thorax drainage": { + "text": "Thorax drainage" + }, + "Thorax nodes": { + "text": "Thorax nodes" + }, + "Thrombolites": { + "text": "Thrombolites" + }, + "Thymus": { + "text": "Thymus" + }, + "Thyroid": { + "text": "Thyroid" + }, + "Tidal flats": { + "text": "Tidal flats" + }, + "Tissue": { + "text": "Tissue" + }, + "Tissue-engineered": { + "text": "Tissue-engineered" + }, + "Tongue": { + "text": "Tongue" + }, + "Tongue dorsum": { + "text": "Tongue dorsum" + }, + "Tooth": { + "text": "Tooth" + }, + "Tooth: Cementum": { + "text": "Tooth: Cementum" + }, + "Tooth: Dental pulp": { + "text": "Tooth: Dental pulp" + }, + "Tooth: Dentin": { + "text": "Tooth: Dentin" + }, + "Tooth: Enamel": { + "text": "Tooth: Enamel" + }, + "Transverse colon": { + "text": "Transverse colon" + }, + "Trees stand": { + "text": "Trees stand" + }, + "Tricuspid valve": { + "text": "Tricuspid valve" + }, + "Tropical rainforest": { + "text": "Tropical rainforest" + }, + "Truffle orchard": { + "text": "Truffle orchard" + }, + "Tubal": { + "text": "Tubal" + }, + "Tubeworm bush": { + "text": "Tubeworm bush" + }, + "Tubiform": { + "text": "Tubiform" + }, + "Udder": { + "text": "Udder" + }, + "Udder dermatitis": { + "text": "Udder dermatitis" + }, + "Ulcer": { + "text": "Ulcer" + }, + "Umbilical cord": { + "text": "Umbilical cord" + }, + "Umbilical cord blood": { + "text": "Umbilical cord blood" + }, + "Umbilicus": { + "text": "Umbilicus" + }, + "Unchlorinated": { + "text": "Unchlorinated" + }, + "Unclassified": { + "text": "Unclassified" + }, + "Unspecified tissue": { + "text": "Unspecified tissue" + }, + "Untreated": { + "text": "Untreated" + }, + "Upland zone": { + "text": "Upland zone" + }, + "Uranium contaminated": { + "text": "Uranium contaminated" + }, + "Urban floodwater": { + "text": "Urban floodwater" + }, + "Urothelial carcinoma/Transitional cell carcinoma (TCC)": { + "text": "Urothelial carcinoma/Transitional cell carcinoma (TCC)" + }, + "Venous": { + "text": "Venous" + }, + "Ventricle": { + "text": "Ventricle" + }, + "Vertebra": { + "text": "Vertebra" + }, + "Viscera": { + "text": "Viscera" + }, + "Visceral fat": { + "text": "Visceral fat" + }, + "Vitreous humor": { + "text": "Vitreous humor" + }, + "Wall biofilm": { + "text": "Wall biofilm" + }, + "Wall surface": { + "text": "Wall surface" + }, + "Wastewater": { + "text": "Wastewater" + }, + "Well": { + "text": "Well" + }, + "Well biofilm": { + "text": "Well biofilm" + }, + "Well sediment": { + "text": "Well sediment" + }, + "Wetland zone": { + "text": "Wetland zone" + }, + "Whale fall": { + "text": "Whale fall" + }, + "Wheat straw": { + "text": "Wheat straw" + }, + "White": { + "text": "White" + }, + "White smokers": { + "text": "White smokers" + }, + "Whole blood": { + "text": "Whole blood" + }, + "Whole body": { + "text": "Whole body" + }, + "Wood decay": { + "text": "Wood decay" + }, + "Wood fall": { + "text": "Wood fall" + }, + "Wood/Secondary xylem": { + "text": "Wood/Secondary xylem" + }, + "Woodchip biofilm": { + "text": "Woodchip biofilm" + }, + "Wooden surface": { + "text": "Wooden surface" + }, + "Xylem vessels": { + "text": "Xylem vessels" + } + } + }, + "EcosystemForSoilEnum": { + "name": "EcosystemForSoilEnum", + "from_schema": "https://example.com/nmdc_submission_schema", + "permissible_values": { + "Environmental": { + "text": "Environmental" + } + } + }, + "EcosystemCategoryForSoilEnum": { + "name": "EcosystemCategoryForSoilEnum", + "from_schema": "https://example.com/nmdc_submission_schema", + "permissible_values": { + "Terrestrial": { + "text": "Terrestrial" + } + } + }, + "EcosystemTypeForSoilEnum": { + "name": "EcosystemTypeForSoilEnum", + "from_schema": "https://example.com/nmdc_submission_schema", + "permissible_values": { + "Soil": { + "text": "Soil" + } + } + }, + "EcosystemSubtypeForSoilEnum": { + "name": "EcosystemSubtypeForSoilEnum", + "from_schema": "https://example.com/nmdc_submission_schema", + "permissible_values": { + "Agricultural land": { + "text": "Agricultural land" + }, + "Alpine": { + "text": "Alpine" + }, + "Arable": { + "text": "Arable" + }, + "Biochar": { + "text": "Biochar" + }, + "Biocrust": { + "text": "Biocrust" + }, + "Biofilm": { + "text": "Biofilm" + }, + "Boreal forest/Taiga": { + "text": "Boreal forest/Taiga" + }, + "Botanical garden": { + "text": "Botanical garden" + }, + "Chaparral": { + "text": "Chaparral" + }, + "City park": { + "text": "City park" + }, + "Clay": { + "text": "Clay" + }, + "Coastal area": { + "text": "Coastal area" + }, + "Contaminated": { + "text": "Contaminated" + }, + "Desert": { + "text": "Desert" + }, + "Drainage basin": { + "text": "Drainage basin" + }, + "Floodplain": { + "text": "Floodplain" + }, + "Forest": { + "text": "Forest" + }, + "Fossil": { + "text": "Fossil" + }, + "Garden": { + "text": "Garden" + }, + "Geothermal field": { + "text": "Geothermal field" + }, + "Glacial till": { + "text": "Glacial till" + }, + "Glacier": { + "text": "Glacier" + }, + "Grasslands": { + "text": "Grasslands" + }, + "Gravesite": { + "text": "Gravesite" + }, + "Greenhouse": { + "text": "Greenhouse" + }, + "Intertidal zone": { + "text": "Intertidal zone" + }, + "Lakeshore": { + "text": "Lakeshore" + }, + "Landfill": { + "text": "Landfill" + }, + "Laurel/Subtropical forest": { + "text": "Laurel/Subtropical forest" + }, + "Leptosol": { + "text": "Leptosol" + }, + "Loam": { + "text": "Loam" + }, + "Mangrove soil": { + "text": "Mangrove soil" + }, + "Manure-fertilized": { + "text": "Manure-fertilized" + }, + "Meadow": { + "text": "Meadow" + }, + "Mineral horizon": { + "text": "Mineral horizon" + }, + "Mud": { + "text": "Mud" + }, + "Nature reserve": { + "text": "Nature reserve" + }, + "Oak savanna": { + "text": "Oak savanna" + }, + "Orchard": { + "text": "Orchard" + }, + "Organic layer": { + "text": "Organic layer" + }, + "Paddy field/soil": { + "text": "Paddy field/soil" + }, + "Palsa": { + "text": "Palsa" + }, + "Pasture": { + "text": "Pasture" + }, + "Peat": { + "text": "Peat" + }, + "Permafrost": { + "text": "Permafrost" + }, + "Potting soil": { + "text": "Potting soil" + }, + "Proglacial area": { + "text": "Proglacial area" + }, + "Ranch": { + "text": "Ranch" + }, + "Riparian zone": { + "text": "Riparian zone" + }, + "Riverside": { + "text": "Riverside" + }, + "Salt flat/Salt pan": { + "text": "Salt flat/Salt pan" + }, + "Sand": { + "text": "Sand" + }, + "Shrubland": { + "text": "Shrubland" + }, + "Silt": { + "text": "Silt" + }, + "Soil crust": { + "text": "Soil crust" + }, + "Sub-biocrust": { + "text": "Sub-biocrust" + }, + "Surface mine": { + "text": "Surface mine" + }, + "Tailings": { + "text": "Tailings" + }, + "Temperate forest": { + "text": "Temperate forest" + }, + "Tree plantation": { + "text": "Tree plantation" + }, + "Tropical forest": { + "text": "Tropical forest" + }, + "Tundra": { + "text": "Tundra" + }, + "Unclassified": { + "text": "Unclassified" + }, + "Urban forest": { + "text": "Urban forest" + }, + "Vadose zone": { + "text": "Vadose zone" + }, + "Watershed": { + "text": "Watershed" + }, + "Wetland-upland transition": { + "text": "Wetland-upland transition" + }, + "Wetlands": { + "text": "Wetlands" + } + } + }, + "SpecificEcosystemForSoilEnum": { + "name": "SpecificEcosystemForSoilEnum", + "from_schema": "https://example.com/nmdc_submission_schema", + "permissible_values": { + "A horizon/Topsoil": { + "text": "A horizon/Topsoil" + }, + "Acid sulfate soil": { + "text": "Acid sulfate soil" + }, + "Agricultural land": { + "text": "Agricultural land" + }, + "Agricultural soil": { + "text": "Agricultural soil" + }, + "Alpine": { + "text": "Alpine" + }, + "B horizon/Subsoil": { + "text": "B horizon/Subsoil" + }, + "Biological": { + "text": "Biological" + }, + "Bog": { + "text": "Bog" + }, + "Boreal forest": { + "text": "Boreal forest" + }, + "Bulk soil": { + "text": "Bulk soil" + }, + "C horizon/Substratum": { + "text": "C horizon/Substratum" + }, + "Contaminated": { + "text": "Contaminated" + }, + "Cover soil": { + "text": "Cover soil" + }, + "Creek": { + "text": "Creek" + }, + "Cryoconite": { + "text": "Cryoconite" + }, + "Deglaciated soil": { + "text": "Deglaciated soil" + }, + "Desert": { + "text": "Desert" + }, + "Dry permafrost": { + "text": "Dry permafrost" + }, + "E horizon/Subsurface": { + "text": "E horizon/Subsurface" + }, + "Eutric": { + "text": "Eutric" + }, + "Farm": { + "text": "Farm" + }, + "Fen": { + "text": "Fen" + }, + "Fluvial sediment": { + "text": "Fluvial sediment" + }, + "Forefield soil": { + "text": "Forefield soil" + }, + "Forest": { + "text": "Forest" + }, + "Forest Soil": { + "text": "Forest Soil" + }, + "Forest soil": { + "text": "Forest soil" + }, + "Freshwater marsh": { + "text": "Freshwater marsh" + }, + "Gibber plain": { + "text": "Gibber plain" + }, + "Glacial till/moraine": { + "text": "Glacial till/moraine" + }, + "Glacier forefield": { + "text": "Glacier forefield" + }, + "Glacier terminus": { + "text": "Glacier terminus" + }, + "Grasslands": { + "text": "Grasslands" + }, + "Green roof": { + "text": "Green roof" + }, + "Humus": { + "text": "Humus" + }, + "Lignite": { + "text": "Lignite" + }, + "Meadow": { + "text": "Meadow" + }, + "Mine": { + "text": "Mine" + }, + "Mine drainage": { + "text": "Mine drainage" + }, + "Mineral soil": { + "text": "Mineral soil" + }, + "Mineral soil core": { + "text": "Mineral soil core" + }, + "Mire": { + "text": "Mire" + }, + "O horizen/Organic layer": { + "text": "O horizen/Organic layer" + }, + "O horizon/Organic": { + "text": "O horizon/Organic" + }, + "O horizon/Organic layer": { + "text": "O horizon/Organic layer" + }, + "Oil-contaminated": { + "text": "Oil-contaminated" + }, + "Orchard soil": { + "text": "Orchard soil" + }, + "Organic layer": { + "text": "Organic layer" + }, + "Palsa": { + "text": "Palsa" + }, + "Pasture": { + "text": "Pasture" + }, + "Peat": { + "text": "Peat" + }, + "Peat permafrost": { + "text": "Peat permafrost" + }, + "Permafrost": { + "text": "Permafrost" + }, + "Pesticide": { + "text": "Pesticide" + }, + "Physical": { + "text": "Physical" + }, + "Reclaimed": { + "text": "Reclaimed" + }, + "Riparian soil": { + "text": "Riparian soil" + }, + "Salt marsh": { + "text": "Salt marsh" + }, + "Saprolite": { + "text": "Saprolite" + }, + "Sediment": { + "text": "Sediment" + }, + "Shrubland": { + "text": "Shrubland" + }, + "Thermokarst pond": { + "text": "Thermokarst pond" + }, + "Trees stand": { + "text": "Trees stand" + }, + "Tropical rainforest": { + "text": "Tropical rainforest" + }, + "Truffle orchard": { + "text": "Truffle orchard" + }, + "Unclassified": { + "text": "Unclassified" + }, + "Upland zone": { + "text": "Upland zone" + }, + "Uranium contaminated": { + "text": "Uranium contaminated" + }, + "Wetland zone": { + "text": "Wetland zone" + } + } + }, + "EnvMediumWaterEnum": { + "name": "EnvMediumWaterEnum", + "from_schema": "https://example.com/nmdc_submission_schema", + "permissible_values": { + "acidic water [ENVO:01000358]": { + "text": "acidic water [ENVO:01000358]" + }, + "alkaline water [ENVO:01000357]": { + "text": "alkaline water [ENVO:01000357]" + }, + "anoxic water [ENVO:01000173]": { + "text": "anoxic water [ENVO:01000173]" + }, + "bacon curing brine [ENVO:00003045]": { + "text": "bacon curing brine [ENVO:00003045]" + }, + "ballast water [ENVO:01000872]": { + "text": "ballast water [ENVO:01000872]" + }, + "borax leachate [ENVO:00002142]": { + "text": "borax leachate [ENVO:00002142]" + }, + "brackish water [ENVO:00002019]": { + "text": "brackish water [ENVO:00002019]" + }, + "brine [ENVO:00003044]": { + "text": "brine [ENVO:00003044]" + }, + "cloud water [ENVO:03600081]": { + "text": "cloud water [ENVO:03600081]" + }, + "coastal sea water [ENVO:00002150]": { + "text": "coastal sea water [ENVO:00002150]" + }, + "cooling water [ENVO:03600002]": { + "text": "cooling water [ENVO:03600002]" + }, + "desalinated water [ENVO:06105269]": { + "text": "desalinated water [ENVO:06105269]" + }, + "distilled water [ENVO:00003065]": { + "text": "distilled water [ENVO:00003065]" + }, + "ditch water [ENVO:00002158]": { + "text": "ditch water [ENVO:00002158]" + }, + "drilling bore water [ENVO:00002159]": { + "text": "drilling bore water [ENVO:00002159]" + }, + "drinking water [ENVO:00003064]": { + "text": "drinking water [ENVO:00003064]" + }, + "estuarine water [ENVO:01000301]": { + "text": "estuarine water [ENVO:01000301]" + }, + "eutrophic water [ENVO:00002224]": { + "text": "eutrophic water [ENVO:00002224]" + }, + "fresh water [ENVO:00002011]": { + "text": "fresh water [ENVO:00002011]" + }, + "groundwater [ENVO:01001004]": { + "text": "groundwater [ENVO:01001004]" + }, + "highly saline water [ENVO:01001039]": { + "text": "highly saline water [ENVO:01001039]" + }, + "hydrothermal fluid [ENVO:01000134]": { + "text": "hydrothermal fluid [ENVO:01000134]" + }, + "hypereutrophic water [ENVO:01001018]": { + "text": "hypereutrophic water [ENVO:01001018]" + }, + "hypersaline water [ENVO:00002012]": { + "text": "hypersaline water [ENVO:00002012]" + }, + "hypoxic water [ENVO:01001064]": { + "text": "hypoxic water [ENVO:01001064]" + }, + "interstitial water [ENVO:03600009]": { + "text": "interstitial water [ENVO:03600009]" + }, + "leachate [ENVO:00002141]": { + "text": "leachate [ENVO:00002141]" + }, + "liquid water [ENVO:00002006]": { + "text": "liquid water [ENVO:00002006]" + }, + "meltwater [ENVO:01000722]": { + "text": "meltwater [ENVO:01000722]" + }, + "mesotrophic water [ENVO:00002225]": { + "text": "mesotrophic water [ENVO:00002225]" + }, + "moderately saline water [ENVO:01001038]": { + "text": "moderately saline water [ENVO:01001038]" + }, + "muddy water [ENVO:00005793]": { + "text": "muddy water [ENVO:00005793]" + }, + "oligotrophic water [ENVO:00002223]": { + "text": "oligotrophic water [ENVO:00002223]" + }, + "oxic water [ENVO:01001063]": { + "text": "oxic water [ENVO:01001063]" + }, + "pond water [ENVO:00002228]": { + "text": "pond water [ENVO:00002228]" + }, + "rainwater [ENVO:01000600]": { + "text": "rainwater [ENVO:01000600]" + }, + "rural stormwater [ENVO:01001270]": { + "text": "rural stormwater [ENVO:01001270]" + }, + "saline shrimp pond water [ENVO:01001257]": { + "text": "saline shrimp pond water [ENVO:01001257]" + }, + "saline water [ENVO:00002010]": { + "text": "saline water [ENVO:00002010]" + }, + "sea water [ENVO:00002149]": { + "text": "sea water [ENVO:00002149]" + }, + "slightly saline water [ENVO:01001037]": { + "text": "slightly saline water [ENVO:01001037]" + }, + "stagnant water [ENVO:03501370]": { + "text": "stagnant water [ENVO:03501370]" + }, + "sterile water [ENVO:00005791]": { + "text": "sterile water [ENVO:00005791]" + }, + "stormwater [ENVO:01001267]": { + "text": "stormwater [ENVO:01001267]" + }, + "subterranean lake [ENVO:02000145]": { + "text": "subterranean lake [ENVO:02000145]" + }, + "surface water [ENVO:00002042]": { + "text": "surface water [ENVO:00002042]" + }, + "tap water [ENVO:00003096]": { + "text": "tap water [ENVO:00003096]" + }, + "underground water [ENVO:00005792]": { + "text": "underground water [ENVO:00005792]" + }, + "urban stormwater [ENVO:01001268]": { + "text": "urban stormwater [ENVO:01001268]" + } + } + }, + "EnvBroadScaleSoilEnum": { + "name": "EnvBroadScaleSoilEnum", + "from_schema": "https://example.com/nmdc_submission_schema", + "permissible_values": { + "alpine tundra biome [ENVO:01001505]": { + "text": "alpine tundra biome [ENVO:01001505]" + }, + "anthropogenic terrestrial biome [ENVO:01000219]": { + "text": "anthropogenic terrestrial biome [ENVO:01000219]" + }, + "broadleaf forest biome [ENVO:01000197]": { + "text": "broadleaf forest biome [ENVO:01000197]" + }, + "coniferous forest biome [ENVO:01000196]": { + "text": "coniferous forest biome [ENVO:01000196]" + }, + "cropland biome [ENVO:01000245]": { + "text": "cropland biome [ENVO:01000245]" + }, + "flooded grassland biome [ENVO:01000195]": { + "text": "flooded grassland biome [ENVO:01000195]" + }, + "flooded savanna biome [ENVO:01000190]": { + "text": "flooded savanna biome [ENVO:01000190]" + }, + "forest biome [ENVO:01000174]": { + "text": "forest biome [ENVO:01000174]" + }, + "grassland biome [ENVO:01000177]": { + "text": "grassland biome [ENVO:01000177]" + }, + "mangrove biome [ENVO:01000181]": { + "text": "mangrove biome [ENVO:01000181]" + }, + "mediterranean forest biome [ENVO:01000199]": { + "text": "mediterranean forest biome [ENVO:01000199]" + }, + "mediterranean grassland biome [ENVO:01000224]": { + "text": "mediterranean grassland biome [ENVO:01000224]" + }, + "mediterranean savanna biome [ENVO:01000229]": { + "text": "mediterranean savanna biome [ENVO:01000229]" + }, + "mediterranean shrubland biome [ENVO:01000217]": { + "text": "mediterranean shrubland biome [ENVO:01000217]" + }, + "mediterranean woodland biome [ENVO:01000208]": { + "text": "mediterranean woodland biome [ENVO:01000208]" + }, + "mixed forest biome [ENVO:01000198]": { + "text": "mixed forest biome [ENVO:01000198]" + }, + "montane grassland biome [ENVO:01000194]": { + "text": "montane grassland biome [ENVO:01000194]" + }, + "montane savanna biome [ENVO:01000223]": { + "text": "montane savanna biome [ENVO:01000223]" + }, + "montane shrubland biome [ENVO:01000216]": { + "text": "montane shrubland biome [ENVO:01000216]" + }, + "rangeland biome [ENVO:01000247]": { + "text": "rangeland biome [ENVO:01000247]" + }, + "savanna biome [ENVO:01000178]": { + "text": "savanna biome [ENVO:01000178]" + }, + "shrubland biome [ENVO:01000176]": { + "text": "shrubland biome [ENVO:01000176]" + }, + "subpolar coniferous forest biome [ENVO:01000250]": { + "text": "subpolar coniferous forest biome [ENVO:01000250]" + }, + "subtropical broadleaf forest biome [ENVO:01000201]": { + "text": "subtropical broadleaf forest biome [ENVO:01000201]" + }, + "subtropical coniferous forest biome [ENVO:01000209]": { + "text": "subtropical coniferous forest biome [ENVO:01000209]" + }, + "subtropical dry broadleaf forest biome [ENVO:01000225]": { + "text": "subtropical dry broadleaf forest biome [ENVO:01000225]" + }, + "subtropical grassland biome [ENVO:01000191]": { + "text": "subtropical grassland biome [ENVO:01000191]" + }, + "subtropical moist broadleaf forest biome [ENVO:01000226]": { + "text": "subtropical moist broadleaf forest biome [ENVO:01000226]" + }, + "subtropical savanna biome [ENVO:01000187]": { + "text": "subtropical savanna biome [ENVO:01000187]" + }, + "subtropical shrubland biome [ENVO:01000213]": { + "text": "subtropical shrubland biome [ENVO:01000213]" + }, + "subtropical woodland biome [ENVO:01000222]": { + "text": "subtropical woodland biome [ENVO:01000222]" + }, + "temperate broadleaf forest biome [ENVO:01000202]": { + "text": "temperate broadleaf forest biome [ENVO:01000202]" + }, + "temperate coniferous forest biome [ENVO:01000211]": { + "text": "temperate coniferous forest biome [ENVO:01000211]" + }, + "temperate grassland biome [ENVO:01000193]": { + "text": "temperate grassland biome [ENVO:01000193]" + }, + "temperate mixed forest biome [ENVO:01000212]": { + "text": "temperate mixed forest biome [ENVO:01000212]" + }, + "temperate savanna biome [ENVO:01000189]": { + "text": "temperate savanna biome [ENVO:01000189]" + }, + "temperate shrubland biome [ENVO:01000215]": { + "text": "temperate shrubland biome [ENVO:01000215]" + }, + "temperate woodland biome [ENVO:01000221]": { + "text": "temperate woodland biome [ENVO:01000221]" + }, + "terrestrial biome [ENVO:00000446]": { + "text": "terrestrial biome [ENVO:00000446]" + }, + "tidal mangrove shrubland [ENVO:01001369]": { + "text": "tidal mangrove shrubland [ENVO:01001369]" + }, + "tropical broadleaf forest biome [ENVO:01000200]": { + "text": "tropical broadleaf forest biome [ENVO:01000200]" + }, + "tropical coniferous forest biome [ENVO:01000210]": { + "text": "tropical coniferous forest biome [ENVO:01000210]" + }, + "tropical dry broadleaf forest biome [ENVO:01000227]": { + "text": "tropical dry broadleaf forest biome [ENVO:01000227]" + }, + "tropical grassland biome [ENVO:01000192]": { + "text": "tropical grassland biome [ENVO:01000192]" + }, + "tropical mixed forest biome [ENVO:01001798]": { + "text": "tropical mixed forest biome [ENVO:01001798]" + }, + "tropical moist broadleaf forest biome [ENVO:01000228]": { + "text": "tropical moist broadleaf forest biome [ENVO:01000228]" + }, + "tropical savanna biome [ENVO:01000188]": { + "text": "tropical savanna biome [ENVO:01000188]" + }, + "tropical shrubland biome [ENVO:01000214]": { + "text": "tropical shrubland biome [ENVO:01000214]" + }, + "tropical woodland biome [ENVO:01000220]": { + "text": "tropical woodland biome [ENVO:01000220]" + }, + "tundra biome [ENVO:01000180]": { + "text": "tundra biome [ENVO:01000180]" + }, + "woodland biome [ENVO:01000175]": { + "text": "woodland biome [ENVO:01000175]" + }, + "xeric shrubland biome [ENVO:01000218]": { + "text": "xeric shrubland biome [ENVO:01000218]" + } + } + }, + "EnvLocalScaleSoilEnum": { + "name": "EnvLocalScaleSoilEnum", + "from_schema": "https://example.com/nmdc_submission_schema", + "permissible_values": { + "active permafrost layer [ENVO:04000009]": { + "text": "active permafrost layer [ENVO:04000009]" + }, + "alas [ENVO:00000438]": { + "text": "alas [ENVO:00000438]" + }, + "badland [ENVO:00000127]": { + "text": "badland [ENVO:00000127]" + }, + "beach [ENVO:00000091]": { + "text": "beach [ENVO:00000091]" + }, + "butte [ENVO:00000287]": { + "text": "butte [ENVO:00000287]" + }, + "caldera [ENVO:00000096]": { + "text": "caldera [ENVO:00000096]" + }, + "campground [ENVO:01000935]": { + "text": "campground [ENVO:01000935]" + }, + "canyon [ENVO:00000169]": { + "text": "canyon [ENVO:00000169]" + }, + "cave [ENVO:00000067]": { + "text": "cave [ENVO:00000067]" + }, + "channel [ENVO:03000117]": { + "text": "channel [ENVO:03000117]" + }, + "cirque [ENVO:00000155]": { + "text": "cirque [ENVO:00000155]" + }, + "cliff [ENVO:00000087]": { + "text": "cliff [ENVO:00000087]" + }, + "crater [ENVO:00000514]": { + "text": "crater [ENVO:00000514]" + }, + "crevasse [ENVO:00000320]": { + "text": "crevasse [ENVO:00000320]" + }, + "cryosphere [ENVO:03000143]": { + "text": "cryosphere [ENVO:03000143]" + }, + "dam [ENVO:00000074]": { + "text": "dam [ENVO:00000074]" + }, + "desert [ENVO:01001357]": { + "text": "desert [ENVO:01001357]" + }, + "drainage basin [ENVO:00000291]": { + "text": "drainage basin [ENVO:00000291]" + }, + "drumlin [ENVO:00000276]": { + "text": "drumlin [ENVO:00000276]" + }, + "dry lake [ENVO:00000277]": { + "text": "dry lake [ENVO:00000277]" + }, + "dune [ENVO:00000170]": { + "text": "dune [ENVO:00000170]" + }, + "endorheic basin [ENVO:00000551]": { + "text": "endorheic basin [ENVO:00000551]" + }, + "escarpment [ENVO:00000280]": { + "text": "escarpment [ENVO:00000280]" + }, + "esker [ENVO:00000282]": { + "text": "esker [ENVO:00000282]" + }, + "farm [ENVO:00000078]": { + "text": "farm [ENVO:00000078]" + }, + "fen [ENVO:00000232]": { + "text": "fen [ENVO:00000232]" + }, + "fjord [ENVO:00000039]": { + "text": "fjord [ENVO:00000039]" + }, + "flood plain [ENVO:00000255]": { + "text": "flood plain [ENVO:00000255]" + }, + "frost heave [ENVO:01001568]": { + "text": "frost heave [ENVO:01001568]" + }, + "fumarole [ENVO:00000216]": { + "text": "fumarole [ENVO:00000216]" + }, + "garden [ENVO:00000011]": { + "text": "garden [ENVO:00000011]" + }, + "glacier [ENVO:00000133]": { + "text": "glacier [ENVO:00000133]" + }, + "greenhouse [ENVO:03600087]": { + "text": "greenhouse [ENVO:03600087]" + }, + "harbour [ENVO:00000463]": { + "text": "harbour [ENVO:00000463]" + }, + "hill [ENVO:00000083]": { + "text": "hill [ENVO:00000083]" + }, + "hummock [ENVO:00000516]": { + "text": "hummock [ENVO:00000516]" + }, + "isthmus [ENVO:00000174]": { + "text": "isthmus [ENVO:00000174]" + }, + "kame [ENVO:00000542]": { + "text": "kame [ENVO:00000542]" + }, + "karst [ENVO:00000175]": { + "text": "karst [ENVO:00000175]" + }, + "kipuka [ENVO:00000410]": { + "text": "kipuka [ENVO:00000410]" + }, + "landfill [ENVO:00000533]": { + "text": "landfill [ENVO:00000533]" + }, + "machair [ENVO:00000417]": { + "text": "machair [ENVO:00000417]" + }, + "marsh [ENVO:00000035]": { + "text": "marsh [ENVO:00000035]" + }, + "meadow ecosystem [ENVO:00000108]": { + "text": "meadow ecosystem [ENVO:00000108]" + }, + "mesa [ENVO:00000179]": { + "text": "mesa [ENVO:00000179]" + }, + "mine [ENVO:00000076]": { + "text": "mine [ENVO:00000076]" + }, + "mine drainage [ENVO:00001996]": { + "text": "mine drainage [ENVO:00001996]" + }, + "monadnock [ENVO:00000432]": { + "text": "monadnock [ENVO:00000432]" + }, + "moraine [ENVO:00000177]": { + "text": "moraine [ENVO:00000177]" + }, + "mountain [ENVO:00000081]": { + "text": "mountain [ENVO:00000081]" + }, + "nunatak [ENVO:00000181]": { + "text": "nunatak [ENVO:00000181]" + }, + "oil spill [ENVO:00002061]": { + "text": "oil spill [ENVO:00002061]" + }, + "palsa [ENVO:00000489]": { + "text": "palsa [ENVO:00000489]" + }, + "park [ENVO:00000562]": { + "text": "park [ENVO:00000562]" + }, + "pasture [ENVO:00000266]": { + "text": "pasture [ENVO:00000266]" + }, + "peatland [ENVO:00000044]": { + "text": "peatland [ENVO:00000044]" + }, + "pit [ENVO:01001871]": { + "text": "pit [ENVO:01001871]" + }, + "plain [ENVO:00000086]": { + "text": "plain [ENVO:00000086]" + }, + "plateau [ENVO:00000182]": { + "text": "plateau [ENVO:00000182]" + }, + "polje [ENVO:00000325]": { + "text": "polje [ENVO:00000325]" + }, + "prairie [ENVO:00000260]": { + "text": "prairie [ENVO:00000260]" + }, + "quarry [ENVO:00000284]": { + "text": "quarry [ENVO:00000284]" + }, + "ranch [ENVO:01001207]": { + "text": "ranch [ENVO:01001207]" + }, + "ravine [ENVO:01000446]": { + "text": "ravine [ENVO:01000446]" + }, + "refinery [ENVO:02000141]": { + "text": "refinery [ENVO:02000141]" + }, + "rhizosphere [ENVO:00005801]": { + "text": "rhizosphere [ENVO:00005801]" + }, + "ria [ENVO:00000418]": { + "text": "ria [ENVO:00000418]" + }, + "ridge [ENVO:00000283]": { + "text": "ridge [ENVO:00000283]" + }, + "rill [ENVO:00000496]": { + "text": "rill [ENVO:00000496]" + }, + "river [ENVO:00000022]": { + "text": "river [ENVO:00000022]" + }, + "riverfront [ENVO:03501239]": { + "text": "riverfront [ENVO:03501239]" + }, + "road [ENVO:00000064]": { + "text": "road [ENVO:00000064]" + }, + "scrubland area [ENVO:00000300]": { + "text": "scrubland area [ENVO:00000300]" + }, + "shingle beach [ENVO:00000545]": { + "text": "shingle beach [ENVO:00000545]" + }, + "shore [ENVO:00000304]": { + "text": "shore [ENVO:00000304]" + }, + "sinkhole [ENVO:00000195]": { + "text": "sinkhole [ENVO:00000195]" + }, + "slope [ENVO:00002000]": { + "text": "slope [ENVO:00002000]" + }, + "soil cryoturbate [ENVO:01001665]": { + "text": "soil cryoturbate [ENVO:01001665]" + }, + "spring [ENVO:00000027]": { + "text": "spring [ENVO:00000027]" + }, + "spur [ENVO:01001489]": { + "text": "spur [ENVO:01001489]" + }, + "stack [ENVO:00000419]": { + "text": "stack [ENVO:00000419]" + }, + "steppe [ENVO:00000262]": { + "text": "steppe [ENVO:00000262]" + }, + "stream [ENVO:00000023]": { + "text": "stream [ENVO:00000023]" + }, + "swale [ENVO:00000543]": { + "text": "swale [ENVO:00000543]" + }, + "terrace [ENVO:00000508]": { + "text": "terrace [ENVO:00000508]" + }, + "thermokarst [ENVO:03000085]": { + "text": "thermokarst [ENVO:03000085]" + }, + "trench [ENVO:01000649]": { + "text": "trench [ENVO:01000649]" + }, + "tunnel [ENVO:00000068]": { + "text": "tunnel [ENVO:00000068]" + }, + "tuya [ENVO:00000370]": { + "text": "tuya [ENVO:00000370]" + }, + "valley [ENVO:00000100]": { + "text": "valley [ENVO:00000100]" + }, + "volcano [ENVO:00000247]": { + "text": "volcano [ENVO:00000247]" + }, + "wadi [ENVO:00000031]": { + "text": "wadi [ENVO:00000031]" + }, + "watershed [ENVO:00000292]": { + "text": "watershed [ENVO:00000292]" + }, + "well [ENVO:00000026]": { + "text": "well [ENVO:00000026]" + }, + "woodland clearing [ENVO:00000444]": { + "text": "woodland clearing [ENVO:00000444]" + } + } + }, + "EnvMediumSoilEnum": { + "name": "EnvMediumSoilEnum", + "from_schema": "https://example.com/nmdc_submission_schema", + "permissible_values": { + "acidic soil [ENVO:01001185]": { + "text": "acidic soil [ENVO:01001185]" + }, + "acrisol [ENVO:00002234]": { + "text": "acrisol [ENVO:00002234]" + }, + "agricultural soil [ENVO:00002259]": { + "text": "agricultural soil [ENVO:00002259]" + }, + "albeluvisol [ENVO:00002233]": { + "text": "albeluvisol [ENVO:00002233]" + }, + "alisol [ENVO:00002231]": { + "text": "alisol [ENVO:00002231]" + }, + "allotment garden soil [ENVO:00005744]": { + "text": "allotment garden soil [ENVO:00005744]" + }, + "alluvial paddy field soil [ENVO:00005759]": { + "text": "alluvial paddy field soil [ENVO:00005759]" + }, + "alluvial soil [ENVO:00002871]": { + "text": "alluvial soil [ENVO:00002871]" + }, + "alluvial swamp soil [ENVO:00005758]": { + "text": "alluvial swamp soil [ENVO:00005758]" + }, + "alpine soil [ENVO:00005741]": { + "text": "alpine soil [ENVO:00005741]" + }, + "andosol [ENVO:00002232]": { + "text": "andosol [ENVO:00002232]" + }, + "anthrosol [ENVO:00002230]": { + "text": "anthrosol [ENVO:00002230]" + }, + "arable soil [ENVO:00005742]": { + "text": "arable soil [ENVO:00005742]" + }, + "arenosol [ENVO:00002229]": { + "text": "arenosol [ENVO:00002229]" + }, + "bare soil [ENVO:01001616]": { + "text": "bare soil [ENVO:01001616]" + }, + "beech forest soil [ENVO:00005770]": { + "text": "beech forest soil [ENVO:00005770]" + }, + "bluegrass field soil [ENVO:00005789]": { + "text": "bluegrass field soil [ENVO:00005789]" + }, + "bulk soil [ENVO:00005802]": { + "text": "bulk soil [ENVO:00005802]" + }, + "burned soil [ENVO:00005760]": { + "text": "burned soil [ENVO:00005760]" + }, + "calcisol [ENVO:00002239]": { + "text": "calcisol [ENVO:00002239]" + }, + "cambisol [ENVO:00002235]": { + "text": "cambisol [ENVO:00002235]" + }, + "chernozem [ENVO:00002237]": { + "text": "chernozem [ENVO:00002237]" + }, + "clay soil [ENVO:00002262]": { + "text": "clay soil [ENVO:00002262]" + }, + "compacted soil [ENVO:06105205]": { + "text": "compacted soil [ENVO:06105205]" + }, + "compost soil [ENVO:00005747]": { + "text": "compost soil [ENVO:00005747]" + }, + "cryosol [ENVO:00002236]": { + "text": "cryosol [ENVO:00002236]" + }, + "dry soil [ENVO:00005748]": { + "text": "dry soil [ENVO:00005748]" + }, + "durisol [ENVO:00002238]": { + "text": "durisol [ENVO:00002238]" + }, + "eucalyptus forest soil [ENVO:00005787]": { + "text": "eucalyptus forest soil [ENVO:00005787]" + }, + "ferralsol [ENVO:00002246]": { + "text": "ferralsol [ENVO:00002246]" + }, + "fertilized soil [ENVO:00005754]": { + "text": "fertilized soil [ENVO:00005754]" + }, + "field soil [ENVO:00005755]": { + "text": "field soil [ENVO:00005755]" + }, + "fluvisol [ENVO:00002273]": { + "text": "fluvisol [ENVO:00002273]" + }, + "forest soil [ENVO:00002261]": { + "text": "forest soil [ENVO:00002261]" + }, + "friable-frozen soil [ENVO:01001528]": { + "text": "friable-frozen soil [ENVO:01001528]" + }, + "frost-susceptible soil [ENVO:01001638]": { + "text": "frost-susceptible soil [ENVO:01001638]" + }, + "frozen compost soil [ENVO:00005765]": { + "text": "frozen compost soil [ENVO:00005765]" + }, + "frozen soil [ENVO:01001526]": { + "text": "frozen soil [ENVO:01001526]" + }, + "gleysol [ENVO:00002244]": { + "text": "gleysol [ENVO:00002244]" + }, + "grassland soil [ENVO:00005750]": { + "text": "grassland soil [ENVO:00005750]" + }, + "gypsisol [ENVO:00002245]": { + "text": "gypsisol [ENVO:00002245]" + }, + "hard-frozen soil [ENVO:01001525]": { + "text": "hard-frozen soil [ENVO:01001525]" + }, + "heat stressed soil [ENVO:00005781]": { + "text": "heat stressed soil [ENVO:00005781]" + }, + "histosol [ENVO:00002243]": { + "text": "histosol [ENVO:00002243]" + }, + "jungle soil [ENVO:00005751]": { + "text": "jungle soil [ENVO:00005751]" + }, + "kastanozem [ENVO:00002240]": { + "text": "kastanozem [ENVO:00002240]" + }, + "lawn soil [ENVO:00005756]": { + "text": "lawn soil [ENVO:00005756]" + }, + "leafy wood soil [ENVO:00005783]": { + "text": "leafy wood soil [ENVO:00005783]" + }, + "leptosol [ENVO:00002241]": { + "text": "leptosol [ENVO:00002241]" + }, + "limed soil [ENVO:00005766]": { + "text": "limed soil [ENVO:00005766]" + }, + "lixisol [ENVO:00002242]": { + "text": "lixisol [ENVO:00002242]" + }, + "loam [ENVO:00002258]": { + "text": "loam [ENVO:00002258]" + }, + "luvisol [ENVO:00002248]": { + "text": "luvisol [ENVO:00002248]" + }, + "manured soil [ENVO:00005767]": { + "text": "manured soil [ENVO:00005767]" + }, + "mountain forest soil [ENVO:00005769]": { + "text": "mountain forest soil [ENVO:00005769]" + }, + "muddy soil [ENVO:00005771]": { + "text": "muddy soil [ENVO:00005771]" + }, + "nitisol [ENVO:00002247]": { + "text": "nitisol [ENVO:00002247]" + }, + "orchid soil [ENVO:00005768]": { + "text": "orchid soil [ENVO:00005768]" + }, + "ornithogenic soil [ENVO:00005782]": { + "text": "ornithogenic soil [ENVO:00005782]" + }, + "paddy field soil [ENVO:00005740]": { + "text": "paddy field soil [ENVO:00005740]" + }, + "pathogen-suppressive soil [ENVO:03600036]": { + "text": "pathogen-suppressive soil [ENVO:03600036]" + }, + "phaeozem [ENVO:00002249]": { + "text": "phaeozem [ENVO:00002249]" + }, + "planosol [ENVO:00002251]": { + "text": "planosol [ENVO:00002251]" + }, + "plastic-frozen soil [ENVO:01001527]": { + "text": "plastic-frozen soil [ENVO:01001527]" + }, + "plinthosol [ENVO:00002250]": { + "text": "plinthosol [ENVO:00002250]" + }, + "podzol [ENVO:00002257]": { + "text": "podzol [ENVO:00002257]" + }, + "pond soil [ENVO:00005764]": { + "text": "pond soil [ENVO:00005764]" + }, + "red soil [ENVO:00005790]": { + "text": "red soil [ENVO:00005790]" + }, + "regosol [ENVO:00002256]": { + "text": "regosol [ENVO:00002256]" + }, + "roadside soil [ENVO:00005743]": { + "text": "roadside soil [ENVO:00005743]" + }, + "rubber plantation soil [ENVO:00005788]": { + "text": "rubber plantation soil [ENVO:00005788]" + }, + "savanna soil [ENVO:00005746]": { + "text": "savanna soil [ENVO:00005746]" + }, + "sawah soil [ENVO:00005752]": { + "text": "sawah soil [ENVO:00005752]" + }, + "soil [ENVO:00001998]": { + "text": "soil [ENVO:00001998]" + }, + "solonchak [ENVO:00002252]": { + "text": "solonchak [ENVO:00002252]" + }, + "solonetz [ENVO:00002255]": { + "text": "solonetz [ENVO:00002255]" + }, + "spruce forest soil [ENVO:00005784]": { + "text": "spruce forest soil [ENVO:00005784]" + }, + "stagnosol [ENVO:00002274]": { + "text": "stagnosol [ENVO:00002274]" + }, + "surface soil [ENVO:02000059]": { + "text": "surface soil [ENVO:02000059]" + }, + "technosol [ENVO:00002275]": { + "text": "technosol [ENVO:00002275]" + }, + "tropical soil [ENVO:00005778]": { + "text": "tropical soil [ENVO:00005778]" + }, + "ultisol [ENVO:01001397]": { + "text": "ultisol [ENVO:01001397]" + }, + "umbrisol [ENVO:00002253]": { + "text": "umbrisol [ENVO:00002253]" + }, + "upland soil [ENVO:00005786]": { + "text": "upland soil [ENVO:00005786]" + }, + "vegetable garden soil [ENVO:00005779]": { + "text": "vegetable garden soil [ENVO:00005779]" + }, + "vertisol [ENVO:00002254]": { + "text": "vertisol [ENVO:00002254]" + } + } + } + }, + "slots": { + "air_data": { + "name": "air_data", + "description": "aggregation slot relating air data collections to a SampleData container", + "from_schema": "https://example.com/nmdc_submission_schema", + "domain_of": [ + "SampleData" + ], + "range": "AirInterface", + "multivalued": true, + "inlined": true, + "inlined_as_list": true + }, + "biofilm_data": { + "name": "biofilm_data", + "description": "aggregation slot relating biofilm data collections to a SampleData container", + "from_schema": "https://example.com/nmdc_submission_schema", + "domain_of": [ + "SampleData" + ], + "range": "BiofilmInterface", + "multivalued": true, + "inlined": true, + "inlined_as_list": true + }, + "built_env_data": { + "name": "built_env_data", + "description": "aggregation slot relating built_env data collections to a SampleData container", + "from_schema": "https://example.com/nmdc_submission_schema", + "domain_of": [ + "SampleData" + ], + "range": "BuiltEnvInterface", + "multivalued": true, + "inlined": true, + "inlined_as_list": true + }, + "emsl_data": { + "name": "emsl_data", + "description": "aggregation slot relating emsl data collections to a SampleData container", + "from_schema": "https://example.com/nmdc_submission_schema", + "domain_of": [ + "SampleData" + ], + "range": "EmslInterface", + "multivalued": true, + "inlined": true, + "inlined_as_list": true + }, + "hcr_cores_data": { + "name": "hcr_cores_data", + "description": "aggregation slot relating hcr_cores data collections to a SampleData container", + "from_schema": "https://example.com/nmdc_submission_schema", + "range": "HcrCoresInterface", + "multivalued": true, + "inlined": true, + "inlined_as_list": true + }, + "hcr_fluids_swabs_data": { + "name": "hcr_fluids_swabs_data", + "description": "aggregation slot relating hcr_fluids_swabs data collections to a SampleData container", + "from_schema": "https://example.com/nmdc_submission_schema", + "range": "HcrFluidsSwabsInterface", + "multivalued": true, + "inlined": true, + "inlined_as_list": true + }, + "host_associated_data": { + "name": "host_associated_data", + "description": "aggregation slot relating host_associated data collections to a SampleData container", + "from_schema": "https://example.com/nmdc_submission_schema", + "domain_of": [ + "SampleData" + ], + "range": "HostAssociatedInterface", + "multivalued": true, + "inlined": true, + "inlined_as_list": true + }, + "jgi_mg_data": { + "name": "jgi_mg_data", + "description": "aggregation slot relating jgi_mg data collections to a SampleData container", + "from_schema": "https://example.com/nmdc_submission_schema", + "domain_of": [ + "SampleData" + ], + "range": "JgiMgInterface", + "multivalued": true, + "inlined": true, + "inlined_as_list": true + }, + "jgi_mg_lr_data": { + "name": "jgi_mg_lr_data", + "description": "aggregation slot relating jgi_mg_lr data collections to a SampleData container", + "from_schema": "https://example.com/nmdc_submission_schema", + "domain_of": [ + "SampleData" + ], + "range": "JgiMgLrInterface", + "multivalued": true, + "inlined": true, + "inlined_as_list": true + }, + "jgi_mt_data": { + "name": "jgi_mt_data", + "description": "aggregation slot relating jgi_mt data collections to a SampleData container", + "from_schema": "https://example.com/nmdc_submission_schema", + "domain_of": [ + "SampleData" + ], + "range": "JgiMtInterface", + "multivalued": true, + "inlined": true, + "inlined_as_list": true + }, + "misc_envs_data": { + "name": "misc_envs_data", + "description": "aggregation slot relating misc_envs data collections to a SampleData container", + "from_schema": "https://example.com/nmdc_submission_schema", + "range": "MiscEnvsInterface", + "multivalued": true, + "inlined": true, + "inlined_as_list": true + }, + "plant_associated_data": { + "name": "plant_associated_data", + "description": "aggregation slot relating plant_associated data collections to a SampleData container", + "from_schema": "https://example.com/nmdc_submission_schema", + "domain_of": [ + "SampleData" + ], + "range": "PlantAssociatedInterface", + "multivalued": true, + "inlined": true, + "inlined_as_list": true + }, + "sediment_data": { + "name": "sediment_data", + "description": "aggregation slot relating sediment data collections to a SampleData container", + "from_schema": "https://example.com/nmdc_submission_schema", + "domain_of": [ + "SampleData" + ], + "range": "SedimentInterface", + "multivalued": true, + "inlined": true, + "inlined_as_list": true + }, + "soil_data": { + "name": "soil_data", + "description": "aggregation slot relating soil data collections to a SampleData container", + "from_schema": "https://example.com/nmdc_submission_schema", + "domain_of": [ + "SampleData" + ], + "range": "SoilInterface", + "multivalued": true, + "inlined": true, + "inlined_as_list": true + }, + "wastewater_sludge_data": { + "name": "wastewater_sludge_data", + "description": "aggregation slot relating wastewater_sludge data collections to a SampleData container", + "from_schema": "https://example.com/nmdc_submission_schema", + "domain_of": [ + "SampleData" + ], + "range": "WastewaterSludgeInterface", + "multivalued": true, + "inlined": true, + "inlined_as_list": true + }, + "water_data": { + "name": "water_data", + "description": "aggregation slot relating water data collections to a SampleData container", + "from_schema": "https://example.com/nmdc_submission_schema", + "domain_of": [ + "SampleData" + ], + "range": "WaterInterface", + "multivalued": true, + "inlined": true, + "inlined_as_list": true + }, + "dh_section": { + "name": "dh_section", + "description": "dh_section grouping slot", + "from_schema": "https://example.com/nmdc_submission_schema" + }, + "emsl_section": { + "name": "emsl_section", + "title": "EMSL", + "from_schema": "https://example.com/nmdc_submission_schema", + "rank": 2, + "is_a": "dh_section" + }, + "jgi_metagenomics_section": { + "name": "jgi_metagenomics_section", + "title": "JGI-Metagenomics", + "from_schema": "https://example.com/nmdc_submission_schema", + "rank": 3, + "is_a": "dh_section" + }, + "jgi_metatranscriptomics_section": { + "name": "jgi_metatranscriptomics_section", + "title": "JGI-Metatranscriptomics", + "from_schema": "https://example.com/nmdc_submission_schema", + "rank": 4, + "is_a": "dh_section" + }, + "mixs_core_section": { + "name": "mixs_core_section", + "title": "MIxS Core", + "from_schema": "https://example.com/nmdc_submission_schema", + "rank": 10, + "is_a": "dh_section" + }, + "mixs_inspired_section": { + "name": "mixs_inspired_section", + "title": "MIxS Inspired", + "from_schema": "https://example.com/nmdc_submission_schema", + "rank": 7, + "is_a": "dh_section" + }, + "mixs_investigation_section": { + "name": "mixs_investigation_section", + "from_schema": "https://example.com/nmdc_submission_schema", + "rank": 8, + "is_a": "dh_section" + }, + "mixs_modified_section": { + "name": "mixs_modified_section", + "title": "MIxS (modified)", + "from_schema": "https://example.com/nmdc_submission_schema", + "rank": 6, + "is_a": "dh_section" + }, + "mixs_nassf_section": { + "name": "mixs_nassf_section", + "from_schema": "https://example.com/nmdc_submission_schema", + "rank": 9, + "is_a": "dh_section" + }, + "mixs_section": { + "name": "mixs_section", + "title": "MIxS", + "from_schema": "https://example.com/nmdc_submission_schema", + "rank": 5, + "is_a": "dh_section" + }, + "sample_id_section": { + "name": "sample_id_section", + "title": "Sample ID", + "from_schema": "https://example.com/nmdc_submission_schema", + "rank": 1, + "is_a": "dh_section" + }, + "abs_air_humidity": { + "name": "abs_air_humidity", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "gram per gram, kilogram per kilogram, kilogram, pound" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Actual mass of water vapor - mh20 - present in the air water vapor mixture", + "title": "absolute air humidity", + "examples": [ + { + "value": "9 gram per gram" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "absolute air humidity" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000122", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "add_recov_method": { + "name": "add_recov_method", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration;timestamp" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Additional (i.e. Secondary, tertiary, etc.) recovery methods deployed for increase of hydrocarbon recovery from resource and start date for each one of them. If \"other\" is specified, please propose entry in \"additional info\" field", + "title": "secondary and tertiary recovery methods and start date", + "examples": [ + { + "value": "Polymer Addition;2018-06-21T14:30Z" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "secondary and tertiary recovery methods and start date" + ], + "is_a": "core field", + "slot_uri": "MIXS:0001009", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "additional_info": { + "name": "additional_info", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "text" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Information that doesn't fit anywhere else. Can also be used to propose new entries for fields with controlled vocabulary", + "title": "additional info", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "additional info" + ], + "is_a": "core field", + "string_serialization": "{text}", + "slot_uri": "MIXS:0000300", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "address": { + "name": "address", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "value" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The street name and building number where the sampling occurred.", + "title": "address", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "address" + ], + "is_a": "core field", + "string_serialization": "{integer}{text}", + "slot_uri": "MIXS:0000218", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "adj_room": { + "name": "adj_room", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "room name;room number" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "List of rooms (room number, room name) immediately adjacent to the sampling room", + "title": "adjacent rooms", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "adjacent rooms" + ], + "is_a": "core field", + "string_serialization": "{text};{integer}", + "slot_uri": "MIXS:0000219", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "aero_struc": { + "name": "aero_struc", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Aerospace structures typically consist of thin plates with stiffeners for the external surfaces, bulkheads and frames to support the shape and fasteners such as welds, rivets, screws and bolts to hold the components together", + "title": "aerospace structure", + "examples": [ + { + "value": "plane" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "aerospace structure" + ], + "is_a": "core field", + "string_serialization": "[plane|glider]", + "slot_uri": "MIXS:0000773", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "agrochem_addition": { + "name": "agrochem_addition", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "agrochemical name;agrochemical amount;timestamp" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "gram, mole per liter, milligram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Addition of fertilizers, pesticides, etc. - amount and time of applications", + "title": "history/agrochemical additions", + "examples": [ + { + "value": "roundup;5 milligram per liter;2018-06-21" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "history/agrochemical additions" + ], + "is_a": "core field", + "string_serialization": "{text};{float} {unit};{timestamp}", + "slot_uri": "MIXS:0000639", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "air_PM_concen": { + "name": "air_PM_concen", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "particulate matter name;measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micrograms per cubic meter" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Concentration of substances that remain suspended in the air, and comprise mixtures of organic and inorganic substances (PM10 and PM2.5); can report multiple PM's by entering numeric values preceded by name of PM", + "title": "air particulate matter concentration", + "examples": [ + { + "value": "PM2.5;10 microgram per cubic meter" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "air particulate matter concentration" + ], + "is_a": "core field", + "string_serialization": "{text};{float} {unit}", + "slot_uri": "MIXS:0000108", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "air_temp": { + "name": "air_temp", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "degree Celsius" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Temperature of the air at the time of sampling", + "title": "air temperature", + "examples": [ + { + "value": "20 degree Celsius" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "air temperature" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000124", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "air_temp_regm": { + "name": "air_temp_regm", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "temperature value;treatment interval and duration" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "meter" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Information about treatment involving an exposure to varying temperatures; should include the temperature, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include different temperature regimens", + "title": "air temperature regimen", + "examples": [ + { + "value": "25 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "air temperature regimen" + ], + "is_a": "core field", + "string_serialization": "{float} {unit};{Rn/start_time/end_time/duration}", + "slot_uri": "MIXS:0000551", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "al_sat": { + "name": "al_sat", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "percentage" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Aluminum saturation (esp. For tropical soils)", + "title": "extreme_unusual_properties/Al saturation", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "extreme_unusual_properties/Al saturation" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000607", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "al_sat_meth": { + "name": "al_sat_meth", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "PMID,DOI or URL" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Reference or method used in determining Al saturation", + "title": "extreme_unusual_properties/Al saturation method", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "extreme_unusual_properties/Al saturation method" + ], + "is_a": "core field", + "string_serialization": "{PMID}|{DOI}|{URL}", + "slot_uri": "MIXS:0000324", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "alkalinity": { + "name": "alkalinity", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milliequivalent per liter, milligram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate", + "title": "alkalinity", + "examples": [ + { + "value": "50 milligram per liter" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "alkalinity" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000421", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "alkalinity_method": { + "name": "alkalinity_method", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "description of method" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Method used for alkalinity measurement", + "title": "alkalinity method", + "examples": [ + { + "value": "titration" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "alkalinity method" + ], + "is_a": "core field", + "string_serialization": "{text}", + "slot_uri": "MIXS:0000298", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "alkyl_diethers": { + "name": "alkyl_diethers", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "mole per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of alkyl diethers", + "title": "alkyl diethers", + "examples": [ + { + "value": "0.005 mole per liter" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "alkyl diethers" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000490", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "alt": { + "name": "alt", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + } + }, + "description": "Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air", + "title": "altitude", + "examples": [ + { + "value": "100 meter" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "altitude" + ], + "is_a": "environment field", + "slot_uri": "MIXS:0000094", + "domain_of": [ + "agriculture", + "air", + "built environment", + "core", + "food-animal and animal feed", + "food-farm environment", + "food-food production facility", + "food-human foods", + "host-associated", + "human-associated", + "human-gut", + "human-oral", + "human-skin", + "human-vaginal", + "hydrocarbon resources-cores", + "hydrocarbon resources-fluids_swabs", + "microbial mat_biofilm", + "miscellaneous natural or artificial environment", + "plant-associated", + "sediment", + "soil", + "symbiont-associated", + "wastewater_sludge", + "water", + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "aminopept_act": { + "name": "aminopept_act", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "mole per liter per hour" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Measurement of aminopeptidase activity", + "title": "aminopeptidase activity", + "examples": [ + { + "value": "0.269 mole per liter per hour" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "aminopeptidase activity" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000172", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "ammonium": { + "name": "ammonium", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per liter, milligram per liter, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of ammonium in the sample", + "title": "ammonium", + "examples": [ + { + "value": "1.5 milligram per liter" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "ammonium" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000427", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "ammonium_nitrogen": { + "name": "ammonium_nitrogen", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "mg/kg" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of ammonium nitrogen in the sample", + "title": "ammonium nitrogen", + "examples": [ + { + "value": "2.3 mg/kg" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "see_also": [ + "https://www.ornl.gov/content/bio-scales-0" + ], + "aliases": [ + "ammonium_nitrogen", + "NH4-N" + ], + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "amount_light": { + "name": "amount_light", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "lux, lumens per square meter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The unit of illuminance and luminous emittance, measuring luminous flux per unit area", + "title": "amount of light", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "amount of light" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000140", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "analysis_type": { + "name": "analysis_type", + "description": "Select all the data types associated or available for this biosample", + "title": "analysis/data type", + "examples": [ + { + "value": "metagenomics; metabolomics; proteomics" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "see_also": [ + "MIxS:investigation_type" + ], + "rank": 3, + "domain_of": [ + "Biosample" + ], + "slot_group": "Sample ID", + "range": "AnalysisTypeEnum", + "recommended": true, + "multivalued": true + }, + "ances_data": { + "name": "ances_data", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "free text" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Information about either pedigree or other ancestral information description (e.g. parental variety in case of mutant or selection), e.g. A/3*B (meaning [(A x B) x B] x B)", + "title": "ancestral data", + "examples": [ + { + "value": "A/3*B" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "ancestral data" + ], + "is_a": "core field", + "string_serialization": "{text}", + "slot_uri": "MIXS:0000247", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "annual_precpt": { + "name": "annual_precpt", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "millimeter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The average of all annual precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or Isohyetal maps.", + "title": "mean annual precipitation", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "mean annual precipitation" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000644", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "annual_temp": { + "name": "annual_temp", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "degree Celsius" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Mean annual temperature", + "title": "mean annual temperature", + "examples": [ + { + "value": "12.5 degree Celsius" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "mean annual temperature" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000642", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "antibiotic_regm": { + "name": "antibiotic_regm", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "antibiotic name;antibiotic amount;treatment interval and duration" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milligram" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Information about treatment involving antibiotic administration; should include the name of antibiotic, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple antibiotic regimens", + "title": "antibiotic regimen", + "examples": [ + { + "value": "penicillin;5 milligram;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "antibiotic regimen" + ], + "is_a": "core field", + "string_serialization": "{text};{float} {unit};{Rn/start_time/end_time/duration}", + "slot_uri": "MIXS:0000553", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "api": { + "name": "api", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "degrees API" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "API gravity is a measure of how heavy or light a petroleum liquid is compared to water (source: https://en.wikipedia.org/wiki/API_gravity) (e.g. 31.1¬∞ API)", + "title": "API gravity", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "API gravity" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000157", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "arch_struc": { + "name": "arch_struc", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "An architectural structure is a human-made, free-standing, immobile outdoor construction", + "title": "architectural structure", + "examples": [ + { + "value": "shed" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "architectural structure" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000774", + "domain_of": [ + "Biosample" + ], + "range": "arch_struc_enum", + "multivalued": false + }, + "aromatics_pc": { + "name": "aromatics_pc", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "name;measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "percent" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene)", + "title": "aromatics wt%", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "aromatics wt%" + ], + "is_a": "core field", + "string_serialization": "{text};{float} {unit}", + "slot_uri": "MIXS:0000133", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "asphaltenes_pc": { + "name": "asphaltenes_pc", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "name;measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "percent" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene)", + "title": "asphaltenes wt%", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "asphaltenes wt%" + ], + "is_a": "core field", + "string_serialization": "{text};{float} {unit}", + "slot_uri": "MIXS:0000135", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "atmospheric_data": { + "name": "atmospheric_data", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "atmospheric data name;measurement value" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Measurement of atmospheric data; can include multiple data", + "title": "atmospheric data", + "examples": [ + { + "value": "wind speed;9 knots" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "atmospheric data" + ], + "is_a": "core field", + "string_serialization": "{text};{float} {unit}", + "slot_uri": "MIXS:0001097", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "avg_dew_point": { + "name": "avg_dew_point", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "degree Celsius" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The average of dew point measures taken at the beginning of every hour over a 24 hour period on the sampling day", + "title": "average dew point", + "examples": [ + { + "value": "25.5 degree Celsius" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "average dew point" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000141", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "avg_occup": { + "name": "avg_occup", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "value" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Daily average occupancy of room. Indicate the number of person(s) daily occupying the sampling room.", + "title": "average daily occupancy", + "examples": [ + { + "value": "2" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "average daily occupancy" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000775", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "avg_temp": { + "name": "avg_temp", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "degree Celsius" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The average of temperatures taken at the beginning of every hour over a 24 hour period on the sampling day", + "title": "average temperature", + "examples": [ + { + "value": "12.5 degree Celsius" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "average temperature" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000142", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "bac_prod": { + "name": "bac_prod", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milligram per cubic meter per day" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Bacterial production in the water column measured by isotope uptake", + "title": "bacterial production", + "examples": [ + { + "value": "5 milligram per cubic meter per day" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "bacterial production" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000683", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "bac_resp": { + "name": "bac_resp", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milligram per cubic meter per day, micromole oxygen per liter per hour" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Measurement of bacterial respiration in the water column", + "title": "bacterial respiration", + "examples": [ + { + "value": "300 micromole oxygen per liter per hour" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "bacterial respiration" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000684", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "bacteria_carb_prod": { + "name": "bacteria_carb_prod", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "nanogram per hour" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Measurement of bacterial carbon production", + "title": "bacterial carbon production", + "examples": [ + { + "value": "2.53 microgram per liter per hour" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "bacterial carbon production" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000173", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "barometric_press": { + "name": "barometric_press", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "millibar" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Force per unit area exerted against a surface by the weight of air above that surface", + "title": "barometric pressure", + "examples": [ + { + "value": "5 millibar" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "barometric pressure" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000096", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "basin": { + "name": "basin", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "name" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Name of the basin (e.g. Campos)", + "title": "basin name", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "basin name" + ], + "is_a": "core field", + "string_serialization": "{text}", + "slot_uri": "MIXS:0000290", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "bathroom_count": { + "name": "bathroom_count", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "value" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The number of bathrooms in the building", + "title": "bathroom count", + "examples": [ + { + "value": "1" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "bathroom count" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000776", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "bedroom_count": { + "name": "bedroom_count", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "value" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The number of bedrooms in the building", + "title": "bedroom count", + "examples": [ + { + "value": "2" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "bedroom count" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000777", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "benzene": { + "name": "benzene", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milligram per liter, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of benzene in the sample", + "title": "benzene", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "benzene" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000153", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "biochem_oxygen_dem": { + "name": "biochem_oxygen_dem", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milligram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Amount of dissolved oxygen needed by aerobic biological organisms in a body of water to break down organic material present in a given water sample at certain temperature over a specific time period", + "title": "biochemical oxygen demand", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "biochemical oxygen demand" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000653", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "biocide": { + "name": "biocide", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "name;name;timestamp" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "List of biocides (commercial name of product and supplier) and date of administration", + "title": "biocide administration", + "examples": [ + { + "value": "ALPHA 1427;Baker Hughes;2008-01-23" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "biocide administration" + ], + "is_a": "core field", + "string_serialization": "{text};{text};{timestamp}", + "slot_uri": "MIXS:0001011", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "biocide_admin_method": { + "name": "biocide_admin_method", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value;frequency;duration;duration" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milligram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Method of biocide administration (dose, frequency, duration, time elapsed between last biociding and sampling) (e.g. 150 mg/l; weekly; 4 hr; 3 days)", + "title": "biocide administration method", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "biocide administration method" + ], + "is_a": "core field", + "string_serialization": "{float} {unit};{Rn/start_time/end_time/duration};{duration}", + "slot_uri": "MIXS:0000456", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "biol_stat": { + "name": "biol_stat", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The level of genome modification.", + "title": "biological status", + "examples": [ + { + "value": "natural" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "biological status" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000858", + "domain_of": [ + "Biosample" + ], + "range": "biol_stat_enum", + "multivalued": false + }, + "biomass": { + "name": "biomass", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "biomass type;measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "ton, kilogram, gram" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements", + "title": "biomass", + "examples": [ + { + "value": "total;20 gram" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "biomass" + ], + "is_a": "core field", + "string_serialization": "{text};{float} {unit}", + "slot_uri": "MIXS:0000174", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "biotic_regm": { + "name": "biotic_regm", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "free text" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Information about treatment(s) involving use of biotic factors, such as bacteria, viruses or fungi.", + "title": "biotic regimen", + "examples": [ + { + "value": "sample inoculated with Rhizobium spp. Culture" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "biotic regimen" + ], + "is_a": "core field", + "string_serialization": "{text}", + "slot_uri": "MIXS:0001038", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "biotic_relationship": { + "name": "biotic_relationship", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + } + }, + "description": "Description of relationship(s) between the subject organism and other organism(s) it is associated with. E.g., parasite on species X; mutualist with species Y. The target organism is the subject of the relationship, and the other organism(s) is the object", + "title": "observed biotic relationship", + "examples": [ + { + "value": "free living" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "observed biotic relationship" + ], + "is_a": "nucleic acid sequence source field", + "slot_uri": "MIXS:0000028", + "domain_of": [ + "Biosample" + ], + "range": "biotic_relationship_enum", + "multivalued": false + }, + "bishomohopanol": { + "name": "bishomohopanol", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "microgram per liter, microgram per gram" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of bishomohopanol", + "title": "bishomohopanol", + "examples": [ + { + "value": "14 microgram per liter" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "bishomohopanol" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000175", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "blood_press_diast": { + "name": "blood_press_diast", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "millimeter mercury" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Resting diastolic blood pressure, measured as mm mercury", + "title": "host blood pressure diastolic", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "host blood pressure diastolic" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000258", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "blood_press_syst": { + "name": "blood_press_syst", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "millimeter mercury" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Resting systolic blood pressure, measured as mm mercury", + "title": "host blood pressure systolic", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "host blood pressure systolic" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000259", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "bromide": { + "name": "bromide", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of bromide", + "title": "bromide", + "examples": [ + { + "value": "0.05 parts per million" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "bromide" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000176", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "build_docs": { + "name": "build_docs", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The building design, construction and operation documents", + "title": "design, construction, and operation documents", + "examples": [ + { + "value": "maintenance plans" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "design, construction, and operation documents" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000787", + "domain_of": [ + "Biosample" + ], + "range": "build_docs_enum", + "multivalued": false + }, + "build_occup_type": { + "name": "build_occup_type", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "The primary function for which a building or discrete part of a building is intended to be used", + "title": "building occupancy type", + "examples": [ + { + "value": "market" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "building occupancy type" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000761", + "domain_of": [ + "Biosample" + ], + "range": "build_occup_type_enum", + "multivalued": true + }, + "building_setting": { + "name": "building_setting", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "A location (geography) where a building is set", + "title": "building setting", + "examples": [ + { + "value": "rural" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "building setting" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000768", + "domain_of": [ + "Biosample" + ], + "range": "building_setting_enum", + "multivalued": false + }, + "built_struc_age": { + "name": "built_struc_age", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "year" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The age of the built structure since construction", + "title": "built structure age", + "examples": [ + { + "value": "15" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "built structure age" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000145", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "built_struc_set": { + "name": "built_struc_set", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The characterization of the location of the built structure as high or low human density", + "title": "built structure setting", + "examples": [ + { + "value": "rural" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "built structure setting" + ], + "is_a": "core field", + "string_serialization": "[urban|rural]", + "slot_uri": "MIXS:0000778", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "built_struc_type": { + "name": "built_struc_type", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "free text" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "A physical structure that is a body or assemblage of bodies in space to form a system capable of supporting loads", + "title": "built structure type", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "built structure type" + ], + "is_a": "core field", + "string_serialization": "{text}", + "slot_uri": "MIXS:0000721", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "bulk_elect_conductivity": { + "name": "bulk_elect_conductivity", + "description": "Electrical conductivity is a measure of the ability to carry electric current, which is mostly dictated by the chemistry of and amount of water.", + "title": "bulk electrical conductivity", + "comments": [ + "Provide the value output of the field instrument." + ], + "examples": [ + { + "value": "JsonObj(has_raw_value='0.017 mS/cm', has_numeric_value=0.017, has_unit='mS/cm')", + "description": "The conductivity measurement was 0.017 millisiemens per centimeter." + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "calcium": { + "name": "calcium", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milligram per liter, micromole per liter, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of calcium in the sample", + "title": "calcium", + "examples": [ + { + "value": "0.2 micromole per liter" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "calcium" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000432", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "carb_dioxide": { + "name": "carb_dioxide", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per liter, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Carbon dioxide (gas) amount or concentration at the time of sampling", + "title": "carbon dioxide", + "examples": [ + { + "value": "410 parts per million" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "carbon dioxide" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000097", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "carb_monoxide": { + "name": "carb_monoxide", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per liter, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Carbon monoxide (gas) amount or concentration at the time of sampling", + "title": "carbon monoxide", + "examples": [ + { + "value": "0.1 parts per million" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "carbon monoxide" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000098", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "carb_nitro_ratio": { + "name": "carb_nitro_ratio", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Ratio of amount or concentrations of carbon to nitrogen", + "title": "carbon/nitrogen ratio", + "examples": [ + { + "value": "0.417361111" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "carbon/nitrogen ratio" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000310", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "ceil_area": { + "name": "ceil_area", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "square meter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The area of the ceiling space within the room", + "title": "ceiling area", + "examples": [ + { + "value": "25 square meter" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "ceiling area" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000148", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "ceil_cond": { + "name": "ceil_cond", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The physical condition of the ceiling at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas", + "title": "ceiling condition", + "examples": [ + { + "value": "damaged" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "ceiling condition" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000779", + "domain_of": [ + "Biosample" + ], + "range": "ceil_cond_enum", + "multivalued": false + }, + "ceil_finish_mat": { + "name": "ceil_finish_mat", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The type of material used to finish a ceiling", + "title": "ceiling finish material", + "examples": [ + { + "value": "stucco" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "ceiling finish material" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000780", + "domain_of": [ + "Biosample" + ], + "range": "ceil_finish_mat_enum", + "multivalued": false + }, + "ceil_struc": { + "name": "ceil_struc", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The construction format of the ceiling", + "title": "ceiling structure", + "examples": [ + { + "value": "concrete" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "ceiling structure" + ], + "is_a": "core field", + "string_serialization": "[wood frame|concrete]", + "slot_uri": "MIXS:0000782", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "ceil_texture": { + "name": "ceil_texture", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The feel, appearance, or consistency of a ceiling surface", + "title": "ceiling texture", + "examples": [ + { + "value": "popcorn" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "ceiling texture" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000783", + "domain_of": [ + "Biosample" + ], + "range": "ceil_texture_enum", + "multivalued": false + }, + "ceil_thermal_mass": { + "name": "ceil_thermal_mass", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "joule per degree Celsius" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The ability of the ceiling to provide inertia against temperature fluctuations. Generally this means concrete that is exposed. A metal deck that supports a concrete slab will act thermally as long as it is exposed to room air flow", + "title": "ceiling thermal mass", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "ceiling thermal mass" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000143", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "ceil_type": { + "name": "ceil_type", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The type of ceiling according to the ceiling's appearance or construction", + "title": "ceiling type", + "examples": [ + { + "value": "coffered" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "ceiling type" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000784", + "domain_of": [ + "Biosample" + ], + "range": "ceil_type_enum", + "multivalued": false + }, + "ceil_water_mold": { + "name": "ceil_water_mold", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Signs of the presence of mold or mildew on the ceiling", + "title": "ceiling signs of water/mold", + "examples": [ + { + "value": "presence of mold visible" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "ceiling signs of water/mold" + ], + "is_a": "core field", + "string_serialization": "[presence of mold visible|no presence of mold visible]", + "slot_uri": "MIXS:0000781", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "chem_administration": { + "name": "chem_administration", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "CHEBI;timestamp" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi", + "title": "chemical administration", + "examples": [ + { + "value": "agar [CHEBI:2509];2018-05-11T20:00Z" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "chemical administration" + ], + "is_a": "core field", + "string_serialization": "{termLabel} {[termID]};{timestamp}", + "slot_uri": "MIXS:0000751", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "chem_mutagen": { + "name": "chem_mutagen", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "mutagen name;mutagen amount;treatment interval and duration" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milligram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Treatment involving use of mutagens; should include the name of mutagen, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple mutagen regimens", + "title": "chemical mutagen", + "examples": [ + { + "value": "nitrous acid;0.5 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "chemical mutagen" + ], + "is_a": "core field", + "string_serialization": "{text};{float} {unit};{Rn/start_time/end_time/duration}", + "slot_uri": "MIXS:0000555", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "chem_oxygen_dem": { + "name": "chem_oxygen_dem", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milligram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "A measure of the capacity of water to consume oxygen during the decomposition of organic matter and the oxidation of inorganic chemicals such as ammonia and nitrite", + "title": "chemical oxygen demand", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "chemical oxygen demand" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000656", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "chem_treat_method": { + "name": "chem_treat_method", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value;frequency;duration;duration" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milligram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Method of chemical administration(dose, frequency, duration, time elapsed between administration and sampling) (e.g. 50 mg/l; twice a week; 1 hr; 0 days)", + "title": "chemical treatment method", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "chemical treatment method" + ], + "is_a": "core field", + "string_serialization": "{float} {unit};{Rn/start_time/end_time/duration};{duration};{duration}", + "slot_uri": "MIXS:0000457", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "chem_treatment": { + "name": "chem_treatment", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "name;name;timestamp" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "List of chemical compounds administered upstream the sampling location where sampling occurred (e.g. Glycols, H2S scavenger, corrosion and scale inhibitors, demulsifiers, and other production chemicals etc.). The commercial name of the product and name of the supplier should be provided. The date of administration should also be included", + "title": "chemical treatment", + "examples": [ + { + "value": "ACCENT 1125;DOW;2010-11-17" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "chemical treatment" + ], + "is_a": "core field", + "string_serialization": "{text};{text};{timestamp}", + "slot_uri": "MIXS:0001012", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "chloride": { + "name": "chloride", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milligram per liter, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of chloride in the sample", + "title": "chloride", + "examples": [ + { + "value": "5000 milligram per liter" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "chloride" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000429", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "chlorophyll": { + "name": "chlorophyll", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milligram per cubic meter, microgram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of chlorophyll", + "title": "chlorophyll", + "examples": [ + { + "value": "5 milligram per cubic meter" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "chlorophyll" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000177", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "climate_environment": { + "name": "climate_environment", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "climate name;treatment interval and duration" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Treatment involving an exposure to a particular climate; treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple climates", + "title": "climate environment", + "examples": [ + { + "value": "tropical climate;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "climate environment" + ], + "is_a": "core field", + "string_serialization": "{text};{Rn/start_time/end_time/duration}", + "slot_uri": "MIXS:0001040", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "collection_date": { + "name": "collection_date", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "date and time" + } + }, + "description": "The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant", + "title": "collection date", + "examples": [ + { + "value": "2018-05-11T10:00:00+01:00; 2018-05-11" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "collection date" + ], + "is_a": "environment field", + "slot_uri": "MIXS:0000011", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "collection_date_inc": { + "name": "collection_date_inc", + "description": "Date the incubation was harvested/collected/ended. Only relevant for incubation samples.", + "title": "incubation collection date", + "notes": [ + "MIxS collection_date accepts (truncated) ISO8601. DH taking arbitrary precision date only" + ], + "comments": [ + "Date should be formatted as YYYY(-MM(-DD)). Ie, 2021-04-15, 2021-04 and 2021 are all acceptable." + ], + "examples": [ + { + "value": "2021-04-15, 2021-04 and 2021 are all acceptable." + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "see_also": [ + "MIXS:0000011" + ], + "rank": 2, + "string_serialization": "{date, arbitrary precision}", + "domain_of": [ + "Biosample" + ], + "slot_group": "MIxS Inspired", + "recommended": true + }, + "collection_time": { + "name": "collection_time", + "description": "The time of sampling, either as an instance (single point) or interval.", + "title": "collection time, GMT", + "notes": [ + "MIxS collection_date accepts (truncated) ISO8601. DH taking seconds optional time only" + ], + "comments": [ + "Time should be entered as HH:MM(:SS) in GMT. See here for a converter: https://www.worldtimebuddy.com/pst-to-gmt-converter" + ], + "examples": [ + { + "value": "13:33 or 13:33:55" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "see_also": [ + "MIXS:0000011" + ], + "rank": 1, + "string_serialization": "{time, seconds optional}", + "domain_of": [ + "Biosample" + ], + "slot_group": "MIxS Inspired", + "recommended": true + }, + "collection_time_inc": { + "name": "collection_time_inc", + "description": "Time the incubation was harvested/collected/ended. Only relevant for incubation samples.", + "title": "incubation collection time, GMT", + "notes": [ + "MIxS collection_date accepts (truncated) ISO8601. DH taking seconds optional time only" + ], + "comments": [ + "Time should be entered as HH:MM(:SS) in GMT. See here for a converter: https://www.worldtimebuddy.com/pst-to-gmt-converter" + ], + "examples": [ + { + "value": "13:33 or 13:33:55" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "see_also": [ + "MIXS:0000011" + ], + "rank": 3, + "string_serialization": "{time, seconds optional}", + "domain_of": [ + "Biosample" + ], + "slot_group": "MIxS Inspired", + "recommended": true + }, + "conduc": { + "name": "conduc", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milliSiemens per centimeter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Electrical conductivity of water", + "title": "conductivity", + "examples": [ + { + "value": "10 milliSiemens per centimeter" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "conductivity" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000692", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "cool_syst_id": { + "name": "cool_syst_id", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "unique identifier" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The cooling system identifier", + "title": "cooling system identifier", + "examples": [ + { + "value": "12345" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "cooling system identifier" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000785", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "crop_rotation": { + "name": "crop_rotation", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "crop rotation status;schedule" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Whether or not crop is rotated, and if yes, rotation schedule", + "title": "history/crop rotation", + "examples": [ + { + "value": "yes;R2/2017-01-01/2018-12-31/P6M" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "history/crop rotation" + ], + "is_a": "core field", + "string_serialization": "{boolean};{Rn/start_time/end_time/duration}", + "slot_uri": "MIXS:0000318", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "cult_root_med": { + "name": "cult_root_med", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "name, PMID,DOI or url" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Name or reference for the hydroponic or in vitro culture rooting medium; can be the name of a commonly used medium or reference to a specific medium, e.g. Murashige and Skoog medium. If the medium has not been formally published, use the rooting medium descriptors.", + "title": "culture rooting medium", + "examples": [ + { + "value": "http://himedialabs.com/TD/PT158.pdf" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "culture rooting medium" + ], + "is_a": "core field", + "string_serialization": "{text}|{PMID}|{DOI}|{URL}", + "slot_uri": "MIXS:0001041", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "cur_land_use": { + "name": "cur_land_use", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Present state of sample site", + "title": "current land use", + "examples": [ + { + "value": "conifers" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "current land use" + ], + "is_a": "core field", + "slot_uri": "MIXS:0001080", + "domain_of": [ + "Biosample" + ], + "range": "cur_land_use_enum", + "multivalued": false + }, + "cur_vegetation": { + "name": "cur_vegetation", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "current vegetation type" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Vegetation classification from one or more standard classification systems, or agricultural crop", + "title": "current vegetation", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "current vegetation" + ], + "is_a": "core field", + "string_serialization": "{text}", + "slot_uri": "MIXS:0000312", + "domain_of": [ + "FieldResearchSite", + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "cur_vegetation_meth": { + "name": "cur_vegetation_meth", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "PMID,DOI or url" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Reference or method used in vegetation classification", + "title": "current vegetation method", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "current vegetation method" + ], + "is_a": "core field", + "string_serialization": "{PMID}|{DOI}|{URL}", + "slot_uri": "MIXS:0000314", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "date_last_rain": { + "name": "date_last_rain", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "timestamp" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The date of the last time it rained", + "title": "date last rain", + "examples": [ + { + "value": "2018-05-11:T14:30Z" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "date last rain" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000786", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "density": { + "name": "density", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "gram per cubic meter, gram per cubic centimeter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Density of the sample, which is its mass per unit volume (aka volumetric mass density)", + "title": "density", + "examples": [ + { + "value": "1000 kilogram per cubic meter" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "density" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000435", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "depos_env": { + "name": "depos_env", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Main depositional environment (https://en.wikipedia.org/wiki/Depositional_environment). If \"other\" is specified, please propose entry in \"additional info\" field", + "title": "depositional environment", + "examples": [ + { + "value": "Continental - Alluvial" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "depositional environment" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000992", + "domain_of": [ + "Biosample" + ], + "range": "depos_env_enum", + "multivalued": false + }, + "depth": { + "name": "depth", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + } + }, + "description": "The vertical distance below local surface, e.g. for sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples.", + "title": "depth", + "examples": [ + { + "value": "10 meter" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "depth" + ], + "is_a": "environment field", + "slot_uri": "MIXS:0000018", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "dew_point": { + "name": "dew_point", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "degree Celsius" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The temperature to which a given parcel of humid air must be cooled, at constant barometric pressure, for water vapor to condense into water.", + "title": "dew point", + "examples": [ + { + "value": "22 degree Celsius" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "dew point" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000129", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "diether_lipids": { + "name": "diether_lipids", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "diether lipid name;measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "nanogram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Concentration of diether lipids; can include multiple types of diether lipids", + "title": "diether lipids", + "examples": [ + { + "value": "0.2 nanogram per liter" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "diether lipids" + ], + "is_a": "core field", + "string_serialization": "{text};{float} {unit}", + "slot_uri": "MIXS:0000178", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "diss_carb_dioxide": { + "name": "diss_carb_dioxide", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per liter, milligram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample", + "title": "dissolved carbon dioxide", + "examples": [ + { + "value": "5 milligram per liter" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "dissolved carbon dioxide" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000436", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "diss_hydrogen": { + "name": "diss_hydrogen", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of dissolved hydrogen", + "title": "dissolved hydrogen", + "examples": [ + { + "value": "0.3 micromole per liter" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "dissolved hydrogen" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000179", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "diss_inorg_carb": { + "name": "diss_inorg_carb", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "microgram per liter, milligram per liter, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter", + "title": "dissolved inorganic carbon", + "examples": [ + { + "value": "2059 micromole per kilogram" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "dissolved inorganic carbon" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000434", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "diss_inorg_nitro": { + "name": "diss_inorg_nitro", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "microgram per liter, micromole per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of dissolved inorganic nitrogen", + "title": "dissolved inorganic nitrogen", + "examples": [ + { + "value": "761 micromole per liter" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "dissolved inorganic nitrogen" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000698", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "diss_inorg_phosp": { + "name": "diss_inorg_phosp", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "microgram per liter, milligram per liter, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of dissolved inorganic phosphorus in the sample", + "title": "dissolved inorganic phosphorus", + "examples": [ + { + "value": "56.5 micromole per liter" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "dissolved inorganic phosphorus" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000106", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "diss_iron": { + "name": "diss_iron", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milligram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of dissolved iron in the sample", + "title": "dissolved iron", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "dissolved iron" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000139", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "diss_org_carb": { + "name": "diss_org_carb", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per liter, milligram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid", + "title": "dissolved organic carbon", + "examples": [ + { + "value": "197 micromole per liter" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "dissolved organic carbon" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000433", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "diss_org_nitro": { + "name": "diss_org_nitro", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "microgram per liter, milligram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2", + "title": "dissolved organic nitrogen", + "examples": [ + { + "value": "0.05 micromole per liter" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "dissolved organic nitrogen" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000162", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "diss_oxygen": { + "name": "diss_oxygen", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per kilogram, milligram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of dissolved oxygen", + "title": "dissolved oxygen", + "examples": [ + { + "value": "175 micromole per kilogram" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "dissolved oxygen" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000119", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "diss_oxygen_fluid": { + "name": "diss_oxygen_fluid", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per kilogram, milligram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of dissolved oxygen in the oil field produced fluids as it contributes to oxgen-corrosion and microbial activity (e.g. Mic).", + "title": "dissolved oxygen in fluids", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "dissolved oxygen in fluids" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000438", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "dna_absorb1": { + "name": "dna_absorb1", + "description": "260/280 measurement of DNA sample purity", + "title": "DNA absorbance 260/280", + "comments": [ + "Recommended value is between 1 and 3." + ], + "examples": [ + { + "value": "2.02" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "rank": 7, + "is_a": "biomaterial_purity", + "domain_of": [ + "Biosample", + "ProcessedSample" + ], + "slot_group": "JGI-Metagenomics", + "range": "float", + "recommended": true + }, + "dna_absorb2": { + "name": "dna_absorb2", + "description": "260/230 measurement of DNA sample purity", + "title": "DNA absorbance 260/230", + "comments": [ + "Recommended value is between 1 and 3." + ], + "examples": [ + { + "value": "2.02" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "rank": 8, + "is_a": "biomaterial_purity", + "domain_of": [ + "Biosample" + ], + "slot_group": "JGI-Metagenomics", + "range": "float", + "recommended": true + }, + "dna_concentration": { + "name": "dna_concentration", + "title": "DNA concentration in ng/ul", + "comments": [ + "Units must be in ng/uL. Enter the numerical part only. Must be calculated using a fluorometric method. Acceptable values are 0-2000." + ], + "examples": [ + { + "value": "100" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "see_also": [ + "nmdc:nucleic_acid_concentration" + ], + "rank": 5, + "domain_of": [ + "Biosample", + "ProcessedSample" + ], + "slot_group": "JGI-Metagenomics", + "range": "float", + "recommended": true, + "minimum_value": 0, + "maximum_value": 2000 + }, + "dna_cont_type": { + "name": "dna_cont_type", + "description": "Tube or plate (96-well)", + "title": "DNA container type", + "examples": [ + { + "value": "plate" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "rank": 10, + "domain_of": [ + "Biosample" + ], + "slot_group": "JGI-Metagenomics", + "range": "JgiContTypeEnum", + "recommended": true + }, + "dna_cont_well": { + "name": "dna_cont_well", + "title": "DNA plate position", + "comments": [ + "Required when 'plate' is selected for container type.", + "Leave blank if the sample will be shipped in a tube.", + "JGI will not process samples in corner wells, so A1, A12, H1 and H12 will not pass validation.", + "For partial plates, fill by columns, like B1-G1,A2-H2,A3-D3 (NOT A2-A11,B1-B8)." + ], + "examples": [ + { + "value": "B2" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "rank": 11, + "string_serialization": "{96 well plate pos}", + "domain_of": [ + "Biosample" + ], + "slot_group": "JGI-Metagenomics", + "recommended": true, + "pattern": "^(?!A1$|A12$|H1$|H12$)(([A-H][1-9])|([A-H]1[0-2]))$" + }, + "dna_container_id": { + "name": "dna_container_id", + "title": "DNA container label", + "comments": [ + "Must be unique across all tubes and plates, and <20 characters. All samples in a plate should have the same plate label." + ], + "examples": [ + { + "value": "Pond_MT_041618" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "rank": 9, + "string_serialization": "{text < 20 characters}", + "domain_of": [ + "Biosample" + ], + "slot_group": "JGI-Metagenomics", + "recommended": true + }, + "dna_dnase": { + "name": "dna_dnase", + "title": "DNase treatment DNA", + "comments": [ + "Note DNase treatment is required for all RNA samples." + ], + "examples": [ + { + "value": "no" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "rank": 13, + "domain_of": [ + "Biosample" + ], + "slot_group": "JGI-Metagenomics", + "range": "YesNoEnum", + "recommended": true + }, + "dna_isolate_meth": { + "name": "dna_isolate_meth", + "description": "Describe the method/protocol/kit used to extract DNA/RNA.", + "title": "DNA isolation method", + "examples": [ + { + "value": "phenol/chloroform extraction" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "Sample Isolation Method" + ], + "rank": 16, + "string_serialization": "{text}", + "domain_of": [ + "Biosample" + ], + "slot_group": "JGI-Metagenomics", + "recommended": true + }, + "dna_project_contact": { + "name": "dna_project_contact", + "title": "DNA seq project contact", + "comments": [ + "Do not edit these values. A template will be provided by NMDC in which these values have been pre-filled." + ], + "examples": [ + { + "value": "John Jones" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "rank": 18, + "string_serialization": "{text}", + "domain_of": [ + "Biosample" + ], + "slot_group": "JGI-Metagenomics", + "recommended": true + }, + "dna_samp_id": { + "name": "dna_samp_id", + "title": "DNA sample ID", + "todos": [ + "Removed identifier = TRUE from dna_samp_ID in JGI_sample_slots, as a class can't have two identifiers. How to force uniqueness? Moot because that column will be prefilled?" + ], + "comments": [ + "Do not edit these values. A template will be provided by NMDC in which these values have been pre-filled." + ], + "examples": [ + { + "value": "187654" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "rank": 3, + "string_serialization": "{text}", + "domain_of": [ + "Biosample" + ], + "slot_group": "JGI-Metagenomics", + "recommended": true + }, + "dna_sample_format": { + "name": "dna_sample_format", + "description": "Solution in which the DNA sample has been suspended", + "title": "DNA sample format", + "examples": [ + { + "value": "Water" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "rank": 12, + "domain_of": [ + "Biosample" + ], + "slot_group": "JGI-Metagenomics", + "range": "DNASampleFormatEnum", + "recommended": true + }, + "dna_sample_name": { + "name": "dna_sample_name", + "description": "Give the DNA sample a name that is meaningful to you. Sample names must be unique across all JGI projects and contain a-z, A-Z, 0-9, - and _ only.", + "title": "DNA sample name", + "examples": [ + { + "value": "JGI_pond_041618" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "rank": 4, + "string_serialization": "{text}", + "domain_of": [ + "Biosample" + ], + "slot_group": "JGI-Metagenomics", + "recommended": true + }, + "dna_seq_project": { + "name": "dna_seq_project", + "title": "DNA seq project ID", + "comments": [ + "Do not edit these values. A template will be provided by NMDC in which these values have been pre-filled." + ], + "examples": [ + { + "value": "1191234" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "Seq Project ID" + ], + "rank": 1, + "string_serialization": "{text}", + "domain_of": [ + "Biosample" + ], + "slot_group": "JGI-Metagenomics", + "recommended": true + }, + "dna_seq_project_name": { + "name": "dna_seq_project_name", + "title": "DNA seq project name", + "comments": [ + "Do not edit these values. A template will be provided by NMDC in which these values have been pre-filled." + ], + "examples": [ + { + "value": "JGI Pond metagenomics" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "rank": 2, + "string_serialization": "{text}", + "domain_of": [ + "Biosample" + ], + "slot_group": "JGI-Metagenomics", + "recommended": true + }, + "dna_seq_project_pi": { + "name": "dna_seq_project_pi", + "title": "DNA seq project PI", + "comments": [ + "Do not edit these values. A template will be provided by NMDC in which these values have been pre-filled." + ], + "examples": [ + { + "value": "Jane Johnson" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "rank": 17, + "string_serialization": "{text}", + "domain_of": [ + "Biosample" + ], + "slot_group": "JGI-Metagenomics", + "recommended": true + }, + "dna_volume": { + "name": "dna_volume", + "title": "DNA volume in ul", + "comments": [ + "Units must be in uL. Enter the numerical part only. Value must be 0-1000. This form accepts values < 25, but JGI may refuse to process them unless permission has been granted by a project manager" + ], + "examples": [ + { + "value": "25" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "rank": 6, + "string_serialization": "{float}", + "domain_of": [ + "Biosample" + ], + "slot_group": "JGI-Metagenomics", + "range": "float", + "recommended": true, + "minimum_value": 0, + "maximum_value": 1000 + }, + "dnase_rna": { + "name": "dnase_rna", + "title": "DNase treated", + "comments": [ + "Note DNase treatment is required for all RNA samples." + ], + "examples": [ + { + "value": "no" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "Was Sample DNAse treated?" + ], + "rank": 13, + "domain_of": [ + "Biosample" + ], + "slot_group": "JGI-Metatranscriptomics", + "range": "YesNoEnum", + "recommended": true + }, + "door_comp_type": { + "name": "door_comp_type", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The composite type of the door", + "title": "door type, composite", + "examples": [ + { + "value": "revolving" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "door type, composite" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000795", + "domain_of": [ + "Biosample" + ], + "range": "door_comp_type_enum", + "multivalued": false + }, + "door_cond": { + "name": "door_cond", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The phsical condition of the door", + "title": "door condition", + "examples": [ + { + "value": "new" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "door condition" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000788", + "domain_of": [ + "Biosample" + ], + "range": "door_cond_enum", + "multivalued": false + }, + "door_direct": { + "name": "door_direct", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The direction the door opens", + "title": "door direction of opening", + "examples": [ + { + "value": "inward" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "door direction of opening" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000789", + "domain_of": [ + "Biosample" + ], + "range": "door_direct_enum", + "multivalued": false + }, + "door_loc": { + "name": "door_loc", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The relative location of the door in the room", + "title": "door location", + "examples": [ + { + "value": "north" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "door location" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000790", + "domain_of": [ + "Biosample" + ], + "range": "door_loc_enum", + "multivalued": false + }, + "door_mat": { + "name": "door_mat", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The material the door is composed of", + "title": "door material", + "examples": [ + { + "value": "wood" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "door material" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000791", + "domain_of": [ + "Biosample" + ], + "range": "door_mat_enum", + "multivalued": false + }, + "door_move": { + "name": "door_move", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The type of movement of the door", + "title": "door movement", + "examples": [ + { + "value": "swinging" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "door movement" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000792", + "domain_of": [ + "Biosample" + ], + "range": "door_move_enum", + "multivalued": false + }, + "door_size": { + "name": "door_size", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "square meter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The size of the door", + "title": "door area or size", + "examples": [ + { + "value": "2.5 square meter" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "door area or size" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000158", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "door_type": { + "name": "door_type", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The type of door material", + "title": "door type", + "examples": [ + { + "value": "wooden" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "door type" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000794", + "domain_of": [ + "Biosample" + ], + "range": "door_type_enum", + "multivalued": false + }, + "door_type_metal": { + "name": "door_type_metal", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The type of metal door", + "title": "door type, metal", + "examples": [ + { + "value": "hollow" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "door type, metal" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000796", + "domain_of": [ + "Biosample" + ], + "range": "door_type_metal_enum", + "multivalued": false + }, + "door_type_wood": { + "name": "door_type_wood", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The type of wood door", + "title": "door type, wood", + "examples": [ + { + "value": "battened" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "door type, wood" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000797", + "domain_of": [ + "Biosample" + ], + "range": "door_type_wood_enum", + "multivalued": false + }, + "door_water_mold": { + "name": "door_water_mold", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Signs of the presence of mold or mildew on a door", + "title": "door signs of water/mold", + "examples": [ + { + "value": "presence of mold visible" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "door signs of water/mold" + ], + "is_a": "core field", + "string_serialization": "[presence of mold visible|no presence of mold visible]", + "slot_uri": "MIXS:0000793", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "down_par": { + "name": "down_par", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "microEinstein per square meter per second, microEinstein per square centimeter per second" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Visible waveband radiance and irradiance measurements in the water column", + "title": "downward PAR", + "examples": [ + { + "value": "28.71 microEinstein per square meter per second" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "downward PAR" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000703", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "drainage_class": { + "name": "drainage_class", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Drainage classification from a standard system such as the USDA system", + "title": "drainage classification", + "examples": [ + { + "value": "well" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "drainage classification" + ], + "is_a": "core field", + "slot_uri": "MIXS:0001085", + "domain_of": [ + "Biosample" + ], + "range": "drainage_class_enum", + "multivalued": false + }, + "drawings": { + "name": "drawings", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The buildings architectural drawings; if design is chosen, indicate phase-conceptual, schematic, design development, and construction documents", + "title": "drawings", + "examples": [ + { + "value": "sketch" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "drawings" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000798", + "domain_of": [ + "Biosample" + ], + "range": "drawings_enum", + "multivalued": false + }, + "ecosystem": { + "name": "ecosystem", + "description": "An ecosystem is a combination of a physical environment (abiotic factors) and all the organisms (biotic factors) that interact with this environment. Ecosystem is in position 1/5 in a GOLD path.", + "comments": [ + "The abiotic factors play a profound role on the type and composition of organisms in a given environment. The GOLD Ecosystem at the top of the five-level classification system is aimed at capturing the broader environment from which an organism or environmental sample is collected. The three broad groups under Ecosystem are Environmental, Host-associated, and Engineered. They represent samples collected from a natural environment or from another organism or from engineered environments like bioreactors respectively." + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "see_also": [ + "https://gold.jgi.doe.gov/help" + ], + "is_a": "gold_path_field", + "domain_of": [ + "Biosample", + "Study" + ] + }, + "ecosystem_category": { + "name": "ecosystem_category", + "description": "Ecosystem categories represent divisions within the ecosystem based on specific characteristics of the environment from where an organism or sample is isolated. Ecosystem category is in position 2/5 in a GOLD path.", + "comments": [ + "The Environmental ecosystem (for example) is divided into Air, Aquatic and Terrestrial. Ecosystem categories for Host-associated samples can be individual hosts or phyla and for engineered samples it may be manipulated environments like bioreactors, solid waste etc." + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "see_also": [ + "https://gold.jgi.doe.gov/help" + ], + "is_a": "gold_path_field", + "domain_of": [ + "Biosample", + "Study" + ] + }, + "ecosystem_subtype": { + "name": "ecosystem_subtype", + "description": "Ecosystem subtypes represent further subdivision of Ecosystem types into more distinct subtypes. Ecosystem subtype is in position 4/5 in a GOLD path.", + "comments": [ + "Ecosystem Type Marine (Environmental -> Aquatic -> Marine) is further divided (for example) into Intertidal zone, Coastal, Pelagic, Intertidal zone etc. in the Ecosystem subtype category." + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "see_also": [ + "https://gold.jgi.doe.gov/help" + ], + "is_a": "gold_path_field", + "domain_of": [ + "Biosample", + "Study" + ] + }, + "ecosystem_type": { + "name": "ecosystem_type", + "description": "Ecosystem types represent things having common characteristics within the Ecosystem Category. These common characteristics based grouping is still broad but specific to the characteristics of a given environment. Ecosystem type is in position 3/5 in a GOLD path.", + "comments": [ + "The Aquatic ecosystem category (for example) may have ecosystem types like Marine or Thermal springs etc. Ecosystem category Air may have Indoor air or Outdoor air as different Ecosystem Types. In the case of Host-associated samples, ecosystem type can represent Respiratory system, Digestive system, Roots etc." + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "see_also": [ + "https://gold.jgi.doe.gov/help" + ], + "is_a": "gold_path_field", + "domain_of": [ + "Biosample", + "Study" + ] + }, + "efficiency_percent": { + "name": "efficiency_percent", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Percentage of volatile solids removed from the anaerobic digestor", + "title": "efficiency percent", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "efficiency percent" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000657", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "elev": { + "name": "elev", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + } + }, + "description": "Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit.", + "title": "elevation", + "examples": [ + { + "value": "100 meter" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "elevation" + ], + "is_a": "environment field", + "slot_uri": "MIXS:0000093", + "domain_of": [ + "FieldResearchSite", + "Biosample" + ], + "range": "float", + "multivalued": false + }, + "elevator": { + "name": "elevator", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "value" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The number of elevators within the built structure", + "title": "elevator count", + "examples": [ + { + "value": "2" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "elevator count" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000799", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "emsl_store_temp": { + "name": "emsl_store_temp", + "description": "The temperature at which the sample should be stored upon delivery to EMSL", + "title": "EMSL sample storage temperature, deg. C", + "todos": [ + "add 'see_alsos' with link to NEXUS info" + ], + "comments": [ + "Enter a temperature in celsius. Numeric portion only." + ], + "examples": [ + { + "value": "-80" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "rank": 4, + "string_serialization": "{float}", + "domain_of": [ + "EmslInterface" + ], + "slot_group": "EMSL", + "recommended": true + }, + "emulsions": { + "name": "emulsions", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "emulsion name;measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "gram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Amount or concentration of substances such as paints, adhesives, mayonnaise, hair colorants, emulsified oils, etc.; can include multiple emulsion types", + "title": "emulsions", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "emulsions" + ], + "is_a": "core field", + "string_serialization": "{text};{float} {unit}", + "slot_uri": "MIXS:0000660", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "env_broad_scale": { + "name": "env_broad_scale", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "The major environment type(s) where the sample was collected. Recommend subclasses of biome [ENVO:00000428]. Multiple terms can be separated by one or more pipes." + }, + "tooltip": { + "tag": "tooltip", + "value": "The biome or major environmental system where the sample or specimen originated. Choose values from subclasses of the 'biome' class [ENVO:00000428] in the Environment Ontology (ENVO). For host-associated or plant-associated samples, use terms from the UBERON or Plant Ontology to describe the broad anatomical or morphological context" + } + }, + "description": "Report the major environmental system the sample or specimen came from. The system(s) identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. in the desert or a rainforest). We recommend using subclasses of EnvO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS", + "title": "broad-scale environmental context", + "examples": [ + { + "value": "oceanic epipelagic zone biome [ENVO:01000033] for annotating a water sample from the photic zone in middle of the Atlantic Ocean" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "broad-scale environmental context" + ], + "is_a": "environment field", + "string_serialization": "{termLabel} {[termID]}", + "slot_uri": "MIXS:0000012", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "env_local_scale": { + "name": "env_local_scale", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "Environmental entities having causal influences upon the entity at time of sampling." + }, + "tooltip": { + "tag": "tooltip", + "value": "The specific environmental entities or features near the sample or specimen that significantly influence its characteristics or composition. These entities are typically smaller in scale than the broad environmental context. Values for this field should be countable, material nouns and must be chosen from subclasses of BFO:0000040 (material entity) that appear in the Environment Ontology (ENVO). For host-associated or plant-associated samples, use terms from the UBERON or Plant Ontology to describe specific anatomical structures or plant parts." + } + }, + "description": "Report the entity or entities which are in the sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. We recommend using EnvO terms which are of smaller spatial grain than your entry for env_broad_scale. Terms, such as anatomical sites, from other OBO Library ontologies which interoperate with EnvO (e.g. UBERON) are accepted in this field. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS.", + "title": "local environmental context", + "examples": [ + { + "value": "litter layer [ENVO:01000338]; Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]." + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "local environmental context" + ], + "is_a": "environment field", + "string_serialization": "{termLabel} {[termID]}", + "slot_uri": "MIXS:0000013", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "env_medium": { + "name": "env_medium", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "The material displaced by the entity at time of sampling. Recommend subclasses of environmental material [ENVO:00010483]." + }, + "tooltip": { + "tag": "tooltip", + "value": "The predominant environmental material or substrate that directly surrounds or hosts the sample or specimen at the time of sampling. Choose values from subclasses of the 'environmental material' class [ENVO:00010483] in the Environment Ontology (ENVO). Values for this field should be measurable or mass material nouns, representing continuous environmental materials. For host-associated or plant-associated samples, use terms from the UBERON or Plant Ontology to indicate a tissue, organ, or plant structure" + } + }, + "description": "Report the environmental material(s) immediately surrounding the sample or specimen at the time of sampling. We recommend using subclasses of 'environmental material' (http://purl.obolibrary.org/obo/ENVO_00010483). EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS . Terms from other OBO ontologies are permissible as long as they reference mass/volume nouns (e.g. air, water, blood) and not discrete, countable entities (e.g. a tree, a leaf, a table top).", + "title": "environmental medium", + "examples": [ + { + "value": "soil [ENVO:00001998]; Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air [ENVO_00002005]" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "environmental medium" + ], + "is_a": "environment field", + "string_serialization": "{termLabel} {[termID]}", + "slot_uri": "MIXS:0000014", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "escalator": { + "name": "escalator", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "value" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The number of escalators within the built structure", + "title": "escalator count", + "examples": [ + { + "value": "4" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "escalator count" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000800", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "ethylbenzene": { + "name": "ethylbenzene", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milligram per liter, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of ethylbenzene in the sample", + "title": "ethylbenzene", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "ethylbenzene" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000155", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "exp_duct": { + "name": "exp_duct", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "square meter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The amount of exposed ductwork in the room", + "title": "exposed ductwork", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "exposed ductwork" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000144", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "exp_pipe": { + "name": "exp_pipe", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The number of exposed pipes in the room", + "title": "exposed pipes", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "exposed pipes" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000220", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "experimental_factor": { + "name": "experimental_factor", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "text or EFO and/or OBI" + } + }, + "description": "Experimental factors are essentially the variable aspects of an experiment design which can be used to describe an experiment, or set of experiments, in an increasingly detailed manner. This field accepts ontology terms from Experimental Factor Ontology (EFO) and/or Ontology for Biomedical Investigations (OBI). For a browser of EFO (v 2.95) terms, please see http://purl.bioontology.org/ontology/EFO; for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI", + "title": "experimental factor", + "examples": [ + { + "value": "time series design [EFO:EFO_0001779]" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "experimental factor" + ], + "is_a": "investigation field", + "string_serialization": "{termLabel} {[termID]}|{text}", + "slot_uri": "MIXS:0000008", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "experimental_factor_other": { + "name": "experimental_factor_other", + "description": "Other details about your sample that you feel can't be accurately represented in the available columns.", + "title": "experimental factor- other", + "comments": [ + "This slot accepts open-ended text about your sample.", + "We recommend using key:value pairs.", + "Provided pairs will be considered for inclusion as future slots/terms in this data collection template." + ], + "examples": [ + { + "value": "experimental treatment: value" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "see_also": [ + "MIXS:0000008", + "MIXS:0000300" + ], + "rank": 7, + "string_serialization": "{text}", + "domain_of": [ + "Biosample" + ], + "slot_group": "MIxS Inspired", + "recommended": true + }, + "ext_door": { + "name": "ext_door", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "value" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The number of exterior doors in the built structure", + "title": "exterior door count", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "exterior door count" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000170", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "ext_wall_orient": { + "name": "ext_wall_orient", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The orientation of the exterior wall", + "title": "orientations of exterior wall", + "examples": [ + { + "value": "northwest" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "orientations of exterior wall" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000817", + "domain_of": [ + "Biosample" + ], + "range": "ext_wall_orient_enum", + "multivalued": false + }, + "ext_window_orient": { + "name": "ext_window_orient", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The compass direction the exterior window of the room is facing", + "title": "orientations of exterior window", + "examples": [ + { + "value": "southwest" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "orientations of exterior window" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000818", + "domain_of": [ + "Biosample" + ], + "range": "ext_window_orient_enum", + "multivalued": false + }, + "extreme_event": { + "name": "extreme_event", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "date" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Unusual physical events that may have affected microbial populations", + "title": "history/extreme events", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "history/extreme events" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000320", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "fao_class": { + "name": "fao_class", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Soil classification from the FAO World Reference Database for Soil Resources. The list can be found at http://www.fao.org/nr/land/sols/soil/wrb-soil-maps/reference-groups", + "title": "soil_taxonomic/FAO classification", + "examples": [ + { + "value": "Luvisols" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "soil_taxonomic/FAO classification" + ], + "is_a": "core field", + "slot_uri": "MIXS:0001083", + "domain_of": [ + "Biosample" + ], + "range": "fao_class_enum", + "multivalued": false + }, + "fertilizer_regm": { + "name": "fertilizer_regm", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "fertilizer name;fertilizer amount;treatment interval and duration" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "gram, mole per liter, milligram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Information about treatment involving the use of fertilizers; should include the name of fertilizer, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple fertilizer regimens", + "title": "fertilizer regimen", + "examples": [ + { + "value": "urea;0.6 milligram per liter;R2/2018-05-11:T14:30/2018-05-11T19:30/P1H30M" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "fertilizer regimen" + ], + "is_a": "core field", + "string_serialization": "{text};{float} {unit};{Rn/start_time/end_time/duration}", + "slot_uri": "MIXS:0000556", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "field": { + "name": "field", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "name" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Name of the hydrocarbon field (e.g. Albacora)", + "title": "field name", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "field name" + ], + "is_a": "core field", + "string_serialization": "{text}", + "slot_uri": "MIXS:0000291", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "filter_method": { + "name": "filter_method", + "description": "Type of filter used or how the sample was filtered", + "title": "filter method", + "comments": [ + "describe the filter or provide a catalog number and manufacturer" + ], + "examples": [ + { + "value": "C18" + }, + { + "value": "Basix PES, 13-100-106 FisherSci" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "see_also": [ + "MIXS:0000765" + ], + "rank": 6, + "string_serialization": "{text}", + "domain_of": [ + "Biosample" + ], + "slot_group": "MIxS Inspired", + "recommended": true + }, + "filter_type": { + "name": "filter_type", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "A device which removes solid particulates or airborne molecular contaminants", + "title": "filter type", + "examples": [ + { + "value": "HEPA" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "filter type" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000765", + "domain_of": [ + "Biosample" + ], + "range": "filter_type_enum", + "multivalued": true + }, + "fire": { + "name": "fire", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "date" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Historical and/or physical evidence of fire", + "title": "history/fire", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "history/fire" + ], + "is_a": "core field", + "slot_uri": "MIXS:0001086", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "fireplace_type": { + "name": "fireplace_type", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "A firebox with chimney", + "title": "fireplace type", + "examples": [ + { + "value": "wood burning" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "fireplace type" + ], + "is_a": "core field", + "string_serialization": "[gas burning|wood burning]", + "slot_uri": "MIXS:0000802", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "flooding": { + "name": "flooding", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "date" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Historical and/or physical evidence of flooding", + "title": "history/flooding", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "history/flooding" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000319", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "floor_age": { + "name": "floor_age", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "years, weeks, days" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The time period since installment of the carpet or flooring", + "title": "floor age", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "floor age" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000164", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "floor_area": { + "name": "floor_area", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "square meter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The area of the floor space within the room", + "title": "floor area", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "floor area" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000165", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "floor_cond": { + "name": "floor_cond", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The physical condition of the floor at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas", + "title": "floor condition", + "examples": [ + { + "value": "new" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "floor condition" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000803", + "domain_of": [ + "Biosample" + ], + "range": "floor_cond_enum", + "multivalued": false + }, + "floor_count": { + "name": "floor_count", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "value" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The number of floors in the building, including basements and mechanical penthouse", + "title": "floor count", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "floor count" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000225", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "floor_finish_mat": { + "name": "floor_finish_mat", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The floor covering type; the finished surface that is walked on", + "title": "floor finish material", + "examples": [ + { + "value": "carpet" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "floor finish material" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000804", + "domain_of": [ + "Biosample" + ], + "range": "floor_finish_mat_enum", + "multivalued": false + }, + "floor_struc": { + "name": "floor_struc", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Refers to the structural elements and subfloor upon which the finish flooring is installed", + "title": "floor structure", + "examples": [ + { + "value": "concrete" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "floor structure" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000806", + "domain_of": [ + "Biosample" + ], + "range": "floor_struc_enum", + "multivalued": false + }, + "floor_thermal_mass": { + "name": "floor_thermal_mass", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "joule per degree Celsius" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The ability of the floor to provide inertia against temperature fluctuations", + "title": "floor thermal mass", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "floor thermal mass" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000166", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "floor_water_mold": { + "name": "floor_water_mold", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Signs of the presence of mold or mildew in a room", + "title": "floor signs of water/mold", + "examples": [ + { + "value": "ceiling discoloration" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "floor signs of water/mold" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000805", + "domain_of": [ + "Biosample" + ], + "range": "floor_water_mold_enum", + "multivalued": false + }, + "fluor": { + "name": "fluor", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milligram chlorophyll a per cubic meter, volts" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Raw or converted fluorescence of water", + "title": "fluorescence", + "examples": [ + { + "value": "2.5 volts" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "fluorescence" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000704", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "freq_clean": { + "name": "freq_clean", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration or {text}" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The number of times the sample location is cleaned. Frequency of cleaning might be on a Daily basis, Weekly, Monthly, Quarterly or Annually.", + "title": "frequency of cleaning", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "frequency of cleaning" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000226", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "freq_cook": { + "name": "freq_cook", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The number of times a meal is cooked per week", + "title": "frequency of cooking", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "frequency of cooking" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000227", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "fungicide_regm": { + "name": "fungicide_regm", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "fungicide name;fungicide amount;treatment interval and duration" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "gram, mole per liter, milligram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Information about treatment involving use of fungicides; should include the name of fungicide, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple fungicide regimens", + "title": "fungicide regimen", + "examples": [ + { + "value": "bifonazole;1 mole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "fungicide regimen" + ], + "is_a": "core field", + "string_serialization": "{text};{float} {unit};{Rn/start_time/end_time/duration}", + "slot_uri": "MIXS:0000557", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "furniture": { + "name": "furniture", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The types of furniture present in the sampled room", + "title": "furniture", + "examples": [ + { + "value": "chair" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "furniture" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000807", + "domain_of": [ + "Biosample" + ], + "range": "furniture_enum", + "multivalued": false + }, + "gaseous_environment": { + "name": "gaseous_environment", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "gaseous compound name;gaseous compound amount;treatment interval and duration" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Use of conditions with differing gaseous environments; should include the name of gaseous compound, amount administered, treatment duration, interval and total experimental duration; can include multiple gaseous environment regimens", + "title": "gaseous environment", + "examples": [ + { + "value": "nitric oxide;0.5 micromole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "gaseous environment" + ], + "is_a": "core field", + "string_serialization": "{text};{float} {unit};{Rn/start_time/end_time/duration}", + "slot_uri": "MIXS:0000558", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "gaseous_substances": { + "name": "gaseous_substances", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "gaseous substance name;measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Amount or concentration of substances such as hydrogen sulfide, carbon dioxide, methane, etc.; can include multiple substances", + "title": "gaseous substances", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "gaseous substances" + ], + "is_a": "core field", + "string_serialization": "{text};{float} {unit}", + "slot_uri": "MIXS:0000661", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "gender_restroom": { + "name": "gender_restroom", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The gender type of the restroom", + "title": "gender of restroom", + "examples": [ + { + "value": "male" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "gender of restroom" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000808", + "domain_of": [ + "Biosample" + ], + "range": "gender_restroom_enum", + "multivalued": false + }, + "genetic_mod": { + "name": "genetic_mod", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "PMID,DOI,url or free text" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Genetic modifications of the genome of an organism, which may occur naturally by spontaneous mutation, or be introduced by some experimental means, e.g. specification of a transgene or the gene knocked-out or details of transient transfection", + "title": "genetic modification", + "examples": [ + { + "value": "aox1A transgenic" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "genetic modification" + ], + "is_a": "core field", + "string_serialization": "{PMID}|{DOI}|{URL}|{text}", + "slot_uri": "MIXS:0000859", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "geo_loc_name": { + "name": "geo_loc_name", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "country or sea name (INSDC or GAZ): region(GAZ), specific location name" + } + }, + "description": "The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (http://purl.bioontology.org/ontology/GAZ)", + "title": "geographic location (country and/or sea,region)", + "examples": [ + { + "value": "USA: Maryland, Bethesda" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "geographic location (country and/or sea,region)" + ], + "is_a": "environment field", + "string_serialization": "{term}: {term}, {text}", + "slot_uri": "MIXS:0000010", + "domain_of": [ + "FieldResearchSite", + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "glucosidase_act": { + "name": "glucosidase_act", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "mol per liter per hour" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Measurement of glucosidase activity", + "title": "glucosidase activity", + "examples": [ + { + "value": "5 mol per liter per hour" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "glucosidase activity" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000137", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "gravidity": { + "name": "gravidity", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "gravidity status;timestamp" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Whether or not subject is gravid, and if yes date due or date post-conception, specifying which is used", + "title": "gravidity", + "examples": [ + { + "value": "yes;due date:2018-05-11" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "gravidity" + ], + "is_a": "core field", + "string_serialization": "{boolean};{timestamp}", + "slot_uri": "MIXS:0000875", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "gravity": { + "name": "gravity", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "gravity factor value;treatment interval and duration" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "meter per square second, g" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Information about treatment involving use of gravity factor to study various types of responses in presence, absence or modified levels of gravity; treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple treatments", + "title": "gravity", + "examples": [ + { + "value": "12 g;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "gravity" + ], + "is_a": "core field", + "string_serialization": "{float} {unit};{Rn/start_time/end_time/duration}", + "slot_uri": "MIXS:0000559", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "growth_facil": { + "name": "growth_facil", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "free text or CO" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Type of facility where the sampled plant was grown; controlled vocabulary: growth chamber, open top chamber, glasshouse, experimental garden, field. Alternatively use Crop Ontology (CO) terms, see http://www.cropontology.org/ontology/CO_715/Crop%20Research", + "title": "growth facility", + "examples": [ + { + "value": "Growth chamber [CO_715:0000189]" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "growth facility" + ], + "is_a": "core field", + "string_serialization": "{text}|{termLabel} {[termID]}", + "slot_uri": "MIXS:0001043", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "growth_habit": { + "name": "growth_habit", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Characteristic shape, appearance or growth form of a plant species", + "title": "growth habit", + "examples": [ + { + "value": "spreading" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "growth habit" + ], + "is_a": "core field", + "slot_uri": "MIXS:0001044", + "domain_of": [ + "Biosample" + ], + "range": "growth_habit_enum", + "multivalued": false + }, + "growth_hormone_regm": { + "name": "growth_hormone_regm", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "growth hormone name;growth hormone amount;treatment interval and duration" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "gram, mole per liter, milligram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Information about treatment involving use of growth hormones; should include the name of growth hormone, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple growth hormone regimens", + "title": "growth hormone regimen", + "examples": [ + { + "value": "abscisic acid;0.5 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "growth hormone regimen" + ], + "is_a": "core field", + "string_serialization": "{text};{float} {unit};{Rn/start_time/end_time/duration}", + "slot_uri": "MIXS:0000560", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "hall_count": { + "name": "hall_count", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "value" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The total count of hallways and cooridors in the built structure", + "title": "hallway/corridor count", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "hallway/corridor count" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000228", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "handidness": { + "name": "handidness", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The handidness of the individual sampled", + "title": "handidness", + "examples": [ + { + "value": "right handedness" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "handidness" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000809", + "domain_of": [ + "Biosample" + ], + "range": "handidness_enum", + "multivalued": false + }, + "hc_produced": { + "name": "hc_produced", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Main hydrocarbon type produced from resource (i.e. Oil, gas, condensate, etc). If \"other\" is specified, please propose entry in \"additional info\" field", + "title": "hydrocarbon type produced", + "examples": [ + { + "value": "Gas" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "hydrocarbon type produced" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000989", + "domain_of": [ + "Biosample" + ], + "range": "hc_produced_enum", + "multivalued": false + }, + "hcr": { + "name": "hcr", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Main Hydrocarbon Resource type. The term \"Hydrocarbon Resource\" HCR defined as a natural environmental feature containing large amounts of hydrocarbons at high concentrations potentially suitable for commercial exploitation. This term should not be confused with the Hydrocarbon Occurrence term which also includes hydrocarbon-rich environments with currently limited commercial interest such as seeps, outcrops, gas hydrates etc. If \"other\" is specified, please propose entry in \"additional info\" field", + "title": "hydrocarbon resource type", + "examples": [ + { + "value": "Oil Sand" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "hydrocarbon resource type" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000988", + "domain_of": [ + "Biosample" + ], + "range": "hcr_enum", + "multivalued": false + }, + "hcr_fw_salinity": { + "name": "hcr_fw_salinity", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milligram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Original formation water salinity (prior to secondary recovery e.g. Waterflooding) expressed as TDS", + "title": "formation water salinity", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "formation water salinity" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000406", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "hcr_geol_age": { + "name": "hcr_geol_age", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Geological age of hydrocarbon resource (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). If \"other\" is specified, please propose entry in \"additional info\" field", + "title": "hydrocarbon resource geological age", + "examples": [ + { + "value": "Silurian" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "hydrocarbon resource geological age" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000993", + "domain_of": [ + "Biosample" + ], + "range": "hcr_geol_age_enum", + "multivalued": false + }, + "hcr_pressure": { + "name": "hcr_pressure", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value range" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "atmosphere, kilopascal" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Original pressure of the hydrocarbon resource", + "title": "hydrocarbon resource original pressure", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "hydrocarbon resource original pressure" + ], + "is_a": "core field", + "string_serialization": "{float} - {float} {unit}", + "slot_uri": "MIXS:0000395", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "hcr_temp": { + "name": "hcr_temp", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value range" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "degree Celsius" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Original temperature of the hydrocarbon resource", + "title": "hydrocarbon resource original temperature", + "examples": [ + { + "value": "150-295 degree Celsius" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "hydrocarbon resource original temperature" + ], + "is_a": "core field", + "string_serialization": "{float} - {float} {unit}", + "slot_uri": "MIXS:0000393", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "heat_cool_type": { + "name": "heat_cool_type", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Methods of conditioning or heating a room or building", + "title": "heating and cooling system type", + "examples": [ + { + "value": "heat pump" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "heating and cooling system type" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000766", + "domain_of": [ + "Biosample" + ], + "range": "heat_cool_type_enum", + "multivalued": true + }, + "heat_deliv_loc": { + "name": "heat_deliv_loc", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The location of heat delivery within the room", + "title": "heating delivery locations", + "examples": [ + { + "value": "north" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "heating delivery locations" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000810", + "domain_of": [ + "Biosample" + ], + "range": "heat_deliv_loc_enum", + "multivalued": false + }, + "heat_sys_deliv_meth": { + "name": "heat_sys_deliv_meth", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The method by which the heat is delivered through the system", + "title": "heating system delivery method", + "examples": [ + { + "value": "radiant" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "heating system delivery method" + ], + "is_a": "core field", + "string_serialization": "[conductive|radiant]", + "slot_uri": "MIXS:0000812", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "heat_system_id": { + "name": "heat_system_id", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "unique identifier" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The heating system identifier", + "title": "heating system identifier", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "heating system identifier" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000833", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "heavy_metals": { + "name": "heavy_metals", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "heavy metal name;measurement value unit" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "microgram per gram" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Heavy metals present in the sequenced sample and their concentrations. For multiple heavy metals and concentrations, add multiple copies of this field.", + "title": "extreme_unusual_properties/heavy metals", + "examples": [ + { + "value": "mercury;0.09 micrograms per gram" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "extreme_unusual_properties/heavy metals" + ], + "is_a": "core field", + "string_serialization": "{text};{float} {unit}", + "slot_uri": "MIXS:0000652", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "heavy_metals_meth": { + "name": "heavy_metals_meth", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "PMID,DOI or url" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Reference or method used in determining heavy metals", + "title": "extreme_unusual_properties/heavy metals method", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "extreme_unusual_properties/heavy metals method" + ], + "is_a": "core field", + "string_serialization": "{PMID}|{DOI}|{URL}", + "slot_uri": "MIXS:0000343", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "height_carper_fiber": { + "name": "height_carper_fiber", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "centimeter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The average carpet fiber height in the indoor environment", + "title": "height carpet fiber mat", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "height carpet fiber mat" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000167", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "herbicide_regm": { + "name": "herbicide_regm", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "herbicide name;herbicide amount;treatment interval and duration" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "gram, mole per liter, milligram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Information about treatment involving use of herbicides; information about treatment involving use of growth hormones; should include the name of herbicide, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens", + "title": "herbicide regimen", + "examples": [ + { + "value": "atrazine;10 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "herbicide regimen" + ], + "is_a": "core field", + "string_serialization": "{text};{float} {unit};{Rn/start_time/end_time/duration}", + "slot_uri": "MIXS:0000561", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "horizon_meth": { + "name": "horizon_meth", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "PMID,DOI or url" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Reference or method used in determining the horizon", + "title": "soil horizon method", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "soil horizon method" + ], + "is_a": "core field", + "string_serialization": "{PMID}|{DOI}|{URL}", + "slot_uri": "MIXS:0000321", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "host_age": { + "name": "host_age", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "year, day, hour" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees", + "title": "host age", + "examples": [ + { + "value": "10 days" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "host age" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000255", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "host_body_habitat": { + "name": "host_body_habitat", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "free text" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Original body habitat where the sample was obtained from", + "title": "host body habitat", + "examples": [ + { + "value": "nasopharynx" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "host body habitat" + ], + "is_a": "core field", + "string_serialization": "{text}", + "slot_uri": "MIXS:0000866", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "host_body_product": { + "name": "host_body_product", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "FMA or UBERON" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon", + "title": "host body product", + "examples": [ + { + "value": "Portion of mucus [fma66938]" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "host body product" + ], + "is_a": "core field", + "string_serialization": "{termLabel} {[termID]}", + "slot_uri": "MIXS:0000888", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "host_body_site": { + "name": "host_body_site", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "FMA or UBERON" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON", + "title": "host body site", + "examples": [ + { + "value": "gill [UBERON:0002535]" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "host body site" + ], + "is_a": "core field", + "string_serialization": "{termLabel} {[termID]}", + "slot_uri": "MIXS:0000867", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "host_body_temp": { + "name": "host_body_temp", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "degree Celsius" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Core body temperature of the host when sample was collected", + "title": "host body temperature", + "examples": [ + { + "value": "15 degree Celsius" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "host body temperature" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000274", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "host_color": { + "name": "host_color", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "color" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The color of host", + "title": "host color", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "host color" + ], + "is_a": "core field", + "string_serialization": "{text}", + "slot_uri": "MIXS:0000260", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "host_common_name": { + "name": "host_common_name", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "common name" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Common name of the host.", + "title": "host common name", + "examples": [ + { + "value": "human" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "host common name" + ], + "is_a": "core field", + "string_serialization": "{text}", + "slot_uri": "MIXS:0000248", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "host_diet": { + "name": "host_diet", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "diet type" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types", + "title": "host diet", + "examples": [ + { + "value": "herbivore" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "host diet" + ], + "is_a": "core field", + "string_serialization": "{text}", + "slot_uri": "MIXS:0000869", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "host_disease_stat": { + "name": "host_disease_stat", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "disease name or Disease Ontology term" + } + }, + "description": "List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text", + "title": "host disease status", + "examples": [ + { + "value": "rabies [DOID:11260]" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "host disease status" + ], + "is_a": "nucleic acid sequence source field", + "string_serialization": "{termLabel} {[termID]}|{text}", + "slot_uri": "MIXS:0000031", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "host_dry_mass": { + "name": "host_dry_mass", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "kilogram, gram" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Measurement of dry mass", + "title": "host dry mass", + "examples": [ + { + "value": "500 gram" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "host dry mass" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000257", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "host_family_relation": { + "name": "host_family_relation", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "relationship type;arbitrary identifier" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Familial relationships to other hosts in the same study; can include multiple relationships", + "title": "host family relationship", + "examples": [ + { + "value": "offspring;Mussel25" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "host family relationship" + ], + "is_a": "core field", + "string_serialization": "{text};{text}", + "slot_uri": "MIXS:0000872", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "host_genotype": { + "name": "host_genotype", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "genotype" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Observed genotype", + "title": "host genotype", + "examples": [ + { + "value": "C57BL/6" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "host genotype" + ], + "is_a": "core field", + "string_serialization": "{text}", + "slot_uri": "MIXS:0000365", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "host_growth_cond": { + "name": "host_growth_cond", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "PMID,DOI,url or free text" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Literature reference giving growth conditions of the host", + "title": "host growth conditions", + "examples": [ + { + "value": "https://academic.oup.com/icesjms/article/68/2/349/617247" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "host growth conditions" + ], + "is_a": "core field", + "string_serialization": "{PMID}|{DOI}|{URL}|{text}", + "slot_uri": "MIXS:0000871", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "host_height": { + "name": "host_height", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "centimeter, millimeter, meter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The height of subject", + "title": "host height", + "examples": [ + { + "value": "0.1 meter" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "host height" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000264", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "host_last_meal": { + "name": "host_last_meal", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "content;duration" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Content of last meal and time since feeding; can include multiple values", + "title": "host last meal", + "examples": [ + { + "value": "corn feed;P2H" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "host last meal" + ], + "is_a": "core field", + "string_serialization": "{text};{duration}", + "slot_uri": "MIXS:0000870", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "host_length": { + "name": "host_length", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "centimeter, millimeter, meter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The length of subject", + "title": "host length", + "examples": [ + { + "value": "1 meter" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "host length" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000256", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "host_life_stage": { + "name": "host_life_stage", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "stage" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Description of life stage of host", + "title": "host life stage", + "examples": [ + { + "value": "adult" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "host life stage" + ], + "is_a": "core field", + "string_serialization": "{text}", + "slot_uri": "MIXS:0000251", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "host_phenotype": { + "name": "host_phenotype", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "PATO or HP" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP", + "title": "host phenotype", + "examples": [ + { + "value": "elongated [PATO:0001154]" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "host phenotype" + ], + "is_a": "core field", + "string_serialization": "{termLabel} {[termID]}", + "slot_uri": "MIXS:0000874", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "host_sex": { + "name": "host_sex", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Gender or physical sex of the host.", + "title": "host sex", + "examples": [ + { + "value": "non-binary" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "host sex" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000811", + "domain_of": [ + "Biosample" + ], + "range": "host_sex_enum", + "multivalued": false + }, + "host_shape": { + "name": "host_shape", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "shape" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Morphological shape of host", + "title": "host shape", + "examples": [ + { + "value": "round" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "host shape" + ], + "is_a": "core field", + "string_serialization": "{text}", + "slot_uri": "MIXS:0000261", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "host_subject_id": { + "name": "host_subject_id", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "unique identifier" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "A unique identifier by which each subject can be referred to, de-identified.", + "title": "host subject id", + "examples": [ + { + "value": "MPI123" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "host subject id" + ], + "is_a": "core field", + "string_serialization": "{text}", + "slot_uri": "MIXS:0000861", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "host_subspecf_genlin": { + "name": "host_subspecf_genlin", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "Genetic lineage below lowest rank of NCBI taxonomy, which is subspecies, e.g. serovar, biotype, ecotype, variety, cultivar." + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Information about the genetic distinctness of the host organism below the subspecies level e.g., serovar, serotype, biotype, ecotype, variety, cultivar, or any relevant genetic typing schemes like Group I plasmid. Subspecies should not be recorded in this term, but in the NCBI taxonomy. Supply both the lineage name and the lineage rank separated by a colon, e.g., biovar:abc123.", + "title": "host subspecific genetic lineage", + "examples": [ + { + "value": "serovar:Newport, variety:glabrum, cultivar: Red Delicious" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "host subspecific genetic lineage" + ], + "is_a": "core field", + "string_serialization": "{rank name}:{text}", + "slot_uri": "MIXS:0001318", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "host_substrate": { + "name": "host_substrate", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "substrate name" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The growth substrate of the host.", + "title": "host substrate", + "examples": [ + { + "value": "rock" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "host substrate" + ], + "is_a": "core field", + "string_serialization": "{text}", + "slot_uri": "MIXS:0000252", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "host_symbiont": { + "name": "host_symbiont", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "species name or common name" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host.", + "title": "observed host symbionts", + "examples": [ + { + "value": "flukeworms" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "observed host symbionts" + ], + "is_a": "core field", + "string_serialization": "{text}", + "slot_uri": "MIXS:0001298", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "host_taxid": { + "name": "host_taxid", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "NCBI taxon identifier" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "NCBI taxon id of the host, e.g. 9606", + "title": "host taxid", + "comments": [ + "Homo sapiens [NCBITaxon:9606] would be a reasonable has_raw_value" + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "host taxid" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000250", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "host_tot_mass": { + "name": "host_tot_mass", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "kilogram, gram" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Total mass of the host at collection, the unit depends on host", + "title": "host total mass", + "examples": [ + { + "value": "2500 gram" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "host total mass" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000263", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "host_wet_mass": { + "name": "host_wet_mass", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "kilogram, gram" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Measurement of wet mass", + "title": "host wet mass", + "examples": [ + { + "value": "1500 gram" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "host wet mass" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000567", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "humidity": { + "name": "humidity", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "gram per cubic meter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Amount of water vapour in the air, at the time of sampling", + "title": "humidity", + "examples": [ + { + "value": "25 gram per cubic meter" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "humidity" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000100", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "humidity_regm": { + "name": "humidity_regm", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "humidity value;treatment interval and duration" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "gram per cubic meter" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Information about treatment involving an exposure to varying degree of humidity; information about treatment involving use of growth hormones; should include amount of humidity administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens", + "title": "humidity regimen", + "examples": [ + { + "value": "25 gram per cubic meter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "humidity regimen" + ], + "is_a": "core field", + "string_serialization": "{float} {unit};{Rn/start_time/end_time/duration}", + "slot_uri": "MIXS:0000568", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "indoor_space": { + "name": "indoor_space", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "A distinguishable space within a structure, the purpose for which discrete areas of a building is used", + "title": "indoor space", + "examples": [ + { + "value": "foyer" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "indoor space" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000763", + "domain_of": [ + "Biosample" + ], + "range": "indoor_space_enum", + "multivalued": false + }, + "indoor_surf": { + "name": "indoor_surf", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Type of indoor surface", + "title": "indoor surface", + "examples": [ + { + "value": "wall" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "indoor surface" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000764", + "domain_of": [ + "Biosample" + ], + "range": "indoor_surf_enum", + "multivalued": false + }, + "indust_eff_percent": { + "name": "indust_eff_percent", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "percentage" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Percentage of industrial effluents received by wastewater treatment plant", + "title": "industrial effluent percent", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "industrial effluent percent" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000662", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "infiltrations": { + "name": "infiltrations", + "description": "The amount of time it takes to complete each infiltration activity", + "examples": [ + { + "value": "['00:01:32', '00:00:53']" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "see_also": [ + "https://www.protocols.io/view/field-sampling-protocol-kqdg3962pg25/v1" + ], + "aliases": [ + "infiltration_1", + "infiltration_2" + ], + "list_elements_ordered": true, + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false, + "pattern": "^(?:[0-9]|[1-9][0-9]|9[0-9]|0[0-9]|0[0-5][0-9]):[0-5][0-9]:[0-5][0-9]$" + }, + "inorg_particles": { + "name": "inorg_particles", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "inorganic particle name;measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "mole per liter, milligram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Concentration of particles such as sand, grit, metal particles, ceramics, etc.; can include multiple particles", + "title": "inorganic particles", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "inorganic particles" + ], + "is_a": "core field", + "string_serialization": "{text};{float} {unit}", + "slot_uri": "MIXS:0000664", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "inside_lux": { + "name": "inside_lux", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "kilowatt per square metre" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The recorded value at sampling time (power density)", + "title": "inside lux light", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "inside lux light" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000168", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "int_wall_cond": { + "name": "int_wall_cond", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The physical condition of the wall at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas", + "title": "interior wall condition", + "examples": [ + { + "value": "damaged" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "interior wall condition" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000813", + "domain_of": [ + "Biosample" + ], + "range": "int_wall_cond_enum", + "multivalued": false + }, + "isotope_exposure": { + "name": "isotope_exposure", + "description": "List isotope exposure or addition applied to your sample.", + "title": "isotope exposure/addition", + "todos": [ + "Can we make the H218O correctly super and subscripted?" + ], + "comments": [ + "This is required when your experimental design includes the use of isotopically labeled compounds" + ], + "examples": [ + { + "value": "13C glucose" + }, + { + "value": "H218O" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "see_also": [ + "MIXS:0000751" + ], + "rank": 16, + "string_serialization": "{termLabel} {[termID]}; {timestamp}", + "domain_of": [ + "Biosample" + ], + "slot_group": "MIxS Inspired", + "recommended": true + }, + "iw_bt_date_well": { + "name": "iw_bt_date_well", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "timestamp" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Injection water breakthrough date per well following a secondary and/or tertiary recovery", + "title": "injection water breakthrough date of specific well", + "examples": [ + { + "value": "2018-05-11" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "injection water breakthrough date of specific well" + ], + "is_a": "core field", + "slot_uri": "MIXS:0001010", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "iwf": { + "name": "iwf", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "percent" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Proportion of the produced fluids derived from injected water at the time of sampling. (e.g. 87%)", + "title": "injection water fraction", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "injection water fraction" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000455", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "last_clean": { + "name": "last_clean", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "timestamp" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The last time the floor was cleaned (swept, mopped, vacuumed)", + "title": "last time swept/mopped/vacuumed", + "examples": [ + { + "value": "2018-05-11:T14:30Z" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "last time swept/mopped/vacuumed" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000814", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "lat_lon": { + "name": "lat_lon", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "decimal degrees, limit to 8 decimal points" + } + }, + "description": "The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system", + "title": "geographic location (latitude and longitude)", + "examples": [ + { + "value": "50.586825 6.408977" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "geographic location (latitude and longitude)" + ], + "is_a": "environment field", + "string_serialization": "{float} {float}", + "slot_uri": "MIXS:0000009", + "domain_of": [ + "FieldResearchSite", + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "lbc_thirty": { + "name": "lbc_thirty", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "ppm CaCO3/pH" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "lime buffer capacity, determined after 30 minute incubation", + "title": "lime buffer capacity (at 30 minutes)", + "comments": [ + "This is the mass of lime, in mg, needed to raise the pH of one kg of soil by one pH unit" + ], + "examples": [ + { + "value": "543 mg/kg" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "see_also": [ + "https://www.ornl.gov/content/bio-scales-0", + "https://secure.caes.uga.edu/extension/publications/files/pdf/C%20874_5.PDF" + ], + "aliases": [ + "lbc_thirty", + "lbc30", + "lime buffer capacity (at 30 minutes)" + ], + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "lbceq": { + "name": "lbceq", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "ppm CaCO3/pH" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "lime buffer capacity, determined at equilibrium after 5 day incubation", + "title": "lime buffer capacity (after 5 day incubation)", + "comments": [ + "This is the mass of lime, in mg, needed to raise the pH of one kg of soil by one pH unit" + ], + "examples": [ + { + "value": "1575 mg/kg" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "see_also": [ + "https://www.ornl.gov/content/bio-scales-0" + ], + "aliases": [ + "lbceq", + "lime buffer capacity (at 5-day equilibrium)" + ], + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "light_intensity": { + "name": "light_intensity", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "lux" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Measurement of light intensity", + "title": "light intensity", + "examples": [ + { + "value": "0.3 lux" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "light intensity" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000706", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "light_regm": { + "name": "light_regm", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "exposure type;light intensity;light quality" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "lux; micrometer, nanometer, angstrom" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Information about treatment(s) involving exposure to light, including both light intensity and quality.", + "title": "light regimen", + "examples": [ + { + "value": "incandescant light;10 lux;450 nanometer" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "light regimen" + ], + "is_a": "core field", + "string_serialization": "{text};{float} {unit};{float} {unit}", + "slot_uri": "MIXS:0000569", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "light_type": { + "name": "light_type", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Application of light to achieve some practical or aesthetic effect. Lighting includes the use of both artificial light sources such as lamps and light fixtures, as well as natural illumination by capturing daylight. Can also include absence of light", + "title": "light type", + "examples": [ + { + "value": "desk lamp" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "light type" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000769", + "domain_of": [ + "Biosample" + ], + "range": "light_type_enum", + "multivalued": true + }, + "link_addit_analys": { + "name": "link_addit_analys", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "PMID,DOI or url" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Link to additional analysis results performed on the sample", + "title": "links to additional analysis", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "links to additional analysis" + ], + "is_a": "core field", + "string_serialization": "{PMID}|{DOI}|{URL}", + "slot_uri": "MIXS:0000340", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "link_class_info": { + "name": "link_class_info", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "PMID,DOI or url" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Link to digitized soil maps or other soil classification information", + "title": "link to classification information", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "link to classification information" + ], + "is_a": "core field", + "string_serialization": "{PMID}|{DOI}|{URL}", + "slot_uri": "MIXS:0000329", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "link_climate_info": { + "name": "link_climate_info", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "PMID,DOI or url" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Link to climate resource", + "title": "link to climate information", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "link to climate information" + ], + "is_a": "core field", + "string_serialization": "{PMID}|{DOI}|{URL}", + "slot_uri": "MIXS:0000328", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "lithology": { + "name": "lithology", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Hydrocarbon resource main lithology (Additional information: http://petrowiki.org/Lithology_and_rock_type_determination). If \"other\" is specified, please propose entry in \"additional info\" field", + "title": "lithology", + "examples": [ + { + "value": "Volcanic" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "lithology" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000990", + "domain_of": [ + "Biosample" + ], + "range": "lithology_enum", + "multivalued": false + }, + "local_class": { + "name": "local_class", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "local classification name" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Soil classification based on local soil classification system", + "title": "soil_taxonomic/local classification", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "soil_taxonomic/local classification" + ], + "is_a": "core field", + "string_serialization": "{text}", + "slot_uri": "MIXS:0000330", + "domain_of": [ + "FieldResearchSite", + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "local_class_meth": { + "name": "local_class_meth", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "PMID,DOI or url" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Reference or method used in determining the local soil classification", + "title": "soil_taxonomic/local classification method", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "soil_taxonomic/local classification method" + ], + "is_a": "core field", + "string_serialization": "{PMID}|{DOI}|{URL}", + "slot_uri": "MIXS:0000331", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "magnesium": { + "name": "magnesium", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "mole per liter, milligram per liter, parts per million, micromole per kilogram" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of magnesium in the sample", + "title": "magnesium", + "examples": [ + { + "value": "52.8 micromole per kilogram" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "magnesium" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000431", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "manganese": { + "name": "manganese", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "mg/kg (ppm)" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of manganese in the sample", + "title": "manganese", + "examples": [ + { + "value": "24.7 mg/kg" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "see_also": [ + "https://www.ornl.gov/content/bio-scales-0" + ], + "aliases": [ + "manganese" + ], + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "max_occup": { + "name": "max_occup", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The maximum amount of people allowed in the indoor environment", + "title": "maximum occupancy", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "maximum occupancy" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000229", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "mean_frict_vel": { + "name": "mean_frict_vel", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "meter per second" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Measurement of mean friction velocity", + "title": "mean friction velocity", + "examples": [ + { + "value": "0.5 meter per second" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "mean friction velocity" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000498", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "mean_peak_frict_vel": { + "name": "mean_peak_frict_vel", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "meter per second" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Measurement of mean peak friction velocity", + "title": "mean peak friction velocity", + "examples": [ + { + "value": "1 meter per second" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "mean peak friction velocity" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000502", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "mech_struc": { + "name": "mech_struc", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "mechanical structure: a moving structure", + "title": "mechanical structure", + "examples": [ + { + "value": "elevator" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "mechanical structure" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000815", + "domain_of": [ + "Biosample" + ], + "range": "mech_struc_enum", + "multivalued": false + }, + "mechanical_damage": { + "name": "mechanical_damage", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "damage type;body site" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Information about any mechanical damage exerted on the plant; can include multiple damages and sites", + "title": "mechanical damage", + "examples": [ + { + "value": "pruning;bark" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "mechanical damage" + ], + "is_a": "core field", + "string_serialization": "{text};{text}", + "slot_uri": "MIXS:0001052", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "methane": { + "name": "methane", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per liter, parts per billion, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Methane (gas) amount or concentration at the time of sampling", + "title": "methane", + "examples": [ + { + "value": "1800 parts per billion" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "methane" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000101", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "micro_biomass_c_meth": { + "name": "micro_biomass_c_meth", + "description": "Reference or method used in determining microbial biomass carbon", + "title": "microbial biomass carbon method", + "todos": [ + "How should we separate values? | or ;? lets be consistent" + ], + "comments": [ + "required if \"microbial_biomass_c\" is provided" + ], + "examples": [ + { + "value": "https://doi.org/10.1016/0038-0717(87)90052-6" + }, + { + "value": "https://doi.org/10.1016/0038-0717(87)90052-6 | https://www.sciencedirect.com/science/article/abs/pii/0038071787900526" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "see_also": [ + "MIXS:0000339" + ], + "rank": 11, + "string_serialization": "{PMID}|{DOI}|{URL}", + "domain_of": [ + "Biosample" + ], + "slot_group": "MIxS Inspired", + "recommended": true + }, + "micro_biomass_meth": { + "name": "micro_biomass_meth", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "PMID,DOI or url" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Reference or method used in determining microbial biomass", + "title": "microbial biomass method", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "microbial biomass method" + ], + "is_a": "core field", + "string_serialization": "{PMID}|{DOI}|{URL}", + "slot_uri": "MIXS:0000339", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "micro_biomass_n_meth": { + "name": "micro_biomass_n_meth", + "description": "Reference or method used in determining microbial biomass nitrogen", + "title": "microbial biomass nitrogen method", + "comments": [ + "required if \"microbial_biomass_n\" is provided" + ], + "examples": [ + { + "value": "https://doi.org/10.1016/0038-0717(87)90052-6" + }, + { + "value": "https://doi.org/10.1016/0038-0717(87)90052-6 | https://www.sciencedirect.com/science/article/abs/pii/0038071787900526" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "see_also": [ + "MIXS:0000339" + ], + "rank": 13, + "string_serialization": "{PMID}|{DOI}|{URL}", + "domain_of": [ + "Biosample" + ], + "slot_group": "MIxS Inspired" + }, + "microbial_biomass": { + "name": "microbial_biomass", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "ton, kilogram, gram per kilogram soil" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The part of the organic matter in the soil that constitutes living microorganisms smaller than 5-10 micrometer. If you keep this, you would need to have correction factors used for conversion to the final units", + "title": "microbial biomass", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "microbial biomass" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000650", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "microbial_biomass_c": { + "name": "microbial_biomass_c", + "description": "The part of the organic matter in the soil that constitutes living microorganisms smaller than 5-10 micrometer.", + "title": "microbial biomass carbon", + "comments": [ + "If you provide this, correction factors used for conversion to the final units and method are required" + ], + "examples": [ + { + "value": "0.05 ug C/g dry soil" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "see_also": [ + "MIXS:0000650" + ], + "rank": 10, + "string_serialization": "{float} {unit}", + "domain_of": [ + "Biosample" + ], + "slot_group": "MIxS Inspired" + }, + "microbial_biomass_n": { + "name": "microbial_biomass_n", + "description": "The part of the organic matter in the soil that constitutes living microorganisms smaller than 5-10 micrometer.", + "title": "microbial biomass nitrogen", + "comments": [ + "If you provide this, correction factors used for conversion to the final units and method are required" + ], + "examples": [ + { + "value": "0.05 ug N/g dry soil" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "see_also": [ + "MIXS:0000650" + ], + "rank": 12, + "string_serialization": "{float} {unit}", + "domain_of": [ + "Biosample" + ], + "slot_group": "MIxS Inspired" + }, + "mineral_nutr_regm": { + "name": "mineral_nutr_regm", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "mineral nutrient name;mineral nutrient amount;treatment interval and duration" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "gram, mole per liter, milligram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Information about treatment involving the use of mineral supplements; should include the name of mineral nutrient, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple mineral nutrient regimens", + "title": "mineral nutrient regimen", + "examples": [ + { + "value": "potassium;15 gram;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "mineral nutrient regimen" + ], + "is_a": "core field", + "string_serialization": "{text};{float} {unit};{Rn/start_time/end_time/duration}", + "slot_uri": "MIXS:0000570", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "misc_param": { + "name": "misc_param", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "parameter name;measurement value" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Any other measurement performed or parameter collected, that is not listed here", + "title": "miscellaneous parameter", + "examples": [ + { + "value": "Bicarbonate ion concentration;2075 micromole per kilogram" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "miscellaneous parameter" + ], + "is_a": "core field", + "string_serialization": "{text};{float} {unit}", + "slot_uri": "MIXS:0000752", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "n_alkanes": { + "name": "n_alkanes", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "n-alkane name;measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Concentration of n-alkanes; can include multiple n-alkanes", + "title": "n-alkanes", + "examples": [ + { + "value": "n-hexadecane;100 milligram per liter" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "n-alkanes" + ], + "is_a": "core field", + "string_serialization": "{text};{float} {unit}", + "slot_uri": "MIXS:0000503", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "nitrate": { + "name": "nitrate", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per liter, milligram per liter, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of nitrate in the sample", + "title": "nitrate", + "examples": [ + { + "value": "65 micromole per liter" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "nitrate" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000425", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "nitrate_nitrogen": { + "name": "nitrate_nitrogen", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "mg/kg" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of nitrate nitrogen in the sample", + "title": "nitrate_nitrogen", + "comments": [ + "often below some specified limit of detection" + ], + "examples": [ + { + "value": "0.29 mg/kg" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "see_also": [ + "https://www.ornl.gov/content/bio-scales-0" + ], + "aliases": [ + "nitrate_nitrogen", + "NO3-N" + ], + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "nitrite": { + "name": "nitrite", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per liter, milligram per liter, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of nitrite in the sample", + "title": "nitrite", + "examples": [ + { + "value": "0.5 micromole per liter" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "nitrite" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000426", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "nitrite_nitrogen": { + "name": "nitrite_nitrogen", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "mg/kg" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of nitrite nitrogen in the sample", + "title": "nitrite_nitrogen", + "examples": [ + { + "value": "1.2 mg/kg" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "see_also": [ + "https://www.ornl.gov/content/bio-scales-0" + ], + "aliases": [ + "nitrite_nitrogen", + "NO2-N" + ], + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "nitro": { + "name": "nitro", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of nitrogen (total)", + "title": "nitrogen", + "examples": [ + { + "value": "4.2 micromole per liter" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "nitrogen" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000504", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "non_microb_biomass": { + "name": "non_microb_biomass", + "description": "Amount of biomass; should include the name for the part of biomass measured, e.g.insect, plant, total. Can include multiple measurements separated by ;", + "title": "non-microbial biomass", + "examples": [ + { + "value": "insect 0.23 ug; plant 1g" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "see_also": [ + "MIXS:0000174", + "MIXS:0000650" + ], + "rank": 8, + "string_serialization": "{text};{float} {unit}", + "domain_of": [ + "Biosample" + ], + "slot_group": "MIxS Inspired" + }, + "non_microb_biomass_method": { + "name": "non_microb_biomass_method", + "description": "Reference or method used in determining biomass", + "title": "non-microbial biomass method", + "comments": [ + "required if \"non-microbial biomass\" is provided" + ], + "examples": [ + { + "value": "https://doi.org/10.1038/s41467-021-26181-3" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "see_also": [ + "MIXS:0000650" + ], + "rank": 9, + "string_serialization": "{PMID}|{DOI}|{URL}", + "domain_of": [ + "Biosample" + ], + "slot_group": "MIxS Inspired" + }, + "non_min_nutr_regm": { + "name": "non_min_nutr_regm", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "non-mineral nutrient name;non-mineral nutrient amount;treatment interval and duration" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "gram, mole per liter, milligram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Information about treatment involving the exposure of plant to non-mineral nutrient such as oxygen, hydrogen or carbon; should include the name of non-mineral nutrient, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple non-mineral nutrient regimens", + "title": "non-mineral nutrient regimen", + "examples": [ + { + "value": "carbon dioxide;10 mole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "non-mineral nutrient regimen" + ], + "is_a": "core field", + "string_serialization": "{text};{float} {unit};{Rn/start_time/end_time/duration}", + "slot_uri": "MIXS:0000571", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "number_pets": { + "name": "number_pets", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The number of pets residing in the sampled space", + "title": "number of pets", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "number of pets" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000231", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "number_plants": { + "name": "number_plants", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The number of plant(s) in the sampling space", + "title": "number of houseplants", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "number of houseplants" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000230", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "number_resident": { + "name": "number_resident", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The number of individuals currently occupying in the sampling location", + "title": "number of residents", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "number of residents" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000232", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "occup_density_samp": { + "name": "occup_density_samp", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Average number of occupants at time of sampling per square footage", + "title": "occupant density at sampling", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "occupant density at sampling" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000217", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "occup_document": { + "name": "occup_document", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The type of documentation of occupancy", + "title": "occupancy documentation", + "examples": [ + { + "value": "estimate" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "occupancy documentation" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000816", + "domain_of": [ + "Biosample" + ], + "range": "occup_document_enum", + "multivalued": false + }, + "occup_samp": { + "name": "occup_samp", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Number of occupants present at time of sample within the given space", + "title": "occupancy at sampling", + "examples": [ + { + "value": "10" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "occupancy at sampling" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000772", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "org_carb": { + "name": "org_carb", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of organic carbon", + "title": "organic carbon", + "examples": [ + { + "value": "1.5 microgram per liter" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "organic carbon" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000508", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "org_count_qpcr_info": { + "name": "org_count_qpcr_info", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "gene name;FWD:forward primer sequence;REV:reverse primer sequence;initial denaturation:degrees_minutes;denaturation:degrees_minutes;annealing:degrees_minutes;elongation:degrees_minutes;final elongation:degrees_minutes; total cycles" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "number of cells per gram (or ml or cm^2)" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "If qpcr was used for the cell count, the target gene name, the primer sequence and the cycling conditions should also be provided. (Example: 16S rrna; FWD:ACGTAGCTATGACGT REV:GTGCTAGTCGAGTAC; initial denaturation:90C_5min; denaturation:90C_2min; annealing:52C_30 sec; elongation:72C_30 sec; 90 C for 1 min; final elongation:72C_5min; 30 cycles)", + "title": "organism count qPCR information", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "organism count qPCR information" + ], + "is_a": "core field", + "string_serialization": "{text};FWD:{dna};REV:{dna};initial denaturation:degrees_minutes;denaturation:degrees_minutes;annealing:degrees_minutes;elongation:degrees_minutes;final elongation:degrees_minutes; total cycles", + "slot_uri": "MIXS:0000099", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "org_matter": { + "name": "org_matter", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "microgram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of organic matter", + "title": "organic matter", + "examples": [ + { + "value": "1.75 milligram per cubic meter" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "organic matter" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000204", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "org_nitro": { + "name": "org_nitro", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "microgram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of organic nitrogen", + "title": "organic nitrogen", + "examples": [ + { + "value": "4 micromole per liter" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "organic nitrogen" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000205", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "org_nitro_method": { + "name": "org_nitro_method", + "description": "Method used for obtaining organic nitrogen", + "title": "organic nitrogen method", + "comments": [ + "required if \"org_nitro\" is provided" + ], + "examples": [ + { + "value": "https://doi.org/10.1016/0038-0717(85)90144-0" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "see_also": [ + "MIXS:0000338", + "MIXS:0000205" + ], + "rank": 14, + "string_serialization": "{PMID}|{DOI}|{URL}", + "domain_of": [ + "Biosample" + ], + "slot_group": "MIxS Inspired" + }, + "org_particles": { + "name": "org_particles", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "particle name;measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "gram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Concentration of particles such as faeces, hairs, food, vomit, paper fibers, plant material, humus, etc.", + "title": "organic particles", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "organic particles" + ], + "is_a": "core field", + "string_serialization": "{text};{float} {unit}", + "slot_uri": "MIXS:0000665", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "organism_count": { + "name": "organism_count", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "organism name;measurement value;enumeration" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "number of cells per cubic meter, number of cells per milliliter, number of cells per cubic centimeter" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr)", + "title": "organism count", + "examples": [ + { + "value": "total prokaryotes;3.5e7 cells per milliliter;qPCR" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "organism count" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000103", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "other_treatment": { + "name": "other_treatment", + "description": "Other treatments applied to your samples that are not applicable to the provided fields", + "title": "other treatments", + "notes": [ + "Values entered here will be used to determine potential new slots." + ], + "comments": [ + "This is an open text field to provide any treatments that cannot be captured in the provided slots." + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "see_also": [ + "MIXS:0000300" + ], + "rank": 15, + "string_serialization": "{text}", + "domain_of": [ + "Biosample" + ], + "slot_group": "MIxS Inspired", + "recommended": true + }, + "owc_tvdss": { + "name": "owc_tvdss", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "meter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Depth of the original oil water contact (OWC) zone (average) (m TVDSS)", + "title": "oil water contact depth", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "oil water contact depth" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000405", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "oxy_stat_samp": { + "name": "oxy_stat_samp", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Oxygenation status of sample", + "title": "oxygenation status of sample", + "examples": [ + { + "value": "aerobic" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "oxygenation status of sample" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000753", + "domain_of": [ + "Biosample" + ], + "range": "OxyStatSampEnum", + "multivalued": false + }, + "oxygen": { + "name": "oxygen", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milligram per liter, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Oxygen (gas) amount or concentration at the time of sampling", + "title": "oxygen", + "examples": [ + { + "value": "600 parts per million" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "oxygen" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000104", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "part_org_carb": { + "name": "part_org_carb", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "microgram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of particulate organic carbon", + "title": "particulate organic carbon", + "examples": [ + { + "value": "1.92 micromole per liter" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "particulate organic carbon" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000515", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "part_org_nitro": { + "name": "part_org_nitro", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "microgram per liter, micromole per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of particulate organic nitrogen", + "title": "particulate organic nitrogen", + "examples": [ + { + "value": "0.3 micromole per liter" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "particulate organic nitrogen" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000719", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "particle_class": { + "name": "particle_class", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "particle name;measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micrometer" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Particles are classified, based on their size, into six general categories:clay, silt, sand, gravel, cobbles, and boulders; should include amount of particle preceded by the name of the particle type; can include multiple values", + "title": "particle classification", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "particle classification" + ], + "is_a": "core field", + "string_serialization": "{text};{float} {unit}", + "slot_uri": "MIXS:0000206", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "permeability": { + "name": "permeability", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value range" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "mD" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Measure of the ability of a hydrocarbon resource to allow fluids to pass through it. (Additional information: https://en.wikipedia.org/wiki/Permeability_(earth_sciences))", + "title": "permeability", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "permeability" + ], + "is_a": "core field", + "string_serialization": "{integer} - {integer} {unit}", + "slot_uri": "MIXS:0000404", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "perturbation": { + "name": "perturbation", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "perturbation type name;perturbation interval and duration" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types", + "title": "perturbation", + "examples": [ + { + "value": "antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "perturbation" + ], + "is_a": "core field", + "string_serialization": "{text};{Rn/start_time/end_time/duration}", + "slot_uri": "MIXS:0000754", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "pesticide_regm": { + "name": "pesticide_regm", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "pesticide name;pesticide amount;treatment interval and duration" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "gram, mole per liter, milligram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Information about treatment involving use of insecticides; should include the name of pesticide, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple pesticide regimens", + "title": "pesticide regimen", + "examples": [ + { + "value": "pyrethrum;0.6 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "pesticide regimen" + ], + "is_a": "core field", + "string_serialization": "{text};{float} {unit};{Rn/start_time/end_time/duration}", + "slot_uri": "MIXS:0000573", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "petroleum_hydrocarb": { + "name": "petroleum_hydrocarb", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of petroleum hydrocarbon", + "title": "petroleum hydrocarbon", + "examples": [ + { + "value": "0.05 micromole per liter" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "petroleum hydrocarbon" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000516", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "ph": { + "name": "ph", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid", + "title": "pH", + "examples": [ + { + "value": "7.2" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "pH" + ], + "is_a": "core field", + "slot_uri": "MIXS:0001001", + "domain_of": [ + "Biosample" + ], + "range": "double", + "multivalued": false + }, + "ph_meth": { + "name": "ph_meth", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "PMID,DOI or url" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Reference or method used in determining ph", + "title": "pH method", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "pH method" + ], + "is_a": "core field", + "string_serialization": "{PMID}|{DOI}|{URL}", + "slot_uri": "MIXS:0001106", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "ph_regm": { + "name": "ph_regm", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value;treatment interval and duration" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Information about treatment involving exposure of plants to varying levels of ph of the growth media, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimen", + "title": "pH regimen", + "examples": [ + { + "value": "7.6;R2/2018-05-11:T14:30/2018-05-11T19:30/P1H30M" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "pH regimen" + ], + "is_a": "core field", + "string_serialization": "{float};{Rn/start_time/end_time/duration}", + "slot_uri": "MIXS:0001056", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "phaeopigments": { + "name": "phaeopigments", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "phaeopigment name;measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milligram per cubic meter" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Concentration of phaeopigments; can include multiple phaeopigments", + "title": "phaeopigments", + "examples": [ + { + "value": "2.5 milligram per cubic meter" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "phaeopigments" + ], + "is_a": "core field", + "string_serialization": "{text};{float} {unit}", + "slot_uri": "MIXS:0000180", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "phosphate": { + "name": "phosphate", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of phosphate", + "title": "phosphate", + "examples": [ + { + "value": "0.7 micromole per liter" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "phosphate" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000505", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "phosplipid_fatt_acid": { + "name": "phosplipid_fatt_acid", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "phospholipid fatty acid name;measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "mole per gram, mole per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Concentration of phospholipid fatty acids; can include multiple values", + "title": "phospholipid fatty acid", + "examples": [ + { + "value": "2.98 milligram per liter" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "phospholipid fatty acid" + ], + "is_a": "core field", + "string_serialization": "{text};{float} {unit}", + "slot_uri": "MIXS:0000181", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "photon_flux": { + "name": "photon_flux", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "number of photons per second per unit area" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Measurement of photon flux", + "title": "photon flux", + "examples": [ + { + "value": "3.926 micromole photons per second per square meter" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "photon flux" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000725", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "plant_growth_med": { + "name": "plant_growth_med", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "EO or enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Specification of the media for growing the plants or tissue cultured samples, e.g. soil, aeroponic, hydroponic, in vitro solid culture medium, in vitro liquid culture medium. Recommended value is a specific value from EO:plant growth medium (follow this link for terms http://purl.obolibrary.org/obo/EO_0007147) or other controlled vocabulary", + "title": "plant growth medium", + "examples": [ + { + "value": "hydroponic plant culture media [EO:0007067]" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "plant growth medium" + ], + "is_a": "core field", + "slot_uri": "MIXS:0001057", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "plant_product": { + "name": "plant_product", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "product name" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Substance produced by the plant, where the sample was obtained from", + "title": "plant product", + "examples": [ + { + "value": "xylem sap [PO:0025539]" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "plant product" + ], + "is_a": "core field", + "string_serialization": "{text}", + "slot_uri": "MIXS:0001058", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "plant_sex": { + "name": "plant_sex", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Sex of the reproductive parts on the whole plant, e.g. pistillate, staminate, monoecieous, hermaphrodite.", + "title": "plant sex", + "examples": [ + { + "value": "Hermaphroditic" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "plant sex" + ], + "is_a": "core field", + "slot_uri": "MIXS:0001059", + "domain_of": [ + "Biosample" + ], + "range": "plant_sex_enum", + "multivalued": false + }, + "plant_struc": { + "name": "plant_struc", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "PO" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Name of plant structure the sample was obtained from; for Plant Ontology (PO) (v releases/2017-12-14) terms, see http://purl.bioontology.org/ontology/PO, e.g. petiole epidermis (PO_0000051). If an individual flower is sampled, the sex of it can be recorded here.", + "title": "plant structure", + "examples": [ + { + "value": "epidermis [PO:0005679]" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "plant structure" + ], + "is_a": "core field", + "string_serialization": "{termLabel} {[termID]}", + "slot_uri": "MIXS:0001060", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "pollutants": { + "name": "pollutants", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "pollutant name;measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "gram, mole per liter, milligram per liter, microgram per cubic meter" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Pollutant types and, amount or concentrations measured at the time of sampling; can report multiple pollutants by entering numeric values preceded by name of pollutant", + "title": "pollutants", + "examples": [ + { + "value": "lead;0.15 microgram per cubic meter" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "pollutants" + ], + "is_a": "core field", + "string_serialization": "{text};{float} {unit}", + "slot_uri": "MIXS:0000107", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "porosity": { + "name": "porosity", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value or range" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "percentage" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Porosity of deposited sediment is volume of voids divided by the total volume of sample", + "title": "porosity", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "porosity" + ], + "is_a": "core field", + "string_serialization": "{float} - {float} {unit}", + "slot_uri": "MIXS:0000211", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "potassium": { + "name": "potassium", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milligram per liter, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of potassium in the sample", + "title": "potassium", + "examples": [ + { + "value": "463 milligram per liter" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "potassium" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000430", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "pour_point": { + "name": "pour_point", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "degree Celsius" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Temperature at which a liquid becomes semi solid and loses its flow characteristics. In crude oil a high¬†pour point¬†is generally associated with a high paraffin content, typically found in crude deriving from a larger proportion of plant material. (soure: https://en.wikipedia.org/wiki/pour_point)", + "title": "pour point", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "pour point" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000127", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "pre_treatment": { + "name": "pre_treatment", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "pre-treatment type" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The process of pre-treatment removes materials that can be easily collected from the raw wastewater", + "title": "pre-treatment", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "pre-treatment" + ], + "is_a": "core field", + "string_serialization": "{text}", + "slot_uri": "MIXS:0000348", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "pres_animal_insect": { + "name": "pres_animal_insect", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration;count" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The type and number of animals or insects present in the sampling space.", + "title": "presence of pets, animals, or insects", + "examples": [ + { + "value": "cat;5" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "presence of pets, animals, or insects" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000819", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false, + "pattern": "^(cat|dog|rodent|snake|other);\\d+$" + }, + "pressure": { + "name": "pressure", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "atmosphere" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Pressure to which the sample is subject to, in atmospheres", + "title": "pressure", + "examples": [ + { + "value": "50 atmosphere" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "pressure" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000412", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "prev_land_use_meth": { + "name": "prev_land_use_meth", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "PMID,DOI or url" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Reference or method used in determining previous land use and dates", + "title": "history/previous land use method", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "history/previous land use method" + ], + "is_a": "core field", + "string_serialization": "{PMID}|{DOI}|{URL}", + "slot_uri": "MIXS:0000316", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "previous_land_use": { + "name": "previous_land_use", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "land use name;date" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Previous land use and dates", + "title": "history/previous land use", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "history/previous land use" + ], + "is_a": "core field", + "string_serialization": "{text};{timestamp}", + "slot_uri": "MIXS:0000315", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "primary_prod": { + "name": "primary_prod", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milligram per cubic meter per day, gram per square meter per day" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Measurement of primary production, generally measured as isotope uptake", + "title": "primary production", + "examples": [ + { + "value": "100 milligram per cubic meter per day" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "primary production" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000728", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "primary_treatment": { + "name": "primary_treatment", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "primary treatment type" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The process to produce both a generally homogeneous liquid capable of being treated biologically and a sludge that can be separately treated or processed", + "title": "primary treatment", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "primary treatment" + ], + "is_a": "core field", + "string_serialization": "{text}", + "slot_uri": "MIXS:0000349", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "prod_rate": { + "name": "prod_rate", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "cubic meter per day" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Oil and/or gas production rates per well (e.g. 524 m3 / day)", + "title": "production rate", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "production rate" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000452", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "prod_start_date": { + "name": "prod_start_date", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "timestamp" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Date of field's first production", + "title": "production start date", + "examples": [ + { + "value": "2018-05-11" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "production start date" + ], + "is_a": "core field", + "slot_uri": "MIXS:0001008", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "profile_position": { + "name": "profile_position", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Cross-sectional position in the hillslope where sample was collected.sample area position in relation to surrounding areas", + "title": "profile position", + "examples": [ + { + "value": "summit" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "profile position" + ], + "is_a": "core field", + "slot_uri": "MIXS:0001084", + "domain_of": [ + "Biosample" + ], + "range": "profile_position_enum", + "multivalued": false + }, + "project_id": { + "name": "project_id", + "description": "Proposal IDs or names associated with dataset", + "title": "project ID", + "from_schema": "https://example.com/nmdc_submission_schema", + "rank": 1, + "string_serialization": "{text}", + "domain_of": [ + "Biosample" + ], + "slot_group": "EMSL", + "recommended": true + }, + "proposal_dna": { + "name": "proposal_dna", + "title": "DNA proposal ID", + "comments": [ + "Do not edit these values. A template will be provided by NMDC in which these values have been pre-filled." + ], + "examples": [ + { + "value": "504000" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "rank": 19, + "string_serialization": "{text}", + "domain_of": [ + "Biosample" + ], + "slot_group": "JGI-Metagenomics", + "recommended": true + }, + "proposal_rna": { + "name": "proposal_rna", + "title": "RNA proposal ID", + "comments": [ + "Do not edit these values. A template will be provided by NMDC in which these values have been pre-filled." + ], + "examples": [ + { + "value": "504000" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "rank": 19, + "string_serialization": "{text}", + "domain_of": [ + "Biosample" + ], + "slot_group": "JGI-Metatranscriptomics", + "recommended": true + }, + "quad_pos": { + "name": "quad_pos", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The quadrant position of the sampling room within the building", + "title": "quadrant position", + "examples": [ + { + "value": "West side" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "quadrant position" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000820", + "domain_of": [ + "Biosample" + ], + "range": "quad_pos_enum", + "multivalued": false + }, + "radiation_regm": { + "name": "radiation_regm", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "radiation type name;radiation amount;treatment interval and duration" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "rad, gray" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Information about treatment involving exposure of plant or a plant part to a particular radiation regimen; should include the radiation type, amount or intensity administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple radiation regimens", + "title": "radiation regimen", + "examples": [ + { + "value": "gamma radiation;60 gray;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "radiation regimen" + ], + "is_a": "core field", + "string_serialization": "{text};{float} {unit};{Rn/start_time/end_time/duration}", + "slot_uri": "MIXS:0000575", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "rainfall_regm": { + "name": "rainfall_regm", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value;treatment interval and duration" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "millimeter" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Information about treatment involving an exposure to a given amount of rainfall, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens", + "title": "rainfall regimen", + "examples": [ + { + "value": "15 millimeter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "rainfall regimen" + ], + "is_a": "core field", + "string_serialization": "{float} {unit};{Rn/start_time/end_time/duration}", + "slot_uri": "MIXS:0000576", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "reactor_type": { + "name": "reactor_type", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "reactor type name" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Anaerobic digesters can be designed and engineered to operate using a number of different process configurations, as batch or continuous, mesophilic, high solid or low solid, and single stage or multistage", + "title": "reactor type", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "reactor type" + ], + "is_a": "core field", + "string_serialization": "{text}", + "slot_uri": "MIXS:0000350", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "redox_potential": { + "name": "redox_potential", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "millivolt" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential", + "title": "redox potential", + "examples": [ + { + "value": "300 millivolt" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "redox potential" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000182", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "rel_air_humidity": { + "name": "rel_air_humidity", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "percentage" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Partial vapor and air pressure, density of the vapor and air, or by the actual mass of the vapor and air", + "title": "relative air humidity", + "examples": [ + { + "value": "80%" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "relative air humidity" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000121", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "rel_humidity_out": { + "name": "rel_humidity_out", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "gram of air, kilogram of air" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The recorded outside relative humidity value at the time of sampling", + "title": "outside relative humidity", + "examples": [ + { + "value": "12 per kilogram of air" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "outside relative humidity" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000188", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "rel_samp_loc": { + "name": "rel_samp_loc", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The sampling location within the train car", + "title": "relative sampling location", + "examples": [ + { + "value": "center of car" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "relative sampling location" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000821", + "domain_of": [ + "Biosample" + ], + "range": "rel_samp_loc_enum", + "multivalued": false + }, + "replicate_number": { + "name": "replicate_number", + "description": "If sending biological replicates, indicate the rep number here.", + "title": "replicate number", + "comments": [ + "This will guide staff in ensuring your samples are blocked & randomized correctly" + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "rank": 6, + "string_serialization": "{integer}", + "domain_of": [ + "Biosample" + ], + "slot_group": "EMSL", + "recommended": true + }, + "reservoir": { + "name": "reservoir", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "name" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Name of the reservoir (e.g. Carapebus)", + "title": "reservoir name", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "reservoir name" + ], + "is_a": "core field", + "string_serialization": "{text}", + "slot_uri": "MIXS:0000303", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "resins_pc": { + "name": "resins_pc", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "name;measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "percent" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene)", + "title": "resins wt%", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "resins wt%" + ], + "is_a": "core field", + "string_serialization": "{text};{float} {unit}", + "slot_uri": "MIXS:0000134", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "rna_absorb1": { + "name": "rna_absorb1", + "description": "260/280 measurement of RNA sample purity", + "title": "RNA absorbance 260/280", + "comments": [ + "Recommended value is between 1 and 3." + ], + "examples": [ + { + "value": "2.02" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "rank": 7, + "string_serialization": "{float}", + "domain_of": [ + "Biosample" + ], + "slot_group": "JGI-Metatranscriptomics", + "range": "float", + "recommended": true + }, + "rna_absorb2": { + "name": "rna_absorb2", + "description": "260/230 measurement of RNA sample purity", + "title": "RNA absorbance 260/230", + "comments": [ + "Recommended value is between 1 and 3." + ], + "examples": [ + { + "value": "2.02" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "rank": 8, + "string_serialization": "{float}", + "domain_of": [ + "Biosample" + ], + "slot_group": "JGI-Metatranscriptomics", + "range": "float", + "recommended": true + }, + "rna_concentration": { + "name": "rna_concentration", + "title": "RNA concentration in ng/ul", + "comments": [ + "Units must be in ng/uL. Enter the numerical part only. Must be calculated using a fluorometric method. Acceptable values are 0-2000." + ], + "examples": [ + { + "value": "100" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "see_also": [ + "nmdc:nucleic_acid_concentration" + ], + "rank": 5, + "string_serialization": "{float}", + "domain_of": [ + "Biosample" + ], + "slot_group": "JGI-Metatranscriptomics", + "range": "float", + "recommended": true, + "minimum_value": 0, + "maximum_value": 1000 + }, + "rna_cont_type": { + "name": "rna_cont_type", + "description": "Tube or plate (96-well)", + "title": "RNA container type", + "examples": [ + { + "value": "plate" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "rank": 10, + "domain_of": [ + "Biosample" + ], + "slot_group": "JGI-Metatranscriptomics", + "range": "JgiContTypeEnum", + "recommended": true + }, + "rna_cont_well": { + "name": "rna_cont_well", + "title": "RNA plate position", + "comments": [ + "Required when 'plate' is selected for container type.", + "Leave blank if the sample will be shipped in a tube.", + "JGI will not process samples in corner wells, so A1, A12, H1 and H12 will not pass validation.", + "For partial plates, fill by columns, like B1-G1,A2-H2,A3-D3 (NOT A2-A11,B1-B8)." + ], + "examples": [ + { + "value": "B2" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "rank": 11, + "string_serialization": "{96 well plate pos}", + "domain_of": [ + "Biosample" + ], + "slot_group": "JGI-Metatranscriptomics", + "recommended": true, + "pattern": "^(?!A1$|A12$|H1$|H12$)(([A-H][1-9])|([A-H]1[0-2]))$" + }, + "rna_container_id": { + "name": "rna_container_id", + "title": "RNA container label", + "comments": [ + "Must be unique across all tubes and plates, and <20 characters. All samples in a plate should have the same plate label." + ], + "examples": [ + { + "value": "Pond_MT_041618" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "rank": 9, + "string_serialization": "{text < 20 characters}", + "domain_of": [ + "Biosample" + ], + "slot_group": "JGI-Metatranscriptomics", + "recommended": true + }, + "rna_isolate_meth": { + "name": "rna_isolate_meth", + "description": "Describe the method/protocol/kit used to extract DNA/RNA.", + "title": "RNA isolation method", + "examples": [ + { + "value": "phenol/chloroform extraction" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "Sample Isolation Method" + ], + "rank": 16, + "string_serialization": "{text}", + "domain_of": [ + "Biosample" + ], + "slot_group": "JGI-Metatranscriptomics", + "recommended": true + }, + "rna_project_contact": { + "name": "rna_project_contact", + "title": "RNA seq project contact", + "comments": [ + "Do not edit these values. A template will be provided by NMDC in which these values have been pre-filled." + ], + "examples": [ + { + "value": "John Jones" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "rank": 18, + "string_serialization": "{text}", + "domain_of": [ + "Biosample" + ], + "slot_group": "JGI-Metatranscriptomics", + "recommended": true + }, + "rna_samp_id": { + "name": "rna_samp_id", + "title": "RNA sample ID", + "comments": [ + "Do not edit these values. A template will be provided by NMDC in which these values have been pre-filled." + ], + "examples": [ + { + "value": "187654" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "rank": 3, + "string_serialization": "{text}", + "domain_of": [ + "Biosample" + ], + "slot_group": "JGI-Metatranscriptomics", + "recommended": true + }, + "rna_sample_format": { + "name": "rna_sample_format", + "description": "Solution in which the RNA sample has been suspended", + "title": "RNA sample format", + "examples": [ + { + "value": "Water" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "rank": 12, + "domain_of": [ + "Biosample" + ], + "slot_group": "JGI-Metatranscriptomics", + "range": "RNASampleFormatEnum", + "recommended": true + }, + "rna_sample_name": { + "name": "rna_sample_name", + "description": "Give the RNA sample a name that is meaningful to you. Sample names must be unique across all JGI projects and contain a-z, A-Z, 0-9, - and _ only.", + "title": "RNA sample name", + "examples": [ + { + "value": "JGI_pond_041618" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "rank": 4, + "string_serialization": "{text}", + "domain_of": [ + "Biosample" + ], + "slot_group": "JGI-Metatranscriptomics", + "recommended": true, + "minimum_value": 0, + "maximum_value": 2000 + }, + "rna_seq_project": { + "name": "rna_seq_project", + "title": "RNA seq project ID", + "comments": [ + "Do not edit these values. A template will be provided by NMDC in which these values have been pre-filled." + ], + "examples": [ + { + "value": "1191234" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "Seq Project ID" + ], + "rank": 1, + "string_serialization": "{text}", + "domain_of": [ + "Biosample" + ], + "slot_group": "JGI-Metatranscriptomics", + "recommended": true + }, + "rna_seq_project_name": { + "name": "rna_seq_project_name", + "title": "RNA seq project name", + "comments": [ + "Do not edit these values. A template will be provided by NMDC in which these values have been pre-filled." + ], + "examples": [ + { + "value": "JGI Pond metatranscriptomics" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "rank": 2, + "string_serialization": "{text}", + "domain_of": [ + "Biosample" + ], + "slot_group": "JGI-Metatranscriptomics", + "recommended": true + }, + "rna_seq_project_pi": { + "name": "rna_seq_project_pi", + "title": "RNA seq project PI", + "comments": [ + "Do not edit these values. A template will be provided by NMDC in which these values have been pre-filled." + ], + "examples": [ + { + "value": "Jane Johnson" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "rank": 17, + "string_serialization": "{text}", + "domain_of": [ + "Biosample" + ], + "slot_group": "JGI-Metatranscriptomics", + "recommended": true + }, + "rna_volume": { + "name": "rna_volume", + "title": "RNA volume in ul", + "comments": [ + "Units must be in uL. Enter the numerical part only. Value must be 0-1000. This form accepts values < 25, but JGI may refuse to process them unless permission has been granted by a project manager" + ], + "examples": [ + { + "value": "25" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "rank": 6, + "string_serialization": "{float}", + "domain_of": [ + "Biosample" + ], + "slot_group": "JGI-Metatranscriptomics", + "range": "float", + "recommended": true, + "minimum_value": 0, + "maximum_value": 1000 + }, + "room_air_exch_rate": { + "name": "room_air_exch_rate", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "liter per hour" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The rate at which outside air replaces indoor air in a given space", + "title": "room air exchange rate", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "room air exchange rate" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000169", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "room_architec_elem": { + "name": "room_architec_elem", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "free text" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The unique details and component parts that, together, form the architecture of a distinguisahable space within a built structure", + "title": "room architectural elements", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "room architectural elements" + ], + "is_a": "core field", + "string_serialization": "{text}", + "slot_uri": "MIXS:0000233", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "room_condt": { + "name": "room_condt", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The condition of the room at the time of sampling", + "title": "room condition", + "examples": [ + { + "value": "new" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "room condition" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000822", + "domain_of": [ + "Biosample" + ], + "range": "room_condt_enum", + "multivalued": false + }, + "room_connected": { + "name": "room_connected", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "List of rooms connected to the sampling room by a doorway", + "title": "rooms connected by a doorway", + "examples": [ + { + "value": "office" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "rooms connected by a doorway" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000826", + "domain_of": [ + "Biosample" + ], + "range": "room_connected_enum", + "multivalued": false + }, + "room_count": { + "name": "room_count", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "value" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The total count of rooms in the built structure including all room types", + "title": "room count", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "room count" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000234", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "room_dim": { + "name": "room_dim", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "meter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The length, width and height of sampling room", + "title": "room dimensions", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "room dimensions" + ], + "is_a": "core field", + "string_serialization": "{integer} {unit} x {integer} {unit} x {integer} {unit}", + "slot_uri": "MIXS:0000192", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "room_door_dist": { + "name": "room_door_dist", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "meter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Distance between doors (meters) in the hallway between the sampling room and adjacent rooms", + "title": "room door distance", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "room door distance" + ], + "is_a": "core field", + "string_serialization": "{integer} {unit}", + "slot_uri": "MIXS:0000193", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "room_door_share": { + "name": "room_door_share", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "room name;room number" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "List of room(s) (room number, room name) sharing a door with the sampling room", + "title": "rooms that share a door with sampling room", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "rooms that share a door with sampling room" + ], + "is_a": "core field", + "string_serialization": "{text};{integer}", + "slot_uri": "MIXS:0000242", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "room_hallway": { + "name": "room_hallway", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "room name;room number" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "List of room(s) (room number, room name) located in the same hallway as sampling room", + "title": "rooms that are on the same hallway", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "rooms that are on the same hallway" + ], + "is_a": "core field", + "string_serialization": "{text};{integer}", + "slot_uri": "MIXS:0000238", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "room_loc": { + "name": "room_loc", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The position of the room within the building", + "title": "room location in building", + "examples": [ + { + "value": "interior room" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "room location in building" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000823", + "domain_of": [ + "Biosample" + ], + "range": "room_loc_enum", + "multivalued": false + }, + "room_moist_dam_hist": { + "name": "room_moist_dam_hist", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "value" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The history of moisture damage or mold in the past 12 months. Number of events of moisture damage or mold observed", + "title": "room moisture damage or mold history", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "room moisture damage or mold history" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000235", + "domain_of": [ + "Biosample" + ], + "range": "integer", + "multivalued": false + }, + "room_net_area": { + "name": "room_net_area", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "square feet, square meter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The net floor area of sampling room. Net area excludes wall thicknesses", + "title": "room net area", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "room net area" + ], + "is_a": "core field", + "string_serialization": "{integer} {unit}", + "slot_uri": "MIXS:0000194", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "room_occup": { + "name": "room_occup", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Count of room occupancy at time of sampling", + "title": "room occupancy", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "room occupancy" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000236", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "room_samp_pos": { + "name": "room_samp_pos", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The horizontal sampling position in the room relative to architectural elements", + "title": "room sampling position", + "examples": [ + { + "value": "south corner" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "room sampling position" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000824", + "domain_of": [ + "Biosample" + ], + "range": "room_samp_pos_enum", + "multivalued": false + }, + "room_type": { + "name": "room_type", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The main purpose or activity of the sampling room. A room is any distinguishable space within a structure", + "title": "room type", + "examples": [ + { + "value": "bathroom" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "room type" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000825", + "domain_of": [ + "Biosample" + ], + "range": "room_type_enum", + "multivalued": false + }, + "room_vol": { + "name": "room_vol", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "cubic feet, cubic meter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Volume of sampling room", + "title": "room volume", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "room volume" + ], + "is_a": "core field", + "string_serialization": "{integer} {unit}", + "slot_uri": "MIXS:0000195", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "room_wall_share": { + "name": "room_wall_share", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "room name;room number" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "List of room(s) (room number, room name) sharing a wall with the sampling room", + "title": "rooms that share a wall with sampling room", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "rooms that share a wall with sampling room" + ], + "is_a": "core field", + "string_serialization": "{text};{integer}", + "slot_uri": "MIXS:0000243", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "room_window_count": { + "name": "room_window_count", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "value" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Number of windows in the room", + "title": "room window count", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "room window count" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000237", + "domain_of": [ + "Biosample" + ], + "range": "integer", + "multivalued": false + }, + "root_cond": { + "name": "root_cond", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "PMID,DOI,url or free text" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Relevant rooting conditions such as field plot size, sowing density, container dimensions, number of plants per container.", + "title": "rooting conditions", + "examples": [ + { + "value": "http://himedialabs.com/TD/PT158.pdf" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "rooting conditions" + ], + "is_a": "core field", + "string_serialization": "{PMID}|{DOI}|{URL}|{text}", + "slot_uri": "MIXS:0001061", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "root_med_carbon": { + "name": "root_med_carbon", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "carbon source name;measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milligram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Source of organic carbon in the culture rooting medium; e.g. sucrose.", + "title": "rooting medium carbon", + "examples": [ + { + "value": "sucrose" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "rooting medium carbon" + ], + "is_a": "core field", + "string_serialization": "{text};{float} {unit}", + "slot_uri": "MIXS:0000577", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "root_med_macronutr": { + "name": "root_med_macronutr", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "macronutrient name;measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milligram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Measurement of the culture rooting medium macronutrients (N,P, K, Ca, Mg, S); e.g. KH2PO4 (170¬†mg/L).", + "title": "rooting medium macronutrients", + "examples": [ + { + "value": "KH2PO4;170¬†milligram per liter" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "rooting medium macronutrients" + ], + "is_a": "core field", + "string_serialization": "{text};{float} {unit}", + "slot_uri": "MIXS:0000578", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "root_med_micronutr": { + "name": "root_med_micronutr", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "micronutrient name;measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milligram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Measurement of the culture rooting medium micronutrients (Fe, Mn, Zn, B, Cu, Mo); e.g. H3BO3 (6.2¬†mg/L).", + "title": "rooting medium micronutrients", + "examples": [ + { + "value": "H3BO3;6.2¬†milligram per liter" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "rooting medium micronutrients" + ], + "is_a": "core field", + "string_serialization": "{text};{float} {unit}", + "slot_uri": "MIXS:0000579", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "root_med_ph": { + "name": "root_med_ph", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "pH measurement of the culture rooting medium; e.g. 5.5.", + "title": "rooting medium pH", + "examples": [ + { + "value": "7.5" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "rooting medium pH" + ], + "is_a": "core field", + "slot_uri": "MIXS:0001062", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "root_med_regl": { + "name": "root_med_regl", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "regulator name;measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milligram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Growth regulators in the culture rooting medium such as cytokinins, auxins, gybberellins, abscisic acid; e.g. 0.5¬†mg/L NAA.", + "title": "rooting medium regulators", + "examples": [ + { + "value": "abscisic acid;0.75 milligram per liter" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "rooting medium regulators" + ], + "is_a": "core field", + "string_serialization": "{text};{float} {unit}", + "slot_uri": "MIXS:0000581", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "root_med_solid": { + "name": "root_med_solid", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "name" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Specification of the solidifying agent in the culture rooting medium; e.g. agar.", + "title": "rooting medium solidifier", + "examples": [ + { + "value": "agar" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "rooting medium solidifier" + ], + "is_a": "core field", + "string_serialization": "{text}", + "slot_uri": "MIXS:0001063", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "root_med_suppl": { + "name": "root_med_suppl", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "supplement name;measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milligram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Organic supplements of the culture rooting medium, such as vitamins, amino acids, organic acids, antibiotics activated charcoal; e.g. nicotinic acid (0.5¬†mg/L).", + "title": "rooting medium organic supplements", + "examples": [ + { + "value": "nicotinic acid;0.5 milligram per liter" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "rooting medium organic supplements" + ], + "is_a": "core field", + "string_serialization": "{text};{float} {unit}", + "slot_uri": "MIXS:0000580", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "salinity": { + "name": "salinity", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "practical salinity unit, percentage" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The total concentration of all dissolved salts in a liquid or solid sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater.", + "title": "salinity", + "examples": [ + { + "value": "25 practical salinity unit" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "salinity" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000183", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "salinity_meth": { + "name": "salinity_meth", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "PMID,DOI or url" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Reference or method used in determining salinity", + "title": "salinity method", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "salinity method" + ], + "is_a": "core field", + "string_serialization": "{PMID}|{DOI}|{URL}", + "slot_uri": "MIXS:0000341", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "salt_regm": { + "name": "salt_regm", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "salt name;salt amount;treatment interval and duration" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "gram, microgram, mole per liter, gram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Information about treatment involving use of salts as supplement to liquid and soil growth media; should include the name of salt, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple salt regimens", + "title": "salt regimen", + "examples": [ + { + "value": "NaCl;5 gram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "salt regimen" + ], + "is_a": "core field", + "string_serialization": "{text};{float} {unit};{Rn/start_time/end_time/duration}", + "slot_uri": "MIXS:0000582", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "samp_capt_status": { + "name": "samp_capt_status", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Reason for the sample", + "title": "sample capture status", + "examples": [ + { + "value": "farm sample" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "sample capture status" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000860", + "domain_of": [ + "Biosample" + ], + "range": "samp_capt_status_enum", + "multivalued": false + }, + "samp_collec_device": { + "name": "samp_collec_device", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "device name" + } + }, + "description": "The device used to collect an environmental sample. This field accepts terms listed under environmental sampling device (http://purl.obolibrary.org/obo/ENVO). This field also accepts terms listed under specimen collection device (http://purl.obolibrary.org/obo/GENEPIO_0002094).", + "title": "sample collection device", + "examples": [ + { + "value": "swab, biopsy, niskin bottle, push core, drag swab [GENEPIO:0002713]" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "sample collection device" + ], + "is_a": "nucleic acid sequence source field", + "string_serialization": "{termLabel} {[termID]}|{text}", + "slot_uri": "MIXS:0000002", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "samp_collec_method": { + "name": "samp_collec_method", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "PMID,DOI,url , or text" + } + }, + "description": "The method employed for collecting the sample.", + "title": "sample collection method", + "examples": [ + { + "value": "swabbing" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "sample collection method" + ], + "is_a": "nucleic acid sequence source field", + "string_serialization": "{PMID}|{DOI}|{URL}|{text}", + "slot_uri": "MIXS:0001225", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "samp_collect_point": { + "name": "samp_collect_point", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Sampling point on the asset were sample was collected (e.g. Wellhead, storage tank, separator, etc). If \"other\" is specified, please propose entry in \"additional info\" field", + "title": "sample collection point", + "examples": [ + { + "value": "well" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "sample collection point" + ], + "is_a": "core field", + "slot_uri": "MIXS:0001015", + "domain_of": [ + "Biosample" + ], + "range": "samp_collect_point_enum", + "multivalued": false + }, + "samp_dis_stage": { + "name": "samp_dis_stage", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Stage of the disease at the time of sample collection, e.g. inoculation, penetration, infection, growth and reproduction, dissemination of pathogen.", + "title": "sample disease stage", + "examples": [ + { + "value": "infection" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "sample disease stage" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000249", + "domain_of": [ + "Biosample" + ], + "range": "samp_dis_stage_enum", + "multivalued": false + }, + "samp_floor": { + "name": "samp_floor", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The floor of the building, where the sampling room is located", + "title": "sampling floor", + "examples": [ + { + "value": "4th floor" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "sampling floor" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000828", + "domain_of": [ + "Biosample" + ], + "range": "samp_floor_enum", + "multivalued": false + }, + "samp_loc_corr_rate": { + "name": "samp_loc_corr_rate", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value range" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "millimeter per year" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Metal corrosion rate is the speed of metal deterioration due to environmental conditions. As environmental conditions change corrosion rates change accordingly. Therefore, long term corrosion rates are generally more informative than short term rates and for that reason they are preferred during reporting. In the case of suspected MIC, corrosion rate measurements at the time of sampling might provide insights into the involvement of certain microbial community members in MIC as well as potential microbial interplays", + "title": "corrosion rate at sample location", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "corrosion rate at sample location" + ], + "is_a": "core field", + "string_serialization": "{float} - {float} {unit}", + "slot_uri": "MIXS:0000136", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "samp_mat_process": { + "name": "samp_mat_process", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "text" + } + }, + "description": "A brief description of any processing applied to the sample during or after retrieving the sample from environment, or a link to the relevant protocol(s) performed.", + "title": "sample material processing", + "examples": [ + { + "value": "filtering of seawater, storing samples in ethanol" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "sample material processing" + ], + "is_a": "nucleic acid sequence source field", + "string_serialization": "{text}", + "slot_uri": "MIXS:0000016", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "samp_md": { + "name": "samp_md", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value;enumeration" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "meter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "In non deviated well, measured depth is equal to the true vertical depth, TVD (TVD=TVDSS plus the reference or datum it refers to). In deviated wells, the MD is the length of trajectory of the borehole measured from the same reference or datum. Common datums used are ground level (GL), drilling rig floor (DF), rotary table (RT), kelly bushing (KB) and mean sea level (MSL). If \"other\" is specified, please propose entry in \"additional info\" field", + "title": "sample measured depth", + "examples": [ + { + "value": "1534 meter;MSL" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "sample measured depth" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000413", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "samp_name": { + "name": "samp_name", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "text" + } + }, + "description": "A local identifier or name that for the material sample used for extracting nucleic acids, and subsequent sequencing. It can refer either to the original material collected or to any derived sub-samples. It can have any format, but we suggest that you make it concise, unique and consistent within your lab, and as informative as possible. INSDC requires every sample name from a single Submitter to be unique. Use of a globally unique identifier for the field source_mat_id is recommended in addition to sample_name.", + "title": "sample name", + "examples": [ + { + "value": "ISDsoil1" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "sample name" + ], + "is_a": "investigation field", + "string_serialization": "{text}", + "slot_uri": "MIXS:0001107", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "samp_preserv": { + "name": "samp_preserv", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "name;measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milliliter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Preservative added to the sample (e.g. Rnalater, alcohol, formaldehyde, etc.). Where appropriate include volume added (e.g. Rnalater; 2 ml)", + "title": "preservative added to sample", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "preservative added to sample" + ], + "is_a": "core field", + "string_serialization": "{text};{float} {unit}", + "slot_uri": "MIXS:0000463", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "samp_room_id": { + "name": "samp_room_id", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "value" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Sampling room number. This ID should be consistent with the designations on the building floor plans", + "title": "sampling room ID or name", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "sampling room ID or name" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000244", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "samp_size": { + "name": "samp_size", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "millliter, gram, milligram, liter" + } + }, + "description": "The total amount or size (volume (ml), mass (g) or area (m2) ) of sample collected.", + "title": "amount or size of sample collected", + "examples": [ + { + "value": "5 liter" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "amount or size of sample collected" + ], + "is_a": "nucleic acid sequence source field", + "slot_uri": "MIXS:0000001", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "samp_sort_meth": { + "name": "samp_sort_meth", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "description of method" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Method by which samples are sorted; open face filter collecting total suspended particles, prefilter to remove particles larger than X micrometers in diameter, where common values of X would be 10 and 2.5 full size sorting in a cascade impactor.", + "title": "sample size sorting method", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "sample size sorting method" + ], + "is_a": "core field", + "string_serialization": "{text}", + "slot_uri": "MIXS:0000216", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "samp_store_dur": { + "name": "samp_store_dur", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "duration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Duration for which the sample was stored", + "title": "sample storage duration", + "examples": [ + { + "value": "P1Y6M" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "sample storage duration" + ], + "is_a": "core field", + "string_serialization": "{duration}", + "slot_uri": "MIXS:0000116", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "samp_store_loc": { + "name": "samp_store_loc", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "location name" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Location at which sample was stored, usually name of a specific freezer/room", + "title": "sample storage location", + "examples": [ + { + "value": "Freezer no:5" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "sample storage location" + ], + "is_a": "core field", + "string_serialization": "{text}", + "slot_uri": "MIXS:0000755", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "samp_store_temp": { + "name": "samp_store_temp", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "degree Celsius" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Temperature at which sample was stored, e.g. -80 degree Celsius", + "title": "sample storage temperature", + "examples": [ + { + "value": "-80 degree Celsius" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "sample storage temperature" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000110", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "samp_subtype": { + "name": "samp_subtype", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Name of sample sub-type. For example if \"sample type\" is \"Produced Water\" then subtype could be \"Oil Phase\" or \"Water Phase\". If \"other\" is specified, please propose entry in \"additional info\" field", + "title": "sample subtype", + "examples": [ + { + "value": "biofilm" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "sample subtype" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000999", + "domain_of": [ + "Biosample" + ], + "range": "samp_subtype_enum", + "multivalued": false + }, + "samp_time_out": { + "name": "samp_time_out", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "time" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "hour" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The recent and long term history of outside sampling", + "title": "sampling time outside", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "sampling time outside" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000196", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "samp_transport_cond": { + "name": "samp_transport_cond", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value;measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "days;degree Celsius" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Sample transport duration (in days or hrs) and temperature the sample was exposed to (e.g. 5.5 days; 20 ¬∞C)", + "title": "sample transport conditions", + "examples": [ + { + "value": "5 days;-20 degree Celsius" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "sample transport conditions" + ], + "is_a": "core field", + "string_serialization": "{float} {unit};{float} {unit}", + "slot_uri": "MIXS:0000410", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "samp_tvdss": { + "name": "samp_tvdss", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value or measurement value range" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "meter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Depth of the sample i.e. The vertical distance between the sea level and the sampled position in the subsurface. Depth can be reported as an interval for subsurface samples e.g. 1325.75-1362.25 m", + "title": "sample true vertical depth subsea", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "sample true vertical depth subsea" + ], + "is_a": "core field", + "string_serialization": "{float}-{float} {unit}", + "slot_uri": "MIXS:0000409", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "samp_type": { + "name": "samp_type", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "GENEPIO:0001246" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The type of material from which the sample was obtained. For the Hydrocarbon package, samples include types like core, rock trimmings, drill cuttings, piping section, coupon, pigging debris, solid deposit, produced fluid, produced water, injected water, swabs, etc. For the Food Package, samples are usually categorized as food, body products or tissues, or environmental material. This field accepts terms listed under environmental specimen (http://purl.obolibrary.org/obo/GENEPIO_0001246).", + "title": "sample type", + "examples": [ + { + "value": "built environment sample [GENEPIO:0001248]" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "sample type" + ], + "is_a": "core field", + "string_serialization": "{termLabel} {[termID]}", + "slot_uri": "MIXS:0000998", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "samp_weather": { + "name": "samp_weather", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The weather on the sampling day", + "title": "sampling day weather", + "examples": [ + { + "value": "foggy" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "sampling day weather" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000827", + "domain_of": [ + "Biosample" + ], + "range": "samp_weather_enum", + "multivalued": false + }, + "samp_well_name": { + "name": "samp_well_name", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "name" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Name of the well (e.g. BXA1123) where sample was taken", + "title": "sample well name", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "sample well name" + ], + "is_a": "core field", + "string_serialization": "{text}", + "slot_uri": "MIXS:0000296", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "sample_link": { + "name": "sample_link", + "description": "A unique identifier to assign parent-child, subsample, or sibling samples. This is relevant when a sample or other material was used to generate the new sample.", + "title": "sample linkage", + "comments": [ + "This field allows multiple entries separated by ; (Examples: Soil collected from the field will link with the soil used in an incubation. The soil a plant was grown in links to the plant sample. An original culture sample was transferred to a new vial and generated a new sample)" + ], + "examples": [ + { + "value": "IGSN:DSJ0284" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "rank": 5, + "string_serialization": "{text}:{text}", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface", + "SampIdNewTermsMixin" + ], + "slot_group": "Sample ID", + "range": "string", + "recommended": true, + "multivalued": false + }, + "sample_shipped": { + "name": "sample_shipped", + "description": "The total amount or size (volume (ml), mass (g) or area (m2) ) of sample sent to EMSL.", + "title": "sample shipped amount", + "comments": [ + "This field is only required when completing metadata for samples being submitted to EMSL for analyses." + ], + "examples": [ + { + "value": "15 g" + }, + { + "value": "100 uL" + }, + { + "value": "5 mL" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "rank": 3, + "string_serialization": "{float} {unit}", + "domain_of": [ + "Biosample" + ], + "slot_group": "EMSL", + "recommended": true + }, + "sample_type": { + "name": "sample_type", + "description": "Type of sample being submitted", + "title": "sample type", + "comments": [ + "This can vary from 'environmental package' if the sample is an extraction." + ], + "examples": [ + { + "value": "water extracted soil" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "rank": 2, + "domain_of": [ + "Biosample" + ], + "slot_group": "EMSL", + "range": "SampleTypeEnum", + "recommended": true + }, + "saturates_pc": { + "name": "saturates_pc", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "name;measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "percent" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene)", + "title": "saturates wt%", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "saturates wt%" + ], + "is_a": "core field", + "string_serialization": "{text};{float} {unit}", + "slot_uri": "MIXS:0000131", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "season": { + "name": "season", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "NCIT:C94729" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The season when sampling occurred. Any of the four periods into which the year is divided by the equinoxes and solstices. This field accepts terms listed under season (http://purl.obolibrary.org/obo/NCIT_C94729).", + "title": "season", + "examples": [ + { + "value": "autumn [NCIT:C94733]" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "season" + ], + "is_a": "core field", + "string_serialization": "{termLabel} {[termID]}", + "slot_uri": "MIXS:0000829", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "season_environment": { + "name": "season_environment", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "seasonal environment name;treatment interval and duration" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Treatment involving an exposure to a particular season (e.g. Winter, summer, rabi, rainy etc.), treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment", + "title": "seasonal environment", + "examples": [ + { + "value": "rainy;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "seasonal environment" + ], + "is_a": "core field", + "string_serialization": "{text};{Rn/start_time/end_time/duration}", + "slot_uri": "MIXS:0001068", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "season_precpt": { + "name": "season_precpt", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "millimeter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The average of all seasonal precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or Isohyetal maps.", + "title": "mean seasonal precipitation", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "mean seasonal precipitation" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000645", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "season_temp": { + "name": "season_temp", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "degree Celsius" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Mean seasonal temperature", + "title": "mean seasonal temperature", + "examples": [ + { + "value": "18 degree Celsius" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "mean seasonal temperature" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000643", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "season_use": { + "name": "season_use", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The seasons the space is occupied", + "title": "seasonal use", + "examples": [ + { + "value": "Winter" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "seasonal use" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000830", + "domain_of": [ + "Biosample" + ], + "range": "season_use_enum", + "multivalued": false + }, + "secondary_treatment": { + "name": "secondary_treatment", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "secondary treatment type" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The process for substantially degrading the biological content of the sewage", + "title": "secondary treatment", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "secondary treatment" + ], + "is_a": "core field", + "string_serialization": "{text}", + "slot_uri": "MIXS:0000351", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "sediment_type": { + "name": "sediment_type", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Information about the sediment type based on major constituents", + "title": "sediment type", + "examples": [ + { + "value": "biogenous" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "sediment type" + ], + "is_a": "core field", + "slot_uri": "MIXS:0001078", + "domain_of": [ + "Biosample" + ], + "range": "sediment_type_enum", + "multivalued": false + }, + "sewage_type": { + "name": "sewage_type", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "sewage type name" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Type of wastewater treatment plant as municipial or industrial", + "title": "sewage type", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "sewage type" + ], + "is_a": "core field", + "string_serialization": "{text}", + "slot_uri": "MIXS:0000215", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "shad_dev_water_mold": { + "name": "shad_dev_water_mold", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Signs of the presence of mold or mildew on the shading device", + "title": "shading device signs of water/mold", + "examples": [ + { + "value": "no presence of mold visible" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "shading device signs of water/mold" + ], + "is_a": "core field", + "string_serialization": "[presence of mold visible|no presence of mold visible]", + "slot_uri": "MIXS:0000834", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "shading_device_cond": { + "name": "shading_device_cond", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The physical condition of the shading device at the time of sampling", + "title": "shading device condition", + "examples": [ + { + "value": "new" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "shading device condition" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000831", + "domain_of": [ + "Biosample" + ], + "range": "shading_device_cond_enum", + "multivalued": false + }, + "shading_device_loc": { + "name": "shading_device_loc", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The location of the shading device in relation to the built structure", + "title": "shading device location", + "examples": [ + { + "value": "exterior" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "shading device location" + ], + "is_a": "core field", + "string_serialization": "[exterior|interior]", + "slot_uri": "MIXS:0000832", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "shading_device_mat": { + "name": "shading_device_mat", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "material name" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The material the shading device is composed of", + "title": "shading device material", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "shading device material" + ], + "is_a": "core field", + "string_serialization": "{text}", + "slot_uri": "MIXS:0000245", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "shading_device_type": { + "name": "shading_device_type", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The type of shading device", + "title": "shading device type", + "examples": [ + { + "value": "slatted aluminum awning" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "shading device type" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000835", + "domain_of": [ + "Biosample" + ], + "range": "shading_device_type_enum", + "multivalued": false + }, + "sieving": { + "name": "sieving", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "design name and/or size;amount" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Collection design of pooled samples and/or sieve size and amount of sample sieved", + "title": "composite design/sieving", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "composite design/sieving" + ], + "is_a": "core field", + "string_serialization": "{{text}|{float} {unit}};{float} {unit}", + "slot_uri": "MIXS:0000322", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "silicate": { + "name": "silicate", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of silicate", + "title": "silicate", + "examples": [ + { + "value": "0.05 micromole per liter" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "silicate" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000184", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "size_frac": { + "name": "size_frac", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "filter size value range" + } + }, + "description": "Filtering pore size used in sample preparation", + "title": "size fraction selected", + "examples": [ + { + "value": "0-0.22 micrometer" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "size fraction selected" + ], + "is_a": "nucleic acid sequence source field", + "string_serialization": "{float}-{float} {unit}", + "slot_uri": "MIXS:0000017", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "size_frac_low": { + "name": "size_frac_low", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micrometer" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Refers to the mesh/pore size used to pre-filter/pre-sort the sample. Materials larger than the size threshold are excluded from the sample", + "title": "size-fraction lower threshold", + "examples": [ + { + "value": "0.2 micrometer" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "size-fraction lower threshold" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000735", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "size_frac_up": { + "name": "size_frac_up", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micrometer" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Refers to the mesh/pore size used to retain the sample. Materials smaller than the size threshold are excluded from the sample", + "title": "size-fraction upper threshold", + "examples": [ + { + "value": "20 micrometer" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "size-fraction upper threshold" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000736", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "slope_aspect": { + "name": "slope_aspect", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "degree" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The direction a slope faces. While looking down a slope use a compass to record the direction you are facing (direction or degrees); e.g., nw or 315 degrees. This measure provides an indication of sun and wind exposure that will influence soil temperature and evapotranspiration.", + "title": "slope aspect", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "slope aspect" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000647", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "slope_gradient": { + "name": "slope_gradient", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "percentage" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Commonly called 'slope'. The angle between ground surface and a horizontal line (in percent). This is the direction that overland water would flow. This measure is usually taken with a hand level meter or clinometer", + "title": "slope gradient", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "slope gradient" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000646", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "sludge_retent_time": { + "name": "sludge_retent_time", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "hours" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The time activated sludge remains in reactor", + "title": "sludge retention time", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "sludge retention time" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000669", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "sodium": { + "name": "sodium", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milligram per liter, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Sodium concentration in the sample", + "title": "sodium", + "examples": [ + { + "value": "10.5 milligram per liter" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "sodium" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000428", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "soil_horizon": { + "name": "soil_horizon", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Specific layer in the land area which measures parallel to the soil surface and possesses physical characteristics which differ from the layers above and beneath", + "title": "soil horizon", + "examples": [ + { + "value": "A horizon" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "soil horizon" + ], + "is_a": "core field", + "slot_uri": "MIXS:0001082", + "domain_of": [ + "Biosample" + ], + "range": "soil_horizon_enum", + "multivalued": false + }, + "soil_text_measure": { + "name": "soil_text_measure", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The relative proportion of different grain sizes of mineral particles in a soil, as described using a standard system; express as % sand (50 um to 2 mm), silt (2 um to 50 um), and clay (<2 um) with textural name (e.g., silty clay loam) optional.", + "title": "soil texture measurement", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "soil texture measurement" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000335", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "soil_texture_meth": { + "name": "soil_texture_meth", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "PMID,DOI or url" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Reference or method used in determining soil texture", + "title": "soil texture method", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "soil texture method" + ], + "is_a": "core field", + "string_serialization": "{PMID}|{DOI}|{URL}", + "slot_uri": "MIXS:0000336", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "soil_type": { + "name": "soil_type", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "ENVO_00001998" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Description of the soil type or classification. This field accepts terms under soil (http://purl.obolibrary.org/obo/ENVO_00001998). Multiple terms can be separated by pipes.", + "title": "soil type", + "examples": [ + { + "value": "plinthosol [ENVO:00002250]" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "soil type" + ], + "is_a": "core field", + "string_serialization": "{termLabel} {[termID]}", + "slot_uri": "MIXS:0000332", + "domain_of": [ + "FieldResearchSite", + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "soil_type_meth": { + "name": "soil_type_meth", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "PMID,DOI or url" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Reference or method used in determining soil series name or other lower-level classification", + "title": "soil type method", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "soil type method" + ], + "is_a": "core field", + "string_serialization": "{PMID}|{DOI}|{URL}", + "slot_uri": "MIXS:0000334", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "solar_irradiance": { + "name": "solar_irradiance", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "kilowatts per square meter per day, ergs per square centimeter per second" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The amount of solar energy that arrives at a specific area of a surface during a specific time interval", + "title": "solar irradiance", + "examples": [ + { + "value": "1.36 kilowatts per square meter per day" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "solar irradiance" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000112", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "soluble_inorg_mat": { + "name": "soluble_inorg_mat", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "soluble inorganic material name;measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "gram, microgram, mole per liter, gram per liter, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Concentration of substances such as ammonia, road-salt, sea-salt, cyanide, hydrogen sulfide, thiocyanates, thiosulfates, etc.", + "title": "soluble inorganic material", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "soluble inorganic material" + ], + "is_a": "core field", + "string_serialization": "{text};{float} {unit}", + "slot_uri": "MIXS:0000672", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "soluble_org_mat": { + "name": "soluble_org_mat", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "soluble organic material name;measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "gram, microgram, mole per liter, gram per liter, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Concentration of substances such as urea, fruit sugars, soluble proteins, drugs, pharmaceuticals, etc.", + "title": "soluble organic material", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "soluble organic material" + ], + "is_a": "core field", + "string_serialization": "{text};{float} {unit}", + "slot_uri": "MIXS:0000673", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "soluble_react_phosp": { + "name": "soluble_react_phosp", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per liter, milligram per liter, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of soluble reactive phosphorus", + "title": "soluble reactive phosphorus", + "examples": [ + { + "value": "0.1 milligram per liter" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "soluble reactive phosphorus" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000738", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "source_mat_id": { + "name": "source_mat_id", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "for cultures of microorganisms: identifiers for two culture collections; for other material a unique arbitrary identifer" + } + }, + "description": "A unique identifier assigned to a material sample (as defined by http://rs.tdwg.org/dwc/terms/materialSampleID, and as opposed to a particular digital record of a material sample) used for extracting nucleic acids, and subsequent sequencing. The identifier can refer either to the original material collected or to any derived sub-samples. The INSDC qualifiers /specimen_voucher, /bio_material, or /culture_collection may or may not share the same value as the source_mat_id field. For instance, the /specimen_voucher qualifier and source_mat_id may both contain 'UAM:Herps:14' , referring to both the specimen voucher and sampled tissue with the same identifier. However, the /culture_collection qualifier may refer to a value from an initial culture (e.g. ATCC:11775) while source_mat_id would refer to an identifier from some derived culture from which the nucleic acids were extracted (e.g. xatc123 or ark:/2154/R2).", + "title": "source material identifiers", + "examples": [ + { + "value": "MPI012345" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "source material identifiers" + ], + "is_a": "nucleic acid sequence source field", + "string_serialization": "{text}", + "slot_uri": "MIXS:0000026", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "space_typ_state": { + "name": "space_typ_state", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Customary or normal state of the space", + "title": "space typical state", + "examples": [ + { + "value": "typically occupied" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "space typical state" + ], + "is_a": "core field", + "string_serialization": "[typically occupied|typically unoccupied]", + "slot_uri": "MIXS:0000770", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "specific": { + "name": "specific", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The building specifications. If design is chosen, indicate phase: conceptual, schematic, design development, construction documents", + "title": "specifications", + "examples": [ + { + "value": "construction" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "specifications" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000836", + "domain_of": [ + "Biosample" + ], + "range": "specific_enum", + "multivalued": false + }, + "specific_ecosystem": { + "name": "specific_ecosystem", + "description": "Specific ecosystems represent specific features of the environment like aphotic zone in an ocean or gastric mucosa within a host digestive system. Specific ecosystem is in position 5/5 in a GOLD path.", + "comments": [ + "Specific ecosystems help to define samples based on very specific characteristics of an environment under the five-level classification system." + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "see_also": [ + "https://gold.jgi.doe.gov/help" + ], + "is_a": "gold_path_field", + "domain_of": [ + "Biosample", + "Study" + ] + }, + "specific_humidity": { + "name": "specific_humidity", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "gram of air, kilogram of air" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The mass of water vapour in a unit mass of moist air, usually expressed as grams of vapour per kilogram of air, or, in air conditioning, as grains per pound.", + "title": "specific humidity", + "examples": [ + { + "value": "15 per kilogram of air" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "specific humidity" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000214", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "sr_dep_env": { + "name": "sr_dep_env", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Source rock depositional environment (https://en.wikipedia.org/wiki/Source_rock). If \"other\" is specified, please propose entry in \"additional info\" field", + "title": "source rock depositional environment", + "examples": [ + { + "value": "Marine" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "source rock depositional environment" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000996", + "domain_of": [ + "Biosample" + ], + "range": "sr_dep_env_enum", + "multivalued": false + }, + "sr_geol_age": { + "name": "sr_geol_age", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Geological age of source rock (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). If \"other\" is specified, please propose entry in \"additional info\" field", + "title": "source rock geological age", + "examples": [ + { + "value": "Silurian" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "source rock geological age" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000997", + "domain_of": [ + "Biosample" + ], + "range": "sr_geol_age_enum", + "multivalued": false + }, + "sr_kerog_type": { + "name": "sr_kerog_type", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Origin of kerogen. Type I: Algal (aquatic), Type II: planktonic and soft plant material (aquatic or terrestrial), Type III: terrestrial woody/ fibrous plant material (terrestrial), Type IV: oxidized recycled woody debris (terrestrial) (additional information: https://en.wikipedia.org/wiki/Kerogen). If \"other\" is specified, please propose entry in \"additional info\" field", + "title": "source rock kerogen type", + "examples": [ + { + "value": "Type IV" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "source rock kerogen type" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000994", + "domain_of": [ + "Biosample" + ], + "range": "sr_kerog_type_enum", + "multivalued": false + }, + "sr_lithology": { + "name": "sr_lithology", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Lithology of source rock (https://en.wikipedia.org/wiki/Source_rock). If \"other\" is specified, please propose entry in \"additional info\" field", + "title": "source rock lithology", + "examples": [ + { + "value": "Coal" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "source rock lithology" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000995", + "domain_of": [ + "Biosample" + ], + "range": "sr_lithology_enum", + "multivalued": false + }, + "standing_water_regm": { + "name": "standing_water_regm", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "standing water type;treatment interval and duration" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Treatment involving an exposure to standing water during a plant's life span, types can be flood water or standing water, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens", + "title": "standing water regimen", + "examples": [ + { + "value": "standing water;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "standing water regimen" + ], + "is_a": "core field", + "string_serialization": "{text};{Rn/start_time/end_time/duration}", + "slot_uri": "MIXS:0001069", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "start_date_inc": { + "name": "start_date_inc", + "description": "Date the incubation was started. Only relevant for incubation samples.", + "title": "incubation start date", + "notes": [ + "MIxS collection_date accepts (truncated) ISO8601. DH taking arbitrary precision date only" + ], + "comments": [ + "Date should be formatted as YYYY(-MM(-DD)). Ie, 2021-04-15, 2021-04 and 2021 are all acceptable." + ], + "examples": [ + { + "value": "2021-04-15, 2021-04 and 2021 are all acceptable." + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "see_also": [ + "MIXS:0000011" + ], + "rank": 4, + "string_serialization": "{date, arbitrary precision}", + "domain_of": [ + "Biosample" + ], + "slot_group": "MIxS Inspired", + "recommended": true + }, + "start_time_inc": { + "name": "start_time_inc", + "description": "Time the incubation was started. Only relevant for incubation samples.", + "title": "incubation start time, GMT", + "notes": [ + "MIxS collection_date accepts (truncated) ISO8601. DH taking seconds optional time only" + ], + "comments": [ + "Time should be entered as HH:MM(:SS) in GMT. See here for a converter: https://www.worldtimebuddy.com/pst-to-gmt-converter" + ], + "examples": [ + { + "value": "13:33 or 13:33:55" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "see_also": [ + "MIXS:0000011" + ], + "rank": 5, + "string_serialization": "{time, seconds optional}", + "domain_of": [ + "Biosample" + ], + "slot_group": "MIxS Inspired", + "recommended": true + }, + "store_cond": { + "name": "store_cond", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "storage condition type;duration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Explain how and for how long the soil sample was stored before DNA extraction (fresh/frozen/other).", + "title": "storage conditions", + "examples": [ + { + "value": "-20 degree Celsius freezer;P2Y10D" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "storage conditions" + ], + "is_a": "core field", + "string_serialization": "{text};{duration}", + "slot_uri": "MIXS:0000327", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "substructure_type": { + "name": "substructure_type", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "The substructure or under building is that largely hidden section of the building which is built off the foundations to the ground floor level", + "title": "substructure type", + "examples": [ + { + "value": "basement" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "substructure type" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000767", + "domain_of": [ + "Biosample" + ], + "range": "substructure_type_enum", + "multivalued": true + }, + "sulfate": { + "name": "sulfate", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per liter, milligram per liter, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of sulfate in the sample", + "title": "sulfate", + "examples": [ + { + "value": "5 micromole per liter" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "sulfate" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000423", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "sulfate_fw": { + "name": "sulfate_fw", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milligram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Original sulfate concentration in the hydrocarbon resource", + "title": "sulfate in formation water", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "sulfate in formation water" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000407", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "sulfide": { + "name": "sulfide", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per liter, milligram per liter, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of sulfide in the sample", + "title": "sulfide", + "examples": [ + { + "value": "2 micromole per liter" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "sulfide" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000424", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "surf_air_cont": { + "name": "surf_air_cont", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Contaminant identified on surface", + "title": "surface-air contaminant", + "examples": [ + { + "value": "radon" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "surface-air contaminant" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000759", + "domain_of": [ + "Biosample" + ], + "range": "surf_air_cont_enum", + "multivalued": true + }, + "surf_humidity": { + "name": "surf_humidity", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "percentage" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Surfaces: water activity as a function of air and material moisture", + "title": "surface humidity", + "examples": [ + { + "value": "10%" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "surface humidity" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000123", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "surf_material": { + "name": "surf_material", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Surface materials at the point of sampling", + "title": "surface material", + "examples": [ + { + "value": "wood" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "surface material" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000758", + "domain_of": [ + "Biosample" + ], + "range": "surf_material_enum", + "multivalued": false + }, + "surf_moisture": { + "name": "surf_moisture", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "parts per million, gram per cubic meter, gram per square meter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Water held on a surface", + "title": "surface moisture", + "examples": [ + { + "value": "0.01 gram per square meter" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "surface moisture" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000128", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "surf_moisture_ph": { + "name": "surf_moisture_ph", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "ph measurement of surface", + "title": "surface moisture pH", + "examples": [ + { + "value": "7" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "surface moisture pH" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000760", + "domain_of": [ + "Biosample" + ], + "range": "double", + "multivalued": false + }, + "surf_temp": { + "name": "surf_temp", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "degree Celsius" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Temperature of the surface at the time of sampling", + "title": "surface temperature", + "examples": [ + { + "value": "15 degree Celsius" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "surface temperature" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000125", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "suspend_part_matter": { + "name": "suspend_part_matter", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milligram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of suspended particulate matter", + "title": "suspended particulate matter", + "examples": [ + { + "value": "0.5 milligram per liter" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "suspended particulate matter" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000741", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "suspend_solids": { + "name": "suspend_solids", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "suspended solid name;measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "gram, microgram, milligram per liter, mole per liter, gram per liter, part per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Concentration of substances including a wide variety of material, such as silt, decaying plant and animal matter; can include multiple substances", + "title": "suspended solids", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "suspended solids" + ], + "is_a": "core field", + "string_serialization": "{text};{float} {unit}", + "slot_uri": "MIXS:0000150", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "tan": { + "name": "tan", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milligram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Total Acid Number¬†(TAN) is a measurement of acidity that is determined by the amount of¬†potassium hydroxide¬†in milligrams that is needed to neutralize the acids in one gram of oil.¬†It is an important quality measurement of¬†crude oil. (source: https://en.wikipedia.org/wiki/Total_acid_number)", + "title": "total acid number", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "total acid number" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000120", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "technical_reps": { + "name": "technical_reps", + "description": "If sending technical replicates of the same sample, indicate the replicate count.", + "title": "number technical replicate", + "comments": [ + "This field is only required when completing metadata for samples being submitted to EMSL for analyses." + ], + "examples": [ + { + "value": "2" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "rank": 5, + "string_serialization": "{integer}", + "domain_of": [ + "Biosample" + ], + "slot_group": "EMSL", + "recommended": true + }, + "temp": { + "name": "temp", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "degree Celsius" + } + }, + "description": "Temperature of the sample at the time of sampling.", + "title": "temperature", + "examples": [ + { + "value": "25 degree Celsius" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "temperature" + ], + "is_a": "environment field", + "slot_uri": "MIXS:0000113", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "temp_out": { + "name": "temp_out", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "degree Celsius" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The recorded temperature value at sampling time outside", + "title": "temperature outside house", + "examples": [ + { + "value": "5 degree Celsius" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "temperature outside house" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000197", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "tertiary_treatment": { + "name": "tertiary_treatment", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "tertiary treatment type" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The process providing a final treatment stage to raise the effluent quality before it is discharged to the receiving environment", + "title": "tertiary treatment", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "tertiary treatment" + ], + "is_a": "core field", + "string_serialization": "{text}", + "slot_uri": "MIXS:0000352", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "tidal_stage": { + "name": "tidal_stage", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Stage of tide", + "title": "tidal stage", + "examples": [ + { + "value": "high tide" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "tidal stage" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000750", + "domain_of": [ + "Biosample" + ], + "range": "tidal_stage_enum", + "multivalued": false + }, + "tillage": { + "name": "tillage", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Note method(s) used for tilling", + "title": "history/tillage", + "examples": [ + { + "value": "chisel" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "history/tillage" + ], + "is_a": "core field", + "slot_uri": "MIXS:0001081", + "domain_of": [ + "Biosample" + ], + "range": "tillage_enum", + "multivalued": true + }, + "tiss_cult_growth_med": { + "name": "tiss_cult_growth_med", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "PMID,DOI,url or free text" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Description of plant tissue culture growth media used", + "title": "tissue culture growth media", + "examples": [ + { + "value": "https://link.springer.com/content/pdf/10.1007/BF02796489.pdf" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "tissue culture growth media" + ], + "is_a": "core field", + "string_serialization": "{PMID}|{DOI}|{URL}|{text}", + "slot_uri": "MIXS:0001070", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "toluene": { + "name": "toluene", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milligram per liter, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of toluene in the sample", + "title": "toluene", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "toluene" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000154", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "tot_carb": { + "name": "tot_carb", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "microgram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Total carbon content", + "title": "total carbon", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "total carbon" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000525", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "tot_depth_water_col": { + "name": "tot_depth_water_col", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "meter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Measurement of total depth of water column", + "title": "total depth of water column", + "examples": [ + { + "value": "500 meter" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "total depth of water column" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000634", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "tot_diss_nitro": { + "name": "tot_diss_nitro", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "microgram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Total dissolved nitrogen concentration, reported as nitrogen, measured by: total dissolved nitrogen = NH4 + NO3NO2 + dissolved organic nitrogen", + "title": "total dissolved nitrogen", + "examples": [ + { + "value": "40 microgram per liter" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "total dissolved nitrogen" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000744", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "tot_inorg_nitro": { + "name": "tot_inorg_nitro", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "microgram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Total inorganic nitrogen content", + "title": "total inorganic nitrogen", + "examples": [ + { + "value": "40 microgram per liter" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "total inorganic nitrogen" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000745", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "tot_iron": { + "name": "tot_iron", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milligram per liter, milligram per kilogram" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of total iron in the sample", + "title": "total iron", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "total iron" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000105", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "tot_nitro": { + "name": "tot_nitro", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "microgram per liter, micromole per liter, milligram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen", + "title": "total nitrogen concentration", + "examples": [ + { + "value": "50 micromole per liter" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "total nitrogen concentration" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000102", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "tot_nitro_cont_meth": { + "name": "tot_nitro_cont_meth", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "PMID,DOI or url" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Reference or method used in determining the total nitrogen", + "title": "total nitrogen content method", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "total nitrogen content method" + ], + "is_a": "core field", + "string_serialization": "{PMID}|{DOI}|{URL}", + "slot_uri": "MIXS:0000338", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "tot_nitro_content": { + "name": "tot_nitro_content", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "microgram per liter, micromole per liter, milligram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Total nitrogen content of the sample", + "title": "total nitrogen content", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "total nitrogen content" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000530", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "tot_org_c_meth": { + "name": "tot_org_c_meth", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "PMID,DOI or url" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Reference or method used in determining total organic carbon", + "title": "total organic carbon method", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "total organic carbon method" + ], + "is_a": "core field", + "string_serialization": "{PMID}|{DOI}|{URL}", + "slot_uri": "MIXS:0000337", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "tot_org_carb": { + "name": "tot_org_carb", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "gram Carbon per kilogram sample material" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content", + "title": "total organic carbon", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "total organic carbon" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000533", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "tot_part_carb": { + "name": "tot_part_carb", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "microgram per liter, micromole per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Total particulate carbon content", + "title": "total particulate carbon", + "examples": [ + { + "value": "35 micromole per liter" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "total particulate carbon" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000747", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "tot_phosp": { + "name": "tot_phosp", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per liter, milligram per liter, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus", + "title": "total phosphorus", + "examples": [ + { + "value": "0.03 milligram per liter" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "total phosphorus" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000117", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "tot_phosphate": { + "name": "tot_phosphate", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "microgram per liter, micromole per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Total amount or concentration of phosphate", + "title": "total phosphate", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "total phosphate" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000689", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "tot_sulfur": { + "name": "tot_sulfur", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milligram per liter, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of total sulfur in the sample", + "title": "total sulfur", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "total sulfur" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000419", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "train_line": { + "name": "train_line", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The subway line name", + "title": "train line", + "examples": [ + { + "value": "red" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "train line" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000837", + "domain_of": [ + "Biosample" + ], + "range": "train_line_enum", + "multivalued": false + }, + "train_stat_loc": { + "name": "train_stat_loc", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The train station collection location", + "title": "train station collection location", + "examples": [ + { + "value": "forest hills" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "train station collection location" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000838", + "domain_of": [ + "Biosample" + ], + "range": "train_stat_loc_enum", + "multivalued": false + }, + "train_stop_loc": { + "name": "train_stop_loc", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The train stop collection location", + "title": "train stop collection location", + "examples": [ + { + "value": "end" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "train stop collection location" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000839", + "domain_of": [ + "Biosample" + ], + "range": "train_stop_loc_enum", + "multivalued": false + }, + "turbidity": { + "name": "turbidity", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "formazin turbidity unit, formazin nephelometric units" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Measure of the amount of cloudiness or haziness in water caused by individual particles", + "title": "turbidity", + "examples": [ + { + "value": "0.3 nephelometric turbidity units" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "turbidity" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000191", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "tvdss_of_hcr_press": { + "name": "tvdss_of_hcr_press", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "meter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original pressure was measured (e.g. 1578 m).", + "title": "depth (TVDSS) of hydrocarbon resource pressure", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "depth (TVDSS) of hydrocarbon resource pressure" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000397", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "tvdss_of_hcr_temp": { + "name": "tvdss_of_hcr_temp", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "meter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original temperature was measured (e.g. 1345 m).", + "title": "depth (TVDSS) of hydrocarbon resource temperature", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "depth (TVDSS) of hydrocarbon resource temperature" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000394", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "typ_occup_density": { + "name": "typ_occup_density", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Customary or normal density of occupants", + "title": "typical occupant density", + "examples": [ + { + "value": "25" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "typical occupant density" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000771", + "domain_of": [ + "Biosample" + ], + "range": "double", + "multivalued": false + }, + "ventilation_rate": { + "name": "ventilation_rate", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "cubic meter per minute, liters per second" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Ventilation rate of the system in the sampled premises", + "title": "ventilation rate", + "examples": [ + { + "value": "750 cubic meter per minute" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "ventilation rate" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000114", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "ventilation_type": { + "name": "ventilation_type", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "ventilation type name" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Ventilation system used in the sampled premises", + "title": "ventilation type", + "examples": [ + { + "value": "Operable windows" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "ventilation type" + ], + "is_a": "core field", + "string_serialization": "{text}", + "slot_uri": "MIXS:0000756", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "vfa": { + "name": "vfa", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milligram per liter, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of Volatile Fatty Acids in the sample", + "title": "volatile fatty acids", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "volatile fatty acids" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000152", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "vfa_fw": { + "name": "vfa_fw", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milligram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Original volatile fatty acid concentration in the hydrocarbon resource", + "title": "vfa in formation water", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "vfa in formation water" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000408", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "vis_media": { + "name": "vis_media", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The building visual media", + "title": "visual media", + "examples": [ + { + "value": "3D scans" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "visual media" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000840", + "domain_of": [ + "Biosample" + ], + "range": "vis_media_enum", + "multivalued": false + }, + "viscosity": { + "name": "viscosity", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value;measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "cP at degree Celsius" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "A measure of oil's resistance¬†to gradual deformation by¬†shear stress¬†or¬†tensile stress (e.g. 3.5 cp; 100 ¬∞C)", + "title": "viscosity", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "viscosity" + ], + "is_a": "core field", + "string_serialization": "{float} {unit};{float} {unit}", + "slot_uri": "MIXS:0000126", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "volatile_org_comp": { + "name": "volatile_org_comp", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "volatile organic compound name;measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "microgram per cubic meter, parts per million, nanogram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Concentration of carbon-based chemicals that easily evaporate at room temperature; can report multiple volatile organic compounds by entering numeric values preceded by name of compound", + "title": "volatile organic compounds", + "examples": [ + { + "value": "formaldehyde;500 nanogram per liter" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "volatile organic compounds" + ], + "is_a": "core field", + "string_serialization": "{text};{float} {unit}", + "slot_uri": "MIXS:0000115", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "wall_area": { + "name": "wall_area", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "square meter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The total area of the sampled room's walls", + "title": "wall area", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "wall area" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000198", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "wall_const_type": { + "name": "wall_const_type", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The building class of the wall defined by the composition of the building elements and fire-resistance rating.", + "title": "wall construction type", + "examples": [ + { + "value": "fire resistive" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "wall construction type" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000841", + "domain_of": [ + "Biosample" + ], + "range": "wall_const_type_enum", + "multivalued": false + }, + "wall_finish_mat": { + "name": "wall_finish_mat", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The material utilized to finish the outer most layer of the wall", + "title": "wall finish material", + "examples": [ + { + "value": "wood" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "wall finish material" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000842", + "domain_of": [ + "Biosample" + ], + "range": "wall_finish_mat_enum", + "multivalued": false + }, + "wall_height": { + "name": "wall_height", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "centimeter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The average height of the walls in the sampled room", + "title": "wall height", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "wall height" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000221", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "wall_loc": { + "name": "wall_loc", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The relative location of the wall within the room", + "title": "wall location", + "examples": [ + { + "value": "north" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "wall location" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000843", + "domain_of": [ + "Biosample" + ], + "range": "wall_loc_enum", + "multivalued": false + }, + "wall_surf_treatment": { + "name": "wall_surf_treatment", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The surface treatment of interior wall", + "title": "wall surface treatment", + "examples": [ + { + "value": "paneling" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "wall surface treatment" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000845", + "domain_of": [ + "Biosample" + ], + "range": "wall_surf_treatment_enum", + "multivalued": false + }, + "wall_texture": { + "name": "wall_texture", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The feel, appearance, or consistency of a wall surface", + "title": "wall texture", + "examples": [ + { + "value": "popcorn" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "wall texture" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000846", + "domain_of": [ + "Biosample" + ], + "range": "wall_texture_enum", + "multivalued": false + }, + "wall_thermal_mass": { + "name": "wall_thermal_mass", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "joule per degree Celsius" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The ability of the wall to provide inertia against temperature fluctuations. Generally this means concrete or concrete block that is either exposed or covered only with paint", + "title": "wall thermal mass", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "wall thermal mass" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000222", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "wall_water_mold": { + "name": "wall_water_mold", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Signs of the presence of mold or mildew on a wall", + "title": "wall signs of water/mold", + "examples": [ + { + "value": "no presence of mold visible" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "wall signs of water/mold" + ], + "is_a": "core field", + "string_serialization": "[presence of mold visible|no presence of mold visible]", + "slot_uri": "MIXS:0000844", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "wastewater_type": { + "name": "wastewater_type", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "wastewater type name" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The origin of wastewater such as human waste, rainfall, storm drains, etc.", + "title": "wastewater type", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "wastewater type" + ], + "is_a": "core field", + "string_serialization": "{text}", + "slot_uri": "MIXS:0000353", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "water_cont_soil_meth": { + "name": "water_cont_soil_meth", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "PMID,DOI or url" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Reference or method used in determining the water content of soil", + "title": "water content method", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "water content method" + ], + "is_a": "core field", + "string_serialization": "{PMID}|{DOI}|{URL}", + "slot_uri": "MIXS:0000323", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "water_content": { + "name": "water_content", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "gram per gram or cubic centimeter per cubic centimeter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Water content measurement", + "title": "water content", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "water content" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000185", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "water_current": { + "name": "water_current", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "cubic meter per second, knots" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Measurement of magnitude and direction of flow within a fluid", + "title": "water current", + "examples": [ + { + "value": "10 cubic meter per second" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "water current" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000203", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "water_cut": { + "name": "water_cut", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "percent" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Current amount of water (%) in a produced fluid stream; or the average of the combined streams", + "title": "water cut", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "water cut" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000454", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "water_feat_size": { + "name": "water_feat_size", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "square meter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The size of the water feature", + "title": "water feature size", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "water feature size" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000223", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "water_feat_type": { + "name": "water_feat_type", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The type of water feature present within the building being sampled", + "title": "water feature type", + "examples": [ + { + "value": "stream" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "water feature type" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000847", + "domain_of": [ + "Biosample" + ], + "range": "water_feat_type_enum", + "multivalued": false + }, + "water_prod_rate": { + "name": "water_prod_rate", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "cubic meter per day" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Water production rates per well (e.g. 987 m3 / day)", + "title": "water production rate", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "water production rate" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000453", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "water_temp_regm": { + "name": "water_temp_regm", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value;treatment interval and duration" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "degree Celsius" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Information about treatment involving an exposure to water with varying degree of temperature, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens", + "title": "water temperature regimen", + "examples": [ + { + "value": "15 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "water temperature regimen" + ], + "is_a": "core field", + "string_serialization": "{float} {unit};{Rn/start_time/end_time/duration}", + "slot_uri": "MIXS:0000590", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "watering_regm": { + "name": "watering_regm", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value;treatment interval and duration" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milliliter, liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Information about treatment involving an exposure to watering frequencies, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens", + "title": "watering regimen", + "examples": [ + { + "value": "1 liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "watering regimen" + ], + "is_a": "core field", + "string_serialization": "{float} {unit};{Rn/start_time/end_time/duration}", + "slot_uri": "MIXS:0000591", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "weekday": { + "name": "weekday", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The day of the week when sampling occurred", + "title": "weekday", + "examples": [ + { + "value": "Sunday" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "weekday" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000848", + "domain_of": [ + "Biosample" + ], + "range": "weekday_enum", + "multivalued": false + }, + "win": { + "name": "win", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "text" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "A unique identifier of a well or wellbore. This is part of the Global Framework for Well Identification initiative which is compiled by the Professional Petroleum Data Management Association (PPDM) in an effort to improve well identification systems. (Supporting information: https://ppdm.org/ and http://dl.ppdm.org/dl/690)", + "title": "well identification number", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "well identification number" + ], + "is_a": "core field", + "string_serialization": "{text}", + "slot_uri": "MIXS:0000297", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "wind_direction": { + "name": "wind_direction", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "wind direction name" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Wind direction is the direction from which a wind originates", + "title": "wind direction", + "examples": [ + { + "value": "Northwest" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "wind direction" + ], + "is_a": "core field", + "string_serialization": "{text}", + "slot_uri": "MIXS:0000757", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "wind_speed": { + "name": "wind_speed", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "meter per second, kilometer per hour" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Speed of wind measured at the time of sampling", + "title": "wind speed", + "examples": [ + { + "value": "21 kilometer per hour" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "wind speed" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000118", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "window_cond": { + "name": "window_cond", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The physical condition of the window at the time of sampling", + "title": "window condition", + "examples": [ + { + "value": "rupture" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "window condition" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000849", + "domain_of": [ + "Biosample" + ], + "range": "window_cond_enum", + "multivalued": false + }, + "window_cover": { + "name": "window_cover", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The type of window covering", + "title": "window covering", + "examples": [ + { + "value": "curtains" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "window covering" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000850", + "domain_of": [ + "Biosample" + ], + "range": "window_cover_enum", + "multivalued": false + }, + "window_horiz_pos": { + "name": "window_horiz_pos", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The horizontal position of the window on the wall", + "title": "window horizontal position", + "examples": [ + { + "value": "middle" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "window horizontal position" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000851", + "domain_of": [ + "Biosample" + ], + "range": "window_horiz_pos_enum", + "multivalued": false + }, + "window_loc": { + "name": "window_loc", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The relative location of the window within the room", + "title": "window location", + "examples": [ + { + "value": "west" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "window location" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000852", + "domain_of": [ + "Biosample" + ], + "range": "window_loc_enum", + "multivalued": false + }, + "window_mat": { + "name": "window_mat", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The type of material used to finish a window", + "title": "window material", + "examples": [ + { + "value": "wood" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "window material" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000853", + "domain_of": [ + "Biosample" + ], + "range": "window_mat_enum", + "multivalued": false + }, + "window_open_freq": { + "name": "window_open_freq", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "value" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The number of times windows are opened per week", + "title": "window open frequency", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "window open frequency" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000246", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "window_size": { + "name": "window_size", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "inch, meter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The window's length and width", + "title": "window area/size", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "window area/size" + ], + "is_a": "core field", + "string_serialization": "{float} {unit} x {float} {unit}", + "slot_uri": "MIXS:0000224", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "window_status": { + "name": "window_status", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Defines whether the windows were open or closed during environmental testing", + "title": "window status", + "examples": [ + { + "value": "open" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "window status" + ], + "is_a": "core field", + "string_serialization": "[closed|open]", + "slot_uri": "MIXS:0000855", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "window_type": { + "name": "window_type", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The type of windows", + "title": "window type", + "examples": [ + { + "value": "fixed window" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "window type" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000856", + "domain_of": [ + "Biosample" + ], + "range": "window_type_enum", + "multivalued": false + }, + "window_vert_pos": { + "name": "window_vert_pos", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The vertical position of the window on the wall", + "title": "window vertical position", + "examples": [ + { + "value": "middle" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "window vertical position" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000857", + "domain_of": [ + "Biosample" + ], + "range": "window_vert_pos_enum", + "multivalued": false + }, + "window_water_mold": { + "name": "window_water_mold", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Signs of the presence of mold or mildew on the window.", + "title": "window signs of water/mold", + "examples": [ + { + "value": "no presence of mold visible" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "window signs of water/mold" + ], + "is_a": "core field", + "string_serialization": "[presence of mold visible|no presence of mold visible]", + "slot_uri": "MIXS:0000854", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "xylene": { + "name": "xylene", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milligram per liter, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of xylene in the sample", + "title": "xylene", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "aliases": [ + "xylene" + ], + "is_a": "core field", + "slot_uri": "MIXS:0000156", + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "zinc": { + "name": "zinc", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "mg/kg (ppm)" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of zinc in the sample", + "title": "zinc", + "examples": [ + { + "value": "2.5 mg/kg" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "see_also": [ + "https://www.ornl.gov/content/bio-scales-0" + ], + "aliases": [ + "zinc" + ], + "domain_of": [ + "Biosample" + ], + "range": "string", + "multivalued": false + }, + "alternative_identifiers": { + "name": "alternative_identifiers", + "description": "A list of alternative identifiers for the entity.", + "from_schema": "https://example.com/nmdc_submission_schema", + "domain_of": [ + "MetaboliteIdentification", + "NamedThing" + ], + "range": "uriorcurie", + "multivalued": true, + "pattern": "^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$" + }, + "core field": { + "name": "core field", + "description": "basic fields", + "from_schema": "https://example.com/nmdc_submission_schema", + "abstract": true, + "domain_of": [ + "Biosample" + ] + }, + "description": { + "name": "description", + "description": "a human-readable description of a thing", + "from_schema": "https://example.com/nmdc_submission_schema", + "slot_uri": "dcterms:description", + "domain_of": [ + "ImageValue", + "NamedThing" + ], + "range": "string", + "multivalued": false + }, + "environment field": { + "name": "environment field", + "description": "field describing environmental aspect of a sample", + "from_schema": "https://example.com/nmdc_submission_schema", + "abstract": true, + "domain_of": [ + "Biosample" + ] + }, + "gold_path_field": { + "name": "gold_path_field", + "annotations": { + "tooltip": { + "tag": "tooltip", + "value": "GOLD Ecosystem Classification paths describe the surroundings from which an environmental sample or an organism is collected.", + "annotations": { + "source": { + "tag": "source", + "value": "https://gold.jgi.doe.gov/ecosystem_classification" + } + } + } + }, + "description": "This is a grouping for any of the gold path fields", + "from_schema": "https://example.com/nmdc_submission_schema", + "abstract": true, + "range": "string", + "multivalued": false + }, + "id": { + "name": "id", + "description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", + "notes": [ + "abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?", + "a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters will be accepted", + "typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked via per-class id slot usage assertions", + "minting authority shoulders should probably be enumerated and checked in the pattern" + ], + "examples": [ + { + "value": "nmdc:mgmag-00-x012.1_7_c1", + "description": "https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "identifier": true, + "domain_of": [ + "NamedThing" + ], + "range": "uriorcurie", + "required": true, + "pattern": "^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$" + }, + "investigation field": { + "name": "investigation field", + "description": "field describing aspect of the investigation/study to which the sample belongs", + "from_schema": "https://example.com/nmdc_submission_schema", + "abstract": true, + "domain_of": [ + "Biosample" + ] + }, + "language": { + "name": "language", + "description": "Should use ISO 639-1 code e.g. \"en\", \"fr\"", + "from_schema": "https://example.com/nmdc_submission_schema", + "domain_of": [ + "TextValue" + ], + "range": "language code" + }, + "name": { + "name": "name", + "description": "A human readable label for an entity", + "from_schema": "https://example.com/nmdc_submission_schema", + "domain_of": [ + "PersonValue", + "NamedThing", + "Protocol" + ], + "range": "string", + "multivalued": false + }, + "nucleic acid sequence source field": { + "name": "nucleic acid sequence source field", + "from_schema": "https://example.com/nmdc_submission_schema", + "abstract": true, + "domain_of": [ + "Biosample" + ] + }, + "type": { + "name": "type", + "description": "the class_uri of the class that has been instantiated", + "notes": [ + "replaces legacy nmdc:type slot", + "makes it easier to read example data files", + "required for polymorphic MongoDB collections" + ], + "examples": [ + { + "value": "nmdc:Biosample" + }, + { + "value": "nmdc:Study" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/issues/1048", + "https://github.com/microbiomedata/nmdc-schema/issues/1233", + "https://github.com/microbiomedata/nmdc-schema/issues/248" + ], + "slot_uri": "rdf:type", + "designates_type": true, + "domain_of": [ + "EukEval", + "FunctionalAnnotationAggMember", + "MobilePhaseSegment", + "PortionOfSubstance", + "MagBin", + "MetaboliteIdentification", + "PeptideQuantification", + "ProteinQuantification", + "GenomeFeature", + "FunctionalAnnotation", + "AttributeValue", + "NamedThing", + "FailureCategorization", + "Protocol", + "CreditAssociation", + "Doi" + ], + "range": "uriorcurie", + "required": true + }, + "biomaterial_purity": { + "name": "biomaterial_purity", + "from_schema": "https://example.com/nmdc_submission_schema", + "range": "string", + "multivalued": false + } + }, + "classes": { + "AirInterface": { + "name": "AirInterface", + "annotations": { + "excel_worksheet_name": { + "tag": "excel_worksheet_name", + "value": "air" + } + }, + "description": "air dh_interface", + "title": "Air", + "from_schema": "https://example.com/nmdc_submission_schema", + "is_a": "DhInterface", + "mixins": [ + "DhMultiviewCommonColumnsMixin", + "SampIdNewTermsMixin" + ], + "slots": [ + "air_PM_concen", + "alt", + "barometric_press", + "carb_dioxide", + "carb_monoxide", + "chem_administration", + "collection_date", + "depth", + "ecosystem", + "ecosystem_category", + "ecosystem_subtype", + "ecosystem_type", + "elev", + "env_broad_scale", + "env_local_scale", + "env_medium", + "experimental_factor", + "geo_loc_name", + "humidity", + "lat_lon", + "methane", + "misc_param", + "organism_count", + "oxy_stat_samp", + "oxygen", + "perturbation", + "pollutants", + "salinity", + "samp_collec_device", + "samp_collec_method", + "samp_mat_process", + "samp_size", + "samp_store_dur", + "samp_store_loc", + "samp_store_temp", + "sample_link", + "size_frac", + "solar_irradiance", + "specific_ecosystem", + "temp", + "ventilation_rate", + "ventilation_type", + "volatile_org_comp", + "wind_direction", + "wind_speed" + ], + "slot_usage": { + "air_PM_concen": { + "name": "air_PM_concen", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "particulate matter name;measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micrograms per cubic meter" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Concentration of substances that remain suspended in the air, and comprise mixtures of organic and inorganic substances (PM10 and PM2.5); can report multiple PM's by entering numeric values preceded by name of PM", + "title": "air particulate matter concentration", + "examples": [ + { + "value": "PM2.5;10 microgram per cubic meter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "air particulate matter concentration" + ], + "rank": 48, + "is_a": "core field", + "string_serialization": "{text};{float} {unit}", + "slot_uri": "MIXS:0000108", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+\\|)*([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+)$" + }, + "alt": { + "name": "alt", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + } + }, + "description": "Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air", + "title": "altitude", + "examples": [ + { + "value": "100 meter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "altitude" + ], + "rank": 26, + "is_a": "environment field", + "slot_uri": "MIXS:0000094", + "owner": "Biosample", + "domain_of": [ + "agriculture", + "air", + "built environment", + "core", + "food-animal and animal feed", + "food-farm environment", + "food-food production facility", + "food-human foods", + "host-associated", + "human-associated", + "human-gut", + "human-oral", + "human-skin", + "human-vaginal", + "hydrocarbon resources-cores", + "hydrocarbon resources-fluids_swabs", + "microbial mat_biofilm", + "miscellaneous natural or artificial environment", + "plant-associated", + "sediment", + "soil", + "symbiont-associated", + "wastewater_sludge", + "water", + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HostAssociatedInterface", + "MiscEnvsInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "recommended": true, + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "barometric_press": { + "name": "barometric_press", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "millibar" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Force per unit area exerted against a surface by the weight of air above that surface", + "title": "barometric pressure", + "examples": [ + { + "value": "5 millibar" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "barometric pressure" + ], + "rank": 49, + "is_a": "core field", + "slot_uri": "MIXS:0000096", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "carb_dioxide": { + "name": "carb_dioxide", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per liter, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Carbon dioxide (gas) amount or concentration at the time of sampling", + "title": "carbon dioxide", + "examples": [ + { + "value": "410 parts per million" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "carbon dioxide" + ], + "rank": 50, + "is_a": "core field", + "slot_uri": "MIXS:0000097", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "carb_monoxide": { + "name": "carb_monoxide", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per liter, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Carbon monoxide (gas) amount or concentration at the time of sampling", + "title": "carbon monoxide", + "examples": [ + { + "value": "0.1 parts per million" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "carbon monoxide" + ], + "rank": 51, + "is_a": "core field", + "slot_uri": "MIXS:0000098", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "chem_administration": { + "name": "chem_administration", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "CHEBI;timestamp" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi", + "title": "chemical administration", + "examples": [ + { + "value": "agar [CHEBI:2509];2018-05-11|agar [CHEBI:2509];2018-05-22" + }, + { + "value": "agar [CHEBI:2509];2018-05" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "chemical administration" + ], + "rank": 17, + "is_a": "core field", + "string_serialization": "{termLabel} {[termID]};{timestamp}", + "slot_uri": "MIXS:0000751", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "recommended": true, + "multivalued": false, + "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\];([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$" + }, + "collection_date": { + "name": "collection_date", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "date and time" + } + }, + "description": "The date of sampling", + "title": "collection date", + "notes": [ + "MIxS collection_date accepts (truncated) ISO8601. DH taking arb prec date only", + "Use modified term (amended definition)" + ], + "examples": [ + { + "value": "2021-04-15" + }, + { + "value": "2021-04" + }, + { + "value": "2021" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "collection date" + ], + "rank": 3, + "is_a": "environment field", + "string_serialization": "{date, arbitrary precision}", + "slot_uri": "MIXS:0000011", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "required": true, + "multivalued": false, + "pattern": "^[12]\\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\\d|3[01]))?)?$" + }, + "depth": { + "name": "depth", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + } + }, + "description": "The vertical distance below local surface, e.g. for sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples.", + "title": "depth, meters", + "notes": [ + "Use modified term" + ], + "comments": [ + "All depths must be reported in meters. Provide the numerical portion only." + ], + "examples": [ + { + "value": "0 - 0.1" + }, + { + "value": "1" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "depth" + ], + "rank": 9, + "is_a": "environment field", + "string_serialization": "{float}|{float}-{float}", + "slot_uri": "MIXS:0000018", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "recommended": true, + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)?(\\s*-\\s*[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)?)?$" + }, + "ecosystem": { + "name": "ecosystem", + "description": "An ecosystem is a combination of a physical environment (abiotic factors) and all the organisms (biotic factors) that interact with this environment. Ecosystem is in position 1/5 in a GOLD path.", + "comments": [ + "The abiotic factors play a profound role on the type and composition of organisms in a given environment. The GOLD Ecosystem at the top of the five-level classification system is aimed at capturing the broader environment from which an organism or environmental sample is collected. The three broad groups under Ecosystem are Environmental, Host-associated, and Engineered. They represent samples collected from a natural environment or from another organism or from engineered environments like bioreactors respectively." + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "https://gold.jgi.doe.gov/help" + ], + "rank": 9, + "is_a": "gold_path_field", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "Study", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "EcosystemEnum", + "recommended": true + }, + "ecosystem_category": { + "name": "ecosystem_category", + "description": "Ecosystem categories represent divisions within the ecosystem based on specific characteristics of the environment from where an organism or sample is isolated. Ecosystem category is in position 2/5 in a GOLD path.", + "comments": [ + "The Environmental ecosystem (for example) is divided into Air, Aquatic and Terrestrial. Ecosystem categories for Host-associated samples can be individual hosts or phyla and for engineered samples it may be manipulated environments like bioreactors, solid waste etc." + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "https://gold.jgi.doe.gov/help" + ], + "rank": 10, + "is_a": "gold_path_field", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "Study", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "EcosystemCategoryEnum", + "recommended": true + }, + "ecosystem_subtype": { + "name": "ecosystem_subtype", + "description": "Ecosystem subtypes represent further subdivision of Ecosystem types into more distinct subtypes. Ecosystem subtype is in position 4/5 in a GOLD path.", + "comments": [ + "Ecosystem Type Marine (Environmental -> Aquatic -> Marine) is further divided (for example) into Intertidal zone, Coastal, Pelagic, Intertidal zone etc. in the Ecosystem subtype category." + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "https://gold.jgi.doe.gov/help" + ], + "rank": 12, + "is_a": "gold_path_field", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "Study", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "EcosystemSubtypeEnum", + "recommended": true + }, + "ecosystem_type": { + "name": "ecosystem_type", + "description": "Ecosystem types represent things having common characteristics within the Ecosystem Category. These common characteristics based grouping is still broad but specific to the characteristics of a given environment. Ecosystem type is in position 3/5 in a GOLD path.", + "comments": [ + "The Aquatic ecosystem category (for example) may have ecosystem types like Marine or Thermal springs etc. Ecosystem category Air may have Indoor air or Outdoor air as different Ecosystem Types. In the case of Host-associated samples, ecosystem type can represent Respiratory system, Digestive system, Roots etc." + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "https://gold.jgi.doe.gov/help" + ], + "rank": 11, + "is_a": "gold_path_field", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "Study", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "EcosystemTypeEnum", + "recommended": true + }, + "elev": { + "name": "elev", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + } + }, + "description": "Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit.", + "title": "elevation, meters", + "comments": [ + "All elevations must be reported in meters. Provide the numerical portion only.", + "Please use https://www.advancedconverter.com/map-tools/find-altitude-by-coordinates, if needed, to help estimate the elevation based on latitude and longitude coordinates." + ], + "examples": [ + { + "value": "225" + }, + { + "value": "0" + }, + { + "value": "1250" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "elevation" + ], + "rank": 6, + "is_a": "environment field", + "slot_uri": "MIXS:0000093", + "owner": "Biosample", + "domain_of": [ + "FieldResearchSite", + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "float", + "required": true, + "multivalued": false + }, + "env_broad_scale": { + "name": "env_broad_scale", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "The major environment type(s) where the sample was collected. Recommend subclasses of biome [ENVO:00000428]. Multiple terms can be separated by one or more pipes." + }, + "tooltip": { + "tag": "tooltip", + "value": "The biome or major environmental system where the sample or specimen originated. Choose values from subclasses of the 'biome' class [ENVO:00000428] in the Environment Ontology (ENVO). For host-associated or plant-associated samples, use terms from the UBERON or Plant Ontology to describe the broad anatomical or morphological context" + } + }, + "description": "In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO's biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html", + "title": "broad-scale environmental context", + "notes": [ + "range changed to enumeration late in makefile, so this is modified (but \"sample ID\" anyway)" + ], + "examples": [ + { + "value": "oceanic epipelagic zone biome [ENVO:01000033] for annotating a water sample from the photic zone in middle of the Atlantic Ocean" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "broad-scale environmental context" + ], + "rank": 6, + "is_a": "environment field", + "string_serialization": "{termLabel} {[termID]}", + "slot_uri": "MIXS:0000012", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "string", + "required": true, + "multivalued": false, + "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$" + }, + "env_local_scale": { + "name": "env_local_scale", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "Environmental entities having causal influences upon the entity at time of sampling." + }, + "tooltip": { + "tag": "tooltip", + "value": "The specific environmental entities or features near the sample or specimen that significantly influence its characteristics or composition. These entities are typically smaller in scale than the broad environmental context. Values for this field should be countable, material nouns and must be chosen from subclasses of BFO:0000040 (material entity) that appear in the Environment Ontology (ENVO). For host-associated or plant-associated samples, use terms from the UBERON or Plant Ontology to describe specific anatomical structures or plant parts." + } + }, + "description": "Report the entity or entities which are in the sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. We recommend using EnvO terms which are of smaller spatial grain than your entry for env_broad_scale. Terms, such as anatomical sites, from other OBO Library ontologies which interoperate with EnvO (e.g. UBERON) are accepted in this field. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS.", + "title": "local environmental context", + "notes": [ + "range changed to enumeration late in makefile, so this is modified (but \"sample ID\" anyway)" + ], + "examples": [ + { + "value": "canopy [ENVO:00000047]" + }, + { + "value": "herb and fern layer [ENVO:01000337]" + }, + { + "value": "litter layer [ENVO:01000338]" + }, + { + "value": "understory [01000335]" + }, + { + "value": "shrub layer [ENVO:01000336]" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "local environmental context" + ], + "rank": 7, + "is_a": "environment field", + "string_serialization": "{termLabel} {[termID]}", + "slot_uri": "MIXS:0000013", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "string", + "required": true, + "multivalued": false, + "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$" + }, + "env_medium": { + "name": "env_medium", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "The material displaced by the entity at time of sampling. Recommend subclasses of environmental material [ENVO:00010483]." + }, + "tooltip": { + "tag": "tooltip", + "value": "The predominant environmental material or substrate that directly surrounds or hosts the sample or specimen at the time of sampling. Choose values from subclasses of the 'environmental material' class [ENVO:00010483] in the Environment Ontology (ENVO). Values for this field should be measurable or mass material nouns, representing continuous environmental materials. For host-associated or plant-associated samples, use terms from the UBERON or Plant Ontology to indicate a tissue, organ, or plant structure" + } + }, + "description": "Report the environmental material(s) immediately surrounding the sample or specimen at the time of sampling. We recommend using subclasses of 'environmental material' (http://purl.obolibrary.org/obo/ENVO_00010483). EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS . Terms from other OBO ontologies are permissible as long as they reference mass/volume nouns (e.g. air, water, blood) and not discrete, countable entities (e.g. a tree, a leaf, a table top).", + "title": "environmental medium", + "notes": [ + "range changed to enumeration late in makefile, so this is modified (but \"sample ID\" anyway)" + ], + "examples": [ + { + "value": "soil [ENVO:00001998]" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "environmental medium" + ], + "rank": 8, + "is_a": "environment field", + "string_serialization": "{termLabel} {[termID]}", + "slot_uri": "MIXS:0000014", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "string", + "required": true, + "multivalued": false, + "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$" + }, + "experimental_factor": { + "name": "experimental_factor", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "text or EFO and/or OBI" + } + }, + "description": "Experimental factors are essentially the variable aspects of an experiment design which can be used to describe an experiment, or set of experiments, in an increasingly detailed manner. This field accepts ontology terms from Experimental Factor Ontology (EFO) and/or Ontology for Biomedical Investigations (OBI). For a browser of EFO (v 2.95) terms, please see http://purl.bioontology.org/ontology/EFO; for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI", + "title": "experimental factor", + "examples": [ + { + "value": "time series design [EFO:EFO_0001779]" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "experimental factor" + ], + "rank": 12, + "is_a": "investigation field", + "string_serialization": "{termLabel} {[termID]}|{text}", + "slot_uri": "MIXS:0000008", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false + }, + "geo_loc_name": { + "name": "geo_loc_name", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "country or sea name (INSDC or GAZ): region(GAZ), specific location name" + } + }, + "description": "The geographical origin of the sample as defined by the country or sea name followed by specific region name.", + "title": "geographic location (country and/or sea,region)", + "examples": [ + { + "value": "USA: Maryland, Bethesda" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "geographic location (country and/or sea,region)" + ], + "rank": 4, + "is_a": "environment field", + "string_serialization": "{text}: {text}, {text}", + "slot_uri": "MIXS:0000010", + "owner": "Biosample", + "domain_of": [ + "FieldResearchSite", + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "required": true, + "multivalued": false, + "pattern": "^[^:, ][^:]*: [^:, ][^,]*, [^:, ].*$" + }, + "humidity": { + "name": "humidity", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "gram per cubic meter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Amount of water vapour in the air, at the time of sampling", + "title": "humidity", + "examples": [ + { + "value": "25 gram per cubic meter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "humidity" + ], + "rank": 52, + "is_a": "core field", + "slot_uri": "MIXS:0000100", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "lat_lon": { + "name": "lat_lon", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "decimal degrees, limit to 8 decimal points" + } + }, + "description": "The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system", + "title": "geographic location (latitude and longitude)", + "notes": [ + "This is currently a required field but it's not clear if this should be required for human hosts" + ], + "examples": [ + { + "value": "50.586825 6.408977" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "geographic location (latitude and longitude)" + ], + "rank": 5, + "is_a": "environment field", + "string_serialization": "{lat lon}", + "slot_uri": "MIXS:0000009", + "owner": "Biosample", + "domain_of": [ + "FieldResearchSite", + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "required": true, + "multivalued": false, + "pattern": "^[-+]?([1-8]?\\d(\\.\\d{1,8})?|90(\\.0{1,8})?)\\s[-+]?(180(\\.0{1,8})?|((1[0-7]\\d)|([1-9]?\\d))(\\.\\d{1,8})?)$" + }, + "methane": { + "name": "methane", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per liter, parts per billion, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Methane (gas) amount or concentration at the time of sampling", + "title": "methane", + "examples": [ + { + "value": "1800 parts per billion" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "methane" + ], + "rank": 24, + "is_a": "core field", + "slot_uri": "MIXS:0000101", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "SedimentInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "misc_param": { + "name": "misc_param", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "parameter name;measurement value" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Any other measurement performed or parameter collected, that is not listed here", + "title": "miscellaneous parameter", + "examples": [ + { + "value": "Bicarbonate ion concentration;2075 micromole per kilogram" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "miscellaneous parameter" + ], + "rank": 23, + "is_a": "core field", + "string_serialization": "{text};{float} {unit}", + "slot_uri": "MIXS:0000752", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false, + "pattern": "^([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+\\|)*([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+)$" + }, + "organism_count": { + "name": "organism_count", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "organism name;measurement value;enumeration" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "number of cells per cubic meter, number of cells per milliliter, number of cells per cubic centimeter" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr)", + "title": "organism count", + "examples": [ + { + "value": "total prokaryotes;3.5e7 cells per milliliter;qPCR" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "organism count" + ], + "rank": 30, + "is_a": "core field", + "slot_uri": "MIXS:0000103", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^([-+]?[0-9]*\\.?[0-9]+ +\\S.*\\|)*([-+]?[0-9]*\\.?[0-9]+ +\\S.*)$" + }, + "oxy_stat_samp": { + "name": "oxy_stat_samp", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Oxygenation status of sample", + "title": "oxygenation status of sample", + "examples": [ + { + "value": "aerobic" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "oxygenation status of sample" + ], + "rank": 25, + "is_a": "core field", + "slot_uri": "MIXS:0000753", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_section", + "range": "OxyStatSampEnum", + "multivalued": false + }, + "oxygen": { + "name": "oxygen", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milligram per liter, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Oxygen (gas) amount or concentration at the time of sampling", + "title": "oxygen", + "examples": [ + { + "value": "600 parts per million" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "oxygen" + ], + "rank": 53, + "is_a": "core field", + "slot_uri": "MIXS:0000104", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "perturbation": { + "name": "perturbation", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "perturbation type name;perturbation interval and duration" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types", + "title": "perturbation", + "examples": [ + { + "value": "antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "perturbation" + ], + "rank": 33, + "is_a": "core field", + "string_serialization": "{text};{Rn/start_time/end_time/duration}", + "slot_uri": "MIXS:0000754", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "pollutants": { + "name": "pollutants", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "pollutant name;measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "gram, mole per liter, milligram per liter, microgram per cubic meter" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Pollutant types and, amount or concentrations measured at the time of sampling; can report multiple pollutants by entering numeric values preceded by name of pollutant", + "title": "pollutants", + "examples": [ + { + "value": "lead;0.15 microgram per cubic meter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "pollutants" + ], + "rank": 54, + "is_a": "core field", + "string_serialization": "{text};{float} {unit}", + "slot_uri": "MIXS:0000107", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+\\|)*([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+)$" + }, + "salinity": { + "name": "salinity", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "practical salinity unit, percentage" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The total concentration of all dissolved salts in a liquid or solid sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater.", + "title": "salinity", + "examples": [ + { + "value": "25 practical salinity unit" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "salinity" + ], + "rank": 54, + "is_a": "core field", + "slot_uri": "MIXS:0000183", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "samp_collec_device": { + "name": "samp_collec_device", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "device name" + } + }, + "description": "The device used to collect an environmental sample. This field accepts terms listed under environmental sampling device (http://purl.obolibrary.org/obo/ENVO). This field also accepts terms listed under specimen collection device (http://purl.obolibrary.org/obo/GENEPIO_0002094).", + "title": "sample collection device", + "comments": [ + "Report dimensions and details when applicable" + ], + "examples": [ + { + "value": "swab, biopsy, niskin bottle, push core, drag swab [GENEPIO:0002713]" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sample collection device" + ], + "rank": 14, + "is_a": "nucleic acid sequence source field", + "string_serialization": "{termLabel} {[termID]}|{text}", + "slot_uri": "MIXS:0000002", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "recommended": true, + "multivalued": false + }, + "samp_collec_method": { + "name": "samp_collec_method", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "PMID,DOI,url , or text" + } + }, + "description": "The method employed for collecting the sample.", + "title": "sample collection method", + "comments": [ + "This can be a citation or description" + ], + "examples": [ + { + "value": "swabbing" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sample collection method" + ], + "rank": 15, + "is_a": "nucleic acid sequence source field", + "string_serialization": "{PMID}|{DOI}|{URL}|{text}", + "slot_uri": "MIXS:0001225", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "multivalued": false + }, + "samp_mat_process": { + "name": "samp_mat_process", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "text" + } + }, + "description": "A brief description of any processing applied to the sample during or after retrieving the sample from environment, or a link to the relevant protocol(s) performed.", + "title": "sample material processing", + "examples": [ + { + "value": "filtering of seawater" + }, + { + "value": "storing samples in ethanol" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sample material processing" + ], + "rank": 12, + "is_a": "nucleic acid sequence source field", + "string_serialization": "{text}", + "slot_uri": "MIXS:0000016", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "multivalued": false + }, + "samp_size": { + "name": "samp_size", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "millliter, gram, milligram, liter" + } + }, + "description": "The total amount or size (volume (ml), mass (g) or area (m2) ) of sample collected.", + "title": "amount or size of sample collected", + "comments": [ + "This refers to the TOTAL amount of sample collected from the experiment. NOT the amount sent to each institution or collected for a specific analysis." + ], + "examples": [ + { + "value": "5 grams" + }, + { + "value": "10 mL" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "amount or size of sample collected" + ], + "rank": 18, + "is_a": "nucleic acid sequence source field", + "string_serialization": "{float} {unit}", + "slot_uri": "MIXS:0000001", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? \\S+$" + }, + "samp_store_dur": { + "name": "samp_store_dur", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "duration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Duration for which the sample was stored", + "title": "sample storage duration", + "examples": [ + { + "value": "P1Y6M" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sample storage duration" + ], + "rank": 353, + "is_a": "core field", + "string_serialization": "{duration}", + "slot_uri": "MIXS:0000116", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "samp_store_loc": { + "name": "samp_store_loc", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "location name" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Location at which sample was stored, usually name of a specific freezer/room", + "title": "sample storage location", + "examples": [ + { + "value": "Freezer no:5" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sample storage location" + ], + "rank": 41, + "is_a": "core field", + "string_serialization": "{text}", + "slot_uri": "MIXS:0000755", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "samp_store_temp": { + "name": "samp_store_temp", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "degree Celsius" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Temperature at which the sample was stored (degrees are assumed)", + "title": "sample storage temperature", + "examples": [ + { + "value": "-80 Celsius" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sample storage temperature" + ], + "rank": 7, + "is_a": "core field", + "slot_uri": "MIXS:0000110", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "required": true, + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "sample_link": { + "name": "sample_link", + "description": "A unique identifier to assign parent-child, subsample, or sibling samples. This is relevant when a sample or other material was used to generate the new sample.", + "title": "sample linkage", + "notes": [ + "also tempted to include SampIdNewTermsMixin but if len(slot_usage.keys()) > 1 and \"placeholder\" in slot_usage.keys():AttributeError: 'list' object has no attribute 'keys'" + ], + "comments": [ + "This field allows multiple entries separated by ; (Examples: Soil collected from the field will link with the soil used in an incubation. The soil a plant was grown in links to the plant sample. An original culture sample was transferred to a new vial and generated a new sample)" + ], + "examples": [ + { + "value": "IGSN:DSJ0284" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "rank": 5, + "string_serialization": "{text}:{text}", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface", + "SampIdNewTermsMixin" + ], + "slot_group": "sample_id_section", + "range": "string", + "recommended": true, + "multivalued": false, + "pattern": "[^\\:\\n\\r]+\\:[^\\:\\n\\r]+" + }, + "size_frac": { + "name": "size_frac", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "filter size value range" + } + }, + "description": "Filtering pore size used in sample preparation", + "title": "size fraction selected", + "examples": [ + { + "value": "0-0.22 micrometer" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "size fraction selected" + ], + "rank": 285, + "is_a": "nucleic acid sequence source field", + "string_serialization": "{float}-{float} {unit}", + "slot_uri": "MIXS:0000017", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "solar_irradiance": { + "name": "solar_irradiance", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "kilowatts per square meter per day, ergs per square centimeter per second" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The amount of solar energy that arrives at a specific area of a surface during a specific time interval", + "title": "solar irradiance", + "examples": [ + { + "value": "1.36 kilowatts per square meter per day" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "solar irradiance" + ], + "rank": 55, + "is_a": "core field", + "slot_uri": "MIXS:0000112", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "specific_ecosystem": { + "name": "specific_ecosystem", + "description": "Specific ecosystems represent specific features of the environment like aphotic zone in an ocean or gastric mucosa within a host digestive system. Specific ecosystem is in position 5/5 in a GOLD path.", + "comments": [ + "Specific ecosystems help to define samples based on very specific characteristics of an environment under the five-level classification system." + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "https://gold.jgi.doe.gov/help" + ], + "rank": 13, + "is_a": "gold_path_field", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "Study", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "SpecificEcosystemEnum", + "recommended": true + }, + "temp": { + "name": "temp", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "degree Celsius" + } + }, + "description": "Temperature of the sample at the time of sampling.", + "title": "temperature", + "examples": [ + { + "value": "25 degree Celsius" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "temperature" + ], + "rank": 37, + "is_a": "environment field", + "slot_uri": "MIXS:0000113", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "ventilation_rate": { + "name": "ventilation_rate", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "cubic meter per minute, liters per second" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Ventilation rate of the system in the sampled premises", + "title": "ventilation rate", + "examples": [ + { + "value": "750 cubic meter per minute" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "ventilation rate" + ], + "rank": 56, + "is_a": "core field", + "slot_uri": "MIXS:0000114", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "ventilation_type": { + "name": "ventilation_type", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "ventilation type name" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Ventilation system used in the sampled premises", + "title": "ventilation type", + "examples": [ + { + "value": "Operable windows" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "ventilation type" + ], + "rank": 57, + "is_a": "core field", + "string_serialization": "{text}", + "slot_uri": "MIXS:0000756", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "volatile_org_comp": { + "name": "volatile_org_comp", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "volatile organic compound name;measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "microgram per cubic meter, parts per million, nanogram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Concentration of carbon-based chemicals that easily evaporate at room temperature; can report multiple volatile organic compounds by entering numeric values preceded by name of compound", + "title": "volatile organic compounds", + "examples": [ + { + "value": "formaldehyde;500 nanogram per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "volatile organic compounds" + ], + "rank": 58, + "is_a": "core field", + "string_serialization": "{text};{float} {unit}", + "slot_uri": "MIXS:0000115", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+\\|)*([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+)$" + }, + "wind_direction": { + "name": "wind_direction", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "wind direction name" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Wind direction is the direction from which a wind originates", + "title": "wind direction", + "examples": [ + { + "value": "Northwest" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "wind direction" + ], + "rank": 59, + "is_a": "core field", + "string_serialization": "{text}", + "slot_uri": "MIXS:0000757", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "wind_speed": { + "name": "wind_speed", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "meter per second, kilometer per hour" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Speed of wind measured at the time of sampling", + "title": "wind speed", + "examples": [ + { + "value": "21 kilometer per hour" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "wind speed" + ], + "rank": 60, + "is_a": "core field", + "slot_uri": "MIXS:0000118", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "horizon_meth": { + "name": "horizon_meth", + "title": "horizon method" + } + }, + "attributes": { + "air_PM_concen": { + "name": "air_PM_concen", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "particulate matter name;measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micrograms per cubic meter" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Concentration of substances that remain suspended in the air, and comprise mixtures of organic and inorganic substances (PM10 and PM2.5); can report multiple PM's by entering numeric values preceded by name of PM", + "title": "air particulate matter concentration", + "examples": [ + { + "value": "PM2.5;10 microgram per cubic meter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "air particulate matter concentration" + ], + "rank": 48, + "is_a": "core field", + "string_serialization": "{text};{float} {unit}", + "slot_uri": "MIXS:0000108", + "alias": "air_PM_concen", + "owner": "AirInterface", + "domain_of": [ + "Biosample", + "AirInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+\\|)*([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+)$" + }, + "alt": { + "name": "alt", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + } + }, + "description": "Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air", + "title": "altitude", + "examples": [ + { + "value": "100 meter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "altitude" + ], + "rank": 26, + "is_a": "environment field", + "slot_uri": "MIXS:0000094", + "alias": "alt", + "owner": "AirInterface", + "domain_of": [ + "agriculture", + "air", + "built environment", + "core", + "food-animal and animal feed", + "food-farm environment", + "food-food production facility", + "food-human foods", + "host-associated", + "human-associated", + "human-gut", + "human-oral", + "human-skin", + "human-vaginal", + "hydrocarbon resources-cores", + "hydrocarbon resources-fluids_swabs", + "microbial mat_biofilm", + "miscellaneous natural or artificial environment", + "plant-associated", + "sediment", + "soil", + "symbiont-associated", + "wastewater_sludge", + "water", + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HostAssociatedInterface", + "MiscEnvsInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "recommended": true, + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "barometric_press": { + "name": "barometric_press", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "millibar" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Force per unit area exerted against a surface by the weight of air above that surface", + "title": "barometric pressure", + "examples": [ + { + "value": "5 millibar" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "barometric pressure" + ], + "rank": 49, + "is_a": "core field", + "slot_uri": "MIXS:0000096", + "alias": "barometric_press", + "owner": "AirInterface", + "domain_of": [ + "Biosample", + "AirInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "carb_dioxide": { + "name": "carb_dioxide", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per liter, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Carbon dioxide (gas) amount or concentration at the time of sampling", + "title": "carbon dioxide", + "examples": [ + { + "value": "410 parts per million" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "carbon dioxide" + ], + "rank": 50, + "is_a": "core field", + "slot_uri": "MIXS:0000097", + "alias": "carb_dioxide", + "owner": "AirInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "carb_monoxide": { + "name": "carb_monoxide", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per liter, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Carbon monoxide (gas) amount or concentration at the time of sampling", + "title": "carbon monoxide", + "examples": [ + { + "value": "0.1 parts per million" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "carbon monoxide" + ], + "rank": 51, + "is_a": "core field", + "slot_uri": "MIXS:0000098", + "alias": "carb_monoxide", + "owner": "AirInterface", + "domain_of": [ + "Biosample", + "AirInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "chem_administration": { + "name": "chem_administration", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "CHEBI;timestamp" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi", + "title": "chemical administration", + "examples": [ + { + "value": "agar [CHEBI:2509];2018-05-11|agar [CHEBI:2509];2018-05-22" + }, + { + "value": "agar [CHEBI:2509];2018-05" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "chemical administration" + ], + "rank": 17, + "is_a": "core field", + "string_serialization": "{termLabel} {[termID]};{timestamp}", + "slot_uri": "MIXS:0000751", + "alias": "chem_administration", + "owner": "AirInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "recommended": true, + "multivalued": false, + "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\];([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$" + }, + "collection_date": { + "name": "collection_date", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "date and time" + } + }, + "description": "The date of sampling", + "title": "collection date", + "notes": [ + "MIxS collection_date accepts (truncated) ISO8601. DH taking arb prec date only", + "Use modified term (amended definition)" + ], + "examples": [ + { + "value": "2021-04-15" + }, + { + "value": "2021-04" + }, + { + "value": "2021" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "collection date" + ], + "rank": 3, + "is_a": "environment field", + "string_serialization": "{date, arbitrary precision}", + "slot_uri": "MIXS:0000011", + "alias": "collection_date", + "owner": "AirInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "required": true, + "multivalued": false, + "pattern": "^[12]\\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\\d|3[01]))?)?$" + }, + "depth": { + "name": "depth", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + } + }, + "description": "The vertical distance below local surface, e.g. for sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples.", + "title": "depth, meters", + "notes": [ + "Use modified term" + ], + "comments": [ + "All depths must be reported in meters. Provide the numerical portion only." + ], + "examples": [ + { + "value": "0 - 0.1" + }, + { + "value": "1" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "depth" + ], + "rank": 9, + "is_a": "environment field", + "string_serialization": "{float}|{float}-{float}", + "slot_uri": "MIXS:0000018", + "alias": "depth", + "owner": "AirInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "recommended": true, + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)?(\\s*-\\s*[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)?)?$" + }, + "ecosystem": { + "name": "ecosystem", + "description": "An ecosystem is a combination of a physical environment (abiotic factors) and all the organisms (biotic factors) that interact with this environment. Ecosystem is in position 1/5 in a GOLD path.", + "comments": [ + "The abiotic factors play a profound role on the type and composition of organisms in a given environment. The GOLD Ecosystem at the top of the five-level classification system is aimed at capturing the broader environment from which an organism or environmental sample is collected. The three broad groups under Ecosystem are Environmental, Host-associated, and Engineered. They represent samples collected from a natural environment or from another organism or from engineered environments like bioreactors respectively." + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "https://gold.jgi.doe.gov/help" + ], + "rank": 9, + "is_a": "gold_path_field", + "alias": "ecosystem", + "owner": "AirInterface", + "domain_of": [ + "Biosample", + "Study", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "EcosystemEnum", + "recommended": true + }, + "ecosystem_category": { + "name": "ecosystem_category", + "description": "Ecosystem categories represent divisions within the ecosystem based on specific characteristics of the environment from where an organism or sample is isolated. Ecosystem category is in position 2/5 in a GOLD path.", + "comments": [ + "The Environmental ecosystem (for example) is divided into Air, Aquatic and Terrestrial. Ecosystem categories for Host-associated samples can be individual hosts or phyla and for engineered samples it may be manipulated environments like bioreactors, solid waste etc." + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "https://gold.jgi.doe.gov/help" + ], + "rank": 10, + "is_a": "gold_path_field", + "alias": "ecosystem_category", + "owner": "AirInterface", + "domain_of": [ + "Biosample", + "Study", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "EcosystemCategoryEnum", + "recommended": true + }, + "ecosystem_subtype": { + "name": "ecosystem_subtype", + "description": "Ecosystem subtypes represent further subdivision of Ecosystem types into more distinct subtypes. Ecosystem subtype is in position 4/5 in a GOLD path.", + "comments": [ + "Ecosystem Type Marine (Environmental -> Aquatic -> Marine) is further divided (for example) into Intertidal zone, Coastal, Pelagic, Intertidal zone etc. in the Ecosystem subtype category." + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "https://gold.jgi.doe.gov/help" + ], + "rank": 12, + "is_a": "gold_path_field", + "alias": "ecosystem_subtype", + "owner": "AirInterface", + "domain_of": [ + "Biosample", + "Study", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "EcosystemSubtypeEnum", + "recommended": true + }, + "ecosystem_type": { + "name": "ecosystem_type", + "description": "Ecosystem types represent things having common characteristics within the Ecosystem Category. These common characteristics based grouping is still broad but specific to the characteristics of a given environment. Ecosystem type is in position 3/5 in a GOLD path.", + "comments": [ + "The Aquatic ecosystem category (for example) may have ecosystem types like Marine or Thermal springs etc. Ecosystem category Air may have Indoor air or Outdoor air as different Ecosystem Types. In the case of Host-associated samples, ecosystem type can represent Respiratory system, Digestive system, Roots etc." + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "https://gold.jgi.doe.gov/help" + ], + "rank": 11, + "is_a": "gold_path_field", + "alias": "ecosystem_type", + "owner": "AirInterface", + "domain_of": [ + "Biosample", + "Study", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "EcosystemTypeEnum", + "recommended": true + }, + "elev": { + "name": "elev", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + } + }, + "description": "Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit.", + "title": "elevation, meters", + "comments": [ + "All elevations must be reported in meters. Provide the numerical portion only.", + "Please use https://www.advancedconverter.com/map-tools/find-altitude-by-coordinates, if needed, to help estimate the elevation based on latitude and longitude coordinates." + ], + "examples": [ + { + "value": "225" + }, + { + "value": "0" + }, + { + "value": "1250" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "elevation" + ], + "rank": 6, + "is_a": "environment field", + "slot_uri": "MIXS:0000093", + "alias": "elev", + "owner": "AirInterface", + "domain_of": [ + "FieldResearchSite", + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "float", + "required": true, + "multivalued": false + }, + "env_broad_scale": { + "name": "env_broad_scale", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "The major environment type(s) where the sample was collected. Recommend subclasses of biome [ENVO:00000428]. Multiple terms can be separated by one or more pipes." + }, + "tooltip": { + "tag": "tooltip", + "value": "The biome or major environmental system where the sample or specimen originated. Choose values from subclasses of the 'biome' class [ENVO:00000428] in the Environment Ontology (ENVO). For host-associated or plant-associated samples, use terms from the UBERON or Plant Ontology to describe the broad anatomical or morphological context" + } + }, + "description": "In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO's biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html", + "title": "broad-scale environmental context", + "notes": [ + "range changed to enumeration late in makefile, so this is modified (but \"sample ID\" anyway)" + ], + "examples": [ + { + "value": "oceanic epipelagic zone biome [ENVO:01000033] for annotating a water sample from the photic zone in middle of the Atlantic Ocean" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "broad-scale environmental context" + ], + "rank": 6, + "is_a": "environment field", + "string_serialization": "{termLabel} {[termID]}", + "slot_uri": "MIXS:0000012", + "alias": "env_broad_scale", + "owner": "AirInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "string", + "required": true, + "multivalued": false, + "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$" + }, + "env_local_scale": { + "name": "env_local_scale", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "Environmental entities having causal influences upon the entity at time of sampling." + }, + "tooltip": { + "tag": "tooltip", + "value": "The specific environmental entities or features near the sample or specimen that significantly influence its characteristics or composition. These entities are typically smaller in scale than the broad environmental context. Values for this field should be countable, material nouns and must be chosen from subclasses of BFO:0000040 (material entity) that appear in the Environment Ontology (ENVO). For host-associated or plant-associated samples, use terms from the UBERON or Plant Ontology to describe specific anatomical structures or plant parts." + } + }, + "description": "Report the entity or entities which are in the sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. We recommend using EnvO terms which are of smaller spatial grain than your entry for env_broad_scale. Terms, such as anatomical sites, from other OBO Library ontologies which interoperate with EnvO (e.g. UBERON) are accepted in this field. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS.", + "title": "local environmental context", + "notes": [ + "range changed to enumeration late in makefile, so this is modified (but \"sample ID\" anyway)" + ], + "examples": [ + { + "value": "canopy [ENVO:00000047]" + }, + { + "value": "herb and fern layer [ENVO:01000337]" + }, + { + "value": "litter layer [ENVO:01000338]" + }, + { + "value": "understory [01000335]" + }, + { + "value": "shrub layer [ENVO:01000336]" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "local environmental context" + ], + "rank": 7, + "is_a": "environment field", + "string_serialization": "{termLabel} {[termID]}", + "slot_uri": "MIXS:0000013", + "alias": "env_local_scale", + "owner": "AirInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "string", + "required": true, + "multivalued": false, + "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$" + }, + "env_medium": { + "name": "env_medium", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "The material displaced by the entity at time of sampling. Recommend subclasses of environmental material [ENVO:00010483]." + }, + "tooltip": { + "tag": "tooltip", + "value": "The predominant environmental material or substrate that directly surrounds or hosts the sample or specimen at the time of sampling. Choose values from subclasses of the 'environmental material' class [ENVO:00010483] in the Environment Ontology (ENVO). Values for this field should be measurable or mass material nouns, representing continuous environmental materials. For host-associated or plant-associated samples, use terms from the UBERON or Plant Ontology to indicate a tissue, organ, or plant structure" + } + }, + "description": "Report the environmental material(s) immediately surrounding the sample or specimen at the time of sampling. We recommend using subclasses of 'environmental material' (http://purl.obolibrary.org/obo/ENVO_00010483). EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS . Terms from other OBO ontologies are permissible as long as they reference mass/volume nouns (e.g. air, water, blood) and not discrete, countable entities (e.g. a tree, a leaf, a table top).", + "title": "environmental medium", + "notes": [ + "range changed to enumeration late in makefile, so this is modified (but \"sample ID\" anyway)" + ], + "examples": [ + { + "value": "soil [ENVO:00001998]" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "environmental medium" + ], + "rank": 8, + "is_a": "environment field", + "string_serialization": "{termLabel} {[termID]}", + "slot_uri": "MIXS:0000014", + "alias": "env_medium", + "owner": "AirInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "string", + "required": true, + "multivalued": false, + "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$" + }, + "experimental_factor": { + "name": "experimental_factor", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "text or EFO and/or OBI" + } + }, + "description": "Experimental factors are essentially the variable aspects of an experiment design which can be used to describe an experiment, or set of experiments, in an increasingly detailed manner. This field accepts ontology terms from Experimental Factor Ontology (EFO) and/or Ontology for Biomedical Investigations (OBI). For a browser of EFO (v 2.95) terms, please see http://purl.bioontology.org/ontology/EFO; for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI", + "title": "experimental factor", + "examples": [ + { + "value": "time series design [EFO:EFO_0001779]" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "experimental factor" + ], + "rank": 12, + "is_a": "investigation field", + "string_serialization": "{termLabel} {[termID]}|{text}", + "slot_uri": "MIXS:0000008", + "alias": "experimental_factor", + "owner": "AirInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false + }, + "geo_loc_name": { + "name": "geo_loc_name", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "country or sea name (INSDC or GAZ): region(GAZ), specific location name" + } + }, + "description": "The geographical origin of the sample as defined by the country or sea name followed by specific region name.", + "title": "geographic location (country and/or sea,region)", + "examples": [ + { + "value": "USA: Maryland, Bethesda" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "geographic location (country and/or sea,region)" + ], + "rank": 4, + "is_a": "environment field", + "string_serialization": "{text}: {text}, {text}", + "slot_uri": "MIXS:0000010", + "alias": "geo_loc_name", + "owner": "AirInterface", + "domain_of": [ + "FieldResearchSite", + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "required": true, + "multivalued": false, + "pattern": "^[^:, ][^:]*: [^:, ][^,]*, [^:, ].*$" + }, + "humidity": { + "name": "humidity", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "gram per cubic meter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Amount of water vapour in the air, at the time of sampling", + "title": "humidity", + "examples": [ + { + "value": "25 gram per cubic meter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "humidity" + ], + "rank": 52, + "is_a": "core field", + "slot_uri": "MIXS:0000100", + "alias": "humidity", + "owner": "AirInterface", + "domain_of": [ + "Biosample", + "AirInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "lat_lon": { + "name": "lat_lon", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "decimal degrees, limit to 8 decimal points" + } + }, + "description": "The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system", + "title": "geographic location (latitude and longitude)", + "notes": [ + "This is currently a required field but it's not clear if this should be required for human hosts" + ], + "examples": [ + { + "value": "50.586825 6.408977" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "geographic location (latitude and longitude)" + ], + "rank": 5, + "is_a": "environment field", + "string_serialization": "{lat lon}", + "slot_uri": "MIXS:0000009", + "alias": "lat_lon", + "owner": "AirInterface", + "domain_of": [ + "FieldResearchSite", + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "required": true, + "multivalued": false, + "pattern": "^[-+]?([1-8]?\\d(\\.\\d{1,8})?|90(\\.0{1,8})?)\\s[-+]?(180(\\.0{1,8})?|((1[0-7]\\d)|([1-9]?\\d))(\\.\\d{1,8})?)$" + }, + "methane": { + "name": "methane", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per liter, parts per billion, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Methane (gas) amount or concentration at the time of sampling", + "title": "methane", + "examples": [ + { + "value": "1800 parts per billion" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "methane" + ], + "rank": 24, + "is_a": "core field", + "slot_uri": "MIXS:0000101", + "alias": "methane", + "owner": "AirInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "SedimentInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "misc_param": { + "name": "misc_param", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "parameter name;measurement value" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Any other measurement performed or parameter collected, that is not listed here", + "title": "miscellaneous parameter", + "examples": [ + { + "value": "Bicarbonate ion concentration;2075 micromole per kilogram" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "miscellaneous parameter" + ], + "rank": 23, + "is_a": "core field", + "string_serialization": "{text};{float} {unit}", + "slot_uri": "MIXS:0000752", + "alias": "misc_param", + "owner": "AirInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false, + "pattern": "^([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+\\|)*([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+)$" + }, + "organism_count": { + "name": "organism_count", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "organism name;measurement value;enumeration" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "number of cells per cubic meter, number of cells per milliliter, number of cells per cubic centimeter" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr)", + "title": "organism count", + "examples": [ + { + "value": "total prokaryotes;3.5e7 cells per milliliter;qPCR" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "organism count" + ], + "rank": 30, + "is_a": "core field", + "slot_uri": "MIXS:0000103", + "alias": "organism_count", + "owner": "AirInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^([-+]?[0-9]*\\.?[0-9]+ +\\S.*\\|)*([-+]?[0-9]*\\.?[0-9]+ +\\S.*)$" + }, + "oxy_stat_samp": { + "name": "oxy_stat_samp", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Oxygenation status of sample", + "title": "oxygenation status of sample", + "examples": [ + { + "value": "aerobic" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "oxygenation status of sample" + ], + "rank": 25, + "is_a": "core field", + "slot_uri": "MIXS:0000753", + "alias": "oxy_stat_samp", + "owner": "AirInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_section", + "range": "OxyStatSampEnum", + "multivalued": false + }, + "oxygen": { + "name": "oxygen", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milligram per liter, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Oxygen (gas) amount or concentration at the time of sampling", + "title": "oxygen", + "examples": [ + { + "value": "600 parts per million" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "oxygen" + ], + "rank": 53, + "is_a": "core field", + "slot_uri": "MIXS:0000104", + "alias": "oxygen", + "owner": "AirInterface", + "domain_of": [ + "Biosample", + "AirInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "perturbation": { + "name": "perturbation", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "perturbation type name;perturbation interval and duration" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types", + "title": "perturbation", + "examples": [ + { + "value": "antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "perturbation" + ], + "rank": 33, + "is_a": "core field", + "string_serialization": "{text};{Rn/start_time/end_time/duration}", + "slot_uri": "MIXS:0000754", + "alias": "perturbation", + "owner": "AirInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "pollutants": { + "name": "pollutants", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "pollutant name;measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "gram, mole per liter, milligram per liter, microgram per cubic meter" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Pollutant types and, amount or concentrations measured at the time of sampling; can report multiple pollutants by entering numeric values preceded by name of pollutant", + "title": "pollutants", + "examples": [ + { + "value": "lead;0.15 microgram per cubic meter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "pollutants" + ], + "rank": 54, + "is_a": "core field", + "string_serialization": "{text};{float} {unit}", + "slot_uri": "MIXS:0000107", + "alias": "pollutants", + "owner": "AirInterface", + "domain_of": [ + "Biosample", + "AirInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+\\|)*([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+)$" + }, + "salinity": { + "name": "salinity", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "practical salinity unit, percentage" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The total concentration of all dissolved salts in a liquid or solid sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater.", + "title": "salinity", + "examples": [ + { + "value": "25 practical salinity unit" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "salinity" + ], + "rank": 54, + "is_a": "core field", + "slot_uri": "MIXS:0000183", + "alias": "salinity", + "owner": "AirInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "samp_collec_device": { + "name": "samp_collec_device", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "device name" + } + }, + "description": "The device used to collect an environmental sample. This field accepts terms listed under environmental sampling device (http://purl.obolibrary.org/obo/ENVO). This field also accepts terms listed under specimen collection device (http://purl.obolibrary.org/obo/GENEPIO_0002094).", + "title": "sample collection device", + "comments": [ + "Report dimensions and details when applicable" + ], + "examples": [ + { + "value": "swab, biopsy, niskin bottle, push core, drag swab [GENEPIO:0002713]" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sample collection device" + ], + "rank": 14, + "is_a": "nucleic acid sequence source field", + "string_serialization": "{termLabel} {[termID]}|{text}", + "slot_uri": "MIXS:0000002", + "alias": "samp_collec_device", + "owner": "AirInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "recommended": true, + "multivalued": false + }, + "samp_collec_method": { + "name": "samp_collec_method", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "PMID,DOI,url , or text" + } + }, + "description": "The method employed for collecting the sample.", + "title": "sample collection method", + "comments": [ + "This can be a citation or description" + ], + "examples": [ + { + "value": "swabbing" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sample collection method" + ], + "rank": 15, + "is_a": "nucleic acid sequence source field", + "string_serialization": "{PMID}|{DOI}|{URL}|{text}", + "slot_uri": "MIXS:0001225", + "alias": "samp_collec_method", + "owner": "AirInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "multivalued": false + }, + "samp_mat_process": { + "name": "samp_mat_process", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "text" + } + }, + "description": "A brief description of any processing applied to the sample during or after retrieving the sample from environment, or a link to the relevant protocol(s) performed.", + "title": "sample material processing", + "examples": [ + { + "value": "filtering of seawater" + }, + { + "value": "storing samples in ethanol" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sample material processing" + ], + "rank": 12, + "is_a": "nucleic acid sequence source field", + "string_serialization": "{text}", + "slot_uri": "MIXS:0000016", + "alias": "samp_mat_process", + "owner": "AirInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "multivalued": false + }, + "samp_size": { + "name": "samp_size", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "millliter, gram, milligram, liter" + } + }, + "description": "The total amount or size (volume (ml), mass (g) or area (m2) ) of sample collected.", + "title": "amount or size of sample collected", + "comments": [ + "This refers to the TOTAL amount of sample collected from the experiment. NOT the amount sent to each institution or collected for a specific analysis." + ], + "examples": [ + { + "value": "5 grams" + }, + { + "value": "10 mL" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "amount or size of sample collected" + ], + "rank": 18, + "is_a": "nucleic acid sequence source field", + "string_serialization": "{float} {unit}", + "slot_uri": "MIXS:0000001", + "alias": "samp_size", + "owner": "AirInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? \\S+$" + }, + "samp_store_dur": { + "name": "samp_store_dur", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "duration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Duration for which the sample was stored", + "title": "sample storage duration", + "examples": [ + { + "value": "P1Y6M" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sample storage duration" + ], + "rank": 353, + "is_a": "core field", + "string_serialization": "{duration}", + "slot_uri": "MIXS:0000116", + "alias": "samp_store_dur", + "owner": "AirInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "samp_store_loc": { + "name": "samp_store_loc", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "location name" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Location at which sample was stored, usually name of a specific freezer/room", + "title": "sample storage location", + "examples": [ + { + "value": "Freezer no:5" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sample storage location" + ], + "rank": 41, + "is_a": "core field", + "string_serialization": "{text}", + "slot_uri": "MIXS:0000755", + "alias": "samp_store_loc", + "owner": "AirInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "samp_store_temp": { + "name": "samp_store_temp", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "degree Celsius" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Temperature at which the sample was stored (degrees are assumed)", + "title": "sample storage temperature", + "examples": [ + { + "value": "-80 Celsius" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sample storage temperature" + ], + "rank": 7, + "is_a": "core field", + "slot_uri": "MIXS:0000110", + "alias": "samp_store_temp", + "owner": "AirInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "required": true, + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "sample_link": { + "name": "sample_link", + "description": "A unique identifier to assign parent-child, subsample, or sibling samples. This is relevant when a sample or other material was used to generate the new sample.", + "title": "sample linkage", + "notes": [ + "also tempted to include SampIdNewTermsMixin but if len(slot_usage.keys()) > 1 and \"placeholder\" in slot_usage.keys():AttributeError: 'list' object has no attribute 'keys'" + ], + "comments": [ + "This field allows multiple entries separated by ; (Examples: Soil collected from the field will link with the soil used in an incubation. The soil a plant was grown in links to the plant sample. An original culture sample was transferred to a new vial and generated a new sample)" + ], + "examples": [ + { + "value": "IGSN:DSJ0284" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "rank": 5, + "string_serialization": "{text}:{text}", + "alias": "sample_link", + "owner": "AirInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface", + "SampIdNewTermsMixin" + ], + "slot_group": "sample_id_section", + "range": "string", + "recommended": true, + "multivalued": false, + "pattern": "[^\\:\\n\\r]+\\:[^\\:\\n\\r]+" + }, + "size_frac": { + "name": "size_frac", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "filter size value range" + } + }, + "description": "Filtering pore size used in sample preparation", + "title": "size fraction selected", + "examples": [ + { + "value": "0-0.22 micrometer" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "size fraction selected" + ], + "rank": 285, + "is_a": "nucleic acid sequence source field", + "string_serialization": "{float}-{float} {unit}", + "slot_uri": "MIXS:0000017", + "alias": "size_frac", + "owner": "AirInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "solar_irradiance": { + "name": "solar_irradiance", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "kilowatts per square meter per day, ergs per square centimeter per second" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The amount of solar energy that arrives at a specific area of a surface during a specific time interval", + "title": "solar irradiance", + "examples": [ + { + "value": "1.36 kilowatts per square meter per day" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "solar irradiance" + ], + "rank": 55, + "is_a": "core field", + "slot_uri": "MIXS:0000112", + "alias": "solar_irradiance", + "owner": "AirInterface", + "domain_of": [ + "Biosample", + "AirInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "specific_ecosystem": { + "name": "specific_ecosystem", + "description": "Specific ecosystems represent specific features of the environment like aphotic zone in an ocean or gastric mucosa within a host digestive system. Specific ecosystem is in position 5/5 in a GOLD path.", + "comments": [ + "Specific ecosystems help to define samples based on very specific characteristics of an environment under the five-level classification system." + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "https://gold.jgi.doe.gov/help" + ], + "rank": 13, + "is_a": "gold_path_field", + "alias": "specific_ecosystem", + "owner": "AirInterface", + "domain_of": [ + "Biosample", + "Study", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "SpecificEcosystemEnum", + "recommended": true + }, + "temp": { + "name": "temp", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "degree Celsius" + } + }, + "description": "Temperature of the sample at the time of sampling.", + "title": "temperature", + "examples": [ + { + "value": "25 degree Celsius" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "temperature" + ], + "rank": 37, + "is_a": "environment field", + "slot_uri": "MIXS:0000113", + "alias": "temp", + "owner": "AirInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "ventilation_rate": { + "name": "ventilation_rate", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "cubic meter per minute, liters per second" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Ventilation rate of the system in the sampled premises", + "title": "ventilation rate", + "examples": [ + { + "value": "750 cubic meter per minute" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "ventilation rate" + ], + "rank": 56, + "is_a": "core field", + "slot_uri": "MIXS:0000114", + "alias": "ventilation_rate", + "owner": "AirInterface", + "domain_of": [ + "Biosample", + "AirInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "ventilation_type": { + "name": "ventilation_type", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "ventilation type name" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Ventilation system used in the sampled premises", + "title": "ventilation type", + "examples": [ + { + "value": "Operable windows" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "ventilation type" + ], + "rank": 57, + "is_a": "core field", + "string_serialization": "{text}", + "slot_uri": "MIXS:0000756", + "alias": "ventilation_type", + "owner": "AirInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "volatile_org_comp": { + "name": "volatile_org_comp", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "volatile organic compound name;measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "microgram per cubic meter, parts per million, nanogram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Concentration of carbon-based chemicals that easily evaporate at room temperature; can report multiple volatile organic compounds by entering numeric values preceded by name of compound", + "title": "volatile organic compounds", + "examples": [ + { + "value": "formaldehyde;500 nanogram per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "volatile organic compounds" + ], + "rank": 58, + "is_a": "core field", + "string_serialization": "{text};{float} {unit}", + "slot_uri": "MIXS:0000115", + "alias": "volatile_org_comp", + "owner": "AirInterface", + "domain_of": [ + "Biosample", + "AirInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+\\|)*([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+)$" + }, + "wind_direction": { + "name": "wind_direction", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "wind direction name" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Wind direction is the direction from which a wind originates", + "title": "wind direction", + "examples": [ + { + "value": "Northwest" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "wind direction" + ], + "rank": 59, + "is_a": "core field", + "string_serialization": "{text}", + "slot_uri": "MIXS:0000757", + "alias": "wind_direction", + "owner": "AirInterface", + "domain_of": [ + "Biosample", + "AirInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "wind_speed": { + "name": "wind_speed", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "meter per second, kilometer per hour" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Speed of wind measured at the time of sampling", + "title": "wind speed", + "examples": [ + { + "value": "21 kilometer per hour" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "wind speed" + ], + "rank": 60, + "is_a": "core field", + "slot_uri": "MIXS:0000118", + "alias": "wind_speed", + "owner": "AirInterface", + "domain_of": [ + "Biosample", + "AirInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "analysis_type": { + "name": "analysis_type", + "description": "Select all the data types associated or available for this biosample", + "title": "analysis/data type", + "examples": [ + { + "value": "metagenomics; metabolomics; proteomics" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "MIxS:investigation_type" + ], + "rank": 3, + "alias": "analysis_type", + "owner": "AirInterface", + "domain_of": [ + "Biosample", + "DhMultiviewCommonColumnsMixin", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "EmslInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "JgiMgInterface", + "JgiMgLrInterface", + "JgiMtInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "AnalysisTypeEnum", + "required": true, + "recommended": false, + "multivalued": true + }, + "samp_name": { + "name": "samp_name", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "text" + } + }, + "description": "A local identifier or name that for the material sample collected. Refers to the original material collected or to any derived sub-samples.", + "title": "sample name", + "comments": [ + "It can have any format, but we suggest that you make it concise, unique and consistent within your lab, and as informative as possible." + ], + "examples": [ + { + "value": "Rock core CB1178(5-6) from NSW" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sample name" + ], + "rank": 1, + "is_a": "investigation field", + "string_serialization": "{text}", + "slot_uri": "MIXS:0001107", + "identifier": true, + "alias": "samp_name", + "owner": "AirInterface", + "domain_of": [ + "Biosample", + "DhMultiviewCommonColumnsMixin", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "EmslInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "JgiMgInterface", + "JgiMgLrInterface", + "JgiMtInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "string", + "required": true, + "multivalued": false + }, + "source_mat_id": { + "name": "source_mat_id", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "for cultures of microorganisms: identifiers for two culture collections; for other material a unique arbitrary identifer" + } + }, + "description": "A globally unique identifier assigned to the biological sample.", + "title": "source material identifier", + "todos": [ + "Currently, the comments say to use UUIDs. However, if we implement assigning NMDC identifiers with the minter we dont need to require a GUID. It can be an optional field to fill out only if they already have a resolvable ID.", + "Currently, the comments say to use UUIDs. However, if we implement assigning NMDC identifiers with the minter we dont need to require a GUID. It can be an optional field to fill out only if they already have a resolvable ID." + ], + "notes": [ + "The source material IS the Globally Unique ID" + ], + "comments": [ + "Identifiers must be prefixed. Possible FAIR prefixes are IGSNs (http://www.geosamples.org/getigsn), NCBI biosample accession numbers, ARK identifiers (https://arks.org/). These IDs enable linking to derived analytes and subsamples. If you have not assigned FAIR identifiers to your samples, you can generate UUIDs (https://www.uuidgenerator.net/).", + "Identifiers must be prefixed. Possible FAIR prefixes are IGSNs (http://www.geosamples.org/getigsn), NCBI biosample accession numbers, ARK identifiers (https://arks.org/). These IDs enable linking to derived analytes and subsamples. If you have not assigned FAIR identifiers to your samples, you can generate UUIDs (https://www.uuidgenerator.net/)." + ], + "examples": [ + { + "value": "IGSN:AU1243" + }, + { + "value": "UUID:24f1467a-40f4-11ed-b878-0242ac120002" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "source material identifiers" + ], + "rank": 2, + "is_a": "nucleic acid sequence source field", + "string_serialization": "{text}:{text}", + "slot_uri": "MIXS:0000026", + "alias": "source_mat_id", + "owner": "AirInterface", + "domain_of": [ + "Biosample", + "DhMultiviewCommonColumnsMixin", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "EmslInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "JgiMgInterface", + "JgiMgLrInterface", + "JgiMtInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "string", + "multivalued": false, + "pattern": "[^\\:\\n\\r]+\\:[^\\:\\n\\r]+" + } + } + }, + "BiofilmInterface": { + "name": "BiofilmInterface", + "annotations": { + "excel_worksheet_name": { + "tag": "excel_worksheet_name", + "value": "microbial mat_biofilm" + } + }, + "description": "biofilm dh_interface", + "title": "Biofilm", + "from_schema": "https://example.com/nmdc_submission_schema", + "is_a": "DhInterface", + "mixins": [ + "DhMultiviewCommonColumnsMixin", + "SampIdNewTermsMixin" + ], + "slots": [ + "alkalinity", + "alkyl_diethers", + "alt", + "aminopept_act", + "ammonium", + "bacteria_carb_prod", + "biomass", + "bishomohopanol", + "bromide", + "calcium", + "carb_nitro_ratio", + "chem_administration", + "chloride", + "chlorophyll", + "collection_date", + "depth", + "diether_lipids", + "diss_carb_dioxide", + "diss_hydrogen", + "diss_inorg_carb", + "diss_org_carb", + "diss_org_nitro", + "diss_oxygen", + "ecosystem", + "ecosystem_category", + "ecosystem_subtype", + "ecosystem_type", + "elev", + "env_broad_scale", + "env_local_scale", + "env_medium", + "experimental_factor", + "geo_loc_name", + "glucosidase_act", + "lat_lon", + "magnesium", + "mean_frict_vel", + "mean_peak_frict_vel", + "methane", + "misc_param", + "n_alkanes", + "nitrate", + "nitrite", + "nitro", + "org_carb", + "org_matter", + "org_nitro", + "organism_count", + "oxy_stat_samp", + "part_org_carb", + "perturbation", + "petroleum_hydrocarb", + "ph", + "ph_meth", + "phaeopigments", + "phosphate", + "phosplipid_fatt_acid", + "potassium", + "pressure", + "redox_potential", + "salinity", + "samp_collec_device", + "samp_collec_method", + "samp_mat_process", + "samp_size", + "samp_store_dur", + "samp_store_loc", + "samp_store_temp", + "sample_link", + "silicate", + "size_frac", + "sodium", + "specific_ecosystem", + "sulfate", + "sulfide", + "temp", + "tot_carb", + "tot_nitro_content", + "tot_org_carb", + "turbidity", + "water_content" + ], + "slot_usage": { + "alkalinity": { + "name": "alkalinity", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milliequivalent per liter, milligram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate", + "title": "alkalinity", + "examples": [ + { + "value": "50 milligram per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "alkalinity" + ], + "rank": 1, + "is_a": "core field", + "slot_uri": "MIXS:0000421", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "alkyl_diethers": { + "name": "alkyl_diethers", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "mole per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of alkyl diethers", + "title": "alkyl diethers", + "examples": [ + { + "value": "0.005 mole per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "alkyl diethers" + ], + "rank": 2, + "is_a": "core field", + "slot_uri": "MIXS:0000490", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "alt": { + "name": "alt", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + } + }, + "description": "Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air", + "title": "altitude", + "examples": [ + { + "value": "100 meter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "altitude" + ], + "rank": 26, + "is_a": "environment field", + "slot_uri": "MIXS:0000094", + "owner": "Biosample", + "domain_of": [ + "agriculture", + "air", + "built environment", + "core", + "food-animal and animal feed", + "food-farm environment", + "food-food production facility", + "food-human foods", + "host-associated", + "human-associated", + "human-gut", + "human-oral", + "human-skin", + "human-vaginal", + "hydrocarbon resources-cores", + "hydrocarbon resources-fluids_swabs", + "microbial mat_biofilm", + "miscellaneous natural or artificial environment", + "plant-associated", + "sediment", + "soil", + "symbiont-associated", + "wastewater_sludge", + "water", + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HostAssociatedInterface", + "MiscEnvsInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "recommended": true, + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "aminopept_act": { + "name": "aminopept_act", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "mole per liter per hour" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Measurement of aminopeptidase activity", + "title": "aminopeptidase activity", + "examples": [ + { + "value": "0.269 mole per liter per hour" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "aminopeptidase activity" + ], + "rank": 3, + "is_a": "core field", + "slot_uri": "MIXS:0000172", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "ammonium": { + "name": "ammonium", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per liter, milligram per liter, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of ammonium in the sample", + "title": "ammonium", + "examples": [ + { + "value": "1.5 milligram per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "ammonium" + ], + "rank": 4, + "is_a": "core field", + "slot_uri": "MIXS:0000427", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "bacteria_carb_prod": { + "name": "bacteria_carb_prod", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "nanogram per hour" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Measurement of bacterial carbon production", + "title": "bacterial carbon production", + "examples": [ + { + "value": "2.53 microgram per liter per hour" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "bacterial carbon production" + ], + "rank": 5, + "is_a": "core field", + "slot_uri": "MIXS:0000173", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "biomass": { + "name": "biomass", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "biomass type;measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "ton, kilogram, gram" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements", + "title": "biomass", + "examples": [ + { + "value": "total;20 gram" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "biomass" + ], + "rank": 6, + "is_a": "core field", + "string_serialization": "{text};{float} {unit}", + "slot_uri": "MIXS:0000174", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+\\|)*([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+)$" + }, + "bishomohopanol": { + "name": "bishomohopanol", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "microgram per liter, microgram per gram" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of bishomohopanol", + "title": "bishomohopanol", + "examples": [ + { + "value": "14 microgram per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "bishomohopanol" + ], + "rank": 7, + "is_a": "core field", + "slot_uri": "MIXS:0000175", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "bromide": { + "name": "bromide", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of bromide", + "title": "bromide", + "examples": [ + { + "value": "0.05 parts per million" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "bromide" + ], + "rank": 8, + "is_a": "core field", + "slot_uri": "MIXS:0000176", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "calcium": { + "name": "calcium", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milligram per liter, micromole per liter, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of calcium in the sample", + "title": "calcium", + "examples": [ + { + "value": "0.2 micromole per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "calcium" + ], + "rank": 9, + "is_a": "core field", + "slot_uri": "MIXS:0000432", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "carb_nitro_ratio": { + "name": "carb_nitro_ratio", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Ratio of amount or concentrations of carbon to nitrogen", + "title": "carbon/nitrogen ratio", + "examples": [ + { + "value": "0.417361111" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "carbon/nitrogen ratio" + ], + "rank": 44, + "is_a": "core field", + "slot_uri": "MIXS:0000310", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "SedimentInterface", + "SoilInterface", + "WaterInterface" + ], + "slot_group": "mixs_section", + "range": "float", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "chem_administration": { + "name": "chem_administration", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "CHEBI;timestamp" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi", + "title": "chemical administration", + "examples": [ + { + "value": "agar [CHEBI:2509];2018-05-11|agar [CHEBI:2509];2018-05-22" + }, + { + "value": "agar [CHEBI:2509];2018-05" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "chemical administration" + ], + "rank": 17, + "is_a": "core field", + "string_serialization": "{termLabel} {[termID]};{timestamp}", + "slot_uri": "MIXS:0000751", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "recommended": true, + "multivalued": false, + "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\];([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$" + }, + "chloride": { + "name": "chloride", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milligram per liter, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of chloride in the sample", + "title": "chloride", + "examples": [ + { + "value": "5000 milligram per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "chloride" + ], + "rank": 10, + "is_a": "core field", + "slot_uri": "MIXS:0000429", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "chlorophyll": { + "name": "chlorophyll", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milligram per cubic meter, microgram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of chlorophyll", + "title": "chlorophyll", + "examples": [ + { + "value": "5 milligram per cubic meter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "chlorophyll" + ], + "rank": 11, + "is_a": "core field", + "slot_uri": "MIXS:0000177", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "collection_date": { + "name": "collection_date", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "date and time" + } + }, + "description": "The date of sampling", + "title": "collection date", + "notes": [ + "MIxS collection_date accepts (truncated) ISO8601. DH taking arb prec date only", + "Use modified term (amended definition)" + ], + "examples": [ + { + "value": "2021-04-15" + }, + { + "value": "2021-04" + }, + { + "value": "2021" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "collection date" + ], + "rank": 3, + "is_a": "environment field", + "string_serialization": "{date, arbitrary precision}", + "slot_uri": "MIXS:0000011", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "required": true, + "multivalued": false, + "pattern": "^[12]\\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\\d|3[01]))?)?$" + }, + "depth": { + "name": "depth", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + } + }, + "description": "The vertical distance below local surface, e.g. for sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples.", + "title": "depth, meters", + "notes": [ + "Use modified term" + ], + "comments": [ + "All depths must be reported in meters. Provide the numerical portion only." + ], + "examples": [ + { + "value": "0 - 0.1" + }, + { + "value": "1" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "depth" + ], + "rank": 9, + "is_a": "environment field", + "string_serialization": "{float}|{float}-{float}", + "slot_uri": "MIXS:0000018", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "recommended": true, + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)?(\\s*-\\s*[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)?)?$" + }, + "diether_lipids": { + "name": "diether_lipids", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "diether lipid name;measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "nanogram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Concentration of diether lipids; can include multiple types of diether lipids", + "title": "diether lipids", + "examples": [ + { + "value": "0.2 nanogram per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "diether lipids" + ], + "rank": 13, + "is_a": "core field", + "string_serialization": "{text};{float} {unit}", + "slot_uri": "MIXS:0000178", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+\\|)*([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+)$" + }, + "diss_carb_dioxide": { + "name": "diss_carb_dioxide", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per liter, milligram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample", + "title": "dissolved carbon dioxide", + "examples": [ + { + "value": "5 milligram per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "dissolved carbon dioxide" + ], + "rank": 14, + "is_a": "core field", + "slot_uri": "MIXS:0000436", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "diss_hydrogen": { + "name": "diss_hydrogen", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of dissolved hydrogen", + "title": "dissolved hydrogen", + "examples": [ + { + "value": "0.3 micromole per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "dissolved hydrogen" + ], + "rank": 15, + "is_a": "core field", + "slot_uri": "MIXS:0000179", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "diss_inorg_carb": { + "name": "diss_inorg_carb", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "microgram per liter, milligram per liter, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter", + "title": "dissolved inorganic carbon", + "examples": [ + { + "value": "2059 micromole per kilogram" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "dissolved inorganic carbon" + ], + "rank": 16, + "is_a": "core field", + "slot_uri": "MIXS:0000434", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "diss_org_carb": { + "name": "diss_org_carb", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per liter, milligram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid", + "title": "dissolved organic carbon", + "examples": [ + { + "value": "197 micromole per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "dissolved organic carbon" + ], + "rank": 17, + "is_a": "core field", + "slot_uri": "MIXS:0000433", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "diss_org_nitro": { + "name": "diss_org_nitro", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "microgram per liter, milligram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2", + "title": "dissolved organic nitrogen", + "examples": [ + { + "value": "0.05 micromole per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "dissolved organic nitrogen" + ], + "rank": 18, + "is_a": "core field", + "slot_uri": "MIXS:0000162", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "diss_oxygen": { + "name": "diss_oxygen", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per kilogram, milligram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of dissolved oxygen", + "title": "dissolved oxygen", + "examples": [ + { + "value": "175 micromole per kilogram" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "dissolved oxygen" + ], + "rank": 19, + "is_a": "core field", + "slot_uri": "MIXS:0000119", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "ecosystem": { + "name": "ecosystem", + "description": "An ecosystem is a combination of a physical environment (abiotic factors) and all the organisms (biotic factors) that interact with this environment. Ecosystem is in position 1/5 in a GOLD path.", + "comments": [ + "The abiotic factors play a profound role on the type and composition of organisms in a given environment. The GOLD Ecosystem at the top of the five-level classification system is aimed at capturing the broader environment from which an organism or environmental sample is collected. The three broad groups under Ecosystem are Environmental, Host-associated, and Engineered. They represent samples collected from a natural environment or from another organism or from engineered environments like bioreactors respectively." + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "https://gold.jgi.doe.gov/help" + ], + "rank": 9, + "is_a": "gold_path_field", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "Study", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "EcosystemEnum", + "recommended": true + }, + "ecosystem_category": { + "name": "ecosystem_category", + "description": "Ecosystem categories represent divisions within the ecosystem based on specific characteristics of the environment from where an organism or sample is isolated. Ecosystem category is in position 2/5 in a GOLD path.", + "comments": [ + "The Environmental ecosystem (for example) is divided into Air, Aquatic and Terrestrial. Ecosystem categories for Host-associated samples can be individual hosts or phyla and for engineered samples it may be manipulated environments like bioreactors, solid waste etc." + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "https://gold.jgi.doe.gov/help" + ], + "rank": 10, + "is_a": "gold_path_field", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "Study", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "EcosystemCategoryEnum", + "recommended": true + }, + "ecosystem_subtype": { + "name": "ecosystem_subtype", + "description": "Ecosystem subtypes represent further subdivision of Ecosystem types into more distinct subtypes. Ecosystem subtype is in position 4/5 in a GOLD path.", + "comments": [ + "Ecosystem Type Marine (Environmental -> Aquatic -> Marine) is further divided (for example) into Intertidal zone, Coastal, Pelagic, Intertidal zone etc. in the Ecosystem subtype category." + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "https://gold.jgi.doe.gov/help" + ], + "rank": 12, + "is_a": "gold_path_field", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "Study", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "EcosystemSubtypeEnum", + "recommended": true + }, + "ecosystem_type": { + "name": "ecosystem_type", + "description": "Ecosystem types represent things having common characteristics within the Ecosystem Category. These common characteristics based grouping is still broad but specific to the characteristics of a given environment. Ecosystem type is in position 3/5 in a GOLD path.", + "comments": [ + "The Aquatic ecosystem category (for example) may have ecosystem types like Marine or Thermal springs etc. Ecosystem category Air may have Indoor air or Outdoor air as different Ecosystem Types. In the case of Host-associated samples, ecosystem type can represent Respiratory system, Digestive system, Roots etc." + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "https://gold.jgi.doe.gov/help" + ], + "rank": 11, + "is_a": "gold_path_field", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "Study", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "EcosystemTypeEnum", + "recommended": true + }, + "elev": { + "name": "elev", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + } + }, + "description": "Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit.", + "title": "elevation, meters", + "comments": [ + "All elevations must be reported in meters. Provide the numerical portion only.", + "Please use https://www.advancedconverter.com/map-tools/find-altitude-by-coordinates, if needed, to help estimate the elevation based on latitude and longitude coordinates." + ], + "examples": [ + { + "value": "225" + }, + { + "value": "0" + }, + { + "value": "1250" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "elevation" + ], + "rank": 6, + "is_a": "environment field", + "slot_uri": "MIXS:0000093", + "owner": "Biosample", + "domain_of": [ + "FieldResearchSite", + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "float", + "required": true, + "multivalued": false + }, + "env_broad_scale": { + "name": "env_broad_scale", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "The major environment type(s) where the sample was collected. Recommend subclasses of biome [ENVO:00000428]. Multiple terms can be separated by one or more pipes." + }, + "tooltip": { + "tag": "tooltip", + "value": "The biome or major environmental system where the sample or specimen originated. Choose values from subclasses of the 'biome' class [ENVO:00000428] in the Environment Ontology (ENVO). For host-associated or plant-associated samples, use terms from the UBERON or Plant Ontology to describe the broad anatomical or morphological context" + } + }, + "description": "In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO's biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html", + "title": "broad-scale environmental context", + "notes": [ + "range changed to enumeration late in makefile, so this is modified (but \"sample ID\" anyway)" + ], + "examples": [ + { + "value": "oceanic epipelagic zone biome [ENVO:01000033] for annotating a water sample from the photic zone in middle of the Atlantic Ocean" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "broad-scale environmental context" + ], + "rank": 6, + "is_a": "environment field", + "string_serialization": "{termLabel} {[termID]}", + "slot_uri": "MIXS:0000012", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "string", + "required": true, + "multivalued": false, + "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$" + }, + "env_local_scale": { + "name": "env_local_scale", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "Environmental entities having causal influences upon the entity at time of sampling." + }, + "tooltip": { + "tag": "tooltip", + "value": "The specific environmental entities or features near the sample or specimen that significantly influence its characteristics or composition. These entities are typically smaller in scale than the broad environmental context. Values for this field should be countable, material nouns and must be chosen from subclasses of BFO:0000040 (material entity) that appear in the Environment Ontology (ENVO). For host-associated or plant-associated samples, use terms from the UBERON or Plant Ontology to describe specific anatomical structures or plant parts." + } + }, + "description": "Report the entity or entities which are in the sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. We recommend using EnvO terms which are of smaller spatial grain than your entry for env_broad_scale. Terms, such as anatomical sites, from other OBO Library ontologies which interoperate with EnvO (e.g. UBERON) are accepted in this field. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS.", + "title": "local environmental context", + "notes": [ + "range changed to enumeration late in makefile, so this is modified (but \"sample ID\" anyway)" + ], + "examples": [ + { + "value": "canopy [ENVO:00000047]" + }, + { + "value": "herb and fern layer [ENVO:01000337]" + }, + { + "value": "litter layer [ENVO:01000338]" + }, + { + "value": "understory [01000335]" + }, + { + "value": "shrub layer [ENVO:01000336]" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "local environmental context" + ], + "rank": 7, + "is_a": "environment field", + "string_serialization": "{termLabel} {[termID]}", + "slot_uri": "MIXS:0000013", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "string", + "required": true, + "multivalued": false, + "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$" + }, + "env_medium": { + "name": "env_medium", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "The material displaced by the entity at time of sampling. Recommend subclasses of environmental material [ENVO:00010483]." + }, + "tooltip": { + "tag": "tooltip", + "value": "The predominant environmental material or substrate that directly surrounds or hosts the sample or specimen at the time of sampling. Choose values from subclasses of the 'environmental material' class [ENVO:00010483] in the Environment Ontology (ENVO). Values for this field should be measurable or mass material nouns, representing continuous environmental materials. For host-associated or plant-associated samples, use terms from the UBERON or Plant Ontology to indicate a tissue, organ, or plant structure" + } + }, + "description": "Report the environmental material(s) immediately surrounding the sample or specimen at the time of sampling. We recommend using subclasses of 'environmental material' (http://purl.obolibrary.org/obo/ENVO_00010483). EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS . Terms from other OBO ontologies are permissible as long as they reference mass/volume nouns (e.g. air, water, blood) and not discrete, countable entities (e.g. a tree, a leaf, a table top).", + "title": "environmental medium", + "notes": [ + "range changed to enumeration late in makefile, so this is modified (but \"sample ID\" anyway)" + ], + "examples": [ + { + "value": "soil [ENVO:00001998]" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "environmental medium" + ], + "rank": 8, + "is_a": "environment field", + "string_serialization": "{termLabel} {[termID]}", + "slot_uri": "MIXS:0000014", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "string", + "required": true, + "multivalued": false, + "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$" + }, + "experimental_factor": { + "name": "experimental_factor", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "text or EFO and/or OBI" + } + }, + "description": "Experimental factors are essentially the variable aspects of an experiment design which can be used to describe an experiment, or set of experiments, in an increasingly detailed manner. This field accepts ontology terms from Experimental Factor Ontology (EFO) and/or Ontology for Biomedical Investigations (OBI). For a browser of EFO (v 2.95) terms, please see http://purl.bioontology.org/ontology/EFO; for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI", + "title": "experimental factor", + "examples": [ + { + "value": "time series design [EFO:EFO_0001779]" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "experimental factor" + ], + "rank": 12, + "is_a": "investigation field", + "string_serialization": "{termLabel} {[termID]}|{text}", + "slot_uri": "MIXS:0000008", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false + }, + "geo_loc_name": { + "name": "geo_loc_name", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "country or sea name (INSDC or GAZ): region(GAZ), specific location name" + } + }, + "description": "The geographical origin of the sample as defined by the country or sea name followed by specific region name.", + "title": "geographic location (country and/or sea,region)", + "examples": [ + { + "value": "USA: Maryland, Bethesda" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "geographic location (country and/or sea,region)" + ], + "rank": 4, + "is_a": "environment field", + "string_serialization": "{text}: {text}, {text}", + "slot_uri": "MIXS:0000010", + "owner": "Biosample", + "domain_of": [ + "FieldResearchSite", + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "required": true, + "multivalued": false, + "pattern": "^[^:, ][^:]*: [^:, ][^,]*, [^:, ].*$" + }, + "glucosidase_act": { + "name": "glucosidase_act", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "mol per liter per hour" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Measurement of glucosidase activity", + "title": "glucosidase activity", + "examples": [ + { + "value": "5 mol per liter per hour" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "glucosidase activity" + ], + "rank": 20, + "is_a": "core field", + "slot_uri": "MIXS:0000137", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "lat_lon": { + "name": "lat_lon", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "decimal degrees, limit to 8 decimal points" + } + }, + "description": "The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system", + "title": "geographic location (latitude and longitude)", + "notes": [ + "This is currently a required field but it's not clear if this should be required for human hosts" + ], + "examples": [ + { + "value": "50.586825 6.408977" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "geographic location (latitude and longitude)" + ], + "rank": 5, + "is_a": "environment field", + "string_serialization": "{lat lon}", + "slot_uri": "MIXS:0000009", + "owner": "Biosample", + "domain_of": [ + "FieldResearchSite", + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "required": true, + "multivalued": false, + "pattern": "^[-+]?([1-8]?\\d(\\.\\d{1,8})?|90(\\.0{1,8})?)\\s[-+]?(180(\\.0{1,8})?|((1[0-7]\\d)|([1-9]?\\d))(\\.\\d{1,8})?)$" + }, + "magnesium": { + "name": "magnesium", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "mole per liter, milligram per liter, parts per million, micromole per kilogram" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of magnesium in the sample", + "title": "magnesium", + "examples": [ + { + "value": "52.8 micromole per kilogram" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "magnesium" + ], + "rank": 21, + "is_a": "core field", + "slot_uri": "MIXS:0000431", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "mean_frict_vel": { + "name": "mean_frict_vel", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "meter per second" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Measurement of mean friction velocity", + "title": "mean friction velocity", + "examples": [ + { + "value": "0.5 meter per second" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "mean friction velocity" + ], + "rank": 22, + "is_a": "core field", + "slot_uri": "MIXS:0000498", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "mean_peak_frict_vel": { + "name": "mean_peak_frict_vel", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "meter per second" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Measurement of mean peak friction velocity", + "title": "mean peak friction velocity", + "examples": [ + { + "value": "1 meter per second" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "mean peak friction velocity" + ], + "rank": 23, + "is_a": "core field", + "slot_uri": "MIXS:0000502", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "methane": { + "name": "methane", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per liter, parts per billion, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Methane (gas) amount or concentration at the time of sampling", + "title": "methane", + "examples": [ + { + "value": "1800 parts per billion" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "methane" + ], + "rank": 24, + "is_a": "core field", + "slot_uri": "MIXS:0000101", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "SedimentInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "misc_param": { + "name": "misc_param", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "parameter name;measurement value" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Any other measurement performed or parameter collected, that is not listed here", + "title": "miscellaneous parameter", + "examples": [ + { + "value": "Bicarbonate ion concentration;2075 micromole per kilogram" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "miscellaneous parameter" + ], + "rank": 23, + "is_a": "core field", + "string_serialization": "{text};{float} {unit}", + "slot_uri": "MIXS:0000752", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false, + "pattern": "^([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+\\|)*([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+)$" + }, + "n_alkanes": { + "name": "n_alkanes", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "n-alkane name;measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Concentration of n-alkanes; can include multiple n-alkanes", + "title": "n-alkanes", + "examples": [ + { + "value": "n-hexadecane;100 milligram per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "n-alkanes" + ], + "rank": 25, + "is_a": "core field", + "string_serialization": "{text};{float} {unit}", + "slot_uri": "MIXS:0000503", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+\\|)*([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+)$" + }, + "nitrate": { + "name": "nitrate", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per liter, milligram per liter, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of nitrate in the sample", + "title": "nitrate", + "examples": [ + { + "value": "65 micromole per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "nitrate" + ], + "rank": 26, + "is_a": "core field", + "slot_uri": "MIXS:0000425", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "nitrite": { + "name": "nitrite", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per liter, milligram per liter, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of nitrite in the sample", + "title": "nitrite", + "examples": [ + { + "value": "0.5 micromole per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "nitrite" + ], + "rank": 27, + "is_a": "core field", + "slot_uri": "MIXS:0000426", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "nitro": { + "name": "nitro", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of nitrogen (total)", + "title": "nitrogen", + "examples": [ + { + "value": "4.2 micromole per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "nitrogen" + ], + "rank": 28, + "is_a": "core field", + "slot_uri": "MIXS:0000504", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "org_carb": { + "name": "org_carb", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of organic carbon", + "title": "organic carbon", + "examples": [ + { + "value": "1.5 microgram per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "organic carbon" + ], + "rank": 29, + "is_a": "core field", + "slot_uri": "MIXS:0000508", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "org_matter": { + "name": "org_matter", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "microgram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of organic matter", + "title": "organic matter", + "examples": [ + { + "value": "1.75 milligram per cubic meter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "organic matter" + ], + "rank": 45, + "is_a": "core field", + "slot_uri": "MIXS:0000204", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "MiscEnvsInterface", + "SedimentInterface", + "SoilInterface", + "WaterInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "org_nitro": { + "name": "org_nitro", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "microgram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of organic nitrogen", + "title": "organic nitrogen", + "examples": [ + { + "value": "4 micromole per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "organic nitrogen" + ], + "rank": 46, + "is_a": "core field", + "slot_uri": "MIXS:0000205", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "MiscEnvsInterface", + "SedimentInterface", + "SoilInterface", + "WaterInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "organism_count": { + "name": "organism_count", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "organism name;measurement value;enumeration" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "number of cells per cubic meter, number of cells per milliliter, number of cells per cubic centimeter" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr)", + "title": "organism count", + "examples": [ + { + "value": "total prokaryotes;3.5e7 cells per milliliter;qPCR" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "organism count" + ], + "rank": 30, + "is_a": "core field", + "slot_uri": "MIXS:0000103", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^([-+]?[0-9]*\\.?[0-9]+ +\\S.*\\|)*([-+]?[0-9]*\\.?[0-9]+ +\\S.*)$" + }, + "oxy_stat_samp": { + "name": "oxy_stat_samp", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Oxygenation status of sample", + "title": "oxygenation status of sample", + "examples": [ + { + "value": "aerobic" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "oxygenation status of sample" + ], + "rank": 25, + "is_a": "core field", + "slot_uri": "MIXS:0000753", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_section", + "range": "OxyStatSampEnum", + "multivalued": false + }, + "part_org_carb": { + "name": "part_org_carb", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "microgram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of particulate organic carbon", + "title": "particulate organic carbon", + "examples": [ + { + "value": "1.92 micromole per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "particulate organic carbon" + ], + "rank": 31, + "is_a": "core field", + "slot_uri": "MIXS:0000515", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "perturbation": { + "name": "perturbation", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "perturbation type name;perturbation interval and duration" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types", + "title": "perturbation", + "examples": [ + { + "value": "antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "perturbation" + ], + "rank": 33, + "is_a": "core field", + "string_serialization": "{text};{Rn/start_time/end_time/duration}", + "slot_uri": "MIXS:0000754", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "petroleum_hydrocarb": { + "name": "petroleum_hydrocarb", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of petroleum hydrocarbon", + "title": "petroleum hydrocarbon", + "examples": [ + { + "value": "0.05 micromole per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "petroleum hydrocarbon" + ], + "rank": 34, + "is_a": "core field", + "slot_uri": "MIXS:0000516", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "ph": { + "name": "ph", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "pH measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid", + "title": "pH", + "notes": [ + "Use modified term" + ], + "examples": [ + { + "value": "7.2" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "pH" + ], + "rank": 27, + "is_a": "core field", + "string_serialization": "{float}", + "slot_uri": "MIXS:0001001", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "MiscEnvsInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "float", + "recommended": true, + "multivalued": false, + "minimum_value": 0, + "maximum_value": 14 + }, + "ph_meth": { + "name": "ph_meth", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "PMID,DOI or url" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Reference or method used in determining ph", + "title": "pH method", + "comments": [ + "This can include a link to the instrument used or a citation for the method." + ], + "examples": [ + { + "value": "https://www.southernlabware.com/pc9500-benchtop-ph-conductivity-meter-kit-ph-accuracy-2000mv-ph-range-2-000-to-20-000.html?gclid=Cj0KCQiAwJWdBhCYARIsAJc4idCO5vtvbVMf545fcvdROFqa6zjzNSoywNx6K4k9Coo9cCc2pybtvGsaAiR0EALw_wcB" + }, + { + "value": "https://doi.org/10.2136/sssabookser5.3.c16" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "pH method" + ], + "rank": 41, + "is_a": "core field", + "string_serialization": "{PMID}|{DOI}|{URL}", + "slot_uri": "MIXS:0001106", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "MiscEnvsInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false + }, + "phaeopigments": { + "name": "phaeopigments", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "phaeopigment name;measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milligram per cubic meter" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Concentration of phaeopigments; can include multiple phaeopigments", + "title": "phaeopigments", + "examples": [ + { + "value": "2.5 milligram per cubic meter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "phaeopigments" + ], + "rank": 35, + "is_a": "core field", + "string_serialization": "{text};{float} {unit}", + "slot_uri": "MIXS:0000180", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+\\|)*([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+)$" + }, + "phosphate": { + "name": "phosphate", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of phosphate", + "title": "phosphate", + "examples": [ + { + "value": "0.7 micromole per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "phosphate" + ], + "rank": 53, + "is_a": "core field", + "slot_uri": "MIXS:0000505", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "MiscEnvsInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "phosplipid_fatt_acid": { + "name": "phosplipid_fatt_acid", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "phospholipid fatty acid name;measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "mole per gram, mole per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Concentration of phospholipid fatty acids; can include multiple values", + "title": "phospholipid fatty acid", + "examples": [ + { + "value": "2.98 milligram per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "phospholipid fatty acid" + ], + "rank": 36, + "is_a": "core field", + "string_serialization": "{text};{float} {unit}", + "slot_uri": "MIXS:0000181", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+\\|)*([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+)$" + }, + "potassium": { + "name": "potassium", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milligram per liter, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of potassium in the sample", + "title": "potassium", + "examples": [ + { + "value": "463 milligram per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "potassium" + ], + "rank": 38, + "is_a": "core field", + "slot_uri": "MIXS:0000430", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "pressure": { + "name": "pressure", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "atmosphere" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Pressure to which the sample is subject to, in atmospheres", + "title": "pressure", + "examples": [ + { + "value": "50 atmosphere" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "pressure" + ], + "rank": 39, + "is_a": "core field", + "slot_uri": "MIXS:0000412", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "redox_potential": { + "name": "redox_potential", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "millivolt" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential", + "title": "redox potential", + "examples": [ + { + "value": "300 millivolt" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "redox potential" + ], + "rank": 40, + "is_a": "core field", + "slot_uri": "MIXS:0000182", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "salinity": { + "name": "salinity", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "practical salinity unit, percentage" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The total concentration of all dissolved salts in a liquid or solid sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater.", + "title": "salinity", + "examples": [ + { + "value": "25 practical salinity unit" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "salinity" + ], + "rank": 54, + "is_a": "core field", + "slot_uri": "MIXS:0000183", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "samp_collec_device": { + "name": "samp_collec_device", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "device name" + } + }, + "description": "The device used to collect an environmental sample. This field accepts terms listed under environmental sampling device (http://purl.obolibrary.org/obo/ENVO). This field also accepts terms listed under specimen collection device (http://purl.obolibrary.org/obo/GENEPIO_0002094).", + "title": "sample collection device", + "comments": [ + "Report dimensions and details when applicable" + ], + "examples": [ + { + "value": "swab, biopsy, niskin bottle, push core, drag swab [GENEPIO:0002713]" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sample collection device" + ], + "rank": 14, + "is_a": "nucleic acid sequence source field", + "string_serialization": "{termLabel} {[termID]}|{text}", + "slot_uri": "MIXS:0000002", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "recommended": true, + "multivalued": false + }, + "samp_collec_method": { + "name": "samp_collec_method", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "PMID,DOI,url , or text" + } + }, + "description": "The method employed for collecting the sample.", + "title": "sample collection method", + "comments": [ + "This can be a citation or description" + ], + "examples": [ + { + "value": "swabbing" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sample collection method" + ], + "rank": 15, + "is_a": "nucleic acid sequence source field", + "string_serialization": "{PMID}|{DOI}|{URL}|{text}", + "slot_uri": "MIXS:0001225", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "multivalued": false + }, + "samp_mat_process": { + "name": "samp_mat_process", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "text" + } + }, + "description": "A brief description of any processing applied to the sample during or after retrieving the sample from environment, or a link to the relevant protocol(s) performed.", + "title": "sample material processing", + "examples": [ + { + "value": "filtering of seawater" + }, + { + "value": "storing samples in ethanol" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sample material processing" + ], + "rank": 12, + "is_a": "nucleic acid sequence source field", + "string_serialization": "{text}", + "slot_uri": "MIXS:0000016", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "multivalued": false + }, + "samp_size": { + "name": "samp_size", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "millliter, gram, milligram, liter" + } + }, + "description": "The total amount or size (volume (ml), mass (g) or area (m2) ) of sample collected.", + "title": "amount or size of sample collected", + "comments": [ + "This refers to the TOTAL amount of sample collected from the experiment. NOT the amount sent to each institution or collected for a specific analysis." + ], + "examples": [ + { + "value": "5 grams" + }, + { + "value": "10 mL" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "amount or size of sample collected" + ], + "rank": 18, + "is_a": "nucleic acid sequence source field", + "string_serialization": "{float} {unit}", + "slot_uri": "MIXS:0000001", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? \\S+$" + }, + "samp_store_dur": { + "name": "samp_store_dur", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "duration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Duration for which the sample was stored", + "title": "sample storage duration", + "examples": [ + { + "value": "P1Y6M" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sample storage duration" + ], + "rank": 353, + "is_a": "core field", + "string_serialization": "{duration}", + "slot_uri": "MIXS:0000116", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "samp_store_loc": { + "name": "samp_store_loc", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "location name" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Location at which sample was stored, usually name of a specific freezer/room", + "title": "sample storage location", + "examples": [ + { + "value": "Freezer no:5" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sample storage location" + ], + "rank": 41, + "is_a": "core field", + "string_serialization": "{text}", + "slot_uri": "MIXS:0000755", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "samp_store_temp": { + "name": "samp_store_temp", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "degree Celsius" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Temperature at which the sample was stored (degrees are assumed)", + "title": "sample storage temperature", + "examples": [ + { + "value": "-80 Celsius" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sample storage temperature" + ], + "rank": 7, + "is_a": "core field", + "slot_uri": "MIXS:0000110", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "required": true, + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "sample_link": { + "name": "sample_link", + "description": "A unique identifier to assign parent-child, subsample, or sibling samples. This is relevant when a sample or other material was used to generate the new sample.", + "title": "sample linkage", + "notes": [ + "also tempted to include SampIdNewTermsMixin but if len(slot_usage.keys()) > 1 and \"placeholder\" in slot_usage.keys():AttributeError: 'list' object has no attribute 'keys'" + ], + "comments": [ + "This field allows multiple entries separated by ; (Examples: Soil collected from the field will link with the soil used in an incubation. The soil a plant was grown in links to the plant sample. An original culture sample was transferred to a new vial and generated a new sample)" + ], + "examples": [ + { + "value": "IGSN:DSJ0284" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "rank": 5, + "string_serialization": "{text}:{text}", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface", + "SampIdNewTermsMixin" + ], + "slot_group": "sample_id_section", + "range": "string", + "recommended": true, + "multivalued": false, + "pattern": "[^\\:\\n\\r]+\\:[^\\:\\n\\r]+" + }, + "silicate": { + "name": "silicate", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of silicate", + "title": "silicate", + "examples": [ + { + "value": "0.05 micromole per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "silicate" + ], + "rank": 43, + "is_a": "core field", + "slot_uri": "MIXS:0000184", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "size_frac": { + "name": "size_frac", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "filter size value range" + } + }, + "description": "Filtering pore size used in sample preparation", + "title": "size fraction selected", + "examples": [ + { + "value": "0-0.22 micrometer" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "size fraction selected" + ], + "rank": 285, + "is_a": "nucleic acid sequence source field", + "string_serialization": "{float}-{float} {unit}", + "slot_uri": "MIXS:0000017", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "sodium": { + "name": "sodium", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milligram per liter, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Sodium concentration in the sample", + "title": "sodium", + "examples": [ + { + "value": "10.5 milligram per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sodium" + ], + "rank": 363, + "is_a": "core field", + "slot_uri": "MIXS:0000428", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "specific_ecosystem": { + "name": "specific_ecosystem", + "description": "Specific ecosystems represent specific features of the environment like aphotic zone in an ocean or gastric mucosa within a host digestive system. Specific ecosystem is in position 5/5 in a GOLD path.", + "comments": [ + "Specific ecosystems help to define samples based on very specific characteristics of an environment under the five-level classification system." + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "https://gold.jgi.doe.gov/help" + ], + "rank": 13, + "is_a": "gold_path_field", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "Study", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "SpecificEcosystemEnum", + "recommended": true + }, + "sulfate": { + "name": "sulfate", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per liter, milligram per liter, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of sulfate in the sample", + "title": "sulfate", + "examples": [ + { + "value": "5 micromole per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sulfate" + ], + "rank": 44, + "is_a": "core field", + "slot_uri": "MIXS:0000423", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "sulfide": { + "name": "sulfide", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per liter, milligram per liter, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of sulfide in the sample", + "title": "sulfide", + "examples": [ + { + "value": "2 micromole per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sulfide" + ], + "rank": 371, + "is_a": "core field", + "slot_uri": "MIXS:0000424", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "temp": { + "name": "temp", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "degree Celsius" + } + }, + "description": "Temperature of the sample at the time of sampling.", + "title": "temperature", + "examples": [ + { + "value": "25 degree Celsius" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "temperature" + ], + "rank": 37, + "is_a": "environment field", + "slot_uri": "MIXS:0000113", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "tot_carb": { + "name": "tot_carb", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "microgram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Total carbon content", + "title": "total carbon", + "todos": [ + "is this inorganic and organic? both? could use some clarification.", + "ug/L doesn't seem like the right units. Should check this slots usage in databases and re-evaluate. I couldn't find any references that provided this data in this format", + "is this inorganic and organic? both? could use some clarification.", + "ug/L doesn't seem like the right units. Should check this slots usage in databases and re-evaluate. I couldn't find any references that provided this data in this format" + ], + "examples": [ + { + "value": "1 ug/L" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "total carbon" + ], + "rank": 47, + "is_a": "core field", + "slot_uri": "MIXS:0000525", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "SedimentInterface", + "SoilInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "tot_nitro_content": { + "name": "tot_nitro_content", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "microgram per liter, micromole per liter, milligram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Total nitrogen content of the sample", + "title": "total nitrogen content", + "examples": [ + { + "value": "5 mg N/ L" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "total nitrogen content" + ], + "rank": 48, + "is_a": "core field", + "slot_uri": "MIXS:0000530", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "SedimentInterface", + "SoilInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "tot_org_carb": { + "name": "tot_org_carb", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "gram Carbon per kilogram sample material" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content", + "title": "total organic carbon", + "todos": [ + "check description. How are they different?", + "check description. How are they different?" + ], + "examples": [ + { + "value": "5 mg N/ L" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "total organic carbon" + ], + "rank": 50, + "is_a": "core field", + "slot_uri": "MIXS:0000533", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "SedimentInterface", + "SoilInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "turbidity": { + "name": "turbidity", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "formazin turbidity unit, formazin nephelometric units" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Measure of the amount of cloudiness or haziness in water caused by individual particles", + "title": "turbidity", + "examples": [ + { + "value": "0.3 nephelometric turbidity units" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "turbidity" + ], + "rank": 47, + "is_a": "core field", + "slot_uri": "MIXS:0000191", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "water_content": { + "name": "water_content", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "string" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "gram per gram or cubic centimeter per cubic centimeter" + } + }, + "description": "Water content measurement", + "title": "water content", + "todos": [ + "value in preferred unit is too limiting. need to change this", + "check and correct validation so examples are accepted", + "how to manage multiple water content methods?" + ], + "examples": [ + { + "value": "0.75 g water/g dry soil" + }, + { + "value": "75% water holding capacity" + }, + { + "value": "1.1 g fresh weight/ dry weight" + }, + { + "value": "10% water filled pore space" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "water content" + ], + "rank": 39, + "is_a": "core field", + "string_serialization": "{float or pct} {unit}", + "slot_uri": "MIXS:0000185", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "SedimentInterface", + "SoilInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)?%? \\S.+$" + }, + "horizon_meth": { + "name": "horizon_meth", + "title": "horizon method" + } + }, + "attributes": { + "alkalinity": { + "name": "alkalinity", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milliequivalent per liter, milligram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate", + "title": "alkalinity", + "examples": [ + { + "value": "50 milligram per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "alkalinity" + ], + "rank": 1, + "is_a": "core field", + "slot_uri": "MIXS:0000421", + "alias": "alkalinity", + "owner": "BiofilmInterface", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "alkyl_diethers": { + "name": "alkyl_diethers", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "mole per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of alkyl diethers", + "title": "alkyl diethers", + "examples": [ + { + "value": "0.005 mole per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "alkyl diethers" + ], + "rank": 2, + "is_a": "core field", + "slot_uri": "MIXS:0000490", + "alias": "alkyl_diethers", + "owner": "BiofilmInterface", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "alt": { + "name": "alt", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + } + }, + "description": "Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. 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Provide the numerical portion only." + ], + "examples": [ + { + "value": "0 - 0.1" + }, + { + "value": "1" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "depth" + ], + "rank": 9, + "is_a": "environment field", + "string_serialization": "{float}|{float}-{float}", + "slot_uri": "MIXS:0000018", + "alias": "depth", + "owner": "BiofilmInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "recommended": true, + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)?(\\s*-\\s*[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)?)?$" + }, + "diether_lipids": { + "name": "diether_lipids", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "diether lipid name;measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "nanogram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Concentration of diether lipids; can include multiple types of diether lipids", + "title": "diether lipids", + "examples": [ + { + "value": "0.2 nanogram per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "diether lipids" + ], + "rank": 13, + "is_a": "core field", + "string_serialization": "{text};{float} {unit}", + "slot_uri": "MIXS:0000178", + "alias": "diether_lipids", + "owner": "BiofilmInterface", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+\\|)*([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+)$" + }, + "diss_carb_dioxide": { + "name": "diss_carb_dioxide", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per liter, milligram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample", + "title": "dissolved carbon dioxide", + "examples": [ + { + "value": "5 milligram per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "dissolved carbon dioxide" + ], + "rank": 14, + "is_a": "core field", + "slot_uri": "MIXS:0000436", + "alias": "diss_carb_dioxide", + "owner": "BiofilmInterface", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "diss_hydrogen": { + "name": "diss_hydrogen", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of dissolved hydrogen", + "title": "dissolved hydrogen", + "examples": [ + { + "value": "0.3 micromole per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "dissolved hydrogen" + ], + "rank": 15, + "is_a": "core field", + "slot_uri": "MIXS:0000179", + "alias": "diss_hydrogen", + "owner": "BiofilmInterface", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "diss_inorg_carb": { + "name": "diss_inorg_carb", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "microgram per liter, milligram per liter, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter", + "title": "dissolved inorganic carbon", + "examples": [ + { + "value": "2059 micromole per kilogram" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "dissolved inorganic carbon" + ], + "rank": 16, + "is_a": "core field", + "slot_uri": "MIXS:0000434", + "alias": "diss_inorg_carb", + "owner": "BiofilmInterface", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "diss_org_carb": { + "name": "diss_org_carb", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per liter, milligram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid", + "title": "dissolved organic carbon", + "examples": [ + { + "value": "197 micromole per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "dissolved organic carbon" + ], + "rank": 17, + "is_a": "core field", + "slot_uri": "MIXS:0000433", + "alias": "diss_org_carb", + "owner": "BiofilmInterface", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "diss_org_nitro": { + "name": "diss_org_nitro", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "microgram per liter, milligram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2", + "title": "dissolved organic nitrogen", + "examples": [ + { + "value": "0.05 micromole per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "dissolved organic nitrogen" + ], + "rank": 18, + "is_a": "core field", + "slot_uri": "MIXS:0000162", + "alias": "diss_org_nitro", + "owner": "BiofilmInterface", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "diss_oxygen": { + "name": "diss_oxygen", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per kilogram, milligram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of dissolved oxygen", + "title": "dissolved oxygen", + "examples": [ + { + "value": "175 micromole per kilogram" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "dissolved oxygen" + ], + "rank": 19, + "is_a": "core field", + "slot_uri": "MIXS:0000119", + "alias": "diss_oxygen", + "owner": "BiofilmInterface", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "ecosystem": { + "name": "ecosystem", + "description": "An ecosystem is a combination of a physical environment (abiotic factors) and all the organisms (biotic factors) that interact with this environment. Ecosystem is in position 1/5 in a GOLD path.", + "comments": [ + "The abiotic factors play a profound role on the type and composition of organisms in a given environment. The GOLD Ecosystem at the top of the five-level classification system is aimed at capturing the broader environment from which an organism or environmental sample is collected. The three broad groups under Ecosystem are Environmental, Host-associated, and Engineered. They represent samples collected from a natural environment or from another organism or from engineered environments like bioreactors respectively." + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "https://gold.jgi.doe.gov/help" + ], + "rank": 9, + "is_a": "gold_path_field", + "alias": "ecosystem", + "owner": "BiofilmInterface", + "domain_of": [ + "Biosample", + "Study", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "EcosystemEnum", + "recommended": true + }, + "ecosystem_category": { + "name": "ecosystem_category", + "description": "Ecosystem categories represent divisions within the ecosystem based on specific characteristics of the environment from where an organism or sample is isolated. Ecosystem category is in position 2/5 in a GOLD path.", + "comments": [ + "The Environmental ecosystem (for example) is divided into Air, Aquatic and Terrestrial. Ecosystem categories for Host-associated samples can be individual hosts or phyla and for engineered samples it may be manipulated environments like bioreactors, solid waste etc." + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "https://gold.jgi.doe.gov/help" + ], + "rank": 10, + "is_a": "gold_path_field", + "alias": "ecosystem_category", + "owner": "BiofilmInterface", + "domain_of": [ + "Biosample", + "Study", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "EcosystemCategoryEnum", + "recommended": true + }, + "ecosystem_subtype": { + "name": "ecosystem_subtype", + "description": "Ecosystem subtypes represent further subdivision of Ecosystem types into more distinct subtypes. Ecosystem subtype is in position 4/5 in a GOLD path.", + "comments": [ + "Ecosystem Type Marine (Environmental -> Aquatic -> Marine) is further divided (for example) into Intertidal zone, Coastal, Pelagic, Intertidal zone etc. in the Ecosystem subtype category." + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "https://gold.jgi.doe.gov/help" + ], + "rank": 12, + "is_a": "gold_path_field", + "alias": "ecosystem_subtype", + "owner": "BiofilmInterface", + "domain_of": [ + "Biosample", + "Study", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "EcosystemSubtypeEnum", + "recommended": true + }, + "ecosystem_type": { + "name": "ecosystem_type", + "description": "Ecosystem types represent things having common characteristics within the Ecosystem Category. These common characteristics based grouping is still broad but specific to the characteristics of a given environment. Ecosystem type is in position 3/5 in a GOLD path.", + "comments": [ + "The Aquatic ecosystem category (for example) may have ecosystem types like Marine or Thermal springs etc. Ecosystem category Air may have Indoor air or Outdoor air as different Ecosystem Types. In the case of Host-associated samples, ecosystem type can represent Respiratory system, Digestive system, Roots etc." + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "https://gold.jgi.doe.gov/help" + ], + "rank": 11, + "is_a": "gold_path_field", + "alias": "ecosystem_type", + "owner": "BiofilmInterface", + "domain_of": [ + "Biosample", + "Study", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "EcosystemTypeEnum", + "recommended": true + }, + "elev": { + "name": "elev", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + } + }, + "description": "Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit.", + "title": "elevation, meters", + "comments": [ + "All elevations must be reported in meters. Provide the numerical portion only.", + "Please use https://www.advancedconverter.com/map-tools/find-altitude-by-coordinates, if needed, to help estimate the elevation based on latitude and longitude coordinates." + ], + "examples": [ + { + "value": "225" + }, + { + "value": "0" + }, + { + "value": "1250" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "elevation" + ], + "rank": 6, + "is_a": "environment field", + "slot_uri": "MIXS:0000093", + "alias": "elev", + "owner": "BiofilmInterface", + "domain_of": [ + "FieldResearchSite", + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "float", + "required": true, + "multivalued": false + }, + "env_broad_scale": { + "name": "env_broad_scale", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "The major environment type(s) where the sample was collected. Recommend subclasses of biome [ENVO:00000428]. Multiple terms can be separated by one or more pipes." + }, + "tooltip": { + "tag": "tooltip", + "value": "The biome or major environmental system where the sample or specimen originated. Choose values from subclasses of the 'biome' class [ENVO:00000428] in the Environment Ontology (ENVO). For host-associated or plant-associated samples, use terms from the UBERON or Plant Ontology to describe the broad anatomical or morphological context" + } + }, + "description": "In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO's biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html", + "title": "broad-scale environmental context", + "notes": [ + "range changed to enumeration late in makefile, so this is modified (but \"sample ID\" anyway)" + ], + "examples": [ + { + "value": "oceanic epipelagic zone biome [ENVO:01000033] for annotating a water sample from the photic zone in middle of the Atlantic Ocean" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "broad-scale environmental context" + ], + "rank": 6, + "is_a": "environment field", + "string_serialization": "{termLabel} {[termID]}", + "slot_uri": "MIXS:0000012", + "alias": "env_broad_scale", + "owner": "BiofilmInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "string", + "required": true, + "multivalued": false, + "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$" + }, + "env_local_scale": { + "name": "env_local_scale", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "Environmental entities having causal influences upon the entity at time of sampling." + }, + "tooltip": { + "tag": "tooltip", + "value": "The specific environmental entities or features near the sample or specimen that significantly influence its characteristics or composition. These entities are typically smaller in scale than the broad environmental context. Values for this field should be countable, material nouns and must be chosen from subclasses of BFO:0000040 (material entity) that appear in the Environment Ontology (ENVO). For host-associated or plant-associated samples, use terms from the UBERON or Plant Ontology to describe specific anatomical structures or plant parts." + } + }, + "description": "Report the entity or entities which are in the sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. We recommend using EnvO terms which are of smaller spatial grain than your entry for env_broad_scale. Terms, such as anatomical sites, from other OBO Library ontologies which interoperate with EnvO (e.g. UBERON) are accepted in this field. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS.", + "title": "local environmental context", + "notes": [ + "range changed to enumeration late in makefile, so this is modified (but \"sample ID\" anyway)" + ], + "examples": [ + { + "value": "canopy [ENVO:00000047]" + }, + { + "value": "herb and fern layer [ENVO:01000337]" + }, + { + "value": "litter layer [ENVO:01000338]" + }, + { + "value": "understory [01000335]" + }, + { + "value": "shrub layer [ENVO:01000336]" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "local environmental context" + ], + "rank": 7, + "is_a": "environment field", + "string_serialization": "{termLabel} {[termID]}", + "slot_uri": "MIXS:0000013", + "alias": "env_local_scale", + "owner": "BiofilmInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "string", + "required": true, + "multivalued": false, + "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$" + }, + "env_medium": { + "name": "env_medium", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "The material displaced by the entity at time of sampling. Recommend subclasses of environmental material [ENVO:00010483]." + }, + "tooltip": { + "tag": "tooltip", + "value": "The predominant environmental material or substrate that directly surrounds or hosts the sample or specimen at the time of sampling. Choose values from subclasses of the 'environmental material' class [ENVO:00010483] in the Environment Ontology (ENVO). Values for this field should be measurable or mass material nouns, representing continuous environmental materials. For host-associated or plant-associated samples, use terms from the UBERON or Plant Ontology to indicate a tissue, organ, or plant structure" + } + }, + "description": "Report the environmental material(s) immediately surrounding the sample or specimen at the time of sampling. We recommend using subclasses of 'environmental material' (http://purl.obolibrary.org/obo/ENVO_00010483). EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS . Terms from other OBO ontologies are permissible as long as they reference mass/volume nouns (e.g. air, water, blood) and not discrete, countable entities (e.g. a tree, a leaf, a table top).", + "title": "environmental medium", + "notes": [ + "range changed to enumeration late in makefile, so this is modified (but \"sample ID\" anyway)" + ], + "examples": [ + { + "value": "soil [ENVO:00001998]" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "environmental medium" + ], + "rank": 8, + "is_a": "environment field", + "string_serialization": "{termLabel} {[termID]}", + "slot_uri": "MIXS:0000014", + "alias": "env_medium", + "owner": "BiofilmInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "string", + "required": true, + "multivalued": false, + "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$" + }, + "experimental_factor": { + "name": "experimental_factor", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "text or EFO and/or OBI" + } + }, + "description": "Experimental factors are essentially the variable aspects of an experiment design which can be used to describe an experiment, or set of experiments, in an increasingly detailed manner. This field accepts ontology terms from Experimental Factor Ontology (EFO) and/or Ontology for Biomedical Investigations (OBI). For a browser of EFO (v 2.95) terms, please see http://purl.bioontology.org/ontology/EFO; for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI", + "title": "experimental factor", + "examples": [ + { + "value": "time series design [EFO:EFO_0001779]" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "experimental factor" + ], + "rank": 12, + "is_a": "investigation field", + "string_serialization": "{termLabel} {[termID]}|{text}", + "slot_uri": "MIXS:0000008", + "alias": "experimental_factor", + "owner": "BiofilmInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false + }, + "geo_loc_name": { + "name": "geo_loc_name", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "country or sea name (INSDC or GAZ): region(GAZ), specific location name" + } + }, + "description": "The geographical origin of the sample as defined by the country or sea name followed by specific region name.", + "title": "geographic location (country and/or sea,region)", + "examples": [ + { + "value": "USA: Maryland, Bethesda" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "geographic location (country and/or sea,region)" + ], + "rank": 4, + "is_a": "environment field", + "string_serialization": "{text}: {text}, {text}", + "slot_uri": "MIXS:0000010", + "alias": "geo_loc_name", + "owner": "BiofilmInterface", + "domain_of": [ + "FieldResearchSite", + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "required": true, + "multivalued": false, + "pattern": "^[^:, ][^:]*: [^:, ][^,]*, [^:, ].*$" + }, + "glucosidase_act": { + "name": "glucosidase_act", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "mol per liter per hour" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Measurement of glucosidase activity", + "title": "glucosidase activity", + "examples": [ + { + "value": "5 mol per liter per hour" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "glucosidase activity" + ], + "rank": 20, + "is_a": "core field", + "slot_uri": "MIXS:0000137", + "alias": "glucosidase_act", + "owner": "BiofilmInterface", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "lat_lon": { + "name": "lat_lon", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "decimal degrees, limit to 8 decimal points" + } + }, + "description": "The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system", + "title": "geographic location (latitude and longitude)", + "notes": [ + "This is currently a required field but it's not clear if this should be required for human hosts" + ], + "examples": [ + { + "value": "50.586825 6.408977" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "geographic location (latitude and longitude)" + ], + "rank": 5, + "is_a": "environment field", + "string_serialization": "{lat lon}", + "slot_uri": "MIXS:0000009", + "alias": "lat_lon", + "owner": "BiofilmInterface", + "domain_of": [ + "FieldResearchSite", + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "required": true, + "multivalued": false, + "pattern": "^[-+]?([1-8]?\\d(\\.\\d{1,8})?|90(\\.0{1,8})?)\\s[-+]?(180(\\.0{1,8})?|((1[0-7]\\d)|([1-9]?\\d))(\\.\\d{1,8})?)$" + }, + "magnesium": { + "name": "magnesium", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "mole per liter, milligram per liter, parts per million, micromole per kilogram" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of magnesium in the sample", + "title": "magnesium", + "examples": [ + { + "value": "52.8 micromole per kilogram" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "magnesium" + ], + "rank": 21, + "is_a": "core field", + "slot_uri": "MIXS:0000431", + "alias": "magnesium", + "owner": "BiofilmInterface", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "mean_frict_vel": { + "name": "mean_frict_vel", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "meter per second" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Measurement of mean friction velocity", + "title": "mean friction velocity", + "examples": [ + { + "value": "0.5 meter per second" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "mean friction velocity" + ], + "rank": 22, + "is_a": "core field", + "slot_uri": "MIXS:0000498", + "alias": "mean_frict_vel", + "owner": "BiofilmInterface", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "mean_peak_frict_vel": { + "name": "mean_peak_frict_vel", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "meter per second" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Measurement of mean peak friction velocity", + "title": "mean peak friction velocity", + "examples": [ + { + "value": "1 meter per second" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "mean peak friction velocity" + ], + "rank": 23, + "is_a": "core field", + "slot_uri": "MIXS:0000502", + "alias": "mean_peak_frict_vel", + "owner": "BiofilmInterface", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "methane": { + "name": "methane", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per liter, parts per billion, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Methane (gas) amount or concentration at the time of sampling", + "title": "methane", + "examples": [ + { + "value": "1800 parts per billion" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "methane" + ], + "rank": 24, + "is_a": "core field", + "slot_uri": "MIXS:0000101", + "alias": "methane", + "owner": "BiofilmInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "SedimentInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "misc_param": { + "name": "misc_param", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "parameter name;measurement value" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Any other measurement performed or parameter collected, that is not listed here", + "title": "miscellaneous parameter", + "examples": [ + { + "value": "Bicarbonate ion concentration;2075 micromole per kilogram" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "miscellaneous parameter" + ], + "rank": 23, + "is_a": "core field", + "string_serialization": "{text};{float} {unit}", + "slot_uri": "MIXS:0000752", + "alias": "misc_param", + "owner": "BiofilmInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false, + "pattern": "^([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+\\|)*([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+)$" + }, + "n_alkanes": { + "name": "n_alkanes", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "n-alkane name;measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Concentration of n-alkanes; can include multiple n-alkanes", + "title": "n-alkanes", + "examples": [ + { + "value": "n-hexadecane;100 milligram per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "n-alkanes" + ], + "rank": 25, + "is_a": "core field", + "string_serialization": "{text};{float} {unit}", + "slot_uri": "MIXS:0000503", + "alias": "n_alkanes", + "owner": "BiofilmInterface", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+\\|)*([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+)$" + }, + "nitrate": { + "name": "nitrate", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per liter, milligram per liter, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of nitrate in the sample", + "title": "nitrate", + "examples": [ + { + "value": "65 micromole per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "nitrate" + ], + "rank": 26, + "is_a": "core field", + "slot_uri": "MIXS:0000425", + "alias": "nitrate", + "owner": "BiofilmInterface", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "nitrite": { + "name": "nitrite", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per liter, milligram per liter, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of nitrite in the sample", + "title": "nitrite", + "examples": [ + { + "value": "0.5 micromole per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "nitrite" + ], + "rank": 27, + "is_a": "core field", + "slot_uri": "MIXS:0000426", + "alias": "nitrite", + "owner": "BiofilmInterface", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "nitro": { + "name": "nitro", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of nitrogen (total)", + "title": "nitrogen", + "examples": [ + { + "value": "4.2 micromole per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "nitrogen" + ], + "rank": 28, + "is_a": "core field", + "slot_uri": "MIXS:0000504", + "alias": "nitro", + "owner": "BiofilmInterface", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "org_carb": { + "name": "org_carb", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of organic carbon", + "title": "organic carbon", + "examples": [ + { + "value": "1.5 microgram per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "organic carbon" + ], + "rank": 29, + "is_a": "core field", + "slot_uri": "MIXS:0000508", + "alias": "org_carb", + "owner": "BiofilmInterface", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "org_matter": { + "name": "org_matter", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "microgram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of organic matter", + "title": "organic matter", + "examples": [ + { + "value": "1.75 milligram per cubic meter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "organic matter" + ], + "rank": 45, + "is_a": "core field", + "slot_uri": "MIXS:0000204", + "alias": "org_matter", + "owner": "BiofilmInterface", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "MiscEnvsInterface", + "SedimentInterface", + "SoilInterface", + "WaterInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "org_nitro": { + "name": "org_nitro", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "microgram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of organic nitrogen", + "title": "organic nitrogen", + "examples": [ + { + "value": "4 micromole per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "organic nitrogen" + ], + "rank": 46, + "is_a": "core field", + "slot_uri": "MIXS:0000205", + "alias": "org_nitro", + "owner": "BiofilmInterface", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "MiscEnvsInterface", + "SedimentInterface", + "SoilInterface", + "WaterInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "organism_count": { + "name": "organism_count", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "organism name;measurement value;enumeration" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "number of cells per cubic meter, number of cells per milliliter, number of cells per cubic centimeter" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr)", + "title": "organism count", + "examples": [ + { + "value": "total prokaryotes;3.5e7 cells per milliliter;qPCR" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "organism count" + ], + "rank": 30, + "is_a": "core field", + "slot_uri": "MIXS:0000103", + "alias": "organism_count", + "owner": "BiofilmInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^([-+]?[0-9]*\\.?[0-9]+ +\\S.*\\|)*([-+]?[0-9]*\\.?[0-9]+ +\\S.*)$" + }, + "oxy_stat_samp": { + "name": "oxy_stat_samp", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Oxygenation status of sample", + "title": "oxygenation status of sample", + "examples": [ + { + "value": "aerobic" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "oxygenation status of sample" + ], + "rank": 25, + "is_a": "core field", + "slot_uri": "MIXS:0000753", + "alias": "oxy_stat_samp", + "owner": "BiofilmInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_section", + "range": "OxyStatSampEnum", + "multivalued": false + }, + "part_org_carb": { + "name": "part_org_carb", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "microgram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of particulate organic carbon", + "title": "particulate organic carbon", + "examples": [ + { + "value": "1.92 micromole per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "particulate organic carbon" + ], + "rank": 31, + "is_a": "core field", + "slot_uri": "MIXS:0000515", + "alias": "part_org_carb", + "owner": "BiofilmInterface", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "perturbation": { + "name": "perturbation", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "perturbation type name;perturbation interval and duration" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types", + "title": "perturbation", + "examples": [ + { + "value": "antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "perturbation" + ], + "rank": 33, + "is_a": "core field", + "string_serialization": "{text};{Rn/start_time/end_time/duration}", + "slot_uri": "MIXS:0000754", + "alias": "perturbation", + "owner": "BiofilmInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "petroleum_hydrocarb": { + "name": "petroleum_hydrocarb", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of petroleum hydrocarbon", + "title": "petroleum hydrocarbon", + "examples": [ + { + "value": "0.05 micromole per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "petroleum hydrocarbon" + ], + "rank": 34, + "is_a": "core field", + "slot_uri": "MIXS:0000516", + "alias": "petroleum_hydrocarb", + "owner": "BiofilmInterface", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "ph": { + "name": "ph", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "pH measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid", + "title": "pH", + "notes": [ + "Use modified term" + ], + "examples": [ + { + "value": "7.2" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "pH" + ], + "rank": 27, + "is_a": "core field", + "string_serialization": "{float}", + "slot_uri": "MIXS:0001001", + "alias": "ph", + "owner": "BiofilmInterface", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "MiscEnvsInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "float", + "recommended": true, + "multivalued": false, + "minimum_value": 0, + "maximum_value": 14 + }, + "ph_meth": { + "name": "ph_meth", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "PMID,DOI or url" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Reference or method used in determining ph", + "title": "pH method", + "comments": [ + "This can include a link to the instrument used or a citation for the method." + ], + "examples": [ + { + "value": "https://www.southernlabware.com/pc9500-benchtop-ph-conductivity-meter-kit-ph-accuracy-2000mv-ph-range-2-000-to-20-000.html?gclid=Cj0KCQiAwJWdBhCYARIsAJc4idCO5vtvbVMf545fcvdROFqa6zjzNSoywNx6K4k9Coo9cCc2pybtvGsaAiR0EALw_wcB" + }, + { + "value": "https://doi.org/10.2136/sssabookser5.3.c16" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "pH method" + ], + "rank": 41, + "is_a": "core field", + "string_serialization": "{PMID}|{DOI}|{URL}", + "slot_uri": "MIXS:0001106", + "alias": "ph_meth", + "owner": "BiofilmInterface", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "MiscEnvsInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false + }, + "phaeopigments": { + "name": "phaeopigments", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "phaeopigment name;measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milligram per cubic meter" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Concentration of phaeopigments; can include multiple phaeopigments", + "title": "phaeopigments", + "examples": [ + { + "value": "2.5 milligram per cubic meter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "phaeopigments" + ], + "rank": 35, + "is_a": "core field", + "string_serialization": "{text};{float} {unit}", + "slot_uri": "MIXS:0000180", + "alias": "phaeopigments", + "owner": "BiofilmInterface", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+\\|)*([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+)$" + }, + "phosphate": { + "name": "phosphate", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of phosphate", + "title": "phosphate", + "examples": [ + { + "value": "0.7 micromole per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "phosphate" + ], + "rank": 53, + "is_a": "core field", + "slot_uri": "MIXS:0000505", + "alias": "phosphate", + "owner": "BiofilmInterface", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "MiscEnvsInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "phosplipid_fatt_acid": { + "name": "phosplipid_fatt_acid", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "phospholipid fatty acid name;measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "mole per gram, mole per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Concentration of phospholipid fatty acids; can include multiple values", + "title": "phospholipid fatty acid", + "examples": [ + { + "value": "2.98 milligram per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "phospholipid fatty acid" + ], + "rank": 36, + "is_a": "core field", + "string_serialization": "{text};{float} {unit}", + "slot_uri": "MIXS:0000181", + "alias": "phosplipid_fatt_acid", + "owner": "BiofilmInterface", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+\\|)*([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+)$" + }, + "potassium": { + "name": "potassium", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milligram per liter, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of potassium in the sample", + "title": "potassium", + "examples": [ + { + "value": "463 milligram per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "potassium" + ], + "rank": 38, + "is_a": "core field", + "slot_uri": "MIXS:0000430", + "alias": "potassium", + "owner": "BiofilmInterface", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "pressure": { + "name": "pressure", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "atmosphere" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Pressure to which the sample is subject to, in atmospheres", + "title": "pressure", + "examples": [ + { + "value": "50 atmosphere" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "pressure" + ], + "rank": 39, + "is_a": "core field", + "slot_uri": "MIXS:0000412", + "alias": "pressure", + "owner": "BiofilmInterface", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "redox_potential": { + "name": "redox_potential", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "millivolt" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential", + "title": "redox potential", + "examples": [ + { + "value": "300 millivolt" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "redox potential" + ], + "rank": 40, + "is_a": "core field", + "slot_uri": "MIXS:0000182", + "alias": "redox_potential", + "owner": "BiofilmInterface", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "salinity": { + "name": "salinity", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "practical salinity unit, percentage" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The total concentration of all dissolved salts in a liquid or solid sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater.", + "title": "salinity", + "examples": [ + { + "value": "25 practical salinity unit" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "salinity" + ], + "rank": 54, + "is_a": "core field", + "slot_uri": "MIXS:0000183", + "alias": "salinity", + "owner": "BiofilmInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "samp_collec_device": { + "name": "samp_collec_device", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "device name" + } + }, + "description": "The device used to collect an environmental sample. This field accepts terms listed under environmental sampling device (http://purl.obolibrary.org/obo/ENVO). This field also accepts terms listed under specimen collection device (http://purl.obolibrary.org/obo/GENEPIO_0002094).", + "title": "sample collection device", + "comments": [ + "Report dimensions and details when applicable" + ], + "examples": [ + { + "value": "swab, biopsy, niskin bottle, push core, drag swab [GENEPIO:0002713]" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sample collection device" + ], + "rank": 14, + "is_a": "nucleic acid sequence source field", + "string_serialization": "{termLabel} {[termID]}|{text}", + "slot_uri": "MIXS:0000002", + "alias": "samp_collec_device", + "owner": "BiofilmInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "recommended": true, + "multivalued": false + }, + "samp_collec_method": { + "name": "samp_collec_method", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "PMID,DOI,url , or text" + } + }, + "description": "The method employed for collecting the sample.", + "title": "sample collection method", + "comments": [ + "This can be a citation or description" + ], + "examples": [ + { + "value": "swabbing" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sample collection method" + ], + "rank": 15, + "is_a": "nucleic acid sequence source field", + "string_serialization": "{PMID}|{DOI}|{URL}|{text}", + "slot_uri": "MIXS:0001225", + "alias": "samp_collec_method", + "owner": "BiofilmInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "multivalued": false + }, + "samp_mat_process": { + "name": "samp_mat_process", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "text" + } + }, + "description": "A brief description of any processing applied to the sample during or after retrieving the sample from environment, or a link to the relevant protocol(s) performed.", + "title": "sample material processing", + "examples": [ + { + "value": "filtering of seawater" + }, + { + "value": "storing samples in ethanol" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sample material processing" + ], + "rank": 12, + "is_a": "nucleic acid sequence source field", + "string_serialization": "{text}", + "slot_uri": "MIXS:0000016", + "alias": "samp_mat_process", + "owner": "BiofilmInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "multivalued": false + }, + "samp_size": { + "name": "samp_size", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "millliter, gram, milligram, liter" + } + }, + "description": "The total amount or size (volume (ml), mass (g) or area (m2) ) of sample collected.", + "title": "amount or size of sample collected", + "comments": [ + "This refers to the TOTAL amount of sample collected from the experiment. NOT the amount sent to each institution or collected for a specific analysis." + ], + "examples": [ + { + "value": "5 grams" + }, + { + "value": "10 mL" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "amount or size of sample collected" + ], + "rank": 18, + "is_a": "nucleic acid sequence source field", + "string_serialization": "{float} {unit}", + "slot_uri": "MIXS:0000001", + "alias": "samp_size", + "owner": "BiofilmInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? \\S+$" + }, + "samp_store_dur": { + "name": "samp_store_dur", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "duration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Duration for which the sample was stored", + "title": "sample storage duration", + "examples": [ + { + "value": "P1Y6M" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sample storage duration" + ], + "rank": 353, + "is_a": "core field", + "string_serialization": "{duration}", + "slot_uri": "MIXS:0000116", + "alias": "samp_store_dur", + "owner": "BiofilmInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "samp_store_loc": { + "name": "samp_store_loc", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "location name" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Location at which sample was stored, usually name of a specific freezer/room", + "title": "sample storage location", + "examples": [ + { + "value": "Freezer no:5" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sample storage location" + ], + "rank": 41, + "is_a": "core field", + "string_serialization": "{text}", + "slot_uri": "MIXS:0000755", + "alias": "samp_store_loc", + "owner": "BiofilmInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "samp_store_temp": { + "name": "samp_store_temp", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "degree Celsius" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Temperature at which the sample was stored (degrees are assumed)", + "title": "sample storage temperature", + "examples": [ + { + "value": "-80 Celsius" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sample storage temperature" + ], + "rank": 7, + "is_a": "core field", + "slot_uri": "MIXS:0000110", + "alias": "samp_store_temp", + "owner": "BiofilmInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "required": true, + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "sample_link": { + "name": "sample_link", + "description": "A unique identifier to assign parent-child, subsample, or sibling samples. This is relevant when a sample or other material was used to generate the new sample.", + "title": "sample linkage", + "notes": [ + "also tempted to include SampIdNewTermsMixin but if len(slot_usage.keys()) > 1 and \"placeholder\" in slot_usage.keys():AttributeError: 'list' object has no attribute 'keys'" + ], + "comments": [ + "This field allows multiple entries separated by ; (Examples: Soil collected from the field will link with the soil used in an incubation. The soil a plant was grown in links to the plant sample. An original culture sample was transferred to a new vial and generated a new sample)" + ], + "examples": [ + { + "value": "IGSN:DSJ0284" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "rank": 5, + "string_serialization": "{text}:{text}", + "alias": "sample_link", + "owner": "BiofilmInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface", + "SampIdNewTermsMixin" + ], + "slot_group": "sample_id_section", + "range": "string", + "recommended": true, + "multivalued": false, + "pattern": "[^\\:\\n\\r]+\\:[^\\:\\n\\r]+" + }, + "silicate": { + "name": "silicate", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of silicate", + "title": "silicate", + "examples": [ + { + "value": "0.05 micromole per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "silicate" + ], + "rank": 43, + "is_a": "core field", + "slot_uri": "MIXS:0000184", + "alias": "silicate", + "owner": "BiofilmInterface", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "size_frac": { + "name": "size_frac", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "filter size value range" + } + }, + "description": "Filtering pore size used in sample preparation", + "title": "size fraction selected", + "examples": [ + { + "value": "0-0.22 micrometer" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "size fraction selected" + ], + "rank": 285, + "is_a": "nucleic acid sequence source field", + "string_serialization": "{float}-{float} {unit}", + "slot_uri": "MIXS:0000017", + "alias": "size_frac", + "owner": "BiofilmInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "sodium": { + "name": "sodium", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milligram per liter, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Sodium concentration in the sample", + "title": "sodium", + "examples": [ + { + "value": "10.5 milligram per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sodium" + ], + "rank": 363, + "is_a": "core field", + "slot_uri": "MIXS:0000428", + "alias": "sodium", + "owner": "BiofilmInterface", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "specific_ecosystem": { + "name": "specific_ecosystem", + "description": "Specific ecosystems represent specific features of the environment like aphotic zone in an ocean or gastric mucosa within a host digestive system. Specific ecosystem is in position 5/5 in a GOLD path.", + "comments": [ + "Specific ecosystems help to define samples based on very specific characteristics of an environment under the five-level classification system." + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "https://gold.jgi.doe.gov/help" + ], + "rank": 13, + "is_a": "gold_path_field", + "alias": "specific_ecosystem", + "owner": "BiofilmInterface", + "domain_of": [ + "Biosample", + "Study", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "SpecificEcosystemEnum", + "recommended": true + }, + "sulfate": { + "name": "sulfate", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per liter, milligram per liter, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of sulfate in the sample", + "title": "sulfate", + "examples": [ + { + "value": "5 micromole per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sulfate" + ], + "rank": 44, + "is_a": "core field", + "slot_uri": "MIXS:0000423", + "alias": "sulfate", + "owner": "BiofilmInterface", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "sulfide": { + "name": "sulfide", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per liter, milligram per liter, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of sulfide in the sample", + "title": "sulfide", + "examples": [ + { + "value": "2 micromole per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sulfide" + ], + "rank": 371, + "is_a": "core field", + "slot_uri": "MIXS:0000424", + "alias": "sulfide", + "owner": "BiofilmInterface", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "temp": { + "name": "temp", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "degree Celsius" + } + }, + "description": "Temperature of the sample at the time of sampling.", + "title": "temperature", + "examples": [ + { + "value": "25 degree Celsius" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "temperature" + ], + "rank": 37, + "is_a": "environment field", + "slot_uri": "MIXS:0000113", + "alias": "temp", + "owner": "BiofilmInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "tot_carb": { + "name": "tot_carb", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "microgram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Total carbon content", + "title": "total carbon", + "todos": [ + "is this inorganic and organic? both? could use some clarification.", + "ug/L doesn't seem like the right units. Should check this slots usage in databases and re-evaluate. I couldn't find any references that provided this data in this format", + "is this inorganic and organic? both? could use some clarification.", + "ug/L doesn't seem like the right units. Should check this slots usage in databases and re-evaluate. I couldn't find any references that provided this data in this format" + ], + "examples": [ + { + "value": "1 ug/L" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "total carbon" + ], + "rank": 47, + "is_a": "core field", + "slot_uri": "MIXS:0000525", + "alias": "tot_carb", + "owner": "BiofilmInterface", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "SedimentInterface", + "SoilInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "tot_nitro_content": { + "name": "tot_nitro_content", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "microgram per liter, micromole per liter, milligram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Total nitrogen content of the sample", + "title": "total nitrogen content", + "examples": [ + { + "value": "5 mg N/ L" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "total nitrogen content" + ], + "rank": 48, + "is_a": "core field", + "slot_uri": "MIXS:0000530", + "alias": "tot_nitro_content", + "owner": "BiofilmInterface", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "SedimentInterface", + "SoilInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "tot_org_carb": { + "name": "tot_org_carb", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "gram Carbon per kilogram sample material" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content", + "title": "total organic carbon", + "todos": [ + "check description. How are they different?", + "check description. How are they different?" + ], + "examples": [ + { + "value": "5 mg N/ L" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "total organic carbon" + ], + "rank": 50, + "is_a": "core field", + "slot_uri": "MIXS:0000533", + "alias": "tot_org_carb", + "owner": "BiofilmInterface", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "SedimentInterface", + "SoilInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "turbidity": { + "name": "turbidity", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "formazin turbidity unit, formazin nephelometric units" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Measure of the amount of cloudiness or haziness in water caused by individual particles", + "title": "turbidity", + "examples": [ + { + "value": "0.3 nephelometric turbidity units" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "turbidity" + ], + "rank": 47, + "is_a": "core field", + "slot_uri": "MIXS:0000191", + "alias": "turbidity", + "owner": "BiofilmInterface", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "water_content": { + "name": "water_content", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "string" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "gram per gram or cubic centimeter per cubic centimeter" + } + }, + "description": "Water content measurement", + "title": "water content", + "todos": [ + "value in preferred unit is too limiting. need to change this", + "check and correct validation so examples are accepted", + "how to manage multiple water content methods?" + ], + "examples": [ + { + "value": "0.75 g water/g dry soil" + }, + { + "value": "75% water holding capacity" + }, + { + "value": "1.1 g fresh weight/ dry weight" + }, + { + "value": "10% water filled pore space" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "water content" + ], + "rank": 39, + "is_a": "core field", + "string_serialization": "{float or pct} {unit}", + "slot_uri": "MIXS:0000185", + "alias": "water_content", + "owner": "BiofilmInterface", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "SedimentInterface", + "SoilInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)?%? \\S.+$" + }, + "analysis_type": { + "name": "analysis_type", + "description": "Select all the data types associated or available for this biosample", + "title": "analysis/data type", + "examples": [ + { + "value": "metagenomics; metabolomics; proteomics" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "MIxS:investigation_type" + ], + "rank": 3, + "alias": "analysis_type", + "owner": "BiofilmInterface", + "domain_of": [ + "Biosample", + "DhMultiviewCommonColumnsMixin", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "EmslInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "JgiMgInterface", + "JgiMgLrInterface", + "JgiMtInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "AnalysisTypeEnum", + "required": true, + "recommended": false, + "multivalued": true + }, + "samp_name": { + "name": "samp_name", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "text" + } + }, + "description": "A local identifier or name that for the material sample collected. Refers to the original material collected or to any derived sub-samples.", + "title": "sample name", + "comments": [ + "It can have any format, but we suggest that you make it concise, unique and consistent within your lab, and as informative as possible." + ], + "examples": [ + { + "value": "Rock core CB1178(5-6) from NSW" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sample name" + ], + "rank": 1, + "is_a": "investigation field", + "string_serialization": "{text}", + "slot_uri": "MIXS:0001107", + "identifier": true, + "alias": "samp_name", + "owner": "BiofilmInterface", + "domain_of": [ + "Biosample", + "DhMultiviewCommonColumnsMixin", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "EmslInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "JgiMgInterface", + "JgiMgLrInterface", + "JgiMtInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "string", + "required": true, + "multivalued": false + }, + "source_mat_id": { + "name": "source_mat_id", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "for cultures of microorganisms: identifiers for two culture collections; for other material a unique arbitrary identifer" + } + }, + "description": "A globally unique identifier assigned to the biological sample.", + "title": "source material identifier", + "todos": [ + "Currently, the comments say to use UUIDs. However, if we implement assigning NMDC identifiers with the minter we dont need to require a GUID. It can be an optional field to fill out only if they already have a resolvable ID.", + "Currently, the comments say to use UUIDs. However, if we implement assigning NMDC identifiers with the minter we dont need to require a GUID. It can be an optional field to fill out only if they already have a resolvable ID." + ], + "notes": [ + "The source material IS the Globally Unique ID" + ], + "comments": [ + "Identifiers must be prefixed. Possible FAIR prefixes are IGSNs (http://www.geosamples.org/getigsn), NCBI biosample accession numbers, ARK identifiers (https://arks.org/). These IDs enable linking to derived analytes and subsamples. If you have not assigned FAIR identifiers to your samples, you can generate UUIDs (https://www.uuidgenerator.net/).", + "Identifiers must be prefixed. Possible FAIR prefixes are IGSNs (http://www.geosamples.org/getigsn), NCBI biosample accession numbers, ARK identifiers (https://arks.org/). These IDs enable linking to derived analytes and subsamples. If you have not assigned FAIR identifiers to your samples, you can generate UUIDs (https://www.uuidgenerator.net/)." + ], + "examples": [ + { + "value": "IGSN:AU1243" + }, + { + "value": "UUID:24f1467a-40f4-11ed-b878-0242ac120002" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "source material identifiers" + ], + "rank": 2, + "is_a": "nucleic acid sequence source field", + "string_serialization": "{text}:{text}", + "slot_uri": "MIXS:0000026", + "alias": "source_mat_id", + "owner": "BiofilmInterface", + "domain_of": [ + "Biosample", + "DhMultiviewCommonColumnsMixin", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "EmslInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "JgiMgInterface", + "JgiMgLrInterface", + "JgiMtInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "string", + "multivalued": false, + "pattern": "[^\\:\\n\\r]+\\:[^\\:\\n\\r]+" + } + } + }, + "BuiltEnvInterface": { + "name": "BuiltEnvInterface", + "annotations": { + "excel_worksheet_name": { + "tag": "excel_worksheet_name", + "value": "built environment" + } + }, + "description": "built_env dh_interface", + "title": "Built Env", + "from_schema": "https://example.com/nmdc_submission_schema", + "is_a": "DhInterface", + "mixins": [ + "DhMultiviewCommonColumnsMixin", + "SampIdNewTermsMixin" + ], + "slots": [ + "abs_air_humidity", + "address", + "adj_room", + "aero_struc", + "air_temp", + "alt", + "amount_light", + "arch_struc", + "avg_dew_point", + "avg_occup", + "avg_temp", + "bathroom_count", + "bedroom_count", + "build_docs", + "build_occup_type", + "building_setting", + "built_struc_age", + "built_struc_set", + "built_struc_type", + "carb_dioxide", + "ceil_area", + "ceil_cond", + "ceil_finish_mat", + "ceil_struc", + "ceil_texture", + "ceil_thermal_mass", + "ceil_type", + "ceil_water_mold", + "collection_date", + "cool_syst_id", + "date_last_rain", + "depth", + "dew_point", + "door_comp_type", + "door_cond", + "door_direct", + "door_loc", + "door_mat", + "door_move", + "door_size", + "door_type", + "door_type_metal", + "door_type_wood", + "door_water_mold", + "drawings", + "ecosystem", + "ecosystem_category", + "ecosystem_subtype", + "ecosystem_type", + "elev", + "elevator", + "env_broad_scale", + "env_local_scale", + "env_medium", + "escalator", + "exp_duct", + "exp_pipe", + "experimental_factor", + "ext_door", + "ext_wall_orient", + "ext_window_orient", + "filter_type", + "fireplace_type", + "floor_age", + "floor_area", + "floor_cond", + "floor_count", + "floor_finish_mat", + "floor_struc", + "floor_thermal_mass", + "floor_water_mold", + "freq_clean", + "freq_cook", + "furniture", + "gender_restroom", + "geo_loc_name", + "hall_count", + "handidness", + "heat_cool_type", + "heat_deliv_loc", + "heat_sys_deliv_meth", + "heat_system_id", + "height_carper_fiber", + "indoor_space", + "indoor_surf", + "inside_lux", + "int_wall_cond", + "last_clean", + "lat_lon", + "light_type", + "max_occup", + "mech_struc", + "number_pets", + "number_plants", + "number_resident", + "occup_density_samp", + "occup_document", + "occup_samp", + "organism_count", + "pres_animal_insect", + "quad_pos", + "rel_air_humidity", + "rel_humidity_out", + "rel_samp_loc", + "room_air_exch_rate", + "room_architec_elem", + "room_condt", + "room_connected", + "room_count", + "room_dim", + "room_door_dist", + "room_door_share", + "room_hallway", + "room_loc", + "room_moist_dam_hist", + "room_net_area", + "room_occup", + "room_samp_pos", + "room_type", + "room_vol", + "room_wall_share", + "room_window_count", + "samp_floor", + "samp_room_id", + "samp_sort_meth", + "samp_time_out", + "samp_weather", + "sample_link", + "season", + "season_use", + "shad_dev_water_mold", + "shading_device_cond", + "shading_device_loc", + "shading_device_mat", + "shading_device_type", + "size_frac", + "space_typ_state", + "specific", + "specific_ecosystem", + "specific_humidity", + "substructure_type", + "surf_air_cont", + "surf_humidity", + "surf_material", + "surf_moisture", + "surf_moisture_ph", + "surf_temp", + "temp", + "temp_out", + "train_line", + "train_stat_loc", + "train_stop_loc", + "typ_occup_density", + "ventilation_type", + "vis_media", + "wall_area", + "wall_const_type", + "wall_finish_mat", + "wall_height", + "wall_loc", + "wall_surf_treatment", + "wall_texture", + "wall_thermal_mass", + "wall_water_mold", + "water_feat_size", + "water_feat_type", + "weekday", + "window_cond", + "window_cover", + "window_horiz_pos", + "window_loc", + "window_mat", + "window_open_freq", + "window_size", + "window_status", + "window_type", + "window_vert_pos", + "window_water_mold" + ], + "slot_usage": { + "abs_air_humidity": { + "name": "abs_air_humidity", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "gram per gram, kilogram per kilogram, kilogram, pound" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Actual mass of water vapor - mh20 - present in the air water vapor mixture", + "title": "absolute air humidity", + "examples": [ + { + "value": "9 gram per gram" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "absolute air humidity" + ], + "rank": 61, + "is_a": "core field", + "slot_uri": "MIXS:0000122", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "address": { + "name": "address", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "value" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The street name and building number where the sampling occurred.", + "title": "address", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "address" + ], + "rank": 62, + "is_a": "core field", + "string_serialization": "{integer}{text}", + "slot_uri": "MIXS:0000218", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "adj_room": { + "name": "adj_room", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "room name;room number" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "List of rooms (room number, room name) immediately adjacent to the sampling room", + "title": "adjacent rooms", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "adjacent rooms" + ], + "rank": 63, + "is_a": "core field", + "string_serialization": "{text};{integer}", + "slot_uri": "MIXS:0000219", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "aero_struc": { + "name": "aero_struc", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Aerospace structures typically consist of thin plates with stiffeners for the external surfaces, bulkheads and frames to support the shape and fasteners such as welds, rivets, screws and bolts to hold the components together", + "title": "aerospace structure", + "examples": [ + { + "value": "plane" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "aerospace structure" + ], + "rank": 64, + "is_a": "core field", + "string_serialization": "[plane|glider]", + "slot_uri": "MIXS:0000773", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "air_temp": { + "name": "air_temp", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "degree Celsius" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Temperature of the air at the time of sampling", + "title": "air temperature", + "examples": [ + { + "value": "20 degree Celsius" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "air temperature" + ], + "rank": 65, + "is_a": "core field", + "slot_uri": "MIXS:0000124", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "alt": { + "name": "alt", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + } + }, + "description": "Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air", + "title": "altitude", + "examples": [ + { + "value": "100 meter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "altitude" + ], + "rank": 26, + "is_a": "environment field", + "slot_uri": "MIXS:0000094", + "owner": "Biosample", + "domain_of": [ + "agriculture", + "air", + "built environment", + "core", + "food-animal and animal feed", + "food-farm environment", + "food-food production facility", + "food-human foods", + "host-associated", + "human-associated", + "human-gut", + "human-oral", + "human-skin", + "human-vaginal", + "hydrocarbon resources-cores", + "hydrocarbon resources-fluids_swabs", + "microbial mat_biofilm", + "miscellaneous natural or artificial environment", + "plant-associated", + "sediment", + "soil", + "symbiont-associated", + "wastewater_sludge", + "water", + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HostAssociatedInterface", + "MiscEnvsInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "recommended": true, + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "amount_light": { + "name": "amount_light", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "lux, lumens per square meter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The unit of illuminance and luminous emittance, measuring luminous flux per unit area", + "title": "amount of light", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "amount of light" + ], + "rank": 66, + "is_a": "core field", + "slot_uri": "MIXS:0000140", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "arch_struc": { + "name": "arch_struc", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "An architectural structure is a human-made, free-standing, immobile outdoor construction", + "title": "architectural structure", + "examples": [ + { + "value": "shed" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "architectural structure" + ], + "rank": 67, + "is_a": "core field", + "slot_uri": "MIXS:0000774", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "arch_struc_enum", + "multivalued": false + }, + "avg_dew_point": { + "name": "avg_dew_point", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "degree Celsius" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The average of dew point measures taken at the beginning of every hour over a 24 hour period on the sampling day", + "title": "average dew point", + "examples": [ + { + "value": "25.5 degree Celsius" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "average dew point" + ], + "rank": 68, + "is_a": "core field", + "slot_uri": "MIXS:0000141", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "avg_occup": { + "name": "avg_occup", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "value" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Daily average occupancy of room. Indicate the number of person(s) daily occupying the sampling room.", + "title": "average daily occupancy", + "examples": [ + { + "value": "2" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "average daily occupancy" + ], + "rank": 69, + "is_a": "core field", + "slot_uri": "MIXS:0000775", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "avg_temp": { + "name": "avg_temp", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "degree Celsius" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The average of temperatures taken at the beginning of every hour over a 24 hour period on the sampling day", + "title": "average temperature", + "examples": [ + { + "value": "12.5 degree Celsius" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "average temperature" + ], + "rank": 70, + "is_a": "core field", + "slot_uri": "MIXS:0000142", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "bathroom_count": { + "name": "bathroom_count", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "value" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The number of bathrooms in the building", + "title": "bathroom count", + "examples": [ + { + "value": "1" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "bathroom count" + ], + "rank": 71, + "is_a": "core field", + "slot_uri": "MIXS:0000776", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "bedroom_count": { + "name": "bedroom_count", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "value" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The number of bedrooms in the building", + "title": "bedroom count", + "examples": [ + { + "value": "2" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "bedroom count" + ], + "rank": 72, + "is_a": "core field", + "slot_uri": "MIXS:0000777", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "build_docs": { + "name": "build_docs", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The building design, construction and operation documents", + "title": "design, 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Generally this means concrete that is exposed. A metal deck that supports a concrete slab will act thermally as long as it is exposed to room air flow", + "title": "ceiling thermal mass", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "ceiling thermal mass" + ], + "rank": 84, + "is_a": "core field", + "slot_uri": "MIXS:0000143", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "ceil_type": { + "name": "ceil_type", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The type of ceiling according to the ceiling's appearance or construction", + "title": "ceiling type", + "examples": [ + { + "value": "coffered" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "ceiling type" + ], + "rank": 85, + "is_a": "core field", + "slot_uri": "MIXS:0000784", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "ceil_type_enum", + "multivalued": false + }, + "ceil_water_mold": { + "name": "ceil_water_mold", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Signs of the presence of mold or mildew on the ceiling", + "title": "ceiling signs of water/mold", + "examples": [ + { + "value": "presence of mold visible" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "ceiling signs of water/mold" + ], + "rank": 86, + "is_a": "core field", + "string_serialization": "[presence of mold visible|no presence of mold visible]", + "slot_uri": "MIXS:0000781", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "collection_date": { + "name": "collection_date", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "date and time" + } + }, + "description": "The date of sampling", + "title": "collection date", + "notes": [ + "MIxS collection_date accepts (truncated) ISO8601. DH taking arb prec date only", + "Use modified term (amended definition)" + ], + "examples": [ + { + "value": "2021-04-15" + }, + { + "value": "2021-04" + }, + { + "value": "2021" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "collection date" + ], + "rank": 3, + "is_a": "environment field", + "string_serialization": "{date, arbitrary precision}", + "slot_uri": "MIXS:0000011", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "required": true, + "multivalued": false, + "pattern": "^[12]\\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\\d|3[01]))?)?$" + }, + "cool_syst_id": { + "name": "cool_syst_id", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "unique identifier" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The cooling system identifier", + "title": "cooling system identifier", + "examples": [ + { + "value": "12345" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "cooling system identifier" + ], + "rank": 87, + "is_a": "core field", + "slot_uri": "MIXS:0000785", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "date_last_rain": { + "name": "date_last_rain", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "timestamp" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The date of the last time it rained", + "title": "date last rain", + "examples": [ + { + "value": "2018-05-11:T14:30Z" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "date last rain" + ], + "rank": 88, + "is_a": "core field", + "slot_uri": "MIXS:0000786", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "depth": { + "name": "depth", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + } + }, + "description": "The vertical distance below local surface, e.g. for sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples.", + "title": "depth, meters", + "notes": [ + "Use modified term" + ], + "comments": [ + "All depths must be reported in meters. Provide the numerical portion only." + ], + "examples": [ + { + "value": "0 - 0.1" + }, + { + "value": "1" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "depth" + ], + "rank": 9, + "is_a": "environment field", + "string_serialization": "{float}|{float}-{float}", + "slot_uri": "MIXS:0000018", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "recommended": true, + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)?(\\s*-\\s*[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)?)?$" + }, + "dew_point": { + "name": "dew_point", + "annotations": { + "expected_value": { + "tag": "expected_value", 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"domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "door_cond_enum", + "multivalued": false + }, + "door_direct": { + "name": "door_direct", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The direction the door opens", + "title": "door direction of opening", + "examples": [ + { + "value": "inward" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "door direction of opening" + ], + "rank": 92, + "is_a": "core field", + "slot_uri": "MIXS:0000789", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "door_direct_enum", + "multivalued": false + }, + "door_loc": { + "name": "door_loc", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The relative location of the door in the room", + "title": "door location", + "examples": [ + { + "value": "north" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "door location" + ], + "rank": 93, + "is_a": "core field", + "slot_uri": "MIXS:0000790", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "door_loc_enum", + "multivalued": false + }, + "door_mat": { + "name": "door_mat", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The material the door is composed of", + "title": "door material", + "examples": [ + { + "value": "wood" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "door material" + ], + "rank": 94, + "is_a": "core field", + "slot_uri": "MIXS:0000791", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "door_mat_enum", + "multivalued": false + }, + "door_move": { + "name": "door_move", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The type of movement of the door", + "title": "door movement", + "examples": [ + { + "value": "swinging" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "door movement" + ], + "rank": 95, + "is_a": "core field", + "slot_uri": "MIXS:0000792", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "door_move_enum", + "multivalued": false + }, + "door_size": { + "name": "door_size", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "square meter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The size of the door", + "title": "door area or size", + "examples": [ + { + "value": "2.5 square meter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "door area or size" + ], + "rank": 96, + "is_a": "core field", + "slot_uri": "MIXS:0000158", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "door_type": { + "name": "door_type", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The type of door material", + "title": "door type", + "examples": [ + { + "value": "wooden" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "door type" + ], + "rank": 97, + "is_a": "core field", + "slot_uri": "MIXS:0000794", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "door_type_enum", + "multivalued": false + }, + "door_type_metal": { + "name": "door_type_metal", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The type of metal door", + "title": "door type, metal", + "examples": [ + { + "value": "hollow" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "door type, metal" + ], + "rank": 98, + "is_a": "core field", + "slot_uri": "MIXS:0000796", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "door_type_metal_enum", + "multivalued": false + }, + "door_type_wood": { + "name": "door_type_wood", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The type of wood door", + "title": "door type, wood", + "examples": [ + { + "value": "battened" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "door type, wood" + ], + "rank": 99, + "is_a": "core field", + "slot_uri": "MIXS:0000797", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "door_type_wood_enum", + "multivalued": false + }, + "door_water_mold": { + "name": "door_water_mold", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Signs of the presence of mold or mildew on a door", + "title": "door signs of water/mold", + "examples": [ + { + "value": "presence of mold visible" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "door signs of water/mold" + ], + "rank": 100, + "is_a": "core field", + "string_serialization": "[presence of mold visible|no presence of mold visible]", + "slot_uri": "MIXS:0000793", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "drawings": { + "name": "drawings", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The buildings architectural drawings; if design is chosen, indicate phase-conceptual, schematic, design development, and construction documents", + "title": "drawings", + "examples": [ + { + "value": "sketch" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "drawings" + ], + "rank": 101, + "is_a": "core field", + "slot_uri": "MIXS:0000798", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "drawings_enum", + "multivalued": false + }, + "ecosystem": { + "name": "ecosystem", + "description": "An ecosystem is a combination of a physical environment (abiotic factors) and all the organisms (biotic factors) that interact with this environment. Ecosystem is in position 1/5 in a GOLD path.", + "comments": [ + "The abiotic factors play a profound role on the type and composition of organisms in a given environment. The GOLD Ecosystem at the top of the five-level classification system is aimed at capturing the broader environment from which an organism or environmental sample is collected. The three broad groups under Ecosystem are Environmental, Host-associated, and Engineered. They represent samples collected from a natural environment or from another organism or from engineered environments like bioreactors respectively." + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "https://gold.jgi.doe.gov/help" + ], + "rank": 9, + "is_a": "gold_path_field", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "Study", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "EcosystemEnum", + "recommended": true + }, + "ecosystem_category": { + "name": "ecosystem_category", + "description": "Ecosystem categories represent divisions within the ecosystem based on specific characteristics of the environment from where an organism or sample is isolated. Ecosystem category is in position 2/5 in a GOLD path.", + "comments": [ + "The Environmental ecosystem (for example) is divided into Air, Aquatic and Terrestrial. Ecosystem categories for Host-associated samples can be individual hosts or phyla and for engineered samples it may be manipulated environments like bioreactors, solid waste etc." + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "https://gold.jgi.doe.gov/help" + ], + "rank": 10, + "is_a": "gold_path_field", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "Study", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "EcosystemCategoryEnum", + "recommended": true + }, + "ecosystem_subtype": { + "name": "ecosystem_subtype", + "description": "Ecosystem subtypes represent further subdivision of Ecosystem types into more distinct subtypes. Ecosystem subtype is in position 4/5 in a GOLD path.", + "comments": [ + "Ecosystem Type Marine (Environmental -> Aquatic -> Marine) is further divided (for example) into Intertidal zone, Coastal, Pelagic, Intertidal zone etc. in the Ecosystem subtype category." + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "https://gold.jgi.doe.gov/help" + ], + "rank": 12, + "is_a": "gold_path_field", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "Study", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "EcosystemSubtypeEnum", + "recommended": true + }, + "ecosystem_type": { + "name": "ecosystem_type", + "description": "Ecosystem types represent things having common characteristics within the Ecosystem Category. These common characteristics based grouping is still broad but specific to the characteristics of a given environment. Ecosystem type is in position 3/5 in a GOLD path.", + "comments": [ + "The Aquatic ecosystem category (for example) may have ecosystem types like Marine or Thermal springs etc. Ecosystem category Air may have Indoor air or Outdoor air as different Ecosystem Types. In the case of Host-associated samples, ecosystem type can represent Respiratory system, Digestive system, Roots etc." + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "https://gold.jgi.doe.gov/help" + ], + "rank": 11, + "is_a": "gold_path_field", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "Study", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "EcosystemTypeEnum", + "recommended": true + }, + "elev": { + "name": "elev", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + } + }, + "description": "Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit.", + "title": "elevation, meters", + "comments": [ + "All elevations must be reported in meters. Provide the numerical portion only.", + "Please use https://www.advancedconverter.com/map-tools/find-altitude-by-coordinates, if needed, to help estimate the elevation based on latitude and longitude coordinates." + ], + "examples": [ + { + "value": "225" + }, + { + "value": "0" + }, + { + "value": "1250" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "elevation" + ], + "rank": 6, + "is_a": "environment field", + "slot_uri": "MIXS:0000093", + "owner": "Biosample", + "domain_of": [ + "FieldResearchSite", + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "float", + "required": true, + "multivalued": false + }, + "elevator": { + "name": "elevator", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "value" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The number of elevators within the built structure", + "title": "elevator count", + "examples": [ + { + "value": "2" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "elevator count" + ], + "rank": 102, + "is_a": "core field", + "slot_uri": "MIXS:0000799", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "env_broad_scale": { + "name": "env_broad_scale", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "The major environment type(s) where the sample was collected. Recommend subclasses of biome [ENVO:00000428]. Multiple terms can be separated by one or more pipes." + }, + "tooltip": { + "tag": "tooltip", + "value": "The biome or major environmental system where the sample or specimen originated. Choose values from subclasses of the 'biome' class [ENVO:00000428] in the Environment Ontology (ENVO). For host-associated or plant-associated samples, use terms from the UBERON or Plant Ontology to describe the broad anatomical or morphological context" + } + }, + "description": "In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO's biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html", + "title": "broad-scale environmental context", + "notes": [ + "range changed to enumeration late in makefile, so this is modified (but \"sample ID\" anyway)" + ], + "examples": [ + { + "value": "oceanic epipelagic zone biome [ENVO:01000033] for annotating a water sample from the photic zone in middle of the Atlantic Ocean" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "broad-scale environmental context" + ], + "rank": 6, + "is_a": "environment field", + "string_serialization": "{termLabel} {[termID]}", + "slot_uri": "MIXS:0000012", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "string", + "required": true, + "multivalued": false, + "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$" + }, + "env_local_scale": { + "name": "env_local_scale", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "Environmental entities having causal influences upon the entity at time of sampling." + }, + "tooltip": { + "tag": "tooltip", + "value": "The specific environmental entities or features near the sample or specimen that significantly influence its characteristics or composition. These entities are typically smaller in scale than the broad environmental context. Values for this field should be countable, material nouns and must be chosen from subclasses of BFO:0000040 (material entity) that appear in the Environment Ontology (ENVO). For host-associated or plant-associated samples, use terms from the UBERON or Plant Ontology to describe specific anatomical structures or plant parts." + } + }, + "description": "Report the entity or entities which are in the sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. We recommend using EnvO terms which are of smaller spatial grain than your entry for env_broad_scale. Terms, such as anatomical sites, from other OBO Library ontologies which interoperate with EnvO (e.g. UBERON) are accepted in this field. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS.", + "title": "local environmental context", + "notes": [ + "range changed to enumeration late in makefile, so this is modified (but \"sample ID\" anyway)" + ], + "examples": [ + { + "value": "canopy [ENVO:00000047]" + }, + { + "value": "herb and fern layer [ENVO:01000337]" + }, + { + "value": "litter layer [ENVO:01000338]" + }, + { + "value": "understory [01000335]" + }, + { + "value": "shrub layer [ENVO:01000336]" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "local environmental context" + ], + "rank": 7, + "is_a": "environment field", + "string_serialization": "{termLabel} {[termID]}", + "slot_uri": "MIXS:0000013", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "string", + "required": true, + "multivalued": false, + "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$" + }, + "env_medium": { + "name": "env_medium", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "The material displaced by the entity at time of sampling. Recommend subclasses of environmental material [ENVO:00010483]." + }, + "tooltip": { + "tag": "tooltip", + "value": "The predominant environmental material or substrate that directly surrounds or hosts the sample or specimen at the time of sampling. Choose values from subclasses of the 'environmental material' class [ENVO:00010483] in the Environment Ontology (ENVO). Values for this field should be measurable or mass material nouns, representing continuous environmental materials. For host-associated or plant-associated samples, use terms from the UBERON or Plant Ontology to indicate a tissue, organ, or plant structure" + } + }, + "description": "Report the environmental material(s) immediately surrounding the sample or specimen at the time of sampling. We recommend using subclasses of 'environmental material' (http://purl.obolibrary.org/obo/ENVO_00010483). EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS . Terms from other OBO ontologies are permissible as long as they reference mass/volume nouns (e.g. air, water, blood) and not discrete, countable entities (e.g. a tree, a leaf, a table top).", + "title": "environmental medium", + "notes": [ + "range changed to enumeration late in makefile, so this is modified (but \"sample ID\" anyway)" + ], + "examples": [ + { + "value": "soil [ENVO:00001998]" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "environmental medium" + ], + "rank": 8, + "is_a": "environment field", + "string_serialization": "{termLabel} {[termID]}", + "slot_uri": "MIXS:0000014", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "string", + "required": true, + "multivalued": false, + "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$" + }, + "escalator": { + "name": "escalator", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "value" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The number of escalators within the built structure", + "title": "escalator count", + "examples": [ + { + "value": "4" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "escalator count" + ], + "rank": 103, + "is_a": "core field", + "slot_uri": "MIXS:0000800", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "exp_duct": { + "name": "exp_duct", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "square meter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The amount of exposed ductwork in the room", + "title": "exposed ductwork", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "exposed ductwork" + ], + "rank": 104, + "is_a": "core field", + "slot_uri": "MIXS:0000144", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "exp_pipe": { + "name": "exp_pipe", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The number of exposed pipes in the room", + "title": "exposed pipes", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "exposed pipes" + ], + "rank": 105, + "is_a": "core field", + "slot_uri": "MIXS:0000220", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "experimental_factor": { + "name": "experimental_factor", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "text or EFO and/or OBI" + } + }, + "description": "Experimental factors are essentially the variable aspects of an experiment design which can be used to describe an experiment, or set of experiments, in an increasingly detailed manner. This field accepts ontology terms from Experimental Factor Ontology (EFO) and/or Ontology for Biomedical Investigations (OBI). For a browser of EFO (v 2.95) terms, please see http://purl.bioontology.org/ontology/EFO; for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI", + "title": "experimental factor", + "examples": [ + { + "value": "time series design [EFO:EFO_0001779]" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "experimental factor" + ], + "rank": 12, + "is_a": "investigation field", + "string_serialization": "{termLabel} {[termID]}|{text}", + "slot_uri": "MIXS:0000008", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false + }, + "ext_door": { + "name": "ext_door", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "value" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The number of exterior doors in the built structure", + "title": "exterior door count", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "exterior door count" + ], + "rank": 106, + "is_a": "core field", + "slot_uri": "MIXS:0000170", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "ext_wall_orient": { + "name": "ext_wall_orient", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The orientation of the exterior wall", + "title": "orientations of exterior wall", + "examples": [ + { + "value": "northwest" + } + ], 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+ }, + "description": "Type of indoor surface", + "title": "indoor surface", + "examples": [ + { + "value": "wall" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "indoor surface" + ], + "rank": 131, + "is_a": "core field", + "slot_uri": "MIXS:0000764", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "indoor_surf_enum", + "multivalued": false + }, + "inside_lux": { + "name": "inside_lux", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "kilowatt per square metre" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The recorded value at sampling time (power density)", + "title": "inside lux light", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "inside lux light" + ], + "rank": 132, + "is_a": "core field", + "slot_uri": "MIXS:0000168", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "int_wall_cond": { + "name": "int_wall_cond", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The physical condition of the wall at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas", + "title": "interior wall condition", + "examples": [ + { + "value": "damaged" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "interior wall condition" + ], + "rank": 133, + "is_a": "core field", + "slot_uri": "MIXS:0000813", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "int_wall_cond_enum", + "multivalued": false + }, + "last_clean": { + "name": "last_clean", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "timestamp" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The last time the floor was cleaned (swept, mopped, vacuumed)", + "title": "last time swept/mopped/vacuumed", + "examples": [ + { + "value": "2018-05-11:T14:30Z" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "last time swept/mopped/vacuumed" + ], + "rank": 134, + "is_a": "core field", + "slot_uri": "MIXS:0000814", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "lat_lon": { + "name": "lat_lon", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "decimal degrees, limit to 8 decimal points" + } + }, + "description": "The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system", + "title": "geographic location (latitude and longitude)", + "notes": [ + "This is currently a required field but it's not clear if this should be required for human hosts" + ], + "examples": [ + { + "value": "50.586825 6.408977" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "geographic location (latitude and longitude)" + ], + "rank": 5, + "is_a": "environment field", + "string_serialization": "{lat lon}", + "slot_uri": "MIXS:0000009", + "owner": "Biosample", + "domain_of": [ + "FieldResearchSite", + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "required": true, + "multivalued": false, + "pattern": "^[-+]?([1-8]?\\d(\\.\\d{1,8})?|90(\\.0{1,8})?)\\s[-+]?(180(\\.0{1,8})?|((1[0-7]\\d)|([1-9]?\\d))(\\.\\d{1,8})?)$" + }, + "light_type": { + "name": "light_type", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Application of light to achieve some practical or aesthetic effect. Lighting includes the use of both artificial light sources such as lamps and light fixtures, as well as natural illumination by capturing daylight. Can also include absence of light", + "title": "light type", + "examples": [ + { + "value": "desk lamp" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "light type" + ], + "rank": 135, + "is_a": "core field", + "slot_uri": "MIXS:0000769", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "light_type_enum", + "multivalued": true + }, + "max_occup": { + "name": "max_occup", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The maximum amount of people allowed in the indoor environment", + "title": "maximum occupancy", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "maximum occupancy" + ], + "rank": 136, + "is_a": "core field", + "slot_uri": "MIXS:0000229", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "mech_struc": { + "name": "mech_struc", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "mechanical structure: a moving structure", + "title": "mechanical structure", + "examples": [ + { + "value": "elevator" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "mechanical structure" + ], + "rank": 137, + "is_a": "core field", + "slot_uri": "MIXS:0000815", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "mech_struc_enum", + "multivalued": false + }, + "number_pets": { + "name": "number_pets", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The number of pets residing in the sampled space", + "title": "number of pets", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "number of pets" + ], + "rank": 138, + "is_a": "core field", + "slot_uri": "MIXS:0000231", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "number_plants": { + "name": "number_plants", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The number of plant(s) in the sampling space", + "title": "number of houseplants", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "number of houseplants" + ], + "rank": 139, + "is_a": "core field", + "slot_uri": "MIXS:0000230", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "number_resident": { + "name": "number_resident", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The number of individuals currently occupying in the sampling location", + "title": "number of residents", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "number of residents" + ], + "rank": 140, + "is_a": "core field", + "slot_uri": "MIXS:0000232", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "occup_density_samp": { + "name": "occup_density_samp", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Average number of occupants at time of sampling per square footage", + "title": "occupant density at sampling", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "occupant density at sampling" + ], + "rank": 141, + "is_a": "core field", + "slot_uri": "MIXS:0000217", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "occup_document": { + "name": "occup_document", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The type of documentation of occupancy", + "title": "occupancy documentation", + "examples": [ + { + "value": "estimate" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "occupancy documentation" + ], + "rank": 142, + "is_a": "core field", + "slot_uri": "MIXS:0000816", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "occup_document_enum", + "multivalued": false + }, + "occup_samp": { + "name": "occup_samp", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Number of occupants present at time of sample within the given space", + "title": "occupancy at sampling", + "examples": [ + { + "value": "10" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "occupancy at sampling" + ], + "rank": 143, + "is_a": "core field", + "slot_uri": "MIXS:0000772", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "organism_count": { + "name": "organism_count", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "organism name;measurement value;enumeration" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "number of cells per cubic meter, number of cells per milliliter, number of cells per cubic centimeter" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr)", + "title": "organism count", + "examples": [ + { + "value": "total prokaryotes;3.5e7 cells per milliliter;qPCR" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "organism count" + ], + "rank": 30, + "is_a": "core field", + "slot_uri": "MIXS:0000103", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^([-+]?[0-9]*\\.?[0-9]+ +\\S.*\\|)*([-+]?[0-9]*\\.?[0-9]+ +\\S.*)$" + }, + "pres_animal_insect": { + "name": "pres_animal_insect", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration;count" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The type and number of animals or insects present in the sampling space.", + "title": "presence of pets, animals, or insects", + "examples": [ + { + "value": "cat;5" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "presence of pets, animals, or insects" + ], + "rank": 144, + "is_a": "core field", + "slot_uri": "MIXS:0000819", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^(cat|dog|rodent|snake|other);\\d+$" + }, + "quad_pos": { + "name": "quad_pos", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The quadrant position of the sampling room within the building", + "title": "quadrant position", + "examples": [ + { + "value": "West side" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "quadrant position" + ], + "rank": 145, + "is_a": "core field", + "slot_uri": "MIXS:0000820", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "quad_pos_enum", + "multivalued": false + }, + "rel_air_humidity": { + "name": "rel_air_humidity", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "percentage" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Partial vapor and air pressure, density of the vapor and air, or by the actual mass of the vapor and air", + "title": "relative air humidity", + "examples": [ + { + "value": "80%" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "relative air humidity" + ], + "rank": 146, + "is_a": "core field", + "slot_uri": "MIXS:0000121", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "rel_humidity_out": { + "name": "rel_humidity_out", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "gram of air, kilogram of air" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The recorded outside relative humidity value at the time of sampling", + "title": "outside relative humidity", + "examples": [ + { + "value": "12 per kilogram of air" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "outside relative humidity" + ], + "rank": 147, + "is_a": "core field", + "slot_uri": "MIXS:0000188", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "rel_samp_loc": { + "name": "rel_samp_loc", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The sampling location within the train car", + "title": "relative sampling location", + "examples": [ + { + "value": "center of car" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "relative sampling location" + ], + "rank": 148, + "is_a": "core field", + "slot_uri": "MIXS:0000821", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "rel_samp_loc_enum", + "multivalued": false + }, + "room_air_exch_rate": { + "name": "room_air_exch_rate", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "liter per hour" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The rate at which outside air replaces indoor air in a given space", + "title": "room air exchange rate", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "room air exchange rate" + ], + "rank": 149, + "is_a": "core field", + "slot_uri": "MIXS:0000169", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "room_architec_elem": { + "name": "room_architec_elem", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "free text" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The unique details and component parts that, together, form the architecture of a distinguisahable space within a built structure", + "title": "room architectural elements", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "room architectural elements" + ], + "rank": 150, + "is_a": "core field", + "string_serialization": "{text}", + "slot_uri": "MIXS:0000233", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "room_condt": { + "name": "room_condt", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The condition of the room at the time of sampling", + "title": "room condition", + "examples": [ + { + "value": "new" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "room condition" + ], + "rank": 151, + "is_a": "core field", + "slot_uri": "MIXS:0000822", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "room_condt_enum", + "multivalued": false + }, + "room_connected": { + "name": "room_connected", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "List of rooms connected to the sampling room by a doorway", + "title": "rooms connected by a doorway", + "examples": [ + { + "value": "office" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "rooms connected by a doorway" + ], + "rank": 152, + "is_a": "core field", + "slot_uri": "MIXS:0000826", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "room_connected_enum", + "multivalued": false + }, + "room_count": { + "name": "room_count", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "value" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The total count of rooms in the built structure including all room types", + "title": "room count", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "room count" + ], + "rank": 153, + "is_a": "core field", + "slot_uri": "MIXS:0000234", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "room_dim": { + "name": "room_dim", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "meter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The length, width and height of sampling room", + "title": "room dimensions", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "room dimensions" + ], + "rank": 154, + "is_a": "core field", + "string_serialization": "{integer} {unit} x {integer} {unit} x {integer} {unit}", + "slot_uri": "MIXS:0000192", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "room_door_dist": { + "name": "room_door_dist", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "meter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Distance between doors (meters) in the hallway between the sampling room and adjacent rooms", + "title": "room door distance", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "room door distance" + ], + "rank": 155, + "is_a": "core field", + "string_serialization": "{integer} {unit}", + "slot_uri": "MIXS:0000193", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "room_door_share": { + "name": "room_door_share", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "room name;room number" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "List of room(s) (room number, room name) sharing a door with the sampling room", + "title": "rooms that share a door with sampling room", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "rooms that share a door with sampling room" + ], + "rank": 156, + "is_a": "core field", + "string_serialization": "{text};{integer}", + "slot_uri": "MIXS:0000242", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "room_hallway": { + "name": "room_hallway", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "room name;room number" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "List of room(s) (room number, room name) located in the same hallway as sampling room", + "title": "rooms that are on the same hallway", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "rooms that are on the same hallway" + ], + "rank": 157, + "is_a": "core field", + "string_serialization": "{text};{integer}", + "slot_uri": "MIXS:0000238", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "room_loc": { + "name": "room_loc", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The position of the room within the building", + "title": "room location in building", + "examples": [ + { + "value": "interior room" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "room location in building" + ], + "rank": 158, + "is_a": "core field", + "slot_uri": "MIXS:0000823", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "room_loc_enum", + "multivalued": false + }, + "room_moist_dam_hist": { + "name": "room_moist_dam_hist", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "value" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The history of moisture damage or mold in the past 12 months. Number of events of moisture damage or mold observed", + "title": "room moisture damage or mold history", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "room moisture damage or mold history" + ], + "rank": 159, + "is_a": "core field", + "slot_uri": "MIXS:0000235", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "integer", + "multivalued": false + }, + "room_net_area": { + "name": "room_net_area", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "square feet, square meter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The net floor area of sampling room. Net area excludes wall thicknesses", + "title": "room net area", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "room net area" + ], + "rank": 160, + "is_a": "core field", + "string_serialization": "{integer} {unit}", + "slot_uri": "MIXS:0000194", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "room_occup": { + "name": "room_occup", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Count of room occupancy at time of sampling", + "title": "room occupancy", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "room occupancy" + ], + "rank": 161, + "is_a": "core field", + "slot_uri": "MIXS:0000236", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "room_samp_pos": { + "name": "room_samp_pos", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The horizontal sampling position in the room relative to architectural elements", + "title": "room sampling position", + "examples": [ + { + "value": "south corner" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "room sampling position" + ], + "rank": 162, + "is_a": "core field", + "slot_uri": "MIXS:0000824", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "room_samp_pos_enum", + "multivalued": false + }, + "room_type": { + "name": "room_type", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The main purpose or activity of the sampling room. A room is any distinguishable space within a structure", + "title": "room type", + "examples": [ + { + "value": "bathroom" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "room type" + ], + "rank": 163, + "is_a": "core field", + "slot_uri": "MIXS:0000825", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "room_type_enum", + "multivalued": false + }, + "room_vol": { + "name": "room_vol", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "cubic feet, cubic meter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Volume of sampling room", + "title": "room volume", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "room volume" + ], + "rank": 164, + "is_a": "core field", + "string_serialization": "{integer} {unit}", + "slot_uri": "MIXS:0000195", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "room_wall_share": { + "name": "room_wall_share", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "room name;room number" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "List of room(s) (room number, room name) sharing a wall with the sampling room", + "title": "rooms that share a wall with sampling room", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "rooms that share a wall with sampling room" + ], + "rank": 165, + "is_a": "core field", + "string_serialization": "{text};{integer}", + "slot_uri": "MIXS:0000243", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "room_window_count": { + "name": "room_window_count", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "value" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Number of windows in the room", + "title": "room window count", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "room window count" + ], + "rank": 166, + "is_a": "core field", + "slot_uri": "MIXS:0000237", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "integer", + "multivalued": false + }, + "samp_floor": { + "name": "samp_floor", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The floor of the building, where the sampling room is located", + "title": "sampling floor", + "examples": [ + { + "value": "4th floor" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sampling floor" + ], + "rank": 167, + "is_a": "core field", + "slot_uri": "MIXS:0000828", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "samp_floor_enum", + "multivalued": false + }, + "samp_room_id": { + "name": "samp_room_id", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "value" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Sampling room number. This ID should be consistent with the designations on the building floor plans", + "title": "sampling room ID or name", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sampling room ID or name" + ], + "rank": 168, + "is_a": "core field", + "slot_uri": "MIXS:0000244", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "samp_sort_meth": { + "name": "samp_sort_meth", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "description of method" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Method by which samples are sorted; open face filter collecting total suspended particles, prefilter to remove particles larger than X micrometers in diameter, where common values of X would be 10 and 2.5 full size sorting in a cascade impactor.", + "title": "sample size sorting method", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sample size sorting method" + ], + "rank": 169, + "is_a": "core field", + "string_serialization": "{text}", + "slot_uri": "MIXS:0000216", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "samp_time_out": { + "name": "samp_time_out", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "time" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "hour" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The recent and long term history of outside sampling", + "title": "sampling time outside", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sampling time outside" + ], + "rank": 170, + "is_a": "core field", + "slot_uri": "MIXS:0000196", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "samp_weather": { + "name": "samp_weather", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The weather on the sampling day", + "title": "sampling day weather", + "examples": [ + { + "value": "foggy" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sampling day weather" + ], + "rank": 171, + "is_a": "core field", + "slot_uri": "MIXS:0000827", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "samp_weather_enum", + "multivalued": false + }, + "sample_link": { + "name": "sample_link", + "description": "A unique identifier to assign parent-child, subsample, or sibling samples. This is relevant when a sample or other material was used to generate the new sample.", + "title": "sample linkage", + "notes": [ + "also tempted to include SampIdNewTermsMixin but if len(slot_usage.keys()) > 1 and \"placeholder\" in slot_usage.keys():AttributeError: 'list' object has no attribute 'keys'" + ], + "comments": [ + "This field allows multiple entries separated by ; (Examples: Soil collected from the field will link with the soil used in an incubation. The soil a plant was grown in links to the plant sample. An original culture sample was transferred to a new vial and generated a new sample)" + ], + "examples": [ + { + "value": "IGSN:DSJ0284" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "rank": 5, + "string_serialization": "{text}:{text}", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface", + "SampIdNewTermsMixin" + ], + "slot_group": "sample_id_section", + "range": "string", + "recommended": true, + "multivalued": false, + "pattern": "[^\\:\\n\\r]+\\:[^\\:\\n\\r]+" + }, + "season": { + "name": "season", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "NCIT:C94729" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The season when sampling occurred. Any of the four periods into which the year is divided by the equinoxes and solstices. This field accepts terms listed under season (http://purl.obolibrary.org/obo/NCIT_C94729).", + "title": "season", + "examples": [ + { + "value": "autumn [NCIT:C94733]" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "season" + ], + "rank": 172, + "is_a": "core field", + "string_serialization": "{termLabel} {[termID]}", + "slot_uri": "MIXS:0000829", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$" + }, + "season_use": { + "name": "season_use", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The seasons the space is occupied", + "title": "seasonal use", + "examples": [ + { + "value": "Winter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "seasonal use" + ], + "rank": 173, + "is_a": "core field", + "slot_uri": "MIXS:0000830", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "season_use_enum", + "multivalued": false + }, + "shad_dev_water_mold": { + "name": "shad_dev_water_mold", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Signs of the presence of mold or mildew on the shading device", + "title": "shading device signs of water/mold", + "examples": [ + { + "value": "no presence of mold visible" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "shading device signs of water/mold" + ], + "rank": 174, + "is_a": "core field", + "string_serialization": "[presence of mold visible|no presence of mold visible]", + "slot_uri": "MIXS:0000834", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "shading_device_cond": { + "name": "shading_device_cond", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The physical condition of the shading device at the time of sampling", + "title": "shading device condition", + "examples": [ + { + "value": "new" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "shading device condition" + ], + "rank": 175, + "is_a": "core field", + "slot_uri": "MIXS:0000831", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "shading_device_cond_enum", + "multivalued": false + }, + "shading_device_loc": { + "name": "shading_device_loc", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The location of the shading device in relation to the built structure", + "title": "shading device location", + "examples": [ + { + "value": "exterior" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "shading device location" + ], + "rank": 176, + "is_a": "core field", + "string_serialization": "[exterior|interior]", + "slot_uri": "MIXS:0000832", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "shading_device_mat": { + "name": "shading_device_mat", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "material name" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The material the shading device is composed of", + "title": "shading device material", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "shading device material" + ], + "rank": 177, + "is_a": "core field", + "string_serialization": "{text}", + "slot_uri": "MIXS:0000245", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "shading_device_type": { + "name": "shading_device_type", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The type of shading device", + "title": "shading device type", + "examples": [ + { + "value": "slatted aluminum awning" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "shading device type" + ], + "rank": 178, + "is_a": "core field", + "slot_uri": "MIXS:0000835", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "shading_device_type_enum", + "multivalued": false + }, + "size_frac": { + "name": "size_frac", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "filter size value range" + } + }, + "description": "Filtering pore size used in sample preparation", + "title": "size fraction selected", + "examples": [ + { + "value": "0-0.22 micrometer" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "size fraction selected" + ], + "rank": 285, + "is_a": "nucleic acid sequence source field", + "string_serialization": "{float}-{float} {unit}", + "slot_uri": "MIXS:0000017", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "space_typ_state": { + "name": "space_typ_state", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Customary or normal state of the space", + "title": "space typical state", + "examples": [ + { + "value": "typically occupied" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "space typical state" + ], + "rank": 179, + "is_a": "core field", + "string_serialization": "[typically occupied|typically unoccupied]", + "slot_uri": "MIXS:0000770", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "specific": { + "name": "specific", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": 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If design is chosen, indicate phase: conceptual, schematic, design development, construction documents", + "title": "specifications", + "examples": [ + { + "value": "construction" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "specifications" + ], + "rank": 180, + "is_a": "core field", + "slot_uri": "MIXS:0000836", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "specific_enum", + "multivalued": false + }, + "specific_ecosystem": { + "name": "specific_ecosystem", + "description": "Specific ecosystems represent specific features of the environment like aphotic zone in an ocean or gastric mucosa within a host digestive system. 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"expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The day of the week when sampling occurred", + "title": "weekday", + "examples": [ + { + "value": "Sunday" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "weekday" + ], + "rank": 206, + "is_a": "core field", + "slot_uri": "MIXS:0000848", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "weekday_enum", + "multivalued": false + }, + "window_cond": { + "name": "window_cond", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The physical condition of the window at the time of sampling", + "title": "window condition", + "examples": [ + { + "value": "rupture" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "window condition" + ], + "rank": 207, + "is_a": "core field", + "slot_uri": "MIXS:0000849", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "window_cond_enum", + "multivalued": false + }, + "window_cover": { + "name": "window_cover", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The type of window covering", + "title": "window covering", + "examples": [ + { + "value": "curtains" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "window covering" + ], + "rank": 208, + "is_a": "core field", + "slot_uri": "MIXS:0000850", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "window_cover_enum", + "multivalued": false + }, + "window_horiz_pos": { + "name": 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"occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The window's length and width", + "title": "window area/size", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "window area/size" + ], + "rank": 213, + "is_a": "core field", + "string_serialization": "{float} {unit} x {float} {unit}", + "slot_uri": "MIXS:0000224", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "window_status": { + "name": "window_status", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Defines whether the windows were open or closed during environmental testing", + "title": "window status", + "examples": [ + { + "value": "open" + } + ], + "from_schema": 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mildew on the window.", + "title": "window signs of water/mold", + "examples": [ + { + "value": "no presence of mold visible" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "window signs of water/mold" + ], + "rank": 217, + "is_a": "core field", + "string_serialization": "[presence of mold visible|no presence of mold visible]", + "slot_uri": "MIXS:0000854", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "horizon_meth": { + "name": "horizon_meth", + "title": "horizon method" + }, + "oxy_stat_samp": { + "name": "oxy_stat_samp", + "range": "OxyStatSampEnum" + } + }, + "attributes": { + "abs_air_humidity": { + "name": "abs_air_humidity", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "gram per gram, kilogram per kilogram, 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"examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "address" + ], + "rank": 62, + "is_a": "core field", + "string_serialization": "{integer}{text}", + "slot_uri": "MIXS:0000218", + "alias": "address", + "owner": "BuiltEnvInterface", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "adj_room": { + "name": "adj_room", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "room name;room number" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "List of rooms (room number, room name) immediately adjacent to the sampling room", + "title": "adjacent rooms", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "adjacent rooms" + ], + "rank": 63, + "is_a": "core field", + "string_serialization": "{text};{integer}", + "slot_uri": 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It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air", + "title": "altitude", + "examples": [ + { + "value": "100 meter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "altitude" + ], + "rank": 26, + "is_a": "environment field", + "slot_uri": "MIXS:0000094", + "alias": "alt", + "owner": "BuiltEnvInterface", + "domain_of": [ + "agriculture", + "air", + "built environment", + "core", + "food-animal and animal feed", + "food-farm environment", + "food-food production facility", + "food-human foods", + "host-associated", + "human-associated", + "human-gut", + "human-oral", + "human-skin", + "human-vaginal", + "hydrocarbon resources-cores", + "hydrocarbon resources-fluids_swabs", + "microbial mat_biofilm", + "miscellaneous natural or artificial environment", + "plant-associated", + "sediment", + "soil", + "symbiont-associated", + "wastewater_sludge", + "water", + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HostAssociatedInterface", + "MiscEnvsInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "recommended": true, + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "amount_light": { + "name": "amount_light", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "lux, lumens per square meter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The unit of illuminance and luminous emittance, measuring luminous flux per unit area", + "title": "amount of light", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "amount of light" + ], + "rank": 66, + "is_a": "core field", + "slot_uri": "MIXS:0000140", + "alias": "amount_light", + "owner": "BuiltEnvInterface", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "arch_struc": { + "name": "arch_struc", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "An architectural structure is a human-made, free-standing, immobile outdoor construction", + "title": "architectural structure", + "examples": [ + { + "value": "shed" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "architectural structure" + ], + "rank": 67, + "is_a": "core field", + "slot_uri": "MIXS:0000774", + "alias": "arch_struc", + "owner": "BuiltEnvInterface", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "arch_struc_enum", + "multivalued": false + }, + "avg_dew_point": { + "name": "avg_dew_point", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "degree Celsius" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The average of dew point measures taken at the beginning of every hour over a 24 hour period on the sampling day", + "title": "average dew point", + "examples": [ + { + "value": "25.5 degree Celsius" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "average dew point" + ], + "rank": 68, + "is_a": "core field", + "slot_uri": "MIXS:0000141", + "alias": "avg_dew_point", + "owner": "BuiltEnvInterface", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "avg_occup": { + "name": "avg_occup", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "value" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Daily average occupancy of room. Indicate the number of person(s) daily occupying the sampling room.", + "title": "average daily occupancy", + "examples": [ + { + "value": "2" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "average daily occupancy" + ], + "rank": 69, + "is_a": "core field", + "slot_uri": "MIXS:0000775", + "alias": "avg_occup", + "owner": "BuiltEnvInterface", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "avg_temp": { + "name": "avg_temp", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "degree Celsius" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The average of temperatures taken at the beginning of every hour over a 24 hour period on the sampling day", + "title": "average temperature", + "examples": [ + { + "value": "12.5 degree Celsius" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "average temperature" + ], + "rank": 70, + "is_a": "core field", + "slot_uri": "MIXS:0000142", + "alias": "avg_temp", + "owner": "BuiltEnvInterface", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "bathroom_count": { + "name": "bathroom_count", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "value" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The number of bathrooms in the building", + "title": "bathroom count", + "examples": [ + { + "value": "1" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "bathroom count" + ], + "rank": 71, + "is_a": "core field", + "slot_uri": "MIXS:0000776", + "alias": "bathroom_count", + "owner": "BuiltEnvInterface", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "bedroom_count": { + "name": "bedroom_count", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "value" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The number of bedrooms in the building", + "title": "bedroom count", + "examples": [ + { + "value": "2" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "bedroom count" + ], + "rank": 72, + "is_a": "core field", + "slot_uri": "MIXS:0000777", + "alias": "bedroom_count", + "owner": "BuiltEnvInterface", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "build_docs": { + "name": "build_docs", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The building design, construction and operation documents", + "title": "design, construction, and operation documents", + "examples": [ + { + "value": "maintenance plans" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "design, construction, and operation documents" + ], + "rank": 73, + "is_a": "core field", + "slot_uri": "MIXS:0000787", + "alias": "build_docs", + "owner": "BuiltEnvInterface", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "build_docs_enum", + "multivalued": false + }, + "build_occup_type": { + "name": "build_occup_type", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "The primary function for which a building or discrete part of a building is intended to be used", + "title": "building 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+ "owner": "BuiltEnvInterface", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "building_setting_enum", + "multivalued": false + }, + "built_struc_age": { + "name": "built_struc_age", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "year" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The age of the built structure since construction", + "title": "built structure age", + "examples": [ + { + "value": "15" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "built structure age" + ], + "rank": 76, + "is_a": "core field", + "slot_uri": "MIXS:0000145", + "alias": "built_struc_age", + "owner": "BuiltEnvInterface", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "built_struc_set": { + "name": "built_struc_set", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The characterization of the location of the built structure as high or low human density", + "title": "built structure setting", + "examples": [ + { + "value": "rural" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "built structure setting" + ], + "rank": 77, + "is_a": "core field", + "string_serialization": "[urban|rural]", + "slot_uri": "MIXS:0000778", + "alias": "built_struc_set", + "owner": "BuiltEnvInterface", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "built_struc_type": { + "name": "built_struc_type", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "free 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"1" + } + }, + "description": "Carbon dioxide (gas) amount or concentration at the time of sampling", + "title": "carbon dioxide", + "examples": [ + { + "value": "410 parts per million" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "carbon dioxide" + ], + "rank": 50, + "is_a": "core field", + "slot_uri": "MIXS:0000097", + "alias": "carb_dioxide", + "owner": "BuiltEnvInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "ceil_area": { + "name": "ceil_area", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "square meter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The area of the ceiling space within the room", + "title": "ceiling area", + "examples": [ + { + "value": "25 square meter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "ceiling area" + ], + "rank": 79, + "is_a": "core field", + "slot_uri": "MIXS:0000148", + "alias": "ceil_area", + "owner": "BuiltEnvInterface", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "ceil_cond": { + "name": "ceil_cond", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The physical condition of the ceiling at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas", + "title": "ceiling condition", + "examples": [ + { + "value": "damaged" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "ceiling condition" + ], + "rank": 80, + "is_a": "core field", + "slot_uri": "MIXS:0000779", + "alias": "ceil_cond", + "owner": "BuiltEnvInterface", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "ceil_cond_enum", + "multivalued": false + }, + "ceil_finish_mat": { + "name": "ceil_finish_mat", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The type of material used to finish a ceiling", + "title": "ceiling finish material", + "examples": [ + { + "value": "stucco" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "ceiling finish material" + ], + "rank": 81, + "is_a": "core field", + "slot_uri": "MIXS:0000780", + "alias": "ceil_finish_mat", + "owner": "BuiltEnvInterface", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "ceil_finish_mat_enum", + "multivalued": false + }, + "ceil_struc": { + "name": "ceil_struc", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The construction format of the ceiling", + "title": "ceiling structure", + "examples": [ + { + "value": "concrete" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "ceiling structure" + ], + "rank": 82, + "is_a": "core field", + "string_serialization": "[wood frame|concrete]", + "slot_uri": "MIXS:0000782", + "alias": "ceil_struc", + "owner": "BuiltEnvInterface", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "ceil_texture": { + "name": "ceil_texture", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The feel, appearance, or consistency of a ceiling surface", + "title": "ceiling texture", + "examples": [ + { + "value": "popcorn" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "ceiling texture" + ], + "rank": 83, + "is_a": "core field", + "slot_uri": "MIXS:0000783", + "alias": "ceil_texture", + "owner": "BuiltEnvInterface", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "ceil_texture_enum", + "multivalued": false + }, + "ceil_thermal_mass": { + "name": "ceil_thermal_mass", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "joule per degree Celsius" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The ability of the ceiling to provide inertia against temperature fluctuations. Generally this means concrete that is exposed. A metal deck that supports a concrete slab will act thermally as long as it is exposed to room air flow", + "title": "ceiling thermal mass", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "ceiling thermal mass" + ], + "rank": 84, + "is_a": "core field", + "slot_uri": "MIXS:0000143", + "alias": "ceil_thermal_mass", + "owner": "BuiltEnvInterface", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "ceil_type": { + "name": "ceil_type", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The type of ceiling according to the ceiling's appearance or construction", + "title": "ceiling type", + "examples": [ + { + "value": "coffered" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "ceiling type" + ], + "rank": 85, + "is_a": "core field", + "slot_uri": "MIXS:0000784", + "alias": "ceil_type", + "owner": "BuiltEnvInterface", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "ceil_type_enum", + "multivalued": false + }, + "ceil_water_mold": { + "name": "ceil_water_mold", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Signs of the presence of mold or mildew on the ceiling", + "title": "ceiling signs of water/mold", + "examples": [ + { + "value": "presence of mold visible" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "ceiling signs of water/mold" + ], + "rank": 86, + "is_a": "core field", + "string_serialization": "[presence of mold visible|no presence of mold visible]", + "slot_uri": "MIXS:0000781", + "alias": "ceil_water_mold", + "owner": "BuiltEnvInterface", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "collection_date": { + "name": "collection_date", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "date and time" + } + }, + "description": "The date of sampling", + "title": "collection date", + "notes": [ + "MIxS collection_date accepts (truncated) ISO8601. DH taking arb prec date only", + "Use modified term (amended definition)" + ], + "examples": [ + { + "value": "2021-04-15" + }, + { + "value": "2021-04" + }, + { + "value": "2021" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "collection date" + ], + "rank": 3, + "is_a": "environment field", + "string_serialization": "{date, arbitrary precision}", + "slot_uri": "MIXS:0000011", + "alias": "collection_date", + "owner": "BuiltEnvInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "required": true, + "multivalued": false, + "pattern": "^[12]\\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\\d|3[01]))?)?$" + }, + "cool_syst_id": { + "name": "cool_syst_id", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "unique identifier" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The cooling system identifier", + "title": "cooling system identifier", + "examples": [ + { + "value": "12345" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "cooling system identifier" + ], + "rank": 87, + "is_a": "core field", + "slot_uri": "MIXS:0000785", + "alias": "cool_syst_id", + "owner": "BuiltEnvInterface", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "date_last_rain": { + "name": "date_last_rain", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "timestamp" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The date of the last time it rained", + "title": "date last rain", + "examples": [ + { + "value": "2018-05-11:T14:30Z" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "date last rain" + ], + "rank": 88, + "is_a": "core field", + "slot_uri": "MIXS:0000786", + "alias": "date_last_rain", + "owner": "BuiltEnvInterface", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "depth": { + "name": "depth", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + } + }, + "description": "The vertical distance below local surface, e.g. for sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples.", + "title": "depth, meters", + "notes": [ + "Use modified term" + ], + "comments": [ + "All depths must be reported in meters. Provide the numerical portion only." + ], + "examples": [ + { + "value": "0 - 0.1" + }, + { + "value": "1" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "depth" + ], + "rank": 9, + "is_a": "environment field", + "string_serialization": "{float}|{float}-{float}", + "slot_uri": "MIXS:0000018", + "alias": "depth", + "owner": "BuiltEnvInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "recommended": true, + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)?(\\s*-\\s*[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)?)?$" + }, + "dew_point": { + "name": "dew_point", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "degree Celsius" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The temperature to which a given parcel of humid air must be cooled, at constant barometric pressure, for water vapor to condense into water.", + "title": "dew point", + "examples": [ + { + "value": "22 degree Celsius" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "dew point" + ], + "rank": 89, + "is_a": "core field", + "slot_uri": "MIXS:0000129", + "alias": "dew_point", + "owner": "BuiltEnvInterface", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "door_comp_type": { + "name": "door_comp_type", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The composite type of the door", + "title": "door type, composite", + "examples": [ + { + "value": "revolving" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "door type, composite" + ], + "rank": 90, + "is_a": "core field", + "slot_uri": "MIXS:0000795", + "alias": "door_comp_type", + "owner": "BuiltEnvInterface", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "door_comp_type_enum", + "multivalued": false + }, + "door_cond": { + "name": "door_cond", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The phsical condition of the door", + "title": "door condition", + "examples": [ + { + "value": "new" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "door condition" + ], + "rank": 91, + "is_a": "core field", + "slot_uri": "MIXS:0000788", + "alias": "door_cond", + "owner": "BuiltEnvInterface", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "door_cond_enum", + "multivalued": false + }, + "door_direct": { + "name": "door_direct", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The direction the door opens", + "title": "door direction of opening", + "examples": [ + { + "value": "inward" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "door direction of opening" + ], + "rank": 92, + "is_a": "core field", + "slot_uri": "MIXS:0000789", + "alias": "door_direct", + "owner": "BuiltEnvInterface", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "door_direct_enum", + "multivalued": false + }, + "door_loc": { + "name": "door_loc", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The relative location of the door in the room", + "title": "door location", + "examples": [ + { + "value": "north" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "door location" + ], + "rank": 93, + "is_a": "core field", + "slot_uri": "MIXS:0000790", + "alias": "door_loc", + "owner": "BuiltEnvInterface", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "door_loc_enum", + "multivalued": false + }, + "door_mat": { + "name": "door_mat", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The material the door is composed of", + "title": "door material", + "examples": [ + { + "value": "wood" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "door material" + ], + "rank": 94, + "is_a": "core field", + "slot_uri": "MIXS:0000791", + "alias": "door_mat", + "owner": "BuiltEnvInterface", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "door_mat_enum", + "multivalued": false + }, + "door_move": { + "name": "door_move", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The type of movement of the door", + "title": "door movement", + "examples": [ + { + "value": "swinging" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "door movement" + ], + "rank": 95, + "is_a": "core field", + "slot_uri": "MIXS:0000792", + "alias": "door_move", + "owner": "BuiltEnvInterface", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "door_move_enum", + "multivalued": false + }, + "door_size": { + "name": "door_size", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "square meter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The size of the door", + "title": "door area or size", + "examples": [ + { + "value": "2.5 square meter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "door area or size" + ], + "rank": 96, + "is_a": "core field", + "slot_uri": "MIXS:0000158", + "alias": "door_size", + "owner": "BuiltEnvInterface", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "door_type": { + "name": "door_type", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The type of door material", + "title": "door type", + "examples": [ + { + "value": "wooden" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "door type" + ], + "rank": 97, + "is_a": "core field", + "slot_uri": "MIXS:0000794", + "alias": "door_type", + "owner": "BuiltEnvInterface", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "door_type_enum", + "multivalued": false + }, + "door_type_metal": { + "name": "door_type_metal", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The type of metal door", + "title": "door type, metal", + "examples": [ + { + "value": "hollow" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "door type, metal" + ], + "rank": 98, + "is_a": "core field", + "slot_uri": "MIXS:0000796", + "alias": "door_type_metal", + "owner": "BuiltEnvInterface", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "door_type_metal_enum", + "multivalued": false + }, + "door_type_wood": { + "name": "door_type_wood", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The type of wood door", + "title": "door type, wood", + "examples": [ + { + "value": "battened" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "door type, wood" + ], + "rank": 99, + "is_a": "core field", + "slot_uri": "MIXS:0000797", + "alias": "door_type_wood", + "owner": "BuiltEnvInterface", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "door_type_wood_enum", + "multivalued": false + }, + "door_water_mold": { + "name": "door_water_mold", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Signs of the presence of mold or mildew on a door", + "title": "door signs of water/mold", + "examples": [ + { + "value": "presence of mold visible" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "door signs of water/mold" + ], + "rank": 100, + "is_a": "core field", + "string_serialization": "[presence of mold visible|no presence of mold visible]", + "slot_uri": "MIXS:0000793", + "alias": "door_water_mold", + "owner": "BuiltEnvInterface", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "drawings": { + "name": "drawings", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The buildings architectural drawings; if design is chosen, indicate phase-conceptual, schematic, design development, and construction documents", + "title": "drawings", + "examples": [ + { + "value": "sketch" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "drawings" + ], + "rank": 101, + "is_a": "core field", + "slot_uri": "MIXS:0000798", + "alias": "drawings", + "owner": "BuiltEnvInterface", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "drawings_enum", + "multivalued": false + }, + "ecosystem": { + "name": "ecosystem", + "description": "An ecosystem is a combination of a physical environment (abiotic factors) and all the organisms (biotic factors) that interact with this environment. Ecosystem is in position 1/5 in a GOLD path.", + "comments": [ + "The abiotic factors play a profound role on the type and composition of organisms in a given environment. The GOLD Ecosystem at the top of the five-level classification system is aimed at capturing the broader environment from which an organism or environmental sample is collected. The three broad groups under Ecosystem are Environmental, Host-associated, and Engineered. They represent samples collected from a natural environment or from another organism or from engineered environments like bioreactors respectively." + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "https://gold.jgi.doe.gov/help" + ], + "rank": 9, + "is_a": "gold_path_field", + "alias": "ecosystem", + "owner": "BuiltEnvInterface", + "domain_of": [ + "Biosample", + "Study", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "EcosystemEnum", + "recommended": true + }, + "ecosystem_category": { + "name": "ecosystem_category", + "description": "Ecosystem categories represent divisions within the ecosystem based on specific characteristics of the environment from where an organism or sample is isolated. Ecosystem category is in position 2/5 in a GOLD path.", + "comments": [ + "The Environmental ecosystem (for example) is divided into Air, Aquatic and Terrestrial. Ecosystem categories for Host-associated samples can be individual hosts or phyla and for engineered samples it may be manipulated environments like bioreactors, solid waste etc." + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "https://gold.jgi.doe.gov/help" + ], + "rank": 10, + "is_a": "gold_path_field", + "alias": "ecosystem_category", + "owner": "BuiltEnvInterface", + "domain_of": [ + "Biosample", + "Study", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "EcosystemCategoryEnum", + "recommended": true + }, + "ecosystem_subtype": { + "name": "ecosystem_subtype", + "description": "Ecosystem subtypes represent further subdivision of Ecosystem types into more distinct subtypes. Ecosystem subtype is in position 4/5 in a GOLD path.", + "comments": [ + "Ecosystem Type Marine (Environmental -> Aquatic -> Marine) is further divided (for example) into Intertidal zone, Coastal, Pelagic, Intertidal zone etc. in the Ecosystem subtype category." + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "https://gold.jgi.doe.gov/help" + ], + "rank": 12, + "is_a": "gold_path_field", + "alias": "ecosystem_subtype", + "owner": "BuiltEnvInterface", + "domain_of": [ + "Biosample", + "Study", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "EcosystemSubtypeEnum", + "recommended": true + }, + "ecosystem_type": { + "name": "ecosystem_type", + "description": "Ecosystem types represent things having common characteristics within the Ecosystem Category. These common characteristics based grouping is still broad but specific to the characteristics of a given environment. Ecosystem type is in position 3/5 in a GOLD path.", + "comments": [ + "The Aquatic ecosystem category (for example) may have ecosystem types like Marine or Thermal springs etc. Ecosystem category Air may have Indoor air or Outdoor air as different Ecosystem Types. In the case of Host-associated samples, ecosystem type can represent Respiratory system, Digestive system, Roots etc." + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "https://gold.jgi.doe.gov/help" + ], + "rank": 11, + "is_a": "gold_path_field", + "alias": "ecosystem_type", + "owner": "BuiltEnvInterface", + "domain_of": [ + "Biosample", + "Study", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "EcosystemTypeEnum", + "recommended": true + }, + "elev": { + "name": "elev", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + } + }, + "description": "Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit.", + "title": "elevation, meters", + "comments": [ + "All elevations must be reported in meters. Provide the numerical portion only.", + "Please use https://www.advancedconverter.com/map-tools/find-altitude-by-coordinates, if needed, to help estimate the elevation based on latitude and longitude coordinates." + ], + "examples": [ + { + "value": "225" + }, + { + "value": "0" + }, + { + "value": "1250" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "elevation" + ], + "rank": 6, + "is_a": "environment field", + "slot_uri": "MIXS:0000093", + "alias": "elev", + "owner": "BuiltEnvInterface", + "domain_of": [ + "FieldResearchSite", + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "float", + "required": true, + "multivalued": false + }, + "elevator": { + "name": "elevator", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "value" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The number of elevators within the built structure", + "title": "elevator count", + "examples": [ + { + "value": "2" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "elevator count" + ], + "rank": 102, + "is_a": "core field", + "slot_uri": "MIXS:0000799", + "alias": "elevator", + "owner": "BuiltEnvInterface", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "env_broad_scale": { + "name": "env_broad_scale", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "The major environment type(s) where the sample was collected. Recommend subclasses of biome [ENVO:00000428]. Multiple terms can be separated by one or more pipes." + }, + "tooltip": { + "tag": "tooltip", + "value": "The biome or major environmental system where the sample or specimen originated. Choose values from subclasses of the 'biome' class [ENVO:00000428] in the Environment Ontology (ENVO). For host-associated or plant-associated samples, use terms from the UBERON or Plant Ontology to describe the broad anatomical or morphological context" + } + }, + "description": "In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO's biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html", + "title": "broad-scale environmental context", + "notes": [ + "range changed to enumeration late in makefile, so this is modified (but \"sample ID\" anyway)" + ], + "examples": [ + { + "value": "oceanic epipelagic zone biome [ENVO:01000033] for annotating a water sample from the photic zone in middle of the Atlantic Ocean" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "broad-scale environmental context" + ], + "rank": 6, + "is_a": "environment field", + "string_serialization": "{termLabel} {[termID]}", + "slot_uri": "MIXS:0000012", + "alias": "env_broad_scale", + "owner": "BuiltEnvInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "string", + "required": true, + "multivalued": false, + "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$" + }, + "env_local_scale": { + "name": "env_local_scale", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "Environmental entities having causal influences upon the entity at time of sampling." + }, + "tooltip": { + "tag": "tooltip", + "value": "The specific environmental entities or features near the sample or specimen that significantly influence its characteristics or composition. These entities are typically smaller in scale than the broad environmental context. Values for this field should be countable, material nouns and must be chosen from subclasses of BFO:0000040 (material entity) that appear in the Environment Ontology (ENVO). For host-associated or plant-associated samples, use terms from the UBERON or Plant Ontology to describe specific anatomical structures or plant parts." + } + }, + "description": "Report the entity or entities which are in the sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. We recommend using EnvO terms which are of smaller spatial grain than your entry for env_broad_scale. Terms, such as anatomical sites, from other OBO Library ontologies which interoperate with EnvO (e.g. UBERON) are accepted in this field. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS.", + "title": "local environmental context", + "notes": [ + "range changed to enumeration late in makefile, so this is modified (but \"sample ID\" anyway)" + ], + "examples": [ + { + "value": "canopy [ENVO:00000047]" + }, + { + "value": "herb and fern layer [ENVO:01000337]" + }, + { + "value": "litter layer [ENVO:01000338]" + }, + { + "value": "understory [01000335]" + }, + { + "value": "shrub layer [ENVO:01000336]" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "local environmental context" + ], + "rank": 7, + "is_a": "environment field", + "string_serialization": "{termLabel} {[termID]}", + "slot_uri": "MIXS:0000013", + "alias": "env_local_scale", + "owner": "BuiltEnvInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "string", + "required": true, + "multivalued": false, + "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$" + }, + "env_medium": { + "name": "env_medium", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "The material displaced by the entity at time of sampling. Recommend subclasses of environmental material [ENVO:00010483]." + }, + "tooltip": { + "tag": "tooltip", + "value": "The predominant environmental material or substrate that directly surrounds or hosts the sample or specimen at the time of sampling. Choose values from subclasses of the 'environmental material' class [ENVO:00010483] in the Environment Ontology (ENVO). Values for this field should be measurable or mass material nouns, representing continuous environmental materials. For host-associated or plant-associated samples, use terms from the UBERON or Plant Ontology to indicate a tissue, organ, or plant structure" + } + }, + "description": "Report the environmental material(s) immediately surrounding the sample or specimen at the time of sampling. We recommend using subclasses of 'environmental material' (http://purl.obolibrary.org/obo/ENVO_00010483). EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS . Terms from other OBO ontologies are permissible as long as they reference mass/volume nouns (e.g. air, water, blood) and not discrete, countable entities (e.g. a tree, a leaf, a table top).", + "title": "environmental medium", + "notes": [ + "range changed to enumeration late in makefile, so this is modified (but \"sample ID\" anyway)" + ], + "examples": [ + { + "value": "soil [ENVO:00001998]" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "environmental medium" + ], + "rank": 8, + "is_a": "environment field", + "string_serialization": "{termLabel} {[termID]}", + "slot_uri": "MIXS:0000014", + "alias": "env_medium", + "owner": "BuiltEnvInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "string", + "required": true, + "multivalued": false, + "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$" + }, + "escalator": { + "name": "escalator", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "value" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The number of escalators within the built structure", + "title": "escalator count", + "examples": [ + { + "value": "4" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "escalator count" + ], + "rank": 103, + "is_a": "core field", + "slot_uri": "MIXS:0000800", + "alias": "escalator", + "owner": "BuiltEnvInterface", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "exp_duct": { + "name": "exp_duct", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "square meter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The amount of exposed ductwork in the room", + "title": "exposed ductwork", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "exposed ductwork" + ], + "rank": 104, + "is_a": "core field", + "slot_uri": "MIXS:0000144", + "alias": "exp_duct", + "owner": "BuiltEnvInterface", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "exp_pipe": { + "name": "exp_pipe", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The number of exposed pipes in the room", + "title": "exposed pipes", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "exposed pipes" + ], + "rank": 105, + "is_a": "core field", + "slot_uri": "MIXS:0000220", + "alias": "exp_pipe", + "owner": "BuiltEnvInterface", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "experimental_factor": { + "name": "experimental_factor", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "text or EFO and/or OBI" + } + }, + "description": "Experimental factors are essentially the variable aspects of an experiment design which can be used to describe an experiment, or set of experiments, in an increasingly detailed manner. This field accepts ontology terms from Experimental Factor Ontology (EFO) and/or Ontology for Biomedical Investigations (OBI). For a browser of EFO (v 2.95) terms, please see http://purl.bioontology.org/ontology/EFO; for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI", + "title": "experimental factor", + "examples": [ + { + "value": "time series design [EFO:EFO_0001779]" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "experimental factor" + ], + "rank": 12, + "is_a": "investigation field", + "string_serialization": "{termLabel} {[termID]}|{text}", + "slot_uri": "MIXS:0000008", + "alias": "experimental_factor", + "owner": "BuiltEnvInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false + }, + "ext_door": { + "name": "ext_door", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "value" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The number of exterior doors in the built structure", + "title": "exterior door count", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "exterior door count" + ], + "rank": 106, + "is_a": "core field", + "slot_uri": "MIXS:0000170", + "alias": "ext_door", + "owner": "BuiltEnvInterface", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "ext_wall_orient": { + "name": "ext_wall_orient", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The orientation of the exterior wall", + "title": "orientations of exterior wall", + "examples": [ + { + "value": "northwest" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "orientations of exterior wall" + ], + "rank": 107, + "is_a": "core field", + "slot_uri": "MIXS:0000817", + "alias": "ext_wall_orient", + "owner": "BuiltEnvInterface", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "ext_wall_orient_enum", + "multivalued": false + }, + "ext_window_orient": { + "name": "ext_window_orient", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The compass direction the exterior window of the room is facing", + "title": "orientations of exterior window", + "examples": [ + { + "value": "southwest" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "orientations of exterior window" + ], + "rank": 108, + "is_a": "core field", + "slot_uri": "MIXS:0000818", + "alias": "ext_window_orient", + "owner": "BuiltEnvInterface", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "ext_window_orient_enum", + "multivalued": false + }, + "filter_type": { + "name": "filter_type", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "A device which removes solid particulates or airborne molecular contaminants", + "title": "filter type", + "examples": [ + { + "value": "HEPA" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "filter type" + ], + "rank": 109, + "is_a": "core field", + "slot_uri": "MIXS:0000765", + "alias": "filter_type", + "owner": "BuiltEnvInterface", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "filter_type_enum", + "multivalued": true + }, + "fireplace_type": { + "name": "fireplace_type", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "A firebox with chimney", + "title": "fireplace type", + "examples": [ + { + "value": "wood burning" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "fireplace type" + ], + "rank": 110, + "is_a": "core field", + "string_serialization": "[gas burning|wood burning]", + "slot_uri": "MIXS:0000802", + "alias": "fireplace_type", + "owner": "BuiltEnvInterface", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "floor_age": { + "name": "floor_age", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "years, weeks, days" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The time period since installment of the carpet or flooring", + "title": "floor age", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "floor age" + ], + "rank": 111, + "is_a": "core field", + "slot_uri": "MIXS:0000164", + "alias": "floor_age", + "owner": "BuiltEnvInterface", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "floor_area": { + "name": "floor_area", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "square meter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The area of the floor space within the room", + "title": "floor area", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "floor area" + ], + "rank": 112, + "is_a": "core field", + "slot_uri": "MIXS:0000165", + "alias": "floor_area", + "owner": "BuiltEnvInterface", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "floor_cond": { + "name": "floor_cond", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The physical condition of the floor at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas", + "title": "floor condition", + "examples": [ + { + "value": "new" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "floor condition" + ], + "rank": 113, + "is_a": "core field", + "slot_uri": "MIXS:0000803", + "alias": "floor_cond", + "owner": "BuiltEnvInterface", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "floor_cond_enum", + "multivalued": false + }, + "floor_count": { + "name": "floor_count", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "value" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The number of floors in the building, including basements and mechanical penthouse", + "title": "floor count", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "floor count" + ], + "rank": 114, + "is_a": "core field", + "slot_uri": "MIXS:0000225", + "alias": "floor_count", + "owner": "BuiltEnvInterface", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "floor_finish_mat": { + "name": "floor_finish_mat", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The floor covering type; the finished surface that is walked on", + "title": "floor finish material", + "examples": [ + { + "value": "carpet" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "floor finish material" + ], + "rank": 115, + "is_a": "core field", + "slot_uri": "MIXS:0000804", + "alias": "floor_finish_mat", + "owner": "BuiltEnvInterface", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "floor_finish_mat_enum", + "multivalued": false + }, + "floor_struc": { + "name": "floor_struc", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Refers to the structural elements and subfloor upon which the finish flooring is installed", + "title": "floor structure", + "examples": [ + { + "value": "concrete" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "floor structure" + ], + "rank": 116, + "is_a": "core field", + "slot_uri": "MIXS:0000806", + "alias": "floor_struc", + "owner": "BuiltEnvInterface", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "floor_struc_enum", + "multivalued": false + }, + "floor_thermal_mass": { + "name": "floor_thermal_mass", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "joule per degree Celsius" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The ability of the floor to provide inertia against temperature fluctuations", + "title": "floor thermal mass", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "floor thermal mass" + ], + "rank": 117, + "is_a": "core field", + "slot_uri": "MIXS:0000166", + "alias": "floor_thermal_mass", + "owner": "BuiltEnvInterface", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "floor_water_mold": { + "name": "floor_water_mold", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Signs of the presence of mold or mildew in a room", + "title": "floor signs of water/mold", + "examples": [ + { + "value": "ceiling discoloration" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "floor signs of water/mold" + ], + "rank": 118, + "is_a": "core field", + "slot_uri": "MIXS:0000805", + "alias": "floor_water_mold", + "owner": "BuiltEnvInterface", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "floor_water_mold_enum", + "multivalued": false + }, + "freq_clean": { + "name": "freq_clean", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration or {text}" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The number of times the sample location is cleaned. Frequency of cleaning might be on a Daily basis, Weekly, Monthly, Quarterly or Annually.", + "title": "frequency of cleaning", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "frequency of cleaning" + ], + "rank": 119, + "is_a": "core field", + "slot_uri": "MIXS:0000226", + "alias": "freq_clean", + "owner": "BuiltEnvInterface", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "freq_cook": { + "name": "freq_cook", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The number of times a meal is cooked per week", + "title": "frequency of cooking", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "frequency of cooking" + ], + "rank": 120, + "is_a": "core field", + "slot_uri": "MIXS:0000227", + "alias": "freq_cook", + "owner": "BuiltEnvInterface", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "furniture": { + "name": "furniture", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The types of furniture present in the sampled room", + "title": "furniture", + "examples": [ + { + "value": "chair" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "furniture" + ], + "rank": 121, + "is_a": "core field", + "slot_uri": "MIXS:0000807", + "alias": "furniture", + "owner": "BuiltEnvInterface", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "furniture_enum", + "multivalued": false + }, + "gender_restroom": { + "name": "gender_restroom", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The gender type of the restroom", + "title": "gender of restroom", + "examples": [ + { + "value": "male" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "gender of restroom" + ], + "rank": 122, + "is_a": "core field", + "slot_uri": "MIXS:0000808", + "alias": "gender_restroom", + "owner": "BuiltEnvInterface", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "gender_restroom_enum", + "multivalued": false + }, + "geo_loc_name": { + "name": "geo_loc_name", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "country or sea name (INSDC or GAZ): region(GAZ), specific location name" + } + }, + "description": "The geographical origin of the sample as defined by the country or sea name followed by specific region name.", + "title": "geographic location (country and/or sea,region)", + "examples": [ + { + "value": "USA: Maryland, Bethesda" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "geographic location (country and/or sea,region)" + ], + "rank": 4, + "is_a": "environment field", + "string_serialization": "{text}: {text}, {text}", + "slot_uri": "MIXS:0000010", + "alias": "geo_loc_name", + "owner": "BuiltEnvInterface", + "domain_of": [ + "FieldResearchSite", + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "required": true, + "multivalued": false, + "pattern": "^[^:, ][^:]*: [^:, ][^,]*, [^:, ].*$" + }, + "hall_count": { + "name": "hall_count", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "value" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The total count of hallways and cooridors in the built structure", + "title": "hallway/corridor count", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "hallway/corridor count" + ], + "rank": 123, + "is_a": "core field", + "slot_uri": "MIXS:0000228", + "alias": "hall_count", + "owner": "BuiltEnvInterface", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "handidness": { + "name": "handidness", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The handidness of the individual sampled", + "title": "handidness", + "examples": [ + { + "value": "right handedness" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "handidness" + ], + "rank": 124, + "is_a": "core field", + "slot_uri": "MIXS:0000809", + "alias": "handidness", + "owner": "BuiltEnvInterface", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "handidness_enum", + "multivalued": false + }, + "heat_cool_type": { + "name": "heat_cool_type", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Methods of conditioning or heating a room or building", + "title": "heating and cooling system type", + "examples": [ + { + "value": "heat pump" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "heating and cooling system type" + ], + "rank": 125, + "is_a": "core field", + "slot_uri": "MIXS:0000766", + "alias": "heat_cool_type", + "owner": "BuiltEnvInterface", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "heat_cool_type_enum", + "multivalued": true + }, + "heat_deliv_loc": { + "name": "heat_deliv_loc", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The location of heat delivery within the room", + "title": "heating delivery locations", + "examples": [ + { + "value": "north" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "heating delivery locations" + ], + "rank": 126, + "is_a": "core field", + "slot_uri": "MIXS:0000810", + "alias": "heat_deliv_loc", + "owner": "BuiltEnvInterface", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "heat_deliv_loc_enum", + "multivalued": false + }, + "heat_sys_deliv_meth": { + "name": "heat_sys_deliv_meth", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The method by which the heat is delivered through the system", + "title": "heating system delivery method", + "examples": [ + { + "value": "radiant" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "heating system delivery method" + ], + "rank": 127, + "is_a": "core field", + "string_serialization": "[conductive|radiant]", + "slot_uri": "MIXS:0000812", + "alias": "heat_sys_deliv_meth", + "owner": "BuiltEnvInterface", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "heat_system_id": { + "name": "heat_system_id", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "unique identifier" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The heating system identifier", + "title": "heating system identifier", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "heating system identifier" + ], + "rank": 128, + "is_a": "core field", + "slot_uri": "MIXS:0000833", + "alias": "heat_system_id", + "owner": "BuiltEnvInterface", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "height_carper_fiber": { + "name": "height_carper_fiber", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "centimeter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The average carpet fiber height in the indoor environment", + "title": "height carpet fiber mat", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "height carpet fiber mat" + ], + "rank": 129, + "is_a": "core field", + "slot_uri": "MIXS:0000167", + "alias": "height_carper_fiber", + "owner": "BuiltEnvInterface", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "indoor_space": { + "name": "indoor_space", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "A distinguishable space within a structure, the purpose for which discrete areas of a building is used", + "title": "indoor space", + "examples": [ + { + "value": "foyer" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "indoor space" + ], + "rank": 130, + "is_a": "core field", + "slot_uri": "MIXS:0000763", + "alias": "indoor_space", + "owner": "BuiltEnvInterface", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "indoor_space_enum", + "multivalued": false + }, + "indoor_surf": { + "name": "indoor_surf", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Type of indoor surface", + "title": "indoor surface", + "examples": [ + { + "value": "wall" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "indoor surface" + ], + "rank": 131, + "is_a": "core field", + "slot_uri": "MIXS:0000764", + "alias": "indoor_surf", + "owner": "BuiltEnvInterface", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "indoor_surf_enum", + "multivalued": false + }, + "inside_lux": { + "name": "inside_lux", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "kilowatt per square metre" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The recorded value at sampling time (power density)", + "title": "inside lux light", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "inside lux light" + ], + "rank": 132, + "is_a": "core field", + "slot_uri": "MIXS:0000168", + "alias": "inside_lux", + "owner": "BuiltEnvInterface", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "int_wall_cond": { + "name": "int_wall_cond", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The physical condition of the wall at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas", + "title": "interior wall condition", + "examples": [ + { + "value": "damaged" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "interior wall condition" + ], + "rank": 133, + "is_a": "core field", + "slot_uri": "MIXS:0000813", + "alias": "int_wall_cond", + "owner": "BuiltEnvInterface", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "int_wall_cond_enum", + "multivalued": false + }, + "last_clean": { + "name": "last_clean", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "timestamp" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The last time the floor was cleaned (swept, mopped, vacuumed)", + "title": "last time swept/mopped/vacuumed", + "examples": [ + { + "value": "2018-05-11:T14:30Z" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "last time swept/mopped/vacuumed" + ], + "rank": 134, + "is_a": "core field", + "slot_uri": "MIXS:0000814", + "alias": "last_clean", + "owner": "BuiltEnvInterface", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "lat_lon": { + "name": "lat_lon", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "decimal degrees, limit to 8 decimal points" + } + }, + "description": "The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system", + "title": "geographic location (latitude and longitude)", + "notes": [ + "This is currently a required field but it's not clear if this should be required for human hosts" + ], + "examples": [ + { + "value": "50.586825 6.408977" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "geographic location (latitude and longitude)" + ], + "rank": 5, + "is_a": "environment field", + "string_serialization": "{lat lon}", + "slot_uri": "MIXS:0000009", + "alias": "lat_lon", + "owner": "BuiltEnvInterface", + "domain_of": [ + "FieldResearchSite", + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "required": true, + "multivalued": false, + "pattern": "^[-+]?([1-8]?\\d(\\.\\d{1,8})?|90(\\.0{1,8})?)\\s[-+]?(180(\\.0{1,8})?|((1[0-7]\\d)|([1-9]?\\d))(\\.\\d{1,8})?)$" + }, + "light_type": { + "name": "light_type", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Application of light to achieve some practical or aesthetic effect. Lighting includes the use of both artificial light sources such as lamps and light fixtures, as well as natural illumination by capturing daylight. Can also include absence of light", + "title": "light type", + "examples": [ + { + "value": "desk lamp" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "light type" + ], + "rank": 135, + "is_a": "core field", + "slot_uri": "MIXS:0000769", + "alias": "light_type", + "owner": "BuiltEnvInterface", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "light_type_enum", + "multivalued": true + }, + "max_occup": { + "name": "max_occup", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The maximum amount of people allowed in the indoor environment", + "title": "maximum occupancy", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "maximum occupancy" + ], + "rank": 136, + "is_a": "core field", + "slot_uri": "MIXS:0000229", + "alias": "max_occup", + "owner": "BuiltEnvInterface", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "mech_struc": { + "name": "mech_struc", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "mechanical structure: a moving structure", + "title": "mechanical structure", + "examples": [ + { + "value": "elevator" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "mechanical structure" + ], + "rank": 137, + "is_a": "core field", + "slot_uri": "MIXS:0000815", + "alias": "mech_struc", + "owner": "BuiltEnvInterface", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "mech_struc_enum", + "multivalued": false + }, + "number_pets": { + "name": "number_pets", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The number of pets residing in the sampled space", + "title": "number of pets", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "number of pets" + ], + "rank": 138, + "is_a": "core field", + "slot_uri": "MIXS:0000231", + "alias": "number_pets", + "owner": "BuiltEnvInterface", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "number_plants": { + "name": "number_plants", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The number of plant(s) in the sampling space", + "title": "number of houseplants", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "number of houseplants" + ], + "rank": 139, + "is_a": "core field", + "slot_uri": "MIXS:0000230", + "alias": "number_plants", + "owner": "BuiltEnvInterface", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "number_resident": { + "name": "number_resident", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The number of individuals currently occupying in the sampling location", + "title": "number of residents", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "number of residents" + ], + "rank": 140, + "is_a": "core field", + "slot_uri": "MIXS:0000232", + "alias": "number_resident", + "owner": "BuiltEnvInterface", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "occup_density_samp": { + "name": "occup_density_samp", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Average number of occupants at time of sampling per square footage", + "title": "occupant density at sampling", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "occupant density at sampling" + ], + "rank": 141, + "is_a": "core field", + "slot_uri": "MIXS:0000217", + "alias": "occup_density_samp", + "owner": "BuiltEnvInterface", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "occup_document": { + "name": "occup_document", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The type of documentation of occupancy", + "title": "occupancy documentation", + "examples": [ + { + "value": "estimate" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "occupancy documentation" + ], + "rank": 142, + "is_a": "core field", + "slot_uri": "MIXS:0000816", + "alias": "occup_document", + "owner": "BuiltEnvInterface", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "occup_document_enum", + "multivalued": false + }, + "occup_samp": { + "name": "occup_samp", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Number of occupants present at time of sample within the given space", + "title": "occupancy at sampling", + "examples": [ + { + "value": "10" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "occupancy at sampling" + ], + "rank": 143, + "is_a": "core field", + "slot_uri": "MIXS:0000772", + "alias": "occup_samp", + "owner": "BuiltEnvInterface", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "organism_count": { + "name": "organism_count", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "organism name;measurement value;enumeration" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "number of cells per cubic meter, number of cells per milliliter, number of cells per cubic centimeter" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr)", + "title": "organism count", + "examples": [ + { + "value": "total prokaryotes;3.5e7 cells per milliliter;qPCR" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "organism count" + ], + "rank": 30, + "is_a": "core field", + "slot_uri": "MIXS:0000103", + "alias": "organism_count", + "owner": "BuiltEnvInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^([-+]?[0-9]*\\.?[0-9]+ +\\S.*\\|)*([-+]?[0-9]*\\.?[0-9]+ +\\S.*)$" + }, + "pres_animal_insect": { + "name": "pres_animal_insect", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration;count" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The type and number of animals or insects present in the sampling space.", + "title": "presence of pets, animals, or insects", + "examples": [ + { + "value": "cat;5" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "presence of pets, animals, or insects" + ], + "rank": 144, + "is_a": "core field", + "slot_uri": "MIXS:0000819", + "alias": "pres_animal_insect", + "owner": "BuiltEnvInterface", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^(cat|dog|rodent|snake|other);\\d+$" + }, + "quad_pos": { + "name": "quad_pos", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The quadrant position of the sampling room within the building", + "title": "quadrant position", + "examples": [ + { + "value": "West side" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "quadrant position" + ], + "rank": 145, + "is_a": "core field", + "slot_uri": "MIXS:0000820", + "alias": "quad_pos", + "owner": "BuiltEnvInterface", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "quad_pos_enum", + "multivalued": false + }, + "rel_air_humidity": { + "name": "rel_air_humidity", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "percentage" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Partial vapor and air pressure, density of the vapor and air, or by the actual mass of the vapor and air", + "title": "relative air humidity", + "examples": [ + { + "value": "80%" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "relative air humidity" + ], + "rank": 146, + "is_a": "core field", + "slot_uri": "MIXS:0000121", + "alias": "rel_air_humidity", + "owner": "BuiltEnvInterface", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "rel_humidity_out": { + "name": "rel_humidity_out", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "gram of air, kilogram of air" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The recorded outside relative humidity value at the time of sampling", + "title": "outside relative humidity", + "examples": [ + { + "value": "12 per kilogram of air" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "outside relative humidity" + ], + "rank": 147, + "is_a": "core field", + "slot_uri": "MIXS:0000188", + "alias": "rel_humidity_out", + "owner": "BuiltEnvInterface", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "rel_samp_loc": { + "name": "rel_samp_loc", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The sampling location within the train car", + "title": "relative sampling location", + "examples": [ + { + "value": "center of car" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "relative sampling location" + ], + "rank": 148, + "is_a": "core field", + "slot_uri": "MIXS:0000821", + "alias": "rel_samp_loc", + "owner": "BuiltEnvInterface", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "rel_samp_loc_enum", + "multivalued": false + }, + "room_air_exch_rate": { + "name": "room_air_exch_rate", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "liter per hour" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The rate at which outside air replaces indoor air in a given space", + "title": "room air exchange rate", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "room air exchange rate" + ], + "rank": 149, + "is_a": "core field", + "slot_uri": "MIXS:0000169", + "alias": "room_air_exch_rate", + "owner": "BuiltEnvInterface", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "room_architec_elem": { + "name": "room_architec_elem", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "free text" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The unique details and component parts that, together, form the architecture of a distinguisahable space within a built structure", + "title": "room architectural elements", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "room architectural elements" + ], + "rank": 150, + "is_a": "core field", + "string_serialization": "{text}", + "slot_uri": "MIXS:0000233", + "alias": "room_architec_elem", + "owner": "BuiltEnvInterface", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "room_condt": { + "name": "room_condt", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The condition of the room at the time of sampling", + "title": "room condition", + "examples": [ + { + "value": "new" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "room condition" + ], + "rank": 151, + "is_a": "core field", + "slot_uri": "MIXS:0000822", + "alias": "room_condt", + "owner": "BuiltEnvInterface", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "room_condt_enum", + "multivalued": false + }, + "room_connected": { + "name": "room_connected", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "List of rooms connected to the sampling room by a doorway", + "title": "rooms connected by a doorway", + "examples": [ + { + "value": "office" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "rooms connected by a doorway" + ], + "rank": 152, + "is_a": "core field", + "slot_uri": "MIXS:0000826", + "alias": "room_connected", + "owner": "BuiltEnvInterface", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "room_connected_enum", + "multivalued": false + }, + "room_count": { + "name": "room_count", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "value" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The total count of rooms in the built structure including all room types", + "title": "room count", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "room count" + ], + "rank": 153, + "is_a": "core field", + "slot_uri": "MIXS:0000234", + "alias": "room_count", + "owner": "BuiltEnvInterface", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "room_dim": { + "name": "room_dim", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "meter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The length, width and height of sampling room", + "title": "room dimensions", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "room dimensions" + ], + "rank": 154, + "is_a": "core field", + "string_serialization": "{integer} {unit} x {integer} {unit} x {integer} {unit}", + "slot_uri": "MIXS:0000192", + "alias": "room_dim", + "owner": "BuiltEnvInterface", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "room_door_dist": { + "name": "room_door_dist", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "meter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Distance between doors (meters) in the hallway between the sampling room and adjacent rooms", + "title": "room door distance", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "room door distance" + ], + "rank": 155, + "is_a": "core field", + "string_serialization": "{integer} {unit}", + "slot_uri": "MIXS:0000193", + "alias": "room_door_dist", + "owner": "BuiltEnvInterface", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "room_door_share": { + "name": "room_door_share", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "room name;room number" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "List of room(s) (room number, room name) sharing a door with the sampling room", + "title": "rooms that share a door with sampling room", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "rooms that share a door with sampling room" + ], + "rank": 156, + "is_a": "core field", + "string_serialization": "{text};{integer}", + "slot_uri": "MIXS:0000242", + "alias": "room_door_share", + "owner": "BuiltEnvInterface", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "room_hallway": { + "name": "room_hallway", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "room name;room number" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "List of room(s) (room number, room name) located in the same hallway as sampling room", + "title": "rooms that are on the same hallway", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "rooms that are on the same hallway" + ], + "rank": 157, + "is_a": "core field", + "string_serialization": "{text};{integer}", + "slot_uri": "MIXS:0000238", + "alias": "room_hallway", + "owner": "BuiltEnvInterface", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "room_loc": { + "name": "room_loc", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The position of the room within the building", + "title": "room location in building", + "examples": [ + { + "value": "interior room" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "room location in building" + ], + "rank": 158, + "is_a": "core field", + "slot_uri": "MIXS:0000823", + "alias": "room_loc", + "owner": "BuiltEnvInterface", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "room_loc_enum", + "multivalued": false + }, + "room_moist_dam_hist": { + "name": "room_moist_dam_hist", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "value" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The history of moisture damage or mold in the past 12 months. Number of events of moisture damage or mold observed", + "title": "room moisture damage or mold history", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "room moisture damage or mold history" + ], + "rank": 159, + "is_a": "core field", + "slot_uri": "MIXS:0000235", + "alias": "room_moist_dam_hist", + "owner": "BuiltEnvInterface", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "integer", + "multivalued": false + }, + "room_net_area": { + "name": "room_net_area", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "square feet, square meter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The net floor area of sampling room. Net area excludes wall thicknesses", + "title": "room net area", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "room net area" + ], + "rank": 160, + "is_a": "core field", + "string_serialization": "{integer} {unit}", + "slot_uri": "MIXS:0000194", + "alias": "room_net_area", + "owner": "BuiltEnvInterface", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "room_occup": { + "name": "room_occup", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Count of room occupancy at time of sampling", + "title": "room occupancy", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "room occupancy" + ], + "rank": 161, + "is_a": "core field", + "slot_uri": "MIXS:0000236", + "alias": "room_occup", + "owner": "BuiltEnvInterface", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "room_samp_pos": { + "name": "room_samp_pos", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The horizontal sampling position in the room relative to architectural elements", + "title": "room sampling position", + "examples": [ + { + "value": "south corner" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "room sampling position" + ], + "rank": 162, + "is_a": "core field", + "slot_uri": "MIXS:0000824", + "alias": "room_samp_pos", + "owner": "BuiltEnvInterface", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "room_samp_pos_enum", + "multivalued": false + }, + "room_type": { + "name": "room_type", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The main purpose or activity of the sampling room. A room is any distinguishable space within a structure", + "title": "room type", + "examples": [ + { + "value": "bathroom" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "room type" + ], + "rank": 163, + "is_a": "core field", + "slot_uri": "MIXS:0000825", + "alias": "room_type", + "owner": "BuiltEnvInterface", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "room_type_enum", + "multivalued": false + }, + "room_vol": { + "name": "room_vol", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "cubic feet, cubic meter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Volume of sampling room", + "title": "room volume", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "room volume" + ], + "rank": 164, + "is_a": "core field", + "string_serialization": "{integer} {unit}", + "slot_uri": "MIXS:0000195", + "alias": "room_vol", + "owner": "BuiltEnvInterface", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "room_wall_share": { + "name": "room_wall_share", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "room name;room number" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "List of room(s) (room number, room name) sharing a wall with the sampling room", + "title": "rooms that share a wall with sampling room", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "rooms that share a wall with sampling room" + ], + "rank": 165, + "is_a": "core field", + "string_serialization": "{text};{integer}", + "slot_uri": "MIXS:0000243", + "alias": "room_wall_share", + "owner": "BuiltEnvInterface", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "room_window_count": { + "name": "room_window_count", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "value" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Number of windows in the room", + "title": "room window count", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "room window count" + ], + "rank": 166, + "is_a": "core field", + "slot_uri": "MIXS:0000237", + "alias": "room_window_count", + "owner": "BuiltEnvInterface", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "integer", + "multivalued": false + }, + "samp_floor": { + "name": "samp_floor", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The floor of the building, where the sampling room is located", + "title": "sampling floor", + "examples": [ + { + "value": "4th floor" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sampling floor" + ], + "rank": 167, + "is_a": "core field", + "slot_uri": "MIXS:0000828", + "alias": "samp_floor", + "owner": "BuiltEnvInterface", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "samp_floor_enum", + "multivalued": false + }, + "samp_room_id": { + "name": "samp_room_id", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "value" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Sampling room number. This ID should be consistent with the designations on the building floor plans", + "title": "sampling room ID or name", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sampling room ID or name" + ], + "rank": 168, + "is_a": "core field", + "slot_uri": "MIXS:0000244", + "alias": "samp_room_id", + "owner": "BuiltEnvInterface", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "samp_sort_meth": { + "name": "samp_sort_meth", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "description of method" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Method by which samples are sorted; open face filter collecting total suspended particles, prefilter to remove particles larger than X micrometers in diameter, where common values of X would be 10 and 2.5 full size sorting in a cascade impactor.", + "title": "sample size sorting method", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sample size sorting method" + ], + "rank": 169, + "is_a": "core field", + "string_serialization": "{text}", + "slot_uri": "MIXS:0000216", + "alias": "samp_sort_meth", + "owner": "BuiltEnvInterface", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "samp_time_out": { + "name": "samp_time_out", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "time" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "hour" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The recent and long term history of outside sampling", + "title": "sampling time outside", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sampling time outside" + ], + "rank": 170, + "is_a": "core field", + "slot_uri": "MIXS:0000196", + "alias": "samp_time_out", + "owner": "BuiltEnvInterface", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "samp_weather": { + "name": "samp_weather", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The weather on the sampling day", + "title": "sampling day weather", + "examples": [ + { + "value": "foggy" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sampling day weather" + ], + "rank": 171, + "is_a": "core field", + "slot_uri": "MIXS:0000827", + "alias": "samp_weather", + "owner": "BuiltEnvInterface", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "samp_weather_enum", + "multivalued": false + }, + "sample_link": { + "name": "sample_link", + "description": "A unique identifier to assign parent-child, subsample, or sibling samples. This is relevant when a sample or other material was used to generate the new sample.", + "title": "sample linkage", + "notes": [ + "also tempted to include SampIdNewTermsMixin but if len(slot_usage.keys()) > 1 and \"placeholder\" in slot_usage.keys():AttributeError: 'list' object has no attribute 'keys'" + ], + "comments": [ + "This field allows multiple entries separated by ; (Examples: Soil collected from the field will link with the soil used in an incubation. The soil a plant was grown in links to the plant sample. An original culture sample was transferred to a new vial and generated a new sample)" + ], + "examples": [ + { + "value": "IGSN:DSJ0284" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "rank": 5, + "string_serialization": "{text}:{text}", + "alias": "sample_link", + "owner": "BuiltEnvInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface", + "SampIdNewTermsMixin" + ], + "slot_group": "sample_id_section", + "range": "string", + "recommended": true, + "multivalued": false, + "pattern": "[^\\:\\n\\r]+\\:[^\\:\\n\\r]+" + }, + "season": { + "name": "season", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "NCIT:C94729" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The season when sampling occurred. Any of the four periods into which the year is divided by the equinoxes and solstices. This field accepts terms listed under season (http://purl.obolibrary.org/obo/NCIT_C94729).", + "title": "season", + "examples": [ + { + "value": "autumn [NCIT:C94733]" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "season" + ], + "rank": 172, + "is_a": "core field", + "string_serialization": "{termLabel} {[termID]}", + "slot_uri": "MIXS:0000829", + "alias": "season", + "owner": "BuiltEnvInterface", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$" + }, + "season_use": { + "name": "season_use", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The seasons the space is occupied", + "title": "seasonal use", + "examples": [ + { + "value": "Winter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "seasonal use" + ], + "rank": 173, + "is_a": "core field", + "slot_uri": "MIXS:0000830", + "alias": "season_use", + "owner": "BuiltEnvInterface", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "season_use_enum", + "multivalued": false + }, + "shad_dev_water_mold": { + "name": "shad_dev_water_mold", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Signs of the presence of mold or mildew on the shading device", + "title": "shading device signs of water/mold", + "examples": [ + { + "value": "no presence of mold visible" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "shading device signs of water/mold" + ], + "rank": 174, + "is_a": "core field", + "string_serialization": "[presence of mold visible|no presence of mold visible]", + "slot_uri": "MIXS:0000834", + "alias": "shad_dev_water_mold", + "owner": "BuiltEnvInterface", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "shading_device_cond": { + "name": "shading_device_cond", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The physical condition of the shading device at the time of sampling", + "title": "shading device condition", + "examples": [ + { + "value": "new" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "shading device condition" + ], + "rank": 175, + "is_a": "core field", + "slot_uri": "MIXS:0000831", + "alias": "shading_device_cond", + "owner": "BuiltEnvInterface", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": 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"tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The surface treatment of interior wall", + "title": "wall surface treatment", + "examples": [ + { + "value": "paneling" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "wall surface treatment" + ], + "rank": 200, + "is_a": "core field", + "slot_uri": "MIXS:0000845", + "alias": "wall_surf_treatment", + "owner": "BuiltEnvInterface", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "wall_surf_treatment_enum", + "multivalued": false + }, + "wall_texture": { + "name": "wall_texture", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The feel, appearance, or consistency of a wall surface", + "title": "wall texture", + "examples": [ + { + "value": "popcorn" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "wall texture" + ], + "rank": 201, + "is_a": "core field", + "slot_uri": "MIXS:0000846", + "alias": "wall_texture", + "owner": "BuiltEnvInterface", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "wall_texture_enum", + "multivalued": false + }, + "wall_thermal_mass": { + "name": "wall_thermal_mass", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "joule per degree Celsius" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The ability of the wall to provide inertia against temperature fluctuations. Generally this means concrete or concrete block that is either exposed or covered only with paint", + "title": "wall thermal mass", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "wall thermal mass" + ], + "rank": 202, + "is_a": "core field", + "slot_uri": "MIXS:0000222", + "alias": "wall_thermal_mass", + "owner": "BuiltEnvInterface", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "wall_water_mold": { + "name": "wall_water_mold", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Signs of the presence of mold or mildew on a wall", + "title": "wall signs of water/mold", + "examples": [ + { + "value": "no presence of mold visible" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "wall signs of water/mold" + ], + "rank": 203, + "is_a": "core field", + "string_serialization": "[presence of mold visible|no presence of mold visible]", + "slot_uri": "MIXS:0000844", + "alias": "wall_water_mold", + "owner": "BuiltEnvInterface", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "water_feat_size": { + "name": "water_feat_size", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "square meter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The size of the water feature", + "title": "water feature size", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "water feature size" + ], + "rank": 204, + "is_a": "core field", + "slot_uri": "MIXS:0000223", + "alias": "water_feat_size", + "owner": "BuiltEnvInterface", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "water_feat_type": { + "name": "water_feat_type", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The type of water feature present within the building being sampled", + "title": "water feature type", + "examples": [ + { + "value": "stream" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "water feature type" + ], + "rank": 205, + "is_a": "core field", + "slot_uri": "MIXS:0000847", + "alias": "water_feat_type", + "owner": "BuiltEnvInterface", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "water_feat_type_enum", + "multivalued": false + }, + "weekday": { + "name": "weekday", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The day of the week when sampling occurred", + "title": "weekday", + "examples": [ + { + "value": "Sunday" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "weekday" + ], + "rank": 206, + "is_a": "core field", + "slot_uri": "MIXS:0000848", + "alias": "weekday", + "owner": "BuiltEnvInterface", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "weekday_enum", + "multivalued": false + }, + "window_cond": { + "name": "window_cond", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The physical condition of the window at the time of sampling", + "title": "window condition", + "examples": [ + { + "value": "rupture" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "window condition" + ], + "rank": 207, + "is_a": "core field", + "slot_uri": "MIXS:0000849", + "alias": "window_cond", + "owner": "BuiltEnvInterface", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "window_cond_enum", + "multivalued": false + }, + "window_cover": { + "name": "window_cover", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The type of window covering", + "title": "window covering", + "examples": [ + { + "value": "curtains" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "window covering" + ], + "rank": 208, + "is_a": "core field", + "slot_uri": "MIXS:0000850", + "alias": "window_cover", + "owner": "BuiltEnvInterface", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "window_cover_enum", + "multivalued": false + }, + "window_horiz_pos": { + "name": "window_horiz_pos", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The horizontal position of the window on the wall", + "title": "window horizontal position", + "examples": [ + { + "value": "middle" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "window horizontal position" + ], + "rank": 209, + "is_a": "core field", + "slot_uri": "MIXS:0000851", + "alias": "window_horiz_pos", + "owner": "BuiltEnvInterface", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "window_horiz_pos_enum", + "multivalued": false + }, + "window_loc": { + "name": "window_loc", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The relative location of the window within the room", + "title": "window location", + "examples": [ + { + "value": "west" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "window location" + ], + "rank": 210, + "is_a": "core field", + "slot_uri": "MIXS:0000852", + "alias": "window_loc", + "owner": "BuiltEnvInterface", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "window_loc_enum", + "multivalued": false + }, + "window_mat": { + "name": "window_mat", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The type of material used to finish a window", + "title": "window material", + "examples": [ + { + "value": "wood" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "window material" + ], + "rank": 211, + "is_a": "core field", + "slot_uri": "MIXS:0000853", + "alias": "window_mat", + "owner": "BuiltEnvInterface", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "window_mat_enum", + "multivalued": false + }, + "window_open_freq": { + "name": "window_open_freq", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "value" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The number of times windows are opened per week", + "title": "window open frequency", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "window open frequency" + ], + "rank": 212, + "is_a": "core field", + "slot_uri": "MIXS:0000246", + "alias": "window_open_freq", + "owner": "BuiltEnvInterface", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "window_size": { + "name": "window_size", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "inch, meter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The window's length and width", + "title": "window area/size", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "window area/size" + ], + "rank": 213, + "is_a": "core field", + "string_serialization": "{float} {unit} x {float} {unit}", + "slot_uri": "MIXS:0000224", + "alias": "window_size", + "owner": "BuiltEnvInterface", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "window_status": { + "name": "window_status", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Defines whether the windows were open or closed during environmental testing", + "title": "window status", + "examples": [ + { + "value": "open" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "window status" + ], + "rank": 214, + "is_a": "core field", + "string_serialization": "[closed|open]", + "slot_uri": "MIXS:0000855", + "alias": "window_status", + "owner": "BuiltEnvInterface", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "window_type": { + "name": "window_type", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The type of windows", + "title": "window type", + "examples": [ + { + "value": "fixed window" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "window type" + ], + "rank": 215, + "is_a": "core field", + "slot_uri": "MIXS:0000856", + "alias": "window_type", + "owner": "BuiltEnvInterface", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "window_type_enum", + "multivalued": false + }, + "window_vert_pos": { + "name": "window_vert_pos", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The vertical position of the window on the wall", + "title": "window vertical position", + "examples": [ + { + "value": "middle" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "window vertical position" + ], + "rank": 216, + "is_a": "core field", + "slot_uri": "MIXS:0000857", + "alias": "window_vert_pos", + "owner": "BuiltEnvInterface", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "window_vert_pos_enum", + "multivalued": false + }, + "window_water_mold": { + "name": "window_water_mold", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Signs of the presence of mold or mildew on the window.", + "title": "window signs of water/mold", + "examples": [ + { + "value": "no presence of mold visible" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "window signs of water/mold" + ], + "rank": 217, + "is_a": "core field", + "string_serialization": "[presence of mold visible|no presence of mold visible]", + "slot_uri": "MIXS:0000854", + "alias": "window_water_mold", + "owner": "BuiltEnvInterface", + "domain_of": [ + "Biosample", + "BuiltEnvInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "analysis_type": { + "name": "analysis_type", + "description": "Select all the data types associated or available for this biosample", + "title": "analysis/data type", + "examples": [ + { + "value": "metagenomics; metabolomics; proteomics" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "MIxS:investigation_type" + ], + "rank": 3, + "alias": "analysis_type", + "owner": "BuiltEnvInterface", + "domain_of": [ + "Biosample", + "DhMultiviewCommonColumnsMixin", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "EmslInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "JgiMgInterface", + "JgiMgLrInterface", + "JgiMtInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "AnalysisTypeEnum", + "required": true, + "recommended": false, + "multivalued": true + }, + "samp_name": { + "name": "samp_name", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "text" + } + }, + "description": "A local identifier or name that for the material sample collected. Refers to the original material collected or to any derived sub-samples.", + "title": "sample name", + "comments": [ + "It can have any format, but we suggest that you make it concise, unique and consistent within your lab, and as informative as possible." + ], + "examples": [ + { + "value": "Rock core CB1178(5-6) from NSW" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sample name" + ], + "rank": 1, + "is_a": "investigation field", + "string_serialization": "{text}", + "slot_uri": "MIXS:0001107", + "identifier": true, + "alias": "samp_name", + "owner": "BuiltEnvInterface", + "domain_of": [ + "Biosample", + "DhMultiviewCommonColumnsMixin", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "EmslInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "JgiMgInterface", + "JgiMgLrInterface", + "JgiMtInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "string", + "required": true, + "multivalued": false + }, + "source_mat_id": { + "name": "source_mat_id", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "for cultures of microorganisms: identifiers for two culture collections; for other material a unique arbitrary identifer" + } + }, + "description": "A globally unique identifier assigned to the biological sample.", + "title": "source material identifier", + "todos": [ + "Currently, the comments say to use UUIDs. However, if we implement assigning NMDC identifiers with the minter we dont need to require a GUID. It can be an optional field to fill out only if they already have a resolvable ID.", + "Currently, the comments say to use UUIDs. However, if we implement assigning NMDC identifiers with the minter we dont need to require a GUID. It can be an optional field to fill out only if they already have a resolvable ID." + ], + "notes": [ + "The source material IS the Globally Unique ID" + ], + "comments": [ + "Identifiers must be prefixed. Possible FAIR prefixes are IGSNs (http://www.geosamples.org/getigsn), NCBI biosample accession numbers, ARK identifiers (https://arks.org/). These IDs enable linking to derived analytes and subsamples. If you have not assigned FAIR identifiers to your samples, you can generate UUIDs (https://www.uuidgenerator.net/).", + "Identifiers must be prefixed. Possible FAIR prefixes are IGSNs (http://www.geosamples.org/getigsn), NCBI biosample accession numbers, ARK identifiers (https://arks.org/). These IDs enable linking to derived analytes and subsamples. If you have not assigned FAIR identifiers to your samples, you can generate UUIDs (https://www.uuidgenerator.net/)." + ], + "examples": [ + { + "value": "IGSN:AU1243" + }, + { + "value": "UUID:24f1467a-40f4-11ed-b878-0242ac120002" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "source material identifiers" + ], + "rank": 2, + "is_a": "nucleic acid sequence source field", + "string_serialization": "{text}:{text}", + "slot_uri": "MIXS:0000026", + "alias": "source_mat_id", + "owner": "BuiltEnvInterface", + "domain_of": [ + "Biosample", + "DhMultiviewCommonColumnsMixin", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "EmslInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "JgiMgInterface", + "JgiMgLrInterface", + "JgiMtInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "string", + "multivalued": false, + "pattern": "[^\\:\\n\\r]+\\:[^\\:\\n\\r]+" + } + } + }, + "EmslInterface": { + "name": "EmslInterface", + "annotations": { + "excel_worksheet_name": { + "tag": "excel_worksheet_name", + "value": "EMSL" + } + }, + "description": "emsl dh_interface", + "title": "Emsl", + "from_schema": "https://example.com/nmdc_submission_schema", + "is_a": "DhInterface", + "mixins": [ + "DhMultiviewCommonColumnsMixin" + ], + "slots": [ + "emsl_store_temp", + "project_id", + "replicate_number", + "sample_shipped", + "sample_type", + "technical_reps", + "emsl_store_temp", + "project_id", + "replicate_number", + "sample_shipped", + "sample_type", + "technical_reps" + ], + "slot_usage": { + "emsl_store_temp": { + "name": "emsl_store_temp", + "description": "The temperature at which the sample should be stored upon delivery to EMSL", + "title": "EMSL sample storage temperature, deg. C", + "todos": [ + "add 'see_alsos' with link to NEXUS info" + ], + "comments": [ + "Enter a temperature in celsius. Numeric portion only." + ], + "examples": [ + { + "value": "-80" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "rank": 4, + "string_serialization": "{float}", + "owner": "Biosample", + "slot_group": "emsl_section", + "range": "float", + "required": true, + "recommended": false + }, + "project_id": { + "name": "project_id", + "description": "Proposal IDs or names associated with dataset", + "title": "project ID", + "from_schema": "https://w3id.org/nmdc/nmdc", + "rank": 1, + "string_serialization": "{text}", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "EmslInterface" + ], + "slot_group": "emsl_section", + "range": "string", + "required": true, + "recommended": false, + "multivalued": false + }, + "replicate_number": { + "name": "replicate_number", + "description": "If sending biological replicates, indicate the rep number here.", + "title": "replicate number", + "comments": [ + "This will guide staff in ensuring your samples are blocked & randomized correctly" + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "rank": 6, + "string_serialization": "{integer}", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "EmslInterface" + ], + "slot_group": "emsl_section", + "range": "integer", + "recommended": true + }, + "sample_shipped": { + "name": "sample_shipped", + "description": "The total amount or size (volume (ml), mass (g) or area (m2) ) of sample sent to EMSL.", + "title": "sample shipped amount", + "comments": [ + "This field is only required when completing metadata for samples being submitted to EMSL for analyses." + ], + "examples": [ + { + "value": "15 g" + }, + { + "value": "100 uL" + }, + { + "value": "5 mL" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "rank": 3, + "string_serialization": "{float} {unit}", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "EmslInterface" + ], + "slot_group": "emsl_section", + "range": "string", + "required": true, + "recommended": false, + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? \\S+$" + }, + "sample_type": { + "name": "sample_type", + "description": "Type of sample being submitted", + "title": "sample type", + "comments": [ + "This can vary from 'environmental package' if the sample is an extraction." + ], + "examples": [ + { + "value": "water extracted soil" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "rank": 2, + "owner": "Biosample", + "domain_of": [ + "Biosample", + "EmslInterface" + ], + "slot_group": "emsl_section", + "range": "SampleTypeEnum", + "required": true, + "recommended": false + }, + "technical_reps": { + "name": "technical_reps", + "description": "If sending technical replicates of the same sample, indicate the replicate count.", + "title": "number technical replicate", + "comments": [ + "This field is only required when completing metadata for samples being submitted to EMSL for analyses." + ], + "examples": [ + { + "value": "2" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "rank": 5, + "string_serialization": "{integer}", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "EmslInterface" + ], + "slot_group": "emsl_section", + "range": "integer", + "recommended": true + }, + "oxy_stat_samp": { + "name": "oxy_stat_samp", + "range": "OxyStatSampEnum" + } + }, + "attributes": { + "emsl_store_temp": { + "name": "emsl_store_temp", + "description": "The temperature at which the sample should be stored upon delivery to EMSL", + "title": "EMSL sample storage temperature, deg. C", + "todos": [ + "add 'see_alsos' with link to NEXUS info" + ], + "comments": [ + "Enter a temperature in celsius. Numeric portion only." + ], + "examples": [ + { + "value": "-80" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "rank": 4, + "string_serialization": "{float}", + "alias": "emsl_store_temp", + "owner": "EmslInterface", + "domain_of": [ + "EmslInterface" + ], + "slot_group": "emsl_section", + "range": "float", + "required": true, + "recommended": false + }, + "project_id": { + "name": "project_id", + "description": "Proposal IDs or names associated with dataset", + "title": "project ID", + "from_schema": "https://w3id.org/nmdc/nmdc", + "rank": 1, + "string_serialization": "{text}", + "alias": "project_id", + "owner": "EmslInterface", + "domain_of": [ + "Biosample", + "EmslInterface" + ], + "slot_group": "emsl_section", + "range": "string", + "required": true, + "recommended": false, + "multivalued": false + }, + "replicate_number": { + "name": "replicate_number", + "description": "If sending biological replicates, indicate the rep number here.", + "title": "replicate number", + "comments": [ + "This will guide staff in ensuring your samples are blocked & randomized correctly" + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "rank": 6, + "string_serialization": "{integer}", + "alias": "replicate_number", + "owner": "EmslInterface", + "domain_of": [ + "Biosample", + "EmslInterface" + ], + "slot_group": "emsl_section", + "range": "integer", + "recommended": true + }, + "sample_shipped": { + "name": "sample_shipped", + "description": "The total amount or size (volume (ml), mass (g) or area (m2) ) of sample sent to EMSL.", + "title": "sample shipped amount", + "comments": [ + "This field is only required when completing metadata for samples being submitted to EMSL for analyses." + ], + "examples": [ + { + "value": "15 g" + }, + { + "value": "100 uL" + }, + { + "value": "5 mL" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "rank": 3, + "string_serialization": "{float} {unit}", + "alias": "sample_shipped", + "owner": "EmslInterface", + "domain_of": [ + "Biosample", + "EmslInterface" + ], + "slot_group": "emsl_section", + "range": "string", + "required": true, + "recommended": false, + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? \\S+$" + }, + "sample_type": { + "name": "sample_type", + "description": "Type of sample being submitted", + "title": "sample type", + "comments": [ + "This can vary from 'environmental package' if the sample is an extraction." + ], + "examples": [ + { + "value": "water extracted soil" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "rank": 2, + "alias": "sample_type", + "owner": "EmslInterface", + "domain_of": [ + "Biosample", + "EmslInterface" + ], + "slot_group": "emsl_section", + "range": "SampleTypeEnum", + "required": true, + "recommended": false + }, + "technical_reps": { + "name": "technical_reps", + "description": "If sending technical replicates of the same sample, indicate the replicate count.", + "title": "number technical replicate", + "comments": [ + "This field is only required when completing metadata for samples being submitted to EMSL for analyses." + ], + "examples": [ + { + "value": "2" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "rank": 5, + "string_serialization": "{integer}", + "alias": "technical_reps", + "owner": "EmslInterface", + "domain_of": [ + "Biosample", + "EmslInterface" + ], + "slot_group": "emsl_section", + "range": "integer", + "recommended": true + }, + "analysis_type": { + "name": "analysis_type", + "description": "Select all the data types associated or available for this biosample", + "title": "analysis/data type", + "examples": [ + { + "value": "metagenomics; metabolomics; proteomics" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "MIxS:investigation_type" + ], + "rank": 3, + "alias": "analysis_type", + "owner": "EmslInterface", + "domain_of": [ + "Biosample", + "DhMultiviewCommonColumnsMixin", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "EmslInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "JgiMgInterface", + "JgiMgLrInterface", + "JgiMtInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "AnalysisTypeEnum", + "required": true, + "recommended": false, + "multivalued": true + }, + "samp_name": { + "name": "samp_name", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "text" + } + }, + "description": "A local identifier or name that for the material sample collected. Refers to the original material collected or to any derived sub-samples.", + "title": "sample name", + "comments": [ + "It can have any format, but we suggest that you make it concise, unique and consistent within your lab, and as informative as possible." + ], + "examples": [ + { + "value": "Rock core CB1178(5-6) from NSW" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sample name" + ], + "rank": 1, + "is_a": "investigation field", + "string_serialization": "{text}", + "slot_uri": "MIXS:0001107", + "identifier": true, + "alias": "samp_name", + "owner": "EmslInterface", + "domain_of": [ + "Biosample", + "DhMultiviewCommonColumnsMixin", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "EmslInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "JgiMgInterface", + "JgiMgLrInterface", + "JgiMtInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "string", + "required": true, + "multivalued": false + }, + "source_mat_id": { + "name": "source_mat_id", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "for cultures of microorganisms: identifiers for two culture collections; for other material a unique arbitrary identifer" + } + }, + "description": "A globally unique identifier assigned to the biological sample.", + "title": "source material identifier", + "todos": [ + "Currently, the comments say to use UUIDs. However, if we implement assigning NMDC identifiers with the minter we dont need to require a GUID. It can be an optional field to fill out only if they already have a resolvable ID.", + "Currently, the comments say to use UUIDs. However, if we implement assigning NMDC identifiers with the minter we dont need to require a GUID. It can be an optional field to fill out only if they already have a resolvable ID." + ], + "notes": [ + "The source material IS the Globally Unique ID" + ], + "comments": [ + "Identifiers must be prefixed. Possible FAIR prefixes are IGSNs (http://www.geosamples.org/getigsn), NCBI biosample accession numbers, ARK identifiers (https://arks.org/). These IDs enable linking to derived analytes and subsamples. If you have not assigned FAIR identifiers to your samples, you can generate UUIDs (https://www.uuidgenerator.net/).", + "Identifiers must be prefixed. Possible FAIR prefixes are IGSNs (http://www.geosamples.org/getigsn), NCBI biosample accession numbers, ARK identifiers (https://arks.org/). These IDs enable linking to derived analytes and subsamples. If you have not assigned FAIR identifiers to your samples, you can generate UUIDs (https://www.uuidgenerator.net/)." + ], + "examples": [ + { + "value": "IGSN:AU1243" + }, + { + "value": "UUID:24f1467a-40f4-11ed-b878-0242ac120002" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "source material identifiers" + ], + "rank": 2, + "is_a": "nucleic acid sequence source field", + "string_serialization": "{text}:{text}", + "slot_uri": "MIXS:0000026", + "alias": "source_mat_id", + "owner": "EmslInterface", + "domain_of": [ + "Biosample", + "DhMultiviewCommonColumnsMixin", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "EmslInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "JgiMgInterface", + "JgiMgLrInterface", + "JgiMtInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "string", + "multivalued": false, + "pattern": "[^\\:\\n\\r]+\\:[^\\:\\n\\r]+" + } + } + }, + "HcrCoresInterface": { + "name": "HcrCoresInterface", + "annotations": { + "excel_worksheet_name": { + "tag": "excel_worksheet_name", + "value": "hcr core" + } + }, + "description": "hcr_cores dh_interface", + "title": "Hcr Cores", + "from_schema": "https://example.com/nmdc_submission_schema", + "is_a": "DhInterface", + "mixins": [ + "DhMultiviewCommonColumnsMixin" + ], + "slots": [ + "additional_info", + "alkalinity", + "alkalinity_method", + "ammonium", + "api", + "aromatics_pc", + "asphaltenes_pc", + "basin", + "benzene", + "calcium", + "chem_administration", + "chloride", + "collection_date", + "density", + "depos_env", + "depth", + "diss_carb_dioxide", + "diss_inorg_carb", + "diss_inorg_phosp", + "diss_iron", + "diss_org_carb", + "diss_oxygen_fluid", + "ecosystem", + "ecosystem_category", + "ecosystem_subtype", + "ecosystem_type", + "elev", + "env_broad_scale", + "env_local_scale", + "env_medium", + "ethylbenzene", + "experimental_factor", + "field", + "geo_loc_name", + "hc_produced", + "hcr", + "hcr_fw_salinity", + "hcr_geol_age", + "hcr_pressure", + "hcr_temp", + "lat_lon", + "lithology", + "magnesium", + "misc_param", + "nitrate", + "nitrite", + "org_count_qpcr_info", + "organism_count", + "owc_tvdss", + "oxy_stat_samp", + "permeability", + "ph", + "ph_meth", + "porosity", + "potassium", + "pour_point", + "pressure", + "reservoir", + "resins_pc", + "salinity", + "samp_collec_device", + "samp_collec_method", + "samp_mat_process", + "samp_md", + "samp_size", + "samp_store_dur", + "samp_store_loc", + "samp_store_temp", + "samp_subtype", + "samp_transport_cond", + "samp_tvdss", + "samp_type", + "samp_well_name", + "sample_link", + "saturates_pc", + "size_frac", + "sodium", + "specific_ecosystem", + "sr_dep_env", + "sr_geol_age", + "sr_kerog_type", + "sr_lithology", + "sulfate", + "sulfate_fw", + "sulfide", + "suspend_solids", + "tan", + "temp", + "toluene", + "tot_iron", + "tot_nitro", + "tot_phosp", + "tot_sulfur", + "tvdss_of_hcr_press", + "tvdss_of_hcr_temp", + "vfa", + "vfa_fw", + "viscosity", + "win", + "xylene" + ], + "slot_usage": { + "additional_info": { + "name": "additional_info", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "text" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Information that doesn't fit anywhere else. Can also be used to propose new entries for fields with controlled vocabulary", + "title": "additional info", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "additional info" + ], + "rank": 290, + "is_a": "core field", + "string_serialization": "{text}", + "slot_uri": "MIXS:0000300", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "HcrCoresInterface", + "HcrFluidsSwabsInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "alkalinity": { + "name": "alkalinity", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milliequivalent per liter, milligram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate", + "title": "alkalinity", + "examples": [ + { + "value": "50 milligram per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "alkalinity" + ], + "rank": 1, + "is_a": "core field", + "slot_uri": "MIXS:0000421", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "alkalinity_method": { + "name": "alkalinity_method", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "description of method" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Method used for alkalinity measurement", + "title": "alkalinity method", + "examples": [ + { + "value": "titration" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "alkalinity method" + ], + "rank": 218, + "is_a": "core field", + "string_serialization": "{text}", + "slot_uri": "MIXS:0000298", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "ammonium": { + "name": "ammonium", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per liter, milligram per liter, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of ammonium in the sample", + "title": "ammonium", + "examples": [ + { + "value": "1.5 milligram per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "ammonium" + ], + "rank": 4, + "is_a": "core field", + "slot_uri": "MIXS:0000427", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "api": { + "name": "api", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "degrees API" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "API gravity is a measure of how heavy or light a petroleum liquid is compared to water (source: https://en.wikipedia.org/wiki/API_gravity) (e.g. 31.1¬∞ API)", + "title": "API gravity", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "API gravity" + ], + "rank": 291, + "is_a": "core field", + "slot_uri": "MIXS:0000157", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "HcrCoresInterface", + "HcrFluidsSwabsInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "aromatics_pc": { + "name": "aromatics_pc", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "name;measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "percent" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene)", + "title": "aromatics wt%", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "aromatics wt%" + ], + "rank": 292, + "is_a": "core field", + "string_serialization": "{text};{float} {unit}", + "slot_uri": "MIXS:0000133", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "HcrCoresInterface", + "HcrFluidsSwabsInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[^;\\t\\r\\x0A\\|]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A\\|]+$" + }, + "asphaltenes_pc": { + "name": "asphaltenes_pc", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "name;measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "percent" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene)", + "title": "asphaltenes wt%", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "asphaltenes wt%" + ], + "rank": 293, + "is_a": "core field", + "string_serialization": "{text};{float} {unit}", + "slot_uri": "MIXS:0000135", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "HcrCoresInterface", + "HcrFluidsSwabsInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[^;\\t\\r\\x0A\\|]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A\\|]+$" + }, + "basin": { + "name": "basin", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "name" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Name of the basin (e.g. Campos)", + "title": "basin name", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "basin name" + ], + "rank": 294, + "is_a": "core field", + "string_serialization": "{text}", + "slot_uri": "MIXS:0000290", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "HcrCoresInterface", + "HcrFluidsSwabsInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "benzene": { + "name": "benzene", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milligram per liter, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of benzene in the sample", + "title": "benzene", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "benzene" + ], + "rank": 295, + "is_a": "core field", + "slot_uri": "MIXS:0000153", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "HcrCoresInterface", + "HcrFluidsSwabsInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "calcium": { + "name": "calcium", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milligram per liter, micromole per liter, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of calcium in the sample", + "title": "calcium", + "examples": [ + { + "value": "0.2 micromole per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "calcium" + ], + "rank": 9, + "is_a": "core field", + "slot_uri": "MIXS:0000432", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "chem_administration": { + "name": "chem_administration", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "CHEBI;timestamp" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi", + "title": "chemical administration", + "examples": [ + { + "value": "agar [CHEBI:2509];2018-05-11|agar [CHEBI:2509];2018-05-22" + }, + { + "value": "agar [CHEBI:2509];2018-05" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "chemical administration" + ], + "rank": 17, + "is_a": "core field", + "string_serialization": "{termLabel} {[termID]};{timestamp}", + "slot_uri": "MIXS:0000751", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "recommended": true, + "multivalued": false, + "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\];([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$" + }, + "chloride": { + "name": "chloride", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milligram per liter, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of chloride in the sample", + "title": "chloride", + "examples": [ + { + "value": "5000 milligram per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "chloride" + ], + "rank": 10, + "is_a": "core field", + "slot_uri": "MIXS:0000429", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "collection_date": { + "name": "collection_date", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "date and time" + } + }, + "description": "The date of sampling", + "title": "collection date", + "notes": [ + "MIxS collection_date accepts (truncated) ISO8601. DH taking arb prec date only", + "Use modified term (amended definition)" + ], + "examples": [ + { + "value": "2021-04-15" + }, + { + "value": "2021-04" + }, + { + "value": "2021" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "collection date" + ], + "rank": 3, + "is_a": "environment field", + "string_serialization": "{date, arbitrary precision}", + "slot_uri": "MIXS:0000011", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "required": true, + "multivalued": false, + "pattern": "^[12]\\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\\d|3[01]))?)?$" + }, + "density": { + "name": "density", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "gram per cubic meter, gram per cubic centimeter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Density of the sample, which is its mass per unit volume (aka volumetric mass density)", + "title": "density", + "examples": [ + { + "value": "1000 kilogram per cubic meter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "density" + ], + "rank": 12, + "is_a": "core field", + "slot_uri": "MIXS:0000435", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "depos_env": { + "name": "depos_env", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Main depositional environment (https://en.wikipedia.org/wiki/Depositional_environment). If \"other\" is specified, please propose entry in \"additional info\" field", + "title": "depositional environment", + "examples": [ + { + "value": "Continental - Alluvial" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "depositional environment" + ], + "rank": 304, + "is_a": "core field", + "slot_uri": "MIXS:0000992", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "HcrCoresInterface", + "HcrFluidsSwabsInterface" + ], + "slot_group": "mixs_core_section", + "range": "depos_env_enum", + "multivalued": false + }, + "depth": { + "name": "depth", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + } + }, + "description": "The vertical distance below local surface, e.g. for sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples.", + "title": "depth, meters", + "notes": [ + "Use modified term" + ], + "comments": [ + "All depths must be reported in meters. Provide the numerical portion only." + ], + "examples": [ + { + "value": "0 - 0.1" + }, + { + "value": "1" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "depth" + ], + "rank": 9, + "is_a": "environment field", + "string_serialization": "{float}|{float}-{float}", + "slot_uri": "MIXS:0000018", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "recommended": true, + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)?(\\s*-\\s*[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)?)?$" + }, + "diss_carb_dioxide": { + "name": "diss_carb_dioxide", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per liter, milligram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample", + "title": "dissolved carbon dioxide", + "examples": [ + { + "value": "5 milligram per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "dissolved carbon dioxide" + ], + "rank": 14, + "is_a": "core field", + "slot_uri": "MIXS:0000436", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "diss_inorg_carb": { + "name": "diss_inorg_carb", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "microgram per liter, milligram per liter, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter", + "title": "dissolved inorganic carbon", + "examples": [ + { + "value": "2059 micromole per kilogram" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "dissolved inorganic carbon" + ], + "rank": 16, + "is_a": "core field", + "slot_uri": "MIXS:0000434", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "diss_inorg_phosp": { + "name": "diss_inorg_phosp", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "microgram per liter, milligram per liter, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of dissolved inorganic phosphorus in the sample", + "title": "dissolved inorganic phosphorus", + "examples": [ + { + "value": "56.5 micromole per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "dissolved inorganic phosphorus" + ], + "rank": 224, + "is_a": "core field", + "slot_uri": "MIXS:0000106", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "diss_iron": { + "name": "diss_iron", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milligram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of dissolved iron in the sample", + "title": "dissolved iron", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "dissolved iron" + ], + "rank": 305, + "is_a": "core field", + "slot_uri": "MIXS:0000139", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "HcrCoresInterface", + "HcrFluidsSwabsInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "diss_org_carb": { + "name": "diss_org_carb", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per liter, milligram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid", + "title": "dissolved organic carbon", + "examples": [ + { + "value": "197 micromole per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "dissolved organic carbon" + ], + "rank": 17, + "is_a": "core field", + "slot_uri": "MIXS:0000433", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "diss_oxygen_fluid": { + "name": "diss_oxygen_fluid", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per kilogram, milligram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of dissolved oxygen in the oil field produced fluids as it contributes to oxgen-corrosion and microbial activity (e.g. Mic).", + "title": "dissolved oxygen in fluids", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "dissolved oxygen in fluids" + ], + "rank": 306, + "is_a": "core field", + "slot_uri": "MIXS:0000438", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "HcrCoresInterface", + "HcrFluidsSwabsInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "ecosystem": { + "name": "ecosystem", + "description": "An ecosystem is a combination of a physical environment (abiotic factors) and all the organisms (biotic factors) that interact with this environment. Ecosystem is in position 1/5 in a GOLD path.", + "comments": [ + "The abiotic factors play a profound role on the type and composition of organisms in a given environment. The GOLD Ecosystem at the top of the five-level classification system is aimed at capturing the broader environment from which an organism or environmental sample is collected. The three broad groups under Ecosystem are Environmental, Host-associated, and Engineered. They represent samples collected from a natural environment or from another organism or from engineered environments like bioreactors respectively." + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "https://gold.jgi.doe.gov/help" + ], + "rank": 9, + "is_a": "gold_path_field", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "Study", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "EcosystemEnum", + "recommended": true + }, + "ecosystem_category": { + "name": "ecosystem_category", + "description": "Ecosystem categories represent divisions within the ecosystem based on specific characteristics of the environment from where an organism or sample is isolated. Ecosystem category is in position 2/5 in a GOLD path.", + "comments": [ + "The Environmental ecosystem (for example) is divided into Air, Aquatic and Terrestrial. Ecosystem categories for Host-associated samples can be individual hosts or phyla and for engineered samples it may be manipulated environments like bioreactors, solid waste etc." + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "https://gold.jgi.doe.gov/help" + ], + "rank": 10, + "is_a": "gold_path_field", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "Study", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "EcosystemCategoryEnum", + "recommended": true + }, + "ecosystem_subtype": { + "name": "ecosystem_subtype", + "description": "Ecosystem subtypes represent further subdivision of Ecosystem types into more distinct subtypes. Ecosystem subtype is in position 4/5 in a GOLD path.", + "comments": [ + "Ecosystem Type Marine (Environmental -> Aquatic -> Marine) is further divided (for example) into Intertidal zone, Coastal, Pelagic, Intertidal zone etc. in the Ecosystem subtype category." + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "https://gold.jgi.doe.gov/help" + ], + "rank": 12, + "is_a": "gold_path_field", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "Study", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "EcosystemSubtypeEnum", + "recommended": true + }, + "ecosystem_type": { + "name": "ecosystem_type", + "description": "Ecosystem types represent things having common characteristics within the Ecosystem Category. These common characteristics based grouping is still broad but specific to the characteristics of a given environment. Ecosystem type is in position 3/5 in a GOLD path.", + "comments": [ + "The Aquatic ecosystem category (for example) may have ecosystem types like Marine or Thermal springs etc. Ecosystem category Air may have Indoor air or Outdoor air as different Ecosystem Types. In the case of Host-associated samples, ecosystem type can represent Respiratory system, Digestive system, Roots etc." + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "https://gold.jgi.doe.gov/help" + ], + "rank": 11, + "is_a": "gold_path_field", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "Study", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "EcosystemTypeEnum", + "recommended": true + }, + "elev": { + "name": "elev", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + } + }, + "description": "Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit.", + "title": "elevation, meters", + "comments": [ + "All elevations must be reported in meters. Provide the numerical portion only.", + "Please use https://www.advancedconverter.com/map-tools/find-altitude-by-coordinates, if needed, to help estimate the elevation based on latitude and longitude coordinates." + ], + "examples": [ + { + "value": "225" + }, + { + "value": "0" + }, + { + "value": "1250" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "elevation" + ], + "rank": 6, + "is_a": "environment field", + "slot_uri": "MIXS:0000093", + "owner": "Biosample", + "domain_of": [ + "FieldResearchSite", + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "float", + "required": true, + "multivalued": false + }, + "env_broad_scale": { + "name": "env_broad_scale", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "The major environment type(s) where the sample was collected. Recommend subclasses of biome [ENVO:00000428]. Multiple terms can be separated by one or more pipes." + }, + "tooltip": { + "tag": "tooltip", + "value": "The biome or major environmental system where the sample or specimen originated. Choose values from subclasses of the 'biome' class [ENVO:00000428] in the Environment Ontology (ENVO). For host-associated or plant-associated samples, use terms from the UBERON or Plant Ontology to describe the broad anatomical or morphological context" + } + }, + "description": "In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO's biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html", + "title": "broad-scale environmental context", + "notes": [ + "range changed to enumeration late in makefile, so this is modified (but \"sample ID\" anyway)" + ], + "examples": [ + { + "value": "oceanic epipelagic zone biome [ENVO:01000033] for annotating a water sample from the photic zone in middle of the Atlantic Ocean" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "broad-scale environmental context" + ], + "rank": 6, + "is_a": "environment field", + "string_serialization": "{termLabel} {[termID]}", + "slot_uri": "MIXS:0000012", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "string", + "required": true, + "multivalued": false, + "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$" + }, + "env_local_scale": { + "name": "env_local_scale", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "Environmental entities having causal influences upon the entity at time of sampling." + }, + "tooltip": { + "tag": "tooltip", + "value": "The specific environmental entities or features near the sample or specimen that significantly influence its characteristics or composition. These entities are typically smaller in scale than the broad environmental context. Values for this field should be countable, material nouns and must be chosen from subclasses of BFO:0000040 (material entity) that appear in the Environment Ontology (ENVO). For host-associated or plant-associated samples, use terms from the UBERON or Plant Ontology to describe specific anatomical structures or plant parts." + } + }, + "description": "Report the entity or entities which are in the sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. We recommend using EnvO terms which are of smaller spatial grain than your entry for env_broad_scale. Terms, such as anatomical sites, from other OBO Library ontologies which interoperate with EnvO (e.g. UBERON) are accepted in this field. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS.", + "title": "local environmental context", + "notes": [ + "range changed to enumeration late in makefile, so this is modified (but \"sample ID\" anyway)" + ], + "examples": [ + { + "value": "canopy [ENVO:00000047]" + }, + { + "value": "herb and fern layer [ENVO:01000337]" + }, + { + "value": "litter layer [ENVO:01000338]" + }, + { + "value": "understory [01000335]" + }, + { + "value": "shrub layer [ENVO:01000336]" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "local environmental context" + ], + "rank": 7, + "is_a": "environment field", + "string_serialization": "{termLabel} {[termID]}", + "slot_uri": "MIXS:0000013", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "string", + "required": true, + "multivalued": false, + "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$" + }, + "env_medium": { + "name": "env_medium", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "The material displaced by the entity at time of sampling. Recommend subclasses of environmental material [ENVO:00010483]." + }, + "tooltip": { + "tag": "tooltip", + "value": "The predominant environmental material or substrate that directly surrounds or hosts the sample or specimen at the time of sampling. Choose values from subclasses of the 'environmental material' class [ENVO:00010483] in the Environment Ontology (ENVO). Values for this field should be measurable or mass material nouns, representing continuous environmental materials. For host-associated or plant-associated samples, use terms from the UBERON or Plant Ontology to indicate a tissue, organ, or plant structure" + } + }, + "description": "Report the environmental material(s) immediately surrounding the sample or specimen at the time of sampling. We recommend using subclasses of 'environmental material' (http://purl.obolibrary.org/obo/ENVO_00010483). EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS . Terms from other OBO ontologies are permissible as long as they reference mass/volume nouns (e.g. air, water, blood) and not discrete, countable entities (e.g. a tree, a leaf, a table top).", + "title": "environmental medium", + "notes": [ + "range changed to enumeration late in makefile, so this is modified (but \"sample ID\" anyway)" + ], + "examples": [ + { + "value": "soil [ENVO:00001998]" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "environmental medium" + ], + "rank": 8, + "is_a": "environment field", + "string_serialization": "{termLabel} {[termID]}", + "slot_uri": "MIXS:0000014", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "string", + "required": true, + "multivalued": false, + "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$" + }, + "ethylbenzene": { + "name": "ethylbenzene", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milligram per liter, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of ethylbenzene in the sample", + "title": "ethylbenzene", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "ethylbenzene" + ], + "rank": 309, + "is_a": "core field", + "slot_uri": "MIXS:0000155", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "HcrCoresInterface", + "HcrFluidsSwabsInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "experimental_factor": { + "name": "experimental_factor", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "text or EFO and/or OBI" + } + }, + "description": "Experimental factors are essentially the variable aspects of an experiment design which can be used to describe an experiment, or set of experiments, in an increasingly detailed manner. This field accepts ontology terms from Experimental Factor Ontology (EFO) and/or Ontology for Biomedical Investigations (OBI). For a browser of EFO (v 2.95) terms, please see http://purl.bioontology.org/ontology/EFO; for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI", + "title": "experimental factor", + "examples": [ + { + "value": "time series design [EFO:EFO_0001779]" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "experimental factor" + ], + "rank": 12, + "is_a": "investigation field", + "string_serialization": "{termLabel} {[termID]}|{text}", + "slot_uri": "MIXS:0000008", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false + }, + "field": { + "name": "field", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "name" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Name of the hydrocarbon field (e.g. Albacora)", + "title": "field name", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "field name" + ], + "rank": 310, + "is_a": "core field", + "string_serialization": "{text}", + "slot_uri": "MIXS:0000291", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "HcrCoresInterface", + "HcrFluidsSwabsInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "geo_loc_name": { + "name": "geo_loc_name", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "country or sea name (INSDC or GAZ): region(GAZ), specific location name" + } + }, + "description": "The geographical origin of the sample as defined by the country or sea name followed by specific region name.", + "title": "geographic location (country and/or sea,region)", + "examples": [ + { + "value": "USA: Maryland, Bethesda" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "geographic location (country and/or sea,region)" + ], + "rank": 4, + "is_a": "environment field", + "string_serialization": "{text}: {text}, {text}", + "slot_uri": "MIXS:0000010", + "owner": "Biosample", + "domain_of": [ + "FieldResearchSite", + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "required": true, + "multivalued": false, + "pattern": "^[^:, ][^:]*: [^:, ][^,]*, [^:, ].*$" + }, + "hc_produced": { + "name": "hc_produced", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Main hydrocarbon type produced from resource (i.e. Oil, gas, condensate, etc). If \"other\" is specified, please propose entry in \"additional info\" field", + "title": "hydrocarbon type produced", + "examples": [ + { + "value": "Gas" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "hydrocarbon type produced" + ], + "rank": 313, + "is_a": "core field", + "slot_uri": "MIXS:0000989", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "HcrCoresInterface", + "HcrFluidsSwabsInterface" + ], + "slot_group": "mixs_core_section", + "range": "hc_produced_enum", + "multivalued": false + }, + "hcr": { + "name": "hcr", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Main Hydrocarbon Resource type. The term \"Hydrocarbon Resource\" HCR defined as a natural environmental feature containing large amounts of hydrocarbons at high concentrations potentially suitable for commercial exploitation. This term should not be confused with the Hydrocarbon Occurrence term which also includes hydrocarbon-rich environments with currently limited commercial interest such as seeps, outcrops, gas hydrates etc. If \"other\" is specified, please propose entry in \"additional info\" field", + "title": "hydrocarbon resource type", + "examples": [ + { + "value": "Oil Sand" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "hydrocarbon resource type" + ], + "rank": 314, + "is_a": "core field", + "slot_uri": "MIXS:0000988", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "HcrCoresInterface", + "HcrFluidsSwabsInterface" + ], + "slot_group": "mixs_core_section", + "range": "hcr_enum", + "multivalued": false + }, + "hcr_fw_salinity": { + "name": "hcr_fw_salinity", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milligram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Original formation water salinity (prior to secondary recovery e.g. Waterflooding) expressed as TDS", + "title": "formation water salinity", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "formation water salinity" + ], + "rank": 315, + "is_a": "core field", + "slot_uri": "MIXS:0000406", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "HcrCoresInterface", + "HcrFluidsSwabsInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "hcr_geol_age": { + "name": "hcr_geol_age", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Geological age of hydrocarbon resource (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). If \"other\" is specified, please propose entry in \"additional info\" field", + "title": "hydrocarbon resource geological age", + "examples": [ + { + "value": "Silurian" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "hydrocarbon resource geological age" + ], + "rank": 316, + "is_a": "core field", + "slot_uri": "MIXS:0000993", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "HcrCoresInterface", + "HcrFluidsSwabsInterface" + ], + "slot_group": "mixs_core_section", + "range": "hcr_geol_age_enum", + "multivalued": false + }, + "hcr_pressure": { + "name": "hcr_pressure", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value range" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "atmosphere, kilopascal" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Original pressure of the hydrocarbon resource", + "title": "hydrocarbon resource original pressure", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "hydrocarbon resource original pressure" + ], + "rank": 317, + "is_a": "core field", + "string_serialization": "{float} - {float} {unit}", + "slot_uri": "MIXS:0000395", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "HcrCoresInterface", + "HcrFluidsSwabsInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "hcr_temp": { + "name": "hcr_temp", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value range" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "degree Celsius" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Original temperature of the hydrocarbon resource", + "title": "hydrocarbon resource original temperature", + "examples": [ + { + "value": "150-295 degree Celsius" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "hydrocarbon resource original temperature" + ], + "rank": 318, + "is_a": "core field", + "string_serialization": "{float} - {float} {unit}", + "slot_uri": "MIXS:0000393", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "HcrCoresInterface", + "HcrFluidsSwabsInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "lat_lon": { + "name": "lat_lon", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "decimal degrees, limit to 8 decimal points" + } + }, + "description": "The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system", + "title": "geographic location (latitude and longitude)", + "notes": [ + "This is currently a required field but it's not clear if this should be required for human hosts" + ], + "examples": [ + { + "value": "50.586825 6.408977" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "geographic location (latitude and longitude)" + ], + "rank": 5, + "is_a": "environment field", + "string_serialization": "{lat lon}", + "slot_uri": "MIXS:0000009", + "owner": "Biosample", + "domain_of": [ + "FieldResearchSite", + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "required": true, + "multivalued": false, + "pattern": "^[-+]?([1-8]?\\d(\\.\\d{1,8})?|90(\\.0{1,8})?)\\s[-+]?(180(\\.0{1,8})?|((1[0-7]\\d)|([1-9]?\\d))(\\.\\d{1,8})?)$" + }, + "lithology": { + "name": "lithology", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Hydrocarbon resource main lithology (Additional information: http://petrowiki.org/Lithology_and_rock_type_determination). If \"other\" is specified, please propose entry in \"additional info\" field", + "title": "lithology", + "examples": [ + { + "value": "Volcanic" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "lithology" + ], + "rank": 336, + "is_a": "core field", + "slot_uri": "MIXS:0000990", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "HcrCoresInterface", + "HcrFluidsSwabsInterface" + ], + "slot_group": "mixs_core_section", + "range": "lithology_enum", + "multivalued": false + }, + "magnesium": { + "name": "magnesium", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "mole per liter, milligram per liter, parts per million, micromole per kilogram" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of magnesium in the sample", + "title": "magnesium", + "examples": [ + { + "value": "52.8 micromole per kilogram" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "magnesium" + ], + "rank": 21, + "is_a": "core field", + "slot_uri": "MIXS:0000431", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "misc_param": { + "name": "misc_param", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "parameter name;measurement value" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Any other measurement performed or parameter collected, that is not listed here", + "title": "miscellaneous parameter", + "examples": [ + { + "value": "Bicarbonate ion concentration;2075 micromole per kilogram" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "miscellaneous parameter" + ], + "rank": 23, + "is_a": "core field", + "string_serialization": "{text};{float} {unit}", + "slot_uri": "MIXS:0000752", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false, + "pattern": "^([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+\\|)*([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+)$" + }, + "nitrate": { + "name": "nitrate", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per liter, milligram per liter, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of nitrate in the sample", + "title": "nitrate", + "examples": [ + { + "value": "65 micromole per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "nitrate" + ], + "rank": 26, + "is_a": "core field", + "slot_uri": "MIXS:0000425", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "nitrite": { + "name": "nitrite", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per liter, milligram per liter, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of nitrite in the sample", + "title": "nitrite", + "examples": [ + { + "value": "0.5 micromole per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "nitrite" + ], + "rank": 27, + "is_a": "core field", + "slot_uri": "MIXS:0000426", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "org_count_qpcr_info": { + "name": "org_count_qpcr_info", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "gene name;FWD:forward primer sequence;REV:reverse primer sequence;initial denaturation:degrees_minutes;denaturation:degrees_minutes;annealing:degrees_minutes;elongation:degrees_minutes;final elongation:degrees_minutes; total cycles" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "number of cells per gram (or ml or cm^2)" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "If qpcr was used for the cell count, the target gene name, the primer sequence and the cycling conditions should also be provided. (Example: 16S rrna; FWD:ACGTAGCTATGACGT REV:GTGCTAGTCGAGTAC; initial denaturation:90C_5min; denaturation:90C_2min; annealing:52C_30 sec; elongation:72C_30 sec; 90 C for 1 min; final elongation:72C_5min; 30 cycles)", + "title": "organism count qPCR information", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "organism count qPCR information" + ], + "rank": 337, + "is_a": "core field", + "string_serialization": "{text};FWD:{dna};REV:{dna};initial denaturation:degrees_minutes;denaturation:degrees_minutes;annealing:degrees_minutes;elongation:degrees_minutes;final elongation:degrees_minutes; total cycles", + "slot_uri": "MIXS:0000099", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "HcrCoresInterface", + "HcrFluidsSwabsInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "organism_count": { + "name": "organism_count", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "organism name;measurement value;enumeration" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "number of cells per cubic meter, number of cells per milliliter, number of cells per cubic centimeter" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr)", + "title": "organism count", + "examples": [ + { + "value": "total prokaryotes;3.5e7 cells per milliliter;qPCR" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "organism count" + ], + "rank": 30, + "is_a": "core field", + "slot_uri": "MIXS:0000103", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^([-+]?[0-9]*\\.?[0-9]+ +\\S.*\\|)*([-+]?[0-9]*\\.?[0-9]+ +\\S.*)$" + }, + "owc_tvdss": { + "name": "owc_tvdss", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "meter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Depth of the original oil water contact (OWC) zone (average) (m TVDSS)", + "title": "oil water contact depth", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "oil water contact depth" + ], + "rank": 339, + "is_a": "core field", + "slot_uri": "MIXS:0000405", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "HcrCoresInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "oxy_stat_samp": { + "name": "oxy_stat_samp", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Oxygenation status of sample", + "title": "oxygenation status of sample", + "examples": [ + { + "value": "aerobic" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "oxygenation status of sample" + ], + "rank": 25, + "is_a": "core field", + "slot_uri": "MIXS:0000753", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_section", + "range": "OxyStatSampEnum", + "multivalued": false + }, + "permeability": { + "name": "permeability", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value range" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "mD" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Measure of the ability of a hydrocarbon resource to allow fluids to pass through it. (Additional information: https://en.wikipedia.org/wiki/Permeability_(earth_sciences))", + "title": "permeability", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "permeability" + ], + "rank": 340, + "is_a": "core field", + "string_serialization": "{integer} - {integer} {unit}", + "slot_uri": "MIXS:0000404", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "HcrCoresInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "ph": { + "name": "ph", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "pH measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid", + "title": "pH", + "notes": [ + "Use modified term" + ], + "examples": [ + { + "value": "7.2" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "pH" + ], + "rank": 27, + "is_a": "core field", + "string_serialization": "{float}", + "slot_uri": "MIXS:0001001", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "MiscEnvsInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "float", + "recommended": true, + "multivalued": false, + "minimum_value": 0, + "maximum_value": 14 + }, + "ph_meth": { + "name": "ph_meth", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "PMID,DOI or url" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Reference or method used in determining ph", + "title": "pH method", + "comments": [ + "This can include a link to the instrument used or a citation for the method." + ], + "examples": [ + { + "value": "https://www.southernlabware.com/pc9500-benchtop-ph-conductivity-meter-kit-ph-accuracy-2000mv-ph-range-2-000-to-20-000.html?gclid=Cj0KCQiAwJWdBhCYARIsAJc4idCO5vtvbVMf545fcvdROFqa6zjzNSoywNx6K4k9Coo9cCc2pybtvGsaAiR0EALw_wcB" + }, + { + "value": "https://doi.org/10.2136/sssabookser5.3.c16" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "pH method" + ], + "rank": 41, + "is_a": "core field", + "string_serialization": "{PMID}|{DOI}|{URL}", + "slot_uri": "MIXS:0001106", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "MiscEnvsInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false + }, + "porosity": { + "name": "porosity", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value or range" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "percentage" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Porosity of deposited sediment is volume of voids divided by the total volume of sample", + "title": "porosity", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "porosity" + ], + "rank": 37, + "is_a": "core field", + "string_serialization": "{float} - {float} {unit}", + "slot_uri": "MIXS:0000211", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "HcrCoresInterface", + "SedimentInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "potassium": { + "name": "potassium", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milligram per liter, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of potassium in the sample", + "title": "potassium", + "examples": [ + { + "value": "463 milligram per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "potassium" + ], + "rank": 38, + "is_a": "core field", + "slot_uri": "MIXS:0000430", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "pour_point": { + "name": "pour_point", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "degree Celsius" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Temperature at which a liquid becomes semi solid and loses its flow characteristics. In crude oil a high¬†pour point¬†is generally associated with a high paraffin content, typically found in crude deriving from a larger proportion of plant material. (soure: https://en.wikipedia.org/wiki/pour_point)", + "title": "pour point", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "pour point" + ], + "rank": 341, + "is_a": "core field", + "slot_uri": "MIXS:0000127", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "HcrCoresInterface", + "HcrFluidsSwabsInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "pressure": { + "name": "pressure", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "atmosphere" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Pressure to which the sample is subject to, in atmospheres", + "title": "pressure", + "examples": [ + { + "value": "50 atmosphere" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "pressure" + ], + "rank": 39, + "is_a": "core field", + "slot_uri": "MIXS:0000412", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "reservoir": { + "name": "reservoir", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "name" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Name of the reservoir (e.g. Carapebus)", + "title": "reservoir name", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "reservoir name" + ], + "rank": 347, + "is_a": "core field", + "string_serialization": "{text}", + "slot_uri": "MIXS:0000303", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "HcrCoresInterface", + "HcrFluidsSwabsInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "resins_pc": { + "name": "resins_pc", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "name;measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "percent" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene)", + "title": "resins wt%", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "resins wt%" + ], + "rank": 348, + "is_a": "core field", + "string_serialization": "{text};{float} {unit}", + "slot_uri": "MIXS:0000134", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "HcrCoresInterface", + "HcrFluidsSwabsInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[^;\\t\\r\\x0A\\|]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A\\|]+$" + }, + "salinity": { + "name": "salinity", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "practical salinity unit, percentage" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The total concentration of all dissolved salts in a liquid or solid sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater.", + "title": "salinity", + "examples": [ + { + "value": "25 practical salinity unit" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "salinity" + ], + "rank": 54, + "is_a": "core field", + "slot_uri": "MIXS:0000183", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "samp_collec_device": { + "name": "samp_collec_device", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "device name" + } + }, + "description": "The device used to collect an environmental sample. This field accepts terms listed under environmental sampling device (http://purl.obolibrary.org/obo/ENVO). This field also accepts terms listed under specimen collection device (http://purl.obolibrary.org/obo/GENEPIO_0002094).", + "title": "sample collection device", + "comments": [ + "Report dimensions and details when applicable" + ], + "examples": [ + { + "value": "swab, biopsy, niskin bottle, push core, drag swab [GENEPIO:0002713]" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sample collection device" + ], + "rank": 14, + "is_a": "nucleic acid sequence source field", + "string_serialization": "{termLabel} {[termID]}|{text}", + "slot_uri": "MIXS:0000002", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "recommended": true, + "multivalued": false + }, + "samp_collec_method": { + "name": "samp_collec_method", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "PMID,DOI,url , or text" + } + }, + "description": "The method employed for collecting the sample.", + "title": "sample collection method", + "comments": [ + "This can be a citation or description" + ], + "examples": [ + { + "value": "swabbing" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sample collection method" + ], + "rank": 15, + "is_a": "nucleic acid sequence source field", + "string_serialization": "{PMID}|{DOI}|{URL}|{text}", + "slot_uri": "MIXS:0001225", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "multivalued": false + }, + "samp_mat_process": { + "name": "samp_mat_process", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "text" + } + }, + "description": "A brief description of any processing applied to the sample during or after retrieving the sample from environment, or a link to the relevant protocol(s) performed.", + "title": "sample material processing", + "examples": [ + { + "value": "filtering of seawater" + }, + { + "value": "storing samples in ethanol" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sample material processing" + ], + "rank": 12, + "is_a": "nucleic acid sequence source field", + "string_serialization": "{text}", + "slot_uri": "MIXS:0000016", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "multivalued": false + }, + "samp_md": { + "name": "samp_md", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value;enumeration" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "meter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "In non deviated well, measured depth is equal to the true vertical depth, TVD (TVD=TVDSS plus the reference or datum it refers to). In deviated wells, the MD is the length of trajectory of the borehole measured from the same reference or datum. Common datums used are ground level (GL), drilling rig floor (DF), rotary table (RT), kelly bushing (KB) and mean sea level (MSL). If \"other\" is specified, please propose entry in \"additional info\" field", + "title": "sample measured depth", + "examples": [ + { + "value": "1534 meter;MSL" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sample measured depth" + ], + "rank": 351, + "is_a": "core field", + "slot_uri": "MIXS:0000413", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "HcrCoresInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "samp_size": { + "name": "samp_size", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "millliter, gram, milligram, liter" + } + }, + "description": "The total amount or size (volume (ml), mass (g) or area (m2) ) of sample collected.", + "title": "amount or size of sample collected", + "comments": [ + "This refers to the TOTAL amount of sample collected from the experiment. NOT the amount sent to each institution or collected for a specific analysis." + ], + "examples": [ + { + "value": "5 grams" + }, + { + "value": "10 mL" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "amount or size of sample collected" + ], + "rank": 18, + "is_a": "nucleic acid sequence source field", + "string_serialization": "{float} {unit}", + "slot_uri": "MIXS:0000001", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? \\S+$" + }, + "samp_store_dur": { + "name": "samp_store_dur", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "duration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Duration for which the sample was stored", + "title": "sample storage duration", + "examples": [ + { + "value": "P1Y6M" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sample storage duration" + ], + "rank": 353, + "is_a": "core field", + "string_serialization": "{duration}", + "slot_uri": "MIXS:0000116", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "samp_store_loc": { + "name": "samp_store_loc", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "location name" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Location at which sample was stored, usually name of a specific freezer/room", + "title": "sample storage location", + "examples": [ + { + "value": "Freezer no:5" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sample storage location" + ], + "rank": 41, + "is_a": "core field", + "string_serialization": "{text}", + "slot_uri": "MIXS:0000755", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "samp_store_temp": { + "name": "samp_store_temp", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "degree Celsius" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Temperature at which the sample was stored (degrees are assumed)", + "title": "sample storage temperature", + "examples": [ + { + "value": "-80 Celsius" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sample storage temperature" + ], + "rank": 7, + "is_a": "core field", + "slot_uri": "MIXS:0000110", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "required": true, + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "samp_subtype": { + "name": "samp_subtype", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Name of sample sub-type. For example if \"sample type\" is \"Produced Water\" then subtype could be \"Oil Phase\" or \"Water Phase\". If \"other\" is specified, please propose entry in \"additional info\" field", + "title": "sample subtype", + "examples": [ + { + "value": "biofilm" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sample subtype" + ], + "rank": 354, + "is_a": "core field", + "slot_uri": "MIXS:0000999", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "HcrCoresInterface", + "HcrFluidsSwabsInterface" + ], + "slot_group": "mixs_core_section", + "range": "samp_subtype_enum", + "multivalued": false + }, + "samp_transport_cond": { + "name": "samp_transport_cond", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value;measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "days;degree Celsius" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Sample transport duration (in days or hrs) and temperature the sample was exposed to (e.g. 5.5 days; 20 ¬∞C)", + "title": "sample transport conditions", + "examples": [ + { + "value": "5 days;-20 degree Celsius" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sample transport conditions" + ], + "rank": 355, + "is_a": "core field", + "string_serialization": "{float} {unit};{float} {unit}", + "slot_uri": "MIXS:0000410", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "HcrCoresInterface", + "HcrFluidsSwabsInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "samp_tvdss": { + "name": "samp_tvdss", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value or measurement value range" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "meter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Depth of the sample i.e. The vertical distance between the sea level and the sampled position in the subsurface. Depth can be reported as an interval for subsurface samples e.g. 1325.75-1362.25 m", + "title": "sample true vertical depth subsea", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sample true vertical depth subsea" + ], + "rank": 356, + "is_a": "core field", + "string_serialization": "{float}-{float} {unit}", + "slot_uri": "MIXS:0000409", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "HcrCoresInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "samp_type": { + "name": "samp_type", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "GENEPIO:0001246" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The type of material from which the sample was obtained. For the Hydrocarbon package, samples include types like core, rock trimmings, drill cuttings, piping section, coupon, pigging debris, solid deposit, produced fluid, produced water, injected water, swabs, etc. For the Food Package, samples are usually categorized as food, body products or tissues, or environmental material. This field accepts terms listed under environmental specimen (http://purl.obolibrary.org/obo/GENEPIO_0001246).", + "title": "sample type", + "examples": [ + { + "value": "built environment sample [GENEPIO:0001248]" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sample type" + ], + "rank": 357, + "is_a": "core field", + "string_serialization": "{termLabel} {[termID]}", + "slot_uri": "MIXS:0000998", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "HcrCoresInterface", + "HcrFluidsSwabsInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$" + }, + "samp_well_name": { + "name": "samp_well_name", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "name" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Name of the well (e.g. BXA1123) where sample was taken", + "title": "sample well name", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sample well name" + ], + "rank": 358, + "is_a": "core field", + "string_serialization": "{text}", + "slot_uri": "MIXS:0000296", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "HcrCoresInterface", + "HcrFluidsSwabsInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "sample_link": { + "name": "sample_link", + "description": "A unique identifier to assign parent-child, subsample, or sibling samples. This is relevant when a sample or other material was used to generate the new sample.", + "title": "sample linkage", + "notes": [ + "also tempted to include SampIdNewTermsMixin but if len(slot_usage.keys()) > 1 and \"placeholder\" in slot_usage.keys():AttributeError: 'list' object has no attribute 'keys'" + ], + "comments": [ + "This field allows multiple entries separated by ; (Examples: Soil collected from the field will link with the soil used in an incubation. The soil a plant was grown in links to the plant sample. An original culture sample was transferred to a new vial and generated a new sample)" + ], + "examples": [ + { + "value": "IGSN:DSJ0284" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "rank": 5, + "string_serialization": "{text}:{text}", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface", + "SampIdNewTermsMixin" + ], + "slot_group": "sample_id_section", + "range": "string", + "recommended": true, + "multivalued": false, + "pattern": "[^\\:\\n\\r]+\\:[^\\:\\n\\r]+" + }, + "saturates_pc": { + "name": "saturates_pc", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "name;measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "percent" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene)", + "title": "saturates wt%", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "saturates wt%" + ], + "rank": 359, + "is_a": "core field", + "string_serialization": "{text};{float} {unit}", + "slot_uri": "MIXS:0000131", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "HcrCoresInterface", + "HcrFluidsSwabsInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[^;\\t\\r\\x0A\\|]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A\\|]+$" + }, + "size_frac": { + "name": "size_frac", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "filter size value range" + } + }, + "description": "Filtering pore size used in sample preparation", + "title": "size fraction selected", + "examples": [ + { + "value": "0-0.22 micrometer" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "size fraction selected" + ], + "rank": 285, + "is_a": "nucleic acid sequence source field", + "string_serialization": "{float}-{float} {unit}", + "slot_uri": "MIXS:0000017", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "sodium": { + "name": "sodium", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milligram per liter, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Sodium concentration in the sample", + "title": "sodium", + "examples": [ + { + "value": "10.5 milligram per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sodium" + ], + "rank": 363, + "is_a": "core field", + "slot_uri": "MIXS:0000428", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "specific_ecosystem": { + "name": "specific_ecosystem", + "description": "Specific ecosystems represent specific features of the environment like aphotic zone in an ocean or gastric mucosa within a host digestive system. Specific ecosystem is in position 5/5 in a GOLD path.", + "comments": [ + "Specific ecosystems help to define samples based on very specific characteristics of an environment under the five-level classification system." + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "https://gold.jgi.doe.gov/help" + ], + "rank": 13, + "is_a": "gold_path_field", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "Study", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "SpecificEcosystemEnum", + "recommended": true + }, + "sr_dep_env": { + "name": "sr_dep_env", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Source rock depositional environment (https://en.wikipedia.org/wiki/Source_rock). If \"other\" is specified, please propose entry in \"additional info\" field", + "title": "source rock depositional environment", + "examples": [ + { + "value": "Marine" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "source rock depositional environment" + ], + "rank": 366, + "is_a": "core field", + "slot_uri": "MIXS:0000996", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "HcrCoresInterface" + ], + "slot_group": "mixs_core_section", + "range": "sr_dep_env_enum", + "multivalued": false + }, + "sr_geol_age": { + "name": "sr_geol_age", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Geological age of source rock (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). If \"other\" is specified, please propose entry in \"additional info\" field", + "title": "source rock geological age", + "examples": [ + { + "value": "Silurian" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "source rock geological age" + ], + "rank": 367, + "is_a": "core field", + "slot_uri": "MIXS:0000997", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "HcrCoresInterface" + ], + "slot_group": "mixs_core_section", + "range": "sr_geol_age_enum", + "multivalued": false + }, + "sr_kerog_type": { + "name": "sr_kerog_type", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Origin of kerogen. Type I: Algal (aquatic), Type II: planktonic and soft plant material (aquatic or terrestrial), Type III: terrestrial woody/ fibrous plant material (terrestrial), Type IV: oxidized recycled woody debris (terrestrial) (additional information: https://en.wikipedia.org/wiki/Kerogen). If \"other\" is specified, please propose entry in \"additional info\" field", + "title": "source rock kerogen type", + "examples": [ + { + "value": "Type IV" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "source rock kerogen type" + ], + "rank": 368, + "is_a": "core field", + "slot_uri": "MIXS:0000994", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "HcrCoresInterface" + ], + "slot_group": "mixs_core_section", + "range": "sr_kerog_type_enum", + "multivalued": false + }, + "sr_lithology": { + "name": "sr_lithology", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Lithology of source rock (https://en.wikipedia.org/wiki/Source_rock). 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This is part of the Global Framework for Well Identification initiative which is compiled by the Professional Petroleum Data Management Association (PPDM) in an effort to improve well identification systems. (Supporting information: https://ppdm.org/ and http://dl.ppdm.org/dl/690)", + "title": "well identification number", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "well identification number" + ], + "rank": 388, + "is_a": "core field", + "string_serialization": "{text}", + "slot_uri": "MIXS:0000297", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "HcrCoresInterface", + "HcrFluidsSwabsInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "xylene": { + "name": "xylene", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milligram per liter, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of xylene in the sample", + "title": "xylene", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "xylene" + ], + "rank": 389, + "is_a": "core field", + "slot_uri": "MIXS:0000156", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "HcrCoresInterface", + "HcrFluidsSwabsInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "horizon_meth": { + "name": "horizon_meth", + "title": "horizon method" + } + }, + "attributes": { + "additional_info": { + "name": "additional_info", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "text" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Information that doesn't fit anywhere else. Can also be used to propose new entries for fields with controlled vocabulary", + "title": "additional info", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "additional info" + ], + "rank": 290, + "is_a": "core field", + "string_serialization": "{text}", + "slot_uri": "MIXS:0000300", + "alias": "additional_info", + "owner": "HcrCoresInterface", + "domain_of": [ + "Biosample", + "HcrCoresInterface", + "HcrFluidsSwabsInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "alkalinity": { + "name": "alkalinity", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milliequivalent per liter, milligram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate", + "title": "alkalinity", + "examples": [ + { + "value": "50 milligram per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "alkalinity" + ], + "rank": 1, + "is_a": "core field", + "slot_uri": "MIXS:0000421", + "alias": "alkalinity", + "owner": "HcrCoresInterface", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "alkalinity_method": { + "name": "alkalinity_method", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "description of method" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Method used for alkalinity measurement", + "title": "alkalinity method", + "examples": [ + { + "value": "titration" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "alkalinity method" + ], + "rank": 218, + "is_a": "core field", + "string_serialization": "{text}", + "slot_uri": "MIXS:0000298", + "alias": "alkalinity_method", + "owner": "HcrCoresInterface", + "domain_of": [ + "Biosample", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "ammonium": { + "name": "ammonium", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per liter, milligram per liter, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of ammonium in the sample", + "title": "ammonium", + "examples": [ + { + "value": "1.5 milligram per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "ammonium" + ], + "rank": 4, + "is_a": "core field", + "slot_uri": "MIXS:0000427", + "alias": "ammonium", + "owner": "HcrCoresInterface", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "api": { + "name": "api", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "degrees API" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "API gravity is a measure of how heavy or light a petroleum liquid is compared to water (source: https://en.wikipedia.org/wiki/API_gravity) (e.g. 31.1¬∞ API)", + "title": "API gravity", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "API gravity" + ], + "rank": 291, + "is_a": "core field", + "slot_uri": "MIXS:0000157", + "alias": "api", + "owner": "HcrCoresInterface", + "domain_of": [ + "Biosample", + "HcrCoresInterface", + "HcrFluidsSwabsInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "aromatics_pc": { + "name": "aromatics_pc", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "name;measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "percent" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene)", + "title": "aromatics wt%", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "aromatics wt%" + ], + "rank": 292, + "is_a": "core field", + "string_serialization": "{text};{float} {unit}", + "slot_uri": "MIXS:0000133", + "alias": "aromatics_pc", + "owner": "HcrCoresInterface", + "domain_of": [ + "Biosample", + "HcrCoresInterface", + "HcrFluidsSwabsInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[^;\\t\\r\\x0A\\|]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A\\|]+$" + }, + "asphaltenes_pc": { + "name": "asphaltenes_pc", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "name;measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "percent" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene)", + "title": "asphaltenes wt%", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "asphaltenes wt%" + ], + "rank": 293, + "is_a": "core field", + "string_serialization": "{text};{float} {unit}", + "slot_uri": "MIXS:0000135", + "alias": "asphaltenes_pc", + "owner": "HcrCoresInterface", + "domain_of": [ + "Biosample", + "HcrCoresInterface", + "HcrFluidsSwabsInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[^;\\t\\r\\x0A\\|]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A\\|]+$" + }, + "basin": { + "name": "basin", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "name" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Name of the basin (e.g. Campos)", + "title": "basin name", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "basin name" + ], + "rank": 294, + "is_a": "core field", + "string_serialization": "{text}", + "slot_uri": "MIXS:0000290", + "alias": "basin", + "owner": "HcrCoresInterface", + "domain_of": [ + "Biosample", + "HcrCoresInterface", + "HcrFluidsSwabsInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "benzene": { + "name": "benzene", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milligram per liter, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of benzene in the sample", + "title": "benzene", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "benzene" + ], + "rank": 295, + "is_a": "core field", + "slot_uri": "MIXS:0000153", + "alias": "benzene", + "owner": "HcrCoresInterface", + "domain_of": [ + "Biosample", + "HcrCoresInterface", + "HcrFluidsSwabsInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "calcium": { + "name": "calcium", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milligram per liter, micromole per liter, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of calcium in the sample", + "title": "calcium", + "examples": [ + { + "value": "0.2 micromole per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "calcium" + ], + "rank": 9, + "is_a": "core field", + "slot_uri": "MIXS:0000432", + "alias": "calcium", + "owner": "HcrCoresInterface", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "chem_administration": { + "name": "chem_administration", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "CHEBI;timestamp" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi", + "title": "chemical administration", + "examples": [ + { + "value": "agar [CHEBI:2509];2018-05-11|agar [CHEBI:2509];2018-05-22" + }, + { + "value": "agar [CHEBI:2509];2018-05" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "chemical administration" + ], + "rank": 17, + "is_a": "core field", + "string_serialization": "{termLabel} {[termID]};{timestamp}", + "slot_uri": "MIXS:0000751", + "alias": "chem_administration", + "owner": "HcrCoresInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "recommended": true, + "multivalued": false, + "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\];([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$" + }, + "chloride": { + "name": "chloride", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milligram per liter, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of chloride in the sample", + "title": "chloride", + "examples": [ + { + "value": "5000 milligram per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "chloride" + ], + "rank": 10, + "is_a": "core field", + "slot_uri": "MIXS:0000429", + "alias": "chloride", + "owner": "HcrCoresInterface", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "collection_date": { + "name": "collection_date", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "date and time" + } + }, + "description": "The date of sampling", + "title": "collection date", + "notes": [ + "MIxS collection_date accepts (truncated) ISO8601. DH taking arb prec date only", + "Use modified term (amended definition)" + ], + "examples": [ + { + "value": "2021-04-15" + }, + { + "value": "2021-04" + }, + { + "value": "2021" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "collection date" + ], + "rank": 3, + "is_a": "environment field", + "string_serialization": "{date, arbitrary precision}", + "slot_uri": "MIXS:0000011", + "alias": "collection_date", + "owner": "HcrCoresInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "required": true, + "multivalued": false, + "pattern": "^[12]\\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\\d|3[01]))?)?$" + }, + "density": { + "name": "density", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "gram per cubic meter, gram per cubic centimeter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Density of the sample, which is its mass per unit volume (aka volumetric mass density)", + "title": "density", + "examples": [ + { + "value": "1000 kilogram per cubic meter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "density" + ], + "rank": 12, + "is_a": "core field", + "slot_uri": "MIXS:0000435", + "alias": "density", + "owner": "HcrCoresInterface", + "domain_of": [ + "Biosample", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "depos_env": { + "name": "depos_env", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Main depositional environment (https://en.wikipedia.org/wiki/Depositional_environment). If \"other\" is specified, please propose entry in \"additional info\" field", + "title": "depositional environment", + "examples": [ + { + "value": "Continental - Alluvial" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "depositional environment" + ], + "rank": 304, + "is_a": "core field", + "slot_uri": "MIXS:0000992", + "alias": "depos_env", + "owner": "HcrCoresInterface", + "domain_of": [ + "Biosample", + "HcrCoresInterface", + "HcrFluidsSwabsInterface" + ], + "slot_group": "mixs_core_section", + "range": "depos_env_enum", + "multivalued": false + }, + "depth": { + "name": "depth", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + } + }, + "description": "The vertical distance below local surface, e.g. for sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples.", + "title": "depth, meters", + "notes": [ + "Use modified term" + ], + "comments": [ + "All depths must be reported in meters. Provide the numerical portion only." + ], + "examples": [ + { + "value": "0 - 0.1" + }, + { + "value": "1" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "depth" + ], + "rank": 9, + "is_a": "environment field", + "string_serialization": "{float}|{float}-{float}", + "slot_uri": "MIXS:0000018", + "alias": "depth", + "owner": "HcrCoresInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "recommended": true, + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)?(\\s*-\\s*[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)?)?$" + }, + "diss_carb_dioxide": { + "name": "diss_carb_dioxide", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per liter, milligram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample", + "title": "dissolved carbon dioxide", + "examples": [ + { + "value": "5 milligram per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "dissolved carbon dioxide" + ], + "rank": 14, + "is_a": "core field", + "slot_uri": "MIXS:0000436", + "alias": "diss_carb_dioxide", + "owner": "HcrCoresInterface", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "diss_inorg_carb": { + "name": "diss_inorg_carb", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "microgram per liter, milligram per liter, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter", + "title": "dissolved inorganic carbon", + "examples": [ + { + "value": "2059 micromole per kilogram" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "dissolved inorganic carbon" + ], + "rank": 16, + "is_a": "core field", + "slot_uri": "MIXS:0000434", + "alias": "diss_inorg_carb", + "owner": "HcrCoresInterface", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "diss_inorg_phosp": { + "name": "diss_inorg_phosp", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "microgram per liter, milligram per liter, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of dissolved inorganic phosphorus in the sample", + "title": "dissolved inorganic phosphorus", + "examples": [ + { + "value": "56.5 micromole per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "dissolved inorganic phosphorus" + ], + "rank": 224, + "is_a": "core field", + "slot_uri": "MIXS:0000106", + "alias": "diss_inorg_phosp", + "owner": "HcrCoresInterface", + "domain_of": [ + "Biosample", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "diss_iron": { + "name": "diss_iron", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milligram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of dissolved iron in the sample", + "title": "dissolved iron", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "dissolved iron" + ], + "rank": 305, + "is_a": "core field", + "slot_uri": "MIXS:0000139", + "alias": "diss_iron", + "owner": "HcrCoresInterface", + "domain_of": [ + "Biosample", + "HcrCoresInterface", + "HcrFluidsSwabsInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "diss_org_carb": { + "name": "diss_org_carb", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per liter, milligram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid", + "title": "dissolved organic carbon", + "examples": [ + { + "value": "197 micromole per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "dissolved organic carbon" + ], + "rank": 17, + "is_a": "core field", + "slot_uri": "MIXS:0000433", + "alias": "diss_org_carb", + "owner": "HcrCoresInterface", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "diss_oxygen_fluid": { + "name": "diss_oxygen_fluid", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per kilogram, milligram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of dissolved oxygen in the oil field produced fluids as it contributes to oxgen-corrosion and microbial activity (e.g. Mic).", + "title": "dissolved oxygen in fluids", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "dissolved oxygen in fluids" + ], + "rank": 306, + "is_a": "core field", + "slot_uri": "MIXS:0000438", + "alias": "diss_oxygen_fluid", + "owner": "HcrCoresInterface", + "domain_of": [ + "Biosample", + "HcrCoresInterface", + "HcrFluidsSwabsInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "ecosystem": { + "name": "ecosystem", + "description": "An ecosystem is a combination of a physical environment (abiotic factors) and all the organisms (biotic factors) that interact with this environment. Ecosystem is in position 1/5 in a GOLD path.", + "comments": [ + "The abiotic factors play a profound role on the type and composition of organisms in a given environment. The GOLD Ecosystem at the top of the five-level classification system is aimed at capturing the broader environment from which an organism or environmental sample is collected. The three broad groups under Ecosystem are Environmental, Host-associated, and Engineered. They represent samples collected from a natural environment or from another organism or from engineered environments like bioreactors respectively." + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "https://gold.jgi.doe.gov/help" + ], + "rank": 9, + "is_a": "gold_path_field", + "alias": "ecosystem", + "owner": "HcrCoresInterface", + "domain_of": [ + "Biosample", + "Study", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "EcosystemEnum", + "recommended": true + }, + "ecosystem_category": { + "name": "ecosystem_category", + "description": "Ecosystem categories represent divisions within the ecosystem based on specific characteristics of the environment from where an organism or sample is isolated. Ecosystem category is in position 2/5 in a GOLD path.", + "comments": [ + "The Environmental ecosystem (for example) is divided into Air, Aquatic and Terrestrial. Ecosystem categories for Host-associated samples can be individual hosts or phyla and for engineered samples it may be manipulated environments like bioreactors, solid waste etc." + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "https://gold.jgi.doe.gov/help" + ], + "rank": 10, + "is_a": "gold_path_field", + "alias": "ecosystem_category", + "owner": "HcrCoresInterface", + "domain_of": [ + "Biosample", + "Study", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "EcosystemCategoryEnum", + "recommended": true + }, + "ecosystem_subtype": { + "name": "ecosystem_subtype", + "description": "Ecosystem subtypes represent further subdivision of Ecosystem types into more distinct subtypes. Ecosystem subtype is in position 4/5 in a GOLD path.", + "comments": [ + "Ecosystem Type Marine (Environmental -> Aquatic -> Marine) is further divided (for example) into Intertidal zone, Coastal, Pelagic, Intertidal zone etc. in the Ecosystem subtype category." + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "https://gold.jgi.doe.gov/help" + ], + "rank": 12, + "is_a": "gold_path_field", + "alias": "ecosystem_subtype", + "owner": "HcrCoresInterface", + "domain_of": [ + "Biosample", + "Study", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "EcosystemSubtypeEnum", + "recommended": true + }, + "ecosystem_type": { + "name": "ecosystem_type", + "description": "Ecosystem types represent things having common characteristics within the Ecosystem Category. These common characteristics based grouping is still broad but specific to the characteristics of a given environment. Ecosystem type is in position 3/5 in a GOLD path.", + "comments": [ + "The Aquatic ecosystem category (for example) may have ecosystem types like Marine or Thermal springs etc. Ecosystem category Air may have Indoor air or Outdoor air as different Ecosystem Types. In the case of Host-associated samples, ecosystem type can represent Respiratory system, Digestive system, Roots etc." + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "https://gold.jgi.doe.gov/help" + ], + "rank": 11, + "is_a": "gold_path_field", + "alias": "ecosystem_type", + "owner": "HcrCoresInterface", + "domain_of": [ + "Biosample", + "Study", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "EcosystemTypeEnum", + "recommended": true + }, + "elev": { + "name": "elev", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + } + }, + "description": "Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit.", + "title": "elevation, meters", + "comments": [ + "All elevations must be reported in meters. Provide the numerical portion only.", + "Please use https://www.advancedconverter.com/map-tools/find-altitude-by-coordinates, if needed, to help estimate the elevation based on latitude and longitude coordinates." + ], + "examples": [ + { + "value": "225" + }, + { + "value": "0" + }, + { + "value": "1250" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "elevation" + ], + "rank": 6, + "is_a": "environment field", + "slot_uri": "MIXS:0000093", + "alias": "elev", + "owner": "HcrCoresInterface", + "domain_of": [ + "FieldResearchSite", + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "float", + "required": true, + "multivalued": false + }, + "env_broad_scale": { + "name": "env_broad_scale", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "The major environment type(s) where the sample was collected. Recommend subclasses of biome [ENVO:00000428]. Multiple terms can be separated by one or more pipes." + }, + "tooltip": { + "tag": "tooltip", + "value": "The biome or major environmental system where the sample or specimen originated. Choose values from subclasses of the 'biome' class [ENVO:00000428] in the Environment Ontology (ENVO). For host-associated or plant-associated samples, use terms from the UBERON or Plant Ontology to describe the broad anatomical or morphological context" + } + }, + "description": "In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO's biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html", + "title": "broad-scale environmental context", + "notes": [ + "range changed to enumeration late in makefile, so this is modified (but \"sample ID\" anyway)" + ], + "examples": [ + { + "value": "oceanic epipelagic zone biome [ENVO:01000033] for annotating a water sample from the photic zone in middle of the Atlantic Ocean" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "broad-scale environmental context" + ], + "rank": 6, + "is_a": "environment field", + "string_serialization": "{termLabel} {[termID]}", + "slot_uri": "MIXS:0000012", + "alias": "env_broad_scale", + "owner": "HcrCoresInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "string", + "required": true, + "multivalued": false, + "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$" + }, + "env_local_scale": { + "name": "env_local_scale", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "Environmental entities having causal influences upon the entity at time of sampling." + }, + "tooltip": { + "tag": "tooltip", + "value": "The specific environmental entities or features near the sample or specimen that significantly influence its characteristics or composition. These entities are typically smaller in scale than the broad environmental context. Values for this field should be countable, material nouns and must be chosen from subclasses of BFO:0000040 (material entity) that appear in the Environment Ontology (ENVO). For host-associated or plant-associated samples, use terms from the UBERON or Plant Ontology to describe specific anatomical structures or plant parts." + } + }, + "description": "Report the entity or entities which are in the sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. We recommend using EnvO terms which are of smaller spatial grain than your entry for env_broad_scale. Terms, such as anatomical sites, from other OBO Library ontologies which interoperate with EnvO (e.g. UBERON) are accepted in this field. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS.", + "title": "local environmental context", + "notes": [ + "range changed to enumeration late in makefile, so this is modified (but \"sample ID\" anyway)" + ], + "examples": [ + { + "value": "canopy [ENVO:00000047]" + }, + { + "value": "herb and fern layer [ENVO:01000337]" + }, + { + "value": "litter layer [ENVO:01000338]" + }, + { + "value": "understory [01000335]" + }, + { + "value": "shrub layer [ENVO:01000336]" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "local environmental context" + ], + "rank": 7, + "is_a": "environment field", + "string_serialization": "{termLabel} {[termID]}", + "slot_uri": "MIXS:0000013", + "alias": "env_local_scale", + "owner": "HcrCoresInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "string", + "required": true, + "multivalued": false, + "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$" + }, + "env_medium": { + "name": "env_medium", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "The material displaced by the entity at time of sampling. Recommend subclasses of environmental material [ENVO:00010483]." + }, + "tooltip": { + "tag": "tooltip", + "value": "The predominant environmental material or substrate that directly surrounds or hosts the sample or specimen at the time of sampling. Choose values from subclasses of the 'environmental material' class [ENVO:00010483] in the Environment Ontology (ENVO). Values for this field should be measurable or mass material nouns, representing continuous environmental materials. For host-associated or plant-associated samples, use terms from the UBERON or Plant Ontology to indicate a tissue, organ, or plant structure" + } + }, + "description": "Report the environmental material(s) immediately surrounding the sample or specimen at the time of sampling. We recommend using subclasses of 'environmental material' (http://purl.obolibrary.org/obo/ENVO_00010483). EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS . Terms from other OBO ontologies are permissible as long as they reference mass/volume nouns (e.g. air, water, blood) and not discrete, countable entities (e.g. a tree, a leaf, a table top).", + "title": "environmental medium", + "notes": [ + "range changed to enumeration late in makefile, so this is modified (but \"sample ID\" anyway)" + ], + "examples": [ + { + "value": "soil [ENVO:00001998]" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "environmental medium" + ], + "rank": 8, + "is_a": "environment field", + "string_serialization": "{termLabel} {[termID]}", + "slot_uri": "MIXS:0000014", + "alias": "env_medium", + "owner": "HcrCoresInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "string", + "required": true, + "multivalued": false, + "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$" + }, + "ethylbenzene": { + "name": "ethylbenzene", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milligram per liter, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of ethylbenzene in the sample", + "title": "ethylbenzene", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "ethylbenzene" + ], + "rank": 309, + "is_a": "core field", + "slot_uri": "MIXS:0000155", + "alias": "ethylbenzene", + "owner": "HcrCoresInterface", + "domain_of": [ + "Biosample", + "HcrCoresInterface", + "HcrFluidsSwabsInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "experimental_factor": { + "name": "experimental_factor", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "text or EFO and/or OBI" + } + }, + "description": "Experimental factors are essentially the variable aspects of an experiment design which can be used to describe an experiment, or set of experiments, in an increasingly detailed manner. This field accepts ontology terms from Experimental Factor Ontology (EFO) and/or Ontology for Biomedical Investigations (OBI). For a browser of EFO (v 2.95) terms, please see http://purl.bioontology.org/ontology/EFO; for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI", + "title": "experimental factor", + "examples": [ + { + "value": "time series design [EFO:EFO_0001779]" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "experimental factor" + ], + "rank": 12, + "is_a": "investigation field", + "string_serialization": "{termLabel} {[termID]}|{text}", + "slot_uri": "MIXS:0000008", + "alias": "experimental_factor", + "owner": "HcrCoresInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false + }, + "field": { + "name": "field", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "name" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Name of the hydrocarbon field (e.g. Albacora)", + "title": "field name", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "field name" + ], + "rank": 310, + "is_a": "core field", + "string_serialization": "{text}", + "slot_uri": "MIXS:0000291", + "alias": "field", + "owner": "HcrCoresInterface", + "domain_of": [ + "Biosample", + "HcrCoresInterface", + "HcrFluidsSwabsInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "geo_loc_name": { + "name": "geo_loc_name", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "country or sea name (INSDC or GAZ): region(GAZ), specific location name" + } + }, + "description": "The geographical origin of the sample as defined by the country or sea name followed by specific region name.", + "title": "geographic location (country and/or sea,region)", + "examples": [ + { + "value": "USA: Maryland, Bethesda" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "geographic location (country and/or sea,region)" + ], + "rank": 4, + "is_a": "environment field", + "string_serialization": "{text}: {text}, {text}", + "slot_uri": "MIXS:0000010", + "alias": "geo_loc_name", + "owner": "HcrCoresInterface", + "domain_of": [ + "FieldResearchSite", + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "required": true, + "multivalued": false, + "pattern": "^[^:, ][^:]*: [^:, ][^,]*, [^:, ].*$" + }, + "hc_produced": { + "name": "hc_produced", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Main hydrocarbon type produced from resource (i.e. Oil, gas, condensate, etc). If \"other\" is specified, please propose entry in \"additional info\" field", + "title": "hydrocarbon type produced", + "examples": [ + { + "value": "Gas" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "hydrocarbon type produced" + ], + "rank": 313, + "is_a": "core field", + "slot_uri": "MIXS:0000989", + "alias": "hc_produced", + "owner": "HcrCoresInterface", + "domain_of": [ + "Biosample", + "HcrCoresInterface", + "HcrFluidsSwabsInterface" + ], + "slot_group": "mixs_core_section", + "range": "hc_produced_enum", + "multivalued": false + }, + "hcr": { + "name": "hcr", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Main Hydrocarbon Resource type. The term \"Hydrocarbon Resource\" HCR defined as a natural environmental feature containing large amounts of hydrocarbons at high concentrations potentially suitable for commercial exploitation. This term should not be confused with the Hydrocarbon Occurrence term which also includes hydrocarbon-rich environments with currently limited commercial interest such as seeps, outcrops, gas hydrates etc. If \"other\" is specified, please propose entry in \"additional info\" field", + "title": "hydrocarbon resource type", + "examples": [ + { + "value": "Oil Sand" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "hydrocarbon resource type" + ], + "rank": 314, + "is_a": "core field", + "slot_uri": "MIXS:0000988", + "alias": "hcr", + "owner": "HcrCoresInterface", + "domain_of": [ + "Biosample", + "HcrCoresInterface", + "HcrFluidsSwabsInterface" + ], + "slot_group": "mixs_core_section", + "range": "hcr_enum", + "multivalued": false + }, + "hcr_fw_salinity": { + "name": "hcr_fw_salinity", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milligram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Original formation water salinity (prior to secondary recovery e.g. Waterflooding) expressed as TDS", + "title": "formation water salinity", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "formation water salinity" + ], + "rank": 315, + "is_a": "core field", + "slot_uri": "MIXS:0000406", + "alias": "hcr_fw_salinity", + "owner": "HcrCoresInterface", + "domain_of": [ + "Biosample", + "HcrCoresInterface", + "HcrFluidsSwabsInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "hcr_geol_age": { + "name": "hcr_geol_age", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Geological age of hydrocarbon resource (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). If \"other\" is specified, please propose entry in \"additional info\" field", + "title": "hydrocarbon resource geological age", + "examples": [ + { + "value": "Silurian" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "hydrocarbon resource geological age" + ], + "rank": 316, + "is_a": "core field", + "slot_uri": "MIXS:0000993", + "alias": "hcr_geol_age", + "owner": "HcrCoresInterface", + "domain_of": [ + "Biosample", + "HcrCoresInterface", + "HcrFluidsSwabsInterface" + ], + "slot_group": "mixs_core_section", + "range": "hcr_geol_age_enum", + "multivalued": false + }, + "hcr_pressure": { + "name": "hcr_pressure", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value range" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "atmosphere, kilopascal" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Original pressure of the hydrocarbon resource", + "title": "hydrocarbon resource original pressure", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "hydrocarbon resource original pressure" + ], + "rank": 317, + "is_a": "core field", + "string_serialization": "{float} - {float} {unit}", + "slot_uri": "MIXS:0000395", + "alias": "hcr_pressure", + "owner": "HcrCoresInterface", + "domain_of": [ + "Biosample", + "HcrCoresInterface", + "HcrFluidsSwabsInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "hcr_temp": { + "name": "hcr_temp", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value range" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "degree Celsius" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Original temperature of the hydrocarbon resource", + "title": "hydrocarbon resource original temperature", + "examples": [ + { + "value": "150-295 degree Celsius" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "hydrocarbon resource original temperature" + ], + "rank": 318, + "is_a": "core field", + "string_serialization": "{float} - {float} {unit}", + "slot_uri": "MIXS:0000393", + "alias": "hcr_temp", + "owner": "HcrCoresInterface", + "domain_of": [ + "Biosample", + "HcrCoresInterface", + "HcrFluidsSwabsInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "lat_lon": { + "name": "lat_lon", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "decimal degrees, limit to 8 decimal points" + } + }, + "description": "The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system", + "title": "geographic location (latitude and longitude)", + "notes": [ + "This is currently a required field but it's not clear if this should be required for human hosts" + ], + "examples": [ + { + "value": "50.586825 6.408977" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "geographic location (latitude and longitude)" + ], + "rank": 5, + "is_a": "environment field", + "string_serialization": "{lat lon}", + "slot_uri": "MIXS:0000009", + "alias": "lat_lon", + "owner": "HcrCoresInterface", + "domain_of": [ + "FieldResearchSite", + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "required": true, + "multivalued": false, + "pattern": "^[-+]?([1-8]?\\d(\\.\\d{1,8})?|90(\\.0{1,8})?)\\s[-+]?(180(\\.0{1,8})?|((1[0-7]\\d)|([1-9]?\\d))(\\.\\d{1,8})?)$" + }, + "lithology": { + "name": "lithology", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Hydrocarbon resource main lithology (Additional information: http://petrowiki.org/Lithology_and_rock_type_determination). If \"other\" is specified, please propose entry in \"additional info\" field", + "title": "lithology", + "examples": [ + { + "value": "Volcanic" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "lithology" + ], + "rank": 336, + "is_a": "core field", + "slot_uri": "MIXS:0000990", + "alias": "lithology", + "owner": "HcrCoresInterface", + "domain_of": [ + "Biosample", + "HcrCoresInterface", + "HcrFluidsSwabsInterface" + ], + "slot_group": "mixs_core_section", + "range": "lithology_enum", + "multivalued": false + }, + "magnesium": { + "name": "magnesium", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "mole per liter, milligram per liter, parts per million, micromole per kilogram" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of magnesium in the sample", + "title": "magnesium", + "examples": [ + { + "value": "52.8 micromole per kilogram" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "magnesium" + ], + "rank": 21, + "is_a": "core field", + "slot_uri": "MIXS:0000431", + "alias": "magnesium", + "owner": "HcrCoresInterface", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "misc_param": { + "name": "misc_param", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "parameter name;measurement value" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Any other measurement performed or parameter collected, that is not listed here", + "title": "miscellaneous parameter", + "examples": [ + { + "value": "Bicarbonate ion concentration;2075 micromole per kilogram" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "miscellaneous parameter" + ], + "rank": 23, + "is_a": "core field", + "string_serialization": "{text};{float} {unit}", + "slot_uri": "MIXS:0000752", + "alias": "misc_param", + "owner": "HcrCoresInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false, + "pattern": "^([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+\\|)*([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+)$" + }, + "nitrate": { + "name": "nitrate", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per liter, milligram per liter, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of nitrate in the sample", + "title": "nitrate", + "examples": [ + { + "value": "65 micromole per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "nitrate" + ], + "rank": 26, + "is_a": "core field", + "slot_uri": "MIXS:0000425", + "alias": "nitrate", + "owner": "HcrCoresInterface", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "nitrite": { + "name": "nitrite", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per liter, milligram per liter, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of nitrite in the sample", + "title": "nitrite", + "examples": [ + { + "value": "0.5 micromole per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "nitrite" + ], + "rank": 27, + "is_a": "core field", + "slot_uri": "MIXS:0000426", + "alias": "nitrite", + "owner": "HcrCoresInterface", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "org_count_qpcr_info": { + "name": "org_count_qpcr_info", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "gene name;FWD:forward primer sequence;REV:reverse primer sequence;initial denaturation:degrees_minutes;denaturation:degrees_minutes;annealing:degrees_minutes;elongation:degrees_minutes;final elongation:degrees_minutes; total cycles" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "number of cells per gram (or ml or cm^2)" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "If qpcr was used for the cell count, the target gene name, the primer sequence and the cycling conditions should also be provided. (Example: 16S rrna; FWD:ACGTAGCTATGACGT REV:GTGCTAGTCGAGTAC; initial denaturation:90C_5min; denaturation:90C_2min; annealing:52C_30 sec; elongation:72C_30 sec; 90 C for 1 min; final elongation:72C_5min; 30 cycles)", + "title": "organism count qPCR information", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "organism count qPCR information" + ], + "rank": 337, + "is_a": "core field", + "string_serialization": "{text};FWD:{dna};REV:{dna};initial denaturation:degrees_minutes;denaturation:degrees_minutes;annealing:degrees_minutes;elongation:degrees_minutes;final elongation:degrees_minutes; total cycles", + "slot_uri": "MIXS:0000099", + "alias": "org_count_qpcr_info", + "owner": "HcrCoresInterface", + "domain_of": [ + "Biosample", + "HcrCoresInterface", + "HcrFluidsSwabsInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "organism_count": { + "name": "organism_count", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "organism name;measurement value;enumeration" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "number of cells per cubic meter, number of cells per milliliter, number of cells per cubic centimeter" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr)", + "title": "organism count", + "examples": [ + { + "value": "total prokaryotes;3.5e7 cells per milliliter;qPCR" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "organism count" + ], + "rank": 30, + "is_a": "core field", + "slot_uri": "MIXS:0000103", + "alias": "organism_count", + "owner": "HcrCoresInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^([-+]?[0-9]*\\.?[0-9]+ +\\S.*\\|)*([-+]?[0-9]*\\.?[0-9]+ +\\S.*)$" + }, + "owc_tvdss": { + "name": "owc_tvdss", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "meter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Depth of the original oil water contact (OWC) zone (average) (m TVDSS)", + "title": "oil water contact depth", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "oil water contact depth" + ], + "rank": 339, + "is_a": "core field", + "slot_uri": "MIXS:0000405", + "alias": "owc_tvdss", + "owner": "HcrCoresInterface", + "domain_of": [ + "Biosample", + "HcrCoresInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "oxy_stat_samp": { + "name": "oxy_stat_samp", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Oxygenation status of sample", + "title": "oxygenation status of sample", + "examples": [ + { + "value": "aerobic" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "oxygenation status of sample" + ], + "rank": 25, + "is_a": "core field", + "slot_uri": "MIXS:0000753", + "alias": "oxy_stat_samp", + "owner": "HcrCoresInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_section", + "range": "OxyStatSampEnum", + "multivalued": false + }, + "permeability": { + "name": "permeability", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value range" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "mD" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Measure of the ability of a hydrocarbon resource to allow fluids to pass through it. (Additional information: https://en.wikipedia.org/wiki/Permeability_(earth_sciences))", + "title": "permeability", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "permeability" + ], + "rank": 340, + "is_a": "core field", + "string_serialization": "{integer} - {integer} {unit}", + "slot_uri": "MIXS:0000404", + "alias": "permeability", + "owner": "HcrCoresInterface", + "domain_of": [ + "Biosample", + "HcrCoresInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "ph": { + "name": "ph", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "pH measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid", + "title": "pH", + "notes": [ + "Use modified term" + ], + "examples": [ + { + "value": "7.2" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "pH" + ], + "rank": 27, + "is_a": "core field", + "string_serialization": "{float}", + "slot_uri": "MIXS:0001001", + "alias": "ph", + "owner": "HcrCoresInterface", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "MiscEnvsInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "float", + "recommended": true, + "multivalued": false, + "minimum_value": 0, + "maximum_value": 14 + }, + "ph_meth": { + "name": "ph_meth", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "PMID,DOI or url" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Reference or method used in determining ph", + "title": "pH method", + "comments": [ + "This can include a link to the instrument used or a citation for the method." + ], + "examples": [ + { + "value": "https://www.southernlabware.com/pc9500-benchtop-ph-conductivity-meter-kit-ph-accuracy-2000mv-ph-range-2-000-to-20-000.html?gclid=Cj0KCQiAwJWdBhCYARIsAJc4idCO5vtvbVMf545fcvdROFqa6zjzNSoywNx6K4k9Coo9cCc2pybtvGsaAiR0EALw_wcB" + }, + { + "value": "https://doi.org/10.2136/sssabookser5.3.c16" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "pH method" + ], + "rank": 41, + "is_a": "core field", + "string_serialization": "{PMID}|{DOI}|{URL}", + "slot_uri": "MIXS:0001106", + "alias": "ph_meth", + "owner": "HcrCoresInterface", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "MiscEnvsInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false + }, + "porosity": { + "name": "porosity", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value or range" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "percentage" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Porosity of deposited sediment is volume of voids divided by the total volume of sample", + "title": "porosity", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "porosity" + ], + "rank": 37, + "is_a": "core field", + "string_serialization": "{float} - {float} {unit}", + "slot_uri": "MIXS:0000211", + "alias": "porosity", + "owner": "HcrCoresInterface", + "domain_of": [ + "Biosample", + "HcrCoresInterface", + "SedimentInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "potassium": { + "name": "potassium", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milligram per liter, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of potassium in the sample", + "title": "potassium", + "examples": [ + { + "value": "463 milligram per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "potassium" + ], + "rank": 38, + "is_a": "core field", + "slot_uri": "MIXS:0000430", + "alias": "potassium", + "owner": "HcrCoresInterface", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "pour_point": { + "name": "pour_point", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "degree Celsius" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Temperature at which a liquid becomes semi solid and loses its flow characteristics. In crude oil a high¬†pour point¬†is generally associated with a high paraffin content, typically found in crude deriving from a larger proportion of plant material. (soure: https://en.wikipedia.org/wiki/pour_point)", + "title": "pour point", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "pour point" + ], + "rank": 341, + "is_a": "core field", + "slot_uri": "MIXS:0000127", + "alias": "pour_point", + "owner": "HcrCoresInterface", + "domain_of": [ + "Biosample", + "HcrCoresInterface", + "HcrFluidsSwabsInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "pressure": { + "name": "pressure", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "atmosphere" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Pressure to which the sample is subject to, in atmospheres", + "title": "pressure", + "examples": [ + { + "value": "50 atmosphere" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "pressure" + ], + "rank": 39, + "is_a": "core field", + "slot_uri": "MIXS:0000412", + "alias": "pressure", + "owner": "HcrCoresInterface", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "reservoir": { + "name": "reservoir", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "name" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Name of the reservoir (e.g. Carapebus)", + "title": "reservoir name", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "reservoir name" + ], + "rank": 347, + "is_a": "core field", + "string_serialization": "{text}", + "slot_uri": "MIXS:0000303", + "alias": "reservoir", + "owner": "HcrCoresInterface", + "domain_of": [ + "Biosample", + "HcrCoresInterface", + "HcrFluidsSwabsInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "resins_pc": { + "name": "resins_pc", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "name;measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "percent" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene)", + "title": "resins wt%", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "resins wt%" + ], + "rank": 348, + "is_a": "core field", + "string_serialization": "{text};{float} {unit}", + "slot_uri": "MIXS:0000134", + "alias": "resins_pc", + "owner": "HcrCoresInterface", + "domain_of": [ + "Biosample", + "HcrCoresInterface", + "HcrFluidsSwabsInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[^;\\t\\r\\x0A\\|]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A\\|]+$" + }, + "salinity": { + "name": "salinity", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "practical salinity unit, percentage" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The total concentration of all dissolved salts in a liquid or solid sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater.", + "title": "salinity", + "examples": [ + { + "value": "25 practical salinity unit" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "salinity" + ], + "rank": 54, + "is_a": "core field", + "slot_uri": "MIXS:0000183", + "alias": "salinity", + "owner": "HcrCoresInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "samp_collec_device": { + "name": "samp_collec_device", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "device name" + } + }, + "description": "The device used to collect an environmental sample. This field accepts terms listed under environmental sampling device (http://purl.obolibrary.org/obo/ENVO). This field also accepts terms listed under specimen collection device (http://purl.obolibrary.org/obo/GENEPIO_0002094).", + "title": "sample collection device", + "comments": [ + "Report dimensions and details when applicable" + ], + "examples": [ + { + "value": "swab, biopsy, niskin bottle, push core, drag swab [GENEPIO:0002713]" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sample collection device" + ], + "rank": 14, + "is_a": "nucleic acid sequence source field", + "string_serialization": "{termLabel} {[termID]}|{text}", + "slot_uri": "MIXS:0000002", + "alias": "samp_collec_device", + "owner": "HcrCoresInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "recommended": true, + "multivalued": false + }, + "samp_collec_method": { + "name": "samp_collec_method", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "PMID,DOI,url , or text" + } + }, + "description": "The method employed for collecting the sample.", + "title": "sample collection method", + "comments": [ + "This can be a citation or description" + ], + "examples": [ + { + "value": "swabbing" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sample collection method" + ], + "rank": 15, + "is_a": "nucleic acid sequence source field", + "string_serialization": "{PMID}|{DOI}|{URL}|{text}", + "slot_uri": "MIXS:0001225", + "alias": "samp_collec_method", + "owner": "HcrCoresInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "multivalued": false + }, + "samp_mat_process": { + "name": "samp_mat_process", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "text" + } + }, + "description": "A brief description of any processing applied to the sample during or after retrieving the sample from environment, or a link to the relevant protocol(s) performed.", + "title": "sample material processing", + "examples": [ + { + "value": "filtering of seawater" + }, + { + "value": "storing samples in ethanol" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sample material processing" + ], + "rank": 12, + "is_a": "nucleic acid sequence source field", + "string_serialization": "{text}", + "slot_uri": "MIXS:0000016", + "alias": "samp_mat_process", + "owner": "HcrCoresInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "multivalued": false + }, + "samp_md": { + "name": "samp_md", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value;enumeration" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "meter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "In non deviated well, measured depth is equal to the true vertical depth, TVD (TVD=TVDSS plus the reference or datum it refers to). In deviated wells, the MD is the length of trajectory of the borehole measured from the same reference or datum. Common datums used are ground level (GL), drilling rig floor (DF), rotary table (RT), kelly bushing (KB) and mean sea level (MSL). If \"other\" is specified, please propose entry in \"additional info\" field", + "title": "sample measured depth", + "examples": [ + { + "value": "1534 meter;MSL" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sample measured depth" + ], + "rank": 351, + "is_a": "core field", + "slot_uri": "MIXS:0000413", + "alias": "samp_md", + "owner": "HcrCoresInterface", + "domain_of": [ + "Biosample", + "HcrCoresInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "samp_size": { + "name": "samp_size", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "millliter, gram, milligram, liter" + } + }, + "description": "The total amount or size (volume (ml), mass (g) or area (m2) ) of sample collected.", + "title": "amount or size of sample collected", + "comments": [ + "This refers to the TOTAL amount of sample collected from the experiment. NOT the amount sent to each institution or collected for a specific analysis." + ], + "examples": [ + { + "value": "5 grams" + }, + { + "value": "10 mL" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "amount or size of sample collected" + ], + "rank": 18, + "is_a": "nucleic acid sequence source field", + "string_serialization": "{float} {unit}", + "slot_uri": "MIXS:0000001", + "alias": "samp_size", + "owner": "HcrCoresInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? \\S+$" + }, + "samp_store_dur": { + "name": "samp_store_dur", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "duration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Duration for which the sample was stored", + "title": "sample storage duration", + "examples": [ + { + "value": "P1Y6M" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sample storage duration" + ], + "rank": 353, + "is_a": "core field", + "string_serialization": "{duration}", + "slot_uri": "MIXS:0000116", + "alias": "samp_store_dur", + "owner": "HcrCoresInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "samp_store_loc": { + "name": "samp_store_loc", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "location name" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Location at which sample was stored, usually name of a specific freezer/room", + "title": "sample storage location", + "examples": [ + { + "value": "Freezer no:5" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sample storage location" + ], + "rank": 41, + "is_a": "core field", + "string_serialization": "{text}", + "slot_uri": "MIXS:0000755", + "alias": "samp_store_loc", + "owner": "HcrCoresInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "samp_store_temp": { + "name": "samp_store_temp", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "degree Celsius" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Temperature at which the sample was stored (degrees are assumed)", + "title": "sample storage temperature", + "examples": [ + { + "value": "-80 Celsius" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sample storage temperature" + ], + "rank": 7, + "is_a": "core field", + "slot_uri": "MIXS:0000110", + "alias": "samp_store_temp", + "owner": "HcrCoresInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "required": true, + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "samp_subtype": { + "name": "samp_subtype", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Name of sample sub-type. For example if \"sample type\" is \"Produced Water\" then subtype could be \"Oil Phase\" or \"Water Phase\". If \"other\" is specified, please propose entry in \"additional info\" field", + "title": "sample subtype", + "examples": [ + { + "value": "biofilm" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sample subtype" + ], + "rank": 354, + "is_a": "core field", + "slot_uri": "MIXS:0000999", + "alias": "samp_subtype", + "owner": "HcrCoresInterface", + "domain_of": [ + "Biosample", + "HcrCoresInterface", + "HcrFluidsSwabsInterface" + ], + "slot_group": "mixs_core_section", + "range": "samp_subtype_enum", + "multivalued": false + }, + "samp_transport_cond": { + "name": "samp_transport_cond", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value;measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "days;degree Celsius" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Sample transport duration (in days or hrs) and temperature the sample was exposed to (e.g. 5.5 days; 20 ¬∞C)", + "title": "sample transport conditions", + "examples": [ + { + "value": "5 days;-20 degree Celsius" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sample transport conditions" + ], + "rank": 355, + "is_a": "core field", + "string_serialization": "{float} {unit};{float} {unit}", + "slot_uri": "MIXS:0000410", + "alias": "samp_transport_cond", + "owner": "HcrCoresInterface", + "domain_of": [ + "Biosample", + "HcrCoresInterface", + "HcrFluidsSwabsInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "samp_tvdss": { + "name": "samp_tvdss", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value or measurement value range" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "meter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Depth of the sample i.e. The vertical distance between the sea level and the sampled position in the subsurface. Depth can be reported as an interval for subsurface samples e.g. 1325.75-1362.25 m", + "title": "sample true vertical depth subsea", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sample true vertical depth subsea" + ], + "rank": 356, + "is_a": "core field", + "string_serialization": "{float}-{float} {unit}", + "slot_uri": "MIXS:0000409", + "alias": "samp_tvdss", + "owner": "HcrCoresInterface", + "domain_of": [ + "Biosample", + "HcrCoresInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "samp_type": { + "name": "samp_type", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "GENEPIO:0001246" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The type of material from which the sample was obtained. For the Hydrocarbon package, samples include types like core, rock trimmings, drill cuttings, piping section, coupon, pigging debris, solid deposit, produced fluid, produced water, injected water, swabs, etc. For the Food Package, samples are usually categorized as food, body products or tissues, or environmental material. This field accepts terms listed under environmental specimen (http://purl.obolibrary.org/obo/GENEPIO_0001246).", + "title": "sample type", + "examples": [ + { + "value": "built environment sample [GENEPIO:0001248]" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sample type" + ], + "rank": 357, + "is_a": "core field", + "string_serialization": "{termLabel} {[termID]}", + "slot_uri": "MIXS:0000998", + "alias": "samp_type", + "owner": "HcrCoresInterface", + "domain_of": [ + "Biosample", + "HcrCoresInterface", + "HcrFluidsSwabsInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$" + }, + "samp_well_name": { + "name": "samp_well_name", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "name" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Name of the well (e.g. BXA1123) where sample was taken", + "title": "sample well name", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sample well name" + ], + "rank": 358, + "is_a": "core field", + "string_serialization": "{text}", + "slot_uri": "MIXS:0000296", + "alias": "samp_well_name", + "owner": "HcrCoresInterface", + "domain_of": [ + "Biosample", + "HcrCoresInterface", + "HcrFluidsSwabsInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "sample_link": { + "name": "sample_link", + "description": "A unique identifier to assign parent-child, subsample, or sibling samples. This is relevant when a sample or other material was used to generate the new sample.", + "title": "sample linkage", + "notes": [ + "also tempted to include SampIdNewTermsMixin but if len(slot_usage.keys()) > 1 and \"placeholder\" in slot_usage.keys():AttributeError: 'list' object has no attribute 'keys'" + ], + "comments": [ + "This field allows multiple entries separated by ; (Examples: Soil collected from the field will link with the soil used in an incubation. The soil a plant was grown in links to the plant sample. An original culture sample was transferred to a new vial and generated a new sample)" + ], + "examples": [ + { + "value": "IGSN:DSJ0284" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "rank": 5, + "string_serialization": "{text}:{text}", + "alias": "sample_link", + "owner": "HcrCoresInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface", + "SampIdNewTermsMixin" + ], + "slot_group": "sample_id_section", + "range": "string", + "recommended": true, + "multivalued": false, + "pattern": "[^\\:\\n\\r]+\\:[^\\:\\n\\r]+" + }, + "saturates_pc": { + "name": "saturates_pc", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "name;measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "percent" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene)", + "title": "saturates wt%", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "saturates wt%" + ], + "rank": 359, + "is_a": "core field", + "string_serialization": "{text};{float} {unit}", + "slot_uri": "MIXS:0000131", + "alias": "saturates_pc", + "owner": "HcrCoresInterface", + "domain_of": [ + "Biosample", + "HcrCoresInterface", + "HcrFluidsSwabsInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[^;\\t\\r\\x0A\\|]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A\\|]+$" + }, + "size_frac": { + "name": "size_frac", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "filter size value range" + } + }, + "description": "Filtering pore size used in sample preparation", + "title": "size fraction selected", + "examples": [ + { + "value": "0-0.22 micrometer" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "size fraction selected" + ], + "rank": 285, + "is_a": "nucleic acid sequence source field", + "string_serialization": "{float}-{float} {unit}", + "slot_uri": "MIXS:0000017", + "alias": "size_frac", + "owner": "HcrCoresInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "sodium": { + "name": "sodium", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milligram per liter, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Sodium concentration in the sample", + "title": "sodium", + "examples": [ + { + "value": "10.5 milligram per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sodium" + ], + "rank": 363, + "is_a": "core field", + "slot_uri": "MIXS:0000428", + "alias": "sodium", + "owner": "HcrCoresInterface", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "specific_ecosystem": { + "name": "specific_ecosystem", + "description": "Specific ecosystems represent specific features of the environment like aphotic zone in an ocean or gastric mucosa within a host digestive system. Specific ecosystem is in position 5/5 in a GOLD path.", + "comments": [ + "Specific ecosystems help to define samples based on very specific characteristics of an environment under the five-level classification system." + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "https://gold.jgi.doe.gov/help" + ], + "rank": 13, + "is_a": "gold_path_field", + "alias": "specific_ecosystem", + "owner": "HcrCoresInterface", + "domain_of": [ + "Biosample", + "Study", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "SpecificEcosystemEnum", + "recommended": true + }, + "sr_dep_env": { + "name": "sr_dep_env", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Source rock depositional environment (https://en.wikipedia.org/wiki/Source_rock). If \"other\" is specified, please propose entry in \"additional info\" field", + "title": "source rock depositional environment", + "examples": [ + { + "value": "Marine" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "source rock depositional environment" + ], + "rank": 366, + "is_a": "core field", + "slot_uri": "MIXS:0000996", + "alias": "sr_dep_env", + "owner": "HcrCoresInterface", + "domain_of": [ + "Biosample", + "HcrCoresInterface" + ], + "slot_group": "mixs_core_section", + "range": "sr_dep_env_enum", + "multivalued": false + }, + "sr_geol_age": { + "name": "sr_geol_age", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Geological age of source rock (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). If \"other\" is specified, please propose entry in \"additional info\" field", + "title": "source rock geological age", + "examples": [ + { + "value": "Silurian" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "source rock geological age" + ], + "rank": 367, + "is_a": "core field", + "slot_uri": "MIXS:0000997", + "alias": "sr_geol_age", + "owner": "HcrCoresInterface", + "domain_of": [ + "Biosample", + "HcrCoresInterface" + ], + "slot_group": "mixs_core_section", + "range": "sr_geol_age_enum", + "multivalued": false + }, + "sr_kerog_type": { + "name": "sr_kerog_type", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Origin of kerogen. Type I: Algal (aquatic), Type II: planktonic and soft plant material (aquatic or terrestrial), Type III: terrestrial woody/ fibrous plant material (terrestrial), Type IV: oxidized recycled woody debris (terrestrial) (additional information: https://en.wikipedia.org/wiki/Kerogen). If \"other\" is specified, please propose entry in \"additional info\" field", + "title": "source rock kerogen type", + "examples": [ + { + "value": "Type IV" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "source rock kerogen type" + ], + "rank": 368, + "is_a": "core field", + "slot_uri": "MIXS:0000994", + "alias": "sr_kerog_type", + "owner": "HcrCoresInterface", + "domain_of": [ + "Biosample", + "HcrCoresInterface" + ], + "slot_group": "mixs_core_section", + "range": "sr_kerog_type_enum", + "multivalued": false + }, + "sr_lithology": { + "name": "sr_lithology", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Lithology of source rock (https://en.wikipedia.org/wiki/Source_rock). If \"other\" is specified, please propose entry in \"additional info\" field", + "title": "source rock lithology", + "examples": [ + { + "value": "Coal" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "source rock lithology" + ], + "rank": 369, + "is_a": "core field", + "slot_uri": "MIXS:0000995", + "alias": "sr_lithology", + "owner": "HcrCoresInterface", + "domain_of": [ + "Biosample", + "HcrCoresInterface" + ], + "slot_group": "mixs_core_section", + "range": "sr_lithology_enum", + "multivalued": false + }, + "sulfate": { + "name": "sulfate", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per liter, milligram per liter, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of sulfate in the sample", + "title": "sulfate", + "examples": [ + { + "value": "5 micromole per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sulfate" + ], + "rank": 44, + "is_a": "core field", + "slot_uri": "MIXS:0000423", + "alias": "sulfate", + "owner": "HcrCoresInterface", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "sulfate_fw": { + "name": "sulfate_fw", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milligram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Original sulfate concentration in the hydrocarbon resource", + "title": "sulfate in formation water", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sulfate in formation water" + ], + "rank": 370, + "is_a": "core field", + "slot_uri": "MIXS:0000407", + "alias": "sulfate_fw", + "owner": "HcrCoresInterface", + "domain_of": [ + "Biosample", + "HcrCoresInterface", + "HcrFluidsSwabsInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "sulfide": { + "name": "sulfide", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per liter, milligram per liter, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of sulfide in the sample", + "title": "sulfide", + "examples": [ + { + "value": "2 micromole per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sulfide" + ], + "rank": 371, + "is_a": "core field", + "slot_uri": "MIXS:0000424", + "alias": "sulfide", + "owner": "HcrCoresInterface", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "suspend_solids": { + "name": "suspend_solids", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "suspended solid name;measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "gram, microgram, milligram per liter, mole per liter, gram per liter, part per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Concentration of substances including a wide variety of material, such as silt, decaying plant and animal matter; can include multiple substances", + "title": "suspended solids", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "suspended solids" + ], + "rank": 372, + "is_a": "core field", + "string_serialization": "{text};{float} {unit}", + "slot_uri": "MIXS:0000150", + "alias": "suspend_solids", + "owner": "HcrCoresInterface", + "domain_of": [ + "Biosample", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "WastewaterSludgeInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+\\|)*([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+)$" + }, + "tan": { + "name": "tan", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milligram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Total Acid Number¬†(TAN) is a measurement of acidity that is determined by the amount of¬†potassium hydroxide¬†in milligrams that is needed to neutralize the acids in one gram of oil.¬†It is an important quality measurement of¬†crude oil. (source: https://en.wikipedia.org/wiki/Total_acid_number)", + "title": "total acid number", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "total acid number" + ], + "rank": 373, + "is_a": "core field", + "slot_uri": "MIXS:0000120", + "alias": "tan", + "owner": "HcrCoresInterface", + "domain_of": [ + "Biosample", + "HcrCoresInterface", + "HcrFluidsSwabsInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "temp": { + "name": "temp", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "degree Celsius" + } + }, + "description": "Temperature of the sample at the time of sampling.", + "title": "temperature", + "examples": [ + { + "value": "25 degree Celsius" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "temperature" + ], + "rank": 37, + "is_a": "environment field", + "slot_uri": "MIXS:0000113", + "alias": "temp", + "owner": "HcrCoresInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "toluene": { + "name": "toluene", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milligram per liter, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of toluene in the sample", + "title": "toluene", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "toluene" + ], + "rank": 375, + "is_a": "core field", + "slot_uri": "MIXS:0000154", + "alias": "toluene", + "owner": "HcrCoresInterface", + "domain_of": [ + "Biosample", + "HcrCoresInterface", + "HcrFluidsSwabsInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "tot_iron": { + "name": "tot_iron", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milligram per liter, milligram per kilogram" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of total iron in the sample", + "title": "total iron", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "total iron" + ], + "rank": 376, + "is_a": "core field", + "slot_uri": "MIXS:0000105", + "alias": "tot_iron", + "owner": "HcrCoresInterface", + "domain_of": [ + "Biosample", + "HcrCoresInterface", + "HcrFluidsSwabsInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "tot_nitro": { + "name": "tot_nitro", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "microgram per liter, micromole per liter, milligram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen", + "title": "total nitrogen concentration", + "examples": [ + { + "value": "50 micromole per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "total nitrogen concentration" + ], + "rank": 377, + "is_a": "core field", + "slot_uri": "MIXS:0000102", + "alias": "tot_nitro", + "owner": "HcrCoresInterface", + "domain_of": [ + "Biosample", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "tot_phosp": { + "name": "tot_phosp", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per liter, milligram per liter, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus", + "title": "total phosphorus", + "examples": [ + { + "value": "0.03 milligram per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "total phosphorus" + ], + "rank": 52, + "is_a": "core field", + "slot_uri": "MIXS:0000117", + "alias": "tot_phosp", + "owner": "HcrCoresInterface", + "domain_of": [ + "Biosample", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "SoilInterface", + "WaterInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "tot_sulfur": { + "name": "tot_sulfur", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milligram per liter, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of total sulfur in the sample", + "title": "total sulfur", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "total sulfur" + ], + "rank": 379, + "is_a": "core field", + "slot_uri": "MIXS:0000419", + "alias": "tot_sulfur", + "owner": "HcrCoresInterface", + "domain_of": [ + "Biosample", + "HcrCoresInterface", + "HcrFluidsSwabsInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "tvdss_of_hcr_press": { + "name": "tvdss_of_hcr_press", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "meter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original pressure was measured (e.g. 1578 m).", + "title": "depth (TVDSS) of hydrocarbon resource pressure", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "depth (TVDSS) of hydrocarbon resource pressure" + ], + "rank": 380, + "is_a": "core field", + "slot_uri": "MIXS:0000397", + "alias": "tvdss_of_hcr_press", + "owner": "HcrCoresInterface", + "domain_of": [ + "Biosample", + "HcrCoresInterface", + "HcrFluidsSwabsInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "tvdss_of_hcr_temp": { + "name": "tvdss_of_hcr_temp", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "meter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original temperature was measured (e.g. 1345 m).", + "title": "depth (TVDSS) of hydrocarbon resource temperature", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "depth (TVDSS) of hydrocarbon resource temperature" + ], + "rank": 381, + "is_a": "core field", + "slot_uri": "MIXS:0000394", + "alias": "tvdss_of_hcr_temp", + "owner": "HcrCoresInterface", + "domain_of": [ + "Biosample", + "HcrCoresInterface", + "HcrFluidsSwabsInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "vfa": { + "name": "vfa", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milligram per liter, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of Volatile Fatty Acids in the sample", + "title": "volatile fatty acids", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "volatile fatty acids" + ], + "rank": 382, + "is_a": "core field", + "slot_uri": "MIXS:0000152", + "alias": "vfa", + "owner": "HcrCoresInterface", + "domain_of": [ + "Biosample", + "HcrCoresInterface", + "HcrFluidsSwabsInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "vfa_fw": { + "name": "vfa_fw", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milligram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Original volatile fatty acid concentration in the hydrocarbon resource", + "title": "vfa in formation water", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "vfa in formation water" + ], + "rank": 383, + "is_a": "core field", + "slot_uri": "MIXS:0000408", + "alias": "vfa_fw", + "owner": "HcrCoresInterface", + "domain_of": [ + "Biosample", + "HcrCoresInterface", + "HcrFluidsSwabsInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "viscosity": { + "name": "viscosity", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value;measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "cP at degree Celsius" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "A measure of oil's resistance¬†to gradual deformation by¬†shear stress¬†or¬†tensile stress (e.g. 3.5 cp; 100 ¬∞C)", + "title": "viscosity", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "viscosity" + ], + "rank": 384, + "is_a": "core field", + "string_serialization": "{float} {unit};{float} {unit}", + "slot_uri": "MIXS:0000126", + "alias": "viscosity", + "owner": "HcrCoresInterface", + "domain_of": [ + "Biosample", + "HcrCoresInterface", + "HcrFluidsSwabsInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "win": { + "name": "win", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "text" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "A unique identifier of a well or wellbore. This is part of the Global Framework for Well Identification initiative which is compiled by the Professional Petroleum Data Management Association (PPDM) in an effort to improve well identification systems. (Supporting information: https://ppdm.org/ and http://dl.ppdm.org/dl/690)", + "title": "well identification number", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "well identification number" + ], + "rank": 388, + "is_a": "core field", + "string_serialization": "{text}", + "slot_uri": "MIXS:0000297", + "alias": "win", + "owner": "HcrCoresInterface", + "domain_of": [ + "Biosample", + "HcrCoresInterface", + "HcrFluidsSwabsInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "xylene": { + "name": "xylene", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milligram per liter, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of xylene in the sample", + "title": "xylene", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "xylene" + ], + "rank": 389, + "is_a": "core field", + "slot_uri": "MIXS:0000156", + "alias": "xylene", + "owner": "HcrCoresInterface", + "domain_of": [ + "Biosample", + "HcrCoresInterface", + "HcrFluidsSwabsInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "analysis_type": { + "name": "analysis_type", + "description": "Select all the data types associated or available for this biosample", + "title": "analysis/data type", + "examples": [ + { + "value": "metagenomics; metabolomics; proteomics" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "MIxS:investigation_type" + ], + "rank": 3, + "alias": "analysis_type", + "owner": "HcrCoresInterface", + "domain_of": [ + "Biosample", + "DhMultiviewCommonColumnsMixin", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "EmslInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "JgiMgInterface", + "JgiMgLrInterface", + "JgiMtInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "AnalysisTypeEnum", + "required": true, + "recommended": false, + "multivalued": true + }, + "samp_name": { + "name": "samp_name", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "text" + } + }, + "description": "A local identifier or name that for the material sample collected. Refers to the original material collected or to any derived sub-samples.", + "title": "sample name", + "comments": [ + "It can have any format, but we suggest that you make it concise, unique and consistent within your lab, and as informative as possible." + ], + "examples": [ + { + "value": "Rock core CB1178(5-6) from NSW" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sample name" + ], + "rank": 1, + "is_a": "investigation field", + "string_serialization": "{text}", + "slot_uri": "MIXS:0001107", + "identifier": true, + "alias": "samp_name", + "owner": "HcrCoresInterface", + "domain_of": [ + "Biosample", + "DhMultiviewCommonColumnsMixin", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "EmslInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "JgiMgInterface", + "JgiMgLrInterface", + "JgiMtInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "string", + "required": true, + "multivalued": false + }, + "source_mat_id": { + "name": "source_mat_id", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "for cultures of microorganisms: identifiers for two culture collections; for other material a unique arbitrary identifer" + } + }, + "description": "A globally unique identifier assigned to the biological sample.", + "title": "source material identifier", + "todos": [ + "Currently, the comments say to use UUIDs. However, if we implement assigning NMDC identifiers with the minter we dont need to require a GUID. It can be an optional field to fill out only if they already have a resolvable ID.", + "Currently, the comments say to use UUIDs. However, if we implement assigning NMDC identifiers with the minter we dont need to require a GUID. It can be an optional field to fill out only if they already have a resolvable ID." + ], + "notes": [ + "The source material IS the Globally Unique ID" + ], + "comments": [ + "Identifiers must be prefixed. Possible FAIR prefixes are IGSNs (http://www.geosamples.org/getigsn), NCBI biosample accession numbers, ARK identifiers (https://arks.org/). These IDs enable linking to derived analytes and subsamples. If you have not assigned FAIR identifiers to your samples, you can generate UUIDs (https://www.uuidgenerator.net/).", + "Identifiers must be prefixed. Possible FAIR prefixes are IGSNs (http://www.geosamples.org/getigsn), NCBI biosample accession numbers, ARK identifiers (https://arks.org/). These IDs enable linking to derived analytes and subsamples. If you have not assigned FAIR identifiers to your samples, you can generate UUIDs (https://www.uuidgenerator.net/)." + ], + "examples": [ + { + "value": "IGSN:AU1243" + }, + { + "value": "UUID:24f1467a-40f4-11ed-b878-0242ac120002" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "source material identifiers" + ], + "rank": 2, + "is_a": "nucleic acid sequence source field", + "string_serialization": "{text}:{text}", + "slot_uri": "MIXS:0000026", + "alias": "source_mat_id", + "owner": "HcrCoresInterface", + "domain_of": [ + "Biosample", + "DhMultiviewCommonColumnsMixin", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "EmslInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "JgiMgInterface", + "JgiMgLrInterface", + "JgiMtInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "string", + "multivalued": false, + "pattern": "[^\\:\\n\\r]+\\:[^\\:\\n\\r]+" + } + } + }, + "HcrFluidsSwabsInterface": { + "name": "HcrFluidsSwabsInterface", + "annotations": { + "excel_worksheet_name": { + "tag": "excel_worksheet_name", + "value": "hcr fluids swab" + } + }, + "description": "hcr_fluids_swabs dh_interface", + "title": "Hcr Fluids Swabs", + "from_schema": "https://example.com/nmdc_submission_schema", + "is_a": "DhInterface", + "mixins": [ + "DhMultiviewCommonColumnsMixin" + ], + "slots": [ + "add_recov_method", + "additional_info", + "alkalinity", + "alkalinity_method", + "ammonium", + "api", + "aromatics_pc", + "asphaltenes_pc", + "basin", + "benzene", + "biocide", + "biocide_admin_method", + "calcium", + "chem_administration", + "chem_treat_method", + "chem_treatment", + "chloride", + "collection_date", + "density", + "depos_env", + "depth", + "diss_carb_dioxide", + "diss_inorg_carb", + "diss_inorg_phosp", + "diss_iron", + "diss_org_carb", + "diss_oxygen_fluid", + "ecosystem", + "ecosystem_category", + "ecosystem_subtype", + "ecosystem_type", + "elev", + "env_broad_scale", + "env_local_scale", + "env_medium", + "ethylbenzene", + "experimental_factor", + "field", + "geo_loc_name", + "hc_produced", + "hcr", + "hcr_fw_salinity", + "hcr_geol_age", + "hcr_pressure", + "hcr_temp", + "iw_bt_date_well", + "iwf", + "lat_lon", + "lithology", + "magnesium", + "misc_param", + "nitrate", + "nitrite", + "org_count_qpcr_info", + "organism_count", + "oxy_stat_samp", + "ph", + "ph_meth", + "potassium", + "pour_point", + "pressure", + "prod_rate", + "prod_start_date", + "reservoir", + "resins_pc", + "salinity", + "samp_collec_device", + "samp_collec_method", + "samp_collect_point", + "samp_loc_corr_rate", + "samp_mat_process", + "samp_preserv", + "samp_size", + "samp_store_dur", + "samp_store_loc", + "samp_store_temp", + "samp_subtype", + "samp_transport_cond", + "samp_type", + "samp_well_name", + "sample_link", + "saturates_pc", + "size_frac", + "sodium", + "specific_ecosystem", + "sulfate", + "sulfate_fw", + "sulfide", + "suspend_solids", + "tan", + "temp", + "toluene", + "tot_iron", + "tot_nitro", + "tot_phosp", + "tot_sulfur", + "tvdss_of_hcr_press", + "tvdss_of_hcr_temp", + "vfa", + "vfa_fw", + "viscosity", + "water_cut", + "water_prod_rate", + "win", + "xylene" + ], + "slot_usage": { + "add_recov_method": { + "name": "add_recov_method", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration;timestamp" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Additional (i.e. Secondary, tertiary, etc.) recovery methods deployed for increase of hydrocarbon recovery from resource and start date for each one of them. If \"other\" is specified, please propose entry in \"additional info\" field", + "title": "secondary and tertiary recovery methods and start date", + "examples": [ + { + "value": "Polymer Addition;2018-06-21T14:30Z" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "secondary and tertiary recovery methods and start date" + ], + "rank": 289, + "is_a": "core field", + "slot_uri": "MIXS:0001009", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "HcrFluidsSwabsInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "additional_info": { + "name": "additional_info", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "text" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Information that doesn't fit anywhere else. Can also be used to propose new entries for fields with controlled vocabulary", + "title": "additional info", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "additional info" + ], + "rank": 290, + "is_a": "core field", + "string_serialization": "{text}", + "slot_uri": "MIXS:0000300", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "HcrCoresInterface", + "HcrFluidsSwabsInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "alkalinity": { + "name": "alkalinity", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milliequivalent per liter, milligram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate", + "title": "alkalinity", + "examples": [ + { + "value": "50 milligram per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "alkalinity" + ], + "rank": 1, + "is_a": "core field", + "slot_uri": "MIXS:0000421", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "alkalinity_method": { + "name": "alkalinity_method", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "description of method" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Method used for alkalinity measurement", + "title": "alkalinity method", + "examples": [ + { + "value": "titration" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "alkalinity method" + ], + "rank": 218, + "is_a": "core field", + "string_serialization": "{text}", + "slot_uri": "MIXS:0000298", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "ammonium": { + "name": "ammonium", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per liter, milligram per liter, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of ammonium in the sample", + "title": "ammonium", + "examples": [ + { + "value": "1.5 milligram per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "ammonium" + ], + "rank": 4, + "is_a": "core field", + "slot_uri": "MIXS:0000427", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "api": { + "name": "api", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "degrees API" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "API gravity is a measure of how heavy or light a petroleum liquid is compared to water (source: https://en.wikipedia.org/wiki/API_gravity) (e.g. 31.1¬∞ API)", + "title": "API gravity", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "API gravity" + ], + "rank": 291, + "is_a": "core field", + "slot_uri": "MIXS:0000157", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "HcrCoresInterface", + "HcrFluidsSwabsInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "aromatics_pc": { + "name": "aromatics_pc", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "name;measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "percent" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene)", + "title": "aromatics wt%", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "aromatics wt%" + ], + "rank": 292, + "is_a": "core field", + "string_serialization": "{text};{float} {unit}", + "slot_uri": "MIXS:0000133", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "HcrCoresInterface", + "HcrFluidsSwabsInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[^;\\t\\r\\x0A\\|]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A\\|]+$" + }, + "asphaltenes_pc": { + "name": "asphaltenes_pc", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "name;measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "percent" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene)", + "title": "asphaltenes wt%", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "asphaltenes wt%" + ], + "rank": 293, + "is_a": "core field", + "string_serialization": "{text};{float} {unit}", + "slot_uri": "MIXS:0000135", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "HcrCoresInterface", + "HcrFluidsSwabsInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[^;\\t\\r\\x0A\\|]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A\\|]+$" + }, + "basin": { + "name": "basin", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "name" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Name of the basin (e.g. Campos)", + "title": "basin name", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "basin name" + ], + "rank": 294, + "is_a": "core field", + "string_serialization": "{text}", + "slot_uri": "MIXS:0000290", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "HcrCoresInterface", + "HcrFluidsSwabsInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "benzene": { + "name": "benzene", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milligram per liter, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of benzene in the sample", + "title": "benzene", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "benzene" + ], + "rank": 295, + "is_a": "core field", + "slot_uri": "MIXS:0000153", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "HcrCoresInterface", + "HcrFluidsSwabsInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "biocide": { + "name": "biocide", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "name;name;timestamp" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "List of biocides (commercial name of product and supplier) and date of administration", + "title": "biocide administration", + "examples": [ + { + "value": "ALPHA 1427;Baker Hughes;2008-01-23" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "biocide administration" + ], + "rank": 297, + "is_a": "core field", + "string_serialization": "{text};{text};{timestamp}", + "slot_uri": "MIXS:0001011", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "HcrFluidsSwabsInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "biocide_admin_method": { + "name": "biocide_admin_method", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value;frequency;duration;duration" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milligram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Method of biocide administration (dose, frequency, duration, time elapsed between last biociding and sampling) (e.g. 150 mg/l; weekly; 4 hr; 3 days)", + "title": "biocide administration method", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "biocide administration method" + ], + "rank": 298, + "is_a": "core field", + "string_serialization": "{float} {unit};{Rn/start_time/end_time/duration};{duration}", + "slot_uri": "MIXS:0000456", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "HcrFluidsSwabsInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "calcium": { + "name": "calcium", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milligram per liter, micromole per liter, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of calcium in the sample", + "title": "calcium", + "examples": [ + { + "value": "0.2 micromole per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "calcium" + ], + "rank": 9, + "is_a": "core field", + "slot_uri": "MIXS:0000432", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "chem_administration": { + "name": "chem_administration", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "CHEBI;timestamp" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi", + "title": "chemical administration", + "examples": [ + { + "value": "agar [CHEBI:2509];2018-05-11|agar [CHEBI:2509];2018-05-22" + }, + { + "value": "agar [CHEBI:2509];2018-05" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "chemical administration" + ], + "rank": 17, + "is_a": "core field", + "string_serialization": "{termLabel} {[termID]};{timestamp}", + "slot_uri": "MIXS:0000751", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "recommended": true, + "multivalued": false, + "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\];([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$" + }, + "chem_treat_method": { + "name": "chem_treat_method", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value;frequency;duration;duration" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milligram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Method of chemical administration(dose, frequency, duration, time elapsed between administration and sampling) (e.g. 50 mg/l; twice a week; 1 hr; 0 days)", + "title": "chemical treatment method", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "chemical treatment method" + ], + "rank": 302, + "is_a": "core field", + "string_serialization": "{float} {unit};{Rn/start_time/end_time/duration};{duration};{duration}", + "slot_uri": "MIXS:0000457", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "HcrFluidsSwabsInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "chem_treatment": { + "name": "chem_treatment", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "name;name;timestamp" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "List of chemical compounds administered upstream the sampling location where sampling occurred (e.g. Glycols, H2S scavenger, corrosion and scale inhibitors, demulsifiers, and other production chemicals etc.). The commercial name of the product and name of the supplier should be provided. The date of administration should also be included", + "title": "chemical treatment", + "examples": [ + { + "value": "ACCENT 1125;DOW;2010-11-17" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "chemical treatment" + ], + "rank": 303, + "is_a": "core field", + "string_serialization": "{text};{text};{timestamp}", + "slot_uri": "MIXS:0001012", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "HcrFluidsSwabsInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "chloride": { + "name": "chloride", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milligram per liter, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of chloride in the sample", + "title": "chloride", + "examples": [ + { + "value": "5000 milligram per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "chloride" + ], + "rank": 10, + "is_a": "core field", + "slot_uri": "MIXS:0000429", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "collection_date": { + "name": "collection_date", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "date and time" + } + }, + "description": "The date of sampling", + "title": "collection date", + "notes": [ + "MIxS collection_date accepts (truncated) ISO8601. DH taking arb prec date only", + "Use modified term (amended definition)" + ], + "examples": [ + { + "value": "2021-04-15" + }, + { + "value": "2021-04" + }, + { + "value": "2021" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "collection date" + ], + "rank": 3, + "is_a": "environment field", + "string_serialization": "{date, arbitrary precision}", + "slot_uri": "MIXS:0000011", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "required": true, + "multivalued": false, + "pattern": "^[12]\\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\\d|3[01]))?)?$" + }, + "density": { + "name": "density", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "gram per cubic meter, gram per cubic centimeter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Density of the sample, which is its mass per unit volume (aka volumetric mass density)", + "title": "density", + "examples": [ + { + "value": "1000 kilogram per cubic meter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "density" + ], + "rank": 12, + "is_a": "core field", + "slot_uri": "MIXS:0000435", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "depos_env": { + "name": "depos_env", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Main depositional environment (https://en.wikipedia.org/wiki/Depositional_environment). If \"other\" is specified, please propose entry in \"additional info\" field", + "title": "depositional environment", + "examples": [ + { + "value": "Continental - Alluvial" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "depositional environment" + ], + "rank": 304, + "is_a": "core field", + "slot_uri": "MIXS:0000992", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "HcrCoresInterface", + "HcrFluidsSwabsInterface" + ], + "slot_group": "mixs_core_section", + "range": "depos_env_enum", + "multivalued": false + }, + "depth": { + "name": "depth", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + } + }, + "description": "The vertical distance below local surface, e.g. for sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples.", + "title": "depth, meters", + "notes": [ + "Use modified term" + ], + "comments": [ + "All depths must be reported in meters. Provide the numerical portion only." + ], + "examples": [ + { + "value": "0 - 0.1" + }, + { + "value": "1" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "depth" + ], + "rank": 9, + "is_a": "environment field", + "string_serialization": "{float}|{float}-{float}", + "slot_uri": "MIXS:0000018", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "recommended": true, + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)?(\\s*-\\s*[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)?)?$" + }, + "diss_carb_dioxide": { + "name": "diss_carb_dioxide", + "annotations": { + "expected_value": { + "tag": 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"annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "microgram per liter, milligram per liter, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter", + "title": "dissolved inorganic carbon", + "examples": [ + { + "value": "2059 micromole per kilogram" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "dissolved inorganic carbon" + ], + "rank": 16, + "is_a": "core field", + "slot_uri": "MIXS:0000434", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "diss_inorg_phosp": { + "name": "diss_inorg_phosp", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "microgram per liter, milligram per liter, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of dissolved inorganic phosphorus in the sample", + "title": "dissolved inorganic phosphorus", + "examples": [ + { + "value": "56.5 micromole per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "dissolved inorganic phosphorus" + ], + "rank": 224, + "is_a": "core field", + "slot_uri": "MIXS:0000106", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "diss_iron": { + "name": "diss_iron", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milligram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of dissolved iron in the sample", + "title": "dissolved iron", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "dissolved iron" + ], + "rank": 305, + "is_a": "core field", + "slot_uri": "MIXS:0000139", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "HcrCoresInterface", + "HcrFluidsSwabsInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "diss_org_carb": { + "name": "diss_org_carb", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per liter, milligram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid", + "title": "dissolved organic carbon", + "examples": [ + { + "value": "197 micromole per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "dissolved organic carbon" + ], + "rank": 17, + "is_a": "core field", + "slot_uri": "MIXS:0000433", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "diss_oxygen_fluid": { + "name": "diss_oxygen_fluid", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per kilogram, milligram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of dissolved oxygen in the oil field produced fluids as it contributes to oxgen-corrosion and microbial activity (e.g. Mic).", + "title": "dissolved oxygen in fluids", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "dissolved oxygen in fluids" + ], + "rank": 306, + "is_a": "core field", + "slot_uri": "MIXS:0000438", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "HcrCoresInterface", + "HcrFluidsSwabsInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "ecosystem": { + "name": "ecosystem", + "description": "An ecosystem is a combination of a physical environment (abiotic factors) and all the organisms (biotic factors) that interact with this environment. Ecosystem is in position 1/5 in a GOLD path.", + "comments": [ + "The abiotic factors play a profound role on the type and composition of organisms in a given environment. The GOLD Ecosystem at the top of the five-level classification system is aimed at capturing the broader environment from which an organism or environmental sample is collected. The three broad groups under Ecosystem are Environmental, Host-associated, and Engineered. They represent samples collected from a natural environment or from another organism or from engineered environments like bioreactors respectively." + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "https://gold.jgi.doe.gov/help" + ], + "rank": 9, + "is_a": "gold_path_field", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "Study", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "EcosystemEnum", + "recommended": true + }, + "ecosystem_category": { + "name": "ecosystem_category", + "description": "Ecosystem categories represent divisions within the ecosystem based on specific characteristics of the environment from where an organism or sample is isolated. Ecosystem category is in position 2/5 in a GOLD path.", + "comments": [ + "The Environmental ecosystem (for example) is divided into Air, Aquatic and Terrestrial. Ecosystem categories for Host-associated samples can be individual hosts or phyla and for engineered samples it may be manipulated environments like bioreactors, solid waste etc." + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "https://gold.jgi.doe.gov/help" + ], + "rank": 10, + "is_a": "gold_path_field", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "Study", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "EcosystemCategoryEnum", + "recommended": true + }, + "ecosystem_subtype": { + "name": "ecosystem_subtype", + "description": "Ecosystem subtypes represent further subdivision of Ecosystem types into more distinct subtypes. Ecosystem subtype is in position 4/5 in a GOLD path.", + "comments": [ + "Ecosystem Type Marine (Environmental -> Aquatic -> Marine) is further divided (for example) into Intertidal zone, Coastal, Pelagic, Intertidal zone etc. in the Ecosystem subtype category." + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "https://gold.jgi.doe.gov/help" + ], + "rank": 12, + "is_a": "gold_path_field", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "Study", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "EcosystemSubtypeEnum", + "recommended": true + }, + "ecosystem_type": { + "name": "ecosystem_type", + "description": "Ecosystem types represent things having common characteristics within the Ecosystem Category. These common characteristics based grouping is still broad but specific to the characteristics of a given environment. Ecosystem type is in position 3/5 in a GOLD path.", + "comments": [ + "The Aquatic ecosystem category (for example) may have ecosystem types like Marine or Thermal springs etc. Ecosystem category Air may have Indoor air or Outdoor air as different Ecosystem Types. In the case of Host-associated samples, ecosystem type can represent Respiratory system, Digestive system, Roots etc." + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "https://gold.jgi.doe.gov/help" + ], + "rank": 11, + "is_a": "gold_path_field", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "Study", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "EcosystemTypeEnum", + "recommended": true + }, + "elev": { + "name": "elev", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + } + }, + "description": "Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit.", + "title": "elevation, meters", + "comments": [ + "All elevations must be reported in meters. Provide the numerical portion only.", + "Please use https://www.advancedconverter.com/map-tools/find-altitude-by-coordinates, if needed, to help estimate the elevation based on latitude and longitude coordinates." + ], + "examples": [ + { + "value": "225" + }, + { + "value": "0" + }, + { + "value": "1250" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "elevation" + ], + "rank": 6, + "is_a": "environment field", + "slot_uri": "MIXS:0000093", + "owner": "Biosample", + "domain_of": [ + "FieldResearchSite", + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "float", + "required": true, + "multivalued": false + }, + "env_broad_scale": { + "name": "env_broad_scale", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "The major environment type(s) where the sample was collected. Recommend subclasses of biome [ENVO:00000428]. Multiple terms can be separated by one or more pipes." + }, + "tooltip": { + "tag": "tooltip", + "value": "The biome or major environmental system where the sample or specimen originated. Choose values from subclasses of the 'biome' class [ENVO:00000428] in the Environment Ontology (ENVO). For host-associated or plant-associated samples, use terms from the UBERON or Plant Ontology to describe the broad anatomical or morphological context" + } + }, + "description": "In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO's biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html", + "title": "broad-scale environmental context", + "notes": [ + "range changed to enumeration late in makefile, so this is modified (but \"sample ID\" anyway)" + ], + "examples": [ + { + "value": "oceanic epipelagic zone biome [ENVO:01000033] for annotating a water sample from the photic zone in middle of the Atlantic Ocean" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "broad-scale environmental context" + ], + "rank": 6, + "is_a": "environment field", + "string_serialization": "{termLabel} {[termID]}", + "slot_uri": "MIXS:0000012", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "string", + "required": true, + "multivalued": false, + "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$" + }, + "env_local_scale": { + "name": "env_local_scale", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "Environmental entities having causal influences upon the entity at time of sampling." + }, + "tooltip": { + "tag": "tooltip", + "value": "The specific environmental entities or features near the sample or specimen that significantly influence its characteristics or composition. These entities are typically smaller in scale than the broad environmental context. Values for this field should be countable, material nouns and must be chosen from subclasses of BFO:0000040 (material entity) that appear in the Environment Ontology (ENVO). For host-associated or plant-associated samples, use terms from the UBERON or Plant Ontology to describe specific anatomical structures or plant parts." + } + }, + "description": "Report the entity or entities which are in the sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. We recommend using EnvO terms which are of smaller spatial grain than your entry for env_broad_scale. Terms, such as anatomical sites, from other OBO Library ontologies which interoperate with EnvO (e.g. UBERON) are accepted in this field. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS.", + "title": "local environmental context", + "notes": [ + "range changed to enumeration late in makefile, so this is modified (but \"sample ID\" anyway)" + ], + "examples": [ + { + "value": "canopy [ENVO:00000047]" + }, + { + "value": "herb and fern layer [ENVO:01000337]" + }, + { + "value": "litter layer [ENVO:01000338]" + }, + { + "value": "understory [01000335]" + }, + { + "value": "shrub layer [ENVO:01000336]" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "local environmental context" + ], + "rank": 7, + "is_a": "environment field", + "string_serialization": "{termLabel} {[termID]}", + "slot_uri": "MIXS:0000013", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "string", + "required": true, + "multivalued": false, + "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$" + }, + "env_medium": { + "name": "env_medium", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "The material displaced by the entity at time of sampling. Recommend subclasses of environmental material [ENVO:00010483]." + }, + "tooltip": { + "tag": "tooltip", + "value": "The predominant environmental material or substrate that directly surrounds or hosts the sample or specimen at the time of sampling. Choose values from subclasses of the 'environmental material' class [ENVO:00010483] in the Environment Ontology (ENVO). Values for this field should be measurable or mass material nouns, representing continuous environmental materials. For host-associated or plant-associated samples, use terms from the UBERON or Plant Ontology to indicate a tissue, organ, or plant structure" + } + }, + "description": "Report the environmental material(s) immediately surrounding the sample or specimen at the time of sampling. We recommend using subclasses of 'environmental material' (http://purl.obolibrary.org/obo/ENVO_00010483). EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS . Terms from other OBO ontologies are permissible as long as they reference mass/volume nouns (e.g. air, water, blood) and not discrete, countable entities (e.g. a tree, a leaf, a table top).", + "title": "environmental medium", + "notes": [ + "range changed to enumeration late in makefile, so this is modified (but \"sample ID\" anyway)" + ], + "examples": [ + { + "value": "soil [ENVO:00001998]" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "environmental medium" + ], + "rank": 8, + "is_a": "environment field", + "string_serialization": "{termLabel} {[termID]}", + "slot_uri": "MIXS:0000014", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "string", + "required": true, + "multivalued": false, + "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$" + }, + "ethylbenzene": { + "name": "ethylbenzene", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milligram per liter, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of ethylbenzene in the sample", + "title": "ethylbenzene", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "ethylbenzene" + ], + "rank": 309, + "is_a": "core field", + "slot_uri": "MIXS:0000155", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "HcrCoresInterface", + "HcrFluidsSwabsInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "experimental_factor": { + "name": "experimental_factor", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "text or EFO and/or OBI" + } + }, + "description": "Experimental factors are essentially the variable aspects of an experiment design which can be used to describe an experiment, or set of experiments, in an increasingly detailed manner. This field accepts ontology terms from Experimental Factor Ontology (EFO) and/or Ontology for Biomedical Investigations (OBI). For a browser of EFO (v 2.95) terms, please see http://purl.bioontology.org/ontology/EFO; for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI", + "title": "experimental factor", + "examples": [ + { + "value": "time series design [EFO:EFO_0001779]" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "experimental factor" + ], + "rank": 12, + "is_a": "investigation field", + "string_serialization": "{termLabel} {[termID]}|{text}", + "slot_uri": "MIXS:0000008", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false + }, + "field": { + "name": "field", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "name" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Name of the hydrocarbon field (e.g. Albacora)", + "title": "field name", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "field name" + ], + "rank": 310, + "is_a": "core field", + "string_serialization": "{text}", + "slot_uri": "MIXS:0000291", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "HcrCoresInterface", + "HcrFluidsSwabsInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "geo_loc_name": { + "name": "geo_loc_name", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "country or sea name (INSDC or GAZ): region(GAZ), specific location name" + } + }, + "description": "The geographical origin of the sample as defined by the country or sea name followed by specific region name.", + "title": "geographic location (country and/or sea,region)", + "examples": [ + { + "value": "USA: Maryland, Bethesda" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "geographic location (country and/or sea,region)" + ], + "rank": 4, + "is_a": "environment field", + "string_serialization": "{text}: {text}, {text}", + "slot_uri": "MIXS:0000010", + "owner": "Biosample", + "domain_of": [ + "FieldResearchSite", + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "required": true, + "multivalued": false, + "pattern": "^[^:, ][^:]*: [^:, ][^,]*, [^:, ].*$" + }, + "hc_produced": { + "name": "hc_produced", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Main hydrocarbon type produced from resource (i.e. Oil, gas, condensate, etc). If \"other\" is specified, please propose entry in \"additional info\" field", + "title": "hydrocarbon type produced", + "examples": [ + { + "value": "Gas" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "hydrocarbon type produced" + ], + "rank": 313, + "is_a": "core field", + "slot_uri": "MIXS:0000989", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "HcrCoresInterface", + "HcrFluidsSwabsInterface" + ], + "slot_group": "mixs_core_section", + "range": "hc_produced_enum", + "multivalued": false + }, + "hcr": { + "name": "hcr", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Main Hydrocarbon Resource type. The term \"Hydrocarbon Resource\" HCR defined as a natural environmental feature containing large amounts of hydrocarbons at high concentrations potentially suitable for commercial exploitation. This term should not be confused with the Hydrocarbon Occurrence term which also includes hydrocarbon-rich environments with currently limited commercial interest such as seeps, outcrops, gas hydrates etc. If \"other\" is specified, please propose entry in \"additional info\" field", + "title": "hydrocarbon resource type", + "examples": [ + { + "value": "Oil Sand" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "hydrocarbon resource type" + ], + "rank": 314, + "is_a": "core field", + "slot_uri": "MIXS:0000988", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "HcrCoresInterface", + "HcrFluidsSwabsInterface" + ], + "slot_group": "mixs_core_section", + "range": "hcr_enum", + "multivalued": false + }, + "hcr_fw_salinity": { + "name": "hcr_fw_salinity", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milligram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Original formation water salinity (prior to secondary recovery e.g. Waterflooding) expressed as TDS", + "title": "formation water salinity", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "formation water salinity" + ], + "rank": 315, + "is_a": "core field", + "slot_uri": "MIXS:0000406", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "HcrCoresInterface", + "HcrFluidsSwabsInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "hcr_geol_age": { + "name": "hcr_geol_age", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Geological age of hydrocarbon resource (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). If \"other\" is specified, please propose entry in \"additional info\" field", + "title": "hydrocarbon resource geological age", + "examples": [ + { + "value": "Silurian" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "hydrocarbon resource geological age" + ], + "rank": 316, + "is_a": "core field", + "slot_uri": "MIXS:0000993", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "HcrCoresInterface", + "HcrFluidsSwabsInterface" + ], + "slot_group": "mixs_core_section", + "range": "hcr_geol_age_enum", + "multivalued": false + }, + "hcr_pressure": { + "name": "hcr_pressure", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value range" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "atmosphere, kilopascal" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Original pressure of the hydrocarbon resource", + "title": "hydrocarbon resource original pressure", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "hydrocarbon resource original pressure" + ], + "rank": 317, + "is_a": "core field", + "string_serialization": "{float} - {float} {unit}", + "slot_uri": "MIXS:0000395", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "HcrCoresInterface", + "HcrFluidsSwabsInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "hcr_temp": { + "name": "hcr_temp", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value range" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "degree Celsius" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Original temperature of the hydrocarbon resource", + "title": "hydrocarbon resource original temperature", + "examples": [ + { + "value": "150-295 degree Celsius" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "hydrocarbon resource original temperature" + ], + "rank": 318, + "is_a": "core field", + "string_serialization": "{float} - {float} {unit}", + "slot_uri": "MIXS:0000393", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "HcrCoresInterface", + "HcrFluidsSwabsInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "iw_bt_date_well": { + "name": "iw_bt_date_well", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "timestamp" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Injection water breakthrough date per well following a secondary and/or tertiary recovery", + "title": "injection water breakthrough date of specific well", + "examples": [ + { + "value": "2018-05-11" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "injection water breakthrough date of specific well" + ], + "rank": 334, + "is_a": "core field", + "slot_uri": "MIXS:0001010", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "HcrFluidsSwabsInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "iwf": { + "name": "iwf", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "percent" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Proportion of the produced fluids derived from injected water at the time of sampling. (e.g. 87%)", + "title": "injection water fraction", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "injection water fraction" + ], + "rank": 335, + "is_a": "core field", + "slot_uri": "MIXS:0000455", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "HcrFluidsSwabsInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "lat_lon": { + "name": "lat_lon", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "decimal degrees, limit to 8 decimal points" + } + }, + "description": "The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system", + "title": "geographic location (latitude and longitude)", + "notes": [ + "This is currently a required field but it's not clear if this should be required for human hosts" + ], + "examples": [ + { + "value": "50.586825 6.408977" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "geographic location (latitude and longitude)" + ], + "rank": 5, + "is_a": "environment field", + "string_serialization": "{lat lon}", + "slot_uri": "MIXS:0000009", + "owner": "Biosample", + "domain_of": [ + "FieldResearchSite", + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "required": true, + "multivalued": false, + "pattern": "^[-+]?([1-8]?\\d(\\.\\d{1,8})?|90(\\.0{1,8})?)\\s[-+]?(180(\\.0{1,8})?|((1[0-7]\\d)|([1-9]?\\d))(\\.\\d{1,8})?)$" + }, + "lithology": { + "name": "lithology", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Hydrocarbon resource main lithology (Additional information: http://petrowiki.org/Lithology_and_rock_type_determination). If \"other\" is specified, please propose entry in \"additional info\" field", + "title": "lithology", + "examples": [ + { + "value": "Volcanic" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "lithology" + ], + "rank": 336, + "is_a": "core field", + "slot_uri": "MIXS:0000990", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "HcrCoresInterface", + "HcrFluidsSwabsInterface" + ], + "slot_group": "mixs_core_section", + "range": "lithology_enum", + "multivalued": false + }, + "magnesium": { + "name": "magnesium", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "mole per liter, milligram per liter, parts per million, micromole per kilogram" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of magnesium in the sample", + "title": "magnesium", + "examples": [ + { + "value": "52.8 micromole per kilogram" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "magnesium" + ], + "rank": 21, + "is_a": "core field", + "slot_uri": "MIXS:0000431", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "misc_param": { + "name": "misc_param", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "parameter name;measurement value" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Any other measurement performed or parameter collected, that is not listed here", + "title": "miscellaneous parameter", + "examples": [ + { + "value": "Bicarbonate ion concentration;2075 micromole per kilogram" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "miscellaneous parameter" + ], + "rank": 23, + "is_a": "core field", + "string_serialization": "{text};{float} {unit}", + "slot_uri": "MIXS:0000752", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false, + "pattern": "^([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+\\|)*([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+)$" + }, + "nitrate": { + "name": "nitrate", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per liter, milligram per liter, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of nitrate in the sample", + "title": "nitrate", + "examples": [ + { + "value": "65 micromole per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "nitrate" + ], + "rank": 26, + "is_a": "core field", + "slot_uri": "MIXS:0000425", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "nitrite": { + "name": "nitrite", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per liter, milligram per liter, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of nitrite in the sample", + "title": "nitrite", + "examples": [ + { + "value": "0.5 micromole per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "nitrite" + ], + "rank": 27, + "is_a": "core field", + "slot_uri": "MIXS:0000426", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "org_count_qpcr_info": { + "name": "org_count_qpcr_info", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "gene name;FWD:forward primer sequence;REV:reverse primer sequence;initial denaturation:degrees_minutes;denaturation:degrees_minutes;annealing:degrees_minutes;elongation:degrees_minutes;final elongation:degrees_minutes; total cycles" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "number of cells per gram (or ml or cm^2)" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "If qpcr was used for the cell count, the target gene name, the primer sequence and the cycling conditions should also be provided. (Example: 16S rrna; FWD:ACGTAGCTATGACGT REV:GTGCTAGTCGAGTAC; initial denaturation:90C_5min; denaturation:90C_2min; annealing:52C_30 sec; elongation:72C_30 sec; 90 C for 1 min; final elongation:72C_5min; 30 cycles)", + "title": "organism count qPCR information", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "organism count qPCR information" + ], + "rank": 337, + "is_a": "core field", + "string_serialization": "{text};FWD:{dna};REV:{dna};initial denaturation:degrees_minutes;denaturation:degrees_minutes;annealing:degrees_minutes;elongation:degrees_minutes;final elongation:degrees_minutes; total cycles", + "slot_uri": "MIXS:0000099", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "HcrCoresInterface", + "HcrFluidsSwabsInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "organism_count": { + "name": "organism_count", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "organism name;measurement value;enumeration" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "number of cells per cubic meter, number of cells per milliliter, number of cells per cubic centimeter" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr)", + "title": "organism count", + "examples": [ + { + "value": "total prokaryotes;3.5e7 cells per milliliter;qPCR" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "organism count" + ], + "rank": 30, + "is_a": "core field", + "slot_uri": "MIXS:0000103", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^([-+]?[0-9]*\\.?[0-9]+ +\\S.*\\|)*([-+]?[0-9]*\\.?[0-9]+ +\\S.*)$" + }, + "oxy_stat_samp": { + "name": "oxy_stat_samp", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Oxygenation status of sample", + "title": "oxygenation status of sample", + "examples": [ + { + "value": "aerobic" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "oxygenation status of sample" + ], + "rank": 25, + "is_a": "core field", + "slot_uri": "MIXS:0000753", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_section", + "range": "OxyStatSampEnum", + "multivalued": false + }, + "ph": { + "name": "ph", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "pH measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid", + "title": "pH", + "notes": [ + "Use modified term" + ], + "examples": [ + { + "value": "7.2" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "pH" + ], + "rank": 27, + "is_a": "core field", + "string_serialization": "{float}", + "slot_uri": "MIXS:0001001", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "MiscEnvsInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "float", + "recommended": true, + "multivalued": false, + "minimum_value": 0, + "maximum_value": 14 + }, + "ph_meth": { + "name": "ph_meth", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "PMID,DOI or url" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Reference or method used in determining ph", + "title": "pH method", + "comments": [ + "This can include a link to the instrument used or a citation for the method." + ], + "examples": [ + { + "value": "https://www.southernlabware.com/pc9500-benchtop-ph-conductivity-meter-kit-ph-accuracy-2000mv-ph-range-2-000-to-20-000.html?gclid=Cj0KCQiAwJWdBhCYARIsAJc4idCO5vtvbVMf545fcvdROFqa6zjzNSoywNx6K4k9Coo9cCc2pybtvGsaAiR0EALw_wcB" + }, + { + "value": "https://doi.org/10.2136/sssabookser5.3.c16" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "pH method" + ], + "rank": 41, + "is_a": "core field", + "string_serialization": "{PMID}|{DOI}|{URL}", + "slot_uri": "MIXS:0001106", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "MiscEnvsInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false + }, + "potassium": { + "name": "potassium", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milligram per liter, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of potassium in the sample", + "title": "potassium", + "examples": [ + { + "value": "463 milligram per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "potassium" + ], + "rank": 38, + "is_a": "core field", + "slot_uri": "MIXS:0000430", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "pour_point": { + "name": "pour_point", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "degree Celsius" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Temperature at which a liquid becomes semi solid and loses its flow characteristics. In crude oil a high¬†pour point¬†is generally associated with a high paraffin content, typically found in crude deriving from a larger proportion of plant material. (soure: https://en.wikipedia.org/wiki/pour_point)", + "title": "pour point", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "pour point" + ], + "rank": 341, + "is_a": "core field", + "slot_uri": "MIXS:0000127", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "HcrCoresInterface", + "HcrFluidsSwabsInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "pressure": { + "name": "pressure", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "atmosphere" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Pressure to which the sample is subject to, in atmospheres", + "title": "pressure", + "examples": [ + { + "value": "50 atmosphere" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "pressure" + ], + "rank": 39, + "is_a": "core field", + "slot_uri": "MIXS:0000412", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "prod_rate": { + "name": "prod_rate", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "cubic meter per day" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Oil and/or gas production rates per well (e.g. 524 m3 / day)", + "title": "production rate", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "production rate" + ], + "rank": 344, + "is_a": "core field", + "slot_uri": "MIXS:0000452", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "HcrFluidsSwabsInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "prod_start_date": { + "name": "prod_start_date", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "timestamp" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Date of field's first production", + "title": "production start date", + "examples": [ + { + "value": "2018-05-11" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "production start date" + ], + "rank": 345, + "is_a": "core field", + "slot_uri": "MIXS:0001008", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "HcrFluidsSwabsInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "reservoir": { + "name": "reservoir", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "name" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Name of the reservoir (e.g. Carapebus)", + "title": "reservoir name", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "reservoir name" + ], + "rank": 347, + "is_a": "core field", + "string_serialization": "{text}", + "slot_uri": "MIXS:0000303", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "HcrCoresInterface", + "HcrFluidsSwabsInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "resins_pc": { + "name": "resins_pc", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "name;measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "percent" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene)", + "title": "resins wt%", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "resins wt%" + ], + "rank": 348, + "is_a": "core field", + "string_serialization": "{text};{float} {unit}", + "slot_uri": "MIXS:0000134", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "HcrCoresInterface", + "HcrFluidsSwabsInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[^;\\t\\r\\x0A\\|]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A\\|]+$" + }, + "salinity": { + "name": "salinity", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "practical salinity unit, percentage" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The total concentration of all dissolved salts in a liquid or solid sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater.", + "title": "salinity", + "examples": [ + { + "value": "25 practical salinity unit" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "salinity" + ], + "rank": 54, + "is_a": "core field", + "slot_uri": "MIXS:0000183", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "samp_collec_device": { + "name": "samp_collec_device", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "device name" + } + }, + "description": "The device used to collect an environmental sample. This field accepts terms listed under environmental sampling device (http://purl.obolibrary.org/obo/ENVO). This field also accepts terms listed under specimen collection device (http://purl.obolibrary.org/obo/GENEPIO_0002094).", + "title": "sample collection device", + "comments": [ + "Report dimensions and details when applicable" + ], + "examples": [ + { + "value": "swab, biopsy, niskin bottle, push core, drag swab [GENEPIO:0002713]" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sample collection device" + ], + "rank": 14, + "is_a": "nucleic acid sequence source field", + "string_serialization": "{termLabel} {[termID]}|{text}", + "slot_uri": "MIXS:0000002", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "recommended": true, + "multivalued": false + }, + "samp_collec_method": { + "name": "samp_collec_method", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "PMID,DOI,url , or text" + } + }, + "description": "The method employed for collecting the sample.", + "title": "sample collection method", + "comments": [ + "This can be a citation or description" + ], + "examples": [ + { + "value": "swabbing" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sample collection method" + ], + "rank": 15, + "is_a": "nucleic acid sequence source field", + "string_serialization": "{PMID}|{DOI}|{URL}|{text}", + "slot_uri": "MIXS:0001225", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "multivalued": false + }, + "samp_collect_point": { + "name": "samp_collect_point", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Sampling point on the asset were sample was collected (e.g. Wellhead, storage tank, separator, etc). If \"other\" is specified, please propose entry in \"additional info\" field", + "title": "sample collection point", + "examples": [ + { + "value": "well" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sample collection point" + ], + "rank": 349, + "is_a": "core field", + "slot_uri": "MIXS:0001015", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "HcrFluidsSwabsInterface" + ], + "slot_group": "mixs_core_section", + "range": "samp_collect_point_enum", + "multivalued": false + }, + "samp_loc_corr_rate": { + "name": "samp_loc_corr_rate", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value range" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "millimeter per year" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Metal corrosion rate is the speed of metal deterioration due to environmental conditions. As environmental conditions change corrosion rates change accordingly. Therefore, long term corrosion rates are generally more informative than short term rates and for that reason they are preferred during reporting. In the case of suspected MIC, corrosion rate measurements at the time of sampling might provide insights into the involvement of certain microbial community members in MIC as well as potential microbial interplays", + "title": "corrosion rate at sample location", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "corrosion rate at sample location" + ], + "rank": 350, + "is_a": "core field", + "string_serialization": "{float} - {float} {unit}", + "slot_uri": "MIXS:0000136", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "HcrFluidsSwabsInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "samp_mat_process": { + "name": "samp_mat_process", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "text" + } + }, + "description": "A brief description of any processing applied to the sample during or after retrieving the sample from environment, or a link to the relevant protocol(s) performed.", + "title": "sample material processing", + "examples": [ + { + "value": "filtering of seawater" + }, + { + "value": "storing samples in ethanol" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sample material processing" + ], + "rank": 12, + "is_a": "nucleic acid sequence source field", + "string_serialization": "{text}", + "slot_uri": "MIXS:0000016", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "multivalued": false + }, + "samp_preserv": { + "name": "samp_preserv", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "name;measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milliliter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Preservative added to the sample (e.g. Rnalater, alcohol, formaldehyde, etc.). Where appropriate include volume added (e.g. Rnalater; 2 ml)", + "title": "preservative added to sample", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "preservative added to sample" + ], + "rank": 352, + "is_a": "core field", + "string_serialization": "{text};{float} {unit}", + "slot_uri": "MIXS:0000463", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "HcrFluidsSwabsInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[^;\\t\\r\\x0A\\|]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A\\|]+$" + }, + "samp_size": { + "name": "samp_size", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "millliter, gram, milligram, liter" + } + }, + "description": "The total amount or size (volume (ml), mass (g) or area (m2) ) of sample collected.", + "title": "amount or size of sample collected", + "comments": [ + "This refers to the TOTAL amount of sample collected from the experiment. NOT the amount sent to each institution or collected for a specific analysis." + ], + "examples": [ + { + "value": "5 grams" + }, + { + "value": "10 mL" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "amount or size of sample collected" + ], + "rank": 18, + "is_a": "nucleic acid sequence source field", + "string_serialization": "{float} {unit}", + "slot_uri": "MIXS:0000001", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? \\S+$" + }, + "samp_store_dur": { + "name": "samp_store_dur", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "duration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Duration for which the sample was stored", + "title": "sample storage duration", + "examples": [ + { + "value": "P1Y6M" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sample storage duration" + ], + "rank": 353, + "is_a": "core field", + "string_serialization": "{duration}", + "slot_uri": "MIXS:0000116", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "samp_store_loc": { + "name": "samp_store_loc", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "location name" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Location at which sample was stored, usually name of a specific freezer/room", + "title": "sample storage location", + "examples": [ + { + "value": "Freezer no:5" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sample storage location" + ], + "rank": 41, + "is_a": "core field", + "string_serialization": "{text}", + "slot_uri": "MIXS:0000755", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "samp_store_temp": { + "name": "samp_store_temp", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "degree Celsius" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Temperature at which the sample was stored (degrees are assumed)", + "title": "sample storage temperature", + "examples": [ + { + "value": "-80 Celsius" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sample storage temperature" + ], + "rank": 7, + "is_a": "core field", + "slot_uri": "MIXS:0000110", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "required": true, + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "samp_subtype": { + "name": "samp_subtype", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Name of sample sub-type. For example if \"sample type\" is \"Produced Water\" then subtype could be \"Oil Phase\" or \"Water Phase\". If \"other\" is specified, please propose entry in \"additional info\" field", + "title": "sample subtype", + "examples": [ + { + "value": "biofilm" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sample subtype" + ], + "rank": 354, + "is_a": "core field", + "slot_uri": "MIXS:0000999", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "HcrCoresInterface", + "HcrFluidsSwabsInterface" + ], + "slot_group": "mixs_core_section", + "range": "samp_subtype_enum", + "multivalued": false + }, + "samp_transport_cond": { + "name": "samp_transport_cond", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value;measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "days;degree Celsius" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Sample transport duration (in days or hrs) and temperature the sample was exposed to (e.g. 5.5 days; 20 ¬∞C)", + "title": "sample transport conditions", + "examples": [ + { + "value": "5 days;-20 degree Celsius" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sample transport conditions" + ], + "rank": 355, + "is_a": "core field", + "string_serialization": "{float} {unit};{float} {unit}", + "slot_uri": "MIXS:0000410", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "HcrCoresInterface", + "HcrFluidsSwabsInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "samp_type": { + "name": "samp_type", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "GENEPIO:0001246" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The type of material from which the sample was obtained. For the Hydrocarbon package, samples include types like core, rock trimmings, drill cuttings, piping section, coupon, pigging debris, solid deposit, produced fluid, produced water, injected water, swabs, etc. For the Food Package, samples are usually categorized as food, body products or tissues, or environmental material. This field accepts terms listed under environmental specimen (http://purl.obolibrary.org/obo/GENEPIO_0001246).", + "title": "sample type", + "examples": [ + { + "value": "built environment sample [GENEPIO:0001248]" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sample type" + ], + "rank": 357, + "is_a": "core field", + "string_serialization": "{termLabel} {[termID]}", + "slot_uri": "MIXS:0000998", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "HcrCoresInterface", + "HcrFluidsSwabsInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$" + }, + "samp_well_name": { + "name": "samp_well_name", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "name" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Name of the well (e.g. BXA1123) where sample was taken", + "title": "sample well name", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sample well name" + ], + "rank": 358, + "is_a": "core field", + "string_serialization": "{text}", + "slot_uri": "MIXS:0000296", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "HcrCoresInterface", + "HcrFluidsSwabsInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "sample_link": { + "name": "sample_link", + "description": "A unique identifier to assign parent-child, subsample, or sibling samples. This is relevant when a sample or other material was used to generate the new sample.", + "title": "sample linkage", + "notes": [ + "also tempted to include SampIdNewTermsMixin but if len(slot_usage.keys()) > 1 and \"placeholder\" in slot_usage.keys():AttributeError: 'list' object has no attribute 'keys'" + ], + "comments": [ + "This field allows multiple entries separated by ; (Examples: Soil collected from the field will link with the soil used in an incubation. The soil a plant was grown in links to the plant sample. An original culture sample was transferred to a new vial and generated a new sample)" + ], + "examples": [ + { + "value": "IGSN:DSJ0284" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "rank": 5, + "string_serialization": "{text}:{text}", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface", + "SampIdNewTermsMixin" + ], + "slot_group": "sample_id_section", + "range": "string", + "recommended": true, + "multivalued": false, + "pattern": "[^\\:\\n\\r]+\\:[^\\:\\n\\r]+" + }, + "saturates_pc": { + "name": "saturates_pc", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "name;measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "percent" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene)", + "title": "saturates wt%", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "saturates wt%" + ], + "rank": 359, + "is_a": "core field", + "string_serialization": "{text};{float} {unit}", + "slot_uri": "MIXS:0000131", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "HcrCoresInterface", + "HcrFluidsSwabsInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[^;\\t\\r\\x0A\\|]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A\\|]+$" + }, + "size_frac": { + "name": "size_frac", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "filter size value range" + } + }, + "description": "Filtering pore size used in sample preparation", + "title": "size fraction selected", + "examples": [ + { + "value": "0-0.22 micrometer" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "size fraction selected" + ], + "rank": 285, + "is_a": "nucleic acid sequence source field", + "string_serialization": "{float}-{float} {unit}", + "slot_uri": "MIXS:0000017", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "sodium": { + "name": "sodium", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milligram per liter, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Sodium concentration in the sample", + "title": "sodium", + "examples": [ + { + "value": "10.5 milligram per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sodium" + ], + "rank": 363, + "is_a": "core field", + "slot_uri": "MIXS:0000428", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "specific_ecosystem": { + "name": "specific_ecosystem", + "description": "Specific ecosystems represent specific features of the environment like aphotic zone in an ocean or gastric mucosa within a host digestive system. 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+ }, + "description": "A unique identifier of a well or wellbore. This is part of the Global Framework for Well Identification initiative which is compiled by the Professional Petroleum Data Management Association (PPDM) in an effort to improve well identification systems. (Supporting information: https://ppdm.org/ and http://dl.ppdm.org/dl/690)", + "title": "well identification number", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "well identification number" + ], + "rank": 388, + "is_a": "core field", + "string_serialization": "{text}", + "slot_uri": "MIXS:0000297", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "HcrCoresInterface", + "HcrFluidsSwabsInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "xylene": { + "name": "xylene", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milligram per liter, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of xylene in the sample", + "title": "xylene", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "xylene" + ], + "rank": 389, + "is_a": "core field", + "slot_uri": "MIXS:0000156", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "HcrCoresInterface", + "HcrFluidsSwabsInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "horizon_meth": { + "name": "horizon_meth", + "title": "horizon method" + } + }, + "attributes": { + "add_recov_method": { + "name": "add_recov_method", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration;timestamp" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Additional (i.e. Secondary, tertiary, etc.) recovery methods deployed for increase of hydrocarbon recovery from resource and start date for each one of them. If \"other\" is specified, please propose entry in \"additional info\" field", + "title": "secondary and tertiary recovery methods and start date", + "examples": [ + { + "value": "Polymer Addition;2018-06-21T14:30Z" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "secondary and tertiary recovery methods and start date" + ], + "rank": 289, + "is_a": "core field", + "slot_uri": "MIXS:0001009", + "alias": "add_recov_method", + "owner": "HcrFluidsSwabsInterface", + "domain_of": [ + "Biosample", + "HcrFluidsSwabsInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "additional_info": { + "name": "additional_info", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "text" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Information that doesn't fit anywhere else. Can also be used to propose new entries for fields with controlled vocabulary", + "title": "additional info", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "additional info" + ], + "rank": 290, + "is_a": "core field", + "string_serialization": "{text}", + "slot_uri": "MIXS:0000300", + "alias": "additional_info", + "owner": "HcrFluidsSwabsInterface", + "domain_of": [ + "Biosample", + "HcrCoresInterface", + "HcrFluidsSwabsInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "alkalinity": { + "name": "alkalinity", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milliequivalent per liter, milligram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate", + "title": "alkalinity", + "examples": [ + { + "value": "50 milligram per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "alkalinity" + ], + "rank": 1, + "is_a": "core field", + "slot_uri": "MIXS:0000421", + "alias": "alkalinity", + "owner": "HcrFluidsSwabsInterface", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "alkalinity_method": { + "name": "alkalinity_method", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "description of method" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Method used for alkalinity measurement", + "title": "alkalinity method", + "examples": [ + { + "value": "titration" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "alkalinity method" + ], + "rank": 218, + "is_a": "core field", + "string_serialization": "{text}", + "slot_uri": "MIXS:0000298", + "alias": "alkalinity_method", + "owner": "HcrFluidsSwabsInterface", + "domain_of": [ + "Biosample", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "ammonium": { + "name": "ammonium", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per liter, milligram per liter, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of ammonium in the sample", + "title": "ammonium", + "examples": [ + { + "value": "1.5 milligram per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "ammonium" + ], + "rank": 4, + "is_a": "core field", + "slot_uri": "MIXS:0000427", + "alias": "ammonium", + "owner": "HcrFluidsSwabsInterface", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "api": { + "name": "api", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "degrees API" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "API gravity is a measure of how heavy or light a petroleum liquid is compared to water (source: https://en.wikipedia.org/wiki/API_gravity) (e.g. 31.1¬∞ API)", + "title": "API gravity", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "API gravity" + ], + "rank": 291, + "is_a": "core field", + "slot_uri": "MIXS:0000157", + "alias": "api", + "owner": "HcrFluidsSwabsInterface", + "domain_of": [ + "Biosample", + "HcrCoresInterface", + "HcrFluidsSwabsInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "aromatics_pc": { + "name": "aromatics_pc", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "name;measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "percent" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene)", + "title": "aromatics wt%", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "aromatics wt%" + ], + "rank": 292, + "is_a": "core field", + "string_serialization": "{text};{float} {unit}", + "slot_uri": "MIXS:0000133", + "alias": "aromatics_pc", + "owner": "HcrFluidsSwabsInterface", + "domain_of": [ + "Biosample", + "HcrCoresInterface", + "HcrFluidsSwabsInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[^;\\t\\r\\x0A\\|]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A\\|]+$" + }, + "asphaltenes_pc": { + "name": "asphaltenes_pc", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "name;measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "percent" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene)", + "title": "asphaltenes wt%", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "asphaltenes wt%" + ], + "rank": 293, + "is_a": "core field", + "string_serialization": "{text};{float} {unit}", + "slot_uri": "MIXS:0000135", + "alias": "asphaltenes_pc", + "owner": "HcrFluidsSwabsInterface", + "domain_of": [ + "Biosample", + "HcrCoresInterface", + "HcrFluidsSwabsInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[^;\\t\\r\\x0A\\|]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A\\|]+$" + }, + "basin": { + "name": "basin", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "name" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Name of the basin (e.g. Campos)", + "title": "basin name", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "basin name" + ], + "rank": 294, + "is_a": "core field", + "string_serialization": "{text}", + "slot_uri": "MIXS:0000290", + "alias": "basin", + "owner": "HcrFluidsSwabsInterface", + "domain_of": [ + "Biosample", + "HcrCoresInterface", + "HcrFluidsSwabsInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "benzene": { + "name": "benzene", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milligram per liter, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of benzene in the sample", + "title": "benzene", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "benzene" + ], + "rank": 295, + "is_a": "core field", + "slot_uri": "MIXS:0000153", + "alias": "benzene", + "owner": "HcrFluidsSwabsInterface", + "domain_of": [ + "Biosample", + "HcrCoresInterface", + "HcrFluidsSwabsInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "biocide": { + "name": "biocide", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "name;name;timestamp" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "List of biocides (commercial name of product and supplier) and date of administration", + "title": "biocide administration", + "examples": [ + { + "value": "ALPHA 1427;Baker Hughes;2008-01-23" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "biocide administration" + ], + "rank": 297, + "is_a": "core field", + "string_serialization": "{text};{text};{timestamp}", + "slot_uri": "MIXS:0001011", + "alias": "biocide", + "owner": "HcrFluidsSwabsInterface", + "domain_of": [ + "Biosample", + "HcrFluidsSwabsInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "biocide_admin_method": { + "name": "biocide_admin_method", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value;frequency;duration;duration" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milligram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Method of biocide administration (dose, frequency, duration, time elapsed between last biociding and sampling) (e.g. 150 mg/l; weekly; 4 hr; 3 days)", + "title": "biocide administration method", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "biocide administration method" + ], + "rank": 298, + "is_a": "core field", + "string_serialization": "{float} {unit};{Rn/start_time/end_time/duration};{duration}", + "slot_uri": "MIXS:0000456", + "alias": "biocide_admin_method", + "owner": "HcrFluidsSwabsInterface", + "domain_of": [ + "Biosample", + "HcrFluidsSwabsInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "calcium": { + "name": "calcium", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milligram per liter, micromole per liter, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of calcium in the sample", + "title": "calcium", + "examples": [ + { + "value": "0.2 micromole per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "calcium" + ], + "rank": 9, + "is_a": "core field", + "slot_uri": "MIXS:0000432", + "alias": "calcium", + "owner": "HcrFluidsSwabsInterface", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "chem_administration": { + "name": "chem_administration", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "CHEBI;timestamp" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi", + "title": "chemical administration", + "examples": [ + { + "value": "agar [CHEBI:2509];2018-05-11|agar [CHEBI:2509];2018-05-22" + }, + { + "value": "agar [CHEBI:2509];2018-05" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "chemical administration" + ], + "rank": 17, + "is_a": "core field", + "string_serialization": "{termLabel} {[termID]};{timestamp}", + "slot_uri": "MIXS:0000751", + "alias": "chem_administration", + "owner": "HcrFluidsSwabsInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "recommended": true, + "multivalued": false, + "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\];([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$" + }, + "chem_treat_method": { + "name": "chem_treat_method", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value;frequency;duration;duration" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milligram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Method of chemical administration(dose, frequency, duration, time elapsed between administration and sampling) (e.g. 50 mg/l; twice a week; 1 hr; 0 days)", + "title": "chemical treatment method", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "chemical treatment method" + ], + "rank": 302, + "is_a": "core field", + "string_serialization": "{float} {unit};{Rn/start_time/end_time/duration};{duration};{duration}", + "slot_uri": "MIXS:0000457", + "alias": "chem_treat_method", + "owner": "HcrFluidsSwabsInterface", + "domain_of": [ + "Biosample", + "HcrFluidsSwabsInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "chem_treatment": { + "name": "chem_treatment", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "name;name;timestamp" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "List of chemical compounds administered upstream the sampling location where sampling occurred (e.g. Glycols, H2S scavenger, corrosion and scale inhibitors, demulsifiers, and other production chemicals etc.). The commercial name of the product and name of the supplier should be provided. The date of administration should also be included", + "title": "chemical treatment", + "examples": [ + { + "value": "ACCENT 1125;DOW;2010-11-17" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "chemical treatment" + ], + "rank": 303, + "is_a": "core field", + "string_serialization": "{text};{text};{timestamp}", + "slot_uri": "MIXS:0001012", + "alias": "chem_treatment", + "owner": "HcrFluidsSwabsInterface", + "domain_of": [ + "Biosample", + "HcrFluidsSwabsInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "chloride": { + "name": "chloride", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milligram per liter, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of chloride in the sample", + "title": "chloride", + "examples": [ + { + "value": "5000 milligram per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "chloride" + ], + "rank": 10, + "is_a": "core field", + "slot_uri": "MIXS:0000429", + "alias": "chloride", + "owner": "HcrFluidsSwabsInterface", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "collection_date": { + "name": "collection_date", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "date and time" + } + }, + "description": "The date of sampling", + "title": "collection date", + "notes": [ + "MIxS collection_date accepts (truncated) ISO8601. DH taking arb prec date only", + "Use modified term (amended definition)" + ], + "examples": [ + { + "value": "2021-04-15" + }, + { + "value": "2021-04" + }, + { + "value": "2021" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "collection date" + ], + "rank": 3, + "is_a": "environment field", + "string_serialization": "{date, arbitrary precision}", + "slot_uri": "MIXS:0000011", + "alias": "collection_date", + "owner": "HcrFluidsSwabsInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "required": true, + "multivalued": false, + "pattern": "^[12]\\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\\d|3[01]))?)?$" + }, + "density": { + "name": "density", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "gram per cubic meter, gram per cubic centimeter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Density of the sample, which is its mass per unit volume (aka volumetric mass density)", + "title": "density", + "examples": [ + { + "value": "1000 kilogram per cubic meter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "density" + ], + "rank": 12, + "is_a": "core field", + "slot_uri": "MIXS:0000435", + "alias": "density", + "owner": "HcrFluidsSwabsInterface", + "domain_of": [ + "Biosample", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "depos_env": { + "name": "depos_env", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Main depositional environment (https://en.wikipedia.org/wiki/Depositional_environment). If \"other\" is specified, please propose entry in \"additional info\" field", + "title": "depositional environment", + "examples": [ + { + "value": "Continental - Alluvial" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "depositional environment" + ], + "rank": 304, + "is_a": "core field", + "slot_uri": "MIXS:0000992", + "alias": "depos_env", + "owner": "HcrFluidsSwabsInterface", + "domain_of": [ + "Biosample", + "HcrCoresInterface", + "HcrFluidsSwabsInterface" + ], + "slot_group": "mixs_core_section", + "range": "depos_env_enum", + "multivalued": false + }, + "depth": { + "name": "depth", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + } + }, + "description": "The vertical distance below local surface, e.g. for sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples.", + "title": "depth, meters", + "notes": [ + "Use modified term" + ], + "comments": [ + "All depths must be reported in meters. Provide the numerical portion only." + ], + "examples": [ + { + "value": "0 - 0.1" + }, + { + "value": "1" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "depth" + ], + "rank": 9, + "is_a": "environment field", + "string_serialization": "{float}|{float}-{float}", + "slot_uri": "MIXS:0000018", + "alias": "depth", + "owner": "HcrFluidsSwabsInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "recommended": true, + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)?(\\s*-\\s*[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)?)?$" + }, + "diss_carb_dioxide": { + "name": "diss_carb_dioxide", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per liter, milligram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample", + "title": "dissolved carbon dioxide", + "examples": [ + { + "value": "5 milligram per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "dissolved carbon dioxide" + ], + "rank": 14, + "is_a": "core field", + "slot_uri": "MIXS:0000436", + "alias": "diss_carb_dioxide", + "owner": "HcrFluidsSwabsInterface", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "diss_inorg_carb": { + "name": "diss_inorg_carb", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "microgram per liter, milligram per liter, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter", + "title": "dissolved inorganic carbon", + "examples": [ + { + "value": "2059 micromole per kilogram" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "dissolved inorganic carbon" + ], + "rank": 16, + "is_a": "core field", + "slot_uri": "MIXS:0000434", + "alias": "diss_inorg_carb", + "owner": "HcrFluidsSwabsInterface", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "diss_inorg_phosp": { + "name": "diss_inorg_phosp", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "microgram per liter, milligram per liter, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of dissolved inorganic phosphorus in the sample", + "title": "dissolved inorganic phosphorus", + "examples": [ + { + "value": "56.5 micromole per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "dissolved inorganic phosphorus" + ], + "rank": 224, + "is_a": "core field", + "slot_uri": "MIXS:0000106", + "alias": "diss_inorg_phosp", + "owner": "HcrFluidsSwabsInterface", + "domain_of": [ + "Biosample", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "diss_iron": { + "name": "diss_iron", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milligram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of dissolved iron in the sample", + "title": "dissolved iron", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "dissolved iron" + ], + "rank": 305, + "is_a": "core field", + "slot_uri": "MIXS:0000139", + "alias": "diss_iron", + "owner": "HcrFluidsSwabsInterface", + "domain_of": [ + "Biosample", + "HcrCoresInterface", + "HcrFluidsSwabsInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "diss_org_carb": { + "name": "diss_org_carb", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per liter, milligram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid", + "title": "dissolved organic carbon", + "examples": [ + { + "value": "197 micromole per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "dissolved organic carbon" + ], + "rank": 17, + "is_a": "core field", + "slot_uri": "MIXS:0000433", + "alias": "diss_org_carb", + "owner": "HcrFluidsSwabsInterface", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "diss_oxygen_fluid": { + "name": "diss_oxygen_fluid", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per kilogram, milligram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of dissolved oxygen in the oil field produced fluids as it contributes to oxgen-corrosion and microbial activity (e.g. Mic).", + "title": "dissolved oxygen in fluids", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "dissolved oxygen in fluids" + ], + "rank": 306, + "is_a": "core field", + "slot_uri": "MIXS:0000438", + "alias": "diss_oxygen_fluid", + "owner": "HcrFluidsSwabsInterface", + "domain_of": [ + "Biosample", + "HcrCoresInterface", + "HcrFluidsSwabsInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "ecosystem": { + "name": "ecosystem", + "description": "An ecosystem is a combination of a physical environment (abiotic factors) and all the organisms (biotic factors) that interact with this environment. Ecosystem is in position 1/5 in a GOLD path.", + "comments": [ + "The abiotic factors play a profound role on the type and composition of organisms in a given environment. The GOLD Ecosystem at the top of the five-level classification system is aimed at capturing the broader environment from which an organism or environmental sample is collected. The three broad groups under Ecosystem are Environmental, Host-associated, and Engineered. They represent samples collected from a natural environment or from another organism or from engineered environments like bioreactors respectively." + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "https://gold.jgi.doe.gov/help" + ], + "rank": 9, + "is_a": "gold_path_field", + "alias": "ecosystem", + "owner": "HcrFluidsSwabsInterface", + "domain_of": [ + "Biosample", + "Study", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "EcosystemEnum", + "recommended": true + }, + "ecosystem_category": { + "name": "ecosystem_category", + "description": "Ecosystem categories represent divisions within the ecosystem based on specific characteristics of the environment from where an organism or sample is isolated. Ecosystem category is in position 2/5 in a GOLD path.", + "comments": [ + "The Environmental ecosystem (for example) is divided into Air, Aquatic and Terrestrial. Ecosystem categories for Host-associated samples can be individual hosts or phyla and for engineered samples it may be manipulated environments like bioreactors, solid waste etc." + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "https://gold.jgi.doe.gov/help" + ], + "rank": 10, + "is_a": "gold_path_field", + "alias": "ecosystem_category", + "owner": "HcrFluidsSwabsInterface", + "domain_of": [ + "Biosample", + "Study", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "EcosystemCategoryEnum", + "recommended": true + }, + "ecosystem_subtype": { + "name": "ecosystem_subtype", + "description": "Ecosystem subtypes represent further subdivision of Ecosystem types into more distinct subtypes. Ecosystem subtype is in position 4/5 in a GOLD path.", + "comments": [ + "Ecosystem Type Marine (Environmental -> Aquatic -> Marine) is further divided (for example) into Intertidal zone, Coastal, Pelagic, Intertidal zone etc. in the Ecosystem subtype category." + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "https://gold.jgi.doe.gov/help" + ], + "rank": 12, + "is_a": "gold_path_field", + "alias": "ecosystem_subtype", + "owner": "HcrFluidsSwabsInterface", + "domain_of": [ + "Biosample", + "Study", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "EcosystemSubtypeEnum", + "recommended": true + }, + "ecosystem_type": { + "name": "ecosystem_type", + "description": "Ecosystem types represent things having common characteristics within the Ecosystem Category. These common characteristics based grouping is still broad but specific to the characteristics of a given environment. Ecosystem type is in position 3/5 in a GOLD path.", + "comments": [ + "The Aquatic ecosystem category (for example) may have ecosystem types like Marine or Thermal springs etc. Ecosystem category Air may have Indoor air or Outdoor air as different Ecosystem Types. In the case of Host-associated samples, ecosystem type can represent Respiratory system, Digestive system, Roots etc." + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "https://gold.jgi.doe.gov/help" + ], + "rank": 11, + "is_a": "gold_path_field", + "alias": "ecosystem_type", + "owner": "HcrFluidsSwabsInterface", + "domain_of": [ + "Biosample", + "Study", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "EcosystemTypeEnum", + "recommended": true + }, + "elev": { + "name": "elev", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + } + }, + "description": "Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit.", + "title": "elevation, meters", + "comments": [ + "All elevations must be reported in meters. Provide the numerical portion only.", + "Please use https://www.advancedconverter.com/map-tools/find-altitude-by-coordinates, if needed, to help estimate the elevation based on latitude and longitude coordinates." + ], + "examples": [ + { + "value": "225" + }, + { + "value": "0" + }, + { + "value": "1250" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "elevation" + ], + "rank": 6, + "is_a": "environment field", + "slot_uri": "MIXS:0000093", + "alias": "elev", + "owner": "HcrFluidsSwabsInterface", + "domain_of": [ + "FieldResearchSite", + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "float", + "required": true, + "multivalued": false + }, + "env_broad_scale": { + "name": "env_broad_scale", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "The major environment type(s) where the sample was collected. Recommend subclasses of biome [ENVO:00000428]. Multiple terms can be separated by one or more pipes." + }, + "tooltip": { + "tag": "tooltip", + "value": "The biome or major environmental system where the sample or specimen originated. Choose values from subclasses of the 'biome' class [ENVO:00000428] in the Environment Ontology (ENVO). For host-associated or plant-associated samples, use terms from the UBERON or Plant Ontology to describe the broad anatomical or morphological context" + } + }, + "description": "In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO's biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html", + "title": "broad-scale environmental context", + "notes": [ + "range changed to enumeration late in makefile, so this is modified (but \"sample ID\" anyway)" + ], + "examples": [ + { + "value": "oceanic epipelagic zone biome [ENVO:01000033] for annotating a water sample from the photic zone in middle of the Atlantic Ocean" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "broad-scale environmental context" + ], + "rank": 6, + "is_a": "environment field", + "string_serialization": "{termLabel} {[termID]}", + "slot_uri": "MIXS:0000012", + "alias": "env_broad_scale", + "owner": "HcrFluidsSwabsInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "string", + "required": true, + "multivalued": false, + "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$" + }, + "env_local_scale": { + "name": "env_local_scale", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "Environmental entities having causal influences upon the entity at time of sampling." + }, + "tooltip": { + "tag": "tooltip", + "value": "The specific environmental entities or features near the sample or specimen that significantly influence its characteristics or composition. These entities are typically smaller in scale than the broad environmental context. Values for this field should be countable, material nouns and must be chosen from subclasses of BFO:0000040 (material entity) that appear in the Environment Ontology (ENVO). For host-associated or plant-associated samples, use terms from the UBERON or Plant Ontology to describe specific anatomical structures or plant parts." + } + }, + "description": "Report the entity or entities which are in the sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. We recommend using EnvO terms which are of smaller spatial grain than your entry for env_broad_scale. Terms, such as anatomical sites, from other OBO Library ontologies which interoperate with EnvO (e.g. UBERON) are accepted in this field. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS.", + "title": "local environmental context", + "notes": [ + "range changed to enumeration late in makefile, so this is modified (but \"sample ID\" anyway)" + ], + "examples": [ + { + "value": "canopy [ENVO:00000047]" + }, + { + "value": "herb and fern layer [ENVO:01000337]" + }, + { + "value": "litter layer [ENVO:01000338]" + }, + { + "value": "understory [01000335]" + }, + { + "value": "shrub layer [ENVO:01000336]" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "local environmental context" + ], + "rank": 7, + "is_a": "environment field", + "string_serialization": "{termLabel} {[termID]}", + "slot_uri": "MIXS:0000013", + "alias": "env_local_scale", + "owner": "HcrFluidsSwabsInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "string", + "required": true, + "multivalued": false, + "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$" + }, + "env_medium": { + "name": "env_medium", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "The material displaced by the entity at time of sampling. Recommend subclasses of environmental material [ENVO:00010483]." + }, + "tooltip": { + "tag": "tooltip", + "value": "The predominant environmental material or substrate that directly surrounds or hosts the sample or specimen at the time of sampling. Choose values from subclasses of the 'environmental material' class [ENVO:00010483] in the Environment Ontology (ENVO). Values for this field should be measurable or mass material nouns, representing continuous environmental materials. For host-associated or plant-associated samples, use terms from the UBERON or Plant Ontology to indicate a tissue, organ, or plant structure" + } + }, + "description": "Report the environmental material(s) immediately surrounding the sample or specimen at the time of sampling. We recommend using subclasses of 'environmental material' (http://purl.obolibrary.org/obo/ENVO_00010483). EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS . Terms from other OBO ontologies are permissible as long as they reference mass/volume nouns (e.g. air, water, blood) and not discrete, countable entities (e.g. a tree, a leaf, a table top).", + "title": "environmental medium", + "notes": [ + "range changed to enumeration late in makefile, so this is modified (but \"sample ID\" anyway)" + ], + "examples": [ + { + "value": "soil [ENVO:00001998]" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "environmental medium" + ], + "rank": 8, + "is_a": "environment field", + "string_serialization": "{termLabel} {[termID]}", + "slot_uri": "MIXS:0000014", + "alias": "env_medium", + "owner": "HcrFluidsSwabsInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "string", + "required": true, + "multivalued": false, + "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$" + }, + "ethylbenzene": { + "name": "ethylbenzene", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milligram per liter, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of ethylbenzene in the sample", + "title": "ethylbenzene", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "ethylbenzene" + ], + "rank": 309, + "is_a": "core field", + "slot_uri": "MIXS:0000155", + "alias": "ethylbenzene", + "owner": "HcrFluidsSwabsInterface", + "domain_of": [ + "Biosample", + "HcrCoresInterface", + "HcrFluidsSwabsInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "experimental_factor": { + "name": "experimental_factor", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "text or EFO and/or OBI" + } + }, + "description": "Experimental factors are essentially the variable aspects of an experiment design which can be used to describe an experiment, or set of experiments, in an increasingly detailed manner. This field accepts ontology terms from Experimental Factor Ontology (EFO) and/or Ontology for Biomedical Investigations (OBI). For a browser of EFO (v 2.95) terms, please see http://purl.bioontology.org/ontology/EFO; for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI", + "title": "experimental factor", + "examples": [ + { + "value": "time series design [EFO:EFO_0001779]" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "experimental factor" + ], + "rank": 12, + "is_a": "investigation field", + "string_serialization": "{termLabel} {[termID]}|{text}", + "slot_uri": "MIXS:0000008", + "alias": "experimental_factor", + "owner": "HcrFluidsSwabsInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false + }, + "field": { + "name": "field", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "name" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Name of the hydrocarbon field (e.g. Albacora)", + "title": "field name", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "field name" + ], + "rank": 310, + "is_a": "core field", + "string_serialization": "{text}", + "slot_uri": "MIXS:0000291", + "alias": "field", + "owner": "HcrFluidsSwabsInterface", + "domain_of": [ + "Biosample", + "HcrCoresInterface", + "HcrFluidsSwabsInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "geo_loc_name": { + "name": "geo_loc_name", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "country or sea name (INSDC or GAZ): region(GAZ), specific location name" + } + }, + "description": "The geographical origin of the sample as defined by the country or sea name followed by specific region name.", + "title": "geographic location (country and/or sea,region)", + "examples": [ + { + "value": "USA: Maryland, Bethesda" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "geographic location (country and/or sea,region)" + ], + "rank": 4, + "is_a": "environment field", + "string_serialization": "{text}: {text}, {text}", + "slot_uri": "MIXS:0000010", + "alias": "geo_loc_name", + "owner": "HcrFluidsSwabsInterface", + "domain_of": [ + "FieldResearchSite", + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "required": true, + "multivalued": false, + "pattern": "^[^:, ][^:]*: [^:, ][^,]*, [^:, ].*$" + }, + "hc_produced": { + "name": "hc_produced", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Main hydrocarbon type produced from resource (i.e. Oil, gas, condensate, etc). If \"other\" is specified, please propose entry in \"additional info\" field", + "title": "hydrocarbon type produced", + "examples": [ + { + "value": "Gas" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "hydrocarbon type produced" + ], + "rank": 313, + "is_a": "core field", + "slot_uri": "MIXS:0000989", + "alias": "hc_produced", + "owner": "HcrFluidsSwabsInterface", + "domain_of": [ + "Biosample", + "HcrCoresInterface", + "HcrFluidsSwabsInterface" + ], + "slot_group": "mixs_core_section", + "range": "hc_produced_enum", + "multivalued": false + }, + "hcr": { + "name": "hcr", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Main Hydrocarbon Resource type. The term \"Hydrocarbon Resource\" HCR defined as a natural environmental feature containing large amounts of hydrocarbons at high concentrations potentially suitable for commercial exploitation. This term should not be confused with the Hydrocarbon Occurrence term which also includes hydrocarbon-rich environments with currently limited commercial interest such as seeps, outcrops, gas hydrates etc. If \"other\" is specified, please propose entry in \"additional info\" field", + "title": "hydrocarbon resource type", + "examples": [ + { + "value": "Oil Sand" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "hydrocarbon resource type" + ], + "rank": 314, + "is_a": "core field", + "slot_uri": "MIXS:0000988", + "alias": "hcr", + "owner": "HcrFluidsSwabsInterface", + "domain_of": [ + "Biosample", + "HcrCoresInterface", + "HcrFluidsSwabsInterface" + ], + "slot_group": "mixs_core_section", + "range": "hcr_enum", + "multivalued": false + }, + "hcr_fw_salinity": { + "name": "hcr_fw_salinity", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milligram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Original formation water salinity (prior to secondary recovery e.g. Waterflooding) expressed as TDS", + "title": "formation water salinity", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "formation water salinity" + ], + "rank": 315, + "is_a": "core field", + "slot_uri": "MIXS:0000406", + "alias": "hcr_fw_salinity", + "owner": "HcrFluidsSwabsInterface", + "domain_of": [ + "Biosample", + "HcrCoresInterface", + "HcrFluidsSwabsInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "hcr_geol_age": { + "name": "hcr_geol_age", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Geological age of hydrocarbon resource (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). If \"other\" is specified, please propose entry in \"additional info\" field", + "title": "hydrocarbon resource geological age", + "examples": [ + { + "value": "Silurian" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "hydrocarbon resource geological age" + ], + "rank": 316, + "is_a": "core field", + "slot_uri": "MIXS:0000993", + "alias": "hcr_geol_age", + "owner": "HcrFluidsSwabsInterface", + "domain_of": [ + "Biosample", + "HcrCoresInterface", + "HcrFluidsSwabsInterface" + ], + "slot_group": "mixs_core_section", + "range": "hcr_geol_age_enum", + "multivalued": false + }, + "hcr_pressure": { + "name": "hcr_pressure", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value range" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "atmosphere, kilopascal" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Original pressure of the hydrocarbon resource", + "title": "hydrocarbon resource original pressure", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "hydrocarbon resource original pressure" + ], + "rank": 317, + "is_a": "core field", + "string_serialization": "{float} - {float} {unit}", + "slot_uri": "MIXS:0000395", + "alias": "hcr_pressure", + "owner": "HcrFluidsSwabsInterface", + "domain_of": [ + "Biosample", + "HcrCoresInterface", + "HcrFluidsSwabsInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "hcr_temp": { + "name": "hcr_temp", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value range" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "degree Celsius" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Original temperature of the hydrocarbon resource", + "title": "hydrocarbon resource original temperature", + "examples": [ + { + "value": "150-295 degree Celsius" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "hydrocarbon resource original temperature" + ], + "rank": 318, + "is_a": "core field", + "string_serialization": "{float} - {float} {unit}", + "slot_uri": "MIXS:0000393", + "alias": "hcr_temp", + "owner": "HcrFluidsSwabsInterface", + "domain_of": [ + "Biosample", + "HcrCoresInterface", + "HcrFluidsSwabsInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "iw_bt_date_well": { + "name": "iw_bt_date_well", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "timestamp" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Injection water breakthrough date per well following a secondary and/or tertiary recovery", + "title": "injection water breakthrough date of specific well", + "examples": [ + { + "value": "2018-05-11" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "injection water breakthrough date of specific well" + ], + "rank": 334, + "is_a": "core field", + "slot_uri": "MIXS:0001010", + "alias": "iw_bt_date_well", + "owner": "HcrFluidsSwabsInterface", + "domain_of": [ + "Biosample", + "HcrFluidsSwabsInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "iwf": { + "name": "iwf", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "percent" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Proportion of the produced fluids derived from injected water at the time of sampling. (e.g. 87%)", + "title": "injection water fraction", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "injection water fraction" + ], + "rank": 335, + "is_a": "core field", + "slot_uri": "MIXS:0000455", + "alias": "iwf", + "owner": "HcrFluidsSwabsInterface", + "domain_of": [ + "Biosample", + "HcrFluidsSwabsInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "lat_lon": { + "name": "lat_lon", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "decimal degrees, limit to 8 decimal points" + } + }, + "description": "The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system", + "title": "geographic location (latitude and longitude)", + "notes": [ + "This is currently a required field but it's not clear if this should be required for human hosts" + ], + "examples": [ + { + "value": "50.586825 6.408977" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "geographic location (latitude and longitude)" + ], + "rank": 5, + "is_a": "environment field", + "string_serialization": "{lat lon}", + "slot_uri": "MIXS:0000009", + "alias": "lat_lon", + "owner": "HcrFluidsSwabsInterface", + "domain_of": [ + "FieldResearchSite", + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "required": true, + "multivalued": false, + "pattern": "^[-+]?([1-8]?\\d(\\.\\d{1,8})?|90(\\.0{1,8})?)\\s[-+]?(180(\\.0{1,8})?|((1[0-7]\\d)|([1-9]?\\d))(\\.\\d{1,8})?)$" + }, + "lithology": { + "name": "lithology", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Hydrocarbon resource main lithology (Additional information: http://petrowiki.org/Lithology_and_rock_type_determination). If \"other\" is specified, please propose entry in \"additional info\" field", + "title": "lithology", + "examples": [ + { + "value": "Volcanic" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "lithology" + ], + "rank": 336, + "is_a": "core field", + "slot_uri": "MIXS:0000990", + "alias": "lithology", + "owner": "HcrFluidsSwabsInterface", + "domain_of": [ + "Biosample", + "HcrCoresInterface", + "HcrFluidsSwabsInterface" + ], + "slot_group": "mixs_core_section", + "range": "lithology_enum", + "multivalued": false + }, + "magnesium": { + "name": "magnesium", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "mole per liter, milligram per liter, parts per million, micromole per kilogram" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of magnesium in the sample", + "title": "magnesium", + "examples": [ + { + "value": "52.8 micromole per kilogram" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "magnesium" + ], + "rank": 21, + "is_a": "core field", + "slot_uri": "MIXS:0000431", + "alias": "magnesium", + "owner": "HcrFluidsSwabsInterface", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "misc_param": { + "name": "misc_param", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "parameter name;measurement value" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Any other measurement performed or parameter collected, that is not listed here", + "title": "miscellaneous parameter", + "examples": [ + { + "value": "Bicarbonate ion concentration;2075 micromole per kilogram" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "miscellaneous parameter" + ], + "rank": 23, + "is_a": "core field", + "string_serialization": "{text};{float} {unit}", + "slot_uri": "MIXS:0000752", + "alias": "misc_param", + "owner": "HcrFluidsSwabsInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false, + "pattern": "^([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+\\|)*([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+)$" + }, + "nitrate": { + "name": "nitrate", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per liter, milligram per liter, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of nitrate in the sample", + "title": "nitrate", + "examples": [ + { + "value": "65 micromole per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "nitrate" + ], + "rank": 26, + "is_a": "core field", + "slot_uri": "MIXS:0000425", + "alias": "nitrate", + "owner": "HcrFluidsSwabsInterface", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "nitrite": { + "name": "nitrite", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per liter, milligram per liter, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of nitrite in the sample", + "title": "nitrite", + "examples": [ + { + "value": "0.5 micromole per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "nitrite" + ], + "rank": 27, + "is_a": "core field", + "slot_uri": "MIXS:0000426", + "alias": "nitrite", + "owner": "HcrFluidsSwabsInterface", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "org_count_qpcr_info": { + "name": "org_count_qpcr_info", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "gene name;FWD:forward primer sequence;REV:reverse primer sequence;initial denaturation:degrees_minutes;denaturation:degrees_minutes;annealing:degrees_minutes;elongation:degrees_minutes;final elongation:degrees_minutes; total cycles" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "number of cells per gram (or ml or cm^2)" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "If qpcr was used for the cell count, the target gene name, the primer sequence and the cycling conditions should also be provided. (Example: 16S rrna; FWD:ACGTAGCTATGACGT REV:GTGCTAGTCGAGTAC; initial denaturation:90C_5min; denaturation:90C_2min; annealing:52C_30 sec; elongation:72C_30 sec; 90 C for 1 min; final elongation:72C_5min; 30 cycles)", + "title": "organism count qPCR information", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "organism count qPCR information" + ], + "rank": 337, + "is_a": "core field", + "string_serialization": "{text};FWD:{dna};REV:{dna};initial denaturation:degrees_minutes;denaturation:degrees_minutes;annealing:degrees_minutes;elongation:degrees_minutes;final elongation:degrees_minutes; total cycles", + "slot_uri": "MIXS:0000099", + "alias": "org_count_qpcr_info", + "owner": "HcrFluidsSwabsInterface", + "domain_of": [ + "Biosample", + "HcrCoresInterface", + "HcrFluidsSwabsInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "organism_count": { + "name": "organism_count", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "organism name;measurement value;enumeration" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "number of cells per cubic meter, number of cells per milliliter, number of cells per cubic centimeter" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr)", + "title": "organism count", + "examples": [ + { + "value": "total prokaryotes;3.5e7 cells per milliliter;qPCR" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "organism count" + ], + "rank": 30, + "is_a": "core field", + "slot_uri": "MIXS:0000103", + "alias": "organism_count", + "owner": "HcrFluidsSwabsInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^([-+]?[0-9]*\\.?[0-9]+ +\\S.*\\|)*([-+]?[0-9]*\\.?[0-9]+ +\\S.*)$" + }, + "oxy_stat_samp": { + "name": "oxy_stat_samp", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Oxygenation status of sample", + "title": "oxygenation status of sample", + "examples": [ + { + "value": "aerobic" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "oxygenation status of sample" + ], + "rank": 25, + "is_a": "core field", + "slot_uri": "MIXS:0000753", + "alias": "oxy_stat_samp", + "owner": "HcrFluidsSwabsInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_section", + "range": "OxyStatSampEnum", + "multivalued": false + }, + "ph": { + "name": "ph", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "pH measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid", + "title": "pH", + "notes": [ + "Use modified term" + ], + "examples": [ + { + "value": "7.2" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "pH" + ], + "rank": 27, + "is_a": "core field", + "string_serialization": "{float}", + "slot_uri": "MIXS:0001001", + "alias": "ph", + "owner": "HcrFluidsSwabsInterface", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "MiscEnvsInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "float", + "recommended": true, + "multivalued": false, + "minimum_value": 0, + "maximum_value": 14 + }, + "ph_meth": { + "name": "ph_meth", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "PMID,DOI or url" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Reference or method used in determining ph", + "title": "pH method", + "comments": [ + "This can include a link to the instrument used or a citation for the method." + ], + "examples": [ + { + "value": "https://www.southernlabware.com/pc9500-benchtop-ph-conductivity-meter-kit-ph-accuracy-2000mv-ph-range-2-000-to-20-000.html?gclid=Cj0KCQiAwJWdBhCYARIsAJc4idCO5vtvbVMf545fcvdROFqa6zjzNSoywNx6K4k9Coo9cCc2pybtvGsaAiR0EALw_wcB" + }, + { + "value": "https://doi.org/10.2136/sssabookser5.3.c16" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "pH method" + ], + "rank": 41, + "is_a": "core field", + "string_serialization": "{PMID}|{DOI}|{URL}", + "slot_uri": "MIXS:0001106", + "alias": "ph_meth", + "owner": "HcrFluidsSwabsInterface", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "MiscEnvsInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false + }, + "potassium": { + "name": "potassium", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milligram per liter, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of potassium in the sample", + "title": "potassium", + "examples": [ + { + "value": "463 milligram per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "potassium" + ], + "rank": 38, + "is_a": "core field", + "slot_uri": "MIXS:0000430", + "alias": "potassium", + "owner": "HcrFluidsSwabsInterface", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "pour_point": { + "name": "pour_point", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "degree Celsius" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Temperature at which a liquid becomes semi solid and loses its flow characteristics. In crude oil a high¬†pour point¬†is generally associated with a high paraffin content, typically found in crude deriving from a larger proportion of plant material. (soure: https://en.wikipedia.org/wiki/pour_point)", + "title": "pour point", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "pour point" + ], + "rank": 341, + "is_a": "core field", + "slot_uri": "MIXS:0000127", + "alias": "pour_point", + "owner": "HcrFluidsSwabsInterface", + "domain_of": [ + "Biosample", + "HcrCoresInterface", + "HcrFluidsSwabsInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "pressure": { + "name": "pressure", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "atmosphere" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Pressure to which the sample is subject to, in atmospheres", + "title": "pressure", + "examples": [ + { + "value": "50 atmosphere" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "pressure" + ], + "rank": 39, + "is_a": "core field", + "slot_uri": "MIXS:0000412", + "alias": "pressure", + "owner": "HcrFluidsSwabsInterface", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "prod_rate": { + "name": "prod_rate", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "cubic meter per day" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Oil and/or gas production rates per well (e.g. 524 m3 / day)", + "title": "production rate", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "production rate" + ], + "rank": 344, + "is_a": "core field", + "slot_uri": "MIXS:0000452", + "alias": "prod_rate", + "owner": "HcrFluidsSwabsInterface", + "domain_of": [ + "Biosample", + "HcrFluidsSwabsInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "prod_start_date": { + "name": "prod_start_date", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "timestamp" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Date of field's first production", + "title": "production start date", + "examples": [ + { + "value": "2018-05-11" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "production start date" + ], + "rank": 345, + "is_a": "core field", + "slot_uri": "MIXS:0001008", + "alias": "prod_start_date", + "owner": "HcrFluidsSwabsInterface", + "domain_of": [ + "Biosample", + "HcrFluidsSwabsInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "reservoir": { + "name": "reservoir", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "name" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Name of the reservoir (e.g. Carapebus)", + "title": "reservoir name", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "reservoir name" + ], + "rank": 347, + "is_a": "core field", + "string_serialization": "{text}", + "slot_uri": "MIXS:0000303", + "alias": "reservoir", + "owner": "HcrFluidsSwabsInterface", + "domain_of": [ + "Biosample", + "HcrCoresInterface", + "HcrFluidsSwabsInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "resins_pc": { + "name": "resins_pc", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "name;measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "percent" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene)", + "title": "resins wt%", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "resins wt%" + ], + "rank": 348, + "is_a": "core field", + "string_serialization": "{text};{float} {unit}", + "slot_uri": "MIXS:0000134", + "alias": "resins_pc", + "owner": "HcrFluidsSwabsInterface", + "domain_of": [ + "Biosample", + "HcrCoresInterface", + "HcrFluidsSwabsInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[^;\\t\\r\\x0A\\|]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A\\|]+$" + }, + "salinity": { + "name": "salinity", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "practical salinity unit, percentage" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The total concentration of all dissolved salts in a liquid or solid sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater.", + "title": "salinity", + "examples": [ + { + "value": "25 practical salinity unit" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "salinity" + ], + "rank": 54, + "is_a": "core field", + "slot_uri": "MIXS:0000183", + "alias": "salinity", + "owner": "HcrFluidsSwabsInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "samp_collec_device": { + "name": "samp_collec_device", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "device name" + } + }, + "description": "The device used to collect an environmental sample. This field accepts terms listed under environmental sampling device (http://purl.obolibrary.org/obo/ENVO). This field also accepts terms listed under specimen collection device (http://purl.obolibrary.org/obo/GENEPIO_0002094).", + "title": "sample collection device", + "comments": [ + "Report dimensions and details when applicable" + ], + "examples": [ + { + "value": "swab, biopsy, niskin bottle, push core, drag swab [GENEPIO:0002713]" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sample collection device" + ], + "rank": 14, + "is_a": "nucleic acid sequence source field", + "string_serialization": "{termLabel} {[termID]}|{text}", + "slot_uri": "MIXS:0000002", + "alias": "samp_collec_device", + "owner": "HcrFluidsSwabsInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "recommended": true, + "multivalued": false + }, + "samp_collec_method": { + "name": "samp_collec_method", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "PMID,DOI,url , or text" + } + }, + "description": "The method employed for collecting the sample.", + "title": "sample collection method", + "comments": [ + "This can be a citation or description" + ], + "examples": [ + { + "value": "swabbing" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sample collection method" + ], + "rank": 15, + "is_a": "nucleic acid sequence source field", + "string_serialization": "{PMID}|{DOI}|{URL}|{text}", + "slot_uri": "MIXS:0001225", + "alias": "samp_collec_method", + "owner": "HcrFluidsSwabsInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "multivalued": false + }, + "samp_collect_point": { + "name": "samp_collect_point", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Sampling point on the asset were sample was collected (e.g. Wellhead, storage tank, separator, etc). If \"other\" is specified, please propose entry in \"additional info\" field", + "title": "sample collection point", + "examples": [ + { + "value": "well" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sample collection point" + ], + "rank": 349, + "is_a": "core field", + "slot_uri": "MIXS:0001015", + "alias": "samp_collect_point", + "owner": "HcrFluidsSwabsInterface", + "domain_of": [ + "Biosample", + "HcrFluidsSwabsInterface" + ], + "slot_group": "mixs_core_section", + "range": "samp_collect_point_enum", + "multivalued": false + }, + "samp_loc_corr_rate": { + "name": "samp_loc_corr_rate", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value range" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "millimeter per year" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Metal corrosion rate is the speed of metal deterioration due to environmental conditions. As environmental conditions change corrosion rates change accordingly. Therefore, long term corrosion rates are generally more informative than short term rates and for that reason they are preferred during reporting. In the case of suspected MIC, corrosion rate measurements at the time of sampling might provide insights into the involvement of certain microbial community members in MIC as well as potential microbial interplays", + "title": "corrosion rate at sample location", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "corrosion rate at sample location" + ], + "rank": 350, + "is_a": "core field", + "string_serialization": "{float} - {float} {unit}", + "slot_uri": "MIXS:0000136", + "alias": "samp_loc_corr_rate", + "owner": "HcrFluidsSwabsInterface", + "domain_of": [ + "Biosample", + "HcrFluidsSwabsInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "samp_mat_process": { + "name": "samp_mat_process", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "text" + } + }, + "description": "A brief description of any processing applied to the sample during or after retrieving the sample from environment, or a link to the relevant protocol(s) performed.", + "title": "sample material processing", + "examples": [ + { + "value": "filtering of seawater" + }, + { + "value": "storing samples in ethanol" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sample material processing" + ], + "rank": 12, + "is_a": "nucleic acid sequence source field", + "string_serialization": "{text}", + "slot_uri": "MIXS:0000016", + "alias": "samp_mat_process", + "owner": "HcrFluidsSwabsInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "multivalued": false + }, + "samp_preserv": { + "name": "samp_preserv", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "name;measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milliliter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Preservative added to the sample (e.g. Rnalater, alcohol, formaldehyde, etc.). 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NOT the amount sent to each institution or collected for a specific analysis." + ], + "examples": [ + { + "value": "5 grams" + }, + { + "value": "10 mL" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "amount or size of sample collected" + ], + "rank": 18, + "is_a": "nucleic acid sequence source field", + "string_serialization": "{float} {unit}", + "slot_uri": "MIXS:0000001", + "alias": "samp_size", + "owner": "HcrFluidsSwabsInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? \\S+$" + }, + "samp_store_dur": { + "name": "samp_store_dur", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "duration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Duration for which the sample was stored", + "title": "sample storage duration", + "examples": [ + { + "value": "P1Y6M" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sample storage duration" + ], + "rank": 353, + "is_a": "core field", + "string_serialization": "{duration}", + "slot_uri": "MIXS:0000116", + "alias": "samp_store_dur", + "owner": "HcrFluidsSwabsInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "samp_store_loc": { + "name": "samp_store_loc", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "location name" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Location at which sample was stored, usually name of a specific freezer/room", + "title": "sample storage location", + "examples": [ + { + "value": "Freezer no:5" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sample storage location" + ], + "rank": 41, + "is_a": "core field", + "string_serialization": "{text}", + "slot_uri": "MIXS:0000755", + "alias": "samp_store_loc", + "owner": "HcrFluidsSwabsInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "samp_store_temp": { + "name": "samp_store_temp", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "degree Celsius" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Temperature at which the sample was stored (degrees are assumed)", + "title": "sample storage temperature", + "examples": [ + { + "value": "-80 Celsius" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sample storage temperature" + ], + "rank": 7, + "is_a": "core field", + "slot_uri": "MIXS:0000110", + "alias": "samp_store_temp", + "owner": "HcrFluidsSwabsInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "required": true, + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "samp_subtype": { + "name": "samp_subtype", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Name of sample sub-type. 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For the Hydrocarbon package, samples include types like core, rock trimmings, drill cuttings, piping section, coupon, pigging debris, solid deposit, produced fluid, produced water, injected water, swabs, etc. For the Food Package, samples are usually categorized as food, body products or tissues, or environmental material. This field accepts terms listed under environmental specimen (http://purl.obolibrary.org/obo/GENEPIO_0001246).", + "title": "sample type", + "examples": [ + { + "value": "built environment sample [GENEPIO:0001248]" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sample type" + ], + "rank": 357, + "is_a": "core field", + "string_serialization": "{termLabel} {[termID]}", + "slot_uri": "MIXS:0000998", + "alias": "samp_type", + "owner": "HcrFluidsSwabsInterface", + "domain_of": [ + "Biosample", + "HcrCoresInterface", + "HcrFluidsSwabsInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$" + }, + "samp_well_name": { + "name": "samp_well_name", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "name" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Name of the well (e.g. BXA1123) where sample was taken", + "title": "sample well name", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sample well name" + ], + "rank": 358, + "is_a": "core field", + "string_serialization": "{text}", + "slot_uri": "MIXS:0000296", + "alias": "samp_well_name", + "owner": "HcrFluidsSwabsInterface", + "domain_of": [ + "Biosample", + "HcrCoresInterface", + "HcrFluidsSwabsInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "sample_link": { + "name": "sample_link", + "description": "A unique identifier to assign parent-child, subsample, or sibling samples. This is relevant when a sample or other material was used to generate the new sample.", + "title": "sample linkage", + "notes": [ + "also tempted to include SampIdNewTermsMixin but if len(slot_usage.keys()) > 1 and \"placeholder\" in slot_usage.keys():AttributeError: 'list' object has no attribute 'keys'" + ], + "comments": [ + "This field allows multiple entries separated by ; (Examples: Soil collected from the field will link with the soil used in an incubation. The soil a plant was grown in links to the plant sample. An original culture sample was transferred to a new vial and generated a new sample)" + ], + "examples": [ + { + "value": "IGSN:DSJ0284" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "rank": 5, + "string_serialization": "{text}:{text}", + "alias": "sample_link", + "owner": "HcrFluidsSwabsInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface", + "SampIdNewTermsMixin" + ], + "slot_group": "sample_id_section", + "range": "string", + "recommended": true, + "multivalued": false, + "pattern": "[^\\:\\n\\r]+\\:[^\\:\\n\\r]+" + }, + "saturates_pc": { + "name": "saturates_pc", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "name;measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "percent" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene)", + "title": "saturates wt%", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "saturates wt%" + ], + "rank": 359, + "is_a": "core field", + "string_serialization": "{text};{float} {unit}", + "slot_uri": "MIXS:0000131", + "alias": "saturates_pc", + "owner": "HcrFluidsSwabsInterface", + "domain_of": [ + "Biosample", + "HcrCoresInterface", + "HcrFluidsSwabsInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[^;\\t\\r\\x0A\\|]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A\\|]+$" + }, + "size_frac": { + "name": "size_frac", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "filter size value range" + } + }, + "description": "Filtering pore size used in sample preparation", + "title": "size fraction selected", + "examples": [ + { + "value": "0-0.22 micrometer" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "size fraction selected" + ], + "rank": 285, + "is_a": "nucleic acid sequence source field", + "string_serialization": "{float}-{float} {unit}", + "slot_uri": "MIXS:0000017", + "alias": "size_frac", + "owner": "HcrFluidsSwabsInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "sodium": { + "name": "sodium", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milligram per liter, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Sodium concentration in the sample", + "title": "sodium", + "examples": [ + { + "value": "10.5 milligram per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sodium" + ], + "rank": 363, + "is_a": "core field", + "slot_uri": "MIXS:0000428", + "alias": "sodium", + "owner": "HcrFluidsSwabsInterface", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "specific_ecosystem": { + "name": "specific_ecosystem", + "description": "Specific ecosystems represent specific features of the environment like aphotic zone in an ocean or gastric mucosa within a host digestive system. Specific ecosystem is in position 5/5 in a GOLD path.", + "comments": [ + "Specific ecosystems help to define samples based on very specific characteristics of an environment under the five-level classification system." + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "https://gold.jgi.doe.gov/help" + ], + "rank": 13, + "is_a": "gold_path_field", + "alias": "specific_ecosystem", + "owner": "HcrFluidsSwabsInterface", + "domain_of": [ + "Biosample", + "Study", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "SpecificEcosystemEnum", + "recommended": true + }, + "sulfate": { + "name": "sulfate", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per liter, milligram per liter, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of sulfate in the sample", + "title": "sulfate", + "examples": [ + { + "value": "5 micromole per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sulfate" + ], + "rank": 44, + "is_a": "core field", + "slot_uri": "MIXS:0000423", + "alias": "sulfate", + "owner": "HcrFluidsSwabsInterface", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "sulfate_fw": { + "name": "sulfate_fw", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milligram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Original sulfate concentration in the hydrocarbon resource", + "title": "sulfate in formation water", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sulfate in formation water" + ], + "rank": 370, + "is_a": "core field", + "slot_uri": "MIXS:0000407", + "alias": "sulfate_fw", + "owner": "HcrFluidsSwabsInterface", + "domain_of": [ + "Biosample", + "HcrCoresInterface", + "HcrFluidsSwabsInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "sulfide": { + "name": "sulfide", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per liter, milligram per liter, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of sulfide in the sample", + "title": "sulfide", + "examples": [ + { + "value": "2 micromole per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sulfide" + ], + "rank": 371, + "is_a": "core field", + "slot_uri": "MIXS:0000424", + "alias": "sulfide", + "owner": "HcrFluidsSwabsInterface", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "suspend_solids": { + "name": "suspend_solids", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "suspended solid name;measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "gram, microgram, milligram per liter, mole per liter, gram per liter, part per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Concentration of substances including a wide variety of material, such as silt, decaying plant and animal matter; can include multiple substances", + "title": "suspended solids", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "suspended solids" + ], + "rank": 372, + "is_a": "core field", + "string_serialization": "{text};{float} {unit}", + "slot_uri": "MIXS:0000150", + "alias": "suspend_solids", + "owner": "HcrFluidsSwabsInterface", + "domain_of": [ + "Biosample", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "WastewaterSludgeInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? 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This is part of the Global Framework for Well Identification initiative which is compiled by the Professional Petroleum Data Management Association (PPDM) in an effort to improve well identification systems. (Supporting information: https://ppdm.org/ and http://dl.ppdm.org/dl/690)", + "title": "well identification number", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "well identification number" + ], + "rank": 388, + "is_a": "core field", + "string_serialization": "{text}", + "slot_uri": "MIXS:0000297", + "alias": "win", + "owner": "HcrFluidsSwabsInterface", + "domain_of": [ + "Biosample", + "HcrCoresInterface", + "HcrFluidsSwabsInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "xylene": { + "name": "xylene", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milligram per liter, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of xylene in the sample", + "title": "xylene", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "xylene" + ], + "rank": 389, + "is_a": "core field", + "slot_uri": "MIXS:0000156", + "alias": "xylene", + "owner": "HcrFluidsSwabsInterface", + "domain_of": [ + "Biosample", + "HcrCoresInterface", + "HcrFluidsSwabsInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "analysis_type": { + "name": "analysis_type", + "description": "Select all the data types associated or available for this biosample", + "title": "analysis/data type", + "examples": [ + { + "value": "metagenomics; metabolomics; proteomics" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "MIxS:investigation_type" + ], + "rank": 3, + "alias": "analysis_type", + "owner": "HcrFluidsSwabsInterface", + "domain_of": [ + "Biosample", + "DhMultiviewCommonColumnsMixin", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "EmslInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "JgiMgInterface", + "JgiMgLrInterface", + "JgiMtInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "AnalysisTypeEnum", + "required": true, + "recommended": false, + "multivalued": true + }, + "samp_name": { + "name": "samp_name", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "text" + } + }, + "description": "A local identifier or name that for the material sample collected. Refers to the original material collected or to any derived sub-samples.", + "title": "sample name", + "comments": [ + "It can have any format, but we suggest that you make it concise, unique and consistent within your lab, and as informative as possible." + ], + "examples": [ + { + "value": "Rock core CB1178(5-6) from NSW" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sample name" + ], + "rank": 1, + "is_a": "investigation field", + "string_serialization": "{text}", + "slot_uri": "MIXS:0001107", + "identifier": true, + "alias": "samp_name", + "owner": "HcrFluidsSwabsInterface", + "domain_of": [ + "Biosample", + "DhMultiviewCommonColumnsMixin", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "EmslInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "JgiMgInterface", + "JgiMgLrInterface", + "JgiMtInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "string", + "required": true, + "multivalued": false + }, + "source_mat_id": { + "name": "source_mat_id", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "for cultures of microorganisms: identifiers for two culture collections; for other material a unique arbitrary identifer" + } + }, + "description": "A globally unique identifier assigned to the biological sample.", + "title": "source material identifier", + "todos": [ + "Currently, the comments say to use UUIDs. However, if we implement assigning NMDC identifiers with the minter we dont need to require a GUID. It can be an optional field to fill out only if they already have a resolvable ID.", + "Currently, the comments say to use UUIDs. However, if we implement assigning NMDC identifiers with the minter we dont need to require a GUID. It can be an optional field to fill out only if they already have a resolvable ID." + ], + "notes": [ + "The source material IS the Globally Unique ID" + ], + "comments": [ + "Identifiers must be prefixed. Possible FAIR prefixes are IGSNs (http://www.geosamples.org/getigsn), NCBI biosample accession numbers, ARK identifiers (https://arks.org/). These IDs enable linking to derived analytes and subsamples. If you have not assigned FAIR identifiers to your samples, you can generate UUIDs (https://www.uuidgenerator.net/).", + "Identifiers must be prefixed. Possible FAIR prefixes are IGSNs (http://www.geosamples.org/getigsn), NCBI biosample accession numbers, ARK identifiers (https://arks.org/). These IDs enable linking to derived analytes and subsamples. If you have not assigned FAIR identifiers to your samples, you can generate UUIDs (https://www.uuidgenerator.net/)." + ], + "examples": [ + { + "value": "IGSN:AU1243" + }, + { + "value": "UUID:24f1467a-40f4-11ed-b878-0242ac120002" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "source material identifiers" + ], + "rank": 2, + "is_a": "nucleic acid sequence source field", + "string_serialization": "{text}:{text}", + "slot_uri": "MIXS:0000026", + "alias": "source_mat_id", + "owner": "HcrFluidsSwabsInterface", + "domain_of": [ + "Biosample", + "DhMultiviewCommonColumnsMixin", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "EmslInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "JgiMgInterface", + "JgiMgLrInterface", + "JgiMtInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "string", + "multivalued": false, + "pattern": "[^\\:\\n\\r]+\\:[^\\:\\n\\r]+" + } + } + }, + "HostAssociatedInterface": { + "name": "HostAssociatedInterface", + "annotations": { + "excel_worksheet_name": { + "tag": "excel_worksheet_name", + "value": "host-associated" + } + }, + "description": "host_associated dh_interface", + "title": "Host Associated", + "from_schema": "https://example.com/nmdc_submission_schema", + "is_a": "DhInterface", + "mixins": [ + "DhMultiviewCommonColumnsMixin", + "SampIdNewTermsMixin" + ], + "slots": [ + "alt", + "ances_data", + "biol_stat", + "blood_press_diast", + "blood_press_syst", + "chem_administration", + "collection_date", + "depth", + "ecosystem", + "ecosystem_category", + "ecosystem_subtype", + "ecosystem_type", + "elev", + "env_broad_scale", + "env_local_scale", + "env_medium", + "experimental_factor", + "genetic_mod", + "geo_loc_name", + "gravidity", + "host_age", + "host_body_habitat", + "host_body_product", + "host_body_site", + "host_body_temp", + "host_color", + "host_common_name", + "host_diet", + "host_disease_stat", + "host_dry_mass", + "host_family_relation", + "host_genotype", + "host_growth_cond", + "host_height", + "host_last_meal", + "host_length", + "host_life_stage", + "host_phenotype", + "host_sex", + "host_shape", + "host_subject_id", + "host_subspecf_genlin", + "host_substrate", + "host_symbiont", + "host_taxid", + "host_tot_mass", + "lat_lon", + "misc_param", + "organism_count", + "oxy_stat_samp", + "perturbation", + "salinity", + "samp_capt_status", + "samp_collec_device", + "samp_collec_method", + "samp_dis_stage", + "samp_mat_process", + "samp_size", + "samp_store_dur", + "samp_store_loc", + "samp_store_temp", + "sample_link", + "size_frac", + "specific_ecosystem", + "temp" + ], + "slot_usage": { + "alt": { + "name": "alt", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + } + }, + "description": "Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air", + "title": "altitude", + "examples": [ + { + "value": "100 meter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "altitude" + ], + "rank": 26, + "is_a": "environment field", + "slot_uri": "MIXS:0000094", + "owner": "Biosample", + "domain_of": [ + "agriculture", + "air", + "built environment", + "core", + "food-animal and animal feed", + "food-farm environment", + "food-food production facility", + "food-human foods", + "host-associated", + "human-associated", + "human-gut", + "human-oral", + "human-skin", + "human-vaginal", + "hydrocarbon resources-cores", + "hydrocarbon resources-fluids_swabs", + "microbial mat_biofilm", + "miscellaneous natural or artificial environment", + "plant-associated", + "sediment", + "soil", + "symbiont-associated", + "wastewater_sludge", + "water", + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HostAssociatedInterface", + "MiscEnvsInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "recommended": true, + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "ances_data": { + "name": "ances_data", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "free text" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Information about either pedigree or other ancestral information description (e.g. parental variety in case of mutant or selection), e.g. A/3*B (meaning [(A x B) x B] x B)", + "title": "ancestral data", + "examples": [ + { + "value": "A/3*B" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "ancestral data" + ], + "rank": 237, + "is_a": "core field", + "string_serialization": "{text}", + "slot_uri": "MIXS:0000247", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "HostAssociatedInterface", + "PlantAssociatedInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "biol_stat": { + "name": "biol_stat", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The level of genome modification.", + "title": "biological status", + "examples": [ + { + "value": "natural" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "biological status" + ], + "rank": 239, + "is_a": "core field", + "slot_uri": "MIXS:0000858", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "HostAssociatedInterface", + "PlantAssociatedInterface" + ], + "slot_group": "mixs_core_section", + "range": "biol_stat_enum", + "multivalued": false + }, + "blood_press_diast": { + "name": "blood_press_diast", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "millimeter mercury" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Resting diastolic blood pressure, measured as mm mercury", + "title": "host blood pressure diastolic", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "host blood pressure diastolic" + ], + "rank": 299, + "is_a": "core field", + "slot_uri": "MIXS:0000258", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "HostAssociatedInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "blood_press_syst": { + "name": "blood_press_syst", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "millimeter mercury" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Resting systolic blood pressure, measured as mm mercury", + "title": "host blood pressure systolic", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "host blood pressure systolic" + ], + "rank": 300, + "is_a": "core field", + "slot_uri": "MIXS:0000259", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "HostAssociatedInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "chem_administration": { + "name": "chem_administration", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "CHEBI;timestamp" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi", + "title": "chemical administration", + "examples": [ + { + "value": "agar [CHEBI:2509];2018-05-11|agar [CHEBI:2509];2018-05-22" + }, + { + "value": "agar [CHEBI:2509];2018-05" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "chemical administration" + ], + "rank": 17, + "is_a": "core field", + "string_serialization": "{termLabel} {[termID]};{timestamp}", + "slot_uri": "MIXS:0000751", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "recommended": true, + "multivalued": false, + "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\];([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$" + }, + "collection_date": { + "name": "collection_date", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "date and time" + } + }, + "description": "The date of sampling", + "title": "collection date", + "notes": [ + "MIxS collection_date accepts (truncated) ISO8601. DH taking arb prec date only", + "Use modified term (amended definition)" + ], + "examples": [ + { + "value": "2021-04-15" + }, + { + "value": "2021-04" + }, + { + "value": "2021" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "collection date" + ], + "rank": 3, + "is_a": "environment field", + "string_serialization": "{date, arbitrary precision}", + "slot_uri": "MIXS:0000011", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "required": true, + "multivalued": false, + "pattern": "^[12]\\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\\d|3[01]))?)?$" + }, + "depth": { + "name": "depth", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + } + }, + "description": "The vertical distance below local surface, e.g. for sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples.", + "title": "depth, meters", + "notes": [ + "Use modified term" + ], + "comments": [ + "All depths must be reported in meters. Provide the numerical portion only." + ], + "examples": [ + { + "value": "0 - 0.1" + }, + { + "value": "1" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "depth" + ], + "rank": 9, + "is_a": "environment field", + "string_serialization": "{float}|{float}-{float}", + "slot_uri": "MIXS:0000018", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "recommended": true, + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)?(\\s*-\\s*[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)?)?$" + }, + "ecosystem": { + "name": "ecosystem", + "description": "An ecosystem is a combination of a physical environment (abiotic factors) and all the organisms (biotic factors) that interact with this environment. Ecosystem is in position 1/5 in a GOLD path.", + "comments": [ + "The abiotic factors play a profound role on the type and composition of organisms in a given environment. The GOLD Ecosystem at the top of the five-level classification system is aimed at capturing the broader environment from which an organism or environmental sample is collected. The three broad groups under Ecosystem are Environmental, Host-associated, and Engineered. They represent samples collected from a natural environment or from another organism or from engineered environments like bioreactors respectively." + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "https://gold.jgi.doe.gov/help" + ], + "rank": 9, + "is_a": "gold_path_field", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "Study", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "EcosystemEnum", + "recommended": true + }, + "ecosystem_category": { + "name": "ecosystem_category", + "description": "Ecosystem categories represent divisions within the ecosystem based on specific characteristics of the environment from where an organism or sample is isolated. Ecosystem category is in position 2/5 in a GOLD path.", + "comments": [ + "The Environmental ecosystem (for example) is divided into Air, Aquatic and Terrestrial. Ecosystem categories for Host-associated samples can be individual hosts or phyla and for engineered samples it may be manipulated environments like bioreactors, solid waste etc." + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "https://gold.jgi.doe.gov/help" + ], + "rank": 10, + "is_a": "gold_path_field", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "Study", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "EcosystemCategoryEnum", + "recommended": true + }, + "ecosystem_subtype": { + "name": "ecosystem_subtype", + "description": "Ecosystem subtypes represent further subdivision of Ecosystem types into more distinct subtypes. Ecosystem subtype is in position 4/5 in a GOLD path.", + "comments": [ + "Ecosystem Type Marine (Environmental -> Aquatic -> Marine) is further divided (for example) into Intertidal zone, Coastal, Pelagic, Intertidal zone etc. in the Ecosystem subtype category." + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "https://gold.jgi.doe.gov/help" + ], + "rank": 12, + "is_a": "gold_path_field", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "Study", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "EcosystemSubtypeEnum", + "recommended": true + }, + "ecosystem_type": { + "name": "ecosystem_type", + "description": "Ecosystem types represent things having common characteristics within the Ecosystem Category. These common characteristics based grouping is still broad but specific to the characteristics of a given environment. Ecosystem type is in position 3/5 in a GOLD path.", + "comments": [ + "The Aquatic ecosystem category (for example) may have ecosystem types like Marine or Thermal springs etc. Ecosystem category Air may have Indoor air or Outdoor air as different Ecosystem Types. In the case of Host-associated samples, ecosystem type can represent Respiratory system, Digestive system, Roots etc." + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "https://gold.jgi.doe.gov/help" + ], + "rank": 11, + "is_a": "gold_path_field", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "Study", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "EcosystemTypeEnum", + "recommended": true + }, + "elev": { + "name": "elev", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + } + }, + "description": "Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit.", + "title": "elevation, meters", + "comments": [ + "All elevations must be reported in meters. Provide the numerical portion only.", + "Please use https://www.advancedconverter.com/map-tools/find-altitude-by-coordinates, if needed, to help estimate the elevation based on latitude and longitude coordinates." + ], + "examples": [ + { + "value": "225" + }, + { + "value": "0" + }, + { + "value": "1250" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "elevation" + ], + "rank": 6, + "is_a": "environment field", + "slot_uri": "MIXS:0000093", + "owner": "Biosample", + "domain_of": [ + "FieldResearchSite", + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "float", + "required": true, + "multivalued": false + }, + "env_broad_scale": { + "name": "env_broad_scale", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "The major environment type(s) where the sample was collected. Recommend subclasses of biome [ENVO:00000428]. Multiple terms can be separated by one or more pipes." + }, + "tooltip": { + "tag": "tooltip", + "value": "The biome or major environmental system where the sample or specimen originated. Choose values from subclasses of the 'biome' class [ENVO:00000428] in the Environment Ontology (ENVO). For host-associated or plant-associated samples, use terms from the UBERON or Plant Ontology to describe the broad anatomical or morphological context" + } + }, + "description": "In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO's biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html", + "title": "broad-scale environmental context", + "notes": [ + "range changed to enumeration late in makefile, so this is modified (but \"sample ID\" anyway)" + ], + "examples": [ + { + "value": "oceanic epipelagic zone biome [ENVO:01000033] for annotating a water sample from the photic zone in middle of the Atlantic Ocean" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "broad-scale environmental context" + ], + "rank": 6, + "is_a": "environment field", + "string_serialization": "{termLabel} {[termID]}", + "slot_uri": "MIXS:0000012", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "string", + "required": true, + "multivalued": false, + "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$" + }, + "env_local_scale": { + "name": "env_local_scale", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "Environmental entities having causal influences upon the entity at time of sampling." + }, + "tooltip": { + "tag": "tooltip", + "value": "The specific environmental entities or features near the sample or specimen that significantly influence its characteristics or composition. These entities are typically smaller in scale than the broad environmental context. Values for this field should be countable, material nouns and must be chosen from subclasses of BFO:0000040 (material entity) that appear in the Environment Ontology (ENVO). For host-associated or plant-associated samples, use terms from the UBERON or Plant Ontology to describe specific anatomical structures or plant parts." + } + }, + "description": "Report the entity or entities which are in the sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. We recommend using EnvO terms which are of smaller spatial grain than your entry for env_broad_scale. Terms, such as anatomical sites, from other OBO Library ontologies which interoperate with EnvO (e.g. UBERON) are accepted in this field. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS.", + "title": "local environmental context", + "notes": [ + "range changed to enumeration late in makefile, so this is modified (but \"sample ID\" anyway)" + ], + "examples": [ + { + "value": "canopy [ENVO:00000047]" + }, + { + "value": "herb and fern layer [ENVO:01000337]" + }, + { + "value": "litter layer [ENVO:01000338]" + }, + { + "value": "understory [01000335]" + }, + { + "value": "shrub layer [ENVO:01000336]" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "local environmental context" + ], + "rank": 7, + "is_a": "environment field", + "string_serialization": "{termLabel} {[termID]}", + "slot_uri": "MIXS:0000013", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "string", + "required": true, + "multivalued": false, + "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$" + }, + "env_medium": { + "name": "env_medium", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "The material displaced by the entity at time of sampling. Recommend subclasses of environmental material [ENVO:00010483]." + }, + "tooltip": { + "tag": "tooltip", + "value": "The predominant environmental material or substrate that directly surrounds or hosts the sample or specimen at the time of sampling. Choose values from subclasses of the 'environmental material' class [ENVO:00010483] in the Environment Ontology (ENVO). Values for this field should be measurable or mass material nouns, representing continuous environmental materials. For host-associated or plant-associated samples, use terms from the UBERON or Plant Ontology to indicate a tissue, organ, or plant structure" + } + }, + "description": "Report the environmental material(s) immediately surrounding the sample or specimen at the time of sampling. We recommend using subclasses of 'environmental material' (http://purl.obolibrary.org/obo/ENVO_00010483). EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS . Terms from other OBO ontologies are permissible as long as they reference mass/volume nouns (e.g. air, water, blood) and not discrete, countable entities (e.g. a tree, a leaf, a table top).", + "title": "environmental medium", + "notes": [ + "range changed to enumeration late in makefile, so this is modified (but \"sample ID\" anyway)" + ], + "examples": [ + { + "value": "soil [ENVO:00001998]" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "environmental medium" + ], + "rank": 8, + "is_a": "environment field", + "string_serialization": "{termLabel} {[termID]}", + "slot_uri": "MIXS:0000014", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "string", + "required": true, + "multivalued": false, + "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$" + }, + "experimental_factor": { + "name": "experimental_factor", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "text or EFO and/or OBI" + } + }, + "description": "Experimental factors are essentially the variable aspects of an experiment design which can be used to describe an experiment, or set of experiments, in an increasingly detailed manner. This field accepts ontology terms from Experimental Factor Ontology (EFO) and/or Ontology for Biomedical Investigations (OBI). For a browser of EFO (v 2.95) terms, please see http://purl.bioontology.org/ontology/EFO; for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI", + "title": "experimental factor", + "examples": [ + { + "value": "time series design [EFO:EFO_0001779]" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "experimental factor" + ], + "rank": 12, + "is_a": "investigation field", + "string_serialization": "{termLabel} {[termID]}|{text}", + "slot_uri": "MIXS:0000008", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false + }, + "genetic_mod": { + "name": "genetic_mod", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "PMID,DOI,url or free text" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Genetic modifications of the genome of an organism, which may occur naturally by spontaneous mutation, or be introduced by some experimental means, e.g. specification of a transgene or the gene knocked-out or details of transient transfection", + "title": "genetic modification", + "examples": [ + { + "value": "aox1A transgenic" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "genetic modification" + ], + "rank": 244, + "is_a": "core field", + "string_serialization": "{PMID}|{DOI}|{URL}|{text}", + "slot_uri": "MIXS:0000859", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "HostAssociatedInterface", + "PlantAssociatedInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "geo_loc_name": { + "name": "geo_loc_name", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "country or sea name (INSDC or GAZ): region(GAZ), specific location name" + } + }, + "description": "The geographical origin of the sample as defined by the country or sea name followed by specific region name.", + "title": "geographic location (country and/or sea,region)", + "examples": [ + { + "value": "USA: Maryland, Bethesda" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "geographic location (country and/or sea,region)" + ], + "rank": 4, + "is_a": "environment field", + "string_serialization": "{text}: {text}, {text}", + "slot_uri": "MIXS:0000010", + "owner": "Biosample", + "domain_of": [ + "FieldResearchSite", + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "required": true, + "multivalued": false, + "pattern": "^[^:, ][^:]*: [^:, ][^,]*, [^:, ].*$" + }, + "gravidity": { + "name": "gravidity", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "gravidity status;timestamp" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Whether or not subject is gravid, and if yes date due or date post-conception, specifying which is used", + "title": "gravidity", + "examples": [ + { + "value": "yes;due date:2018-05-11" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "gravidity" + ], + "rank": 312, + "is_a": "core field", + "string_serialization": "{boolean};{timestamp}", + "slot_uri": "MIXS:0000875", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "HostAssociatedInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "host_age": { + "name": "host_age", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "year, day, hour" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees", + "title": "host age", + "examples": [ + { + "value": "10 days" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "host age" + ], + "rank": 249, + "is_a": "core field", + "slot_uri": "MIXS:0000255", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "HostAssociatedInterface", + "PlantAssociatedInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "host_body_habitat": { + "name": "host_body_habitat", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "free text" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Original body habitat where the sample was obtained from", + "title": "host body habitat", + "examples": [ + { + "value": "nasopharynx" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "host body habitat" + ], + "rank": 319, + "is_a": "core field", + "string_serialization": "{text}", + "slot_uri": "MIXS:0000866", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "HostAssociatedInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "host_body_product": { + "name": "host_body_product", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "FMA or UBERON" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon", + "title": "host body product", + "examples": [ + { + "value": "Portion of mucus [fma66938]" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "host body product" + ], + "rank": 320, + "is_a": "core field", + "string_serialization": "{termLabel} {[termID]}", + "slot_uri": "MIXS:0000888", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "HostAssociatedInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$" + }, + "host_body_site": { + "name": "host_body_site", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "FMA or UBERON" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON", + "title": "host body site", + "examples": [ + { + "value": "gill [UBERON:0002535]" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "host body site" + ], + "rank": 321, + "is_a": "core field", + "string_serialization": "{termLabel} {[termID]}", + "slot_uri": "MIXS:0000867", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "HostAssociatedInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$" + }, + "host_body_temp": { + "name": "host_body_temp", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "degree Celsius" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Core body temperature of the host when sample was collected", + "title": "host body temperature", + "examples": [ + { + "value": "15 degree Celsius" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "host body temperature" + ], + "rank": 322, + "is_a": "core field", + "slot_uri": "MIXS:0000274", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "HostAssociatedInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "host_color": { + "name": "host_color", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "color" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The color of host", + "title": "host color", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "host color" + ], + "rank": 323, + "is_a": "core field", + "string_serialization": "{text}", + "slot_uri": "MIXS:0000260", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "HostAssociatedInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "host_common_name": { + "name": "host_common_name", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "common name" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Common name of the host.", + "title": "host common name", + "examples": [ + { + "value": "human" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "host common name" + ], + "rank": 250, + "is_a": "core field", + "string_serialization": "{text}", + "slot_uri": "MIXS:0000248", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "HostAssociatedInterface", + "PlantAssociatedInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "host_diet": { + "name": "host_diet", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "diet type" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types", + "title": "host diet", + "examples": [ + { + "value": "herbivore" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "host diet" + ], + "rank": 324, + "is_a": "core field", + "string_serialization": "{text}", + "slot_uri": "MIXS:0000869", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "HostAssociatedInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "host_disease_stat": { + "name": "host_disease_stat", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "disease name or Disease Ontology term" + } + }, + "description": "List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text", + "title": "host disease status", + "examples": [ + { + "value": "rabies [DOID:11260]" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "host disease status" + ], + "rank": 390, + "is_a": "nucleic acid sequence source field", + "string_serialization": "{termLabel} {[termID]}|{text}", + "slot_uri": "MIXS:0000031", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "HostAssociatedInterface", + "PlantAssociatedInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "host_dry_mass": { + "name": "host_dry_mass", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "kilogram, gram" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Measurement of dry mass", + "title": "host dry mass", + "examples": [ + { + "value": "500 gram" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "host dry mass" + ], + "rank": 251, + "is_a": "core field", + "slot_uri": "MIXS:0000257", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "HostAssociatedInterface", + "PlantAssociatedInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "host_family_relation": { + "name": "host_family_relation", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "relationship type;arbitrary identifier" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Familial relationships to other hosts in the same study; can include multiple relationships", + "title": "host family relationship", + "examples": [ + { + "value": "offspring;Mussel25" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "host family relationship" + ], + "rank": 325, + "is_a": "core field", + "string_serialization": "{text};{text}", + "slot_uri": "MIXS:0000872", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "HostAssociatedInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "host_genotype": { + "name": "host_genotype", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "genotype" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Observed genotype", + "title": "host genotype", + "examples": [ + { + "value": "C57BL/6" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "host genotype" + ], + "rank": 252, + "is_a": "core field", + "string_serialization": "{text}", + "slot_uri": "MIXS:0000365", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "HostAssociatedInterface", + "PlantAssociatedInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "host_growth_cond": { + "name": "host_growth_cond", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "PMID,DOI,url or free text" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Literature reference giving growth conditions of the host", + "title": "host growth conditions", + "examples": [ + { + "value": "https://academic.oup.com/icesjms/article/68/2/349/617247" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "host growth conditions" + ], + "rank": 326, + "is_a": "core field", + "string_serialization": "{PMID}|{DOI}|{URL}|{text}", + "slot_uri": "MIXS:0000871", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "HostAssociatedInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "host_height": { + "name": "host_height", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "centimeter, millimeter, meter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The height of subject", + "title": "host height", + "examples": [ + { + "value": "0.1 meter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "host height" + ], + "rank": 253, + "is_a": "core field", + "slot_uri": "MIXS:0000264", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "HostAssociatedInterface", + "PlantAssociatedInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "host_last_meal": { + "name": "host_last_meal", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "content;duration" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Content of last meal and time since feeding; can include multiple values", + "title": "host last meal", + "examples": [ + { + "value": "corn feed;P2H" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "host last meal" + ], + "rank": 327, + "is_a": "core field", + "string_serialization": "{text};{duration}", + "slot_uri": "MIXS:0000870", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "HostAssociatedInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "host_length": { + "name": "host_length", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "centimeter, millimeter, meter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The length of subject", + "title": "host length", + "examples": [ + { + "value": "1 meter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "host length" + ], + "rank": 254, + "is_a": "core field", + "slot_uri": "MIXS:0000256", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "HostAssociatedInterface", + "PlantAssociatedInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "host_life_stage": { + "name": "host_life_stage", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "stage" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Description of life stage of host", + "title": "host life stage", + "examples": [ + { + "value": "adult" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "host life stage" + ], + "rank": 255, + "is_a": "core field", + "string_serialization": "{text}", + "slot_uri": "MIXS:0000251", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "HostAssociatedInterface", + "PlantAssociatedInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "host_phenotype": { + "name": "host_phenotype", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "PATO or HP" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP", + "title": "host phenotype", + "examples": [ + { + "value": "elongated [PATO:0001154]" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "host phenotype" + ], + "rank": 256, + "is_a": "core field", + "string_serialization": "{termLabel} {[termID]}", + "slot_uri": "MIXS:0000874", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "HostAssociatedInterface", + "PlantAssociatedInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$" + }, + "host_sex": { + "name": "host_sex", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Gender or physical sex of the host.", + "title": "host sex", + "examples": [ + { + "value": "non-binary" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "host sex" + ], + "rank": 328, + "is_a": "core field", + "slot_uri": "MIXS:0000811", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "HostAssociatedInterface" + ], + "slot_group": "mixs_core_section", + "range": "host_sex_enum", + "multivalued": false + }, + "host_shape": { + "name": "host_shape", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "shape" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Morphological shape of host", + "title": "host shape", + "examples": [ + { + "value": "round" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "host shape" + ], + "rank": 329, + "is_a": "core field", + "string_serialization": "{text}", + "slot_uri": "MIXS:0000261", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "HostAssociatedInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "host_subject_id": { + "name": "host_subject_id", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "unique identifier" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "A unique identifier by which each subject can be referred to, de-identified.", + "title": "host subject id", + "examples": [ + { + "value": "MPI123" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "host subject id" + ], + "rank": 330, + "is_a": "core field", + "string_serialization": "{text}", + "slot_uri": "MIXS:0000861", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "HostAssociatedInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "host_subspecf_genlin": { + "name": "host_subspecf_genlin", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "Genetic lineage below lowest rank of NCBI taxonomy, which is subspecies, e.g. serovar, biotype, ecotype, variety, cultivar." + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Information about the genetic distinctness of the host organism below the subspecies level e.g., serovar, serotype, biotype, ecotype, variety, cultivar, or any relevant genetic typing schemes like Group I plasmid. Subspecies should not be recorded in this term, but in the NCBI taxonomy. Supply both the lineage name and the lineage rank separated by a colon, e.g., biovar:abc123.", + "title": "host subspecific genetic lineage", + "examples": [ + { + "value": "serovar:Newport, variety:glabrum, cultivar: Red Delicious" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "host subspecific genetic lineage" + ], + "rank": 257, + "is_a": "core field", + "string_serialization": "{rank name}:{text}", + "slot_uri": "MIXS:0001318", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "HostAssociatedInterface", + "PlantAssociatedInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "host_substrate": { + "name": "host_substrate", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "substrate name" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The growth substrate of the host.", + "title": "host substrate", + "examples": [ + { + "value": "rock" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "host substrate" + ], + "rank": 331, + "is_a": "core field", + "string_serialization": "{text}", + "slot_uri": "MIXS:0000252", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "HostAssociatedInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "host_symbiont": { + "name": "host_symbiont", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "species name or common name" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host.", + "title": "observed host symbionts", + "examples": [ + { + "value": "flukeworms" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "observed host symbionts" + ], + "rank": 258, + "is_a": "core field", + "string_serialization": "{text}", + "slot_uri": "MIXS:0001298", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "HostAssociatedInterface", + "PlantAssociatedInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "host_taxid": { + "name": "host_taxid", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "NCBI taxon identifier" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "NCBI taxon id of the host, e.g. 9606", + "title": "host taxid", + "comments": [ + "Homo sapiens [NCBITaxon:9606] would be a reasonable has_raw_value" + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "host taxid" + ], + "rank": 259, + "is_a": "core field", + "slot_uri": "MIXS:0000250", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "HostAssociatedInterface", + "PlantAssociatedInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "host_tot_mass": { + "name": "host_tot_mass", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "kilogram, gram" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Total mass of the host at collection, the unit depends on host", + "title": "host total mass", + "examples": [ + { + "value": "2500 gram" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "host total mass" + ], + "rank": 260, + "is_a": "core field", + "slot_uri": "MIXS:0000263", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "HostAssociatedInterface", + "PlantAssociatedInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "lat_lon": { + "name": "lat_lon", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "decimal degrees, limit to 8 decimal points" + } + }, + "description": "The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system", + "title": "geographic location (latitude and longitude)", + "notes": [ + "This is currently a required field but it's not clear if this should be required for human hosts" + ], + "examples": [ + { + "value": "50.586825 6.408977" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "geographic location (latitude and longitude)" + ], + "rank": 5, + "is_a": "environment field", + "string_serialization": "{lat lon}", + "slot_uri": "MIXS:0000009", + "owner": "Biosample", + "domain_of": [ + "FieldResearchSite", + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "required": true, + "multivalued": false, + "pattern": "^[-+]?([1-8]?\\d(\\.\\d{1,8})?|90(\\.0{1,8})?)\\s[-+]?(180(\\.0{1,8})?|((1[0-7]\\d)|([1-9]?\\d))(\\.\\d{1,8})?)$" + }, + "misc_param": { + "name": "misc_param", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "parameter name;measurement value" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Any other measurement performed or parameter collected, that is not listed here", + "title": "miscellaneous parameter", + "examples": [ + { + "value": "Bicarbonate ion concentration;2075 micromole per kilogram" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "miscellaneous parameter" + ], + "rank": 23, + "is_a": "core field", + "string_serialization": "{text};{float} {unit}", + "slot_uri": "MIXS:0000752", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false, + "pattern": "^([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+\\|)*([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+)$" + }, + "organism_count": { + "name": "organism_count", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "organism name;measurement value;enumeration" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "number of cells per cubic meter, number of cells per milliliter, number of cells per cubic centimeter" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr)", + "title": "organism count", + "examples": [ + { + "value": "total prokaryotes;3.5e7 cells per milliliter;qPCR" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "organism count" + ], + "rank": 30, + "is_a": "core field", + "slot_uri": "MIXS:0000103", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^([-+]?[0-9]*\\.?[0-9]+ +\\S.*\\|)*([-+]?[0-9]*\\.?[0-9]+ +\\S.*)$" + }, + "oxy_stat_samp": { + "name": "oxy_stat_samp", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Oxygenation status of sample", + "title": "oxygenation status of sample", + "examples": [ + { + "value": "aerobic" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "oxygenation status of sample" + ], + "rank": 25, + "is_a": "core field", + "slot_uri": "MIXS:0000753", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_section", + "range": "OxyStatSampEnum", + "multivalued": false + }, + "perturbation": { + "name": "perturbation", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "perturbation type name;perturbation interval and duration" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types", + "title": "perturbation", + "examples": [ + { + "value": "antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "perturbation" + ], + "rank": 33, + "is_a": "core field", + "string_serialization": "{text};{Rn/start_time/end_time/duration}", + "slot_uri": "MIXS:0000754", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "salinity": { + "name": "salinity", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "practical salinity unit, percentage" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The total concentration of all dissolved salts in a liquid or solid sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater.", + "title": "salinity", + "examples": [ + { + "value": "25 practical salinity unit" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "salinity" + ], + "rank": 54, + "is_a": "core field", + "slot_uri": "MIXS:0000183", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "samp_capt_status": { + "name": "samp_capt_status", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Reason for the sample", + "title": "sample capture status", + "examples": [ + { + "value": "farm sample" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sample capture status" + ], + "rank": 282, + "is_a": "core field", + "slot_uri": "MIXS:0000860", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "HostAssociatedInterface", + "PlantAssociatedInterface" + ], + "slot_group": "mixs_core_section", + "range": "samp_capt_status_enum", + "multivalued": false + }, + "samp_collec_device": { + "name": "samp_collec_device", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "device name" + } + }, + "description": "The device used to collect an environmental sample. This field accepts terms listed under environmental sampling device (http://purl.obolibrary.org/obo/ENVO). This field also accepts terms listed under specimen collection device (http://purl.obolibrary.org/obo/GENEPIO_0002094).", + "title": "sample collection device", + "comments": [ + "Report dimensions and details when applicable" + ], + "examples": [ + { + "value": "swab, biopsy, niskin bottle, push core, drag swab [GENEPIO:0002713]" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sample collection device" + ], + "rank": 14, + "is_a": "nucleic acid sequence source field", + "string_serialization": "{termLabel} {[termID]}|{text}", + "slot_uri": "MIXS:0000002", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "recommended": true, + "multivalued": false + }, + "samp_collec_method": { + "name": "samp_collec_method", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "PMID,DOI,url , or text" + } + }, + "description": "The method employed for collecting the sample.", + "title": "sample collection method", + "comments": [ + "This can be a citation or description" + ], + "examples": [ + { + "value": "swabbing" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sample collection method" + ], + "rank": 15, + "is_a": "nucleic acid sequence source field", + "string_serialization": "{PMID}|{DOI}|{URL}|{text}", + "slot_uri": "MIXS:0001225", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "multivalued": false + }, + "samp_dis_stage": { + "name": "samp_dis_stage", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Stage of the disease at the time of sample collection, e.g. inoculation, penetration, infection, growth and reproduction, dissemination of pathogen.", + "title": "sample disease stage", + "examples": [ + { + "value": "infection" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sample disease stage" + ], + "rank": 283, + "is_a": "core field", + "slot_uri": "MIXS:0000249", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "HostAssociatedInterface", + "PlantAssociatedInterface" + ], + "slot_group": "mixs_core_section", + "range": "samp_dis_stage_enum", + "multivalued": false + }, + "samp_mat_process": { + "name": "samp_mat_process", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "text" + } + }, + "description": "A brief description of any processing applied to the sample during or after retrieving the sample from environment, or a link to the relevant protocol(s) performed.", + "title": "sample material processing", + "examples": [ + { + "value": "filtering of seawater" + }, + { + "value": "storing samples in ethanol" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sample material processing" + ], + "rank": 12, + "is_a": "nucleic acid sequence source field", + "string_serialization": "{text}", + "slot_uri": "MIXS:0000016", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "multivalued": false + }, + "samp_size": { + "name": "samp_size", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "millliter, gram, milligram, liter" + } + }, + "description": "The total amount or size (volume (ml), mass (g) or area (m2) ) of sample collected.", + "title": "amount or size of sample collected", + "comments": [ + "This refers to the TOTAL amount of sample collected from the experiment. NOT the amount sent to each institution or collected for a specific analysis." + ], + "examples": [ + { + "value": "5 grams" + }, + { + "value": "10 mL" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "amount or size of sample collected" + ], + "rank": 18, + "is_a": "nucleic acid sequence source field", + "string_serialization": "{float} {unit}", + "slot_uri": "MIXS:0000001", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? \\S+$" + }, + "samp_store_dur": { + "name": "samp_store_dur", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "duration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Duration for which the sample was stored", + "title": "sample storage duration", + "examples": [ + { + "value": "P1Y6M" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sample storage duration" + ], + "rank": 353, + "is_a": "core field", + "string_serialization": "{duration}", + "slot_uri": "MIXS:0000116", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "samp_store_loc": { + "name": "samp_store_loc", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "location name" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Location at which sample was stored, usually name of a specific freezer/room", + "title": "sample storage location", + "examples": [ + { + "value": "Freezer no:5" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sample storage location" + ], + "rank": 41, + "is_a": "core field", + "string_serialization": "{text}", + "slot_uri": "MIXS:0000755", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "samp_store_temp": { + "name": "samp_store_temp", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "degree Celsius" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Temperature at which the sample was stored (degrees are assumed)", + "title": "sample storage temperature", + "examples": [ + { + "value": "-80 Celsius" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sample storage temperature" + ], + "rank": 7, + "is_a": "core field", + "slot_uri": "MIXS:0000110", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "required": true, + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "sample_link": { + "name": "sample_link", + "description": "A unique identifier to assign parent-child, subsample, or sibling samples. This is relevant when a sample or other material was used to generate the new sample.", + "title": "sample linkage", + "notes": [ + "also tempted to include SampIdNewTermsMixin but if len(slot_usage.keys()) > 1 and \"placeholder\" in slot_usage.keys():AttributeError: 'list' object has no attribute 'keys'" + ], + "comments": [ + "This field allows multiple entries separated by ; (Examples: Soil collected from the field will link with the soil used in an incubation. The soil a plant was grown in links to the plant sample. An original culture sample was transferred to a new vial and generated a new sample)" + ], + "examples": [ + { + "value": "IGSN:DSJ0284" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "rank": 5, + "string_serialization": "{text}:{text}", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface", + "SampIdNewTermsMixin" + ], + "slot_group": "sample_id_section", + "range": "string", + "recommended": true, + "multivalued": false, + "pattern": "[^\\:\\n\\r]+\\:[^\\:\\n\\r]+" + }, + "size_frac": { + "name": "size_frac", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "filter size value range" + } + }, + "description": "Filtering pore size used in sample preparation", + "title": "size fraction selected", + "examples": [ + { + "value": "0-0.22 micrometer" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "size fraction selected" + ], + "rank": 285, + "is_a": "nucleic acid sequence source field", + "string_serialization": "{float}-{float} {unit}", + "slot_uri": "MIXS:0000017", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "specific_ecosystem": { + "name": "specific_ecosystem", + "description": "Specific ecosystems represent specific features of the environment like aphotic zone in an ocean or gastric mucosa within a host digestive system. Specific ecosystem is in position 5/5 in a GOLD path.", + "comments": [ + "Specific ecosystems help to define samples based on very specific characteristics of an environment under the five-level classification system." + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "https://gold.jgi.doe.gov/help" + ], + "rank": 13, + "is_a": "gold_path_field", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "Study", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "SpecificEcosystemEnum", + "recommended": true + }, + "temp": { + "name": "temp", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "degree Celsius" + } + }, + "description": "Temperature of the sample at the time of sampling.", + "title": "temperature", + "examples": [ + { + "value": "25 degree Celsius" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "temperature" + ], + "rank": 37, + "is_a": "environment field", + "slot_uri": "MIXS:0000113", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "horizon_meth": { + "name": "horizon_meth", + "title": "horizon method" + } + }, + "attributes": { + "alt": { + "name": "alt", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + } + }, + "description": "Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air", + "title": "altitude", + "examples": [ + { + "value": "100 meter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "altitude" + ], + "rank": 26, + "is_a": "environment field", + "slot_uri": "MIXS:0000094", + "alias": "alt", + "owner": "HostAssociatedInterface", + "domain_of": [ + "agriculture", + "air", + "built environment", + "core", + "food-animal and animal feed", + "food-farm environment", + "food-food production facility", + "food-human foods", + "host-associated", + "human-associated", + "human-gut", + "human-oral", + "human-skin", + "human-vaginal", + "hydrocarbon resources-cores", + "hydrocarbon resources-fluids_swabs", + "microbial mat_biofilm", + "miscellaneous natural or artificial environment", + "plant-associated", + "sediment", + "soil", + "symbiont-associated", + "wastewater_sludge", + "water", + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HostAssociatedInterface", + "MiscEnvsInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "recommended": true, + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "ances_data": { + "name": "ances_data", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "free text" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Information about either pedigree or other ancestral information description (e.g. parental variety in case of mutant or selection), e.g. A/3*B (meaning [(A x B) x B] x B)", + "title": "ancestral data", + "examples": [ + { + "value": "A/3*B" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "ancestral data" + ], + "rank": 237, + "is_a": "core field", + "string_serialization": "{text}", + "slot_uri": "MIXS:0000247", + "alias": "ances_data", + "owner": "HostAssociatedInterface", + "domain_of": [ + "Biosample", + "HostAssociatedInterface", + "PlantAssociatedInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "biol_stat": { + "name": "biol_stat", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The level of genome modification.", + "title": "biological status", + "examples": [ + { + "value": "natural" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "biological status" + ], + "rank": 239, + "is_a": "core field", + "slot_uri": "MIXS:0000858", + "alias": "biol_stat", + "owner": "HostAssociatedInterface", + "domain_of": [ + "Biosample", + "HostAssociatedInterface", + "PlantAssociatedInterface" + ], + "slot_group": "mixs_core_section", + "range": "biol_stat_enum", + "multivalued": false + }, + "blood_press_diast": { + "name": "blood_press_diast", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "millimeter mercury" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Resting diastolic blood pressure, measured as mm mercury", + "title": "host blood pressure diastolic", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "host blood pressure diastolic" + ], + "rank": 299, + "is_a": "core field", + "slot_uri": "MIXS:0000258", + "alias": "blood_press_diast", + "owner": "HostAssociatedInterface", + "domain_of": [ + "Biosample", + "HostAssociatedInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "blood_press_syst": { + "name": "blood_press_syst", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "millimeter mercury" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Resting systolic blood pressure, measured as mm mercury", + "title": "host blood pressure systolic", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "host blood pressure systolic" + ], + "rank": 300, + "is_a": "core field", + "slot_uri": "MIXS:0000259", + "alias": "blood_press_syst", + "owner": "HostAssociatedInterface", + "domain_of": [ + "Biosample", + "HostAssociatedInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "chem_administration": { + "name": "chem_administration", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "CHEBI;timestamp" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi", + "title": "chemical administration", + "examples": [ + { + "value": "agar [CHEBI:2509];2018-05-11|agar [CHEBI:2509];2018-05-22" + }, + { + "value": "agar [CHEBI:2509];2018-05" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "chemical administration" + ], + "rank": 17, + "is_a": "core field", + "string_serialization": "{termLabel} {[termID]};{timestamp}", + "slot_uri": "MIXS:0000751", + "alias": "chem_administration", + "owner": "HostAssociatedInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "recommended": true, + "multivalued": false, + "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\];([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$" + }, + "collection_date": { + "name": "collection_date", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "date and time" + } + }, + "description": "The date of sampling", + "title": "collection date", + "notes": [ + "MIxS collection_date accepts (truncated) ISO8601. DH taking arb prec date only", + "Use modified term (amended definition)" + ], + "examples": [ + { + "value": "2021-04-15" + }, + { + "value": "2021-04" + }, + { + "value": "2021" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "collection date" + ], + "rank": 3, + "is_a": "environment field", + "string_serialization": "{date, arbitrary precision}", + "slot_uri": "MIXS:0000011", + "alias": "collection_date", + "owner": "HostAssociatedInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "required": true, + "multivalued": false, + "pattern": "^[12]\\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\\d|3[01]))?)?$" + }, + "depth": { + "name": "depth", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + } + }, + "description": "The vertical distance below local surface, e.g. for sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples.", + "title": "depth, meters", + "notes": [ + "Use modified term" + ], + "comments": [ + "All depths must be reported in meters. Provide the numerical portion only." + ], + "examples": [ + { + "value": "0 - 0.1" + }, + { + "value": "1" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "depth" + ], + "rank": 9, + "is_a": "environment field", + "string_serialization": "{float}|{float}-{float}", + "slot_uri": "MIXS:0000018", + "alias": "depth", + "owner": "HostAssociatedInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "recommended": true, + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)?(\\s*-\\s*[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)?)?$" + }, + "ecosystem": { + "name": "ecosystem", + "description": "An ecosystem is a combination of a physical environment (abiotic factors) and all the organisms (biotic factors) that interact with this environment. Ecosystem is in position 1/5 in a GOLD path.", + "comments": [ + "The abiotic factors play a profound role on the type and composition of organisms in a given environment. The GOLD Ecosystem at the top of the five-level classification system is aimed at capturing the broader environment from which an organism or environmental sample is collected. The three broad groups under Ecosystem are Environmental, Host-associated, and Engineered. They represent samples collected from a natural environment or from another organism or from engineered environments like bioreactors respectively." + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "https://gold.jgi.doe.gov/help" + ], + "rank": 9, + "is_a": "gold_path_field", + "alias": "ecosystem", + "owner": "HostAssociatedInterface", + "domain_of": [ + "Biosample", + "Study", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "EcosystemEnum", + "recommended": true + }, + "ecosystem_category": { + "name": "ecosystem_category", + "description": "Ecosystem categories represent divisions within the ecosystem based on specific characteristics of the environment from where an organism or sample is isolated. Ecosystem category is in position 2/5 in a GOLD path.", + "comments": [ + "The Environmental ecosystem (for example) is divided into Air, Aquatic and Terrestrial. Ecosystem categories for Host-associated samples can be individual hosts or phyla and for engineered samples it may be manipulated environments like bioreactors, solid waste etc." + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "https://gold.jgi.doe.gov/help" + ], + "rank": 10, + "is_a": "gold_path_field", + "alias": "ecosystem_category", + "owner": "HostAssociatedInterface", + "domain_of": [ + "Biosample", + "Study", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "EcosystemCategoryEnum", + "recommended": true + }, + "ecosystem_subtype": { + "name": "ecosystem_subtype", + "description": "Ecosystem subtypes represent further subdivision of Ecosystem types into more distinct subtypes. Ecosystem subtype is in position 4/5 in a GOLD path.", + "comments": [ + "Ecosystem Type Marine (Environmental -> Aquatic -> Marine) is further divided (for example) into Intertidal zone, Coastal, Pelagic, Intertidal zone etc. in the Ecosystem subtype category." + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "https://gold.jgi.doe.gov/help" + ], + "rank": 12, + "is_a": "gold_path_field", + "alias": "ecosystem_subtype", + "owner": "HostAssociatedInterface", + "domain_of": [ + "Biosample", + "Study", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "EcosystemSubtypeEnum", + "recommended": true + }, + "ecosystem_type": { + "name": "ecosystem_type", + "description": "Ecosystem types represent things having common characteristics within the Ecosystem Category. These common characteristics based grouping is still broad but specific to the characteristics of a given environment. Ecosystem type is in position 3/5 in a GOLD path.", + "comments": [ + "The Aquatic ecosystem category (for example) may have ecosystem types like Marine or Thermal springs etc. Ecosystem category Air may have Indoor air or Outdoor air as different Ecosystem Types. In the case of Host-associated samples, ecosystem type can represent Respiratory system, Digestive system, Roots etc." + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "https://gold.jgi.doe.gov/help" + ], + "rank": 11, + "is_a": "gold_path_field", + "alias": "ecosystem_type", + "owner": "HostAssociatedInterface", + "domain_of": [ + "Biosample", + "Study", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "EcosystemTypeEnum", + "recommended": true + }, + "elev": { + "name": "elev", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + } + }, + "description": "Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit.", + "title": "elevation, meters", + "comments": [ + "All elevations must be reported in meters. Provide the numerical portion only.", + "Please use https://www.advancedconverter.com/map-tools/find-altitude-by-coordinates, if needed, to help estimate the elevation based on latitude and longitude coordinates." + ], + "examples": [ + { + "value": "225" + }, + { + "value": "0" + }, + { + "value": "1250" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "elevation" + ], + "rank": 6, + "is_a": "environment field", + "slot_uri": "MIXS:0000093", + "alias": "elev", + "owner": "HostAssociatedInterface", + "domain_of": [ + "FieldResearchSite", + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "float", + "required": true, + "multivalued": false + }, + "env_broad_scale": { + "name": "env_broad_scale", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "The major environment type(s) where the sample was collected. Recommend subclasses of biome [ENVO:00000428]. Multiple terms can be separated by one or more pipes." + }, + "tooltip": { + "tag": "tooltip", + "value": "The biome or major environmental system where the sample or specimen originated. Choose values from subclasses of the 'biome' class [ENVO:00000428] in the Environment Ontology (ENVO). For host-associated or plant-associated samples, use terms from the UBERON or Plant Ontology to describe the broad anatomical or morphological context" + } + }, + "description": "In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO's biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html", + "title": "broad-scale environmental context", + "notes": [ + "range changed to enumeration late in makefile, so this is modified (but \"sample ID\" anyway)" + ], + "examples": [ + { + "value": "oceanic epipelagic zone biome [ENVO:01000033] for annotating a water sample from the photic zone in middle of the Atlantic Ocean" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "broad-scale environmental context" + ], + "rank": 6, + "is_a": "environment field", + "string_serialization": "{termLabel} {[termID]}", + "slot_uri": "MIXS:0000012", + "alias": "env_broad_scale", + "owner": "HostAssociatedInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "string", + "required": true, + "multivalued": false, + "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$" + }, + "env_local_scale": { + "name": "env_local_scale", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "Environmental entities having causal influences upon the entity at time of sampling." + }, + "tooltip": { + "tag": "tooltip", + "value": "The specific environmental entities or features near the sample or specimen that significantly influence its characteristics or composition. These entities are typically smaller in scale than the broad environmental context. Values for this field should be countable, material nouns and must be chosen from subclasses of BFO:0000040 (material entity) that appear in the Environment Ontology (ENVO). For host-associated or plant-associated samples, use terms from the UBERON or Plant Ontology to describe specific anatomical structures or plant parts." + } + }, + "description": "Report the entity or entities which are in the sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. We recommend using EnvO terms which are of smaller spatial grain than your entry for env_broad_scale. Terms, such as anatomical sites, from other OBO Library ontologies which interoperate with EnvO (e.g. UBERON) are accepted in this field. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS.", + "title": "local environmental context", + "notes": [ + "range changed to enumeration late in makefile, so this is modified (but \"sample ID\" anyway)" + ], + "examples": [ + { + "value": "canopy [ENVO:00000047]" + }, + { + "value": "herb and fern layer [ENVO:01000337]" + }, + { + "value": "litter layer [ENVO:01000338]" + }, + { + "value": "understory [01000335]" + }, + { + "value": "shrub layer [ENVO:01000336]" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "local environmental context" + ], + "rank": 7, + "is_a": "environment field", + "string_serialization": "{termLabel} {[termID]}", + "slot_uri": "MIXS:0000013", + "alias": "env_local_scale", + "owner": "HostAssociatedInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "string", + "required": true, + "multivalued": false, + "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$" + }, + "env_medium": { + "name": "env_medium", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "The material displaced by the entity at time of sampling. Recommend subclasses of environmental material [ENVO:00010483]." + }, + "tooltip": { + "tag": "tooltip", + "value": "The predominant environmental material or substrate that directly surrounds or hosts the sample or specimen at the time of sampling. Choose values from subclasses of the 'environmental material' class [ENVO:00010483] in the Environment Ontology (ENVO). Values for this field should be measurable or mass material nouns, representing continuous environmental materials. For host-associated or plant-associated samples, use terms from the UBERON or Plant Ontology to indicate a tissue, organ, or plant structure" + } + }, + "description": "Report the environmental material(s) immediately surrounding the sample or specimen at the time of sampling. We recommend using subclasses of 'environmental material' (http://purl.obolibrary.org/obo/ENVO_00010483). EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS . Terms from other OBO ontologies are permissible as long as they reference mass/volume nouns (e.g. air, water, blood) and not discrete, countable entities (e.g. a tree, a leaf, a table top).", + "title": "environmental medium", + "notes": [ + "range changed to enumeration late in makefile, so this is modified (but \"sample ID\" anyway)" + ], + "examples": [ + { + "value": "soil [ENVO:00001998]" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "environmental medium" + ], + "rank": 8, + "is_a": "environment field", + "string_serialization": "{termLabel} {[termID]}", + "slot_uri": "MIXS:0000014", + "alias": "env_medium", + "owner": "HostAssociatedInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "string", + "required": true, + "multivalued": false, + "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$" + }, + "experimental_factor": { + "name": "experimental_factor", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "text or EFO and/or OBI" + } + }, + "description": "Experimental factors are essentially the variable aspects of an experiment design which can be used to describe an experiment, or set of experiments, in an increasingly detailed manner. This field accepts ontology terms from Experimental Factor Ontology (EFO) and/or Ontology for Biomedical Investigations (OBI). For a browser of EFO (v 2.95) terms, please see http://purl.bioontology.org/ontology/EFO; for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI", + "title": "experimental factor", + "examples": [ + { + "value": "time series design [EFO:EFO_0001779]" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "experimental factor" + ], + "rank": 12, + "is_a": "investigation field", + "string_serialization": "{termLabel} {[termID]}|{text}", + "slot_uri": "MIXS:0000008", + "alias": "experimental_factor", + "owner": "HostAssociatedInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false + }, + "genetic_mod": { + "name": "genetic_mod", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "PMID,DOI,url or free text" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Genetic modifications of the genome of an organism, which may occur naturally by spontaneous mutation, or be introduced by some experimental means, e.g. specification of a transgene or the gene knocked-out or details of transient transfection", + "title": "genetic modification", + "examples": [ + { + "value": "aox1A transgenic" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "genetic modification" + ], + "rank": 244, + "is_a": "core field", + "string_serialization": "{PMID}|{DOI}|{URL}|{text}", + "slot_uri": "MIXS:0000859", + "alias": "genetic_mod", + "owner": "HostAssociatedInterface", + "domain_of": [ + "Biosample", + "HostAssociatedInterface", + "PlantAssociatedInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "geo_loc_name": { + "name": "geo_loc_name", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "country or sea name (INSDC or GAZ): region(GAZ), specific location name" + } + }, + "description": "The geographical origin of the sample as defined by the country or sea name followed by specific region name.", + "title": "geographic location (country and/or sea,region)", + "examples": [ + { + "value": "USA: Maryland, Bethesda" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "geographic location (country and/or sea,region)" + ], + "rank": 4, + "is_a": "environment field", + "string_serialization": "{text}: {text}, {text}", + "slot_uri": "MIXS:0000010", + "alias": "geo_loc_name", + "owner": "HostAssociatedInterface", + "domain_of": [ + "FieldResearchSite", + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "required": true, + "multivalued": false, + "pattern": "^[^:, ][^:]*: [^:, ][^,]*, [^:, ].*$" + }, + "gravidity": { + "name": "gravidity", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "gravidity status;timestamp" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Whether or not subject is gravid, and if yes date due or date post-conception, specifying which is used", + "title": "gravidity", + "examples": [ + { + "value": "yes;due date:2018-05-11" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "gravidity" + ], + "rank": 312, + "is_a": "core field", + "string_serialization": "{boolean};{timestamp}", + "slot_uri": "MIXS:0000875", + "alias": "gravidity", + "owner": "HostAssociatedInterface", + "domain_of": [ + "Biosample", + "HostAssociatedInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "host_age": { + "name": "host_age", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "year, day, hour" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees", + "title": "host age", + "examples": [ + { + "value": "10 days" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "host age" + ], + "rank": 249, + "is_a": "core field", + "slot_uri": "MIXS:0000255", + "alias": "host_age", + "owner": "HostAssociatedInterface", + "domain_of": [ + "Biosample", + "HostAssociatedInterface", + "PlantAssociatedInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "host_body_habitat": { + "name": "host_body_habitat", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "free text" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Original body habitat where the sample was obtained from", + "title": "host body habitat", + "examples": [ + { + "value": "nasopharynx" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "host body habitat" + ], + "rank": 319, + "is_a": "core field", + "string_serialization": "{text}", + "slot_uri": "MIXS:0000866", + "alias": "host_body_habitat", + "owner": "HostAssociatedInterface", + "domain_of": [ + "Biosample", + "HostAssociatedInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "host_body_product": { + "name": "host_body_product", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "FMA or UBERON" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon", + "title": "host body product", + "examples": [ + { + "value": "Portion of mucus [fma66938]" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "host body product" + ], + "rank": 320, + "is_a": "core field", + "string_serialization": "{termLabel} {[termID]}", + "slot_uri": "MIXS:0000888", + "alias": "host_body_product", + "owner": "HostAssociatedInterface", + "domain_of": [ + "Biosample", + "HostAssociatedInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$" + }, + "host_body_site": { + "name": "host_body_site", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "FMA or UBERON" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON", + "title": "host body site", + "examples": [ + { + "value": "gill [UBERON:0002535]" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "host body site" + ], + "rank": 321, + "is_a": "core field", + "string_serialization": "{termLabel} {[termID]}", + "slot_uri": "MIXS:0000867", + "alias": "host_body_site", + "owner": "HostAssociatedInterface", + "domain_of": [ + "Biosample", + "HostAssociatedInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$" + }, + "host_body_temp": { + "name": "host_body_temp", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "degree Celsius" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Core body temperature of the host when sample was collected", + "title": "host body temperature", + "examples": [ + { + "value": "15 degree Celsius" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "host body temperature" + ], + "rank": 322, + "is_a": "core field", + "slot_uri": "MIXS:0000274", + "alias": "host_body_temp", + "owner": "HostAssociatedInterface", + "domain_of": [ + "Biosample", + "HostAssociatedInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "host_color": { + "name": "host_color", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "color" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The color of host", + "title": "host color", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "host color" + ], + "rank": 323, + "is_a": "core field", + "string_serialization": "{text}", + "slot_uri": "MIXS:0000260", + "alias": "host_color", + "owner": "HostAssociatedInterface", + "domain_of": [ + "Biosample", + "HostAssociatedInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "host_common_name": { + "name": "host_common_name", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "common name" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Common name of the host.", + "title": "host common name", + "examples": [ + { + "value": "human" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "host common name" + ], + "rank": 250, + "is_a": "core field", + "string_serialization": "{text}", + "slot_uri": "MIXS:0000248", + "alias": "host_common_name", + "owner": "HostAssociatedInterface", + "domain_of": [ + "Biosample", + "HostAssociatedInterface", + "PlantAssociatedInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "host_diet": { + "name": "host_diet", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "diet type" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types", + "title": "host diet", + "examples": [ + { + "value": "herbivore" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "host diet" + ], + "rank": 324, + "is_a": "core field", + "string_serialization": "{text}", + "slot_uri": "MIXS:0000869", + "alias": "host_diet", + "owner": "HostAssociatedInterface", + "domain_of": [ + "Biosample", + "HostAssociatedInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "host_disease_stat": { + "name": "host_disease_stat", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "disease name or Disease Ontology term" + } + }, + "description": "List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text", + "title": "host disease status", + "examples": [ + { + "value": "rabies [DOID:11260]" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "host disease status" + ], + "rank": 390, + "is_a": "nucleic acid sequence source field", + "string_serialization": "{termLabel} {[termID]}|{text}", + "slot_uri": "MIXS:0000031", + "alias": "host_disease_stat", + "owner": "HostAssociatedInterface", + "domain_of": [ + "Biosample", + "HostAssociatedInterface", + "PlantAssociatedInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "host_dry_mass": { + "name": "host_dry_mass", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "kilogram, gram" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Measurement of dry mass", + "title": "host dry mass", + "examples": [ + { + "value": "500 gram" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "host dry mass" + ], + "rank": 251, + "is_a": "core field", + "slot_uri": "MIXS:0000257", + "alias": "host_dry_mass", + "owner": "HostAssociatedInterface", + "domain_of": [ + "Biosample", + "HostAssociatedInterface", + "PlantAssociatedInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "host_family_relation": { + "name": "host_family_relation", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "relationship type;arbitrary identifier" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Familial relationships to other hosts in the same study; can include multiple relationships", + "title": "host family relationship", + "examples": [ + { + "value": "offspring;Mussel25" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "host family relationship" + ], + "rank": 325, + "is_a": "core field", + "string_serialization": "{text};{text}", + "slot_uri": "MIXS:0000872", + "alias": "host_family_relation", + "owner": "HostAssociatedInterface", + "domain_of": [ + "Biosample", + "HostAssociatedInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "host_genotype": { + "name": "host_genotype", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "genotype" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Observed genotype", + "title": "host genotype", + "examples": [ + { + "value": "C57BL/6" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "host genotype" + ], + "rank": 252, + "is_a": "core field", + "string_serialization": "{text}", + "slot_uri": "MIXS:0000365", + "alias": "host_genotype", + "owner": "HostAssociatedInterface", + "domain_of": [ + "Biosample", + "HostAssociatedInterface", + "PlantAssociatedInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "host_growth_cond": { + "name": "host_growth_cond", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "PMID,DOI,url or free text" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Literature reference giving growth conditions of the host", + "title": "host growth conditions", + "examples": [ + { + "value": "https://academic.oup.com/icesjms/article/68/2/349/617247" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "host growth conditions" + ], + "rank": 326, + "is_a": "core field", + "string_serialization": "{PMID}|{DOI}|{URL}|{text}", + "slot_uri": "MIXS:0000871", + "alias": "host_growth_cond", + "owner": "HostAssociatedInterface", + "domain_of": [ + "Biosample", + "HostAssociatedInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "host_height": { + "name": "host_height", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "centimeter, millimeter, meter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The height of subject", + "title": "host height", + "examples": [ + { + "value": "0.1 meter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "host height" + ], + "rank": 253, + "is_a": "core field", + "slot_uri": "MIXS:0000264", + "alias": "host_height", + "owner": "HostAssociatedInterface", + "domain_of": [ + "Biosample", + "HostAssociatedInterface", + "PlantAssociatedInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "host_last_meal": { + "name": "host_last_meal", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "content;duration" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Content of last meal and time since feeding; can include multiple values", + "title": "host last meal", + "examples": [ + { + "value": "corn feed;P2H" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "host last meal" + ], + "rank": 327, + "is_a": "core field", + "string_serialization": "{text};{duration}", + "slot_uri": "MIXS:0000870", + "alias": "host_last_meal", + "owner": "HostAssociatedInterface", + "domain_of": [ + "Biosample", + "HostAssociatedInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "host_length": { + "name": "host_length", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "centimeter, millimeter, meter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The length of subject", + "title": "host length", + "examples": [ + { + "value": "1 meter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "host length" + ], + "rank": 254, + "is_a": "core field", + "slot_uri": "MIXS:0000256", + "alias": "host_length", + "owner": "HostAssociatedInterface", + "domain_of": [ + "Biosample", + "HostAssociatedInterface", + "PlantAssociatedInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "host_life_stage": { + "name": "host_life_stage", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "stage" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Description of life stage of host", + "title": "host life stage", + "examples": [ + { + "value": "adult" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "host life stage" + ], + "rank": 255, + "is_a": "core field", + "string_serialization": "{text}", + "slot_uri": "MIXS:0000251", + "alias": "host_life_stage", + "owner": "HostAssociatedInterface", + "domain_of": [ + "Biosample", + "HostAssociatedInterface", + "PlantAssociatedInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "host_phenotype": { + "name": "host_phenotype", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "PATO or HP" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP", + "title": "host phenotype", + "examples": [ + { + "value": "elongated [PATO:0001154]" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "host phenotype" + ], + "rank": 256, + "is_a": "core field", + "string_serialization": "{termLabel} {[termID]}", + "slot_uri": "MIXS:0000874", + "alias": "host_phenotype", + "owner": "HostAssociatedInterface", + "domain_of": [ + "Biosample", + "HostAssociatedInterface", + "PlantAssociatedInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$" + }, + "host_sex": { + "name": "host_sex", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Gender or physical sex of the host.", + "title": "host sex", + "examples": [ + { + "value": "non-binary" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "host sex" + ], + "rank": 328, + "is_a": "core field", + "slot_uri": "MIXS:0000811", + "alias": "host_sex", + "owner": "HostAssociatedInterface", + "domain_of": [ + "Biosample", + "HostAssociatedInterface" + ], + "slot_group": "mixs_core_section", + "range": "host_sex_enum", + "multivalued": false + }, + "host_shape": { + "name": "host_shape", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "shape" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Morphological shape of host", + "title": "host shape", + "examples": [ + { + "value": "round" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "host shape" + ], + "rank": 329, + "is_a": "core field", + "string_serialization": "{text}", + "slot_uri": "MIXS:0000261", + "alias": "host_shape", + "owner": "HostAssociatedInterface", + "domain_of": [ + "Biosample", + "HostAssociatedInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "host_subject_id": { + "name": "host_subject_id", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "unique identifier" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "A unique identifier by which each subject can be referred to, de-identified.", + "title": "host subject id", + "examples": [ + { + "value": "MPI123" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "host subject id" + ], + "rank": 330, + "is_a": "core field", + "string_serialization": "{text}", + "slot_uri": "MIXS:0000861", + "alias": "host_subject_id", + "owner": "HostAssociatedInterface", + "domain_of": [ + "Biosample", + "HostAssociatedInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "host_subspecf_genlin": { + "name": "host_subspecf_genlin", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "Genetic lineage below lowest rank of NCBI taxonomy, which is subspecies, e.g. serovar, biotype, ecotype, variety, cultivar." + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Information about the genetic distinctness of the host organism below the subspecies level e.g., serovar, serotype, biotype, ecotype, variety, cultivar, or any relevant genetic typing schemes like Group I plasmid. Subspecies should not be recorded in this term, but in the NCBI taxonomy. Supply both the lineage name and the lineage rank separated by a colon, e.g., biovar:abc123.", + "title": "host subspecific genetic lineage", + "examples": [ + { + "value": "serovar:Newport, variety:glabrum, cultivar: Red Delicious" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "host subspecific genetic lineage" + ], + "rank": 257, + "is_a": "core field", + "string_serialization": "{rank name}:{text}", + "slot_uri": "MIXS:0001318", + "alias": "host_subspecf_genlin", + "owner": "HostAssociatedInterface", + "domain_of": [ + "Biosample", + "HostAssociatedInterface", + "PlantAssociatedInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "host_substrate": { + "name": "host_substrate", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "substrate name" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The growth substrate of the host.", + "title": "host substrate", + "examples": [ + { + "value": "rock" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "host substrate" + ], + "rank": 331, + "is_a": "core field", + "string_serialization": "{text}", + "slot_uri": "MIXS:0000252", + "alias": "host_substrate", + "owner": "HostAssociatedInterface", + "domain_of": [ + "Biosample", + "HostAssociatedInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "host_symbiont": { + "name": "host_symbiont", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "species name or common name" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host.", + "title": "observed host symbionts", + "examples": [ + { + "value": "flukeworms" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "observed host symbionts" + ], + "rank": 258, + "is_a": "core field", + "string_serialization": "{text}", + "slot_uri": "MIXS:0001298", + "alias": "host_symbiont", + "owner": "HostAssociatedInterface", + "domain_of": [ + "Biosample", + "HostAssociatedInterface", + "PlantAssociatedInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "host_taxid": { + "name": "host_taxid", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "NCBI taxon identifier" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "NCBI taxon id of the host, e.g. 9606", + "title": "host taxid", + "comments": [ + "Homo sapiens [NCBITaxon:9606] would be a reasonable has_raw_value" + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "host taxid" + ], + "rank": 259, + "is_a": "core field", + "slot_uri": "MIXS:0000250", + "alias": "host_taxid", + "owner": "HostAssociatedInterface", + "domain_of": [ + "Biosample", + "HostAssociatedInterface", + "PlantAssociatedInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "host_tot_mass": { + "name": "host_tot_mass", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "kilogram, gram" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Total mass of the host at collection, the unit depends on host", + "title": "host total mass", + "examples": [ + { + "value": "2500 gram" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "host total mass" + ], + "rank": 260, + "is_a": "core field", + "slot_uri": "MIXS:0000263", + "alias": "host_tot_mass", + "owner": "HostAssociatedInterface", + "domain_of": [ + "Biosample", + "HostAssociatedInterface", + "PlantAssociatedInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "lat_lon": { + "name": "lat_lon", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "decimal degrees, limit to 8 decimal points" + } + }, + "description": "The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system", + "title": "geographic location (latitude and longitude)", + "notes": [ + "This is currently a required field but it's not clear if this should be required for human hosts" + ], + "examples": [ + { + "value": "50.586825 6.408977" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "geographic location (latitude and longitude)" + ], + "rank": 5, + "is_a": "environment field", + "string_serialization": "{lat lon}", + "slot_uri": "MIXS:0000009", + "alias": "lat_lon", + "owner": "HostAssociatedInterface", + "domain_of": [ + "FieldResearchSite", + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "required": true, + "multivalued": false, + "pattern": "^[-+]?([1-8]?\\d(\\.\\d{1,8})?|90(\\.0{1,8})?)\\s[-+]?(180(\\.0{1,8})?|((1[0-7]\\d)|([1-9]?\\d))(\\.\\d{1,8})?)$" + }, + "misc_param": { + "name": "misc_param", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "parameter name;measurement value" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Any other measurement performed or parameter collected, that is not listed here", + "title": "miscellaneous parameter", + "examples": [ + { + "value": "Bicarbonate ion concentration;2075 micromole per kilogram" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "miscellaneous parameter" + ], + "rank": 23, + "is_a": "core field", + "string_serialization": "{text};{float} {unit}", + "slot_uri": "MIXS:0000752", + "alias": "misc_param", + "owner": "HostAssociatedInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false, + "pattern": "^([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+\\|)*([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+)$" + }, + "organism_count": { + "name": "organism_count", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "organism name;measurement value;enumeration" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "number of cells per cubic meter, number of cells per milliliter, number of cells per cubic centimeter" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr)", + "title": "organism count", + "examples": [ + { + "value": "total prokaryotes;3.5e7 cells per milliliter;qPCR" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "organism count" + ], + "rank": 30, + "is_a": "core field", + "slot_uri": "MIXS:0000103", + "alias": "organism_count", + "owner": "HostAssociatedInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^([-+]?[0-9]*\\.?[0-9]+ +\\S.*\\|)*([-+]?[0-9]*\\.?[0-9]+ +\\S.*)$" + }, + "oxy_stat_samp": { + "name": "oxy_stat_samp", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Oxygenation status of sample", + "title": "oxygenation status of sample", + "examples": [ + { + "value": "aerobic" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "oxygenation status of sample" + ], + "rank": 25, + "is_a": "core field", + "slot_uri": "MIXS:0000753", + "alias": "oxy_stat_samp", + "owner": "HostAssociatedInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_section", + "range": "OxyStatSampEnum", + "multivalued": false + }, + "perturbation": { + "name": "perturbation", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "perturbation type name;perturbation interval and duration" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types", + "title": "perturbation", + "examples": [ + { + "value": "antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "perturbation" + ], + "rank": 33, + "is_a": "core field", + "string_serialization": "{text};{Rn/start_time/end_time/duration}", + "slot_uri": "MIXS:0000754", + "alias": "perturbation", + "owner": "HostAssociatedInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "salinity": { + "name": "salinity", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "practical salinity unit, percentage" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The total concentration of all dissolved salts in a liquid or solid sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater.", + "title": "salinity", + "examples": [ + { + "value": "25 practical salinity unit" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "salinity" + ], + "rank": 54, + "is_a": "core field", + "slot_uri": "MIXS:0000183", + "alias": "salinity", + "owner": "HostAssociatedInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "samp_capt_status": { + "name": "samp_capt_status", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Reason for the sample", + "title": "sample capture status", + "examples": [ + { + "value": "farm sample" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sample capture status" + ], + "rank": 282, + "is_a": "core field", + "slot_uri": "MIXS:0000860", + "alias": "samp_capt_status", + "owner": "HostAssociatedInterface", + "domain_of": [ + "Biosample", + "HostAssociatedInterface", + "PlantAssociatedInterface" + ], + "slot_group": "mixs_core_section", + "range": "samp_capt_status_enum", + "multivalued": false + }, + "samp_collec_device": { + "name": "samp_collec_device", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "device name" + } + }, + "description": "The device used to collect an environmental sample. This field accepts terms listed under environmental sampling device (http://purl.obolibrary.org/obo/ENVO). This field also accepts terms listed under specimen collection device (http://purl.obolibrary.org/obo/GENEPIO_0002094).", + "title": "sample collection device", + "comments": [ + "Report dimensions and details when applicable" + ], + "examples": [ + { + "value": "swab, biopsy, niskin bottle, push core, drag swab [GENEPIO:0002713]" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sample collection device" + ], + "rank": 14, + "is_a": "nucleic acid sequence source field", + "string_serialization": "{termLabel} {[termID]}|{text}", + "slot_uri": "MIXS:0000002", + "alias": "samp_collec_device", + "owner": "HostAssociatedInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "recommended": true, + "multivalued": false + }, + "samp_collec_method": { + "name": "samp_collec_method", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "PMID,DOI,url , or text" + } + }, + "description": "The method employed for collecting the sample.", + "title": "sample collection method", + "comments": [ + "This can be a citation or description" + ], + "examples": [ + { + "value": "swabbing" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sample collection method" + ], + "rank": 15, + "is_a": "nucleic acid sequence source field", + "string_serialization": "{PMID}|{DOI}|{URL}|{text}", + "slot_uri": "MIXS:0001225", + "alias": "samp_collec_method", + "owner": "HostAssociatedInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "multivalued": false + }, + "samp_dis_stage": { + "name": "samp_dis_stage", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Stage of the disease at the time of sample collection, e.g. inoculation, penetration, infection, growth and reproduction, dissemination of pathogen.", + "title": "sample disease stage", + "examples": [ + { + "value": "infection" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sample disease stage" + ], + "rank": 283, + "is_a": "core field", + "slot_uri": "MIXS:0000249", + "alias": "samp_dis_stage", + "owner": "HostAssociatedInterface", + "domain_of": [ + "Biosample", + "HostAssociatedInterface", + "PlantAssociatedInterface" + ], + "slot_group": "mixs_core_section", + "range": "samp_dis_stage_enum", + "multivalued": false + }, + "samp_mat_process": { + "name": "samp_mat_process", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "text" + } + }, + "description": "A brief description of any processing applied to the sample during or after retrieving the sample from environment, or a link to the relevant protocol(s) performed.", + "title": "sample material processing", + "examples": [ + { + "value": "filtering of seawater" + }, + { + "value": "storing samples in ethanol" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sample material processing" + ], + "rank": 12, + "is_a": "nucleic acid sequence source field", + "string_serialization": "{text}", + "slot_uri": "MIXS:0000016", + "alias": "samp_mat_process", + "owner": "HostAssociatedInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "multivalued": false + }, + "samp_size": { + "name": "samp_size", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "millliter, gram, milligram, liter" + } + }, + "description": "The total amount or size (volume (ml), mass (g) or area (m2) ) of sample collected.", + "title": "amount or size of sample collected", + "comments": [ + "This refers to the TOTAL amount of sample collected from the experiment. NOT the amount sent to each institution or collected for a specific analysis." + ], + "examples": [ + { + "value": "5 grams" + }, + { + "value": "10 mL" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "amount or size of sample collected" + ], + "rank": 18, + "is_a": "nucleic acid sequence source field", + "string_serialization": "{float} {unit}", + "slot_uri": "MIXS:0000001", + "alias": "samp_size", + "owner": "HostAssociatedInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? \\S+$" + }, + "samp_store_dur": { + "name": "samp_store_dur", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "duration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Duration for which the sample was stored", + "title": "sample storage duration", + "examples": [ + { + "value": "P1Y6M" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sample storage duration" + ], + "rank": 353, + "is_a": "core field", + "string_serialization": "{duration}", + "slot_uri": "MIXS:0000116", + "alias": "samp_store_dur", + "owner": "HostAssociatedInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "samp_store_loc": { + "name": "samp_store_loc", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "location name" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Location at which sample was stored, usually name of a specific freezer/room", + "title": "sample storage location", + "examples": [ + { + "value": "Freezer no:5" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sample storage location" + ], + "rank": 41, + "is_a": "core field", + "string_serialization": "{text}", + "slot_uri": "MIXS:0000755", + "alias": "samp_store_loc", + "owner": "HostAssociatedInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "samp_store_temp": { + "name": "samp_store_temp", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "degree Celsius" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Temperature at which the sample was stored (degrees are assumed)", + "title": "sample storage temperature", + "examples": [ + { + "value": "-80 Celsius" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sample storage temperature" + ], + "rank": 7, + "is_a": "core field", + "slot_uri": "MIXS:0000110", + "alias": "samp_store_temp", + "owner": "HostAssociatedInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "required": true, + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "sample_link": { + "name": "sample_link", + "description": "A unique identifier to assign parent-child, subsample, or sibling samples. This is relevant when a sample or other material was used to generate the new sample.", + "title": "sample linkage", + "notes": [ + "also tempted to include SampIdNewTermsMixin but if len(slot_usage.keys()) > 1 and \"placeholder\" in slot_usage.keys():AttributeError: 'list' object has no attribute 'keys'" + ], + "comments": [ + "This field allows multiple entries separated by ; (Examples: Soil collected from the field will link with the soil used in an incubation. The soil a plant was grown in links to the plant sample. An original culture sample was transferred to a new vial and generated a new sample)" + ], + "examples": [ + { + "value": "IGSN:DSJ0284" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "rank": 5, + "string_serialization": "{text}:{text}", + "alias": "sample_link", + "owner": "HostAssociatedInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface", + "SampIdNewTermsMixin" + ], + "slot_group": "sample_id_section", + "range": "string", + "recommended": true, + "multivalued": false, + "pattern": "[^\\:\\n\\r]+\\:[^\\:\\n\\r]+" + }, + "size_frac": { + "name": "size_frac", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "filter size value range" + } + }, + "description": "Filtering pore size used in sample preparation", + "title": "size fraction selected", + "examples": [ + { + "value": "0-0.22 micrometer" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "size fraction selected" + ], + "rank": 285, + "is_a": "nucleic acid sequence source field", + "string_serialization": "{float}-{float} {unit}", + "slot_uri": "MIXS:0000017", + "alias": "size_frac", + "owner": "HostAssociatedInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "specific_ecosystem": { + "name": "specific_ecosystem", + "description": "Specific ecosystems represent specific features of the environment like aphotic zone in an ocean or gastric mucosa within a host digestive system. Specific ecosystem is in position 5/5 in a GOLD path.", + "comments": [ + "Specific ecosystems help to define samples based on very specific characteristics of an environment under the five-level classification system." + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "https://gold.jgi.doe.gov/help" + ], + "rank": 13, + "is_a": "gold_path_field", + "alias": "specific_ecosystem", + "owner": "HostAssociatedInterface", + "domain_of": [ + "Biosample", + "Study", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "SpecificEcosystemEnum", + "recommended": true + }, + "temp": { + "name": "temp", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "degree Celsius" + } + }, + "description": "Temperature of the sample at the time of sampling.", + "title": "temperature", + "examples": [ + { + "value": "25 degree Celsius" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "temperature" + ], + "rank": 37, + "is_a": "environment field", + "slot_uri": "MIXS:0000113", + "alias": "temp", + "owner": "HostAssociatedInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "analysis_type": { + "name": "analysis_type", + "description": "Select all the data types associated or available for this biosample", + "title": "analysis/data type", + "examples": [ + { + "value": "metagenomics; metabolomics; proteomics" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "MIxS:investigation_type" + ], + "rank": 3, + "alias": "analysis_type", + "owner": "HostAssociatedInterface", + "domain_of": [ + "Biosample", + "DhMultiviewCommonColumnsMixin", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "EmslInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "JgiMgInterface", + "JgiMgLrInterface", + "JgiMtInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "AnalysisTypeEnum", + "required": true, + "recommended": false, + "multivalued": true + }, + "samp_name": { + "name": "samp_name", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "text" + } + }, + "description": "A local identifier or name that for the material sample collected. Refers to the original material collected or to any derived sub-samples.", + "title": "sample name", + "comments": [ + "It can have any format, but we suggest that you make it concise, unique and consistent within your lab, and as informative as possible." + ], + "examples": [ + { + "value": "Rock core CB1178(5-6) from NSW" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sample name" + ], + "rank": 1, + "is_a": "investigation field", + "string_serialization": "{text}", + "slot_uri": "MIXS:0001107", + "identifier": true, + "alias": "samp_name", + "owner": "HostAssociatedInterface", + "domain_of": [ + "Biosample", + "DhMultiviewCommonColumnsMixin", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "EmslInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "JgiMgInterface", + "JgiMgLrInterface", + "JgiMtInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "string", + "required": true, + "multivalued": false + }, + "source_mat_id": { + "name": "source_mat_id", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "for cultures of microorganisms: identifiers for two culture collections; for other material a unique arbitrary identifer" + } + }, + "description": "A globally unique identifier assigned to the biological sample.", + "title": "source material identifier", + "todos": [ + "Currently, the comments say to use UUIDs. However, if we implement assigning NMDC identifiers with the minter we dont need to require a GUID. It can be an optional field to fill out only if they already have a resolvable ID.", + "Currently, the comments say to use UUIDs. However, if we implement assigning NMDC identifiers with the minter we dont need to require a GUID. It can be an optional field to fill out only if they already have a resolvable ID." + ], + "notes": [ + "The source material IS the Globally Unique ID" + ], + "comments": [ + "Identifiers must be prefixed. Possible FAIR prefixes are IGSNs (http://www.geosamples.org/getigsn), NCBI biosample accession numbers, ARK identifiers (https://arks.org/). These IDs enable linking to derived analytes and subsamples. If you have not assigned FAIR identifiers to your samples, you can generate UUIDs (https://www.uuidgenerator.net/).", + "Identifiers must be prefixed. Possible FAIR prefixes are IGSNs (http://www.geosamples.org/getigsn), NCBI biosample accession numbers, ARK identifiers (https://arks.org/). These IDs enable linking to derived analytes and subsamples. If you have not assigned FAIR identifiers to your samples, you can generate UUIDs (https://www.uuidgenerator.net/)." + ], + "examples": [ + { + "value": "IGSN:AU1243" + }, + { + "value": "UUID:24f1467a-40f4-11ed-b878-0242ac120002" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "source material identifiers" + ], + "rank": 2, + "is_a": "nucleic acid sequence source field", + "string_serialization": "{text}:{text}", + "slot_uri": "MIXS:0000026", + "alias": "source_mat_id", + "owner": "HostAssociatedInterface", + "domain_of": [ + "Biosample", + "DhMultiviewCommonColumnsMixin", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "EmslInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "JgiMgInterface", + "JgiMgLrInterface", + "JgiMtInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "string", + "multivalued": false, + "pattern": "[^\\:\\n\\r]+\\:[^\\:\\n\\r]+" + } + } + }, + "JgiMgInterface": { + "name": "JgiMgInterface", + "annotations": { + "excel_worksheet_name": { + "tag": "excel_worksheet_name", + "value": "JGI MG" + } + }, + "description": "Metadata for samples sent to JGI for standard metagenome sequencing", + "title": "JGI MG", + "from_schema": "https://example.com/nmdc_submission_schema", + "is_a": "DhInterface", + "mixins": [ + "DhMultiviewCommonColumnsMixin" + ], + "slots": [ + "dna_absorb1", + "dna_absorb2", + "dna_concentration", + "dna_cont_type", + "dna_cont_well", + "dna_container_id", + "dna_dnase", + "dna_isolate_meth", + "dna_project_contact", + "dna_samp_id", + "dna_sample_format", + "dna_sample_name", + "dna_seq_project", + "dna_seq_project_name", + "dna_seq_project_pi", + "dna_volume", + "proposal_dna", + "dna_absorb1", + "dna_absorb2", + "dna_concentration", + "dna_cont_type", + "dna_cont_well", + "dna_container_id", + "dna_dnase", + "dna_isolate_meth", + "dna_project_contact", + "dna_samp_id", + "dna_sample_format", + "dna_sample_name", + "dna_seq_project", + "dna_seq_project_name", + "dna_seq_project_pi", + "dna_volume", + "proposal_dna" + ], + "slot_usage": { + "dna_absorb1": { + "name": "dna_absorb1", + "description": "260/280 measurement of DNA sample purity", + "title": "DNA absorbance 260/280", + "comments": [ + "Recommended value is between 1 and 3." + ], + "examples": [ + { + "value": "2.02" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "rank": 7, + "is_a": "biomaterial_purity", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "ProcessedSample", + "JgiMgInterface", + "JgiMgLrInterface" + ], + "slot_group": "jgi_metagenomics_section", + "range": "float", + "recommended": true + }, + "dna_absorb2": { + "name": "dna_absorb2", + "description": "260/230 measurement of DNA sample purity", + "title": "DNA absorbance 260/230", + "comments": [ + "Recommended value is between 1 and 3." + ], + "examples": [ + { + "value": "2.02" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "rank": 8, + "is_a": "biomaterial_purity", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "JgiMgInterface", + "JgiMgLrInterface" + ], + "slot_group": "jgi_metagenomics_section", + "range": "float", + "recommended": true + }, + "dna_concentration": { + "name": "dna_concentration", + "title": "DNA concentration in ng/ul", + "comments": [ + "Units must be in ng/uL. Enter the numerical part only. Must be calculated using a fluorometric method. Acceptable values are 0-2000." + ], + "examples": [ + { + "value": "100" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "nmdc:nucleic_acid_concentration" + ], + "rank": 5, + "owner": "Biosample", + "domain_of": [ + "Biosample", + "ProcessedSample", + "JgiMgInterface", + "JgiMgLrInterface" + ], + "slot_group": "jgi_metagenomics_section", + "range": "float", + "required": true, + "recommended": false, + "minimum_value": 0, + "maximum_value": 2000 + }, + "dna_cont_type": { + "name": "dna_cont_type", + "description": "Tube or plate (96-well)", + "title": "DNA container type", + "examples": [ + { + "value": "plate" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "rank": 10, + "owner": "Biosample", + "domain_of": [ + "Biosample", + "JgiMgInterface", + "JgiMgLrInterface" + ], + "slot_group": "jgi_metagenomics_section", + "range": "JgiContTypeEnum", + "required": true, + "recommended": false + }, + "dna_cont_well": { + "name": "dna_cont_well", + "title": "DNA plate position", + "comments": [ + "Required when 'plate' is selected for container type.", + "Leave blank if the sample will be shipped in a tube.", + "JGI will not process samples in corner wells, so A1, A12, H1 and H12 will not pass validation.", + "For partial plates, fill by columns, like B1-G1,A2-H2,A3-D3 (NOT A2-A11,B1-B8)." + ], + "examples": [ + { + "value": "B2" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "rank": 11, + "string_serialization": "{96 well plate pos}", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "JgiMgInterface", + "JgiMgLrInterface" + ], + "slot_group": "jgi_metagenomics_section", + "range": "string", + "recommended": true, + "multivalued": false, + "pattern": "^(?!A1$|A12$|H1$|H12$)(([A-H][1-9])|([A-H]1[0-2]))$" + }, + "dna_container_id": { + "name": "dna_container_id", + "title": "DNA container label", + "comments": [ + "Must be unique across all tubes and plates, and <20 characters. All samples in a plate should have the same plate label." + ], + "examples": [ + { + "value": "Pond_MT_041618" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "rank": 9, + "string_serialization": "{text < 20 characters}", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "JgiMgInterface", + "JgiMgLrInterface" + ], + "slot_group": "jgi_metagenomics_section", + "range": "string", + "required": true, + "recommended": false, + "multivalued": false, + "pattern": "^.{1,20}$" + }, + "dna_dnase": { + "name": "dna_dnase", + "title": "DNase treatment DNA", + "comments": [ + "Note DNase treatment is required for all RNA samples." + ], + "examples": [ + { + "value": "no" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "rank": 13, + "owner": "Biosample", + "domain_of": [ + "Biosample", + "JgiMgInterface", + "JgiMgLrInterface" + ], + "slot_group": "jgi_metagenomics_section", + "range": "YesNoEnum", + "required": true, + "recommended": false + }, + "dna_isolate_meth": { + "name": "dna_isolate_meth", + "description": "Describe the method/protocol/kit used to extract DNA/RNA.", + "title": "DNA isolation method", + "examples": [ + { + "value": "phenol/chloroform extraction" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "Sample Isolation Method" + ], + "rank": 16, + "string_serialization": "{text}", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "JgiMgInterface", + "JgiMgLrInterface" + ], + "slot_group": "jgi_metagenomics_section", + "range": "string", + "required": true, + "recommended": false, + "multivalued": false + }, + "dna_project_contact": { + "name": "dna_project_contact", + "title": "DNA seq project contact", + "comments": [ + "Do not edit these values. A template will be provided by NMDC in which these values have been pre-filled." + ], + "examples": [ + { + "value": "John Jones" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "rank": 18, + "string_serialization": "{text}", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "JgiMgInterface", + "JgiMgLrInterface" + ], + "slot_group": "jgi_metagenomics_section", + "range": "string", + "required": true, + "recommended": false, + "multivalued": false + }, + "dna_samp_id": { + "name": "dna_samp_id", + "title": "DNA sample ID", + "todos": [ + "Removed identifier = TRUE from dna_samp_ID in JGI_sample_slots, as a class can't have two identifiers. How to force uniqueness? Moot because that column will be prefilled?" + ], + "comments": [ + "Do not edit these values. A template will be provided by NMDC in which these values have been pre-filled." + ], + "examples": [ + { + "value": "187654" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "rank": 3, + "string_serialization": "{text}", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "JgiMgInterface", + "JgiMgLrInterface" + ], + "slot_group": "jgi_metagenomics_section", + "range": "string", + "required": true, + "recommended": false, + "multivalued": false + }, + "dna_sample_format": { + "name": "dna_sample_format", + "description": "Solution in which the DNA sample has been suspended", + "title": "DNA sample format", + "examples": [ + { + "value": "Water" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "rank": 12, + "owner": "Biosample", + "domain_of": [ + "Biosample", + "JgiMgInterface", + "JgiMgLrInterface" + ], + "slot_group": "jgi_metagenomics_section", + "range": "DNASampleFormatEnum", + "required": true, + "recommended": false + }, + "dna_sample_name": { + "name": "dna_sample_name", + "description": "Give the DNA sample a name that is meaningful to you. Sample names must be unique across all JGI projects and contain a-z, A-Z, 0-9, - and _ only.", + "title": "DNA sample name", + "examples": [ + { + "value": "JGI_pond_041618" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "rank": 4, + "string_serialization": "{text}", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "JgiMgInterface", + "JgiMgLrInterface" + ], + "slot_group": "jgi_metagenomics_section", + "range": "string", + "required": true, + "recommended": false, + "multivalued": false, + "pattern": "^[_a-zA-Z0-9-]*$" + }, + "dna_seq_project": { + "name": "dna_seq_project", + "title": "DNA seq project ID", + "comments": [ + "Do not edit these values. A template will be provided by NMDC in which these values have been pre-filled." + ], + "examples": [ + { + "value": "1191234" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "Seq Project ID" + ], + "rank": 1, + "string_serialization": "{text}", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "JgiMgInterface", + "JgiMgLrInterface" + ], + "slot_group": "jgi_metagenomics_section", + "range": "string", + "required": true, + "recommended": false, + "multivalued": false + }, + "dna_seq_project_name": { + "name": "dna_seq_project_name", + "title": "DNA seq project name", + "comments": [ + "Do not edit these values. A template will be provided by NMDC in which these values have been pre-filled." + ], + "examples": [ + { + "value": "JGI Pond metagenomics" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "rank": 2, + "string_serialization": "{text}", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "JgiMgInterface", + "JgiMgLrInterface" + ], + "slot_group": "jgi_metagenomics_section", + "range": "string", + "required": true, + "recommended": false, + "multivalued": false + }, + "dna_seq_project_pi": { + "name": "dna_seq_project_pi", + "title": "DNA seq project PI", + "comments": [ + "Do not edit these values. A template will be provided by NMDC in which these values have been pre-filled." + ], + "examples": [ + { + "value": "Jane Johnson" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "rank": 17, + "string_serialization": "{text}", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "JgiMgInterface", + "JgiMgLrInterface" + ], + "slot_group": "jgi_metagenomics_section", + "range": "string", + "required": true, + "recommended": false, + "multivalued": false + }, + "dna_volume": { + "name": "dna_volume", + "title": "DNA volume in ul", + "comments": [ + "Units must be in uL. Enter the numerical part only. Value must be 0-1000. This form accepts values < 25, but JGI may refuse to process them unless permission has been granted by a project manager" + ], + "examples": [ + { + "value": "25" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "rank": 6, + "string_serialization": "{float}", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "JgiMgInterface", + "JgiMgLrInterface" + ], + "slot_group": "jgi_metagenomics_section", + "range": "float", + "required": true, + "recommended": false, + "minimum_value": 0, + "maximum_value": 1000 + }, + "proposal_dna": { + "name": "proposal_dna", + "title": "DNA proposal ID", + "comments": [ + "Do not edit these values. A template will be provided by NMDC in which these values have been pre-filled." + ], + "examples": [ + { + "value": "504000" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "rank": 19, + "string_serialization": "{text}", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "JgiMgInterface", + "JgiMgLrInterface" + ], + "slot_group": "jgi_metagenomics_section", + "range": "string", + "required": true, + "recommended": false, + "multivalued": false + }, + "oxy_stat_samp": { + "name": "oxy_stat_samp", + "range": "OxyStatSampEnum" + } + }, + "attributes": { + "dna_absorb1": { + "name": "dna_absorb1", + "description": "260/280 measurement of DNA sample purity", + "title": "DNA absorbance 260/280", + "comments": [ + "Recommended value is between 1 and 3." + ], + "examples": [ + { + "value": "2.02" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "rank": 7, + "is_a": "biomaterial_purity", + "alias": "dna_absorb1", + "owner": "JgiMgInterface", + "domain_of": [ + "Biosample", + "ProcessedSample", + "JgiMgInterface", + "JgiMgLrInterface" + ], + "slot_group": "jgi_metagenomics_section", + "range": "float", + "recommended": true + }, + "dna_absorb2": { + "name": "dna_absorb2", + "description": "260/230 measurement of DNA sample purity", + "title": "DNA absorbance 260/230", + "comments": [ + "Recommended value is between 1 and 3." + ], + "examples": [ + { + "value": "2.02" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "rank": 8, + "is_a": "biomaterial_purity", + "alias": "dna_absorb2", + "owner": "JgiMgInterface", + "domain_of": [ + "Biosample", + "JgiMgInterface", + "JgiMgLrInterface" + ], + "slot_group": "jgi_metagenomics_section", + "range": "float", + "recommended": true + }, + "dna_concentration": { + "name": "dna_concentration", + "title": "DNA concentration in ng/ul", + "comments": [ + "Units must be in ng/uL. Enter the numerical part only. Must be calculated using a fluorometric method. Acceptable values are 0-2000." + ], + "examples": [ + { + "value": "100" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "nmdc:nucleic_acid_concentration" + ], + "rank": 5, + "alias": "dna_concentration", + "owner": "JgiMgInterface", + "domain_of": [ + "Biosample", + "ProcessedSample", + "JgiMgInterface", + "JgiMgLrInterface" + ], + "slot_group": "jgi_metagenomics_section", + "range": "float", + "required": true, + "recommended": false, + "minimum_value": 0, + "maximum_value": 2000 + }, + "dna_cont_type": { + "name": "dna_cont_type", + "description": "Tube or plate (96-well)", + "title": "DNA container type", + "examples": [ + { + "value": "plate" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "rank": 10, + "alias": "dna_cont_type", + "owner": "JgiMgInterface", + "domain_of": [ + "Biosample", + "JgiMgInterface", + "JgiMgLrInterface" + ], + "slot_group": "jgi_metagenomics_section", + "range": "JgiContTypeEnum", + "required": true, + "recommended": false + }, + "dna_cont_well": { + "name": "dna_cont_well", + "title": "DNA plate position", + "comments": [ + "Required when 'plate' is selected for container type.", + "Leave blank if the sample will be shipped in a tube.", + "JGI will not process samples in corner wells, so A1, A12, H1 and H12 will not pass validation.", + "For partial plates, fill by columns, like B1-G1,A2-H2,A3-D3 (NOT A2-A11,B1-B8)." + ], + "examples": [ + { + "value": "B2" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "rank": 11, + "string_serialization": "{96 well plate pos}", + "alias": "dna_cont_well", + "owner": "JgiMgInterface", + "domain_of": [ + "Biosample", + "JgiMgInterface", + "JgiMgLrInterface" + ], + "slot_group": "jgi_metagenomics_section", + "range": "string", + "recommended": true, + "multivalued": false, + "pattern": "^(?!A1$|A12$|H1$|H12$)(([A-H][1-9])|([A-H]1[0-2]))$" + }, + "dna_container_id": { + "name": "dna_container_id", + "title": "DNA container label", + "comments": [ + "Must be unique across all tubes and plates, and <20 characters. All samples in a plate should have the same plate label." + ], + "examples": [ + { + "value": "Pond_MT_041618" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "rank": 9, + "string_serialization": "{text < 20 characters}", + "alias": "dna_container_id", + "owner": "JgiMgInterface", + "domain_of": [ + "Biosample", + "JgiMgInterface", + "JgiMgLrInterface" + ], + "slot_group": "jgi_metagenomics_section", + "range": "string", + "required": true, + "recommended": false, + "multivalued": false, + "pattern": "^.{1,20}$" + }, + "dna_dnase": { + "name": "dna_dnase", + "title": "DNase treatment DNA", + "comments": [ + "Note DNase treatment is required for all RNA samples." + ], + "examples": [ + { + "value": "no" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "rank": 13, + "alias": "dna_dnase", + "owner": "JgiMgInterface", + "domain_of": [ + "Biosample", + "JgiMgInterface", + "JgiMgLrInterface" + ], + "slot_group": "jgi_metagenomics_section", + "range": "YesNoEnum", + "required": true, + "recommended": false + }, + "dna_isolate_meth": { + "name": "dna_isolate_meth", + "description": "Describe the method/protocol/kit used to extract DNA/RNA.", + "title": "DNA isolation method", + "examples": [ + { + "value": "phenol/chloroform extraction" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "Sample Isolation Method" + ], + "rank": 16, + "string_serialization": "{text}", + "alias": "dna_isolate_meth", + "owner": "JgiMgInterface", + "domain_of": [ + "Biosample", + "JgiMgInterface", + "JgiMgLrInterface" + ], + "slot_group": "jgi_metagenomics_section", + "range": "string", + "required": true, + "recommended": false, + "multivalued": false + }, + "dna_project_contact": { + "name": "dna_project_contact", + "title": "DNA seq project contact", + "comments": [ + "Do not edit these values. A template will be provided by NMDC in which these values have been pre-filled." + ], + "examples": [ + { + "value": "John Jones" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "rank": 18, + "string_serialization": "{text}", + "alias": "dna_project_contact", + "owner": "JgiMgInterface", + "domain_of": [ + "Biosample", + "JgiMgInterface", + "JgiMgLrInterface" + ], + "slot_group": "jgi_metagenomics_section", + "range": "string", + "required": true, + "recommended": false, + "multivalued": false + }, + "dna_samp_id": { + "name": "dna_samp_id", + "title": "DNA sample ID", + "todos": [ + "Removed identifier = TRUE from dna_samp_ID in JGI_sample_slots, as a class can't have two identifiers. How to force uniqueness? Moot because that column will be prefilled?" + ], + "comments": [ + "Do not edit these values. A template will be provided by NMDC in which these values have been pre-filled." + ], + "examples": [ + { + "value": "187654" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "rank": 3, + "string_serialization": "{text}", + "alias": "dna_samp_id", + "owner": "JgiMgInterface", + "domain_of": [ + "Biosample", + "JgiMgInterface", + "JgiMgLrInterface" + ], + "slot_group": "jgi_metagenomics_section", + "range": "string", + "required": true, + "recommended": false, + "multivalued": false + }, + "dna_sample_format": { + "name": "dna_sample_format", + "description": "Solution in which the DNA sample has been suspended", + "title": "DNA sample format", + "examples": [ + { + "value": "Water" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "rank": 12, + "alias": "dna_sample_format", + "owner": "JgiMgInterface", + "domain_of": [ + "Biosample", + "JgiMgInterface", + "JgiMgLrInterface" + ], + "slot_group": "jgi_metagenomics_section", + "range": "DNASampleFormatEnum", + "required": true, + "recommended": false + }, + "dna_sample_name": { + "name": "dna_sample_name", + "description": "Give the DNA sample a name that is meaningful to you. Sample names must be unique across all JGI projects and contain a-z, A-Z, 0-9, - and _ only.", + "title": "DNA sample name", + "examples": [ + { + "value": "JGI_pond_041618" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "rank": 4, + "string_serialization": "{text}", + "alias": "dna_sample_name", + "owner": "JgiMgInterface", + "domain_of": [ + "Biosample", + "JgiMgInterface", + "JgiMgLrInterface" + ], + "slot_group": "jgi_metagenomics_section", + "range": "string", + "required": true, + "recommended": false, + "multivalued": false, + "pattern": "^[_a-zA-Z0-9-]*$" + }, + "dna_seq_project": { + "name": "dna_seq_project", + "title": "DNA seq project ID", + "comments": [ + "Do not edit these values. A template will be provided by NMDC in which these values have been pre-filled." + ], + "examples": [ + { + "value": "1191234" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "Seq Project ID" + ], + "rank": 1, + "string_serialization": "{text}", + "alias": "dna_seq_project", + "owner": "JgiMgInterface", + "domain_of": [ + "Biosample", + "JgiMgInterface", + "JgiMgLrInterface" + ], + "slot_group": "jgi_metagenomics_section", + "range": "string", + "required": true, + "recommended": false, + "multivalued": false + }, + "dna_seq_project_name": { + "name": "dna_seq_project_name", + "title": "DNA seq project name", + "comments": [ + "Do not edit these values. A template will be provided by NMDC in which these values have been pre-filled." + ], + "examples": [ + { + "value": "JGI Pond metagenomics" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "rank": 2, + "string_serialization": "{text}", + "alias": "dna_seq_project_name", + "owner": "JgiMgInterface", + "domain_of": [ + "Biosample", + "JgiMgInterface", + "JgiMgLrInterface" + ], + "slot_group": "jgi_metagenomics_section", + "range": "string", + "required": true, + "recommended": false, + "multivalued": false + }, + "dna_seq_project_pi": { + "name": "dna_seq_project_pi", + "title": "DNA seq project PI", + "comments": [ + "Do not edit these values. A template will be provided by NMDC in which these values have been pre-filled." + ], + "examples": [ + { + "value": "Jane Johnson" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "rank": 17, + "string_serialization": "{text}", + "alias": "dna_seq_project_pi", + "owner": "JgiMgInterface", + "domain_of": [ + "Biosample", + "JgiMgInterface", + "JgiMgLrInterface" + ], + "slot_group": "jgi_metagenomics_section", + "range": "string", + "required": true, + "recommended": false, + "multivalued": false + }, + "dna_volume": { + "name": "dna_volume", + "title": "DNA volume in ul", + "comments": [ + "Units must be in uL. Enter the numerical part only. Value must be 0-1000. This form accepts values < 25, but JGI may refuse to process them unless permission has been granted by a project manager" + ], + "examples": [ + { + "value": "25" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "rank": 6, + "string_serialization": "{float}", + "alias": "dna_volume", + "owner": "JgiMgInterface", + "domain_of": [ + "Biosample", + "JgiMgInterface", + "JgiMgLrInterface" + ], + "slot_group": "jgi_metagenomics_section", + "range": "float", + "required": true, + "recommended": false, + "minimum_value": 0, + "maximum_value": 1000 + }, + "proposal_dna": { + "name": "proposal_dna", + "title": "DNA proposal ID", + "comments": [ + "Do not edit these values. A template will be provided by NMDC in which these values have been pre-filled." + ], + "examples": [ + { + "value": "504000" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "rank": 19, + "string_serialization": "{text}", + "alias": "proposal_dna", + "owner": "JgiMgInterface", + "domain_of": [ + "Biosample", + "JgiMgInterface", + "JgiMgLrInterface" + ], + "slot_group": "jgi_metagenomics_section", + "range": "string", + "required": true, + "recommended": false, + "multivalued": false + }, + "analysis_type": { + "name": "analysis_type", + "description": "Select all the data types associated or available for this biosample", + "title": "analysis/data type", + "examples": [ + { + "value": "metagenomics; metabolomics; proteomics" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "MIxS:investigation_type" + ], + "rank": 3, + "alias": "analysis_type", + "owner": "JgiMgInterface", + "domain_of": [ + "Biosample", + "DhMultiviewCommonColumnsMixin", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "EmslInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "JgiMgInterface", + "JgiMgLrInterface", + "JgiMtInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "AnalysisTypeEnum", + "required": true, + "recommended": false, + "multivalued": true + }, + "samp_name": { + "name": "samp_name", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "text" + } + }, + "description": "A local identifier or name that for the material sample collected. Refers to the original material collected or to any derived sub-samples.", + "title": "sample name", + "comments": [ + "It can have any format, but we suggest that you make it concise, unique and consistent within your lab, and as informative as possible." + ], + "examples": [ + { + "value": "Rock core CB1178(5-6) from NSW" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sample name" + ], + "rank": 1, + "is_a": "investigation field", + "string_serialization": "{text}", + "slot_uri": "MIXS:0001107", + "identifier": true, + "alias": "samp_name", + "owner": "JgiMgInterface", + "domain_of": [ + "Biosample", + "DhMultiviewCommonColumnsMixin", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "EmslInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "JgiMgInterface", + "JgiMgLrInterface", + "JgiMtInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "string", + "required": true, + "multivalued": false + }, + "source_mat_id": { + "name": "source_mat_id", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "for cultures of microorganisms: identifiers for two culture collections; for other material a unique arbitrary identifer" + } + }, + "description": "A globally unique identifier assigned to the biological sample.", + "title": "source material identifier", + "todos": [ + "Currently, the comments say to use UUIDs. However, if we implement assigning NMDC identifiers with the minter we dont need to require a GUID. It can be an optional field to fill out only if they already have a resolvable ID.", + "Currently, the comments say to use UUIDs. However, if we implement assigning NMDC identifiers with the minter we dont need to require a GUID. It can be an optional field to fill out only if they already have a resolvable ID." + ], + "notes": [ + "The source material IS the Globally Unique ID" + ], + "comments": [ + "Identifiers must be prefixed. Possible FAIR prefixes are IGSNs (http://www.geosamples.org/getigsn), NCBI biosample accession numbers, ARK identifiers (https://arks.org/). These IDs enable linking to derived analytes and subsamples. If you have not assigned FAIR identifiers to your samples, you can generate UUIDs (https://www.uuidgenerator.net/).", + "Identifiers must be prefixed. Possible FAIR prefixes are IGSNs (http://www.geosamples.org/getigsn), NCBI biosample accession numbers, ARK identifiers (https://arks.org/). These IDs enable linking to derived analytes and subsamples. If you have not assigned FAIR identifiers to your samples, you can generate UUIDs (https://www.uuidgenerator.net/)." + ], + "examples": [ + { + "value": "IGSN:AU1243" + }, + { + "value": "UUID:24f1467a-40f4-11ed-b878-0242ac120002" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "source material identifiers" + ], + "rank": 2, + "is_a": "nucleic acid sequence source field", + "string_serialization": "{text}:{text}", + "slot_uri": "MIXS:0000026", + "alias": "source_mat_id", + "owner": "JgiMgInterface", + "domain_of": [ + "Biosample", + "DhMultiviewCommonColumnsMixin", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "EmslInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "JgiMgInterface", + "JgiMgLrInterface", + "JgiMtInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "string", + "multivalued": false, + "pattern": "[^\\:\\n\\r]+\\:[^\\:\\n\\r]+" + } + }, + "rules": [ + { + "preconditions": { + "slot_conditions": { + "dna_cont_well": { + "name": "dna_cont_well", + "pattern": ".+" + } + } + }, + "postconditions": { + "slot_conditions": { + "dna_cont_type": { + "name": "dna_cont_type", + "equals_string": "plate" + } + } + }, + "description": "DNA samples shipped to JGI for metagenomic analysis in tubes can't have any value for their plate position.", + "title": "dna_well_requires_plate" + }, + { + "preconditions": { + "slot_conditions": { + "dna_cont_type": { + "name": "dna_cont_type", + "equals_string": "plate" + } + } + }, + "postconditions": { + "slot_conditions": { + "dna_cont_well": { + "name": "dna_cont_well", + "pattern": "^(?!A1$|A12$|H1$|H12$)(([A-H][1-9])|([A-H]1[0-2]))$" + } + } + }, + "description": "DNA samples in plates must have a plate position that matches the regex. Note the requirement for an empty string in the tube case. Waiting for value_present validation to be added to runtime", + "title": "dna_plate_requires_well" + } + ] + }, + "JgiMgLrInterface": { + "name": "JgiMgLrInterface", + "annotations": { + "excel_worksheet_name": { + "tag": "excel_worksheet_name", + "value": "JGI MG (Long Read)" + } + }, + "description": "Metadata for samples sent to JGI for long read metagenome sequecning", + "title": "JGI MG (Long Read)", + "from_schema": "https://example.com/nmdc_submission_schema", + "is_a": "DhInterface", + "mixins": [ + "DhMultiviewCommonColumnsMixin" + ], + "slots": [ + "dna_absorb1", + "dna_absorb2", + "dna_concentration", + "dna_cont_type", + "dna_cont_well", + "dna_container_id", + "dna_dnase", + "dna_isolate_meth", + "dna_project_contact", + "dna_samp_id", + "dna_sample_format", + "dna_sample_name", + "dna_seq_project", + "dna_seq_project_name", + "dna_seq_project_pi", + "dna_volume", + "proposal_dna", + "dna_absorb1", + "dna_absorb2", + "dna_concentration", + "dna_cont_type", + "dna_cont_well", + "dna_container_id", + "dna_dnase", + "dna_isolate_meth", + "dna_project_contact", + "dna_samp_id", + "dna_sample_format", + "dna_sample_name", + "dna_seq_project", + "dna_seq_project_name", + "dna_seq_project_pi", + "dna_volume", + "proposal_dna" + ], + "slot_usage": { + "dna_absorb1": { + "name": "dna_absorb1", + "description": "260/280 measurement of DNA sample purity", + "title": "DNA absorbance 260/280", + "comments": [ + "Recommended value is between 1 and 3." + ], + "examples": [ + { + "value": "2.02" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "rank": 7, + "is_a": "biomaterial_purity", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "ProcessedSample", + "JgiMgInterface", + "JgiMgLrInterface" + ], + "slot_group": "jgi_metagenomics_section", + "range": "float", + "required": true, + "recommended": false + }, + "dna_absorb2": { + "name": "dna_absorb2", + "description": "260/230 measurement of DNA sample purity", + "title": "DNA absorbance 260/230", + "comments": [ + "Recommended value is between 1 and 3." + ], + "examples": [ + { + "value": "2.02" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "rank": 8, + "is_a": "biomaterial_purity", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "JgiMgInterface", + "JgiMgLrInterface" + ], + "slot_group": "jgi_metagenomics_section", + "range": "float", + "required": true, + "recommended": false + }, + "dna_concentration": { + "name": "dna_concentration", + "title": "DNA concentration in ng/ul", + "comments": [ + "Units must be in ng/uL. Enter the numerical part only. Must be calculated using a fluorometric method. Acceptable values are 0-2000." + ], + "examples": [ + { + "value": "100" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "nmdc:nucleic_acid_concentration" + ], + "rank": 5, + "owner": "Biosample", + "domain_of": [ + "Biosample", + "ProcessedSample", + "JgiMgInterface", + "JgiMgLrInterface" + ], + "slot_group": "jgi_metagenomics_section", + "range": "float", + "required": true, + "recommended": false, + "minimum_value": 0, + "maximum_value": 2000 + }, + "dna_cont_type": { + "name": "dna_cont_type", + "description": "Tube or plate (96-well)", + "title": "DNA container type", + "examples": [ + { + "value": "plate" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "rank": 10, + "owner": "Biosample", + "domain_of": [ + "Biosample", + "JgiMgInterface", + "JgiMgLrInterface" + ], + "slot_group": "jgi_metagenomics_section", + "range": "JgiContTypeEnum", + "required": true, + "recommended": false + }, + "dna_cont_well": { + "name": "dna_cont_well", + "title": "DNA plate position", + "comments": [ + "Required when 'plate' is selected for container type.", + "Leave blank if the sample will be shipped in a tube.", + "JGI will not process samples in corner wells, so A1, A12, H1 and H12 will not pass validation.", + "For partial plates, fill by columns, like B1-G1,A2-H2,A3-D3 (NOT A2-A11,B1-B8)." + ], + "examples": [ + { + "value": "B2" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "rank": 11, + "string_serialization": "{96 well plate pos}", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "JgiMgInterface", + "JgiMgLrInterface" + ], + "slot_group": "jgi_metagenomics_section", + "range": "string", + "recommended": true, + "multivalued": false, + "pattern": "^(?!A1$|A12$|H1$|H12$)(([A-H][1-9])|([A-H]1[0-2]))$" + }, + "dna_container_id": { + "name": "dna_container_id", + "title": "DNA container label", + "comments": [ + "Must be unique across all tubes and plates, and <20 characters. All samples in a plate should have the same plate label." + ], + "examples": [ + { + "value": "Pond_MT_041618" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "rank": 9, + "string_serialization": "{text < 20 characters}", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "JgiMgInterface", + "JgiMgLrInterface" + ], + "slot_group": "jgi_metagenomics_section", + "range": "string", + "required": true, + "recommended": false, + "multivalued": false, + "pattern": "^.{1,20}$" + }, + "dna_dnase": { + "name": "dna_dnase", + "title": "DNase treatment DNA", + "comments": [ + "Note DNase treatment is required for all RNA samples." + ], + "examples": [ + { + "value": "no" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "rank": 13, + "owner": "Biosample", + "domain_of": [ + "Biosample", + "JgiMgInterface", + "JgiMgLrInterface" + ], + "slot_group": "jgi_metagenomics_section", + "range": "YesNoEnum", + "required": true, + "recommended": false + }, + "dna_isolate_meth": { + "name": "dna_isolate_meth", + "description": "Describe the method/protocol/kit used to extract DNA/RNA.", + "title": "DNA isolation method", + "examples": [ + { + "value": "phenol/chloroform extraction" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "Sample Isolation Method" + ], + "rank": 16, + "string_serialization": "{text}", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "JgiMgInterface", + "JgiMgLrInterface" + ], + "slot_group": "jgi_metagenomics_section", + "range": "string", + "required": true, + "recommended": false, + "multivalued": false + }, + "dna_project_contact": { + "name": "dna_project_contact", + "title": "DNA seq project contact", + "comments": [ + "Do not edit these values. A template will be provided by NMDC in which these values have been pre-filled." + ], + "examples": [ + { + "value": "John Jones" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "rank": 18, + "string_serialization": "{text}", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "JgiMgInterface", + "JgiMgLrInterface" + ], + "slot_group": "jgi_metagenomics_section", + "range": "string", + "required": true, + "recommended": false, + "multivalued": false + }, + "dna_samp_id": { + "name": "dna_samp_id", + "title": "DNA sample ID", + "todos": [ + "Removed identifier = TRUE from dna_samp_ID in JGI_sample_slots, as a class can't have two identifiers. How to force uniqueness? Moot because that column will be prefilled?" + ], + "comments": [ + "Do not edit these values. A template will be provided by NMDC in which these values have been pre-filled." + ], + "examples": [ + { + "value": "187654" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "rank": 3, + "string_serialization": "{text}", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "JgiMgInterface", + "JgiMgLrInterface" + ], + "slot_group": "jgi_metagenomics_section", + "range": "string", + "required": true, + "recommended": false, + "multivalued": false + }, + "dna_sample_format": { + "name": "dna_sample_format", + "description": "Solution in which the DNA sample has been suspended", + "title": "DNA sample format", + "examples": [ + { + "value": "Water" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "rank": 12, + "owner": "Biosample", + "domain_of": [ + "Biosample", + "JgiMgInterface", + "JgiMgLrInterface" + ], + "slot_group": "jgi_metagenomics_section", + "range": "DNASampleFormatEnum", + "required": true, + "recommended": false + }, + "dna_sample_name": { + "name": "dna_sample_name", + "description": "Give the DNA sample a name that is meaningful to you. Sample names must be unique across all JGI projects and contain a-z, A-Z, 0-9, - and _ only.", + "title": "DNA sample name", + "examples": [ + { + "value": "JGI_pond_041618" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "rank": 4, + "string_serialization": "{text}", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "JgiMgInterface", + "JgiMgLrInterface" + ], + "slot_group": "jgi_metagenomics_section", + "range": "string", + "required": true, + "recommended": false, + "multivalued": false, + "pattern": "^[_a-zA-Z0-9-]*$" + }, + "dna_seq_project": { + "name": "dna_seq_project", + "title": "DNA seq project ID", + "comments": [ + "Do not edit these values. A template will be provided by NMDC in which these values have been pre-filled." + ], + "examples": [ + { + "value": "1191234" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "Seq Project ID" + ], + "rank": 1, + "string_serialization": "{text}", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "JgiMgInterface", + "JgiMgLrInterface" + ], + "slot_group": "jgi_metagenomics_section", + "range": "string", + "required": true, + "recommended": false, + "multivalued": false + }, + "dna_seq_project_name": { + "name": "dna_seq_project_name", + "title": "DNA seq project name", + "comments": [ + "Do not edit these values. A template will be provided by NMDC in which these values have been pre-filled." + ], + "examples": [ + { + "value": "JGI Pond metagenomics" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "rank": 2, + "string_serialization": "{text}", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "JgiMgInterface", + "JgiMgLrInterface" + ], + "slot_group": "jgi_metagenomics_section", + "range": "string", + "required": true, + "recommended": false, + "multivalued": false + }, + "dna_seq_project_pi": { + "name": "dna_seq_project_pi", + "title": "DNA seq project PI", + "comments": [ + "Do not edit these values. A template will be provided by NMDC in which these values have been pre-filled." + ], + "examples": [ + { + "value": "Jane Johnson" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "rank": 17, + "string_serialization": "{text}", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "JgiMgInterface", + "JgiMgLrInterface" + ], + "slot_group": "jgi_metagenomics_section", + "range": "string", + "required": true, + "recommended": false, + "multivalued": false + }, + "dna_volume": { + "name": "dna_volume", + "title": "DNA volume in ul", + "comments": [ + "Units must be in uL. Enter the numerical part only. Value must be 0-1000. This form accepts values < 25, but JGI may refuse to process them unless permission has been granted by a project manager" + ], + "examples": [ + { + "value": "25" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "rank": 6, + "string_serialization": "{float}", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "JgiMgInterface", + "JgiMgLrInterface" + ], + "slot_group": "jgi_metagenomics_section", + "range": "float", + "required": true, + "recommended": false, + "minimum_value": 0, + "maximum_value": 1000 + }, + "proposal_dna": { + "name": "proposal_dna", + "title": "DNA proposal ID", + "comments": [ + "Do not edit these values. A template will be provided by NMDC in which these values have been pre-filled." + ], + "examples": [ + { + "value": "504000" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "rank": 19, + "string_serialization": "{text}", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "JgiMgInterface", + "JgiMgLrInterface" + ], + "slot_group": "jgi_metagenomics_section", + "range": "string", + "required": true, + "recommended": false, + "multivalued": false + }, + "oxy_stat_samp": { + "name": "oxy_stat_samp", + "range": "OxyStatSampEnum" + } + }, + "attributes": { + "dna_absorb1": { + "name": "dna_absorb1", + "description": "260/280 measurement of DNA sample purity", + "title": "DNA absorbance 260/280", + "comments": [ + "Recommended value is between 1 and 3." + ], + "examples": [ + { + "value": "2.02" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "rank": 7, + "is_a": "biomaterial_purity", + "alias": "dna_absorb1", + "owner": "JgiMgLrInterface", + "domain_of": [ + "Biosample", + "ProcessedSample", + "JgiMgInterface", + "JgiMgLrInterface" + ], + "slot_group": "jgi_metagenomics_section", + "range": "float", + "required": true, + "recommended": false + }, + "dna_absorb2": { + "name": "dna_absorb2", + "description": "260/230 measurement of DNA sample purity", + "title": "DNA absorbance 260/230", + "comments": [ + "Recommended value is between 1 and 3." + ], + "examples": [ + { + "value": "2.02" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "rank": 8, + "is_a": "biomaterial_purity", + "alias": "dna_absorb2", + "owner": "JgiMgLrInterface", + "domain_of": [ + "Biosample", + "JgiMgInterface", + "JgiMgLrInterface" + ], + "slot_group": "jgi_metagenomics_section", + "range": "float", + "required": true, + "recommended": false + }, + "dna_concentration": { + "name": "dna_concentration", + "title": "DNA concentration in ng/ul", + "comments": [ + "Units must be in ng/uL. Enter the numerical part only. Must be calculated using a fluorometric method. Acceptable values are 0-2000." + ], + "examples": [ + { + "value": "100" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "nmdc:nucleic_acid_concentration" + ], + "rank": 5, + "alias": "dna_concentration", + "owner": "JgiMgLrInterface", + "domain_of": [ + "Biosample", + "ProcessedSample", + "JgiMgInterface", + "JgiMgLrInterface" + ], + "slot_group": "jgi_metagenomics_section", + "range": "float", + "required": true, + "recommended": false, + "minimum_value": 0, + "maximum_value": 2000 + }, + "dna_cont_type": { + "name": "dna_cont_type", + "description": "Tube or plate (96-well)", + "title": "DNA container type", + "examples": [ + { + "value": "plate" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "rank": 10, + "alias": "dna_cont_type", + "owner": "JgiMgLrInterface", + "domain_of": [ + "Biosample", + "JgiMgInterface", + "JgiMgLrInterface" + ], + "slot_group": "jgi_metagenomics_section", + "range": "JgiContTypeEnum", + "required": true, + "recommended": false + }, + "dna_cont_well": { + "name": "dna_cont_well", + "title": "DNA plate position", + "comments": [ + "Required when 'plate' is selected for container type.", + "Leave blank if the sample will be shipped in a tube.", + "JGI will not process samples in corner wells, so A1, A12, H1 and H12 will not pass validation.", + "For partial plates, fill by columns, like B1-G1,A2-H2,A3-D3 (NOT A2-A11,B1-B8)." + ], + "examples": [ + { + "value": "B2" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "rank": 11, + "string_serialization": "{96 well plate pos}", + "alias": "dna_cont_well", + "owner": "JgiMgLrInterface", + "domain_of": [ + "Biosample", + "JgiMgInterface", + "JgiMgLrInterface" + ], + "slot_group": "jgi_metagenomics_section", + "range": "string", + "recommended": true, + "multivalued": false, + "pattern": "^(?!A1$|A12$|H1$|H12$)(([A-H][1-9])|([A-H]1[0-2]))$" + }, + "dna_container_id": { + "name": "dna_container_id", + "title": "DNA container label", + "comments": [ + "Must be unique across all tubes and plates, and <20 characters. All samples in a plate should have the same plate label." + ], + "examples": [ + { + "value": "Pond_MT_041618" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "rank": 9, + "string_serialization": "{text < 20 characters}", + "alias": "dna_container_id", + "owner": "JgiMgLrInterface", + "domain_of": [ + "Biosample", + "JgiMgInterface", + "JgiMgLrInterface" + ], + "slot_group": "jgi_metagenomics_section", + "range": "string", + "required": true, + "recommended": false, + "multivalued": false, + "pattern": "^.{1,20}$" + }, + "dna_dnase": { + "name": "dna_dnase", + "title": "DNase treatment DNA", + "comments": [ + "Note DNase treatment is required for all RNA samples." + ], + "examples": [ + { + "value": "no" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "rank": 13, + "alias": "dna_dnase", + "owner": "JgiMgLrInterface", + "domain_of": [ + "Biosample", + "JgiMgInterface", + "JgiMgLrInterface" + ], + "slot_group": "jgi_metagenomics_section", + "range": "YesNoEnum", + "required": true, + "recommended": false + }, + "dna_isolate_meth": { + "name": "dna_isolate_meth", + "description": "Describe the method/protocol/kit used to extract DNA/RNA.", + "title": "DNA isolation method", + "examples": [ + { + "value": "phenol/chloroform extraction" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "Sample Isolation Method" + ], + "rank": 16, + "string_serialization": "{text}", + "alias": "dna_isolate_meth", + "owner": "JgiMgLrInterface", + "domain_of": [ + "Biosample", + "JgiMgInterface", + "JgiMgLrInterface" + ], + "slot_group": "jgi_metagenomics_section", + "range": "string", + "required": true, + "recommended": false, + "multivalued": false + }, + "dna_project_contact": { + "name": "dna_project_contact", + "title": "DNA seq project contact", + "comments": [ + "Do not edit these values. A template will be provided by NMDC in which these values have been pre-filled." + ], + "examples": [ + { + "value": "John Jones" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "rank": 18, + "string_serialization": "{text}", + "alias": "dna_project_contact", + "owner": "JgiMgLrInterface", + "domain_of": [ + "Biosample", + "JgiMgInterface", + "JgiMgLrInterface" + ], + "slot_group": "jgi_metagenomics_section", + "range": "string", + "required": true, + "recommended": false, + "multivalued": false + }, + "dna_samp_id": { + "name": "dna_samp_id", + "title": "DNA sample ID", + "todos": [ + "Removed identifier = TRUE from dna_samp_ID in JGI_sample_slots, as a class can't have two identifiers. How to force uniqueness? Moot because that column will be prefilled?" + ], + "comments": [ + "Do not edit these values. A template will be provided by NMDC in which these values have been pre-filled." + ], + "examples": [ + { + "value": "187654" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "rank": 3, + "string_serialization": "{text}", + "alias": "dna_samp_id", + "owner": "JgiMgLrInterface", + "domain_of": [ + "Biosample", + "JgiMgInterface", + "JgiMgLrInterface" + ], + "slot_group": "jgi_metagenomics_section", + "range": "string", + "required": true, + "recommended": false, + "multivalued": false + }, + "dna_sample_format": { + "name": "dna_sample_format", + "description": "Solution in which the DNA sample has been suspended", + "title": "DNA sample format", + "examples": [ + { + "value": "Water" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "rank": 12, + "alias": "dna_sample_format", + "owner": "JgiMgLrInterface", + "domain_of": [ + "Biosample", + "JgiMgInterface", + "JgiMgLrInterface" + ], + "slot_group": "jgi_metagenomics_section", + "range": "DNASampleFormatEnum", + "required": true, + "recommended": false + }, + "dna_sample_name": { + "name": "dna_sample_name", + "description": "Give the DNA sample a name that is meaningful to you. Sample names must be unique across all JGI projects and contain a-z, A-Z, 0-9, - and _ only.", + "title": "DNA sample name", + "examples": [ + { + "value": "JGI_pond_041618" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "rank": 4, + "string_serialization": "{text}", + "alias": "dna_sample_name", + "owner": "JgiMgLrInterface", + "domain_of": [ + "Biosample", + "JgiMgInterface", + "JgiMgLrInterface" + ], + "slot_group": "jgi_metagenomics_section", + "range": "string", + "required": true, + "recommended": false, + "multivalued": false, + "pattern": "^[_a-zA-Z0-9-]*$" + }, + "dna_seq_project": { + "name": "dna_seq_project", + "title": "DNA seq project ID", + "comments": [ + "Do not edit these values. A template will be provided by NMDC in which these values have been pre-filled." + ], + "examples": [ + { + "value": "1191234" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "Seq Project ID" + ], + "rank": 1, + "string_serialization": "{text}", + "alias": "dna_seq_project", + "owner": "JgiMgLrInterface", + "domain_of": [ + "Biosample", + "JgiMgInterface", + "JgiMgLrInterface" + ], + "slot_group": "jgi_metagenomics_section", + "range": "string", + "required": true, + "recommended": false, + "multivalued": false + }, + "dna_seq_project_name": { + "name": "dna_seq_project_name", + "title": "DNA seq project name", + "comments": [ + "Do not edit these values. A template will be provided by NMDC in which these values have been pre-filled." + ], + "examples": [ + { + "value": "JGI Pond metagenomics" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "rank": 2, + "string_serialization": "{text}", + "alias": "dna_seq_project_name", + "owner": "JgiMgLrInterface", + "domain_of": [ + "Biosample", + "JgiMgInterface", + "JgiMgLrInterface" + ], + "slot_group": "jgi_metagenomics_section", + "range": "string", + "required": true, + "recommended": false, + "multivalued": false + }, + "dna_seq_project_pi": { + "name": "dna_seq_project_pi", + "title": "DNA seq project PI", + "comments": [ + "Do not edit these values. A template will be provided by NMDC in which these values have been pre-filled." + ], + "examples": [ + { + "value": "Jane Johnson" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "rank": 17, + "string_serialization": "{text}", + "alias": "dna_seq_project_pi", + "owner": "JgiMgLrInterface", + "domain_of": [ + "Biosample", + "JgiMgInterface", + "JgiMgLrInterface" + ], + "slot_group": "jgi_metagenomics_section", + "range": "string", + "required": true, + "recommended": false, + "multivalued": false + }, + "dna_volume": { + "name": "dna_volume", + "title": "DNA volume in ul", + "comments": [ + "Units must be in uL. Enter the numerical part only. Value must be 0-1000. This form accepts values < 25, but JGI may refuse to process them unless permission has been granted by a project manager" + ], + "examples": [ + { + "value": "25" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "rank": 6, + "string_serialization": "{float}", + "alias": "dna_volume", + "owner": "JgiMgLrInterface", + "domain_of": [ + "Biosample", + "JgiMgInterface", + "JgiMgLrInterface" + ], + "slot_group": "jgi_metagenomics_section", + "range": "float", + "required": true, + "recommended": false, + "minimum_value": 0, + "maximum_value": 1000 + }, + "proposal_dna": { + "name": "proposal_dna", + "title": "DNA proposal ID", + "comments": [ + "Do not edit these values. A template will be provided by NMDC in which these values have been pre-filled." + ], + "examples": [ + { + "value": "504000" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "rank": 19, + "string_serialization": "{text}", + "alias": "proposal_dna", + "owner": "JgiMgLrInterface", + "domain_of": [ + "Biosample", + "JgiMgInterface", + "JgiMgLrInterface" + ], + "slot_group": "jgi_metagenomics_section", + "range": "string", + "required": true, + "recommended": false, + "multivalued": false + }, + "analysis_type": { + "name": "analysis_type", + "description": "Select all the data types associated or available for this biosample", + "title": "analysis/data type", + "examples": [ + { + "value": "metagenomics; metabolomics; proteomics" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "MIxS:investigation_type" + ], + "rank": 3, + "alias": "analysis_type", + "owner": "JgiMgLrInterface", + "domain_of": [ + "Biosample", + "DhMultiviewCommonColumnsMixin", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "EmslInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "JgiMgInterface", + "JgiMgLrInterface", + "JgiMtInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "AnalysisTypeEnum", + "required": true, + "recommended": false, + "multivalued": true + }, + "samp_name": { + "name": "samp_name", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "text" + } + }, + "description": "A local identifier or name that for the material sample collected. Refers to the original material collected or to any derived sub-samples.", + "title": "sample name", + "comments": [ + "It can have any format, but we suggest that you make it concise, unique and consistent within your lab, and as informative as possible." + ], + "examples": [ + { + "value": "Rock core CB1178(5-6) from NSW" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sample name" + ], + "rank": 1, + "is_a": "investigation field", + "string_serialization": "{text}", + "slot_uri": "MIXS:0001107", + "identifier": true, + "alias": "samp_name", + "owner": "JgiMgLrInterface", + "domain_of": [ + "Biosample", + "DhMultiviewCommonColumnsMixin", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "EmslInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "JgiMgInterface", + "JgiMgLrInterface", + "JgiMtInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "string", + "required": true, + "multivalued": false + }, + "source_mat_id": { + "name": "source_mat_id", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "for cultures of microorganisms: identifiers for two culture collections; for other material a unique arbitrary identifer" + } + }, + "description": "A globally unique identifier assigned to the biological sample.", + "title": "source material identifier", + "todos": [ + "Currently, the comments say to use UUIDs. However, if we implement assigning NMDC identifiers with the minter we dont need to require a GUID. It can be an optional field to fill out only if they already have a resolvable ID.", + "Currently, the comments say to use UUIDs. However, if we implement assigning NMDC identifiers with the minter we dont need to require a GUID. It can be an optional field to fill out only if they already have a resolvable ID." + ], + "notes": [ + "The source material IS the Globally Unique ID" + ], + "comments": [ + "Identifiers must be prefixed. Possible FAIR prefixes are IGSNs (http://www.geosamples.org/getigsn), NCBI biosample accession numbers, ARK identifiers (https://arks.org/). These IDs enable linking to derived analytes and subsamples. If you have not assigned FAIR identifiers to your samples, you can generate UUIDs (https://www.uuidgenerator.net/).", + "Identifiers must be prefixed. Possible FAIR prefixes are IGSNs (http://www.geosamples.org/getigsn), NCBI biosample accession numbers, ARK identifiers (https://arks.org/). These IDs enable linking to derived analytes and subsamples. If you have not assigned FAIR identifiers to your samples, you can generate UUIDs (https://www.uuidgenerator.net/)." + ], + "examples": [ + { + "value": "IGSN:AU1243" + }, + { + "value": "UUID:24f1467a-40f4-11ed-b878-0242ac120002" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "source material identifiers" + ], + "rank": 2, + "is_a": "nucleic acid sequence source field", + "string_serialization": "{text}:{text}", + "slot_uri": "MIXS:0000026", + "alias": "source_mat_id", + "owner": "JgiMgLrInterface", + "domain_of": [ + "Biosample", + "DhMultiviewCommonColumnsMixin", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "EmslInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "JgiMgInterface", + "JgiMgLrInterface", + "JgiMtInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "string", + "multivalued": false, + "pattern": "[^\\:\\n\\r]+\\:[^\\:\\n\\r]+" + } + } + }, + "JgiMtInterface": { + "name": "JgiMtInterface", + "annotations": { + "excel_worksheet_name": { + "tag": "excel_worksheet_name", + "value": "JGI MT" + } + }, + "description": "jgi_mt dh_interface", + "title": "JGI MT", + "from_schema": "https://example.com/nmdc_submission_schema", + "is_a": "DhInterface", + "mixins": [ + "DhMultiviewCommonColumnsMixin" + ], + "slots": [ + "dnase_rna", + "proposal_rna", + "rna_absorb1", + "rna_absorb2", + "rna_concentration", + "rna_cont_type", + "rna_cont_well", + "rna_container_id", + "rna_isolate_meth", + "rna_project_contact", + "rna_samp_id", + "rna_sample_format", + "rna_sample_name", + "rna_seq_project", + "rna_seq_project_name", + "rna_seq_project_pi", + "rna_volume", + "dnase_rna", + "proposal_rna", + "rna_absorb1", + "rna_absorb2", + "rna_concentration", + "rna_cont_type", + "rna_cont_well", + "rna_container_id", + "rna_isolate_meth", + "rna_project_contact", + "rna_samp_id", + "rna_sample_format", + "rna_sample_name", + "rna_seq_project", + "rna_seq_project_name", + "rna_seq_project_pi", + "rna_volume" + ], + "slot_usage": { + "dnase_rna": { + "name": "dnase_rna", + "title": "DNase treated", + "comments": [ + "Note DNase treatment is required for all RNA samples." + ], + "examples": [ + { + "value": "no" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "Was Sample DNAse treated?" + ], + "rank": 13, + "owner": "Biosample", + "domain_of": [ + "Biosample", + "JgiMtInterface" + ], + "slot_group": "jgi_metatranscriptomics_section", + "range": "YesNoEnum", + "required": true, + "recommended": false + }, + "proposal_rna": { + "name": "proposal_rna", + "title": "RNA proposal ID", + "comments": [ + "Do not edit these values. A template will be provided by NMDC in which these values have been pre-filled." + ], + "examples": [ + { + "value": "504000" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "rank": 19, + "string_serialization": "{text}", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "JgiMtInterface" + ], + "slot_group": "jgi_metatranscriptomics_section", + "range": "string", + "required": true, + "recommended": false, + "multivalued": false + }, + "rna_absorb1": { + "name": "rna_absorb1", + "description": "260/280 measurement of RNA sample purity", + "title": "RNA absorbance 260/280", + "comments": [ + "Recommended value is between 1 and 3." + ], + "examples": [ + { + "value": "2.02" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "rank": 7, + "string_serialization": "{float}", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "JgiMtInterface" + ], + "slot_group": "jgi_metatranscriptomics_section", + "range": "float", + "recommended": true + }, + "rna_absorb2": { + "name": "rna_absorb2", + "description": "260/230 measurement of RNA sample purity", + "title": "RNA absorbance 260/230", + "comments": [ + "Recommended value is between 1 and 3." + ], + "examples": [ + { + "value": "2.02" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "rank": 8, + "string_serialization": "{float}", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "JgiMtInterface" + ], + "slot_group": "jgi_metatranscriptomics_section", + "range": "float", + "recommended": true + }, + "rna_concentration": { + "name": "rna_concentration", + "title": "RNA concentration in ng/ul", + "comments": [ + "Units must be in ng/uL. Enter the numerical part only. Must be calculated using a fluorometric method. Acceptable values are 0-2000." + ], + "examples": [ + { + "value": "100" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "nmdc:nucleic_acid_concentration" + ], + "rank": 5, + "string_serialization": "{float}", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "JgiMtInterface" + ], + "slot_group": "jgi_metatranscriptomics_section", + "range": "float", + "required": true, + "recommended": false, + "minimum_value": 0, + "maximum_value": 1000 + }, + "rna_cont_type": { + "name": "rna_cont_type", + "description": "Tube or plate (96-well)", + "title": "RNA container type", + "examples": [ + { + "value": "plate" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "rank": 10, + "owner": "Biosample", + "domain_of": [ + "Biosample", + "JgiMtInterface" + ], + "slot_group": "jgi_metatranscriptomics_section", + "range": "JgiContTypeEnum", + "required": true, + "recommended": false + }, + "rna_cont_well": { + "name": "rna_cont_well", + "title": "RNA plate position", + "comments": [ + "Required when 'plate' is selected for container type.", + "Leave blank if the sample will be shipped in a tube.", + "JGI will not process samples in corner wells, so A1, A12, H1 and H12 will not pass validation.", + "For partial plates, fill by columns, like B1-G1,A2-H2,A3-D3 (NOT A2-A11,B1-B8)." + ], + "examples": [ + { + "value": "B2" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "rank": 11, + "string_serialization": "{96 well plate pos}", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "JgiMtInterface" + ], + "slot_group": "jgi_metatranscriptomics_section", + "range": "string", + "recommended": true, + "multivalued": false, + "pattern": "^(?!A1$|A12$|H1$|H12$)(([A-H][1-9])|([A-H]1[0-2]))$" + }, + "rna_container_id": { + "name": "rna_container_id", + "title": "RNA container label", + "comments": [ + "Must be unique across all tubes and plates, and <20 characters. All samples in a plate should have the same plate label." + ], + "examples": [ + { + "value": "Pond_MT_041618" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "rank": 9, + "string_serialization": "{text < 20 characters}", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "JgiMtInterface" + ], + "slot_group": "jgi_metatranscriptomics_section", + "range": "string", + "required": true, + "recommended": false, + "multivalued": false, + "pattern": "^.{1,20}$" + }, + "rna_isolate_meth": { + "name": "rna_isolate_meth", + "description": "Describe the method/protocol/kit used to extract DNA/RNA.", + "title": "RNA isolation method", + "examples": [ + { + "value": "phenol/chloroform extraction" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "Sample Isolation Method" + ], + "rank": 16, + "string_serialization": "{text}", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "JgiMtInterface" + ], + "slot_group": "jgi_metatranscriptomics_section", + "range": "string", + "required": true, + "recommended": false, + "multivalued": false + }, + "rna_project_contact": { + "name": "rna_project_contact", + "title": "RNA seq project contact", + "comments": [ + "Do not edit these values. A template will be provided by NMDC in which these values have been pre-filled." + ], + "examples": [ + { + "value": "John Jones" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "rank": 18, + "string_serialization": "{text}", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "JgiMtInterface" + ], + "slot_group": "jgi_metatranscriptomics_section", + "range": "string", + "required": true, + "recommended": false, + "multivalued": false + }, + "rna_samp_id": { + "name": "rna_samp_id", + "title": "RNA sample ID", + "comments": [ + "Do not edit these values. A template will be provided by NMDC in which these values have been pre-filled." + ], + "examples": [ + { + "value": "187654" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "rank": 3, + "string_serialization": "{text}", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "JgiMtInterface" + ], + "slot_group": "jgi_metatranscriptomics_section", + "range": "string", + "required": true, + "recommended": false, + "multivalued": false + }, + "rna_sample_format": { + "name": "rna_sample_format", + "description": "Solution in which the RNA sample has been suspended", + "title": "RNA sample format", + "examples": [ + { + "value": "Water" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "rank": 12, + "owner": "Biosample", + "domain_of": [ + "Biosample", + "JgiMtInterface" + ], + "slot_group": "jgi_metatranscriptomics_section", + "range": "RNASampleFormatEnum", + "required": true, + "recommended": false + }, + "rna_sample_name": { + "name": "rna_sample_name", + "description": "Give the RNA sample a name that is meaningful to you. Sample names must be unique across all JGI projects and contain a-z, A-Z, 0-9, - and _ only.", + "title": "RNA sample name", + "examples": [ + { + "value": "JGI_pond_041618" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "rank": 4, + "string_serialization": "{text}", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "JgiMtInterface" + ], + "slot_group": "jgi_metatranscriptomics_section", + "range": "string", + "required": true, + "recommended": false, + "multivalued": false, + "minimum_value": 0, + "maximum_value": 2000, + "pattern": "^[_a-zA-Z0-9-]*$" + }, + "rna_seq_project": { + "name": "rna_seq_project", + "title": "RNA seq project ID", + "comments": [ + "Do not edit these values. A template will be provided by NMDC in which these values have been pre-filled." + ], + "examples": [ + { + "value": "1191234" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "Seq Project ID" + ], + "rank": 1, + "string_serialization": "{text}", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "JgiMtInterface" + ], + "slot_group": "jgi_metatranscriptomics_section", + "range": "string", + "required": true, + "recommended": false, + "multivalued": false + }, + "rna_seq_project_name": { + "name": "rna_seq_project_name", + "title": "RNA seq project name", + "comments": [ + "Do not edit these values. A template will be provided by NMDC in which these values have been pre-filled." + ], + "examples": [ + { + "value": "JGI Pond metatranscriptomics" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "rank": 2, + "string_serialization": "{text}", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "JgiMtInterface" + ], + "slot_group": "jgi_metatranscriptomics_section", + "range": "string", + "required": true, + "recommended": false, + "multivalued": false + }, + "rna_seq_project_pi": { + "name": "rna_seq_project_pi", + "title": "RNA seq project PI", + "comments": [ + "Do not edit these values. A template will be provided by NMDC in which these values have been pre-filled." + ], + "examples": [ + { + "value": "Jane Johnson" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "rank": 17, + "string_serialization": "{text}", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "JgiMtInterface" + ], + "slot_group": "jgi_metatranscriptomics_section", + "range": "string", + "required": true, + "recommended": false, + "multivalued": false + }, + "rna_volume": { + "name": "rna_volume", + "title": "RNA volume in ul", + "comments": [ + "Units must be in uL. Enter the numerical part only. Value must be 0-1000. This form accepts values < 25, but JGI may refuse to process them unless permission has been granted by a project manager" + ], + "examples": [ + { + "value": "25" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "rank": 6, + "string_serialization": "{float}", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "JgiMtInterface" + ], + "slot_group": "jgi_metatranscriptomics_section", + "range": "float", + "required": true, + "recommended": false, + "minimum_value": 0, + "maximum_value": 1000 + }, + "oxy_stat_samp": { + "name": "oxy_stat_samp", + "range": "OxyStatSampEnum" + } + }, + "attributes": { + "dnase_rna": { + "name": "dnase_rna", + "title": "DNase treated", + "comments": [ + "Note DNase treatment is required for all RNA samples." + ], + "examples": [ + { + "value": "no" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "Was Sample DNAse treated?" + ], + "rank": 13, + "alias": "dnase_rna", + "owner": "JgiMtInterface", + "domain_of": [ + "Biosample", + "JgiMtInterface" + ], + "slot_group": "jgi_metatranscriptomics_section", + "range": "YesNoEnum", + "required": true, + "recommended": false + }, + "proposal_rna": { + "name": "proposal_rna", + "title": "RNA proposal ID", + "comments": [ + "Do not edit these values. A template will be provided by NMDC in which these values have been pre-filled." + ], + "examples": [ + { + "value": "504000" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "rank": 19, + "string_serialization": "{text}", + "alias": "proposal_rna", + "owner": "JgiMtInterface", + "domain_of": [ + "Biosample", + "JgiMtInterface" + ], + "slot_group": "jgi_metatranscriptomics_section", + "range": "string", + "required": true, + "recommended": false, + "multivalued": false + }, + "rna_absorb1": { + "name": "rna_absorb1", + "description": "260/280 measurement of RNA sample purity", + "title": "RNA absorbance 260/280", + "comments": [ + "Recommended value is between 1 and 3." + ], + "examples": [ + { + "value": "2.02" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "rank": 7, + "string_serialization": "{float}", + "alias": "rna_absorb1", + "owner": "JgiMtInterface", + "domain_of": [ + "Biosample", + "JgiMtInterface" + ], + "slot_group": "jgi_metatranscriptomics_section", + "range": "float", + "recommended": true + }, + "rna_absorb2": { + "name": "rna_absorb2", + "description": "260/230 measurement of RNA sample purity", + "title": "RNA absorbance 260/230", + "comments": [ + "Recommended value is between 1 and 3." + ], + "examples": [ + { + "value": "2.02" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "rank": 8, + "string_serialization": "{float}", + "alias": "rna_absorb2", + "owner": "JgiMtInterface", + "domain_of": [ + "Biosample", + "JgiMtInterface" + ], + "slot_group": "jgi_metatranscriptomics_section", + "range": "float", + "recommended": true + }, + "rna_concentration": { + "name": "rna_concentration", + "title": "RNA concentration in ng/ul", + "comments": [ + "Units must be in ng/uL. Enter the numerical part only. Must be calculated using a fluorometric method. Acceptable values are 0-2000." + ], + "examples": [ + { + "value": "100" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "nmdc:nucleic_acid_concentration" + ], + "rank": 5, + "string_serialization": "{float}", + "alias": "rna_concentration", + "owner": "JgiMtInterface", + "domain_of": [ + "Biosample", + "JgiMtInterface" + ], + "slot_group": "jgi_metatranscriptomics_section", + "range": "float", + "required": true, + "recommended": false, + "minimum_value": 0, + "maximum_value": 1000 + }, + "rna_cont_type": { + "name": "rna_cont_type", + "description": "Tube or plate (96-well)", + "title": "RNA container type", + "examples": [ + { + "value": "plate" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "rank": 10, + "alias": "rna_cont_type", + "owner": "JgiMtInterface", + "domain_of": [ + "Biosample", + "JgiMtInterface" + ], + "slot_group": "jgi_metatranscriptomics_section", + "range": "JgiContTypeEnum", + "required": true, + "recommended": false + }, + "rna_cont_well": { + "name": "rna_cont_well", + "title": "RNA plate position", + "comments": [ + "Required when 'plate' is selected for container type.", + "Leave blank if the sample will be shipped in a tube.", + "JGI will not process samples in corner wells, so A1, A12, H1 and H12 will not pass validation.", + "For partial plates, fill by columns, like B1-G1,A2-H2,A3-D3 (NOT A2-A11,B1-B8)." + ], + "examples": [ + { + "value": "B2" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "rank": 11, + "string_serialization": "{96 well plate pos}", + "alias": "rna_cont_well", + "owner": "JgiMtInterface", + "domain_of": [ + "Biosample", + "JgiMtInterface" + ], + "slot_group": "jgi_metatranscriptomics_section", + "range": "string", + "recommended": true, + "multivalued": false, + "pattern": "^(?!A1$|A12$|H1$|H12$)(([A-H][1-9])|([A-H]1[0-2]))$" + }, + "rna_container_id": { + "name": "rna_container_id", + "title": "RNA container label", + "comments": [ + "Must be unique across all tubes and plates, and <20 characters. All samples in a plate should have the same plate label." + ], + "examples": [ + { + "value": "Pond_MT_041618" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "rank": 9, + "string_serialization": "{text < 20 characters}", + "alias": "rna_container_id", + "owner": "JgiMtInterface", + "domain_of": [ + "Biosample", + "JgiMtInterface" + ], + "slot_group": "jgi_metatranscriptomics_section", + "range": "string", + "required": true, + "recommended": false, + "multivalued": false, + "pattern": "^.{1,20}$" + }, + "rna_isolate_meth": { + "name": "rna_isolate_meth", + "description": "Describe the method/protocol/kit used to extract DNA/RNA.", + "title": "RNA isolation method", + "examples": [ + { + "value": "phenol/chloroform extraction" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "Sample Isolation Method" + ], + "rank": 16, + "string_serialization": "{text}", + "alias": "rna_isolate_meth", + "owner": "JgiMtInterface", + "domain_of": [ + "Biosample", + "JgiMtInterface" + ], + "slot_group": "jgi_metatranscriptomics_section", + "range": "string", + "required": true, + "recommended": false, + "multivalued": false + }, + "rna_project_contact": { + "name": "rna_project_contact", + "title": "RNA seq project contact", + "comments": [ + "Do not edit these values. A template will be provided by NMDC in which these values have been pre-filled." + ], + "examples": [ + { + "value": "John Jones" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "rank": 18, + "string_serialization": "{text}", + "alias": "rna_project_contact", + "owner": "JgiMtInterface", + "domain_of": [ + "Biosample", + "JgiMtInterface" + ], + "slot_group": "jgi_metatranscriptomics_section", + "range": "string", + "required": true, + "recommended": false, + "multivalued": false + }, + "rna_samp_id": { + "name": "rna_samp_id", + "title": "RNA sample ID", + "comments": [ + "Do not edit these values. A template will be provided by NMDC in which these values have been pre-filled." + ], + "examples": [ + { + "value": "187654" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "rank": 3, + "string_serialization": "{text}", + "alias": "rna_samp_id", + "owner": "JgiMtInterface", + "domain_of": [ + "Biosample", + "JgiMtInterface" + ], + "slot_group": "jgi_metatranscriptomics_section", + "range": "string", + "required": true, + "recommended": false, + "multivalued": false + }, + "rna_sample_format": { + "name": "rna_sample_format", + "description": "Solution in which the RNA sample has been suspended", + "title": "RNA sample format", + "examples": [ + { + "value": "Water" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "rank": 12, + "alias": "rna_sample_format", + "owner": "JgiMtInterface", + "domain_of": [ + "Biosample", + "JgiMtInterface" + ], + "slot_group": "jgi_metatranscriptomics_section", + "range": "RNASampleFormatEnum", + "required": true, + "recommended": false + }, + "rna_sample_name": { + "name": "rna_sample_name", + "description": "Give the RNA sample a name that is meaningful to you. Sample names must be unique across all JGI projects and contain a-z, A-Z, 0-9, - and _ only.", + "title": "RNA sample name", + "examples": [ + { + "value": "JGI_pond_041618" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "rank": 4, + "string_serialization": "{text}", + "alias": "rna_sample_name", + "owner": "JgiMtInterface", + "domain_of": [ + "Biosample", + "JgiMtInterface" + ], + "slot_group": "jgi_metatranscriptomics_section", + "range": "string", + "required": true, + "recommended": false, + "multivalued": false, + "minimum_value": 0, + "maximum_value": 2000, + "pattern": "^[_a-zA-Z0-9-]*$" + }, + "rna_seq_project": { + "name": "rna_seq_project", + "title": "RNA seq project ID", + "comments": [ + "Do not edit these values. A template will be provided by NMDC in which these values have been pre-filled." + ], + "examples": [ + { + "value": "1191234" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "Seq Project ID" + ], + "rank": 1, + "string_serialization": "{text}", + "alias": "rna_seq_project", + "owner": "JgiMtInterface", + "domain_of": [ + "Biosample", + "JgiMtInterface" + ], + "slot_group": "jgi_metatranscriptomics_section", + "range": "string", + "required": true, + "recommended": false, + "multivalued": false + }, + "rna_seq_project_name": { + "name": "rna_seq_project_name", + "title": "RNA seq project name", + "comments": [ + "Do not edit these values. A template will be provided by NMDC in which these values have been pre-filled." + ], + "examples": [ + { + "value": "JGI Pond metatranscriptomics" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "rank": 2, + "string_serialization": "{text}", + "alias": "rna_seq_project_name", + "owner": "JgiMtInterface", + "domain_of": [ + "Biosample", + "JgiMtInterface" + ], + "slot_group": "jgi_metatranscriptomics_section", + "range": "string", + "required": true, + "recommended": false, + "multivalued": false + }, + "rna_seq_project_pi": { + "name": "rna_seq_project_pi", + "title": "RNA seq project PI", + "comments": [ + "Do not edit these values. A template will be provided by NMDC in which these values have been pre-filled." + ], + "examples": [ + { + "value": "Jane Johnson" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "rank": 17, + "string_serialization": "{text}", + "alias": "rna_seq_project_pi", + "owner": "JgiMtInterface", + "domain_of": [ + "Biosample", + "JgiMtInterface" + ], + "slot_group": "jgi_metatranscriptomics_section", + "range": "string", + "required": true, + "recommended": false, + "multivalued": false + }, + "rna_volume": { + "name": "rna_volume", + "title": "RNA volume in ul", + "comments": [ + "Units must be in uL. Enter the numerical part only. Value must be 0-1000. This form accepts values < 25, but JGI may refuse to process them unless permission has been granted by a project manager" + ], + "examples": [ + { + "value": "25" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "rank": 6, + "string_serialization": "{float}", + "alias": "rna_volume", + "owner": "JgiMtInterface", + "domain_of": [ + "Biosample", + "JgiMtInterface" + ], + "slot_group": "jgi_metatranscriptomics_section", + "range": "float", + "required": true, + "recommended": false, + "minimum_value": 0, + "maximum_value": 1000 + }, + "analysis_type": { + "name": "analysis_type", + "description": "Select all the data types associated or available for this biosample", + "title": "analysis/data type", + "examples": [ + { + "value": "metagenomics; metabolomics; proteomics" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "MIxS:investigation_type" + ], + "rank": 3, + "alias": "analysis_type", + "owner": "JgiMtInterface", + "domain_of": [ + "Biosample", + "DhMultiviewCommonColumnsMixin", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "EmslInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "JgiMgInterface", + "JgiMgLrInterface", + "JgiMtInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "AnalysisTypeEnum", + "required": true, + "recommended": false, + "multivalued": true + }, + "samp_name": { + "name": "samp_name", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "text" + } + }, + "description": "A local identifier or name that for the material sample collected. Refers to the original material collected or to any derived sub-samples.", + "title": "sample name", + "comments": [ + "It can have any format, but we suggest that you make it concise, unique and consistent within your lab, and as informative as possible." + ], + "examples": [ + { + "value": "Rock core CB1178(5-6) from NSW" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sample name" + ], + "rank": 1, + "is_a": "investigation field", + "string_serialization": "{text}", + "slot_uri": "MIXS:0001107", + "identifier": true, + "alias": "samp_name", + "owner": "JgiMtInterface", + "domain_of": [ + "Biosample", + "DhMultiviewCommonColumnsMixin", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "EmslInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "JgiMgInterface", + "JgiMgLrInterface", + "JgiMtInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "string", + "required": true, + "multivalued": false + }, + "source_mat_id": { + "name": "source_mat_id", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "for cultures of microorganisms: identifiers for two culture collections; for other material a unique arbitrary identifer" + } + }, + "description": "A globally unique identifier assigned to the biological sample.", + "title": "source material identifier", + "todos": [ + "Currently, the comments say to use UUIDs. However, if we implement assigning NMDC identifiers with the minter we dont need to require a GUID. It can be an optional field to fill out only if they already have a resolvable ID.", + "Currently, the comments say to use UUIDs. However, if we implement assigning NMDC identifiers with the minter we dont need to require a GUID. It can be an optional field to fill out only if they already have a resolvable ID." + ], + "notes": [ + "The source material IS the Globally Unique ID" + ], + "comments": [ + "Identifiers must be prefixed. Possible FAIR prefixes are IGSNs (http://www.geosamples.org/getigsn), NCBI biosample accession numbers, ARK identifiers (https://arks.org/). These IDs enable linking to derived analytes and subsamples. If you have not assigned FAIR identifiers to your samples, you can generate UUIDs (https://www.uuidgenerator.net/).", + "Identifiers must be prefixed. Possible FAIR prefixes are IGSNs (http://www.geosamples.org/getigsn), NCBI biosample accession numbers, ARK identifiers (https://arks.org/). These IDs enable linking to derived analytes and subsamples. If you have not assigned FAIR identifiers to your samples, you can generate UUIDs (https://www.uuidgenerator.net/)." + ], + "examples": [ + { + "value": "IGSN:AU1243" + }, + { + "value": "UUID:24f1467a-40f4-11ed-b878-0242ac120002" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "source material identifiers" + ], + "rank": 2, + "is_a": "nucleic acid sequence source field", + "string_serialization": "{text}:{text}", + "slot_uri": "MIXS:0000026", + "alias": "source_mat_id", + "owner": "JgiMtInterface", + "domain_of": [ + "Biosample", + "DhMultiviewCommonColumnsMixin", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "EmslInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "JgiMgInterface", + "JgiMgLrInterface", + "JgiMtInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "string", + "multivalued": false, + "pattern": "[^\\:\\n\\r]+\\:[^\\:\\n\\r]+" + } + }, + "rules": [ + { + "preconditions": { + "slot_conditions": { + "rna_cont_well": { + "name": "rna_cont_well", + "pattern": ".+" + } + } + }, + "postconditions": { + "slot_conditions": { + "rna_cont_type": { + "name": "rna_cont_type", + "equals_string": "plate" + } + } + }, + "description": "RNA samples shipped to JGI for metagenomic analysis in tubes can't have any value for their plate position.", + "title": "rna_well_requires_plate" + }, + { + "preconditions": { + "slot_conditions": { + "rna_cont_type": { + "name": "rna_cont_type", + "equals_string": "plate" + } + } + }, + "postconditions": { + "slot_conditions": { + "rna_cont_well": { + "name": "rna_cont_well", + "pattern": "^(?!A1$|A12$|H1$|H12$)(([A-H][1-9])|([A-H]1[0-2]))$" + } + } + }, + "description": "RNA samples in plates must have a plate position that matches the regex. Note the requirement for an empty string in the tube case. Waiting for value_present validation to be added to runtime", + "title": "rna_plate_requires_well" + } + ] + }, + "MiscEnvsInterface": { + "name": "MiscEnvsInterface", + "annotations": { + "excel_worksheet_name": { + "tag": "excel_worksheet_name", + "value": "misc natural or artificial" + } + }, + "description": "misc_envs dh_interface", + "title": "Misc Envs", + "from_schema": "https://example.com/nmdc_submission_schema", + "is_a": "DhInterface", + "mixins": [ + "DhMultiviewCommonColumnsMixin" + ], + "slots": [ + "alkalinity", + "alt", + "ammonium", + "biomass", + "bromide", + "calcium", + "chem_administration", + "chloride", + "chlorophyll", + "collection_date", + "density", + "depth", + "diether_lipids", + "diss_carb_dioxide", + "diss_hydrogen", + "diss_inorg_carb", + "diss_org_nitro", + "diss_oxygen", + "ecosystem", + "ecosystem_category", + "ecosystem_subtype", + "ecosystem_type", + "elev", + "env_broad_scale", + "env_local_scale", + "env_medium", + "experimental_factor", + "geo_loc_name", + "lat_lon", + "misc_param", + "nitrate", + "nitrite", + "nitro", + "org_carb", + "org_matter", + "org_nitro", + "organism_count", + "oxy_stat_samp", + "perturbation", + "ph", + "ph_meth", + "phosphate", + "phosplipid_fatt_acid", + "potassium", + "pressure", + "salinity", + "samp_collec_device", + "samp_collec_method", + "samp_mat_process", + "samp_size", + "samp_store_dur", + "samp_store_loc", + "samp_store_temp", + "sample_link", + "silicate", + "size_frac", + "sodium", + "specific_ecosystem", + "sulfate", + "sulfide", + "temp", + "water_current" + ], + "slot_usage": { + "alkalinity": { + "name": "alkalinity", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milliequivalent per liter, milligram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate", + "title": "alkalinity", + "examples": [ + { + "value": "50 milligram per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "alkalinity" + ], + "rank": 1, + "is_a": "core field", + "slot_uri": "MIXS:0000421", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "alt": { + "name": "alt", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + } + }, + "description": "Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air", + "title": "altitude", + "examples": [ + { + "value": "100 meter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "altitude" + ], + "rank": 26, + "is_a": "environment field", + "slot_uri": "MIXS:0000094", + "owner": "Biosample", + "domain_of": [ + "agriculture", + "air", + "built environment", + "core", + "food-animal and animal feed", + "food-farm environment", + "food-food production facility", + "food-human foods", + "host-associated", + "human-associated", + "human-gut", + "human-oral", + "human-skin", + "human-vaginal", + "hydrocarbon resources-cores", + "hydrocarbon resources-fluids_swabs", + "microbial mat_biofilm", + "miscellaneous natural or artificial environment", + "plant-associated", + "sediment", + "soil", + "symbiont-associated", + "wastewater_sludge", + "water", + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HostAssociatedInterface", + "MiscEnvsInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "recommended": true, + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "ammonium": { + "name": "ammonium", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per liter, milligram per liter, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of ammonium in the sample", + "title": "ammonium", + "examples": [ + { + "value": "1.5 milligram per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "ammonium" + ], + "rank": 4, + "is_a": "core field", + "slot_uri": "MIXS:0000427", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "biomass": { + "name": "biomass", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "biomass type;measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "ton, kilogram, gram" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements", + "title": "biomass", + "examples": [ + { + "value": "total;20 gram" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "biomass" + ], + "rank": 6, + "is_a": "core field", + "string_serialization": "{text};{float} {unit}", + "slot_uri": "MIXS:0000174", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+\\|)*([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+)$" + }, + "bromide": { + "name": "bromide", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of bromide", + "title": "bromide", + "examples": [ + { + "value": "0.05 parts per million" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "bromide" + ], + "rank": 8, + "is_a": "core field", + "slot_uri": "MIXS:0000176", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "calcium": { + "name": "calcium", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milligram per liter, micromole per liter, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of calcium in the sample", + "title": "calcium", + "examples": [ + { + "value": "0.2 micromole per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "calcium" + ], + "rank": 9, + "is_a": "core field", + "slot_uri": "MIXS:0000432", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "chem_administration": { + "name": "chem_administration", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "CHEBI;timestamp" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi", + "title": "chemical administration", + "examples": [ + { + "value": "agar [CHEBI:2509];2018-05-11|agar [CHEBI:2509];2018-05-22" + }, + { + "value": "agar [CHEBI:2509];2018-05" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "chemical administration" + ], + "rank": 17, + "is_a": "core field", + "string_serialization": "{termLabel} {[termID]};{timestamp}", + "slot_uri": "MIXS:0000751", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "recommended": true, + "multivalued": false, + "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\];([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$" + }, + "chloride": { + "name": "chloride", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milligram per liter, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of chloride in the sample", + "title": "chloride", + "examples": [ + { + "value": "5000 milligram per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "chloride" + ], + "rank": 10, + "is_a": "core field", + "slot_uri": "MIXS:0000429", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "chlorophyll": { + "name": "chlorophyll", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milligram per cubic meter, microgram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of chlorophyll", + "title": "chlorophyll", + "examples": [ + { + "value": "5 milligram per cubic meter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "chlorophyll" + ], + "rank": 11, + "is_a": "core field", + "slot_uri": "MIXS:0000177", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "collection_date": { + "name": "collection_date", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "date and time" + } + }, + "description": "The date of sampling", + "title": "collection date", + "notes": [ + "MIxS collection_date accepts (truncated) ISO8601. DH taking arb prec date only", + "Use modified term (amended definition)" + ], + "examples": [ + { + "value": "2021-04-15" + }, + { + "value": "2021-04" + }, + { + "value": "2021" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "collection date" + ], + "rank": 3, + "is_a": "environment field", + "string_serialization": "{date, arbitrary precision}", + "slot_uri": "MIXS:0000011", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "required": true, + "multivalued": false, + "pattern": "^[12]\\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\\d|3[01]))?)?$" + }, + "density": { + "name": "density", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "gram per cubic meter, gram per cubic centimeter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Density of the sample, which is its mass per unit volume (aka volumetric mass density)", + "title": "density", + "examples": [ + { + "value": "1000 kilogram per cubic meter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "density" + ], + "rank": 12, + "is_a": "core field", + "slot_uri": "MIXS:0000435", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "depth": { + "name": "depth", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + } + }, + "description": "The vertical distance below local surface, e.g. for sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples.", + "title": "depth, meters", + "notes": [ + "Use modified term" + ], + "comments": [ + "All depths must be reported in meters. Provide the numerical portion only." + ], + "examples": [ + { + "value": "0 - 0.1" + }, + { + "value": "1" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "depth" + ], + "rank": 9, + "is_a": "environment field", + "string_serialization": "{float}|{float}-{float}", + "slot_uri": "MIXS:0000018", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "recommended": true, + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)?(\\s*-\\s*[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)?)?$" + }, + "diether_lipids": { + "name": "diether_lipids", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "diether lipid name;measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "nanogram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Concentration of diether lipids; can include multiple types of diether lipids", + "title": "diether lipids", + "examples": [ + { + "value": "0.2 nanogram per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "diether lipids" + ], + "rank": 13, + "is_a": "core field", + "string_serialization": "{text};{float} {unit}", + "slot_uri": "MIXS:0000178", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+\\|)*([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+)$" + }, + "diss_carb_dioxide": { + "name": "diss_carb_dioxide", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per liter, milligram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample", + "title": "dissolved carbon dioxide", + "examples": [ + { + "value": "5 milligram per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "dissolved carbon dioxide" + ], + "rank": 14, + "is_a": "core field", + "slot_uri": "MIXS:0000436", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "diss_hydrogen": { + "name": "diss_hydrogen", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of dissolved hydrogen", + "title": "dissolved hydrogen", + "examples": [ + { + "value": "0.3 micromole per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "dissolved hydrogen" + ], + "rank": 15, + "is_a": "core field", + "slot_uri": "MIXS:0000179", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "diss_inorg_carb": { + "name": "diss_inorg_carb", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "microgram per liter, milligram per liter, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter", + "title": "dissolved inorganic carbon", + "examples": [ + { + "value": "2059 micromole per kilogram" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "dissolved inorganic carbon" + ], + "rank": 16, + "is_a": "core field", + "slot_uri": "MIXS:0000434", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "diss_org_nitro": { + "name": "diss_org_nitro", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "microgram per liter, milligram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2", + "title": "dissolved organic nitrogen", + "examples": [ + { + "value": "0.05 micromole per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "dissolved organic nitrogen" + ], + "rank": 18, + "is_a": "core field", + "slot_uri": "MIXS:0000162", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "diss_oxygen": { + "name": "diss_oxygen", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per kilogram, milligram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of dissolved oxygen", + "title": "dissolved oxygen", + "examples": [ + { + "value": "175 micromole per kilogram" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "dissolved oxygen" + ], + "rank": 19, + "is_a": "core field", + "slot_uri": "MIXS:0000119", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "ecosystem": { + "name": "ecosystem", + "description": "An ecosystem is a combination of a physical environment (abiotic factors) and all the organisms (biotic factors) that interact with this environment. Ecosystem is in position 1/5 in a GOLD path.", + "comments": [ + "The abiotic factors play a profound role on the type and composition of organisms in a given environment. The GOLD Ecosystem at the top of the five-level classification system is aimed at capturing the broader environment from which an organism or environmental sample is collected. The three broad groups under Ecosystem are Environmental, Host-associated, and Engineered. They represent samples collected from a natural environment or from another organism or from engineered environments like bioreactors respectively." + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "https://gold.jgi.doe.gov/help" + ], + "rank": 9, + "is_a": "gold_path_field", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "Study", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "EcosystemEnum", + "recommended": true + }, + "ecosystem_category": { + "name": "ecosystem_category", + "description": "Ecosystem categories represent divisions within the ecosystem based on specific characteristics of the environment from where an organism or sample is isolated. Ecosystem category is in position 2/5 in a GOLD path.", + "comments": [ + "The Environmental ecosystem (for example) is divided into Air, Aquatic and Terrestrial. Ecosystem categories for Host-associated samples can be individual hosts or phyla and for engineered samples it may be manipulated environments like bioreactors, solid waste etc." + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "https://gold.jgi.doe.gov/help" + ], + "rank": 10, + "is_a": "gold_path_field", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "Study", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "EcosystemCategoryEnum", + "recommended": true + }, + "ecosystem_subtype": { + "name": "ecosystem_subtype", + "description": "Ecosystem subtypes represent further subdivision of Ecosystem types into more distinct subtypes. Ecosystem subtype is in position 4/5 in a GOLD path.", + "comments": [ + "Ecosystem Type Marine (Environmental -> Aquatic -> Marine) is further divided (for example) into Intertidal zone, Coastal, Pelagic, Intertidal zone etc. in the Ecosystem subtype category." + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "https://gold.jgi.doe.gov/help" + ], + "rank": 12, + "is_a": "gold_path_field", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "Study", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "EcosystemSubtypeEnum", + "recommended": true + }, + "ecosystem_type": { + "name": "ecosystem_type", + "description": "Ecosystem types represent things having common characteristics within the Ecosystem Category. These common characteristics based grouping is still broad but specific to the characteristics of a given environment. Ecosystem type is in position 3/5 in a GOLD path.", + "comments": [ + "The Aquatic ecosystem category (for example) may have ecosystem types like Marine or Thermal springs etc. Ecosystem category Air may have Indoor air or Outdoor air as different Ecosystem Types. In the case of Host-associated samples, ecosystem type can represent Respiratory system, Digestive system, Roots etc." + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "https://gold.jgi.doe.gov/help" + ], + "rank": 11, + "is_a": "gold_path_field", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "Study", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "EcosystemTypeEnum", + "recommended": true + }, + "elev": { + "name": "elev", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + } + }, + "description": "Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit.", + "title": "elevation, meters", + "comments": [ + "All elevations must be reported in meters. Provide the numerical portion only.", + "Please use https://www.advancedconverter.com/map-tools/find-altitude-by-coordinates, if needed, to help estimate the elevation based on latitude and longitude coordinates." + ], + "examples": [ + { + "value": "225" + }, + { + "value": "0" + }, + { + "value": "1250" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "elevation" + ], + "rank": 6, + "is_a": "environment field", + "slot_uri": "MIXS:0000093", + "owner": "Biosample", + "domain_of": [ + "FieldResearchSite", + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "float", + "required": true, + "multivalued": false + }, + "env_broad_scale": { + "name": "env_broad_scale", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "The major environment type(s) where the sample was collected. Recommend subclasses of biome [ENVO:00000428]. Multiple terms can be separated by one or more pipes." + }, + "tooltip": { + "tag": "tooltip", + "value": "The biome or major environmental system where the sample or specimen originated. Choose values from subclasses of the 'biome' class [ENVO:00000428] in the Environment Ontology (ENVO). For host-associated or plant-associated samples, use terms from the UBERON or Plant Ontology to describe the broad anatomical or morphological context" + } + }, + "description": "In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO's biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html", + "title": "broad-scale environmental context", + "notes": [ + "range changed to enumeration late in makefile, so this is modified (but \"sample ID\" anyway)" + ], + "examples": [ + { + "value": "oceanic epipelagic zone biome [ENVO:01000033] for annotating a water sample from the photic zone in middle of the Atlantic Ocean" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "broad-scale environmental context" + ], + "rank": 6, + "is_a": "environment field", + "string_serialization": "{termLabel} {[termID]}", + "slot_uri": "MIXS:0000012", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "string", + "required": true, + "multivalued": false, + "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$" + }, + "env_local_scale": { + "name": "env_local_scale", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "Environmental entities having causal influences upon the entity at time of sampling." + }, + "tooltip": { + "tag": "tooltip", + "value": "The specific environmental entities or features near the sample or specimen that significantly influence its characteristics or composition. These entities are typically smaller in scale than the broad environmental context. Values for this field should be countable, material nouns and must be chosen from subclasses of BFO:0000040 (material entity) that appear in the Environment Ontology (ENVO). For host-associated or plant-associated samples, use terms from the UBERON or Plant Ontology to describe specific anatomical structures or plant parts." + } + }, + "description": "Report the entity or entities which are in the sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. We recommend using EnvO terms which are of smaller spatial grain than your entry for env_broad_scale. Terms, such as anatomical sites, from other OBO Library ontologies which interoperate with EnvO (e.g. UBERON) are accepted in this field. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS.", + "title": "local environmental context", + "notes": [ + "range changed to enumeration late in makefile, so this is modified (but \"sample ID\" anyway)" + ], + "examples": [ + { + "value": "canopy [ENVO:00000047]" + }, + { + "value": "herb and fern layer [ENVO:01000337]" + }, + { + "value": "litter layer [ENVO:01000338]" + }, + { + "value": "understory [01000335]" + }, + { + "value": "shrub layer [ENVO:01000336]" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "local environmental context" + ], + "rank": 7, + "is_a": "environment field", + "string_serialization": "{termLabel} {[termID]}", + "slot_uri": "MIXS:0000013", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "string", + "required": true, + "multivalued": false, + "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$" + }, + "env_medium": { + "name": "env_medium", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "The material displaced by the entity at time of sampling. Recommend subclasses of environmental material [ENVO:00010483]." + }, + "tooltip": { + "tag": "tooltip", + "value": "The predominant environmental material or substrate that directly surrounds or hosts the sample or specimen at the time of sampling. Choose values from subclasses of the 'environmental material' class [ENVO:00010483] in the Environment Ontology (ENVO). Values for this field should be measurable or mass material nouns, representing continuous environmental materials. For host-associated or plant-associated samples, use terms from the UBERON or Plant Ontology to indicate a tissue, organ, or plant structure" + } + }, + "description": "Report the environmental material(s) immediately surrounding the sample or specimen at the time of sampling. We recommend using subclasses of 'environmental material' (http://purl.obolibrary.org/obo/ENVO_00010483). EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS . Terms from other OBO ontologies are permissible as long as they reference mass/volume nouns (e.g. air, water, blood) and not discrete, countable entities (e.g. a tree, a leaf, a table top).", + "title": "environmental medium", + "notes": [ + "range changed to enumeration late in makefile, so this is modified (but \"sample ID\" anyway)" + ], + "examples": [ + { + "value": "soil [ENVO:00001998]" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "environmental medium" + ], + "rank": 8, + "is_a": "environment field", + "string_serialization": "{termLabel} {[termID]}", + "slot_uri": "MIXS:0000014", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "string", + "required": true, + "multivalued": false, + "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$" + }, + "experimental_factor": { + "name": "experimental_factor", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "text or EFO and/or OBI" + } + }, + "description": "Experimental factors are essentially the variable aspects of an experiment design which can be used to describe an experiment, or set of experiments, in an increasingly detailed manner. This field accepts ontology terms from Experimental Factor Ontology (EFO) and/or Ontology for Biomedical Investigations (OBI). For a browser of EFO (v 2.95) terms, please see http://purl.bioontology.org/ontology/EFO; for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI", + "title": "experimental factor", + "examples": [ + { + "value": "time series design [EFO:EFO_0001779]" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "experimental factor" + ], + "rank": 12, + "is_a": "investigation field", + "string_serialization": "{termLabel} {[termID]}|{text}", + "slot_uri": "MIXS:0000008", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false + }, + "geo_loc_name": { + "name": "geo_loc_name", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "country or sea name (INSDC or GAZ): region(GAZ), specific location name" + } + }, + "description": "The geographical origin of the sample as defined by the country or sea name followed by specific region name.", + "title": "geographic location (country and/or sea,region)", + "examples": [ + { + "value": "USA: Maryland, Bethesda" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "geographic location (country and/or sea,region)" + ], + "rank": 4, + "is_a": "environment field", + "string_serialization": "{text}: {text}, {text}", + "slot_uri": "MIXS:0000010", + "owner": "Biosample", + "domain_of": [ + "FieldResearchSite", + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "required": true, + "multivalued": false, + "pattern": "^[^:, ][^:]*: [^:, ][^,]*, [^:, ].*$" + }, + "lat_lon": { + "name": "lat_lon", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "decimal degrees, limit to 8 decimal points" + } + }, + "description": "The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system", + "title": "geographic location (latitude and longitude)", + "notes": [ + "This is currently a required field but it's not clear if this should be required for human hosts" + ], + "examples": [ + { + "value": "50.586825 6.408977" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "geographic location (latitude and longitude)" + ], + "rank": 5, + "is_a": "environment field", + "string_serialization": "{lat lon}", + "slot_uri": "MIXS:0000009", + "owner": "Biosample", + "domain_of": [ + "FieldResearchSite", + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "required": true, + "multivalued": false, + "pattern": "^[-+]?([1-8]?\\d(\\.\\d{1,8})?|90(\\.0{1,8})?)\\s[-+]?(180(\\.0{1,8})?|((1[0-7]\\d)|([1-9]?\\d))(\\.\\d{1,8})?)$" + }, + "misc_param": { + "name": "misc_param", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "parameter name;measurement value" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Any other measurement performed or parameter collected, that is not listed here", + "title": "miscellaneous parameter", + "examples": [ + { + "value": "Bicarbonate ion concentration;2075 micromole per kilogram" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "miscellaneous parameter" + ], + "rank": 23, + "is_a": "core field", + "string_serialization": "{text};{float} {unit}", + "slot_uri": "MIXS:0000752", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false, + "pattern": "^([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+\\|)*([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+)$" + }, + "nitrate": { + "name": "nitrate", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per liter, milligram per liter, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of nitrate in the sample", + "title": "nitrate", + "examples": [ + { + "value": "65 micromole per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "nitrate" + ], + "rank": 26, + "is_a": "core field", + "slot_uri": "MIXS:0000425", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ 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"examples": [ + { + "value": "4 micromole per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "organic nitrogen" + ], + "rank": 46, + "is_a": "core field", + "slot_uri": "MIXS:0000205", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "MiscEnvsInterface", + "SedimentInterface", + "SoilInterface", + "WaterInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "organism_count": { + "name": "organism_count", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "organism name;measurement value;enumeration" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "number of cells per cubic meter, number of cells per milliliter, number of cells per cubic centimeter" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Total cell count of any organism (or group of 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(example: total prokaryotes; 3.5e7 cells per ml; qpcr)", + "title": "organism count", + "examples": [ + { + "value": "total prokaryotes;3.5e7 cells per milliliter;qPCR" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "organism count" + ], + "rank": 30, + "is_a": "core field", + "slot_uri": "MIXS:0000103", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^([-+]?[0-9]*\\.?[0-9]+ +\\S.*\\|)*([-+]?[0-9]*\\.?[0-9]+ +\\S.*)$" + }, + "oxy_stat_samp": { + "name": "oxy_stat_samp", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Oxygenation status of sample", + "title": "oxygenation status of sample", + "examples": [ + { + "value": "aerobic" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "oxygenation status of sample" + ], + "rank": 25, + "is_a": "core field", + "slot_uri": "MIXS:0000753", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_section", + "range": "OxyStatSampEnum", + "multivalued": false + }, + "perturbation": { + "name": "perturbation", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "perturbation type name;perturbation interval and duration" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; 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can include multiple values", + "title": "phospholipid fatty acid", + "examples": [ + { + "value": "2.98 milligram per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "phospholipid fatty acid" + ], + "rank": 36, + "is_a": "core field", + "string_serialization": "{text};{float} {unit}", + "slot_uri": "MIXS:0000181", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+\\|)*([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? 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While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater.", + "title": "salinity", + "examples": [ + { + "value": "25 practical salinity unit" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "salinity" + ], + "rank": 54, + "is_a": "core field", + "slot_uri": "MIXS:0000183", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "samp_collec_device": { + "name": "samp_collec_device", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "device name" + } + }, + "description": "The device used to collect an environmental sample. This field accepts terms listed under environmental sampling device (http://purl.obolibrary.org/obo/ENVO). This field also accepts terms listed under specimen collection device (http://purl.obolibrary.org/obo/GENEPIO_0002094).", + "title": "sample collection device", + "comments": [ + "Report dimensions and details when applicable" + ], + "examples": [ + { + "value": "swab, biopsy, niskin bottle, push core, drag swab [GENEPIO:0002713]" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sample collection device" + ], + "rank": 14, + "is_a": "nucleic acid sequence source field", + "string_serialization": "{termLabel} {[termID]}|{text}", + "slot_uri": "MIXS:0000002", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "recommended": true, + "multivalued": false + }, + "samp_collec_method": { + "name": "samp_collec_method", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "PMID,DOI,url , or text" + } + }, + "description": "The method employed for collecting the sample.", + "title": "sample collection method", + "comments": [ + "This can be a citation or description" + ], + "examples": [ + { + "value": "swabbing" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sample collection method" + ], + "rank": 15, + "is_a": "nucleic acid sequence source field", + "string_serialization": "{PMID}|{DOI}|{URL}|{text}", + "slot_uri": "MIXS:0001225", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "multivalued": false + }, + "samp_mat_process": { + "name": "samp_mat_process", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "text" + } + }, + "description": "A brief description of any processing applied to the sample during or after retrieving the sample from environment, or a link to the relevant protocol(s) performed.", + "title": "sample material processing", + "examples": [ + { + "value": "filtering of seawater" + }, + { + "value": "storing samples in ethanol" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sample material processing" + ], + "rank": 12, + "is_a": "nucleic acid sequence source field", + "string_serialization": "{text}", + "slot_uri": "MIXS:0000016", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "multivalued": false + }, + "samp_size": { + "name": "samp_size", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "millliter, gram, milligram, liter" + } + }, + "description": "The total amount or size (volume (ml), mass (g) or area (m2) ) of sample collected.", + "title": "amount or size of sample collected", + "comments": [ + "This refers to the TOTAL amount of sample collected from the experiment. NOT the amount sent to each institution or collected for a specific analysis." + ], + "examples": [ + { + "value": "5 grams" + }, + { + "value": "10 mL" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "amount or size of sample collected" + ], + "rank": 18, + "is_a": "nucleic acid sequence source field", + "string_serialization": "{float} {unit}", + "slot_uri": "MIXS:0000001", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? \\S+$" + }, + "samp_store_dur": { + "name": "samp_store_dur", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "duration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Duration for which the sample was stored", + "title": "sample storage duration", + "examples": [ + { + "value": "P1Y6M" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sample storage duration" + ], + "rank": 353, + "is_a": "core field", + "string_serialization": "{duration}", + "slot_uri": "MIXS:0000116", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "samp_store_loc": { + "name": "samp_store_loc", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "location name" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Location at which sample was stored, usually name of a specific freezer/room", + "title": "sample storage location", + "examples": [ + { + "value": "Freezer no:5" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sample storage location" + ], + "rank": 41, + "is_a": "core field", + "string_serialization": "{text}", + "slot_uri": "MIXS:0000755", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "samp_store_temp": { + "name": "samp_store_temp", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "degree Celsius" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Temperature at which the sample was stored (degrees are assumed)", + "title": "sample storage temperature", + "examples": [ + { + "value": "-80 Celsius" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sample storage temperature" + ], + "rank": 7, + "is_a": "core field", + "slot_uri": "MIXS:0000110", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "required": true, + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "sample_link": { + "name": "sample_link", + "description": "A unique identifier to assign parent-child, subsample, or sibling samples. This is relevant when a sample or other material was used to generate the new sample.", + "title": "sample linkage", + "notes": [ + "also tempted to include SampIdNewTermsMixin but if len(slot_usage.keys()) > 1 and \"placeholder\" in slot_usage.keys():AttributeError: 'list' object has no attribute 'keys'" + ], + "comments": [ + "This field allows multiple entries separated by ; (Examples: Soil collected from the field will link with the soil used in an incubation. The soil a plant was grown in links to the plant sample. An original culture sample was transferred to a new vial and generated a new sample)" + ], + "examples": [ + { + "value": "IGSN:DSJ0284" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "rank": 5, + "string_serialization": "{text}:{text}", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface", + "SampIdNewTermsMixin" + ], + "slot_group": "sample_id_section", + "range": "string", + "recommended": true, + "multivalued": false, + "pattern": "[^\\:\\n\\r]+\\:[^\\:\\n\\r]+" + }, + "silicate": { + "name": "silicate", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of silicate", + "title": "silicate", + "examples": [ + { + "value": "0.05 micromole per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "silicate" + ], + "rank": 43, + "is_a": "core field", + "slot_uri": "MIXS:0000184", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "size_frac": { + "name": "size_frac", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "filter size value range" + } + }, + "description": "Filtering pore size used in sample preparation", + "title": "size fraction selected", + "examples": [ + { + "value": "0-0.22 micrometer" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "size fraction selected" + ], + "rank": 285, + "is_a": "nucleic acid sequence source field", + "string_serialization": "{float}-{float} {unit}", + "slot_uri": "MIXS:0000017", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "sodium": { + "name": "sodium", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milligram per liter, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Sodium concentration in the sample", + "title": "sodium", + "examples": [ + { + "value": "10.5 milligram per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sodium" + ], + "rank": 363, + "is_a": "core field", + "slot_uri": "MIXS:0000428", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "specific_ecosystem": { + "name": "specific_ecosystem", + "description": "Specific ecosystems represent specific features of the environment like aphotic zone in an ocean or gastric mucosa within a host digestive system. Specific ecosystem is in position 5/5 in a GOLD path.", + "comments": [ + "Specific ecosystems help to define samples based on very specific characteristics of an environment under the five-level classification system." + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "https://gold.jgi.doe.gov/help" + ], + "rank": 13, + "is_a": "gold_path_field", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "Study", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "SpecificEcosystemEnum", + "recommended": true + }, + "sulfate": { + "name": "sulfate", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per liter, milligram per liter, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of sulfate in the sample", + "title": "sulfate", + "examples": [ + { + "value": "5 micromole per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sulfate" + ], + "rank": 44, + "is_a": "core field", + "slot_uri": "MIXS:0000423", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "sulfide": { + "name": "sulfide", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per liter, milligram per liter, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of sulfide in the sample", + "title": "sulfide", + "examples": [ + { + "value": "2 micromole per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sulfide" + ], + "rank": 371, + "is_a": "core field", + "slot_uri": "MIXS:0000424", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "temp": { + "name": "temp", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "degree Celsius" + } + }, + "description": "Temperature of the sample at the time of sampling.", + "title": "temperature", + "examples": [ + { + "value": "25 degree Celsius" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "temperature" + ], + "rank": 37, + "is_a": "environment field", + "slot_uri": "MIXS:0000113", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "water_current": { + "name": "water_current", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "cubic meter per second, knots" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Measurement of magnitude and direction of flow within a fluid", + "title": "water current", + "examples": [ + { + "value": "10 cubic meter per second" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "water current" + ], + "rank": 236, + "is_a": "core field", + "slot_uri": "MIXS:0000203", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "MiscEnvsInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "horizon_meth": { + "name": "horizon_meth", + "title": "horizon method" + } + }, + "attributes": { + "alkalinity": { + "name": "alkalinity", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milliequivalent per liter, milligram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate", + "title": "alkalinity", + "examples": [ + { + "value": "50 milligram per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "alkalinity" + ], + "rank": 1, + "is_a": "core field", + "slot_uri": "MIXS:0000421", + "alias": "alkalinity", + "owner": "MiscEnvsInterface", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "alt": { + "name": "alt", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + } + }, + "description": "Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air", + "title": "altitude", + "examples": [ + { + "value": "100 meter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "altitude" + ], + "rank": 26, + "is_a": "environment field", + "slot_uri": "MIXS:0000094", + "alias": "alt", + "owner": "MiscEnvsInterface", + "domain_of": [ + "agriculture", + "air", + "built environment", + "core", + "food-animal and animal feed", + "food-farm environment", + "food-food production facility", + "food-human foods", + "host-associated", + "human-associated", + "human-gut", + "human-oral", + "human-skin", + "human-vaginal", + "hydrocarbon resources-cores", + "hydrocarbon resources-fluids_swabs", + "microbial mat_biofilm", + "miscellaneous natural or artificial environment", + "plant-associated", + "sediment", + "soil", + "symbiont-associated", + "wastewater_sludge", + "water", + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HostAssociatedInterface", + "MiscEnvsInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "recommended": true, + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "ammonium": { + "name": "ammonium", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per liter, milligram per liter, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of ammonium in the sample", + "title": "ammonium", + "examples": [ + { + "value": "1.5 milligram per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "ammonium" + ], + "rank": 4, + "is_a": "core field", + "slot_uri": "MIXS:0000427", + "alias": "ammonium", + "owner": "MiscEnvsInterface", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "biomass": { + "name": "biomass", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "biomass type;measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "ton, kilogram, gram" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements", + "title": "biomass", + "examples": [ + { + "value": "total;20 gram" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "biomass" + ], + "rank": 6, + "is_a": "core field", + "string_serialization": "{text};{float} {unit}", + "slot_uri": "MIXS:0000174", + "alias": "biomass", + "owner": "MiscEnvsInterface", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+\\|)*([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+)$" + }, + "bromide": { + "name": "bromide", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of bromide", + "title": "bromide", + "examples": [ + { + "value": "0.05 parts per million" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "bromide" + ], + "rank": 8, + "is_a": "core field", + "slot_uri": "MIXS:0000176", + "alias": "bromide", + "owner": "MiscEnvsInterface", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "calcium": { + "name": "calcium", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milligram per liter, micromole per liter, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of calcium in the sample", + "title": "calcium", + "examples": [ + { + "value": "0.2 micromole per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "calcium" + ], + "rank": 9, + "is_a": "core field", + "slot_uri": "MIXS:0000432", + "alias": "calcium", + "owner": "MiscEnvsInterface", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "chem_administration": { + "name": "chem_administration", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "CHEBI;timestamp" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi", + "title": "chemical administration", + "examples": [ + { + "value": "agar [CHEBI:2509];2018-05-11|agar [CHEBI:2509];2018-05-22" + }, + { + "value": "agar [CHEBI:2509];2018-05" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "chemical administration" + ], + "rank": 17, + "is_a": "core field", + "string_serialization": "{termLabel} {[termID]};{timestamp}", + "slot_uri": "MIXS:0000751", + "alias": "chem_administration", + "owner": "MiscEnvsInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "recommended": true, + "multivalued": false, + "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\];([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$" + }, + "chloride": { + "name": "chloride", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milligram per liter, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of chloride in the sample", + "title": "chloride", + "examples": [ + { + "value": "5000 milligram per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "chloride" + ], + "rank": 10, + "is_a": "core field", + "slot_uri": "MIXS:0000429", + "alias": "chloride", + "owner": "MiscEnvsInterface", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "chlorophyll": { + "name": "chlorophyll", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milligram per cubic meter, microgram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of chlorophyll", + "title": "chlorophyll", + "examples": [ + { + "value": "5 milligram per cubic meter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "chlorophyll" + ], + "rank": 11, + "is_a": "core field", + "slot_uri": "MIXS:0000177", + "alias": "chlorophyll", + "owner": "MiscEnvsInterface", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "collection_date": { + "name": "collection_date", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "date and time" + } + }, + "description": "The date of sampling", + "title": "collection date", + "notes": [ + "MIxS collection_date accepts (truncated) ISO8601. DH taking arb prec date only", + "Use modified term (amended definition)" + ], + "examples": [ + { + "value": "2021-04-15" + }, + { + "value": "2021-04" + }, + { + "value": "2021" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "collection date" + ], + "rank": 3, + "is_a": "environment field", + "string_serialization": "{date, arbitrary precision}", + "slot_uri": "MIXS:0000011", + "alias": "collection_date", + "owner": "MiscEnvsInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "required": true, + "multivalued": false, + "pattern": "^[12]\\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\\d|3[01]))?)?$" + }, + "density": { + "name": "density", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "gram per cubic meter, gram per cubic centimeter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Density of the sample, which is its mass per unit volume (aka volumetric mass density)", + "title": "density", + "examples": [ + { + "value": "1000 kilogram per cubic meter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "density" + ], + "rank": 12, + "is_a": "core field", + "slot_uri": "MIXS:0000435", + "alias": "density", + "owner": "MiscEnvsInterface", + "domain_of": [ + "Biosample", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "depth": { + "name": "depth", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + } + }, + "description": "The vertical distance below local surface, e.g. for sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples.", + "title": "depth, meters", + "notes": [ + "Use modified term" + ], + "comments": [ + "All depths must be reported in meters. 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total dissolved nitrogen - NH4 - NO3 - NO2", + "title": "dissolved organic nitrogen", + "examples": [ + { + "value": "0.05 micromole per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "dissolved organic nitrogen" + ], + "rank": 18, + "is_a": "core field", + "slot_uri": "MIXS:0000162", + "alias": "diss_org_nitro", + "owner": "MiscEnvsInterface", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "diss_oxygen": { + "name": "diss_oxygen", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per kilogram, milligram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of dissolved oxygen", + "title": "dissolved oxygen", + "examples": [ + { + "value": "175 micromole per kilogram" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "dissolved oxygen" + ], + "rank": 19, + "is_a": "core field", + "slot_uri": "MIXS:0000119", + "alias": "diss_oxygen", + "owner": "MiscEnvsInterface", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "ecosystem": { + "name": "ecosystem", + "description": "An ecosystem is a combination of a physical environment (abiotic factors) and all the organisms (biotic factors) that interact with this environment. Ecosystem is in position 1/5 in a GOLD path.", + "comments": [ + "The abiotic factors play a profound role on the type and composition of organisms in a given environment. The GOLD Ecosystem at the top of the five-level classification system is aimed at capturing the broader environment from which an organism or environmental sample is collected. The three broad groups under Ecosystem are Environmental, Host-associated, and Engineered. They represent samples collected from a natural environment or from another organism or from engineered environments like bioreactors respectively." + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "https://gold.jgi.doe.gov/help" + ], + "rank": 9, + "is_a": "gold_path_field", + "alias": "ecosystem", + "owner": "MiscEnvsInterface", + "domain_of": [ + "Biosample", + "Study", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "EcosystemEnum", + "recommended": true + }, + "ecosystem_category": { + "name": "ecosystem_category", + "description": "Ecosystem categories represent divisions within the ecosystem based on specific characteristics of the environment from where an organism or sample is isolated. Ecosystem category is in position 2/5 in a GOLD path.", + "comments": [ + "The Environmental ecosystem (for example) is divided into Air, Aquatic and Terrestrial. Ecosystem categories for Host-associated samples can be individual hosts or phyla and for engineered samples it may be manipulated environments like bioreactors, solid waste etc." + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "https://gold.jgi.doe.gov/help" + ], + "rank": 10, + "is_a": "gold_path_field", + "alias": "ecosystem_category", + "owner": "MiscEnvsInterface", + "domain_of": [ + "Biosample", + "Study", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "EcosystemCategoryEnum", + "recommended": true + }, + "ecosystem_subtype": { + "name": "ecosystem_subtype", + "description": "Ecosystem subtypes represent further subdivision of Ecosystem types into more distinct subtypes. Ecosystem subtype is in position 4/5 in a GOLD path.", + "comments": [ + "Ecosystem Type Marine (Environmental -> Aquatic -> Marine) is further divided (for example) into Intertidal zone, Coastal, Pelagic, Intertidal zone etc. in the Ecosystem subtype category." + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "https://gold.jgi.doe.gov/help" + ], + "rank": 12, + "is_a": "gold_path_field", + "alias": "ecosystem_subtype", + "owner": "MiscEnvsInterface", + "domain_of": [ + "Biosample", + "Study", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "EcosystemSubtypeEnum", + "recommended": true + }, + "ecosystem_type": { + "name": "ecosystem_type", + "description": "Ecosystem types represent things having common characteristics within the Ecosystem Category. These common characteristics based grouping is still broad but specific to the characteristics of a given environment. Ecosystem type is in position 3/5 in a GOLD path.", + "comments": [ + "The Aquatic ecosystem category (for example) may have ecosystem types like Marine or Thermal springs etc. Ecosystem category Air may have Indoor air or Outdoor air as different Ecosystem Types. In the case of Host-associated samples, ecosystem type can represent Respiratory system, Digestive system, Roots etc." + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "https://gold.jgi.doe.gov/help" + ], + "rank": 11, + "is_a": "gold_path_field", + "alias": "ecosystem_type", + "owner": "MiscEnvsInterface", + "domain_of": [ + "Biosample", + "Study", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "EcosystemTypeEnum", + "recommended": true + }, + "elev": { + "name": "elev", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + } + }, + "description": "Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit.", + "title": "elevation, meters", + "comments": [ + "All elevations must be reported in meters. Provide the numerical portion only.", + "Please use https://www.advancedconverter.com/map-tools/find-altitude-by-coordinates, if needed, to help estimate the elevation based on latitude and longitude coordinates." + ], + "examples": [ + { + "value": "225" + }, + { + "value": "0" + }, + { + "value": "1250" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "elevation" + ], + "rank": 6, + "is_a": "environment field", + "slot_uri": "MIXS:0000093", + "alias": "elev", + "owner": "MiscEnvsInterface", + "domain_of": [ + "FieldResearchSite", + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "float", + "required": true, + "multivalued": false + }, + "env_broad_scale": { + "name": "env_broad_scale", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "The major environment type(s) where the sample was collected. Recommend subclasses of biome [ENVO:00000428]. Multiple terms can be separated by one or more pipes." + }, + "tooltip": { + "tag": "tooltip", + "value": "The biome or major environmental system where the sample or specimen originated. Choose values from subclasses of the 'biome' class [ENVO:00000428] in the Environment Ontology (ENVO). For host-associated or plant-associated samples, use terms from the UBERON or Plant Ontology to describe the broad anatomical or morphological context" + } + }, + "description": "In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO's biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html", + "title": "broad-scale environmental context", + "notes": [ + "range changed to enumeration late in makefile, so this is modified (but \"sample ID\" anyway)" + ], + "examples": [ + { + "value": "oceanic epipelagic zone biome [ENVO:01000033] for annotating a water sample from the photic zone in middle of the Atlantic Ocean" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "broad-scale environmental context" + ], + "rank": 6, + "is_a": "environment field", + "string_serialization": "{termLabel} {[termID]}", + "slot_uri": "MIXS:0000012", + "alias": "env_broad_scale", + "owner": "MiscEnvsInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "string", + "required": true, + "multivalued": false, + "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$" + }, + "env_local_scale": { + "name": "env_local_scale", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "Environmental entities having causal influences upon the entity at time of sampling." + }, + "tooltip": { + "tag": "tooltip", + "value": "The specific environmental entities or features near the sample or specimen that significantly influence its characteristics or composition. These entities are typically smaller in scale than the broad environmental context. Values for this field should be countable, material nouns and must be chosen from subclasses of BFO:0000040 (material entity) that appear in the Environment Ontology (ENVO). For host-associated or plant-associated samples, use terms from the UBERON or Plant Ontology to describe specific anatomical structures or plant parts." + } + }, + "description": "Report the entity or entities which are in the sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. We recommend using EnvO terms which are of smaller spatial grain than your entry for env_broad_scale. Terms, such as anatomical sites, from other OBO Library ontologies which interoperate with EnvO (e.g. UBERON) are accepted in this field. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS.", + "title": "local environmental context", + "notes": [ + "range changed to enumeration late in makefile, so this is modified (but \"sample ID\" anyway)" + ], + "examples": [ + { + "value": "canopy [ENVO:00000047]" + }, + { + "value": "herb and fern layer [ENVO:01000337]" + }, + { + "value": "litter layer [ENVO:01000338]" + }, + { + "value": "understory [01000335]" + }, + { + "value": "shrub layer [ENVO:01000336]" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "local environmental context" + ], + "rank": 7, + "is_a": "environment field", + "string_serialization": "{termLabel} {[termID]}", + "slot_uri": "MIXS:0000013", + "alias": "env_local_scale", + "owner": "MiscEnvsInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "string", + "required": true, + "multivalued": false, + "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$" + }, + "env_medium": { + "name": "env_medium", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "The material displaced by the entity at time of sampling. Recommend subclasses of environmental material [ENVO:00010483]." + }, + "tooltip": { + "tag": "tooltip", + "value": "The predominant environmental material or substrate that directly surrounds or hosts the sample or specimen at the time of sampling. Choose values from subclasses of the 'environmental material' class [ENVO:00010483] in the Environment Ontology (ENVO). Values for this field should be measurable or mass material nouns, representing continuous environmental materials. For host-associated or plant-associated samples, use terms from the UBERON or Plant Ontology to indicate a tissue, organ, or plant structure" + } + }, + "description": "Report the environmental material(s) immediately surrounding the sample or specimen at the time of sampling. We recommend using subclasses of 'environmental material' (http://purl.obolibrary.org/obo/ENVO_00010483). EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS . Terms from other OBO ontologies are permissible as long as they reference mass/volume nouns (e.g. air, water, blood) and not discrete, countable entities (e.g. a tree, a leaf, a table top).", + "title": "environmental medium", + "notes": [ + "range changed to enumeration late in makefile, so this is modified (but \"sample ID\" anyway)" + ], + "examples": [ + { + "value": "soil [ENVO:00001998]" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "environmental medium" + ], + "rank": 8, + "is_a": "environment field", + "string_serialization": "{termLabel} {[termID]}", + "slot_uri": "MIXS:0000014", + "alias": "env_medium", + "owner": "MiscEnvsInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "string", + "required": true, + "multivalued": false, + "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$" + }, + "experimental_factor": { + "name": "experimental_factor", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "text or EFO and/or OBI" + } + }, + "description": "Experimental factors are essentially the variable aspects of an experiment design which can be used to describe an experiment, or set of experiments, in an increasingly detailed manner. This field accepts ontology terms from Experimental Factor Ontology (EFO) and/or Ontology for Biomedical Investigations (OBI). For a browser of EFO (v 2.95) terms, please see http://purl.bioontology.org/ontology/EFO; for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI", + "title": "experimental factor", + "examples": [ + { + "value": "time series design [EFO:EFO_0001779]" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "experimental factor" + ], + "rank": 12, + "is_a": "investigation field", + "string_serialization": "{termLabel} {[termID]}|{text}", + "slot_uri": "MIXS:0000008", + "alias": "experimental_factor", + "owner": "MiscEnvsInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false + }, + "geo_loc_name": { + "name": "geo_loc_name", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "country or sea name (INSDC or GAZ): region(GAZ), specific location name" + } + }, + "description": "The geographical origin of the sample as defined by the country or sea name followed by specific region name.", + "title": "geographic location (country and/or sea,region)", + "examples": [ + { + "value": "USA: Maryland, Bethesda" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "geographic location (country and/or sea,region)" + ], + "rank": 4, + "is_a": "environment field", + "string_serialization": "{text}: {text}, {text}", + "slot_uri": "MIXS:0000010", + "alias": "geo_loc_name", + "owner": "MiscEnvsInterface", + "domain_of": [ + "FieldResearchSite", + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "required": true, + "multivalued": false, + "pattern": "^[^:, ][^:]*: [^:, ][^,]*, [^:, ].*$" + }, + "lat_lon": { + "name": "lat_lon", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "decimal degrees, limit to 8 decimal points" + } + }, + "description": "The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system", + "title": "geographic location (latitude and longitude)", + "notes": [ + "This is currently a required field but it's not clear if this should be required for human hosts" + ], + "examples": [ + { + "value": "50.586825 6.408977" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "geographic location (latitude and longitude)" + ], + "rank": 5, + "is_a": "environment field", + "string_serialization": "{lat lon}", + "slot_uri": "MIXS:0000009", + "alias": "lat_lon", + "owner": "MiscEnvsInterface", + "domain_of": [ + "FieldResearchSite", + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "required": true, + "multivalued": false, + "pattern": "^[-+]?([1-8]?\\d(\\.\\d{1,8})?|90(\\.0{1,8})?)\\s[-+]?(180(\\.0{1,8})?|((1[0-7]\\d)|([1-9]?\\d))(\\.\\d{1,8})?)$" + }, + "misc_param": { + "name": "misc_param", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "parameter name;measurement value" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Any other measurement performed or parameter collected, that is not listed here", + "title": "miscellaneous parameter", + "examples": [ + { + "value": "Bicarbonate ion concentration;2075 micromole per kilogram" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "miscellaneous parameter" + ], + "rank": 23, + "is_a": "core field", + "string_serialization": "{text};{float} {unit}", + "slot_uri": "MIXS:0000752", + "alias": "misc_param", + "owner": "MiscEnvsInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false, + "pattern": "^([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+\\|)*([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+)$" + }, + "nitrate": { + "name": "nitrate", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per liter, milligram per liter, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of nitrate in the sample", + "title": "nitrate", + "examples": [ + { + "value": "65 micromole per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "nitrate" + ], + "rank": 26, + "is_a": "core field", + "slot_uri": "MIXS:0000425", + "alias": "nitrate", + "owner": "MiscEnvsInterface", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "nitrite": { + "name": "nitrite", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per liter, milligram per liter, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of nitrite in the sample", + "title": "nitrite", + "examples": [ + { + "value": "0.5 micromole per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "nitrite" + ], + "rank": 27, + "is_a": "core field", + "slot_uri": "MIXS:0000426", + "alias": "nitrite", + "owner": "MiscEnvsInterface", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "nitro": { + "name": "nitro", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of nitrogen (total)", + "title": "nitrogen", + "examples": [ + { + "value": "4.2 micromole per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "nitrogen" + ], + "rank": 28, + "is_a": "core field", + "slot_uri": "MIXS:0000504", + "alias": "nitro", + "owner": "MiscEnvsInterface", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "org_carb": { + "name": "org_carb", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of organic carbon", + "title": "organic carbon", + "examples": [ + { + "value": "1.5 microgram per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "organic carbon" + ], + "rank": 29, + "is_a": "core field", + "slot_uri": "MIXS:0000508", + "alias": "org_carb", + "owner": "MiscEnvsInterface", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "org_matter": { + "name": "org_matter", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "microgram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of organic matter", + "title": "organic matter", + "examples": [ + { + "value": "1.75 milligram per cubic meter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "organic matter" + ], + "rank": 45, + "is_a": "core field", + "slot_uri": "MIXS:0000204", + "alias": "org_matter", + "owner": "MiscEnvsInterface", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "MiscEnvsInterface", + "SedimentInterface", + "SoilInterface", + "WaterInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "org_nitro": { + "name": "org_nitro", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "microgram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of organic nitrogen", + "title": "organic nitrogen", + "examples": [ + { + "value": "4 micromole per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "organic nitrogen" + ], + "rank": 46, + "is_a": "core field", + "slot_uri": "MIXS:0000205", + "alias": "org_nitro", + "owner": "MiscEnvsInterface", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "MiscEnvsInterface", + "SedimentInterface", + "SoilInterface", + "WaterInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "organism_count": { + "name": "organism_count", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "organism name;measurement value;enumeration" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "number of cells per cubic meter, number of cells per milliliter, number of cells per cubic centimeter" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr)", + "title": "organism count", + "examples": [ + { + "value": "total prokaryotes;3.5e7 cells per milliliter;qPCR" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "organism count" + ], + "rank": 30, + "is_a": "core field", + "slot_uri": "MIXS:0000103", + "alias": "organism_count", + "owner": "MiscEnvsInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^([-+]?[0-9]*\\.?[0-9]+ +\\S.*\\|)*([-+]?[0-9]*\\.?[0-9]+ +\\S.*)$" + }, + "oxy_stat_samp": { + "name": "oxy_stat_samp", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Oxygenation status of sample", + "title": "oxygenation status of sample", + "examples": [ + { + "value": "aerobic" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "oxygenation status of sample" + ], + "rank": 25, + "is_a": "core field", + "slot_uri": "MIXS:0000753", + "alias": "oxy_stat_samp", + "owner": "MiscEnvsInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_section", + "range": "OxyStatSampEnum", + "multivalued": false + }, + "perturbation": { + "name": "perturbation", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "perturbation type name;perturbation interval and duration" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types", + "title": "perturbation", + "examples": [ + { + "value": "antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "perturbation" + ], + "rank": 33, + "is_a": "core field", + "string_serialization": "{text};{Rn/start_time/end_time/duration}", + "slot_uri": "MIXS:0000754", + "alias": "perturbation", + "owner": "MiscEnvsInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "ph": { + "name": "ph", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "pH measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid", + "title": "pH", + "notes": [ + "Use modified term" + ], + "examples": [ + { + "value": "7.2" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "pH" + ], + "rank": 27, + "is_a": "core field", + "string_serialization": "{float}", + "slot_uri": "MIXS:0001001", + "alias": "ph", + "owner": "MiscEnvsInterface", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "MiscEnvsInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "float", + "recommended": true, + "multivalued": false, + "minimum_value": 0, + "maximum_value": 14 + }, + "ph_meth": { + "name": "ph_meth", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "PMID,DOI or url" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Reference or method used in determining ph", + "title": "pH method", + "comments": [ + "This can include a link to the instrument used or a citation for the method." + ], + "examples": [ + { + "value": "https://www.southernlabware.com/pc9500-benchtop-ph-conductivity-meter-kit-ph-accuracy-2000mv-ph-range-2-000-to-20-000.html?gclid=Cj0KCQiAwJWdBhCYARIsAJc4idCO5vtvbVMf545fcvdROFqa6zjzNSoywNx6K4k9Coo9cCc2pybtvGsaAiR0EALw_wcB" + }, + { + "value": "https://doi.org/10.2136/sssabookser5.3.c16" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "pH method" + ], + "rank": 41, + "is_a": "core field", + "string_serialization": "{PMID}|{DOI}|{URL}", + "slot_uri": "MIXS:0001106", + "alias": "ph_meth", + "owner": "MiscEnvsInterface", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "MiscEnvsInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false + }, + "phosphate": { + "name": "phosphate", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of phosphate", + "title": "phosphate", + "examples": [ + { + "value": "0.7 micromole per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "phosphate" + ], + "rank": 53, + "is_a": "core field", + "slot_uri": "MIXS:0000505", + "alias": "phosphate", + "owner": "MiscEnvsInterface", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "MiscEnvsInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "phosplipid_fatt_acid": { + "name": "phosplipid_fatt_acid", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "phospholipid fatty acid name;measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "mole per gram, mole per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Concentration of phospholipid fatty acids; can include multiple values", + "title": "phospholipid fatty acid", + "examples": [ + { + "value": "2.98 milligram per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "phospholipid fatty acid" + ], + "rank": 36, + "is_a": "core field", + "string_serialization": "{text};{float} {unit}", + "slot_uri": "MIXS:0000181", + "alias": "phosplipid_fatt_acid", + "owner": "MiscEnvsInterface", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+\\|)*([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+)$" + }, + "potassium": { + "name": "potassium", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milligram per liter, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of potassium in the sample", + "title": "potassium", + "examples": [ + { + "value": "463 milligram per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "potassium" + ], + "rank": 38, + "is_a": "core field", + "slot_uri": "MIXS:0000430", + "alias": "potassium", + "owner": "MiscEnvsInterface", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "pressure": { + "name": "pressure", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "atmosphere" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Pressure to which the sample is subject to, in atmospheres", + "title": "pressure", + "examples": [ + { + "value": "50 atmosphere" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "pressure" + ], + "rank": 39, + "is_a": "core field", + "slot_uri": "MIXS:0000412", + "alias": "pressure", + "owner": "MiscEnvsInterface", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "salinity": { + "name": "salinity", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "practical salinity unit, percentage" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The total concentration of all dissolved salts in a liquid or solid sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater.", + "title": "salinity", + "examples": [ + { + "value": "25 practical salinity unit" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "salinity" + ], + "rank": 54, + "is_a": "core field", + "slot_uri": "MIXS:0000183", + "alias": "salinity", + "owner": "MiscEnvsInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "samp_collec_device": { + "name": "samp_collec_device", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "device name" + } + }, + "description": "The device used to collect an environmental sample. This field accepts terms listed under environmental sampling device (http://purl.obolibrary.org/obo/ENVO). This field also accepts terms listed under specimen collection device (http://purl.obolibrary.org/obo/GENEPIO_0002094).", + "title": "sample collection device", + "comments": [ + "Report dimensions and details when applicable" + ], + "examples": [ + { + "value": "swab, biopsy, niskin bottle, push core, drag swab [GENEPIO:0002713]" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sample collection device" + ], + "rank": 14, + "is_a": "nucleic acid sequence source field", + "string_serialization": "{termLabel} {[termID]}|{text}", + "slot_uri": "MIXS:0000002", + "alias": "samp_collec_device", + "owner": "MiscEnvsInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "recommended": true, + "multivalued": false + }, + "samp_collec_method": { + "name": "samp_collec_method", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "PMID,DOI,url , or text" + } + }, + "description": "The method employed for collecting the sample.", + "title": "sample collection method", + "comments": [ + "This can be a citation or description" + ], + "examples": [ + { + "value": "swabbing" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sample collection method" + ], + "rank": 15, + "is_a": "nucleic acid sequence source field", + "string_serialization": "{PMID}|{DOI}|{URL}|{text}", + "slot_uri": "MIXS:0001225", + "alias": "samp_collec_method", + "owner": "MiscEnvsInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "multivalued": false + }, + "samp_mat_process": { + "name": "samp_mat_process", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "text" + } + }, + "description": "A brief description of any processing applied to the sample during or after retrieving the sample from environment, or a link to the relevant protocol(s) performed.", + "title": "sample material processing", + "examples": [ + { + "value": "filtering of seawater" + }, + { + "value": "storing samples in ethanol" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sample material processing" + ], + "rank": 12, + "is_a": "nucleic acid sequence source field", + "string_serialization": "{text}", + "slot_uri": "MIXS:0000016", + "alias": "samp_mat_process", + "owner": "MiscEnvsInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "multivalued": false + }, + "samp_size": { + "name": "samp_size", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "millliter, gram, milligram, liter" + } + }, + "description": "The total amount or size (volume (ml), mass (g) or area (m2) ) of sample collected.", + "title": "amount or size of sample collected", + "comments": [ + "This refers to the TOTAL amount of sample collected from the experiment. NOT the amount sent to each institution or collected for a specific analysis." + ], + "examples": [ + { + "value": "5 grams" + }, + { + "value": "10 mL" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "amount or size of sample collected" + ], + "rank": 18, + "is_a": "nucleic acid sequence source field", + "string_serialization": "{float} {unit}", + "slot_uri": "MIXS:0000001", + "alias": "samp_size", + "owner": "MiscEnvsInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? \\S+$" + }, + "samp_store_dur": { + "name": "samp_store_dur", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "duration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Duration for which the sample was stored", + "title": "sample storage duration", + "examples": [ + { + "value": "P1Y6M" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sample storage duration" + ], + "rank": 353, + "is_a": "core field", + "string_serialization": "{duration}", + "slot_uri": "MIXS:0000116", + "alias": "samp_store_dur", + "owner": "MiscEnvsInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "samp_store_loc": { + "name": "samp_store_loc", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "location name" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Location at which sample was stored, usually name of a specific freezer/room", + "title": "sample storage location", + "examples": [ + { + "value": "Freezer no:5" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sample storage location" + ], + "rank": 41, + "is_a": "core field", + "string_serialization": "{text}", + "slot_uri": "MIXS:0000755", + "alias": "samp_store_loc", + "owner": "MiscEnvsInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "samp_store_temp": { + "name": "samp_store_temp", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "degree Celsius" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Temperature at which the sample was stored (degrees are assumed)", + "title": "sample storage temperature", + "examples": [ + { + "value": "-80 Celsius" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sample storage temperature" + ], + "rank": 7, + "is_a": "core field", + "slot_uri": "MIXS:0000110", + "alias": "samp_store_temp", + "owner": "MiscEnvsInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "required": true, + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "sample_link": { + "name": "sample_link", + "description": "A unique identifier to assign parent-child, subsample, or sibling samples. This is relevant when a sample or other material was used to generate the new sample.", + "title": "sample linkage", + "notes": [ + "also tempted to include SampIdNewTermsMixin but if len(slot_usage.keys()) > 1 and \"placeholder\" in slot_usage.keys():AttributeError: 'list' object has no attribute 'keys'" + ], + "comments": [ + "This field allows multiple entries separated by ; (Examples: Soil collected from the field will link with the soil used in an incubation. The soil a plant was grown in links to the plant sample. An original culture sample was transferred to a new vial and generated a new sample)" + ], + "examples": [ + { + "value": "IGSN:DSJ0284" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "rank": 5, + "string_serialization": "{text}:{text}", + "alias": "sample_link", + "owner": "MiscEnvsInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface", + "SampIdNewTermsMixin" + ], + "slot_group": "sample_id_section", + "range": "string", + "recommended": true, + "multivalued": false, + "pattern": "[^\\:\\n\\r]+\\:[^\\:\\n\\r]+" + }, + "silicate": { + "name": "silicate", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of silicate", + "title": "silicate", + "examples": [ + { + "value": "0.05 micromole per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "silicate" + ], + "rank": 43, + "is_a": "core field", + "slot_uri": "MIXS:0000184", + "alias": "silicate", + "owner": "MiscEnvsInterface", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "size_frac": { + "name": "size_frac", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "filter size value range" + } + }, + "description": "Filtering pore size used in sample preparation", + "title": "size fraction selected", + "examples": [ + { + "value": "0-0.22 micrometer" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "size fraction selected" + ], + "rank": 285, + "is_a": "nucleic acid sequence source field", + "string_serialization": "{float}-{float} {unit}", + "slot_uri": "MIXS:0000017", + "alias": "size_frac", + "owner": "MiscEnvsInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "sodium": { + "name": "sodium", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milligram per liter, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Sodium concentration in the sample", + "title": "sodium", + "examples": [ + { + "value": "10.5 milligram per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sodium" + ], + "rank": 363, + "is_a": "core field", + "slot_uri": "MIXS:0000428", + "alias": "sodium", + "owner": "MiscEnvsInterface", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "specific_ecosystem": { + "name": "specific_ecosystem", + "description": "Specific ecosystems represent specific features of the environment like aphotic zone in an ocean or gastric mucosa within a host digestive system. Specific ecosystem is in position 5/5 in a GOLD path.", + "comments": [ + "Specific ecosystems help to define samples based on very specific characteristics of an environment under the five-level classification system." + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "https://gold.jgi.doe.gov/help" + ], + "rank": 13, + "is_a": "gold_path_field", + "alias": "specific_ecosystem", + "owner": "MiscEnvsInterface", + "domain_of": [ + "Biosample", + "Study", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "SpecificEcosystemEnum", + "recommended": true + }, + "sulfate": { + "name": "sulfate", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per liter, milligram per liter, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of sulfate in the sample", + "title": "sulfate", + "examples": [ + { + "value": "5 micromole per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sulfate" + ], + "rank": 44, + "is_a": "core field", + "slot_uri": "MIXS:0000423", + "alias": "sulfate", + "owner": "MiscEnvsInterface", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "sulfide": { + "name": "sulfide", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per liter, milligram per liter, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of sulfide in the sample", + "title": "sulfide", + "examples": [ + { + "value": "2 micromole per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sulfide" + ], + "rank": 371, + "is_a": "core field", + "slot_uri": "MIXS:0000424", + "alias": "sulfide", + "owner": "MiscEnvsInterface", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "temp": { + "name": "temp", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "degree Celsius" + } + }, + "description": "Temperature of the sample at the time of sampling.", + "title": "temperature", + "examples": [ + { + "value": "25 degree Celsius" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "temperature" + ], + "rank": 37, + "is_a": "environment field", + "slot_uri": "MIXS:0000113", + "alias": "temp", + "owner": "MiscEnvsInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "water_current": { + "name": "water_current", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "cubic meter per second, knots" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Measurement of magnitude and direction of flow within a fluid", + "title": "water current", + "examples": [ + { + "value": "10 cubic meter per second" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "water current" + ], + "rank": 236, + "is_a": "core field", + "slot_uri": "MIXS:0000203", + "alias": "water_current", + "owner": "MiscEnvsInterface", + "domain_of": [ + "Biosample", + "MiscEnvsInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "analysis_type": { + "name": "analysis_type", + "description": "Select all the data types associated or available for this biosample", + "title": "analysis/data type", + "examples": [ + { + "value": "metagenomics; metabolomics; proteomics" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "MIxS:investigation_type" + ], + "rank": 3, + "alias": "analysis_type", + "owner": "MiscEnvsInterface", + "domain_of": [ + "Biosample", + "DhMultiviewCommonColumnsMixin", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "EmslInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "JgiMgInterface", + "JgiMgLrInterface", + "JgiMtInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "AnalysisTypeEnum", + "required": true, + "recommended": false, + "multivalued": true + }, + "samp_name": { + "name": "samp_name", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "text" + } + }, + "description": "A local identifier or name that for the material sample collected. Refers to the original material collected or to any derived sub-samples.", + "title": "sample name", + "comments": [ + "It can have any format, but we suggest that you make it concise, unique and consistent within your lab, and as informative as possible." + ], + "examples": [ + { + "value": "Rock core CB1178(5-6) from NSW" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sample name" + ], + "rank": 1, + "is_a": "investigation field", + "string_serialization": "{text}", + "slot_uri": "MIXS:0001107", + "identifier": true, + "alias": "samp_name", + "owner": "MiscEnvsInterface", + "domain_of": [ + "Biosample", + "DhMultiviewCommonColumnsMixin", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "EmslInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "JgiMgInterface", + "JgiMgLrInterface", + "JgiMtInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "string", + "required": true, + "multivalued": false + }, + "source_mat_id": { + "name": "source_mat_id", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "for cultures of microorganisms: identifiers for two culture collections; for other material a unique arbitrary identifer" + } + }, + "description": "A globally unique identifier assigned to the biological sample.", + "title": "source material identifier", + "todos": [ + "Currently, the comments say to use UUIDs. However, if we implement assigning NMDC identifiers with the minter we dont need to require a GUID. It can be an optional field to fill out only if they already have a resolvable ID.", + "Currently, the comments say to use UUIDs. However, if we implement assigning NMDC identifiers with the minter we dont need to require a GUID. It can be an optional field to fill out only if they already have a resolvable ID." + ], + "notes": [ + "The source material IS the Globally Unique ID" + ], + "comments": [ + "Identifiers must be prefixed. Possible FAIR prefixes are IGSNs (http://www.geosamples.org/getigsn), NCBI biosample accession numbers, ARK identifiers (https://arks.org/). These IDs enable linking to derived analytes and subsamples. If you have not assigned FAIR identifiers to your samples, you can generate UUIDs (https://www.uuidgenerator.net/).", + "Identifiers must be prefixed. Possible FAIR prefixes are IGSNs (http://www.geosamples.org/getigsn), NCBI biosample accession numbers, ARK identifiers (https://arks.org/). These IDs enable linking to derived analytes and subsamples. If you have not assigned FAIR identifiers to your samples, you can generate UUIDs (https://www.uuidgenerator.net/)." + ], + "examples": [ + { + "value": "IGSN:AU1243" + }, + { + "value": "UUID:24f1467a-40f4-11ed-b878-0242ac120002" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "source material identifiers" + ], + "rank": 2, + "is_a": "nucleic acid sequence source field", + "string_serialization": "{text}:{text}", + "slot_uri": "MIXS:0000026", + "alias": "source_mat_id", + "owner": "MiscEnvsInterface", + "domain_of": [ + "Biosample", + "DhMultiviewCommonColumnsMixin", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "EmslInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "JgiMgInterface", + "JgiMgLrInterface", + "JgiMtInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "string", + "multivalued": false, + "pattern": "[^\\:\\n\\r]+\\:[^\\:\\n\\r]+" + } + } + }, + "PlantAssociatedInterface": { + "name": "PlantAssociatedInterface", + "annotations": { + "excel_worksheet_name": { + "tag": "excel_worksheet_name", + "value": "plant-associated" + } + }, + "description": "plant_associated dh_interface", + "title": "Plant Associated", + "from_schema": "https://example.com/nmdc_submission_schema", + "is_a": "DhInterface", + "mixins": [ + "DhMultiviewCommonColumnsMixin", + "SampIdNewTermsMixin" + ], + "slots": [ + "air_temp_regm", + "ances_data", + "antibiotic_regm", + "biol_stat", + "biotic_regm", + "biotic_relationship", + "chem_administration", + "chem_mutagen", + "climate_environment", + "collection_date", + "collection_date_inc", + "collection_time", + "cult_root_med", + "depth", + "ecosystem", + "ecosystem_category", + "ecosystem_subtype", + "ecosystem_type", + "elev", + "env_broad_scale", + "env_local_scale", + "env_medium", + "experimental_factor", + "fertilizer_regm", + "fungicide_regm", + "gaseous_environment", + "genetic_mod", + "geo_loc_name", + "gravity", + "growth_facil", + "growth_habit", + "growth_hormone_regm", + "herbicide_regm", + "host_age", + "host_common_name", + "host_disease_stat", + "host_dry_mass", + "host_genotype", + "host_height", + "host_length", + "host_life_stage", + "host_phenotype", + "host_subspecf_genlin", + "host_symbiont", + "host_taxid", + "host_tot_mass", + "host_wet_mass", + "humidity_regm", + "isotope_exposure", + "lat_lon", + "light_regm", + "mechanical_damage", + "mineral_nutr_regm", + "misc_param", + "non_min_nutr_regm", + "organism_count", + "oxy_stat_samp", + "perturbation", + "pesticide_regm", + "ph_regm", + "plant_growth_med", + "plant_product", + "plant_sex", + "plant_struc", + "radiation_regm", + "rainfall_regm", + "root_cond", + "root_med_carbon", + "root_med_macronutr", + "root_med_micronutr", + "root_med_ph", + "root_med_regl", + "root_med_solid", + "root_med_suppl", + "salinity", + "salinity_meth", + "salt_regm", + "samp_capt_status", + "samp_collec_device", + "samp_collec_method", + "samp_dis_stage", + "samp_mat_process", + "samp_size", + "samp_store_dur", + "samp_store_loc", + "samp_store_temp", + "sample_link", + "season_environment", + "size_frac", + "specific_ecosystem", + "standing_water_regm", + "start_date_inc", + "temp", + "tiss_cult_growth_med", + "water_temp_regm", + "watering_regm" + ], + "slot_usage": { + "air_temp_regm": { + "name": "air_temp_regm", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "temperature value;treatment interval and duration" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "meter" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Information about treatment involving an exposure to varying temperatures; should include the temperature, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include different temperature regimens", + "title": "air temperature regimen", + "examples": [ + { + "value": "25 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "air temperature regimen" + ], + "rank": 16, + "is_a": "core field", + "string_serialization": "{float} {unit};{Rn/start_time/end_time/duration}", + "slot_uri": "MIXS:0000551", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "recommended": true, + "multivalued": false + }, + "ances_data": { + "name": "ances_data", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "free text" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Information about either pedigree or other ancestral information description (e.g. parental variety in case of mutant or selection), e.g. A/3*B (meaning [(A x B) x B] x B)", + "title": "ancestral data", + "examples": [ + { + "value": "A/3*B" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "ancestral data" + ], + "rank": 237, + "is_a": "core field", + "string_serialization": "{text}", + "slot_uri": "MIXS:0000247", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "HostAssociatedInterface", + "PlantAssociatedInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "antibiotic_regm": { + "name": "antibiotic_regm", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "antibiotic name;antibiotic amount;treatment interval and duration" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milligram" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Information about treatment involving antibiotic administration; should include the name of antibiotic, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple antibiotic regimens", + "title": "antibiotic regimen", + "examples": [ + { + "value": "penicillin;5 milligram;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "antibiotic regimen" + ], + "rank": 238, + "is_a": "core field", + "string_serialization": "{text};{float} {unit};{Rn/start_time/end_time/duration}", + "slot_uri": "MIXS:0000553", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "PlantAssociatedInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "biol_stat": { + "name": "biol_stat", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The level of genome modification.", + "title": "biological status", + "examples": [ + { + "value": "natural" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "biological status" + ], + "rank": 239, + "is_a": "core field", + "slot_uri": "MIXS:0000858", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "HostAssociatedInterface", + "PlantAssociatedInterface" + ], + "slot_group": "mixs_core_section", + "range": "biol_stat_enum", + "multivalued": false + }, + "biotic_regm": { + "name": "biotic_regm", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "free text" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Information about treatment(s) involving use of biotic factors, such as bacteria, viruses or fungi.", + "title": "biotic regimen", + "examples": [ + { + "value": "sample inoculated with Rhizobium spp. Culture" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "biotic regimen" + ], + "rank": 13, + "is_a": "core field", + "string_serialization": "{text}", + "slot_uri": "MIXS:0001038", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "recommended": true, + "multivalued": false + }, + "biotic_relationship": { + "name": "biotic_relationship", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + } + }, + "description": "Description of relationship(s) between the subject organism and other organism(s) it is associated with. E.g., parasite on species X; mutualist with species Y. The target organism is the subject of the relationship, and the other organism(s) is the object", + "title": "observed biotic relationship", + "examples": [ + { + "value": "free living" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "observed biotic relationship" + ], + "rank": 22, + "is_a": "nucleic acid sequence source field", + "slot_uri": "MIXS:0000028", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface" + ], + "slot_group": "mixs_modified_section", + "range": "biotic_relationship_enum", + "multivalued": false + }, + "chem_administration": { + "name": "chem_administration", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "CHEBI;timestamp" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi", + "title": "chemical administration", + "examples": [ + { + "value": "agar [CHEBI:2509];2018-05-11|agar [CHEBI:2509];2018-05-22" + }, + { + "value": "agar [CHEBI:2509];2018-05" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "chemical administration" + ], + "rank": 17, + "is_a": "core field", + "string_serialization": "{termLabel} {[termID]};{timestamp}", + "slot_uri": "MIXS:0000751", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "recommended": true, + "multivalued": false, + "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\];([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$" + }, + "chem_mutagen": { + "name": "chem_mutagen", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "mutagen name;mutagen amount;treatment interval and duration" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milligram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Treatment involving use of mutagens; should include the name of mutagen, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple mutagen regimens", + "title": "chemical mutagen", + "examples": [ + { + "value": "nitrous acid;0.5 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "chemical mutagen" + ], + "rank": 240, + "is_a": "core field", + "string_serialization": "{text};{float} {unit};{Rn/start_time/end_time/duration}", + "slot_uri": "MIXS:0000555", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "PlantAssociatedInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "climate_environment": { + "name": "climate_environment", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "climate name;treatment interval and duration" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Treatment involving an exposure to a particular climate; treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple climates", + "title": "climate environment", + "todos": [ + "description says \"can include multiple climates\" but multivalued is set to false", + "add examples, i need to see some examples to add correctly formatted example.", + "description says \"can include multiple climates\" but multivalued is set to false", + "add examples, i need to see some examples to add correctly formatted example." + ], + "examples": [ + { + "value": "tropical climate;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "climate environment" + ], + "rank": 19, + "is_a": "core field", + "string_serialization": "{text};{Rn/start_time/end_time/duration}", + "slot_uri": "MIXS:0001040", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "recommended": true, + "multivalued": false + }, + "collection_date": { + "name": "collection_date", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "date and time" + } + }, + "description": "The date of sampling", + "title": "collection date", + "notes": [ + "MIxS collection_date accepts (truncated) ISO8601. DH taking arb prec date only", + "Use modified term (amended definition)" + ], + "examples": [ + { + "value": "2021-04-15" + }, + { + "value": "2021-04" + }, + { + "value": "2021" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "collection date" + ], + "rank": 3, + "is_a": "environment field", + "string_serialization": "{date, arbitrary precision}", + "slot_uri": "MIXS:0000011", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "required": true, + "multivalued": false, + "pattern": "^[12]\\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\\d|3[01]))?)?$" + }, + "collection_date_inc": { + "name": "collection_date_inc", + "description": "Date the incubation was harvested/collected/ended. Only relevant for incubation samples.", + "title": "incubation collection date", + "notes": [ + "MIxS collection_date accepts (truncated) ISO8601. DH taking arbitrary precision date only" + ], + "comments": [ + "Date should be formatted as YYYY(-MM(-DD)). Ie, 2021-04-15, 2021-04 and 2021 are all acceptable." + ], + "examples": [ + { + "value": "2021-04-15, 2021-04 and 2021 are all acceptable." + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "MIXS:0000011" + ], + "rank": 2, + "string_serialization": "{date, arbitrary precision}", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WaterInterface", + "SoilMixsInspiredMixin" + ], + "slot_group": "mixs_inspired_section", + "range": "string", + "recommended": true, + "multivalued": false, + "pattern": "^[12]\\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\\d|3[01]))?)?$" + }, + "collection_time": { + "name": "collection_time", + "description": "The time of sampling, either as an instance (single point) or interval.", + "title": "collection time, GMT", + "notes": [ + "MIxS collection_date accepts (truncated) ISO8601. DH taking seconds optional time only" + ], + "comments": [ + "Time should be entered as HH:MM(:SS) in GMT. See here for a converter: https://www.worldtimebuddy.com/pst-to-gmt-converter" + ], + "examples": [ + { + "value": "13:33 or 13:33:55" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "MIXS:0000011" + ], + "rank": 1, + "string_serialization": "{time, seconds optional}", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WaterInterface", + "SoilMixsInspiredMixin" + ], + "slot_group": "mixs_inspired_section", + "range": "string", + "recommended": true, + "multivalued": false, + "pattern": "^([01]?\\d|2[0-3]|24(?=:00?:00?$)):([0-5]\\d)(:([0-5]\\d))?$" + }, + "cult_root_med": { + "name": "cult_root_med", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "name, PMID,DOI or url" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Name or reference for the hydroponic or in vitro culture rooting medium; can be the name of a commonly used medium or reference to a specific medium, e.g. Murashige and Skoog medium. If the medium has not been formally published, use the rooting medium descriptors.", + "title": "culture rooting medium", + "examples": [ + { + "value": "http://himedialabs.com/TD/PT158.pdf" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "culture rooting medium" + ], + "rank": 241, + "is_a": "core field", + "string_serialization": "{text}|{PMID}|{DOI}|{URL}", + "slot_uri": "MIXS:0001041", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "PlantAssociatedInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "depth": { + "name": "depth", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + } + }, + "description": "The vertical distance below local surface, e.g. for sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples.", + "title": "depth, meters", + "notes": [ + "Use modified term" + ], + "comments": [ + "All depths must be reported in meters. Provide the numerical portion only." + ], + "examples": [ + { + "value": "0 - 0.1" + }, + { + "value": "1" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "depth" + ], + "rank": 9, + "is_a": "environment field", + "string_serialization": "{float}|{float}-{float}", + "slot_uri": "MIXS:0000018", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "recommended": true, + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)?(\\s*-\\s*[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)?)?$" + }, + "ecosystem": { + "name": "ecosystem", + "description": "An ecosystem is a combination of a physical environment (abiotic factors) and all the organisms (biotic factors) that interact with this environment. Ecosystem is in position 1/5 in a GOLD path.", + "comments": [ + "The abiotic factors play a profound role on the type and composition of organisms in a given environment. The GOLD Ecosystem at the top of the five-level classification system is aimed at capturing the broader environment from which an organism or environmental sample is collected. The three broad groups under Ecosystem are Environmental, Host-associated, and Engineered. They represent samples collected from a natural environment or from another organism or from engineered environments like bioreactors respectively." + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "https://gold.jgi.doe.gov/help" + ], + "rank": 9, + "is_a": "gold_path_field", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "Study", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "EcosystemEnum", + "recommended": true + }, + "ecosystem_category": { + "name": "ecosystem_category", + "description": "Ecosystem categories represent divisions within the ecosystem based on specific characteristics of the environment from where an organism or sample is isolated. Ecosystem category is in position 2/5 in a GOLD path.", + "comments": [ + "The Environmental ecosystem (for example) is divided into Air, Aquatic and Terrestrial. Ecosystem categories for Host-associated samples can be individual hosts or phyla and for engineered samples it may be manipulated environments like bioreactors, solid waste etc." + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "https://gold.jgi.doe.gov/help" + ], + "rank": 10, + "is_a": "gold_path_field", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "Study", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "EcosystemCategoryEnum", + "recommended": true + }, + "ecosystem_subtype": { + "name": "ecosystem_subtype", + "description": "Ecosystem subtypes represent further subdivision of Ecosystem types into more distinct subtypes. Ecosystem subtype is in position 4/5 in a GOLD path.", + "comments": [ + "Ecosystem Type Marine (Environmental -> Aquatic -> Marine) is further divided (for example) into Intertidal zone, Coastal, Pelagic, Intertidal zone etc. in the Ecosystem subtype category." + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "https://gold.jgi.doe.gov/help" + ], + "rank": 12, + "is_a": "gold_path_field", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "Study", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "EcosystemSubtypeEnum", + "recommended": true + }, + "ecosystem_type": { + "name": "ecosystem_type", + "description": "Ecosystem types represent things having common characteristics within the Ecosystem Category. These common characteristics based grouping is still broad but specific to the characteristics of a given environment. Ecosystem type is in position 3/5 in a GOLD path.", + "comments": [ + "The Aquatic ecosystem category (for example) may have ecosystem types like Marine or Thermal springs etc. Ecosystem category Air may have Indoor air or Outdoor air as different Ecosystem Types. In the case of Host-associated samples, ecosystem type can represent Respiratory system, Digestive system, Roots etc." + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "https://gold.jgi.doe.gov/help" + ], + "rank": 11, + "is_a": "gold_path_field", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "Study", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "EcosystemTypeEnum", + "recommended": true + }, + "elev": { + "name": "elev", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + } + }, + "description": "Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit.", + "title": "elevation, meters", + "comments": [ + "All elevations must be reported in meters. Provide the numerical portion only.", + "Please use https://www.advancedconverter.com/map-tools/find-altitude-by-coordinates, if needed, to help estimate the elevation based on latitude and longitude coordinates." + ], + "examples": [ + { + "value": "225" + }, + { + "value": "0" + }, + { + "value": "1250" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "elevation" + ], + "rank": 6, + "is_a": "environment field", + "slot_uri": "MIXS:0000093", + "owner": "Biosample", + "domain_of": [ + "FieldResearchSite", + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "float", + "required": true, + "multivalued": false + }, + "env_broad_scale": { + "name": "env_broad_scale", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "The major environment type(s) where the sample was collected. Recommend subclasses of biome [ENVO:00000428]. Multiple terms can be separated by one or more pipes." + }, + "tooltip": { + "tag": "tooltip", + "value": "The biome or major environmental system where the sample or specimen originated. Choose values from subclasses of the 'biome' class [ENVO:00000428] in the Environment Ontology (ENVO). For host-associated or plant-associated samples, use terms from the UBERON or Plant Ontology to describe the broad anatomical or morphological context" + } + }, + "description": "In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO's biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html", + "title": "broad-scale environmental context", + "notes": [ + "range changed to enumeration late in makefile, so this is modified (but \"sample ID\" anyway)" + ], + "examples": [ + { + "value": "oceanic epipelagic zone biome [ENVO:01000033] for annotating a water sample from the photic zone in middle of the Atlantic Ocean" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "broad-scale environmental context" + ], + "rank": 6, + "is_a": "environment field", + "string_serialization": "{termLabel} {[termID]}", + "slot_uri": "MIXS:0000012", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "string", + "required": true, + "multivalued": false, + "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$" + }, + "env_local_scale": { + "name": "env_local_scale", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "Environmental entities having causal influences upon the entity at time of sampling." + }, + "tooltip": { + "tag": "tooltip", + "value": "The specific environmental entities or features near the sample or specimen that significantly influence its characteristics or composition. These entities are typically smaller in scale than the broad environmental context. Values for this field should be countable, material nouns and must be chosen from subclasses of BFO:0000040 (material entity) that appear in the Environment Ontology (ENVO). For host-associated or plant-associated samples, use terms from the UBERON or Plant Ontology to describe specific anatomical structures or plant parts." + } + }, + "description": "Report the entity or entities which are in the sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. We recommend using EnvO terms which are of smaller spatial grain than your entry for env_broad_scale. Terms, such as anatomical sites, from other OBO Library ontologies which interoperate with EnvO (e.g. UBERON) are accepted in this field. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS.", + "title": "local environmental context", + "notes": [ + "range changed to enumeration late in makefile, so this is modified (but \"sample ID\" anyway)" + ], + "examples": [ + { + "value": "canopy [ENVO:00000047]" + }, + { + "value": "herb and fern layer [ENVO:01000337]" + }, + { + "value": "litter layer [ENVO:01000338]" + }, + { + "value": "understory [01000335]" + }, + { + "value": "shrub layer [ENVO:01000336]" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "local environmental context" + ], + "rank": 7, + "is_a": "environment field", + "string_serialization": "{termLabel} {[termID]}", + "slot_uri": "MIXS:0000013", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "string", + "required": true, + "multivalued": false, + "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$" + }, + "env_medium": { + "name": "env_medium", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "The material displaced by the entity at time of sampling. Recommend subclasses of environmental material [ENVO:00010483]." + }, + "tooltip": { + "tag": "tooltip", + "value": "The predominant environmental material or substrate that directly surrounds or hosts the sample or specimen at the time of sampling. Choose values from subclasses of the 'environmental material' class [ENVO:00010483] in the Environment Ontology (ENVO). Values for this field should be measurable or mass material nouns, representing continuous environmental materials. For host-associated or plant-associated samples, use terms from the UBERON or Plant Ontology to indicate a tissue, organ, or plant structure" + } + }, + "description": "Report the environmental material(s) immediately surrounding the sample or specimen at the time of sampling. We recommend using subclasses of 'environmental material' (http://purl.obolibrary.org/obo/ENVO_00010483). EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS . Terms from other OBO ontologies are permissible as long as they reference mass/volume nouns (e.g. air, water, blood) and not discrete, countable entities (e.g. a tree, a leaf, a table top).", + "title": "environmental medium", + "notes": [ + "range changed to enumeration late in makefile, so this is modified (but \"sample ID\" anyway)" + ], + "examples": [ + { + "value": "soil [ENVO:00001998]" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "environmental medium" + ], + "rank": 8, + "is_a": "environment field", + "string_serialization": "{termLabel} {[termID]}", + "slot_uri": "MIXS:0000014", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "string", + "required": true, + "multivalued": false, + "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$" + }, + "experimental_factor": { + "name": "experimental_factor", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "text or EFO and/or OBI" + } + }, + "description": "Experimental factors are essentially the variable aspects of an experiment design which can be used to describe an experiment, or set of experiments, in an increasingly detailed manner. This field accepts ontology terms from Experimental Factor Ontology (EFO) and/or Ontology for Biomedical Investigations (OBI). For a browser of EFO (v 2.95) terms, please see http://purl.bioontology.org/ontology/EFO; for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI", + "title": "experimental factor", + "examples": [ + { + "value": "time series design [EFO:EFO_0001779]" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "experimental factor" + ], + "rank": 12, + "is_a": "investigation field", + "string_serialization": "{termLabel} {[termID]}|{text}", + "slot_uri": "MIXS:0000008", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false + }, + "fertilizer_regm": { + "name": "fertilizer_regm", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "fertilizer name;fertilizer amount;treatment interval and duration" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "gram, mole per liter, milligram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Information about treatment involving the use of fertilizers; should include the name of fertilizer, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple fertilizer regimens", + "title": "fertilizer regimen", + "examples": [ + { + "value": "urea;0.6 milligram per liter;R2/2018-05-11:T14:30/2018-05-11T19:30/P1H30M" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "fertilizer regimen" + ], + "rank": 242, + "is_a": "core field", + "string_serialization": "{text};{float} {unit};{Rn/start_time/end_time/duration}", + "slot_uri": "MIXS:0000556", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "PlantAssociatedInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "fungicide_regm": { + "name": "fungicide_regm", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "fungicide name;fungicide amount;treatment interval and duration" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "gram, mole per liter, milligram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Information about treatment involving use of fungicides; should include the name of fungicide, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple fungicide regimens", + "title": "fungicide regimen", + "examples": [ + { + "value": "bifonazole;1 mole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "fungicide regimen" + ], + "rank": 243, + "is_a": "core field", + "string_serialization": "{text};{float} {unit};{Rn/start_time/end_time/duration}", + "slot_uri": "MIXS:0000557", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "PlantAssociatedInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "gaseous_environment": { + "name": "gaseous_environment", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "gaseous compound name;gaseous compound amount;treatment interval and duration" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Use of conditions with differing gaseous environments; should include the name of gaseous compound, amount administered, treatment duration, interval and total experimental duration; can include multiple gaseous environment regimens", + "title": "gaseous environment", + "todos": [ + "would like to see usage examples for this slot. Requiring micromole/L seems too limiting and doesn't match expected_value value", + "did I do this right? keep the example that's provided and add another? so as to not override", + "would like to see usage examples for this slot. Requiring micromole/L seems too limiting and doesn't match expected_value value", + "did I do this right? keep the example that's provided and add another? so as to not override" + ], + "examples": [ + { + "value": "CO2; 500ppm above ambient; constant" + }, + { + "value": "nitric oxide;0.5 micromole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "gaseous environment" + ], + "rank": 20, + "is_a": "core field", + "string_serialization": "{text};{float} {unit};{Rn/start_time/end_time/duration}", + "slot_uri": "MIXS:0000558", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "recommended": true, + "multivalued": false + }, + "genetic_mod": { + "name": "genetic_mod", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "PMID,DOI,url or free text" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Genetic modifications of the genome of an organism, which may occur naturally by spontaneous mutation, or be introduced by some experimental means, e.g. specification of a transgene or the gene knocked-out or details of transient transfection", + "title": "genetic modification", + "examples": [ + { + "value": "aox1A transgenic" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "genetic modification" + ], + "rank": 244, + "is_a": "core field", + "string_serialization": "{PMID}|{DOI}|{URL}|{text}", + "slot_uri": "MIXS:0000859", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "HostAssociatedInterface", + "PlantAssociatedInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "geo_loc_name": { + "name": "geo_loc_name", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "country or sea name (INSDC or GAZ): region(GAZ), specific location name" + } + }, + "description": "The geographical origin of the sample as defined by the country or sea name followed by specific region name.", + "title": "geographic location (country and/or sea,region)", + "examples": [ + { + "value": "USA: Maryland, Bethesda" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "geographic location (country and/or sea,region)" + ], + "rank": 4, + "is_a": "environment field", + "string_serialization": "{text}: {text}, {text}", + "slot_uri": "MIXS:0000010", + "owner": "Biosample", + "domain_of": [ + "FieldResearchSite", + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "required": true, + "multivalued": false, + "pattern": "^[^:, ][^:]*: [^:, ][^,]*, [^:, ].*$" + }, + "gravity": { + "name": "gravity", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "gravity factor value;treatment interval and duration" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "meter per square second, g" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Information about treatment involving use of gravity factor to study various types of responses in presence, absence or modified levels of gravity; treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple treatments", + "title": "gravity", + "examples": [ + { + "value": "12 g;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "gravity" + ], + "rank": 245, + "is_a": "core field", + "string_serialization": "{float} {unit};{Rn/start_time/end_time/duration}", + "slot_uri": "MIXS:0000559", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "PlantAssociatedInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "growth_facil": { + "name": "growth_facil", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "free text or CO" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Type of facility/location where the sample was harvested; controlled vocabulary: growth chamber, open top chamber, glasshouse, experimental garden, field.", + "title": "growth facility", + "notes": [ + "Removed from description: Alternatively use Crop Ontology (CO) terms" + ], + "examples": [ + { + "value": "Growth chamber [CO_715:0000189]" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "growth facility" + ], + "rank": 1, + "is_a": "core field", + "string_serialization": "{text}|{termLabel} {[termID]}", + "slot_uri": "MIXS:0001043", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "PlantAssociatedInterface", + "SoilInterface" + ], + "slot_group": "mixs_modified_section", + "range": "GrowthFacilEnum", + "required": true, + "multivalued": false + }, + "growth_habit": { + "name": "growth_habit", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Characteristic shape, appearance or growth form of a plant species", + "title": "growth habit", + "examples": [ + { + "value": "spreading" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "growth habit" + ], + "rank": 246, + "is_a": "core field", + "slot_uri": "MIXS:0001044", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "PlantAssociatedInterface" + ], + "slot_group": "mixs_core_section", + "range": "growth_habit_enum", + "multivalued": false + }, + "growth_hormone_regm": { + "name": "growth_hormone_regm", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "growth hormone name;growth hormone amount;treatment interval and duration" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "gram, mole per liter, milligram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Information about treatment involving use of growth hormones; should include the name of growth hormone, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple growth hormone regimens", + "title": "growth hormone regimen", + "examples": [ + { + "value": "abscisic acid;0.5 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "growth hormone regimen" + ], + "rank": 247, + "is_a": "core field", + "string_serialization": "{text};{float} {unit};{Rn/start_time/end_time/duration}", + "slot_uri": "MIXS:0000560", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "PlantAssociatedInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "herbicide_regm": { + "name": "herbicide_regm", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "herbicide name;herbicide amount;treatment interval and duration" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "gram, mole per liter, milligram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Information about treatment involving use of herbicides; information about treatment involving use of growth hormones; should include the name of herbicide, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens", + "title": "herbicide regimen", + "examples": [ + { + "value": "atrazine;10 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "herbicide regimen" + ], + "rank": 248, + "is_a": "core field", + "string_serialization": "{text};{float} {unit};{Rn/start_time/end_time/duration}", + "slot_uri": "MIXS:0000561", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "PlantAssociatedInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "host_age": { + "name": "host_age", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "year, day, hour" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees", + "title": "host age", + "examples": [ + { + "value": "10 days" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "host age" + ], + "rank": 249, + "is_a": "core field", + "slot_uri": "MIXS:0000255", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "HostAssociatedInterface", + "PlantAssociatedInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "host_common_name": { + "name": "host_common_name", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "common name" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Common name of the host.", + "title": "host common name", + "examples": [ + { + "value": "human" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "host common name" + ], + "rank": 250, + "is_a": "core field", + "string_serialization": "{text}", + "slot_uri": "MIXS:0000248", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "HostAssociatedInterface", + "PlantAssociatedInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "host_disease_stat": { + "name": "host_disease_stat", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "disease name or Disease Ontology term" + } + }, + "description": "List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text", + "title": "host disease status", + "examples": [ + { + "value": "rabies [DOID:11260]" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "host disease status" + ], + "rank": 390, + "is_a": "nucleic acid sequence source field", + "string_serialization": "{termLabel} {[termID]}|{text}", + "slot_uri": "MIXS:0000031", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "HostAssociatedInterface", + "PlantAssociatedInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "host_dry_mass": { + "name": "host_dry_mass", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "kilogram, gram" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Measurement of dry mass", + "title": "host dry mass", + "examples": [ + { + "value": "500 gram" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "host dry mass" + ], + "rank": 251, + "is_a": "core field", + "slot_uri": "MIXS:0000257", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "HostAssociatedInterface", + "PlantAssociatedInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "host_genotype": { + "name": "host_genotype", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "genotype" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Observed genotype", + "title": "host genotype", + "examples": [ + { + "value": "C57BL/6" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "host genotype" + ], + "rank": 252, + "is_a": "core field", + "string_serialization": "{text}", + "slot_uri": "MIXS:0000365", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "HostAssociatedInterface", + "PlantAssociatedInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "host_height": { + "name": "host_height", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "centimeter, millimeter, meter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The height of subject", + "title": "host height", + "examples": [ + { + "value": "0.1 meter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "host height" + ], + "rank": 253, + "is_a": "core field", + "slot_uri": "MIXS:0000264", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "HostAssociatedInterface", + "PlantAssociatedInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "host_length": { + "name": "host_length", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "centimeter, millimeter, meter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The length of subject", + "title": "host length", + "examples": [ + { + "value": "1 meter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "host length" + ], + "rank": 254, + "is_a": "core field", + "slot_uri": "MIXS:0000256", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "HostAssociatedInterface", + "PlantAssociatedInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "host_life_stage": { + "name": "host_life_stage", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "stage" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Description of life stage of host", + "title": "host life stage", + "examples": [ + { + "value": "adult" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "host life stage" + ], + "rank": 255, + "is_a": "core field", + "string_serialization": "{text}", + "slot_uri": "MIXS:0000251", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "HostAssociatedInterface", + "PlantAssociatedInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "host_phenotype": { + "name": "host_phenotype", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "PATO or HP" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP", + "title": "host phenotype", + "examples": [ + { + "value": "elongated [PATO:0001154]" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "host phenotype" + ], + "rank": 256, + "is_a": "core field", + "string_serialization": "{termLabel} {[termID]}", + "slot_uri": "MIXS:0000874", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "HostAssociatedInterface", + "PlantAssociatedInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$" + }, + "host_subspecf_genlin": { + "name": "host_subspecf_genlin", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "Genetic lineage below lowest rank of NCBI taxonomy, which is subspecies, e.g. serovar, biotype, ecotype, variety, cultivar." + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Information about the genetic distinctness of the host organism below the subspecies level e.g., serovar, serotype, biotype, ecotype, variety, cultivar, or any relevant genetic typing schemes like Group I plasmid. Subspecies should not be recorded in this term, but in the NCBI taxonomy. Supply both the lineage name and the lineage rank separated by a colon, e.g., biovar:abc123.", + "title": "host subspecific genetic lineage", + "examples": [ + { + "value": "serovar:Newport, variety:glabrum, cultivar: Red Delicious" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "host subspecific genetic lineage" + ], + "rank": 257, + "is_a": "core field", + "string_serialization": "{rank name}:{text}", + "slot_uri": "MIXS:0001318", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "HostAssociatedInterface", + "PlantAssociatedInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "host_symbiont": { + "name": "host_symbiont", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "species name or common name" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host.", + "title": "observed host symbionts", + "examples": [ + { + "value": "flukeworms" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "observed host symbionts" + ], + "rank": 258, + "is_a": "core field", + "string_serialization": "{text}", + "slot_uri": "MIXS:0001298", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "HostAssociatedInterface", + "PlantAssociatedInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "host_taxid": { + "name": "host_taxid", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "NCBI taxon identifier" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "NCBI taxon id of the host, e.g. 9606", + "title": "host taxid", + "comments": [ + "Homo sapiens [NCBITaxon:9606] would be a reasonable has_raw_value" + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "host taxid" + ], + "rank": 259, + "is_a": "core field", + "slot_uri": "MIXS:0000250", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "HostAssociatedInterface", + "PlantAssociatedInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "host_tot_mass": { + "name": "host_tot_mass", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "kilogram, gram" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Total mass of the host at collection, the unit depends on host", + "title": "host total mass", + "examples": [ + { + "value": "2500 gram" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "host total mass" + ], + "rank": 260, + "is_a": "core field", + "slot_uri": "MIXS:0000263", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "HostAssociatedInterface", + "PlantAssociatedInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "host_wet_mass": { + "name": "host_wet_mass", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "kilogram, gram" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Measurement of wet mass", + "title": "host wet mass", + "examples": [ + { + "value": "1500 gram" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "host wet mass" + ], + "rank": 261, + "is_a": "core field", + "slot_uri": "MIXS:0000567", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "PlantAssociatedInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "humidity_regm": { + "name": "humidity_regm", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "humidity value;treatment interval and duration" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "gram per cubic meter" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Information about treatment involving an exposure to varying degree of humidity; information about treatment involving use of growth hormones; should include amount of humidity administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens", + "title": "humidity regimen", + "examples": [ + { + "value": "25 gram per cubic meter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "humidity regimen" + ], + "rank": 21, + "is_a": "core field", + "string_serialization": "{float} {unit};{Rn/start_time/end_time/duration}", + "slot_uri": "MIXS:0000568", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "recommended": true, + "multivalued": false + }, + "isotope_exposure": { + "name": "isotope_exposure", + "description": "List isotope exposure or addition applied to your sample.", + "title": "isotope exposure/addition", + "todos": [ + "Can we make the H218O correctly super and subscripted?" + ], + "comments": [ + "This is required when your experimental design includes the use of isotopically labeled compounds" + ], + "examples": [ + { + "value": "13C glucose" + }, + { + "value": "H218O" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "MIXS:0000751" + ], + "rank": 16, + "string_serialization": "{termLabel} {[termID]}; {timestamp}", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WaterInterface", + "SoilMixsInspiredMixin" + ], + "slot_group": "mixs_inspired_section", + "range": "string", + "recommended": true, + "multivalued": false, + "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]; ([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$" + }, + "lat_lon": { + "name": "lat_lon", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "decimal degrees, limit to 8 decimal points" + } + }, + "description": "The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system", + "title": "geographic location (latitude and longitude)", + "notes": [ + "This is currently a required field but it's not clear if this should be required for human hosts" + ], + "examples": [ + { + "value": "50.586825 6.408977" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "geographic location (latitude and longitude)" + ], + "rank": 5, + "is_a": "environment field", + "string_serialization": "{lat lon}", + "slot_uri": "MIXS:0000009", + "owner": "Biosample", + "domain_of": [ + "FieldResearchSite", + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "required": true, + "multivalued": false, + "pattern": "^[-+]?([1-8]?\\d(\\.\\d{1,8})?|90(\\.0{1,8})?)\\s[-+]?(180(\\.0{1,8})?|((1[0-7]\\d)|([1-9]?\\d))(\\.\\d{1,8})?)$" + }, + "light_regm": { + "name": "light_regm", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "exposure type;light intensity;light quality" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "lux; micrometer, nanometer, angstrom" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Information about treatment(s) involving exposure to light, including both light intensity and quality.", + "title": "light regimen", + "examples": [ + { + "value": "incandescant light;10 lux;450 nanometer" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "light regimen" + ], + "rank": 24, + "is_a": "core field", + "string_serialization": "{text};{float} {unit};{float} {unit}", + "slot_uri": "MIXS:0000569", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "recommended": true, + "multivalued": false, + "pattern": "^\\S+.*\\S+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? \\S+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? \\S+$" + }, + "mechanical_damage": { + "name": "mechanical_damage", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "damage type;body site" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Information about any mechanical damage exerted on the plant; can include multiple damages and sites", + "title": "mechanical damage", + "examples": [ + { + "value": "pruning;bark" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "mechanical damage" + ], + "rank": 262, + "is_a": "core field", + "string_serialization": "{text};{text}", + "slot_uri": "MIXS:0001052", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "PlantAssociatedInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "mineral_nutr_regm": { + "name": "mineral_nutr_regm", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "mineral nutrient name;mineral nutrient amount;treatment interval and duration" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "gram, mole per liter, milligram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Information about treatment involving the use of mineral supplements; should include the name of mineral nutrient, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple mineral nutrient regimens", + "title": "mineral nutrient regimen", + "examples": [ + { + "value": "potassium;15 gram;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "mineral nutrient regimen" + ], + "rank": 263, + "is_a": "core field", + "string_serialization": "{text};{float} {unit};{Rn/start_time/end_time/duration}", + "slot_uri": "MIXS:0000570", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "PlantAssociatedInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "misc_param": { + "name": "misc_param", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "parameter name;measurement value" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Any other measurement performed or parameter collected, that is not listed here", + "title": "miscellaneous parameter", + "examples": [ + { + "value": "Bicarbonate ion concentration;2075 micromole per kilogram" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "miscellaneous parameter" + ], + "rank": 23, + "is_a": "core field", + "string_serialization": "{text};{float} {unit}", + "slot_uri": "MIXS:0000752", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false, + "pattern": "^([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+\\|)*([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+)$" + }, + "non_min_nutr_regm": { + "name": "non_min_nutr_regm", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "non-mineral nutrient name;non-mineral nutrient amount;treatment interval and duration" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "gram, mole per liter, milligram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Information about treatment involving the exposure of plant to non-mineral nutrient such as oxygen, hydrogen or carbon; should include the name of non-mineral nutrient, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple non-mineral nutrient regimens", + "title": "non-mineral nutrient regimen", + "examples": [ + { + "value": "carbon dioxide;10 mole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "non-mineral nutrient regimen" + ], + "rank": 264, + "is_a": "core field", + "string_serialization": "{text};{float} {unit};{Rn/start_time/end_time/duration}", + "slot_uri": "MIXS:0000571", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "PlantAssociatedInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "organism_count": { + "name": "organism_count", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "organism name;measurement value;enumeration" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "number of cells per cubic meter, number of cells per milliliter, number of cells per cubic centimeter" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr)", + "title": "organism count", + "examples": [ + { + "value": "total prokaryotes;3.5e7 cells per milliliter;qPCR" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "organism count" + ], + "rank": 30, + "is_a": "core field", + "slot_uri": "MIXS:0000103", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^([-+]?[0-9]*\\.?[0-9]+ +\\S.*\\|)*([-+]?[0-9]*\\.?[0-9]+ +\\S.*)$" + }, + "oxy_stat_samp": { + "name": "oxy_stat_samp", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Oxygenation status of sample", + "title": "oxygenation status of sample", + "examples": [ + { + "value": "aerobic" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "oxygenation status of sample" + ], + "rank": 25, + "is_a": "core field", + "slot_uri": "MIXS:0000753", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_section", + "range": "OxyStatSampEnum", + "multivalued": false + }, + "perturbation": { + "name": "perturbation", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "perturbation type name;perturbation interval and duration" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types", + "title": "perturbation", + "examples": [ + { + "value": "antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "perturbation" + ], + "rank": 33, + "is_a": "core field", + "string_serialization": "{text};{Rn/start_time/end_time/duration}", + "slot_uri": "MIXS:0000754", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "pesticide_regm": { + "name": "pesticide_regm", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "pesticide name;pesticide amount;treatment interval and duration" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "gram, mole per liter, milligram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Information about treatment involving use of insecticides; should include the name of pesticide, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple pesticide regimens", + "title": "pesticide regimen", + "examples": [ + { + "value": "pyrethrum;0.6 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "pesticide regimen" + ], + "rank": 265, + "is_a": "core field", + "string_serialization": "{text};{float} {unit};{Rn/start_time/end_time/duration}", + "slot_uri": "MIXS:0000573", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "PlantAssociatedInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "ph_regm": { + "name": "ph_regm", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value;treatment interval and duration" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Information about treatment involving exposure of plants to varying levels of ph of the growth media, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimen", + "title": "pH regimen", + "examples": [ + { + "value": "7.6;R2/2018-05-11:T14:30/2018-05-11T19:30/P1H30M" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "pH regimen" + ], + "rank": 266, + "is_a": "core field", + "string_serialization": "{float};{Rn/start_time/end_time/duration}", + "slot_uri": "MIXS:0001056", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "PlantAssociatedInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "plant_growth_med": { + "name": "plant_growth_med", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "EO or enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Specification of the media for growing the plants or tissue cultured samples, e.g. soil, aeroponic, hydroponic, in vitro solid culture medium, in vitro liquid culture medium. Recommended value is a specific value from EO:plant growth medium (follow this link for terms http://purl.obolibrary.org/obo/EO_0007147) or other controlled vocabulary", + "title": "plant growth medium", + "examples": [ + { + "value": "hydroponic plant culture media [EO:0007067]" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "plant growth medium" + ], + "rank": 267, + "is_a": "core field", + "slot_uri": "MIXS:0001057", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "PlantAssociatedInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "plant_product": { + "name": "plant_product", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "product name" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Substance produced by the plant, where the sample was obtained from", + "title": "plant product", + "examples": [ + { + "value": "xylem sap [PO:0025539]" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "plant product" + ], + "rank": 268, + "is_a": "core field", + "string_serialization": "{text}", + "slot_uri": "MIXS:0001058", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "PlantAssociatedInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "plant_sex": { + "name": "plant_sex", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Sex of the reproductive parts on the whole plant, e.g. pistillate, staminate, monoecieous, hermaphrodite.", + "title": "plant sex", + "examples": [ + { + "value": "Hermaphroditic" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "plant sex" + ], + "rank": 269, + "is_a": "core field", + "slot_uri": "MIXS:0001059", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "PlantAssociatedInterface" + ], + "slot_group": "mixs_core_section", + "range": "plant_sex_enum", + "multivalued": false + }, + "plant_struc": { + "name": "plant_struc", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "PO" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Name of plant structure the sample was obtained from; for Plant Ontology (PO) (v releases/2017-12-14) terms, see http://purl.bioontology.org/ontology/PO, e.g. petiole epidermis (PO_0000051). If an individual flower is sampled, the sex of it can be recorded here.", + "title": "plant structure", + "examples": [ + { + "value": "epidermis [PO:0005679]" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "plant structure" + ], + "rank": 270, + "is_a": "core field", + "string_serialization": "{termLabel} {[termID]}", + "slot_uri": "MIXS:0001060", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "PlantAssociatedInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$" + }, + "radiation_regm": { + "name": "radiation_regm", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "radiation type name;radiation amount;treatment interval and duration" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "rad, gray" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Information about treatment involving exposure of plant or a plant part to a particular radiation regimen; should include the radiation type, amount or intensity administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple radiation regimens", + "title": "radiation regimen", + "examples": [ + { + "value": "gamma radiation;60 gray;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "radiation regimen" + ], + "rank": 271, + "is_a": "core field", + "string_serialization": "{text};{float} {unit};{Rn/start_time/end_time/duration}", + "slot_uri": "MIXS:0000575", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "PlantAssociatedInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "rainfall_regm": { + "name": "rainfall_regm", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value;treatment interval and duration" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "millimeter" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Information about treatment involving an exposure to a given amount of rainfall, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens", + "title": "rainfall regimen", + "examples": [ + { + "value": "15 millimeter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "rainfall regimen" + ], + "rank": 272, + "is_a": "core field", + "string_serialization": "{float} {unit};{Rn/start_time/end_time/duration}", + "slot_uri": "MIXS:0000576", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "PlantAssociatedInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "root_cond": { + "name": "root_cond", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "PMID,DOI,url or free text" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Relevant rooting conditions such as field plot size, sowing density, container dimensions, number of plants per container.", + "title": "rooting conditions", + "examples": [ + { + "value": "http://himedialabs.com/TD/PT158.pdf" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "rooting conditions" + ], + "rank": 273, + "is_a": "core field", + "string_serialization": "{PMID}|{DOI}|{URL}|{text}", + "slot_uri": "MIXS:0001061", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "PlantAssociatedInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "root_med_carbon": { + "name": "root_med_carbon", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "carbon source name;measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milligram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Source of organic carbon in the culture rooting medium; e.g. sucrose.", + "title": "rooting medium carbon", + "examples": [ + { + "value": "sucrose" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "rooting medium carbon" + ], + "rank": 274, + "is_a": "core field", + "string_serialization": "{text};{float} {unit}", + "slot_uri": "MIXS:0000577", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "PlantAssociatedInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[^;\\t\\r\\x0A\\|]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A\\|]+$" + }, + "root_med_macronutr": { + "name": "root_med_macronutr", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "macronutrient name;measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milligram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Measurement of the culture rooting medium macronutrients (N,P, K, Ca, Mg, S); e.g. KH2PO4 (170¬†mg/L).", + "title": "rooting medium macronutrients", + "examples": [ + { + "value": "KH2PO4;170¬†milligram per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "rooting medium macronutrients" + ], + "rank": 275, + "is_a": "core field", + "string_serialization": "{text};{float} {unit}", + "slot_uri": "MIXS:0000578", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "PlantAssociatedInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[^;\\t\\r\\x0A\\|]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A\\|]+$" + }, + "root_med_micronutr": { + "name": "root_med_micronutr", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "micronutrient name;measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milligram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Measurement of the culture rooting medium micronutrients (Fe, Mn, Zn, B, Cu, Mo); e.g. H3BO3 (6.2¬†mg/L).", + "title": "rooting medium micronutrients", + "examples": [ + { + "value": "H3BO3;6.2¬†milligram per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "rooting medium micronutrients" + ], + "rank": 276, + "is_a": "core field", + "string_serialization": "{text};{float} {unit}", + "slot_uri": "MIXS:0000579", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "PlantAssociatedInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[^;\\t\\r\\x0A\\|]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A\\|]+$" + }, + "root_med_ph": { + "name": "root_med_ph", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "pH measurement of the culture rooting medium; e.g. 5.5.", + "title": "rooting medium pH", + "examples": [ + { + "value": "7.5" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "rooting medium pH" + ], + "rank": 277, + "is_a": "core field", + "slot_uri": "MIXS:0001062", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "PlantAssociatedInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "root_med_regl": { + "name": "root_med_regl", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "regulator name;measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milligram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Growth regulators in the culture rooting medium such as cytokinins, auxins, gybberellins, abscisic acid; e.g. 0.5¬†mg/L NAA.", + "title": "rooting medium regulators", + "examples": [ + { + "value": "abscisic acid;0.75 milligram per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "rooting medium regulators" + ], + "rank": 278, + "is_a": "core field", + "string_serialization": "{text};{float} {unit}", + "slot_uri": "MIXS:0000581", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "PlantAssociatedInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[^;\\t\\r\\x0A\\|]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A\\|]+$" + }, + "root_med_solid": { + "name": "root_med_solid", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "name" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Specification of the solidifying agent in the culture rooting medium; e.g. agar.", + "title": "rooting medium solidifier", + "examples": [ + { + "value": "agar" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "rooting medium solidifier" + ], + "rank": 279, + "is_a": "core field", + "string_serialization": "{text}", + "slot_uri": "MIXS:0001063", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "PlantAssociatedInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "root_med_suppl": { + "name": "root_med_suppl", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "supplement name;measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milligram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Organic supplements of the culture rooting medium, such as vitamins, amino acids, organic acids, antibiotics activated charcoal; e.g. nicotinic acid (0.5¬†mg/L).", + "title": "rooting medium organic supplements", + "examples": [ + { + "value": "nicotinic acid;0.5 milligram per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "rooting medium organic supplements" + ], + "rank": 280, + "is_a": "core field", + "string_serialization": "{text};{float} {unit}", + "slot_uri": "MIXS:0000580", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "PlantAssociatedInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[^;\\t\\r\\x0A\\|]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A\\|]+$" + }, + "salinity": { + "name": "salinity", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "practical salinity unit, percentage" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The total concentration of all dissolved salts in a liquid or solid sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater.", + "title": "salinity", + "examples": [ + { + "value": "25 practical salinity unit" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "salinity" + ], + "rank": 54, + "is_a": "core field", + "slot_uri": "MIXS:0000183", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "salinity_meth": { + "name": "salinity_meth", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "PMID,DOI or url" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Reference or method used in determining salinity", + "title": "salinity method", + "examples": [ + { + "value": "https://doi.org/10.1007/978-1-61779-986-0_28" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "salinity method" + ], + "rank": 55, + "is_a": "core field", + "string_serialization": "{PMID}|{DOI}|{URL}", + "slot_uri": "MIXS:0000341", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WaterInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false + }, + "salt_regm": { + "name": "salt_regm", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "salt name;salt amount;treatment interval and duration" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "gram, microgram, mole per liter, gram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Information about treatment involving use of salts as supplement to liquid and soil growth media; should include the name of salt, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple salt regimens", + "title": "salt regimen", + "examples": [ + { + "value": "NaCl;5 gram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "salt regimen" + ], + "rank": 281, + "is_a": "core field", + "string_serialization": "{text};{float} {unit};{Rn/start_time/end_time/duration}", + "slot_uri": "MIXS:0000582", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "PlantAssociatedInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "samp_capt_status": { + "name": "samp_capt_status", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Reason for the sample", + "title": "sample capture status", + "examples": [ + { + "value": "farm sample" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sample capture status" + ], + "rank": 282, + "is_a": "core field", + "slot_uri": "MIXS:0000860", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "HostAssociatedInterface", + "PlantAssociatedInterface" + ], + "slot_group": "mixs_core_section", + "range": "samp_capt_status_enum", + "multivalued": false + }, + "samp_collec_device": { + "name": "samp_collec_device", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "device name" + } + }, + "description": "The device used to collect an environmental sample. This field accepts terms listed under environmental sampling device (http://purl.obolibrary.org/obo/ENVO). This field also accepts terms listed under specimen collection device (http://purl.obolibrary.org/obo/GENEPIO_0002094).", + "title": "sample collection device", + "comments": [ + "Report dimensions and details when applicable" + ], + "examples": [ + { + "value": "swab, biopsy, niskin bottle, push core, drag swab [GENEPIO:0002713]" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sample collection device" + ], + "rank": 14, + "is_a": "nucleic acid sequence source field", + "string_serialization": "{termLabel} {[termID]}|{text}", + "slot_uri": "MIXS:0000002", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "recommended": true, + "multivalued": false + }, + "samp_collec_method": { + "name": "samp_collec_method", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "PMID,DOI,url , or text" + } + }, + "description": "The method employed for collecting the sample.", + "title": "sample collection method", + "comments": [ + "This can be a citation or description" + ], + "examples": [ + { + "value": "swabbing" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sample collection method" + ], + "rank": 15, + "is_a": "nucleic acid sequence source field", + "string_serialization": "{PMID}|{DOI}|{URL}|{text}", + "slot_uri": "MIXS:0001225", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "multivalued": false + }, + "samp_dis_stage": { + "name": "samp_dis_stage", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Stage of the disease at the time of sample collection, e.g. inoculation, penetration, infection, growth and reproduction, dissemination of pathogen.", + "title": "sample disease stage", + "examples": [ + { + "value": "infection" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sample disease stage" + ], + "rank": 283, + "is_a": "core field", + "slot_uri": "MIXS:0000249", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "HostAssociatedInterface", + "PlantAssociatedInterface" + ], + "slot_group": "mixs_core_section", + "range": "samp_dis_stage_enum", + "multivalued": false + }, + "samp_mat_process": { + "name": "samp_mat_process", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "text" + } + }, + "description": "A brief description of any processing applied to the sample during or after retrieving the sample from environment, or a link to the relevant protocol(s) performed.", + "title": "sample material processing", + "examples": [ + { + "value": "filtering of seawater" + }, + { + "value": "storing samples in ethanol" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sample material processing" + ], + "rank": 12, + "is_a": "nucleic acid sequence source field", + "string_serialization": "{text}", + "slot_uri": "MIXS:0000016", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "multivalued": false + }, + "samp_size": { + "name": "samp_size", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "millliter, gram, milligram, liter" + } + }, + "description": "The total amount or size (volume (ml), mass (g) or area (m2) ) of sample collected.", + "title": "amount or size of sample collected", + "comments": [ + "This refers to the TOTAL amount of sample collected from the experiment. NOT the amount sent to each institution or collected for a specific analysis." + ], + "examples": [ + { + "value": "5 grams" + }, + { + "value": "10 mL" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "amount or size of sample collected" + ], + "rank": 18, + "is_a": "nucleic acid sequence source field", + "string_serialization": "{float} {unit}", + "slot_uri": "MIXS:0000001", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? \\S+$" + }, + "samp_store_dur": { + "name": "samp_store_dur", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "duration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Duration for which the sample was stored", + "title": "sample storage duration", + "examples": [ + { + "value": "P1Y6M" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sample storage duration" + ], + "rank": 353, + "is_a": "core field", + "string_serialization": "{duration}", + "slot_uri": "MIXS:0000116", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "samp_store_loc": { + "name": "samp_store_loc", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "location name" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Location at which sample was stored, usually name of a specific freezer/room", + "title": "sample storage location", + "examples": [ + { + "value": "Freezer no:5" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sample storage location" + ], + "rank": 41, + "is_a": "core field", + "string_serialization": "{text}", + "slot_uri": "MIXS:0000755", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "samp_store_temp": { + "name": "samp_store_temp", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "degree Celsius" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Temperature at which the sample was stored (degrees are assumed)", + "title": "sample storage temperature", + "examples": [ + { + "value": "-80 Celsius" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sample storage temperature" + ], + "rank": 7, + "is_a": "core field", + "slot_uri": "MIXS:0000110", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "required": true, + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "sample_link": { + "name": "sample_link", + "description": "A unique identifier to assign parent-child, subsample, or sibling samples. This is relevant when a sample or other material was used to generate the new sample.", + "title": "sample linkage", + "notes": [ + "also tempted to include SampIdNewTermsMixin but if len(slot_usage.keys()) > 1 and \"placeholder\" in slot_usage.keys():AttributeError: 'list' object has no attribute 'keys'" + ], + "comments": [ + "This field allows multiple entries separated by ; (Examples: Soil collected from the field will link with the soil used in an incubation. The soil a plant was grown in links to the plant sample. An original culture sample was transferred to a new vial and generated a new sample)" + ], + "examples": [ + { + "value": "IGSN:DSJ0284" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "rank": 5, + "string_serialization": "{text}:{text}", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface", + "SampIdNewTermsMixin" + ], + "slot_group": "sample_id_section", + "range": "string", + "recommended": true, + "multivalued": false, + "pattern": "[^\\:\\n\\r]+\\:[^\\:\\n\\r]+" + }, + "season_environment": { + "name": "season_environment", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "seasonal environment name;treatment interval and duration" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Treatment involving an exposure to a particular season (e.g. Winter, summer, rabi, rainy etc.), treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment", + "title": "seasonal environment", + "examples": [ + { + "value": "rainy;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "seasonal environment" + ], + "rank": 284, + "is_a": "core field", + "string_serialization": "{text};{Rn/start_time/end_time/duration}", + "slot_uri": "MIXS:0001068", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "PlantAssociatedInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "size_frac": { + "name": "size_frac", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "filter size value range" + } + }, + "description": "Filtering pore size used in sample preparation", + "title": "size fraction selected", + "examples": [ + { + "value": "0-0.22 micrometer" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "size fraction selected" + ], + "rank": 285, + "is_a": "nucleic acid sequence source field", + "string_serialization": "{float}-{float} {unit}", + "slot_uri": "MIXS:0000017", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "specific_ecosystem": { + "name": "specific_ecosystem", + "description": "Specific ecosystems represent specific features of the environment like aphotic zone in an ocean or gastric mucosa within a host digestive system. Specific ecosystem is in position 5/5 in a GOLD path.", + "comments": [ + "Specific ecosystems help to define samples based on very specific characteristics of an environment under the five-level classification system." + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "https://gold.jgi.doe.gov/help" + ], + "rank": 13, + "is_a": "gold_path_field", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "Study", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "SpecificEcosystemEnum", + "recommended": true + }, + "standing_water_regm": { + "name": "standing_water_regm", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "standing water type;treatment interval and duration" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Treatment involving an exposure to standing water during a plant's life span, types can be flood water or standing water, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens", + "title": "standing water regimen", + "examples": [ + { + "value": "standing water;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "standing water regimen" + ], + "rank": 286, + "is_a": "core field", + "string_serialization": "{text};{Rn/start_time/end_time/duration}", + "slot_uri": "MIXS:0001069", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "PlantAssociatedInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "start_date_inc": { + "name": "start_date_inc", + "description": "Date the incubation was started. Only relevant for incubation samples.", + "title": "incubation start date", + "notes": [ + "MIxS collection_date accepts (truncated) ISO8601. DH taking arbitrary precision date only" + ], + "comments": [ + "Date should be formatted as YYYY(-MM(-DD)). Ie, 2021-04-15, 2021-04 and 2021 are all acceptable." + ], + "examples": [ + { + "value": "2021-04-15, 2021-04 and 2021 are all acceptable." + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "MIXS:0000011" + ], + "rank": 4, + "string_serialization": "{date, arbitrary precision}", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WaterInterface", + "SoilMixsInspiredMixin" + ], + "slot_group": "mixs_inspired_section", + "range": "string", + "recommended": true, + "multivalued": false, + "pattern": "^[12]\\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\\d|3[01]))?)?$" + }, + "temp": { + "name": "temp", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "degree Celsius" + } + }, + "description": "Temperature of the sample at the time of sampling.", + "title": "temperature", + "examples": [ + { + "value": "25 degree Celsius" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "temperature" + ], + "rank": 37, + "is_a": "environment field", + "slot_uri": "MIXS:0000113", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "tiss_cult_growth_med": { + "name": "tiss_cult_growth_med", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "PMID,DOI,url or free text" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Description of plant tissue culture growth media used", + "title": "tissue culture growth media", + "examples": [ + { + "value": "https://link.springer.com/content/pdf/10.1007/BF02796489.pdf" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "tissue culture growth media" + ], + "rank": 287, + "is_a": "core field", + "string_serialization": "{PMID}|{DOI}|{URL}|{text}", + "slot_uri": "MIXS:0001070", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "PlantAssociatedInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "water_temp_regm": { + "name": "water_temp_regm", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value;treatment interval and duration" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "degree Celsius" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Information about treatment involving an exposure to water with varying degree of temperature, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens", + "title": "water temperature regimen", + "examples": [ + { + "value": "15 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "water temperature regimen" + ], + "rank": 288, + "is_a": "core field", + "string_serialization": "{float} {unit};{Rn/start_time/end_time/duration}", + "slot_uri": "MIXS:0000590", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "PlantAssociatedInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "watering_regm": { + "name": "watering_regm", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value;treatment interval and duration" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milliliter, liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Information about treatment involving an exposure to watering frequencies, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens", + "title": "watering regimen", + "examples": [ + { + "value": "1 liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" + }, + { + "value": "75% water holding capacity; constant" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "watering regimen" + ], + "rank": 25, + "is_a": "core field", + "string_serialization": "{float} {unit};{Rn/start_time/end_time/duration}", + "slot_uri": "MIXS:0000591", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "recommended": true, + "multivalued": false + }, + "horizon_meth": { + "name": "horizon_meth", + "title": "horizon method" + } + }, + "attributes": { + "air_temp_regm": { + "name": "air_temp_regm", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "temperature value;treatment interval and duration" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "meter" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Information about treatment involving an exposure to varying temperatures; should include the temperature, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include different temperature regimens", + "title": "air temperature regimen", + "examples": [ + { + "value": "25 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "air temperature regimen" + ], + "rank": 16, + "is_a": "core field", + "string_serialization": "{float} {unit};{Rn/start_time/end_time/duration}", + "slot_uri": "MIXS:0000551", + "alias": "air_temp_regm", + "owner": "PlantAssociatedInterface", + "domain_of": [ + "Biosample", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "recommended": true, + "multivalued": false + }, + "ances_data": { + "name": "ances_data", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "free text" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Information about either pedigree or other ancestral information description (e.g. parental variety in case of mutant or selection), e.g. A/3*B (meaning [(A x B) x B] x B)", + "title": "ancestral data", + "examples": [ + { + "value": "A/3*B" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "ancestral data" + ], + "rank": 237, + "is_a": "core field", + "string_serialization": "{text}", + "slot_uri": "MIXS:0000247", + "alias": "ances_data", + "owner": "PlantAssociatedInterface", + "domain_of": [ + "Biosample", + "HostAssociatedInterface", + "PlantAssociatedInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "antibiotic_regm": { + "name": "antibiotic_regm", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "antibiotic name;antibiotic amount;treatment interval and duration" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milligram" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Information about treatment involving antibiotic administration; should include the name of antibiotic, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple antibiotic regimens", + "title": "antibiotic regimen", + "examples": [ + { + "value": "penicillin;5 milligram;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "antibiotic regimen" + ], + "rank": 238, + "is_a": "core field", + "string_serialization": "{text};{float} {unit};{Rn/start_time/end_time/duration}", + "slot_uri": "MIXS:0000553", + "alias": "antibiotic_regm", + "owner": "PlantAssociatedInterface", + "domain_of": [ + "Biosample", + "PlantAssociatedInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "biol_stat": { + "name": "biol_stat", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The level of genome modification.", + "title": "biological status", + "examples": [ + { + "value": "natural" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "biological status" + ], + "rank": 239, + "is_a": "core field", + "slot_uri": "MIXS:0000858", + "alias": "biol_stat", + "owner": "PlantAssociatedInterface", + "domain_of": [ + "Biosample", + "HostAssociatedInterface", + "PlantAssociatedInterface" + ], + "slot_group": "mixs_core_section", + "range": "biol_stat_enum", + "multivalued": false + }, + "biotic_regm": { + "name": "biotic_regm", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "free text" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Information about treatment(s) involving use of biotic factors, such as bacteria, viruses or fungi.", + "title": "biotic regimen", + "examples": [ + { + "value": "sample inoculated with Rhizobium spp. Culture" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "biotic regimen" + ], + "rank": 13, + "is_a": "core field", + "string_serialization": "{text}", + "slot_uri": "MIXS:0001038", + "alias": "biotic_regm", + "owner": "PlantAssociatedInterface", + "domain_of": [ + "Biosample", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "recommended": true, + "multivalued": false + }, + "biotic_relationship": { + "name": "biotic_relationship", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + } + }, + "description": "Description of relationship(s) between the subject organism and other organism(s) it is associated with. E.g., parasite on species X; mutualist with species Y. The target organism is the subject of the relationship, and the other organism(s) is the object", + "title": "observed biotic relationship", + "examples": [ + { + "value": "free living" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "observed biotic relationship" + ], + "rank": 22, + "is_a": "nucleic acid sequence source field", + "slot_uri": "MIXS:0000028", + "alias": "biotic_relationship", + "owner": "PlantAssociatedInterface", + "domain_of": [ + "Biosample", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface" + ], + "slot_group": "mixs_modified_section", + "range": "biotic_relationship_enum", + "multivalued": false + }, + "chem_administration": { + "name": "chem_administration", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "CHEBI;timestamp" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi", + "title": "chemical administration", + "examples": [ + { + "value": "agar [CHEBI:2509];2018-05-11|agar [CHEBI:2509];2018-05-22" + }, + { + "value": "agar [CHEBI:2509];2018-05" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "chemical administration" + ], + "rank": 17, + "is_a": "core field", + "string_serialization": "{termLabel} {[termID]};{timestamp}", + "slot_uri": "MIXS:0000751", + "alias": "chem_administration", + "owner": "PlantAssociatedInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "recommended": true, + "multivalued": false, + "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\];([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$" + }, + "chem_mutagen": { + "name": "chem_mutagen", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "mutagen name;mutagen amount;treatment interval and duration" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milligram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Treatment involving use of mutagens; should include the name of mutagen, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple mutagen regimens", + "title": "chemical mutagen", + "examples": [ + { + "value": "nitrous acid;0.5 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "chemical mutagen" + ], + "rank": 240, + "is_a": "core field", + "string_serialization": "{text};{float} {unit};{Rn/start_time/end_time/duration}", + "slot_uri": "MIXS:0000555", + "alias": "chem_mutagen", + "owner": "PlantAssociatedInterface", + "domain_of": [ + "Biosample", + "PlantAssociatedInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "climate_environment": { + "name": "climate_environment", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "climate name;treatment interval and duration" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Treatment involving an exposure to a particular climate; treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple climates", + "title": "climate environment", + "todos": [ + "description says \"can include multiple climates\" but multivalued is set to false", + "add examples, i need to see some examples to add correctly formatted example.", + "description says \"can include multiple climates\" but multivalued is set to false", + "add examples, i need to see some examples to add correctly formatted example." + ], + "examples": [ + { + "value": "tropical climate;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "climate environment" + ], + "rank": 19, + "is_a": "core field", + "string_serialization": "{text};{Rn/start_time/end_time/duration}", + "slot_uri": "MIXS:0001040", + "alias": "climate_environment", + "owner": "PlantAssociatedInterface", + "domain_of": [ + "Biosample", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "recommended": true, + "multivalued": false + }, + "collection_date": { + "name": "collection_date", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "date and time" + } + }, + "description": "The date of sampling", + "title": "collection date", + "notes": [ + "MIxS collection_date accepts (truncated) ISO8601. DH taking arb prec date only", + "Use modified term (amended definition)" + ], + "examples": [ + { + "value": "2021-04-15" + }, + { + "value": "2021-04" + }, + { + "value": "2021" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "collection date" + ], + "rank": 3, + "is_a": "environment field", + "string_serialization": "{date, arbitrary precision}", + "slot_uri": "MIXS:0000011", + "alias": "collection_date", + "owner": "PlantAssociatedInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "required": true, + "multivalued": false, + "pattern": "^[12]\\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\\d|3[01]))?)?$" + }, + "collection_date_inc": { + "name": "collection_date_inc", + "description": "Date the incubation was harvested/collected/ended. Only relevant for incubation samples.", + "title": "incubation collection date", + "notes": [ + "MIxS collection_date accepts (truncated) ISO8601. DH taking arbitrary precision date only" + ], + "comments": [ + "Date should be formatted as YYYY(-MM(-DD)). Ie, 2021-04-15, 2021-04 and 2021 are all acceptable." + ], + "examples": [ + { + "value": "2021-04-15, 2021-04 and 2021 are all acceptable." + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "MIXS:0000011" + ], + "rank": 2, + "string_serialization": "{date, arbitrary precision}", + "alias": "collection_date_inc", + "owner": "PlantAssociatedInterface", + "domain_of": [ + "Biosample", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WaterInterface", + "SoilMixsInspiredMixin" + ], + "slot_group": "mixs_inspired_section", + "range": "string", + "recommended": true, + "multivalued": false, + "pattern": "^[12]\\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\\d|3[01]))?)?$" + }, + "collection_time": { + "name": "collection_time", + "description": "The time of sampling, either as an instance (single point) or interval.", + "title": "collection time, GMT", + "notes": [ + "MIxS collection_date accepts (truncated) ISO8601. DH taking seconds optional time only" + ], + "comments": [ + "Time should be entered as HH:MM(:SS) in GMT. See here for a converter: https://www.worldtimebuddy.com/pst-to-gmt-converter" + ], + "examples": [ + { + "value": "13:33 or 13:33:55" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "MIXS:0000011" + ], + "rank": 1, + "string_serialization": "{time, seconds optional}", + "alias": "collection_time", + "owner": "PlantAssociatedInterface", + "domain_of": [ + "Biosample", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WaterInterface", + "SoilMixsInspiredMixin" + ], + "slot_group": "mixs_inspired_section", + "range": "string", + "recommended": true, + "multivalued": false, + "pattern": "^([01]?\\d|2[0-3]|24(?=:00?:00?$)):([0-5]\\d)(:([0-5]\\d))?$" + }, + "cult_root_med": { + "name": "cult_root_med", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "name, PMID,DOI or url" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Name or reference for the hydroponic or in vitro culture rooting medium; can be the name of a commonly used medium or reference to a specific medium, e.g. Murashige and Skoog medium. If the medium has not been formally published, use the rooting medium descriptors.", + "title": "culture rooting medium", + "examples": [ + { + "value": "http://himedialabs.com/TD/PT158.pdf" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "culture rooting medium" + ], + "rank": 241, + "is_a": "core field", + "string_serialization": "{text}|{PMID}|{DOI}|{URL}", + "slot_uri": "MIXS:0001041", + "alias": "cult_root_med", + "owner": "PlantAssociatedInterface", + "domain_of": [ + "Biosample", + "PlantAssociatedInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "depth": { + "name": "depth", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + } + }, + "description": "The vertical distance below local surface, e.g. for sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples.", + "title": "depth, meters", + "notes": [ + "Use modified term" + ], + "comments": [ + "All depths must be reported in meters. Provide the numerical portion only." + ], + "examples": [ + { + "value": "0 - 0.1" + }, + { + "value": "1" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "depth" + ], + "rank": 9, + "is_a": "environment field", + "string_serialization": "{float}|{float}-{float}", + "slot_uri": "MIXS:0000018", + "alias": "depth", + "owner": "PlantAssociatedInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "recommended": true, + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)?(\\s*-\\s*[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)?)?$" + }, + "ecosystem": { + "name": "ecosystem", + "description": "An ecosystem is a combination of a physical environment (abiotic factors) and all the organisms (biotic factors) that interact with this environment. Ecosystem is in position 1/5 in a GOLD path.", + "comments": [ + "The abiotic factors play a profound role on the type and composition of organisms in a given environment. The GOLD Ecosystem at the top of the five-level classification system is aimed at capturing the broader environment from which an organism or environmental sample is collected. The three broad groups under Ecosystem are Environmental, Host-associated, and Engineered. They represent samples collected from a natural environment or from another organism or from engineered environments like bioreactors respectively." + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "https://gold.jgi.doe.gov/help" + ], + "rank": 9, + "is_a": "gold_path_field", + "alias": "ecosystem", + "owner": "PlantAssociatedInterface", + "domain_of": [ + "Biosample", + "Study", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "EcosystemEnum", + "recommended": true + }, + "ecosystem_category": { + "name": "ecosystem_category", + "description": "Ecosystem categories represent divisions within the ecosystem based on specific characteristics of the environment from where an organism or sample is isolated. Ecosystem category is in position 2/5 in a GOLD path.", + "comments": [ + "The Environmental ecosystem (for example) is divided into Air, Aquatic and Terrestrial. Ecosystem categories for Host-associated samples can be individual hosts or phyla and for engineered samples it may be manipulated environments like bioreactors, solid waste etc." + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "https://gold.jgi.doe.gov/help" + ], + "rank": 10, + "is_a": "gold_path_field", + "alias": "ecosystem_category", + "owner": "PlantAssociatedInterface", + "domain_of": [ + "Biosample", + "Study", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "EcosystemCategoryEnum", + "recommended": true + }, + "ecosystem_subtype": { + "name": "ecosystem_subtype", + "description": "Ecosystem subtypes represent further subdivision of Ecosystem types into more distinct subtypes. Ecosystem subtype is in position 4/5 in a GOLD path.", + "comments": [ + "Ecosystem Type Marine (Environmental -> Aquatic -> Marine) is further divided (for example) into Intertidal zone, Coastal, Pelagic, Intertidal zone etc. in the Ecosystem subtype category." + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "https://gold.jgi.doe.gov/help" + ], + "rank": 12, + "is_a": "gold_path_field", + "alias": "ecosystem_subtype", + "owner": "PlantAssociatedInterface", + "domain_of": [ + "Biosample", + "Study", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "EcosystemSubtypeEnum", + "recommended": true + }, + "ecosystem_type": { + "name": "ecosystem_type", + "description": "Ecosystem types represent things having common characteristics within the Ecosystem Category. These common characteristics based grouping is still broad but specific to the characteristics of a given environment. Ecosystem type is in position 3/5 in a GOLD path.", + "comments": [ + "The Aquatic ecosystem category (for example) may have ecosystem types like Marine or Thermal springs etc. Ecosystem category Air may have Indoor air or Outdoor air as different Ecosystem Types. In the case of Host-associated samples, ecosystem type can represent Respiratory system, Digestive system, Roots etc." + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "https://gold.jgi.doe.gov/help" + ], + "rank": 11, + "is_a": "gold_path_field", + "alias": "ecosystem_type", + "owner": "PlantAssociatedInterface", + "domain_of": [ + "Biosample", + "Study", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "EcosystemTypeEnum", + "recommended": true + }, + "elev": { + "name": "elev", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + } + }, + "description": "Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit.", + "title": "elevation, meters", + "comments": [ + "All elevations must be reported in meters. Provide the numerical portion only.", + "Please use https://www.advancedconverter.com/map-tools/find-altitude-by-coordinates, if needed, to help estimate the elevation based on latitude and longitude coordinates." + ], + "examples": [ + { + "value": "225" + }, + { + "value": "0" + }, + { + "value": "1250" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "elevation" + ], + "rank": 6, + "is_a": "environment field", + "slot_uri": "MIXS:0000093", + "alias": "elev", + "owner": "PlantAssociatedInterface", + "domain_of": [ + "FieldResearchSite", + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "float", + "required": true, + "multivalued": false + }, + "env_broad_scale": { + "name": "env_broad_scale", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "The major environment type(s) where the sample was collected. Recommend subclasses of biome [ENVO:00000428]. Multiple terms can be separated by one or more pipes." + }, + "tooltip": { + "tag": "tooltip", + "value": "The biome or major environmental system where the sample or specimen originated. Choose values from subclasses of the 'biome' class [ENVO:00000428] in the Environment Ontology (ENVO). For host-associated or plant-associated samples, use terms from the UBERON or Plant Ontology to describe the broad anatomical or morphological context" + } + }, + "description": "In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO's biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html", + "title": "broad-scale environmental context", + "notes": [ + "range changed to enumeration late in makefile, so this is modified (but \"sample ID\" anyway)" + ], + "examples": [ + { + "value": "oceanic epipelagic zone biome [ENVO:01000033] for annotating a water sample from the photic zone in middle of the Atlantic Ocean" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "broad-scale environmental context" + ], + "rank": 6, + "is_a": "environment field", + "string_serialization": "{termLabel} {[termID]}", + "slot_uri": "MIXS:0000012", + "alias": "env_broad_scale", + "owner": "PlantAssociatedInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "string", + "required": true, + "multivalued": false, + "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$" + }, + "env_local_scale": { + "name": "env_local_scale", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "Environmental entities having causal influences upon the entity at time of sampling." + }, + "tooltip": { + "tag": "tooltip", + "value": "The specific environmental entities or features near the sample or specimen that significantly influence its characteristics or composition. These entities are typically smaller in scale than the broad environmental context. Values for this field should be countable, material nouns and must be chosen from subclasses of BFO:0000040 (material entity) that appear in the Environment Ontology (ENVO). For host-associated or plant-associated samples, use terms from the UBERON or Plant Ontology to describe specific anatomical structures or plant parts." + } + }, + "description": "Report the entity or entities which are in the sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. We recommend using EnvO terms which are of smaller spatial grain than your entry for env_broad_scale. Terms, such as anatomical sites, from other OBO Library ontologies which interoperate with EnvO (e.g. UBERON) are accepted in this field. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS.", + "title": "local environmental context", + "notes": [ + "range changed to enumeration late in makefile, so this is modified (but \"sample ID\" anyway)" + ], + "examples": [ + { + "value": "canopy [ENVO:00000047]" + }, + { + "value": "herb and fern layer [ENVO:01000337]" + }, + { + "value": "litter layer [ENVO:01000338]" + }, + { + "value": "understory [01000335]" + }, + { + "value": "shrub layer [ENVO:01000336]" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "local environmental context" + ], + "rank": 7, + "is_a": "environment field", + "string_serialization": "{termLabel} {[termID]}", + "slot_uri": "MIXS:0000013", + "alias": "env_local_scale", + "owner": "PlantAssociatedInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "string", + "required": true, + "multivalued": false, + "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$" + }, + "env_medium": { + "name": "env_medium", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "The material displaced by the entity at time of sampling. Recommend subclasses of environmental material [ENVO:00010483]." + }, + "tooltip": { + "tag": "tooltip", + "value": "The predominant environmental material or substrate that directly surrounds or hosts the sample or specimen at the time of sampling. Choose values from subclasses of the 'environmental material' class [ENVO:00010483] in the Environment Ontology (ENVO). Values for this field should be measurable or mass material nouns, representing continuous environmental materials. For host-associated or plant-associated samples, use terms from the UBERON or Plant Ontology to indicate a tissue, organ, or plant structure" + } + }, + "description": "Report the environmental material(s) immediately surrounding the sample or specimen at the time of sampling. We recommend using subclasses of 'environmental material' (http://purl.obolibrary.org/obo/ENVO_00010483). EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS . Terms from other OBO ontologies are permissible as long as they reference mass/volume nouns (e.g. air, water, blood) and not discrete, countable entities (e.g. a tree, a leaf, a table top).", + "title": "environmental medium", + "notes": [ + "range changed to enumeration late in makefile, so this is modified (but \"sample ID\" anyway)" + ], + "examples": [ + { + "value": "soil [ENVO:00001998]" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "environmental medium" + ], + "rank": 8, + "is_a": "environment field", + "string_serialization": "{termLabel} {[termID]}", + "slot_uri": "MIXS:0000014", + "alias": "env_medium", + "owner": "PlantAssociatedInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "string", + "required": true, + "multivalued": false, + "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$" + }, + "experimental_factor": { + "name": "experimental_factor", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "text or EFO and/or OBI" + } + }, + "description": "Experimental factors are essentially the variable aspects of an experiment design which can be used to describe an experiment, or set of experiments, in an increasingly detailed manner. This field accepts ontology terms from Experimental Factor Ontology (EFO) and/or Ontology for Biomedical Investigations (OBI). For a browser of EFO (v 2.95) terms, please see http://purl.bioontology.org/ontology/EFO; for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI", + "title": "experimental factor", + "examples": [ + { + "value": "time series design [EFO:EFO_0001779]" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "experimental factor" + ], + "rank": 12, + "is_a": "investigation field", + "string_serialization": "{termLabel} {[termID]}|{text}", + "slot_uri": "MIXS:0000008", + "alias": "experimental_factor", + "owner": "PlantAssociatedInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false + }, + "fertilizer_regm": { + "name": "fertilizer_regm", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "fertilizer name;fertilizer amount;treatment interval and duration" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "gram, mole per liter, milligram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Information about treatment involving the use of fertilizers; should include the name of fertilizer, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple fertilizer regimens", + "title": "fertilizer regimen", + "examples": [ + { + "value": "urea;0.6 milligram per liter;R2/2018-05-11:T14:30/2018-05-11T19:30/P1H30M" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "fertilizer regimen" + ], + "rank": 242, + "is_a": "core field", + "string_serialization": "{text};{float} {unit};{Rn/start_time/end_time/duration}", + "slot_uri": "MIXS:0000556", + "alias": "fertilizer_regm", + "owner": "PlantAssociatedInterface", + "domain_of": [ + "Biosample", + "PlantAssociatedInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "fungicide_regm": { + "name": "fungicide_regm", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "fungicide name;fungicide amount;treatment interval and duration" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "gram, mole per liter, milligram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Information about treatment involving use of fungicides; should include the name of fungicide, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple fungicide regimens", + "title": "fungicide regimen", + "examples": [ + { + "value": "bifonazole;1 mole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "fungicide regimen" + ], + "rank": 243, + "is_a": "core field", + "string_serialization": "{text};{float} {unit};{Rn/start_time/end_time/duration}", + "slot_uri": "MIXS:0000557", + "alias": "fungicide_regm", + "owner": "PlantAssociatedInterface", + "domain_of": [ + "Biosample", + "PlantAssociatedInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "gaseous_environment": { + "name": "gaseous_environment", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "gaseous compound name;gaseous compound amount;treatment interval and duration" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Use of conditions with differing gaseous environments; should include the name of gaseous compound, amount administered, treatment duration, interval and total experimental duration; can include multiple gaseous environment regimens", + "title": "gaseous environment", + "todos": [ + "would like to see usage examples for this slot. Requiring micromole/L seems too limiting and doesn't match expected_value value", + "did I do this right? keep the example that's provided and add another? so as to not override", + "would like to see usage examples for this slot. Requiring micromole/L seems too limiting and doesn't match expected_value value", + "did I do this right? keep the example that's provided and add another? so as to not override" + ], + "examples": [ + { + "value": "CO2; 500ppm above ambient; constant" + }, + { + "value": "nitric oxide;0.5 micromole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "gaseous environment" + ], + "rank": 20, + "is_a": "core field", + "string_serialization": "{text};{float} {unit};{Rn/start_time/end_time/duration}", + "slot_uri": "MIXS:0000558", + "alias": "gaseous_environment", + "owner": "PlantAssociatedInterface", + "domain_of": [ + "Biosample", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "recommended": true, + "multivalued": false + }, + "genetic_mod": { + "name": "genetic_mod", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "PMID,DOI,url or free text" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Genetic modifications of the genome of an organism, which may occur naturally by spontaneous mutation, or be introduced by some experimental means, e.g. specification of a transgene or the gene knocked-out or details of transient transfection", + "title": "genetic modification", + "examples": [ + { + "value": "aox1A transgenic" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "genetic modification" + ], + "rank": 244, + "is_a": "core field", + "string_serialization": "{PMID}|{DOI}|{URL}|{text}", + "slot_uri": "MIXS:0000859", + "alias": "genetic_mod", + "owner": "PlantAssociatedInterface", + "domain_of": [ + "Biosample", + "HostAssociatedInterface", + "PlantAssociatedInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "geo_loc_name": { + "name": "geo_loc_name", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "country or sea name (INSDC or GAZ): region(GAZ), specific location name" + } + }, + "description": "The geographical origin of the sample as defined by the country or sea name followed by specific region name.", + "title": "geographic location (country and/or sea,region)", + "examples": [ + { + "value": "USA: Maryland, Bethesda" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "geographic location (country and/or sea,region)" + ], + "rank": 4, + "is_a": "environment field", + "string_serialization": "{text}: {text}, {text}", + "slot_uri": "MIXS:0000010", + "alias": "geo_loc_name", + "owner": "PlantAssociatedInterface", + "domain_of": [ + "FieldResearchSite", + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "required": true, + "multivalued": false, + "pattern": "^[^:, ][^:]*: [^:, ][^,]*, [^:, ].*$" + }, + "gravity": { + "name": "gravity", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "gravity factor value;treatment interval and duration" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "meter per square second, g" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Information about treatment involving use of gravity factor to study various types of responses in presence, absence or modified levels of gravity; treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple treatments", + "title": "gravity", + "examples": [ + { + "value": "12 g;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "gravity" + ], + "rank": 245, + "is_a": "core field", + "string_serialization": "{float} {unit};{Rn/start_time/end_time/duration}", + "slot_uri": "MIXS:0000559", + "alias": "gravity", + "owner": "PlantAssociatedInterface", + "domain_of": [ + "Biosample", + "PlantAssociatedInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "growth_facil": { + "name": "growth_facil", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "free text or CO" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Type of facility/location where the sample was harvested; controlled vocabulary: growth chamber, open top chamber, glasshouse, experimental garden, field.", + "title": "growth facility", + "notes": [ + "Removed from description: Alternatively use Crop Ontology (CO) terms" + ], + "examples": [ + { + "value": "Growth chamber [CO_715:0000189]" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "growth facility" + ], + "rank": 1, + "is_a": "core field", + "string_serialization": "{text}|{termLabel} {[termID]}", + "slot_uri": "MIXS:0001043", + "alias": "growth_facil", + "owner": "PlantAssociatedInterface", + "domain_of": [ + "Biosample", + "PlantAssociatedInterface", + "SoilInterface" + ], + "slot_group": "mixs_modified_section", + "range": "GrowthFacilEnum", + "required": true, + "multivalued": false + }, + "growth_habit": { + "name": "growth_habit", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Characteristic shape, appearance or growth form of a plant species", + "title": "growth habit", + "examples": [ + { + "value": "spreading" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "growth habit" + ], + "rank": 246, + "is_a": "core field", + "slot_uri": "MIXS:0001044", + "alias": "growth_habit", + "owner": "PlantAssociatedInterface", + "domain_of": [ + "Biosample", + "PlantAssociatedInterface" + ], + "slot_group": "mixs_core_section", + "range": "growth_habit_enum", + "multivalued": false + }, + "growth_hormone_regm": { + "name": "growth_hormone_regm", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "growth hormone name;growth hormone amount;treatment interval and duration" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "gram, mole per liter, milligram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Information about treatment involving use of growth hormones; should include the name of growth hormone, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple growth hormone regimens", + "title": "growth hormone regimen", + "examples": [ + { + "value": "abscisic acid;0.5 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "growth hormone regimen" + ], + "rank": 247, + "is_a": "core field", + "string_serialization": "{text};{float} {unit};{Rn/start_time/end_time/duration}", + "slot_uri": "MIXS:0000560", + "alias": "growth_hormone_regm", + "owner": "PlantAssociatedInterface", + "domain_of": [ + "Biosample", + "PlantAssociatedInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "herbicide_regm": { + "name": "herbicide_regm", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "herbicide name;herbicide amount;treatment interval and duration" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "gram, mole per liter, milligram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Information about treatment involving use of herbicides; information about treatment involving use of growth hormones; should include the name of herbicide, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens", + "title": "herbicide regimen", + "examples": [ + { + "value": "atrazine;10 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "herbicide regimen" + ], + "rank": 248, + "is_a": "core field", + "string_serialization": "{text};{float} {unit};{Rn/start_time/end_time/duration}", + "slot_uri": "MIXS:0000561", + "alias": "herbicide_regm", + "owner": "PlantAssociatedInterface", + "domain_of": [ + "Biosample", + "PlantAssociatedInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "host_age": { + "name": "host_age", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "year, day, hour" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees", + "title": "host age", + "examples": [ + { + "value": "10 days" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "host age" + ], + "rank": 249, + "is_a": "core field", + "slot_uri": "MIXS:0000255", + "alias": "host_age", + "owner": "PlantAssociatedInterface", + "domain_of": [ + "Biosample", + "HostAssociatedInterface", + "PlantAssociatedInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "host_common_name": { + "name": "host_common_name", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "common name" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Common name of the host.", + "title": "host common name", + "examples": [ + { + "value": "human" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "host common name" + ], + "rank": 250, + "is_a": "core field", + "string_serialization": "{text}", + "slot_uri": "MIXS:0000248", + "alias": "host_common_name", + "owner": "PlantAssociatedInterface", + "domain_of": [ + "Biosample", + "HostAssociatedInterface", + "PlantAssociatedInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "host_disease_stat": { + "name": "host_disease_stat", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "disease name or Disease Ontology term" + } + }, + "description": "List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text", + "title": "host disease status", + "examples": [ + { + "value": "rabies [DOID:11260]" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "host disease status" + ], + "rank": 390, + "is_a": "nucleic acid sequence source field", + "string_serialization": "{termLabel} {[termID]}|{text}", + "slot_uri": "MIXS:0000031", + "alias": "host_disease_stat", + "owner": "PlantAssociatedInterface", + "domain_of": [ + "Biosample", + "HostAssociatedInterface", + "PlantAssociatedInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "host_dry_mass": { + "name": "host_dry_mass", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "kilogram, gram" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Measurement of dry mass", + "title": "host dry mass", + "examples": [ + { + "value": "500 gram" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "host dry mass" + ], + "rank": 251, + "is_a": "core field", + "slot_uri": "MIXS:0000257", + "alias": "host_dry_mass", + "owner": "PlantAssociatedInterface", + "domain_of": [ + "Biosample", + "HostAssociatedInterface", + "PlantAssociatedInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "host_genotype": { + "name": "host_genotype", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "genotype" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Observed genotype", + "title": "host genotype", + "examples": [ + { + "value": "C57BL/6" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "host genotype" + ], + "rank": 252, + "is_a": "core field", + "string_serialization": "{text}", + "slot_uri": "MIXS:0000365", + "alias": "host_genotype", + "owner": "PlantAssociatedInterface", + "domain_of": [ + "Biosample", + "HostAssociatedInterface", + "PlantAssociatedInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "host_height": { + "name": "host_height", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "centimeter, millimeter, meter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The height of subject", + "title": "host height", + "examples": [ + { + "value": "0.1 meter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "host height" + ], + "rank": 253, + "is_a": "core field", + "slot_uri": "MIXS:0000264", + "alias": "host_height", + "owner": "PlantAssociatedInterface", + "domain_of": [ + "Biosample", + "HostAssociatedInterface", + "PlantAssociatedInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "host_length": { + "name": "host_length", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "centimeter, millimeter, meter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The length of subject", + "title": "host length", + "examples": [ + { + "value": "1 meter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "host length" + ], + "rank": 254, + "is_a": "core field", + "slot_uri": "MIXS:0000256", + "alias": "host_length", + "owner": "PlantAssociatedInterface", + "domain_of": [ + "Biosample", + "HostAssociatedInterface", + "PlantAssociatedInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "host_life_stage": { + "name": "host_life_stage", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "stage" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Description of life stage of host", + "title": "host life stage", + "examples": [ + { + "value": "adult" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "host life stage" + ], + "rank": 255, + "is_a": "core field", + "string_serialization": "{text}", + "slot_uri": "MIXS:0000251", + "alias": "host_life_stage", + "owner": "PlantAssociatedInterface", + "domain_of": [ + "Biosample", + "HostAssociatedInterface", + "PlantAssociatedInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "host_phenotype": { + "name": "host_phenotype", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "PATO or HP" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP", + "title": "host phenotype", + "examples": [ + { + "value": "elongated [PATO:0001154]" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "host phenotype" + ], + "rank": 256, + "is_a": "core field", + "string_serialization": "{termLabel} {[termID]}", + "slot_uri": "MIXS:0000874", + "alias": "host_phenotype", + "owner": "PlantAssociatedInterface", + "domain_of": [ + "Biosample", + "HostAssociatedInterface", + "PlantAssociatedInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$" + }, + "host_subspecf_genlin": { + "name": "host_subspecf_genlin", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "Genetic lineage below lowest rank of NCBI taxonomy, which is subspecies, e.g. serovar, biotype, ecotype, variety, cultivar." + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Information about the genetic distinctness of the host organism below the subspecies level e.g., serovar, serotype, biotype, ecotype, variety, cultivar, or any relevant genetic typing schemes like Group I plasmid. Subspecies should not be recorded in this term, but in the NCBI taxonomy. Supply both the lineage name and the lineage rank separated by a colon, e.g., biovar:abc123.", + "title": "host subspecific genetic lineage", + "examples": [ + { + "value": "serovar:Newport, variety:glabrum, cultivar: Red Delicious" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "host subspecific genetic lineage" + ], + "rank": 257, + "is_a": "core field", + "string_serialization": "{rank name}:{text}", + "slot_uri": "MIXS:0001318", + "alias": "host_subspecf_genlin", + "owner": "PlantAssociatedInterface", + "domain_of": [ + "Biosample", + "HostAssociatedInterface", + "PlantAssociatedInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "host_symbiont": { + "name": "host_symbiont", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "species name or common name" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host.", + "title": "observed host symbionts", + "examples": [ + { + "value": "flukeworms" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "observed host symbionts" + ], + "rank": 258, + "is_a": "core field", + "string_serialization": "{text}", + "slot_uri": "MIXS:0001298", + "alias": "host_symbiont", + "owner": "PlantAssociatedInterface", + "domain_of": [ + "Biosample", + "HostAssociatedInterface", + "PlantAssociatedInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "host_taxid": { + "name": "host_taxid", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "NCBI taxon identifier" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "NCBI taxon id of the host, e.g. 9606", + "title": "host taxid", + "comments": [ + "Homo sapiens [NCBITaxon:9606] would be a reasonable has_raw_value" + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "host taxid" + ], + "rank": 259, + "is_a": "core field", + "slot_uri": "MIXS:0000250", + "alias": "host_taxid", + "owner": "PlantAssociatedInterface", + "domain_of": [ + "Biosample", + "HostAssociatedInterface", + "PlantAssociatedInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "host_tot_mass": { + "name": "host_tot_mass", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "kilogram, gram" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Total mass of the host at collection, the unit depends on host", + "title": "host total mass", + "examples": [ + { + "value": "2500 gram" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "host total mass" + ], + "rank": 260, + "is_a": "core field", + "slot_uri": "MIXS:0000263", + "alias": "host_tot_mass", + "owner": "PlantAssociatedInterface", + "domain_of": [ + "Biosample", + "HostAssociatedInterface", + "PlantAssociatedInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "host_wet_mass": { + "name": "host_wet_mass", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "kilogram, gram" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Measurement of wet mass", + "title": "host wet mass", + "examples": [ + { + "value": "1500 gram" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "host wet mass" + ], + "rank": 261, + "is_a": "core field", + "slot_uri": "MIXS:0000567", + "alias": "host_wet_mass", + "owner": "PlantAssociatedInterface", + "domain_of": [ + "Biosample", + "PlantAssociatedInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "humidity_regm": { + "name": "humidity_regm", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "humidity value;treatment interval and duration" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "gram per cubic meter" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Information about treatment involving an exposure to varying degree of humidity; information about treatment involving use of growth hormones; should include amount of humidity administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens", + "title": "humidity regimen", + "examples": [ + { + "value": "25 gram per cubic meter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "humidity regimen" + ], + "rank": 21, + "is_a": "core field", + "string_serialization": "{float} {unit};{Rn/start_time/end_time/duration}", + "slot_uri": "MIXS:0000568", + "alias": "humidity_regm", + "owner": "PlantAssociatedInterface", + "domain_of": [ + "Biosample", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "recommended": true, + "multivalued": false + }, + "isotope_exposure": { + "name": "isotope_exposure", + "description": "List isotope exposure or addition applied to your sample.", + "title": "isotope exposure/addition", + "todos": [ + "Can we make the H218O correctly super and subscripted?" + ], + "comments": [ + "This is required when your experimental design includes the use of isotopically labeled compounds" + ], + "examples": [ + { + "value": "13C glucose" + }, + { + "value": "H218O" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "MIXS:0000751" + ], + "rank": 16, + "string_serialization": "{termLabel} {[termID]}; {timestamp}", + "alias": "isotope_exposure", + "owner": "PlantAssociatedInterface", + "domain_of": [ + "Biosample", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WaterInterface", + "SoilMixsInspiredMixin" + ], + "slot_group": "mixs_inspired_section", + "range": "string", + "recommended": true, + "multivalued": false, + "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]; ([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$" + }, + "lat_lon": { + "name": "lat_lon", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "decimal degrees, limit to 8 decimal points" + } + }, + "description": "The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system", + "title": "geographic location (latitude and longitude)", + "notes": [ + "This is currently a required field but it's not clear if this should be required for human hosts" + ], + "examples": [ + { + "value": "50.586825 6.408977" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "geographic location (latitude and longitude)" + ], + "rank": 5, + "is_a": "environment field", + "string_serialization": "{lat lon}", + "slot_uri": "MIXS:0000009", + "alias": "lat_lon", + "owner": "PlantAssociatedInterface", + "domain_of": [ + "FieldResearchSite", + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "required": true, + "multivalued": false, + "pattern": "^[-+]?([1-8]?\\d(\\.\\d{1,8})?|90(\\.0{1,8})?)\\s[-+]?(180(\\.0{1,8})?|((1[0-7]\\d)|([1-9]?\\d))(\\.\\d{1,8})?)$" + }, + "light_regm": { + "name": "light_regm", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "exposure type;light intensity;light quality" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "lux; micrometer, nanometer, angstrom" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Information about treatment(s) involving exposure to light, including both light intensity and quality.", + "title": "light regimen", + "examples": [ + { + "value": "incandescant light;10 lux;450 nanometer" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "light regimen" + ], + "rank": 24, + "is_a": "core field", + "string_serialization": "{text};{float} {unit};{float} {unit}", + "slot_uri": "MIXS:0000569", + "alias": "light_regm", + "owner": "PlantAssociatedInterface", + "domain_of": [ + "Biosample", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "recommended": true, + "multivalued": false, + "pattern": "^\\S+.*\\S+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? \\S+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? \\S+$" + }, + "mechanical_damage": { + "name": "mechanical_damage", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "damage type;body site" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Information about any mechanical damage exerted on the plant; can include multiple damages and sites", + "title": "mechanical damage", + "examples": [ + { + "value": "pruning;bark" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "mechanical damage" + ], + "rank": 262, + "is_a": "core field", + "string_serialization": "{text};{text}", + "slot_uri": "MIXS:0001052", + "alias": "mechanical_damage", + "owner": "PlantAssociatedInterface", + "domain_of": [ + "Biosample", + "PlantAssociatedInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "mineral_nutr_regm": { + "name": "mineral_nutr_regm", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "mineral nutrient name;mineral nutrient amount;treatment interval and duration" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "gram, mole per liter, milligram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Information about treatment involving the use of mineral supplements; should include the name of mineral nutrient, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple mineral nutrient regimens", + "title": "mineral nutrient regimen", + "examples": [ + { + "value": "potassium;15 gram;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "mineral nutrient regimen" + ], + "rank": 263, + "is_a": "core field", + "string_serialization": "{text};{float} {unit};{Rn/start_time/end_time/duration}", + "slot_uri": "MIXS:0000570", + "alias": "mineral_nutr_regm", + "owner": "PlantAssociatedInterface", + "domain_of": [ + "Biosample", + "PlantAssociatedInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "misc_param": { + "name": "misc_param", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "parameter name;measurement value" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Any other measurement performed or parameter collected, that is not listed here", + "title": "miscellaneous parameter", + "examples": [ + { + "value": "Bicarbonate ion concentration;2075 micromole per kilogram" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "miscellaneous parameter" + ], + "rank": 23, + "is_a": "core field", + "string_serialization": "{text};{float} {unit}", + "slot_uri": "MIXS:0000752", + "alias": "misc_param", + "owner": "PlantAssociatedInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false, + "pattern": "^([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+\\|)*([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+)$" + }, + "non_min_nutr_regm": { + "name": "non_min_nutr_regm", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "non-mineral nutrient name;non-mineral nutrient amount;treatment interval and duration" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "gram, mole per liter, milligram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Information about treatment involving the exposure of plant to non-mineral nutrient such as oxygen, hydrogen or carbon; should include the name of non-mineral nutrient, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple non-mineral nutrient regimens", + "title": "non-mineral nutrient regimen", + "examples": [ + { + "value": "carbon dioxide;10 mole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "non-mineral nutrient regimen" + ], + "rank": 264, + "is_a": "core field", + "string_serialization": "{text};{float} {unit};{Rn/start_time/end_time/duration}", + "slot_uri": "MIXS:0000571", + "alias": "non_min_nutr_regm", + "owner": "PlantAssociatedInterface", + "domain_of": [ + "Biosample", + "PlantAssociatedInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "organism_count": { + "name": "organism_count", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "organism name;measurement value;enumeration" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "number of cells per cubic meter, number of cells per milliliter, number of cells per cubic centimeter" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr)", + "title": "organism count", + "examples": [ + { + "value": "total prokaryotes;3.5e7 cells per milliliter;qPCR" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "organism count" + ], + "rank": 30, + "is_a": "core field", + "slot_uri": "MIXS:0000103", + "alias": "organism_count", + "owner": "PlantAssociatedInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^([-+]?[0-9]*\\.?[0-9]+ +\\S.*\\|)*([-+]?[0-9]*\\.?[0-9]+ +\\S.*)$" + }, + "oxy_stat_samp": { + "name": "oxy_stat_samp", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Oxygenation status of sample", + "title": "oxygenation status of sample", + "examples": [ + { + "value": "aerobic" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "oxygenation status of sample" + ], + "rank": 25, + "is_a": "core field", + "slot_uri": "MIXS:0000753", + "alias": "oxy_stat_samp", + "owner": "PlantAssociatedInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_section", + "range": "OxyStatSampEnum", + "multivalued": false + }, + "perturbation": { + "name": "perturbation", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "perturbation type name;perturbation interval and duration" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types", + "title": "perturbation", + "examples": [ + { + "value": "antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "perturbation" + ], + "rank": 33, + "is_a": "core field", + "string_serialization": "{text};{Rn/start_time/end_time/duration}", + "slot_uri": "MIXS:0000754", + "alias": "perturbation", + "owner": "PlantAssociatedInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "pesticide_regm": { + "name": "pesticide_regm", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "pesticide name;pesticide amount;treatment interval and duration" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "gram, mole per liter, milligram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Information about treatment involving use of insecticides; should include the name of pesticide, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple pesticide regimens", + "title": "pesticide regimen", + "examples": [ + { + "value": "pyrethrum;0.6 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "pesticide regimen" + ], + "rank": 265, + "is_a": "core field", + "string_serialization": "{text};{float} {unit};{Rn/start_time/end_time/duration}", + "slot_uri": "MIXS:0000573", + "alias": "pesticide_regm", + "owner": "PlantAssociatedInterface", + "domain_of": [ + "Biosample", + "PlantAssociatedInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "ph_regm": { + "name": "ph_regm", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value;treatment interval and duration" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Information about treatment involving exposure of plants to varying levels of ph of the growth media, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimen", + "title": "pH regimen", + "examples": [ + { + "value": "7.6;R2/2018-05-11:T14:30/2018-05-11T19:30/P1H30M" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "pH regimen" + ], + "rank": 266, + "is_a": "core field", + "string_serialization": "{float};{Rn/start_time/end_time/duration}", + "slot_uri": "MIXS:0001056", + "alias": "ph_regm", + "owner": "PlantAssociatedInterface", + "domain_of": [ + "Biosample", + "PlantAssociatedInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "plant_growth_med": { + "name": "plant_growth_med", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "EO or enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Specification of the media for growing the plants or tissue cultured samples, e.g. soil, aeroponic, hydroponic, in vitro solid culture medium, in vitro liquid culture medium. Recommended value is a specific value from EO:plant growth medium (follow this link for terms http://purl.obolibrary.org/obo/EO_0007147) or other controlled vocabulary", + "title": "plant growth medium", + "examples": [ + { + "value": "hydroponic plant culture media [EO:0007067]" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "plant growth medium" + ], + "rank": 267, + "is_a": "core field", + "slot_uri": "MIXS:0001057", + "alias": "plant_growth_med", + "owner": "PlantAssociatedInterface", + "domain_of": [ + "Biosample", + "PlantAssociatedInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "plant_product": { + "name": "plant_product", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "product name" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Substance produced by the plant, where the sample was obtained from", + "title": "plant product", + "examples": [ + { + "value": "xylem sap [PO:0025539]" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "plant product" + ], + "rank": 268, + "is_a": "core field", + "string_serialization": "{text}", + "slot_uri": "MIXS:0001058", + "alias": "plant_product", + "owner": "PlantAssociatedInterface", + "domain_of": [ + "Biosample", + "PlantAssociatedInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "plant_sex": { + "name": "plant_sex", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Sex of the reproductive parts on the whole plant, e.g. pistillate, staminate, monoecieous, hermaphrodite.", + "title": "plant sex", + "examples": [ + { + "value": "Hermaphroditic" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "plant sex" + ], + "rank": 269, + "is_a": "core field", + "slot_uri": "MIXS:0001059", + "alias": "plant_sex", + "owner": "PlantAssociatedInterface", + "domain_of": [ + "Biosample", + "PlantAssociatedInterface" + ], + "slot_group": "mixs_core_section", + "range": "plant_sex_enum", + "multivalued": false + }, + "plant_struc": { + "name": "plant_struc", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "PO" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Name of plant structure the sample was obtained from; for Plant Ontology (PO) (v releases/2017-12-14) terms, see http://purl.bioontology.org/ontology/PO, e.g. petiole epidermis (PO_0000051). If an individual flower is sampled, the sex of it can be recorded here.", + "title": "plant structure", + "examples": [ + { + "value": "epidermis [PO:0005679]" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "plant structure" + ], + "rank": 270, + "is_a": "core field", + "string_serialization": "{termLabel} {[termID]}", + "slot_uri": "MIXS:0001060", + "alias": "plant_struc", + "owner": "PlantAssociatedInterface", + "domain_of": [ + "Biosample", + "PlantAssociatedInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$" + }, + "radiation_regm": { + "name": "radiation_regm", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "radiation type name;radiation amount;treatment interval and duration" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "rad, gray" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Information about treatment involving exposure of plant or a plant part to a particular radiation regimen; should include the radiation type, amount or intensity administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple radiation regimens", + "title": "radiation regimen", + "examples": [ + { + "value": "gamma radiation;60 gray;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "radiation regimen" + ], + "rank": 271, + "is_a": "core field", + "string_serialization": "{text};{float} {unit};{Rn/start_time/end_time/duration}", + "slot_uri": "MIXS:0000575", + "alias": "radiation_regm", + "owner": "PlantAssociatedInterface", + "domain_of": [ + "Biosample", + "PlantAssociatedInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "rainfall_regm": { + "name": "rainfall_regm", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value;treatment interval and duration" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "millimeter" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Information about treatment involving an exposure to a given amount of rainfall, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens", + "title": "rainfall regimen", + "examples": [ + { + "value": "15 millimeter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "rainfall regimen" + ], + "rank": 272, + "is_a": "core field", + "string_serialization": "{float} {unit};{Rn/start_time/end_time/duration}", + "slot_uri": "MIXS:0000576", + "alias": "rainfall_regm", + "owner": "PlantAssociatedInterface", + "domain_of": [ + "Biosample", + "PlantAssociatedInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "root_cond": { + "name": "root_cond", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "PMID,DOI,url or free text" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Relevant rooting conditions such as field plot size, sowing density, container dimensions, number of plants per container.", + "title": "rooting conditions", + "examples": [ + { + "value": "http://himedialabs.com/TD/PT158.pdf" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "rooting conditions" + ], + "rank": 273, + "is_a": "core field", + "string_serialization": "{PMID}|{DOI}|{URL}|{text}", + "slot_uri": "MIXS:0001061", + "alias": "root_cond", + "owner": "PlantAssociatedInterface", + "domain_of": [ + "Biosample", + "PlantAssociatedInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "root_med_carbon": { + "name": "root_med_carbon", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "carbon source name;measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milligram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Source of organic carbon in the culture rooting medium; e.g. sucrose.", + "title": "rooting medium carbon", + "examples": [ + { + "value": "sucrose" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "rooting medium carbon" + ], + "rank": 274, + "is_a": "core field", + "string_serialization": "{text};{float} {unit}", + "slot_uri": "MIXS:0000577", + "alias": "root_med_carbon", + "owner": "PlantAssociatedInterface", + "domain_of": [ + "Biosample", + "PlantAssociatedInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[^;\\t\\r\\x0A\\|]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A\\|]+$" + }, + "root_med_macronutr": { + "name": "root_med_macronutr", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "macronutrient name;measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milligram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Measurement of the culture rooting medium macronutrients (N,P, K, Ca, Mg, S); e.g. KH2PO4 (170¬†mg/L).", + "title": "rooting medium macronutrients", + "examples": [ + { + "value": "KH2PO4;170¬†milligram per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "rooting medium macronutrients" + ], + "rank": 275, + "is_a": "core field", + "string_serialization": "{text};{float} {unit}", + "slot_uri": "MIXS:0000578", + "alias": "root_med_macronutr", + "owner": "PlantAssociatedInterface", + "domain_of": [ + "Biosample", + "PlantAssociatedInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[^;\\t\\r\\x0A\\|]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A\\|]+$" + }, + "root_med_micronutr": { + "name": "root_med_micronutr", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "micronutrient name;measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milligram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Measurement of the culture rooting medium micronutrients (Fe, Mn, Zn, B, Cu, Mo); e.g. H3BO3 (6.2¬†mg/L).", + "title": "rooting medium micronutrients", + "examples": [ + { + "value": "H3BO3;6.2¬†milligram per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "rooting medium micronutrients" + ], + "rank": 276, + "is_a": "core field", + "string_serialization": "{text};{float} {unit}", + "slot_uri": "MIXS:0000579", + "alias": "root_med_micronutr", + "owner": "PlantAssociatedInterface", + "domain_of": [ + "Biosample", + "PlantAssociatedInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[^;\\t\\r\\x0A\\|]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A\\|]+$" + }, + "root_med_ph": { + "name": "root_med_ph", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "pH measurement of the culture rooting medium; e.g. 5.5.", + "title": "rooting medium pH", + "examples": [ + { + "value": "7.5" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "rooting medium pH" + ], + "rank": 277, + "is_a": "core field", + "slot_uri": "MIXS:0001062", + "alias": "root_med_ph", + "owner": "PlantAssociatedInterface", + "domain_of": [ + "Biosample", + "PlantAssociatedInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "root_med_regl": { + "name": "root_med_regl", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "regulator name;measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milligram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Growth regulators in the culture rooting medium such as cytokinins, auxins, gybberellins, abscisic acid; e.g. 0.5¬†mg/L NAA.", + "title": "rooting medium regulators", + "examples": [ + { + "value": "abscisic acid;0.75 milligram per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "rooting medium regulators" + ], + "rank": 278, + "is_a": "core field", + "string_serialization": "{text};{float} {unit}", + "slot_uri": "MIXS:0000581", + "alias": "root_med_regl", + "owner": "PlantAssociatedInterface", + "domain_of": [ + "Biosample", + "PlantAssociatedInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[^;\\t\\r\\x0A\\|]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A\\|]+$" + }, + "root_med_solid": { + "name": "root_med_solid", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "name" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Specification of the solidifying agent in the culture rooting medium; e.g. agar.", + "title": "rooting medium solidifier", + "examples": [ + { + "value": "agar" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "rooting medium solidifier" + ], + "rank": 279, + "is_a": "core field", + "string_serialization": "{text}", + "slot_uri": "MIXS:0001063", + "alias": "root_med_solid", + "owner": "PlantAssociatedInterface", + "domain_of": [ + "Biosample", + "PlantAssociatedInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "root_med_suppl": { + "name": "root_med_suppl", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "supplement name;measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milligram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Organic supplements of the culture rooting medium, such as vitamins, amino acids, organic acids, antibiotics activated charcoal; e.g. nicotinic acid (0.5¬†mg/L).", + "title": "rooting medium organic supplements", + "examples": [ + { + "value": "nicotinic acid;0.5 milligram per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "rooting medium organic supplements" + ], + "rank": 280, + "is_a": "core field", + "string_serialization": "{text};{float} {unit}", + "slot_uri": "MIXS:0000580", + "alias": "root_med_suppl", + "owner": "PlantAssociatedInterface", + "domain_of": [ + "Biosample", + "PlantAssociatedInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[^;\\t\\r\\x0A\\|]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A\\|]+$" + }, + "salinity": { + "name": "salinity", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "practical salinity unit, percentage" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The total concentration of all dissolved salts in a liquid or solid sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater.", + "title": "salinity", + "examples": [ + { + "value": "25 practical salinity unit" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "salinity" + ], + "rank": 54, + "is_a": "core field", + "slot_uri": "MIXS:0000183", + "alias": "salinity", + "owner": "PlantAssociatedInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "salinity_meth": { + "name": "salinity_meth", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "PMID,DOI or url" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Reference or method used in determining salinity", + "title": "salinity method", + "examples": [ + { + "value": "https://doi.org/10.1007/978-1-61779-986-0_28" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "salinity method" + ], + "rank": 55, + "is_a": "core field", + "string_serialization": "{PMID}|{DOI}|{URL}", + "slot_uri": "MIXS:0000341", + "alias": "salinity_meth", + "owner": "PlantAssociatedInterface", + "domain_of": [ + "Biosample", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WaterInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false + }, + "salt_regm": { + "name": "salt_regm", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "salt name;salt amount;treatment interval and duration" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "gram, microgram, mole per liter, gram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Information about treatment involving use of salts as supplement to liquid and soil growth media; should include the name of salt, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple salt regimens", + "title": "salt regimen", + "examples": [ + { + "value": "NaCl;5 gram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "salt regimen" + ], + "rank": 281, + "is_a": "core field", + "string_serialization": "{text};{float} {unit};{Rn/start_time/end_time/duration}", + "slot_uri": "MIXS:0000582", + "alias": "salt_regm", + "owner": "PlantAssociatedInterface", + "domain_of": [ + "Biosample", + "PlantAssociatedInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "samp_capt_status": { + "name": "samp_capt_status", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Reason for the sample", + "title": "sample capture status", + "examples": [ + { + "value": "farm sample" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sample capture status" + ], + "rank": 282, + "is_a": "core field", + "slot_uri": "MIXS:0000860", + "alias": "samp_capt_status", + "owner": "PlantAssociatedInterface", + "domain_of": [ + "Biosample", + "HostAssociatedInterface", + "PlantAssociatedInterface" + ], + "slot_group": "mixs_core_section", + "range": "samp_capt_status_enum", + "multivalued": false + }, + "samp_collec_device": { + "name": "samp_collec_device", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "device name" + } + }, + "description": "The device used to collect an environmental sample. This field accepts terms listed under environmental sampling device (http://purl.obolibrary.org/obo/ENVO). This field also accepts terms listed under specimen collection device (http://purl.obolibrary.org/obo/GENEPIO_0002094).", + "title": "sample collection device", + "comments": [ + "Report dimensions and details when applicable" + ], + "examples": [ + { + "value": "swab, biopsy, niskin bottle, push core, drag swab [GENEPIO:0002713]" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sample collection device" + ], + "rank": 14, + "is_a": "nucleic acid sequence source field", + "string_serialization": "{termLabel} {[termID]}|{text}", + "slot_uri": "MIXS:0000002", + "alias": "samp_collec_device", + "owner": "PlantAssociatedInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "recommended": true, + "multivalued": false + }, + "samp_collec_method": { + "name": "samp_collec_method", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "PMID,DOI,url , or text" + } + }, + "description": "The method employed for collecting the sample.", + "title": "sample collection method", + "comments": [ + "This can be a citation or description" + ], + "examples": [ + { + "value": "swabbing" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sample collection method" + ], + "rank": 15, + "is_a": "nucleic acid sequence source field", + "string_serialization": "{PMID}|{DOI}|{URL}|{text}", + "slot_uri": "MIXS:0001225", + "alias": "samp_collec_method", + "owner": "PlantAssociatedInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "multivalued": false + }, + "samp_dis_stage": { + "name": "samp_dis_stage", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Stage of the disease at the time of sample collection, e.g. inoculation, penetration, infection, growth and reproduction, dissemination of pathogen.", + "title": "sample disease stage", + "examples": [ + { + "value": "infection" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sample disease stage" + ], + "rank": 283, + "is_a": "core field", + "slot_uri": "MIXS:0000249", + "alias": "samp_dis_stage", + "owner": "PlantAssociatedInterface", + "domain_of": [ + "Biosample", + "HostAssociatedInterface", + "PlantAssociatedInterface" + ], + "slot_group": "mixs_core_section", + "range": "samp_dis_stage_enum", + "multivalued": false + }, + "samp_mat_process": { + "name": "samp_mat_process", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "text" + } + }, + "description": "A brief description of any processing applied to the sample during or after retrieving the sample from environment, or a link to the relevant protocol(s) performed.", + "title": "sample material processing", + "examples": [ + { + "value": "filtering of seawater" + }, + { + "value": "storing samples in ethanol" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sample material processing" + ], + "rank": 12, + "is_a": "nucleic acid sequence source field", + "string_serialization": "{text}", + "slot_uri": "MIXS:0000016", + "alias": "samp_mat_process", + "owner": "PlantAssociatedInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "multivalued": false + }, + "samp_size": { + "name": "samp_size", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "millliter, gram, milligram, liter" + } + }, + "description": "The total amount or size (volume (ml), mass (g) or area (m2) ) of sample collected.", + "title": "amount or size of sample collected", + "comments": [ + "This refers to the TOTAL amount of sample collected from the experiment. NOT the amount sent to each institution or collected for a specific analysis." + ], + "examples": [ + { + "value": "5 grams" + }, + { + "value": "10 mL" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "amount or size of sample collected" + ], + "rank": 18, + "is_a": "nucleic acid sequence source field", + "string_serialization": "{float} {unit}", + "slot_uri": "MIXS:0000001", + "alias": "samp_size", + "owner": "PlantAssociatedInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? \\S+$" + }, + "samp_store_dur": { + "name": "samp_store_dur", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "duration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Duration for which the sample was stored", + "title": "sample storage duration", + "examples": [ + { + "value": "P1Y6M" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sample storage duration" + ], + "rank": 353, + "is_a": "core field", + "string_serialization": "{duration}", + "slot_uri": "MIXS:0000116", + "alias": "samp_store_dur", + "owner": "PlantAssociatedInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "samp_store_loc": { + "name": "samp_store_loc", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "location name" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Location at which sample was stored, usually name of a specific freezer/room", + "title": "sample storage location", + "examples": [ + { + "value": "Freezer no:5" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sample storage location" + ], + "rank": 41, + "is_a": "core field", + "string_serialization": "{text}", + "slot_uri": "MIXS:0000755", + "alias": "samp_store_loc", + "owner": "PlantAssociatedInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "samp_store_temp": { + "name": "samp_store_temp", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "degree Celsius" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Temperature at which the sample was stored (degrees are assumed)", + "title": "sample storage temperature", + "examples": [ + { + "value": "-80 Celsius" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sample storage temperature" + ], + "rank": 7, + "is_a": "core field", + "slot_uri": "MIXS:0000110", + "alias": "samp_store_temp", + "owner": "PlantAssociatedInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "required": true, + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "sample_link": { + "name": "sample_link", + "description": "A unique identifier to assign parent-child, subsample, or sibling samples. This is relevant when a sample or other material was used to generate the new sample.", + "title": "sample linkage", + "notes": [ + "also tempted to include SampIdNewTermsMixin but if len(slot_usage.keys()) > 1 and \"placeholder\" in slot_usage.keys():AttributeError: 'list' object has no attribute 'keys'" + ], + "comments": [ + "This field allows multiple entries separated by ; (Examples: Soil collected from the field will link with the soil used in an incubation. The soil a plant was grown in links to the plant sample. An original culture sample was transferred to a new vial and generated a new sample)" + ], + "examples": [ + { + "value": "IGSN:DSJ0284" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "rank": 5, + "string_serialization": "{text}:{text}", + "alias": "sample_link", + "owner": "PlantAssociatedInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface", + "SampIdNewTermsMixin" + ], + "slot_group": "sample_id_section", + "range": "string", + "recommended": true, + "multivalued": false, + "pattern": "[^\\:\\n\\r]+\\:[^\\:\\n\\r]+" + }, + "season_environment": { + "name": "season_environment", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "seasonal environment name;treatment interval and duration" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Treatment involving an exposure to a particular season (e.g. Winter, summer, rabi, rainy etc.), treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment", + "title": "seasonal environment", + "examples": [ + { + "value": "rainy;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "seasonal environment" + ], + "rank": 284, + "is_a": "core field", + "string_serialization": "{text};{Rn/start_time/end_time/duration}", + "slot_uri": "MIXS:0001068", + "alias": "season_environment", + "owner": "PlantAssociatedInterface", + "domain_of": [ + "Biosample", + "PlantAssociatedInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "size_frac": { + "name": "size_frac", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "filter size value range" + } + }, + "description": "Filtering pore size used in sample preparation", + "title": "size fraction selected", + "examples": [ + { + "value": "0-0.22 micrometer" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "size fraction selected" + ], + "rank": 285, + "is_a": "nucleic acid sequence source field", + "string_serialization": "{float}-{float} {unit}", + "slot_uri": "MIXS:0000017", + "alias": "size_frac", + "owner": "PlantAssociatedInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "specific_ecosystem": { + "name": "specific_ecosystem", + "description": "Specific ecosystems represent specific features of the environment like aphotic zone in an ocean or gastric mucosa within a host digestive system. Specific ecosystem is in position 5/5 in a GOLD path.", + "comments": [ + "Specific ecosystems help to define samples based on very specific characteristics of an environment under the five-level classification system." + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "https://gold.jgi.doe.gov/help" + ], + "rank": 13, + "is_a": "gold_path_field", + "alias": "specific_ecosystem", + "owner": "PlantAssociatedInterface", + "domain_of": [ + "Biosample", + "Study", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "SpecificEcosystemEnum", + "recommended": true + }, + "standing_water_regm": { + "name": "standing_water_regm", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "standing water type;treatment interval and duration" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Treatment involving an exposure to standing water during a plant's life span, types can be flood water or standing water, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens", + "title": "standing water regimen", + "examples": [ + { + "value": "standing water;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "standing water regimen" + ], + "rank": 286, + "is_a": "core field", + "string_serialization": "{text};{Rn/start_time/end_time/duration}", + "slot_uri": "MIXS:0001069", + "alias": "standing_water_regm", + "owner": "PlantAssociatedInterface", + "domain_of": [ + "Biosample", + "PlantAssociatedInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "start_date_inc": { + "name": "start_date_inc", + "description": "Date the incubation was started. Only relevant for incubation samples.", + "title": "incubation start date", + "notes": [ + "MIxS collection_date accepts (truncated) ISO8601. DH taking arbitrary precision date only" + ], + "comments": [ + "Date should be formatted as YYYY(-MM(-DD)). Ie, 2021-04-15, 2021-04 and 2021 are all acceptable." + ], + "examples": [ + { + "value": "2021-04-15, 2021-04 and 2021 are all acceptable." + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "MIXS:0000011" + ], + "rank": 4, + "string_serialization": "{date, arbitrary precision}", + "alias": "start_date_inc", + "owner": "PlantAssociatedInterface", + "domain_of": [ + "Biosample", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WaterInterface", + "SoilMixsInspiredMixin" + ], + "slot_group": "mixs_inspired_section", + "range": "string", + "recommended": true, + "multivalued": false, + "pattern": "^[12]\\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\\d|3[01]))?)?$" + }, + "temp": { + "name": "temp", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "degree Celsius" + } + }, + "description": "Temperature of the sample at the time of sampling.", + "title": "temperature", + "examples": [ + { + "value": "25 degree Celsius" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "temperature" + ], + "rank": 37, + "is_a": "environment field", + "slot_uri": "MIXS:0000113", + "alias": "temp", + "owner": "PlantAssociatedInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "tiss_cult_growth_med": { + "name": "tiss_cult_growth_med", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "PMID,DOI,url or free text" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Description of plant tissue culture growth media used", + "title": "tissue culture growth media", + "examples": [ + { + "value": "https://link.springer.com/content/pdf/10.1007/BF02796489.pdf" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "tissue culture growth media" + ], + "rank": 287, + "is_a": "core field", + "string_serialization": "{PMID}|{DOI}|{URL}|{text}", + "slot_uri": "MIXS:0001070", + "alias": "tiss_cult_growth_med", + "owner": "PlantAssociatedInterface", + "domain_of": [ + "Biosample", + "PlantAssociatedInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "water_temp_regm": { + "name": "water_temp_regm", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value;treatment interval and duration" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "degree Celsius" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Information about treatment involving an exposure to water with varying degree of temperature, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens", + "title": "water temperature regimen", + "examples": [ + { + "value": "15 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "water temperature regimen" + ], + "rank": 288, + "is_a": "core field", + "string_serialization": "{float} {unit};{Rn/start_time/end_time/duration}", + "slot_uri": "MIXS:0000590", + "alias": "water_temp_regm", + "owner": "PlantAssociatedInterface", + "domain_of": [ + "Biosample", + "PlantAssociatedInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "watering_regm": { + "name": "watering_regm", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value;treatment interval and duration" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milliliter, liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Information about treatment involving an exposure to watering frequencies, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens", + "title": "watering regimen", + "examples": [ + { + "value": "1 liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" + }, + { + "value": "75% water holding capacity; constant" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "watering regimen" + ], + "rank": 25, + "is_a": "core field", + "string_serialization": "{float} {unit};{Rn/start_time/end_time/duration}", + "slot_uri": "MIXS:0000591", + "alias": "watering_regm", + "owner": "PlantAssociatedInterface", + "domain_of": [ + "Biosample", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "recommended": true, + "multivalued": false + }, + "analysis_type": { + "name": "analysis_type", + "description": "Select all the data types associated or available for this biosample", + "title": "analysis/data type", + "examples": [ + { + "value": "metagenomics; metabolomics; proteomics" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "MIxS:investigation_type" + ], + "rank": 3, + "alias": "analysis_type", + "owner": "PlantAssociatedInterface", + "domain_of": [ + "Biosample", + "DhMultiviewCommonColumnsMixin", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "EmslInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "JgiMgInterface", + "JgiMgLrInterface", + "JgiMtInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "AnalysisTypeEnum", + "required": true, + "recommended": false, + "multivalued": true + }, + "samp_name": { + "name": "samp_name", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "text" + } + }, + "description": "A local identifier or name that for the material sample collected. Refers to the original material collected or to any derived sub-samples.", + "title": "sample name", + "comments": [ + "It can have any format, but we suggest that you make it concise, unique and consistent within your lab, and as informative as possible." + ], + "examples": [ + { + "value": "Rock core CB1178(5-6) from NSW" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sample name" + ], + "rank": 1, + "is_a": "investigation field", + "string_serialization": "{text}", + "slot_uri": "MIXS:0001107", + "identifier": true, + "alias": "samp_name", + "owner": "PlantAssociatedInterface", + "domain_of": [ + "Biosample", + "DhMultiviewCommonColumnsMixin", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "EmslInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "JgiMgInterface", + "JgiMgLrInterface", + "JgiMtInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "string", + "required": true, + "multivalued": false + }, + "source_mat_id": { + "name": "source_mat_id", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "for cultures of microorganisms: identifiers for two culture collections; for other material a unique arbitrary identifer" + } + }, + "description": "A globally unique identifier assigned to the biological sample.", + "title": "source material identifier", + "todos": [ + "Currently, the comments say to use UUIDs. However, if we implement assigning NMDC identifiers with the minter we dont need to require a GUID. It can be an optional field to fill out only if they already have a resolvable ID.", + "Currently, the comments say to use UUIDs. However, if we implement assigning NMDC identifiers with the minter we dont need to require a GUID. It can be an optional field to fill out only if they already have a resolvable ID." + ], + "notes": [ + "The source material IS the Globally Unique ID" + ], + "comments": [ + "Identifiers must be prefixed. Possible FAIR prefixes are IGSNs (http://www.geosamples.org/getigsn), NCBI biosample accession numbers, ARK identifiers (https://arks.org/). These IDs enable linking to derived analytes and subsamples. If you have not assigned FAIR identifiers to your samples, you can generate UUIDs (https://www.uuidgenerator.net/).", + "Identifiers must be prefixed. Possible FAIR prefixes are IGSNs (http://www.geosamples.org/getigsn), NCBI biosample accession numbers, ARK identifiers (https://arks.org/). These IDs enable linking to derived analytes and subsamples. If you have not assigned FAIR identifiers to your samples, you can generate UUIDs (https://www.uuidgenerator.net/)." + ], + "examples": [ + { + "value": "IGSN:AU1243" + }, + { + "value": "UUID:24f1467a-40f4-11ed-b878-0242ac120002" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "source material identifiers" + ], + "rank": 2, + "is_a": "nucleic acid sequence source field", + "string_serialization": "{text}:{text}", + "slot_uri": "MIXS:0000026", + "alias": "source_mat_id", + "owner": "PlantAssociatedInterface", + "domain_of": [ + "Biosample", + "DhMultiviewCommonColumnsMixin", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "EmslInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "JgiMgInterface", + "JgiMgLrInterface", + "JgiMtInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "string", + "multivalued": false, + "pattern": "[^\\:\\n\\r]+\\:[^\\:\\n\\r]+" + } + } + }, + "SedimentInterface": { + "name": "SedimentInterface", + "annotations": { + "excel_worksheet_name": { + "tag": "excel_worksheet_name", + "value": "sediment" + } + }, + "description": "sediment dh_interface", + "title": "Sediment", + "from_schema": "https://example.com/nmdc_submission_schema", + "is_a": "DhInterface", + "mixins": [ + "DhMultiviewCommonColumnsMixin", + "SampIdNewTermsMixin" + ], + "slots": [ + "air_temp_regm", + "alkalinity", + "alkalinity_method", + "alkyl_diethers", + "aminopept_act", + "ammonium", + "bacteria_carb_prod", + "biomass", + "biotic_regm", + "biotic_relationship", + "bishomohopanol", + "bromide", + "calcium", + "carb_nitro_ratio", + "chem_administration", + "chloride", + "chlorophyll", + "climate_environment", + "collection_date", + "collection_date_inc", + "collection_time", + "density", + "depth", + "diether_lipids", + "diss_carb_dioxide", + "diss_hydrogen", + "diss_inorg_carb", + "diss_org_carb", + "diss_org_nitro", + "diss_oxygen", + "ecosystem", + "ecosystem_category", + "ecosystem_subtype", + "ecosystem_type", + "elev", + "env_broad_scale", + "env_local_scale", + "env_medium", + "experimental_factor", + "extreme_event", + "fire", + "flooding", + "gaseous_environment", + "geo_loc_name", + "glucosidase_act", + "humidity_regm", + "isotope_exposure", + "lat_lon", + "light_regm", + "magnesium", + "mean_frict_vel", + "mean_peak_frict_vel", + "methane", + "micro_biomass_c_meth", + "micro_biomass_meth", + "micro_biomass_n_meth", + "microbial_biomass", + "microbial_biomass_c", + "microbial_biomass_n", + "misc_param", + "n_alkanes", + "nitrate", + "nitrite", + "nitro", + "org_carb", + "org_matter", + "org_nitro", + "org_nitro_method", + "organism_count", + "oxy_stat_samp", + "part_org_carb", + "particle_class", + "perturbation", + "petroleum_hydrocarb", + "ph", + "ph_meth", + "phaeopigments", + "phosphate", + "phosplipid_fatt_acid", + "porosity", + "potassium", + "pressure", + "redox_potential", + "salinity", + "salinity_meth", + "samp_collec_device", + "samp_collec_method", + "samp_mat_process", + "samp_size", + "samp_store_dur", + "samp_store_loc", + "samp_store_temp", + "sample_link", + "sediment_type", + "sieving", + "silicate", + "size_frac", + "sodium", + "specific_ecosystem", + "start_date_inc", + "sulfate", + "sulfide", + "temp", + "tidal_stage", + "tot_carb", + "tot_depth_water_col", + "tot_nitro_cont_meth", + "tot_nitro_content", + "tot_org_c_meth", + "tot_org_carb", + "turbidity", + "water_cont_soil_meth", + "water_content", + "watering_regm" + ], + "slot_usage": { + "air_temp_regm": { + "name": "air_temp_regm", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "temperature value;treatment interval and duration" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "meter" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Information about treatment involving an exposure to varying temperatures; should include the temperature, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include different temperature regimens", + "title": "air temperature regimen", + "examples": [ + { + "value": "25 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "air temperature regimen" + ], + "rank": 16, + "is_a": "core field", + "string_serialization": "{float} {unit};{Rn/start_time/end_time/duration}", + "slot_uri": "MIXS:0000551", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "multivalued": false + }, + "alkalinity": { + "name": "alkalinity", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milliequivalent per liter, milligram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate", + "title": "alkalinity", + "examples": [ + { + "value": "50 milligram per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "alkalinity" + ], + "rank": 1, + "is_a": "core field", + "slot_uri": "MIXS:0000421", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "alkalinity_method": { + "name": "alkalinity_method", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "description of method" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Method used for alkalinity measurement", + "title": "alkalinity method", + "examples": [ + { + "value": "titration" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "alkalinity method" + ], + "rank": 218, + "is_a": "core field", + "string_serialization": "{text}", + "slot_uri": "MIXS:0000298", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "alkyl_diethers": { + "name": "alkyl_diethers", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "mole per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of alkyl diethers", + "title": "alkyl diethers", + "examples": [ + { + "value": "0.005 mole per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "alkyl diethers" + ], + "rank": 2, + "is_a": "core field", + "slot_uri": "MIXS:0000490", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "aminopept_act": { + "name": "aminopept_act", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "mole per liter per hour" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Measurement of aminopeptidase activity", + "title": "aminopeptidase activity", + "examples": [ + { + "value": "0.269 mole per liter per hour" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "aminopeptidase activity" + ], + "rank": 3, + "is_a": "core field", + "slot_uri": "MIXS:0000172", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "ammonium": { + "name": "ammonium", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per liter, milligram per liter, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of ammonium in the sample", + "title": "ammonium", + "examples": [ + { + "value": "1.5 milligram per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "ammonium" + ], + "rank": 4, + "is_a": "core field", + "slot_uri": "MIXS:0000427", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "bacteria_carb_prod": { + "name": "bacteria_carb_prod", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "nanogram per hour" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Measurement of bacterial carbon production", + "title": "bacterial carbon production", + "examples": [ + { + "value": "2.53 microgram per liter per hour" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "bacterial carbon production" + ], + "rank": 5, + "is_a": "core field", + "slot_uri": "MIXS:0000173", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "biomass": { + "name": "biomass", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "biomass type;measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "ton, kilogram, gram" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements", + "title": "biomass", + "examples": [ + { + "value": "total;20 gram" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "biomass" + ], + "rank": 6, + "is_a": "core field", + "string_serialization": "{text};{float} {unit}", + "slot_uri": "MIXS:0000174", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+\\|)*([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+)$" + }, + "biotic_regm": { + "name": "biotic_regm", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "free text" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Information about treatment(s) involving use of biotic factors, such as bacteria, viruses or fungi.", + "title": "biotic regimen", + "examples": [ + { + "value": "sample inoculated with Rhizobium spp. Culture" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "biotic regimen" + ], + "rank": 13, + "is_a": "core field", + "string_serialization": "{text}", + "slot_uri": "MIXS:0001038", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "multivalued": false + }, + "biotic_relationship": { + "name": "biotic_relationship", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + } + }, + "description": "Description of relationship(s) between the subject organism and other organism(s) it is associated with. E.g., parasite on species X; mutualist with species Y. The target organism is the subject of the relationship, and the other organism(s) is the object", + "title": "observed biotic relationship", + "examples": [ + { + "value": "free living" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "observed biotic relationship" + ], + "rank": 22, + "is_a": "nucleic acid sequence source field", + "slot_uri": "MIXS:0000028", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface" + ], + "slot_group": "mixs_modified_section", + "range": "biotic_relationship_enum", + "multivalued": false + }, + "bishomohopanol": { + "name": "bishomohopanol", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "microgram per liter, microgram per gram" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of bishomohopanol", + "title": "bishomohopanol", + "examples": [ + { + "value": "14 microgram per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "bishomohopanol" + ], + "rank": 7, + "is_a": "core field", + "slot_uri": "MIXS:0000175", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "bromide": { + "name": "bromide", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of bromide", + "title": "bromide", + "examples": [ + { + "value": "0.05 parts per million" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "bromide" + ], + "rank": 8, + "is_a": "core field", + "slot_uri": "MIXS:0000176", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "calcium": { + "name": "calcium", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milligram per liter, micromole per liter, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of calcium in the sample", + "title": "calcium", + "examples": [ + { + "value": "0.2 micromole per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "calcium" + ], + "rank": 9, + "is_a": "core field", + "slot_uri": "MIXS:0000432", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "carb_nitro_ratio": { + "name": "carb_nitro_ratio", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Ratio of amount or concentrations of carbon to nitrogen", + "title": "carbon/nitrogen ratio", + "examples": [ + { + "value": "0.417361111" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "carbon/nitrogen ratio" + ], + "rank": 44, + "is_a": "core field", + "slot_uri": "MIXS:0000310", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "SedimentInterface", + "SoilInterface", + "WaterInterface" + ], + "slot_group": "mixs_section", + "range": "float", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "chem_administration": { + "name": "chem_administration", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "CHEBI;timestamp" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi", + "title": "chemical administration", + "examples": [ + { + "value": "agar [CHEBI:2509];2018-05-11|agar [CHEBI:2509];2018-05-22" + }, + { + "value": "agar [CHEBI:2509];2018-05" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "chemical administration" + ], + "rank": 17, + "is_a": "core field", + "string_serialization": "{termLabel} {[termID]};{timestamp}", + "slot_uri": "MIXS:0000751", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "recommended": true, + "multivalued": false, + "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\];([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$" + }, + "chloride": { + "name": "chloride", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milligram per liter, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of chloride in the sample", + "title": "chloride", + "examples": [ + { + "value": "5000 milligram per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "chloride" + ], + "rank": 10, + "is_a": "core field", + "slot_uri": "MIXS:0000429", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "chlorophyll": { + "name": "chlorophyll", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milligram per cubic meter, microgram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of chlorophyll", + "title": "chlorophyll", + "examples": [ + { + "value": "5 milligram per cubic meter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "chlorophyll" + ], + "rank": 11, + "is_a": "core field", + "slot_uri": "MIXS:0000177", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "climate_environment": { + "name": "climate_environment", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "climate name;treatment interval and duration" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Treatment involving an exposure to a particular climate; treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple climates", + "title": "climate environment", + "todos": [ + "description says \"can include multiple climates\" but multivalued is set to false", + "add examples, i need to see some examples to add correctly formatted example." + ], + "examples": [ + { + "value": "tropical climate;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "climate environment" + ], + "rank": 19, + "is_a": "core field", + "string_serialization": "{text};{Rn/start_time/end_time/duration}", + "slot_uri": "MIXS:0001040", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "multivalued": false + }, + "collection_date": { + "name": "collection_date", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "date and time" + } + }, + "description": "The date of sampling", + "title": "collection date", + "notes": [ + "MIxS collection_date accepts (truncated) ISO8601. DH taking arb prec date only", + "Use modified term (amended definition)" + ], + "examples": [ + { + "value": "2021-04-15" + }, + { + "value": "2021-04" + }, + { + "value": "2021" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "collection date" + ], + "rank": 3, + "is_a": "environment field", + "string_serialization": "{date, arbitrary precision}", + "slot_uri": "MIXS:0000011", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "required": true, + "multivalued": false, + "pattern": "^[12]\\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\\d|3[01]))?)?$" + }, + "collection_date_inc": { + "name": "collection_date_inc", + "description": "Date the incubation was harvested/collected/ended. Only relevant for incubation samples.", + "title": "incubation collection date", + "notes": [ + "MIxS collection_date accepts (truncated) ISO8601. DH taking arbitrary precision date only" + ], + "comments": [ + "Date should be formatted as YYYY(-MM(-DD)). Ie, 2021-04-15, 2021-04 and 2021 are all acceptable." + ], + "examples": [ + { + "value": "2021-04-15, 2021-04 and 2021 are all acceptable." + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "MIXS:0000011" + ], + "rank": 2, + "string_serialization": "{date, arbitrary precision}", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WaterInterface", + "SoilMixsInspiredMixin" + ], + "slot_group": "mixs_inspired_section", + "range": "string", + "recommended": true, + "multivalued": false, + "pattern": "^[12]\\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\\d|3[01]))?)?$" + }, + "collection_time": { + "name": "collection_time", + "description": "The time of sampling, either as an instance (single point) or interval.", + "title": "collection time, GMT", + "notes": [ + "MIxS collection_date accepts (truncated) ISO8601. DH taking seconds optional time only" + ], + "comments": [ + "Time should be entered as HH:MM(:SS) in GMT. See here for a converter: https://www.worldtimebuddy.com/pst-to-gmt-converter" + ], + "examples": [ + { + "value": "13:33 or 13:33:55" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "MIXS:0000011" + ], + "rank": 1, + "string_serialization": "{time, seconds optional}", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WaterInterface", + "SoilMixsInspiredMixin" + ], + "slot_group": "mixs_inspired_section", + "range": "string", + "recommended": true, + "multivalued": false, + "pattern": "^([01]?\\d|2[0-3]|24(?=:00?:00?$)):([0-5]\\d)(:([0-5]\\d))?$" + }, + "density": { + "name": "density", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "gram per cubic meter, gram per cubic centimeter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Density of the sample, which is its mass per unit volume (aka volumetric mass density)", + "title": "density", + "examples": [ + { + "value": "1000 kilogram per cubic meter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "density" + ], + "rank": 12, + "is_a": "core field", + "slot_uri": "MIXS:0000435", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "depth": { + "name": "depth", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + } + }, + "description": "The vertical distance below local surface, e.g. for sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples.", + "title": "depth, meters", + "notes": [ + "Use modified term" + ], + "comments": [ + "All depths must be reported in meters. Provide the numerical portion only." + ], + "examples": [ + { + "value": "0 - 0.1" + }, + { + "value": "1" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "depth" + ], + "rank": 9, + "is_a": "environment field", + "string_serialization": "{float}-{float}", + "slot_uri": "MIXS:0000018", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "required": true, + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)?\\s*-\\s*[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)?$" + }, + "diether_lipids": { + "name": "diether_lipids", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "diether lipid name;measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "nanogram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Concentration of diether lipids; can include multiple types of diether lipids", + "title": "diether lipids", + "examples": [ + { + "value": "0.2 nanogram per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "diether lipids" + ], + "rank": 13, + "is_a": "core field", + "string_serialization": "{text};{float} {unit}", + "slot_uri": "MIXS:0000178", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+\\|)*([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+)$" + }, + "diss_carb_dioxide": { + "name": "diss_carb_dioxide", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per liter, milligram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample", + "title": "dissolved carbon dioxide", + "examples": [ + { + "value": "5 milligram per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "dissolved carbon dioxide" + ], + "rank": 14, + "is_a": "core field", + "slot_uri": "MIXS:0000436", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "diss_hydrogen": { + "name": "diss_hydrogen", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of dissolved hydrogen", + "title": "dissolved hydrogen", + "examples": [ + { + "value": "0.3 micromole per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "dissolved hydrogen" + ], + "rank": 15, + "is_a": "core field", + "slot_uri": "MIXS:0000179", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "diss_inorg_carb": { + "name": "diss_inorg_carb", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "microgram per liter, milligram per liter, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter", + "title": "dissolved inorganic carbon", + "examples": [ + { + "value": "2059 micromole per kilogram" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "dissolved inorganic carbon" + ], + "rank": 16, + "is_a": "core field", + "slot_uri": "MIXS:0000434", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "diss_org_carb": { + "name": "diss_org_carb", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per liter, milligram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid", + "title": "dissolved organic carbon", + "examples": [ + { + "value": "197 micromole per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "dissolved organic carbon" + ], + "rank": 17, + "is_a": "core field", + "slot_uri": "MIXS:0000433", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "diss_org_nitro": { + "name": "diss_org_nitro", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "microgram per liter, milligram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2", + "title": "dissolved organic nitrogen", + "examples": [ + { + "value": "0.05 micromole per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "dissolved organic nitrogen" + ], + "rank": 18, + "is_a": "core field", + "slot_uri": "MIXS:0000162", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "diss_oxygen": { + "name": "diss_oxygen", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per kilogram, milligram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of dissolved oxygen", + "title": "dissolved oxygen", + "examples": [ + { + "value": "175 micromole per kilogram" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "dissolved oxygen" + ], + "rank": 19, + "is_a": "core field", + "slot_uri": "MIXS:0000119", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "ecosystem": { + "name": "ecosystem", + "description": "An ecosystem is a combination of a physical environment (abiotic factors) and all the organisms (biotic factors) that interact with this environment. Ecosystem is in position 1/5 in a GOLD path.", + "comments": [ + "The abiotic factors play a profound role on the type and composition of organisms in a given environment. The GOLD Ecosystem at the top of the five-level classification system is aimed at capturing the broader environment from which an organism or environmental sample is collected. The three broad groups under Ecosystem are Environmental, Host-associated, and Engineered. They represent samples collected from a natural environment or from another organism or from engineered environments like bioreactors respectively." + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "https://gold.jgi.doe.gov/help" + ], + "rank": 9, + "is_a": "gold_path_field", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "Study", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "EcosystemEnum", + "recommended": true + }, + "ecosystem_category": { + "name": "ecosystem_category", + "description": "Ecosystem categories represent divisions within the ecosystem based on specific characteristics of the environment from where an organism or sample is isolated. Ecosystem category is in position 2/5 in a GOLD path.", + "comments": [ + "The Environmental ecosystem (for example) is divided into Air, Aquatic and Terrestrial. Ecosystem categories for Host-associated samples can be individual hosts or phyla and for engineered samples it may be manipulated environments like bioreactors, solid waste etc." + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "https://gold.jgi.doe.gov/help" + ], + "rank": 10, + "is_a": "gold_path_field", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "Study", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "EcosystemCategoryEnum", + "recommended": true + }, + "ecosystem_subtype": { + "name": "ecosystem_subtype", + "description": "Ecosystem subtypes represent further subdivision of Ecosystem types into more distinct subtypes. Ecosystem subtype is in position 4/5 in a GOLD path.", + "comments": [ + "Ecosystem Type Marine (Environmental -> Aquatic -> Marine) is further divided (for example) into Intertidal zone, Coastal, Pelagic, Intertidal zone etc. in the Ecosystem subtype category." + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "https://gold.jgi.doe.gov/help" + ], + "rank": 12, + "is_a": "gold_path_field", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "Study", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "EcosystemSubtypeEnum", + "recommended": true + }, + "ecosystem_type": { + "name": "ecosystem_type", + "description": "Ecosystem types represent things having common characteristics within the Ecosystem Category. These common characteristics based grouping is still broad but specific to the characteristics of a given environment. Ecosystem type is in position 3/5 in a GOLD path.", + "comments": [ + "The Aquatic ecosystem category (for example) may have ecosystem types like Marine or Thermal springs etc. Ecosystem category Air may have Indoor air or Outdoor air as different Ecosystem Types. In the case of Host-associated samples, ecosystem type can represent Respiratory system, Digestive system, Roots etc." + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "https://gold.jgi.doe.gov/help" + ], + "rank": 11, + "is_a": "gold_path_field", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "Study", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "EcosystemTypeEnum", + "recommended": true + }, + "elev": { + "name": "elev", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + } + }, + "description": "Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit.", + "title": "elevation, meters", + "comments": [ + "All elevations must be reported in meters. Provide the numerical portion only.", + "Please use https://www.advancedconverter.com/map-tools/find-altitude-by-coordinates, if needed, to help estimate the elevation based on latitude and longitude coordinates." + ], + "examples": [ + { + "value": "225" + }, + { + "value": "0" + }, + { + "value": "1250" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "elevation" + ], + "rank": 6, + "is_a": "environment field", + "slot_uri": "MIXS:0000093", + "owner": "Biosample", + "domain_of": [ + "FieldResearchSite", + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "float", + "required": true, + "multivalued": false + }, + "env_broad_scale": { + "name": "env_broad_scale", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "The major environment type(s) where the sample was collected. Recommend subclasses of biome [ENVO:00000428]. Multiple terms can be separated by one or more pipes." + }, + "tooltip": { + "tag": "tooltip", + "value": "The biome or major environmental system where the sample or specimen originated. Choose values from subclasses of the 'biome' class [ENVO:00000428] in the Environment Ontology (ENVO). For host-associated or plant-associated samples, use terms from the UBERON or Plant Ontology to describe the broad anatomical or morphological context" + } + }, + "description": "In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO's biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html", + "title": "broad-scale environmental context", + "notes": [ + "range changed to enumeration late in makefile, so this is modified (but \"sample ID\" anyway)" + ], + "examples": [ + { + "value": "oceanic epipelagic zone biome [ENVO:01000033] for annotating a water sample from the photic zone in middle of the Atlantic Ocean" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "broad-scale environmental context" + ], + "rank": 6, + "is_a": "environment field", + "string_serialization": "{termLabel} {[termID]}", + "slot_uri": "MIXS:0000012", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "string", + "required": true, + "multivalued": false, + "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$" + }, + "env_local_scale": { + "name": "env_local_scale", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "Environmental entities having causal influences upon the entity at time of sampling." + }, + "tooltip": { + "tag": "tooltip", + "value": "The specific environmental entities or features near the sample or specimen that significantly influence its characteristics or composition. These entities are typically smaller in scale than the broad environmental context. Values for this field should be countable, material nouns and must be chosen from subclasses of BFO:0000040 (material entity) that appear in the Environment Ontology (ENVO). For host-associated or plant-associated samples, use terms from the UBERON or Plant Ontology to describe specific anatomical structures or plant parts." + } + }, + "description": "Report the entity or entities which are in the sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. We recommend using EnvO terms which are of smaller spatial grain than your entry for env_broad_scale. Terms, such as anatomical sites, from other OBO Library ontologies which interoperate with EnvO (e.g. UBERON) are accepted in this field. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS.", + "title": "local environmental context", + "notes": [ + "range changed to enumeration late in makefile, so this is modified (but \"sample ID\" anyway)" + ], + "examples": [ + { + "value": "canopy [ENVO:00000047]" + }, + { + "value": "herb and fern layer [ENVO:01000337]" + }, + { + "value": "litter layer [ENVO:01000338]" + }, + { + "value": "understory [01000335]" + }, + { + "value": "shrub layer [ENVO:01000336]" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "local environmental context" + ], + "rank": 7, + "is_a": "environment field", + "string_serialization": "{termLabel} {[termID]}", + "slot_uri": "MIXS:0000013", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "string", + "required": true, + "multivalued": false, + "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$" + }, + "env_medium": { + "name": "env_medium", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "The material displaced by the entity at time of sampling. Recommend subclasses of environmental material [ENVO:00010483]." + }, + "tooltip": { + "tag": "tooltip", + "value": "The predominant environmental material or substrate that directly surrounds or hosts the sample or specimen at the time of sampling. Choose values from subclasses of the 'environmental material' class [ENVO:00010483] in the Environment Ontology (ENVO). Values for this field should be measurable or mass material nouns, representing continuous environmental materials. For host-associated or plant-associated samples, use terms from the UBERON or Plant Ontology to indicate a tissue, organ, or plant structure" + } + }, + "description": "Report the environmental material(s) immediately surrounding the sample or specimen at the time of sampling. We recommend using subclasses of 'environmental material' (http://purl.obolibrary.org/obo/ENVO_00010483). EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS . Terms from other OBO ontologies are permissible as long as they reference mass/volume nouns (e.g. air, water, blood) and not discrete, countable entities (e.g. a tree, a leaf, a table top).", + "title": "environmental medium", + "notes": [ + "range changed to enumeration late in makefile, so this is modified (but \"sample ID\" anyway)" + ], + "examples": [ + { + "value": "soil [ENVO:00001998]" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "environmental medium" + ], + "rank": 8, + "is_a": "environment field", + "string_serialization": "{termLabel} {[termID]}", + "slot_uri": "MIXS:0000014", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "string", + "required": true, + "multivalued": false, + "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$" + }, + "experimental_factor": { + "name": "experimental_factor", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "text or EFO and/or OBI" + } + }, + "description": "Experimental factors are essentially the variable aspects of an experiment design which can be used to describe an experiment, or set of experiments, in an increasingly detailed manner. This field accepts ontology terms from Experimental Factor Ontology (EFO) and/or Ontology for Biomedical Investigations (OBI). For a browser of EFO (v 2.95) terms, please see http://purl.bioontology.org/ontology/EFO; for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI", + "title": "experimental factor", + "examples": [ + { + "value": "time series design [EFO:EFO_0001779]" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "experimental factor" + ], + "rank": 12, + "is_a": "investigation field", + "string_serialization": "{termLabel} {[termID]}|{text}", + "slot_uri": "MIXS:0000008", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false + }, + "extreme_event": { + "name": "extreme_event", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "date, string" + } + }, + "description": "Unusual physical events that may have affected microbial populations", + "title": "history/extreme events", + "examples": [ + { + "value": "1980-05-18, volcanic eruption" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "history/extreme events" + ], + "rank": 13, + "is_a": "core field", + "slot_uri": "MIXS:0000320", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "SedimentInterface", + "SoilInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false + }, + "fire": { + "name": "fire", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "date string" + } + }, + "description": "Historical and/or physical evidence of fire", + "title": "history/fire", + "todos": [ + "is \"to\" acceptable? Is there a better way to request that be written?" + ], + "comments": [ + "Provide the date the fire occurred. If extended burning occurred provide the date range." + ], + "examples": [ + { + "value": "1871-10-10" + }, + { + "value": "1871-10-01 to 1871-10-31" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "history/fire" + ], + "rank": 15, + "is_a": "core field", + "slot_uri": "MIXS:0001086", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "SedimentInterface", + "SoilInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false, + "pattern": "^[12]\\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\\d|3[01]))?)?(\\s+to\\s+[12]\\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\\d|3[01]))?)?)?$" + }, + "flooding": { + "name": "flooding", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "date string" + } + }, + "description": "Historical and/or physical evidence of flooding", + "title": "history/flooding", + "todos": [ + "is \"to\" acceptable? Is there a better way to request that be written?", + "What about if the \"day\" isn't known? Is this ok?" + ], + "comments": [ + "Provide the date the flood occurred. If extended flooding occurred provide the date range." + ], + "examples": [ + { + "value": "1927-04-15" + }, + { + "value": "1927-04 to 1927-05" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "history/flooding" + ], + "rank": 16, + "is_a": "core field", + "slot_uri": "MIXS:0000319", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "SedimentInterface", + "SoilInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false + }, + "gaseous_environment": { + "name": "gaseous_environment", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "gaseous compound name;gaseous compound amount;treatment interval and duration" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Use of conditions with differing gaseous environments; should include the name of gaseous compound, amount administered, treatment duration, interval and total experimental duration; can include multiple gaseous environment regimens", + "title": "gaseous environment", + "todos": [ + "would like to see usage examples for this slot. Requiring micromole/L seems too limiting and doesn't match expected_value value", + "did I do this right? keep the example that's provided and add another? so as to not override" + ], + "examples": [ + { + "value": "CO2; 500ppm above ambient; constant" + }, + { + "value": "nitric oxide;0.5 micromole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "gaseous environment" + ], + "rank": 20, + "is_a": "core field", + "string_serialization": "{text};{float} {unit};{Rn/start_time/end_time/duration}", + "slot_uri": "MIXS:0000558", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "multivalued": false + }, + "geo_loc_name": { + "name": "geo_loc_name", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "country or sea name (INSDC or GAZ): region(GAZ), specific location name" + } + }, + "description": "The geographical origin of the sample as defined by the country or sea name followed by specific region name.", + "title": "geographic location (country and/or sea,region)", + "examples": [ + { + "value": "USA: Maryland, Bethesda" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "geographic location (country and/or sea,region)" + ], + "rank": 4, + "is_a": "environment field", + "string_serialization": "{text}: {text}, {text}", + "slot_uri": "MIXS:0000010", + "owner": "Biosample", + "domain_of": [ + "FieldResearchSite", + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "required": true, + "multivalued": false, + "pattern": "^[^:, ][^:]*: [^:, ][^,]*, [^:, ].*$" + }, + "glucosidase_act": { + "name": "glucosidase_act", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "mol per liter per hour" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Measurement of glucosidase activity", + "title": "glucosidase activity", + "examples": [ + { + "value": "5 mol per liter per hour" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "glucosidase activity" + ], + "rank": 20, + "is_a": "core field", + "slot_uri": "MIXS:0000137", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "humidity_regm": { + "name": "humidity_regm", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "humidity value;treatment interval and duration" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "gram per cubic meter" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Information about treatment involving an exposure to varying degree of humidity; information about treatment involving use of growth hormones; should include amount of humidity administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens", + "title": "humidity regimen", + "examples": [ + { + "value": "25 gram per cubic meter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "humidity regimen" + ], + "rank": 21, + "is_a": "core field", + "string_serialization": "{float} {unit};{Rn/start_time/end_time/duration}", + "slot_uri": "MIXS:0000568", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "multivalued": false + }, + "isotope_exposure": { + "name": "isotope_exposure", + "description": "List isotope exposure or addition applied to your sample.", + "title": "isotope exposure/addition", + "todos": [ + "Can we make the H218O correctly super and subscripted?" + ], + "comments": [ + "This is required when your experimental design includes the use of isotopically labeled compounds" + ], + "examples": [ + { + "value": "13C glucose" + }, + { + "value": "H218O" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "MIXS:0000751" + ], + "rank": 16, + "string_serialization": "{termLabel} {[termID]}; {timestamp}", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WaterInterface", + "SoilMixsInspiredMixin" + ], + "slot_group": "mixs_inspired_section", + "range": "string", + "recommended": true, + "multivalued": false, + "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]; ([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$" + }, + "lat_lon": { + "name": "lat_lon", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "decimal degrees, limit to 8 decimal points" + } + }, + "description": "The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system", + "title": "geographic location (latitude and longitude)", + "notes": [ + "This is currently a required field but it's not clear if this should be required for human hosts" + ], + "examples": [ + { + "value": "50.586825 6.408977" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "geographic location (latitude and longitude)" + ], + "rank": 5, + "is_a": "environment field", + "string_serialization": "{lat lon}", + "slot_uri": "MIXS:0000009", + "owner": "Biosample", + "domain_of": [ + "FieldResearchSite", + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "required": true, + "multivalued": false, + "pattern": "^[-+]?([1-8]?\\d(\\.\\d{1,8})?|90(\\.0{1,8})?)\\s[-+]?(180(\\.0{1,8})?|((1[0-7]\\d)|([1-9]?\\d))(\\.\\d{1,8})?)$" + }, + "light_regm": { + "name": "light_regm", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "exposure type;light intensity;light quality" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "lux; micrometer, nanometer, angstrom" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Information about treatment(s) involving exposure to light, including both light intensity and quality.", + "title": "light regimen", + "examples": [ + { + "value": "incandescant light;10 lux;450 nanometer" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "light regimen" + ], + "rank": 24, + "is_a": "core field", + "string_serialization": "{text};{float} {unit};{float} {unit}", + "slot_uri": "MIXS:0000569", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "multivalued": false, + "pattern": "^\\S+.*\\S+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? \\S+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? \\S+$" + }, + "magnesium": { + "name": "magnesium", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "mole per liter, milligram per liter, parts per million, micromole per kilogram" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of magnesium in the sample", + "title": "magnesium", + "examples": [ + { + "value": "52.8 micromole per kilogram" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "magnesium" + ], + "rank": 21, + "is_a": "core field", + "slot_uri": "MIXS:0000431", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "mean_frict_vel": { + "name": "mean_frict_vel", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "meter per second" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Measurement of mean friction velocity", + "title": "mean friction velocity", + "examples": [ + { + "value": "0.5 meter per second" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "mean friction velocity" + ], + "rank": 22, + "is_a": "core field", + "slot_uri": "MIXS:0000498", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "mean_peak_frict_vel": { + "name": "mean_peak_frict_vel", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "meter per second" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Measurement of mean peak friction velocity", + "title": "mean peak friction velocity", + "examples": [ + { + "value": "1 meter per second" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "mean peak friction velocity" + ], + "rank": 23, + "is_a": "core field", + "slot_uri": "MIXS:0000502", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "methane": { + "name": "methane", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per liter, parts per billion, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Methane (gas) amount or concentration at the time of sampling", + "title": "methane", + "examples": [ + { + "value": "1800 parts per billion" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "methane" + ], + "rank": 24, + "is_a": "core field", + "slot_uri": "MIXS:0000101", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "SedimentInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "micro_biomass_c_meth": { + "name": "micro_biomass_c_meth", + "description": "Reference or method used in determining microbial biomass carbon", + "title": "microbial biomass carbon method", + "todos": [ + "How should we separate values? | or ;? lets be consistent" + ], + "comments": [ + "required if \"microbial_biomass_c\" is provided" + ], + "examples": [ + { + "value": "https://doi.org/10.1016/0038-0717(87)90052-6" + }, + { + "value": "https://doi.org/10.1016/0038-0717(87)90052-6 | https://www.sciencedirect.com/science/article/abs/pii/0038071787900526" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "MIXS:0000339" + ], + "rank": 1004, + "string_serialization": "{PMID}|{DOI}|{URL}", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "SedimentInterface", + "SoilInterface", + "SoilMixsInspiredMixin" + ], + "slot_group": "mixs_inspired_section", + "range": "string", + "recommended": true, + "multivalued": false + }, + "micro_biomass_meth": { + "name": "micro_biomass_meth", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "PMID,DOI or url" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Reference or method used in determining microbial biomass", + "title": "microbial biomass method", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "microbial biomass method" + ], + "rank": 43, + "is_a": "core field", + "string_serialization": "{PMID}|{DOI}|{URL}", + "slot_uri": "MIXS:0000339", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "SedimentInterface", + "SoilInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false + }, + "micro_biomass_n_meth": { + "name": "micro_biomass_n_meth", + "description": "Reference or method used in determining microbial biomass nitrogen", + "title": "microbial biomass nitrogen method", + "comments": [ + "required if \"microbial_biomass_n\" is provided" + ], + "examples": [ + { + "value": "https://doi.org/10.1016/0038-0717(87)90052-6" + }, + { + "value": "https://doi.org/10.1016/0038-0717(87)90052-6 | https://www.sciencedirect.com/science/article/abs/pii/0038071787900526" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "MIXS:0000339" + ], + "rank": 1004, + "string_serialization": "{PMID}|{DOI}|{URL}", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "SedimentInterface", + "SoilInterface", + "SoilMixsInspiredMixin" + ], + "slot_group": "mixs_inspired_section", + "range": "string", + "multivalued": false + }, + "microbial_biomass": { + "name": "microbial_biomass", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "ton, kilogram, gram per kilogram soil" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The part of the organic matter in the soil that constitutes living microorganisms smaller than 5-10 micrometer. If you keep this, you would need to have correction factors used for conversion to the final units", + "title": "microbial biomass", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "microbial biomass" + ], + "rank": 42, + "is_a": "core field", + "slot_uri": "MIXS:0000650", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "SedimentInterface", + "SoilInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "microbial_biomass_c": { + "name": "microbial_biomass_c", + "description": "The part of the organic matter in the soil that constitutes living microorganisms smaller than 5-10 micrometer.", + "title": "microbial biomass carbon", + "comments": [ + "If you provide this, correction factors used for conversion to the final units and method are required" + ], + "examples": [ + { + "value": "0.05 ug C/g dry soil" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "MIXS:0000650" + ], + "rank": 1004, + "string_serialization": "{float} {unit}", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "SedimentInterface", + "SoilInterface", + "SoilMixsInspiredMixin" + ], + "slot_group": "mixs_inspired_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? \\S+$" + }, + "microbial_biomass_n": { + "name": "microbial_biomass_n", + "description": "The part of the organic matter in the soil that constitutes living microorganisms smaller than 5-10 micrometer.", + "title": "microbial biomass nitrogen", + "comments": [ + "If you provide this, correction factors used for conversion to the final units and method are required" + ], + "examples": [ + { + "value": "0.05 ug N/g dry soil" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "MIXS:0000650" + ], + "rank": 1004, + "string_serialization": "{float} {unit}", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "SedimentInterface", + "SoilInterface", + "SoilMixsInspiredMixin" + ], + "slot_group": "mixs_inspired_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? \\S+$" + }, + "misc_param": { + "name": "misc_param", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "parameter name;measurement value" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Any other measurement performed or parameter collected, that is not listed here", + "title": "miscellaneous parameter", + "examples": [ + { + "value": "Bicarbonate ion concentration;2075 micromole per kilogram" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "miscellaneous parameter" + ], + "rank": 23, + "is_a": "core field", + "string_serialization": "{text};{float} {unit}", + "slot_uri": "MIXS:0000752", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false, + "pattern": "^([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+\\|)*([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+)$" + }, + "n_alkanes": { + "name": "n_alkanes", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "n-alkane name;measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Concentration of n-alkanes; can include multiple n-alkanes", + "title": "n-alkanes", + "examples": [ + { + "value": "n-hexadecane;100 milligram per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "n-alkanes" + ], + "rank": 25, + "is_a": "core field", + "string_serialization": "{text};{float} {unit}", + "slot_uri": "MIXS:0000503", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+\\|)*([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+)$" + }, + "nitrate": { + "name": "nitrate", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per liter, milligram per liter, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of nitrate in the sample", + "title": "nitrate", + "examples": [ + { + "value": "65 micromole per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "nitrate" + ], + "rank": 26, + "is_a": "core field", + "slot_uri": "MIXS:0000425", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "nitrite": { + "name": "nitrite", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per liter, milligram per liter, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of nitrite in the sample", + "title": "nitrite", + "examples": [ + { + "value": "0.5 micromole per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "nitrite" + ], + "rank": 27, + "is_a": "core field", + "slot_uri": "MIXS:0000426", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "nitro": { + "name": 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+ } + }, + "description": "Concentration of organic matter", + "title": "organic matter", + "examples": [ + { + "value": "1.75 milligram per cubic meter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "organic matter" + ], + "rank": 45, + "is_a": "core field", + "slot_uri": "MIXS:0000204", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "MiscEnvsInterface", + "SedimentInterface", + "SoilInterface", + "WaterInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "org_nitro": { + "name": "org_nitro", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "microgram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of organic nitrogen", + "title": "organic nitrogen", + 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can include multiple phaeopigments", + "title": "phaeopigments", + "examples": [ + { + "value": "2.5 milligram per cubic meter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "phaeopigments" + ], + "rank": 35, + "is_a": "core field", + "string_serialization": "{text};{float} {unit}", + "slot_uri": "MIXS:0000180", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? 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[^;\\t\\r\\x0A]+)$" + }, + "porosity": { + "name": "porosity", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value or range" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "percentage" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Porosity of deposited sediment is volume of voids divided by the total volume of sample", + "title": "porosity", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "porosity" + ], + "rank": 37, + "is_a": "core field", + "string_serialization": "{float} - {float} {unit}", + "slot_uri": "MIXS:0000211", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "HcrCoresInterface", + "SedimentInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "potassium": { + "name": "potassium", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milligram per liter, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of potassium in the sample", + "title": "potassium", + "examples": [ + { + "value": "463 milligram per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "potassium" + ], + "rank": 38, + "is_a": "core field", + "slot_uri": "MIXS:0000430", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "pressure": { + "name": "pressure", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "atmosphere" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Pressure to which the sample is subject to, in atmospheres", + "title": "pressure", + "examples": [ + { + "value": "50 atmosphere" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "pressure" + ], + "rank": 39, + "is_a": "core field", + "slot_uri": "MIXS:0000412", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "redox_potential": { + "name": "redox_potential", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "millivolt" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential", + "title": "redox potential", + "examples": [ + { + "value": "300 millivolt" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "redox potential" + ], + "rank": 40, + "is_a": "core field", + "slot_uri": "MIXS:0000182", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "salinity": { + "name": "salinity", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "practical salinity unit, percentage" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The total concentration of all dissolved salts in a liquid or solid sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater.", + "title": "salinity", + "examples": [ + { + "value": "25 practical salinity unit" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "salinity" + ], + "rank": 54, + "is_a": "core field", + "slot_uri": "MIXS:0000183", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "salinity_meth": { + "name": "salinity_meth", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "PMID,DOI or url" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Reference or method used in determining salinity", + "title": "salinity method", + "examples": [ + { + "value": "https://doi.org/10.1007/978-1-61779-986-0_28" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "salinity method" + ], + "rank": 55, + "is_a": "core field", + "string_serialization": "{PMID}|{DOI}|{URL}", + "slot_uri": "MIXS:0000341", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WaterInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false + }, + "samp_collec_device": { + "name": "samp_collec_device", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "device name" + } + }, + "description": "The device used to collect an environmental sample. This field accepts terms listed under environmental sampling device (http://purl.obolibrary.org/obo/ENVO). This field also accepts terms listed under specimen collection device (http://purl.obolibrary.org/obo/GENEPIO_0002094).", + "title": "sample collection device", + "comments": [ + "Report dimensions and details when applicable" + ], + "examples": [ + { + "value": "swab, biopsy, niskin bottle, push core, drag swab [GENEPIO:0002713]" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sample collection device" + ], + "rank": 14, + "is_a": "nucleic acid sequence source field", + "string_serialization": "{termLabel} {[termID]}|{text}", + "slot_uri": "MIXS:0000002", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "recommended": true, + "multivalued": false + }, + "samp_collec_method": { + "name": "samp_collec_method", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "PMID,DOI,url , or text" + } + }, + "description": "The method employed for collecting the sample.", + "title": "sample collection method", + "comments": [ + "This can be a citation or description" + ], + "examples": [ + { + "value": "swabbing" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sample collection method" + ], + "rank": 15, + "is_a": "nucleic acid sequence source field", + "string_serialization": "{PMID}|{DOI}|{URL}|{text}", + "slot_uri": "MIXS:0001225", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "multivalued": false + }, + "samp_mat_process": { + "name": "samp_mat_process", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "text" + } + }, + "description": "A brief description of any processing applied to the sample during or after retrieving the sample from environment, or a link to the relevant protocol(s) performed.", + "title": "sample material processing", + "examples": [ + { + "value": "filtering of seawater" + }, + { + "value": "storing samples in ethanol" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sample material processing" + ], + "rank": 12, + "is_a": "nucleic acid sequence source field", + "string_serialization": "{text}", + "slot_uri": "MIXS:0000016", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "multivalued": false + }, + "samp_size": { + "name": "samp_size", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "millliter, gram, milligram, liter" + } + }, + "description": "The total amount or size (volume (ml), mass (g) or area (m2) ) of sample collected.", + "title": "amount or size of sample collected", + "comments": [ + "This refers to the TOTAL amount of sample collected from the experiment. NOT the amount sent to each institution or collected for a specific analysis." + ], + "examples": [ + { + "value": "5 grams" + }, + { + "value": "10 mL" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "amount or size of sample collected" + ], + "rank": 18, + "is_a": "nucleic acid sequence source field", + "string_serialization": "{float} {unit}", + "slot_uri": "MIXS:0000001", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? \\S+$" + }, + "samp_store_dur": { + "name": "samp_store_dur", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "duration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Duration for which the sample was stored", + "title": "sample storage duration", + "examples": [ + { + "value": "P1Y6M" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sample storage duration" + ], + "rank": 353, + "is_a": "core field", + "string_serialization": "{duration}", + "slot_uri": "MIXS:0000116", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "samp_store_loc": { + "name": "samp_store_loc", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "location name" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Location at which sample was stored, usually name of a specific freezer/room", + "title": "sample storage location", + "examples": [ + { + "value": "Freezer no:5" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sample storage location" + ], + "rank": 41, + "is_a": "core field", + "string_serialization": "{text}", + "slot_uri": "MIXS:0000755", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "samp_store_temp": { + "name": "samp_store_temp", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "degree Celsius" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Temperature at which the sample was stored (degrees are assumed)", + "title": "sample storage temperature", + "examples": [ + { + "value": "-80 Celsius" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sample storage temperature" + ], + "rank": 7, + "is_a": "core field", + "slot_uri": "MIXS:0000110", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "required": true, + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "sample_link": { + "name": "sample_link", + "description": "A unique identifier to assign parent-child, subsample, or sibling samples. This is relevant when a sample or other material was used to generate the new sample.", + "title": "sample linkage", + "notes": [ + "also tempted to include SampIdNewTermsMixin but if len(slot_usage.keys()) > 1 and \"placeholder\" in slot_usage.keys():AttributeError: 'list' object has no attribute 'keys'" + ], + "comments": [ + "This field allows multiple entries separated by ; (Examples: Soil collected from the field will link with the soil used in an incubation. The soil a plant was grown in links to the plant sample. An original culture sample was transferred to a new vial and generated a new sample)" + ], + "examples": [ + { + "value": "IGSN:DSJ0284" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "rank": 5, + "string_serialization": "{text}:{text}", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface", + "SampIdNewTermsMixin" + ], + "slot_group": "sample_id_section", + "range": "string", + "recommended": true, + "multivalued": false, + "pattern": "[^\\:\\n\\r]+\\:[^\\:\\n\\r]+" + }, + "sediment_type": { + "name": "sediment_type", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Information about the sediment type based on major constituents", + "title": "sediment type", + "examples": [ + { + "value": "biogenous" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sediment type" + ], + "rank": 42, + "is_a": "core field", + "slot_uri": "MIXS:0001078", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "SedimentInterface" + ], + "slot_group": "mixs_core_section", + "range": "sediment_type_enum", + "multivalued": false + }, + "sieving": { + "name": "sieving", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "design name and/or size;amount" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Collection design of pooled samples and/or sieve size and amount of sample sieved", + "title": "composite design/sieving", + "todos": [ + "check validation and examples" + ], + "comments": [ + "Describe how samples were composited or sieved.", + "Use 'sample link' to indicate which samples were combined." + ], + "examples": [ + { + "value": "combined 2 cores | 4mm sieved" + }, + { + "value": "4 mm sieved and homogenized" + }, + { + "value": "50 g | 5 cores | 2 mm sieved" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "composite design/sieving" + ], + "rank": 8, + "is_a": "core field", + "string_serialization": "{{text}|{float} {unit}};{float} {unit}", + "slot_uri": "MIXS:0000322", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "SedimentInterface", + "SoilInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "multivalued": false + }, + "silicate": { + "name": "silicate", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of silicate", + "title": "silicate", + "examples": [ + { + "value": "0.05 micromole per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "silicate" + ], + "rank": 43, + "is_a": "core field", + "slot_uri": "MIXS:0000184", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "size_frac": { + "name": "size_frac", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "filter size value range" + } + }, + "description": "Filtering pore size used in sample preparation", + "title": "size fraction selected", + "examples": [ + { + "value": "0-0.22 micrometer" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "size fraction selected" + ], + "rank": 285, + "is_a": "nucleic acid sequence source field", + "string_serialization": "{float}-{float} {unit}", + "slot_uri": "MIXS:0000017", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "sodium": { + "name": "sodium", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milligram per liter, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Sodium concentration in the sample", + "title": "sodium", + "examples": [ + { + "value": "10.5 milligram per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sodium" + ], + "rank": 363, + "is_a": "core field", + "slot_uri": "MIXS:0000428", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "specific_ecosystem": { + "name": "specific_ecosystem", + "description": "Specific ecosystems represent specific features of the environment like aphotic zone in an ocean or gastric mucosa within a host digestive system. Specific ecosystem is in position 5/5 in a GOLD path.", + "comments": [ + "Specific ecosystems help to define samples based on very specific characteristics of an environment under the five-level classification system." + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "https://gold.jgi.doe.gov/help" + ], + "rank": 13, + "is_a": "gold_path_field", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "Study", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "SpecificEcosystemEnum", + "recommended": true + }, + "start_date_inc": { + "name": "start_date_inc", + "description": "Date the incubation was started. Only relevant for incubation samples.", + "title": "incubation start date", + "notes": [ + "MIxS collection_date accepts (truncated) ISO8601. DH taking arbitrary precision date only" + ], + "comments": [ + "Date should be formatted as YYYY(-MM(-DD)). Ie, 2021-04-15, 2021-04 and 2021 are all acceptable." + ], + "examples": [ + { + "value": "2021-04-15, 2021-04 and 2021 are all acceptable." + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "MIXS:0000011" + ], + "rank": 4, + "string_serialization": "{date, arbitrary precision}", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WaterInterface", + "SoilMixsInspiredMixin" + ], + "slot_group": "mixs_inspired_section", + "range": "string", + "recommended": true, + "multivalued": false, + "pattern": "^[12]\\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\\d|3[01]))?)?$" + }, + "sulfate": { + "name": "sulfate", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per liter, milligram per liter, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of sulfate in the sample", + "title": "sulfate", + "examples": [ + { + "value": "5 micromole per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sulfate" + ], + "rank": 44, + "is_a": "core field", + "slot_uri": "MIXS:0000423", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "sulfide": { + "name": "sulfide", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per liter, milligram per liter, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of sulfide in the sample", + "title": "sulfide", + "examples": [ + { + "value": "2 micromole per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sulfide" + ], + "rank": 371, + "is_a": "core field", + "slot_uri": "MIXS:0000424", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "temp": { + "name": "temp", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "degree Celsius" + } + }, + "description": "Temperature of the sample at the time of sampling.", + "title": "temperature", + "examples": [ + { + "value": "25 degree Celsius" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "temperature" + ], + "rank": 37, + "is_a": "environment field", + "slot_uri": "MIXS:0000113", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "tidal_stage": { + "name": "tidal_stage", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Stage of tide", + "title": "tidal stage", + "examples": [ + { + "value": "high tide" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "tidal stage" + ], + "rank": 45, + "is_a": "core field", + "slot_uri": "MIXS:0000750", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "tidal_stage_enum", + "multivalued": false + }, + "tot_carb": { + "name": "tot_carb", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "microgram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Total carbon content", + "title": "total carbon", + "todos": [ + "is this inorganic and organic? both? could use some clarification.", + "ug/L doesn't seem like the right units. Should check this slots usage in databases and re-evaluate. I couldn't find any references that provided this data in this format", + "is this inorganic and organic? both? could use some clarification.", + "ug/L doesn't seem like the right units. Should check this slots usage in databases and re-evaluate. I couldn't find any references that provided this data in this format" + ], + "examples": [ + { + "value": "1 ug/L" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "total carbon" + ], + "rank": 47, + "is_a": "core field", + "slot_uri": "MIXS:0000525", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "SedimentInterface", + "SoilInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "tot_depth_water_col": { + "name": "tot_depth_water_col", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "meter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Measurement of total depth of water column", + "title": "total depth of water column", + "examples": [ + { + "value": "500 meter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "total depth of water column" + ], + "rank": 46, + "is_a": "core field", + "slot_uri": "MIXS:0000634", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "tot_nitro_cont_meth": { + "name": "tot_nitro_cont_meth", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "PMID,DOI or url" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Reference or method used in determining the total nitrogen", + "title": "total nitrogen content method", + "examples": [ + { + "value": "https://doi.org/10.2134/agronmonogr9.2.c32" + }, + { + "value": "https://acsess.onlinelibrary.wiley.com/doi/full/10.2136/sssaj2009.0389?casa_token=bm0pYIUdNMgAAAAA%3AOWVRR0STHaOe-afTcTdxn5m1hM8n2ltM0wY-b1iYpYdD9dhwppk5j3LvC2IO5yhOIvyLVeQz4NZRCZo" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "total nitrogen content method" + ], + "rank": 49, + "is_a": "core field", + "string_serialization": "{PMID}|{DOI}|{URL}", + "slot_uri": "MIXS:0000338", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "SedimentInterface", + "SoilInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false + }, + "tot_nitro_content": { + "name": "tot_nitro_content", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "microgram per liter, micromole per liter, milligram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Total nitrogen content of the sample", + "title": "total nitrogen content", + "examples": [ + { + "value": "5 mg N/ L" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "total nitrogen content" + ], + "rank": 48, + "is_a": "core field", + "slot_uri": "MIXS:0000530", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "SedimentInterface", + "SoilInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "tot_org_c_meth": { + "name": "tot_org_c_meth", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "PMID,DOI or url" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Reference or method used in determining total organic carbon", + "title": "total organic carbon method", + "examples": [ + { + "value": "https://doi.org/10.1080/07352680902776556" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "total organic carbon method" + ], + "rank": 51, + "is_a": "core field", + "string_serialization": "{PMID}|{DOI}|{URL}", + "slot_uri": "MIXS:0000337", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "SedimentInterface", + "SoilInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false + }, + "tot_org_carb": { + "name": "tot_org_carb", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "gram Carbon per kilogram sample material" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content", + "title": "total organic carbon", + "todos": [ + "check description. How are they different?", + "check description. How are they different?" + ], + "examples": [ + { + "value": "5 mg N/ L" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "total organic carbon" + ], + "rank": 50, + "is_a": "core field", + "slot_uri": "MIXS:0000533", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "SedimentInterface", + "SoilInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "turbidity": { + "name": "turbidity", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "formazin turbidity unit, formazin nephelometric units" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Measure of the amount of cloudiness or haziness in water caused by individual particles", + "title": "turbidity", + "examples": [ + { + "value": "0.3 nephelometric turbidity units" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "turbidity" + ], + "rank": 47, + "is_a": "core field", + "slot_uri": "MIXS:0000191", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "water_cont_soil_meth": { + "name": "water_cont_soil_meth", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "PMID,DOI or url" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Reference or method used in determining the water content of soil", + "title": "water content method", + "todos": [ + "Why is it soil water content method in the name but not the title? Is this slot used in other samples?", + "Soil water content can be measure MANY ways and often, multiple ways are used in one experiment (gravimetric water content and water holding capacity and water filled pore space, to name a few).", + "Should this be multi valued? How to we manage and validate this?" + ], + "comments": [ + "Required if providing water content" + ], + "examples": [ + { + "value": "J. Nat. Prod. Plant Resour., 2012, 2 (4):500-503" + }, + { + "value": "https://dec.alaska.gov/applications/spar/webcalc/definitions.htm" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "water content method" + ], + "rank": 40, + "is_a": "core field", + "string_serialization": "{PMID}|{DOI}|{URL}", + "slot_uri": "MIXS:0000323", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "SedimentInterface", + "SoilInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false + }, + "water_content": { + "name": "water_content", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "string" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "gram per gram or cubic centimeter per cubic centimeter" + } + }, + "description": "Water content measurement", + "title": "water content", + "todos": [ + "value in preferred unit is too limiting. need to change this", + "check and correct validation so examples are accepted", + "how to manage multiple water content methods?" + ], + "examples": [ + { + "value": "0.75 g water/g dry soil" + }, + { + "value": "75% water holding capacity" + }, + { + "value": "1.1 g fresh weight/ dry weight" + }, + { + "value": "10% water filled pore space" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "water content" + ], + "rank": 39, + "is_a": "core field", + "string_serialization": "{float or pct} {unit}", + "slot_uri": "MIXS:0000185", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "SedimentInterface", + "SoilInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)?%? \\S.+$" + }, + "watering_regm": { + "name": "watering_regm", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value;treatment interval and duration" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milliliter, liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Information about treatment involving an exposure to watering frequencies, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens", + "title": "watering regimen", + "examples": [ + { + "value": "1 liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" + }, + { + "value": "75% water holding capacity; constant" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "watering regimen" + ], + "rank": 25, + "is_a": "core field", + "string_serialization": "{float} {unit};{Rn/start_time/end_time/duration}", + "slot_uri": "MIXS:0000591", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "multivalued": false + }, + "horizon_meth": { + "name": "horizon_meth", + "title": "horizon method" + } + }, + "attributes": { + "air_temp_regm": { + "name": "air_temp_regm", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "temperature value;treatment interval and duration" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "meter" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Information about treatment involving an exposure to varying temperatures; should include the temperature, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include different temperature regimens", + "title": "air temperature regimen", + "examples": [ + { + "value": "25 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "air temperature regimen" + ], + "rank": 16, + "is_a": "core field", + "string_serialization": "{float} {unit};{Rn/start_time/end_time/duration}", + "slot_uri": "MIXS:0000551", + "alias": "air_temp_regm", + "owner": "SedimentInterface", + "domain_of": [ + "Biosample", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "multivalued": false + }, + "alkalinity": { + "name": "alkalinity", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milliequivalent per liter, milligram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate", + "title": "alkalinity", + "examples": [ + { + "value": "50 milligram per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "alkalinity" + ], + "rank": 1, + "is_a": "core field", + "slot_uri": "MIXS:0000421", + "alias": "alkalinity", + "owner": "SedimentInterface", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "alkalinity_method": { + "name": "alkalinity_method", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "description of method" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Method used for alkalinity measurement", + "title": "alkalinity method", + "examples": [ + { + "value": "titration" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "alkalinity method" + ], + "rank": 218, + "is_a": "core field", + "string_serialization": "{text}", + "slot_uri": "MIXS:0000298", + "alias": "alkalinity_method", + "owner": "SedimentInterface", + "domain_of": [ + "Biosample", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "alkyl_diethers": { + "name": "alkyl_diethers", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "mole per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of alkyl diethers", + "title": "alkyl diethers", + "examples": [ + { + "value": "0.005 mole per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "alkyl diethers" + ], + "rank": 2, + "is_a": "core field", + "slot_uri": "MIXS:0000490", + "alias": "alkyl_diethers", + "owner": "SedimentInterface", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "aminopept_act": { + "name": "aminopept_act", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "mole per liter per hour" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Measurement of aminopeptidase activity", + "title": "aminopeptidase activity", + "examples": [ + { + "value": "0.269 mole per liter per hour" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "aminopeptidase activity" + ], + "rank": 3, + "is_a": "core field", + "slot_uri": "MIXS:0000172", + "alias": "aminopept_act", + "owner": "SedimentInterface", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "ammonium": { + "name": "ammonium", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per liter, milligram per liter, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of ammonium in the sample", + "title": "ammonium", + "examples": [ + { + "value": "1.5 milligram per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "ammonium" + ], + "rank": 4, + "is_a": "core field", + "slot_uri": "MIXS:0000427", + "alias": "ammonium", + "owner": "SedimentInterface", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "bacteria_carb_prod": { + "name": "bacteria_carb_prod", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "nanogram per hour" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Measurement of bacterial carbon production", + "title": "bacterial carbon production", + "examples": [ + { + "value": "2.53 microgram per liter per hour" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "bacterial carbon production" + ], + "rank": 5, + "is_a": "core field", + "slot_uri": "MIXS:0000173", + "alias": "bacteria_carb_prod", + "owner": "SedimentInterface", + "domain_of": [ + "Biosample", + 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Only relevant for incubation samples.", + "title": "incubation collection date", + "notes": [ + "MIxS collection_date accepts (truncated) ISO8601. DH taking arbitrary precision date only" + ], + "comments": [ + "Date should be formatted as YYYY(-MM(-DD)). 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DH taking seconds optional time only" + ], + "comments": [ + "Time should be entered as HH:MM(:SS) in GMT. See here for a converter: https://www.worldtimebuddy.com/pst-to-gmt-converter" + ], + "examples": [ + { + "value": "13:33 or 13:33:55" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "MIXS:0000011" + ], + "rank": 1, + "string_serialization": "{time, seconds optional}", + "alias": "collection_time", + "owner": "SedimentInterface", + "domain_of": [ + "Biosample", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WaterInterface", + "SoilMixsInspiredMixin" + ], + "slot_group": "mixs_inspired_section", + "range": "string", + "recommended": true, + "multivalued": false, + "pattern": "^([01]?\\d|2[0-3]|24(?=:00?:00?$)):([0-5]\\d)(:([0-5]\\d))?$" + }, + "density": { + "name": "density", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "gram per cubic meter, gram per cubic centimeter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Density of the sample, which is its mass per unit volume (aka volumetric mass density)", + "title": "density", + "examples": [ + { + "value": "1000 kilogram per cubic meter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "density" + ], + "rank": 12, + "is_a": "core field", + "slot_uri": "MIXS:0000435", + "alias": "density", + "owner": "SedimentInterface", + "domain_of": [ + "Biosample", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "depth": { + "name": "depth", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + } + }, + "description": "The vertical distance below local surface, e.g. for sediment or soil samples depth is measured from sediment or soil surface, respectively. 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Provide the numerical portion only." + ], + "examples": [ + { + "value": "0 - 0.1" + }, + { + "value": "1" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "depth" + ], + "rank": 9, + "is_a": "environment field", + "string_serialization": "{float}-{float}", + "slot_uri": "MIXS:0000018", + "alias": "depth", + "owner": "SedimentInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "required": true, + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)?\\s*-\\s*[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)?$" + }, + "diether_lipids": { + "name": "diether_lipids", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "diether lipid name;measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "nanogram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Concentration of diether lipids; can include multiple types of diether lipids", + "title": "diether lipids", + "examples": [ + { + "value": "0.2 nanogram per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "diether lipids" + ], + "rank": 13, + "is_a": "core field", + "string_serialization": "{text};{float} {unit}", + "slot_uri": "MIXS:0000178", + "alias": "diether_lipids", + "owner": "SedimentInterface", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+\\|)*([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+)$" + }, + "diss_carb_dioxide": { + "name": "diss_carb_dioxide", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per liter, milligram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample", + "title": "dissolved carbon dioxide", + "examples": [ + { + "value": "5 milligram per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "dissolved carbon dioxide" + ], + "rank": 14, + "is_a": "core field", + "slot_uri": "MIXS:0000436", + "alias": "diss_carb_dioxide", + "owner": "SedimentInterface", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "diss_hydrogen": { + "name": "diss_hydrogen", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of dissolved hydrogen", + "title": "dissolved hydrogen", + "examples": [ + { + "value": "0.3 micromole per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "dissolved hydrogen" + ], + "rank": 15, + "is_a": "core field", + "slot_uri": "MIXS:0000179", + "alias": "diss_hydrogen", + "owner": "SedimentInterface", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "diss_inorg_carb": { + "name": "diss_inorg_carb", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "microgram per liter, milligram per liter, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter", + "title": "dissolved inorganic carbon", + "examples": [ + { + "value": "2059 micromole per kilogram" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "dissolved inorganic carbon" + ], + "rank": 16, + "is_a": "core field", + "slot_uri": "MIXS:0000434", + "alias": "diss_inorg_carb", + "owner": "SedimentInterface", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "diss_org_carb": { + "name": "diss_org_carb", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per liter, milligram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid", + "title": "dissolved organic carbon", + "examples": [ + { + "value": "197 micromole per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "dissolved organic carbon" + ], + "rank": 17, + "is_a": "core field", + "slot_uri": "MIXS:0000433", + "alias": "diss_org_carb", + "owner": "SedimentInterface", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "diss_org_nitro": { + "name": "diss_org_nitro", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "microgram per liter, milligram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2", + "title": "dissolved organic nitrogen", + "examples": [ + { + "value": "0.05 micromole per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "dissolved organic nitrogen" + ], + "rank": 18, + "is_a": "core field", + "slot_uri": "MIXS:0000162", + "alias": "diss_org_nitro", + "owner": "SedimentInterface", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "diss_oxygen": { + "name": "diss_oxygen", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per kilogram, milligram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of dissolved oxygen", + "title": "dissolved oxygen", + "examples": [ + { + "value": "175 micromole per kilogram" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "dissolved oxygen" + ], + "rank": 19, + "is_a": "core field", + "slot_uri": "MIXS:0000119", + "alias": "diss_oxygen", + "owner": "SedimentInterface", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "ecosystem": { + "name": "ecosystem", + "description": "An ecosystem is a combination of a physical environment (abiotic factors) and all the organisms (biotic factors) that interact with this environment. Ecosystem is in position 1/5 in a GOLD path.", + "comments": [ + "The abiotic factors play a profound role on the type and composition of organisms in a given environment. The GOLD Ecosystem at the top of the five-level classification system is aimed at capturing the broader environment from which an organism or environmental sample is collected. The three broad groups under Ecosystem are Environmental, Host-associated, and Engineered. They represent samples collected from a natural environment or from another organism or from engineered environments like bioreactors respectively." + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "https://gold.jgi.doe.gov/help" + ], + "rank": 9, + "is_a": "gold_path_field", + "alias": "ecosystem", + "owner": "SedimentInterface", + "domain_of": [ + "Biosample", + "Study", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "EcosystemEnum", + "recommended": true + }, + "ecosystem_category": { + "name": "ecosystem_category", + "description": "Ecosystem categories represent divisions within the ecosystem based on specific characteristics of the environment from where an organism or sample is isolated. Ecosystem category is in position 2/5 in a GOLD path.", + "comments": [ + "The Environmental ecosystem (for example) is divided into Air, Aquatic and Terrestrial. Ecosystem categories for Host-associated samples can be individual hosts or phyla and for engineered samples it may be manipulated environments like bioreactors, solid waste etc." + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "https://gold.jgi.doe.gov/help" + ], + "rank": 10, + "is_a": "gold_path_field", + "alias": "ecosystem_category", + "owner": "SedimentInterface", + "domain_of": [ + "Biosample", + "Study", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "EcosystemCategoryEnum", + "recommended": true + }, + "ecosystem_subtype": { + "name": "ecosystem_subtype", + "description": "Ecosystem subtypes represent further subdivision of Ecosystem types into more distinct subtypes. Ecosystem subtype is in position 4/5 in a GOLD path.", + "comments": [ + "Ecosystem Type Marine (Environmental -> Aquatic -> Marine) is further divided (for example) into Intertidal zone, Coastal, Pelagic, Intertidal zone etc. in the Ecosystem subtype category." + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "https://gold.jgi.doe.gov/help" + ], + "rank": 12, + "is_a": "gold_path_field", + "alias": "ecosystem_subtype", + "owner": "SedimentInterface", + "domain_of": [ + "Biosample", + "Study", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "EcosystemSubtypeEnum", + "recommended": true + }, + "ecosystem_type": { + "name": "ecosystem_type", + "description": "Ecosystem types represent things having common characteristics within the Ecosystem Category. These common characteristics based grouping is still broad but specific to the characteristics of a given environment. Ecosystem type is in position 3/5 in a GOLD path.", + "comments": [ + "The Aquatic ecosystem category (for example) may have ecosystem types like Marine or Thermal springs etc. Ecosystem category Air may have Indoor air or Outdoor air as different Ecosystem Types. In the case of Host-associated samples, ecosystem type can represent Respiratory system, Digestive system, Roots etc." + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "https://gold.jgi.doe.gov/help" + ], + "rank": 11, + "is_a": "gold_path_field", + "alias": "ecosystem_type", + "owner": "SedimentInterface", + "domain_of": [ + "Biosample", + "Study", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "EcosystemTypeEnum", + "recommended": true + }, + "elev": { + "name": "elev", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + } + }, + "description": "Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit.", + "title": "elevation, meters", + "comments": [ + "All elevations must be reported in meters. Provide the numerical portion only.", + "Please use https://www.advancedconverter.com/map-tools/find-altitude-by-coordinates, if needed, to help estimate the elevation based on latitude and longitude coordinates." + ], + "examples": [ + { + "value": "225" + }, + { + "value": "0" + }, + { + "value": "1250" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "elevation" + ], + "rank": 6, + "is_a": "environment field", + "slot_uri": "MIXS:0000093", + "alias": "elev", + "owner": "SedimentInterface", + "domain_of": [ + "FieldResearchSite", + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "float", + "required": true, + "multivalued": false + }, + "env_broad_scale": { + "name": "env_broad_scale", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "The major environment type(s) where the sample was collected. Recommend subclasses of biome [ENVO:00000428]. Multiple terms can be separated by one or more pipes." + }, + "tooltip": { + "tag": "tooltip", + "value": "The biome or major environmental system where the sample or specimen originated. Choose values from subclasses of the 'biome' class [ENVO:00000428] in the Environment Ontology (ENVO). For host-associated or plant-associated samples, use terms from the UBERON or Plant Ontology to describe the broad anatomical or morphological context" + } + }, + "description": "In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO's biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html", + "title": "broad-scale environmental context", + "notes": [ + "range changed to enumeration late in makefile, so this is modified (but \"sample ID\" anyway)" + ], + "examples": [ + { + "value": "oceanic epipelagic zone biome [ENVO:01000033] for annotating a water sample from the photic zone in middle of the Atlantic Ocean" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "broad-scale environmental context" + ], + "rank": 6, + "is_a": "environment field", + "string_serialization": "{termLabel} {[termID]}", + "slot_uri": "MIXS:0000012", + "alias": "env_broad_scale", + "owner": "SedimentInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "string", + "required": true, + "multivalued": false, + "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$" + }, + "env_local_scale": { + "name": "env_local_scale", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "Environmental entities having causal influences upon the entity at time of sampling." + }, + "tooltip": { + "tag": "tooltip", + "value": "The specific environmental entities or features near the sample or specimen that significantly influence its characteristics or composition. These entities are typically smaller in scale than the broad environmental context. Values for this field should be countable, material nouns and must be chosen from subclasses of BFO:0000040 (material entity) that appear in the Environment Ontology (ENVO). For host-associated or plant-associated samples, use terms from the UBERON or Plant Ontology to describe specific anatomical structures or plant parts." + } + }, + "description": "Report the entity or entities which are in the sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. We recommend using EnvO terms which are of smaller spatial grain than your entry for env_broad_scale. Terms, such as anatomical sites, from other OBO Library ontologies which interoperate with EnvO (e.g. UBERON) are accepted in this field. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS.", + "title": "local environmental context", + "notes": [ + "range changed to enumeration late in makefile, so this is modified (but \"sample ID\" anyway)" + ], + "examples": [ + { + "value": "canopy [ENVO:00000047]" + }, + { + "value": "herb and fern layer [ENVO:01000337]" + }, + { + "value": "litter layer [ENVO:01000338]" + }, + { + "value": "understory [01000335]" + }, + { + "value": "shrub layer [ENVO:01000336]" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "local environmental context" + ], + "rank": 7, + "is_a": "environment field", + "string_serialization": "{termLabel} {[termID]}", + "slot_uri": "MIXS:0000013", + "alias": "env_local_scale", + "owner": "SedimentInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "string", + "required": true, + "multivalued": false, + "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$" + }, + "env_medium": { + "name": "env_medium", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "The material displaced by the entity at time of sampling. Recommend subclasses of environmental material [ENVO:00010483]." + }, + "tooltip": { + "tag": "tooltip", + "value": "The predominant environmental material or substrate that directly surrounds or hosts the sample or specimen at the time of sampling. Choose values from subclasses of the 'environmental material' class [ENVO:00010483] in the Environment Ontology (ENVO). Values for this field should be measurable or mass material nouns, representing continuous environmental materials. For host-associated or plant-associated samples, use terms from the UBERON or Plant Ontology to indicate a tissue, organ, or plant structure" + } + }, + "description": "Report the environmental material(s) immediately surrounding the sample or specimen at the time of sampling. We recommend using subclasses of 'environmental material' (http://purl.obolibrary.org/obo/ENVO_00010483). EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS . Terms from other OBO ontologies are permissible as long as they reference mass/volume nouns (e.g. air, water, blood) and not discrete, countable entities (e.g. a tree, a leaf, a table top).", + "title": "environmental medium", + "notes": [ + "range changed to enumeration late in makefile, so this is modified (but \"sample ID\" anyway)" + ], + "examples": [ + { + "value": "soil [ENVO:00001998]" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "environmental medium" + ], + "rank": 8, + "is_a": "environment field", + "string_serialization": "{termLabel} {[termID]}", + "slot_uri": "MIXS:0000014", + "alias": "env_medium", + "owner": "SedimentInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "string", + "required": true, + "multivalued": false, + "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$" + }, + "experimental_factor": { + "name": "experimental_factor", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "text or EFO and/or OBI" + } + }, + "description": "Experimental factors are essentially the variable aspects of an experiment design which can be used to describe an experiment, or set of experiments, in an increasingly detailed manner. This field accepts ontology terms from Experimental Factor Ontology (EFO) and/or Ontology for Biomedical Investigations (OBI). For a browser of EFO (v 2.95) terms, please see http://purl.bioontology.org/ontology/EFO; for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI", + "title": "experimental factor", + "examples": [ + { + "value": "time series design [EFO:EFO_0001779]" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "experimental factor" + ], + "rank": 12, + "is_a": "investigation field", + "string_serialization": "{termLabel} {[termID]}|{text}", + "slot_uri": "MIXS:0000008", + "alias": "experimental_factor", + "owner": "SedimentInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false + }, + "extreme_event": { + "name": "extreme_event", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "date, string" + } + }, + "description": "Unusual physical events that may have affected microbial populations", + "title": "history/extreme events", + "examples": [ + { + "value": "1980-05-18, volcanic eruption" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "history/extreme events" + ], + "rank": 13, + "is_a": "core field", + "slot_uri": "MIXS:0000320", + "alias": "extreme_event", + "owner": "SedimentInterface", + "domain_of": [ + "Biosample", + "SedimentInterface", + "SoilInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false + }, + "fire": { + "name": "fire", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "date string" + } + }, + "description": "Historical and/or physical evidence of fire", + "title": "history/fire", + "todos": [ + "is \"to\" acceptable? Is there a better way to request that be written?" + ], + "comments": [ + "Provide the date the fire occurred. If extended burning occurred provide the date range." + ], + "examples": [ + { + "value": "1871-10-10" + }, + { + "value": "1871-10-01 to 1871-10-31" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "history/fire" + ], + "rank": 15, + "is_a": "core field", + "slot_uri": "MIXS:0001086", + "alias": "fire", + "owner": "SedimentInterface", + "domain_of": [ + "Biosample", + "SedimentInterface", + "SoilInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false, + "pattern": "^[12]\\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\\d|3[01]))?)?(\\s+to\\s+[12]\\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\\d|3[01]))?)?)?$" + }, + "flooding": { + "name": "flooding", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "date string" + } + }, + "description": "Historical and/or physical evidence of flooding", + "title": "history/flooding", + "todos": [ + "is \"to\" acceptable? Is there a better way to request that be written?", + "What about if the \"day\" isn't known? Is this ok?" + ], + "comments": [ + "Provide the date the flood occurred. If extended flooding occurred provide the date range." + ], + "examples": [ + { + "value": "1927-04-15" + }, + { + "value": "1927-04 to 1927-05" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "history/flooding" + ], + "rank": 16, + "is_a": "core field", + "slot_uri": "MIXS:0000319", + "alias": "flooding", + "owner": "SedimentInterface", + "domain_of": [ + "Biosample", + "SedimentInterface", + "SoilInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false + }, + "gaseous_environment": { + "name": "gaseous_environment", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "gaseous compound name;gaseous compound amount;treatment interval and duration" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Use of conditions with differing gaseous environments; should include the name of gaseous compound, amount administered, treatment duration, interval and total experimental duration; can include multiple gaseous environment regimens", + "title": "gaseous environment", + "todos": [ + "would like to see usage examples for this slot. Requiring micromole/L seems too limiting and doesn't match expected_value value", + "did I do this right? keep the example that's provided and add another? so as to not override" + ], + "examples": [ + { + "value": "CO2; 500ppm above ambient; constant" + }, + { + "value": "nitric oxide;0.5 micromole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "gaseous environment" + ], + "rank": 20, + "is_a": "core field", + "string_serialization": "{text};{float} {unit};{Rn/start_time/end_time/duration}", + "slot_uri": "MIXS:0000558", + "alias": "gaseous_environment", + "owner": "SedimentInterface", + "domain_of": [ + "Biosample", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "multivalued": false + }, + "geo_loc_name": { + "name": "geo_loc_name", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "country or sea name (INSDC or GAZ): region(GAZ), specific location name" + } + }, + "description": "The geographical origin of the sample as defined by the country or sea name followed by specific region name.", + "title": "geographic location (country and/or sea,region)", + "examples": [ + { + "value": "USA: Maryland, Bethesda" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "geographic location (country and/or sea,region)" + ], + "rank": 4, + "is_a": "environment field", + "string_serialization": "{text}: {text}, {text}", + "slot_uri": "MIXS:0000010", + "alias": "geo_loc_name", + "owner": "SedimentInterface", + "domain_of": [ + "FieldResearchSite", + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "required": true, + "multivalued": false, + "pattern": "^[^:, ][^:]*: [^:, ][^,]*, [^:, ].*$" + }, + "glucosidase_act": { + "name": "glucosidase_act", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "mol per liter per hour" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Measurement of glucosidase activity", + "title": "glucosidase activity", + "examples": [ + { + "value": "5 mol per liter per hour" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "glucosidase activity" + ], + "rank": 20, + "is_a": "core field", + "slot_uri": "MIXS:0000137", + "alias": "glucosidase_act", + "owner": "SedimentInterface", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "humidity_regm": { + "name": "humidity_regm", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "humidity value;treatment interval and duration" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "gram per cubic meter" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Information about treatment involving an exposure to varying degree of humidity; information about treatment involving use of growth hormones; should include amount of humidity administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens", + "title": "humidity regimen", + "examples": [ + { + "value": "25 gram per cubic meter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "humidity regimen" + ], + "rank": 21, + "is_a": "core field", + "string_serialization": "{float} {unit};{Rn/start_time/end_time/duration}", + "slot_uri": "MIXS:0000568", + "alias": "humidity_regm", + "owner": "SedimentInterface", + "domain_of": [ + "Biosample", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "multivalued": false + }, + "isotope_exposure": { + "name": "isotope_exposure", + "description": "List isotope exposure or addition applied to your sample.", + "title": "isotope exposure/addition", + "todos": [ + "Can we make the H218O correctly super and subscripted?" + ], + "comments": [ + "This is required when your experimental design includes the use of isotopically labeled compounds" + ], + "examples": [ + { + "value": "13C glucose" + }, + { + "value": "H218O" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "MIXS:0000751" + ], + "rank": 16, + "string_serialization": "{termLabel} {[termID]}; {timestamp}", + "alias": "isotope_exposure", + "owner": "SedimentInterface", + "domain_of": [ + "Biosample", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WaterInterface", + "SoilMixsInspiredMixin" + ], + "slot_group": "mixs_inspired_section", + "range": "string", + "recommended": true, + "multivalued": false, + "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]; ([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$" + }, + "lat_lon": { + "name": "lat_lon", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "decimal degrees, limit to 8 decimal points" + } + }, + "description": "The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system", + "title": "geographic location (latitude and longitude)", + "notes": [ + "This is currently a required field but it's not clear if this should be required for human hosts" + ], + "examples": [ + { + "value": "50.586825 6.408977" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "geographic location (latitude and longitude)" + ], + "rank": 5, + "is_a": "environment field", + "string_serialization": "{lat lon}", + "slot_uri": "MIXS:0000009", + "alias": "lat_lon", + "owner": "SedimentInterface", + "domain_of": [ + "FieldResearchSite", + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "required": true, + "multivalued": false, + "pattern": "^[-+]?([1-8]?\\d(\\.\\d{1,8})?|90(\\.0{1,8})?)\\s[-+]?(180(\\.0{1,8})?|((1[0-7]\\d)|([1-9]?\\d))(\\.\\d{1,8})?)$" + }, + "light_regm": { + "name": "light_regm", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "exposure type;light intensity;light quality" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "lux; micrometer, nanometer, angstrom" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Information about treatment(s) involving exposure to light, including both light intensity and quality.", + "title": "light regimen", + "examples": [ + { + "value": "incandescant light;10 lux;450 nanometer" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "light regimen" + ], + "rank": 24, + "is_a": "core field", + "string_serialization": "{text};{float} {unit};{float} {unit}", + "slot_uri": "MIXS:0000569", + "alias": "light_regm", + "owner": "SedimentInterface", + "domain_of": [ + "Biosample", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "multivalued": false, + "pattern": "^\\S+.*\\S+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? \\S+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? \\S+$" + }, + "magnesium": { + "name": "magnesium", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "mole per liter, milligram per liter, parts per million, micromole per kilogram" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of magnesium in the sample", + "title": "magnesium", + "examples": [ + { + "value": "52.8 micromole per kilogram" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "magnesium" + ], + "rank": 21, + "is_a": "core field", + "slot_uri": "MIXS:0000431", + "alias": "magnesium", + "owner": "SedimentInterface", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "mean_frict_vel": { + "name": "mean_frict_vel", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "meter per second" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Measurement of mean friction velocity", + "title": "mean friction velocity", + "examples": [ + { + "value": "0.5 meter per second" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "mean friction velocity" + ], + "rank": 22, + "is_a": "core field", + "slot_uri": "MIXS:0000498", + "alias": "mean_frict_vel", + "owner": "SedimentInterface", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "mean_peak_frict_vel": { + "name": "mean_peak_frict_vel", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "meter per second" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Measurement of mean peak friction velocity", + "title": "mean peak friction velocity", + "examples": [ + { + "value": "1 meter per second" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "mean peak friction velocity" + ], + "rank": 23, + "is_a": "core field", + "slot_uri": "MIXS:0000502", + "alias": "mean_peak_frict_vel", + "owner": "SedimentInterface", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "methane": { + "name": "methane", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per liter, parts per billion, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Methane (gas) amount or concentration at the time of sampling", + "title": "methane", + "examples": [ + { + "value": "1800 parts per billion" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "methane" + ], + "rank": 24, + "is_a": "core field", + "slot_uri": "MIXS:0000101", + "alias": "methane", + "owner": "SedimentInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "SedimentInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "micro_biomass_c_meth": { + "name": "micro_biomass_c_meth", + "description": "Reference or method used in determining microbial biomass carbon", + "title": "microbial biomass carbon method", + "todos": [ + "How should we separate values? | or ;? lets be consistent" + ], + "comments": [ + "required if \"microbial_biomass_c\" is provided" + ], + "examples": [ + { + "value": "https://doi.org/10.1016/0038-0717(87)90052-6" + }, + { + "value": "https://doi.org/10.1016/0038-0717(87)90052-6 | https://www.sciencedirect.com/science/article/abs/pii/0038071787900526" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "MIXS:0000339" + ], + "rank": 1004, + "string_serialization": "{PMID}|{DOI}|{URL}", + "alias": "micro_biomass_c_meth", + "owner": "SedimentInterface", + "domain_of": [ + "Biosample", + "SedimentInterface", + "SoilInterface", + "SoilMixsInspiredMixin" + ], + "slot_group": "mixs_inspired_section", + "range": "string", + "recommended": true, + "multivalued": false + }, + "micro_biomass_meth": { + "name": "micro_biomass_meth", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "PMID,DOI or url" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Reference or method used in determining microbial biomass", + "title": "microbial biomass method", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "microbial biomass method" + ], + "rank": 43, + "is_a": "core field", + "string_serialization": "{PMID}|{DOI}|{URL}", + "slot_uri": "MIXS:0000339", + "alias": "micro_biomass_meth", + "owner": "SedimentInterface", + "domain_of": [ + "Biosample", + "SedimentInterface", + "SoilInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false + }, + "micro_biomass_n_meth": { + "name": "micro_biomass_n_meth", + "description": "Reference or method used in determining microbial biomass nitrogen", + "title": "microbial biomass nitrogen method", + "comments": [ + "required if \"microbial_biomass_n\" is provided" + ], + "examples": [ + { + "value": "https://doi.org/10.1016/0038-0717(87)90052-6" + }, + { + "value": "https://doi.org/10.1016/0038-0717(87)90052-6 | https://www.sciencedirect.com/science/article/abs/pii/0038071787900526" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "MIXS:0000339" + ], + "rank": 1004, + "string_serialization": "{PMID}|{DOI}|{URL}", + "alias": "micro_biomass_n_meth", + "owner": "SedimentInterface", + "domain_of": [ + "Biosample", + "SedimentInterface", + "SoilInterface", + "SoilMixsInspiredMixin" + ], + "slot_group": "mixs_inspired_section", + "range": "string", + "multivalued": false + }, + "microbial_biomass": { + "name": "microbial_biomass", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "ton, kilogram, gram per kilogram soil" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The part of the organic matter in the soil that constitutes living microorganisms smaller than 5-10 micrometer. If you keep this, you would need to have correction factors used for conversion to the final units", + "title": "microbial biomass", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "microbial biomass" + ], + "rank": 42, + "is_a": "core field", + "slot_uri": "MIXS:0000650", + "alias": "microbial_biomass", + "owner": "SedimentInterface", + "domain_of": [ + "Biosample", + "SedimentInterface", + "SoilInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "microbial_biomass_c": { + "name": "microbial_biomass_c", + "description": "The part of the organic matter in the soil that constitutes living microorganisms smaller than 5-10 micrometer.", + "title": "microbial biomass carbon", + "comments": [ + "If you provide this, correction factors used for conversion to the final units and method are required" + ], + "examples": [ + { + "value": "0.05 ug C/g dry soil" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "MIXS:0000650" + ], + "rank": 1004, + "string_serialization": "{float} {unit}", + "alias": "microbial_biomass_c", + "owner": "SedimentInterface", + "domain_of": [ + "Biosample", + "SedimentInterface", + "SoilInterface", + "SoilMixsInspiredMixin" + ], + "slot_group": "mixs_inspired_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? \\S+$" + }, + "microbial_biomass_n": { + "name": "microbial_biomass_n", + "description": "The part of the organic matter in the soil that constitutes living microorganisms smaller than 5-10 micrometer.", + "title": "microbial biomass nitrogen", + "comments": [ + "If you provide this, correction factors used for conversion to the final units and method are required" + ], + "examples": [ + { + "value": "0.05 ug N/g dry soil" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "MIXS:0000650" + ], + "rank": 1004, + "string_serialization": "{float} {unit}", + "alias": "microbial_biomass_n", + "owner": "SedimentInterface", + "domain_of": [ + "Biosample", + "SedimentInterface", + "SoilInterface", + "SoilMixsInspiredMixin" + ], + "slot_group": "mixs_inspired_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? \\S+$" + }, + "misc_param": { + "name": "misc_param", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "parameter name;measurement value" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Any other measurement performed or parameter collected, that is not listed here", + "title": "miscellaneous parameter", + "examples": [ + { + "value": "Bicarbonate ion concentration;2075 micromole per kilogram" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "miscellaneous parameter" + ], + "rank": 23, + "is_a": "core field", + "string_serialization": "{text};{float} {unit}", + "slot_uri": "MIXS:0000752", + "alias": "misc_param", + "owner": "SedimentInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false, + "pattern": "^([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+\\|)*([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+)$" + }, + "n_alkanes": { + "name": "n_alkanes", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "n-alkane name;measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Concentration of n-alkanes; can include multiple n-alkanes", + "title": "n-alkanes", + "examples": [ + { + "value": "n-hexadecane;100 milligram per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "n-alkanes" + ], + "rank": 25, + "is_a": "core field", + "string_serialization": "{text};{float} {unit}", + "slot_uri": "MIXS:0000503", + "alias": "n_alkanes", + "owner": "SedimentInterface", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+\\|)*([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+)$" + }, + "nitrate": { + "name": "nitrate", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per liter, milligram per liter, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of nitrate in the sample", + "title": "nitrate", + "examples": [ + { + "value": "65 micromole per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "nitrate" + ], + "rank": 26, + "is_a": "core field", + "slot_uri": "MIXS:0000425", + "alias": "nitrate", + "owner": "SedimentInterface", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "nitrite": { + "name": "nitrite", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per liter, milligram per liter, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of nitrite in the sample", + "title": "nitrite", + "examples": [ + { + "value": "0.5 micromole per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "nitrite" + ], + "rank": 27, + "is_a": "core field", + "slot_uri": "MIXS:0000426", + "alias": "nitrite", + "owner": "SedimentInterface", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "nitro": { + "name": "nitro", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of nitrogen (total)", + "title": "nitrogen", + "examples": [ + { + "value": "4.2 micromole per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "nitrogen" + ], + "rank": 28, + "is_a": "core field", + "slot_uri": "MIXS:0000504", + "alias": "nitro", + "owner": "SedimentInterface", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "org_carb": { + "name": "org_carb", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of organic carbon", + "title": "organic carbon", + "examples": [ + { + "value": "1.5 microgram per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "organic carbon" + ], + "rank": 29, + "is_a": "core field", + "slot_uri": "MIXS:0000508", + "alias": "org_carb", + "owner": "SedimentInterface", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "org_matter": { + "name": "org_matter", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "microgram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of organic matter", + "title": "organic matter", + "examples": [ + { + "value": "1.75 milligram per cubic meter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "organic matter" + ], + "rank": 45, + "is_a": "core field", + "slot_uri": "MIXS:0000204", + "alias": "org_matter", + "owner": "SedimentInterface", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "MiscEnvsInterface", + "SedimentInterface", + "SoilInterface", + "WaterInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "org_nitro": { + "name": "org_nitro", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "microgram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of organic nitrogen", + "title": "organic nitrogen", + "examples": [ + { + "value": "4 micromole per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "organic nitrogen" + ], + "rank": 46, + "is_a": "core field", + "slot_uri": "MIXS:0000205", + "alias": "org_nitro", + "owner": "SedimentInterface", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "MiscEnvsInterface", + "SedimentInterface", + "SoilInterface", + "WaterInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "org_nitro_method": { + "name": "org_nitro_method", + "description": "Method used for obtaining organic nitrogen", + "title": "organic nitrogen method", + "comments": [ + "required if \"org_nitro\" is provided" + ], + "examples": [ + { + "value": "https://doi.org/10.1016/0038-0717(85)90144-0" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "MIXS:0000338", + "MIXS:0000205" + ], + "rank": 14, + "string_serialization": "{PMID}|{DOI}|{URL}", + "alias": "org_nitro_method", + "owner": "SedimentInterface", + "domain_of": [ + "Biosample", + "SedimentInterface", + "SoilInterface", + "SoilMixsInspiredMixin" + ], + "slot_group": "mixs_inspired_section", + "range": "string", + "multivalued": false + }, + "organism_count": { + "name": "organism_count", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "organism name;measurement value;enumeration" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "number of cells per cubic meter, number of cells per milliliter, number of cells per cubic centimeter" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr)", + "title": "organism count", + "examples": [ + { + "value": "total prokaryotes;3.5e7 cells per milliliter;qPCR" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "organism count" + ], + "rank": 30, + "is_a": "core field", + "slot_uri": "MIXS:0000103", + "alias": "organism_count", + "owner": "SedimentInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^([-+]?[0-9]*\\.?[0-9]+ +\\S.*\\|)*([-+]?[0-9]*\\.?[0-9]+ +\\S.*)$" + }, + "oxy_stat_samp": { + "name": "oxy_stat_samp", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Oxygenation status of sample", + "title": "oxygenation status of sample", + "examples": [ + { + "value": "aerobic" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "oxygenation status of sample" + ], + "rank": 25, + "is_a": "core field", + "slot_uri": "MIXS:0000753", + "alias": "oxy_stat_samp", + "owner": "SedimentInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_section", + "range": "OxyStatSampEnum", + "multivalued": false + }, + "part_org_carb": { + "name": "part_org_carb", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "microgram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of particulate organic carbon", + "title": "particulate organic carbon", + "examples": [ + { + "value": "1.92 micromole per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "particulate organic carbon" + ], + "rank": 31, + "is_a": "core field", + "slot_uri": "MIXS:0000515", + "alias": "part_org_carb", + "owner": "SedimentInterface", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "particle_class": { + "name": "particle_class", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "particle name;measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micrometer" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Particles are classified, based on their size, into six general categories:clay, silt, sand, gravel, cobbles, and boulders; should include amount of particle preceded by the name of the particle type; can include multiple values", + "title": "particle classification", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "particle classification" + ], + "rank": 32, + "is_a": "core field", + "string_serialization": "{text};{float} {unit}", + "slot_uri": "MIXS:0000206", + "alias": "particle_class", + "owner": "SedimentInterface", + "domain_of": [ + "Biosample", + "SedimentInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+\\|)*([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+)$" + }, + "perturbation": { + "name": "perturbation", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "perturbation type name;perturbation interval and duration" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types", + "title": "perturbation", + "examples": [ + { + "value": "antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "perturbation" + ], + "rank": 33, + "is_a": "core field", + "string_serialization": "{text};{Rn/start_time/end_time/duration}", + "slot_uri": "MIXS:0000754", + "alias": "perturbation", + "owner": "SedimentInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "petroleum_hydrocarb": { + "name": "petroleum_hydrocarb", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of petroleum hydrocarbon", + "title": "petroleum hydrocarbon", + "examples": [ + { + "value": "0.05 micromole per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "petroleum hydrocarbon" + ], + "rank": 34, + "is_a": "core field", + "slot_uri": "MIXS:0000516", + "alias": "petroleum_hydrocarb", + "owner": "SedimentInterface", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "ph": { + "name": "ph", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "pH measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid", + "title": "pH", + "notes": [ + "Use modified term" + ], + "examples": [ + { + "value": "7.2" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "pH" + ], + "rank": 27, + "is_a": "core field", + "string_serialization": "{float}", + "slot_uri": "MIXS:0001001", + "alias": "ph", + "owner": "SedimentInterface", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "MiscEnvsInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "float", + "recommended": true, + "multivalued": false, + "minimum_value": 0, + "maximum_value": 14 + }, + "ph_meth": { + "name": "ph_meth", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "PMID,DOI or url" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Reference or method used in determining ph", + "title": "pH method", + "comments": [ + "This can include a link to the instrument used or a citation for the method." + ], + "examples": [ + { + "value": "https://www.southernlabware.com/pc9500-benchtop-ph-conductivity-meter-kit-ph-accuracy-2000mv-ph-range-2-000-to-20-000.html?gclid=Cj0KCQiAwJWdBhCYARIsAJc4idCO5vtvbVMf545fcvdROFqa6zjzNSoywNx6K4k9Coo9cCc2pybtvGsaAiR0EALw_wcB" + }, + { + "value": "https://doi.org/10.2136/sssabookser5.3.c16" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "pH method" + ], + "rank": 41, + "is_a": "core field", + "string_serialization": "{PMID}|{DOI}|{URL}", + "slot_uri": "MIXS:0001106", + "alias": "ph_meth", + "owner": "SedimentInterface", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "MiscEnvsInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false + }, + "phaeopigments": { + "name": "phaeopigments", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "phaeopigment name;measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milligram per cubic meter" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Concentration of phaeopigments; can include multiple phaeopigments", + "title": "phaeopigments", + "examples": [ + { + "value": "2.5 milligram per cubic meter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "phaeopigments" + ], + "rank": 35, + "is_a": "core field", + "string_serialization": "{text};{float} {unit}", + "slot_uri": "MIXS:0000180", + "alias": "phaeopigments", + "owner": "SedimentInterface", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+\\|)*([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+)$" + }, + "phosphate": { + "name": "phosphate", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of phosphate", + "title": "phosphate", + "examples": [ + { + "value": "0.7 micromole per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "phosphate" + ], + "rank": 53, + "is_a": "core field", + "slot_uri": "MIXS:0000505", + "alias": "phosphate", + "owner": "SedimentInterface", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "MiscEnvsInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "phosplipid_fatt_acid": { + "name": "phosplipid_fatt_acid", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "phospholipid fatty acid name;measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "mole per gram, mole per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Concentration of phospholipid fatty acids; can include multiple values", + "title": "phospholipid fatty acid", + "examples": [ + { + "value": "2.98 milligram per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "phospholipid fatty acid" + ], + "rank": 36, + "is_a": "core field", + "string_serialization": "{text};{float} {unit}", + "slot_uri": "MIXS:0000181", + "alias": "phosplipid_fatt_acid", + "owner": "SedimentInterface", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+\\|)*([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+)$" + }, + "porosity": { + "name": "porosity", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value or range" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "percentage" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Porosity of deposited sediment is volume of voids divided by the total volume of sample", + "title": "porosity", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "porosity" + ], + "rank": 37, + "is_a": "core field", + "string_serialization": "{float} - {float} {unit}", + "slot_uri": "MIXS:0000211", + "alias": "porosity", + "owner": "SedimentInterface", + "domain_of": [ + "Biosample", + "HcrCoresInterface", + "SedimentInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "potassium": { + "name": "potassium", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milligram per liter, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of potassium in the sample", + "title": "potassium", + "examples": [ + { + "value": "463 milligram per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "potassium" + ], + "rank": 38, + "is_a": "core field", + "slot_uri": "MIXS:0000430", + "alias": "potassium", + "owner": "SedimentInterface", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "pressure": { + "name": "pressure", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "atmosphere" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Pressure to which the sample is subject to, in atmospheres", + "title": "pressure", + "examples": [ + { + "value": "50 atmosphere" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "pressure" + ], + "rank": 39, + "is_a": "core field", + "slot_uri": "MIXS:0000412", + "alias": "pressure", + "owner": "SedimentInterface", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "redox_potential": { + "name": "redox_potential", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "millivolt" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential", + "title": "redox potential", + "examples": [ + { + "value": "300 millivolt" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "redox potential" + ], + "rank": 40, + "is_a": "core field", + "slot_uri": "MIXS:0000182", + "alias": "redox_potential", + "owner": "SedimentInterface", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "salinity": { + "name": "salinity", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "practical salinity unit, percentage" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The total concentration of all dissolved salts in a liquid or solid sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater.", + "title": "salinity", + "examples": [ + { + "value": "25 practical salinity unit" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "salinity" + ], + "rank": 54, + "is_a": "core field", + "slot_uri": "MIXS:0000183", + "alias": "salinity", + "owner": "SedimentInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "salinity_meth": { + "name": "salinity_meth", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "PMID,DOI or url" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Reference or method used in determining salinity", + "title": "salinity method", + "examples": [ + { + "value": "https://doi.org/10.1007/978-1-61779-986-0_28" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "salinity method" + ], + "rank": 55, + "is_a": "core field", + "string_serialization": "{PMID}|{DOI}|{URL}", + "slot_uri": "MIXS:0000341", + "alias": "salinity_meth", + "owner": "SedimentInterface", + "domain_of": [ + "Biosample", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WaterInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false + }, + "samp_collec_device": { + "name": "samp_collec_device", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "device name" + } + }, + "description": "The device used to collect an environmental sample. This field accepts terms listed under environmental sampling device (http://purl.obolibrary.org/obo/ENVO). This field also accepts terms listed under specimen collection device (http://purl.obolibrary.org/obo/GENEPIO_0002094).", + "title": "sample collection device", + "comments": [ + "Report dimensions and details when applicable" + ], + "examples": [ + { + "value": "swab, biopsy, niskin bottle, push core, drag swab [GENEPIO:0002713]" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sample collection device" + ], + "rank": 14, + "is_a": "nucleic acid sequence source field", + "string_serialization": "{termLabel} {[termID]}|{text}", + "slot_uri": "MIXS:0000002", + "alias": "samp_collec_device", + "owner": "SedimentInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "recommended": true, + "multivalued": false + }, + "samp_collec_method": { + "name": "samp_collec_method", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "PMID,DOI,url , or text" + } + }, + "description": "The method employed for collecting the sample.", + "title": "sample collection method", + "comments": [ + "This can be a citation or description" + ], + "examples": [ + { + "value": "swabbing" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sample collection method" + ], + "rank": 15, + "is_a": "nucleic acid sequence source field", + "string_serialization": "{PMID}|{DOI}|{URL}|{text}", + "slot_uri": "MIXS:0001225", + "alias": "samp_collec_method", + "owner": "SedimentInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "multivalued": false + }, + "samp_mat_process": { + "name": "samp_mat_process", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "text" + } + }, + "description": "A brief description of any processing applied to the sample during or after retrieving the sample from environment, or a link to the relevant protocol(s) performed.", + "title": "sample material processing", + "examples": [ + { + "value": "filtering of seawater" + }, + { + "value": "storing samples in ethanol" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sample material processing" + ], + "rank": 12, + "is_a": "nucleic acid sequence source field", + "string_serialization": "{text}", + "slot_uri": "MIXS:0000016", + "alias": "samp_mat_process", + "owner": "SedimentInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "multivalued": false + }, + "samp_size": { + "name": "samp_size", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "millliter, gram, milligram, liter" + } + }, + "description": "The total amount or size (volume (ml), mass (g) or area (m2) ) of sample collected.", + "title": "amount or size of sample collected", + "comments": [ + "This refers to the TOTAL amount of sample collected from the experiment. NOT the amount sent to each institution or collected for a specific analysis." + ], + "examples": [ + { + "value": "5 grams" + }, + { + "value": "10 mL" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "amount or size of sample collected" + ], + "rank": 18, + "is_a": "nucleic acid sequence source field", + "string_serialization": "{float} {unit}", + "slot_uri": "MIXS:0000001", + "alias": "samp_size", + "owner": "SedimentInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? \\S+$" + }, + "samp_store_dur": { + "name": "samp_store_dur", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "duration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Duration for which the sample was stored", + "title": "sample storage duration", + "examples": [ + { + "value": "P1Y6M" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sample storage duration" + ], + "rank": 353, + "is_a": "core field", + "string_serialization": "{duration}", + "slot_uri": "MIXS:0000116", + "alias": "samp_store_dur", + "owner": "SedimentInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "samp_store_loc": { + "name": "samp_store_loc", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "location name" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Location at which sample was stored, usually name of a specific freezer/room", + "title": "sample storage location", + "examples": [ + { + "value": "Freezer no:5" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sample storage location" + ], + "rank": 41, + "is_a": "core field", + "string_serialization": "{text}", + "slot_uri": "MIXS:0000755", + "alias": "samp_store_loc", + "owner": "SedimentInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "samp_store_temp": { + "name": "samp_store_temp", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "degree Celsius" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Temperature at which the sample was stored (degrees are assumed)", + "title": "sample storage temperature", + "examples": [ + { + "value": "-80 Celsius" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sample storage temperature" + ], + "rank": 7, + "is_a": "core field", + "slot_uri": "MIXS:0000110", + "alias": "samp_store_temp", + "owner": "SedimentInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "required": true, + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "sample_link": { + "name": "sample_link", + "description": "A unique identifier to assign parent-child, subsample, or sibling samples. This is relevant when a sample or other material was used to generate the new sample.", + "title": "sample linkage", + "notes": [ + "also tempted to include SampIdNewTermsMixin but if len(slot_usage.keys()) > 1 and \"placeholder\" in slot_usage.keys():AttributeError: 'list' object has no attribute 'keys'" + ], + "comments": [ + "This field allows multiple entries separated by ; (Examples: Soil collected from the field will link with the soil used in an incubation. The soil a plant was grown in links to the plant sample. An original culture sample was transferred to a new vial and generated a new sample)" + ], + "examples": [ + { + "value": "IGSN:DSJ0284" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "rank": 5, + "string_serialization": "{text}:{text}", + "alias": "sample_link", + "owner": "SedimentInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface", + "SampIdNewTermsMixin" + ], + "slot_group": "sample_id_section", + "range": "string", + "recommended": true, + "multivalued": false, + "pattern": "[^\\:\\n\\r]+\\:[^\\:\\n\\r]+" + }, + "sediment_type": { + "name": "sediment_type", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Information about the sediment type based on major constituents", + "title": "sediment type", + "examples": [ + { + "value": "biogenous" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sediment type" + ], + "rank": 42, + "is_a": "core field", + "slot_uri": "MIXS:0001078", + "alias": "sediment_type", + "owner": "SedimentInterface", + "domain_of": [ + "Biosample", + "SedimentInterface" + ], + "slot_group": "mixs_core_section", + "range": "sediment_type_enum", + "multivalued": false + }, + "sieving": { + "name": "sieving", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "design name and/or size;amount" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Collection design of pooled samples and/or sieve size and amount of sample sieved", + "title": "composite design/sieving", + "todos": [ + "check validation and examples" + ], + "comments": [ + "Describe how samples were composited or sieved.", + "Use 'sample link' to indicate which samples were combined." + ], + "examples": [ + { + "value": "combined 2 cores | 4mm sieved" + }, + { + "value": "4 mm sieved and homogenized" + }, + { + "value": "50 g | 5 cores | 2 mm sieved" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "composite design/sieving" + ], + "rank": 8, + "is_a": "core field", + "string_serialization": "{{text}|{float} {unit}};{float} {unit}", + "slot_uri": "MIXS:0000322", + "alias": "sieving", + "owner": "SedimentInterface", + "domain_of": [ + "Biosample", + "SedimentInterface", + "SoilInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "multivalued": false + }, + "silicate": { + "name": "silicate", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of silicate", + "title": "silicate", + "examples": [ + { + "value": "0.05 micromole per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "silicate" + ], + "rank": 43, + "is_a": "core field", + "slot_uri": "MIXS:0000184", + "alias": "silicate", + "owner": "SedimentInterface", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "size_frac": { + "name": "size_frac", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "filter size value range" + } + }, + "description": "Filtering pore size used in sample preparation", + "title": "size fraction selected", + "examples": [ + { + "value": "0-0.22 micrometer" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "size fraction selected" + ], + "rank": 285, + "is_a": "nucleic acid sequence source field", + "string_serialization": "{float}-{float} {unit}", + "slot_uri": "MIXS:0000017", + "alias": "size_frac", + "owner": "SedimentInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "sodium": { + "name": "sodium", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milligram per liter, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Sodium concentration in the sample", + "title": "sodium", + "examples": [ + { + "value": "10.5 milligram per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sodium" + ], + "rank": 363, + "is_a": "core field", + "slot_uri": "MIXS:0000428", + "alias": "sodium", + "owner": "SedimentInterface", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "specific_ecosystem": { + "name": "specific_ecosystem", + "description": "Specific ecosystems represent specific features of the environment like aphotic zone in an ocean or gastric mucosa within a host digestive system. Specific ecosystem is in position 5/5 in a GOLD path.", + "comments": [ + "Specific ecosystems help to define samples based on very specific characteristics of an environment under the five-level classification system." + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "https://gold.jgi.doe.gov/help" + ], + "rank": 13, + "is_a": "gold_path_field", + "alias": "specific_ecosystem", + "owner": "SedimentInterface", + "domain_of": [ + "Biosample", + "Study", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "SpecificEcosystemEnum", + "recommended": true + }, + "start_date_inc": { + "name": "start_date_inc", + "description": "Date the incubation was started. Only relevant for incubation samples.", + "title": "incubation start date", + "notes": [ + "MIxS collection_date accepts (truncated) ISO8601. DH taking arbitrary precision date only" + ], + "comments": [ + "Date should be formatted as YYYY(-MM(-DD)). Ie, 2021-04-15, 2021-04 and 2021 are all acceptable." + ], + "examples": [ + { + "value": "2021-04-15, 2021-04 and 2021 are all acceptable." + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "MIXS:0000011" + ], + "rank": 4, + "string_serialization": "{date, arbitrary precision}", + "alias": "start_date_inc", + "owner": "SedimentInterface", + "domain_of": [ + "Biosample", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WaterInterface", + "SoilMixsInspiredMixin" + ], + "slot_group": "mixs_inspired_section", + "range": "string", + "recommended": true, + "multivalued": false, + "pattern": "^[12]\\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\\d|3[01]))?)?$" + }, + "sulfate": { + "name": "sulfate", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per liter, milligram per liter, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of sulfate in the sample", + "title": "sulfate", + "examples": [ + { + "value": "5 micromole per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sulfate" + ], + "rank": 44, + "is_a": "core field", + "slot_uri": "MIXS:0000423", + "alias": "sulfate", + "owner": "SedimentInterface", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "sulfide": { + "name": "sulfide", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per liter, milligram per liter, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of sulfide in the sample", + "title": "sulfide", + "examples": [ + { + "value": "2 micromole per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sulfide" + ], + "rank": 371, + "is_a": "core field", + "slot_uri": "MIXS:0000424", + "alias": "sulfide", + "owner": "SedimentInterface", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "temp": { + "name": "temp", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "degree Celsius" + } + }, + "description": "Temperature of the sample at the time of sampling.", + "title": "temperature", + "examples": [ + { + "value": "25 degree Celsius" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "temperature" + ], + "rank": 37, + "is_a": "environment field", + "slot_uri": "MIXS:0000113", + "alias": "temp", + "owner": "SedimentInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "tidal_stage": { + "name": "tidal_stage", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Stage of tide", + "title": "tidal stage", + "examples": [ + { + "value": "high tide" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "tidal stage" + ], + "rank": 45, + "is_a": "core field", + "slot_uri": "MIXS:0000750", + "alias": "tidal_stage", + "owner": "SedimentInterface", + "domain_of": [ + "Biosample", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "tidal_stage_enum", + "multivalued": false + }, + "tot_carb": { + "name": "tot_carb", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "microgram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Total carbon content", + "title": "total carbon", + "todos": [ + "is this inorganic and organic? both? could use some clarification.", + "ug/L doesn't seem like the right units. Should check this slots usage in databases and re-evaluate. I couldn't find any references that provided this data in this format", + "is this inorganic and organic? both? could use some clarification.", + "ug/L doesn't seem like the right units. Should check this slots usage in databases and re-evaluate. I couldn't find any references that provided this data in this format" + ], + "examples": [ + { + "value": "1 ug/L" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "total carbon" + ], + "rank": 47, + "is_a": "core field", + "slot_uri": "MIXS:0000525", + "alias": "tot_carb", + "owner": "SedimentInterface", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "SedimentInterface", + "SoilInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "tot_depth_water_col": { + "name": "tot_depth_water_col", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "meter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Measurement of total depth of water column", + "title": "total depth of water column", + "examples": [ + { + "value": "500 meter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "total depth of water column" + ], + "rank": 46, + "is_a": "core field", + "slot_uri": "MIXS:0000634", + "alias": "tot_depth_water_col", + "owner": "SedimentInterface", + "domain_of": [ + "Biosample", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "tot_nitro_cont_meth": { + "name": "tot_nitro_cont_meth", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "PMID,DOI or url" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Reference or method used in determining the total nitrogen", + "title": "total nitrogen content method", + "examples": [ + { + "value": "https://doi.org/10.2134/agronmonogr9.2.c32" + }, + { + "value": "https://acsess.onlinelibrary.wiley.com/doi/full/10.2136/sssaj2009.0389?casa_token=bm0pYIUdNMgAAAAA%3AOWVRR0STHaOe-afTcTdxn5m1hM8n2ltM0wY-b1iYpYdD9dhwppk5j3LvC2IO5yhOIvyLVeQz4NZRCZo" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "total nitrogen content method" + ], + "rank": 49, + "is_a": "core field", + "string_serialization": "{PMID}|{DOI}|{URL}", + "slot_uri": "MIXS:0000338", + "alias": "tot_nitro_cont_meth", + "owner": "SedimentInterface", + "domain_of": [ + "Biosample", + "SedimentInterface", + "SoilInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false + }, + "tot_nitro_content": { + "name": "tot_nitro_content", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "microgram per liter, micromole per liter, milligram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Total nitrogen content of the sample", + "title": "total nitrogen content", + "examples": [ + { + "value": "5 mg N/ L" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "total nitrogen content" + ], + "rank": 48, + "is_a": "core field", + "slot_uri": "MIXS:0000530", + "alias": "tot_nitro_content", + "owner": "SedimentInterface", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "SedimentInterface", + "SoilInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "tot_org_c_meth": { + "name": "tot_org_c_meth", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "PMID,DOI or url" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Reference or method used in determining total organic carbon", + "title": "total organic carbon method", + "examples": [ + { + "value": "https://doi.org/10.1080/07352680902776556" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "total organic carbon method" + ], + "rank": 51, + "is_a": "core field", + "string_serialization": "{PMID}|{DOI}|{URL}", + "slot_uri": "MIXS:0000337", + "alias": "tot_org_c_meth", + "owner": "SedimentInterface", + "domain_of": [ + "Biosample", + "SedimentInterface", + "SoilInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false + }, + "tot_org_carb": { + "name": "tot_org_carb", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "gram Carbon per kilogram sample material" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content", + "title": "total organic carbon", + "todos": [ + "check description. How are they different?", + "check description. How are they different?" + ], + "examples": [ + { + "value": "5 mg N/ L" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "total organic carbon" + ], + "rank": 50, + "is_a": "core field", + "slot_uri": "MIXS:0000533", + "alias": "tot_org_carb", + "owner": "SedimentInterface", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "SedimentInterface", + "SoilInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "turbidity": { + "name": "turbidity", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "formazin turbidity unit, formazin nephelometric units" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Measure of the amount of cloudiness or haziness in water caused by individual particles", + "title": "turbidity", + "examples": [ + { + "value": "0.3 nephelometric turbidity units" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "turbidity" + ], + "rank": 47, + "is_a": "core field", + "slot_uri": "MIXS:0000191", + "alias": "turbidity", + "owner": "SedimentInterface", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "water_cont_soil_meth": { + "name": "water_cont_soil_meth", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "PMID,DOI or url" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Reference or method used in determining the water content of soil", + "title": "water content method", + "todos": [ + "Why is it soil water content method in the name but not the title? Is this slot used in other samples?", + "Soil water content can be measure MANY ways and often, multiple ways are used in one experiment (gravimetric water content and water holding capacity and water filled pore space, to name a few).", + "Should this be multi valued? How to we manage and validate this?" + ], + "comments": [ + "Required if providing water content" + ], + "examples": [ + { + "value": "J. Nat. Prod. Plant Resour., 2012, 2 (4):500-503" + }, + { + "value": "https://dec.alaska.gov/applications/spar/webcalc/definitions.htm" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "water content method" + ], + "rank": 40, + "is_a": "core field", + "string_serialization": "{PMID}|{DOI}|{URL}", + "slot_uri": "MIXS:0000323", + "alias": "water_cont_soil_meth", + "owner": "SedimentInterface", + "domain_of": [ + "Biosample", + "SedimentInterface", + "SoilInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false + }, + "water_content": { + "name": "water_content", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "string" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "gram per gram or cubic centimeter per cubic centimeter" + } + }, + "description": "Water content measurement", + "title": "water content", + "todos": [ + "value in preferred unit is too limiting. need to change this", + "check and correct validation so examples are accepted", + "how to manage multiple water content methods?" + ], + "examples": [ + { + "value": "0.75 g water/g dry soil" + }, + { + "value": "75% water holding capacity" + }, + { + "value": "1.1 g fresh weight/ dry weight" + }, + { + "value": "10% water filled pore space" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "water content" + ], + "rank": 39, + "is_a": "core field", + "string_serialization": "{float or pct} {unit}", + "slot_uri": "MIXS:0000185", + "alias": "water_content", + "owner": "SedimentInterface", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "SedimentInterface", + "SoilInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)?%? \\S.+$" + }, + "watering_regm": { + "name": "watering_regm", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value;treatment interval and duration" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milliliter, liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Information about treatment involving an exposure to watering frequencies, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens", + "title": "watering regimen", + "examples": [ + { + "value": "1 liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" + }, + { + "value": "75% water holding capacity; constant" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "watering regimen" + ], + "rank": 25, + "is_a": "core field", + "string_serialization": "{float} {unit};{Rn/start_time/end_time/duration}", + "slot_uri": "MIXS:0000591", + "alias": "watering_regm", + "owner": "SedimentInterface", + "domain_of": [ + "Biosample", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "multivalued": false + }, + "analysis_type": { + "name": "analysis_type", + "description": "Select all the data types associated or available for this biosample", + "title": "analysis/data type", + "examples": [ + { + "value": "metagenomics; metabolomics; proteomics" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "MIxS:investigation_type" + ], + "rank": 3, + "alias": "analysis_type", + "owner": "SedimentInterface", + "domain_of": [ + "Biosample", + "DhMultiviewCommonColumnsMixin", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "EmslInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "JgiMgInterface", + "JgiMgLrInterface", + "JgiMtInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "AnalysisTypeEnum", + "required": true, + "recommended": false, + "multivalued": true + }, + "samp_name": { + "name": "samp_name", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "text" + } + }, + "description": "A local identifier or name that for the material sample collected. Refers to the original material collected or to any derived sub-samples.", + "title": "sample name", + "comments": [ + "It can have any format, but we suggest that you make it concise, unique and consistent within your lab, and as informative as possible." + ], + "examples": [ + { + "value": "Rock core CB1178(5-6) from NSW" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sample name" + ], + "rank": 1, + "is_a": "investigation field", + "string_serialization": "{text}", + "slot_uri": "MIXS:0001107", + "identifier": true, + "alias": "samp_name", + "owner": "SedimentInterface", + "domain_of": [ + "Biosample", + "DhMultiviewCommonColumnsMixin", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "EmslInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "JgiMgInterface", + "JgiMgLrInterface", + "JgiMtInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "string", + "required": true, + "multivalued": false + }, + "source_mat_id": { + "name": "source_mat_id", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "for cultures of microorganisms: identifiers for two culture collections; for other material a unique arbitrary identifer" + } + }, + "description": "A globally unique identifier assigned to the biological sample.", + "title": "source material identifier", + "todos": [ + "Currently, the comments say to use UUIDs. However, if we implement assigning NMDC identifiers with the minter we dont need to require a GUID. It can be an optional field to fill out only if they already have a resolvable ID.", + "Currently, the comments say to use UUIDs. However, if we implement assigning NMDC identifiers with the minter we dont need to require a GUID. It can be an optional field to fill out only if they already have a resolvable ID." + ], + "notes": [ + "The source material IS the Globally Unique ID" + ], + "comments": [ + "Identifiers must be prefixed. Possible FAIR prefixes are IGSNs (http://www.geosamples.org/getigsn), NCBI biosample accession numbers, ARK identifiers (https://arks.org/). These IDs enable linking to derived analytes and subsamples. If you have not assigned FAIR identifiers to your samples, you can generate UUIDs (https://www.uuidgenerator.net/).", + "Identifiers must be prefixed. Possible FAIR prefixes are IGSNs (http://www.geosamples.org/getigsn), NCBI biosample accession numbers, ARK identifiers (https://arks.org/). These IDs enable linking to derived analytes and subsamples. If you have not assigned FAIR identifiers to your samples, you can generate UUIDs (https://www.uuidgenerator.net/)." + ], + "examples": [ + { + "value": "IGSN:AU1243" + }, + { + "value": "UUID:24f1467a-40f4-11ed-b878-0242ac120002" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "source material identifiers" + ], + "rank": 2, + "is_a": "nucleic acid sequence source field", + "string_serialization": "{text}:{text}", + "slot_uri": "MIXS:0000026", + "alias": "source_mat_id", + "owner": "SedimentInterface", + "domain_of": [ + "Biosample", + "DhMultiviewCommonColumnsMixin", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "EmslInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "JgiMgInterface", + "JgiMgLrInterface", + "JgiMtInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "string", + "multivalued": false, + "pattern": "[^\\:\\n\\r]+\\:[^\\:\\n\\r]+" + } + } + }, + "SoilInterface": { + "name": "SoilInterface", + "annotations": { + "excel_worksheet_name": { + "tag": "excel_worksheet_name", + "value": "soil" + } + }, + "description": "soil dh_interface", + "title": "Soil", + "from_schema": "https://example.com/nmdc_submission_schema", + "is_a": "DhInterface", + "mixins": [ + "DhMultiviewCommonColumnsMixin", + "SampIdNewTermsMixin", + "SoilMixsInspiredMixin" + ], + "slots": [ + "agrochem_addition", + "air_temp_regm", + "al_sat", + "al_sat_meth", + "ammonium_nitrogen", + "annual_precpt", + "annual_temp", + "biotic_regm", + "biotic_relationship", + "bulk_elect_conductivity", + "carb_nitro_ratio", + "chem_administration", + "climate_environment", + "collection_date", + "collection_date_inc", + "collection_time", + "collection_time_inc", + "crop_rotation", + "cur_land_use", + "cur_vegetation", + "cur_vegetation_meth", + "depth", + "drainage_class", + "ecosystem", + "ecosystem_category", + "ecosystem_subtype", + "ecosystem_type", + "elev", + "env_broad_scale", + "env_local_scale", + "env_medium", + "experimental_factor", + "experimental_factor_other", + "extreme_event", + "fao_class", + "filter_method", + "fire", + "flooding", + "gaseous_environment", + "geo_loc_name", + "growth_facil", + "heavy_metals", + "heavy_metals_meth", + "horizon_meth", + "humidity_regm", + "infiltrations", + "isotope_exposure", + "lat_lon", + "lbc_thirty", + "lbceq", + "light_regm", + "link_addit_analys", + "link_class_info", + "link_climate_info", + "local_class", + "local_class_meth", + "manganese", + "micro_biomass_c_meth", + "micro_biomass_c_meth", + "micro_biomass_meth", + "micro_biomass_n_meth", + "micro_biomass_n_meth", + "microbial_biomass", + "microbial_biomass_c", + "microbial_biomass_c", + "microbial_biomass_n", + "microbial_biomass_n", + "misc_param", + "nitrate_nitrogen", + "nitrite_nitrogen", + "non_microb_biomass", + "non_microb_biomass_method", + "org_matter", + "org_nitro", + "org_nitro_method", + "other_treatment", + "oxy_stat_samp", + "ph", + "ph_meth", + "phosphate", + "prev_land_use_meth", + "previous_land_use", + "profile_position", + "salinity", + "salinity_meth", + "samp_collec_device", + "samp_collec_method", + "samp_mat_process", + "samp_size", + "samp_store_temp", + "sample_link", + "season_precpt", + "season_temp", + "sieving", + "size_frac_low", + "size_frac_up", + "slope_aspect", + "slope_gradient", + "soil_horizon", + "soil_text_measure", + "soil_texture_meth", + "soil_type", + "soil_type_meth", + "specific_ecosystem", + "start_date_inc", + "start_time_inc", + "store_cond", + "temp", + "tillage", + "tot_carb", + "tot_nitro_cont_meth", + "tot_nitro_content", + "tot_org_c_meth", + "tot_org_carb", + "tot_phosp", + "water_cont_soil_meth", + "water_content", + "watering_regm", + "zinc" + ], + "slot_usage": { + "agrochem_addition": { + "name": "agrochem_addition", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "agrochemical name;agrochemical amount;timestamp" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "gram, mole per liter, milligram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Addition of fertilizers, pesticides, etc. - amount and time of applications", + "title": "history/agrochemical additions", + "examples": [ + { + "value": "roundup;5 milligram per liter;2018-06-21" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "history/agrochemical additions" + ], + "rank": 2, + "is_a": "core field", + "string_serialization": "{text};{float} {unit};{timestamp}", + "slot_uri": "MIXS:0000639", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "SoilInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false, + "pattern": ".*" + }, + "air_temp_regm": { + "name": "air_temp_regm", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "temperature value;treatment interval and duration" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "meter" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Information about treatment involving an exposure to varying temperatures; should include the temperature, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include different temperature regimens", + "title": "air temperature regimen", + "examples": [ + { + "value": "25 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "air temperature regimen" + ], + "rank": 16, + "is_a": "core field", + "string_serialization": "{float} {unit};{Rn/start_time/end_time/duration}", + "slot_uri": "MIXS:0000551", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "recommended": true, + "multivalued": false + }, + "al_sat": { + "name": "al_sat", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "percentage" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The relative abundance of aluminum in the sample", + "title": "aluminum saturation/ extreme unusual properties", + "todos": [ + "Example & validation. Can we configure things so that 27% & 27 % & 0.27 will validate?", + "I think it's weird the way GSC writes the title. I recommend this change. Thoughts? I would argue this isn't an extreme unusual property. It's just a biogeochemical measurement.", + "This is no longer matching the listed IRI from GSC. When NMDC has its own slots, map this to the MIxS slot", + "Example & validation. Can we make rules that 27% & 27 % & 0.27 will validate?", + "I think it's weird the way GSC writes the title. I recommend this change. Thoughts? I would argue this isn't an extreme unusual property. It's just a biogeochemical measurement." + ], + "notes": [ + "Aluminum saturation is the percentage of the CEC occupies by aluminum. Like all cations, aluminum held by the cation exchange complex is in equilibrium with aluminum in the soil solution." + ], + "examples": [ + { + "value": "0.27" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "extreme_unusual_properties/Al saturation" + ], + "rank": 3, + "is_a": "core field", + "slot_uri": "MIXS:0000607", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "SoilInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "al_sat_meth": { + "name": "al_sat_meth", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "PMID,DOI or URL" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Reference or method used in determining Aluminum saturation", + "title": "aluminum saturation method/ extreme unusual properties", + "todos": [ + "I think it's weird the way GSC writes the title. I recommend this change. Thoughts?", + "This is no longer matching the listed IRI from GSC. When NMDC has its own slots, map this to the MIxS slot", + "I think it's weird the way GSC writes the title. I recommend this change. Thoughts?" + ], + "comments": [ + "Required when aluminum saturation is provided." + ], + "examples": [ + { + "value": "https://doi.org/10.1371/journal.pone.0176357" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "extreme_unusual_properties/Al saturation method" + ], + "rank": 4, + "is_a": "core field", + "string_serialization": "{PMID}|{DOI}|{URL}", + "slot_uri": "MIXS:0000324", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "SoilInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false + }, + "ammonium_nitrogen": { + "name": "ammonium_nitrogen", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "mg/kg" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of ammonium nitrogen in the sample", + "title": "ammonium nitrogen", + "examples": [ + { + "value": "2.3 mg/kg" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "https://www.ornl.gov/content/bio-scales-0" + ], + "aliases": [ + "ammonium_nitrogen", + "NH4-N" + ], + "rank": 1005, + "owner": "Biosample", + "domain_of": [ + "Biosample", + "SoilInterface" + ], + "slot_group": "mixs_inspired_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "annual_precpt": { + "name": "annual_precpt", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "millimeter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The average of all annual precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or Isohyetal maps.", + "title": "mean annual precipitation", + "todos": [ + "This is no longer matching the listed IRI from GSC, added example. When NMDC has its own slots, map this to the MIxS slot" + ], + "examples": [ + { + "value": "8.94 inch" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "mean annual precipitation" + ], + "rank": 5, + "is_a": "core field", + "slot_uri": "MIXS:0000644", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "SoilInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "annual_temp": { + "name": "annual_temp", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "degree Celsius" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Mean annual temperature", + "title": "mean annual temperature", + "examples": [ + { + "value": "12.5 degree Celsius" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "mean annual temperature" + ], + "rank": 6, + "is_a": "core field", + "slot_uri": "MIXS:0000642", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "SoilInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "biotic_regm": { + "name": "biotic_regm", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "free text" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Information about treatment(s) involving use of biotic factors, such as bacteria, viruses or fungi.", + "title": "biotic regimen", + "examples": [ + { + "value": "sample inoculated with Rhizobium spp. Culture" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "biotic regimen" + ], + "rank": 13, + "is_a": "core field", + "string_serialization": "{text}", + "slot_uri": "MIXS:0001038", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "recommended": true, + "multivalued": false + }, + "biotic_relationship": { + "name": "biotic_relationship", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + } + }, + "description": "Description of relationship(s) between the subject organism and other organism(s) it is associated with. E.g., parasite on species X; mutualist with species Y. The target organism is the subject of the relationship, and the other organism(s) is the object", + "title": "observed biotic relationship", + "examples": [ + { + "value": "free living" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "observed biotic relationship" + ], + "rank": 22, + "is_a": "nucleic acid sequence source field", + "slot_uri": "MIXS:0000028", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface" + ], + "slot_group": "mixs_modified_section", + "range": "biotic_relationship_enum", + "multivalued": false + }, + "bulk_elect_conductivity": { + "name": "bulk_elect_conductivity", + "description": "Electrical conductivity is a measure of the ability to carry electric current, which is mostly dictated by the chemistry of and amount of water.", + "title": "bulk electrical conductivity", + "comments": [ + "Provide the value output of the field instrument." + ], + "examples": [ + { + "value": "0.017 mS/cm" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "rank": 1008, + "owner": "Biosample", + "domain_of": [ + "Biosample", + "SoilInterface" + ], + "slot_group": "mixs_inspired_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "carb_nitro_ratio": { + "name": "carb_nitro_ratio", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Ratio of amount or concentrations of carbon to nitrogen", + "title": "carbon/nitrogen ratio", + "examples": [ + { + "value": "0.417361111" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "carbon/nitrogen ratio" + ], + "rank": 44, + "is_a": "core field", + "slot_uri": "MIXS:0000310", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "SedimentInterface", + "SoilInterface", + "WaterInterface" + ], + "slot_group": "mixs_section", + "range": "float", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "chem_administration": { + "name": "chem_administration", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "CHEBI;timestamp" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi", + "title": "chemical administration", + "examples": [ + { + "value": "agar [CHEBI:2509];2018-05-11|agar [CHEBI:2509];2018-05-22" + }, + { + "value": "agar [CHEBI:2509];2018-05" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "chemical administration" + ], + "rank": 17, + "is_a": "core field", + "string_serialization": "{termLabel} {[termID]};{timestamp}", + "slot_uri": "MIXS:0000751", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "recommended": true, + "multivalued": false, + "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\];([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$" + }, + "climate_environment": { + "name": "climate_environment", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "climate name;treatment interval and duration" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Treatment involving an exposure to a particular climate; treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple climates", + "title": "climate environment", + "todos": [ + "description says \"can include multiple climates\" but multivalued is set to false", + "add examples, i need to see some examples to add correctly formatted example.", + "description says \"can include multiple climates\" but multivalued is set to false", + "add examples, i need to see some examples to add correctly formatted example." + ], + "examples": [ + { + "value": "tropical climate;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "climate environment" + ], + "rank": 19, + "is_a": "core field", + "string_serialization": "{text};{Rn/start_time/end_time/duration}", + "slot_uri": "MIXS:0001040", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "recommended": true, + "multivalued": false + }, + "collection_date": { + "name": "collection_date", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "date and time" + } + }, + "description": "The date of sampling", + "title": "collection date", + "notes": [ + "MIxS collection_date accepts (truncated) ISO8601. DH taking arb prec date only", + "Use modified term (amended definition)" + ], + "examples": [ + { + "value": "2021-04-15" + }, + { + "value": "2021-04" + }, + { + "value": "2021" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "collection date" + ], + "rank": 3, + "is_a": "environment field", + "string_serialization": "{date, arbitrary precision}", + "slot_uri": "MIXS:0000011", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "required": true, + "multivalued": false, + "pattern": "^[12]\\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\\d|3[01]))?)?$" + }, + "collection_date_inc": { + "name": "collection_date_inc", + "description": "Date the incubation was harvested/collected/ended. Only relevant for incubation samples.", + "title": "incubation collection date", + "notes": [ + "MIxS collection_date accepts (truncated) ISO8601. DH taking arbitrary precision date only" + ], + "comments": [ + "Date should be formatted as YYYY(-MM(-DD)). Ie, 2021-04-15, 2021-04 and 2021 are all acceptable." + ], + "examples": [ + { + "value": "2021-04-15, 2021-04 and 2021 are all acceptable." + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "MIXS:0000011" + ], + "rank": 2, + "string_serialization": "{date, arbitrary precision}", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WaterInterface", + "SoilMixsInspiredMixin" + ], + "slot_group": "mixs_inspired_section", + "range": "string", + "recommended": true, + "multivalued": false, + "pattern": "^[12]\\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\\d|3[01]))?)?$" + }, + "collection_time": { + "name": "collection_time", + "description": "The time of sampling, either as an instance (single point) or interval.", + "title": "collection time, GMT", + "notes": [ + "MIxS collection_date accepts (truncated) ISO8601. DH taking seconds optional time only" + ], + "comments": [ + "Time should be entered as HH:MM(:SS) in GMT. See here for a converter: https://www.worldtimebuddy.com/pst-to-gmt-converter" + ], + "examples": [ + { + "value": "13:33 or 13:33:55" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "MIXS:0000011" + ], + "rank": 1, + "string_serialization": "{time, seconds optional}", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WaterInterface", + "SoilMixsInspiredMixin" + ], + "slot_group": "mixs_inspired_section", + "range": "string", + "recommended": true, + "multivalued": false, + "pattern": "^([01]?\\d|2[0-3]|24(?=:00?:00?$)):([0-5]\\d)(:([0-5]\\d))?$" + }, + "collection_time_inc": { + "name": "collection_time_inc", + "description": "Time the incubation was harvested/collected/ended. Only relevant for incubation samples.", + "title": "incubation collection time, GMT", + "notes": [ + "MIxS collection_date accepts (truncated) ISO8601. DH taking seconds optional time only" + ], + "comments": [ + "Time should be entered as HH:MM(:SS) in GMT. See here for a converter: https://www.worldtimebuddy.com/pst-to-gmt-converter" + ], + "examples": [ + { + "value": "13:33 or 13:33:55" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "MIXS:0000011" + ], + "rank": 3, + "string_serialization": "{time, seconds optional}", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "SoilInterface", + "SoilMixsInspiredMixin" + ], + "slot_group": "mixs_inspired_section", + "range": "string", + "recommended": true, + "multivalued": false, + "pattern": "^([01]?\\d|2[0-3]|24(?=:00?:00?$)):([0-5]\\d)(:([0-5]\\d))?$" + }, + "crop_rotation": { + "name": "crop_rotation", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "crop rotation status;schedule" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Whether or not crop is rotated, and if yes, rotation schedule", + "title": "history/crop rotation", + "examples": [ + { + "value": "yes;R2/2017-01-01/2018-12-31/P6M" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "history/crop rotation" + ], + "rank": 7, + "is_a": "core field", + "string_serialization": "{boolean};{Rn/start_time/end_time/duration}", + "slot_uri": "MIXS:0000318", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "SoilInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false + }, + "cur_land_use": { + "name": "cur_land_use", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Present state of sample site", + "title": "current land use", + "examples": [ + { + "value": "conifers" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "current land use" + ], + "rank": 8, + "is_a": "core field", + "slot_uri": "MIXS:0001080", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "SoilInterface" + ], + "slot_group": "mixs_section", + "range": "cur_land_use_enum", + "multivalued": false + }, + "cur_vegetation": { + "name": "cur_vegetation", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "current vegetation type" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Vegetation classification from one or more standard classification systems, or agricultural crop", + "title": "current vegetation", + "todos": [ + "Recommend changing this from text value to some king of ontology?", + "This is no longer matching the listed IRI from GSC. When NMDC has its own slots, map this to the MIxS slot", + "Recommend changing this from text value to some kind of ontology?" + ], + "comments": [ + "Values provided here can be specific species of vegetation or vegetation regions", + "See for vegetation regions- https://education.nationalgeographic.org/resource/vegetation-region" + ], + "examples": [ + { + "value": "deciduous forest" + }, + { + "value": "forest" + }, + { + "value": "Bauhinia variegata" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "current vegetation" + ], + "rank": 9, + "is_a": "core field", + "string_serialization": "{text}", + "slot_uri": "MIXS:0000312", + "owner": "Biosample", + "domain_of": [ + "FieldResearchSite", + "Biosample", + "SoilInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false + }, + "cur_vegetation_meth": { + "name": "cur_vegetation_meth", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "PMID,DOI or url" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Reference or method used in vegetation classification", + "title": "current vegetation method", + "todos": [ + "I'm not sure this is a DOI, PMID, or URI. Should pool the community and find out how they accomplish this if provided.", + "This is no longer matching the listed IRI from GSC. When NMDC has its own slots, map this to the MIxS slot", + "I'm not sure this is a DOI, PMID, or URI. Should pool the community and find out how they accomplish this if provided." + ], + "comments": [ + "Required when current vegetation is provided." + ], + "examples": [ + { + "value": "https://doi.org/10.1111/j.1654-109X.2011.01154.x" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "current vegetation method" + ], + "rank": 10, + "is_a": "core field", + "string_serialization": "{PMID}|{DOI}|{URL}", + "slot_uri": "MIXS:0000314", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "SoilInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false + }, + "depth": { + "name": "depth", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + } + }, + "description": "The vertical distance below local surface, e.g. for sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples.", + "title": "depth, meters", + "notes": [ + "Use modified term" + ], + "comments": [ + "All depths must be reported in meters. Provide the numerical portion only." + ], + "examples": [ + { + "value": "0 - 0.1" + }, + { + "value": "1" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "depth" + ], + "rank": 9, + "is_a": "environment field", + "string_serialization": "{float}-{float}", + "slot_uri": "MIXS:0000018", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "required": true, + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)?\\s*-\\s*[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)?$" + }, + "drainage_class": { + "name": "drainage_class", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Drainage classification from a standard system such as the USDA system", + "title": "drainage classification", + "examples": [ + { + "value": "well" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "drainage classification" + ], + "rank": 11, + "is_a": "core field", + "slot_uri": "MIXS:0001085", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "SoilInterface" + ], + "slot_group": "mixs_section", + "range": "drainage_class_enum", + "multivalued": false + }, + "ecosystem": { + "name": "ecosystem", + "description": "An ecosystem is a combination of a physical environment (abiotic factors) and all the organisms (biotic factors) that interact with this environment. Ecosystem is in position 1/5 in a GOLD path.", + "comments": [ + "The abiotic factors play a profound role on the type and composition of organisms in a given environment. The GOLD Ecosystem at the top of the five-level classification system is aimed at capturing the broader environment from which an organism or environmental sample is collected. The three broad groups under Ecosystem are Environmental, Host-associated, and Engineered. They represent samples collected from a natural environment or from another organism or from engineered environments like bioreactors respectively." + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "https://gold.jgi.doe.gov/help" + ], + "rank": 9, + "is_a": "gold_path_field", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "Study", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "EcosystemForSoilEnum", + "recommended": true + }, + "ecosystem_category": { + "name": "ecosystem_category", + "description": "Ecosystem categories represent divisions within the ecosystem based on specific characteristics of the environment from where an organism or sample is isolated. Ecosystem category is in position 2/5 in a GOLD path.", + "comments": [ + "The Environmental ecosystem (for example) is divided into Air, Aquatic and Terrestrial. Ecosystem categories for Host-associated samples can be individual hosts or phyla and for engineered samples it may be manipulated environments like bioreactors, solid waste etc." + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "https://gold.jgi.doe.gov/help" + ], + "rank": 10, + "is_a": "gold_path_field", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "Study", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "EcosystemCategoryForSoilEnum", + "recommended": true + }, + "ecosystem_subtype": { + "name": "ecosystem_subtype", + "description": "Ecosystem subtypes represent further subdivision of Ecosystem types into more distinct subtypes. Ecosystem subtype is in position 4/5 in a GOLD path.", + "comments": [ + "Ecosystem Type Marine (Environmental -> Aquatic -> Marine) is further divided (for example) into Intertidal zone, Coastal, Pelagic, Intertidal zone etc. in the Ecosystem subtype category." + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "https://gold.jgi.doe.gov/help" + ], + "rank": 12, + "is_a": "gold_path_field", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "Study", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "EcosystemSubtypeForSoilEnum", + "recommended": true + }, + "ecosystem_type": { + "name": "ecosystem_type", + "description": "Ecosystem types represent things having common characteristics within the Ecosystem Category. These common characteristics based grouping is still broad but specific to the characteristics of a given environment. Ecosystem type is in position 3/5 in a GOLD path.", + "comments": [ + "The Aquatic ecosystem category (for example) may have ecosystem types like Marine or Thermal springs etc. Ecosystem category Air may have Indoor air or Outdoor air as different Ecosystem Types. In the case of Host-associated samples, ecosystem type can represent Respiratory system, Digestive system, Roots etc." + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "https://gold.jgi.doe.gov/help" + ], + "rank": 11, + "is_a": "gold_path_field", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "Study", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "EcosystemTypeForSoilEnum", + "recommended": true + }, + "elev": { + "name": "elev", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + } + }, + "description": "Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit.", + "title": "elevation, meters", + "comments": [ + "All elevations must be reported in meters. Provide the numerical portion only.", + "Please use https://www.advancedconverter.com/map-tools/find-altitude-by-coordinates, if needed, to help estimate the elevation based on latitude and longitude coordinates." + ], + "examples": [ + { + "value": "225" + }, + { + "value": "0" + }, + { + "value": "1250" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "elevation" + ], + "rank": 6, + "is_a": "environment field", + "slot_uri": "MIXS:0000093", + "owner": "Biosample", + "domain_of": [ + "FieldResearchSite", + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "float", + "required": true, + "multivalued": false + }, + "env_broad_scale": { + "name": "env_broad_scale", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "The major environment type(s) where the sample was collected. Recommend subclasses of biome [ENVO:00000428]. Multiple terms can be separated by one or more pipes." + }, + "tooltip": { + "tag": "tooltip", + "value": "The biome or major environmental system where the sample or specimen originated. Choose values from subclasses of the 'biome' class [ENVO:00000428] in the Environment Ontology (ENVO). For host-associated or plant-associated samples, use terms from the UBERON or Plant Ontology to describe the broad anatomical or morphological context" + } + }, + "description": "In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO's biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html", + "title": "broad-scale environmental context", + "notes": [ + "range changed to enumeration late in makefile, so this is modified (but \"sample ID\" anyway)" + ], + "examples": [ + { + "value": "oceanic epipelagic zone biome [ENVO:01000033] for annotating a water sample from the photic zone in middle of the Atlantic Ocean" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "broad-scale environmental context" + ], + "rank": 6, + "is_a": "environment field", + "string_serialization": "{termLabel} {[termID]}", + "slot_uri": "MIXS:0000012", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "required": true, + "multivalued": false, + "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$", + "any_of": [ + { + "range": "EnvBroadScaleSoilEnum" + }, + { + "range": "string" + } + ] + }, + "env_local_scale": { + "name": "env_local_scale", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "Environmental entities having causal influences upon the entity at time of sampling." + }, + "tooltip": { + "tag": "tooltip", + "value": "The specific environmental entities or features near the sample or specimen that significantly influence its characteristics or composition. These entities are typically smaller in scale than the broad environmental context. Values for this field should be countable, material nouns and must be chosen from subclasses of BFO:0000040 (material entity) that appear in the Environment Ontology (ENVO). For host-associated or plant-associated samples, use terms from the UBERON or Plant Ontology to describe specific anatomical structures or plant parts." + } + }, + "description": "Report the entity or entities which are in the sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. We recommend using EnvO terms which are of smaller spatial grain than your entry for env_broad_scale. Terms, such as anatomical sites, from other OBO Library ontologies which interoperate with EnvO (e.g. UBERON) are accepted in this field. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS.", + "title": "local environmental context", + "notes": [ + "range changed to enumeration late in makefile, so this is modified (but \"sample ID\" anyway)" + ], + "examples": [ + { + "value": "canopy [ENVO:00000047]" + }, + { + "value": "herb and fern layer [ENVO:01000337]" + }, + { + "value": "litter layer [ENVO:01000338]" + }, + { + "value": "understory [01000335]" + }, + { + "value": "shrub layer [ENVO:01000336]" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "local environmental context" + ], + "rank": 7, + "is_a": "environment field", + "string_serialization": "{termLabel} {[termID]}", + "slot_uri": "MIXS:0000013", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "required": true, + "multivalued": false, + "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$", + "any_of": [ + { + "range": "EnvLocalScaleSoilEnum" + }, + { + "range": "string" + } + ] + }, + "env_medium": { + "name": "env_medium", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "The material displaced by the entity at time of sampling. Recommend subclasses of environmental material [ENVO:00010483]." + }, + "tooltip": { + "tag": "tooltip", + "value": "The predominant environmental material or substrate that directly surrounds or hosts the sample or specimen at the time of sampling. Choose values from subclasses of the 'environmental material' class [ENVO:00010483] in the Environment Ontology (ENVO). Values for this field should be measurable or mass material nouns, representing continuous environmental materials. For host-associated or plant-associated samples, use terms from the UBERON or Plant Ontology to indicate a tissue, organ, or plant structure" + } + }, + "description": "Report the environmental material(s) immediately surrounding the sample or specimen at the time of sampling. We recommend using subclasses of 'environmental material' (http://purl.obolibrary.org/obo/ENVO_00010483). EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS . Terms from other OBO ontologies are permissible as long as they reference mass/volume nouns (e.g. air, water, blood) and not discrete, countable entities (e.g. a tree, a leaf, a table top).", + "title": "environmental medium", + "notes": [ + "range changed to enumeration late in makefile, so this is modified (but \"sample ID\" anyway)" + ], + "examples": [ + { + "value": "soil [ENVO:00001998]" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "environmental medium" + ], + "rank": 8, + "is_a": "environment field", + "string_serialization": "{termLabel} {[termID]}", + "slot_uri": "MIXS:0000014", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "required": true, + "multivalued": false, + "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$", + "any_of": [ + { + "range": "EnvMediumSoilEnum" + }, + { + "range": "string" + } + ] + }, + "experimental_factor": { + "name": "experimental_factor", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "text or EFO and/or OBI" + } + }, + "description": "Experimental factors are essentially the variable aspects of an experiment design which can be used to describe an experiment, or set of experiments, in an increasingly detailed manner. This field accepts ontology terms from Experimental Factor Ontology (EFO) and/or Ontology for Biomedical Investigations (OBI). For a browser of EFO (v 2.95) terms, please see http://purl.bioontology.org/ontology/EFO; for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI", + "title": "experimental factor", + "examples": [ + { + "value": "time series design [EFO:0001779]" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "experimental factor" + ], + "rank": 12, + "is_a": "investigation field", + "string_serialization": "{termLabel} {[termID]}|{text}", + "slot_uri": "MIXS:0000008", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false + }, + "experimental_factor_other": { + "name": "experimental_factor_other", + "description": "Other details about your sample that you feel can't be accurately represented in the available columns.", + "title": "experimental factor- other", + "comments": [ + "This slot accepts open-ended text about your sample.", + "We recommend using key:value pairs.", + "Provided pairs will be considered for inclusion as future slots/terms in this data collection template." + ], + "examples": [ + { + "value": "experimental treatment: value" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "MIXS:0000008", + "MIXS:0000300" + ], + "rank": 7, + "string_serialization": "{text}", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "SoilInterface", + "SoilMixsInspiredMixin" + ], + "slot_group": "mixs_inspired_section", + "range": "string", + "recommended": true, + "multivalued": false + }, + "extreme_event": { + "name": "extreme_event", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "date, string" + } + }, + "description": "Unusual physical events that may have affected microbial populations", + "title": "history/extreme events", + "todos": [ + "This is no longer matching the listed IRI from GSC. When NMDC has its own slots, map this to the MIxS slot" + ], + "examples": [ + { + "value": "1980-05-18, volcanic eruption" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "history/extreme events" + ], + "rank": 13, + "is_a": "core field", + "slot_uri": "MIXS:0000320", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "SedimentInterface", + "SoilInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false + }, + "fao_class": { + "name": "fao_class", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Soil classification from the FAO World Reference Database for Soil Resources. The list can be found at http://www.fao.org/nr/land/sols/soil/wrb-soil-maps/reference-groups", + "title": "soil_taxonomic/FAO classification", + "examples": [ + { + "value": "Luvisols" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "soil_taxonomic/FAO classification" + ], + "rank": 14, + "is_a": "core field", + "slot_uri": "MIXS:0001083", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "SoilInterface" + ], + "slot_group": "mixs_section", + "range": "fao_class_enum", + "multivalued": false + }, + "filter_method": { + "name": "filter_method", + "description": "Type of filter used or how the sample was filtered", + "title": "filter method", + "comments": [ + "describe the filter or provide a catalog number and manufacturer" + ], + "examples": [ + { + "value": "C18" + }, + { + "value": "Basix PES, 13-100-106 FisherSci" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "MIXS:0000765" + ], + "rank": 6, + "string_serialization": "{text}", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "SoilInterface", + "WaterInterface", + "SoilMixsInspiredMixin" + ], + "slot_group": "mixs_inspired_section", + "range": "string", + "recommended": true, + "multivalued": false + }, + "fire": { + "name": "fire", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "date string" + } + }, + "description": "Historical and/or physical evidence of fire", + "title": "history/fire", + "todos": [ + "is \"to\" acceptable? Is there a better way to request that be written?", + "is \"to\" acceptable? Is there a better way to request that be written?", + "This is no longer matching the listed IRI from GSC. When NMDC has its own slots, map this to the MIxS slot" + ], + "comments": [ + "Provide the date the fire occurred. If extended burning occurred provide the date range." + ], + "examples": [ + { + "value": "1871-10-10" + }, + { + "value": "1871-10-01 to 1871-10-31" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "history/fire" + ], + "rank": 15, + "is_a": "core field", + "slot_uri": "MIXS:0001086", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "SedimentInterface", + "SoilInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false, + "pattern": "^[12]\\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\\d|3[01]))?)?(\\s+to\\s+[12]\\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\\d|3[01]))?)?)?$" + }, + "flooding": { + "name": "flooding", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "date string" + } + }, + "description": "Historical and/or physical evidence of flooding", + "title": "history/flooding", + "todos": [ + "is \"to\" acceptable? Is there a better way to request that be written?", + "What about if the \"day\" isn't known? Is this ok?", + "is \"to\" acceptable? Is there a better way to request that be written?", + "What about if the \"day\" isn't known? Is this ok?", + "This is no longer matching the listed IRI from GSC. When NMDC has its own slots, map this to the MIxS slot" + ], + "comments": [ + "Provide the date the flood occurred. If extended flooding occurred provide the date range." + ], + "examples": [ + { + "value": "1927-04-15" + }, + { + "value": "1927-04 to 1927-05" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "history/flooding" + ], + "rank": 16, + "is_a": "core field", + "slot_uri": "MIXS:0000319", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "SedimentInterface", + "SoilInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false + }, + "gaseous_environment": { + "name": "gaseous_environment", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "gaseous compound name;gaseous compound amount;treatment interval and duration" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Use of conditions with differing gaseous environments; should include the name of gaseous compound, amount administered, treatment duration, interval and total experimental duration; can include multiple gaseous environment regimens", + "title": "gaseous environment", + "todos": [ + "would like to see usage examples for this slot. Requiring micromole/L seems too limiting and doesn't match expected_value value", + "did I do this right? keep the example that's provided and add another? so as to not override", + "would like to see usage examples for this slot. Requiring micromole/L seems too limiting and doesn't match expected_value value", + "did I do this right? keep the example that's provided and add another? so as to not override" + ], + "examples": [ + { + "value": "CO2; 500ppm above ambient; constant" + }, + { + "value": "nitric oxide;0.5 micromole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "gaseous environment" + ], + "rank": 20, + "is_a": "core field", + "string_serialization": "{text};{float} {unit};{Rn/start_time/end_time/duration}", + "slot_uri": "MIXS:0000558", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "recommended": true, + "multivalued": false + }, + "geo_loc_name": { + "name": "geo_loc_name", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "country or sea name (INSDC or GAZ): region(GAZ), specific location name" + } + }, + "description": "The geographical origin of the sample as defined by the country or sea name followed by specific region name.", + "title": "geographic location (country and/or sea,region)", + "examples": [ + { + "value": "USA: Maryland, Bethesda" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "geographic location (country and/or sea,region)" + ], + "rank": 4, + "is_a": "environment field", + "string_serialization": "{text}: {text}, {text}", + "slot_uri": "MIXS:0000010", + "owner": "Biosample", + "domain_of": [ + "FieldResearchSite", + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "required": true, + "multivalued": false, + "pattern": "^[^:, ][^:]*: [^:, ][^,]*, [^:, ].*$" + }, + "growth_facil": { + "name": "growth_facil", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "free text or CO" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Type of facility/location where the sample was harvested; controlled vocabulary: growth chamber, open top chamber, glasshouse, experimental garden, field.", + "title": "growth facility", + "notes": [ + "Removed from description: Alternatively use Crop Ontology (CO) terms" + ], + "examples": [ + { + "value": "Growth chamber [CO_715:0000189]" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "growth facility" + ], + "rank": 1, + "is_a": "core field", + "string_serialization": "{text}|{termLabel} {[termID]}", + "slot_uri": "MIXS:0001043", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "PlantAssociatedInterface", + "SoilInterface" + ], + "slot_group": "mixs_modified_section", + "range": "GrowthFacilEnum", + "required": true, + "multivalued": false + }, + "heavy_metals": { + "name": "heavy_metals", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "heavy metal name;measurement value unit" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "microgram per gram" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Heavy metals present in the sample and their concentrations.", + "title": "heavy metals/ extreme unusual properties", + "todos": [ + "Example & validation. Can we configure things so that 27% & 27 % & 0.27 will validate?", + "I think it's weird the way GSC writes the title. I recommend this change. Thoughts? I would argue this isn't an extreme unusual property. It's just a biogeochemical measurement.", + "This is no longer matching the listed IRI from GSC. When NMDC has its own slots, map this to the MIxS slot", + "Example & validation. Can we make rules that 27% & 27 % & 0.27 will validate?", + "I think it's weird the way GSC writes the title. I recommend this change. Thoughts? I would argue this isn't an extreme unusual property. It's just a biogeochemical measurement." + ], + "notes": [ + "Changed to multi-valued. In MIxS, you add another column to denote multiple heavy metals. We don't have that ability in the submission portal." + ], + "comments": [ + "For multiple heavy metals and concentrations, separate by ;" + ], + "examples": [ + { + "value": "mercury 0.09 micrograms per gram" + }, + { + "value": "mercury 0.09 ug/g; chromium 0.03 ug/g" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "extreme_unusual_properties/heavy metals" + ], + "rank": 17, + "is_a": "core field", + "string_serialization": "{text};{float} {unit}", + "slot_uri": "MIXS:0000652", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "SoilInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false, + "pattern": "^([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+\\|)*([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+)$" + }, + "heavy_metals_meth": { + "name": "heavy_metals_meth", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "PMID,DOI or url" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Reference or method used in determining heavy metals", + "title": "heavy metals method/ extreme unusual properties", + "todos": [ + "This is no longer matching the listed IRI from GSC. When NMDC has its own slots, map this to the MIxS slot" + ], + "comments": [ + "Required when heavy metals are provided", + "If different methods are used for multiple metals, indicate the metal and method. Separate metals by ;" + ], + "examples": [ + { + "value": "https://doi.org/10.3390/ijms9040434" + }, + { + "value": "mercury https://doi.org/10.1007/BF01056090; chromium https://doi.org/10.1007/s00216-006-0322-8" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "extreme_unusual_properties/heavy metals method" + ], + "rank": 18, + "is_a": "core field", + "string_serialization": "{PMID}|{DOI}|{URL}", + "slot_uri": "MIXS:0000343", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "SoilInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false + }, + "horizon_meth": { + "name": "horizon_meth", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "PMID,DOI or url" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Reference or method used in determining the horizon", + "title": "soil horizon method", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "soil horizon method" + ], + "rank": 19, + "is_a": "core field", + "string_serialization": "{PMID}|{DOI}|{URL}", + "slot_uri": "MIXS:0000321", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "SoilInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false + }, + "humidity_regm": { + "name": "humidity_regm", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "humidity value;treatment interval and duration" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "gram per cubic meter" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Information about treatment involving an exposure to varying degree of humidity; information about treatment involving use of growth hormones; should include amount of humidity administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens", + "title": "humidity regimen", + "examples": [ + { + "value": "25 gram per cubic meter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "humidity regimen" + ], + "rank": 21, + "is_a": "core field", + "string_serialization": "{float} {unit};{Rn/start_time/end_time/duration}", + "slot_uri": "MIXS:0000568", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "recommended": true, + "multivalued": false + }, + "infiltrations": { + "name": "infiltrations", + "description": "The amount of time it takes to complete each infiltration activity", + "examples": [ + { + "value": "00:01:32;00:00:53" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "https://www.protocols.io/view/field-sampling-protocol-kqdg3962pg25/v1" + ], + "aliases": [ + "infiltration_1", + "infiltration_2" + ], + "rank": 1009, + "list_elements_ordered": true, + "owner": "Biosample", + "domain_of": [ + "Biosample", + "SoilInterface" + ], + "slot_group": "mixs_inspired_section", + "range": "string", + "multivalued": false, + "pattern": "^(?:(?:[0-9]|[1-9][0-9]|9[0-9]|0[0-9]|0[0-5][0-9]):[0-5][0-9]:[0-5][0-9])(?:;(?:[0-9]|[1-9][0-9]|9[0-9]|0[0-9]|0[0-5][0-9]):[0-5][0-9]:[0-5][0-9])*$" + }, + "isotope_exposure": { + "name": "isotope_exposure", + "description": "List isotope exposure or addition applied to your sample.", + "title": "isotope exposure/addition", + "todos": [ + "Can we make the H218O correctly super and subscripted?" + ], + "comments": [ + "This is required when your experimental design includes the use of isotopically labeled compounds" + ], + "examples": [ + { + "value": "13C glucose" + }, + { + "value": "H218O" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "MIXS:0000751" + ], + "rank": 16, + "string_serialization": "{termLabel} {[termID]}; {timestamp}", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WaterInterface", + "SoilMixsInspiredMixin" + ], + "slot_group": "mixs_inspired_section", + "range": "string", + "recommended": true, + "multivalued": false, + "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]; ([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$" + }, + "lat_lon": { + "name": "lat_lon", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "decimal degrees, limit to 8 decimal points" + } + }, + "description": "The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system", + "title": "geographic location (latitude and longitude)", + "notes": [ + "This is currently a required field but it's not clear if this should be required for human hosts" + ], + "examples": [ + { + "value": "50.586825 6.408977" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "geographic location (latitude and longitude)" + ], + "rank": 5, + "is_a": "environment field", + "string_serialization": "{lat lon}", + "slot_uri": "MIXS:0000009", + "owner": "Biosample", + "domain_of": [ + "FieldResearchSite", + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "required": true, + "multivalued": false, + "pattern": "^[-+]?([1-8]?\\d(\\.\\d{1,8})?|90(\\.0{1,8})?)\\s[-+]?(180(\\.0{1,8})?|((1[0-7]\\d)|([1-9]?\\d))(\\.\\d{1,8})?)$" + }, + "lbc_thirty": { + "name": "lbc_thirty", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "ppm CaCO3/pH" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "lime buffer capacity, determined after 30 minute incubation", + "title": "lime buffer capacity (at 30 minutes)", + "comments": [ + "This is the mass of lime, in mg, needed to raise the pH of one kg of soil by one pH unit" + ], + "examples": [ + { + "value": "543 mg/kg" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "https://www.ornl.gov/content/bio-scales-0", + "https://secure.caes.uga.edu/extension/publications/files/pdf/C%20874_5.PDF" + ], + "aliases": [ + "lbc_thirty", + "lbc30", + "lime buffer capacity (at 30 minutes)" + ], + "rank": 1001, + "owner": "Biosample", + "domain_of": [ + "Biosample", + "SoilInterface" + ], + "slot_group": "mixs_inspired_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "lbceq": { + "name": "lbceq", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "ppm CaCO3/pH" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "lime buffer capacity, determined at equilibrium after 5 day incubation", + "title": "lime buffer capacity (after 5 day incubation)", + "comments": [ + "This is the mass of lime, in mg, needed to raise the pH of one kg of soil by one pH unit" + ], + "examples": [ + { + "value": "1575 mg/kg" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "https://www.ornl.gov/content/bio-scales-0" + ], + "aliases": [ + "lbceq", + "lime buffer capacity (at 5-day equilibrium)" + ], + "rank": 1002, + "owner": "Biosample", + "domain_of": [ + "Biosample", + "SoilInterface" + ], + "slot_group": "mixs_inspired_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "light_regm": { + "name": "light_regm", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "exposure type;light intensity;light quality" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "lux; micrometer, nanometer, angstrom" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Information about treatment(s) involving exposure to light, including both light intensity and quality.", + "title": "light regimen", + "examples": [ + { + "value": "incandescant light;10 lux;450 nanometer" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "light regimen" + ], + "rank": 24, + "is_a": "core field", + "string_serialization": "{text};{float} {unit};{float} {unit}", + "slot_uri": "MIXS:0000569", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "recommended": true, + "multivalued": false, + "pattern": "^\\S+.*\\S+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? 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| or ;? lets be consistent" + ], + "comments": [ + "required if \"microbial_biomass_c\" is provided" + ], + "examples": [ + { + "value": "https://doi.org/10.1016/0038-0717(87)90052-6" + }, + { + "value": "https://doi.org/10.1016/0038-0717(87)90052-6 | https://www.sciencedirect.com/science/article/abs/pii/0038071787900526" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "MIXS:0000339" + ], + "rank": 1004, + "string_serialization": "{PMID}|{DOI}|{URL}", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "SedimentInterface", + "SoilInterface", + "SoilMixsInspiredMixin" + ], + "slot_group": "mixs_inspired_section", + "range": "string", + "recommended": true, + "multivalued": false + }, + "micro_biomass_meth": { + "name": "micro_biomass_meth", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "PMID,DOI or url" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Reference or method used in determining microbial biomass", + "title": "microbial biomass method", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "microbial biomass method" + ], + "rank": 43, + "is_a": "core field", + "string_serialization": "{PMID}|{DOI}|{URL}", + "slot_uri": "MIXS:0000339", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "SedimentInterface", + "SoilInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false + }, + "micro_biomass_n_meth": { + "name": "micro_biomass_n_meth", + "description": "Reference or method used in determining microbial biomass nitrogen", + "title": "microbial biomass nitrogen method", + "comments": [ + "required if \"microbial_biomass_n\" is provided" + ], + "examples": [ + { + "value": "https://doi.org/10.1016/0038-0717(87)90052-6" + }, + { + "value": "https://doi.org/10.1016/0038-0717(87)90052-6 | https://www.sciencedirect.com/science/article/abs/pii/0038071787900526" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "MIXS:0000339" + ], + "rank": 1004, + "string_serialization": "{PMID}|{DOI}|{URL}", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "SedimentInterface", + "SoilInterface", + "SoilMixsInspiredMixin" + ], + "slot_group": "mixs_inspired_section", + "range": "string", + "multivalued": false + }, + "microbial_biomass": { + "name": "microbial_biomass", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "ton, kilogram, gram per kilogram soil" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The part of the organic matter in the soil that constitutes living microorganisms smaller than 5-10 micrometer. If you keep this, you would need to have correction factors used for conversion to the final units", + "title": "microbial biomass", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "microbial biomass" + ], + "rank": 42, + "is_a": "core field", + "slot_uri": "MIXS:0000650", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "SedimentInterface", + "SoilInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "microbial_biomass_c": { + "name": "microbial_biomass_c", + "description": "The part of the organic matter in the soil that constitutes living microorganisms smaller than 5-10 micrometer.", + "title": "microbial biomass carbon", + "comments": [ + "If you provide this, correction factors used for conversion to the final units and method are required" + ], + "examples": [ + { + "value": "0.05 ug C/g dry soil" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "MIXS:0000650" + ], + "rank": 1004, + "string_serialization": "{float} {unit}", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "SedimentInterface", + "SoilInterface", + "SoilMixsInspiredMixin" + ], + "slot_group": "mixs_inspired_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? \\S+$" + }, + "microbial_biomass_n": { + "name": "microbial_biomass_n", + "description": "The part of the organic matter in the soil that constitutes living microorganisms smaller than 5-10 micrometer.", + "title": "microbial biomass nitrogen", + "comments": [ + "If you provide this, correction factors used for conversion to the final units and method are required" + ], + "examples": [ + { + "value": "0.05 ug N/g dry soil" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "MIXS:0000650" + ], + "rank": 1004, + "string_serialization": "{float} {unit}", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "SedimentInterface", + "SoilInterface", + "SoilMixsInspiredMixin" + ], + "slot_group": "mixs_inspired_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? \\S+$" + }, + "misc_param": { + "name": "misc_param", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "parameter name;measurement value" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Any other measurement performed or parameter collected, that is not listed here", + "title": "miscellaneous parameter", + "examples": [ + { + "value": "Bicarbonate ion concentration;2075 micromole per kilogram" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "miscellaneous parameter" + ], + "rank": 23, + "is_a": "core field", + "string_serialization": "{text};{float} {unit}", + "slot_uri": "MIXS:0000752", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false, + "pattern": "^([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? 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Can include multiple measurements separated by ;", + "title": "non-microbial biomass", + "examples": [ + { + "value": "insect 0.23 ug; plant 1g" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "MIXS:0000174", + "MIXS:0000650" + ], + "rank": 8, + "string_serialization": "{text};{float} {unit}", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "SoilInterface", + "SoilMixsInspiredMixin" + ], + "slot_group": "mixs_inspired_section", + "range": "string", + "multivalued": false, + "pattern": "^[^;\\t\\r\\x0A\\|]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A\\|]+$" + }, + "non_microb_biomass_method": { + "name": "non_microb_biomass_method", + "description": "Reference or method used in determining biomass", + "title": "non-microbial biomass method", + "comments": [ + "required if \"non-microbial biomass\" is provided" + ], + "examples": [ + { + "value": "https://doi.org/10.1038/s41467-021-26181-3" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "MIXS:0000650" + ], + "rank": 9, + "string_serialization": "{PMID}|{DOI}|{URL}", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "SoilInterface", + "SoilMixsInspiredMixin" + ], + "slot_group": "mixs_inspired_section", + "range": "string", + "multivalued": false + }, + "org_matter": { + "name": "org_matter", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "microgram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of organic matter", + "title": "organic matter", + "examples": [ + { + "value": "1.75 milligram per cubic meter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "organic matter" + ], + "rank": 45, + "is_a": "core field", + "slot_uri": "MIXS:0000204", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "MiscEnvsInterface", + "SedimentInterface", + "SoilInterface", + "WaterInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "org_nitro": { + "name": "org_nitro", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "microgram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of organic nitrogen", + "title": "organic nitrogen", + "examples": [ + { + "value": "4 micromole per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "organic nitrogen" + ], + "rank": 46, + "is_a": "core field", + "slot_uri": "MIXS:0000205", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "MiscEnvsInterface", + "SedimentInterface", + "SoilInterface", + "WaterInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "org_nitro_method": { + "name": "org_nitro_method", + "description": "Method used for obtaining organic nitrogen", + "title": "organic nitrogen method", + "comments": [ + "required if \"org_nitro\" is provided" + ], + "examples": [ + { + "value": "https://doi.org/10.1016/0038-0717(85)90144-0" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "MIXS:0000338", + "MIXS:0000205" + ], + "rank": 14, + "string_serialization": "{PMID}|{DOI}|{URL}", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "SedimentInterface", + "SoilInterface", + "SoilMixsInspiredMixin" + ], + "slot_group": "mixs_inspired_section", + "range": "string", + "multivalued": false + }, + "other_treatment": { + "name": "other_treatment", + "description": "Other treatments applied to your samples that are not applicable to the provided fields", + "title": "other treatments", + "notes": [ + "Values entered here will be used to determine potential new slots." + ], + "comments": [ + "This is an open text field to provide any treatments that cannot be captured in the provided slots." + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "MIXS:0000300" + ], + "rank": 15, + "string_serialization": "{text}", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "SoilInterface", + "SoilMixsInspiredMixin" + ], + "slot_group": "mixs_inspired_section", + "range": "string", + "recommended": true, + "multivalued": false + }, + "oxy_stat_samp": { + "name": "oxy_stat_samp", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Oxygenation status of sample", + "title": "oxygenation status of sample", + "examples": [ + { + "value": "aerobic" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "oxygenation status of sample" + ], + "rank": 25, + "is_a": "core field", + "slot_uri": "MIXS:0000753", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_section", + "range": "OxyStatSampEnum", + "multivalued": false + }, + "ph": { + "name": "ph", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "pH measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid", + "title": "pH", + "notes": [ + "Use modified term" + ], + "examples": [ + { + "value": "7.2" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "pH" + ], + "rank": 27, + "is_a": "core field", + "string_serialization": "{float}", + "slot_uri": "MIXS:0001001", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "MiscEnvsInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "float", + "recommended": true, + "multivalued": false, + "minimum_value": 0, + "maximum_value": 14 + }, + "ph_meth": { + "name": "ph_meth", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "PMID,DOI or url" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Reference or method used in determining ph", + "title": "pH method", + "comments": [ + "This can include a link to the instrument used or a citation for the method." + ], + "examples": [ + { + "value": "https://www.southernlabware.com/pc9500-benchtop-ph-conductivity-meter-kit-ph-accuracy-2000mv-ph-range-2-000-to-20-000.html?gclid=Cj0KCQiAwJWdBhCYARIsAJc4idCO5vtvbVMf545fcvdROFqa6zjzNSoywNx6K4k9Coo9cCc2pybtvGsaAiR0EALw_wcB" + }, + { + "value": "https://doi.org/10.2136/sssabookser5.3.c16" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "pH method" + ], + "rank": 41, + "is_a": "core field", + "string_serialization": "{PMID}|{DOI}|{URL}", + "slot_uri": "MIXS:0001106", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "MiscEnvsInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false + }, + "phosphate": { + "name": "phosphate", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of phosphate", + "title": "phosphate", + "examples": [ + { + "value": "0.7 micromole per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "phosphate" + ], + "rank": 53, + "is_a": "core field", + "slot_uri": "MIXS:0000505", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "MiscEnvsInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "prev_land_use_meth": { + "name": "prev_land_use_meth", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "PMID,DOI or url" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Reference or method used in determining previous land use and dates", + "title": "history/previous land use method", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "history/previous land use method" + ], + "rank": 26, + "is_a": "core field", + "string_serialization": "{PMID}|{DOI}|{URL}", + "slot_uri": "MIXS:0000316", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "SoilInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false + }, + "previous_land_use": { + "name": "previous_land_use", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "land use name;date" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Previous land use and dates", + "title": "history/previous land use", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "history/previous land use" + ], + "rank": 27, + "is_a": "core field", + "string_serialization": "{text};{timestamp}", + "slot_uri": "MIXS:0000315", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "SoilInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false, + "pattern": "^\\S+.*\\S+;([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$" + }, + "profile_position": { + "name": "profile_position", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Cross-sectional position in the hillslope where sample was collected.sample area position in relation to surrounding areas", + "title": "profile position", + "examples": [ + { + "value": "summit" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "profile position" + ], + "rank": 28, + "is_a": "core field", + "slot_uri": "MIXS:0001084", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "SoilInterface" + ], + "slot_group": "mixs_section", + "range": "profile_position_enum", + "multivalued": false + }, + "salinity": { + "name": "salinity", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "practical salinity unit, percentage" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The total concentration of all dissolved salts in a liquid or solid sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater.", + "title": "salinity", + "examples": [ + { + "value": "25 practical salinity unit" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "salinity" + ], + "rank": 54, + "is_a": "core field", + "slot_uri": "MIXS:0000183", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "salinity_meth": { + "name": "salinity_meth", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "PMID,DOI or url" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Reference or method used in determining salinity", + "title": "salinity method", + "examples": [ + { + "value": "https://doi.org/10.1007/978-1-61779-986-0_28" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "salinity method" + ], + "rank": 55, + "is_a": "core field", + "string_serialization": "{PMID}|{DOI}|{URL}", + "slot_uri": "MIXS:0000341", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WaterInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false + }, + "samp_collec_device": { + "name": "samp_collec_device", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "device name" + } + }, + "description": "The device used to collect an environmental sample. This field accepts terms listed under environmental sampling device (http://purl.obolibrary.org/obo/ENVO). This field also accepts terms listed under specimen collection device (http://purl.obolibrary.org/obo/GENEPIO_0002094).", + "title": "sample collection device", + "comments": [ + "Report dimensions and details when applicable" + ], + "examples": [ + { + "value": "swab, biopsy, niskin bottle, push core, drag swab [GENEPIO:0002713]" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sample collection device" + ], + "rank": 14, + "is_a": "nucleic acid sequence source field", + "string_serialization": "{termLabel} {[termID]}|{text}", + "slot_uri": "MIXS:0000002", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "recommended": true, + "multivalued": false + }, + "samp_collec_method": { + "name": "samp_collec_method", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "PMID,DOI,url , or text" + } + }, + "description": "The method employed for collecting the sample.", + "title": "sample collection method", + "comments": [ + "This can be a citation or description" + ], + "examples": [ + { + "value": "swabbing" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sample collection method" + ], + "rank": 15, + "is_a": "nucleic acid sequence source field", + "string_serialization": "{PMID}|{DOI}|{URL}|{text}", + "slot_uri": "MIXS:0001225", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "multivalued": false + }, + "samp_mat_process": { + "name": "samp_mat_process", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "text" + } + }, + "description": "A brief description of any processing applied to the sample during or after retrieving the sample from environment, or a link to the relevant protocol(s) performed.", + "title": "sample material processing", + "examples": [ + { + "value": "filtering of seawater" + }, + { + "value": "storing samples in ethanol" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sample material processing" + ], + "rank": 12, + "is_a": "nucleic acid sequence source field", + "string_serialization": "{text}", + "slot_uri": "MIXS:0000016", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "multivalued": false + }, + "samp_size": { + "name": "samp_size", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "millliter, gram, milligram, liter" + } + }, + "description": "The total amount or size (volume (ml), mass (g) or area (m2) ) of sample collected.", + "title": "amount or size of sample collected", + "comments": [ + "This refers to the TOTAL amount of sample collected from the experiment. NOT the amount sent to each institution or collected for a specific analysis." + ], + "examples": [ + { + "value": "5 grams" + }, + { + "value": "10 mL" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "amount or size of sample collected" + ], + "rank": 18, + "is_a": "nucleic acid sequence source field", + "string_serialization": "{float} {unit}", + "slot_uri": "MIXS:0000001", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? \\S+$" + }, + "samp_store_temp": { + "name": "samp_store_temp", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "degree Celsius" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Temperature at which the sample was stored (degrees are assumed)", + "title": "sample storage temperature", + "examples": [ + { + "value": "-80 Celsius" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sample storage temperature" + ], + "rank": 7, + "is_a": "core field", + "slot_uri": "MIXS:0000110", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "required": true, + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "sample_link": { + "name": "sample_link", + "description": "A unique identifier to assign parent-child, subsample, or sibling samples. This is relevant when a sample or other material was used to generate the new sample.", + "title": "sample linkage", + "notes": [ + "also tempted to include SampIdNewTermsMixin but if len(slot_usage.keys()) > 1 and \"placeholder\" in slot_usage.keys():AttributeError: 'list' object has no attribute 'keys'" + ], + "comments": [ + "This field allows multiple entries separated by ; (Examples: Soil collected from the field will link with the soil used in an incubation. The soil a plant was grown in links to the plant sample. An original culture sample was transferred to a new vial and generated a new sample)" + ], + "examples": [ + { + "value": "IGSN:DSJ0284" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "rank": 5, + "string_serialization": "{text}:{text}", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface", + "SampIdNewTermsMixin" + ], + "slot_group": "sample_id_section", + "range": "string", + "recommended": true, + "multivalued": false, + "pattern": "[^\\:\\n\\r]+\\:[^\\:\\n\\r]+" + }, + "season_precpt": { + "name": "season_precpt", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "millimeter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The average of all seasonal precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or Isohyetal maps.", + "title": "average seasonal precipitation", + "todos": [ + "check validation & examples. always mm? so value only? Or value + unit", + "This is no longer matching the listed IRI from GSC. When NMDC has its own slots, map this to the MIxS slot", + "check validation & examples. always mm? so value only? Or value + unit" + ], + "notes": [ + "mean and average are the same thing, but it seems like bad practice to not be consistent. Changed mean to average", + "mean and average are the same thing, but it seems like bad practice to not be consistent. Changed mean to average" + ], + "comments": [ + "Seasons are defined as spring (March, April, May), summer (June, July, August), autumn (September, October, November) and winter (December, January, February)." + ], + "examples": [ + { + "value": "0.4 inch" + }, + { + "value": "10.16 mm" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "mean seasonal precipitation" + ], + "rank": 29, + "is_a": "core field", + "slot_uri": "MIXS:0000645", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "SoilInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "season_temp": { + "name": "season_temp", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "degree Celsius" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Mean seasonal temperature", + "title": "mean seasonal temperature", + "examples": [ + { + "value": "18 degree Celsius" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "mean seasonal temperature" + ], + "rank": 30, + "is_a": "core field", + "slot_uri": "MIXS:0000643", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "SoilInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "sieving": { + "name": "sieving", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "design name and/or size;amount" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Collection design of pooled samples and/or sieve size and amount of sample sieved", + "title": "composite design/sieving", + "todos": [ + "check validation and examples", + "check validation and examples" + ], + "comments": [ + "Describe how samples were composited or sieved.", + "Use 'sample link' to indicate which samples were combined." + ], + "examples": [ + { + "value": "combined 2 cores" + }, + { + "value": "4mm sieved" + }, + { + "value": "4 mm sieved and homogenized" + }, + { + "value": "50 g" + }, + { + "value": "5 cores" + }, + { + "value": "2 mm sieved" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "composite design/sieving" + ], + "rank": 8, + "is_a": "core field", + "string_serialization": "{{text}|{float} {unit}};{float} {unit}", + "slot_uri": "MIXS:0000322", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "SedimentInterface", + "SoilInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "recommended": true, + "multivalued": false + }, + "size_frac_low": { + "name": "size_frac_low", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micrometer" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Refers to the mesh/pore size used to pre-filter/pre-sort the sample. Materials larger than the size threshold are excluded from the sample", + "title": "size-fraction lower threshold", + "examples": [ + { + "value": "0.2 micrometer" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "size-fraction lower threshold" + ], + "rank": 10, + "is_a": "core field", + "slot_uri": "MIXS:0000735", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "SoilInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "recommended": false, + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "size_frac_up": { + "name": "size_frac_up", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micrometer" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Refers to the mesh/pore size used to retain the sample. Materials smaller than the size threshold are excluded from the sample", + "title": "size-fraction upper threshold", + "examples": [ + { + "value": "20 micrometer" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "size-fraction upper threshold" + ], + "rank": 11, + "is_a": "core field", + "slot_uri": "MIXS:0000736", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "SoilInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "recommended": false, + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "slope_aspect": { + "name": "slope_aspect", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "degree" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The direction a slope faces. While looking down a slope use a compass to record the direction you are facing (direction or degrees). - This measure provides an indication of sun and wind exposure that will influence soil temperature and evapotranspiration.", + "title": "slope aspect", + "todos": [ + "This is no longer matching the listed IRI from GSC. When NMDC has its own slots, map this to the MIxS slot" + ], + "comments": [ + "Aspect is the orientation of slope, measured clockwise in degrees from 0 to 360, where 0 is north-facing, 90 is east-facing, 180 is south-facing, and 270 is west-facing." + ], + "examples": [ + { + "value": "35" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "slope aspect" + ], + "rank": 1, + "is_a": "core field", + "slot_uri": "MIXS:0000647", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "SoilInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "slope_gradient": { + "name": "slope_gradient", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "percentage" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Commonly called 'slope'. The angle between ground surface and a horizontal line (in percent). This is the direction that overland water would flow. This measure is usually taken with a hand level meter or clinometer", + "title": "slope gradient", + "todos": [ + "Slope is a percent. How does the validation work? Check to correct examples", + "Slope is a percent. How does the validation work? Check to correct examples" + ], + "examples": [ + { + "value": "10%" + }, + { + "value": "10 %" + }, + { + "value": "0.1" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "slope gradient" + ], + "rank": 31, + "is_a": "core field", + "slot_uri": "MIXS:0000646", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "SoilInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "soil_horizon": { + "name": "soil_horizon", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Specific layer in the land area which measures parallel to the soil surface and possesses physical characteristics which differ from the layers above and beneath", + "title": "soil horizon", + "examples": [ + { + "value": "A horizon" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "soil horizon" + ], + "rank": 32, + "is_a": "core field", + "slot_uri": "MIXS:0001082", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "SoilInterface" + ], + "slot_group": "mixs_section", + "range": "soil_horizon_enum", + "multivalued": false + }, + "soil_text_measure": { + "name": "soil_text_measure", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The relative proportion of different grain sizes of mineral particles in a soil, as described using a standard system; express as % sand (50 um to 2 mm), silt (2 um to 50 um), and clay (<2 um) with textural name (e.g., silty clay loam) optional.", + "title": "soil texture measurement", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "soil texture measurement" + ], + "rank": 33, + "is_a": "core field", + "slot_uri": "MIXS:0000335", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "SoilInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "soil_texture_meth": { + "name": "soil_texture_meth", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "PMID,DOI or url" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Reference or method used in determining soil texture", + "title": "soil texture method", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "soil texture method" + ], + "rank": 34, + "is_a": "core field", + "string_serialization": "{PMID}|{DOI}|{URL}", + "slot_uri": "MIXS:0000336", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "SoilInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false + }, + "soil_type": { + "name": "soil_type", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "ENVO_00001998" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Description of the soil type or classification. This field accepts terms under soil (http://purl.obolibrary.org/obo/ENVO_00001998). Multiple terms can be separated by pipes.", + "title": "soil type", + "examples": [ + { + "value": "plinthosol [ENVO:00002250]" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "soil type" + ], + "rank": 35, + "is_a": "core field", + "string_serialization": "{termLabel} {[termID]}", + "slot_uri": "MIXS:0000332", + "owner": "Biosample", + "domain_of": [ + "FieldResearchSite", + "Biosample", + "SoilInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false, + "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$" + }, + "soil_type_meth": { + "name": "soil_type_meth", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "PMID,DOI or url" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Reference or method used in determining soil series name or other lower-level classification", + "title": "soil type method", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "soil type method" + ], + "rank": 36, + "is_a": "core field", + "string_serialization": "{PMID}|{DOI}|{URL}", + "slot_uri": "MIXS:0000334", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "SoilInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false + }, + "specific_ecosystem": { + "name": "specific_ecosystem", + "description": "Specific ecosystems represent specific features of the environment like aphotic zone in an ocean or gastric mucosa within a host digestive system. Specific ecosystem is in position 5/5 in a GOLD path.", + "comments": [ + "Specific ecosystems help to define samples based on very specific characteristics of an environment under the five-level classification system." + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "https://gold.jgi.doe.gov/help" + ], + "rank": 13, + "is_a": "gold_path_field", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "Study", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "SpecificEcosystemForSoilEnum", + "recommended": true + }, + "start_date_inc": { + "name": "start_date_inc", + "description": "Date the incubation was started. Only relevant for incubation samples.", + "title": "incubation start date", + "notes": [ + "MIxS collection_date accepts (truncated) ISO8601. DH taking arbitrary precision date only" + ], + "comments": [ + "Date should be formatted as YYYY(-MM(-DD)). Ie, 2021-04-15, 2021-04 and 2021 are all acceptable." + ], + "examples": [ + { + "value": "2021-04-15, 2021-04 and 2021 are all acceptable." + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "MIXS:0000011" + ], + "rank": 4, + "string_serialization": "{date, arbitrary precision}", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WaterInterface", + "SoilMixsInspiredMixin" + ], + "slot_group": "mixs_inspired_section", + "range": "string", + "recommended": true, + "multivalued": false, + "pattern": "^[12]\\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\\d|3[01]))?)?$" + }, + "start_time_inc": { + "name": "start_time_inc", + "description": "Time the incubation was started. Only relevant for incubation samples.", + "title": "incubation start time, GMT", + "notes": [ + "MIxS collection_date accepts (truncated) ISO8601. DH taking seconds optional time only" + ], + "comments": [ + "Time should be entered as HH:MM(:SS) in GMT. See here for a converter: https://www.worldtimebuddy.com/pst-to-gmt-converter" + ], + "examples": [ + { + "value": "13:33 or 13:33:55" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "MIXS:0000011" + ], + "rank": 5, + "string_serialization": "{time, seconds optional}", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "SoilInterface", + "SoilMixsInspiredMixin" + ], + "slot_group": "mixs_inspired_section", + "range": "string", + "recommended": true, + "multivalued": false, + "pattern": "^([01]?\\d|2[0-3]|24(?=:00?:00?$)):([0-5]\\d)(:([0-5]\\d))?$" + }, + "store_cond": { + "name": "store_cond", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "storage condition type;duration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Explain how the soil sample is stored (fresh/frozen/other).", + "title": "storage conditions", + "examples": [ + { + "value": "-20 degree Celsius freezer;P2Y10D" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "storage conditions" + ], + "rank": 2, + "is_a": "core field", + "string_serialization": "{text};{duration}", + "slot_uri": "MIXS:0000327", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "SoilInterface" + ], + "slot_group": "mixs_modified_section", + "range": "StoreCondEnum", + "required": true, + "multivalued": false + }, + "temp": { + "name": "temp", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "degree Celsius" + } + }, + "description": "Temperature of the sample at the time of sampling.", + "title": "temperature", + "examples": [ + { + "value": "25 degree Celsius" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "temperature" + ], + "rank": 37, + "is_a": "environment field", + "slot_uri": "MIXS:0000113", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "tillage": { + "name": "tillage", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Note method(s) used for tilling", + "title": "history/tillage", + "examples": [ + { + "value": "chisel" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "history/tillage" + ], + "rank": 38, + "is_a": "core field", + "slot_uri": "MIXS:0001081", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "SoilInterface" + ], + "slot_group": "mixs_section", + "range": "tillage_enum", + "multivalued": true + }, + "tot_carb": { + "name": "tot_carb", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "microgram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Total carbon content", + "title": "total carbon", + "todos": [ + "is this inorganic and organic? both? could use some clarification.", + "ug/L doesn't seem like the right units. Should check this slots usage in databases and re-evaluate. I couldn't find any references that provided this data in this format", + "is this inorganic and organic? both? could use some clarification.", + "ug/L doesn't seem like the right units. Should check this slots usage in databases and re-evaluate. I couldn't find any references that provided this data in this format" + ], + "examples": [ + { + "value": "1 ug/L" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "total carbon" + ], + "rank": 47, + "is_a": "core field", + "slot_uri": "MIXS:0000525", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "SedimentInterface", + "SoilInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "tot_nitro_cont_meth": { + "name": "tot_nitro_cont_meth", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "PMID,DOI or url" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Reference or method used in determining the total nitrogen", + "title": "total nitrogen content method", + "examples": [ + { + "value": "https://doi.org/10.2134/agronmonogr9.2.c32" + }, + { + "value": "https://acsess.onlinelibrary.wiley.com/doi/full/10.2136/sssaj2009.0389?casa_token=bm0pYIUdNMgAAAAA%3AOWVRR0STHaOe-afTcTdxn5m1hM8n2ltM0wY-b1iYpYdD9dhwppk5j3LvC2IO5yhOIvyLVeQz4NZRCZo" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "total nitrogen content method" + ], + "rank": 49, + "is_a": "core field", + "string_serialization": "{PMID}|{DOI}|{URL}", + "slot_uri": "MIXS:0000338", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "SedimentInterface", + "SoilInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false + }, + "tot_nitro_content": { + "name": "tot_nitro_content", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "microgram per liter, micromole per liter, milligram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Total nitrogen content of the sample", + "title": "total nitrogen content", + "examples": [ + { + "value": "5 mg N/ L" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "total nitrogen content" + ], + "rank": 48, + "is_a": "core field", + "slot_uri": "MIXS:0000530", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "SedimentInterface", + "SoilInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "tot_org_c_meth": { + "name": "tot_org_c_meth", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "PMID,DOI or url" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Reference or method used in determining total organic carbon", + "title": "total organic carbon method", + "examples": [ + { + "value": "https://doi.org/10.1080/07352680902776556" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "total organic carbon method" + ], + "rank": 51, + "is_a": "core field", + "string_serialization": "{PMID}|{DOI}|{URL}", + "slot_uri": "MIXS:0000337", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "SedimentInterface", + "SoilInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false + }, + "tot_org_carb": { + "name": "tot_org_carb", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "gram Carbon per kilogram sample material" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content", + "title": "total organic carbon", + "todos": [ + "check description. How are they different?", + "check description. How are they different?" + ], + "examples": [ + { + "value": "5 mg N/ L" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "total organic carbon" + ], + "rank": 50, + "is_a": "core field", + "slot_uri": "MIXS:0000533", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "SedimentInterface", + "SoilInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "tot_phosp": { + "name": "tot_phosp", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per liter, milligram per liter, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus", + "title": "total phosphorus", + "examples": [ + { + "value": "0.03 milligram per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "total phosphorus" + ], + "rank": 52, + "is_a": "core field", + "slot_uri": "MIXS:0000117", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "SoilInterface", + "WaterInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "water_cont_soil_meth": { + "name": "water_cont_soil_meth", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "PMID,DOI or url" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Reference or method used in determining the water content of soil", + "title": "water content method", + "todos": [ + "Why is it soil water content method in the name but not the title? Is this slot used in other samples?", + "Soil water content can be measure MANY ways and often, multiple ways are used in one experiment (gravimetric water content and water holding capacity and water filled pore space, to name a few).", + "Should this be multi valued? How to we manage and validate this?", + "Why is it soil water content method in the name but not the title? Is this slot used in other samples?", + "Soil water content can be measure MANY ways and often, multiple ways are used in one experiment (gravimetric water content and water holding capacity and water filled pore space, to name a few).", + "Should this be multi valued? How to we manage and validate this?" + ], + "comments": [ + "Required if providing water content" + ], + "examples": [ + { + "value": "J. Nat. Prod. Plant Resour., 2012, 2 (4):500-503" + }, + { + "value": "https://dec.alaska.gov/applications/spar/webcalc/definitions.htm" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "water content method" + ], + "rank": 40, + "is_a": "core field", + "string_serialization": "{PMID}|{DOI}|{URL}", + "slot_uri": "MIXS:0000323", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "SedimentInterface", + "SoilInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false + }, + "water_content": { + "name": "water_content", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "string" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "gram per gram or cubic centimeter per cubic centimeter" + } + }, + "description": "Water content measurement", + "title": "water content", + "todos": [ + "value in preferred unit is too limiting. need to change this", + "check and correct validation so examples are accepted", + "how to manage multiple water content methods?" + ], + "examples": [ + { + "value": "0.75 g water/g dry soil" + }, + { + "value": "75% water holding capacity" + }, + { + "value": "1.1 g fresh weight/ dry weight" + }, + { + "value": "10% water filled pore space" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "water content" + ], + "rank": 39, + "is_a": "core field", + "string_serialization": "{float or pct} {unit}", + "slot_uri": "MIXS:0000185", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "SedimentInterface", + "SoilInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)?%? \\S.+$" + }, + "watering_regm": { + "name": "watering_regm", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value;treatment interval and duration" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milliliter, liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Information about treatment involving an exposure to watering frequencies, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens", + "title": "watering regimen", + "examples": [ + { + "value": "1 liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" + }, + { + "value": "75% water holding capacity; constant" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "watering regimen" + ], + "rank": 25, + "is_a": "core field", + "string_serialization": "{float} {unit};{Rn/start_time/end_time/duration}", + "slot_uri": "MIXS:0000591", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "recommended": true, + "multivalued": false + }, + "zinc": { + "name": "zinc", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "mg/kg (ppm)" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of zinc in the sample", + "title": "zinc", + "examples": [ + { + "value": "2.5 mg/kg" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "https://www.ornl.gov/content/bio-scales-0" + ], + "aliases": [ + "zinc" + ], + "rank": 1004, + "owner": "Biosample", + "domain_of": [ + "Biosample", + "SoilInterface" + ], + "slot_group": "mixs_inspired_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "organism_count": { + "name": "organism_count", + "range": "string", + "multivalued": false, + "pattern": "^(\\S+.*\\S+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? \\S+.*\\S+;(qPCR|ATP|MPN|other)\\|)*(\\S+.*\\S+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? \\S+.*\\S+;(qPCR|ATP|MPN|other))$" + } + }, + "attributes": { + "agrochem_addition": { + "name": "agrochem_addition", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "agrochemical name;agrochemical amount;timestamp" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "gram, mole per liter, milligram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Addition of fertilizers, pesticides, etc. - amount and time of applications", + "title": "history/agrochemical additions", + "examples": [ + { + "value": "roundup;5 milligram per liter;2018-06-21" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "history/agrochemical additions" + ], + "rank": 2, + "is_a": "core field", + "string_serialization": "{text};{float} {unit};{timestamp}", + "slot_uri": "MIXS:0000639", + "alias": "agrochem_addition", + "owner": "SoilInterface", + "domain_of": [ + "Biosample", + "SoilInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false, + "pattern": ".*" + }, + "air_temp_regm": { + "name": "air_temp_regm", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "temperature value;treatment interval and duration" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "meter" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Information about treatment involving an exposure to varying temperatures; should include the temperature, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include different temperature regimens", + "title": "air temperature regimen", + "examples": [ + { + "value": "25 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "air temperature regimen" + ], + "rank": 16, + "is_a": "core field", + "string_serialization": "{float} {unit};{Rn/start_time/end_time/duration}", + "slot_uri": "MIXS:0000551", + "alias": "air_temp_regm", + "owner": "SoilInterface", + "domain_of": [ + "Biosample", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "recommended": true, + "multivalued": false + }, + "al_sat": { + "name": "al_sat", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "percentage" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The relative abundance of aluminum in the sample", + "title": "aluminum saturation/ extreme unusual properties", + "todos": [ + "Example & validation. Can we configure things so that 27% & 27 % & 0.27 will validate?", + "I think it's weird the way GSC writes the title. I recommend this change. Thoughts? I would argue this isn't an extreme unusual property. It's just a biogeochemical measurement.", + "This is no longer matching the listed IRI from GSC. When NMDC has its own slots, map this to the MIxS slot", + "Example & validation. Can we make rules that 27% & 27 % & 0.27 will validate?", + "I think it's weird the way GSC writes the title. I recommend this change. Thoughts? I would argue this isn't an extreme unusual property. It's just a biogeochemical measurement." + ], + "notes": [ + "Aluminum saturation is the percentage of the CEC occupies by aluminum. Like all cations, aluminum held by the cation exchange complex is in equilibrium with aluminum in the soil solution." + ], + "examples": [ + { + "value": "0.27" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "extreme_unusual_properties/Al saturation" + ], + "rank": 3, + "is_a": "core field", + "slot_uri": "MIXS:0000607", + "alias": "al_sat", + "owner": "SoilInterface", + "domain_of": [ + "Biosample", + "SoilInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "al_sat_meth": { + "name": "al_sat_meth", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "PMID,DOI or URL" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Reference or method used in determining Aluminum saturation", + "title": "aluminum saturation method/ extreme unusual properties", + "todos": [ + "I think it's weird the way GSC writes the title. I recommend this change. Thoughts?", + "This is no longer matching the listed IRI from GSC. When NMDC has its own slots, map this to the MIxS slot", + "I think it's weird the way GSC writes the title. I recommend this change. Thoughts?" + ], + "comments": [ + "Required when aluminum saturation is provided." + ], + "examples": [ + { + "value": "https://doi.org/10.1371/journal.pone.0176357" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "extreme_unusual_properties/Al saturation method" + ], + "rank": 4, + "is_a": "core field", + "string_serialization": "{PMID}|{DOI}|{URL}", + "slot_uri": "MIXS:0000324", + "alias": "al_sat_meth", + "owner": "SoilInterface", + "domain_of": [ + "Biosample", + "SoilInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false + }, + "ammonium_nitrogen": { + "name": "ammonium_nitrogen", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "mg/kg" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of ammonium nitrogen in the sample", + "title": "ammonium nitrogen", + "examples": [ + { + "value": "2.3 mg/kg" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "https://www.ornl.gov/content/bio-scales-0" + ], + "aliases": [ + "ammonium_nitrogen", + "NH4-N" + ], + "rank": 1005, + "alias": "ammonium_nitrogen", + "owner": "SoilInterface", + "domain_of": [ + "Biosample", + "SoilInterface" + ], + "slot_group": "mixs_inspired_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "annual_precpt": { + "name": "annual_precpt", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "millimeter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The average of all annual precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or Isohyetal maps.", + "title": "mean annual precipitation", + "todos": [ + "This is no longer matching the listed IRI from GSC, added example. When NMDC has its own slots, map this to the MIxS slot" + ], + "examples": [ + { + "value": "8.94 inch" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "mean annual precipitation" + ], + "rank": 5, + "is_a": "core field", + "slot_uri": "MIXS:0000644", + "alias": "annual_precpt", + "owner": "SoilInterface", + "domain_of": [ + "Biosample", + "SoilInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "annual_temp": { + "name": "annual_temp", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "degree Celsius" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Mean annual temperature", + "title": "mean annual temperature", + "examples": [ + { + "value": "12.5 degree Celsius" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "mean annual temperature" + ], + "rank": 6, + "is_a": "core field", + "slot_uri": "MIXS:0000642", + "alias": "annual_temp", + "owner": "SoilInterface", + "domain_of": [ + "Biosample", + "SoilInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "biotic_regm": { + "name": "biotic_regm", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "free text" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Information about treatment(s) involving use of biotic factors, such as bacteria, viruses or fungi.", + "title": "biotic regimen", + "examples": [ + { + "value": "sample inoculated with Rhizobium spp. Culture" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "biotic regimen" + ], + "rank": 13, + "is_a": "core field", + "string_serialization": "{text}", + "slot_uri": "MIXS:0001038", + "alias": "biotic_regm", + "owner": "SoilInterface", + "domain_of": [ + "Biosample", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "recommended": true, + "multivalued": false + }, + "biotic_relationship": { + "name": "biotic_relationship", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + } + }, + "description": "Description of relationship(s) between the subject organism and other organism(s) it is associated with. E.g., parasite on species X; mutualist with species Y. The target organism is the subject of the relationship, and the other organism(s) is the object", + "title": "observed biotic relationship", + "examples": [ + { + "value": "free living" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "observed biotic relationship" + ], + "rank": 22, + "is_a": "nucleic acid sequence source field", + "slot_uri": "MIXS:0000028", + "alias": "biotic_relationship", + "owner": "SoilInterface", + "domain_of": [ + "Biosample", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface" + ], + "slot_group": "mixs_modified_section", + "range": "biotic_relationship_enum", + "multivalued": false + }, + "bulk_elect_conductivity": { + "name": "bulk_elect_conductivity", + "description": "Electrical conductivity is a measure of the ability to carry electric current, which is mostly dictated by the chemistry of and amount of water.", + "title": "bulk electrical conductivity", + "comments": [ + "Provide the value output of the field instrument." + ], + "examples": [ + { + "value": "0.017 mS/cm" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "rank": 1008, + "alias": "bulk_elect_conductivity", + "owner": "SoilInterface", + "domain_of": [ + "Biosample", + "SoilInterface" + ], + "slot_group": "mixs_inspired_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "carb_nitro_ratio": { + "name": "carb_nitro_ratio", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Ratio of amount or concentrations of carbon to nitrogen", + "title": "carbon/nitrogen ratio", + "examples": [ + { + "value": "0.417361111" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "carbon/nitrogen ratio" + ], + "rank": 44, + "is_a": "core field", + "slot_uri": "MIXS:0000310", + "alias": "carb_nitro_ratio", + "owner": "SoilInterface", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "SedimentInterface", + "SoilInterface", + "WaterInterface" + ], + "slot_group": "mixs_section", + "range": "float", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "chem_administration": { + "name": "chem_administration", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "CHEBI;timestamp" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi", + "title": "chemical administration", + "examples": [ + { + "value": "agar [CHEBI:2509];2018-05-11|agar [CHEBI:2509];2018-05-22" + }, + { + "value": "agar [CHEBI:2509];2018-05" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "chemical administration" + ], + "rank": 17, + "is_a": "core field", + "string_serialization": "{termLabel} {[termID]};{timestamp}", + "slot_uri": "MIXS:0000751", + "alias": "chem_administration", + "owner": "SoilInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "recommended": true, + "multivalued": false, + "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\];([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$" + }, + "climate_environment": { + "name": "climate_environment", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "climate name;treatment interval and duration" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Treatment involving an exposure to a particular climate; treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple climates", + "title": "climate environment", + "todos": [ + "description says \"can include multiple climates\" but multivalued is set to false", + "add examples, i need to see some examples to add correctly formatted example.", + "description says \"can include multiple climates\" but multivalued is set to false", + "add examples, i need to see some examples to add correctly formatted example." + ], + "examples": [ + { + "value": "tropical climate;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "climate environment" + ], + "rank": 19, + "is_a": "core field", + "string_serialization": "{text};{Rn/start_time/end_time/duration}", + "slot_uri": "MIXS:0001040", + "alias": "climate_environment", + "owner": "SoilInterface", + "domain_of": [ + "Biosample", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "recommended": true, + "multivalued": false + }, + "collection_date": { + "name": "collection_date", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "date and time" + } + }, + "description": "The date of sampling", + "title": "collection date", + "notes": [ + "MIxS collection_date accepts (truncated) ISO8601. DH taking arb prec date only", + "Use modified term (amended definition)" + ], + "examples": [ + { + "value": "2021-04-15" + }, + { + "value": "2021-04" + }, + { + "value": "2021" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "collection date" + ], + "rank": 3, + "is_a": "environment field", + "string_serialization": "{date, arbitrary precision}", + "slot_uri": "MIXS:0000011", + "alias": "collection_date", + "owner": "SoilInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "required": true, + "multivalued": false, + "pattern": "^[12]\\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\\d|3[01]))?)?$" + }, + "collection_date_inc": { + "name": "collection_date_inc", + "description": "Date the incubation was harvested/collected/ended. Only relevant for incubation samples.", + "title": "incubation collection date", + "notes": [ + "MIxS collection_date accepts (truncated) ISO8601. DH taking arbitrary precision date only" + ], + "comments": [ + "Date should be formatted as YYYY(-MM(-DD)). Ie, 2021-04-15, 2021-04 and 2021 are all acceptable." + ], + "examples": [ + { + "value": "2021-04-15, 2021-04 and 2021 are all acceptable." + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "MIXS:0000011" + ], + "rank": 2, + "string_serialization": "{date, arbitrary precision}", + "alias": "collection_date_inc", + "owner": "SoilInterface", + "domain_of": [ + "Biosample", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WaterInterface", + "SoilMixsInspiredMixin" + ], + "slot_group": "mixs_inspired_section", + "range": "string", + "recommended": true, + "multivalued": false, + "pattern": "^[12]\\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\\d|3[01]))?)?$" + }, + "collection_time": { + "name": "collection_time", + "description": "The time of sampling, either as an instance (single point) or interval.", + "title": "collection time, GMT", + "notes": [ + "MIxS collection_date accepts (truncated) ISO8601. DH taking seconds optional time only" + ], + "comments": [ + "Time should be entered as HH:MM(:SS) in GMT. See here for a converter: https://www.worldtimebuddy.com/pst-to-gmt-converter" + ], + "examples": [ + { + "value": "13:33 or 13:33:55" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "MIXS:0000011" + ], + "rank": 1, + "string_serialization": "{time, seconds optional}", + "alias": "collection_time", + "owner": "SoilInterface", + "domain_of": [ + "Biosample", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WaterInterface", + "SoilMixsInspiredMixin" + ], + "slot_group": "mixs_inspired_section", + "range": "string", + "recommended": true, + "multivalued": false, + "pattern": "^([01]?\\d|2[0-3]|24(?=:00?:00?$)):([0-5]\\d)(:([0-5]\\d))?$" + }, + "collection_time_inc": { + "name": "collection_time_inc", + "description": "Time the incubation was harvested/collected/ended. Only relevant for incubation samples.", + "title": "incubation collection time, GMT", + "notes": [ + "MIxS collection_date accepts (truncated) ISO8601. DH taking seconds optional time only" + ], + "comments": [ + "Time should be entered as HH:MM(:SS) in GMT. See here for a converter: https://www.worldtimebuddy.com/pst-to-gmt-converter" + ], + "examples": [ + { + "value": "13:33 or 13:33:55" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "MIXS:0000011" + ], + "rank": 3, + "string_serialization": "{time, seconds optional}", + "alias": "collection_time_inc", + "owner": "SoilInterface", + "domain_of": [ + "Biosample", + "SoilInterface", + "SoilMixsInspiredMixin" + ], + "slot_group": "mixs_inspired_section", + "range": "string", + "recommended": true, + "multivalued": false, + "pattern": "^([01]?\\d|2[0-3]|24(?=:00?:00?$)):([0-5]\\d)(:([0-5]\\d))?$" + }, + "crop_rotation": { + "name": "crop_rotation", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "crop rotation status;schedule" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Whether or not crop is rotated, and if yes, rotation schedule", + "title": "history/crop rotation", + "examples": [ + { + "value": "yes;R2/2017-01-01/2018-12-31/P6M" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "history/crop rotation" + ], + "rank": 7, + "is_a": "core field", + "string_serialization": "{boolean};{Rn/start_time/end_time/duration}", + "slot_uri": "MIXS:0000318", + "alias": "crop_rotation", + "owner": "SoilInterface", + "domain_of": [ + "Biosample", + "SoilInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false + }, + "cur_land_use": { + "name": "cur_land_use", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Present state of sample site", + "title": "current land use", + "examples": [ + { + "value": "conifers" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "current land use" + ], + "rank": 8, + "is_a": "core field", + "slot_uri": "MIXS:0001080", + "alias": "cur_land_use", + "owner": "SoilInterface", + "domain_of": [ + "Biosample", + "SoilInterface" + ], + "slot_group": "mixs_section", + "range": "cur_land_use_enum", + "multivalued": false + }, + "cur_vegetation": { + "name": "cur_vegetation", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "current vegetation type" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Vegetation classification from one or more standard classification systems, or agricultural crop", + "title": "current vegetation", + "todos": [ + "Recommend changing this from text value to some king of ontology?", + "This is no longer matching the listed IRI from GSC. When NMDC has its own slots, map this to the MIxS slot", + "Recommend changing this from text value to some kind of ontology?" + ], + "comments": [ + "Values provided here can be specific species of vegetation or vegetation regions", + "See for vegetation regions- https://education.nationalgeographic.org/resource/vegetation-region" + ], + "examples": [ + { + "value": "deciduous forest" + }, + { + "value": "forest" + }, + { + "value": "Bauhinia variegata" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "current vegetation" + ], + "rank": 9, + "is_a": "core field", + "string_serialization": "{text}", + "slot_uri": "MIXS:0000312", + "alias": "cur_vegetation", + "owner": "SoilInterface", + "domain_of": [ + "FieldResearchSite", + "Biosample", + "SoilInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false + }, + "cur_vegetation_meth": { + "name": "cur_vegetation_meth", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "PMID,DOI or url" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Reference or method used in vegetation classification", + "title": "current vegetation method", + "todos": [ + "I'm not sure this is a DOI, PMID, or URI. Should pool the community and find out how they accomplish this if provided.", + "This is no longer matching the listed IRI from GSC. When NMDC has its own slots, map this to the MIxS slot", + "I'm not sure this is a DOI, PMID, or URI. Should pool the community and find out how they accomplish this if provided." + ], + "comments": [ + "Required when current vegetation is provided." + ], + "examples": [ + { + "value": "https://doi.org/10.1111/j.1654-109X.2011.01154.x" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "current vegetation method" + ], + "rank": 10, + "is_a": "core field", + "string_serialization": "{PMID}|{DOI}|{URL}", + "slot_uri": "MIXS:0000314", + "alias": "cur_vegetation_meth", + "owner": "SoilInterface", + "domain_of": [ + "Biosample", + "SoilInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false + }, + "depth": { + "name": "depth", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + } + }, + "description": "The vertical distance below local surface, e.g. for sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples.", + "title": "depth, meters", + "notes": [ + "Use modified term" + ], + "comments": [ + "All depths must be reported in meters. Provide the numerical portion only." + ], + "examples": [ + { + "value": "0 - 0.1" + }, + { + "value": "1" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "depth" + ], + "rank": 9, + "is_a": "environment field", + "string_serialization": "{float}-{float}", + "slot_uri": "MIXS:0000018", + "alias": "depth", + "owner": "SoilInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "required": true, + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)?\\s*-\\s*[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)?$" + }, + "drainage_class": { + "name": "drainage_class", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Drainage classification from a standard system such as the USDA system", + "title": "drainage classification", + "examples": [ + { + "value": "well" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "drainage classification" + ], + "rank": 11, + "is_a": "core field", + "slot_uri": "MIXS:0001085", + "alias": "drainage_class", + "owner": "SoilInterface", + "domain_of": [ + "Biosample", + "SoilInterface" + ], + "slot_group": "mixs_section", + "range": "drainage_class_enum", + "multivalued": false + }, + "ecosystem": { + "name": "ecosystem", + "description": "An ecosystem is a combination of a physical environment (abiotic factors) and all the organisms (biotic factors) that interact with this environment. Ecosystem is in position 1/5 in a GOLD path.", + "comments": [ + "The abiotic factors play a profound role on the type and composition of organisms in a given environment. The GOLD Ecosystem at the top of the five-level classification system is aimed at capturing the broader environment from which an organism or environmental sample is collected. The three broad groups under Ecosystem are Environmental, Host-associated, and Engineered. They represent samples collected from a natural environment or from another organism or from engineered environments like bioreactors respectively." + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "https://gold.jgi.doe.gov/help" + ], + "rank": 9, + "is_a": "gold_path_field", + "alias": "ecosystem", + "owner": "SoilInterface", + "domain_of": [ + "Biosample", + "Study", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "EcosystemForSoilEnum", + "recommended": true + }, + "ecosystem_category": { + "name": "ecosystem_category", + "description": "Ecosystem categories represent divisions within the ecosystem based on specific characteristics of the environment from where an organism or sample is isolated. Ecosystem category is in position 2/5 in a GOLD path.", + "comments": [ + "The Environmental ecosystem (for example) is divided into Air, Aquatic and Terrestrial. Ecosystem categories for Host-associated samples can be individual hosts or phyla and for engineered samples it may be manipulated environments like bioreactors, solid waste etc." + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "https://gold.jgi.doe.gov/help" + ], + "rank": 10, + "is_a": "gold_path_field", + "alias": "ecosystem_category", + "owner": "SoilInterface", + "domain_of": [ + "Biosample", + "Study", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "EcosystemCategoryForSoilEnum", + "recommended": true + }, + "ecosystem_subtype": { + "name": "ecosystem_subtype", + "description": "Ecosystem subtypes represent further subdivision of Ecosystem types into more distinct subtypes. Ecosystem subtype is in position 4/5 in a GOLD path.", + "comments": [ + "Ecosystem Type Marine (Environmental -> Aquatic -> Marine) is further divided (for example) into Intertidal zone, Coastal, Pelagic, Intertidal zone etc. in the Ecosystem subtype category." + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "https://gold.jgi.doe.gov/help" + ], + "rank": 12, + "is_a": "gold_path_field", + "alias": "ecosystem_subtype", + "owner": "SoilInterface", + "domain_of": [ + "Biosample", + "Study", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "EcosystemSubtypeForSoilEnum", + "recommended": true + }, + "ecosystem_type": { + "name": "ecosystem_type", + "description": "Ecosystem types represent things having common characteristics within the Ecosystem Category. These common characteristics based grouping is still broad but specific to the characteristics of a given environment. Ecosystem type is in position 3/5 in a GOLD path.", + "comments": [ + "The Aquatic ecosystem category (for example) may have ecosystem types like Marine or Thermal springs etc. Ecosystem category Air may have Indoor air or Outdoor air as different Ecosystem Types. In the case of Host-associated samples, ecosystem type can represent Respiratory system, Digestive system, Roots etc." + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "https://gold.jgi.doe.gov/help" + ], + "rank": 11, + "is_a": "gold_path_field", + "alias": "ecosystem_type", + "owner": "SoilInterface", + "domain_of": [ + "Biosample", + "Study", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "EcosystemTypeForSoilEnum", + "recommended": true + }, + "elev": { + "name": "elev", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + } + }, + "description": "Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit.", + "title": "elevation, meters", + "comments": [ + "All elevations must be reported in meters. Provide the numerical portion only.", + "Please use https://www.advancedconverter.com/map-tools/find-altitude-by-coordinates, if needed, to help estimate the elevation based on latitude and longitude coordinates." + ], + "examples": [ + { + "value": "225" + }, + { + "value": "0" + }, + { + "value": "1250" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "elevation" + ], + "rank": 6, + "is_a": "environment field", + "slot_uri": "MIXS:0000093", + "alias": "elev", + "owner": "SoilInterface", + "domain_of": [ + "FieldResearchSite", + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "float", + "required": true, + "multivalued": false + }, + "env_broad_scale": { + "name": "env_broad_scale", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "The major environment type(s) where the sample was collected. Recommend subclasses of biome [ENVO:00000428]. Multiple terms can be separated by one or more pipes." + }, + "tooltip": { + "tag": "tooltip", + "value": "The biome or major environmental system where the sample or specimen originated. Choose values from subclasses of the 'biome' class [ENVO:00000428] in the Environment Ontology (ENVO). For host-associated or plant-associated samples, use terms from the UBERON or Plant Ontology to describe the broad anatomical or morphological context" + } + }, + "description": "In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO's biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html", + "title": "broad-scale environmental context", + "notes": [ + "range changed to enumeration late in makefile, so this is modified (but \"sample ID\" anyway)" + ], + "examples": [ + { + "value": "oceanic epipelagic zone biome [ENVO:01000033] for annotating a water sample from the photic zone in middle of the Atlantic Ocean" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "broad-scale environmental context" + ], + "rank": 6, + "is_a": "environment field", + "string_serialization": "{termLabel} {[termID]}", + "slot_uri": "MIXS:0000012", + "alias": "env_broad_scale", + "owner": "SoilInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "string", + "required": true, + "multivalued": false, + "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$", + "any_of": [ + { + "range": "EnvBroadScaleSoilEnum" + }, + { + "range": "string" + } + ] + }, + "env_local_scale": { + "name": "env_local_scale", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "Environmental entities having causal influences upon the entity at time of sampling." + }, + "tooltip": { + "tag": "tooltip", + "value": "The specific environmental entities or features near the sample or specimen that significantly influence its characteristics or composition. These entities are typically smaller in scale than the broad environmental context. Values for this field should be countable, material nouns and must be chosen from subclasses of BFO:0000040 (material entity) that appear in the Environment Ontology (ENVO). For host-associated or plant-associated samples, use terms from the UBERON or Plant Ontology to describe specific anatomical structures or plant parts." + } + }, + "description": "Report the entity or entities which are in the sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. We recommend using EnvO terms which are of smaller spatial grain than your entry for env_broad_scale. Terms, such as anatomical sites, from other OBO Library ontologies which interoperate with EnvO (e.g. UBERON) are accepted in this field. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS.", + "title": "local environmental context", + "notes": [ + "range changed to enumeration late in makefile, so this is modified (but \"sample ID\" anyway)" + ], + "examples": [ + { + "value": "canopy [ENVO:00000047]" + }, + { + "value": "herb and fern layer [ENVO:01000337]" + }, + { + "value": "litter layer [ENVO:01000338]" + }, + { + "value": "understory [01000335]" + }, + { + "value": "shrub layer [ENVO:01000336]" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "local environmental context" + ], + "rank": 7, + "is_a": "environment field", + "string_serialization": "{termLabel} {[termID]}", + "slot_uri": "MIXS:0000013", + "alias": "env_local_scale", + "owner": "SoilInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "string", + "required": true, + "multivalued": false, + "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$", + "any_of": [ + { + "range": "EnvLocalScaleSoilEnum" + }, + { + "range": "string" + } + ] + }, + "env_medium": { + "name": "env_medium", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "The material displaced by the entity at time of sampling. Recommend subclasses of environmental material [ENVO:00010483]." + }, + "tooltip": { + "tag": "tooltip", + "value": "The predominant environmental material or substrate that directly surrounds or hosts the sample or specimen at the time of sampling. Choose values from subclasses of the 'environmental material' class [ENVO:00010483] in the Environment Ontology (ENVO). Values for this field should be measurable or mass material nouns, representing continuous environmental materials. For host-associated or plant-associated samples, use terms from the UBERON or Plant Ontology to indicate a tissue, organ, or plant structure" + } + }, + "description": "Report the environmental material(s) immediately surrounding the sample or specimen at the time of sampling. We recommend using subclasses of 'environmental material' (http://purl.obolibrary.org/obo/ENVO_00010483). EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS . Terms from other OBO ontologies are permissible as long as they reference mass/volume nouns (e.g. air, water, blood) and not discrete, countable entities (e.g. a tree, a leaf, a table top).", + "title": "environmental medium", + "notes": [ + "range changed to enumeration late in makefile, so this is modified (but \"sample ID\" anyway)" + ], + "examples": [ + { + "value": "soil [ENVO:00001998]" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "environmental medium" + ], + "rank": 8, + "is_a": "environment field", + "string_serialization": "{termLabel} {[termID]}", + "slot_uri": "MIXS:0000014", + "alias": "env_medium", + "owner": "SoilInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "string", + "required": true, + "multivalued": false, + "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$", + "any_of": [ + { + "range": "EnvMediumSoilEnum" + }, + { + "range": "string" + } + ] + }, + "experimental_factor": { + "name": "experimental_factor", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "text or EFO and/or OBI" + } + }, + "description": "Experimental factors are essentially the variable aspects of an experiment design which can be used to describe an experiment, or set of experiments, in an increasingly detailed manner. This field accepts ontology terms from Experimental Factor Ontology (EFO) and/or Ontology for Biomedical Investigations (OBI). For a browser of EFO (v 2.95) terms, please see http://purl.bioontology.org/ontology/EFO; for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI", + "title": "experimental factor", + "examples": [ + { + "value": "time series design [EFO:0001779]" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "experimental factor" + ], + "rank": 12, + "is_a": "investigation field", + "string_serialization": "{termLabel} {[termID]}|{text}", + "slot_uri": "MIXS:0000008", + "alias": "experimental_factor", + "owner": "SoilInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false + }, + "experimental_factor_other": { + "name": "experimental_factor_other", + "description": "Other details about your sample that you feel can't be accurately represented in the available columns.", + "title": "experimental factor- other", + "comments": [ + "This slot accepts open-ended text about your sample.", + "We recommend using key:value pairs.", + "Provided pairs will be considered for inclusion as future slots/terms in this data collection template." + ], + "examples": [ + { + "value": "experimental treatment: value" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "MIXS:0000008", + "MIXS:0000300" + ], + "rank": 7, + "string_serialization": "{text}", + "alias": "experimental_factor_other", + "owner": "SoilInterface", + "domain_of": [ + "Biosample", + "SoilInterface", + "SoilMixsInspiredMixin" + ], + "slot_group": "mixs_inspired_section", + "range": "string", + "recommended": true, + "multivalued": false + }, + "extreme_event": { + "name": "extreme_event", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "date, string" + } + }, + "description": "Unusual physical events that may have affected microbial populations", + "title": "history/extreme events", + "todos": [ + "This is no longer matching the listed IRI from GSC. When NMDC has its own slots, map this to the MIxS slot" + ], + "examples": [ + { + "value": "1980-05-18, volcanic eruption" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "history/extreme events" + ], + "rank": 13, + "is_a": "core field", + "slot_uri": "MIXS:0000320", + "alias": "extreme_event", + "owner": "SoilInterface", + "domain_of": [ + "Biosample", + "SedimentInterface", + "SoilInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false + }, + "fao_class": { + "name": "fao_class", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Soil classification from the FAO World Reference Database for Soil Resources. The list can be found at http://www.fao.org/nr/land/sols/soil/wrb-soil-maps/reference-groups", + "title": "soil_taxonomic/FAO classification", + "examples": [ + { + "value": "Luvisols" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "soil_taxonomic/FAO classification" + ], + "rank": 14, + "is_a": "core field", + "slot_uri": "MIXS:0001083", + "alias": "fao_class", + "owner": "SoilInterface", + "domain_of": [ + "Biosample", + "SoilInterface" + ], + "slot_group": "mixs_section", + "range": "fao_class_enum", + "multivalued": false + }, + "filter_method": { + "name": "filter_method", + "description": "Type of filter used or how the sample was filtered", + "title": "filter method", + "comments": [ + "describe the filter or provide a catalog number and manufacturer" + ], + "examples": [ + { + "value": "C18" + }, + { + "value": "Basix PES, 13-100-106 FisherSci" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "MIXS:0000765" + ], + "rank": 6, + "string_serialization": "{text}", + "alias": "filter_method", + "owner": "SoilInterface", + "domain_of": [ + "Biosample", + "SoilInterface", + "WaterInterface", + "SoilMixsInspiredMixin" + ], + "slot_group": "mixs_inspired_section", + "range": "string", + "recommended": true, + "multivalued": false + }, + "fire": { + "name": "fire", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "date string" + } + }, + "description": "Historical and/or physical evidence of fire", + "title": "history/fire", + "todos": [ + "is \"to\" acceptable? Is there a better way to request that be written?", + "is \"to\" acceptable? Is there a better way to request that be written?", + "This is no longer matching the listed IRI from GSC. When NMDC has its own slots, map this to the MIxS slot" + ], + "comments": [ + "Provide the date the fire occurred. If extended burning occurred provide the date range." + ], + "examples": [ + { + "value": "1871-10-10" + }, + { + "value": "1871-10-01 to 1871-10-31" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "history/fire" + ], + "rank": 15, + "is_a": "core field", + "slot_uri": "MIXS:0001086", + "alias": "fire", + "owner": "SoilInterface", + "domain_of": [ + "Biosample", + "SedimentInterface", + "SoilInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false, + "pattern": "^[12]\\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\\d|3[01]))?)?(\\s+to\\s+[12]\\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\\d|3[01]))?)?)?$" + }, + "flooding": { + "name": "flooding", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "date string" + } + }, + "description": "Historical and/or physical evidence of flooding", + "title": "history/flooding", + "todos": [ + "is \"to\" acceptable? Is there a better way to request that be written?", + "What about if the \"day\" isn't known? Is this ok?", + "is \"to\" acceptable? Is there a better way to request that be written?", + "What about if the \"day\" isn't known? Is this ok?", + "This is no longer matching the listed IRI from GSC. When NMDC has its own slots, map this to the MIxS slot" + ], + "comments": [ + "Provide the date the flood occurred. If extended flooding occurred provide the date range." + ], + "examples": [ + { + "value": "1927-04-15" + }, + { + "value": "1927-04 to 1927-05" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "history/flooding" + ], + "rank": 16, + "is_a": "core field", + "slot_uri": "MIXS:0000319", + "alias": "flooding", + "owner": "SoilInterface", + "domain_of": [ + "Biosample", + "SedimentInterface", + "SoilInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false + }, + "gaseous_environment": { + "name": "gaseous_environment", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "gaseous compound name;gaseous compound amount;treatment interval and duration" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Use of conditions with differing gaseous environments; should include the name of gaseous compound, amount administered, treatment duration, interval and total experimental duration; can include multiple gaseous environment regimens", + "title": "gaseous environment", + "todos": [ + "would like to see usage examples for this slot. Requiring micromole/L seems too limiting and doesn't match expected_value value", + "did I do this right? keep the example that's provided and add another? so as to not override", + "would like to see usage examples for this slot. Requiring micromole/L seems too limiting and doesn't match expected_value value", + "did I do this right? keep the example that's provided and add another? so as to not override" + ], + "examples": [ + { + "value": "CO2; 500ppm above ambient; constant" + }, + { + "value": "nitric oxide;0.5 micromole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "gaseous environment" + ], + "rank": 20, + "is_a": "core field", + "string_serialization": "{text};{float} {unit};{Rn/start_time/end_time/duration}", + "slot_uri": "MIXS:0000558", + "alias": "gaseous_environment", + "owner": "SoilInterface", + "domain_of": [ + "Biosample", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "recommended": true, + "multivalued": false + }, + "geo_loc_name": { + "name": "geo_loc_name", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "country or sea name (INSDC or GAZ): region(GAZ), specific location name" + } + }, + "description": "The geographical origin of the sample as defined by the country or sea name followed by specific region name.", + "title": "geographic location (country and/or sea,region)", + "examples": [ + { + "value": "USA: Maryland, Bethesda" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "geographic location (country and/or sea,region)" + ], + "rank": 4, + "is_a": "environment field", + "string_serialization": "{text}: {text}, {text}", + "slot_uri": "MIXS:0000010", + "alias": "geo_loc_name", + "owner": "SoilInterface", + "domain_of": [ + "FieldResearchSite", + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "required": true, + "multivalued": false, + "pattern": "^[^:, ][^:]*: [^:, ][^,]*, [^:, ].*$" + }, + "growth_facil": { + "name": "growth_facil", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "free text or CO" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Type of facility/location where the sample was harvested; controlled vocabulary: growth chamber, open top chamber, glasshouse, experimental garden, field.", + "title": "growth facility", + "notes": [ + "Removed from description: Alternatively use Crop Ontology (CO) terms" + ], + "examples": [ + { + "value": "Growth chamber [CO_715:0000189]" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "growth facility" + ], + "rank": 1, + "is_a": "core field", + "string_serialization": "{text}|{termLabel} {[termID]}", + "slot_uri": "MIXS:0001043", + "alias": "growth_facil", + "owner": "SoilInterface", + "domain_of": [ + "Biosample", + "PlantAssociatedInterface", + "SoilInterface" + ], + "slot_group": "mixs_modified_section", + "range": "GrowthFacilEnum", + "required": true, + "multivalued": false + }, + "heavy_metals": { + "name": "heavy_metals", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "heavy metal name;measurement value unit" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "microgram per gram" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Heavy metals present in the sample and their concentrations.", + "title": "heavy metals/ extreme unusual properties", + "todos": [ + "Example & validation. Can we configure things so that 27% & 27 % & 0.27 will validate?", + "I think it's weird the way GSC writes the title. I recommend this change. Thoughts? I would argue this isn't an extreme unusual property. It's just a biogeochemical measurement.", + "This is no longer matching the listed IRI from GSC. When NMDC has its own slots, map this to the MIxS slot", + "Example & validation. Can we make rules that 27% & 27 % & 0.27 will validate?", + "I think it's weird the way GSC writes the title. I recommend this change. Thoughts? I would argue this isn't an extreme unusual property. It's just a biogeochemical measurement." + ], + "notes": [ + "Changed to multi-valued. In MIxS, you add another column to denote multiple heavy metals. We don't have that ability in the submission portal." + ], + "comments": [ + "For multiple heavy metals and concentrations, separate by ;" + ], + "examples": [ + { + "value": "mercury 0.09 micrograms per gram" + }, + { + "value": "mercury 0.09 ug/g; chromium 0.03 ug/g" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "extreme_unusual_properties/heavy metals" + ], + "rank": 17, + "is_a": "core field", + "string_serialization": "{text};{float} {unit}", + "slot_uri": "MIXS:0000652", + "alias": "heavy_metals", + "owner": "SoilInterface", + "domain_of": [ + "Biosample", + "SoilInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false, + "pattern": "^([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+\\|)*([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+)$" + }, + "heavy_metals_meth": { + "name": "heavy_metals_meth", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "PMID,DOI or url" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Reference or method used in determining heavy metals", + "title": "heavy metals method/ extreme unusual properties", + "todos": [ + "This is no longer matching the listed IRI from GSC. When NMDC has its own slots, map this to the MIxS slot" + ], + "comments": [ + "Required when heavy metals are provided", + "If different methods are used for multiple metals, indicate the metal and method. Separate metals by ;" + ], + "examples": [ + { + "value": "https://doi.org/10.3390/ijms9040434" + }, + { + "value": "mercury https://doi.org/10.1007/BF01056090; chromium https://doi.org/10.1007/s00216-006-0322-8" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "extreme_unusual_properties/heavy metals method" + ], + "rank": 18, + "is_a": "core field", + "string_serialization": "{PMID}|{DOI}|{URL}", + "slot_uri": "MIXS:0000343", + "alias": "heavy_metals_meth", + "owner": "SoilInterface", + "domain_of": [ + "Biosample", + "SoilInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false + }, + "horizon_meth": { + "name": "horizon_meth", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "PMID,DOI or url" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Reference or method used in determining the horizon", + "title": "soil horizon method", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "soil horizon method" + ], + "rank": 19, + "is_a": "core field", + "string_serialization": "{PMID}|{DOI}|{URL}", + "slot_uri": "MIXS:0000321", + "alias": "horizon_meth", + "owner": "SoilInterface", + "domain_of": [ + "Biosample", + "SoilInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false + }, + "humidity_regm": { + "name": "humidity_regm", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "humidity value;treatment interval and duration" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "gram per cubic meter" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Information about treatment involving an exposure to varying degree of humidity; information about treatment involving use of growth hormones; should include amount of humidity administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens", + "title": "humidity regimen", + "examples": [ + { + "value": "25 gram per cubic meter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "humidity regimen" + ], + "rank": 21, + "is_a": "core field", + "string_serialization": "{float} {unit};{Rn/start_time/end_time/duration}", + "slot_uri": "MIXS:0000568", + "alias": "humidity_regm", + "owner": "SoilInterface", + "domain_of": [ + "Biosample", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "recommended": true, + "multivalued": false + }, + "infiltrations": { + "name": "infiltrations", + "description": "The amount of time it takes to complete each infiltration activity", + "examples": [ + { + "value": "00:01:32;00:00:53" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "https://www.protocols.io/view/field-sampling-protocol-kqdg3962pg25/v1" + ], + "aliases": [ + "infiltration_1", + "infiltration_2" + ], + "rank": 1009, + "list_elements_ordered": true, + "alias": "infiltrations", + "owner": "SoilInterface", + "domain_of": [ + "Biosample", + "SoilInterface" + ], + "slot_group": "mixs_inspired_section", + "range": "string", + "multivalued": false, + "pattern": "^(?:(?:[0-9]|[1-9][0-9]|9[0-9]|0[0-9]|0[0-5][0-9]):[0-5][0-9]:[0-5][0-9])(?:;(?:[0-9]|[1-9][0-9]|9[0-9]|0[0-9]|0[0-5][0-9]):[0-5][0-9]:[0-5][0-9])*$" + }, + "isotope_exposure": { + "name": "isotope_exposure", + "description": "List isotope exposure or addition applied to your sample.", + "title": "isotope exposure/addition", + "todos": [ + "Can we make the H218O correctly super and subscripted?" + ], + "comments": [ + "This is required when your experimental design includes the use of isotopically labeled compounds" + ], + "examples": [ + { + "value": "13C glucose" + }, + { + "value": "H218O" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "MIXS:0000751" + ], + "rank": 16, + "string_serialization": "{termLabel} {[termID]}; {timestamp}", + "alias": "isotope_exposure", + "owner": "SoilInterface", + "domain_of": [ + "Biosample", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WaterInterface", + "SoilMixsInspiredMixin" + ], + "slot_group": "mixs_inspired_section", + "range": "string", + "recommended": true, + "multivalued": false, + "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]; ([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$" + }, + "lat_lon": { + "name": "lat_lon", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "decimal degrees, limit to 8 decimal points" + } + }, + "description": "The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system", + "title": "geographic location (latitude and longitude)", + "notes": [ + "This is currently a required field but it's not clear if this should be required for human hosts" + ], + "examples": [ + { + "value": "50.586825 6.408977" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "geographic location (latitude and longitude)" + ], + "rank": 5, + "is_a": "environment field", + "string_serialization": "{lat lon}", + "slot_uri": "MIXS:0000009", + "alias": "lat_lon", + "owner": "SoilInterface", + "domain_of": [ + "FieldResearchSite", + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "required": true, + "multivalued": false, + "pattern": "^[-+]?([1-8]?\\d(\\.\\d{1,8})?|90(\\.0{1,8})?)\\s[-+]?(180(\\.0{1,8})?|((1[0-7]\\d)|([1-9]?\\d))(\\.\\d{1,8})?)$" + }, + "lbc_thirty": { + "name": "lbc_thirty", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "ppm CaCO3/pH" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "lime buffer capacity, determined after 30 minute incubation", + "title": "lime buffer capacity (at 30 minutes)", + "comments": [ + "This is the mass of lime, in mg, needed to raise the pH of one kg of soil by one pH unit" + ], + "examples": [ + { + "value": "543 mg/kg" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "https://www.ornl.gov/content/bio-scales-0", + "https://secure.caes.uga.edu/extension/publications/files/pdf/C%20874_5.PDF" + ], + "aliases": [ + "lbc_thirty", + "lbc30", + "lime buffer capacity (at 30 minutes)" + ], + "rank": 1001, + "alias": "lbc_thirty", + "owner": "SoilInterface", + "domain_of": [ + "Biosample", + "SoilInterface" + ], + "slot_group": "mixs_inspired_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "lbceq": { + "name": "lbceq", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "ppm CaCO3/pH" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "lime buffer capacity, determined at equilibrium after 5 day incubation", + "title": "lime buffer capacity (after 5 day incubation)", + "comments": [ + "This is the mass of lime, in mg, needed to raise the pH of one kg of soil by one pH unit" + ], + "examples": [ + { + "value": "1575 mg/kg" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "https://www.ornl.gov/content/bio-scales-0" + ], + "aliases": [ + "lbceq", + "lime buffer capacity (at 5-day equilibrium)" + ], + "rank": 1002, + "alias": "lbceq", + "owner": "SoilInterface", + "domain_of": [ + "Biosample", + "SoilInterface" + ], + "slot_group": "mixs_inspired_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "light_regm": { + "name": "light_regm", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "exposure type;light intensity;light quality" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "lux; micrometer, nanometer, angstrom" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Information about treatment(s) involving exposure to light, including both light intensity and quality.", + "title": "light regimen", + "examples": [ + { + "value": "incandescant light;10 lux;450 nanometer" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "light regimen" + ], + "rank": 24, + "is_a": "core field", + "string_serialization": "{text};{float} {unit};{float} {unit}", + "slot_uri": "MIXS:0000569", + "alias": "light_regm", + "owner": "SoilInterface", + "domain_of": [ + "Biosample", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "recommended": true, + "multivalued": false, + "pattern": "^\\S+.*\\S+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? \\S+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? \\S+$" + }, + "link_addit_analys": { + "name": "link_addit_analys", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "PMID,DOI or url" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Link to additional analysis results performed on the sample", + "title": "links to additional analysis", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "links to additional analysis" + ], + "rank": 56, + "is_a": "core field", + "string_serialization": "{PMID}|{DOI}|{URL}", + "slot_uri": "MIXS:0000340", + "alias": "link_addit_analys", + "owner": "SoilInterface", + "domain_of": [ + "Biosample", + "SoilInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false + }, + "link_class_info": { + "name": "link_class_info", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "PMID,DOI or url" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Link to digitized soil maps or other soil classification information", + "title": "link to classification information", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "link to classification information" + ], + "rank": 20, + "is_a": "core field", + "string_serialization": "{PMID}|{DOI}|{URL}", + "slot_uri": "MIXS:0000329", + "alias": "link_class_info", + "owner": "SoilInterface", + "domain_of": [ + "Biosample", + "SoilInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false + }, + "link_climate_info": { + "name": "link_climate_info", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "PMID,DOI or url" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Link to climate resource", + "title": "link to climate information", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "link to climate information" + ], + "rank": 21, + "is_a": "core field", + "string_serialization": "{PMID}|{DOI}|{URL}", + "slot_uri": "MIXS:0000328", + "alias": "link_climate_info", + "owner": "SoilInterface", + "domain_of": [ + "Biosample", + "SoilInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false + }, + "local_class": { + "name": "local_class", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "local classification name" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Soil classification based on local soil classification system", + "title": "soil_taxonomic/local classification", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "soil_taxonomic/local classification" + ], + "rank": 22, + "is_a": "core field", + "string_serialization": "{text}", + "slot_uri": "MIXS:0000330", + "alias": "local_class", + "owner": "SoilInterface", + "domain_of": [ + "FieldResearchSite", + "Biosample", + "SoilInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false + }, + "local_class_meth": { + "name": "local_class_meth", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "PMID,DOI or url" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Reference or method used in determining the local soil classification", + "title": "soil_taxonomic/local classification method", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "soil_taxonomic/local classification method" + ], + "rank": 24, + "is_a": "core field", + "string_serialization": "{PMID}|{DOI}|{URL}", + "slot_uri": "MIXS:0000331", + "alias": "local_class_meth", + "owner": "SoilInterface", + "domain_of": [ + "Biosample", + "SoilInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false + }, + "manganese": { + "name": "manganese", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "mg/kg (ppm)" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of manganese in the sample", + "title": "manganese", + "examples": [ + { + "value": "24.7 mg/kg" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "https://www.ornl.gov/content/bio-scales-0" + ], + "aliases": [ + "manganese" + ], + "rank": 1003, + "alias": "manganese", + "owner": "SoilInterface", + "domain_of": [ + "Biosample", + "SoilInterface" + ], + "slot_group": "mixs_inspired_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "micro_biomass_c_meth": { + "name": "micro_biomass_c_meth", + "description": "Reference or method used in determining microbial biomass carbon", + "title": "microbial biomass carbon method", + "todos": [ + "How should we separate values? | or ;? lets be consistent" + ], + "comments": [ + "required if \"microbial_biomass_c\" is provided" + ], + "examples": [ + { + "value": "https://doi.org/10.1016/0038-0717(87)90052-6" + }, + { + "value": "https://doi.org/10.1016/0038-0717(87)90052-6 | https://www.sciencedirect.com/science/article/abs/pii/0038071787900526" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "MIXS:0000339" + ], + "rank": 1004, + "string_serialization": "{PMID}|{DOI}|{URL}", + "alias": "micro_biomass_c_meth", + "owner": "SoilInterface", + "domain_of": [ + "Biosample", + "SedimentInterface", + "SoilInterface", + "SoilMixsInspiredMixin" + ], + "slot_group": "mixs_inspired_section", + "range": "string", + "recommended": true, + "multivalued": false + }, + "micro_biomass_meth": { + "name": "micro_biomass_meth", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "PMID,DOI or url" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Reference or method used in determining microbial biomass", + "title": "microbial biomass method", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "microbial biomass method" + ], + "rank": 43, + "is_a": "core field", + "string_serialization": "{PMID}|{DOI}|{URL}", + "slot_uri": "MIXS:0000339", + "alias": "micro_biomass_meth", + "owner": "SoilInterface", + "domain_of": [ + "Biosample", + "SedimentInterface", + "SoilInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false + }, + "micro_biomass_n_meth": { + "name": "micro_biomass_n_meth", + "description": "Reference or method used in determining microbial biomass nitrogen", + "title": "microbial biomass nitrogen method", + "comments": [ + "required if \"microbial_biomass_n\" is provided" + ], + "examples": [ + { + "value": "https://doi.org/10.1016/0038-0717(87)90052-6" + }, + { + "value": "https://doi.org/10.1016/0038-0717(87)90052-6 | https://www.sciencedirect.com/science/article/abs/pii/0038071787900526" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "MIXS:0000339" + ], + "rank": 1004, + "string_serialization": "{PMID}|{DOI}|{URL}", + "alias": "micro_biomass_n_meth", + "owner": "SoilInterface", + "domain_of": [ + "Biosample", + "SedimentInterface", + "SoilInterface", + "SoilMixsInspiredMixin" + ], + "slot_group": "mixs_inspired_section", + "range": "string", + "multivalued": false + }, + "microbial_biomass": { + "name": "microbial_biomass", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "ton, kilogram, gram per kilogram soil" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The part of the organic matter in the soil that constitutes living microorganisms smaller than 5-10 micrometer. If you keep this, you would need to have correction factors used for conversion to the final units", + "title": "microbial biomass", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "microbial biomass" + ], + "rank": 42, + "is_a": "core field", + "slot_uri": "MIXS:0000650", + "alias": "microbial_biomass", + "owner": "SoilInterface", + "domain_of": [ + "Biosample", + "SedimentInterface", + "SoilInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "microbial_biomass_c": { + "name": "microbial_biomass_c", + "description": "The part of the organic matter in the soil that constitutes living microorganisms smaller than 5-10 micrometer.", + "title": "microbial biomass carbon", + "comments": [ + "If you provide this, correction factors used for conversion to the final units and method are required" + ], + "examples": [ + { + "value": "0.05 ug C/g dry soil" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "MIXS:0000650" + ], + "rank": 1004, + "string_serialization": "{float} {unit}", + "alias": "microbial_biomass_c", + "owner": "SoilInterface", + "domain_of": [ + "Biosample", + "SedimentInterface", + "SoilInterface", + "SoilMixsInspiredMixin" + ], + "slot_group": "mixs_inspired_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? \\S+$" + }, + "microbial_biomass_n": { + "name": "microbial_biomass_n", + "description": "The part of the organic matter in the soil that constitutes living microorganisms smaller than 5-10 micrometer.", + "title": "microbial biomass nitrogen", + "comments": [ + "If you provide this, correction factors used for conversion to the final units and method are required" + ], + "examples": [ + { + "value": "0.05 ug N/g dry soil" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "MIXS:0000650" + ], + "rank": 1004, + "string_serialization": "{float} {unit}", + "alias": "microbial_biomass_n", + "owner": "SoilInterface", + "domain_of": [ + "Biosample", + "SedimentInterface", + "SoilInterface", + "SoilMixsInspiredMixin" + ], + "slot_group": "mixs_inspired_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? \\S+$" + }, + "misc_param": { + "name": "misc_param", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "parameter name;measurement value" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Any other measurement performed or parameter collected, that is not listed here", + "title": "miscellaneous parameter", + "examples": [ + { + "value": "Bicarbonate ion concentration;2075 micromole per kilogram" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "miscellaneous parameter" + ], + "rank": 23, + "is_a": "core field", + "string_serialization": "{text};{float} {unit}", + "slot_uri": "MIXS:0000752", + "alias": "misc_param", + "owner": "SoilInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false, + "pattern": "^([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+\\|)*([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+)$" + }, + "nitrate_nitrogen": { + "name": "nitrate_nitrogen", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "mg/kg" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of nitrate nitrogen in the sample", + "title": "nitrate_nitrogen", + "comments": [ + "often below some specified limit of detection" + ], + "examples": [ + { + "value": "0.29 mg/kg" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "https://www.ornl.gov/content/bio-scales-0" + ], + "aliases": [ + "nitrate_nitrogen", + "NO3-N" + ], + "rank": 1006, + "alias": "nitrate_nitrogen", + "owner": "SoilInterface", + "domain_of": [ + "Biosample", + "SoilInterface" + ], + "slot_group": "mixs_inspired_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "nitrite_nitrogen": { + "name": "nitrite_nitrogen", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "mg/kg" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of nitrite nitrogen in the sample", + "title": "nitrite_nitrogen", + "examples": [ + { + "value": "1.2 mg/kg" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "https://www.ornl.gov/content/bio-scales-0" + ], + "aliases": [ + "nitrite_nitrogen", + "NO2-N" + ], + "rank": 1007, + "alias": "nitrite_nitrogen", + "owner": "SoilInterface", + "domain_of": [ + "Biosample", + "SoilInterface" + ], + "slot_group": "mixs_inspired_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "non_microb_biomass": { + "name": "non_microb_biomass", + "description": "Amount of biomass; should include the name for the part of biomass measured, e.g.insect, plant, total. Can include multiple measurements separated by ;", + "title": "non-microbial biomass", + "examples": [ + { + "value": "insect 0.23 ug; plant 1g" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "MIXS:0000174", + "MIXS:0000650" + ], + "rank": 8, + "string_serialization": "{text};{float} {unit}", + "alias": "non_microb_biomass", + "owner": "SoilInterface", + "domain_of": [ + "Biosample", + "SoilInterface", + "SoilMixsInspiredMixin" + ], + "slot_group": "mixs_inspired_section", + "range": "string", + "multivalued": false, + "pattern": "^[^;\\t\\r\\x0A\\|]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A\\|]+$" + }, + "non_microb_biomass_method": { + "name": "non_microb_biomass_method", + "description": "Reference or method used in determining biomass", + "title": "non-microbial biomass method", + "comments": [ + "required if \"non-microbial biomass\" is provided" + ], + "examples": [ + { + "value": "https://doi.org/10.1038/s41467-021-26181-3" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "MIXS:0000650" + ], + "rank": 9, + "string_serialization": "{PMID}|{DOI}|{URL}", + "alias": "non_microb_biomass_method", + "owner": "SoilInterface", + "domain_of": [ + "Biosample", + "SoilInterface", + "SoilMixsInspiredMixin" + ], + "slot_group": "mixs_inspired_section", + "range": "string", + "multivalued": false + }, + "org_matter": { + "name": "org_matter", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "microgram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of organic matter", + "title": "organic matter", + "examples": [ + { + "value": "1.75 milligram per cubic meter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "organic matter" + ], + "rank": 45, + "is_a": "core field", + "slot_uri": "MIXS:0000204", + "alias": "org_matter", + "owner": "SoilInterface", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "MiscEnvsInterface", + "SedimentInterface", + "SoilInterface", + "WaterInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "org_nitro": { + "name": "org_nitro", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "microgram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of organic nitrogen", + "title": "organic nitrogen", + "examples": [ + { + "value": "4 micromole per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "organic nitrogen" + ], + "rank": 46, + "is_a": "core field", + "slot_uri": "MIXS:0000205", + "alias": "org_nitro", + "owner": "SoilInterface", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "MiscEnvsInterface", + "SedimentInterface", + "SoilInterface", + "WaterInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "org_nitro_method": { + "name": "org_nitro_method", + "description": "Method used for obtaining organic nitrogen", + "title": "organic nitrogen method", + "comments": [ + "required if \"org_nitro\" is provided" + ], + "examples": [ + { + "value": "https://doi.org/10.1016/0038-0717(85)90144-0" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "MIXS:0000338", + "MIXS:0000205" + ], + "rank": 14, + "string_serialization": "{PMID}|{DOI}|{URL}", + "alias": "org_nitro_method", + "owner": "SoilInterface", + "domain_of": [ + "Biosample", + "SedimentInterface", + "SoilInterface", + "SoilMixsInspiredMixin" + ], + "slot_group": "mixs_inspired_section", + "range": "string", + "multivalued": false + }, + "other_treatment": { + "name": "other_treatment", + "description": "Other treatments applied to your samples that are not applicable to the provided fields", + "title": "other treatments", + "notes": [ + "Values entered here will be used to determine potential new slots." + ], + "comments": [ + "This is an open text field to provide any treatments that cannot be captured in the provided slots." + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "MIXS:0000300" + ], + "rank": 15, + "string_serialization": "{text}", + "alias": "other_treatment", + "owner": "SoilInterface", + "domain_of": [ + "Biosample", + "SoilInterface", + "SoilMixsInspiredMixin" + ], + "slot_group": "mixs_inspired_section", + "range": "string", + "recommended": true, + "multivalued": false + }, + "oxy_stat_samp": { + "name": "oxy_stat_samp", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Oxygenation status of sample", + "title": "oxygenation status of sample", + "examples": [ + { + "value": "aerobic" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "oxygenation status of sample" + ], + "rank": 25, + "is_a": "core field", + "slot_uri": "MIXS:0000753", + "alias": "oxy_stat_samp", + "owner": "SoilInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_section", + "range": "OxyStatSampEnum", + "multivalued": false + }, + "ph": { + "name": "ph", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "pH measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid", + "title": "pH", + "notes": [ + "Use modified term" + ], + "examples": [ + { + "value": "7.2" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "pH" + ], + "rank": 27, + "is_a": "core field", + "string_serialization": "{float}", + "slot_uri": "MIXS:0001001", + "alias": "ph", + "owner": "SoilInterface", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "MiscEnvsInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "float", + "recommended": true, + "multivalued": false, + "minimum_value": 0, + "maximum_value": 14 + }, + "ph_meth": { + "name": "ph_meth", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "PMID,DOI or url" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Reference or method used in determining ph", + "title": "pH method", + "comments": [ + "This can include a link to the instrument used or a citation for the method." + ], + "examples": [ + { + "value": "https://www.southernlabware.com/pc9500-benchtop-ph-conductivity-meter-kit-ph-accuracy-2000mv-ph-range-2-000-to-20-000.html?gclid=Cj0KCQiAwJWdBhCYARIsAJc4idCO5vtvbVMf545fcvdROFqa6zjzNSoywNx6K4k9Coo9cCc2pybtvGsaAiR0EALw_wcB" + }, + { + "value": "https://doi.org/10.2136/sssabookser5.3.c16" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "pH method" + ], + "rank": 41, + "is_a": "core field", + "string_serialization": "{PMID}|{DOI}|{URL}", + "slot_uri": "MIXS:0001106", + "alias": "ph_meth", + "owner": "SoilInterface", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "MiscEnvsInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false + }, + "phosphate": { + "name": "phosphate", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of phosphate", + "title": "phosphate", + "examples": [ + { + "value": "0.7 micromole per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "phosphate" + ], + "rank": 53, + "is_a": "core field", + "slot_uri": "MIXS:0000505", + "alias": "phosphate", + "owner": "SoilInterface", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "MiscEnvsInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "prev_land_use_meth": { + "name": "prev_land_use_meth", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "PMID,DOI or url" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Reference or method used in determining previous land use and dates", + "title": "history/previous land use method", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "history/previous land use method" + ], + "rank": 26, + "is_a": "core field", + "string_serialization": "{PMID}|{DOI}|{URL}", + "slot_uri": "MIXS:0000316", + "alias": "prev_land_use_meth", + "owner": "SoilInterface", + "domain_of": [ + "Biosample", + "SoilInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false + }, + "previous_land_use": { + "name": "previous_land_use", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "land use name;date" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Previous land use and dates", + "title": "history/previous land use", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "history/previous land use" + ], + "rank": 27, + "is_a": "core field", + "string_serialization": "{text};{timestamp}", + "slot_uri": "MIXS:0000315", + "alias": "previous_land_use", + "owner": "SoilInterface", + "domain_of": [ + "Biosample", + "SoilInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false, + "pattern": "^\\S+.*\\S+;([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$" + }, + "profile_position": { + "name": "profile_position", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Cross-sectional position in the hillslope where sample was collected.sample area position in relation to surrounding areas", + "title": "profile position", + "examples": [ + { + "value": "summit" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "profile position" + ], + "rank": 28, + "is_a": "core field", + "slot_uri": "MIXS:0001084", + "alias": "profile_position", + "owner": "SoilInterface", + "domain_of": [ + "Biosample", + "SoilInterface" + ], + "slot_group": "mixs_section", + "range": "profile_position_enum", + "multivalued": false + }, + "salinity": { + "name": "salinity", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "practical salinity unit, percentage" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The total concentration of all dissolved salts in a liquid or solid sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater.", + "title": "salinity", + "examples": [ + { + "value": "25 practical salinity unit" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "salinity" + ], + "rank": 54, + "is_a": "core field", + "slot_uri": "MIXS:0000183", + "alias": "salinity", + "owner": "SoilInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "salinity_meth": { + "name": "salinity_meth", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "PMID,DOI or url" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Reference or method used in determining salinity", + "title": "salinity method", + "examples": [ + { + "value": "https://doi.org/10.1007/978-1-61779-986-0_28" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "salinity method" + ], + "rank": 55, + "is_a": "core field", + "string_serialization": "{PMID}|{DOI}|{URL}", + "slot_uri": "MIXS:0000341", + "alias": "salinity_meth", + "owner": "SoilInterface", + "domain_of": [ + "Biosample", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WaterInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false + }, + "samp_collec_device": { + "name": "samp_collec_device", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "device name" + } + }, + "description": "The device used to collect an environmental sample. This field accepts terms listed under environmental sampling device (http://purl.obolibrary.org/obo/ENVO). This field also accepts terms listed under specimen collection device (http://purl.obolibrary.org/obo/GENEPIO_0002094).", + "title": "sample collection device", + "comments": [ + "Report dimensions and details when applicable" + ], + "examples": [ + { + "value": "swab, biopsy, niskin bottle, push core, drag swab [GENEPIO:0002713]" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sample collection device" + ], + "rank": 14, + "is_a": "nucleic acid sequence source field", + "string_serialization": "{termLabel} {[termID]}|{text}", + "slot_uri": "MIXS:0000002", + "alias": "samp_collec_device", + "owner": "SoilInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "recommended": true, + "multivalued": false + }, + "samp_collec_method": { + "name": "samp_collec_method", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "PMID,DOI,url , or text" + } + }, + "description": "The method employed for collecting the sample.", + "title": "sample collection method", + "comments": [ + "This can be a citation or description" + ], + "examples": [ + { + "value": "swabbing" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sample collection method" + ], + "rank": 15, + "is_a": "nucleic acid sequence source field", + "string_serialization": "{PMID}|{DOI}|{URL}|{text}", + "slot_uri": "MIXS:0001225", + "alias": "samp_collec_method", + "owner": "SoilInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "multivalued": false + }, + "samp_mat_process": { + "name": "samp_mat_process", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "text" + } + }, + "description": "A brief description of any processing applied to the sample during or after retrieving the sample from environment, or a link to the relevant protocol(s) performed.", + "title": "sample material processing", + "examples": [ + { + "value": "filtering of seawater" + }, + { + "value": "storing samples in ethanol" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sample material processing" + ], + "rank": 12, + "is_a": "nucleic acid sequence source field", + "string_serialization": "{text}", + "slot_uri": "MIXS:0000016", + "alias": "samp_mat_process", + "owner": "SoilInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "multivalued": false + }, + "samp_size": { + "name": "samp_size", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "millliter, gram, milligram, liter" + } + }, + "description": "The total amount or size (volume (ml), mass (g) or area (m2) ) of sample collected.", + "title": "amount or size of sample collected", + "comments": [ + "This refers to the TOTAL amount of sample collected from the experiment. NOT the amount sent to each institution or collected for a specific analysis." + ], + "examples": [ + { + "value": "5 grams" + }, + { + "value": "10 mL" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "amount or size of sample collected" + ], + "rank": 18, + "is_a": "nucleic acid sequence source field", + "string_serialization": "{float} {unit}", + "slot_uri": "MIXS:0000001", + "alias": "samp_size", + "owner": "SoilInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? \\S+$" + }, + "samp_store_temp": { + "name": "samp_store_temp", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "degree Celsius" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Temperature at which the sample was stored (degrees are assumed)", + "title": "sample storage temperature", + "examples": [ + { + "value": "-80 Celsius" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sample storage temperature" + ], + "rank": 7, + "is_a": "core field", + "slot_uri": "MIXS:0000110", + "alias": "samp_store_temp", + "owner": "SoilInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "required": true, + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "sample_link": { + "name": "sample_link", + "description": "A unique identifier to assign parent-child, subsample, or sibling samples. This is relevant when a sample or other material was used to generate the new sample.", + "title": "sample linkage", + "notes": [ + "also tempted to include SampIdNewTermsMixin but if len(slot_usage.keys()) > 1 and \"placeholder\" in slot_usage.keys():AttributeError: 'list' object has no attribute 'keys'" + ], + "comments": [ + "This field allows multiple entries separated by ; (Examples: Soil collected from the field will link with the soil used in an incubation. The soil a plant was grown in links to the plant sample. An original culture sample was transferred to a new vial and generated a new sample)" + ], + "examples": [ + { + "value": "IGSN:DSJ0284" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "rank": 5, + "string_serialization": "{text}:{text}", + "alias": "sample_link", + "owner": "SoilInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface", + "SampIdNewTermsMixin" + ], + "slot_group": "sample_id_section", + "range": "string", + "recommended": true, + "multivalued": false, + "pattern": "[^\\:\\n\\r]+\\:[^\\:\\n\\r]+" + }, + "season_precpt": { + "name": "season_precpt", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "millimeter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The average of all seasonal precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or Isohyetal maps.", + "title": "average seasonal precipitation", + "todos": [ + "check validation & examples. always mm? so value only? Or value + unit", + "This is no longer matching the listed IRI from GSC. When NMDC has its own slots, map this to the MIxS slot", + "check validation & examples. always mm? so value only? Or value + unit" + ], + "notes": [ + "mean and average are the same thing, but it seems like bad practice to not be consistent. Changed mean to average", + "mean and average are the same thing, but it seems like bad practice to not be consistent. Changed mean to average" + ], + "comments": [ + "Seasons are defined as spring (March, April, May), summer (June, July, August), autumn (September, October, November) and winter (December, January, February)." + ], + "examples": [ + { + "value": "0.4 inch" + }, + { + "value": "10.16 mm" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "mean seasonal precipitation" + ], + "rank": 29, + "is_a": "core field", + "slot_uri": "MIXS:0000645", + "alias": "season_precpt", + "owner": "SoilInterface", + "domain_of": [ + "Biosample", + "SoilInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "season_temp": { + "name": "season_temp", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "degree Celsius" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Mean seasonal temperature", + "title": "mean seasonal temperature", + "examples": [ + { + "value": "18 degree Celsius" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "mean seasonal temperature" + ], + "rank": 30, + "is_a": "core field", + "slot_uri": "MIXS:0000643", + "alias": "season_temp", + "owner": "SoilInterface", + "domain_of": [ + "Biosample", + "SoilInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "sieving": { + "name": "sieving", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "design name and/or size;amount" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Collection design of pooled samples and/or sieve size and amount of sample sieved", + "title": "composite design/sieving", + "todos": [ + "check validation and examples", + "check validation and examples" + ], + "comments": [ + "Describe how samples were composited or sieved.", + "Use 'sample link' to indicate which samples were combined." + ], + "examples": [ + { + "value": "combined 2 cores" + }, + { + "value": "4mm sieved" + }, + { + "value": "4 mm sieved and homogenized" + }, + { + "value": "50 g" + }, + { + "value": "5 cores" + }, + { + "value": "2 mm sieved" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "composite design/sieving" + ], + "rank": 8, + "is_a": "core field", + "string_serialization": "{{text}|{float} {unit}};{float} {unit}", + "slot_uri": "MIXS:0000322", + "alias": "sieving", + "owner": "SoilInterface", + "domain_of": [ + "Biosample", + "SedimentInterface", + "SoilInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "recommended": true, + "multivalued": false + }, + "size_frac_low": { + "name": "size_frac_low", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micrometer" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Refers to the mesh/pore size used to pre-filter/pre-sort the sample. Materials larger than the size threshold are excluded from the sample", + "title": "size-fraction lower threshold", + "examples": [ + { + "value": "0.2 micrometer" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "size-fraction lower threshold" + ], + "rank": 10, + "is_a": "core field", + "slot_uri": "MIXS:0000735", + "alias": "size_frac_low", + "owner": "SoilInterface", + "domain_of": [ + "Biosample", + "SoilInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "recommended": false, + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "size_frac_up": { + "name": "size_frac_up", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micrometer" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Refers to the mesh/pore size used to retain the sample. Materials smaller than the size threshold are excluded from the sample", + "title": "size-fraction upper threshold", + "examples": [ + { + "value": "20 micrometer" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "size-fraction upper threshold" + ], + "rank": 11, + "is_a": "core field", + "slot_uri": "MIXS:0000736", + "alias": "size_frac_up", + "owner": "SoilInterface", + "domain_of": [ + "Biosample", + "SoilInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "recommended": false, + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "slope_aspect": { + "name": "slope_aspect", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "degree" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The direction a slope faces. While looking down a slope use a compass to record the direction you are facing (direction or degrees). - This measure provides an indication of sun and wind exposure that will influence soil temperature and evapotranspiration.", + "title": "slope aspect", + "todos": [ + "This is no longer matching the listed IRI from GSC. When NMDC has its own slots, map this to the MIxS slot" + ], + "comments": [ + "Aspect is the orientation of slope, measured clockwise in degrees from 0 to 360, where 0 is north-facing, 90 is east-facing, 180 is south-facing, and 270 is west-facing." + ], + "examples": [ + { + "value": "35" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "slope aspect" + ], + "rank": 1, + "is_a": "core field", + "slot_uri": "MIXS:0000647", + "alias": "slope_aspect", + "owner": "SoilInterface", + "domain_of": [ + "Biosample", + "SoilInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "slope_gradient": { + "name": "slope_gradient", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "percentage" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Commonly called 'slope'. The angle between ground surface and a horizontal line (in percent). This is the direction that overland water would flow. This measure is usually taken with a hand level meter or clinometer", + "title": "slope gradient", + "todos": [ + "Slope is a percent. How does the validation work? Check to correct examples", + "Slope is a percent. How does the validation work? Check to correct examples" + ], + "examples": [ + { + "value": "10%" + }, + { + "value": "10 %" + }, + { + "value": "0.1" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "slope gradient" + ], + "rank": 31, + "is_a": "core field", + "slot_uri": "MIXS:0000646", + "alias": "slope_gradient", + "owner": "SoilInterface", + "domain_of": [ + "Biosample", + "SoilInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "soil_horizon": { + "name": "soil_horizon", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Specific layer in the land area which measures parallel to the soil surface and possesses physical characteristics which differ from the layers above and beneath", + "title": "soil horizon", + "examples": [ + { + "value": "A horizon" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "soil horizon" + ], + "rank": 32, + "is_a": "core field", + "slot_uri": "MIXS:0001082", + "alias": "soil_horizon", + "owner": "SoilInterface", + "domain_of": [ + "Biosample", + "SoilInterface" + ], + "slot_group": "mixs_section", + "range": "soil_horizon_enum", + "multivalued": false + }, + "soil_text_measure": { + "name": "soil_text_measure", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The relative proportion of different grain sizes of mineral particles in a soil, as described using a standard system; express as % sand (50 um to 2 mm), silt (2 um to 50 um), and clay (<2 um) with textural name (e.g., silty clay loam) optional.", + "title": "soil texture measurement", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "soil texture measurement" + ], + "rank": 33, + "is_a": "core field", + "slot_uri": "MIXS:0000335", + "alias": "soil_text_measure", + "owner": "SoilInterface", + "domain_of": [ + "Biosample", + "SoilInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "soil_texture_meth": { + "name": "soil_texture_meth", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "PMID,DOI or url" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Reference or method used in determining soil texture", + "title": "soil texture method", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "soil texture method" + ], + "rank": 34, + "is_a": "core field", + "string_serialization": "{PMID}|{DOI}|{URL}", + "slot_uri": "MIXS:0000336", + "alias": "soil_texture_meth", + "owner": "SoilInterface", + "domain_of": [ + "Biosample", + "SoilInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false + }, + "soil_type": { + "name": "soil_type", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "ENVO_00001998" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Description of the soil type or classification. This field accepts terms under soil (http://purl.obolibrary.org/obo/ENVO_00001998). Multiple terms can be separated by pipes.", + "title": "soil type", + "examples": [ + { + "value": "plinthosol [ENVO:00002250]" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "soil type" + ], + "rank": 35, + "is_a": "core field", + "string_serialization": "{termLabel} {[termID]}", + "slot_uri": "MIXS:0000332", + "alias": "soil_type", + "owner": "SoilInterface", + "domain_of": [ + "FieldResearchSite", + "Biosample", + "SoilInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false, + "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$" + }, + "soil_type_meth": { + "name": "soil_type_meth", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "PMID,DOI or url" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Reference or method used in determining soil series name or other lower-level classification", + "title": "soil type method", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "soil type method" + ], + "rank": 36, + "is_a": "core field", + "string_serialization": "{PMID}|{DOI}|{URL}", + "slot_uri": "MIXS:0000334", + "alias": "soil_type_meth", + "owner": "SoilInterface", + "domain_of": [ + "Biosample", + "SoilInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false + }, + "specific_ecosystem": { + "name": "specific_ecosystem", + "description": "Specific ecosystems represent specific features of the environment like aphotic zone in an ocean or gastric mucosa within a host digestive system. Specific ecosystem is in position 5/5 in a GOLD path.", + "comments": [ + "Specific ecosystems help to define samples based on very specific characteristics of an environment under the five-level classification system." + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "https://gold.jgi.doe.gov/help" + ], + "rank": 13, + "is_a": "gold_path_field", + "alias": "specific_ecosystem", + "owner": "SoilInterface", + "domain_of": [ + "Biosample", + "Study", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "SpecificEcosystemForSoilEnum", + "recommended": true + }, + "start_date_inc": { + "name": "start_date_inc", + "description": "Date the incubation was started. Only relevant for incubation samples.", + "title": "incubation start date", + "notes": [ + "MIxS collection_date accepts (truncated) ISO8601. DH taking arbitrary precision date only" + ], + "comments": [ + "Date should be formatted as YYYY(-MM(-DD)). Ie, 2021-04-15, 2021-04 and 2021 are all acceptable." + ], + "examples": [ + { + "value": "2021-04-15, 2021-04 and 2021 are all acceptable." + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "MIXS:0000011" + ], + "rank": 4, + "string_serialization": "{date, arbitrary precision}", + "alias": "start_date_inc", + "owner": "SoilInterface", + "domain_of": [ + "Biosample", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WaterInterface", + "SoilMixsInspiredMixin" + ], + "slot_group": "mixs_inspired_section", + "range": "string", + "recommended": true, + "multivalued": false, + "pattern": "^[12]\\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\\d|3[01]))?)?$" + }, + "start_time_inc": { + "name": "start_time_inc", + "description": "Time the incubation was started. Only relevant for incubation samples.", + "title": "incubation start time, GMT", + "notes": [ + "MIxS collection_date accepts (truncated) ISO8601. DH taking seconds optional time only" + ], + "comments": [ + "Time should be entered as HH:MM(:SS) in GMT. See here for a converter: https://www.worldtimebuddy.com/pst-to-gmt-converter" + ], + "examples": [ + { + "value": "13:33 or 13:33:55" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "MIXS:0000011" + ], + "rank": 5, + "string_serialization": "{time, seconds optional}", + "alias": "start_time_inc", + "owner": "SoilInterface", + "domain_of": [ + "Biosample", + "SoilInterface", + "SoilMixsInspiredMixin" + ], + "slot_group": "mixs_inspired_section", + "range": "string", + "recommended": true, + "multivalued": false, + "pattern": "^([01]?\\d|2[0-3]|24(?=:00?:00?$)):([0-5]\\d)(:([0-5]\\d))?$" + }, + "store_cond": { + "name": "store_cond", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "storage condition type;duration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Explain how the soil sample is stored (fresh/frozen/other).", + "title": "storage conditions", + "examples": [ + { + "value": "-20 degree Celsius freezer;P2Y10D" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "storage conditions" + ], + "rank": 2, + "is_a": "core field", + "string_serialization": "{text};{duration}", + "slot_uri": "MIXS:0000327", + "alias": "store_cond", + "owner": "SoilInterface", + "domain_of": [ + "Biosample", + "SoilInterface" + ], + "slot_group": "mixs_modified_section", + "range": "StoreCondEnum", + "required": true, + "multivalued": false + }, + "temp": { + "name": "temp", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "degree Celsius" + } + }, + "description": "Temperature of the sample at the time of sampling.", + "title": "temperature", + "examples": [ + { + "value": "25 degree Celsius" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "temperature" + ], + "rank": 37, + "is_a": "environment field", + "slot_uri": "MIXS:0000113", + "alias": "temp", + "owner": "SoilInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "tillage": { + "name": "tillage", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Note method(s) used for tilling", + "title": "history/tillage", + "examples": [ + { + "value": "chisel" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "history/tillage" + ], + "rank": 38, + "is_a": "core field", + "slot_uri": "MIXS:0001081", + "alias": "tillage", + "owner": "SoilInterface", + "domain_of": [ + "Biosample", + "SoilInterface" + ], + "slot_group": "mixs_section", + "range": "tillage_enum", + "multivalued": true + }, + "tot_carb": { + "name": "tot_carb", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "microgram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Total carbon content", + "title": "total carbon", + "todos": [ + "is this inorganic and organic? both? could use some clarification.", + "ug/L doesn't seem like the right units. Should check this slots usage in databases and re-evaluate. I couldn't find any references that provided this data in this format", + "is this inorganic and organic? both? could use some clarification.", + "ug/L doesn't seem like the right units. Should check this slots usage in databases and re-evaluate. I couldn't find any references that provided this data in this format" + ], + "examples": [ + { + "value": "1 ug/L" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "total carbon" + ], + "rank": 47, + "is_a": "core field", + "slot_uri": "MIXS:0000525", + "alias": "tot_carb", + "owner": "SoilInterface", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "SedimentInterface", + "SoilInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "tot_nitro_cont_meth": { + "name": "tot_nitro_cont_meth", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "PMID,DOI or url" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Reference or method used in determining the total nitrogen", + "title": "total nitrogen content method", + "examples": [ + { + "value": "https://doi.org/10.2134/agronmonogr9.2.c32" + }, + { + "value": "https://acsess.onlinelibrary.wiley.com/doi/full/10.2136/sssaj2009.0389?casa_token=bm0pYIUdNMgAAAAA%3AOWVRR0STHaOe-afTcTdxn5m1hM8n2ltM0wY-b1iYpYdD9dhwppk5j3LvC2IO5yhOIvyLVeQz4NZRCZo" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "total nitrogen content method" + ], + "rank": 49, + "is_a": "core field", + "string_serialization": "{PMID}|{DOI}|{URL}", + "slot_uri": "MIXS:0000338", + "alias": "tot_nitro_cont_meth", + "owner": "SoilInterface", + "domain_of": [ + "Biosample", + "SedimentInterface", + "SoilInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false + }, + "tot_nitro_content": { + "name": "tot_nitro_content", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "microgram per liter, micromole per liter, milligram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Total nitrogen content of the sample", + "title": "total nitrogen content", + "examples": [ + { + "value": "5 mg N/ L" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "total nitrogen content" + ], + "rank": 48, + "is_a": "core field", + "slot_uri": "MIXS:0000530", + "alias": "tot_nitro_content", + "owner": "SoilInterface", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "SedimentInterface", + "SoilInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "tot_org_c_meth": { + "name": "tot_org_c_meth", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "PMID,DOI or url" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Reference or method used in determining total organic carbon", + "title": "total organic carbon method", + "examples": [ + { + "value": "https://doi.org/10.1080/07352680902776556" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "total organic carbon method" + ], + "rank": 51, + "is_a": "core field", + "string_serialization": "{PMID}|{DOI}|{URL}", + "slot_uri": "MIXS:0000337", + "alias": "tot_org_c_meth", + "owner": "SoilInterface", + "domain_of": [ + "Biosample", + "SedimentInterface", + "SoilInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false + }, + "tot_org_carb": { + "name": "tot_org_carb", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "gram Carbon per kilogram sample material" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content", + "title": "total organic carbon", + "todos": [ + "check description. How are they different?", + "check description. How are they different?" + ], + "examples": [ + { + "value": "5 mg N/ L" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "total organic carbon" + ], + "rank": 50, + "is_a": "core field", + "slot_uri": "MIXS:0000533", + "alias": "tot_org_carb", + "owner": "SoilInterface", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "SedimentInterface", + "SoilInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "tot_phosp": { + "name": "tot_phosp", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per liter, milligram per liter, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus", + "title": "total phosphorus", + "examples": [ + { + "value": "0.03 milligram per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "total phosphorus" + ], + "rank": 52, + "is_a": "core field", + "slot_uri": "MIXS:0000117", + "alias": "tot_phosp", + "owner": "SoilInterface", + "domain_of": [ + "Biosample", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "SoilInterface", + "WaterInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "water_cont_soil_meth": { + "name": "water_cont_soil_meth", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "PMID,DOI or url" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Reference or method used in determining the water content of soil", + "title": "water content method", + "todos": [ + "Why is it soil water content method in the name but not the title? Is this slot used in other samples?", + "Soil water content can be measure MANY ways and often, multiple ways are used in one experiment (gravimetric water content and water holding capacity and water filled pore space, to name a few).", + "Should this be multi valued? How to we manage and validate this?", + "Why is it soil water content method in the name but not the title? Is this slot used in other samples?", + "Soil water content can be measure MANY ways and often, multiple ways are used in one experiment (gravimetric water content and water holding capacity and water filled pore space, to name a few).", + "Should this be multi valued? How to we manage and validate this?" + ], + "comments": [ + "Required if providing water content" + ], + "examples": [ + { + "value": "J. Nat. Prod. Plant Resour., 2012, 2 (4):500-503" + }, + { + "value": "https://dec.alaska.gov/applications/spar/webcalc/definitions.htm" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "water content method" + ], + "rank": 40, + "is_a": "core field", + "string_serialization": "{PMID}|{DOI}|{URL}", + "slot_uri": "MIXS:0000323", + "alias": "water_cont_soil_meth", + "owner": "SoilInterface", + "domain_of": [ + "Biosample", + "SedimentInterface", + "SoilInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false + }, + "water_content": { + "name": "water_content", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "string" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "gram per gram or cubic centimeter per cubic centimeter" + } + }, + "description": "Water content measurement", + "title": "water content", + "todos": [ + "value in preferred unit is too limiting. need to change this", + "check and correct validation so examples are accepted", + "how to manage multiple water content methods?" + ], + "examples": [ + { + "value": "0.75 g water/g dry soil" + }, + { + "value": "75% water holding capacity" + }, + { + "value": "1.1 g fresh weight/ dry weight" + }, + { + "value": "10% water filled pore space" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "water content" + ], + "rank": 39, + "is_a": "core field", + "string_serialization": "{float or pct} {unit}", + "slot_uri": "MIXS:0000185", + "alias": "water_content", + "owner": "SoilInterface", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "SedimentInterface", + "SoilInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)?%? \\S.+$" + }, + "watering_regm": { + "name": "watering_regm", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value;treatment interval and duration" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milliliter, liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Information about treatment involving an exposure to watering frequencies, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens", + "title": "watering regimen", + "examples": [ + { + "value": "1 liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" + }, + { + "value": "75% water holding capacity; constant" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "watering regimen" + ], + "rank": 25, + "is_a": "core field", + "string_serialization": "{float} {unit};{Rn/start_time/end_time/duration}", + "slot_uri": "MIXS:0000591", + "alias": "watering_regm", + "owner": "SoilInterface", + "domain_of": [ + "Biosample", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "recommended": true, + "multivalued": false + }, + "zinc": { + "name": "zinc", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "mg/kg (ppm)" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of zinc in the sample", + "title": "zinc", + "examples": [ + { + "value": "2.5 mg/kg" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "https://www.ornl.gov/content/bio-scales-0" + ], + "aliases": [ + "zinc" + ], + "rank": 1004, + "alias": "zinc", + "owner": "SoilInterface", + "domain_of": [ + "Biosample", + "SoilInterface" + ], + "slot_group": "mixs_inspired_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "analysis_type": { + "name": "analysis_type", + "description": "Select all the data types associated or available for this biosample", + "title": "analysis/data type", + "examples": [ + { + "value": "metagenomics; metabolomics; proteomics" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "MIxS:investigation_type" + ], + "rank": 3, + "alias": "analysis_type", + "owner": "SoilInterface", + "domain_of": [ + "Biosample", + "DhMultiviewCommonColumnsMixin", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "EmslInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "JgiMgInterface", + "JgiMgLrInterface", + "JgiMtInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "AnalysisTypeEnum", + "required": true, + "recommended": false, + "multivalued": true + }, + "samp_name": { + "name": "samp_name", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "text" + } + }, + "description": "A local identifier or name that for the material sample collected. Refers to the original material collected or to any derived sub-samples.", + "title": "sample name", + "comments": [ + "It can have any format, but we suggest that you make it concise, unique and consistent within your lab, and as informative as possible." + ], + "examples": [ + { + "value": "Rock core CB1178(5-6) from NSW" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sample name" + ], + "rank": 1, + "is_a": "investigation field", + "string_serialization": "{text}", + "slot_uri": "MIXS:0001107", + "identifier": true, + "alias": "samp_name", + "owner": "SoilInterface", + "domain_of": [ + "Biosample", + "DhMultiviewCommonColumnsMixin", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "EmslInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "JgiMgInterface", + "JgiMgLrInterface", + "JgiMtInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "string", + "required": true, + "multivalued": false + }, + "source_mat_id": { + "name": "source_mat_id", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "for cultures of microorganisms: identifiers for two culture collections; for other material a unique arbitrary identifer" + } + }, + "description": "A globally unique identifier assigned to the biological sample.", + "title": "source material identifier", + "todos": [ + "Currently, the comments say to use UUIDs. However, if we implement assigning NMDC identifiers with the minter we dont need to require a GUID. It can be an optional field to fill out only if they already have a resolvable ID.", + "Currently, the comments say to use UUIDs. However, if we implement assigning NMDC identifiers with the minter we dont need to require a GUID. It can be an optional field to fill out only if they already have a resolvable ID." + ], + "notes": [ + "The source material IS the Globally Unique ID" + ], + "comments": [ + "Identifiers must be prefixed. Possible FAIR prefixes are IGSNs (http://www.geosamples.org/getigsn), NCBI biosample accession numbers, ARK identifiers (https://arks.org/). These IDs enable linking to derived analytes and subsamples. If you have not assigned FAIR identifiers to your samples, you can generate UUIDs (https://www.uuidgenerator.net/).", + "Identifiers must be prefixed. Possible FAIR prefixes are IGSNs (http://www.geosamples.org/getigsn), NCBI biosample accession numbers, ARK identifiers (https://arks.org/). These IDs enable linking to derived analytes and subsamples. If you have not assigned FAIR identifiers to your samples, you can generate UUIDs (https://www.uuidgenerator.net/)." + ], + "examples": [ + { + "value": "IGSN:AU1243" + }, + { + "value": "UUID:24f1467a-40f4-11ed-b878-0242ac120002" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "source material identifiers" + ], + "rank": 2, + "is_a": "nucleic acid sequence source field", + "string_serialization": "{text}:{text}", + "slot_uri": "MIXS:0000026", + "alias": "source_mat_id", + "owner": "SoilInterface", + "domain_of": [ + "Biosample", + "DhMultiviewCommonColumnsMixin", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "EmslInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "JgiMgInterface", + "JgiMgLrInterface", + "JgiMtInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "string", + "multivalued": false, + "pattern": "[^\\:\\n\\r]+\\:[^\\:\\n\\r]+" + } + } + }, + "WastewaterSludgeInterface": { + "name": "WastewaterSludgeInterface", + "annotations": { + "excel_worksheet_name": { + "tag": "excel_worksheet_name", + "value": "wastewater sludge" + } + }, + "description": "wastewater_sludge dh_interface", + "title": "Wastewater Sludge", + "from_schema": "https://example.com/nmdc_submission_schema", + "is_a": "DhInterface", + "mixins": [ + "DhMultiviewCommonColumnsMixin", + "SampIdNewTermsMixin" + ], + "slots": [ + "alkalinity", + "biochem_oxygen_dem", + "chem_administration", + "chem_oxygen_dem", + "collection_date", + "depth", + "ecosystem", + "ecosystem_category", + "ecosystem_subtype", + "ecosystem_type", + "efficiency_percent", + "elev", + "emulsions", + "env_broad_scale", + "env_local_scale", + "env_medium", + "experimental_factor", + "gaseous_substances", + "geo_loc_name", + "indust_eff_percent", + "inorg_particles", + "lat_lon", + "misc_param", + "nitrate", + "org_particles", + "organism_count", + "oxy_stat_samp", + "perturbation", + "ph", + "ph_meth", + "phosphate", + "pre_treatment", + "primary_treatment", + "reactor_type", + "salinity", + "samp_collec_device", + "samp_collec_method", + "samp_mat_process", + "samp_size", + "samp_store_dur", + "samp_store_loc", + "samp_store_temp", + "sample_link", + "secondary_treatment", + "sewage_type", + "size_frac", + "sludge_retent_time", + "sodium", + "soluble_inorg_mat", + "soluble_org_mat", + "specific_ecosystem", + "suspend_solids", + "temp", + "tertiary_treatment", + "tot_nitro", + "tot_phosphate", + "wastewater_type" + ], + "slot_usage": { + "alkalinity": { + "name": "alkalinity", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milliequivalent per liter, milligram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate", + "title": "alkalinity", + "examples": [ + { + "value": "50 milligram per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "alkalinity" + ], + "rank": 1, + "is_a": "core field", + "slot_uri": "MIXS:0000421", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "biochem_oxygen_dem": { + "name": "biochem_oxygen_dem", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milligram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Amount of dissolved oxygen needed by aerobic biological organisms in a body of water to break down organic material present in a given water sample at certain temperature over a specific time period", + "title": "biochemical oxygen demand", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "biochemical oxygen demand" + ], + "rank": 296, + "is_a": "core field", + "slot_uri": "MIXS:0000653", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "WastewaterSludgeInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "chem_administration": { + "name": "chem_administration", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "CHEBI;timestamp" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi", + "title": "chemical administration", + "examples": [ + { + "value": "agar [CHEBI:2509];2018-05-11|agar [CHEBI:2509];2018-05-22" + }, + { + "value": "agar [CHEBI:2509];2018-05" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "chemical administration" + ], + "rank": 17, + "is_a": "core field", + "string_serialization": "{termLabel} {[termID]};{timestamp}", + "slot_uri": "MIXS:0000751", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "recommended": true, + "multivalued": false, + "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\];([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$" + }, + "chem_oxygen_dem": { + "name": "chem_oxygen_dem", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milligram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "A measure of the capacity of water to consume oxygen during the decomposition of organic matter and the oxidation of inorganic chemicals such as ammonia and nitrite", + "title": "chemical oxygen demand", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "chemical oxygen demand" + ], + "rank": 301, + "is_a": "core field", + "slot_uri": "MIXS:0000656", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "WastewaterSludgeInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "collection_date": { + "name": "collection_date", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "date and time" + } + }, + "description": "The date of sampling", + "title": "collection date", + "notes": [ + "MIxS collection_date accepts (truncated) ISO8601. DH taking arb prec date only", + "Use modified term (amended definition)" + ], + "examples": [ + { + "value": "2021-04-15" + }, + { + "value": "2021-04" + }, + { + "value": "2021" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "collection date" + ], + "rank": 3, + "is_a": "environment field", + "string_serialization": "{date, arbitrary precision}", + "slot_uri": "MIXS:0000011", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "required": true, + "multivalued": false, + "pattern": "^[12]\\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\\d|3[01]))?)?$" + }, + "depth": { + "name": "depth", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + } + }, + "description": "The vertical distance below local surface, e.g. for sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples.", + "title": "depth, meters", + "notes": [ + "Use modified term" + ], + "comments": [ + "All depths must be reported in meters. Provide the numerical portion only." + ], + "examples": [ + { + "value": "0 - 0.1" + }, + { + "value": "1" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "depth" + ], + "rank": 9, + "is_a": "environment field", + "string_serialization": "{float}|{float}-{float}", + "slot_uri": "MIXS:0000018", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "recommended": true, + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)?(\\s*-\\s*[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)?)?$" + }, + "ecosystem": { + "name": "ecosystem", + "description": "An ecosystem is a combination of a physical environment (abiotic factors) and all the organisms (biotic factors) that interact with this environment. Ecosystem is in position 1/5 in a GOLD path.", + "comments": [ + "The abiotic factors play a profound role on the type and composition of organisms in a given environment. The GOLD Ecosystem at the top of the five-level classification system is aimed at capturing the broader environment from which an organism or environmental sample is collected. The three broad groups under Ecosystem are Environmental, Host-associated, and Engineered. They represent samples collected from a natural environment or from another organism or from engineered environments like bioreactors respectively." + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "https://gold.jgi.doe.gov/help" + ], + "rank": 9, + "is_a": "gold_path_field", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "Study", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "EcosystemEnum", + "recommended": true + }, + "ecosystem_category": { + "name": "ecosystem_category", + "description": "Ecosystem categories represent divisions within the ecosystem based on specific characteristics of the environment from where an organism or sample is isolated. Ecosystem category is in position 2/5 in a GOLD path.", + "comments": [ + "The Environmental ecosystem (for example) is divided into Air, Aquatic and Terrestrial. Ecosystem categories for Host-associated samples can be individual hosts or phyla and for engineered samples it may be manipulated environments like bioreactors, solid waste etc." + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "https://gold.jgi.doe.gov/help" + ], + "rank": 10, + "is_a": "gold_path_field", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "Study", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "EcosystemCategoryEnum", + "recommended": true + }, + "ecosystem_subtype": { + "name": "ecosystem_subtype", + "description": "Ecosystem subtypes represent further subdivision of Ecosystem types into more distinct subtypes. Ecosystem subtype is in position 4/5 in a GOLD path.", + "comments": [ + "Ecosystem Type Marine (Environmental -> Aquatic -> Marine) is further divided (for example) into Intertidal zone, Coastal, Pelagic, Intertidal zone etc. in the Ecosystem subtype category." + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "https://gold.jgi.doe.gov/help" + ], + "rank": 12, + "is_a": "gold_path_field", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "Study", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "EcosystemSubtypeEnum", + "recommended": true + }, + "ecosystem_type": { + "name": "ecosystem_type", + "description": "Ecosystem types represent things having common characteristics within the Ecosystem Category. These common characteristics based grouping is still broad but specific to the characteristics of a given environment. Ecosystem type is in position 3/5 in a GOLD path.", + "comments": [ + "The Aquatic ecosystem category (for example) may have ecosystem types like Marine or Thermal springs etc. Ecosystem category Air may have Indoor air or Outdoor air as different Ecosystem Types. In the case of Host-associated samples, ecosystem type can represent Respiratory system, Digestive system, Roots etc." + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "https://gold.jgi.doe.gov/help" + ], + "rank": 11, + "is_a": "gold_path_field", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "Study", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "EcosystemTypeEnum", + "recommended": true + }, + "efficiency_percent": { + "name": "efficiency_percent", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Percentage of volatile solids removed from the anaerobic digestor", + "title": "efficiency percent", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "efficiency percent" + ], + "rank": 307, + "is_a": "core field", + "slot_uri": "MIXS:0000657", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "WastewaterSludgeInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "elev": { + "name": "elev", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + } + }, + "description": "Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit.", + "title": "elevation, meters", + "comments": [ + "All elevations must be reported in meters. Provide the numerical portion only.", + "Please use https://www.advancedconverter.com/map-tools/find-altitude-by-coordinates, if needed, to help estimate the elevation based on latitude and longitude coordinates." + ], + "examples": [ + { + "value": "225" + }, + { + "value": "0" + }, + { + "value": "1250" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "elevation" + ], + "rank": 6, + "is_a": "environment field", + "slot_uri": "MIXS:0000093", + "owner": "Biosample", + "domain_of": [ + "FieldResearchSite", + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "float", + "required": true, + "multivalued": false + }, + "emulsions": { + "name": "emulsions", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "emulsion name;measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "gram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Amount or concentration of substances such as paints, adhesives, mayonnaise, hair colorants, emulsified oils, etc.; can include multiple emulsion types", + "title": "emulsions", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "emulsions" + ], + "rank": 308, + "is_a": "core field", + "string_serialization": "{text};{float} {unit}", + "slot_uri": "MIXS:0000660", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "WastewaterSludgeInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+\\|)*([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+)$" + }, + "env_broad_scale": { + "name": "env_broad_scale", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "The major environment type(s) where the sample was collected. Recommend subclasses of biome [ENVO:00000428]. Multiple terms can be separated by one or more pipes." + }, + "tooltip": { + "tag": "tooltip", + "value": "The biome or major environmental system where the sample or specimen originated. Choose values from subclasses of the 'biome' class [ENVO:00000428] in the Environment Ontology (ENVO). For host-associated or plant-associated samples, use terms from the UBERON or Plant Ontology to describe the broad anatomical or morphological context" + } + }, + "description": "In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO's biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html", + "title": "broad-scale environmental context", + "notes": [ + "range changed to enumeration late in makefile, so this is modified (but \"sample ID\" anyway)" + ], + "examples": [ + { + "value": "oceanic epipelagic zone biome [ENVO:01000033] for annotating a water sample from the photic zone in middle of the Atlantic Ocean" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "broad-scale environmental context" + ], + "rank": 6, + "is_a": "environment field", + "string_serialization": "{termLabel} {[termID]}", + "slot_uri": "MIXS:0000012", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "string", + "required": true, + "multivalued": false, + "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$" + }, + "env_local_scale": { + "name": "env_local_scale", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "Environmental entities having causal influences upon the entity at time of sampling." + }, + "tooltip": { + "tag": "tooltip", + "value": "The specific environmental entities or features near the sample or specimen that significantly influence its characteristics or composition. These entities are typically smaller in scale than the broad environmental context. Values for this field should be countable, material nouns and must be chosen from subclasses of BFO:0000040 (material entity) that appear in the Environment Ontology (ENVO). For host-associated or plant-associated samples, use terms from the UBERON or Plant Ontology to describe specific anatomical structures or plant parts." + } + }, + "description": "Report the entity or entities which are in the sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. We recommend using EnvO terms which are of smaller spatial grain than your entry for env_broad_scale. Terms, such as anatomical sites, from other OBO Library ontologies which interoperate with EnvO (e.g. UBERON) are accepted in this field. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS.", + "title": "local environmental context", + "notes": [ + "range changed to enumeration late in makefile, so this is modified (but \"sample ID\" anyway)" + ], + "examples": [ + { + "value": "canopy [ENVO:00000047]" + }, + { + "value": "herb and fern layer [ENVO:01000337]" + }, + { + "value": "litter layer [ENVO:01000338]" + }, + { + "value": "understory [01000335]" + }, + { + "value": "shrub layer [ENVO:01000336]" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "local environmental context" + ], + "rank": 7, + "is_a": "environment field", + "string_serialization": "{termLabel} {[termID]}", + "slot_uri": "MIXS:0000013", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "string", + "required": true, + "multivalued": false, + "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$" + }, + "env_medium": { + "name": "env_medium", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "The material displaced by the entity at time of sampling. Recommend subclasses of environmental material [ENVO:00010483]." + }, + "tooltip": { + "tag": "tooltip", + "value": "The predominant environmental material or substrate that directly surrounds or hosts the sample or specimen at the time of sampling. Choose values from subclasses of the 'environmental material' class [ENVO:00010483] in the Environment Ontology (ENVO). Values for this field should be measurable or mass material nouns, representing continuous environmental materials. For host-associated or plant-associated samples, use terms from the UBERON or Plant Ontology to indicate a tissue, organ, or plant structure" + } + }, + "description": "Report the environmental material(s) immediately surrounding the sample or specimen at the time of sampling. We recommend using subclasses of 'environmental material' (http://purl.obolibrary.org/obo/ENVO_00010483). EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS . Terms from other OBO ontologies are permissible as long as they reference mass/volume nouns (e.g. air, water, blood) and not discrete, countable entities (e.g. a tree, a leaf, a table top).", + "title": "environmental medium", + "notes": [ + "range changed to enumeration late in makefile, so this is modified (but \"sample ID\" anyway)" + ], + "examples": [ + { + "value": "soil [ENVO:00001998]" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "environmental medium" + ], + "rank": 8, + "is_a": "environment field", + "string_serialization": "{termLabel} {[termID]}", + "slot_uri": "MIXS:0000014", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "string", + "required": true, + "multivalued": false, + "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$" + }, + "experimental_factor": { + "name": "experimental_factor", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "text or EFO and/or OBI" + } + }, + "description": "Experimental factors are essentially the variable aspects of an experiment design which can be used to describe an experiment, or set of experiments, in an increasingly detailed manner. This field accepts ontology terms from Experimental Factor Ontology (EFO) and/or Ontology for Biomedical Investigations (OBI). For a browser of EFO (v 2.95) terms, please see http://purl.bioontology.org/ontology/EFO; for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI", + "title": "experimental factor", + "examples": [ + { + "value": "time series design [EFO:EFO_0001779]" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "experimental factor" + ], + "rank": 12, + "is_a": "investigation field", + "string_serialization": "{termLabel} {[termID]}|{text}", + "slot_uri": "MIXS:0000008", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false + }, + "gaseous_substances": { + "name": "gaseous_substances", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "gaseous substance name;measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Amount or concentration of substances such as hydrogen sulfide, carbon dioxide, methane, etc.; can include multiple substances", + "title": "gaseous substances", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "gaseous substances" + ], + "rank": 311, + "is_a": "core field", + "string_serialization": "{text};{float} {unit}", + "slot_uri": "MIXS:0000661", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "WastewaterSludgeInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+\\|)*([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+)$" + }, + "geo_loc_name": { + "name": "geo_loc_name", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "country or sea name (INSDC or GAZ): region(GAZ), specific location name" + } + }, + "description": "The geographical origin of the sample as defined by the country or sea name followed by specific region name.", + "title": "geographic location (country and/or sea,region)", + "examples": [ + { + "value": "USA: Maryland, Bethesda" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "geographic location (country and/or sea,region)" + ], + "rank": 4, + "is_a": "environment field", + "string_serialization": "{text}: {text}, {text}", + "slot_uri": "MIXS:0000010", + "owner": "Biosample", + "domain_of": [ + "FieldResearchSite", + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "required": true, + "multivalued": false, + "pattern": "^[^:, ][^:]*: [^:, ][^,]*, [^:, ].*$" + }, + "indust_eff_percent": { + "name": "indust_eff_percent", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "percentage" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Percentage of industrial effluents received by wastewater treatment plant", + "title": "industrial effluent percent", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "industrial effluent percent" + ], + "rank": 332, + "is_a": "core field", + "slot_uri": "MIXS:0000662", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "WastewaterSludgeInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "inorg_particles": { + "name": "inorg_particles", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "inorganic particle name;measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "mole per liter, milligram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Concentration of particles such as sand, grit, metal particles, ceramics, etc.; can include multiple particles", + "title": "inorganic particles", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "inorganic particles" + ], + "rank": 333, + "is_a": "core field", + "string_serialization": "{text};{float} {unit}", + "slot_uri": "MIXS:0000664", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "WastewaterSludgeInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+\\|)*([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+)$" + }, + "lat_lon": { + "name": "lat_lon", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "decimal degrees, limit to 8 decimal points" + } + }, + "description": "The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system", + "title": "geographic location (latitude and longitude)", + "notes": [ + "This is currently a required field but it's not clear if this should be required for human hosts" + ], + "examples": [ + { + "value": "50.586825 6.408977" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "geographic location (latitude and longitude)" + ], + "rank": 5, + "is_a": "environment field", + "string_serialization": "{lat lon}", + "slot_uri": "MIXS:0000009", + "owner": "Biosample", + "domain_of": [ + "FieldResearchSite", + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "required": true, + "multivalued": false, + "pattern": "^[-+]?([1-8]?\\d(\\.\\d{1,8})?|90(\\.0{1,8})?)\\s[-+]?(180(\\.0{1,8})?|((1[0-7]\\d)|([1-9]?\\d))(\\.\\d{1,8})?)$" + }, + "misc_param": { + "name": "misc_param", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "parameter name;measurement value" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Any other measurement performed or parameter collected, that is not listed here", + "title": "miscellaneous parameter", + "examples": [ + { + "value": "Bicarbonate ion concentration;2075 micromole per kilogram" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "miscellaneous parameter" + ], + "rank": 23, + "is_a": "core field", + "string_serialization": "{text};{float} {unit}", + "slot_uri": "MIXS:0000752", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false, + "pattern": "^([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+\\|)*([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+)$" + }, + "nitrate": { + "name": "nitrate", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per liter, milligram per liter, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of nitrate in the sample", + "title": "nitrate", + "examples": [ + { + "value": "65 micromole per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "nitrate" + ], + "rank": 26, + "is_a": "core field", + "slot_uri": "MIXS:0000425", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "org_particles": { + "name": "org_particles", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "particle name;measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "gram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Concentration of particles such as faeces, hairs, food, vomit, paper fibers, plant material, humus, etc.", + "title": "organic particles", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "organic particles" + ], + "rank": 338, + "is_a": "core field", + "string_serialization": "{text};{float} {unit}", + "slot_uri": "MIXS:0000665", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "WastewaterSludgeInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+\\|)*([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+)$" + }, + "organism_count": { + "name": "organism_count", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "organism name;measurement value;enumeration" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "number of cells per cubic meter, number of cells per milliliter, number of cells per cubic centimeter" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr)", + "title": "organism count", + "examples": [ + { + "value": "total prokaryotes;3.5e7 cells per milliliter;qPCR" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "organism count" + ], + "rank": 30, + "is_a": "core field", + "slot_uri": "MIXS:0000103", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^([-+]?[0-9]*\\.?[0-9]+ +\\S.*\\|)*([-+]?[0-9]*\\.?[0-9]+ +\\S.*)$" + }, + "oxy_stat_samp": { + "name": "oxy_stat_samp", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Oxygenation status of sample", + "title": "oxygenation status of sample", + "examples": [ + { + "value": "aerobic" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "oxygenation status of sample" + ], + "rank": 25, + "is_a": "core field", + "slot_uri": "MIXS:0000753", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_section", + "range": "OxyStatSampEnum", + "multivalued": false + }, + "perturbation": { + "name": "perturbation", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "perturbation type name;perturbation interval and duration" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types", + "title": "perturbation", + "examples": [ + { + "value": "antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "perturbation" + ], + "rank": 33, + "is_a": "core field", + "string_serialization": "{text};{Rn/start_time/end_time/duration}", + "slot_uri": "MIXS:0000754", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "ph": { + "name": "ph", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "pH measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid", + "title": "pH", + "notes": [ + "Use modified term" + ], + "examples": [ + { + "value": "7.2" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "pH" + ], + "rank": 27, + "is_a": "core field", + "string_serialization": "{float}", + "slot_uri": "MIXS:0001001", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "MiscEnvsInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "float", + "recommended": true, + "multivalued": false, + "minimum_value": 0, + "maximum_value": 14 + }, + "ph_meth": { + "name": "ph_meth", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "PMID,DOI or url" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Reference or method used in determining ph", + "title": "pH method", + "comments": [ + "This can include a link to the instrument used or a citation for the method." + ], + "examples": [ + { + "value": "https://www.southernlabware.com/pc9500-benchtop-ph-conductivity-meter-kit-ph-accuracy-2000mv-ph-range-2-000-to-20-000.html?gclid=Cj0KCQiAwJWdBhCYARIsAJc4idCO5vtvbVMf545fcvdROFqa6zjzNSoywNx6K4k9Coo9cCc2pybtvGsaAiR0EALw_wcB" + }, + { + "value": "https://doi.org/10.2136/sssabookser5.3.c16" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "pH method" + ], + "rank": 41, + "is_a": "core field", + "string_serialization": "{PMID}|{DOI}|{URL}", + "slot_uri": "MIXS:0001106", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "MiscEnvsInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false + }, + "phosphate": { + "name": "phosphate", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of phosphate", + "title": "phosphate", + "examples": [ + { + "value": "0.7 micromole per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "phosphate" + ], + "rank": 53, + "is_a": "core field", + "slot_uri": "MIXS:0000505", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "MiscEnvsInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "pre_treatment": { + "name": "pre_treatment", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "pre-treatment type" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The process of pre-treatment removes materials that can be easily collected from the raw wastewater", + "title": "pre-treatment", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "pre-treatment" + ], + "rank": 342, + "is_a": "core field", + "string_serialization": "{text}", + "slot_uri": "MIXS:0000348", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "WastewaterSludgeInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "primary_treatment": { + "name": "primary_treatment", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "primary treatment type" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The process to produce both a generally homogeneous liquid capable of being treated biologically and a sludge that can be separately treated or processed", + "title": "primary treatment", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "primary treatment" + ], + "rank": 343, + "is_a": "core field", + "string_serialization": "{text}", + "slot_uri": "MIXS:0000349", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "WastewaterSludgeInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "reactor_type": { + "name": "reactor_type", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "reactor type name" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Anaerobic digesters can be designed and engineered to operate using a number of different process configurations, as batch or continuous, mesophilic, high solid or low solid, and single stage or multistage", + "title": "reactor type", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "reactor type" + ], + "rank": 346, + "is_a": "core field", + "string_serialization": "{text}", + "slot_uri": "MIXS:0000350", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "WastewaterSludgeInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "salinity": { + "name": "salinity", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "practical salinity unit, percentage" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The total concentration of all dissolved salts in a liquid or solid sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater.", + "title": "salinity", + "examples": [ + { + "value": "25 practical salinity unit" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "salinity" + ], + "rank": 54, + "is_a": "core field", + "slot_uri": "MIXS:0000183", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "samp_collec_device": { + "name": "samp_collec_device", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "device name" + } + }, + "description": "The device used to collect an environmental sample. This field accepts terms listed under environmental sampling device (http://purl.obolibrary.org/obo/ENVO). This field also accepts terms listed under specimen collection device (http://purl.obolibrary.org/obo/GENEPIO_0002094).", + "title": "sample collection device", + "comments": [ + "Report dimensions and details when applicable" + ], + "examples": [ + { + "value": "swab, biopsy, niskin bottle, push core, drag swab [GENEPIO:0002713]" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sample collection device" + ], + "rank": 14, + "is_a": "nucleic acid sequence source field", + "string_serialization": "{termLabel} {[termID]}|{text}", + "slot_uri": "MIXS:0000002", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "recommended": true, + "multivalued": false + }, + "samp_collec_method": { + "name": "samp_collec_method", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "PMID,DOI,url , or text" + } + }, + "description": "The method employed for collecting the sample.", + "title": "sample collection method", + "comments": [ + "This can be a citation or description" + ], + "examples": [ + { + "value": "swabbing" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sample collection method" + ], + "rank": 15, + "is_a": "nucleic acid sequence source field", + "string_serialization": "{PMID}|{DOI}|{URL}|{text}", + "slot_uri": "MIXS:0001225", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "multivalued": false + }, + "samp_mat_process": { + "name": "samp_mat_process", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "text" + } + }, + "description": "A brief description of any processing applied to the sample during or after retrieving the sample from environment, or a link to the relevant protocol(s) performed.", + "title": "sample material processing", + "examples": [ + { + "value": "filtering of seawater" + }, + { + "value": "storing samples in ethanol" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sample material processing" + ], + "rank": 12, + "is_a": "nucleic acid sequence source field", + "string_serialization": "{text}", + "slot_uri": "MIXS:0000016", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "multivalued": false + }, + "samp_size": { + "name": "samp_size", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "millliter, gram, milligram, liter" + } + }, + "description": "The total amount or size (volume (ml), mass (g) or area (m2) ) of sample collected.", + "title": "amount or size of sample collected", + "comments": [ + "This refers to the TOTAL amount of sample collected from the experiment. NOT the amount sent to each institution or collected for a specific analysis." + ], + "examples": [ + { + "value": "5 grams" + }, + { + "value": "10 mL" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "amount or size of sample collected" + ], + "rank": 18, + "is_a": "nucleic acid sequence source field", + "string_serialization": "{float} {unit}", + "slot_uri": "MIXS:0000001", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? \\S+$" + }, + "samp_store_dur": { + "name": "samp_store_dur", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "duration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Duration for which the sample was stored", + "title": "sample storage duration", + "examples": [ + { + "value": "P1Y6M" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sample storage duration" + ], + "rank": 353, + "is_a": "core field", + "string_serialization": "{duration}", + "slot_uri": "MIXS:0000116", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "samp_store_loc": { + "name": "samp_store_loc", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "location name" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Location at which sample was stored, usually name of a specific freezer/room", + "title": "sample storage location", + "examples": [ + { + "value": "Freezer no:5" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sample storage location" + ], + "rank": 41, + "is_a": "core field", + "string_serialization": "{text}", + "slot_uri": "MIXS:0000755", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "samp_store_temp": { + "name": "samp_store_temp", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "degree Celsius" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Temperature at which the sample was stored (degrees are assumed)", + "title": "sample storage temperature", + "examples": [ + { + "value": "-80 Celsius" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sample storage temperature" + ], + "rank": 7, + "is_a": "core field", + "slot_uri": "MIXS:0000110", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "required": true, + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "sample_link": { + "name": "sample_link", + "description": "A unique identifier to assign parent-child, subsample, or sibling samples. This is relevant when a sample or other material was used to generate the new sample.", + "title": "sample linkage", + "notes": [ + "also tempted to include SampIdNewTermsMixin but if len(slot_usage.keys()) > 1 and \"placeholder\" in slot_usage.keys():AttributeError: 'list' object has no attribute 'keys'" + ], + "comments": [ + "This field allows multiple entries separated by ; (Examples: Soil collected from the field will link with the soil used in an incubation. The soil a plant was grown in links to the plant sample. An original culture sample was transferred to a new vial and generated a new sample)" + ], + "examples": [ + { + "value": "IGSN:DSJ0284" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "rank": 5, + "string_serialization": "{text}:{text}", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface", + "SampIdNewTermsMixin" + ], + "slot_group": "sample_id_section", + "range": "string", + "recommended": true, + "multivalued": false, + "pattern": "[^\\:\\n\\r]+\\:[^\\:\\n\\r]+" + }, + "secondary_treatment": { + "name": "secondary_treatment", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "secondary treatment type" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The process for substantially degrading the biological content of the sewage", + "title": "secondary treatment", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "secondary treatment" + ], + "rank": 360, + "is_a": "core field", + "string_serialization": "{text}", + "slot_uri": "MIXS:0000351", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "WastewaterSludgeInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "sewage_type": { + "name": "sewage_type", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "sewage type name" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Type of wastewater treatment plant as municipial or industrial", + "title": "sewage type", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sewage type" + ], + "rank": 361, + "is_a": "core field", + "string_serialization": "{text}", + "slot_uri": "MIXS:0000215", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "WastewaterSludgeInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "size_frac": { + "name": "size_frac", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "filter size value range" + } + }, + "description": "Filtering pore size used in sample preparation", + "title": "size fraction selected", + "examples": [ + { + "value": "0-0.22 micrometer" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "size fraction selected" + ], + "rank": 285, + "is_a": "nucleic acid sequence source field", + "string_serialization": "{float}-{float} {unit}", + "slot_uri": "MIXS:0000017", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "sludge_retent_time": { + "name": "sludge_retent_time", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "hours" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The time activated sludge remains in reactor", + "title": "sludge retention time", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sludge retention time" + ], + "rank": 362, + "is_a": "core field", + "slot_uri": "MIXS:0000669", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "WastewaterSludgeInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "sodium": { + "name": "sodium", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milligram per liter, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Sodium concentration in the sample", + "title": "sodium", + "examples": [ + { + "value": "10.5 milligram per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sodium" + ], + "rank": 363, + "is_a": "core field", + "slot_uri": "MIXS:0000428", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "soluble_inorg_mat": { + "name": "soluble_inorg_mat", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "soluble inorganic material name;measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "gram, microgram, mole per liter, gram per liter, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Concentration of substances such as ammonia, road-salt, sea-salt, cyanide, hydrogen sulfide, thiocyanates, thiosulfates, etc.", + "title": "soluble inorganic material", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "soluble inorganic material" + ], + "rank": 364, + "is_a": "core field", + "string_serialization": "{text};{float} {unit}", + "slot_uri": "MIXS:0000672", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "WastewaterSludgeInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+\\|)*([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+)$" + }, + "soluble_org_mat": { + "name": "soluble_org_mat", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "soluble organic material name;measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "gram, microgram, mole per liter, gram per liter, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Concentration of substances such as urea, fruit sugars, soluble proteins, drugs, pharmaceuticals, etc.", + "title": "soluble organic material", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "soluble organic material" + ], + "rank": 365, + "is_a": "core field", + "string_serialization": "{text};{float} {unit}", + "slot_uri": "MIXS:0000673", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "WastewaterSludgeInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+\\|)*([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+)$" + }, + "specific_ecosystem": { + "name": "specific_ecosystem", + "description": "Specific ecosystems represent specific features of the environment like aphotic zone in an ocean or gastric mucosa within a host digestive system. Specific ecosystem is in position 5/5 in a GOLD path.", + "comments": [ + "Specific ecosystems help to define samples based on very specific characteristics of an environment under the five-level classification system." + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "https://gold.jgi.doe.gov/help" + ], + "rank": 13, + "is_a": "gold_path_field", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "Study", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "SpecificEcosystemEnum", + "recommended": true + }, + "suspend_solids": { + "name": "suspend_solids", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "suspended solid name;measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "gram, microgram, milligram per liter, mole per liter, gram per liter, part per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Concentration of substances including a wide variety of material, such as silt, decaying plant and animal matter; can include multiple substances", + "title": "suspended solids", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "suspended solids" + ], + "rank": 372, + "is_a": "core field", + "string_serialization": "{text};{float} {unit}", + "slot_uri": "MIXS:0000150", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "WastewaterSludgeInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+\\|)*([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+)$" + }, + "temp": { + "name": "temp", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "degree Celsius" + } + }, + "description": "Temperature of the sample at the time of sampling.", + "title": "temperature", + "examples": [ + { + "value": "25 degree Celsius" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "temperature" + ], + "rank": 37, + "is_a": "environment field", + "slot_uri": "MIXS:0000113", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "tertiary_treatment": { + "name": "tertiary_treatment", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "tertiary treatment type" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The process providing a final treatment stage to raise the effluent quality before it is discharged to the receiving environment", + "title": "tertiary treatment", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "tertiary treatment" + ], + "rank": 374, + "is_a": "core field", + "string_serialization": "{text}", + "slot_uri": "MIXS:0000352", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "WastewaterSludgeInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "tot_nitro": { + "name": "tot_nitro", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "microgram per liter, micromole per liter, milligram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen", + "title": "total nitrogen concentration", + "examples": [ + { + "value": "50 micromole per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "total nitrogen concentration" + ], + "rank": 377, + "is_a": "core field", + "slot_uri": "MIXS:0000102", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "tot_phosphate": { + "name": "tot_phosphate", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "microgram per liter, micromole per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Total amount or concentration of phosphate", + "title": "total phosphate", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "total phosphate" + ], + "rank": 378, + "is_a": "core field", + "slot_uri": "MIXS:0000689", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "WastewaterSludgeInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "wastewater_type": { + "name": "wastewater_type", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "wastewater type name" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The origin of wastewater such as human waste, rainfall, storm drains, etc.", + "title": "wastewater type", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "wastewater type" + ], + "rank": 385, + "is_a": "core field", + "string_serialization": "{text}", + "slot_uri": "MIXS:0000353", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "WastewaterSludgeInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "horizon_meth": { + "name": "horizon_meth", + "title": "horizon method" + } + }, + "attributes": { + "alkalinity": { + "name": "alkalinity", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milliequivalent per liter, milligram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate", + "title": "alkalinity", + "examples": [ + { + "value": "50 milligram per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "alkalinity" + ], + "rank": 1, + "is_a": "core field", + "slot_uri": "MIXS:0000421", + "alias": "alkalinity", + "owner": "WastewaterSludgeInterface", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "biochem_oxygen_dem": { + "name": "biochem_oxygen_dem", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milligram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Amount of dissolved oxygen needed by aerobic biological organisms in a body of water to break down organic material present in a given water sample at certain temperature over a specific time period", + "title": "biochemical oxygen demand", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "biochemical oxygen demand" + ], + "rank": 296, + "is_a": "core field", + "slot_uri": "MIXS:0000653", + "alias": "biochem_oxygen_dem", + "owner": "WastewaterSludgeInterface", + "domain_of": [ + "Biosample", + "WastewaterSludgeInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "chem_administration": { + "name": "chem_administration", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "CHEBI;timestamp" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi", + "title": "chemical administration", + "examples": [ + { + "value": "agar [CHEBI:2509];2018-05-11|agar [CHEBI:2509];2018-05-22" + }, + { + "value": "agar [CHEBI:2509];2018-05" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "chemical administration" + ], + "rank": 17, + "is_a": "core field", + "string_serialization": "{termLabel} {[termID]};{timestamp}", + "slot_uri": "MIXS:0000751", + "alias": "chem_administration", + "owner": "WastewaterSludgeInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "recommended": true, + "multivalued": false, + "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\];([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$" + }, + "chem_oxygen_dem": { + "name": "chem_oxygen_dem", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milligram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "A measure of the capacity of water to consume oxygen during the decomposition of organic matter and the oxidation of inorganic chemicals such as ammonia and nitrite", + "title": "chemical oxygen demand", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "chemical oxygen demand" + ], + "rank": 301, + "is_a": "core field", + "slot_uri": "MIXS:0000656", + "alias": "chem_oxygen_dem", + "owner": "WastewaterSludgeInterface", + "domain_of": [ + "Biosample", + "WastewaterSludgeInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "collection_date": { + "name": "collection_date", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "date and time" + } + }, + "description": "The date of sampling", + "title": "collection date", + "notes": [ + "MIxS collection_date accepts (truncated) ISO8601. DH taking arb prec date only", + "Use modified term (amended definition)" + ], + "examples": [ + { + "value": "2021-04-15" + }, + { + "value": "2021-04" + }, + { + "value": "2021" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "collection date" + ], + "rank": 3, + "is_a": "environment field", + "string_serialization": "{date, arbitrary precision}", + "slot_uri": "MIXS:0000011", + "alias": "collection_date", + "owner": "WastewaterSludgeInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "required": true, + "multivalued": false, + "pattern": "^[12]\\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\\d|3[01]))?)?$" + }, + "depth": { + "name": "depth", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + } + }, + "description": "The vertical distance below local surface, e.g. for sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples.", + "title": "depth, meters", + "notes": [ + "Use modified term" + ], + "comments": [ + "All depths must be reported in meters. Provide the numerical portion only." + ], + "examples": [ + { + "value": "0 - 0.1" + }, + { + "value": "1" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "depth" + ], + "rank": 9, + "is_a": "environment field", + "string_serialization": "{float}|{float}-{float}", + "slot_uri": "MIXS:0000018", + "alias": "depth", + "owner": "WastewaterSludgeInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "recommended": true, + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)?(\\s*-\\s*[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)?)?$" + }, + "ecosystem": { + "name": "ecosystem", + "description": "An ecosystem is a combination of a physical environment (abiotic factors) and all the organisms (biotic factors) that interact with this environment. Ecosystem is in position 1/5 in a GOLD path.", + "comments": [ + "The abiotic factors play a profound role on the type and composition of organisms in a given environment. The GOLD Ecosystem at the top of the five-level classification system is aimed at capturing the broader environment from which an organism or environmental sample is collected. The three broad groups under Ecosystem are Environmental, Host-associated, and Engineered. They represent samples collected from a natural environment or from another organism or from engineered environments like bioreactors respectively." + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "https://gold.jgi.doe.gov/help" + ], + "rank": 9, + "is_a": "gold_path_field", + "alias": "ecosystem", + "owner": "WastewaterSludgeInterface", + "domain_of": [ + "Biosample", + "Study", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "EcosystemEnum", + "recommended": true + }, + "ecosystem_category": { + "name": "ecosystem_category", + "description": "Ecosystem categories represent divisions within the ecosystem based on specific characteristics of the environment from where an organism or sample is isolated. Ecosystem category is in position 2/5 in a GOLD path.", + "comments": [ + "The Environmental ecosystem (for example) is divided into Air, Aquatic and Terrestrial. Ecosystem categories for Host-associated samples can be individual hosts or phyla and for engineered samples it may be manipulated environments like bioreactors, solid waste etc." + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "https://gold.jgi.doe.gov/help" + ], + "rank": 10, + "is_a": "gold_path_field", + "alias": "ecosystem_category", + "owner": "WastewaterSludgeInterface", + "domain_of": [ + "Biosample", + "Study", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "EcosystemCategoryEnum", + "recommended": true + }, + "ecosystem_subtype": { + "name": "ecosystem_subtype", + "description": "Ecosystem subtypes represent further subdivision of Ecosystem types into more distinct subtypes. Ecosystem subtype is in position 4/5 in a GOLD path.", + "comments": [ + "Ecosystem Type Marine (Environmental -> Aquatic -> Marine) is further divided (for example) into Intertidal zone, Coastal, Pelagic, Intertidal zone etc. in the Ecosystem subtype category." + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "https://gold.jgi.doe.gov/help" + ], + "rank": 12, + "is_a": "gold_path_field", + "alias": "ecosystem_subtype", + "owner": "WastewaterSludgeInterface", + "domain_of": [ + "Biosample", + "Study", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "EcosystemSubtypeEnum", + "recommended": true + }, + "ecosystem_type": { + "name": "ecosystem_type", + "description": "Ecosystem types represent things having common characteristics within the Ecosystem Category. These common characteristics based grouping is still broad but specific to the characteristics of a given environment. Ecosystem type is in position 3/5 in a GOLD path.", + "comments": [ + "The Aquatic ecosystem category (for example) may have ecosystem types like Marine or Thermal springs etc. Ecosystem category Air may have Indoor air or Outdoor air as different Ecosystem Types. In the case of Host-associated samples, ecosystem type can represent Respiratory system, Digestive system, Roots etc." + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "https://gold.jgi.doe.gov/help" + ], + "rank": 11, + "is_a": "gold_path_field", + "alias": "ecosystem_type", + "owner": "WastewaterSludgeInterface", + "domain_of": [ + "Biosample", + "Study", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "EcosystemTypeEnum", + "recommended": true + }, + "efficiency_percent": { + "name": "efficiency_percent", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Percentage of volatile solids removed from the anaerobic digestor", + "title": "efficiency percent", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "efficiency percent" + ], + "rank": 307, + "is_a": "core field", + "slot_uri": "MIXS:0000657", + "alias": "efficiency_percent", + "owner": "WastewaterSludgeInterface", + "domain_of": [ + "Biosample", + "WastewaterSludgeInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "elev": { + "name": "elev", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + } + }, + "description": "Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit.", + "title": "elevation, meters", + "comments": [ + "All elevations must be reported in meters. Provide the numerical portion only.", + "Please use https://www.advancedconverter.com/map-tools/find-altitude-by-coordinates, if needed, to help estimate the elevation based on latitude and longitude coordinates." + ], + "examples": [ + { + "value": "225" + }, + { + "value": "0" + }, + { + "value": "1250" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "elevation" + ], + "rank": 6, + "is_a": "environment field", + "slot_uri": "MIXS:0000093", + "alias": "elev", + "owner": "WastewaterSludgeInterface", + "domain_of": [ + "FieldResearchSite", + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "float", + "required": true, + "multivalued": false + }, + "emulsions": { + "name": "emulsions", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "emulsion name;measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "gram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Amount or concentration of substances such as paints, adhesives, mayonnaise, hair colorants, emulsified oils, etc.; can include multiple emulsion types", + "title": "emulsions", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "emulsions" + ], + "rank": 308, + "is_a": "core field", + "string_serialization": "{text};{float} {unit}", + "slot_uri": "MIXS:0000660", + "alias": "emulsions", + "owner": "WastewaterSludgeInterface", + "domain_of": [ + "Biosample", + "WastewaterSludgeInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+\\|)*([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+)$" + }, + "env_broad_scale": { + "name": "env_broad_scale", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "The major environment type(s) where the sample was collected. Recommend subclasses of biome [ENVO:00000428]. Multiple terms can be separated by one or more pipes." + }, + "tooltip": { + "tag": "tooltip", + "value": "The biome or major environmental system where the sample or specimen originated. Choose values from subclasses of the 'biome' class [ENVO:00000428] in the Environment Ontology (ENVO). For host-associated or plant-associated samples, use terms from the UBERON or Plant Ontology to describe the broad anatomical or morphological context" + } + }, + "description": "In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO's biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html", + "title": "broad-scale environmental context", + "notes": [ + "range changed to enumeration late in makefile, so this is modified (but \"sample ID\" anyway)" + ], + "examples": [ + { + "value": "oceanic epipelagic zone biome [ENVO:01000033] for annotating a water sample from the photic zone in middle of the Atlantic Ocean" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "broad-scale environmental context" + ], + "rank": 6, + "is_a": "environment field", + "string_serialization": "{termLabel} {[termID]}", + "slot_uri": "MIXS:0000012", + "alias": "env_broad_scale", + "owner": "WastewaterSludgeInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "string", + "required": true, + "multivalued": false, + "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$" + }, + "env_local_scale": { + "name": "env_local_scale", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "Environmental entities having causal influences upon the entity at time of sampling." + }, + "tooltip": { + "tag": "tooltip", + "value": "The specific environmental entities or features near the sample or specimen that significantly influence its characteristics or composition. These entities are typically smaller in scale than the broad environmental context. Values for this field should be countable, material nouns and must be chosen from subclasses of BFO:0000040 (material entity) that appear in the Environment Ontology (ENVO). For host-associated or plant-associated samples, use terms from the UBERON or Plant Ontology to describe specific anatomical structures or plant parts." + } + }, + "description": "Report the entity or entities which are in the sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. We recommend using EnvO terms which are of smaller spatial grain than your entry for env_broad_scale. Terms, such as anatomical sites, from other OBO Library ontologies which interoperate with EnvO (e.g. UBERON) are accepted in this field. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS.", + "title": "local environmental context", + "notes": [ + "range changed to enumeration late in makefile, so this is modified (but \"sample ID\" anyway)" + ], + "examples": [ + { + "value": "canopy [ENVO:00000047]" + }, + { + "value": "herb and fern layer [ENVO:01000337]" + }, + { + "value": "litter layer [ENVO:01000338]" + }, + { + "value": "understory [01000335]" + }, + { + "value": "shrub layer [ENVO:01000336]" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "local environmental context" + ], + "rank": 7, + "is_a": "environment field", + "string_serialization": "{termLabel} {[termID]}", + "slot_uri": "MIXS:0000013", + "alias": "env_local_scale", + "owner": "WastewaterSludgeInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "string", + "required": true, + "multivalued": false, + "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$" + }, + "env_medium": { + "name": "env_medium", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "The material displaced by the entity at time of sampling. Recommend subclasses of environmental material [ENVO:00010483]." + }, + "tooltip": { + "tag": "tooltip", + "value": "The predominant environmental material or substrate that directly surrounds or hosts the sample or specimen at the time of sampling. Choose values from subclasses of the 'environmental material' class [ENVO:00010483] in the Environment Ontology (ENVO). Values for this field should be measurable or mass material nouns, representing continuous environmental materials. For host-associated or plant-associated samples, use terms from the UBERON or Plant Ontology to indicate a tissue, organ, or plant structure" + } + }, + "description": "Report the environmental material(s) immediately surrounding the sample or specimen at the time of sampling. We recommend using subclasses of 'environmental material' (http://purl.obolibrary.org/obo/ENVO_00010483). EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS . Terms from other OBO ontologies are permissible as long as they reference mass/volume nouns (e.g. air, water, blood) and not discrete, countable entities (e.g. a tree, a leaf, a table top).", + "title": "environmental medium", + "notes": [ + "range changed to enumeration late in makefile, so this is modified (but \"sample ID\" anyway)" + ], + "examples": [ + { + "value": "soil [ENVO:00001998]" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "environmental medium" + ], + "rank": 8, + "is_a": "environment field", + "string_serialization": "{termLabel} {[termID]}", + "slot_uri": "MIXS:0000014", + "alias": "env_medium", + "owner": "WastewaterSludgeInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "string", + "required": true, + "multivalued": false, + "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$" + }, + "experimental_factor": { + "name": "experimental_factor", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "text or EFO and/or OBI" + } + }, + "description": "Experimental factors are essentially the variable aspects of an experiment design which can be used to describe an experiment, or set of experiments, in an increasingly detailed manner. This field accepts ontology terms from Experimental Factor Ontology (EFO) and/or Ontology for Biomedical Investigations (OBI). For a browser of EFO (v 2.95) terms, please see http://purl.bioontology.org/ontology/EFO; for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI", + "title": "experimental factor", + "examples": [ + { + "value": "time series design [EFO:EFO_0001779]" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "experimental factor" + ], + "rank": 12, + "is_a": "investigation field", + "string_serialization": "{termLabel} {[termID]}|{text}", + "slot_uri": "MIXS:0000008", + "alias": "experimental_factor", + "owner": "WastewaterSludgeInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false + }, + "gaseous_substances": { + "name": "gaseous_substances", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "gaseous substance name;measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Amount or concentration of substances such as hydrogen sulfide, carbon dioxide, methane, etc.; can include multiple substances", + "title": "gaseous substances", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "gaseous substances" + ], + "rank": 311, + "is_a": "core field", + "string_serialization": "{text};{float} {unit}", + "slot_uri": "MIXS:0000661", + "alias": "gaseous_substances", + "owner": "WastewaterSludgeInterface", + "domain_of": [ + "Biosample", + "WastewaterSludgeInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+\\|)*([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+)$" + }, + "geo_loc_name": { + "name": "geo_loc_name", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "country or sea name (INSDC or GAZ): region(GAZ), specific location name" + } + }, + "description": "The geographical origin of the sample as defined by the country or sea name followed by specific region name.", + "title": "geographic location (country and/or sea,region)", + "examples": [ + { + "value": "USA: Maryland, Bethesda" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "geographic location (country and/or sea,region)" + ], + "rank": 4, + "is_a": "environment field", + "string_serialization": "{text}: {text}, {text}", + "slot_uri": "MIXS:0000010", + "alias": "geo_loc_name", + "owner": "WastewaterSludgeInterface", + "domain_of": [ + "FieldResearchSite", + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "required": true, + "multivalued": false, + "pattern": "^[^:, ][^:]*: [^:, ][^,]*, [^:, ].*$" + }, + "indust_eff_percent": { + "name": "indust_eff_percent", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "percentage" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Percentage of industrial effluents received by wastewater treatment plant", + "title": "industrial effluent percent", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "industrial effluent percent" + ], + "rank": 332, + "is_a": "core field", + "slot_uri": "MIXS:0000662", + "alias": "indust_eff_percent", + "owner": "WastewaterSludgeInterface", + "domain_of": [ + "Biosample", + "WastewaterSludgeInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "inorg_particles": { + "name": "inorg_particles", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "inorganic particle name;measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "mole per liter, milligram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Concentration of particles such as sand, grit, metal particles, ceramics, etc.; can include multiple particles", + "title": "inorganic particles", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "inorganic particles" + ], + "rank": 333, + "is_a": "core field", + "string_serialization": "{text};{float} {unit}", + "slot_uri": "MIXS:0000664", + "alias": "inorg_particles", + "owner": "WastewaterSludgeInterface", + "domain_of": [ + "Biosample", + "WastewaterSludgeInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+\\|)*([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+)$" + }, + "lat_lon": { + "name": "lat_lon", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "decimal degrees, limit to 8 decimal points" + } + }, + "description": "The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system", + "title": "geographic location (latitude and longitude)", + "notes": [ + "This is currently a required field but it's not clear if this should be required for human hosts" + ], + "examples": [ + { + "value": "50.586825 6.408977" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "geographic location (latitude and longitude)" + ], + "rank": 5, + "is_a": "environment field", + "string_serialization": "{lat lon}", + "slot_uri": "MIXS:0000009", + "alias": "lat_lon", + "owner": "WastewaterSludgeInterface", + "domain_of": [ + "FieldResearchSite", + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "required": true, + "multivalued": false, + "pattern": "^[-+]?([1-8]?\\d(\\.\\d{1,8})?|90(\\.0{1,8})?)\\s[-+]?(180(\\.0{1,8})?|((1[0-7]\\d)|([1-9]?\\d))(\\.\\d{1,8})?)$" + }, + "misc_param": { + "name": "misc_param", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "parameter name;measurement value" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Any other measurement performed or parameter collected, that is not listed here", + "title": "miscellaneous parameter", + "examples": [ + { + "value": "Bicarbonate ion concentration;2075 micromole per kilogram" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "miscellaneous parameter" + ], + "rank": 23, + "is_a": "core field", + "string_serialization": "{text};{float} {unit}", + "slot_uri": "MIXS:0000752", + "alias": "misc_param", + "owner": "WastewaterSludgeInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false, + "pattern": "^([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+\\|)*([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+)$" + }, + "nitrate": { + "name": "nitrate", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per liter, milligram per liter, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of nitrate in the sample", + "title": "nitrate", + "examples": [ + { + "value": "65 micromole per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "nitrate" + ], + "rank": 26, + "is_a": "core field", + "slot_uri": "MIXS:0000425", + "alias": "nitrate", + "owner": "WastewaterSludgeInterface", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "org_particles": { + "name": "org_particles", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "particle name;measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "gram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Concentration of particles such as faeces, hairs, food, vomit, paper fibers, plant material, humus, etc.", + "title": "organic particles", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "organic particles" + ], + "rank": 338, + "is_a": "core field", + "string_serialization": "{text};{float} {unit}", + "slot_uri": "MIXS:0000665", + "alias": "org_particles", + "owner": "WastewaterSludgeInterface", + "domain_of": [ + "Biosample", + "WastewaterSludgeInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+\\|)*([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+)$" + }, + "organism_count": { + "name": "organism_count", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "organism name;measurement value;enumeration" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "number of cells per cubic meter, number of cells per milliliter, number of cells per cubic centimeter" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr)", + "title": "organism count", + "examples": [ + { + "value": "total prokaryotes;3.5e7 cells per milliliter;qPCR" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "organism count" + ], + "rank": 30, + "is_a": "core field", + "slot_uri": "MIXS:0000103", + "alias": "organism_count", + "owner": "WastewaterSludgeInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^([-+]?[0-9]*\\.?[0-9]+ +\\S.*\\|)*([-+]?[0-9]*\\.?[0-9]+ +\\S.*)$" + }, + "oxy_stat_samp": { + "name": "oxy_stat_samp", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Oxygenation status of sample", + "title": "oxygenation status of sample", + "examples": [ + { + "value": "aerobic" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "oxygenation status of sample" + ], + "rank": 25, + "is_a": "core field", + "slot_uri": "MIXS:0000753", + "alias": "oxy_stat_samp", + "owner": "WastewaterSludgeInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_section", + "range": "OxyStatSampEnum", + "multivalued": false + }, + "perturbation": { + "name": "perturbation", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "perturbation type name;perturbation interval and duration" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types", + "title": "perturbation", + "examples": [ + { + "value": "antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "perturbation" + ], + "rank": 33, + "is_a": "core field", + "string_serialization": "{text};{Rn/start_time/end_time/duration}", + "slot_uri": "MIXS:0000754", + "alias": "perturbation", + "owner": "WastewaterSludgeInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "ph": { + "name": "ph", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "pH measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid", + "title": "pH", + "notes": [ + "Use modified term" + ], + "examples": [ + { + "value": "7.2" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "pH" + ], + "rank": 27, + "is_a": "core field", + "string_serialization": "{float}", + "slot_uri": "MIXS:0001001", + "alias": "ph", + "owner": "WastewaterSludgeInterface", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "MiscEnvsInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "float", + "recommended": true, + "multivalued": false, + "minimum_value": 0, + "maximum_value": 14 + }, + "ph_meth": { + "name": "ph_meth", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "PMID,DOI or url" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Reference or method used in determining ph", + "title": "pH method", + "comments": [ + "This can include a link to the instrument used or a citation for the method." + ], + "examples": [ + { + "value": "https://www.southernlabware.com/pc9500-benchtop-ph-conductivity-meter-kit-ph-accuracy-2000mv-ph-range-2-000-to-20-000.html?gclid=Cj0KCQiAwJWdBhCYARIsAJc4idCO5vtvbVMf545fcvdROFqa6zjzNSoywNx6K4k9Coo9cCc2pybtvGsaAiR0EALw_wcB" + }, + { + "value": "https://doi.org/10.2136/sssabookser5.3.c16" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "pH method" + ], + "rank": 41, + "is_a": "core field", + "string_serialization": "{PMID}|{DOI}|{URL}", + "slot_uri": "MIXS:0001106", + "alias": "ph_meth", + "owner": "WastewaterSludgeInterface", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "MiscEnvsInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false + }, + "phosphate": { + "name": "phosphate", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of phosphate", + "title": "phosphate", + "examples": [ + { + "value": "0.7 micromole per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "phosphate" + ], + "rank": 53, + "is_a": "core field", + "slot_uri": "MIXS:0000505", + "alias": "phosphate", + "owner": "WastewaterSludgeInterface", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "MiscEnvsInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "pre_treatment": { + "name": "pre_treatment", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "pre-treatment type" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The process of pre-treatment removes materials that can be easily collected from the raw wastewater", + "title": "pre-treatment", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "pre-treatment" + ], + "rank": 342, + "is_a": "core field", + "string_serialization": "{text}", + "slot_uri": "MIXS:0000348", + "alias": "pre_treatment", + "owner": "WastewaterSludgeInterface", + "domain_of": [ + "Biosample", + "WastewaterSludgeInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "primary_treatment": { + "name": "primary_treatment", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "primary treatment type" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The process to produce both a generally homogeneous liquid capable of being treated biologically and a sludge that can be separately treated or processed", + "title": "primary treatment", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "primary treatment" + ], + "rank": 343, + "is_a": "core field", + "string_serialization": "{text}", + "slot_uri": "MIXS:0000349", + "alias": "primary_treatment", + "owner": "WastewaterSludgeInterface", + "domain_of": [ + "Biosample", + "WastewaterSludgeInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "reactor_type": { + "name": "reactor_type", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "reactor type name" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Anaerobic digesters can be designed and engineered to operate using a number of different process configurations, as batch or continuous, mesophilic, high solid or low solid, and single stage or multistage", + "title": "reactor type", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "reactor type" + ], + "rank": 346, + "is_a": "core field", + "string_serialization": "{text}", + "slot_uri": "MIXS:0000350", + "alias": "reactor_type", + "owner": "WastewaterSludgeInterface", + "domain_of": [ + "Biosample", + "WastewaterSludgeInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "salinity": { + "name": "salinity", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "practical salinity unit, percentage" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The total concentration of all dissolved salts in a liquid or solid sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater.", + "title": "salinity", + "examples": [ + { + "value": "25 practical salinity unit" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "salinity" + ], + "rank": 54, + "is_a": "core field", + "slot_uri": "MIXS:0000183", + "alias": "salinity", + "owner": "WastewaterSludgeInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "samp_collec_device": { + "name": "samp_collec_device", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "device name" + } + }, + "description": "The device used to collect an environmental sample. This field accepts terms listed under environmental sampling device (http://purl.obolibrary.org/obo/ENVO). This field also accepts terms listed under specimen collection device (http://purl.obolibrary.org/obo/GENEPIO_0002094).", + "title": "sample collection device", + "comments": [ + "Report dimensions and details when applicable" + ], + "examples": [ + { + "value": "swab, biopsy, niskin bottle, push core, drag swab [GENEPIO:0002713]" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sample collection device" + ], + "rank": 14, + "is_a": "nucleic acid sequence source field", + "string_serialization": "{termLabel} {[termID]}|{text}", + "slot_uri": "MIXS:0000002", + "alias": "samp_collec_device", + "owner": "WastewaterSludgeInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "recommended": true, + "multivalued": false + }, + "samp_collec_method": { + "name": "samp_collec_method", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "PMID,DOI,url , or text" + } + }, + "description": "The method employed for collecting the sample.", + "title": "sample collection method", + "comments": [ + "This can be a citation or description" + ], + "examples": [ + { + "value": "swabbing" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sample collection method" + ], + "rank": 15, + "is_a": "nucleic acid sequence source field", + "string_serialization": "{PMID}|{DOI}|{URL}|{text}", + "slot_uri": "MIXS:0001225", + "alias": "samp_collec_method", + "owner": "WastewaterSludgeInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "multivalued": false + }, + "samp_mat_process": { + "name": "samp_mat_process", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "text" + } + }, + "description": "A brief description of any processing applied to the sample during or after retrieving the sample from environment, or a link to the relevant protocol(s) performed.", + "title": "sample material processing", + "examples": [ + { + "value": "filtering of seawater" + }, + { + "value": "storing samples in ethanol" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sample material processing" + ], + "rank": 12, + "is_a": "nucleic acid sequence source field", + "string_serialization": "{text}", + "slot_uri": "MIXS:0000016", + "alias": "samp_mat_process", + "owner": "WastewaterSludgeInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "multivalued": false + }, + "samp_size": { + "name": "samp_size", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "millliter, gram, milligram, liter" + } + }, + "description": "The total amount or size (volume (ml), mass (g) or area (m2) ) of sample collected.", + "title": "amount or size of sample collected", + "comments": [ + "This refers to the TOTAL amount of sample collected from the experiment. NOT the amount sent to each institution or collected for a specific analysis." + ], + "examples": [ + { + "value": "5 grams" + }, + { + "value": "10 mL" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "amount or size of sample collected" + ], + "rank": 18, + "is_a": "nucleic acid sequence source field", + "string_serialization": "{float} {unit}", + "slot_uri": "MIXS:0000001", + "alias": "samp_size", + "owner": "WastewaterSludgeInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? \\S+$" + }, + "samp_store_dur": { + "name": "samp_store_dur", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "duration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Duration for which the sample was stored", + "title": "sample storage duration", + "examples": [ + { + "value": "P1Y6M" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sample storage duration" + ], + "rank": 353, + "is_a": "core field", + "string_serialization": "{duration}", + "slot_uri": "MIXS:0000116", + "alias": "samp_store_dur", + "owner": "WastewaterSludgeInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "samp_store_loc": { + "name": "samp_store_loc", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "location name" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Location at which sample was stored, usually name of a specific freezer/room", + "title": "sample storage location", + "examples": [ + { + "value": "Freezer no:5" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sample storage location" + ], + "rank": 41, + "is_a": "core field", + "string_serialization": "{text}", + "slot_uri": "MIXS:0000755", + "alias": "samp_store_loc", + "owner": "WastewaterSludgeInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "samp_store_temp": { + "name": "samp_store_temp", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "degree Celsius" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Temperature at which the sample was stored (degrees are assumed)", + "title": "sample storage temperature", + "examples": [ + { + "value": "-80 Celsius" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sample storage temperature" + ], + "rank": 7, + "is_a": "core field", + "slot_uri": "MIXS:0000110", + "alias": "samp_store_temp", + "owner": "WastewaterSludgeInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "required": true, + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "sample_link": { + "name": "sample_link", + "description": "A unique identifier to assign parent-child, subsample, or sibling samples. This is relevant when a sample or other material was used to generate the new sample.", + "title": "sample linkage", + "notes": [ + "also tempted to include SampIdNewTermsMixin but if len(slot_usage.keys()) > 1 and \"placeholder\" in slot_usage.keys():AttributeError: 'list' object has no attribute 'keys'" + ], + "comments": [ + "This field allows multiple entries separated by ; (Examples: Soil collected from the field will link with the soil used in an incubation. The soil a plant was grown in links to the plant sample. An original culture sample was transferred to a new vial and generated a new sample)" + ], + "examples": [ + { + "value": "IGSN:DSJ0284" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "rank": 5, + "string_serialization": "{text}:{text}", + "alias": "sample_link", + "owner": "WastewaterSludgeInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface", + "SampIdNewTermsMixin" + ], + "slot_group": "sample_id_section", + "range": "string", + "recommended": true, + "multivalued": false, + "pattern": "[^\\:\\n\\r]+\\:[^\\:\\n\\r]+" + }, + "secondary_treatment": { + "name": "secondary_treatment", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "secondary treatment type" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The process for substantially degrading the biological content of the sewage", + "title": "secondary treatment", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "secondary treatment" + ], + "rank": 360, + "is_a": "core field", + "string_serialization": "{text}", + "slot_uri": "MIXS:0000351", + "alias": "secondary_treatment", + "owner": "WastewaterSludgeInterface", + "domain_of": [ + "Biosample", + "WastewaterSludgeInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "sewage_type": { + "name": "sewage_type", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "sewage type name" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Type of wastewater treatment plant as municipial or industrial", + "title": "sewage type", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sewage type" + ], + "rank": 361, + "is_a": "core field", + "string_serialization": "{text}", + "slot_uri": "MIXS:0000215", + "alias": "sewage_type", + "owner": "WastewaterSludgeInterface", + "domain_of": [ + "Biosample", + "WastewaterSludgeInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "size_frac": { + "name": "size_frac", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "filter size value range" + } + }, + "description": "Filtering pore size used in sample preparation", + "title": "size fraction selected", + "examples": [ + { + "value": "0-0.22 micrometer" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "size fraction selected" + ], + "rank": 285, + "is_a": "nucleic acid sequence source field", + "string_serialization": "{float}-{float} {unit}", + "slot_uri": "MIXS:0000017", + "alias": "size_frac", + "owner": "WastewaterSludgeInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "sludge_retent_time": { + "name": "sludge_retent_time", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "hours" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The time activated sludge remains in reactor", + "title": "sludge retention time", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sludge retention time" + ], + "rank": 362, + "is_a": "core field", + "slot_uri": "MIXS:0000669", + "alias": "sludge_retent_time", + "owner": "WastewaterSludgeInterface", + "domain_of": [ + "Biosample", + "WastewaterSludgeInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "sodium": { + "name": "sodium", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milligram per liter, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Sodium concentration in the sample", + "title": "sodium", + "examples": [ + { + "value": "10.5 milligram per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sodium" + ], + "rank": 363, + "is_a": "core field", + "slot_uri": "MIXS:0000428", + "alias": "sodium", + "owner": "WastewaterSludgeInterface", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "soluble_inorg_mat": { + "name": "soluble_inorg_mat", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "soluble inorganic material name;measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "gram, microgram, mole per liter, gram per liter, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Concentration of substances such as ammonia, road-salt, sea-salt, cyanide, hydrogen sulfide, thiocyanates, thiosulfates, etc.", + "title": "soluble inorganic material", + "examples": [ + { + "value": "" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "soluble inorganic material" + ], + "rank": 364, + "is_a": "core field", + "string_serialization": "{text};{float} {unit}", + "slot_uri": "MIXS:0000672", + "alias": "soluble_inorg_mat", + "owner": "WastewaterSludgeInterface", + "domain_of": [ + "Biosample", + "WastewaterSludgeInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+\\|)*([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? 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Refers to the original material collected or to any derived sub-samples.", + "title": "sample name", + "comments": [ + "It can have any format, but we suggest that you make it concise, unique and consistent within your lab, and as informative as possible." + ], + "examples": [ + { + "value": "Rock core CB1178(5-6) from NSW" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sample name" + ], + "rank": 1, + "is_a": "investigation field", + "string_serialization": "{text}", + "slot_uri": "MIXS:0001107", + "identifier": true, + "alias": "samp_name", + "owner": "WastewaterSludgeInterface", + "domain_of": [ + "Biosample", + "DhMultiviewCommonColumnsMixin", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "EmslInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "JgiMgInterface", + "JgiMgLrInterface", + "JgiMtInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "string", + "required": true, + "multivalued": false + }, + "source_mat_id": { + "name": "source_mat_id", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "for cultures of microorganisms: identifiers for two culture collections; for other material a unique arbitrary identifer" + } + }, + "description": "A globally unique identifier assigned to the biological sample.", + "title": "source material identifier", + "todos": [ + "Currently, the comments say to use UUIDs. However, if we implement assigning NMDC identifiers with the minter we dont need to require a GUID. It can be an optional field to fill out only if they already have a resolvable ID.", + "Currently, the comments say to use UUIDs. However, if we implement assigning NMDC identifiers with the minter we dont need to require a GUID. It can be an optional field to fill out only if they already have a resolvable ID." + ], + "notes": [ + "The source material IS the Globally Unique ID" + ], + "comments": [ + "Identifiers must be prefixed. Possible FAIR prefixes are IGSNs (http://www.geosamples.org/getigsn), NCBI biosample accession numbers, ARK identifiers (https://arks.org/). These IDs enable linking to derived analytes and subsamples. If you have not assigned FAIR identifiers to your samples, you can generate UUIDs (https://www.uuidgenerator.net/).", + "Identifiers must be prefixed. Possible FAIR prefixes are IGSNs (http://www.geosamples.org/getigsn), NCBI biosample accession numbers, ARK identifiers (https://arks.org/). These IDs enable linking to derived analytes and subsamples. If you have not assigned FAIR identifiers to your samples, you can generate UUIDs (https://www.uuidgenerator.net/)." + ], + "examples": [ + { + "value": "IGSN:AU1243" + }, + { + "value": "UUID:24f1467a-40f4-11ed-b878-0242ac120002" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "source material identifiers" + ], + "rank": 2, + "is_a": "nucleic acid sequence source field", + "string_serialization": "{text}:{text}", + "slot_uri": "MIXS:0000026", + "alias": "source_mat_id", + "owner": "WastewaterSludgeInterface", + "domain_of": [ + "Biosample", + "DhMultiviewCommonColumnsMixin", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "EmslInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "JgiMgInterface", + "JgiMgLrInterface", + "JgiMtInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": 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involving an exposure to varying temperatures; should include the temperature, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include different temperature regimens", + "title": "air temperature regimen", + "examples": [ + { + "value": "25 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "air temperature regimen" + ], + "rank": 16, + "is_a": "core field", + "string_serialization": "{float} {unit};{Rn/start_time/end_time/duration}", + "slot_uri": "MIXS:0000551", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "multivalued": false + }, + "alkalinity": { + "name": "alkalinity", + "annotations": { + "expected_value": { + "tag": 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activity", + "title": "aminopeptidase activity", + "examples": [ + { + "value": "0.269 mole per liter per hour" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "aminopeptidase activity" + ], + "rank": 3, + "is_a": "core field", + "slot_uri": "MIXS:0000172", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "ammonium": { + "name": "ammonium", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per liter, milligram per liter, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of ammonium in the sample", + "title": "ammonium", + "examples": [ + { + "value": "1.5 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DH taking arb prec date only", + "Use modified term (amended definition)" + ], + "examples": [ + { + "value": "2021-04-15" + }, + { + "value": "2021-04" + }, + { + "value": "2021" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "collection date" + ], + "rank": 3, + "is_a": "environment field", + "string_serialization": "{date, arbitrary precision}", + "slot_uri": "MIXS:0000011", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "required": true, + "multivalued": false, + "pattern": "^[12]\\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\\d|3[01]))?)?$" + }, + "collection_date_inc": { + "name": "collection_date_inc", + "description": "Date the incubation was harvested/collected/ended. Only relevant for incubation samples.", + "title": "incubation collection date", + "notes": [ + "MIxS collection_date accepts (truncated) ISO8601. DH taking arbitrary precision date only" + ], + "comments": [ + "Date should be formatted as YYYY(-MM(-DD)). Ie, 2021-04-15, 2021-04 and 2021 are all acceptable." + ], + "examples": [ + { + "value": "2021-04-15, 2021-04 and 2021 are all acceptable." + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "MIXS:0000011" + ], + "rank": 2, + "string_serialization": "{date, arbitrary precision}", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WaterInterface", + "SoilMixsInspiredMixin" + ], + "slot_group": "mixs_inspired_section", + "range": "string", + "recommended": true, + "multivalued": false, + "pattern": "^[12]\\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\\d|3[01]))?)?$" + }, + "collection_time": { + "name": "collection_time", + "description": "The time of sampling, either as an instance (single point) or interval.", + "title": "collection time, GMT", + "notes": [ + "MIxS collection_date accepts (truncated) ISO8601. DH taking seconds optional time only" + ], + "comments": [ + "Time should be entered as HH:MM(:SS) in GMT. See here for a converter: https://www.worldtimebuddy.com/pst-to-gmt-converter" + ], + "examples": [ + { + "value": "13:33 or 13:33:55" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "MIXS:0000011" + ], + "rank": 1, + "string_serialization": "{time, seconds optional}", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WaterInterface", + "SoilMixsInspiredMixin" + ], + "slot_group": "mixs_inspired_section", + "range": "string", + "recommended": true, + "multivalued": false, + "pattern": "^([01]?\\d|2[0-3]|24(?=:00?:00?$)):([0-5]\\d)(:([0-5]\\d))?$" + }, + "conduc": { + "name": "conduc", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milliSiemens per centimeter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Electrical conductivity of water", + "title": "conductivity", + "examples": [ + { + "value": "10 milliSiemens per centimeter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "conductivity" + ], + "rank": 222, + "is_a": "core field", + "slot_uri": "MIXS:0000692", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "density": { + "name": "density", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "gram per cubic meter, gram per cubic centimeter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Density of the sample, which is its mass per unit volume (aka volumetric mass density)", + "title": "density", + "examples": [ + { + "value": "1000 kilogram per cubic meter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "density" + ], + "rank": 12, + "is_a": "core field", + "slot_uri": "MIXS:0000435", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "depth": { + "name": "depth", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + } + }, + "description": "The vertical distance below local surface, e.g. for sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples.", + "title": "depth, meters", + "notes": [ + "Use modified term" + ], + "comments": [ + "All depths must be reported in meters. Provide the numerical portion only." + ], + "examples": [ + { + "value": "0 - 0.1" + }, + { + "value": "1" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "depth" + ], + "rank": 9, + "is_a": "environment field", + "string_serialization": "{float}|{float}-{float}", + "slot_uri": "MIXS:0000018", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "required": true, + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)?(\\s*-\\s*[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)?)?$" + }, + "diether_lipids": { + "name": "diether_lipids", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "diether lipid name;measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "nanogram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Concentration of diether lipids; can include multiple types of diether lipids", + "title": "diether lipids", + "examples": [ + { + "value": "0.2 nanogram per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "diether lipids" + ], + "rank": 13, + "is_a": "core field", + "string_serialization": "{text};{float} {unit}", + "slot_uri": "MIXS:0000178", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+\\|)*([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+)$" + }, + "diss_carb_dioxide": { + "name": "diss_carb_dioxide", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per liter, milligram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample", + "title": "dissolved carbon dioxide", + "examples": [ + { + "value": "5 milligram per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "dissolved carbon dioxide" + ], + "rank": 14, + "is_a": "core field", + "slot_uri": "MIXS:0000436", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "diss_hydrogen": { + "name": "diss_hydrogen", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of dissolved hydrogen", + "title": "dissolved hydrogen", + "examples": [ + { + "value": "0.3 micromole per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "dissolved hydrogen" + ], + "rank": 15, + "is_a": "core field", + "slot_uri": "MIXS:0000179", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "diss_inorg_carb": { + "name": "diss_inorg_carb", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "microgram per liter, milligram per liter, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter", + "title": "dissolved inorganic carbon", + "examples": [ + { + "value": "2059 micromole per kilogram" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "dissolved inorganic carbon" + ], + "rank": 16, + "is_a": "core field", + "slot_uri": "MIXS:0000434", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "diss_inorg_nitro": { + "name": "diss_inorg_nitro", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "microgram per liter, micromole per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of dissolved inorganic nitrogen", + "title": "dissolved inorganic nitrogen", + "examples": [ + { + "value": "761 micromole per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "dissolved inorganic nitrogen" + ], + "rank": 223, + "is_a": "core field", + "slot_uri": "MIXS:0000698", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "diss_inorg_phosp": { + "name": "diss_inorg_phosp", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "microgram per liter, milligram per liter, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of dissolved inorganic phosphorus in the sample", + "title": "dissolved inorganic phosphorus", + "examples": [ + { + "value": "56.5 micromole per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "dissolved inorganic phosphorus" + ], + "rank": 224, + "is_a": "core field", + "slot_uri": "MIXS:0000106", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "diss_org_carb": { + "name": "diss_org_carb", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per liter, milligram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid", + "title": "dissolved organic carbon", + "examples": [ + { + "value": "197 micromole per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "dissolved organic carbon" + ], + "rank": 17, + "is_a": "core field", + "slot_uri": "MIXS:0000433", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "diss_org_nitro": { + "name": "diss_org_nitro", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "microgram per liter, milligram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2", + "title": "dissolved organic nitrogen", + "examples": [ + { + "value": "0.05 micromole per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "dissolved organic nitrogen" + ], + "rank": 18, + "is_a": "core field", + "slot_uri": "MIXS:0000162", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "diss_oxygen": { + "name": "diss_oxygen", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per kilogram, milligram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of dissolved oxygen", + "title": "dissolved oxygen", + "examples": [ + { + "value": "175 micromole per kilogram" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "dissolved oxygen" + ], + "rank": 19, + "is_a": "core field", + "slot_uri": "MIXS:0000119", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "down_par": { + "name": "down_par", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "microEinstein per square meter per second, microEinstein per square centimeter per second" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Visible waveband radiance and irradiance measurements in the water column", + "title": "downward PAR", + "examples": [ + { + "value": "28.71 microEinstein per square meter per second" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "downward PAR" + ], + "rank": 225, + "is_a": "core field", + "slot_uri": "MIXS:0000703", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "ecosystem": { + "name": "ecosystem", + "description": "An ecosystem is a combination of a physical environment (abiotic factors) and all the organisms (biotic factors) that interact with this environment. Ecosystem is in position 1/5 in a GOLD path.", + "comments": [ + "The abiotic factors play a profound role on the type and composition of organisms in a given environment. The GOLD Ecosystem at the top of the five-level classification system is aimed at capturing the broader environment from which an organism or environmental sample is collected. The three broad groups under Ecosystem are Environmental, Host-associated, and Engineered. They represent samples collected from a natural environment or from another organism or from engineered environments like bioreactors respectively." + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "https://gold.jgi.doe.gov/help" + ], + "rank": 9, + "is_a": "gold_path_field", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "Study", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "string", + "recommended": true, + "multivalued": false + }, + "ecosystem_category": { + "name": "ecosystem_category", + "description": "Ecosystem categories represent divisions within the ecosystem based on specific characteristics of the environment from where an organism or sample is isolated. Ecosystem category is in position 2/5 in a GOLD path.", + "comments": [ + "The Environmental ecosystem (for example) is divided into Air, Aquatic and Terrestrial. Ecosystem categories for Host-associated samples can be individual hosts or phyla and for engineered samples it may be manipulated environments like bioreactors, solid waste etc." + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "https://gold.jgi.doe.gov/help" + ], + "rank": 10, + "is_a": "gold_path_field", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "Study", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "string", + "recommended": true, + "multivalued": false + }, + "ecosystem_subtype": { + "name": "ecosystem_subtype", + "description": "Ecosystem subtypes represent further subdivision of Ecosystem types into more distinct subtypes. Ecosystem subtype is in position 4/5 in a GOLD path.", + "comments": [ + "Ecosystem Type Marine (Environmental -> Aquatic -> Marine) is further divided (for example) into Intertidal zone, Coastal, Pelagic, Intertidal zone etc. in the Ecosystem subtype category." + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "https://gold.jgi.doe.gov/help" + ], + "rank": 12, + "is_a": "gold_path_field", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "Study", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "string", + "recommended": true, + "multivalued": false + }, + "ecosystem_type": { + "name": "ecosystem_type", + "description": "Ecosystem types represent things having common characteristics within the Ecosystem Category. These common characteristics based grouping is still broad but specific to the characteristics of a given environment. Ecosystem type is in position 3/5 in a GOLD path.", + "comments": [ + "The Aquatic ecosystem category (for example) may have ecosystem types like Marine or Thermal springs etc. Ecosystem category Air may have Indoor air or Outdoor air as different Ecosystem Types. In the case of Host-associated samples, ecosystem type can represent Respiratory system, Digestive system, Roots etc." + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "https://gold.jgi.doe.gov/help" + ], + "rank": 11, + "is_a": "gold_path_field", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "Study", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "string", + "recommended": true, + "multivalued": false + }, + "elev": { + "name": "elev", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + } + }, + "description": "Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit.", + "title": "elevation, meters", + "comments": [ + "All elevations must be reported in meters. Provide the numerical portion only.", + "Please use https://www.advancedconverter.com/map-tools/find-altitude-by-coordinates, if needed, to help estimate the elevation based on latitude and longitude coordinates." + ], + "examples": [ + { + "value": "100" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "elevation" + ], + "rank": 6, + "is_a": "environment field", + "slot_uri": "MIXS:0000093", + "owner": "Biosample", + "domain_of": [ + "FieldResearchSite", + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "float", + "multivalued": false + }, + "env_broad_scale": { + "name": "env_broad_scale", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "The major environment type(s) where the sample was collected. Recommend subclasses of biome [ENVO:00000428]. Multiple terms can be separated by one or more pipes." + }, + "tooltip": { + "tag": "tooltip", + "value": "The biome or major environmental system where the sample or specimen originated. Choose values from subclasses of the 'biome' class [ENVO:00000428] in the Environment Ontology (ENVO). For host-associated or plant-associated samples, use terms from the UBERON or Plant Ontology to describe the broad anatomical or morphological context" + } + }, + "description": "Report the major environmental system the sample or specimen came from. The system(s) identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. in the desert or a rainforest). We recommend using subclasses of EnvO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS", + "title": "broad-scale environmental context", + "examples": [ + { + "value": "oceanic epipelagic zone biome [ENVO:01000033] for annotating a water sample from the photic zone in middle of the Atlantic Ocean" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "broad-scale environmental context" + ], + "rank": 6, + "is_a": "environment field", + "string_serialization": "{termLabel} {[termID]}", + "slot_uri": "MIXS:0000012", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "string", + "required": true, + "multivalued": false, + "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$" + }, + "env_local_scale": { + "name": "env_local_scale", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "Environmental entities having causal influences upon the entity at time of sampling." + }, + "tooltip": { + "tag": "tooltip", + "value": "The specific environmental entities or features near the sample or specimen that significantly influence its characteristics or composition. These entities are typically smaller in scale than the broad environmental context. Values for this field should be countable, material nouns and must be chosen from subclasses of BFO:0000040 (material entity) that appear in the Environment Ontology (ENVO). For host-associated or plant-associated samples, use terms from the UBERON or Plant Ontology to describe specific anatomical structures or plant parts." + } + }, + "description": "Report the entity or entities which are in the sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. We recommend using EnvO terms which are of smaller spatial grain than your entry for env_broad_scale. Terms, such as anatomical sites, from other OBO Library ontologies which interoperate with EnvO (e.g. UBERON) are accepted in this field. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS.", + "title": "local environmental context", + "examples": [ + { + "value": "litter layer [ENVO:01000338]; Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]." + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "local environmental context" + ], + "rank": 7, + "is_a": "environment field", + "string_serialization": "{termLabel} {[termID]}", + "slot_uri": "MIXS:0000013", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "string", + "required": true, + "multivalued": false, + "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$" + }, + "env_medium": { + "name": "env_medium", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "The material displaced by the entity at time of sampling. Recommend subclasses of environmental material [ENVO:00010483]." + }, + "tooltip": { + "tag": "tooltip", + "value": "The predominant environmental material or substrate that directly surrounds or hosts the sample or specimen at the time of sampling. Choose values from subclasses of the 'environmental material' class [ENVO:00010483] in the Environment Ontology (ENVO). Values for this field should be measurable or mass material nouns, representing continuous environmental materials. For host-associated or plant-associated samples, use terms from the UBERON or Plant Ontology to indicate a tissue, organ, or plant structure" + } + }, + "description": "Report the environmental material(s) immediately surrounding the sample or specimen at the time of sampling. We recommend using subclasses of 'environmental material' (http://purl.obolibrary.org/obo/ENVO_00010483). EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS . Terms from other OBO ontologies are permissible as long as they reference mass/volume nouns (e.g. air, water, blood) and not discrete, countable entities (e.g. a tree, a leaf, a table top).", + "title": "environmental medium", + "examples": [ + { + "value": "soil [ENVO:00001998]; Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air [ENVO_00002005]" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "environmental medium" + ], + "rank": 8, + "is_a": "environment field", + "string_serialization": "{termLabel} {[termID]}", + "slot_uri": "MIXS:0000014", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "string", + "required": true, + "multivalued": false, + "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$" + }, + "experimental_factor": { + "name": "experimental_factor", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "text or EFO and/or OBI" + } + }, + "description": "Experimental factors are essentially the variable aspects of an experiment design which can be used to describe an experiment, or set of experiments, in an increasingly detailed manner. This field accepts ontology terms from Experimental Factor Ontology (EFO) and/or Ontology for Biomedical Investigations (OBI). For a browser of EFO (v 2.95) terms, please see http://purl.bioontology.org/ontology/EFO; for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI", + "title": "experimental factor", + "examples": [ + { + "value": "time series design [EFO:0001779]" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "experimental factor" + ], + "rank": 12, + "is_a": "investigation field", + "string_serialization": "{termLabel} {[termID]}|{text}", + "slot_uri": "MIXS:0000008", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false + }, + "filter_method": { + "name": "filter_method", + "description": "Type of filter used or how the sample was filtered", + "title": "filter method", + "comments": [ + "describe the filter or provide a catalog number and manufacturer" + ], + "examples": [ + { + "value": "C18" + }, + { + "value": "Basix PES, 13-100-106 FisherSci" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "MIXS:0000765" + ], + "rank": 6, + "string_serialization": "{text}", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "SoilInterface", + "WaterInterface", + "SoilMixsInspiredMixin" + ], + "slot_group": "mixs_inspired_section", + "range": "string", + "recommended": true, + "multivalued": false + }, + "fluor": { + "name": "fluor", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milligram chlorophyll a per cubic meter, volts" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Raw or converted fluorescence of water", + "title": "fluorescence", + "examples": [ + { + "value": "2.5 volts" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "fluorescence" + ], + "rank": 226, + "is_a": "core field", + "slot_uri": "MIXS:0000704", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "gaseous_environment": { + "name": "gaseous_environment", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "gaseous compound name;gaseous compound amount;treatment interval and duration" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Use of conditions with differing gaseous environments; should include the name of gaseous compound, amount administered, treatment duration, interval and total experimental duration; can include multiple gaseous environment regimens", + "title": "gaseous environment", + "todos": [ + "would like to see usage examples for this slot. Requiring micromole/L seems too limiting and doesn't match expected_value value", + "did I do this right? keep the example that's provided and add another? so as to not override" + ], + "examples": [ + { + "value": "CO2; 500ppm above ambient; constant" + }, + { + "value": "nitric oxide;0.5 micromole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "gaseous environment" + ], + "rank": 20, + "is_a": "core field", + "string_serialization": "{text};{float} {unit};{Rn/start_time/end_time/duration}", + "slot_uri": "MIXS:0000558", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "multivalued": false + }, + "geo_loc_name": { + "name": "geo_loc_name", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "country or sea name (INSDC or GAZ): region(GAZ), specific location name" + } + }, + "description": "The geographical origin of the sample as defined by the country or sea name followed by specific region name.", + "title": "geographic location (country and/or sea,region)", + "examples": [ + { + "value": "USA: Maryland, Bethesda" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "geographic location (country and/or sea,region)" + ], + "rank": 4, + "is_a": "environment field", + "string_serialization": "{term}: {term}, {text}", + "slot_uri": "MIXS:0000010", + "owner": "Biosample", + "domain_of": [ + "FieldResearchSite", + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "required": true, + "multivalued": false + }, + "glucosidase_act": { + "name": "glucosidase_act", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "mol per liter per hour" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Measurement of glucosidase activity", + "title": "glucosidase activity", + "examples": [ + { + "value": "5 mol per liter per hour" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "glucosidase activity" + ], + "rank": 20, + "is_a": "core field", + "slot_uri": "MIXS:0000137", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "humidity_regm": { + "name": "humidity_regm", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "humidity value;treatment interval and duration" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "gram per cubic meter" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Information about treatment involving an exposure to varying degree of humidity; information about treatment involving use of growth hormones; should include amount of humidity administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens", + "title": "humidity regimen", + "examples": [ + { + "value": "25 gram per cubic meter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "humidity regimen" + ], + "rank": 21, + "is_a": "core field", + "string_serialization": "{float} {unit};{Rn/start_time/end_time/duration}", + "slot_uri": "MIXS:0000568", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "multivalued": false + }, + "isotope_exposure": { + "name": "isotope_exposure", + "description": "List isotope exposure or addition applied to your sample.", + "title": "isotope exposure/addition", + "todos": [ + "Can we make the H218O correctly super and subscripted?" + ], + "comments": [ + "This is required when your experimental design includes the use of isotopically labeled compounds" + ], + "examples": [ + { + "value": "13C glucose" + }, + { + "value": "H218O" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "MIXS:0000751" + ], + "rank": 16, + "string_serialization": "{termLabel} {[termID]}; {timestamp}", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WaterInterface", + "SoilMixsInspiredMixin" + ], + "slot_group": "mixs_inspired_section", + "range": "string", + "recommended": true, + "multivalued": false, + "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]; ([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$" + }, + "lat_lon": { + "name": "lat_lon", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "decimal degrees, limit to 8 decimal points" + } + }, + "description": "The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system", + "title": "geographic location (latitude and longitude)", + "notes": [ + "This is currently a required field but it's not clear if this should be required for human hosts" + ], + "examples": [ + { + "value": "50.586825 6.408977" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "geographic location (latitude and longitude)" + ], + "rank": 5, + "is_a": "environment field", + "string_serialization": "{float} {float}", + "slot_uri": "MIXS:0000009", + "owner": "Biosample", + "domain_of": [ + "FieldResearchSite", + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)?$" + }, + "light_intensity": { + "name": "light_intensity", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "lux" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Measurement of light intensity", + "title": "light intensity", + "examples": [ + { + "value": "0.3 lux" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "light intensity" + ], + "rank": 227, + "is_a": "core field", + "slot_uri": "MIXS:0000706", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "light_regm": { + "name": "light_regm", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "exposure type;light intensity;light quality" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "lux; micrometer, nanometer, angstrom" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Information about treatment(s) involving exposure to light, including both light intensity and quality.", + "title": "light regimen", + "examples": [ + { + "value": "incandescant light;10 lux;450 nanometer" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "light regimen" + ], + "rank": 24, + "is_a": "core field", + "string_serialization": "{text};{float} {unit};{float} {unit}", + "slot_uri": "MIXS:0000569", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "multivalued": false, + "pattern": "^\\S+.*\\S+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? \\S+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? \\S+$" + }, + "magnesium": { + "name": "magnesium", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "mole per liter, milligram per liter, parts per million, micromole per kilogram" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of magnesium in the sample", + "title": "magnesium", + "examples": [ + { + "value": "52.8 micromole per kilogram" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "magnesium" + ], + "rank": 21, + "is_a": "core field", + "slot_uri": "MIXS:0000431", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "mean_frict_vel": { + "name": "mean_frict_vel", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "meter per second" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Measurement of mean friction velocity", + "title": "mean friction velocity", + "examples": [ + { + "value": "0.5 meter per second" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "mean friction velocity" + ], + "rank": 22, + "is_a": "core field", + "slot_uri": "MIXS:0000498", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "mean_peak_frict_vel": { + "name": "mean_peak_frict_vel", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "meter per second" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Measurement of mean peak friction velocity", + "title": "mean peak friction velocity", + "examples": [ + { + "value": "1 meter per second" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "mean peak friction velocity" + ], + "rank": 23, + "is_a": "core field", + "slot_uri": "MIXS:0000502", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "misc_param": { + "name": "misc_param", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "parameter name;measurement value" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Any other measurement performed or parameter collected, that is not listed here", + "title": "miscellaneous parameter", + "examples": [ + { + "value": "Bicarbonate ion concentration;2075 micromole per kilogram" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "miscellaneous parameter" + ], + "rank": 23, + "is_a": "core field", + "string_serialization": "{text};{float} {unit}", + "slot_uri": "MIXS:0000752", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false, + "pattern": "^([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+\\|)*([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+)$" + }, + "n_alkanes": { + "name": "n_alkanes", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "n-alkane name;measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Concentration of n-alkanes; can include multiple n-alkanes", + "title": "n-alkanes", + "examples": [ + { + "value": "n-hexadecane;100 milligram per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "n-alkanes" + ], + "rank": 25, + "is_a": "core field", + "string_serialization": "{text};{float} {unit}", + "slot_uri": "MIXS:0000503", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+\\|)*([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+)$" + }, + "nitrate": { + "name": "nitrate", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per liter, milligram per liter, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of nitrate in the sample", + "title": "nitrate", + "examples": [ + { + "value": "65 micromole per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "nitrate" + ], + "rank": 26, + "is_a": "core field", + "slot_uri": "MIXS:0000425", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "nitrite": { + "name": "nitrite", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per liter, milligram per liter, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of nitrite in the sample", + "title": "nitrite", + "examples": [ + { + "value": "0.5 micromole per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "nitrite" + ], + "rank": 27, + "is_a": "core field", + "slot_uri": "MIXS:0000426", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "nitro": { + "name": "nitro", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of nitrogen (total)", + "title": "nitrogen", + "examples": [ + { + "value": "4.2 micromole per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "nitrogen" + ], + "rank": 28, + "is_a": "core field", + "slot_uri": "MIXS:0000504", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "org_carb": { + "name": "org_carb", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of organic carbon", + "title": "organic carbon", + "examples": [ + { + "value": "1.5 microgram per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "organic carbon" + ], + "rank": 29, + "is_a": "core field", + "slot_uri": "MIXS:0000508", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "org_matter": { + "name": "org_matter", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "microgram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of organic matter", + "title": "organic matter", + "examples": [ + { + "value": "1.75 milligram per cubic meter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "organic matter" + ], + "rank": 45, + "is_a": "core field", + "slot_uri": "MIXS:0000204", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "MiscEnvsInterface", + "SedimentInterface", + "SoilInterface", + "WaterInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "org_nitro": { + "name": "org_nitro", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "microgram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of organic nitrogen", + "title": "organic nitrogen", + "examples": [ + { + "value": "4 micromole per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "organic nitrogen" + ], + "rank": 46, + "is_a": "core field", + "slot_uri": "MIXS:0000205", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "MiscEnvsInterface", + "SedimentInterface", + "SoilInterface", + "WaterInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "organism_count": { + "name": "organism_count", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "organism name;measurement value;enumeration" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "number of cells per cubic meter, number of cells per milliliter, number of cells per cubic centimeter" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Total cell count of any organism (or group of 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(example: total prokaryotes; 3.5e7 cells per ml; qpcr)", + "title": "organism count", + "examples": [ + { + "value": "total prokaryotes;3.5e7 cells per milliliter;qPCR" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "organism count" + ], + "rank": 30, + "is_a": "core field", + "slot_uri": "MIXS:0000103", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^(\\S+.*\\S+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? \\S+.*\\S+;(qPCR|ATP|MPN|other)\\|)*(\\S+.*\\S+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? \\S+.*\\S+;(qPCR|ATP|MPN|other))$" + }, + "oxy_stat_samp": { + "name": "oxy_stat_samp", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Oxygenation status of sample", + "title": "oxygenation status of sample", + "examples": [ + { + "value": "aerobic" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "oxygenation status of sample" + ], + "rank": 25, + "is_a": "core field", + "slot_uri": "MIXS:0000753", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_section", + "range": "OxyStatSampEnum", + "multivalued": false + }, + "part_org_carb": { + "name": "part_org_carb", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "microgram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of particulate organic carbon", + "title": "particulate organic carbon", + "examples": [ + { + "value": "1.92 micromole per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "particulate organic carbon" + ], + "rank": 31, + "is_a": "core field", + "slot_uri": "MIXS:0000515", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "part_org_nitro": { + "name": "part_org_nitro", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "microgram per liter, micromole per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of particulate organic nitrogen", + "title": "particulate organic nitrogen", + "examples": [ + { + "value": "0.3 micromole per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "particulate organic nitrogen" + ], + "rank": 228, + "is_a": "core field", + "slot_uri": "MIXS:0000719", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "perturbation": { + "name": "perturbation", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "perturbation type name;perturbation interval and duration" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types", + "title": "perturbation", + "examples": [ + { + "value": "antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "perturbation" + ], + "rank": 33, + "is_a": "core field", + "string_serialization": "{text};{Rn/start_time/end_time/duration}", + "slot_uri": "MIXS:0000754", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "petroleum_hydrocarb": { + "name": "petroleum_hydrocarb", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of petroleum hydrocarbon", + "title": "petroleum hydrocarbon", + "examples": [ + { + "value": "0.05 micromole per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "petroleum hydrocarbon" + ], + "rank": 34, + "is_a": "core field", + "slot_uri": "MIXS:0000516", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "ph": { + "name": "ph", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid", + "title": "pH", + "examples": [ + { + "value": "7.2" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "pH" + ], + "rank": 27, + "is_a": "core field", + "slot_uri": "MIXS:0001001", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "MiscEnvsInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "double", + "multivalued": false + }, + "ph_meth": { + "name": "ph_meth", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "PMID,DOI or url" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Reference or method used in determining ph", + "title": "pH method", + "comments": [ + "This can include a link to the instrument used or a citation for the method." + ], + "examples": [ + { + "value": "https://www.southernlabware.com/pc9500-benchtop-ph-conductivity-meter-kit-ph-accuracy-2000mv-ph-range-2-000-to-20-000.html?gclid=Cj0KCQiAwJWdBhCYARIsAJc4idCO5vtvbVMf545fcvdROFqa6zjzNSoywNx6K4k9Coo9cCc2pybtvGsaAiR0EALw_wcB" + }, + { + "value": "https://doi.org/10.2136/sssabookser5.3.c16" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "pH method" + ], + "rank": 41, + "is_a": "core field", + "string_serialization": "{PMID}|{DOI}|{URL}", + "slot_uri": "MIXS:0001106", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "MiscEnvsInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false + }, + "phaeopigments": { + "name": "phaeopigments", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "phaeopigment name;measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milligram per cubic meter" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Concentration of phaeopigments; can include multiple phaeopigments", + "title": "phaeopigments", + "examples": [ + { + "value": "2.5 milligram per cubic meter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "phaeopigments" + ], + "rank": 35, + "is_a": "core field", + "string_serialization": "{text};{float} {unit}", + "slot_uri": "MIXS:0000180", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? 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[^;\\t\\r\\x0A]+)$" + }, + "photon_flux": { + "name": "photon_flux", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "number of photons per second per unit area" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Measurement of photon flux", + "title": "photon flux", + "examples": [ + { + "value": "3.926 micromole photons per second per square meter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "photon flux" + ], + "rank": 229, + "is_a": "core field", + "slot_uri": "MIXS:0000725", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "potassium": { + "name": "potassium", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milligram per liter, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of potassium in the sample", + "title": "potassium", + "examples": [ + { + "value": "463 milligram per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "potassium" + ], + "rank": 38, + "is_a": "core field", + "slot_uri": "MIXS:0000430", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "pressure": { + "name": "pressure", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "atmosphere" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Pressure to which the sample is subject to, in atmospheres", + "title": "pressure", + "examples": [ + { + "value": "50 atmosphere" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "pressure" + ], + "rank": 39, + "is_a": "core field", + "slot_uri": "MIXS:0000412", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "primary_prod": { + "name": "primary_prod", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milligram per cubic meter per day, gram per square meter per day" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Measurement of primary production, generally measured as isotope uptake", + "title": "primary production", + "examples": [ + { + "value": "100 milligram per cubic meter per day" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "primary production" + ], + "rank": 230, + "is_a": "core field", + "slot_uri": "MIXS:0000728", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "redox_potential": { + "name": "redox_potential", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "millivolt" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential", + "title": "redox potential", + "examples": [ + { + "value": "300 millivolt" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "redox potential" + ], + "rank": 40, + "is_a": "core field", + "slot_uri": "MIXS:0000182", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "salinity": { + "name": "salinity", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "practical salinity unit, percentage" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The total concentration of all dissolved salts in a liquid or solid sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater.", + "title": "salinity", + "examples": [ + { + "value": "25 practical salinity unit" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "salinity" + ], + "rank": 54, + "is_a": "core field", + "slot_uri": "MIXS:0000183", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "salinity_meth": { + "name": "salinity_meth", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "PMID,DOI or url" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Reference or method used in determining salinity", + "title": "salinity method", + "examples": [ + { + "value": "https://doi.org/10.1007/978-1-61779-986-0_28" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "salinity method" + ], + "rank": 55, + "is_a": "core field", + "string_serialization": "{PMID}|{DOI}|{URL}", + "slot_uri": "MIXS:0000341", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WaterInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false + }, + "samp_collec_device": { + "name": "samp_collec_device", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "device name" + } + }, + "description": "The device used to collect an environmental sample. This field accepts terms listed under environmental sampling device (http://purl.obolibrary.org/obo/ENVO). This field also accepts terms listed under specimen collection device (http://purl.obolibrary.org/obo/GENEPIO_0002094).", + "title": "sample collection device", + "examples": [ + { + "value": "swab, biopsy, niskin bottle, push core, drag swab [GENEPIO:0002713]" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sample collection device" + ], + "rank": 14, + "is_a": "nucleic acid sequence source field", + "string_serialization": "{termLabel} {[termID]}|{text}", + "slot_uri": "MIXS:0000002", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "multivalued": false + }, + "samp_collec_method": { + "name": "samp_collec_method", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "PMID,DOI,url , or text" + } + }, + "description": "The method employed for collecting the sample.", + "title": "sample collection method", + "examples": [ + { + "value": "swabbing" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sample collection method" + ], + "rank": 15, + "is_a": "nucleic acid sequence source field", + "string_serialization": "{PMID}|{DOI}|{URL}|{text}", + "slot_uri": "MIXS:0001225", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "multivalued": false + }, + "samp_mat_process": { + "name": "samp_mat_process", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "text" + } + }, + "description": "A brief description of any processing applied to the sample during or after retrieving the sample from environment, or a link to the relevant protocol(s) performed.", + "title": "sample material processing", + "examples": [ + { + "value": "filtering of seawater" + }, + { + "value": "storing samples in ethanol" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sample material processing" + ], + "rank": 12, + "is_a": "nucleic acid sequence source field", + "string_serialization": "{text}", + "slot_uri": "MIXS:0000016", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "multivalued": false + }, + "samp_size": { + "name": "samp_size", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "millliter, gram, milligram, liter" + } + }, + "description": "The total amount or size (volume (ml), mass (g) or area (m2) ) of sample collected.", + "title": "amount or size of sample collected", + "examples": [ + { + "value": "5 liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "amount or size of sample collected" + ], + "rank": 18, + "is_a": "nucleic acid sequence source field", + "slot_uri": "MIXS:0000001", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "samp_store_dur": { + "name": "samp_store_dur", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "duration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Duration for which the sample was stored", + "title": "sample storage duration", + "examples": [ + { + "value": "P1Y6M" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sample storage duration" + ], + "rank": 353, + "is_a": "core field", + "string_serialization": "{duration}", + "slot_uri": "MIXS:0000116", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "samp_store_loc": { + "name": "samp_store_loc", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "location name" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Location at which sample was stored, usually name of a specific freezer/room", + "title": "sample storage location", + "examples": [ + { + "value": "Freezer no:5" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sample storage location" + ], + "rank": 41, + "is_a": "core field", + "string_serialization": "{text}", + "slot_uri": "MIXS:0000755", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "samp_store_temp": { + "name": "samp_store_temp", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "degree Celsius" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Temperature at which sample was stored, e.g. -80 degree Celsius", + "title": "sample storage temperature", + "examples": [ + { + "value": "-80 degree Celsius" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sample storage temperature" + ], + "rank": 7, + "is_a": "core field", + "slot_uri": "MIXS:0000110", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "sample_link": { + "name": "sample_link", + "description": "A unique identifier to assign parent-child, subsample, or sibling samples. This is relevant when a sample or other material was used to generate the new sample.", + "title": "sample linkage", + "notes": [ + "also tempted to include SampIdNewTermsMixin but if len(slot_usage.keys()) > 1 and \"placeholder\" in slot_usage.keys():AttributeError: 'list' object has no attribute 'keys'" + ], + "comments": [ + "This field allows multiple entries separated by ; (Examples: Soil collected from the field will link with the soil used in an incubation. The soil a plant was grown in links to the plant sample. An original culture sample was transferred to a new vial and generated a new sample)" + ], + "examples": [ + { + "value": "IGSN:DSJ0284" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "rank": 5, + "string_serialization": "{text}:{text}", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface", + "SampIdNewTermsMixin" + ], + "slot_group": "sample_id_section", + "range": "string", + "recommended": true, + "multivalued": false, + "pattern": "[^\\:\\n\\r]+\\:[^\\:\\n\\r]+" + }, + "silicate": { + "name": "silicate", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of silicate", + "title": "silicate", + "examples": [ + { + "value": "0.05 micromole per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "silicate" + ], + "rank": 43, + "is_a": "core field", + "slot_uri": "MIXS:0000184", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "size_frac": { + "name": "size_frac", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "filter size value range" + } + }, + "description": "Filtering pore size used in sample preparation", + "title": "size fraction selected", + "examples": [ + { + "value": "0-0.22 micrometer" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "size fraction selected" + ], + "rank": 285, + "is_a": "nucleic acid sequence source field", + "string_serialization": "{float}-{float} {unit}", + "slot_uri": "MIXS:0000017", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "size_frac_low": { + "name": "size_frac_low", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micrometer" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Refers to the mesh/pore size used to pre-filter/pre-sort the sample. Materials larger than the size threshold are excluded from the sample", + "title": "size-fraction lower threshold", + "examples": [ + { + "value": "0.2 micrometer" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "size-fraction lower threshold" + ], + "rank": 10, + "is_a": "core field", + "slot_uri": "MIXS:0000735", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "SoilInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "size_frac_up": { + "name": "size_frac_up", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micrometer" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Refers to the mesh/pore size used to retain the sample. Materials smaller than the size threshold are excluded from the sample", + "title": "size-fraction upper threshold", + "examples": [ + { + "value": "20 micrometer" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "size-fraction upper threshold" + ], + "rank": 11, + "is_a": "core field", + "slot_uri": "MIXS:0000736", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "SoilInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "sodium": { + "name": "sodium", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milligram per liter, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Sodium concentration in the sample", + "title": "sodium", + "examples": [ + { + "value": "10.5 milligram per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sodium" + ], + "rank": 363, + "is_a": "core field", + "slot_uri": "MIXS:0000428", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "soluble_react_phosp": { + "name": "soluble_react_phosp", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per liter, milligram per liter, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of soluble reactive phosphorus", + "title": "soluble reactive phosphorus", + "examples": [ + { + "value": "0.1 milligram per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "soluble reactive phosphorus" + ], + "rank": 231, + "is_a": "core field", + "slot_uri": "MIXS:0000738", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "specific_ecosystem": { + "name": "specific_ecosystem", + "description": "Specific ecosystems represent specific features of the environment like aphotic zone in an ocean or gastric mucosa within a host digestive system. Specific ecosystem is in position 5/5 in a GOLD path.", + "comments": [ + "Specific ecosystems help to define samples based on very specific characteristics of an environment under the five-level classification system." + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "https://gold.jgi.doe.gov/help" + ], + "rank": 13, + "is_a": "gold_path_field", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "Study", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "string", + "recommended": true, + "multivalued": false + }, + "start_date_inc": { + "name": "start_date_inc", + "description": "Date the incubation was started. Only relevant for incubation samples.", + "title": "incubation start date", + "notes": [ + "MIxS collection_date accepts (truncated) ISO8601. DH taking arbitrary precision date only" + ], + "comments": [ + "Date should be formatted as YYYY(-MM(-DD)). Ie, 2021-04-15, 2021-04 and 2021 are all acceptable." + ], + "examples": [ + { + "value": "2021-04-15, 2021-04 and 2021 are all acceptable." + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "MIXS:0000011" + ], + "rank": 4, + "string_serialization": "{date, arbitrary precision}", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WaterInterface", + "SoilMixsInspiredMixin" + ], + "slot_group": "mixs_inspired_section", + "range": "string", + "recommended": true, + "multivalued": false, + "pattern": "^[12]\\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\\d|3[01]))?)?$" + }, + "sulfate": { + "name": "sulfate", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per liter, milligram per liter, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of sulfate in the sample", + "title": "sulfate", + "examples": [ + { + "value": "5 micromole per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sulfate" + ], + "rank": 44, + "is_a": "core field", + "slot_uri": "MIXS:0000423", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "sulfide": { + "name": "sulfide", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per liter, milligram per liter, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of sulfide in the sample", + "title": "sulfide", + "examples": [ + { + "value": "2 micromole per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sulfide" + ], + "rank": 371, + "is_a": "core field", + "slot_uri": "MIXS:0000424", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "suspend_part_matter": { + "name": "suspend_part_matter", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milligram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of suspended particulate matter", + "title": "suspended particulate matter", + "examples": [ + { + "value": "0.5 milligram per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "suspended particulate matter" + ], + "rank": 232, + "is_a": "core field", + "slot_uri": "MIXS:0000741", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "temp": { + "name": "temp", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "degree Celsius" + } + }, + "description": "Temperature of the sample at the time of sampling.", + "title": "temperature", + "examples": [ + { + "value": "25 degree Celsius" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "temperature" + ], + "rank": 37, + "is_a": "environment field", + "slot_uri": "MIXS:0000113", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "tidal_stage": { + "name": "tidal_stage", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Stage of tide", + "title": "tidal stage", + "examples": [ + { + "value": "high tide" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "tidal stage" + ], + "rank": 45, + "is_a": "core field", + "slot_uri": "MIXS:0000750", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "tidal_stage_enum", + "multivalued": false + }, + "tot_depth_water_col": { + "name": "tot_depth_water_col", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "meter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Measurement of total depth of water column", + "title": "total depth of water column", + "examples": [ + { + "value": "500 meter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "total depth of water column" + ], + "rank": 46, + "is_a": "core field", + "slot_uri": "MIXS:0000634", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": 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For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi", + "title": "chemical administration", + "examples": [ + { + "value": "agar [CHEBI:2509];2018-05-11|agar [CHEBI:2509];2018-05-22" + }, + { + "value": "agar [CHEBI:2509];2018-05" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "chemical administration" + ], + "rank": 17, + "is_a": "core field", + "string_serialization": "{termLabel} {[termID]};{timestamp}", + "slot_uri": "MIXS:0000751", + "alias": "chem_administration", + "owner": "WaterInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "recommended": true, + "multivalued": false, + "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\];([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$" + }, + "chloride": { + "name": "chloride", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milligram per liter, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of chloride in the sample", + "title": "chloride", + "examples": [ + { + "value": "5000 milligram per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "chloride" + ], + "rank": 10, + "is_a": "core field", + "slot_uri": "MIXS:0000429", + "alias": "chloride", + "owner": "WaterInterface", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "chlorophyll": { + "name": "chlorophyll", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milligram per cubic meter, microgram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of chlorophyll", + "title": "chlorophyll", + "examples": [ + { + "value": "5 milligram per cubic meter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "chlorophyll" + ], + "rank": 11, + "is_a": "core field", + "slot_uri": "MIXS:0000177", + "alias": "chlorophyll", + "owner": "WaterInterface", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "climate_environment": { + "name": "climate_environment", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "climate name;treatment interval and duration" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Treatment involving an exposure to a particular climate; treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple climates", + "title": "climate environment", + "todos": [ + "description says \"can include multiple climates\" but multivalued is set to false", + "add examples, i need to see some examples to add correctly formatted example." + ], + "examples": [ + { + "value": "tropical climate;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "climate environment" + ], + "rank": 19, + "is_a": "core field", + "string_serialization": "{text};{Rn/start_time/end_time/duration}", + "slot_uri": "MIXS:0001040", + "alias": "climate_environment", + "owner": "WaterInterface", + "domain_of": [ + "Biosample", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "multivalued": false + }, + "collection_date": { + "name": "collection_date", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "date and time" + } + }, + "description": "The date of sampling", + "title": "collection date", + "notes": [ + "MIxS collection_date accepts (truncated) ISO8601. DH taking arb prec date only", + "Use modified term (amended definition)" + ], + "examples": [ + { + "value": "2021-04-15" + }, + { + "value": "2021-04" + }, + { + "value": "2021" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "collection date" + ], + "rank": 3, + "is_a": "environment field", + "string_serialization": "{date, arbitrary precision}", + "slot_uri": "MIXS:0000011", + "alias": "collection_date", + "owner": "WaterInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "required": true, + "multivalued": false, + "pattern": "^[12]\\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\\d|3[01]))?)?$" + }, + "collection_date_inc": { + "name": "collection_date_inc", + "description": "Date the incubation was harvested/collected/ended. Only relevant for incubation samples.", + "title": "incubation collection date", + "notes": [ + "MIxS collection_date accepts (truncated) ISO8601. DH taking arbitrary precision date only" + ], + "comments": [ + "Date should be formatted as YYYY(-MM(-DD)). Ie, 2021-04-15, 2021-04 and 2021 are all acceptable." + ], + "examples": [ + { + "value": "2021-04-15, 2021-04 and 2021 are all acceptable." + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "MIXS:0000011" + ], + "rank": 2, + "string_serialization": "{date, arbitrary precision}", + "alias": "collection_date_inc", + "owner": "WaterInterface", + "domain_of": [ + "Biosample", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WaterInterface", + "SoilMixsInspiredMixin" + ], + "slot_group": "mixs_inspired_section", + "range": "string", + "recommended": true, + "multivalued": false, + "pattern": "^[12]\\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\\d|3[01]))?)?$" + }, + "collection_time": { + "name": "collection_time", + "description": "The time of sampling, either as an instance (single point) or interval.", + "title": "collection time, GMT", + "notes": [ + "MIxS collection_date accepts (truncated) ISO8601. DH taking seconds optional time only" + ], + "comments": [ + "Time should be entered as HH:MM(:SS) in GMT. See here for a converter: https://www.worldtimebuddy.com/pst-to-gmt-converter" + ], + "examples": [ + { + "value": "13:33 or 13:33:55" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "MIXS:0000011" + ], + "rank": 1, + "string_serialization": "{time, seconds optional}", + "alias": "collection_time", + "owner": "WaterInterface", + "domain_of": [ + "Biosample", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WaterInterface", + "SoilMixsInspiredMixin" + ], + "slot_group": "mixs_inspired_section", + "range": "string", + "recommended": true, + "multivalued": false, + "pattern": "^([01]?\\d|2[0-3]|24(?=:00?:00?$)):([0-5]\\d)(:([0-5]\\d))?$" + }, + "conduc": { + "name": "conduc", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milliSiemens per centimeter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Electrical conductivity of water", + "title": "conductivity", + "examples": [ + { + "value": "10 milliSiemens per centimeter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "conductivity" + ], + "rank": 222, + "is_a": "core field", + "slot_uri": "MIXS:0000692", + "alias": "conduc", + "owner": "WaterInterface", + "domain_of": [ + "Biosample", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "density": { + "name": "density", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "gram per cubic meter, gram per cubic centimeter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Density of the sample, which is its mass per unit volume (aka volumetric mass density)", + "title": "density", + "examples": [ + { + "value": "1000 kilogram per cubic meter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "density" + ], + "rank": 12, + "is_a": "core field", + "slot_uri": "MIXS:0000435", + "alias": "density", + "owner": "WaterInterface", + "domain_of": [ + "Biosample", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "depth": { + "name": "depth", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + } + }, + "description": "The vertical distance below local surface, e.g. for sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples.", + "title": "depth, meters", + "notes": [ + "Use modified term" + ], + "comments": [ + "All depths must be reported in meters. Provide the numerical portion only." + ], + "examples": [ + { + "value": "0 - 0.1" + }, + { + "value": "1" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "depth" + ], + "rank": 9, + "is_a": "environment field", + "string_serialization": "{float}|{float}-{float}", + "slot_uri": "MIXS:0000018", + "alias": "depth", + "owner": "WaterInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "required": true, + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)?(\\s*-\\s*[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)?)?$" + }, + "diether_lipids": { + "name": "diether_lipids", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "diether lipid name;measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "nanogram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Concentration of diether lipids; can include multiple types of diether lipids", + "title": "diether lipids", + "examples": [ + { + "value": "0.2 nanogram per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "diether lipids" + ], + "rank": 13, + "is_a": "core field", + "string_serialization": "{text};{float} {unit}", + "slot_uri": "MIXS:0000178", + "alias": "diether_lipids", + "owner": "WaterInterface", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+\\|)*([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+)$" + }, + "diss_carb_dioxide": { + "name": "diss_carb_dioxide", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per liter, milligram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample", + "title": "dissolved carbon dioxide", + "examples": [ + { + "value": "5 milligram per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "dissolved carbon dioxide" + ], + "rank": 14, + "is_a": "core field", + "slot_uri": "MIXS:0000436", + "alias": "diss_carb_dioxide", + "owner": "WaterInterface", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "diss_hydrogen": { + "name": "diss_hydrogen", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of dissolved hydrogen", + "title": "dissolved hydrogen", + "examples": [ + { + "value": "0.3 micromole per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "dissolved hydrogen" + ], + "rank": 15, + "is_a": "core field", + "slot_uri": "MIXS:0000179", + "alias": "diss_hydrogen", + "owner": "WaterInterface", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "diss_inorg_carb": { + "name": "diss_inorg_carb", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "microgram per liter, milligram per liter, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter", + "title": "dissolved inorganic carbon", + "examples": [ + { + "value": "2059 micromole per kilogram" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "dissolved inorganic carbon" + ], + "rank": 16, + "is_a": "core field", + "slot_uri": "MIXS:0000434", + "alias": "diss_inorg_carb", + "owner": "WaterInterface", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "diss_inorg_nitro": { + "name": "diss_inorg_nitro", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "microgram per liter, micromole per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of dissolved inorganic nitrogen", + "title": "dissolved inorganic nitrogen", + "examples": [ + { + "value": "761 micromole per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "dissolved inorganic nitrogen" + ], + "rank": 223, + "is_a": "core field", + "slot_uri": "MIXS:0000698", + "alias": "diss_inorg_nitro", + "owner": "WaterInterface", + "domain_of": [ + "Biosample", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "diss_inorg_phosp": { + "name": "diss_inorg_phosp", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "microgram per liter, milligram per liter, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of dissolved inorganic phosphorus in the sample", + "title": "dissolved inorganic phosphorus", + "examples": [ + { + "value": "56.5 micromole per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "dissolved inorganic phosphorus" + ], + "rank": 224, + "is_a": "core field", + "slot_uri": "MIXS:0000106", + "alias": "diss_inorg_phosp", + "owner": "WaterInterface", + "domain_of": [ + "Biosample", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "diss_org_carb": { + "name": "diss_org_carb", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per liter, milligram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid", + "title": "dissolved organic carbon", + "examples": [ + { + "value": "197 micromole per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "dissolved organic carbon" + ], + "rank": 17, + "is_a": "core field", + "slot_uri": "MIXS:0000433", + "alias": "diss_org_carb", + "owner": "WaterInterface", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "diss_org_nitro": { + "name": "diss_org_nitro", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "microgram per liter, milligram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2", + "title": "dissolved organic nitrogen", + "examples": [ + { + "value": "0.05 micromole per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "dissolved organic nitrogen" + ], + "rank": 18, + "is_a": "core field", + "slot_uri": "MIXS:0000162", + "alias": "diss_org_nitro", + "owner": "WaterInterface", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "diss_oxygen": { + "name": "diss_oxygen", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per kilogram, milligram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of dissolved oxygen", + "title": "dissolved oxygen", + "examples": [ + { + "value": "175 micromole per kilogram" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "dissolved oxygen" + ], + "rank": 19, + "is_a": "core field", + "slot_uri": "MIXS:0000119", + "alias": "diss_oxygen", + "owner": "WaterInterface", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "down_par": { + "name": "down_par", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "microEinstein per square meter per second, microEinstein per square centimeter per second" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Visible waveband radiance and irradiance measurements in the water column", + "title": "downward PAR", + "examples": [ + { + "value": "28.71 microEinstein per square meter per second" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "downward PAR" + ], + "rank": 225, + "is_a": "core field", + "slot_uri": "MIXS:0000703", + "alias": "down_par", + "owner": "WaterInterface", + "domain_of": [ + "Biosample", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "ecosystem": { + "name": "ecosystem", + "description": "An ecosystem is a combination of a physical environment (abiotic factors) and all the organisms (biotic factors) that interact with this environment. Ecosystem is in position 1/5 in a GOLD path.", + "comments": [ + "The abiotic factors play a profound role on the type and composition of organisms in a given environment. The GOLD Ecosystem at the top of the five-level classification system is aimed at capturing the broader environment from which an organism or environmental sample is collected. The three broad groups under Ecosystem are Environmental, Host-associated, and Engineered. They represent samples collected from a natural environment or from another organism or from engineered environments like bioreactors respectively." + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "https://gold.jgi.doe.gov/help" + ], + "rank": 9, + "is_a": "gold_path_field", + "alias": "ecosystem", + "owner": "WaterInterface", + "domain_of": [ + "Biosample", + "Study", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "string", + "recommended": true, + "multivalued": false + }, + "ecosystem_category": { + "name": "ecosystem_category", + "description": "Ecosystem categories represent divisions within the ecosystem based on specific characteristics of the environment from where an organism or sample is isolated. Ecosystem category is in position 2/5 in a GOLD path.", + "comments": [ + "The Environmental ecosystem (for example) is divided into Air, Aquatic and Terrestrial. Ecosystem categories for Host-associated samples can be individual hosts or phyla and for engineered samples it may be manipulated environments like bioreactors, solid waste etc." + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "https://gold.jgi.doe.gov/help" + ], + "rank": 10, + "is_a": "gold_path_field", + "alias": "ecosystem_category", + "owner": "WaterInterface", + "domain_of": [ + "Biosample", + "Study", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "string", + "recommended": true, + "multivalued": false + }, + "ecosystem_subtype": { + "name": "ecosystem_subtype", + "description": "Ecosystem subtypes represent further subdivision of Ecosystem types into more distinct subtypes. Ecosystem subtype is in position 4/5 in a GOLD path.", + "comments": [ + "Ecosystem Type Marine (Environmental -> Aquatic -> Marine) is further divided (for example) into Intertidal zone, Coastal, Pelagic, Intertidal zone etc. in the Ecosystem subtype category." + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "https://gold.jgi.doe.gov/help" + ], + "rank": 12, + "is_a": "gold_path_field", + "alias": "ecosystem_subtype", + "owner": "WaterInterface", + "domain_of": [ + "Biosample", + "Study", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "string", + "recommended": true, + "multivalued": false + }, + "ecosystem_type": { + "name": "ecosystem_type", + "description": "Ecosystem types represent things having common characteristics within the Ecosystem Category. These common characteristics based grouping is still broad but specific to the characteristics of a given environment. Ecosystem type is in position 3/5 in a GOLD path.", + "comments": [ + "The Aquatic ecosystem category (for example) may have ecosystem types like Marine or Thermal springs etc. Ecosystem category Air may have Indoor air or Outdoor air as different Ecosystem Types. In the case of Host-associated samples, ecosystem type can represent Respiratory system, Digestive system, Roots etc." + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "https://gold.jgi.doe.gov/help" + ], + "rank": 11, + "is_a": "gold_path_field", + "alias": "ecosystem_type", + "owner": "WaterInterface", + "domain_of": [ + "Biosample", + "Study", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "string", + "recommended": true, + "multivalued": false + }, + "elev": { + "name": "elev", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + } + }, + "description": "Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit.", + "title": "elevation, meters", + "comments": [ + "All elevations must be reported in meters. Provide the numerical portion only.", + "Please use https://www.advancedconverter.com/map-tools/find-altitude-by-coordinates, if needed, to help estimate the elevation based on latitude and longitude coordinates." + ], + "examples": [ + { + "value": "100" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "elevation" + ], + "rank": 6, + "is_a": "environment field", + "slot_uri": "MIXS:0000093", + "alias": "elev", + "owner": "WaterInterface", + "domain_of": [ + "FieldResearchSite", + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "float", + "multivalued": false + }, + "env_broad_scale": { + "name": "env_broad_scale", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "The major environment type(s) where the sample was collected. Recommend subclasses of biome [ENVO:00000428]. Multiple terms can be separated by one or more pipes." + }, + "tooltip": { + "tag": "tooltip", + "value": "The biome or major environmental system where the sample or specimen originated. Choose values from subclasses of the 'biome' class [ENVO:00000428] in the Environment Ontology (ENVO). For host-associated or plant-associated samples, use terms from the UBERON or Plant Ontology to describe the broad anatomical or morphological context" + } + }, + "description": "Report the major environmental system the sample or specimen came from. The system(s) identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. in the desert or a rainforest). We recommend using subclasses of EnvO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS", + "title": "broad-scale environmental context", + "examples": [ + { + "value": "oceanic epipelagic zone biome [ENVO:01000033] for annotating a water sample from the photic zone in middle of the Atlantic Ocean" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "broad-scale environmental context" + ], + "rank": 6, + "is_a": "environment field", + "string_serialization": "{termLabel} {[termID]}", + "slot_uri": "MIXS:0000012", + "alias": "env_broad_scale", + "owner": "WaterInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "string", + "required": true, + "multivalued": false, + "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$" + }, + "env_local_scale": { + "name": "env_local_scale", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "Environmental entities having causal influences upon the entity at time of sampling." + }, + "tooltip": { + "tag": "tooltip", + "value": "The specific environmental entities or features near the sample or specimen that significantly influence its characteristics or composition. These entities are typically smaller in scale than the broad environmental context. Values for this field should be countable, material nouns and must be chosen from subclasses of BFO:0000040 (material entity) that appear in the Environment Ontology (ENVO). For host-associated or plant-associated samples, use terms from the UBERON or Plant Ontology to describe specific anatomical structures or plant parts." + } + }, + "description": "Report the entity or entities which are in the sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. We recommend using EnvO terms which are of smaller spatial grain than your entry for env_broad_scale. Terms, such as anatomical sites, from other OBO Library ontologies which interoperate with EnvO (e.g. UBERON) are accepted in this field. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS.", + "title": "local environmental context", + "examples": [ + { + "value": "litter layer [ENVO:01000338]; Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]." + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "local environmental context" + ], + "rank": 7, + "is_a": "environment field", + "string_serialization": "{termLabel} {[termID]}", + "slot_uri": "MIXS:0000013", + "alias": "env_local_scale", + "owner": "WaterInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "string", + "required": true, + "multivalued": false, + "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$" + }, + "env_medium": { + "name": "env_medium", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "The material displaced by the entity at time of sampling. Recommend subclasses of environmental material [ENVO:00010483]." + }, + "tooltip": { + "tag": "tooltip", + "value": "The predominant environmental material or substrate that directly surrounds or hosts the sample or specimen at the time of sampling. Choose values from subclasses of the 'environmental material' class [ENVO:00010483] in the Environment Ontology (ENVO). Values for this field should be measurable or mass material nouns, representing continuous environmental materials. For host-associated or plant-associated samples, use terms from the UBERON or Plant Ontology to indicate a tissue, organ, or plant structure" + } + }, + "description": "Report the environmental material(s) immediately surrounding the sample or specimen at the time of sampling. We recommend using subclasses of 'environmental material' (http://purl.obolibrary.org/obo/ENVO_00010483). EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS . Terms from other OBO ontologies are permissible as long as they reference mass/volume nouns (e.g. air, water, blood) and not discrete, countable entities (e.g. a tree, a leaf, a table top).", + "title": "environmental medium", + "examples": [ + { + "value": "soil [ENVO:00001998]; Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air [ENVO_00002005]" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "environmental medium" + ], + "rank": 8, + "is_a": "environment field", + "string_serialization": "{termLabel} {[termID]}", + "slot_uri": "MIXS:0000014", + "alias": "env_medium", + "owner": "WaterInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "string", + "required": true, + "multivalued": false, + "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$" + }, + "experimental_factor": { + "name": "experimental_factor", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "text or EFO and/or OBI" + } + }, + "description": "Experimental factors are essentially the variable aspects of an experiment design which can be used to describe an experiment, or set of experiments, in an increasingly detailed manner. This field accepts ontology terms from Experimental Factor Ontology (EFO) and/or Ontology for Biomedical Investigations (OBI). For a browser of EFO (v 2.95) terms, please see http://purl.bioontology.org/ontology/EFO; for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI", + "title": "experimental factor", + "examples": [ + { + "value": "time series design [EFO:0001779]" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "experimental factor" + ], + "rank": 12, + "is_a": "investigation field", + "string_serialization": "{termLabel} {[termID]}|{text}", + "slot_uri": "MIXS:0000008", + "alias": "experimental_factor", + "owner": "WaterInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false + }, + "filter_method": { + "name": "filter_method", + "description": "Type of filter used or how the sample was filtered", + "title": "filter method", + "comments": [ + "describe the filter or provide a catalog number and manufacturer" + ], + "examples": [ + { + "value": "C18" + }, + { + "value": "Basix PES, 13-100-106 FisherSci" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "MIXS:0000765" + ], + "rank": 6, + "string_serialization": "{text}", + "alias": "filter_method", + "owner": "WaterInterface", + "domain_of": [ + "Biosample", + "SoilInterface", + "WaterInterface", + "SoilMixsInspiredMixin" + ], + "slot_group": "mixs_inspired_section", + "range": "string", + "recommended": true, + "multivalued": false + }, + "fluor": { + "name": "fluor", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milligram chlorophyll a per cubic meter, volts" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Raw or converted fluorescence of water", + "title": "fluorescence", + "examples": [ + { + "value": "2.5 volts" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "fluorescence" + ], + "rank": 226, + "is_a": "core field", + "slot_uri": "MIXS:0000704", + "alias": "fluor", + "owner": "WaterInterface", + "domain_of": [ + "Biosample", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "gaseous_environment": { + "name": "gaseous_environment", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "gaseous compound name;gaseous compound amount;treatment interval and duration" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Use of conditions with differing gaseous environments; should include the name of gaseous compound, amount administered, treatment duration, interval and total experimental duration; can include multiple gaseous environment regimens", + "title": "gaseous environment", + "todos": [ + "would like to see usage examples for this slot. Requiring micromole/L seems too limiting and doesn't match expected_value value", + "did I do this right? keep the example that's provided and add another? so as to not override" + ], + "examples": [ + { + "value": "CO2; 500ppm above ambient; constant" + }, + { + "value": "nitric oxide;0.5 micromole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "gaseous environment" + ], + "rank": 20, + "is_a": "core field", + "string_serialization": "{text};{float} {unit};{Rn/start_time/end_time/duration}", + "slot_uri": "MIXS:0000558", + "alias": "gaseous_environment", + "owner": "WaterInterface", + "domain_of": [ + "Biosample", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "multivalued": false + }, + "geo_loc_name": { + "name": "geo_loc_name", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "country or sea name (INSDC or GAZ): region(GAZ), specific location name" + } + }, + "description": "The geographical origin of the sample as defined by the country or sea name followed by specific region name.", + "title": "geographic location (country and/or sea,region)", + "examples": [ + { + "value": "USA: Maryland, Bethesda" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "geographic location (country and/or sea,region)" + ], + "rank": 4, + "is_a": "environment field", + "string_serialization": "{term}: {term}, {text}", + "slot_uri": "MIXS:0000010", + "alias": "geo_loc_name", + "owner": "WaterInterface", + "domain_of": [ + "FieldResearchSite", + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "required": true, + "multivalued": false + }, + "glucosidase_act": { + "name": "glucosidase_act", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "mol per liter per hour" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Measurement of glucosidase activity", + "title": "glucosidase activity", + "examples": [ + { + "value": "5 mol per liter per hour" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "glucosidase activity" + ], + "rank": 20, + "is_a": "core field", + "slot_uri": "MIXS:0000137", + "alias": "glucosidase_act", + "owner": "WaterInterface", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "humidity_regm": { + "name": "humidity_regm", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "humidity value;treatment interval and duration" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "gram per cubic meter" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Information about treatment involving an exposure to varying degree of humidity; information about treatment involving use of growth hormones; should include amount of humidity administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens", + "title": "humidity regimen", + "examples": [ + { + "value": "25 gram per cubic meter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "humidity regimen" + ], + "rank": 21, + "is_a": "core field", + "string_serialization": "{float} {unit};{Rn/start_time/end_time/duration}", + "slot_uri": "MIXS:0000568", + "alias": "humidity_regm", + "owner": "WaterInterface", + "domain_of": [ + "Biosample", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "multivalued": false + }, + "isotope_exposure": { + "name": "isotope_exposure", + "description": "List isotope exposure or addition applied to your sample.", + "title": "isotope exposure/addition", + "todos": [ + "Can we make the H218O correctly super and subscripted?" + ], + "comments": [ + "This is required when your experimental design includes the use of isotopically labeled compounds" + ], + "examples": [ + { + "value": "13C glucose" + }, + { + "value": "H218O" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "MIXS:0000751" + ], + "rank": 16, + "string_serialization": "{termLabel} {[termID]}; {timestamp}", + "alias": "isotope_exposure", + "owner": "WaterInterface", + "domain_of": [ + "Biosample", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WaterInterface", + "SoilMixsInspiredMixin" + ], + "slot_group": "mixs_inspired_section", + "range": "string", + "recommended": true, + "multivalued": false, + "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]; ([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$" + }, + "lat_lon": { + "name": "lat_lon", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "decimal degrees, limit to 8 decimal points" + } + }, + "description": "The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system", + "title": "geographic location (latitude and longitude)", + "notes": [ + "This is currently a required field but it's not clear if this should be required for human hosts" + ], + "examples": [ + { + "value": "50.586825 6.408977" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "geographic location (latitude and longitude)" + ], + "rank": 5, + "is_a": "environment field", + "string_serialization": "{float} {float}", + "slot_uri": "MIXS:0000009", + "alias": "lat_lon", + "owner": "WaterInterface", + "domain_of": [ + "FieldResearchSite", + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)?$" + }, + "light_intensity": { + "name": "light_intensity", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "lux" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Measurement of light intensity", + "title": "light intensity", + "examples": [ + { + "value": "0.3 lux" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "light intensity" + ], + "rank": 227, + "is_a": "core field", + "slot_uri": "MIXS:0000706", + "alias": "light_intensity", + "owner": "WaterInterface", + "domain_of": [ + "Biosample", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "light_regm": { + "name": "light_regm", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "exposure type;light intensity;light quality" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "lux; micrometer, nanometer, angstrom" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Information about treatment(s) involving exposure to light, including both light intensity and quality.", + "title": "light regimen", + "examples": [ + { + "value": "incandescant light;10 lux;450 nanometer" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "light regimen" + ], + "rank": 24, + "is_a": "core field", + "string_serialization": "{text};{float} {unit};{float} {unit}", + "slot_uri": "MIXS:0000569", + "alias": "light_regm", + "owner": "WaterInterface", + "domain_of": [ + "Biosample", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "multivalued": false, + "pattern": "^\\S+.*\\S+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? \\S+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? \\S+$" + }, + "magnesium": { + "name": "magnesium", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "mole per liter, milligram per liter, parts per million, micromole per kilogram" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of magnesium in the sample", + "title": "magnesium", + "examples": [ + { + "value": "52.8 micromole per kilogram" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "magnesium" + ], + "rank": 21, + "is_a": "core field", + "slot_uri": "MIXS:0000431", + "alias": "magnesium", + "owner": "WaterInterface", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "mean_frict_vel": { + "name": "mean_frict_vel", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "meter per second" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Measurement of mean friction velocity", + "title": "mean friction velocity", + "examples": [ + { + "value": "0.5 meter per second" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "mean friction velocity" + ], + "rank": 22, + "is_a": "core field", + "slot_uri": "MIXS:0000498", + "alias": "mean_frict_vel", + "owner": "WaterInterface", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "mean_peak_frict_vel": { + "name": "mean_peak_frict_vel", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "meter per second" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Measurement of mean peak friction velocity", + "title": "mean peak friction velocity", + "examples": [ + { + "value": "1 meter per second" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "mean peak friction velocity" + ], + "rank": 23, + "is_a": "core field", + "slot_uri": "MIXS:0000502", + "alias": "mean_peak_frict_vel", + "owner": "WaterInterface", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "misc_param": { + "name": "misc_param", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "parameter name;measurement value" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Any other measurement performed or parameter collected, that is not listed here", + "title": "miscellaneous parameter", + "examples": [ + { + "value": "Bicarbonate ion concentration;2075 micromole per kilogram" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "miscellaneous parameter" + ], + "rank": 23, + "is_a": "core field", + "string_serialization": "{text};{float} {unit}", + "slot_uri": "MIXS:0000752", + "alias": "misc_param", + "owner": "WaterInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false, + "pattern": "^([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+\\|)*([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+)$" + }, + "n_alkanes": { + "name": "n_alkanes", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "n-alkane name;measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Concentration of n-alkanes; can include multiple n-alkanes", + "title": "n-alkanes", + "examples": [ + { + "value": "n-hexadecane;100 milligram per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "n-alkanes" + ], + "rank": 25, + "is_a": "core field", + "string_serialization": "{text};{float} {unit}", + "slot_uri": "MIXS:0000503", + "alias": "n_alkanes", + "owner": "WaterInterface", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+\\|)*([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+)$" + }, + "nitrate": { + "name": "nitrate", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per liter, milligram per liter, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of nitrate in the sample", + "title": "nitrate", + "examples": [ + { + "value": "65 micromole per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "nitrate" + ], + "rank": 26, + "is_a": "core field", + "slot_uri": "MIXS:0000425", + "alias": "nitrate", + "owner": "WaterInterface", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "nitrite": { + "name": "nitrite", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per liter, milligram per liter, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of nitrite in the sample", + "title": "nitrite", + "examples": [ + { + "value": "0.5 micromole per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "nitrite" + ], + "rank": 27, + "is_a": "core field", + "slot_uri": "MIXS:0000426", + "alias": "nitrite", + "owner": "WaterInterface", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "nitro": { + "name": "nitro", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of nitrogen (total)", + "title": "nitrogen", + "examples": [ + { + "value": "4.2 micromole per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "nitrogen" + ], + "rank": 28, + "is_a": "core field", + "slot_uri": "MIXS:0000504", + "alias": "nitro", + "owner": "WaterInterface", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "org_carb": { + "name": "org_carb", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of organic carbon", + "title": "organic carbon", + "examples": [ + { + "value": "1.5 microgram per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "organic carbon" + ], + "rank": 29, + "is_a": "core field", + "slot_uri": "MIXS:0000508", + "alias": "org_carb", + "owner": "WaterInterface", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "org_matter": { + "name": "org_matter", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + 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can include multiple phaeopigments", + "title": "phaeopigments", + "examples": [ + { + "value": "2.5 milligram per cubic meter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "phaeopigments" + ], + "rank": 35, + "is_a": "core field", + "string_serialization": "{text};{float} {unit}", + "slot_uri": "MIXS:0000180", + "alias": "phaeopigments", + "owner": "WaterInterface", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? 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percentage" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The total concentration of all dissolved salts in a liquid or solid sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater.", + "title": "salinity", + "examples": [ + { + "value": "25 practical salinity unit" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "salinity" + ], + "rank": 54, + "is_a": "core field", + "slot_uri": "MIXS:0000183", + "alias": "salinity", + "owner": "WaterInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "salinity_meth": { + "name": "salinity_meth", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "PMID,DOI or url" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Reference or method used in determining salinity", + "title": "salinity method", + "examples": [ + { + "value": "https://doi.org/10.1007/978-1-61779-986-0_28" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "salinity method" + ], + "rank": 55, + "is_a": "core field", + "string_serialization": "{PMID}|{DOI}|{URL}", + "slot_uri": "MIXS:0000341", + "alias": "salinity_meth", + "owner": "WaterInterface", + "domain_of": [ + "Biosample", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WaterInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false + }, + "samp_collec_device": { + "name": "samp_collec_device", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "device name" + } + }, + "description": "The device used to collect an environmental sample. This field accepts terms listed under environmental sampling device (http://purl.obolibrary.org/obo/ENVO). This field also accepts terms listed under specimen collection device (http://purl.obolibrary.org/obo/GENEPIO_0002094).", + "title": "sample collection device", + "examples": [ + { + "value": "swab, biopsy, niskin bottle, push core, drag swab [GENEPIO:0002713]" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sample collection device" + ], + "rank": 14, + "is_a": "nucleic acid sequence source field", + "string_serialization": "{termLabel} {[termID]}|{text}", + "slot_uri": "MIXS:0000002", + "alias": "samp_collec_device", + "owner": "WaterInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "multivalued": false + }, + "samp_collec_method": { + "name": "samp_collec_method", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "PMID,DOI,url , or text" + } + }, + "description": "The method employed for collecting the sample.", + "title": "sample collection method", + "examples": [ + { + "value": "swabbing" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sample collection method" + ], + "rank": 15, + "is_a": "nucleic acid sequence source field", + "string_serialization": "{PMID}|{DOI}|{URL}|{text}", + "slot_uri": "MIXS:0001225", + "alias": "samp_collec_method", + "owner": "WaterInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "multivalued": false + }, + "samp_mat_process": { + "name": "samp_mat_process", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "text" + } + }, + "description": "A brief description of any processing applied to the sample during or after retrieving the sample from environment, or a link to the relevant protocol(s) performed.", + "title": "sample material processing", + "examples": [ + { + "value": "filtering of seawater" + }, + { + "value": "storing samples in ethanol" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sample material processing" + ], + "rank": 12, + "is_a": "nucleic acid sequence source field", + "string_serialization": "{text}", + "slot_uri": "MIXS:0000016", + "alias": "samp_mat_process", + "owner": "WaterInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "multivalued": false + }, + "samp_size": { + "name": "samp_size", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "millliter, gram, milligram, liter" + } + }, + "description": "The total amount or size (volume (ml), mass (g) or area (m2) ) of sample collected.", + "title": "amount or size of sample collected", + "examples": [ + { + "value": "5 liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "amount or size of sample collected" + ], + "rank": 18, + "is_a": "nucleic acid sequence source field", + "slot_uri": "MIXS:0000001", + "alias": "samp_size", + "owner": "WaterInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "samp_store_dur": { + "name": "samp_store_dur", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "duration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Duration for which the sample was stored", + "title": "sample storage duration", + "examples": [ + { + "value": "P1Y6M" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sample storage duration" + ], + "rank": 353, + "is_a": "core field", + "string_serialization": "{duration}", + "slot_uri": "MIXS:0000116", + "alias": "samp_store_dur", + "owner": "WaterInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "samp_store_loc": { + "name": "samp_store_loc", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "location name" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Location at which sample was stored, usually name of a specific freezer/room", + "title": "sample storage location", + "examples": [ + { + "value": "Freezer no:5" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sample storage location" + ], + "rank": 41, + "is_a": "core field", + "string_serialization": "{text}", + "slot_uri": "MIXS:0000755", + "alias": "samp_store_loc", + "owner": "WaterInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "samp_store_temp": { + "name": "samp_store_temp", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "degree Celsius" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Temperature at which sample was stored, e.g. -80 degree Celsius", + "title": "sample storage temperature", + "examples": [ + { + "value": "-80 degree Celsius" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sample storage temperature" + ], + "rank": 7, + "is_a": "core field", + "slot_uri": "MIXS:0000110", + "alias": "samp_store_temp", + "owner": "WaterInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "sample_link": { + "name": "sample_link", + "description": "A unique identifier to assign parent-child, subsample, or sibling samples. This is relevant when a sample or other material was used to generate the new sample.", + "title": "sample linkage", + "notes": [ + "also tempted to include SampIdNewTermsMixin but if len(slot_usage.keys()) > 1 and \"placeholder\" in slot_usage.keys():AttributeError: 'list' object has no attribute 'keys'" + ], + "comments": [ + "This field allows multiple entries separated by ; (Examples: Soil collected from the field will link with the soil used in an incubation. The soil a plant was grown in links to the plant sample. An original culture sample was transferred to a new vial and generated a new sample)" + ], + "examples": [ + { + "value": "IGSN:DSJ0284" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "rank": 5, + "string_serialization": "{text}:{text}", + "alias": "sample_link", + "owner": "WaterInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface", + "SampIdNewTermsMixin" + ], + "slot_group": "sample_id_section", + "range": "string", + "recommended": true, + "multivalued": false, + "pattern": "[^\\:\\n\\r]+\\:[^\\:\\n\\r]+" + }, + "silicate": { + "name": "silicate", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of silicate", + "title": "silicate", + "examples": [ + { + "value": "0.05 micromole per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "silicate" + ], + "rank": 43, + "is_a": "core field", + "slot_uri": "MIXS:0000184", + "alias": "silicate", + "owner": "WaterInterface", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "size_frac": { + "name": "size_frac", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "filter size value range" + } + }, + "description": "Filtering pore size used in sample preparation", + "title": "size fraction selected", + "examples": [ + { + "value": "0-0.22 micrometer" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "size fraction selected" + ], + "rank": 285, + "is_a": "nucleic acid sequence source field", + "string_serialization": "{float}-{float} {unit}", + "slot_uri": "MIXS:0000017", + "alias": "size_frac", + "owner": "WaterInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false + }, + "size_frac_low": { + "name": "size_frac_low", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micrometer" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Refers to the mesh/pore size used to pre-filter/pre-sort the sample. Materials larger than the size threshold are excluded from the sample", + "title": "size-fraction lower threshold", + "examples": [ + { + "value": "0.2 micrometer" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "size-fraction lower threshold" + ], + "rank": 10, + "is_a": "core field", + "slot_uri": "MIXS:0000735", + "alias": "size_frac_low", + "owner": "WaterInterface", + "domain_of": [ + "Biosample", + "SoilInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "size_frac_up": { + "name": "size_frac_up", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micrometer" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Refers to the mesh/pore size used to retain the sample. Materials smaller than the size threshold are excluded from the sample", + "title": "size-fraction upper threshold", + "examples": [ + { + "value": "20 micrometer" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "size-fraction upper threshold" + ], + "rank": 11, + "is_a": "core field", + "slot_uri": "MIXS:0000736", + "alias": "size_frac_up", + "owner": "WaterInterface", + "domain_of": [ + "Biosample", + "SoilInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "sodium": { + "name": "sodium", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milligram per liter, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Sodium concentration in the sample", + "title": "sodium", + "examples": [ + { + "value": "10.5 milligram per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sodium" + ], + "rank": 363, + "is_a": "core field", + "slot_uri": "MIXS:0000428", + "alias": "sodium", + "owner": "WaterInterface", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "soluble_react_phosp": { + "name": "soluble_react_phosp", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per liter, milligram per liter, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of soluble reactive phosphorus", + "title": "soluble reactive phosphorus", + "examples": [ + { + "value": "0.1 milligram per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "soluble reactive phosphorus" + ], + "rank": 231, + "is_a": "core field", + "slot_uri": "MIXS:0000738", + "alias": "soluble_react_phosp", + "owner": "WaterInterface", + "domain_of": [ + "Biosample", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "specific_ecosystem": { + "name": "specific_ecosystem", + "description": "Specific ecosystems represent specific features of the environment like aphotic zone in an ocean or gastric mucosa within a host digestive system. Specific ecosystem is in position 5/5 in a GOLD path.", + "comments": [ + "Specific ecosystems help to define samples based on very specific characteristics of an environment under the five-level classification system." + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "https://gold.jgi.doe.gov/help" + ], + "rank": 13, + "is_a": "gold_path_field", + "alias": "specific_ecosystem", + "owner": "WaterInterface", + "domain_of": [ + "Biosample", + "Study", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "string", + "recommended": true, + "multivalued": false + }, + "start_date_inc": { + "name": "start_date_inc", + "description": "Date the incubation was started. Only relevant for incubation samples.", + "title": "incubation start date", + "notes": [ + "MIxS collection_date accepts (truncated) ISO8601. DH taking arbitrary precision date only" + ], + "comments": [ + "Date should be formatted as YYYY(-MM(-DD)). Ie, 2021-04-15, 2021-04 and 2021 are all acceptable." + ], + "examples": [ + { + "value": "2021-04-15, 2021-04 and 2021 are all acceptable." + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "MIXS:0000011" + ], + "rank": 4, + "string_serialization": "{date, arbitrary precision}", + "alias": "start_date_inc", + "owner": "WaterInterface", + "domain_of": [ + "Biosample", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WaterInterface", + "SoilMixsInspiredMixin" + ], + "slot_group": "mixs_inspired_section", + "range": "string", + "recommended": true, + "multivalued": false, + "pattern": "^[12]\\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\\d|3[01]))?)?$" + }, + "sulfate": { + "name": "sulfate", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per liter, milligram per liter, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of sulfate in the sample", + "title": "sulfate", + "examples": [ + { + "value": "5 micromole per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sulfate" + ], + "rank": 44, + "is_a": "core field", + "slot_uri": "MIXS:0000423", + "alias": "sulfate", + "owner": "WaterInterface", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "sulfide": { + "name": "sulfide", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per liter, milligram per liter, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of sulfide in the sample", + "title": "sulfide", + "examples": [ + { + "value": "2 micromole per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sulfide" + ], + "rank": 371, + "is_a": "core field", + "slot_uri": "MIXS:0000424", + "alias": "sulfide", + "owner": "WaterInterface", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "MiscEnvsInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "suspend_part_matter": { + "name": "suspend_part_matter", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milligram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of suspended particulate matter", + "title": "suspended particulate matter", + "examples": [ + { + "value": "0.5 milligram per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "suspended particulate matter" + ], + "rank": 232, + "is_a": "core field", + "slot_uri": "MIXS:0000741", + "alias": "suspend_part_matter", + "owner": "WaterInterface", + "domain_of": [ + "Biosample", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "temp": { + "name": "temp", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "degree Celsius" + } + }, + "description": "Temperature of the sample at the time of sampling.", + "title": "temperature", + "examples": [ + { + "value": "25 degree Celsius" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "temperature" + ], + "rank": 37, + "is_a": "environment field", + "slot_uri": "MIXS:0000113", + "alias": "temp", + "owner": "WaterInterface", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "tidal_stage": { + "name": "tidal_stage", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Stage of tide", + "title": "tidal stage", + "examples": [ + { + "value": "high tide" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "tidal stage" + ], + "rank": 45, + "is_a": "core field", + "slot_uri": "MIXS:0000750", + "alias": "tidal_stage", + "owner": "WaterInterface", + "domain_of": [ + "Biosample", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "tidal_stage_enum", + "multivalued": false + }, + "tot_depth_water_col": { + "name": "tot_depth_water_col", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "meter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Measurement of total depth of water column", + "title": "total depth of water column", + "examples": [ + { + "value": "500 meter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "total depth of water column" + ], + "rank": 46, + "is_a": "core field", + "slot_uri": "MIXS:0000634", + "alias": "tot_depth_water_col", + "owner": "WaterInterface", + "domain_of": [ + "Biosample", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "tot_diss_nitro": { + "name": "tot_diss_nitro", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "microgram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Total dissolved nitrogen concentration, reported as nitrogen, measured by: total dissolved nitrogen = NH4 + NO3NO2 + dissolved organic nitrogen", + "title": "total dissolved nitrogen", + "examples": [ + { + "value": "40 microgram per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "total dissolved nitrogen" + ], + "rank": 233, + "is_a": "core field", + "slot_uri": "MIXS:0000744", + "alias": "tot_diss_nitro", + "owner": "WaterInterface", + "domain_of": [ + "Biosample", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "tot_inorg_nitro": { + "name": "tot_inorg_nitro", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "microgram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Total inorganic nitrogen content", + "title": "total inorganic nitrogen", + "examples": [ + { + "value": "40 microgram per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "total inorganic nitrogen" + ], + "rank": 234, + "is_a": "core field", + "slot_uri": "MIXS:0000745", + "alias": "tot_inorg_nitro", + "owner": "WaterInterface", + "domain_of": [ + "Biosample", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "tot_nitro": { + "name": "tot_nitro", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "microgram per liter, micromole per liter, milligram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen", + "title": "total nitrogen concentration", + "examples": [ + { + "value": "50 micromole per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "total nitrogen concentration" + ], + "rank": 377, + "is_a": "core field", + "slot_uri": "MIXS:0000102", + "alias": "tot_nitro", + "owner": "WaterInterface", + "domain_of": [ + "Biosample", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "tot_part_carb": { + "name": "tot_part_carb", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "microgram per liter, micromole per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Total particulate carbon content", + "title": "total particulate carbon", + "examples": [ + { + "value": "35 micromole per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "total particulate carbon" + ], + "rank": 235, + "is_a": "core field", + "slot_uri": "MIXS:0000747", + "alias": "tot_part_carb", + "owner": "WaterInterface", + "domain_of": [ + "Biosample", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "tot_phosp": { + "name": "tot_phosp", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per liter, milligram per liter, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus", + "title": "total phosphorus", + "examples": [ + { + "value": "0.03 milligram per liter" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "total phosphorus" + ], + "rank": 52, + "is_a": "core field", + "slot_uri": "MIXS:0000117", + "alias": "tot_phosp", + "owner": "WaterInterface", + "domain_of": [ + "Biosample", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "SoilInterface", + "WaterInterface" + ], + "slot_group": "mixs_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "turbidity": { + "name": "turbidity", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "formazin turbidity unit, formazin nephelometric units" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Measure of the amount of cloudiness or haziness in water caused by individual particles", + "title": "turbidity", + "examples": [ + { + "value": "0.3 nephelometric turbidity units" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "turbidity" + ], + "rank": 47, + "is_a": "core field", + "slot_uri": "MIXS:0000191", + "alias": "turbidity", + "owner": "WaterInterface", + "domain_of": [ + "Biosample", + "BiofilmInterface", + "SedimentInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "water_current": { + "name": "water_current", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "cubic meter per second, knots" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Measurement of magnitude and direction of flow within a fluid", + "title": "water current", + "examples": [ + { + "value": "10 cubic meter per second" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "water current" + ], + "rank": 236, + "is_a": "core field", + "slot_uri": "MIXS:0000203", + "alias": "water_current", + "owner": "WaterInterface", + "domain_of": [ + "Biosample", + "MiscEnvsInterface", + "WaterInterface" + ], + "slot_group": "mixs_core_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" + }, + "watering_regm": { + "name": "watering_regm", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value;treatment interval and duration" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milliliter, liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Information about treatment involving an exposure to watering frequencies, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens", + "title": "watering regimen", + "examples": [ + { + "value": "1 liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" + }, + { + "value": "75% water holding capacity; constant" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "watering regimen" + ], + "rank": 25, + "is_a": "core field", + "string_serialization": "{float} {unit};{Rn/start_time/end_time/duration}", + "slot_uri": "MIXS:0000591", + "alias": "watering_regm", + "owner": "WaterInterface", + "domain_of": [ + "Biosample", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WaterInterface" + ], + "slot_group": "mixs_modified_section", + "range": "string", + "multivalued": false + }, + "analysis_type": { + "name": "analysis_type", + "description": "Select all the data types associated or available for this biosample", + "title": "analysis/data type", + "examples": [ + { + "value": "metagenomics; metabolomics; proteomics" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "MIxS:investigation_type" + ], + "rank": 3, + "alias": "analysis_type", + "owner": "WaterInterface", + "domain_of": [ + "Biosample", + "DhMultiviewCommonColumnsMixin", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "EmslInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "JgiMgInterface", + "JgiMgLrInterface", + "JgiMtInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "AnalysisTypeEnum", + "required": true, + "recommended": false, + "multivalued": true + }, + "samp_name": { + "name": "samp_name", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "text" + } + }, + "description": "A local identifier or name that for the material sample collected. Refers to the original material collected or to any derived sub-samples.", + "title": "sample name", + "comments": [ + "It can have any format, but we suggest that you make it concise, unique and consistent within your lab, and as informative as possible." + ], + "examples": [ + { + "value": "Rock core CB1178(5-6) from NSW" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sample name" + ], + "rank": 1, + "is_a": "investigation field", + "string_serialization": "{text}", + "slot_uri": "MIXS:0001107", + "identifier": true, + "alias": "samp_name", + "owner": "WaterInterface", + "domain_of": [ + "Biosample", + "DhMultiviewCommonColumnsMixin", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "EmslInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "JgiMgInterface", + "JgiMgLrInterface", + "JgiMtInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "string", + "required": true, + "multivalued": false + }, + "source_mat_id": { + "name": "source_mat_id", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "for cultures of microorganisms: identifiers for two culture collections; for other material a unique arbitrary identifer" + } + }, + "description": "A globally unique identifier assigned to the biological sample.", + "title": "source material identifier", + "todos": [ + "Currently, the comments say to use UUIDs. However, if we implement assigning NMDC identifiers with the minter we dont need to require a GUID. It can be an optional field to fill out only if they already have a resolvable ID.", + "Currently, the comments say to use UUIDs. However, if we implement assigning NMDC identifiers with the minter we dont need to require a GUID. It can be an optional field to fill out only if they already have a resolvable ID." + ], + "notes": [ + "The source material IS the Globally Unique ID" + ], + "comments": [ + "Identifiers must be prefixed. Possible FAIR prefixes are IGSNs (http://www.geosamples.org/getigsn), NCBI biosample accession numbers, ARK identifiers (https://arks.org/). These IDs enable linking to derived analytes and subsamples. If you have not assigned FAIR identifiers to your samples, you can generate UUIDs (https://www.uuidgenerator.net/).", + "Identifiers must be prefixed. Possible FAIR prefixes are IGSNs (http://www.geosamples.org/getigsn), NCBI biosample accession numbers, ARK identifiers (https://arks.org/). These IDs enable linking to derived analytes and subsamples. If you have not assigned FAIR identifiers to your samples, you can generate UUIDs (https://www.uuidgenerator.net/)." + ], + "examples": [ + { + "value": "IGSN:AU1243" + }, + { + "value": "UUID:24f1467a-40f4-11ed-b878-0242ac120002" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "source material identifiers" + ], + "rank": 2, + "is_a": "nucleic acid sequence source field", + "string_serialization": "{text}:{text}", + "slot_uri": "MIXS:0000026", + "alias": "source_mat_id", + "owner": "WaterInterface", + "domain_of": [ + "Biosample", + "DhMultiviewCommonColumnsMixin", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "EmslInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "JgiMgInterface", + "JgiMgLrInterface", + "JgiMtInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "string", + "multivalued": false, + "pattern": "[^\\:\\n\\r]+\\:[^\\:\\n\\r]+" + } + } + }, + "DhMultiviewCommonColumnsMixin": { + "name": "DhMultiviewCommonColumnsMixin", + "description": "Mixin with DhMutliviewCommon Columns", + "title": "Dh Mutliview Common Columns", + "from_schema": "https://example.com/nmdc_submission_schema", + "mixin": true, + "slots": [ + "analysis_type", + "samp_name", + "source_mat_id" + ], + "slot_usage": { + "analysis_type": { + "name": "analysis_type", + "description": "Select all the data types associated or available for this biosample", + "title": "analysis/data type", + "examples": [ + { + "value": "metagenomics; metabolomics; proteomics" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "MIxS:investigation_type" + ], + "rank": 3, + "owner": "Biosample", + "domain_of": [ + "Biosample", + "DhMultiviewCommonColumnsMixin", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "EmslInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "JgiMgInterface", + "JgiMgLrInterface", + "JgiMtInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "AnalysisTypeEnum", + "required": true, + "recommended": false, + "multivalued": true + }, + "samp_name": { + "name": "samp_name", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "text" + } + }, + "description": "A local identifier or name that for the material sample collected. Refers to the original material collected or to any derived sub-samples.", + "title": "sample name", + "comments": [ + "It can have any format, but we suggest that you make it concise, unique and consistent within your lab, and as informative as possible." + ], + "examples": [ + { + "value": "Rock core CB1178(5-6) from NSW" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sample name" + ], + "rank": 1, + "is_a": "investigation field", + "string_serialization": "{text}", + "slot_uri": "MIXS:0001107", + "identifier": true, + "owner": "Biosample", + "domain_of": [ + "Biosample", + "DhMultiviewCommonColumnsMixin", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "EmslInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "JgiMgInterface", + "JgiMgLrInterface", + "JgiMtInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "string", + "required": true, + "multivalued": false + }, + "source_mat_id": { + "name": "source_mat_id", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "for cultures of microorganisms: identifiers for two culture collections; for other material a unique arbitrary identifer" + } + }, + "description": "A globally unique identifier assigned to the biological sample.", + "title": "source material identifier", + "todos": [ + "Currently, the comments say to use UUIDs. However, if we implement assigning NMDC identifiers with the minter we dont need to require a GUID. It can be an optional field to fill out only if they already have a resolvable ID.", + "Currently, the comments say to use UUIDs. However, if we implement assigning NMDC identifiers with the minter we dont need to require a GUID. It can be an optional field to fill out only if they already have a resolvable ID." + ], + "notes": [ + "The source material IS the Globally Unique ID" + ], + "comments": [ + "Identifiers must be prefixed. Possible FAIR prefixes are IGSNs (http://www.geosamples.org/getigsn), NCBI biosample accession numbers, ARK identifiers (https://arks.org/). These IDs enable linking to derived analytes and subsamples. If you have not assigned FAIR identifiers to your samples, you can generate UUIDs (https://www.uuidgenerator.net/).", + "Identifiers must be prefixed. Possible FAIR prefixes are IGSNs (http://www.geosamples.org/getigsn), NCBI biosample accession numbers, ARK identifiers (https://arks.org/). These IDs enable linking to derived analytes and subsamples. If you have not assigned FAIR identifiers to your samples, you can generate UUIDs (https://www.uuidgenerator.net/)." + ], + "examples": [ + { + "value": "IGSN:AU1243" + }, + { + "value": "UUID:24f1467a-40f4-11ed-b878-0242ac120002" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "source material identifiers" + ], + "rank": 2, + "is_a": "nucleic acid sequence source field", + "string_serialization": "{text}:{text}", + "slot_uri": "MIXS:0000026", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "DhMultiviewCommonColumnsMixin", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "EmslInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "JgiMgInterface", + "JgiMgLrInterface", + "JgiMtInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "string", + "multivalued": false, + "pattern": "[^\\:\\n\\r]+\\:[^\\:\\n\\r]+" + }, + "oxy_stat_samp": { + "name": "oxy_stat_samp", + "range": "OxyStatSampEnum" + } + }, + "attributes": { + "analysis_type": { + "name": "analysis_type", + "description": "Select all the data types associated or available for this biosample", + "title": "analysis/data type", + "examples": [ + { + "value": "metagenomics; metabolomics; proteomics" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "MIxS:investigation_type" + ], + "rank": 3, + "alias": "analysis_type", + "owner": "DhMultiviewCommonColumnsMixin", + "domain_of": [ + "Biosample", + "DhMultiviewCommonColumnsMixin", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "EmslInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "JgiMgInterface", + "JgiMgLrInterface", + "JgiMtInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "AnalysisTypeEnum", + "required": true, + "recommended": false, + "multivalued": true + }, + "samp_name": { + "name": "samp_name", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "text" + } + }, + "description": "A local identifier or name that for the material sample collected. Refers to the original material collected or to any derived sub-samples.", + "title": "sample name", + "comments": [ + "It can have any format, but we suggest that you make it concise, unique and consistent within your lab, and as informative as possible." + ], + "examples": [ + { + "value": "Rock core CB1178(5-6) from NSW" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "sample name" + ], + "rank": 1, + "is_a": "investigation field", + "string_serialization": "{text}", + "slot_uri": "MIXS:0001107", + "identifier": true, + "alias": "samp_name", + "owner": "DhMultiviewCommonColumnsMixin", + "domain_of": [ + "Biosample", + "DhMultiviewCommonColumnsMixin", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "EmslInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "JgiMgInterface", + "JgiMgLrInterface", + "JgiMtInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "string", + "required": true, + "multivalued": false + }, + "source_mat_id": { + "name": "source_mat_id", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "for cultures of microorganisms: identifiers for two culture collections; for other material a unique arbitrary identifer" + } + }, + "description": "A globally unique identifier assigned to the biological sample.", + "title": "source material identifier", + "todos": [ + "Currently, the comments say to use UUIDs. However, if we implement assigning NMDC identifiers with the minter we dont need to require a GUID. It can be an optional field to fill out only if they already have a resolvable ID.", + "Currently, the comments say to use UUIDs. However, if we implement assigning NMDC identifiers with the minter we dont need to require a GUID. It can be an optional field to fill out only if they already have a resolvable ID." + ], + "notes": [ + "The source material IS the Globally Unique ID" + ], + "comments": [ + "Identifiers must be prefixed. Possible FAIR prefixes are IGSNs (http://www.geosamples.org/getigsn), NCBI biosample accession numbers, ARK identifiers (https://arks.org/). These IDs enable linking to derived analytes and subsamples. If you have not assigned FAIR identifiers to your samples, you can generate UUIDs (https://www.uuidgenerator.net/).", + "Identifiers must be prefixed. Possible FAIR prefixes are IGSNs (http://www.geosamples.org/getigsn), NCBI biosample accession numbers, ARK identifiers (https://arks.org/). These IDs enable linking to derived analytes and subsamples. If you have not assigned FAIR identifiers to your samples, you can generate UUIDs (https://www.uuidgenerator.net/)." + ], + "examples": [ + { + "value": "IGSN:AU1243" + }, + { + "value": "UUID:24f1467a-40f4-11ed-b878-0242ac120002" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "aliases": [ + "source material identifiers" + ], + "rank": 2, + "is_a": "nucleic acid sequence source field", + "string_serialization": "{text}:{text}", + "slot_uri": "MIXS:0000026", + "alias": "source_mat_id", + "owner": "DhMultiviewCommonColumnsMixin", + "domain_of": [ + "Biosample", + "DhMultiviewCommonColumnsMixin", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "EmslInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "JgiMgInterface", + "JgiMgLrInterface", + "JgiMtInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface" + ], + "slot_group": "sample_id_section", + "range": "string", + "multivalued": false, + "pattern": "[^\\:\\n\\r]+\\:[^\\:\\n\\r]+" + } + } + }, + "SampIdNewTermsMixin": { + "name": "SampIdNewTermsMixin", + "description": "Mixin with SampIdNew Terms", + "title": "SampId New Terms", + "from_schema": "https://example.com/nmdc_submission_schema", + "mixin": true, + "slots": [ + "sample_link" + ], + "attributes": { + "sample_link": { + "name": "sample_link", + "description": "A unique identifier to assign parent-child, subsample, or sibling samples. This is relevant when a sample or other material was used to generate the new sample.", + "title": "sample linkage", + "comments": [ + "This field allows multiple entries separated by ; (Examples: Soil collected from the field will link with the soil used in an incubation. The soil a plant was grown in links to the plant sample. An original culture sample was transferred to a new vial and generated a new sample)" + ], + "examples": [ + { + "value": "IGSN:DSJ0284" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "rank": 5, + "string_serialization": "{text}:{text}", + "alias": "sample_link", + "owner": "SampIdNewTermsMixin", + "domain_of": [ + "Biosample", + "AirInterface", + "BiofilmInterface", + "BuiltEnvInterface", + "HcrCoresInterface", + "HcrFluidsSwabsInterface", + "HostAssociatedInterface", + "MiscEnvsInterface", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WastewaterSludgeInterface", + "WaterInterface", + "SampIdNewTermsMixin" + ], + "slot_group": "Sample ID", + "range": "string", + "recommended": true, + "multivalued": false + } + } + }, + "SoilMixsInspiredMixin": { + "name": "SoilMixsInspiredMixin", + "description": "Mixin with SoilMixsInspired Terms", + "title": "Soil MIxS Inspired Mixin", + "from_schema": "https://example.com/nmdc_submission_schema", + "mixin": true, + "slots": [ + "collection_date_inc", + "collection_time", + "collection_time_inc", + "experimental_factor_other", + "filter_method", + "isotope_exposure", + "micro_biomass_c_meth", + "micro_biomass_n_meth", + "microbial_biomass_c", + "microbial_biomass_n", + "non_microb_biomass", + "non_microb_biomass_method", + "org_nitro_method", + "other_treatment", + "start_date_inc", + "start_time_inc", + "collection_date_inc", + "collection_time", + "collection_time_inc", + "experimental_factor_other", + "filter_method", + "isotope_exposure", + "micro_biomass_c_meth", + "micro_biomass_n_meth", + "microbial_biomass_c", + "microbial_biomass_n", + "non_microb_biomass", + "non_microb_biomass_method", + "org_nitro_method", + "other_treatment", + "start_date_inc", + "start_time_inc" + ], + "slot_usage": { + "collection_date_inc": { + "name": "collection_date_inc", + "description": "Date the incubation was harvested/collected/ended. Only relevant for incubation samples.", + "title": "incubation collection date", + "notes": [ + "MIxS collection_date accepts (truncated) ISO8601. DH taking arbitrary precision date only" + ], + "comments": [ + "Date should be formatted as YYYY(-MM(-DD)). Ie, 2021-04-15, 2021-04 and 2021 are all acceptable." + ], + "examples": [ + { + "value": "2021-04-15, 2021-04 and 2021 are all acceptable." + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "MIXS:0000011" + ], + "rank": 2, + "string_serialization": "{date, arbitrary precision}", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WaterInterface", + "SoilMixsInspiredMixin" + ], + "slot_group": "mixs_inspired_section", + "range": "string", + "recommended": true, + "multivalued": false, + "pattern": "^[12]\\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\\d|3[01]))?)?$" + }, + "collection_time": { + "name": "collection_time", + "description": "The time of sampling, either as an instance (single point) or interval.", + "title": "collection time, GMT", + "notes": [ + "MIxS collection_date accepts (truncated) ISO8601. DH taking seconds optional time only" + ], + "comments": [ + "Time should be entered as HH:MM(:SS) in GMT. See here for a converter: https://www.worldtimebuddy.com/pst-to-gmt-converter" + ], + "examples": [ + { + "value": "13:33 or 13:33:55" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "MIXS:0000011" + ], + "rank": 1, + "string_serialization": "{time, seconds optional}", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WaterInterface", + "SoilMixsInspiredMixin" + ], + "slot_group": "mixs_inspired_section", + "range": "string", + "recommended": true, + "multivalued": false, + "pattern": "^([01]?\\d|2[0-3]|24(?=:00?:00?$)):([0-5]\\d)(:([0-5]\\d))?$" + }, + "collection_time_inc": { + "name": "collection_time_inc", + "description": "Time the incubation was harvested/collected/ended. Only relevant for incubation samples.", + "title": "incubation collection time, GMT", + "notes": [ + "MIxS collection_date accepts (truncated) ISO8601. DH taking seconds optional time only" + ], + "comments": [ + "Time should be entered as HH:MM(:SS) in GMT. See here for a converter: https://www.worldtimebuddy.com/pst-to-gmt-converter" + ], + "examples": [ + { + "value": "13:33 or 13:33:55" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "MIXS:0000011" + ], + "rank": 3, + "string_serialization": "{time, seconds optional}", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "SoilInterface", + "SoilMixsInspiredMixin" + ], + "slot_group": "mixs_inspired_section", + "range": "string", + "recommended": true, + "multivalued": false, + "pattern": "^([01]?\\d|2[0-3]|24(?=:00?:00?$)):([0-5]\\d)(:([0-5]\\d))?$" + }, + "experimental_factor_other": { + "name": "experimental_factor_other", + "description": "Other details about your sample that you feel can't be accurately represented in the available columns.", + "title": "experimental factor- other", + "comments": [ + "This slot accepts open-ended text about your sample.", + "We recommend using key:value pairs.", + "Provided pairs will be considered for inclusion as future slots/terms in this data collection template." + ], + "examples": [ + { + "value": "experimental treatment: value" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "MIXS:0000008", + "MIXS:0000300" + ], + "rank": 7, + "string_serialization": "{text}", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "SoilInterface", + "SoilMixsInspiredMixin" + ], + "slot_group": "mixs_inspired_section", + "range": "string", + "recommended": true, + "multivalued": false + }, + "filter_method": { + "name": "filter_method", + "description": "Type of filter used or how the sample was filtered", + "title": "filter method", + "comments": [ + "describe the filter or provide a catalog number and manufacturer" + ], + "examples": [ + { + "value": "C18" + }, + { + "value": "Basix PES, 13-100-106 FisherSci" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "MIXS:0000765" + ], + "rank": 6, + "string_serialization": "{text}", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "SoilInterface", + "WaterInterface", + "SoilMixsInspiredMixin" + ], + "slot_group": "mixs_inspired_section", + "range": "string", + "recommended": true, + "multivalued": false + }, + "isotope_exposure": { + "name": "isotope_exposure", + "description": "List isotope exposure or addition applied to your sample.", + "title": "isotope exposure/addition", + "todos": [ + "Can we make the H218O correctly super and subscripted?" + ], + "comments": [ + "This is required when your experimental design includes the use of isotopically labeled compounds" + ], + "examples": [ + { + "value": "13C glucose" + }, + { + "value": "H218O" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "MIXS:0000751" + ], + "rank": 16, + "string_serialization": "{termLabel} {[termID]}; {timestamp}", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WaterInterface", + "SoilMixsInspiredMixin" + ], + "slot_group": "mixs_inspired_section", + "range": "string", + "recommended": true, + "multivalued": false, + "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]; ([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$" + }, + "micro_biomass_c_meth": { + "name": "micro_biomass_c_meth", + "description": "Reference or method used in determining microbial biomass carbon", + "title": "microbial biomass carbon method", + "todos": [ + "How should we separate values? | or ;? lets be consistent" + ], + "comments": [ + "required if \"microbial_biomass_c\" is provided" + ], + "examples": [ + { + "value": "https://doi.org/10.1016/0038-0717(87)90052-6" + }, + { + "value": "https://doi.org/10.1016/0038-0717(87)90052-6 | https://www.sciencedirect.com/science/article/abs/pii/0038071787900526" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "MIXS:0000339" + ], + "rank": 1004, + "string_serialization": "{PMID}|{DOI}|{URL}", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "SedimentInterface", + "SoilInterface", + "SoilMixsInspiredMixin" + ], + "slot_group": "mixs_inspired_section", + "range": "string", + "recommended": true, + "multivalued": false + }, + "micro_biomass_n_meth": { + "name": "micro_biomass_n_meth", + "description": "Reference or method used in determining microbial biomass nitrogen", + "title": "microbial biomass nitrogen method", + "comments": [ + "required if \"microbial_biomass_n\" is provided" + ], + "examples": [ + { + "value": "https://doi.org/10.1016/0038-0717(87)90052-6" + }, + { + "value": "https://doi.org/10.1016/0038-0717(87)90052-6 | https://www.sciencedirect.com/science/article/abs/pii/0038071787900526" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "MIXS:0000339" + ], + "rank": 1004, + "string_serialization": "{PMID}|{DOI}|{URL}", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "SedimentInterface", + "SoilInterface", + "SoilMixsInspiredMixin" + ], + "slot_group": "mixs_inspired_section", + "range": "string", + "multivalued": false + }, + "microbial_biomass_c": { + "name": "microbial_biomass_c", + "description": "The part of the organic matter in the soil that constitutes living microorganisms smaller than 5-10 micrometer.", + "title": "microbial biomass carbon", + "comments": [ + "If you provide this, correction factors used for conversion to the final units and method are required" + ], + "examples": [ + { + "value": "0.05 ug C/g dry soil" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "MIXS:0000650" + ], + "rank": 1004, + "string_serialization": "{float} {unit}", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "SedimentInterface", + "SoilInterface", + "SoilMixsInspiredMixin" + ], + "slot_group": "mixs_inspired_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? \\S+$" + }, + "microbial_biomass_n": { + "name": "microbial_biomass_n", + "description": "The part of the organic matter in the soil that constitutes living microorganisms smaller than 5-10 micrometer.", + "title": "microbial biomass nitrogen", + "comments": [ + "If you provide this, correction factors used for conversion to the final units and method are required" + ], + "examples": [ + { + "value": "0.05 ug N/g dry soil" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "MIXS:0000650" + ], + "rank": 1004, + "string_serialization": "{float} {unit}", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "SedimentInterface", + "SoilInterface", + "SoilMixsInspiredMixin" + ], + "slot_group": "mixs_inspired_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? \\S+$" + }, + "non_microb_biomass": { + "name": "non_microb_biomass", + "description": "Amount of biomass; should include the name for the part of biomass measured, e.g.insect, plant, total. Can include multiple measurements separated by ;", + "title": "non-microbial biomass", + "examples": [ + { + "value": "insect 0.23 ug; plant 1g" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "MIXS:0000174", + "MIXS:0000650" + ], + "rank": 8, + "string_serialization": "{text};{float} {unit}", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "SoilInterface", + "SoilMixsInspiredMixin" + ], + "slot_group": "mixs_inspired_section", + "range": "string", + "multivalued": false, + "pattern": "^[^;\\t\\r\\x0A\\|]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A\\|]+$" + }, + "non_microb_biomass_method": { + "name": "non_microb_biomass_method", + "description": "Reference or method used in determining biomass", + "title": "non-microbial biomass method", + "comments": [ + "required if \"non-microbial biomass\" is provided" + ], + "examples": [ + { + "value": "https://doi.org/10.1038/s41467-021-26181-3" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "MIXS:0000650" + ], + "rank": 9, + "string_serialization": "{PMID}|{DOI}|{URL}", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "SoilInterface", + "SoilMixsInspiredMixin" + ], + "slot_group": "mixs_inspired_section", + "range": "string", + "multivalued": false + }, + "org_nitro_method": { + "name": "org_nitro_method", + "description": "Method used for obtaining organic nitrogen", + "title": "organic nitrogen method", + "comments": [ + "required if \"org_nitro\" is provided" + ], + "examples": [ + { + "value": "https://doi.org/10.1016/0038-0717(85)90144-0" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "MIXS:0000338", + "MIXS:0000205" + ], + "rank": 14, + "string_serialization": "{PMID}|{DOI}|{URL}", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "SedimentInterface", + "SoilInterface", + "SoilMixsInspiredMixin" + ], + "slot_group": "mixs_inspired_section", + "range": "string", + "multivalued": false + }, + "other_treatment": { + "name": "other_treatment", + "description": "Other treatments applied to your samples that are not applicable to the provided fields", + "title": "other treatments", + "notes": [ + "Values entered here will be used to determine potential new slots." + ], + "comments": [ + "This is an open text field to provide any treatments that cannot be captured in the provided slots." + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "MIXS:0000300" + ], + "rank": 15, + "string_serialization": "{text}", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "SoilInterface", + "SoilMixsInspiredMixin" + ], + "slot_group": "mixs_inspired_section", + "range": "string", + "recommended": true, + "multivalued": false + }, + "start_date_inc": { + "name": "start_date_inc", + "description": "Date the incubation was started. Only relevant for incubation samples.", + "title": "incubation start date", + "notes": [ + "MIxS collection_date accepts (truncated) ISO8601. DH taking arbitrary precision date only" + ], + "comments": [ + "Date should be formatted as YYYY(-MM(-DD)). Ie, 2021-04-15, 2021-04 and 2021 are all acceptable." + ], + "examples": [ + { + "value": "2021-04-15, 2021-04 and 2021 are all acceptable." + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "MIXS:0000011" + ], + "rank": 4, + "string_serialization": "{date, arbitrary precision}", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WaterInterface", + "SoilMixsInspiredMixin" + ], + "slot_group": "mixs_inspired_section", + "range": "string", + "recommended": true, + "multivalued": false, + "pattern": "^[12]\\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\\d|3[01]))?)?$" + }, + "start_time_inc": { + "name": "start_time_inc", + "description": "Time the incubation was started. Only relevant for incubation samples.", + "title": "incubation start time, GMT", + "notes": [ + "MIxS collection_date accepts (truncated) ISO8601. DH taking seconds optional time only" + ], + "comments": [ + "Time should be entered as HH:MM(:SS) in GMT. See here for a converter: https://www.worldtimebuddy.com/pst-to-gmt-converter" + ], + "examples": [ + { + "value": "13:33 or 13:33:55" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "MIXS:0000011" + ], + "rank": 5, + "string_serialization": "{time, seconds optional}", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "SoilInterface", + "SoilMixsInspiredMixin" + ], + "slot_group": "mixs_inspired_section", + "range": "string", + "recommended": true, + "multivalued": false, + "pattern": "^([01]?\\d|2[0-3]|24(?=:00?:00?$)):([0-5]\\d)(:([0-5]\\d))?$" + } + }, + "attributes": { + "collection_date_inc": { + "name": "collection_date_inc", + "description": "Date the incubation was harvested/collected/ended. Only relevant for incubation samples.", + "title": "incubation collection date", + "notes": [ + "MIxS collection_date accepts (truncated) ISO8601. DH taking arbitrary precision date only" + ], + "comments": [ + "Date should be formatted as YYYY(-MM(-DD)). Ie, 2021-04-15, 2021-04 and 2021 are all acceptable." + ], + "examples": [ + { + "value": "2021-04-15, 2021-04 and 2021 are all acceptable." + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "MIXS:0000011" + ], + "rank": 2, + "string_serialization": "{date, arbitrary precision}", + "alias": "collection_date_inc", + "owner": "SoilMixsInspiredMixin", + "domain_of": [ + "Biosample", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WaterInterface", + "SoilMixsInspiredMixin" + ], + "slot_group": "mixs_inspired_section", + "range": "string", + "recommended": true, + "multivalued": false, + "pattern": "^[12]\\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\\d|3[01]))?)?$" + }, + "collection_time": { + "name": "collection_time", + "description": "The time of sampling, either as an instance (single point) or interval.", + "title": "collection time, GMT", + "notes": [ + "MIxS collection_date accepts (truncated) ISO8601. DH taking seconds optional time only" + ], + "comments": [ + "Time should be entered as HH:MM(:SS) in GMT. See here for a converter: https://www.worldtimebuddy.com/pst-to-gmt-converter" + ], + "examples": [ + { + "value": "13:33 or 13:33:55" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "MIXS:0000011" + ], + "rank": 1, + "string_serialization": "{time, seconds optional}", + "alias": "collection_time", + "owner": "SoilMixsInspiredMixin", + "domain_of": [ + "Biosample", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WaterInterface", + "SoilMixsInspiredMixin" + ], + "slot_group": "mixs_inspired_section", + "range": "string", + "recommended": true, + "multivalued": false, + "pattern": "^([01]?\\d|2[0-3]|24(?=:00?:00?$)):([0-5]\\d)(:([0-5]\\d))?$" + }, + "collection_time_inc": { + "name": "collection_time_inc", + "description": "Time the incubation was harvested/collected/ended. Only relevant for incubation samples.", + "title": "incubation collection time, GMT", + "notes": [ + "MIxS collection_date accepts (truncated) ISO8601. DH taking seconds optional time only" + ], + "comments": [ + "Time should be entered as HH:MM(:SS) in GMT. See here for a converter: https://www.worldtimebuddy.com/pst-to-gmt-converter" + ], + "examples": [ + { + "value": "13:33 or 13:33:55" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "MIXS:0000011" + ], + "rank": 3, + "string_serialization": "{time, seconds optional}", + "alias": "collection_time_inc", + "owner": "SoilMixsInspiredMixin", + "domain_of": [ + "Biosample", + "SoilInterface", + "SoilMixsInspiredMixin" + ], + "slot_group": "mixs_inspired_section", + "range": "string", + "recommended": true, + "multivalued": false, + "pattern": "^([01]?\\d|2[0-3]|24(?=:00?:00?$)):([0-5]\\d)(:([0-5]\\d))?$" + }, + "experimental_factor_other": { + "name": "experimental_factor_other", + "description": "Other details about your sample that you feel can't be accurately represented in the available columns.", + "title": "experimental factor- other", + "comments": [ + "This slot accepts open-ended text about your sample.", + "We recommend using key:value pairs.", + "Provided pairs will be considered for inclusion as future slots/terms in this data collection template." + ], + "examples": [ + { + "value": "experimental treatment: value" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "MIXS:0000008", + "MIXS:0000300" + ], + "rank": 7, + "string_serialization": "{text}", + "alias": "experimental_factor_other", + "owner": "SoilMixsInspiredMixin", + "domain_of": [ + "Biosample", + "SoilInterface", + "SoilMixsInspiredMixin" + ], + "slot_group": "mixs_inspired_section", + "range": "string", + "recommended": true, + "multivalued": false + }, + "filter_method": { + "name": "filter_method", + "description": "Type of filter used or how the sample was filtered", + "title": "filter method", + "comments": [ + "describe the filter or provide a catalog number and manufacturer" + ], + "examples": [ + { + "value": "C18" + }, + { + "value": "Basix PES, 13-100-106 FisherSci" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "MIXS:0000765" + ], + "rank": 6, + "string_serialization": "{text}", + "alias": "filter_method", + "owner": "SoilMixsInspiredMixin", + "domain_of": [ + "Biosample", + "SoilInterface", + "WaterInterface", + "SoilMixsInspiredMixin" + ], + "slot_group": "mixs_inspired_section", + "range": "string", + "recommended": true, + "multivalued": false + }, + "isotope_exposure": { + "name": "isotope_exposure", + "description": "List isotope exposure or addition applied to your sample.", + "title": "isotope exposure/addition", + "todos": [ + "Can we make the H218O correctly super and subscripted?" + ], + "comments": [ + "This is required when your experimental design includes the use of isotopically labeled compounds" + ], + "examples": [ + { + "value": "13C glucose" + }, + { + "value": "H218O" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "MIXS:0000751" + ], + "rank": 16, + "string_serialization": "{termLabel} {[termID]}; {timestamp}", + "alias": "isotope_exposure", + "owner": "SoilMixsInspiredMixin", + "domain_of": [ + "Biosample", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WaterInterface", + "SoilMixsInspiredMixin" + ], + "slot_group": "mixs_inspired_section", + "range": "string", + "recommended": true, + "multivalued": false, + "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]; ([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$" + }, + "micro_biomass_c_meth": { + "name": "micro_biomass_c_meth", + "description": "Reference or method used in determining microbial biomass carbon", + "title": "microbial biomass carbon method", + "todos": [ + "How should we separate values? | or ;? lets be consistent" + ], + "comments": [ + "required if \"microbial_biomass_c\" is provided" + ], + "examples": [ + { + "value": "https://doi.org/10.1016/0038-0717(87)90052-6" + }, + { + "value": "https://doi.org/10.1016/0038-0717(87)90052-6 | https://www.sciencedirect.com/science/article/abs/pii/0038071787900526" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "MIXS:0000339" + ], + "rank": 1004, + "string_serialization": "{PMID}|{DOI}|{URL}", + "alias": "micro_biomass_c_meth", + "owner": "SoilMixsInspiredMixin", + "domain_of": [ + "Biosample", + "SedimentInterface", + "SoilInterface", + "SoilMixsInspiredMixin" + ], + "slot_group": "mixs_inspired_section", + "range": "string", + "recommended": true, + "multivalued": false + }, + "micro_biomass_n_meth": { + "name": "micro_biomass_n_meth", + "description": "Reference or method used in determining microbial biomass nitrogen", + "title": "microbial biomass nitrogen method", + "comments": [ + "required if \"microbial_biomass_n\" is provided" + ], + "examples": [ + { + "value": "https://doi.org/10.1016/0038-0717(87)90052-6" + }, + { + "value": "https://doi.org/10.1016/0038-0717(87)90052-6 | https://www.sciencedirect.com/science/article/abs/pii/0038071787900526" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "MIXS:0000339" + ], + "rank": 1004, + "string_serialization": "{PMID}|{DOI}|{URL}", + "alias": "micro_biomass_n_meth", + "owner": "SoilMixsInspiredMixin", + "domain_of": [ + "Biosample", + "SedimentInterface", + "SoilInterface", + "SoilMixsInspiredMixin" + ], + "slot_group": "mixs_inspired_section", + "range": "string", + "multivalued": false + }, + "microbial_biomass_c": { + "name": "microbial_biomass_c", + "description": "The part of the organic matter in the soil that constitutes living microorganisms smaller than 5-10 micrometer.", + "title": "microbial biomass carbon", + "comments": [ + "If you provide this, correction factors used for conversion to the final units and method are required" + ], + "examples": [ + { + "value": "0.05 ug C/g dry soil" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "MIXS:0000650" + ], + "rank": 1004, + "string_serialization": "{float} {unit}", + "alias": "microbial_biomass_c", + "owner": "SoilMixsInspiredMixin", + "domain_of": [ + "Biosample", + "SedimentInterface", + "SoilInterface", + "SoilMixsInspiredMixin" + ], + "slot_group": "mixs_inspired_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? \\S+$" + }, + "microbial_biomass_n": { + "name": "microbial_biomass_n", + "description": "The part of the organic matter in the soil that constitutes living microorganisms smaller than 5-10 micrometer.", + "title": "microbial biomass nitrogen", + "comments": [ + "If you provide this, correction factors used for conversion to the final units and method are required" + ], + "examples": [ + { + "value": "0.05 ug N/g dry soil" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "MIXS:0000650" + ], + "rank": 1004, + "string_serialization": "{float} {unit}", + "alias": "microbial_biomass_n", + "owner": "SoilMixsInspiredMixin", + "domain_of": [ + "Biosample", + "SedimentInterface", + "SoilInterface", + "SoilMixsInspiredMixin" + ], + "slot_group": "mixs_inspired_section", + "range": "string", + "multivalued": false, + "pattern": "^[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? \\S+$" + }, + "non_microb_biomass": { + "name": "non_microb_biomass", + "description": "Amount of biomass; should include the name for the part of biomass measured, e.g.insect, plant, total. Can include multiple measurements separated by ;", + "title": "non-microbial biomass", + "examples": [ + { + "value": "insect 0.23 ug; plant 1g" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "MIXS:0000174", + "MIXS:0000650" + ], + "rank": 8, + "string_serialization": "{text};{float} {unit}", + "alias": "non_microb_biomass", + "owner": "SoilMixsInspiredMixin", + "domain_of": [ + "Biosample", + "SoilInterface", + "SoilMixsInspiredMixin" + ], + "slot_group": "mixs_inspired_section", + "range": "string", + "multivalued": false, + "pattern": "^[^;\\t\\r\\x0A\\|]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A\\|]+$" + }, + "non_microb_biomass_method": { + "name": "non_microb_biomass_method", + "description": "Reference or method used in determining biomass", + "title": "non-microbial biomass method", + "comments": [ + "required if \"non-microbial biomass\" is provided" + ], + "examples": [ + { + "value": "https://doi.org/10.1038/s41467-021-26181-3" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "MIXS:0000650" + ], + "rank": 9, + "string_serialization": "{PMID}|{DOI}|{URL}", + "alias": "non_microb_biomass_method", + "owner": "SoilMixsInspiredMixin", + "domain_of": [ + "Biosample", + "SoilInterface", + "SoilMixsInspiredMixin" + ], + "slot_group": "mixs_inspired_section", + "range": "string", + "multivalued": false + }, + "org_nitro_method": { + "name": "org_nitro_method", + "description": "Method used for obtaining organic nitrogen", + "title": "organic nitrogen method", + "comments": [ + "required if \"org_nitro\" is provided" + ], + "examples": [ + { + "value": "https://doi.org/10.1016/0038-0717(85)90144-0" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "MIXS:0000338", + "MIXS:0000205" + ], + "rank": 14, + "string_serialization": "{PMID}|{DOI}|{URL}", + "alias": "org_nitro_method", + "owner": "SoilMixsInspiredMixin", + "domain_of": [ + "Biosample", + "SedimentInterface", + "SoilInterface", + "SoilMixsInspiredMixin" + ], + "slot_group": "mixs_inspired_section", + "range": "string", + "multivalued": false + }, + "other_treatment": { + "name": "other_treatment", + "description": "Other treatments applied to your samples that are not applicable to the provided fields", + "title": "other treatments", + "notes": [ + "Values entered here will be used to determine potential new slots." + ], + "comments": [ + "This is an open text field to provide any treatments that cannot be captured in the provided slots." + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "MIXS:0000300" + ], + "rank": 15, + "string_serialization": "{text}", + "alias": "other_treatment", + "owner": "SoilMixsInspiredMixin", + "domain_of": [ + "Biosample", + "SoilInterface", + "SoilMixsInspiredMixin" + ], + "slot_group": "mixs_inspired_section", + "range": "string", + "recommended": true, + "multivalued": false + }, + "start_date_inc": { + "name": "start_date_inc", + "description": "Date the incubation was started. Only relevant for incubation samples.", + "title": "incubation start date", + "notes": [ + "MIxS collection_date accepts (truncated) ISO8601. DH taking arbitrary precision date only" + ], + "comments": [ + "Date should be formatted as YYYY(-MM(-DD)). Ie, 2021-04-15, 2021-04 and 2021 are all acceptable." + ], + "examples": [ + { + "value": "2021-04-15, 2021-04 and 2021 are all acceptable." + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "MIXS:0000011" + ], + "rank": 4, + "string_serialization": "{date, arbitrary precision}", + "alias": "start_date_inc", + "owner": "SoilMixsInspiredMixin", + "domain_of": [ + "Biosample", + "PlantAssociatedInterface", + "SedimentInterface", + "SoilInterface", + "WaterInterface", + "SoilMixsInspiredMixin" + ], + "slot_group": "mixs_inspired_section", + "range": "string", + "recommended": true, + "multivalued": false, + "pattern": "^[12]\\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\\d|3[01]))?)?$" + }, + "start_time_inc": { + "name": "start_time_inc", + "description": "Time the incubation was started. Only relevant for incubation samples.", + "title": "incubation start time, GMT", + "notes": [ + "MIxS collection_date accepts (truncated) ISO8601. DH taking seconds optional time only" + ], + "comments": [ + "Time should be entered as HH:MM(:SS) in GMT. See here for a converter: https://www.worldtimebuddy.com/pst-to-gmt-converter" + ], + "examples": [ + { + "value": "13:33 or 13:33:55" + } + ], + "from_schema": "https://w3id.org/nmdc/nmdc", + "see_also": [ + "MIXS:0000011" + ], + "rank": 5, + "string_serialization": "{time, seconds optional}", + "alias": "start_time_inc", + "owner": "SoilMixsInspiredMixin", + "domain_of": [ + "Biosample", + "SoilInterface", + "SoilMixsInspiredMixin" + ], + "slot_group": "mixs_inspired_section", + "range": "string", + "recommended": true, + "multivalued": false, + "pattern": "^([01]?\\d|2[0-3]|24(?=:00?:00?$)):([0-5]\\d)(:([0-5]\\d))?$" + } + } + }, + "DhInterface": { + "name": "DhInterface", + "description": "One DataHarmonizer interface, for the specified combination of a checklist, enviornmental_package, and various standards, user facilities or analysis types", + "title": "Dh Root Interface", + "from_schema": "https://example.com/nmdc_submission_schema" + }, + "SampleData": { + "name": "SampleData", + "description": "represents data produced by the DataHarmonizer tabs of the submission portal", + "title": "SampleData", + "from_schema": "https://example.com/nmdc_submission_schema", + "slots": [ + "air_data", + "biofilm_data", + "built_env_data", + "host_associated_data", + "plant_associated_data", + "sediment_data", + "soil_data", + "wastewater_sludge_data", + "water_data", + "emsl_data", + "jgi_mg_lr_data", + "jgi_mg_data", + "jgi_mt_data" + ], + "attributes": { + "air_data": { + "name": "air_data", + "description": "aggregation slot relating air data collections to a SampleData container", + "from_schema": "https://example.com/nmdc_submission_schema", + "alias": "air_data", + "owner": "SampleData", + "domain_of": [ + "SampleData" + ], + "range": "AirInterface", + "multivalued": true, + "inlined": true, + "inlined_as_list": true + }, + "biofilm_data": { + "name": "biofilm_data", + "description": "aggregation slot relating biofilm data collections to a SampleData container", + "from_schema": "https://example.com/nmdc_submission_schema", + "alias": "biofilm_data", + "owner": "SampleData", + "domain_of": [ + "SampleData" + ], + "range": "BiofilmInterface", + "multivalued": true, + "inlined": true, + "inlined_as_list": true + }, + "built_env_data": { + "name": "built_env_data", + "description": "aggregation slot relating built_env data collections to a SampleData container", + "from_schema": "https://example.com/nmdc_submission_schema", + "alias": "built_env_data", + "owner": "SampleData", + "domain_of": [ + "SampleData" + ], + "range": "BuiltEnvInterface", + "multivalued": true, + "inlined": true, + "inlined_as_list": true + }, + "host_associated_data": { + "name": "host_associated_data", + "description": "aggregation slot relating host_associated data collections to a SampleData container", + "from_schema": "https://example.com/nmdc_submission_schema", + "alias": "host_associated_data", + "owner": "SampleData", + "domain_of": [ + "SampleData" + ], + "range": "HostAssociatedInterface", + "multivalued": true, + "inlined": true, + "inlined_as_list": true + }, + "plant_associated_data": { + "name": "plant_associated_data", + "description": "aggregation slot relating plant_associated data collections to a SampleData container", + "from_schema": "https://example.com/nmdc_submission_schema", + "alias": "plant_associated_data", + "owner": "SampleData", + "domain_of": [ + "SampleData" + ], + "range": "PlantAssociatedInterface", + "multivalued": true, + "inlined": true, + "inlined_as_list": true + }, + "sediment_data": { + "name": "sediment_data", + "description": "aggregation slot relating sediment data collections to a SampleData container", + "from_schema": "https://example.com/nmdc_submission_schema", + "alias": "sediment_data", + "owner": "SampleData", + "domain_of": [ + "SampleData" + ], + "range": "SedimentInterface", + "multivalued": true, + "inlined": true, + "inlined_as_list": true + }, + "soil_data": { + "name": "soil_data", + "description": "aggregation slot relating soil data collections to a SampleData container", + "from_schema": "https://example.com/nmdc_submission_schema", + "alias": "soil_data", + "owner": "SampleData", + "domain_of": [ + "SampleData" + ], + "range": "SoilInterface", + "multivalued": true, + "inlined": true, + "inlined_as_list": true + }, + "wastewater_sludge_data": { + "name": "wastewater_sludge_data", + "description": "aggregation slot relating wastewater_sludge data collections to a SampleData container", + "from_schema": "https://example.com/nmdc_submission_schema", + "alias": "wastewater_sludge_data", + "owner": "SampleData", + "domain_of": [ + "SampleData" + ], + "range": "WastewaterSludgeInterface", + "multivalued": true, + "inlined": true, + "inlined_as_list": true + }, + "water_data": { + "name": "water_data", + "description": "aggregation slot relating water data collections to a SampleData container", + "from_schema": "https://example.com/nmdc_submission_schema", + "alias": "water_data", + "owner": "SampleData", + "domain_of": [ + "SampleData" + ], + "range": "WaterInterface", + "multivalued": true, + "inlined": true, + "inlined_as_list": true + }, + "emsl_data": { + "name": "emsl_data", + "description": "aggregation slot relating emsl data collections to a SampleData container", + "from_schema": "https://example.com/nmdc_submission_schema", + "alias": "emsl_data", + "owner": "SampleData", + "domain_of": [ + "SampleData" + ], + "range": "EmslInterface", + "multivalued": true, + "inlined": true, + "inlined_as_list": true + }, + "jgi_mg_lr_data": { + "name": "jgi_mg_lr_data", + "description": "aggregation slot relating jgi_mg_lr data collections to a SampleData container", + "from_schema": "https://example.com/nmdc_submission_schema", + "alias": "jgi_mg_lr_data", + "owner": "SampleData", + "domain_of": [ + "SampleData" + ], + "range": "JgiMgLrInterface", + "multivalued": true, + "inlined": true, + "inlined_as_list": true + }, + "jgi_mg_data": { + "name": "jgi_mg_data", + "description": "aggregation slot relating jgi_mg data collections to a SampleData container", + "from_schema": "https://example.com/nmdc_submission_schema", + "alias": "jgi_mg_data", + "owner": "SampleData", + "domain_of": [ + "SampleData" + ], + "range": "JgiMgInterface", + "multivalued": true, + "inlined": true, + "inlined_as_list": true + }, + "jgi_mt_data": { + "name": "jgi_mt_data", + "description": "aggregation slot relating jgi_mt data collections to a SampleData container", + "from_schema": "https://example.com/nmdc_submission_schema", + "alias": "jgi_mt_data", + "owner": "SampleData", + "domain_of": [ + "SampleData" + ], + "range": "JgiMtInterface", + "multivalued": true, + "inlined": true, + "inlined_as_list": true + } + }, + "tree_root": true + }, + "NamedThing": { + "name": "NamedThing", + "description": "a databased entity or concept/class", + "from_schema": "https://example.com/nmdc_submission_schema", + "abstract": true, + "slots": [ + "id", + "name", + "description", + "alternative_identifiers", + "type" + ], + "attributes": { + "id": { + "name": "id", + "description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", + "notes": [ + "abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?", + "a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters will be accepted", + "typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked via per-class id slot usage assertions", + "minting authority shoulders should probably be enumerated and checked in the pattern" + ], + "examples": [ + { + "value": "nmdc:mgmag-00-x012.1_7_c1", + "description": "https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "identifier": true, + "alias": "id", + "owner": "NamedThing", + "domain_of": [ + "NamedThing" + ], + "range": "uriorcurie", + "required": true, + "pattern": "^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$" + }, + "name": { + "name": "name", + "description": "A human readable label for an entity", + "from_schema": "https://example.com/nmdc_submission_schema", + "alias": "name", + "owner": "NamedThing", + "domain_of": [ + "PersonValue", + "NamedThing", + "Protocol" + ], + "range": "string", + "multivalued": false + }, + "description": { + "name": "description", + "description": "a human-readable description of a thing", + "from_schema": "https://example.com/nmdc_submission_schema", + "slot_uri": "dcterms:description", + "alias": "description", + "owner": "NamedThing", + "domain_of": [ + "ImageValue", + "NamedThing" + ], + "range": "string", + "multivalued": false + }, + "alternative_identifiers": { + "name": "alternative_identifiers", + "description": "A list of alternative identifiers for the entity.", + "from_schema": "https://example.com/nmdc_submission_schema", + "alias": "alternative_identifiers", + "owner": "NamedThing", + "domain_of": [ + "MetaboliteIdentification", + "NamedThing" + ], + "range": "uriorcurie", + "multivalued": true, + "pattern": "^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$" + }, + "type": { + "name": "type", + "description": "the class_uri of the class that has been instantiated", + "notes": [ + "replaces legacy nmdc:type slot", + "makes it easier to read example data files", + "required for polymorphic MongoDB collections" + ], + "examples": [ + { + "value": "nmdc:Biosample" + }, + { + "value": "nmdc:Study" + } + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/issues/1048", + "https://github.com/microbiomedata/nmdc-schema/issues/1233", + "https://github.com/microbiomedata/nmdc-schema/issues/248" + ], + "slot_uri": "rdf:type", + "designates_type": true, + "alias": "type", + "owner": "NamedThing", + "domain_of": [ + "EukEval", + "FunctionalAnnotationAggMember", + "MobilePhaseSegment", + "PortionOfSubstance", + "MagBin", + "MetaboliteIdentification", + "PeptideQuantification", + "ProteinQuantification", + "GenomeFeature", + "FunctionalAnnotation", + "AttributeValue", + "NamedThing", + "FailureCategorization", + "Protocol", + "CreditAssociation", + "Doi" + ], + "range": "uriorcurie", + "required": true + } + }, + "class_uri": "nmdc:NamedThing" + } + }, + "source_file": "src/nmdc_submission_schema/schema/nmdc_submission_schema.yaml", + "@type": "SchemaDefinition" +} diff --git a/project/jsonschema/nmdc_submission_schema.schema.json b/project/jsonschema/nmdc_submission_schema.schema.json new file mode 100644 index 00000000..ab5d2232 --- /dev/null +++ b/project/jsonschema/nmdc_submission_schema.schema.json @@ -0,0 +1,12897 @@ +{ + "$defs": { + "AirInterface": { + "additionalProperties": false, + "description": "air dh_interface", + "properties": { + "air_PM_concen": { + "description": "Concentration of substances that remain suspended in the air, and comprise mixtures of organic and inorganic substances (PM10 and PM2.5); can report multiple PM's by entering numeric values preceded by name of PM", + "pattern": "^([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+\\|)*([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+)$", + "type": [ + "string", + "null" + ] + }, + "alt": { + "description": "Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "analysis_type": { + "description": "Select all the data types associated or available for this biosample", + "items": { + "$ref": "#/$defs/AnalysisTypeEnum" + }, + "type": "array" + }, + "barometric_press": { + "description": "Force per unit area exerted against a surface by the weight of air above that surface", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "carb_dioxide": { + "description": "Carbon dioxide (gas) amount or concentration at the time of sampling", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "carb_monoxide": { + "description": "Carbon monoxide (gas) amount or concentration at the time of sampling", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "chem_administration": { + "description": "List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi", + "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\];([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", + "type": [ + "string", + "null" + ] + }, + "collection_date": { + "description": "The date of sampling", + "pattern": "^[12]\\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\\d|3[01]))?)?$", + "type": "string" + }, + "depth": { + "description": "The vertical distance below local surface, e.g. for sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples.", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)?(\\s*-\\s*[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)?)?$", + "type": [ + "string", + "null" + ] + }, + "ecosystem": { + "$ref": "#/$defs/EcosystemEnum", + "description": "An ecosystem is a combination of a physical environment (abiotic factors) and all the organisms (biotic factors) that interact with this environment. Ecosystem is in position 1/5 in a GOLD path." + }, + "ecosystem_category": { + "$ref": "#/$defs/EcosystemCategoryEnum", + "description": "Ecosystem categories represent divisions within the ecosystem based on specific characteristics of the environment from where an organism or sample is isolated. Ecosystem category is in position 2/5 in a GOLD path." + }, + "ecosystem_subtype": { + "$ref": "#/$defs/EcosystemSubtypeEnum", + "description": "Ecosystem subtypes represent further subdivision of Ecosystem types into more distinct subtypes. Ecosystem subtype is in position 4/5 in a GOLD path." + }, + "ecosystem_type": { + "$ref": "#/$defs/EcosystemTypeEnum", + "description": "Ecosystem types represent things having common characteristics within the Ecosystem Category. These common characteristics based grouping is still broad but specific to the characteristics of a given environment. Ecosystem type is in position 3/5 in a GOLD path." + }, + "elev": { + "description": "Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit.", + "type": "number" + }, + "env_broad_scale": { + "description": "In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO's biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html", + "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$", + "type": "string" + }, + "env_local_scale": { + "description": "Report the entity or entities which are in the sample or specimen\u2019s local vicinity and which you believe have significant causal influences on your sample or specimen. We recommend using EnvO terms which are of smaller spatial grain than your entry for env_broad_scale. Terms, such as anatomical sites, from other OBO Library ontologies which interoperate with EnvO (e.g. UBERON) are accepted in this field. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS.", + "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$", + "type": "string" + }, + "env_medium": { + "description": "Report the environmental material(s) immediately surrounding the sample or specimen at the time of sampling. We recommend using subclasses of 'environmental material' (http://purl.obolibrary.org/obo/ENVO_00010483). EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS . Terms from other OBO ontologies are permissible as long as they reference mass/volume nouns (e.g. air, water, blood) and not discrete, countable entities (e.g. a tree, a leaf, a table top).", + "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$", + "type": "string" + }, + "experimental_factor": { + "description": "Experimental factors are essentially the variable aspects of an experiment design which can be used to describe an experiment, or set of experiments, in an increasingly detailed manner. This field accepts ontology terms from Experimental Factor Ontology (EFO) and/or Ontology for Biomedical Investigations (OBI). For a browser of EFO (v 2.95) terms, please see http://purl.bioontology.org/ontology/EFO; for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI", + "type": [ + "string", + "null" + ] + }, + "geo_loc_name": { + "description": "The geographical origin of the sample as defined by the country or sea name followed by specific region name.", + "pattern": "^[^:, ][^:]*: [^:, ][^,]*, [^:, ].*$", + "type": "string" + }, + "humidity": { + "description": "Amount of water vapour in the air, at the time of sampling", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "lat_lon": { + "description": "The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system", + "pattern": "^[-+]?([1-8]?\\d(\\.\\d{1,8})?|90(\\.0{1,8})?)\\s[-+]?(180(\\.0{1,8})?|((1[0-7]\\d)|([1-9]?\\d))(\\.\\d{1,8})?)$", + "type": "string" + }, + "methane": { + "description": "Methane (gas) amount or concentration at the time of sampling", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "misc_param": { + "description": "Any other measurement performed or parameter collected, that is not listed here", + "pattern": "^([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+\\|)*([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+)$", + "type": [ + "string", + "null" + ] + }, + "organism_count": { + "description": "Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr)", + "pattern": "^([-+]?[0-9]*\\.?[0-9]+ +\\S.*\\|)*([-+]?[0-9]*\\.?[0-9]+ +\\S.*)$", + "type": [ + "string", + "null" + ] + }, + "oxy_stat_samp": { + "$ref": "#/$defs/OxyStatSampEnum", + "description": "Oxygenation status of sample" + }, + "oxygen": { + "description": "Oxygen (gas) amount or concentration at the time of sampling", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "perturbation": { + "description": "Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types", + "type": [ + "string", + "null" + ] + }, + "pollutants": { + "description": "Pollutant types and, amount or concentrations measured at the time of sampling; can report multiple pollutants by entering numeric values preceded by name of pollutant", + "pattern": "^([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+\\|)*([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+)$", + "type": [ + "string", + "null" + ] + }, + "salinity": { + "description": "The total concentration of all dissolved salts in a liquid or solid sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater.", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "samp_collec_device": { + "description": "The device used to collect an environmental sample. This field accepts terms listed under environmental sampling device (http://purl.obolibrary.org/obo/ENVO). This field also accepts terms listed under specimen collection device (http://purl.obolibrary.org/obo/GENEPIO_0002094).", + "type": [ + "string", + "null" + ] + }, + "samp_collec_method": { + "description": "The method employed for collecting the sample.", + "type": [ + "string", + "null" + ] + }, + "samp_mat_process": { + "description": "A brief description of any processing applied to the sample during or after retrieving the sample from environment, or a link to the relevant protocol(s) performed.", + "type": [ + "string", + "null" + ] + }, + "samp_name": { + "description": "A local identifier or name that for the material sample collected. Refers to the original material collected or to any derived sub-samples.", + "type": "string" + }, + "samp_size": { + "description": "The total amount or size (volume (ml), mass (g) or area (m2) ) of sample collected.", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? \\S+$", + "type": [ + "string", + "null" + ] + }, + "samp_store_dur": { + "description": "Duration for which the sample was stored", + "type": [ + "string", + "null" + ] + }, + "samp_store_loc": { + "description": "Location at which sample was stored, usually name of a specific freezer/room", + "type": [ + "string", + "null" + ] + }, + "samp_store_temp": { + "description": "Temperature at which the sample was stored (degrees are assumed)", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": "string" + }, + "sample_link": { + "description": "A unique identifier to assign parent-child, subsample, or sibling samples. This is relevant when a sample or other material was used to generate the new sample.", + "pattern": "[^\\:\\n\\r]+\\:[^\\:\\n\\r]+", + "type": [ + "string", + "null" + ] + }, + "size_frac": { + "description": "Filtering pore size used in sample preparation", + "type": [ + "string", + "null" + ] + }, + "solar_irradiance": { + "description": "The amount of solar energy that arrives at a specific area of a surface during a specific time interval", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "source_mat_id": { + "description": "A globally unique identifier assigned to the biological sample.", + "pattern": "[^\\:\\n\\r]+\\:[^\\:\\n\\r]+", + "type": [ + "string", + "null" + ] + }, + "specific_ecosystem": { + "$ref": "#/$defs/SpecificEcosystemEnum", + "description": "Specific ecosystems represent specific features of the environment like aphotic zone in an ocean or gastric mucosa within a host digestive system. Specific ecosystem is in position 5/5 in a GOLD path." + }, + "temp": { + "description": "Temperature of the sample at the time of sampling.", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "ventilation_rate": { + "description": "Ventilation rate of the system in the sampled premises", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "ventilation_type": { + "description": "Ventilation system used in the sampled premises", + "type": [ + "string", + "null" + ] + }, + "volatile_org_comp": { + "description": "Concentration of carbon-based chemicals that easily evaporate at room temperature; can report multiple volatile organic compounds by entering numeric values preceded by name of compound", + "pattern": "^([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+\\|)*([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+)$", + "type": [ + "string", + "null" + ] + }, + "wind_direction": { + "description": "Wind direction is the direction from which a wind originates", + "type": [ + "string", + "null" + ] + }, + "wind_speed": { + "description": "Speed of wind measured at the time of sampling", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + } + }, + "required": [ + "collection_date", + "elev", + "env_broad_scale", + "env_local_scale", + "env_medium", + "geo_loc_name", + "lat_lon", + "samp_store_temp", + "analysis_type", + "samp_name" + ], + "title": "AirInterface", + "type": "object" + }, + "AnalysisTypeEnum": { + "description": "", + "enum": [ + "metabolomics", + "metagenomics", + "metagenomics_long_read", + "metaproteomics", + "metatranscriptomics", + "natural organic matter", + "bulk chemistry" + ], + "title": "AnalysisTypeEnum", + "type": "string" + }, + "ArchStrucEnum": { + "description": "", + "enum": [ + "building", + "shed", + "home" + ], + "title": "ArchStrucEnum", + "type": "string" + }, + "BiofilmInterface": { + "additionalProperties": false, + "description": "biofilm dh_interface", + "properties": { + "alkalinity": { + "description": "Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "alkyl_diethers": { + "description": "Concentration of alkyl diethers", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "alt": { + "description": "Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "aminopept_act": { + "description": "Measurement of aminopeptidase activity", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "ammonium": { + "description": "Concentration of ammonium in the sample", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "analysis_type": { + "description": "Select all the data types associated or available for this biosample", + "items": { + "$ref": "#/$defs/AnalysisTypeEnum" + }, + "type": "array" + }, + "bacteria_carb_prod": { + "description": "Measurement of bacterial carbon production", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "biomass": { + "description": "Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements", + "pattern": "^([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+\\|)*([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+)$", + "type": [ + "string", + "null" + ] + }, + "bishomohopanol": { + "description": "Concentration of bishomohopanol", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "bromide": { + "description": "Concentration of bromide", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "calcium": { + "description": "Concentration of calcium in the sample", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "carb_nitro_ratio": { + "description": "Ratio of amount or concentrations of carbon to nitrogen", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "number", + "null" + ] + }, + "chem_administration": { + "description": "List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi", + "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\];([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", + "type": [ + "string", + "null" + ] + }, + "chloride": { + "description": "Concentration of chloride in the sample", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "chlorophyll": { + "description": "Concentration of chlorophyll", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "collection_date": { + "description": "The date of sampling", + "pattern": "^[12]\\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\\d|3[01]))?)?$", + "type": "string" + }, + "depth": { + "description": "The vertical distance below local surface, e.g. for sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples.", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)?(\\s*-\\s*[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)?)?$", + "type": [ + "string", + "null" + ] + }, + "diether_lipids": { + "description": "Concentration of diether lipids; can include multiple types of diether lipids", + "pattern": "^([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+\\|)*([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+)$", + "type": [ + "string", + "null" + ] + }, + "diss_carb_dioxide": { + "description": "Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "diss_hydrogen": { + "description": "Concentration of dissolved hydrogen", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "diss_inorg_carb": { + "description": "Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "diss_org_carb": { + "description": "Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "diss_org_nitro": { + "description": "Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "diss_oxygen": { + "description": "Concentration of dissolved oxygen", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "ecosystem": { + "$ref": "#/$defs/EcosystemEnum", + "description": "An ecosystem is a combination of a physical environment (abiotic factors) and all the organisms (biotic factors) that interact with this environment. Ecosystem is in position 1/5 in a GOLD path." + }, + "ecosystem_category": { + "$ref": "#/$defs/EcosystemCategoryEnum", + "description": "Ecosystem categories represent divisions within the ecosystem based on specific characteristics of the environment from where an organism or sample is isolated. Ecosystem category is in position 2/5 in a GOLD path." + }, + "ecosystem_subtype": { + "$ref": "#/$defs/EcosystemSubtypeEnum", + "description": "Ecosystem subtypes represent further subdivision of Ecosystem types into more distinct subtypes. Ecosystem subtype is in position 4/5 in a GOLD path." + }, + "ecosystem_type": { + "$ref": "#/$defs/EcosystemTypeEnum", + "description": "Ecosystem types represent things having common characteristics within the Ecosystem Category. These common characteristics based grouping is still broad but specific to the characteristics of a given environment. Ecosystem type is in position 3/5 in a GOLD path." + }, + "elev": { + "description": "Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit.", + "type": "number" + }, + "env_broad_scale": { + "description": "In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO's biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html", + "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$", + "type": "string" + }, + "env_local_scale": { + "description": "Report the entity or entities which are in the sample or specimen\u2019s local vicinity and which you believe have significant causal influences on your sample or specimen. We recommend using EnvO terms which are of smaller spatial grain than your entry for env_broad_scale. Terms, such as anatomical sites, from other OBO Library ontologies which interoperate with EnvO (e.g. UBERON) are accepted in this field. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS.", + "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$", + "type": "string" + }, + "env_medium": { + "description": "Report the environmental material(s) immediately surrounding the sample or specimen at the time of sampling. We recommend using subclasses of 'environmental material' (http://purl.obolibrary.org/obo/ENVO_00010483). EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS . Terms from other OBO ontologies are permissible as long as they reference mass/volume nouns (e.g. air, water, blood) and not discrete, countable entities (e.g. a tree, a leaf, a table top).", + "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$", + "type": "string" + }, + "experimental_factor": { + "description": "Experimental factors are essentially the variable aspects of an experiment design which can be used to describe an experiment, or set of experiments, in an increasingly detailed manner. This field accepts ontology terms from Experimental Factor Ontology (EFO) and/or Ontology for Biomedical Investigations (OBI). For a browser of EFO (v 2.95) terms, please see http://purl.bioontology.org/ontology/EFO; for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI", + "type": [ + "string", + "null" + ] + }, + "geo_loc_name": { + "description": "The geographical origin of the sample as defined by the country or sea name followed by specific region name.", + "pattern": "^[^:, ][^:]*: [^:, ][^,]*, [^:, ].*$", + "type": "string" + }, + "glucosidase_act": { + "description": "Measurement of glucosidase activity", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "lat_lon": { + "description": "The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system", + "pattern": "^[-+]?([1-8]?\\d(\\.\\d{1,8})?|90(\\.0{1,8})?)\\s[-+]?(180(\\.0{1,8})?|((1[0-7]\\d)|([1-9]?\\d))(\\.\\d{1,8})?)$", + "type": "string" + }, + "magnesium": { + "description": "Concentration of magnesium in the sample", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "mean_frict_vel": { + "description": "Measurement of mean friction velocity", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "mean_peak_frict_vel": { + "description": "Measurement of mean peak friction velocity", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "methane": { + "description": "Methane (gas) amount or concentration at the time of sampling", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "misc_param": { + "description": "Any other measurement performed or parameter collected, that is not listed here", + "pattern": "^([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+\\|)*([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+)$", + "type": [ + "string", + "null" + ] + }, + "n_alkanes": { + "description": "Concentration of n-alkanes; can include multiple n-alkanes", + "pattern": "^([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+\\|)*([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+)$", + "type": [ + "string", + "null" + ] + }, + "nitrate": { + "description": "Concentration of nitrate in the sample", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "nitrite": { + "description": "Concentration of nitrite in the sample", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "nitro": { + "description": "Concentration of nitrogen (total)", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "org_carb": { + "description": "Concentration of organic carbon", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "org_matter": { + "description": "Concentration of organic matter", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "org_nitro": { + "description": "Concentration of organic nitrogen", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "organism_count": { + "description": "Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr)", + "pattern": "^([-+]?[0-9]*\\.?[0-9]+ +\\S.*\\|)*([-+]?[0-9]*\\.?[0-9]+ +\\S.*)$", + "type": [ + "string", + "null" + ] + }, + "oxy_stat_samp": { + "$ref": "#/$defs/OxyStatSampEnum", + "description": "Oxygenation status of sample" + }, + "part_org_carb": { + "description": "Concentration of particulate organic carbon", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "perturbation": { + "description": "Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types", + "type": [ + "string", + "null" + ] + }, + "petroleum_hydrocarb": { + "description": "Concentration of petroleum hydrocarbon", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "ph": { + "description": "pH measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid", + "maximum": 14, + "minimum": 0, + "type": [ + "number", + "null" + ] + }, + "ph_meth": { + "description": "Reference or method used in determining ph", + "type": [ + "string", + "null" + ] + }, + "phaeopigments": { + "description": "Concentration of phaeopigments; can include multiple phaeopigments", + "pattern": "^([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+\\|)*([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+)$", + "type": [ + "string", + "null" + ] + }, + "phosphate": { + "description": "Concentration of phosphate", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "phosplipid_fatt_acid": { + "description": "Concentration of phospholipid fatty acids; can include multiple values", + "pattern": "^([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+\\|)*([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+)$", + "type": [ + "string", + "null" + ] + }, + "potassium": { + "description": "Concentration of potassium in the sample", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "pressure": { + "description": "Pressure to which the sample is subject to, in atmospheres", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "redox_potential": { + "description": "Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "salinity": { + "description": "The total concentration of all dissolved salts in a liquid or solid sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater.", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "samp_collec_device": { + "description": "The device used to collect an environmental sample. This field accepts terms listed under environmental sampling device (http://purl.obolibrary.org/obo/ENVO). This field also accepts terms listed under specimen collection device (http://purl.obolibrary.org/obo/GENEPIO_0002094).", + "type": [ + "string", + "null" + ] + }, + "samp_collec_method": { + "description": "The method employed for collecting the sample.", + "type": [ + "string", + "null" + ] + }, + "samp_mat_process": { + "description": "A brief description of any processing applied to the sample during or after retrieving the sample from environment, or a link to the relevant protocol(s) performed.", + "type": [ + "string", + "null" + ] + }, + "samp_name": { + "description": "A local identifier or name that for the material sample collected. Refers to the original material collected or to any derived sub-samples.", + "type": "string" + }, + "samp_size": { + "description": "The total amount or size (volume (ml), mass (g) or area (m2) ) of sample collected.", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? \\S+$", + "type": [ + "string", + "null" + ] + }, + "samp_store_dur": { + "description": "Duration for which the sample was stored", + "type": [ + "string", + "null" + ] + }, + "samp_store_loc": { + "description": "Location at which sample was stored, usually name of a specific freezer/room", + "type": [ + "string", + "null" + ] + }, + "samp_store_temp": { + "description": "Temperature at which the sample was stored (degrees are assumed)", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": "string" + }, + "sample_link": { + "description": "A unique identifier to assign parent-child, subsample, or sibling samples. This is relevant when a sample or other material was used to generate the new sample.", + "pattern": "[^\\:\\n\\r]+\\:[^\\:\\n\\r]+", + "type": [ + "string", + "null" + ] + }, + "silicate": { + "description": "Concentration of silicate", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "size_frac": { + "description": "Filtering pore size used in sample preparation", + "type": [ + "string", + "null" + ] + }, + "sodium": { + "description": "Sodium concentration in the sample", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "source_mat_id": { + "description": "A globally unique identifier assigned to the biological sample.", + "pattern": "[^\\:\\n\\r]+\\:[^\\:\\n\\r]+", + "type": [ + "string", + "null" + ] + }, + "specific_ecosystem": { + "$ref": "#/$defs/SpecificEcosystemEnum", + "description": "Specific ecosystems represent specific features of the environment like aphotic zone in an ocean or gastric mucosa within a host digestive system. Specific ecosystem is in position 5/5 in a GOLD path." + }, + "sulfate": { + "description": "Concentration of sulfate in the sample", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "sulfide": { + "description": "Concentration of sulfide in the sample", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "temp": { + "description": "Temperature of the sample at the time of sampling.", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "tot_carb": { + "description": "Total carbon content", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "tot_nitro_content": { + "description": "Total nitrogen content of the sample", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "tot_org_carb": { + "description": "Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "turbidity": { + "description": "Measure of the amount of cloudiness or haziness in water caused by individual particles", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "water_content": { + "description": "Water content measurement", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)?%? \\S.+$", + "type": [ + "string", + "null" + ] + } + }, + "required": [ + "collection_date", + "elev", + "env_broad_scale", + "env_local_scale", + "env_medium", + "geo_loc_name", + "lat_lon", + "samp_store_temp", + "analysis_type", + "samp_name" + ], + "title": "BiofilmInterface", + "type": "object" + }, + "BiolStatEnum": { + "description": "", + "enum": [ + "wild", + "natural", + "semi-natural", + "inbred line", + "breeder's line", + "hybrid", + "clonal selection", + "mutant" + ], + "title": "BiolStatEnum", + "type": "string" + }, + "BioticRelationshipEnum": { + "description": "", + "enum": [ + "free living", + "parasite", + "commensal", + "symbiont" + ], + "title": "BioticRelationshipEnum", + "type": "string" + }, + "BuildDocsEnum": { + "description": "", + "enum": [ + "building information model", + "commissioning report", + "complaint logs", + "contract administration", + "cost estimate", + "janitorial schedules or logs", + "maintenance plans", + "schedule", + "sections", + "shop drawings", + "submittals", + "ventilation system", + "windows" + ], + "title": "BuildDocsEnum", + "type": "string" + }, + "BuildOccupTypeEnum": { + "description": "", + "enum": [ + "office", + "market", + "restaurant", + "residence", + "school", + "residential", + "commercial", + "low rise", + "high rise", + "wood framed", + "health care", + "airport", + "sports complex" + ], + "title": "BuildOccupTypeEnum", + "type": "string" + }, + "BuildingSettingEnum": { + "description": "", + "enum": [ + "urban", + "suburban", + "exurban", + "rural" + ], + "title": "BuildingSettingEnum", + "type": "string" + }, + "BuiltEnvInterface": { + "additionalProperties": false, + "description": "built_env dh_interface", + "properties": { + "abs_air_humidity": { + "description": "Actual mass of water vapor - mh20 - present in the air water vapor mixture", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "address": { + "description": "The street name and building number where the sampling occurred.", + "type": [ + "string", + "null" + ] + }, + "adj_room": { + "description": "List of rooms (room number, room name) immediately adjacent to the sampling room", + "type": [ + "string", + "null" + ] + }, + "aero_struc": { + "description": "Aerospace structures typically consist of thin plates with stiffeners for the external surfaces, bulkheads and frames to support the shape and fasteners such as welds, rivets, screws and bolts to hold the components together", + "type": [ + "string", + "null" + ] + }, + "air_temp": { + "description": "Temperature of the air at the time of sampling", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "alt": { + "description": "Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "amount_light": { + "description": "The unit of illuminance and luminous emittance, measuring luminous flux per unit area", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "analysis_type": { + "description": "Select all the data types associated or available for this biosample", + "items": { + "$ref": "#/$defs/AnalysisTypeEnum" + }, + "type": "array" + }, + "arch_struc": { + "$ref": "#/$defs/ArchStrucEnum", + "description": "An architectural structure is a human-made, free-standing, immobile outdoor construction" + }, + "avg_dew_point": { + "description": "The average of dew point measures taken at the beginning of every hour over a 24 hour period on the sampling day", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "avg_occup": { + "description": "Daily average occupancy of room. Indicate the number of person(s) daily occupying the sampling room.", + "type": [ + "string", + "null" + ] + }, + "avg_temp": { + "description": "The average of temperatures taken at the beginning of every hour over a 24 hour period on the sampling day", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "bathroom_count": { + "description": "The number of bathrooms in the building", + "type": [ + "string", + "null" + ] + }, + "bedroom_count": { + "description": "The number of bedrooms in the building", + "type": [ + "string", + "null" + ] + }, + "build_docs": { + "$ref": "#/$defs/BuildDocsEnum", + "description": "The building design, construction and operation documents" + }, + "build_occup_type": { + "description": "The primary function for which a building or discrete part of a building is intended to be used", + "items": { + "$ref": "#/$defs/BuildOccupTypeEnum" + }, + "type": [ + "array", + "null" + ] + }, + "building_setting": { + "$ref": "#/$defs/BuildingSettingEnum", + "description": "A location (geography) where a building is set" + }, + "built_struc_age": { + "description": "The age of the built structure since construction", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "built_struc_set": { + "description": "The characterization of the location of the built structure as high or low human density", + "type": [ + "string", + "null" + ] + }, + "built_struc_type": { + "description": "A physical structure that is a body or assemblage of bodies in space to form a system capable of supporting loads", + "type": [ + "string", + "null" + ] + }, + "carb_dioxide": { + "description": "Carbon dioxide (gas) amount or concentration at the time of sampling", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "ceil_area": { + "description": "The area of the ceiling space within the room", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "ceil_cond": { + "$ref": "#/$defs/CeilCondEnum", + "description": "The physical condition of the ceiling at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas" + }, + "ceil_finish_mat": { + "$ref": "#/$defs/CeilFinishMatEnum", + "description": "The type of material used to finish a ceiling" + }, + "ceil_struc": { + "description": "The construction format of the ceiling", + "type": [ + "string", + "null" + ] + }, + "ceil_texture": { + "$ref": "#/$defs/CeilTextureEnum", + "description": "The feel, appearance, or consistency of a ceiling surface" + }, + "ceil_thermal_mass": { + "description": "The ability of the ceiling to provide inertia against temperature fluctuations. Generally this means concrete that is exposed. A metal deck that supports a concrete slab will act thermally as long as it is exposed to room air flow", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "ceil_type": { + "$ref": "#/$defs/CeilTypeEnum", + "description": "The type of ceiling according to the ceiling's appearance or construction" + }, + "ceil_water_mold": { + "description": "Signs of the presence of mold or mildew on the ceiling", + "type": [ + "string", + "null" + ] + }, + "collection_date": { + "description": "The date of sampling", + "pattern": "^[12]\\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\\d|3[01]))?)?$", + "type": "string" + }, + "cool_syst_id": { + "description": "The cooling system identifier", + "type": [ + "string", + "null" + ] + }, + "date_last_rain": { + "description": "The date of the last time it rained", + "type": [ + "string", + "null" + ] + }, + "depth": { + "description": "The vertical distance below local surface, e.g. for sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples.", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)?(\\s*-\\s*[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)?)?$", + "type": [ + "string", + "null" + ] + }, + "dew_point": { + "description": "The temperature to which a given parcel of humid air must be cooled, at constant barometric pressure, for water vapor to condense into water.", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "door_comp_type": { + "$ref": "#/$defs/DoorCompTypeEnum", + "description": "The composite type of the door" + }, + "door_cond": { + "$ref": "#/$defs/DoorCondEnum", + "description": "The phsical condition of the door" + }, + "door_direct": { + "$ref": "#/$defs/DoorDirectEnum", + "description": "The direction the door opens" + }, + "door_loc": { + "$ref": "#/$defs/DoorLocEnum", + "description": "The relative location of the door in the room" + }, + "door_mat": { + "$ref": "#/$defs/DoorMatEnum", + "description": "The material the door is composed of" + }, + "door_move": { + "$ref": "#/$defs/DoorMoveEnum", + "description": "The type of movement of the door" + }, + "door_size": { + "description": "The size of the door", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "door_type": { + "$ref": "#/$defs/DoorTypeEnum", + "description": "The type of door material" + }, + "door_type_metal": { + "$ref": "#/$defs/DoorTypeMetalEnum", + "description": "The type of metal door" + }, + "door_type_wood": { + "$ref": "#/$defs/DoorTypeWoodEnum", + "description": "The type of wood door" + }, + "door_water_mold": { + "description": "Signs of the presence of mold or mildew on a door", + "type": [ + "string", + "null" + ] + }, + "drawings": { + "$ref": "#/$defs/DrawingsEnum", + "description": "The buildings architectural drawings; if design is chosen, indicate phase-conceptual, schematic, design development, and construction documents" + }, + "ecosystem": { + "$ref": "#/$defs/EcosystemEnum", + "description": "An ecosystem is a combination of a physical environment (abiotic factors) and all the organisms (biotic factors) that interact with this environment. Ecosystem is in position 1/5 in a GOLD path." + }, + "ecosystem_category": { + "$ref": "#/$defs/EcosystemCategoryEnum", + "description": "Ecosystem categories represent divisions within the ecosystem based on specific characteristics of the environment from where an organism or sample is isolated. Ecosystem category is in position 2/5 in a GOLD path." + }, + "ecosystem_subtype": { + "$ref": "#/$defs/EcosystemSubtypeEnum", + "description": "Ecosystem subtypes represent further subdivision of Ecosystem types into more distinct subtypes. Ecosystem subtype is in position 4/5 in a GOLD path." + }, + "ecosystem_type": { + "$ref": "#/$defs/EcosystemTypeEnum", + "description": "Ecosystem types represent things having common characteristics within the Ecosystem Category. These common characteristics based grouping is still broad but specific to the characteristics of a given environment. Ecosystem type is in position 3/5 in a GOLD path." + }, + "elev": { + "description": "Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit.", + "type": "number" + }, + "elevator": { + "description": "The number of elevators within the built structure", + "type": [ + "string", + "null" + ] + }, + "env_broad_scale": { + "description": "In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO's biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html", + "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$", + "type": "string" + }, + "env_local_scale": { + "description": "Report the entity or entities which are in the sample or specimen\u2019s local vicinity and which you believe have significant causal influences on your sample or specimen. We recommend using EnvO terms which are of smaller spatial grain than your entry for env_broad_scale. Terms, such as anatomical sites, from other OBO Library ontologies which interoperate with EnvO (e.g. UBERON) are accepted in this field. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS.", + "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$", + "type": "string" + }, + "env_medium": { + "description": "Report the environmental material(s) immediately surrounding the sample or specimen at the time of sampling. We recommend using subclasses of 'environmental material' (http://purl.obolibrary.org/obo/ENVO_00010483). EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS . Terms from other OBO ontologies are permissible as long as they reference mass/volume nouns (e.g. air, water, blood) and not discrete, countable entities (e.g. a tree, a leaf, a table top).", + "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$", + "type": "string" + }, + "escalator": { + "description": "The number of escalators within the built structure", + "type": [ + "string", + "null" + ] + }, + "exp_duct": { + "description": "The amount of exposed ductwork in the room", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "exp_pipe": { + "description": "The number of exposed pipes in the room", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "experimental_factor": { + "description": "Experimental factors are essentially the variable aspects of an experiment design which can be used to describe an experiment, or set of experiments, in an increasingly detailed manner. This field accepts ontology terms from Experimental Factor Ontology (EFO) and/or Ontology for Biomedical Investigations (OBI). For a browser of EFO (v 2.95) terms, please see http://purl.bioontology.org/ontology/EFO; for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI", + "type": [ + "string", + "null" + ] + }, + "ext_door": { + "description": "The number of exterior doors in the built structure", + "type": [ + "string", + "null" + ] + }, + "ext_wall_orient": { + "$ref": "#/$defs/ExtWallOrientEnum", + "description": "The orientation of the exterior wall" + }, + "ext_window_orient": { + "$ref": "#/$defs/ExtWindowOrientEnum", + "description": "The compass direction the exterior window of the room is facing" + }, + "filter_type": { + "description": "A device which removes solid particulates or airborne molecular contaminants", + "items": { + "$ref": "#/$defs/FilterTypeEnum" + }, + "type": [ + "array", + "null" + ] + }, + "fireplace_type": { + "description": "A firebox with chimney", + "type": [ + "string", + "null" + ] + }, + "floor_age": { + "description": "The time period since installment of the carpet or flooring", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "floor_area": { + "description": "The area of the floor space within the room", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "floor_cond": { + "$ref": "#/$defs/FloorCondEnum", + "description": "The physical condition of the floor at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas" + }, + "floor_count": { + "description": "The number of floors in the building, including basements and mechanical penthouse", + "type": [ + "string", + "null" + ] + }, + "floor_finish_mat": { + "$ref": "#/$defs/FloorFinishMatEnum", + "description": "The floor covering type; the finished surface that is walked on" + }, + "floor_struc": { + "$ref": "#/$defs/FloorStrucEnum", + "description": "Refers to the structural elements and subfloor upon which the finish flooring is installed" + }, + "floor_thermal_mass": { + "description": "The ability of the floor to provide inertia against temperature fluctuations", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "floor_water_mold": { + "$ref": "#/$defs/FloorWaterMoldEnum", + "description": "Signs of the presence of mold or mildew in a room" + }, + "freq_clean": { + "description": "The number of times the sample location is cleaned. Frequency of cleaning might be on a Daily basis, Weekly, Monthly, Quarterly or Annually.", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "freq_cook": { + "description": "The number of times a meal is cooked per week", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "furniture": { + "$ref": "#/$defs/FurnitureEnum", + "description": "The types of furniture present in the sampled room" + }, + "gender_restroom": { + "$ref": "#/$defs/GenderRestroomEnum", + "description": "The gender type of the restroom" + }, + "geo_loc_name": { + "description": "The geographical origin of the sample as defined by the country or sea name followed by specific region name.", + "pattern": "^[^:, ][^:]*: [^:, ][^,]*, [^:, ].*$", + "type": "string" + }, + "hall_count": { + "description": "The total count of hallways and cooridors in the built structure", + "type": [ + "string", + "null" + ] + }, + "handidness": { + "$ref": "#/$defs/HandidnessEnum", + "description": "The handidness of the individual sampled" + }, + "heat_cool_type": { + "description": "Methods of conditioning or heating a room or building", + "items": { + "$ref": "#/$defs/HeatCoolTypeEnum" + }, + "type": [ + "array", + "null" + ] + }, + "heat_deliv_loc": { + "$ref": "#/$defs/HeatDelivLocEnum", + "description": "The location of heat delivery within the room" + }, + "heat_sys_deliv_meth": { + "description": "The method by which the heat is delivered through the system", + "type": [ + "string", + "null" + ] + }, + "heat_system_id": { + "description": "The heating system identifier", + "type": [ + "string", + "null" + ] + }, + "height_carper_fiber": { + "description": "The average carpet fiber height in the indoor environment", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "indoor_space": { + "$ref": "#/$defs/IndoorSpaceEnum", + "description": "A distinguishable space within a structure, the purpose for which discrete areas of a building is used" + }, + "indoor_surf": { + "$ref": "#/$defs/IndoorSurfEnum", + "description": "Type of indoor surface" + }, + "inside_lux": { + "description": "The recorded value at sampling time (power density)", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "int_wall_cond": { + "$ref": "#/$defs/IntWallCondEnum", + "description": "The physical condition of the wall at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas" + }, + "last_clean": { + "description": "The last time the floor was cleaned (swept, mopped, vacuumed)", + "type": [ + "string", + "null" + ] + }, + "lat_lon": { + "description": "The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system", + "pattern": "^[-+]?([1-8]?\\d(\\.\\d{1,8})?|90(\\.0{1,8})?)\\s[-+]?(180(\\.0{1,8})?|((1[0-7]\\d)|([1-9]?\\d))(\\.\\d{1,8})?)$", + "type": "string" + }, + "light_type": { + "description": "Application of light to achieve some practical or aesthetic effect. Lighting includes the use of both artificial light sources such as lamps and light fixtures, as well as natural illumination by capturing daylight. Can also include absence of light", + "items": { + "$ref": "#/$defs/LightTypeEnum" + }, + "type": [ + "array", + "null" + ] + }, + "max_occup": { + "description": "The maximum amount of people allowed in the indoor environment", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "mech_struc": { + "$ref": "#/$defs/MechStrucEnum", + "description": "mechanical structure: a moving structure" + }, + "number_pets": { + "description": "The number of pets residing in the sampled space", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "number_plants": { + "description": "The number of plant(s) in the sampling space", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "number_resident": { + "description": "The number of individuals currently occupying in the sampling location", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "occup_density_samp": { + "description": "Average number of occupants at time of sampling per square footage", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "occup_document": { + "$ref": "#/$defs/OccupDocumentEnum", + "description": "The type of documentation of occupancy" + }, + "occup_samp": { + "description": "Number of occupants present at time of sample within the given space", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "organism_count": { + "description": "Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr)", + "pattern": "^([-+]?[0-9]*\\.?[0-9]+ +\\S.*\\|)*([-+]?[0-9]*\\.?[0-9]+ +\\S.*)$", + "type": [ + "string", + "null" + ] + }, + "pres_animal_insect": { + "description": "The type and number of animals or insects present in the sampling space.", + "pattern": "^(cat|dog|rodent|snake|other);\\d+$", + "type": [ + "string", + "null" + ] + }, + "quad_pos": { + "$ref": "#/$defs/QuadPosEnum", + "description": "The quadrant position of the sampling room within the building" + }, + "rel_air_humidity": { + "description": "Partial vapor and air pressure, density of the vapor and air, or by the actual mass of the vapor and air", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "rel_humidity_out": { + "description": "The recorded outside relative humidity value at the time of sampling", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "rel_samp_loc": { + "$ref": "#/$defs/RelSampLocEnum", + "description": "The sampling location within the train car" + }, + "room_air_exch_rate": { + "description": "The rate at which outside air replaces indoor air in a given space", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "room_architec_elem": { + "description": "The unique details and component parts that, together, form the architecture of a distinguisahable space within a built structure", + "type": [ + "string", + "null" + ] + }, + "room_condt": { + "$ref": "#/$defs/RoomCondtEnum", + "description": "The condition of the room at the time of sampling" + }, + "room_connected": { + "$ref": "#/$defs/RoomConnectedEnum", + "description": "List of rooms connected to the sampling room by a doorway" + }, + "room_count": { + "description": "The total count of rooms in the built structure including all room types", + "type": [ + "string", + "null" + ] + }, + "room_dim": { + "description": "The length, width and height of sampling room", + "type": [ + "string", + "null" + ] + }, + "room_door_dist": { + "description": "Distance between doors (meters) in the hallway between the sampling room and adjacent rooms", + "type": [ + "string", + "null" + ] + }, + "room_door_share": { + "description": "List of room(s) (room number, room name) sharing a door with the sampling room", + "type": [ + "string", + "null" + ] + }, + "room_hallway": { + "description": "List of room(s) (room number, room name) located in the same hallway as sampling room", + "type": [ + "string", + "null" + ] + }, + "room_loc": { + "$ref": "#/$defs/RoomLocEnum", + "description": "The position of the room within the building" + }, + "room_moist_dam_hist": { + "description": "The history of moisture damage or mold in the past 12 months. Number of events of moisture damage or mold observed", + "type": [ + "integer", + "null" + ] + }, + "room_net_area": { + "description": "The net floor area of sampling room. Net area excludes wall thicknesses", + "type": [ + "string", + "null" + ] + }, + "room_occup": { + "description": "Count of room occupancy at time of sampling", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "room_samp_pos": { + "$ref": "#/$defs/RoomSampPosEnum", + "description": "The horizontal sampling position in the room relative to architectural elements" + }, + "room_type": { + "$ref": "#/$defs/RoomTypeEnum", + "description": "The main purpose or activity of the sampling room. A room is any distinguishable space within a structure" + }, + "room_vol": { + "description": "Volume of sampling room", + "type": [ + "string", + "null" + ] + }, + "room_wall_share": { + "description": "List of room(s) (room number, room name) sharing a wall with the sampling room", + "type": [ + "string", + "null" + ] + }, + "room_window_count": { + "description": "Number of windows in the room", + "type": [ + "integer", + "null" + ] + }, + "samp_floor": { + "$ref": "#/$defs/SampFloorEnum", + "description": "The floor of the building, where the sampling room is located" + }, + "samp_name": { + "description": "A local identifier or name that for the material sample collected. Refers to the original material collected or to any derived sub-samples.", + "type": "string" + }, + "samp_room_id": { + "description": "Sampling room number. This ID should be consistent with the designations on the building floor plans", + "type": [ + "string", + "null" + ] + }, + "samp_sort_meth": { + "description": "Method by which samples are sorted; open face filter collecting total suspended particles, prefilter to remove particles larger than X micrometers in diameter, where common values of X would be 10 and 2.5 full size sorting in a cascade impactor.", + "type": [ + "string", + "null" + ] + }, + "samp_time_out": { + "description": "The recent and long term history of outside sampling", + "type": [ + "string", + "null" + ] + }, + "samp_weather": { + "$ref": "#/$defs/SampWeatherEnum", + "description": "The weather on the sampling day" + }, + "sample_link": { + "description": "A unique identifier to assign parent-child, subsample, or sibling samples. This is relevant when a sample or other material was used to generate the new sample.", + "pattern": "[^\\:\\n\\r]+\\:[^\\:\\n\\r]+", + "type": [ + "string", + "null" + ] + }, + "season": { + "description": "The season when sampling occurred. Any of the four periods into which the year is divided by the equinoxes and solstices. This field accepts terms listed under season (http://purl.obolibrary.org/obo/NCIT_C94729).", + "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$", + "type": [ + "string", + "null" + ] + }, + "season_use": { + "$ref": "#/$defs/SeasonUseEnum", + "description": "The seasons the space is occupied" + }, + "shad_dev_water_mold": { + "description": "Signs of the presence of mold or mildew on the shading device", + "type": [ + "string", + "null" + ] + }, + "shading_device_cond": { + "$ref": "#/$defs/ShadingDeviceCondEnum", + "description": "The physical condition of the shading device at the time of sampling" + }, + "shading_device_loc": { + "description": "The location of the shading device in relation to the built structure", + "type": [ + "string", + "null" + ] + }, + "shading_device_mat": { + "description": "The material the shading device is composed of", + "type": [ + "string", + "null" + ] + }, + "shading_device_type": { + "$ref": "#/$defs/ShadingDeviceTypeEnum", + "description": "The type of shading device" + }, + "size_frac": { + "description": "Filtering pore size used in sample preparation", + "type": [ + "string", + "null" + ] + }, + "source_mat_id": { + "description": "A globally unique identifier assigned to the biological sample.", + "pattern": "[^\\:\\n\\r]+\\:[^\\:\\n\\r]+", + "type": [ + "string", + "null" + ] + }, + "space_typ_state": { + "description": "Customary or normal state of the space", + "type": [ + "string", + "null" + ] + }, + "specific": { + "$ref": "#/$defs/SpecificEnum", + "description": "The building specifications. If design is chosen, indicate phase: conceptual, schematic, design development, construction documents" + }, + "specific_ecosystem": { + "$ref": "#/$defs/SpecificEcosystemEnum", + "description": "Specific ecosystems represent specific features of the environment like aphotic zone in an ocean or gastric mucosa within a host digestive system. Specific ecosystem is in position 5/5 in a GOLD path." + }, + "specific_humidity": { + "description": "The mass of water vapour in a unit mass of moist air, usually expressed as grams of vapour per kilogram of air, or, in air conditioning, as grains per pound.", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "substructure_type": { + "description": "The substructure or under building is that largely hidden section of the building which is built off the foundations to the ground floor level", + "items": { + "$ref": "#/$defs/SubstructureTypeEnum" + }, + "type": [ + "array", + "null" + ] + }, + "surf_air_cont": { + "description": "Contaminant identified on surface", + "items": { + "$ref": "#/$defs/SurfAirContEnum" + }, + "type": [ + "array", + "null" + ] + }, + "surf_humidity": { + "description": "Surfaces: water activity as a function of air and material moisture", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "surf_material": { + "$ref": "#/$defs/SurfMaterialEnum", + "description": "Surface materials at the point of sampling" + }, + "surf_moisture": { + "description": "Water held on a surface", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "surf_moisture_ph": { + "description": "ph measurement of surface", + "type": [ + "number", + "null" + ] + }, + "surf_temp": { + "description": "Temperature of the surface at the time of sampling", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "temp": { + "description": "Temperature of the sample at the time of sampling.", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "temp_out": { + "description": "The recorded temperature value at sampling time outside", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "train_line": { + "$ref": "#/$defs/TrainLineEnum", + "description": "The subway line name" + }, + "train_stat_loc": { + "$ref": "#/$defs/TrainStatLocEnum", + "description": "The train station collection location" + }, + "train_stop_loc": { + "$ref": "#/$defs/TrainStopLocEnum", + "description": "The train stop collection location" + }, + "typ_occup_density": { + "description": "Customary or normal density of occupants", + "type": [ + "number", + "null" + ] + }, + "ventilation_type": { + "description": "Ventilation system used in the sampled premises", + "type": [ + "string", + "null" + ] + }, + "vis_media": { + "$ref": "#/$defs/VisMediaEnum", + "description": "The building visual media" + }, + "wall_area": { + "description": "The total area of the sampled room's walls", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "wall_const_type": { + "$ref": "#/$defs/WallConstTypeEnum", + "description": "The building class of the wall defined by the composition of the building elements and fire-resistance rating." + }, + "wall_finish_mat": { + "$ref": "#/$defs/WallFinishMatEnum", + "description": "The material utilized to finish the outer most layer of the wall" + }, + "wall_height": { + "description": "The average height of the walls in the sampled room", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "wall_loc": { + "$ref": "#/$defs/WallLocEnum", + "description": "The relative location of the wall within the room" + }, + "wall_surf_treatment": { + "$ref": "#/$defs/WallSurfTreatmentEnum", + "description": "The surface treatment of interior wall" + }, + "wall_texture": { + "$ref": "#/$defs/WallTextureEnum", + "description": "The feel, appearance, or consistency of a wall surface" + }, + "wall_thermal_mass": { + "description": "The ability of the wall to provide inertia against temperature fluctuations. Generally this means concrete or concrete block that is either exposed or covered only with paint", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "wall_water_mold": { + "description": "Signs of the presence of mold or mildew on a wall", + "type": [ + "string", + "null" + ] + }, + "water_feat_size": { + "description": "The size of the water feature", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "water_feat_type": { + "$ref": "#/$defs/WaterFeatTypeEnum", + "description": "The type of water feature present within the building being sampled" + }, + "weekday": { + "$ref": "#/$defs/WeekdayEnum", + "description": "The day of the week when sampling occurred" + }, + "window_cond": { + "$ref": "#/$defs/WindowCondEnum", + "description": "The physical condition of the window at the time of sampling" + }, + "window_cover": { + "$ref": "#/$defs/WindowCoverEnum", + "description": "The type of window covering" + }, + "window_horiz_pos": { + "$ref": "#/$defs/WindowHorizPosEnum", + "description": "The horizontal position of the window on the wall" + }, + "window_loc": { + "$ref": "#/$defs/WindowLocEnum", + "description": "The relative location of the window within the room" + }, + "window_mat": { + "$ref": "#/$defs/WindowMatEnum", + "description": "The type of material used to finish a window" + }, + "window_open_freq": { + "description": "The number of times windows are opened per week", + "type": [ + "string", + "null" + ] + }, + "window_size": { + "description": "The window's length and width", + "type": [ + "string", + "null" + ] + }, + "window_status": { + "description": "Defines whether the windows were open or closed during environmental testing", + "type": [ + "string", + "null" + ] + }, + "window_type": { + "$ref": "#/$defs/WindowTypeEnum", + "description": "The type of windows" + }, + "window_vert_pos": { + "$ref": "#/$defs/WindowVertPosEnum", + "description": "The vertical position of the window on the wall" + }, + "window_water_mold": { + "description": "Signs of the presence of mold or mildew on the window.", + "type": [ + "string", + "null" + ] + } + }, + "required": [ + "collection_date", + "elev", + "env_broad_scale", + "env_local_scale", + "env_medium", + "geo_loc_name", + "lat_lon", + "analysis_type", + "samp_name" + ], + "title": "BuiltEnvInterface", + "type": "object" + }, + "CeilCondEnum": { + "description": "", + "enum": [ + "new", + "visible wear", + "needs repair", + "damaged", + "rupture" + ], + "title": "CeilCondEnum", + "type": "string" + }, + "CeilFinishMatEnum": { + "description": "", + "enum": [ + "drywall", + "mineral fibre", + "tiles", + "PVC", + "plasterboard", + "metal", + "fiberglass", + "stucco", + "mineral wool/calcium silicate", + "wood" + ], + "title": "CeilFinishMatEnum", + "type": "string" + }, + "CeilTextureEnum": { + "description": "", + "enum": [ + "crows feet", + "crows-foot stomp", + "double skip", + "hawk and trowel", + "knockdown", + "popcorn", + "orange peel", + "rosebud stomp", + "Santa-Fe texture", + "skip trowel", + "smooth", + "stomp knockdown", + "swirl" + ], + "title": "CeilTextureEnum", + "type": "string" + }, + "CeilTypeEnum": { + "description": "", + "enum": [ + "cathedral", + "dropped", + "concave", + "barrel-shaped", + "coffered", + "cove", + "stretched" + ], + "title": "CeilTypeEnum", + "type": "string" + }, + "CurLandUseEnum": { + "description": "", + "enum": [ + "badlands", + "cities", + "conifers", + "crop trees", + "farmstead", + "gravel", + "hardwoods", + "hayland", + "horticultural plants", + "industrial areas", + "intermixed hardwood and conifers", + "marshlands", + "meadows", + "mines/quarries", + "mudflats", + "oil waste areas", + "pastureland", + "permanent snow or ice", + "rainforest", + "rangeland", + "roads/railroads", + "rock", + "row crops", + "saline seeps", + "salt flats", + "sand", + "shrub crops", + "shrub land", + "small grains", + "successional shrub land", + "swamp", + "tropical", + "tundra", + "vegetable crops", + "vine crops" + ], + "title": "CurLandUseEnum", + "type": "string" + }, + "DNASampleFormatEnum": { + "description": "", + "enum": [ + "10 mM Tris-HCl", + "DNAStable", + "Ethanol", + "Low EDTA TE", + "MDA reaction buffer", + "PBS", + "Pellet", + "RNAStable", + "TE", + "Water", + "Gentegra-DNA", + "Gentegra-RNA" + ], + "title": "DNASampleFormatEnum", + "type": "string" + }, + "DeposEnvEnum": { + "description": "", + "enum": [ + "Continental - Alluvial", + "Continental - Aeolian", + "Continental - Fluvial", + "Continental - Lacustrine", + "Transitional - Deltaic", + "Transitional - Tidal", + "Transitional - Lagoonal", + "Transitional - Beach", + "Transitional - Lake", + "Marine - Shallow", + "Marine - Deep", + "Marine - Reef", + "Other - Evaporite", + "Other - Glacial", + "Other - Volcanic", + "other" + ], + "title": "DeposEnvEnum", + "type": "string" + }, + "DhInterface": { + "additionalProperties": false, + "description": "One DataHarmonizer interface, for the specified combination of a checklist, enviornmental_package, and various standards, user facilities or analysis types", + "title": "DhInterface", + "type": "object" + }, + "DnaSampleFormatEnum": { + "description": "", + "enum": [ + "10 mM Tris-HCl", + "DNAStable", + "Ethanol", + "Low EDTA TE", + "MDA reaction buffer", + "PBS", + "Pellet", + "RNAStable", + "TE", + "Water" + ], + "title": "DnaSampleFormatEnum", + "type": "string" + }, + "DoorCompTypeEnum": { + "description": "", + "enum": [ + "metal covered", + "revolving", + "sliding", + "telescopic" + ], + "title": "DoorCompTypeEnum", + "type": "string" + }, + "DoorCondEnum": { + "description": "", + "enum": [ + "damaged", + "needs repair", + "new", + "rupture", + "visible wear" + ], + "title": "DoorCondEnum", + "type": "string" + }, + "DoorDirectEnum": { + "description": "", + "enum": [ + "inward", + "outward", + "sideways" + ], + "title": "DoorDirectEnum", + "type": "string" + }, + "DoorLocEnum": { + "description": "", + "enum": [ + "north", + "south", + "east", + "west" + ], + "title": "DoorLocEnum", + "type": "string" + }, + "DoorMatEnum": { + "description": "", + "enum": [ + "aluminum", + "cellular PVC", + "engineered plastic", + "fiberboard", + "fiberglass", + "metal", + "thermoplastic alloy", + "vinyl", + "wood", + "wood/plastic composite" + ], + "title": "DoorMatEnum", + "type": "string" + }, + "DoorMoveEnum": { + "description": "", + "enum": [ + "collapsible", + "folding", + "revolving", + "rolling shutter", + "sliding", + "swinging" + ], + "title": "DoorMoveEnum", + "type": "string" + }, + "DoorTypeEnum": { + "description": "", + "enum": [ + "composite", + "metal", + "wooden" + ], + "title": "DoorTypeEnum", + "type": "string" + }, + "DoorTypeMetalEnum": { + "description": "", + "enum": [ + "collapsible", + "corrugated steel", + "hollow", + "rolling shutters", + "steel plate" + ], + "title": "DoorTypeMetalEnum", + "type": "string" + }, + "DoorTypeWoodEnum": { + "description": "", + "enum": [ + "bettened and ledged", + "battened", + "ledged and braced", + "ledged and framed", + "ledged, braced and frame", + "framed and paneled", + "glashed or sash", + "flush", + "louvered", + "wire gauged" + ], + "title": "DoorTypeWoodEnum", + "type": "string" + }, + "DrainageClassEnum": { + "description": "", + "enum": [ + "very poorly", + "poorly", + "somewhat poorly", + "moderately well", + "well", + "excessively drained" + ], + "title": "DrainageClassEnum", + "type": "string" + }, + "DrawingsEnum": { + "description": "", + "enum": [ + "operation", + "as built", + "construction", + "bid", + "design", + "building navigation map", + "diagram", + "sketch" + ], + "title": "DrawingsEnum", + "type": "string" + }, + "EcosystemCategoryEnum": { + "description": "", + "enum": [ + "Air", + "Algae", + "Amoebozoa", + "Amphibia", + "Animal feed production", + "Annelida", + "Aquatic", + "Arthropoda: Chelicerates", + "Arthropoda: Crustaceans", + "Arthropoda: Insects", + "Arthropoda: Myriapoda", + "Artificial ecosystem", + "Bioreactor", + "Bioremediation", + "Biotransformation", + "Birds", + "Bryozoa", + "Built environment", + "Cephalochordata", + "Cnidaria", + "Drugs production", + "Endosymbionts", + "Feedstock", + "Fish", + "Food production", + "Fungi", + "Industrial production", + "Invertebrates", + "Lab culture", + "Lab enrichment", + "Lab synthesis", + "Laboratory developed", + "Mammals", + "Mammals: Human", + "Microbial", + "Modeled", + "Mollusca", + "Paper", + "Plants", + "Porifera", + "Protists", + "Protozoa", + "Reptilia", + "Sewage treatment plant", + "Solid waste", + "Terrestrial", + "Tunicates", + "Unclassified", + "WWTP", + "Wastewater" + ], + "title": "EcosystemCategoryEnum", + "type": "string" + }, + "EcosystemCategoryForSoilEnum": { + "description": "", + "enum": [ + "Terrestrial" + ], + "title": "EcosystemCategoryForSoilEnum", + "type": "string" + }, + "EcosystemEnum": { + "description": "", + "enum": [ + "Engineered", + "Environmental", + "Host-associated" + ], + "title": "EcosystemEnum", + "type": "string" + }, + "EcosystemForSoilEnum": { + "description": "", + "enum": [ + "Environmental" + ], + "title": "EcosystemForSoilEnum", + "type": "string" + }, + "EcosystemSubtypeEnum": { + "description": "", + "enum": [ + "A/O bioreactor", + "AGS (Aerobic granular sludge)", + "Abdomen", + "Abdomen/Pleon", + "Abscess", + "Abyssopelagic", + "Accessory nidamental gland (ANG)", + "Acid lake", + "Acid mine drainage", + "Acidic", + "Acidic hypersaline lake", + "Acidic lake", + "Activated sludge", + "Adenoma", + "Adipose tissue", + "Aerial root", + "Aerobic", + "Aerobic media", + "Agricultural field", + "Agricultural land", + "Agricultural wastewater", + "Air", + "Air sacs", + "Air scrubber", + "Algae", + "Algae cultivation tank", + "Algae raceway pond", + "Alkaline", + "Alligator nest", + "Alpine", + "Amniotic sac", + "Anaerobic", + "Anaerobic media", + "Anaerobic-Aerobic", + "Anode", + "Antennal/Green glands", + "Anthosphere", + "Antlers", + "Apocrine sweat glands", + "Apoeccrine sweat glands", + "Aquaculture farm", + "Aquatic biofilm", + "Aquifer", + "Arable", + "Archaea", + "Archipelago", + "Arterial ulcer", + "Ascites", + "Atoll lagoon", + "Autotrophic (ANF)", + "Aviation fuel", + "BHK", + "Bacteria", + "Bark", + "Bathypelagic", + "Beef", + "Benign tumor tissue", + "Benthic", + "Benthic zone", + "Benzene", + "Biliary tract", + "Bioanode", + "Biocathode", + "Biochar", + "Biocrust", + "Biofilm", + "Biofouling", + "Biogas", + "Biological phosphorus removal", + "Biomass", + "Blade", + "Blood", + "Bog lake", + "Bone", + "Bones", + "Boreal forest/Taiga", + "Botanical garden", + "Brain", + "Bread", + "Bronchi", + "Buffer", + "Bulb", + "Bursa of Fabricius", + "CHO", + "CaSki", + "Canthus", + "Carcinoid", + "Carcinoma", + "Carposphere", + "Cartilage", + "Cathode", + "Cattle barn", + "Caulosphere", + "Cave", + "Ceca", + "Cephalothorax", + "Cerebrospinal fluid", + "Ceros", + "Ceruminous glands", + "Chaparral", + "Chelicerates nest", + "Chloroethene", + "Cholesteatoma", + "City park", + "Claws", + "Claws/Talon", + "Clay", + "Coalbed methane well", + "Coastal", + "Coastal area", + "Coastal lagoon", + "Cob", + "Cocoon", + "Cold seeps", + "Cold smoked fish", + "Composting", + "Composting facility", + "Conjunctiva", + "Contaminated", + "Contaminated soil", + "Continental margin", + "Cooked fish", + "Cooked meat", + "Cooling water", + "Coral", + "Cortex", + "Cosmetic products", + "Creek", + "Crop", + "Crude oil sludge", + "Crustaceans pond", + "Crustaceans raceway", + "Crustaceans tank", + "Cultivation substrate", + "Cuticle", + "Cyanide/thiocyanate", + "Dairy farm", + "Decayed wood", + "Decomposed body", + "Deep subsurface", + "Deepwater/Brine lake", + "Demersal zone", + "Dermoid", + "Desert", + "Desert springs", + "Diabetic foot ulcer (DFU)", + "Diaphragm", + "Digestate", + "Digestive system", + "Digestive tube", + "Dissolved organics (aerobic)", + "Dissolved organics (anaerobic)", + "Distilled water", + "Doormat", + "Drainage basin", + "Drainage ditch", + "Dried seaweeds", + "Drinking water", + "Drinking water filter", + "Drinking water pipeline", + "Dust", + "Ear", + "Eccrine sweat glands", + "Ectosymbionts", + "Effluent", + "Egg capsule", + "Eggs", + "Embryo", + "Endocrine gland", + "Endosphere", + "Endosymbionts", + "Epidermoid", + "Epipelagic", + "Epithelial lining fluid", + "Esophagus", + "Evaporite", + "External genitalia", + "External genitalia/Vulva", + "External organs", + "Eye", + "Eye: Ciliary body", + "Eye: Vitreous chamber", + "Fallopian tubes", + "Fascia", + "Feedlot", + "Fermentation", + "Fermented dairy products", + "Fermented fish", + "Fermented meat products", + "Fetal tissue", + "Fibroma", + "Filter", + "Fish pond", + "Fish tank", + "Fjord", + "Floodplain", + "Floodplain lake", + "Floor", + "Foregut", + "Forest", + "Fossil", + "Fossilized remains", + "Fracking water", + "Fresh manure", + "Freshwater", + "Freshwater RAS", + "Freshwater aquarium", + "Freshwater debries", + "Frozen remains", + "Frozen seafood", + "Fruit processing", + "Fumaroles", + "Fungi", + "Galls", + "Ganglion", + "Garden", + "Geothermal field", + "Geothermal pool/Hot lake", + "Germ cell tumor", + "Gill rakers", + "Gill/Bronchial chamber", + "Gills", + "Glacial till", + "Glacier", + "Glands", + "Gonopore", + "Gowning room", + "Granuloma", + "Grasslands", + "Gravesite", + "Greenhouse", + "Groundwater", + "Guano", + "Gulf", + "Gut", + "Gymnolaemates", + "HEK293", + "Hadalpelagic", + "Haemal node", + "Hair", + "Hair/Fur", + "Halite", + "Harbor", + "Hay", + "HeLa", + "Head", + "Head/Cephalon", + "Heart", + "Heart/Dorsal vessel", + "Hemolymph", + "Herpetarium", + "Heterotrophic (HNF)", + "Hindgut", + "Hoof", + "Horn", + "Hornworts", + "Hospital bedroom", + "Hospital wastewater", + "Hot (42-90C)", + "Hotel", + "HuSC", + "Hydroponic media", + "Hydrothermal vents", + "Hyperplastic/Inflammatory polyps", + "Hypersaline", + "Hypersaline lake", + "Hypersaline soda lake", + "Hypoxic zone", + "ICU", + "ISE6", + "Ice", + "Ice cream", + "Infraorbital sinus", + "Inlet", + "Inner ear", + "Inner tissue", + "Inoculum", + "Input fracking water", + "Insectarium", + "Insects nest", + "Interior wall", + "Interstitial water", + "Intertidal zone", + "Intestine", + "Intestine: Anterior", + "Intestine: Mid", + "Intrathoracic space", + "Intromittent organ", + "Irrigation canal", + "Jakobids", + "Joint capsule", + "Juice", + "Kettle hole", + "Kidney", + "Kidneys", + "Lab-grade water", + "Lacrimal apparatus", + "Lake", + "Lake water", + "Lakeshore", + "Landfill", + "Landfill leachate", + "Large intestine", + "Laurel/Subtropical forest", + "Leachate", + "Lentic", + "Leptosol", + "Ligament", + "Light organ", + "Lipoma", + "Litterfall", + "Littoral zone", + "Liverworts", + "Loam", + "Lotic", + "Lower gastrointestinal tract", + "Lung", + "Lymph duct", + "Lymph nodes", + "Lymphoid tissue", + "Lymphoma", + "Malignant tumor tissue", + "Malpighian tubules", + "Mammary gland", + "Mangrove soil", + "Mantle", + "Manure", + "Manure slurry", + "Manure-fertilized", + "Marginal Sea", + "Marine basin floor", + "Marine debries", + "Marine fish farm", + "Marine lake", + "Marine media", + "Marine sediment inoculum", + "Material", + "Maxillary glands", + "Meadow", + "Meat/Poultry processing plant", + "Meibomian glands", + "Melanoma", + "Mesopelagic", + "Metalworking fluids", + "Metasoma", + "Methane", + "Microbial mats", + "Microbialites", + "Middle ear", + "Midgut", + "Milk glands", + "Mine", + "Mine pit lake", + "Mine pit pond", + "Mine water", + "Mineral horizon", + "Mixed liquor", + "Mixed type", + "Mixotrophic (MNF)", + "Molluscs farm", + "Molluscs pond", + "Molluscs tank", + "Morphine", + "Moss", + "Mouse myeloma", + "Mouth", + "Mud", + "Mud volcano", + "Multiple organs", + "Mummified remains", + "Muscles", + "Myeloma", + "Myoma", + "Nails", + "Nasal cavity", + "Nature reserve", + "Near-boiling (>90C)", + "Necrotizing soft tissue infections (NSTI)", + "Nephridia", + "Neritic zone/Coastal water", + "Nevi/Moles", + "Nitrogen removal", + "No head", + "No thorax", + "Nodule", + "Oak savanna", + "Ocean trench", + "Oceanarium", + "Oceanic", + "Oil", + "Oil palm", + "Oil sands", + "Oil sands pit lake", + "Oil seeps", + "Oil well", + "Oil-contaminated sediment", + "Oil/Gas pipeline", + "Olfactory pit", + "Optical Instruments", + "Oral cavity", + "Oral/Buccal cavity", + "Orchard", + "Organic dairy farm", + "Organic layer", + "Osteoma", + "Outer ear", + "Ovaries", + "Ovicells", + "PCR blank control", + "Paddy field/soil", + "Palsa", + "Pancreas", + "Papillomas", + "Parabasalids", + "Paranasal sinuses", + "Park", + "Pasture", + "Peat", + "Pelagic zone", + "Periprosthetic joint", + "Periprosthetic joint: Hip", + "Periprosthetic joint: Knee", + "Peritoneal fluid", + "Peritoneum", + "Permafrost", + "Petiole", + "Petrochemical", + "Petroleum reservoir", + "Petroleum sludge", + "Peyer's patches", + "Pharyngeal glands", + "Pharynx", + "Pharynx/Throat", + "Photobioreactor (PBR)", + "Photophore", + "Phycosphere", + "Phylloplane/Leaf", + "Phylloplane/Leaf surface", + "Phytotelma", + "Pilomatrixoma", + "Pine litter on sand", + "Pit mud", + "Plant nodule", + "Pleural cavity", + "Pleural space/cavity", + "Polycyclic aromatic hydrocarbons", + "Polyps", + "Pond", + "Potting soil", + "Poultry farm", + "Poultry litter", + "Probiotics", + "Processed milk", + "Produced water", + "Proglacial area", + "Pronghorn", + "Prostate", + "Prothorax", + "Puddle", + "Pulp and paper wastewater", + "Pyloric ceca", + "Pyogenic granuloma", + "R2A agar", + "Radioactive waste", + "Rainwater", + "Ranch", + "Rat myeloma", + "Raw meat", + "Raw milk", + "Raw wastewater", + "Reagent blank", + "Reptile cage", + "Reservoir", + "Respiratory tract fluid", + "Rhizoplane", + "Rhizosphere", + "Rice straw", + "Riparian zone", + "River", + "River plume", + "River water", + "Riverside", + "Rock", + "Rock core/Sediment", + "Rodent burrow", + "Runoff channel", + "Saline", + "Saline lake", + "Salt crystallizer ponds", + "Salt flat/Salt pan", + "Salt marsh", + "Salt mine", + "Salt pan/flat", + "Salted fish", + "Sand", + "Sand filter", + "Sanger", + "Saprolite", + "Sarcoma", + "Scale", + "Scales", + "Sea Star", + "Sea Urchin", + "Sea cucumber", + "Sea ice", + "Seat surface", + "Seawater", + "Seawater RAS", + "Seawater aquarium", + "Seaweed", + "Sebaceous glands", + "Sediment", + "Seed radicle", + "Semen/Seminal fluid", + "Seminal glands", + "Settled granule", + "Settling tank", + "Shale gas reservoir", + "Shale gas/oil reservoir", + "Sheath fluid", + "Shell", + "Shipwreck", + "Shrimp pond", + "Shrubland", + "Silt", + "Simulated rainfall", + "Sink", + "Sinkhole", + "Skeletal muscle", + "Skeletonized remains", + "Skin", + "Skin tag", + "Sludge", + "Slums/Informal settlements", + "Small intestine", + "Smooth muscle", + "Smooth muscles", + "Snow", + "Soda lake", + "Soft tissue", + "Soft tissues", + "Soil", + "Soil crust", + "Solar salt", + "Solar solterns", + "Soy sauce", + "Soybean paste", + "Spacecraft", + "Spat", + "Spent mushroom substrate", + "Spermathecae", + "Spinal cord", + "Spiracles", + "Spleen", + "Sporeling", + "Sputum/Phlegm", + "Stadium", + "Stem", + "Stem tuber", + "Sterile water", + "Stomach", + "Stone", + "Storm water", + "Strait", + "Sub-biocrust", + "Sub-saline lake", + "Sub-seafloor", + "Subarachnoid space", + "Subcuticular space", + "Subglacial lake", + "Subterranean lake", + "Subtidal zone", + "Subway", + "Supratidal zone", + "Surface", + "Surface biofilm", + "Surface mine", + "Swine waste with corn", + "Tailings", + "Tailings pond", + "Tap water", + "Taproot", + "Tar", + "Temperate forest", + "Tendons", + "Tepid (25-34C)", + "Terrarium", + "Tertiary lymphoid organ", + "Testes", + "Tetrachloroethylene", + "Thermophilic digester", + "Thorax", + "Thorax/Pereon", + "Tissue", + "Tobacco product", + "Tonsils", + "Trachea", + "Transient pool", + "Tree plantation", + "Trophosome", + "Tropical forest", + "Tundra", + "Unclassified", + "Unspecified organ", + "Urban forest", + "Ureter", + "Urethra", + "Urinary bladder", + "Urine", + "Uropygial/Preen gland", + "Uterus", + "Vaccine", + "Vadose zone", + "Vagina", + "Vas deferens", + "Venous ulcer", + "Verrucas", + "Vinegar", + "Volcanic", + "Wall", + "Warm (34-42C)", + "Wart", + "Wastewater", + "Wastewater effluent", + "Water", + "Water tank", + "Water well", + "Watershed", + "Wetland sediment", + "Wetland-upland transition", + "Wetlands", + "Wetsalted hide", + "Whole body", + "Wood chips", + "Woodchip Bioreactor (WBR)", + "Xylene" + ], + "title": "EcosystemSubtypeEnum", + "type": "string" + }, + "EcosystemSubtypeForSoilEnum": { + "description": "", + "enum": [ + "Agricultural land", + "Alpine", + "Arable", + "Biochar", + "Biocrust", + "Biofilm", + "Boreal forest/Taiga", + "Botanical garden", + "Chaparral", + "City park", + "Clay", + "Coastal area", + "Contaminated", + "Desert", + "Drainage basin", + "Floodplain", + "Forest", + "Fossil", + "Garden", + "Geothermal field", + "Glacial till", + "Glacier", + "Grasslands", + "Gravesite", + "Greenhouse", + "Intertidal zone", + "Lakeshore", + "Landfill", + "Laurel/Subtropical forest", + "Leptosol", + "Loam", + "Mangrove soil", + "Manure-fertilized", + "Meadow", + "Mineral horizon", + "Mud", + "Nature reserve", + "Oak savanna", + "Orchard", + "Organic layer", + "Paddy field/soil", + "Palsa", + "Pasture", + "Peat", + "Permafrost", + "Potting soil", + "Proglacial area", + "Ranch", + "Riparian zone", + "Riverside", + "Salt flat/Salt pan", + "Sand", + "Shrubland", + "Silt", + "Soil crust", + "Sub-biocrust", + "Surface mine", + "Tailings", + "Temperate forest", + "Tree plantation", + "Tropical forest", + "Tundra", + "Unclassified", + "Urban forest", + "Vadose zone", + "Watershed", + "Wetland-upland transition", + "Wetlands" + ], + "title": "EcosystemSubtypeForSoilEnum", + "type": "string" + }, + "EcosystemTypeEnum": { + "description": "", + "enum": [ + "A/O treatment system", + "Abdomen", + "Abdominal cavity", + "Abdominal/Peritoneal cavity", + "Acidic", + "Activated Sludge", + "Activated sludge", + "Aerobic", + "Aerobic digester", + "Agricultural field", + "Agricultural waste", + "Amoebozoa", + "Anaerobic", + "Anaerobic digester", + "Anaerobic digestor", + "Animal cage", + "Animal waste", + "Appressorium", + "Aquaculture", + "Artesian spring", + "Ascidians", + "Asphalt lakes", + "Auditory/Hearing system", + "Baby formula", + "Bacteria", + "Bacterivore", + "Bagasse", + "Beans", + "Benign tumor", + "Beverages", + "Bio- and green waste (BGW)", + "Biochar", + "Biocrust", + "Bivalves", + "Bread production", + "Breviatea", + "Brown Algae", + "Brown waste", + "Bryophytes", + "Bryozoans", + "Building", + "Canal", + "Cave", + "Cell Line", + "Cell culture", + "Cellulose associated waste", + "Cement wall", + "Chemical products", + "Circulatory system", + "City", + "Cnidaria", + "Coal", + "Composting", + "Connective tissue", + "Continuous culture", + "Cryptomonads/Cryptophytes", + "Ctenophora", + "Culture media", + "Currency notes", + "DHS reactor", + "Dairy processing facility", + "Dairy products", + "Debries", + "Deep subsurface", + "Defined media", + "Denitrification", + "Desert", + "Diatoms", + "Digestive system", + "Dinoflagellata", + "Dinoflagellates", + "Drinking water treatment plant", + "Drugs/Supplements", + "EBPR", + "Echinodermata", + "Effluent", + "Egg products", + "Embryo", + "Endocrine system", + "Endosphere", + "Engineered product", + "Equipment/Utensils", + "Excavata", + "Excretory system", + "Fat body", + "Feedstock", + "Fermentation", + "Fermentation cellar", + "Fermentation pit", + "Fermentation starter", + "Fermented beverages", + "Fermented food", + "Fermented seafood", + "Fermented vegetables", + "Fetus", + "Fish products", + "Floodplain", + "Food sample", + "Food waste", + "Freshwater", + "Fruiting body", + "Fungi", + "Genetic cross", + "Genetically modified", + "Geologic", + "Germ tube", + "Gills", + "Golden Algae", + "Grains/Grain products", + "Grass", + "Green algae", + "Green waste", + "Haptophytes", + "Head", + "High-salinity/high-pH", + "Hospital", + "House", + "Household waste", + "Human waste", + "Hydrocarbon", + "Indoor Air", + "Industrial waste", + "Industrial wastewater", + "Influent", + "Integument", + "Integumentary system", + "International Space Station", + "Intracellular endosymbionts", + "Landfill", + "Larva", + "Larva: Nauplius", + "Larva: Zoea", + "Larvae", + "Latrine chamber", + "Legs and wings", + "Lichen", + "Lymphatic system", + "MBR (Membrane bioreactor)", + "Malignant tumor", + "Marine", + "Meat products", + "Mesocosm", + "Metal", + "Microalgae", + "Microbial enhanced oil recovery", + "Microbial fuel cells/MFC", + "Microbial solubilization of coal", + "Microcosm", + "Mine", + "Mixed alcohol bioreactor", + "Mixed algae turf", + "Mixed feedstock", + "Mixed liquor", + "Mixed parts", + "Monument", + "Mud microcosm", + "Mud volcano", + "Multiple systems", + "Multisystem conditions", + "Municipal landfill", + "Muscular system", + "Mushroom farm", + "Mycelium", + "Mycorrhiza", + "Nanoflagellates", + "Nematoda", + "Nervous system", + "Nest", + "Nodule", + "Non-marine Saline and Alkaline", + "Nuclear test reactor", + "Nutrient removal", + "Nutrient-poor", + "Nutrient-rich", + "Nuts", + "Nymph/Instar", + "Oil refinery", + "Oil reservoir", + "Olfactory system", + "Oomycetes", + "Ootheca/Egg mass", + "Outdoor Air", + "Oxymonads", + "Oyster", + "Pastry", + "Peat moss", + "Percolator", + "Persistent organic pollutants (POP)", + "Pessonella", + "Photobioreactor (PBR)", + "Phyllosphere", + "Pipeline", + "Pit lake", + "Pitcher", + "Plant callus", + "Plant growth chamber", + "Plant litter", + "Plant products", + "Plastic waste", + "Platyhelminthes", + "Post-larva", + "Poultry confinement building", + "Prepupa", + "Pupa", + "Reclaimed/Recycled wastewater", + "Red algae", + "Remains", + "Reproductive system", + "Respiratory system", + "Rhizoid", + "Rhizome", + "River", + "Rock-dwelling (endoliths)", + "Rock-dwelling (subaerial biofilms)", + "Roots", + "SBR-EBPR", + "SSF (Solid state fermentation)", + "Salt", + "Sand microcosm", + "Saprolite\u2013Bedrock interface", + "Sargassum", + "Sclerotium", + "Seafood", + "Seafood product", + "Seawater microcosm", + "Sediment", + "Sediment microcosm", + "Seeds", + "Semi-continuous", + "Sensory organs", + "Sewage", + "Shell", + "Silage fermentation", + "Simulated communities (DNA mixture)", + "Simulated communities (contig mixture)", + "Simulated communities (microbial mixture)", + "Simulated communities (sequence read mixture)", + "Skeletal system", + "Slaughterhouse/Abattoir", + "Sludge", + "Soil", + "Soil microcosm", + "Soil-bedrock interface", + "Solar panel", + "Sourdough", + "Spacecraft Assembly Cleanrooms", + "Spices", + "Sponge", + "Spore", + "Sporozoa", + "Stroma", + "Subsurface", + "Sulphur Autotrophic Denitrification", + "Sweets", + "Swim bladder", + "Swimming pool", + "Swine confinement building", + "Tailings pond", + "Terephthalate", + "Tetrachloroethylene and derivatives", + "Thermal springs", + "Thiocyanate", + "Thiocyanate-remediating", + "Thoracic cavity", + "Thorax", + "Tissue", + "Train car", + "Tumor", + "UASB (Upflow anaerobic sludge blanket)", + "Unclassified", + "Undefined media", + "Unknown material", + "Unspecified system", + "Urban waste", + "Urban wastewater", + "Urinary system", + "Vegetable", + "Vermicompost", + "Visual system", + "Vivarium", + "Volcanic", + "Wastewater", + "Water microcosm", + "Water treatment plant", + "Whole body", + "Whole plant body", + "Wood", + "Yellow-green algae", + "Zoo waste" + ], + "title": "EcosystemTypeEnum", + "type": "string" + }, + "EcosystemTypeForSoilEnum": { + "description": "", + "enum": [ + "Soil" + ], + "title": "EcosystemTypeForSoilEnum", + "type": "string" + }, + "EmslInterface": { + "additionalProperties": false, + "description": "emsl dh_interface", + "properties": { + "analysis_type": { + "description": "Select all the data types associated or available for this biosample", + "items": { + "$ref": "#/$defs/AnalysisTypeEnum" + }, + "type": "array" + }, + "emsl_store_temp": { + "description": "The temperature at which the sample should be stored upon delivery to EMSL", + "type": "number" + }, + "project_id": { + "description": "Proposal IDs or names associated with dataset", + "type": "string" + }, + "replicate_number": { + "description": "If sending biological replicates, indicate the rep number here.", + "type": [ + "integer", + "null" + ] + }, + "samp_name": { + "description": "A local identifier or name that for the material sample collected. Refers to the original material collected or to any derived sub-samples.", + "type": "string" + }, + "sample_shipped": { + "description": "The total amount or size (volume (ml), mass (g) or area (m2) ) of sample sent to EMSL.", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? \\S+$", + "type": "string" + }, + "sample_type": { + "$ref": "#/$defs/SampleTypeEnum", + "description": "Type of sample being submitted" + }, + "source_mat_id": { + "description": "A globally unique identifier assigned to the biological sample.", + "pattern": "[^\\:\\n\\r]+\\:[^\\:\\n\\r]+", + "type": [ + "string", + "null" + ] + }, + "technical_reps": { + "description": "If sending technical replicates of the same sample, indicate the replicate count.", + "type": [ + "integer", + "null" + ] + } + }, + "required": [ + "emsl_store_temp", + "project_id", + "sample_shipped", + "sample_type", + "analysis_type", + "samp_name" + ], + "title": "EmslInterface", + "type": "object" + }, + "EnvBroadScaleSoilEnum": { + "description": "", + "enum": [ + "alpine tundra biome [ENVO:01001505]", + "anthropogenic terrestrial biome [ENVO:01000219]", + "broadleaf forest biome [ENVO:01000197]", + "coniferous forest biome [ENVO:01000196]", + "cropland biome [ENVO:01000245]", + "flooded grassland biome [ENVO:01000195]", + "flooded savanna biome [ENVO:01000190]", + "forest biome [ENVO:01000174]", + "grassland biome [ENVO:01000177]", + "mangrove biome [ENVO:01000181]", + "mediterranean forest biome [ENVO:01000199]", + "mediterranean grassland biome [ENVO:01000224]", + "mediterranean savanna biome [ENVO:01000229]", + "mediterranean shrubland biome [ENVO:01000217]", + "mediterranean woodland biome [ENVO:01000208]", + "mixed forest biome [ENVO:01000198]", + "montane grassland biome [ENVO:01000194]", + "montane savanna biome [ENVO:01000223]", + "montane shrubland biome [ENVO:01000216]", + "rangeland biome [ENVO:01000247]", + "savanna biome [ENVO:01000178]", + "shrubland biome [ENVO:01000176]", + "subpolar coniferous forest biome [ENVO:01000250]", + "subtropical broadleaf forest biome [ENVO:01000201]", + "subtropical coniferous forest biome [ENVO:01000209]", + "subtropical dry broadleaf forest biome [ENVO:01000225]", + "subtropical grassland biome [ENVO:01000191]", + "subtropical moist broadleaf forest biome [ENVO:01000226]", + "subtropical savanna biome [ENVO:01000187]", + "subtropical shrubland biome [ENVO:01000213]", + "subtropical woodland biome [ENVO:01000222]", + "temperate broadleaf forest biome [ENVO:01000202]", + "temperate coniferous forest biome [ENVO:01000211]", + "temperate grassland biome [ENVO:01000193]", + "temperate mixed forest biome [ENVO:01000212]", + "temperate savanna biome [ENVO:01000189]", + "temperate shrubland biome [ENVO:01000215]", + "temperate woodland biome [ENVO:01000221]", + "terrestrial biome [ENVO:00000446]", + "tidal mangrove shrubland [ENVO:01001369]", + "tropical broadleaf forest biome [ENVO:01000200]", + "tropical coniferous forest biome [ENVO:01000210]", + "tropical dry broadleaf forest biome [ENVO:01000227]", + "tropical grassland biome [ENVO:01000192]", + "tropical mixed forest biome [ENVO:01001798]", + "tropical moist broadleaf forest biome [ENVO:01000228]", + "tropical savanna biome [ENVO:01000188]", + "tropical shrubland biome [ENVO:01000214]", + "tropical woodland biome [ENVO:01000220]", + "tundra biome [ENVO:01000180]", + "woodland biome [ENVO:01000175]", + "xeric shrubland biome [ENVO:01000218]" + ], + "title": "EnvBroadScaleSoilEnum", + "type": "string" + }, + "EnvLocalScaleSoilEnum": { + "description": "", + "enum": [ + "active permafrost layer [ENVO:04000009]", + "alas [ENVO:00000438]", + "badland [ENVO:00000127]", + "beach [ENVO:00000091]", + "butte [ENVO:00000287]", + "caldera [ENVO:00000096]", + "campground [ENVO:01000935]", + "canyon [ENVO:00000169]", + "cave [ENVO:00000067]", + "channel [ENVO:03000117]", + "cirque [ENVO:00000155]", + "cliff [ENVO:00000087]", + "crater [ENVO:00000514]", + "crevasse [ENVO:00000320]", + "cryosphere [ENVO:03000143]", + "dam [ENVO:00000074]", + "desert [ENVO:01001357]", + "drainage basin [ENVO:00000291]", + "drumlin [ENVO:00000276]", + "dry lake [ENVO:00000277]", + "dune [ENVO:00000170]", + "endorheic basin [ENVO:00000551]", + "escarpment [ENVO:00000280]", + "esker [ENVO:00000282]", + "farm [ENVO:00000078]", + "fen [ENVO:00000232]", + "fjord [ENVO:00000039]", + "flood plain [ENVO:00000255]", + "frost heave [ENVO:01001568]", + "fumarole [ENVO:00000216]", + "garden [ENVO:00000011]", + "glacier [ENVO:00000133]", + "greenhouse [ENVO:03600087]", + "harbour [ENVO:00000463]", + "hill [ENVO:00000083]", + "hummock [ENVO:00000516]", + "isthmus [ENVO:00000174]", + "kame [ENVO:00000542]", + "karst [ENVO:00000175]", + "kipuka [ENVO:00000410]", + "landfill [ENVO:00000533]", + "machair [ENVO:00000417]", + "marsh [ENVO:00000035]", + "meadow ecosystem [ENVO:00000108]", + "mesa [ENVO:00000179]", + "mine [ENVO:00000076]", + "mine drainage [ENVO:00001996]", + "monadnock [ENVO:00000432]", + "moraine [ENVO:00000177]", + "mountain [ENVO:00000081]", + "nunatak [ENVO:00000181]", + "oil spill [ENVO:00002061]", + "palsa [ENVO:00000489]", + "park [ENVO:00000562]", + "pasture [ENVO:00000266]", + "peatland [ENVO:00000044]", + "pit [ENVO:01001871]", + "plain [ENVO:00000086]", + "plateau [ENVO:00000182]", + "polje [ENVO:00000325]", + "prairie [ENVO:00000260]", + "quarry [ENVO:00000284]", + "ranch [ENVO:01001207]", + "ravine [ENVO:01000446]", + "refinery [ENVO:02000141]", + "rhizosphere [ENVO:00005801]", + "ria [ENVO:00000418]", + "ridge [ENVO:00000283]", + "rill [ENVO:00000496]", + "river [ENVO:00000022]", + "riverfront [ENVO:03501239]", + "road [ENVO:00000064]", + "scrubland area [ENVO:00000300]", + "shingle beach [ENVO:00000545]", + "shore [ENVO:00000304]", + "sinkhole [ENVO:00000195]", + "slope [ENVO:00002000]", + "soil cryoturbate [ENVO:01001665]", + "spring [ENVO:00000027]", + "spur [ENVO:01001489]", + "stack [ENVO:00000419]", + "steppe [ENVO:00000262]", + "stream [ENVO:00000023]", + "swale [ENVO:00000543]", + "terrace [ENVO:00000508]", + "thermokarst [ENVO:03000085]", + "trench [ENVO:01000649]", + "tunnel [ENVO:00000068]", + "tuya [ENVO:00000370]", + "valley [ENVO:00000100]", + "volcano [ENVO:00000247]", + "wadi [ENVO:00000031]", + "watershed [ENVO:00000292]", + "well [ENVO:00000026]", + "woodland clearing [ENVO:00000444]" + ], + "title": "EnvLocalScaleSoilEnum", + "type": "string" + }, + "EnvMediumSoilEnum": { + "description": "", + "enum": [ + "acidic soil [ENVO:01001185]", + "acrisol [ENVO:00002234]", + "agricultural soil [ENVO:00002259]", + "albeluvisol [ENVO:00002233]", + "alisol [ENVO:00002231]", + "allotment garden soil [ENVO:00005744]", + "alluvial paddy field soil [ENVO:00005759]", + "alluvial soil [ENVO:00002871]", + "alluvial swamp soil [ENVO:00005758]", + "alpine soil [ENVO:00005741]", + "andosol [ENVO:00002232]", + "anthrosol [ENVO:00002230]", + "arable soil [ENVO:00005742]", + "arenosol [ENVO:00002229]", + "bare soil [ENVO:01001616]", + "beech forest soil [ENVO:00005770]", + "bluegrass field soil [ENVO:00005789]", + "bulk soil [ENVO:00005802]", + "burned soil [ENVO:00005760]", + "calcisol [ENVO:00002239]", + "cambisol [ENVO:00002235]", + "chernozem [ENVO:00002237]", + "clay soil [ENVO:00002262]", + "compacted soil [ENVO:06105205]", + "compost soil [ENVO:00005747]", + "cryosol [ENVO:00002236]", + "dry soil [ENVO:00005748]", + "durisol [ENVO:00002238]", + "eucalyptus forest soil [ENVO:00005787]", + "ferralsol [ENVO:00002246]", + "fertilized soil [ENVO:00005754]", + "field soil [ENVO:00005755]", + "fluvisol [ENVO:00002273]", + "forest soil [ENVO:00002261]", + "friable-frozen soil [ENVO:01001528]", + "frost-susceptible soil [ENVO:01001638]", + "frozen compost soil [ENVO:00005765]", + "frozen soil [ENVO:01001526]", + "gleysol [ENVO:00002244]", + "grassland soil [ENVO:00005750]", + "gypsisol [ENVO:00002245]", + "hard-frozen soil [ENVO:01001525]", + "heat stressed soil [ENVO:00005781]", + "histosol [ENVO:00002243]", + "jungle soil [ENVO:00005751]", + "kastanozem [ENVO:00002240]", + "lawn soil [ENVO:00005756]", + "leafy wood soil [ENVO:00005783]", + "leptosol [ENVO:00002241]", + "limed soil [ENVO:00005766]", + "lixisol [ENVO:00002242]", + "loam [ENVO:00002258]", + "luvisol [ENVO:00002248]", + "manured soil [ENVO:00005767]", + "mountain forest soil [ENVO:00005769]", + "muddy soil [ENVO:00005771]", + "nitisol [ENVO:00002247]", + "orchid soil [ENVO:00005768]", + "ornithogenic soil [ENVO:00005782]", + "paddy field soil [ENVO:00005740]", + "pathogen-suppressive soil [ENVO:03600036]", + "phaeozem [ENVO:00002249]", + "planosol [ENVO:00002251]", + "plastic-frozen soil [ENVO:01001527]", + "plinthosol [ENVO:00002250]", + "podzol [ENVO:00002257]", + "pond soil [ENVO:00005764]", + "red soil [ENVO:00005790]", + "regosol [ENVO:00002256]", + "roadside soil [ENVO:00005743]", + "rubber plantation soil [ENVO:00005788]", + "savanna soil [ENVO:00005746]", + "sawah soil [ENVO:00005752]", + "soil [ENVO:00001998]", + "solonchak [ENVO:00002252]", + "solonetz [ENVO:00002255]", + "spruce forest soil [ENVO:00005784]", + "stagnosol [ENVO:00002274]", + "surface soil [ENVO:02000059]", + "technosol [ENVO:00002275]", + "tropical soil [ENVO:00005778]", + "ultisol [ENVO:01001397]", + "umbrisol [ENVO:00002253]", + "upland soil [ENVO:00005786]", + "vegetable garden soil [ENVO:00005779]", + "vertisol [ENVO:00002254]" + ], + "title": "EnvMediumSoilEnum", + "type": "string" + }, + "EnvMediumWaterEnum": { + "description": "", + "enum": [ + "acidic water [ENVO:01000358]", + "alkaline water [ENVO:01000357]", + "anoxic water [ENVO:01000173]", + "bacon curing brine [ENVO:00003045]", + "ballast water [ENVO:01000872]", + "borax leachate [ENVO:00002142]", + "brackish water [ENVO:00002019]", + "brine [ENVO:00003044]", + "cloud water [ENVO:03600081]", + "coastal sea water [ENVO:00002150]", + "cooling water [ENVO:03600002]", + "desalinated water [ENVO:06105269]", + "distilled water [ENVO:00003065]", + "ditch water [ENVO:00002158]", + "drilling bore water [ENVO:00002159]", + "drinking water [ENVO:00003064]", + "estuarine water [ENVO:01000301]", + "eutrophic water [ENVO:00002224]", + "fresh water [ENVO:00002011]", + "groundwater [ENVO:01001004]", + "highly saline water [ENVO:01001039]", + "hydrothermal fluid [ENVO:01000134]", + "hypereutrophic water [ENVO:01001018]", + "hypersaline water [ENVO:00002012]", + "hypoxic water [ENVO:01001064]", + "interstitial water [ENVO:03600009]", + "leachate [ENVO:00002141]", + "liquid water [ENVO:00002006]", + "meltwater [ENVO:01000722]", + "mesotrophic water [ENVO:00002225]", + "moderately saline water [ENVO:01001038]", + "muddy water [ENVO:00005793]", + "oligotrophic water [ENVO:00002223]", + "oxic water [ENVO:01001063]", + "pond water [ENVO:00002228]", + "rainwater [ENVO:01000600]", + "rural stormwater [ENVO:01001270]", + "saline shrimp pond water [ENVO:01001257]", + "saline water [ENVO:00002010]", + "sea water [ENVO:00002149]", + "slightly saline water [ENVO:01001037]", + "stagnant water [ENVO:03501370]", + "sterile water [ENVO:00005791]", + "stormwater [ENVO:01001267]", + "subterranean lake [ENVO:02000145]", + "surface water [ENVO:00002042]", + "tap water [ENVO:00003096]", + "underground water [ENVO:00005792]", + "urban stormwater [ENVO:01001268]" + ], + "title": "EnvMediumWaterEnum", + "type": "string" + }, + "EnvPackageEnum": { + "description": "", + "enum": [ + "soil" + ], + "title": "EnvPackageEnum", + "type": "string" + }, + "ExtWallOrientEnum": { + "description": "", + "enum": [ + "north", + "south", + "east", + "west", + "northeast", + "southeast", + "southwest", + "northwest" + ], + "title": "ExtWallOrientEnum", + "type": "string" + }, + "ExtWindowOrientEnum": { + "description": "", + "enum": [ + "north", + "south", + "east", + "west", + "northeast", + "southeast", + "southwest", + "northwest" + ], + "title": "ExtWindowOrientEnum", + "type": "string" + }, + "FaoClassEnum": { + "description": "", + "enum": [ + "Acrisols", + "Andosols", + "Arenosols", + "Cambisols", + "Chernozems", + "Ferralsols", + "Fluvisols", + "Gleysols", + "Greyzems", + "Gypsisols", + "Histosols", + "Kastanozems", + "Lithosols", + "Luvisols", + "Nitosols", + "Phaeozems", + "Planosols", + "Podzols", + "Podzoluvisols", + "Rankers", + "Regosols", + "Rendzinas", + "Solonchaks", + "Solonetz", + "Vertisols", + "Yermosols" + ], + "title": "FaoClassEnum", + "type": "string" + }, + "FilterTypeEnum": { + "description": "", + "enum": [ + "particulate air filter", + "chemical air filter", + "low-MERV pleated media", + "HEPA", + "electrostatic", + "gas-phase or ultraviolet air treatments" + ], + "title": "FilterTypeEnum", + "type": "string" + }, + "FloorCondEnum": { + "description": "", + "enum": [ + "new", + "visible wear", + "needs repair", + "damaged", + "rupture" + ], + "title": "FloorCondEnum", + "type": "string" + }, + "FloorFinishMatEnum": { + "description": "", + "enum": [ + "tile", + "wood strip or parquet", + "carpet", + "rug", + "laminate wood", + "lineoleum", + "vinyl composition tile", + "sheet vinyl", + "stone", + "bamboo", + "cork", + "terrazo", + "concrete", + "none", + "sealed", + "clear finish", + "paint", + "none or unfinished" + ], + "title": "FloorFinishMatEnum", + "type": "string" + }, + "FloorStrucEnum": { + "description": "", + "enum": [ + "balcony", + "floating floor", + "glass floor", + "raised floor", + "sprung floor", + "wood-framed", + "concrete" + ], + "title": "FloorStrucEnum", + "type": "string" + }, + "FloorWaterMoldEnum": { + "description": "", + "enum": [ + "mold odor", + "wet floor", + "water stains", + "wall discoloration", + "floor discoloration", + "ceiling discoloration", + "peeling paint or wallpaper", + "bulging walls", + "condensation" + ], + "title": "FloorWaterMoldEnum", + "type": "string" + }, + "FurnitureEnum": { + "description": "", + "enum": [ + "cabinet", + "chair", + "desks" + ], + "title": "FurnitureEnum", + "type": "string" + }, + "GenderRestroomEnum": { + "description": "", + "enum": [ + "all gender", + "female", + "gender neurtral", + "male", + "male and female", + "unisex" + ], + "title": "GenderRestroomEnum", + "type": "string" + }, + "GrowthFacilEnum": { + "description": "", + "enum": [ + "experimental_garden", + "field", + "field_incubation", + "glasshouse", + "greenhouse", + "growth_chamber", + "lab_incubation", + "open_top_chamber", + "other" + ], + "title": "GrowthFacilEnum", + "type": "string" + }, + "GrowthHabitEnum": { + "description": "", + "enum": [ + "erect", + "semi-erect", + "spreading", + "prostrate" + ], + "title": "GrowthHabitEnum", + "type": "string" + }, + "HandidnessEnum": { + "description": "", + "enum": [ + "ambidexterity", + "left handedness", + "mixed-handedness", + "right handedness" + ], + "title": "HandidnessEnum", + "type": "string" + }, + "HcProducedEnum": { + "description": "", + "enum": [ + "Oil", + "Gas-Condensate", + "Gas", + "Bitumen", + "Coalbed Methane", + "other" + ], + "title": "HcProducedEnum", + "type": "string" + }, + "HcrCoresInterface": { + "additionalProperties": false, + "description": "hcr_cores dh_interface", + "properties": { + "additional_info": { + "description": "Information that doesn't fit anywhere else. Can also be used to propose new entries for fields with controlled vocabulary", + "type": [ + "string", + "null" + ] + }, + "alkalinity": { + "description": "Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "alkalinity_method": { + "description": "Method used for alkalinity measurement", + "type": [ + "string", + "null" + ] + }, + "ammonium": { + "description": "Concentration of ammonium in the sample", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "analysis_type": { + "description": "Select all the data types associated or available for this biosample", + "items": { + "$ref": "#/$defs/AnalysisTypeEnum" + }, + "type": "array" + }, + "api": { + "description": "API gravity is a measure of how heavy or light a petroleum liquid is compared to water (source: https://en.wikipedia.org/wiki/API_gravity) (e.g. 31.1\u00ac\u221e API)", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "aromatics_pc": { + "description": "Saturate, Aromatic, Resin and Asphaltene\u00ac\u2020(SARA) is an analysis method that divides\u00ac\u2020crude oil\u00ac\u2020components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene)", + "pattern": "^[^;\\t\\r\\x0A\\|]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A\\|]+$", + "type": [ + "string", + "null" + ] + }, + "asphaltenes_pc": { + "description": "Saturate, Aromatic, Resin and Asphaltene\u00ac\u2020(SARA) is an analysis method that divides\u00ac\u2020crude oil\u00ac\u2020components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene)", + "pattern": "^[^;\\t\\r\\x0A\\|]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A\\|]+$", + "type": [ + "string", + "null" + ] + }, + "basin": { + "description": "Name of the basin (e.g. Campos)", + "type": [ + "string", + "null" + ] + }, + "benzene": { + "description": "Concentration of benzene in the sample", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "calcium": { + "description": "Concentration of calcium in the sample", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "chem_administration": { + "description": "List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi", + "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\];([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", + "type": [ + "string", + "null" + ] + }, + "chloride": { + "description": "Concentration of chloride in the sample", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "collection_date": { + "description": "The date of sampling", + "pattern": "^[12]\\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\\d|3[01]))?)?$", + "type": "string" + }, + "density": { + "description": "Density of the sample, which is its mass per unit volume (aka volumetric mass density)", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "depos_env": { + "$ref": "#/$defs/DeposEnvEnum", + "description": "Main depositional environment (https://en.wikipedia.org/wiki/Depositional_environment). If \"other\" is specified, please propose entry in \"additional info\" field" + }, + "depth": { + "description": "The vertical distance below local surface, e.g. for sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples.", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)?(\\s*-\\s*[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)?)?$", + "type": [ + "string", + "null" + ] + }, + "diss_carb_dioxide": { + "description": "Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "diss_inorg_carb": { + "description": "Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "diss_inorg_phosp": { + "description": "Concentration of dissolved inorganic phosphorus in the sample", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "diss_iron": { + "description": "Concentration of dissolved iron in the sample", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "diss_org_carb": { + "description": "Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "diss_oxygen_fluid": { + "description": "Concentration of dissolved oxygen in the oil field produced fluids as it contributes to oxgen-corrosion and microbial activity (e.g. Mic).", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "ecosystem": { + "$ref": "#/$defs/EcosystemEnum", + "description": "An ecosystem is a combination of a physical environment (abiotic factors) and all the organisms (biotic factors) that interact with this environment. Ecosystem is in position 1/5 in a GOLD path." + }, + "ecosystem_category": { + "$ref": "#/$defs/EcosystemCategoryEnum", + "description": "Ecosystem categories represent divisions within the ecosystem based on specific characteristics of the environment from where an organism or sample is isolated. Ecosystem category is in position 2/5 in a GOLD path." + }, + "ecosystem_subtype": { + "$ref": "#/$defs/EcosystemSubtypeEnum", + "description": "Ecosystem subtypes represent further subdivision of Ecosystem types into more distinct subtypes. Ecosystem subtype is in position 4/5 in a GOLD path." + }, + "ecosystem_type": { + "$ref": "#/$defs/EcosystemTypeEnum", + "description": "Ecosystem types represent things having common characteristics within the Ecosystem Category. These common characteristics based grouping is still broad but specific to the characteristics of a given environment. Ecosystem type is in position 3/5 in a GOLD path." + }, + "elev": { + "description": "Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit.", + "type": "number" + }, + "env_broad_scale": { + "description": "In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO's biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html", + "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$", + "type": "string" + }, + "env_local_scale": { + "description": "Report the entity or entities which are in the sample or specimen\u2019s local vicinity and which you believe have significant causal influences on your sample or specimen. We recommend using EnvO terms which are of smaller spatial grain than your entry for env_broad_scale. Terms, such as anatomical sites, from other OBO Library ontologies which interoperate with EnvO (e.g. UBERON) are accepted in this field. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS.", + "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$", + "type": "string" + }, + "env_medium": { + "description": "Report the environmental material(s) immediately surrounding the sample or specimen at the time of sampling. We recommend using subclasses of 'environmental material' (http://purl.obolibrary.org/obo/ENVO_00010483). EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS . Terms from other OBO ontologies are permissible as long as they reference mass/volume nouns (e.g. air, water, blood) and not discrete, countable entities (e.g. a tree, a leaf, a table top).", + "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$", + "type": "string" + }, + "ethylbenzene": { + "description": "Concentration of ethylbenzene in the sample", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "experimental_factor": { + "description": "Experimental factors are essentially the variable aspects of an experiment design which can be used to describe an experiment, or set of experiments, in an increasingly detailed manner. This field accepts ontology terms from Experimental Factor Ontology (EFO) and/or Ontology for Biomedical Investigations (OBI). For a browser of EFO (v 2.95) terms, please see http://purl.bioontology.org/ontology/EFO; for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI", + "type": [ + "string", + "null" + ] + }, + "field": { + "description": "Name of the hydrocarbon field (e.g. Albacora)", + "type": [ + "string", + "null" + ] + }, + "geo_loc_name": { + "description": "The geographical origin of the sample as defined by the country or sea name followed by specific region name.", + "pattern": "^[^:, ][^:]*: [^:, ][^,]*, [^:, ].*$", + "type": "string" + }, + "hc_produced": { + "$ref": "#/$defs/HcProducedEnum", + "description": "Main hydrocarbon type produced from resource (i.e. Oil, gas, condensate, etc). If \"other\" is specified, please propose entry in \"additional info\" field" + }, + "hcr": { + "$ref": "#/$defs/HcrEnum", + "description": "Main Hydrocarbon Resource type. The term \"Hydrocarbon Resource\" HCR defined as a natural environmental feature containing large amounts of hydrocarbons at high concentrations potentially suitable for commercial exploitation. This term should not be confused with the Hydrocarbon Occurrence term which also includes hydrocarbon-rich environments with currently limited commercial interest such as seeps, outcrops, gas hydrates etc. If \"other\" is specified, please propose entry in \"additional info\" field" + }, + "hcr_fw_salinity": { + "description": "Original formation water salinity (prior to secondary recovery e.g. Waterflooding) expressed as TDS", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "hcr_geol_age": { + "$ref": "#/$defs/HcrGeolAgeEnum", + "description": "Geological age of hydrocarbon resource (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). If \"other\" is specified, please propose entry in \"additional info\" field" + }, + "hcr_pressure": { + "description": "Original pressure of the hydrocarbon resource", + "type": [ + "string", + "null" + ] + }, + "hcr_temp": { + "description": "Original temperature of the hydrocarbon resource", + "type": [ + "string", + "null" + ] + }, + "lat_lon": { + "description": "The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system", + "pattern": "^[-+]?([1-8]?\\d(\\.\\d{1,8})?|90(\\.0{1,8})?)\\s[-+]?(180(\\.0{1,8})?|((1[0-7]\\d)|([1-9]?\\d))(\\.\\d{1,8})?)$", + "type": "string" + }, + "lithology": { + "$ref": "#/$defs/LithologyEnum", + "description": "Hydrocarbon resource main lithology (Additional information: http://petrowiki.org/Lithology_and_rock_type_determination). If \"other\" is specified, please propose entry in \"additional info\" field" + }, + "magnesium": { + "description": "Concentration of magnesium in the sample", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "misc_param": { + "description": "Any other measurement performed or parameter collected, that is not listed here", + "pattern": "^([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+\\|)*([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+)$", + "type": [ + "string", + "null" + ] + }, + "nitrate": { + "description": "Concentration of nitrate in the sample", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "nitrite": { + "description": "Concentration of nitrite in the sample", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "org_count_qpcr_info": { + "description": "If qpcr was used for the cell count, the target gene name, the primer sequence and the cycling conditions should also be provided. (Example: 16S rrna; FWD:ACGTAGCTATGACGT REV:GTGCTAGTCGAGTAC; initial denaturation:90C_5min; denaturation:90C_2min; annealing:52C_30 sec; elongation:72C_30 sec; 90 C for 1 min; final elongation:72C_5min; 30 cycles)", + "type": [ + "string", + "null" + ] + }, + "organism_count": { + "description": "Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr)", + "pattern": "^([-+]?[0-9]*\\.?[0-9]+ +\\S.*\\|)*([-+]?[0-9]*\\.?[0-9]+ +\\S.*)$", + "type": [ + "string", + "null" + ] + }, + "owc_tvdss": { + "description": "Depth of the original oil water contact (OWC) zone (average) (m TVDSS)", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "oxy_stat_samp": { + "$ref": "#/$defs/OxyStatSampEnum", + "description": "Oxygenation status of sample" + }, + "permeability": { + "description": "Measure of the ability of a hydrocarbon resource to allow fluids to pass through it. (Additional information: https://en.wikipedia.org/wiki/Permeability_(earth_sciences))", + "type": [ + "string", + "null" + ] + }, + "ph": { + "description": "pH measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid", + "maximum": 14, + "minimum": 0, + "type": [ + "number", + "null" + ] + }, + "ph_meth": { + "description": "Reference or method used in determining ph", + "type": [ + "string", + "null" + ] + }, + "porosity": { + "description": "Porosity of deposited sediment is volume of voids divided by the total volume of sample", + "type": [ + "string", + "null" + ] + }, + "potassium": { + "description": "Concentration of potassium in the sample", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "pour_point": { + "description": "Temperature at which a liquid becomes semi solid and loses its flow characteristics. In crude oil a high\u00ac\u2020pour point\u00ac\u2020is generally associated with a high paraffin content, typically found in crude deriving from a larger proportion of plant material. (soure: https://en.wikipedia.org/wiki/pour_point)", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "pressure": { + "description": "Pressure to which the sample is subject to, in atmospheres", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "reservoir": { + "description": "Name of the reservoir (e.g. Carapebus)", + "type": [ + "string", + "null" + ] + }, + "resins_pc": { + "description": "Saturate, Aromatic, Resin and Asphaltene\u00ac\u2020(SARA) is an analysis method that divides\u00ac\u2020crude oil\u00ac\u2020components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene)", + "pattern": "^[^;\\t\\r\\x0A\\|]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A\\|]+$", + "type": [ + "string", + "null" + ] + }, + "salinity": { + "description": "The total concentration of all dissolved salts in a liquid or solid sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater.", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "samp_collec_device": { + "description": "The device used to collect an environmental sample. This field accepts terms listed under environmental sampling device (http://purl.obolibrary.org/obo/ENVO). This field also accepts terms listed under specimen collection device (http://purl.obolibrary.org/obo/GENEPIO_0002094).", + "type": [ + "string", + "null" + ] + }, + "samp_collec_method": { + "description": "The method employed for collecting the sample.", + "type": [ + "string", + "null" + ] + }, + "samp_mat_process": { + "description": "A brief description of any processing applied to the sample during or after retrieving the sample from environment, or a link to the relevant protocol(s) performed.", + "type": [ + "string", + "null" + ] + }, + "samp_md": { + "description": "In non deviated well, measured depth is equal to the true vertical depth, TVD (TVD=TVDSS plus the reference or datum it refers to). In deviated wells, the MD is the length of trajectory of the borehole measured from the same reference or datum. Common datums used are ground level (GL), drilling rig floor (DF), rotary table (RT), kelly bushing (KB) and mean sea level (MSL). If \"other\" is specified, please propose entry in \"additional info\" field", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "samp_name": { + "description": "A local identifier or name that for the material sample collected. Refers to the original material collected or to any derived sub-samples.", + "type": "string" + }, + "samp_size": { + "description": "The total amount or size (volume (ml), mass (g) or area (m2) ) of sample collected.", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? \\S+$", + "type": [ + "string", + "null" + ] + }, + "samp_store_dur": { + "description": "Duration for which the sample was stored", + "type": [ + "string", + "null" + ] + }, + "samp_store_loc": { + "description": "Location at which sample was stored, usually name of a specific freezer/room", + "type": [ + "string", + "null" + ] + }, + "samp_store_temp": { + "description": "Temperature at which the sample was stored (degrees are assumed)", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": "string" + }, + "samp_subtype": { + "$ref": "#/$defs/SampSubtypeEnum", + "description": "Name of sample sub-type. For example if \"sample type\" is \"Produced Water\" then subtype could be \"Oil Phase\" or \"Water Phase\". If \"other\" is specified, please propose entry in \"additional info\" field" + }, + "samp_transport_cond": { + "description": "Sample transport duration (in days or hrs) and temperature the sample was exposed to (e.g. 5.5 days; 20 \u00ac\u221eC)", + "type": [ + "string", + "null" + ] + }, + "samp_tvdss": { + "description": "Depth of the sample i.e. The vertical distance between the sea level and the sampled position in the subsurface. Depth can be reported as an interval for subsurface samples e.g. 1325.75-1362.25 m", + "type": [ + "string", + "null" + ] + }, + "samp_type": { + "description": "The type of material from which the sample was obtained. For the Hydrocarbon package, samples include types like core, rock trimmings, drill cuttings, piping section, coupon, pigging debris, solid deposit, produced fluid, produced water, injected water, swabs, etc. For the Food Package, samples are usually categorized as food, body products or tissues, or environmental material. This field accepts terms listed under environmental specimen (http://purl.obolibrary.org/obo/GENEPIO_0001246).", + "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$", + "type": [ + "string", + "null" + ] + }, + "samp_well_name": { + "description": "Name of the well (e.g. BXA1123) where sample was taken", + "type": [ + "string", + "null" + ] + }, + "sample_link": { + "description": "A unique identifier to assign parent-child, subsample, or sibling samples. This is relevant when a sample or other material was used to generate the new sample.", + "pattern": "[^\\:\\n\\r]+\\:[^\\:\\n\\r]+", + "type": [ + "string", + "null" + ] + }, + "saturates_pc": { + "description": "Saturate, Aromatic, Resin and Asphaltene\u00ac\u2020(SARA) is an analysis method that divides\u00ac\u2020crude oil\u00ac\u2020components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene)", + "pattern": "^[^;\\t\\r\\x0A\\|]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A\\|]+$", + "type": [ + "string", + "null" + ] + }, + "size_frac": { + "description": "Filtering pore size used in sample preparation", + "type": [ + "string", + "null" + ] + }, + "sodium": { + "description": "Sodium concentration in the sample", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "source_mat_id": { + "description": "A globally unique identifier assigned to the biological sample.", + "pattern": "[^\\:\\n\\r]+\\:[^\\:\\n\\r]+", + "type": [ + "string", + "null" + ] + }, + "specific_ecosystem": { + "$ref": "#/$defs/SpecificEcosystemEnum", + "description": "Specific ecosystems represent specific features of the environment like aphotic zone in an ocean or gastric mucosa within a host digestive system. Specific ecosystem is in position 5/5 in a GOLD path." + }, + "sr_dep_env": { + "$ref": "#/$defs/SrDepEnvEnum", + "description": "Source rock depositional environment (https://en.wikipedia.org/wiki/Source_rock). If \"other\" is specified, please propose entry in \"additional info\" field" + }, + "sr_geol_age": { + "$ref": "#/$defs/SrGeolAgeEnum", + "description": "Geological age of source rock (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). If \"other\" is specified, please propose entry in \"additional info\" field" + }, + "sr_kerog_type": { + "$ref": "#/$defs/SrKerogTypeEnum", + "description": "Origin of kerogen. Type I: Algal (aquatic), Type II: planktonic and soft plant material (aquatic or terrestrial), Type III: terrestrial woody/ fibrous plant material (terrestrial), Type IV: oxidized recycled woody debris (terrestrial) (additional information: https://en.wikipedia.org/wiki/Kerogen). If \"other\" is specified, please propose entry in \"additional info\" field" + }, + "sr_lithology": { + "$ref": "#/$defs/SrLithologyEnum", + "description": "Lithology of source rock (https://en.wikipedia.org/wiki/Source_rock). If \"other\" is specified, please propose entry in \"additional info\" field" + }, + "sulfate": { + "description": "Concentration of sulfate in the sample", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "sulfate_fw": { + "description": "Original sulfate concentration in the hydrocarbon resource", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "sulfide": { + "description": "Concentration of sulfide in the sample", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "suspend_solids": { + "description": "Concentration of substances including a wide variety of material, such as silt, decaying plant and animal matter; can include multiple substances", + "pattern": "^([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+\\|)*([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+)$", + "type": [ + "string", + "null" + ] + }, + "tan": { + "description": "Total Acid Number\u00ac\u2020(TAN) is a measurement of acidity that is determined by the amount of\u00ac\u2020potassium hydroxide\u00ac\u2020in milligrams that is needed to neutralize the acids in one gram of oil.\u00ac\u2020It is an important quality measurement of\u00ac\u2020crude oil. (source: https://en.wikipedia.org/wiki/Total_acid_number)", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "temp": { + "description": "Temperature of the sample at the time of sampling.", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "toluene": { + "description": "Concentration of toluene in the sample", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "tot_iron": { + "description": "Concentration of total iron in the sample", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "tot_nitro": { + "description": "Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "tot_phosp": { + "description": "Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "tot_sulfur": { + "description": "Concentration of total sulfur in the sample", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "tvdss_of_hcr_press": { + "description": "True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original pressure was measured (e.g. 1578 m).", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "tvdss_of_hcr_temp": { + "description": "True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original temperature was measured (e.g. 1345 m).", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "vfa": { + "description": "Concentration of Volatile Fatty Acids in the sample", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "vfa_fw": { + "description": "Original volatile fatty acid concentration in the hydrocarbon resource", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "viscosity": { + "description": "A measure of oil's resistance\u00ac\u2020to gradual deformation by\u00ac\u2020shear stress\u00ac\u2020or\u00ac\u2020tensile stress (e.g. 3.5 cp; 100 \u00ac\u221eC)", + "type": [ + "string", + "null" + ] + }, + "win": { + "description": "A unique identifier of a well or wellbore. This is part of the Global Framework for Well Identification initiative which is compiled by the Professional Petroleum Data Management Association (PPDM) in an effort to improve well identification systems. (Supporting information: https://ppdm.org/ and http://dl.ppdm.org/dl/690)", + "type": [ + "string", + "null" + ] + }, + "xylene": { + "description": "Concentration of xylene in the sample", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + } + }, + "required": [ + "collection_date", + "elev", + "env_broad_scale", + "env_local_scale", + "env_medium", + "geo_loc_name", + "lat_lon", + "samp_store_temp", + "analysis_type", + "samp_name" + ], + "title": "HcrCoresInterface", + "type": "object" + }, + "HcrEnum": { + "description": "", + "enum": [ + "Oil Reservoir", + "Gas Reservoir", + "Oil Sand", + "Coalbed", + "Shale", + "Tight Oil Reservoir", + "Tight Gas Reservoir", + "other" + ], + "title": "HcrEnum", + "type": "string" + }, + "HcrFluidsSwabsInterface": { + "additionalProperties": false, + "description": "hcr_fluids_swabs dh_interface", + "properties": { + "add_recov_method": { + "description": "Additional (i.e. Secondary, tertiary, etc.) recovery methods deployed for increase of hydrocarbon recovery from resource and start date for each one of them. If \"other\" is specified, please propose entry in \"additional info\" field", + "type": [ + "string", + "null" + ] + }, + "additional_info": { + "description": "Information that doesn't fit anywhere else. Can also be used to propose new entries for fields with controlled vocabulary", + "type": [ + "string", + "null" + ] + }, + "alkalinity": { + "description": "Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "alkalinity_method": { + "description": "Method used for alkalinity measurement", + "type": [ + "string", + "null" + ] + }, + "ammonium": { + "description": "Concentration of ammonium in the sample", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "analysis_type": { + "description": "Select all the data types associated or available for this biosample", + "items": { + "$ref": "#/$defs/AnalysisTypeEnum" + }, + "type": "array" + }, + "api": { + "description": "API gravity is a measure of how heavy or light a petroleum liquid is compared to water (source: https://en.wikipedia.org/wiki/API_gravity) (e.g. 31.1\u00ac\u221e API)", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "aromatics_pc": { + "description": "Saturate, Aromatic, Resin and Asphaltene\u00ac\u2020(SARA) is an analysis method that divides\u00ac\u2020crude oil\u00ac\u2020components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene)", + "pattern": "^[^;\\t\\r\\x0A\\|]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A\\|]+$", + "type": [ + "string", + "null" + ] + }, + "asphaltenes_pc": { + "description": "Saturate, Aromatic, Resin and Asphaltene\u00ac\u2020(SARA) is an analysis method that divides\u00ac\u2020crude oil\u00ac\u2020components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene)", + "pattern": "^[^;\\t\\r\\x0A\\|]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A\\|]+$", + "type": [ + "string", + "null" + ] + }, + "basin": { + "description": "Name of the basin (e.g. Campos)", + "type": [ + "string", + "null" + ] + }, + "benzene": { + "description": "Concentration of benzene in the sample", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "biocide": { + "description": "List of biocides (commercial name of product and supplier) and date of administration", + "type": [ + "string", + "null" + ] + }, + "biocide_admin_method": { + "description": "Method of biocide administration (dose, frequency, duration, time elapsed between last biociding and sampling) (e.g. 150 mg/l; weekly; 4 hr; 3 days)", + "type": [ + "string", + "null" + ] + }, + "calcium": { + "description": "Concentration of calcium in the sample", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "chem_administration": { + "description": "List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi", + "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\];([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", + "type": [ + "string", + "null" + ] + }, + "chem_treat_method": { + "description": "Method of chemical administration(dose, frequency, duration, time elapsed between administration and sampling) (e.g. 50 mg/l; twice a week; 1 hr; 0 days)", + "type": [ + "string", + "null" + ] + }, + "chem_treatment": { + "description": "List of chemical compounds administered upstream the sampling location where sampling occurred (e.g. Glycols, H2S scavenger, corrosion and scale inhibitors, demulsifiers, and other production chemicals etc.). The commercial name of the product and name of the supplier should be provided. The date of administration should also be included", + "type": [ + "string", + "null" + ] + }, + "chloride": { + "description": "Concentration of chloride in the sample", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "collection_date": { + "description": "The date of sampling", + "pattern": "^[12]\\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\\d|3[01]))?)?$", + "type": "string" + }, + "density": { + "description": "Density of the sample, which is its mass per unit volume (aka volumetric mass density)", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "depos_env": { + "$ref": "#/$defs/DeposEnvEnum", + "description": "Main depositional environment (https://en.wikipedia.org/wiki/Depositional_environment). If \"other\" is specified, please propose entry in \"additional info\" field" + }, + "depth": { + "description": "The vertical distance below local surface, e.g. for sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples.", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)?(\\s*-\\s*[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)?)?$", + "type": [ + "string", + "null" + ] + }, + "diss_carb_dioxide": { + "description": "Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "diss_inorg_carb": { + "description": "Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "diss_inorg_phosp": { + "description": "Concentration of dissolved inorganic phosphorus in the sample", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "diss_iron": { + "description": "Concentration of dissolved iron in the sample", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "diss_org_carb": { + "description": "Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "diss_oxygen_fluid": { + "description": "Concentration of dissolved oxygen in the oil field produced fluids as it contributes to oxgen-corrosion and microbial activity (e.g. Mic).", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "ecosystem": { + "$ref": "#/$defs/EcosystemEnum", + "description": "An ecosystem is a combination of a physical environment (abiotic factors) and all the organisms (biotic factors) that interact with this environment. Ecosystem is in position 1/5 in a GOLD path." + }, + "ecosystem_category": { + "$ref": "#/$defs/EcosystemCategoryEnum", + "description": "Ecosystem categories represent divisions within the ecosystem based on specific characteristics of the environment from where an organism or sample is isolated. Ecosystem category is in position 2/5 in a GOLD path." + }, + "ecosystem_subtype": { + "$ref": "#/$defs/EcosystemSubtypeEnum", + "description": "Ecosystem subtypes represent further subdivision of Ecosystem types into more distinct subtypes. Ecosystem subtype is in position 4/5 in a GOLD path." + }, + "ecosystem_type": { + "$ref": "#/$defs/EcosystemTypeEnum", + "description": "Ecosystem types represent things having common characteristics within the Ecosystem Category. These common characteristics based grouping is still broad but specific to the characteristics of a given environment. Ecosystem type is in position 3/5 in a GOLD path." + }, + "elev": { + "description": "Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit.", + "type": "number" + }, + "env_broad_scale": { + "description": "In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO's biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html", + "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$", + "type": "string" + }, + "env_local_scale": { + "description": "Report the entity or entities which are in the sample or specimen\u2019s local vicinity and which you believe have significant causal influences on your sample or specimen. We recommend using EnvO terms which are of smaller spatial grain than your entry for env_broad_scale. Terms, such as anatomical sites, from other OBO Library ontologies which interoperate with EnvO (e.g. UBERON) are accepted in this field. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS.", + "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$", + "type": "string" + }, + "env_medium": { + "description": "Report the environmental material(s) immediately surrounding the sample or specimen at the time of sampling. We recommend using subclasses of 'environmental material' (http://purl.obolibrary.org/obo/ENVO_00010483). EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS . Terms from other OBO ontologies are permissible as long as they reference mass/volume nouns (e.g. air, water, blood) and not discrete, countable entities (e.g. a tree, a leaf, a table top).", + "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$", + "type": "string" + }, + "ethylbenzene": { + "description": "Concentration of ethylbenzene in the sample", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "experimental_factor": { + "description": "Experimental factors are essentially the variable aspects of an experiment design which can be used to describe an experiment, or set of experiments, in an increasingly detailed manner. This field accepts ontology terms from Experimental Factor Ontology (EFO) and/or Ontology for Biomedical Investigations (OBI). For a browser of EFO (v 2.95) terms, please see http://purl.bioontology.org/ontology/EFO; for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI", + "type": [ + "string", + "null" + ] + }, + "field": { + "description": "Name of the hydrocarbon field (e.g. Albacora)", + "type": [ + "string", + "null" + ] + }, + "geo_loc_name": { + "description": "The geographical origin of the sample as defined by the country or sea name followed by specific region name.", + "pattern": "^[^:, ][^:]*: [^:, ][^,]*, [^:, ].*$", + "type": "string" + }, + "hc_produced": { + "$ref": "#/$defs/HcProducedEnum", + "description": "Main hydrocarbon type produced from resource (i.e. Oil, gas, condensate, etc). If \"other\" is specified, please propose entry in \"additional info\" field" + }, + "hcr": { + "$ref": "#/$defs/HcrEnum", + "description": "Main Hydrocarbon Resource type. The term \"Hydrocarbon Resource\" HCR defined as a natural environmental feature containing large amounts of hydrocarbons at high concentrations potentially suitable for commercial exploitation. This term should not be confused with the Hydrocarbon Occurrence term which also includes hydrocarbon-rich environments with currently limited commercial interest such as seeps, outcrops, gas hydrates etc. If \"other\" is specified, please propose entry in \"additional info\" field" + }, + "hcr_fw_salinity": { + "description": "Original formation water salinity (prior to secondary recovery e.g. Waterflooding) expressed as TDS", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "hcr_geol_age": { + "$ref": "#/$defs/HcrGeolAgeEnum", + "description": "Geological age of hydrocarbon resource (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). If \"other\" is specified, please propose entry in \"additional info\" field" + }, + "hcr_pressure": { + "description": "Original pressure of the hydrocarbon resource", + "type": [ + "string", + "null" + ] + }, + "hcr_temp": { + "description": "Original temperature of the hydrocarbon resource", + "type": [ + "string", + "null" + ] + }, + "iw_bt_date_well": { + "description": "Injection water breakthrough date per well following a secondary and/or tertiary recovery", + "type": [ + "string", + "null" + ] + }, + "iwf": { + "description": "Proportion of the produced fluids derived from injected water at the time of sampling. (e.g. 87%)", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "lat_lon": { + "description": "The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system", + "pattern": "^[-+]?([1-8]?\\d(\\.\\d{1,8})?|90(\\.0{1,8})?)\\s[-+]?(180(\\.0{1,8})?|((1[0-7]\\d)|([1-9]?\\d))(\\.\\d{1,8})?)$", + "type": "string" + }, + "lithology": { + "$ref": "#/$defs/LithologyEnum", + "description": "Hydrocarbon resource main lithology (Additional information: http://petrowiki.org/Lithology_and_rock_type_determination). If \"other\" is specified, please propose entry in \"additional info\" field" + }, + "magnesium": { + "description": "Concentration of magnesium in the sample", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "misc_param": { + "description": "Any other measurement performed or parameter collected, that is not listed here", + "pattern": "^([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+\\|)*([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+)$", + "type": [ + "string", + "null" + ] + }, + "nitrate": { + "description": "Concentration of nitrate in the sample", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "nitrite": { + "description": "Concentration of nitrite in the sample", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "org_count_qpcr_info": { + "description": "If qpcr was used for the cell count, the target gene name, the primer sequence and the cycling conditions should also be provided. (Example: 16S rrna; FWD:ACGTAGCTATGACGT REV:GTGCTAGTCGAGTAC; initial denaturation:90C_5min; denaturation:90C_2min; annealing:52C_30 sec; elongation:72C_30 sec; 90 C for 1 min; final elongation:72C_5min; 30 cycles)", + "type": [ + "string", + "null" + ] + }, + "organism_count": { + "description": "Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr)", + "pattern": "^([-+]?[0-9]*\\.?[0-9]+ +\\S.*\\|)*([-+]?[0-9]*\\.?[0-9]+ +\\S.*)$", + "type": [ + "string", + "null" + ] + }, + "oxy_stat_samp": { + "$ref": "#/$defs/OxyStatSampEnum", + "description": "Oxygenation status of sample" + }, + "ph": { + "description": "pH measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid", + "maximum": 14, + "minimum": 0, + "type": [ + "number", + "null" + ] + }, + "ph_meth": { + "description": "Reference or method used in determining ph", + "type": [ + "string", + "null" + ] + }, + "potassium": { + "description": "Concentration of potassium in the sample", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "pour_point": { + "description": "Temperature at which a liquid becomes semi solid and loses its flow characteristics. In crude oil a high\u00ac\u2020pour point\u00ac\u2020is generally associated with a high paraffin content, typically found in crude deriving from a larger proportion of plant material. (soure: https://en.wikipedia.org/wiki/pour_point)", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "pressure": { + "description": "Pressure to which the sample is subject to, in atmospheres", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "prod_rate": { + "description": "Oil and/or gas production rates per well (e.g. 524 m3 / day)", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "prod_start_date": { + "description": "Date of field's first production", + "type": [ + "string", + "null" + ] + }, + "reservoir": { + "description": "Name of the reservoir (e.g. Carapebus)", + "type": [ + "string", + "null" + ] + }, + "resins_pc": { + "description": "Saturate, Aromatic, Resin and Asphaltene\u00ac\u2020(SARA) is an analysis method that divides\u00ac\u2020crude oil\u00ac\u2020components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene)", + "pattern": "^[^;\\t\\r\\x0A\\|]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A\\|]+$", + "type": [ + "string", + "null" + ] + }, + "salinity": { + "description": "The total concentration of all dissolved salts in a liquid or solid sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater.", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "samp_collec_device": { + "description": "The device used to collect an environmental sample. This field accepts terms listed under environmental sampling device (http://purl.obolibrary.org/obo/ENVO). This field also accepts terms listed under specimen collection device (http://purl.obolibrary.org/obo/GENEPIO_0002094).", + "type": [ + "string", + "null" + ] + }, + "samp_collec_method": { + "description": "The method employed for collecting the sample.", + "type": [ + "string", + "null" + ] + }, + "samp_collect_point": { + "$ref": "#/$defs/SampCollectPointEnum", + "description": "Sampling point on the asset were sample was collected (e.g. Wellhead, storage tank, separator, etc). If \"other\" is specified, please propose entry in \"additional info\" field" + }, + "samp_loc_corr_rate": { + "description": "Metal corrosion rate is the speed of metal deterioration due to environmental conditions. As environmental conditions change corrosion rates change accordingly. Therefore, long term corrosion rates are generally more informative than short term rates and for that reason they are preferred during reporting. In the case of suspected MIC, corrosion rate measurements at the time of sampling might provide insights into the involvement of certain microbial community members in MIC as well as potential microbial interplays", + "type": [ + "string", + "null" + ] + }, + "samp_mat_process": { + "description": "A brief description of any processing applied to the sample during or after retrieving the sample from environment, or a link to the relevant protocol(s) performed.", + "type": [ + "string", + "null" + ] + }, + "samp_name": { + "description": "A local identifier or name that for the material sample collected. Refers to the original material collected or to any derived sub-samples.", + "type": "string" + }, + "samp_preserv": { + "description": "Preservative added to the sample (e.g. Rnalater, alcohol, formaldehyde, etc.). Where appropriate include volume added (e.g. Rnalater; 2 ml)", + "pattern": "^[^;\\t\\r\\x0A\\|]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A\\|]+$", + "type": [ + "string", + "null" + ] + }, + "samp_size": { + "description": "The total amount or size (volume (ml), mass (g) or area (m2) ) of sample collected.", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? \\S+$", + "type": [ + "string", + "null" + ] + }, + "samp_store_dur": { + "description": "Duration for which the sample was stored", + "type": [ + "string", + "null" + ] + }, + "samp_store_loc": { + "description": "Location at which sample was stored, usually name of a specific freezer/room", + "type": [ + "string", + "null" + ] + }, + "samp_store_temp": { + "description": "Temperature at which the sample was stored (degrees are assumed)", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": "string" + }, + "samp_subtype": { + "$ref": "#/$defs/SampSubtypeEnum", + "description": "Name of sample sub-type. For example if \"sample type\" is \"Produced Water\" then subtype could be \"Oil Phase\" or \"Water Phase\". If \"other\" is specified, please propose entry in \"additional info\" field" + }, + "samp_transport_cond": { + "description": "Sample transport duration (in days or hrs) and temperature the sample was exposed to (e.g. 5.5 days; 20 \u00ac\u221eC)", + "type": [ + "string", + "null" + ] + }, + "samp_type": { + "description": "The type of material from which the sample was obtained. For the Hydrocarbon package, samples include types like core, rock trimmings, drill cuttings, piping section, coupon, pigging debris, solid deposit, produced fluid, produced water, injected water, swabs, etc. For the Food Package, samples are usually categorized as food, body products or tissues, or environmental material. This field accepts terms listed under environmental specimen (http://purl.obolibrary.org/obo/GENEPIO_0001246).", + "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$", + "type": [ + "string", + "null" + ] + }, + "samp_well_name": { + "description": "Name of the well (e.g. BXA1123) where sample was taken", + "type": [ + "string", + "null" + ] + }, + "sample_link": { + "description": "A unique identifier to assign parent-child, subsample, or sibling samples. This is relevant when a sample or other material was used to generate the new sample.", + "pattern": "[^\\:\\n\\r]+\\:[^\\:\\n\\r]+", + "type": [ + "string", + "null" + ] + }, + "saturates_pc": { + "description": "Saturate, Aromatic, Resin and Asphaltene\u00ac\u2020(SARA) is an analysis method that divides\u00ac\u2020crude oil\u00ac\u2020components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene)", + "pattern": "^[^;\\t\\r\\x0A\\|]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A\\|]+$", + "type": [ + "string", + "null" + ] + }, + "size_frac": { + "description": "Filtering pore size used in sample preparation", + "type": [ + "string", + "null" + ] + }, + "sodium": { + "description": "Sodium concentration in the sample", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "source_mat_id": { + "description": "A globally unique identifier assigned to the biological sample.", + "pattern": "[^\\:\\n\\r]+\\:[^\\:\\n\\r]+", + "type": [ + "string", + "null" + ] + }, + "specific_ecosystem": { + "$ref": "#/$defs/SpecificEcosystemEnum", + "description": "Specific ecosystems represent specific features of the environment like aphotic zone in an ocean or gastric mucosa within a host digestive system. Specific ecosystem is in position 5/5 in a GOLD path." + }, + "sulfate": { + "description": "Concentration of sulfate in the sample", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "sulfate_fw": { + "description": "Original sulfate concentration in the hydrocarbon resource", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "sulfide": { + "description": "Concentration of sulfide in the sample", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "suspend_solids": { + "description": "Concentration of substances including a wide variety of material, such as silt, decaying plant and animal matter; can include multiple substances", + "pattern": "^([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+\\|)*([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+)$", + "type": [ + "string", + "null" + ] + }, + "tan": { + "description": "Total Acid Number\u00ac\u2020(TAN) is a measurement of acidity that is determined by the amount of\u00ac\u2020potassium hydroxide\u00ac\u2020in milligrams that is needed to neutralize the acids in one gram of oil.\u00ac\u2020It is an important quality measurement of\u00ac\u2020crude oil. (source: https://en.wikipedia.org/wiki/Total_acid_number)", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "temp": { + "description": "Temperature of the sample at the time of sampling.", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "toluene": { + "description": "Concentration of toluene in the sample", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "tot_iron": { + "description": "Concentration of total iron in the sample", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "tot_nitro": { + "description": "Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "tot_phosp": { + "description": "Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "tot_sulfur": { + "description": "Concentration of total sulfur in the sample", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "tvdss_of_hcr_press": { + "description": "True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original pressure was measured (e.g. 1578 m).", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "tvdss_of_hcr_temp": { + "description": "True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original temperature was measured (e.g. 1345 m).", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "vfa": { + "description": "Concentration of Volatile Fatty Acids in the sample", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "vfa_fw": { + "description": "Original volatile fatty acid concentration in the hydrocarbon resource", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "viscosity": { + "description": "A measure of oil's resistance\u00ac\u2020to gradual deformation by\u00ac\u2020shear stress\u00ac\u2020or\u00ac\u2020tensile stress (e.g. 3.5 cp; 100 \u00ac\u221eC)", + "type": [ + "string", + "null" + ] + }, + "water_cut": { + "description": "Current amount of water (%) in a produced fluid stream; or the average of the combined streams", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "water_prod_rate": { + "description": "Water production rates per well (e.g. 987 m3 / day)", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "win": { + "description": "A unique identifier of a well or wellbore. This is part of the Global Framework for Well Identification initiative which is compiled by the Professional Petroleum Data Management Association (PPDM) in an effort to improve well identification systems. (Supporting information: https://ppdm.org/ and http://dl.ppdm.org/dl/690)", + "type": [ + "string", + "null" + ] + }, + "xylene": { + "description": "Concentration of xylene in the sample", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + } + }, + "required": [ + "collection_date", + "elev", + "env_broad_scale", + "env_local_scale", + "env_medium", + "geo_loc_name", + "lat_lon", + "samp_store_temp", + "analysis_type", + "samp_name" + ], + "title": "HcrFluidsSwabsInterface", + "type": "object" + }, + "HcrGeolAgeEnum": { + "description": "", + "enum": [ + "Archean", + "Cambrian", + "Carboniferous", + "Cenozoic", + "Cretaceous", + "Devonian", + "Jurassic", + "Mesozoic", + "Neogene", + "Ordovician", + "Paleogene", + "Paleozoic", + "Permian", + "Precambrian", + "Proterozoic", + "Silurian", + "Triassic", + "other" + ], + "title": "HcrGeolAgeEnum", + "type": "string" + }, + "HeatCoolTypeEnum": { + "description": "", + "enum": [ + "radiant system", + "heat pump", + "forced air system", + "steam forced heat", + "wood stove" + ], + "title": "HeatCoolTypeEnum", + "type": "string" + }, + "HeatDelivLocEnum": { + "description": "", + "enum": [ + "north", + "south", + "east", + "west" + ], + "title": "HeatDelivLocEnum", + "type": "string" + }, + "HostAssociatedInterface": { + "additionalProperties": false, + "description": "host_associated dh_interface", + "properties": { + "alt": { + "description": "Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "analysis_type": { + "description": "Select all the data types associated or available for this biosample", + "items": { + "$ref": "#/$defs/AnalysisTypeEnum" + }, + "type": "array" + }, + "ances_data": { + "description": "Information about either pedigree or other ancestral information description (e.g. parental variety in case of mutant or selection), e.g. A/3*B (meaning [(A x B) x B] x B)", + "type": [ + "string", + "null" + ] + }, + "biol_stat": { + "$ref": "#/$defs/BiolStatEnum", + "description": "The level of genome modification." + }, + "blood_press_diast": { + "description": "Resting diastolic blood pressure, measured as mm mercury", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "blood_press_syst": { + "description": "Resting systolic blood pressure, measured as mm mercury", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "chem_administration": { + "description": "List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi", + "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\];([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", + "type": [ + "string", + "null" + ] + }, + "collection_date": { + "description": "The date of sampling", + "pattern": "^[12]\\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\\d|3[01]))?)?$", + "type": "string" + }, + "depth": { + "description": "The vertical distance below local surface, e.g. for sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples.", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)?(\\s*-\\s*[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)?)?$", + "type": [ + "string", + "null" + ] + }, + "ecosystem": { + "$ref": "#/$defs/EcosystemEnum", + "description": "An ecosystem is a combination of a physical environment (abiotic factors) and all the organisms (biotic factors) that interact with this environment. Ecosystem is in position 1/5 in a GOLD path." + }, + "ecosystem_category": { + "$ref": "#/$defs/EcosystemCategoryEnum", + "description": "Ecosystem categories represent divisions within the ecosystem based on specific characteristics of the environment from where an organism or sample is isolated. Ecosystem category is in position 2/5 in a GOLD path." + }, + "ecosystem_subtype": { + "$ref": "#/$defs/EcosystemSubtypeEnum", + "description": "Ecosystem subtypes represent further subdivision of Ecosystem types into more distinct subtypes. Ecosystem subtype is in position 4/5 in a GOLD path." + }, + "ecosystem_type": { + "$ref": "#/$defs/EcosystemTypeEnum", + "description": "Ecosystem types represent things having common characteristics within the Ecosystem Category. These common characteristics based grouping is still broad but specific to the characteristics of a given environment. Ecosystem type is in position 3/5 in a GOLD path." + }, + "elev": { + "description": "Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit.", + "type": "number" + }, + "env_broad_scale": { + "description": "In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO's biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html", + "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$", + "type": "string" + }, + "env_local_scale": { + "description": "Report the entity or entities which are in the sample or specimen\u2019s local vicinity and which you believe have significant causal influences on your sample or specimen. We recommend using EnvO terms which are of smaller spatial grain than your entry for env_broad_scale. Terms, such as anatomical sites, from other OBO Library ontologies which interoperate with EnvO (e.g. UBERON) are accepted in this field. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS.", + "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$", + "type": "string" + }, + "env_medium": { + "description": "Report the environmental material(s) immediately surrounding the sample or specimen at the time of sampling. We recommend using subclasses of 'environmental material' (http://purl.obolibrary.org/obo/ENVO_00010483). EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS . Terms from other OBO ontologies are permissible as long as they reference mass/volume nouns (e.g. air, water, blood) and not discrete, countable entities (e.g. a tree, a leaf, a table top).", + "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$", + "type": "string" + }, + "experimental_factor": { + "description": "Experimental factors are essentially the variable aspects of an experiment design which can be used to describe an experiment, or set of experiments, in an increasingly detailed manner. This field accepts ontology terms from Experimental Factor Ontology (EFO) and/or Ontology for Biomedical Investigations (OBI). For a browser of EFO (v 2.95) terms, please see http://purl.bioontology.org/ontology/EFO; for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI", + "type": [ + "string", + "null" + ] + }, + "genetic_mod": { + "description": "Genetic modifications of the genome of an organism, which may occur naturally by spontaneous mutation, or be introduced by some experimental means, e.g. specification of a transgene or the gene knocked-out or details of transient transfection", + "type": [ + "string", + "null" + ] + }, + "geo_loc_name": { + "description": "The geographical origin of the sample as defined by the country or sea name followed by specific region name.", + "pattern": "^[^:, ][^:]*: [^:, ][^,]*, [^:, ].*$", + "type": "string" + }, + "gravidity": { + "description": "Whether or not subject is gravid, and if yes date due or date post-conception, specifying which is used", + "type": [ + "string", + "null" + ] + }, + "host_age": { + "description": "Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "host_body_habitat": { + "description": "Original body habitat where the sample was obtained from", + "type": [ + "string", + "null" + ] + }, + "host_body_product": { + "description": "Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon", + "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$", + "type": [ + "string", + "null" + ] + }, + "host_body_site": { + "description": "Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON", + "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$", + "type": [ + "string", + "null" + ] + }, + "host_body_temp": { + "description": "Core body temperature of the host when sample was collected", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "host_color": { + "description": "The color of host", + "type": [ + "string", + "null" + ] + }, + "host_common_name": { + "description": "Common name of the host.", + "type": [ + "string", + "null" + ] + }, + "host_diet": { + "description": "Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types", + "type": [ + "string", + "null" + ] + }, + "host_disease_stat": { + "description": "List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text", + "type": [ + "string", + "null" + ] + }, + "host_dry_mass": { + "description": "Measurement of dry mass", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "host_family_relation": { + "description": "Familial relationships to other hosts in the same study; can include multiple relationships", + "type": [ + "string", + "null" + ] + }, + "host_genotype": { + "description": "Observed genotype", + "type": [ + "string", + "null" + ] + }, + "host_growth_cond": { + "description": "Literature reference giving growth conditions of the host", + "type": [ + "string", + "null" + ] + }, + "host_height": { + "description": "The height of subject", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "host_last_meal": { + "description": "Content of last meal and time since feeding; can include multiple values", + "type": [ + "string", + "null" + ] + }, + "host_length": { + "description": "The length of subject", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "host_life_stage": { + "description": "Description of life stage of host", + "type": [ + "string", + "null" + ] + }, + "host_phenotype": { + "description": "Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP", + "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$", + "type": [ + "string", + "null" + ] + }, + "host_sex": { + "$ref": "#/$defs/HostSexEnum", + "description": "Gender or physical sex of the host." + }, + "host_shape": { + "description": "Morphological shape of host", + "type": [ + "string", + "null" + ] + }, + "host_subject_id": { + "description": "A unique identifier by which each subject can be referred to, de-identified.", + "type": [ + "string", + "null" + ] + }, + "host_subspecf_genlin": { + "description": "Information about the genetic distinctness of the host organism below the subspecies level e.g., serovar, serotype, biotype, ecotype, variety, cultivar, or any relevant genetic typing schemes like Group I plasmid. Subspecies should not be recorded in this term, but in the NCBI taxonomy. Supply both the lineage name and the lineage rank separated by a colon, e.g., biovar:abc123.", + "type": [ + "string", + "null" + ] + }, + "host_substrate": { + "description": "The growth substrate of the host.", + "type": [ + "string", + "null" + ] + }, + "host_symbiont": { + "description": "The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host.", + "type": [ + "string", + "null" + ] + }, + "host_taxid": { + "description": "NCBI taxon id of the host, e.g. 9606", + "type": [ + "string", + "null" + ] + }, + "host_tot_mass": { + "description": "Total mass of the host at collection, the unit depends on host", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "lat_lon": { + "description": "The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system", + "pattern": "^[-+]?([1-8]?\\d(\\.\\d{1,8})?|90(\\.0{1,8})?)\\s[-+]?(180(\\.0{1,8})?|((1[0-7]\\d)|([1-9]?\\d))(\\.\\d{1,8})?)$", + "type": "string" + }, + "misc_param": { + "description": "Any other measurement performed or parameter collected, that is not listed here", + "pattern": "^([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+\\|)*([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+)$", + "type": [ + "string", + "null" + ] + }, + "organism_count": { + "description": "Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr)", + "pattern": "^([-+]?[0-9]*\\.?[0-9]+ +\\S.*\\|)*([-+]?[0-9]*\\.?[0-9]+ +\\S.*)$", + "type": [ + "string", + "null" + ] + }, + "oxy_stat_samp": { + "$ref": "#/$defs/OxyStatSampEnum", + "description": "Oxygenation status of sample" + }, + "perturbation": { + "description": "Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types", + "type": [ + "string", + "null" + ] + }, + "salinity": { + "description": "The total concentration of all dissolved salts in a liquid or solid sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater.", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "samp_capt_status": { + "$ref": "#/$defs/SampCaptStatusEnum", + "description": "Reason for the sample" + }, + "samp_collec_device": { + "description": "The device used to collect an environmental sample. This field accepts terms listed under environmental sampling device (http://purl.obolibrary.org/obo/ENVO). This field also accepts terms listed under specimen collection device (http://purl.obolibrary.org/obo/GENEPIO_0002094).", + "type": [ + "string", + "null" + ] + }, + "samp_collec_method": { + "description": "The method employed for collecting the sample.", + "type": [ + "string", + "null" + ] + }, + "samp_dis_stage": { + "$ref": "#/$defs/SampDisStageEnum", + "description": "Stage of the disease at the time of sample collection, e.g. inoculation, penetration, infection, growth and reproduction, dissemination of pathogen." + }, + "samp_mat_process": { + "description": "A brief description of any processing applied to the sample during or after retrieving the sample from environment, or a link to the relevant protocol(s) performed.", + "type": [ + "string", + "null" + ] + }, + "samp_name": { + "description": "A local identifier or name that for the material sample collected. Refers to the original material collected or to any derived sub-samples.", + "type": "string" + }, + "samp_size": { + "description": "The total amount or size (volume (ml), mass (g) or area (m2) ) of sample collected.", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? \\S+$", + "type": [ + "string", + "null" + ] + }, + "samp_store_dur": { + "description": "Duration for which the sample was stored", + "type": [ + "string", + "null" + ] + }, + "samp_store_loc": { + "description": "Location at which sample was stored, usually name of a specific freezer/room", + "type": [ + "string", + "null" + ] + }, + "samp_store_temp": { + "description": "Temperature at which the sample was stored (degrees are assumed)", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": "string" + }, + "sample_link": { + "description": "A unique identifier to assign parent-child, subsample, or sibling samples. This is relevant when a sample or other material was used to generate the new sample.", + "pattern": "[^\\:\\n\\r]+\\:[^\\:\\n\\r]+", + "type": [ + "string", + "null" + ] + }, + "size_frac": { + "description": "Filtering pore size used in sample preparation", + "type": [ + "string", + "null" + ] + }, + "source_mat_id": { + "description": "A globally unique identifier assigned to the biological sample.", + "pattern": "[^\\:\\n\\r]+\\:[^\\:\\n\\r]+", + "type": [ + "string", + "null" + ] + }, + "specific_ecosystem": { + "$ref": "#/$defs/SpecificEcosystemEnum", + "description": "Specific ecosystems represent specific features of the environment like aphotic zone in an ocean or gastric mucosa within a host digestive system. Specific ecosystem is in position 5/5 in a GOLD path." + }, + "temp": { + "description": "Temperature of the sample at the time of sampling.", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + } + }, + "required": [ + "collection_date", + "elev", + "env_broad_scale", + "env_local_scale", + "env_medium", + "geo_loc_name", + "lat_lon", + "samp_store_temp", + "analysis_type", + "samp_name" + ], + "title": "HostAssociatedInterface", + "type": "object" + }, + "HostSexEnum": { + "description": "", + "enum": [ + "female", + "hermaphrodite", + "male", + "neuter" + ], + "title": "HostSexEnum", + "type": "string" + }, + "IndoorSpaceEnum": { + "description": "", + "enum": [ + "bedroom", + "office", + "bathroom", + "foyer", + "kitchen", + "locker room", + "hallway", + "elevator" + ], + "title": "IndoorSpaceEnum", + "type": "string" + }, + "IndoorSurfEnum": { + "description": "", + "enum": [ + "cabinet", + "ceiling", + "counter top", + "door", + "shelving", + "vent cover", + "window", + "wall" + ], + "title": "IndoorSurfEnum", + "type": "string" + }, + "IntWallCondEnum": { + "description": "", + "enum": [ + "new", + "visible wear", + "needs repair", + "damaged", + "rupture" + ], + "title": "IntWallCondEnum", + "type": "string" + }, + "JgiContTypeEnum": { + "description": "", + "enum": [ + "plate", + "tube" + ], + "title": "JgiContTypeEnum", + "type": "string" + }, + "JgiMgInterface": { + "additionalProperties": false, + "allOf": [ + { + "if": { + "properties": { + "dna_cont_well": { + "pattern": ".+" + } + }, + "required": [ + "dna_cont_well" + ] + }, + "then": { + "properties": { + "dna_cont_type": { + "const": "plate" + } + }, + "required": [ + "dna_cont_type" + ] + } + }, + { + "if": { + "properties": { + "dna_cont_type": { + "const": "plate" + } + }, + "required": [ + "dna_cont_type" + ] + }, + "then": { + "properties": { + "dna_cont_well": { + "pattern": "^(?!A1$|A12$|H1$|H12$)(([A-H][1-9])|([A-H]1[0-2]))$" + } + }, + "required": [ + "dna_cont_well" + ] + } + } + ], + "description": "Metadata for samples sent to JGI for standard metagenome sequencing", + "properties": { + "analysis_type": { + "description": "Select all the data types associated or available for this biosample", + "items": { + "$ref": "#/$defs/AnalysisTypeEnum" + }, + "type": "array" + }, + "dna_absorb1": { + "description": "260/280 measurement of DNA sample purity", + "type": [ + "number", + "null" + ] + }, + "dna_absorb2": { + "description": "260/230 measurement of DNA sample purity", + "type": [ + "number", + "null" + ] + }, + "dna_concentration": { + "maximum": 2000, + "minimum": 0, + "type": "number" + }, + "dna_cont_type": { + "$ref": "#/$defs/JgiContTypeEnum", + "description": "Tube or plate (96-well)" + }, + "dna_cont_well": { + "pattern": "^(?!A1$|A12$|H1$|H12$)(([A-H][1-9])|([A-H]1[0-2]))$", + "type": [ + "string", + "null" + ] + }, + "dna_container_id": { + "pattern": "^.{1,20}$", + "type": "string" + }, + "dna_dnase": { + "$ref": "#/$defs/YesNoEnum" + }, + "dna_isolate_meth": { + "description": "Describe the method/protocol/kit used to extract DNA/RNA.", + "type": "string" + }, + "dna_project_contact": { + "type": "string" + }, + "dna_samp_id": { + "type": "string" + }, + "dna_sample_format": { + "$ref": "#/$defs/DNASampleFormatEnum", + "description": "Solution in which the DNA sample has been suspended" + }, + "dna_sample_name": { + "description": "Give the DNA sample a name that is meaningful to you. Sample names must be unique across all JGI projects and contain a-z, A-Z, 0-9, - and _ only.", + "pattern": "^[_a-zA-Z0-9-]*$", + "type": "string" + }, + "dna_seq_project": { + "type": "string" + }, + "dna_seq_project_name": { + "type": "string" + }, + "dna_seq_project_pi": { + "type": "string" + }, + "dna_volume": { + "maximum": 1000, + "minimum": 0, + "type": "number" + }, + "proposal_dna": { + "type": "string" + }, + "samp_name": { + "description": "A local identifier or name that for the material sample collected. Refers to the original material collected or to any derived sub-samples.", + "type": "string" + }, + "source_mat_id": { + "description": "A globally unique identifier assigned to the biological sample.", + "pattern": "[^\\:\\n\\r]+\\:[^\\:\\n\\r]+", + "type": [ + "string", + "null" + ] + } + }, + "required": [ + "dna_concentration", + "dna_cont_type", + "dna_container_id", + "dna_dnase", + "dna_isolate_meth", + "dna_project_contact", + "dna_samp_id", + "dna_sample_format", + "dna_sample_name", + "dna_seq_project", + "dna_seq_project_name", + "dna_seq_project_pi", + "dna_volume", + "proposal_dna", + "analysis_type", + "samp_name" + ], + "title": "JgiMgInterface", + "type": "object" + }, + "JgiMgLrInterface": { + "additionalProperties": false, + "description": "Metadata for samples sent to JGI for long read metagenome sequecning", + "properties": { + "analysis_type": { + "description": "Select all the data types associated or available for this biosample", + "items": { + "$ref": "#/$defs/AnalysisTypeEnum" + }, + "type": "array" + }, + "dna_absorb1": { + "description": "260/280 measurement of DNA sample purity", + "type": "number" + }, + "dna_absorb2": { + "description": "260/230 measurement of DNA sample purity", + "type": "number" + }, + "dna_concentration": { + "maximum": 2000, + "minimum": 0, + "type": "number" + }, + "dna_cont_type": { + "$ref": "#/$defs/JgiContTypeEnum", + "description": "Tube or plate (96-well)" + }, + "dna_cont_well": { + "pattern": "^(?!A1$|A12$|H1$|H12$)(([A-H][1-9])|([A-H]1[0-2]))$", + "type": [ + "string", + "null" + ] + }, + "dna_container_id": { + "pattern": "^.{1,20}$", + "type": "string" + }, + "dna_dnase": { + "$ref": "#/$defs/YesNoEnum" + }, + "dna_isolate_meth": { + "description": "Describe the method/protocol/kit used to extract DNA/RNA.", + "type": "string" + }, + "dna_project_contact": { + "type": "string" + }, + "dna_samp_id": { + "type": "string" + }, + "dna_sample_format": { + "$ref": "#/$defs/DNASampleFormatEnum", + "description": "Solution in which the DNA sample has been suspended" + }, + "dna_sample_name": { + "description": "Give the DNA sample a name that is meaningful to you. Sample names must be unique across all JGI projects and contain a-z, A-Z, 0-9, - and _ only.", + "pattern": "^[_a-zA-Z0-9-]*$", + "type": "string" + }, + "dna_seq_project": { + "type": "string" + }, + "dna_seq_project_name": { + "type": "string" + }, + "dna_seq_project_pi": { + "type": "string" + }, + "dna_volume": { + "maximum": 1000, + "minimum": 0, + "type": "number" + }, + "proposal_dna": { + "type": "string" + }, + "samp_name": { + "description": "A local identifier or name that for the material sample collected. Refers to the original material collected or to any derived sub-samples.", + "type": "string" + }, + "source_mat_id": { + "description": "A globally unique identifier assigned to the biological sample.", + "pattern": "[^\\:\\n\\r]+\\:[^\\:\\n\\r]+", + "type": [ + "string", + "null" + ] + } + }, + "required": [ + "dna_absorb1", + "dna_absorb2", + "dna_concentration", + "dna_cont_type", + "dna_container_id", + "dna_dnase", + "dna_isolate_meth", + "dna_project_contact", + "dna_samp_id", + "dna_sample_format", + "dna_sample_name", + "dna_seq_project", + "dna_seq_project_name", + "dna_seq_project_pi", + "dna_volume", + "proposal_dna", + "analysis_type", + "samp_name" + ], + "title": "JgiMgLrInterface", + "type": "object" + }, + "JgiMtInterface": { + "additionalProperties": false, + "allOf": [ + { + "if": { + "properties": { + "rna_cont_well": { + "pattern": ".+" + } + }, + "required": [ + "rna_cont_well" + ] + }, + "then": { + "properties": { + "rna_cont_type": { + "const": "plate" + } + }, + "required": [ + "rna_cont_type" + ] + } + }, + { + "if": { + "properties": { + "rna_cont_type": { + "const": "plate" + } + }, + "required": [ + "rna_cont_type" + ] + }, + "then": { + "properties": { + "rna_cont_well": { + "pattern": "^(?!A1$|A12$|H1$|H12$)(([A-H][1-9])|([A-H]1[0-2]))$" + } + }, + "required": [ + "rna_cont_well" + ] + } + } + ], + "description": "jgi_mt dh_interface", + "properties": { + "analysis_type": { + "description": "Select all the data types associated or available for this biosample", + "items": { + "$ref": "#/$defs/AnalysisTypeEnum" + }, + "type": "array" + }, + "dnase_rna": { + "$ref": "#/$defs/YesNoEnum" + }, + "proposal_rna": { + "type": "string" + }, + "rna_absorb1": { + "description": "260/280 measurement of RNA sample purity", + "type": [ + "number", + "null" + ] + }, + "rna_absorb2": { + "description": "260/230 measurement of RNA sample purity", + "type": [ + "number", + "null" + ] + }, + "rna_concentration": { + "maximum": 1000, + "minimum": 0, + "type": "number" + }, + "rna_cont_type": { + "$ref": "#/$defs/JgiContTypeEnum", + "description": "Tube or plate (96-well)" + }, + "rna_cont_well": { + "pattern": "^(?!A1$|A12$|H1$|H12$)(([A-H][1-9])|([A-H]1[0-2]))$", + "type": [ + "string", + "null" + ] + }, + "rna_container_id": { + "pattern": "^.{1,20}$", + "type": "string" + }, + "rna_isolate_meth": { + "description": "Describe the method/protocol/kit used to extract DNA/RNA.", + "type": "string" + }, + "rna_project_contact": { + "type": "string" + }, + "rna_samp_id": { + "type": "string" + }, + "rna_sample_format": { + "$ref": "#/$defs/RNASampleFormatEnum", + "description": "Solution in which the RNA sample has been suspended" + }, + "rna_sample_name": { + "description": "Give the RNA sample a name that is meaningful to you. Sample names must be unique across all JGI projects and contain a-z, A-Z, 0-9, - and _ only.", + "maximum": 2000, + "minimum": 0, + "pattern": "^[_a-zA-Z0-9-]*$", + "type": "string" + }, + "rna_seq_project": { + "type": "string" + }, + "rna_seq_project_name": { + "type": "string" + }, + "rna_seq_project_pi": { + "type": "string" + }, + "rna_volume": { + "maximum": 1000, + "minimum": 0, + "type": "number" + }, + "samp_name": { + "description": "A local identifier or name that for the material sample collected. Refers to the original material collected or to any derived sub-samples.", + "type": "string" + }, + "source_mat_id": { + "description": "A globally unique identifier assigned to the biological sample.", + "pattern": "[^\\:\\n\\r]+\\:[^\\:\\n\\r]+", + "type": [ + "string", + "null" + ] + } + }, + "required": [ + "dnase_rna", + "proposal_rna", + "rna_concentration", + "rna_cont_type", + "rna_container_id", + "rna_isolate_meth", + "rna_project_contact", + "rna_samp_id", + "rna_sample_format", + "rna_sample_name", + "rna_seq_project", + "rna_seq_project_name", + "rna_seq_project_pi", + "rna_volume", + "analysis_type", + "samp_name" + ], + "title": "JgiMtInterface", + "type": "object" + }, + "LightTypeEnum": { + "description": "", + "enum": [ + "natural light", + "electric light", + "desk lamp", + "flourescent lights", + "none" + ], + "title": "LightTypeEnum", + "type": "string" + }, + "LithologyEnum": { + "description": "", + "enum": [ + "Basement", + "Chalk", + "Chert", + "Coal", + "Conglomerate", + "Diatomite", + "Dolomite", + "Limestone", + "Sandstone", + "Shale", + "Siltstone", + "Volcanic", + "other" + ], + "title": "LithologyEnum", + "type": "string" + }, + "MechStrucEnum": { + "description": "", + "enum": [ + "subway", + "coach", + "carriage", + "elevator", + "escalator", + "boat", + "train", + "car", + "bus" + ], + "title": "MechStrucEnum", + "type": "string" + }, + "MiscEnvsInterface": { + "additionalProperties": false, + "description": "misc_envs dh_interface", + "properties": { + "alkalinity": { + "description": "Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "alt": { + "description": "Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "ammonium": { + "description": "Concentration of ammonium in the sample", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "analysis_type": { + "description": "Select all the data types associated or available for this biosample", + "items": { + "$ref": "#/$defs/AnalysisTypeEnum" + }, + "type": "array" + }, + "biomass": { + "description": "Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements", + "pattern": "^([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+\\|)*([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+)$", + "type": [ + "string", + "null" + ] + }, + "bromide": { + "description": "Concentration of bromide", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "calcium": { + "description": "Concentration of calcium in the sample", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "chem_administration": { + "description": "List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi", + "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\];([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", + "type": [ + "string", + "null" + ] + }, + "chloride": { + "description": "Concentration of chloride in the sample", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "chlorophyll": { + "description": "Concentration of chlorophyll", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "collection_date": { + "description": "The date of sampling", + "pattern": "^[12]\\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\\d|3[01]))?)?$", + "type": "string" + }, + "density": { + "description": "Density of the sample, which is its mass per unit volume (aka volumetric mass density)", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "depth": { + "description": "The vertical distance below local surface, e.g. for sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples.", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)?(\\s*-\\s*[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)?)?$", + "type": [ + "string", + "null" + ] + }, + "diether_lipids": { + "description": "Concentration of diether lipids; can include multiple types of diether lipids", + "pattern": "^([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+\\|)*([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+)$", + "type": [ + "string", + "null" + ] + }, + "diss_carb_dioxide": { + "description": "Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "diss_hydrogen": { + "description": "Concentration of dissolved hydrogen", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "diss_inorg_carb": { + "description": "Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "diss_org_nitro": { + "description": "Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "diss_oxygen": { + "description": "Concentration of dissolved oxygen", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "ecosystem": { + "$ref": "#/$defs/EcosystemEnum", + "description": "An ecosystem is a combination of a physical environment (abiotic factors) and all the organisms (biotic factors) that interact with this environment. Ecosystem is in position 1/5 in a GOLD path." + }, + "ecosystem_category": { + "$ref": "#/$defs/EcosystemCategoryEnum", + "description": "Ecosystem categories represent divisions within the ecosystem based on specific characteristics of the environment from where an organism or sample is isolated. Ecosystem category is in position 2/5 in a GOLD path." + }, + "ecosystem_subtype": { + "$ref": "#/$defs/EcosystemSubtypeEnum", + "description": "Ecosystem subtypes represent further subdivision of Ecosystem types into more distinct subtypes. Ecosystem subtype is in position 4/5 in a GOLD path." + }, + "ecosystem_type": { + "$ref": "#/$defs/EcosystemTypeEnum", + "description": "Ecosystem types represent things having common characteristics within the Ecosystem Category. These common characteristics based grouping is still broad but specific to the characteristics of a given environment. Ecosystem type is in position 3/5 in a GOLD path." + }, + "elev": { + "description": "Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit.", + "type": "number" + }, + "env_broad_scale": { + "description": "In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO's biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html", + "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$", + "type": "string" + }, + "env_local_scale": { + "description": "Report the entity or entities which are in the sample or specimen\u2019s local vicinity and which you believe have significant causal influences on your sample or specimen. We recommend using EnvO terms which are of smaller spatial grain than your entry for env_broad_scale. Terms, such as anatomical sites, from other OBO Library ontologies which interoperate with EnvO (e.g. UBERON) are accepted in this field. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS.", + "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$", + "type": "string" + }, + "env_medium": { + "description": "Report the environmental material(s) immediately surrounding the sample or specimen at the time of sampling. We recommend using subclasses of 'environmental material' (http://purl.obolibrary.org/obo/ENVO_00010483). EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS . Terms from other OBO ontologies are permissible as long as they reference mass/volume nouns (e.g. air, water, blood) and not discrete, countable entities (e.g. a tree, a leaf, a table top).", + "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$", + "type": "string" + }, + "experimental_factor": { + "description": "Experimental factors are essentially the variable aspects of an experiment design which can be used to describe an experiment, or set of experiments, in an increasingly detailed manner. This field accepts ontology terms from Experimental Factor Ontology (EFO) and/or Ontology for Biomedical Investigations (OBI). For a browser of EFO (v 2.95) terms, please see http://purl.bioontology.org/ontology/EFO; for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI", + "type": [ + "string", + "null" + ] + }, + "geo_loc_name": { + "description": "The geographical origin of the sample as defined by the country or sea name followed by specific region name.", + "pattern": "^[^:, ][^:]*: [^:, ][^,]*, [^:, ].*$", + "type": "string" + }, + "lat_lon": { + "description": "The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system", + "pattern": "^[-+]?([1-8]?\\d(\\.\\d{1,8})?|90(\\.0{1,8})?)\\s[-+]?(180(\\.0{1,8})?|((1[0-7]\\d)|([1-9]?\\d))(\\.\\d{1,8})?)$", + "type": "string" + }, + "misc_param": { + "description": "Any other measurement performed or parameter collected, that is not listed here", + "pattern": "^([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+\\|)*([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+)$", + "type": [ + "string", + "null" + ] + }, + "nitrate": { + "description": "Concentration of nitrate in the sample", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "nitrite": { + "description": "Concentration of nitrite in the sample", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "nitro": { + "description": "Concentration of nitrogen (total)", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "org_carb": { + "description": "Concentration of organic carbon", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "org_matter": { + "description": "Concentration of organic matter", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "org_nitro": { + "description": "Concentration of organic nitrogen", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "organism_count": { + "description": "Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr)", + "pattern": "^([-+]?[0-9]*\\.?[0-9]+ +\\S.*\\|)*([-+]?[0-9]*\\.?[0-9]+ +\\S.*)$", + "type": [ + "string", + "null" + ] + }, + "oxy_stat_samp": { + "$ref": "#/$defs/OxyStatSampEnum", + "description": "Oxygenation status of sample" + }, + "perturbation": { + "description": "Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types", + "type": [ + "string", + "null" + ] + }, + "ph": { + "description": "pH measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid", + "maximum": 14, + "minimum": 0, + "type": [ + "number", + "null" + ] + }, + "ph_meth": { + "description": "Reference or method used in determining ph", + "type": [ + "string", + "null" + ] + }, + "phosphate": { + "description": "Concentration of phosphate", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "phosplipid_fatt_acid": { + "description": "Concentration of phospholipid fatty acids; can include multiple values", + "pattern": "^([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+\\|)*([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+)$", + "type": [ + "string", + "null" + ] + }, + "potassium": { + "description": "Concentration of potassium in the sample", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "pressure": { + "description": "Pressure to which the sample is subject to, in atmospheres", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "salinity": { + "description": "The total concentration of all dissolved salts in a liquid or solid sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater.", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "samp_collec_device": { + "description": "The device used to collect an environmental sample. This field accepts terms listed under environmental sampling device (http://purl.obolibrary.org/obo/ENVO). This field also accepts terms listed under specimen collection device (http://purl.obolibrary.org/obo/GENEPIO_0002094).", + "type": [ + "string", + "null" + ] + }, + "samp_collec_method": { + "description": "The method employed for collecting the sample.", + "type": [ + "string", + "null" + ] + }, + "samp_mat_process": { + "description": "A brief description of any processing applied to the sample during or after retrieving the sample from environment, or a link to the relevant protocol(s) performed.", + "type": [ + "string", + "null" + ] + }, + "samp_name": { + "description": "A local identifier or name that for the material sample collected. Refers to the original material collected or to any derived sub-samples.", + "type": "string" + }, + "samp_size": { + "description": "The total amount or size (volume (ml), mass (g) or area (m2) ) of sample collected.", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? \\S+$", + "type": [ + "string", + "null" + ] + }, + "samp_store_dur": { + "description": "Duration for which the sample was stored", + "type": [ + "string", + "null" + ] + }, + "samp_store_loc": { + "description": "Location at which sample was stored, usually name of a specific freezer/room", + "type": [ + "string", + "null" + ] + }, + "samp_store_temp": { + "description": "Temperature at which the sample was stored (degrees are assumed)", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": "string" + }, + "sample_link": { + "description": "A unique identifier to assign parent-child, subsample, or sibling samples. This is relevant when a sample or other material was used to generate the new sample.", + "pattern": "[^\\:\\n\\r]+\\:[^\\:\\n\\r]+", + "type": [ + "string", + "null" + ] + }, + "silicate": { + "description": "Concentration of silicate", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "size_frac": { + "description": "Filtering pore size used in sample preparation", + "type": [ + "string", + "null" + ] + }, + "sodium": { + "description": "Sodium concentration in the sample", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "source_mat_id": { + "description": "A globally unique identifier assigned to the biological sample.", + "pattern": "[^\\:\\n\\r]+\\:[^\\:\\n\\r]+", + "type": [ + "string", + "null" + ] + }, + "specific_ecosystem": { + "$ref": "#/$defs/SpecificEcosystemEnum", + "description": "Specific ecosystems represent specific features of the environment like aphotic zone in an ocean or gastric mucosa within a host digestive system. Specific ecosystem is in position 5/5 in a GOLD path." + }, + "sulfate": { + "description": "Concentration of sulfate in the sample", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "sulfide": { + "description": "Concentration of sulfide in the sample", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "temp": { + "description": "Temperature of the sample at the time of sampling.", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "water_current": { + "description": "Measurement of magnitude and direction of flow within a fluid", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + } + }, + "required": [ + "collection_date", + "elev", + "env_broad_scale", + "env_local_scale", + "env_medium", + "geo_loc_name", + "lat_lon", + "samp_store_temp", + "analysis_type", + "samp_name" + ], + "title": "MiscEnvsInterface", + "type": "object" + }, + "OccupDocumentEnum": { + "description": "", + "enum": [ + "automated count", + "estimate", + "manual count", + "videos" + ], + "title": "OccupDocumentEnum", + "type": "string" + }, + "OxyStatSampEnum": { + "description": "", + "enum": [ + "aerobic", + "anaerobic", + "other" + ], + "title": "OxyStatSampEnum", + "type": "string" + }, + "PlantAssociatedInterface": { + "additionalProperties": false, + "description": "plant_associated dh_interface", + "properties": { + "air_temp_regm": { + "description": "Information about treatment involving an exposure to varying temperatures; should include the temperature, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include different temperature regimens", + "type": [ + "string", + "null" + ] + }, + "analysis_type": { + "description": "Select all the data types associated or available for this biosample", + "items": { + "$ref": "#/$defs/AnalysisTypeEnum" + }, + "type": "array" + }, + "ances_data": { + "description": "Information about either pedigree or other ancestral information description (e.g. parental variety in case of mutant or selection), e.g. A/3*B (meaning [(A x B) x B] x B)", + "type": [ + "string", + "null" + ] + }, + "antibiotic_regm": { + "description": "Information about treatment involving antibiotic administration; should include the name of antibiotic, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple antibiotic regimens", + "type": [ + "string", + "null" + ] + }, + "biol_stat": { + "$ref": "#/$defs/BiolStatEnum", + "description": "The level of genome modification." + }, + "biotic_regm": { + "description": "Information about treatment(s) involving use of biotic factors, such as bacteria, viruses or fungi.", + "type": [ + "string", + "null" + ] + }, + "biotic_relationship": { + "$ref": "#/$defs/BioticRelationshipEnum", + "description": "Description of relationship(s) between the subject organism and other organism(s) it is associated with. E.g., parasite on species X; mutualist with species Y. The target organism is the subject of the relationship, and the other organism(s) is the object" + }, + "chem_administration": { + "description": "List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi", + "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\];([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", + "type": [ + "string", + "null" + ] + }, + "chem_mutagen": { + "description": "Treatment involving use of mutagens; should include the name of mutagen, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple mutagen regimens", + "type": [ + "string", + "null" + ] + }, + "climate_environment": { + "description": "Treatment involving an exposure to a particular climate; treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple climates", + "type": [ + "string", + "null" + ] + }, + "collection_date": { + "description": "The date of sampling", + "pattern": "^[12]\\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\\d|3[01]))?)?$", + "type": "string" + }, + "collection_date_inc": { + "description": "Date the incubation was harvested/collected/ended. Only relevant for incubation samples.", + "pattern": "^[12]\\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\\d|3[01]))?)?$", + "type": [ + "string", + "null" + ] + }, + "collection_time": { + "description": "The time of sampling, either as an instance (single point) or interval.", + "pattern": "^([01]?\\d|2[0-3]|24(?=:00?:00?$)):([0-5]\\d)(:([0-5]\\d))?$", + "type": [ + "string", + "null" + ] + }, + "cult_root_med": { + "description": "Name or reference for the hydroponic or in vitro culture rooting medium; can be the name of a commonly used medium or reference to a specific medium, e.g. Murashige and Skoog medium. If the medium has not been formally published, use the rooting medium descriptors.", + "type": [ + "string", + "null" + ] + }, + "depth": { + "description": "The vertical distance below local surface, e.g. for sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples.", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)?(\\s*-\\s*[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)?)?$", + "type": [ + "string", + "null" + ] + }, + "ecosystem": { + "$ref": "#/$defs/EcosystemEnum", + "description": "An ecosystem is a combination of a physical environment (abiotic factors) and all the organisms (biotic factors) that interact with this environment. Ecosystem is in position 1/5 in a GOLD path." + }, + "ecosystem_category": { + "$ref": "#/$defs/EcosystemCategoryEnum", + "description": "Ecosystem categories represent divisions within the ecosystem based on specific characteristics of the environment from where an organism or sample is isolated. Ecosystem category is in position 2/5 in a GOLD path." + }, + "ecosystem_subtype": { + "$ref": "#/$defs/EcosystemSubtypeEnum", + "description": "Ecosystem subtypes represent further subdivision of Ecosystem types into more distinct subtypes. Ecosystem subtype is in position 4/5 in a GOLD path." + }, + "ecosystem_type": { + "$ref": "#/$defs/EcosystemTypeEnum", + "description": "Ecosystem types represent things having common characteristics within the Ecosystem Category. These common characteristics based grouping is still broad but specific to the characteristics of a given environment. Ecosystem type is in position 3/5 in a GOLD path." + }, + "elev": { + "description": "Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit.", + "type": "number" + }, + "env_broad_scale": { + "description": "In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO's biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html", + "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$", + "type": "string" + }, + "env_local_scale": { + "description": "Report the entity or entities which are in the sample or specimen\u2019s local vicinity and which you believe have significant causal influences on your sample or specimen. We recommend using EnvO terms which are of smaller spatial grain than your entry for env_broad_scale. Terms, such as anatomical sites, from other OBO Library ontologies which interoperate with EnvO (e.g. UBERON) are accepted in this field. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS.", + "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$", + "type": "string" + }, + "env_medium": { + "description": "Report the environmental material(s) immediately surrounding the sample or specimen at the time of sampling. We recommend using subclasses of 'environmental material' (http://purl.obolibrary.org/obo/ENVO_00010483). EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS . Terms from other OBO ontologies are permissible as long as they reference mass/volume nouns (e.g. air, water, blood) and not discrete, countable entities (e.g. a tree, a leaf, a table top).", + "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$", + "type": "string" + }, + "experimental_factor": { + "description": "Experimental factors are essentially the variable aspects of an experiment design which can be used to describe an experiment, or set of experiments, in an increasingly detailed manner. This field accepts ontology terms from Experimental Factor Ontology (EFO) and/or Ontology for Biomedical Investigations (OBI). For a browser of EFO (v 2.95) terms, please see http://purl.bioontology.org/ontology/EFO; for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI", + "type": [ + "string", + "null" + ] + }, + "fertilizer_regm": { + "description": "Information about treatment involving the use of fertilizers; should include the name of fertilizer, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple fertilizer regimens", + "type": [ + "string", + "null" + ] + }, + "fungicide_regm": { + "description": "Information about treatment involving use of fungicides; should include the name of fungicide, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple fungicide regimens", + "type": [ + "string", + "null" + ] + }, + "gaseous_environment": { + "description": "Use of conditions with differing gaseous environments; should include the name of gaseous compound, amount administered, treatment duration, interval and total experimental duration; can include multiple gaseous environment regimens", + "type": [ + "string", + "null" + ] + }, + "genetic_mod": { + "description": "Genetic modifications of the genome of an organism, which may occur naturally by spontaneous mutation, or be introduced by some experimental means, e.g. specification of a transgene or the gene knocked-out or details of transient transfection", + "type": [ + "string", + "null" + ] + }, + "geo_loc_name": { + "description": "The geographical origin of the sample as defined by the country or sea name followed by specific region name.", + "pattern": "^[^:, ][^:]*: [^:, ][^,]*, [^:, ].*$", + "type": "string" + }, + "gravity": { + "description": "Information about treatment involving use of gravity factor to study various types of responses in presence, absence or modified levels of gravity; treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple treatments", + "type": [ + "string", + "null" + ] + }, + "growth_facil": { + "$ref": "#/$defs/GrowthFacilEnum", + "description": "Type of facility/location where the sample was harvested; controlled vocabulary: growth chamber, open top chamber, glasshouse, experimental garden, field." + }, + "growth_habit": { + "$ref": "#/$defs/GrowthHabitEnum", + "description": "Characteristic shape, appearance or growth form of a plant species" + }, + "growth_hormone_regm": { + "description": "Information about treatment involving use of growth hormones; should include the name of growth hormone, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple growth hormone regimens", + "type": [ + "string", + "null" + ] + }, + "herbicide_regm": { + "description": "Information about treatment involving use of herbicides; information about treatment involving use of growth hormones; should include the name of herbicide, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens", + "type": [ + "string", + "null" + ] + }, + "host_age": { + "description": "Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "host_common_name": { + "description": "Common name of the host.", + "type": [ + "string", + "null" + ] + }, + "host_disease_stat": { + "description": "List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text", + "type": [ + "string", + "null" + ] + }, + "host_dry_mass": { + "description": "Measurement of dry mass", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "host_genotype": { + "description": "Observed genotype", + "type": [ + "string", + "null" + ] + }, + "host_height": { + "description": "The height of subject", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "host_length": { + "description": "The length of subject", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "host_life_stage": { + "description": "Description of life stage of host", + "type": [ + "string", + "null" + ] + }, + "host_phenotype": { + "description": "Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP", + "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$", + "type": [ + "string", + "null" + ] + }, + "host_subspecf_genlin": { + "description": "Information about the genetic distinctness of the host organism below the subspecies level e.g., serovar, serotype, biotype, ecotype, variety, cultivar, or any relevant genetic typing schemes like Group I plasmid. Subspecies should not be recorded in this term, but in the NCBI taxonomy. Supply both the lineage name and the lineage rank separated by a colon, e.g., biovar:abc123.", + "type": [ + "string", + "null" + ] + }, + "host_symbiont": { + "description": "The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host.", + "type": [ + "string", + "null" + ] + }, + "host_taxid": { + "description": "NCBI taxon id of the host, e.g. 9606", + "type": [ + "string", + "null" + ] + }, + "host_tot_mass": { + "description": "Total mass of the host at collection, the unit depends on host", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "host_wet_mass": { + "description": "Measurement of wet mass", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "humidity_regm": { + "description": "Information about treatment involving an exposure to varying degree of humidity; information about treatment involving use of growth hormones; should include amount of humidity administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens", + "type": [ + "string", + "null" + ] + }, + "isotope_exposure": { + "description": "List isotope exposure or addition applied to your sample.", + "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]; ([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", + "type": [ + "string", + "null" + ] + }, + "lat_lon": { + "description": "The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system", + "pattern": "^[-+]?([1-8]?\\d(\\.\\d{1,8})?|90(\\.0{1,8})?)\\s[-+]?(180(\\.0{1,8})?|((1[0-7]\\d)|([1-9]?\\d))(\\.\\d{1,8})?)$", + "type": "string" + }, + "light_regm": { + "description": "Information about treatment(s) involving exposure to light, including both light intensity and quality.", + "pattern": "^\\S+.*\\S+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? \\S+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? \\S+$", + "type": [ + "string", + "null" + ] + }, + "mechanical_damage": { + "description": "Information about any mechanical damage exerted on the plant; can include multiple damages and sites", + "type": [ + "string", + "null" + ] + }, + "mineral_nutr_regm": { + "description": "Information about treatment involving the use of mineral supplements; should include the name of mineral nutrient, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple mineral nutrient regimens", + "type": [ + "string", + "null" + ] + }, + "misc_param": { + "description": "Any other measurement performed or parameter collected, that is not listed here", + "pattern": "^([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+\\|)*([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+)$", + "type": [ + "string", + "null" + ] + }, + "non_min_nutr_regm": { + "description": "Information about treatment involving the exposure of plant to non-mineral nutrient such as oxygen, hydrogen or carbon; should include the name of non-mineral nutrient, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple non-mineral nutrient regimens", + "type": [ + "string", + "null" + ] + }, + "organism_count": { + "description": "Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr)", + "pattern": "^([-+]?[0-9]*\\.?[0-9]+ +\\S.*\\|)*([-+]?[0-9]*\\.?[0-9]+ +\\S.*)$", + "type": [ + "string", + "null" + ] + }, + "oxy_stat_samp": { + "$ref": "#/$defs/OxyStatSampEnum", + "description": "Oxygenation status of sample" + }, + "perturbation": { + "description": "Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types", + "type": [ + "string", + "null" + ] + }, + "pesticide_regm": { + "description": "Information about treatment involving use of insecticides; should include the name of pesticide, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple pesticide regimens", + "type": [ + "string", + "null" + ] + }, + "ph_regm": { + "description": "Information about treatment involving exposure of plants to varying levels of ph of the growth media, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimen", + "type": [ + "string", + "null" + ] + }, + "plant_growth_med": { + "description": "Specification of the media for growing the plants or tissue cultured samples, e.g. soil, aeroponic, hydroponic, in vitro solid culture medium, in vitro liquid culture medium. Recommended value is a specific value from EO:plant growth medium (follow this link for terms http://purl.obolibrary.org/obo/EO_0007147) or other controlled vocabulary", + "type": [ + "string", + "null" + ] + }, + "plant_product": { + "description": "Substance produced by the plant, where the sample was obtained from", + "type": [ + "string", + "null" + ] + }, + "plant_sex": { + "$ref": "#/$defs/PlantSexEnum", + "description": "Sex of the reproductive parts on the whole plant, e.g. pistillate, staminate, monoecieous, hermaphrodite." + }, + "plant_struc": { + "description": "Name of plant structure the sample was obtained from; for Plant Ontology (PO) (v releases/2017-12-14) terms, see http://purl.bioontology.org/ontology/PO, e.g. petiole epidermis (PO_0000051). If an individual flower is sampled, the sex of it can be recorded here.", + "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$", + "type": [ + "string", + "null" + ] + }, + "radiation_regm": { + "description": "Information about treatment involving exposure of plant or a plant part to a particular radiation regimen; should include the radiation type, amount or intensity administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple radiation regimens", + "type": [ + "string", + "null" + ] + }, + "rainfall_regm": { + "description": "Information about treatment involving an exposure to a given amount of rainfall, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens", + "type": [ + "string", + "null" + ] + }, + "root_cond": { + "description": "Relevant rooting conditions such as field plot size, sowing density, container dimensions, number of plants per container.", + "type": [ + "string", + "null" + ] + }, + "root_med_carbon": { + "description": "Source of organic carbon in the culture rooting medium; e.g. sucrose.", + "pattern": "^[^;\\t\\r\\x0A\\|]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A\\|]+$", + "type": [ + "string", + "null" + ] + }, + "root_med_macronutr": { + "description": "Measurement of the culture rooting medium macronutrients (N,P, K, Ca, Mg, S); e.g. KH2PO4 (170\u00ac\u2020mg/L).", + "pattern": "^[^;\\t\\r\\x0A\\|]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A\\|]+$", + "type": [ + "string", + "null" + ] + }, + "root_med_micronutr": { + "description": "Measurement of the culture rooting medium micronutrients (Fe, Mn, Zn, B, Cu, Mo); e.g. H3BO3 (6.2\u00ac\u2020mg/L).", + "pattern": "^[^;\\t\\r\\x0A\\|]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A\\|]+$", + "type": [ + "string", + "null" + ] + }, + "root_med_ph": { + "description": "pH measurement of the culture rooting medium; e.g. 5.5.", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "root_med_regl": { + "description": "Growth regulators in the culture rooting medium such as cytokinins, auxins, gybberellins, abscisic acid; e.g. 0.5\u00ac\u2020mg/L NAA.", + "pattern": "^[^;\\t\\r\\x0A\\|]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A\\|]+$", + "type": [ + "string", + "null" + ] + }, + "root_med_solid": { + "description": "Specification of the solidifying agent in the culture rooting medium; e.g. agar.", + "type": [ + "string", + "null" + ] + }, + "root_med_suppl": { + "description": "Organic supplements of the culture rooting medium, such as vitamins, amino acids, organic acids, antibiotics activated charcoal; e.g. nicotinic acid (0.5\u00ac\u2020mg/L).", + "pattern": "^[^;\\t\\r\\x0A\\|]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A\\|]+$", + "type": [ + "string", + "null" + ] + }, + "salinity": { + "description": "The total concentration of all dissolved salts in a liquid or solid sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater.", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "salinity_meth": { + "description": "Reference or method used in determining salinity", + "type": [ + "string", + "null" + ] + }, + "salt_regm": { + "description": "Information about treatment involving use of salts as supplement to liquid and soil growth media; should include the name of salt, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple salt regimens", + "type": [ + "string", + "null" + ] + }, + "samp_capt_status": { + "$ref": "#/$defs/SampCaptStatusEnum", + "description": "Reason for the sample" + }, + "samp_collec_device": { + "description": "The device used to collect an environmental sample. This field accepts terms listed under environmental sampling device (http://purl.obolibrary.org/obo/ENVO). This field also accepts terms listed under specimen collection device (http://purl.obolibrary.org/obo/GENEPIO_0002094).", + "type": [ + "string", + "null" + ] + }, + "samp_collec_method": { + "description": "The method employed for collecting the sample.", + "type": [ + "string", + "null" + ] + }, + "samp_dis_stage": { + "$ref": "#/$defs/SampDisStageEnum", + "description": "Stage of the disease at the time of sample collection, e.g. inoculation, penetration, infection, growth and reproduction, dissemination of pathogen." + }, + "samp_mat_process": { + "description": "A brief description of any processing applied to the sample during or after retrieving the sample from environment, or a link to the relevant protocol(s) performed.", + "type": [ + "string", + "null" + ] + }, + "samp_name": { + "description": "A local identifier or name that for the material sample collected. Refers to the original material collected or to any derived sub-samples.", + "type": "string" + }, + "samp_size": { + "description": "The total amount or size (volume (ml), mass (g) or area (m2) ) of sample collected.", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? \\S+$", + "type": [ + "string", + "null" + ] + }, + "samp_store_dur": { + "description": "Duration for which the sample was stored", + "type": [ + "string", + "null" + ] + }, + "samp_store_loc": { + "description": "Location at which sample was stored, usually name of a specific freezer/room", + "type": [ + "string", + "null" + ] + }, + "samp_store_temp": { + "description": "Temperature at which the sample was stored (degrees are assumed)", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": "string" + }, + "sample_link": { + "description": "A unique identifier to assign parent-child, subsample, or sibling samples. This is relevant when a sample or other material was used to generate the new sample.", + "pattern": "[^\\:\\n\\r]+\\:[^\\:\\n\\r]+", + "type": [ + "string", + "null" + ] + }, + "season_environment": { + "description": "Treatment involving an exposure to a particular season (e.g. Winter, summer, rabi, rainy etc.), treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment", + "type": [ + "string", + "null" + ] + }, + "size_frac": { + "description": "Filtering pore size used in sample preparation", + "type": [ + "string", + "null" + ] + }, + "source_mat_id": { + "description": "A globally unique identifier assigned to the biological sample.", + "pattern": "[^\\:\\n\\r]+\\:[^\\:\\n\\r]+", + "type": [ + "string", + "null" + ] + }, + "specific_ecosystem": { + "$ref": "#/$defs/SpecificEcosystemEnum", + "description": "Specific ecosystems represent specific features of the environment like aphotic zone in an ocean or gastric mucosa within a host digestive system. Specific ecosystem is in position 5/5 in a GOLD path." + }, + "standing_water_regm": { + "description": "Treatment involving an exposure to standing water during a plant's life span, types can be flood water or standing water, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens", + "type": [ + "string", + "null" + ] + }, + "start_date_inc": { + "description": "Date the incubation was started. Only relevant for incubation samples.", + "pattern": "^[12]\\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\\d|3[01]))?)?$", + "type": [ + "string", + "null" + ] + }, + "temp": { + "description": "Temperature of the sample at the time of sampling.", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "tiss_cult_growth_med": { + "description": "Description of plant tissue culture growth media used", + "type": [ + "string", + "null" + ] + }, + "water_temp_regm": { + "description": "Information about treatment involving an exposure to water with varying degree of temperature, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens", + "type": [ + "string", + "null" + ] + }, + "watering_regm": { + "description": "Information about treatment involving an exposure to watering frequencies, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens", + "type": [ + "string", + "null" + ] + } + }, + "required": [ + "collection_date", + "elev", + "env_broad_scale", + "env_local_scale", + "env_medium", + "geo_loc_name", + "growth_facil", + "lat_lon", + "samp_store_temp", + "analysis_type", + "samp_name" + ], + "title": "PlantAssociatedInterface", + "type": "object" + }, + "PlantSexEnum": { + "description": "", + "enum": [ + "Androdioecious", + "Androecious", + "Androgynous", + "Androgynomonoecious", + "Andromonoecious", + "Bisexual", + "Dichogamous", + "Diclinous", + "Dioecious", + "Gynodioecious", + "Gynoecious", + "Gynomonoecious", + "Hermaphroditic", + "Imperfect", + "Monoclinous", + "Monoecious", + "Perfect", + "Polygamodioecious", + "Polygamomonoecious", + "Polygamous", + "Protandrous", + "Protogynous", + "Subandroecious", + "Subdioecious", + "Subgynoecious", + "Synoecious", + "Trimonoecious", + "Trioecious", + "Unisexual" + ], + "title": "PlantSexEnum", + "type": "string" + }, + "ProfilePositionEnum": { + "description": "", + "enum": [ + "summit", + "shoulder", + "backslope", + "footslope", + "toeslope" + ], + "title": "ProfilePositionEnum", + "type": "string" + }, + "QuadPosEnum": { + "description": "", + "enum": [ + "North side", + "West side", + "South side", + "East side" + ], + "title": "QuadPosEnum", + "type": "string" + }, + "RNASampleFormatEnum": { + "description": "", + "enum": [ + "10 mM Tris-HCl", + "DNAStable", + "Ethanol", + "Low EDTA TE", + "MDA reaction buffer", + "PBS", + "Pellet", + "RNAStable", + "TE", + "Water", + "Gentegra-DNA", + "Gentegra-RNA" + ], + "title": "RNASampleFormatEnum", + "type": "string" + }, + "RelSampLocEnum": { + "description": "", + "enum": [ + "edge of car", + "center of car", + "under a seat" + ], + "title": "RelSampLocEnum", + "type": "string" + }, + "RelToOxygenEnum": { + "description": "", + "enum": [ + "aerobe", + "anaerobe", + "facultative", + "microaerophilic", + "microanaerobe", + "obligate aerobe", + "obligate anaerobe" + ], + "title": "RelToOxygenEnum", + "type": "string" + }, + "RnaSampleFormatEnum": { + "description": "", + "enum": [ + "10 mM Tris-HCl", + "DNAStable", + "Ethanol", + "Low EDTA TE", + "MDA reaction buffer", + "PBS", + "Pellet", + "RNAStable", + "TE", + "Water" + ], + "title": "RnaSampleFormatEnum", + "type": "string" + }, + "RoomCondtEnum": { + "description": "", + "enum": [ + "new", + "visible wear", + "needs repair", + "damaged", + "rupture", + "visible signs of mold/mildew" + ], + "title": "RoomCondtEnum", + "type": "string" + }, + "RoomConnectedEnum": { + "description": "", + "enum": [ + "attic", + "bathroom", + "closet", + "conference room", + "elevator", + "examining room", + "hallway", + "kitchen", + "mail room", + "office", + "stairwell" + ], + "title": "RoomConnectedEnum", + "type": "string" + }, + "RoomLocEnum": { + "description": "", + "enum": [ + "corner room", + "interior room", + "exterior wall" + ], + "title": "RoomLocEnum", + "type": "string" + }, + "RoomSampPosEnum": { + "description": "", + "enum": [ + "north corner", + "south corner", + "west corner", + "east corner", + "northeast corner", + "northwest corner", + "southeast corner", + "southwest corner", + "center" + ], + "title": "RoomSampPosEnum", + "type": "string" + }, + "RoomTypeEnum": { + "description": "", + "enum": [ + "attic", + "bathroom", + "closet", + "conference room", + "elevator", + "examining room", + "hallway", + "kitchen", + "mail room", + "private office", + "open office", + "stairwell", + ",restroom", + "lobby", + "vestibule", + "mechanical or electrical room", + "data center", + "laboratory_wet", + "laboratory_dry", + "gymnasium", + "natatorium", + "auditorium", + "lockers", + "cafe", + "warehouse" + ], + "title": "RoomTypeEnum", + "type": "string" + }, + "SampCaptStatusEnum": { + "description": "", + "enum": [ + "active surveillance in response to an outbreak", + "active surveillance not initiated by an outbreak", + "farm sample", + "market sample", + "other" + ], + "title": "SampCaptStatusEnum", + "type": "string" + }, + "SampCollectPointEnum": { + "description": "", + "enum": [ + "well", + "test well", + "drilling rig", + "wellhead", + "separator", + "storage tank", + "other" + ], + "title": "SampCollectPointEnum", + "type": "string" + }, + "SampDisStageEnum": { + "description": "", + "enum": [ + "dissemination", + "growth and reproduction", + "infection", + "inoculation", + "penetration", + "other" + ], + "title": "SampDisStageEnum", + "type": "string" + }, + "SampFloorEnum": { + "description": "", + "enum": [ + "1st floor", + "2nd floor", + "basement", + "lobby" + ], + "title": "SampFloorEnum", + "type": "string" + }, + "SampSubtypeEnum": { + "description": "", + "enum": [ + "oil phase", + "water phase", + "biofilm", + "not applicable", + "other" + ], + "title": "SampSubtypeEnum", + "type": "string" + }, + "SampWeatherEnum": { + "description": "", + "enum": [ + "clear sky", + "cloudy", + "foggy", + "hail", + "rain", + "snow", + "sleet", + "sunny", + "windy" + ], + "title": "SampWeatherEnum", + "type": "string" + }, + "SampleData": { + "additionalProperties": false, + "description": "represents data produced by the DataHarmonizer tabs of the submission portal", + "properties": { + "air_data": { + "description": "aggregation slot relating air data collections to a SampleData container", + "items": { + "$ref": "#/$defs/AirInterface" + }, + "type": [ + "array", + "null" + ] + }, + "biofilm_data": { + "description": "aggregation slot relating biofilm data collections to a SampleData container", + "items": { + "$ref": "#/$defs/BiofilmInterface" + }, + "type": [ + "array", + "null" + ] + }, + "built_env_data": { + "description": "aggregation slot relating built_env data collections to a SampleData container", + "items": { + "$ref": "#/$defs/BuiltEnvInterface" + }, + "type": [ + "array", + "null" + ] + }, + "emsl_data": { + "description": "aggregation slot relating emsl data collections to a SampleData container", + "items": { + "$ref": "#/$defs/EmslInterface" + }, + "type": [ + "array", + "null" + ] + }, + "host_associated_data": { + "description": "aggregation slot relating host_associated data collections to a SampleData container", + "items": { + "$ref": "#/$defs/HostAssociatedInterface" + }, + "type": [ + "array", + "null" + ] + }, + "jgi_mg_data": { + "description": "aggregation slot relating jgi_mg data collections to a SampleData container", + "items": { + "$ref": "#/$defs/JgiMgInterface" + }, + "type": [ + "array", + "null" + ] + }, + "jgi_mg_lr_data": { + "description": "aggregation slot relating jgi_mg_lr data collections to a SampleData container", + "items": { + "$ref": "#/$defs/JgiMgLrInterface" + }, + "type": [ + "array", + "null" + ] + }, + "jgi_mt_data": { + "description": "aggregation slot relating jgi_mt data collections to a SampleData container", + "items": { + "$ref": "#/$defs/JgiMtInterface" + }, + "type": [ + "array", + "null" + ] + }, + "plant_associated_data": { + "description": "aggregation slot relating plant_associated data collections to a SampleData container", + "items": { + "$ref": "#/$defs/PlantAssociatedInterface" + }, + "type": [ + "array", + "null" + ] + }, + "sediment_data": { + "description": "aggregation slot relating sediment data collections to a SampleData container", + "items": { + "$ref": "#/$defs/SedimentInterface" + }, + "type": [ + "array", + "null" + ] + }, + "soil_data": { + "description": "aggregation slot relating soil data collections to a SampleData container", + "items": { + "$ref": "#/$defs/SoilInterface" + }, + "type": [ + "array", + "null" + ] + }, + "wastewater_sludge_data": { + "description": "aggregation slot relating wastewater_sludge data collections to a SampleData container", + "items": { + "$ref": "#/$defs/WastewaterSludgeInterface" + }, + "type": [ + "array", + "null" + ] + }, + "water_data": { + "description": "aggregation slot relating water data collections to a SampleData container", + "items": { + "$ref": "#/$defs/WaterInterface" + }, + "type": [ + "array", + "null" + ] + } + }, + "title": "SampleData", + "type": "object" + }, + "SampleTypeEnum": { + "description": "", + "enum": [ + "soil", + "soil - water extract", + "plant associated", + "sediment", + "water" + ], + "title": "SampleTypeEnum", + "type": "string" + }, + "SeasonUseEnum": { + "description": "", + "enum": [ + "Spring", + "Summer", + "Fall", + "Winter" + ], + "title": "SeasonUseEnum", + "type": "string" + }, + "SedimentInterface": { + "additionalProperties": false, + "description": "sediment dh_interface", + "properties": { + "air_temp_regm": { + "description": "Information about treatment involving an exposure to varying temperatures; should include the temperature, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include different temperature regimens", + "type": [ + "string", + "null" + ] + }, + "alkalinity": { + "description": "Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "alkalinity_method": { + "description": "Method used for alkalinity measurement", + "type": [ + "string", + "null" + ] + }, + "alkyl_diethers": { + "description": "Concentration of alkyl diethers", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "aminopept_act": { + "description": "Measurement of aminopeptidase activity", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "ammonium": { + "description": "Concentration of ammonium in the sample", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "analysis_type": { + "description": "Select all the data types associated or available for this biosample", + "items": { + "$ref": "#/$defs/AnalysisTypeEnum" + }, + "type": "array" + }, + "bacteria_carb_prod": { + "description": "Measurement of bacterial carbon production", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "biomass": { + "description": "Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements", + "pattern": "^([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+\\|)*([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+)$", + "type": [ + "string", + "null" + ] + }, + "biotic_regm": { + "description": "Information about treatment(s) involving use of biotic factors, such as bacteria, viruses or fungi.", + "type": [ + "string", + "null" + ] + }, + "biotic_relationship": { + "$ref": "#/$defs/BioticRelationshipEnum", + "description": "Description of relationship(s) between the subject organism and other organism(s) it is associated with. E.g., parasite on species X; mutualist with species Y. The target organism is the subject of the relationship, and the other organism(s) is the object" + }, + "bishomohopanol": { + "description": "Concentration of bishomohopanol", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "bromide": { + "description": "Concentration of bromide", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "calcium": { + "description": "Concentration of calcium in the sample", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "carb_nitro_ratio": { + "description": "Ratio of amount or concentrations of carbon to nitrogen", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "number", + "null" + ] + }, + "chem_administration": { + "description": "List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi", + "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\];([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", + "type": [ + "string", + "null" + ] + }, + "chloride": { + "description": "Concentration of chloride in the sample", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "chlorophyll": { + "description": "Concentration of chlorophyll", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "climate_environment": { + "description": "Treatment involving an exposure to a particular climate; treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple climates", + "type": [ + "string", + "null" + ] + }, + "collection_date": { + "description": "The date of sampling", + "pattern": "^[12]\\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\\d|3[01]))?)?$", + "type": "string" + }, + "collection_date_inc": { + "description": "Date the incubation was harvested/collected/ended. Only relevant for incubation samples.", + "pattern": "^[12]\\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\\d|3[01]))?)?$", + "type": [ + "string", + "null" + ] + }, + "collection_time": { + "description": "The time of sampling, either as an instance (single point) or interval.", + "pattern": "^([01]?\\d|2[0-3]|24(?=:00?:00?$)):([0-5]\\d)(:([0-5]\\d))?$", + "type": [ + "string", + "null" + ] + }, + "density": { + "description": "Density of the sample, which is its mass per unit volume (aka volumetric mass density)", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "depth": { + "description": "The vertical distance below local surface, e.g. for sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples.", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)?\\s*-\\s*[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)?$", + "type": "string" + }, + "diether_lipids": { + "description": "Concentration of diether lipids; can include multiple types of diether lipids", + "pattern": "^([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+\\|)*([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+)$", + "type": [ + "string", + "null" + ] + }, + "diss_carb_dioxide": { + "description": "Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "diss_hydrogen": { + "description": "Concentration of dissolved hydrogen", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "diss_inorg_carb": { + "description": "Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "diss_org_carb": { + "description": "Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "diss_org_nitro": { + "description": "Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "diss_oxygen": { + "description": "Concentration of dissolved oxygen", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "ecosystem": { + "$ref": "#/$defs/EcosystemEnum", + "description": "An ecosystem is a combination of a physical environment (abiotic factors) and all the organisms (biotic factors) that interact with this environment. Ecosystem is in position 1/5 in a GOLD path." + }, + "ecosystem_category": { + "$ref": "#/$defs/EcosystemCategoryEnum", + "description": "Ecosystem categories represent divisions within the ecosystem based on specific characteristics of the environment from where an organism or sample is isolated. Ecosystem category is in position 2/5 in a GOLD path." + }, + "ecosystem_subtype": { + "$ref": "#/$defs/EcosystemSubtypeEnum", + "description": "Ecosystem subtypes represent further subdivision of Ecosystem types into more distinct subtypes. Ecosystem subtype is in position 4/5 in a GOLD path." + }, + "ecosystem_type": { + "$ref": "#/$defs/EcosystemTypeEnum", + "description": "Ecosystem types represent things having common characteristics within the Ecosystem Category. These common characteristics based grouping is still broad but specific to the characteristics of a given environment. Ecosystem type is in position 3/5 in a GOLD path." + }, + "elev": { + "description": "Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit.", + "type": "number" + }, + "env_broad_scale": { + "description": "In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO's biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html", + "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$", + "type": "string" + }, + "env_local_scale": { + "description": "Report the entity or entities which are in the sample or specimen\u2019s local vicinity and which you believe have significant causal influences on your sample or specimen. We recommend using EnvO terms which are of smaller spatial grain than your entry for env_broad_scale. Terms, such as anatomical sites, from other OBO Library ontologies which interoperate with EnvO (e.g. UBERON) are accepted in this field. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS.", + "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$", + "type": "string" + }, + "env_medium": { + "description": "Report the environmental material(s) immediately surrounding the sample or specimen at the time of sampling. We recommend using subclasses of 'environmental material' (http://purl.obolibrary.org/obo/ENVO_00010483). EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS . Terms from other OBO ontologies are permissible as long as they reference mass/volume nouns (e.g. air, water, blood) and not discrete, countable entities (e.g. a tree, a leaf, a table top).", + "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$", + "type": "string" + }, + "experimental_factor": { + "description": "Experimental factors are essentially the variable aspects of an experiment design which can be used to describe an experiment, or set of experiments, in an increasingly detailed manner. This field accepts ontology terms from Experimental Factor Ontology (EFO) and/or Ontology for Biomedical Investigations (OBI). For a browser of EFO (v 2.95) terms, please see http://purl.bioontology.org/ontology/EFO; for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI", + "type": [ + "string", + "null" + ] + }, + "extreme_event": { + "description": "Unusual physical events that may have affected microbial populations", + "type": [ + "string", + "null" + ] + }, + "fire": { + "description": "Historical and/or physical evidence of fire", + "pattern": "^[12]\\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\\d|3[01]))?)?(\\s+to\\s+[12]\\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\\d|3[01]))?)?)?$", + "type": [ + "string", + "null" + ] + }, + "flooding": { + "description": "Historical and/or physical evidence of flooding", + "type": [ + "string", + "null" + ] + }, + "gaseous_environment": { + "description": "Use of conditions with differing gaseous environments; should include the name of gaseous compound, amount administered, treatment duration, interval and total experimental duration; can include multiple gaseous environment regimens", + "type": [ + "string", + "null" + ] + }, + "geo_loc_name": { + "description": "The geographical origin of the sample as defined by the country or sea name followed by specific region name.", + "pattern": "^[^:, ][^:]*: [^:, ][^,]*, [^:, ].*$", + "type": "string" + }, + "glucosidase_act": { + "description": "Measurement of glucosidase activity", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "humidity_regm": { + "description": "Information about treatment involving an exposure to varying degree of humidity; information about treatment involving use of growth hormones; should include amount of humidity administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens", + "type": [ + "string", + "null" + ] + }, + "isotope_exposure": { + "description": "List isotope exposure or addition applied to your sample.", + "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]; ([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", + "type": [ + "string", + "null" + ] + }, + "lat_lon": { + "description": "The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system", + "pattern": "^[-+]?([1-8]?\\d(\\.\\d{1,8})?|90(\\.0{1,8})?)\\s[-+]?(180(\\.0{1,8})?|((1[0-7]\\d)|([1-9]?\\d))(\\.\\d{1,8})?)$", + "type": "string" + }, + "light_regm": { + "description": "Information about treatment(s) involving exposure to light, including both light intensity and quality.", + "pattern": "^\\S+.*\\S+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? \\S+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? \\S+$", + "type": [ + "string", + "null" + ] + }, + "magnesium": { + "description": "Concentration of magnesium in the sample", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "mean_frict_vel": { + "description": "Measurement of mean friction velocity", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "mean_peak_frict_vel": { + "description": "Measurement of mean peak friction velocity", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "methane": { + "description": "Methane (gas) amount or concentration at the time of sampling", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "micro_biomass_c_meth": { + "description": "Reference or method used in determining microbial biomass carbon", + "type": [ + "string", + "null" + ] + }, + "micro_biomass_meth": { + "description": "Reference or method used in determining microbial biomass", + "type": [ + "string", + "null" + ] + }, + "micro_biomass_n_meth": { + "description": "Reference or method used in determining microbial biomass nitrogen", + "type": [ + "string", + "null" + ] + }, + "microbial_biomass": { + "description": "The part of the organic matter in the soil that constitutes living microorganisms smaller than 5-10 micrometer. If you keep this, you would need to have correction factors used for conversion to the final units", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "microbial_biomass_c": { + "description": "The part of the organic matter in the soil that constitutes living microorganisms smaller than 5-10 micrometer.", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? \\S+$", + "type": [ + "string", + "null" + ] + }, + "microbial_biomass_n": { + "description": "The part of the organic matter in the soil that constitutes living microorganisms smaller than 5-10 micrometer.", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? \\S+$", + "type": [ + "string", + "null" + ] + }, + "misc_param": { + "description": "Any other measurement performed or parameter collected, that is not listed here", + "pattern": "^([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+\\|)*([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+)$", + "type": [ + "string", + "null" + ] + }, + "n_alkanes": { + "description": "Concentration of n-alkanes; can include multiple n-alkanes", + "pattern": "^([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+\\|)*([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+)$", + "type": [ + "string", + "null" + ] + }, + "nitrate": { + "description": "Concentration of nitrate in the sample", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "nitrite": { + "description": "Concentration of nitrite in the sample", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "nitro": { + "description": "Concentration of nitrogen (total)", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "org_carb": { + "description": "Concentration of organic carbon", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "org_matter": { + "description": "Concentration of organic matter", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "org_nitro": { + "description": "Concentration of organic nitrogen", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "org_nitro_method": { + "description": "Method used for obtaining organic nitrogen", + "type": [ + "string", + "null" + ] + }, + "organism_count": { + "description": "Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr)", + "pattern": "^([-+]?[0-9]*\\.?[0-9]+ +\\S.*\\|)*([-+]?[0-9]*\\.?[0-9]+ +\\S.*)$", + "type": [ + "string", + "null" + ] + }, + "oxy_stat_samp": { + "$ref": "#/$defs/OxyStatSampEnum", + "description": "Oxygenation status of sample" + }, + "part_org_carb": { + "description": "Concentration of particulate organic carbon", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "particle_class": { + "description": "Particles are classified, based on their size, into six general categories:clay, silt, sand, gravel, cobbles, and boulders; should include amount of particle preceded by the name of the particle type; can include multiple values", + "pattern": "^([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+\\|)*([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+)$", + "type": [ + "string", + "null" + ] + }, + "perturbation": { + "description": "Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types", + "type": [ + "string", + "null" + ] + }, + "petroleum_hydrocarb": { + "description": "Concentration of petroleum hydrocarbon", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "ph": { + "description": "pH measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid", + "maximum": 14, + "minimum": 0, + "type": [ + "number", + "null" + ] + }, + "ph_meth": { + "description": "Reference or method used in determining ph", + "type": [ + "string", + "null" + ] + }, + "phaeopigments": { + "description": "Concentration of phaeopigments; can include multiple phaeopigments", + "pattern": "^([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+\\|)*([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+)$", + "type": [ + "string", + "null" + ] + }, + "phosphate": { + "description": "Concentration of phosphate", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "phosplipid_fatt_acid": { + "description": "Concentration of phospholipid fatty acids; can include multiple values", + "pattern": "^([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+\\|)*([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+)$", + "type": [ + "string", + "null" + ] + }, + "porosity": { + "description": "Porosity of deposited sediment is volume of voids divided by the total volume of sample", + "type": [ + "string", + "null" + ] + }, + "potassium": { + "description": "Concentration of potassium in the sample", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "pressure": { + "description": "Pressure to which the sample is subject to, in atmospheres", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "redox_potential": { + "description": "Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "salinity": { + "description": "The total concentration of all dissolved salts in a liquid or solid sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater.", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "salinity_meth": { + "description": "Reference or method used in determining salinity", + "type": [ + "string", + "null" + ] + }, + "samp_collec_device": { + "description": "The device used to collect an environmental sample. This field accepts terms listed under environmental sampling device (http://purl.obolibrary.org/obo/ENVO). This field also accepts terms listed under specimen collection device (http://purl.obolibrary.org/obo/GENEPIO_0002094).", + "type": [ + "string", + "null" + ] + }, + "samp_collec_method": { + "description": "The method employed for collecting the sample.", + "type": [ + "string", + "null" + ] + }, + "samp_mat_process": { + "description": "A brief description of any processing applied to the sample during or after retrieving the sample from environment, or a link to the relevant protocol(s) performed.", + "type": [ + "string", + "null" + ] + }, + "samp_name": { + "description": "A local identifier or name that for the material sample collected. Refers to the original material collected or to any derived sub-samples.", + "type": "string" + }, + "samp_size": { + "description": "The total amount or size (volume (ml), mass (g) or area (m2) ) of sample collected.", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? \\S+$", + "type": [ + "string", + "null" + ] + }, + "samp_store_dur": { + "description": "Duration for which the sample was stored", + "type": [ + "string", + "null" + ] + }, + "samp_store_loc": { + "description": "Location at which sample was stored, usually name of a specific freezer/room", + "type": [ + "string", + "null" + ] + }, + "samp_store_temp": { + "description": "Temperature at which the sample was stored (degrees are assumed)", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": "string" + }, + "sample_link": { + "description": "A unique identifier to assign parent-child, subsample, or sibling samples. This is relevant when a sample or other material was used to generate the new sample.", + "pattern": "[^\\:\\n\\r]+\\:[^\\:\\n\\r]+", + "type": [ + "string", + "null" + ] + }, + "sediment_type": { + "$ref": "#/$defs/SedimentTypeEnum", + "description": "Information about the sediment type based on major constituents" + }, + "sieving": { + "description": "Collection design of pooled samples and/or sieve size and amount of sample sieved", + "type": [ + "string", + "null" + ] + }, + "silicate": { + "description": "Concentration of silicate", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "size_frac": { + "description": "Filtering pore size used in sample preparation", + "type": [ + "string", + "null" + ] + }, + "sodium": { + "description": "Sodium concentration in the sample", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "source_mat_id": { + "description": "A globally unique identifier assigned to the biological sample.", + "pattern": "[^\\:\\n\\r]+\\:[^\\:\\n\\r]+", + "type": [ + "string", + "null" + ] + }, + "specific_ecosystem": { + "$ref": "#/$defs/SpecificEcosystemEnum", + "description": "Specific ecosystems represent specific features of the environment like aphotic zone in an ocean or gastric mucosa within a host digestive system. Specific ecosystem is in position 5/5 in a GOLD path." + }, + "start_date_inc": { + "description": "Date the incubation was started. Only relevant for incubation samples.", + "pattern": "^[12]\\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\\d|3[01]))?)?$", + "type": [ + "string", + "null" + ] + }, + "sulfate": { + "description": "Concentration of sulfate in the sample", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "sulfide": { + "description": "Concentration of sulfide in the sample", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "temp": { + "description": "Temperature of the sample at the time of sampling.", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "tidal_stage": { + "$ref": "#/$defs/TidalStageEnum", + "description": "Stage of tide" + }, + "tot_carb": { + "description": "Total carbon content", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "tot_depth_water_col": { + "description": "Measurement of total depth of water column", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "tot_nitro_cont_meth": { + "description": "Reference or method used in determining the total nitrogen", + "type": [ + "string", + "null" + ] + }, + "tot_nitro_content": { + "description": "Total nitrogen content of the sample", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "tot_org_c_meth": { + "description": "Reference or method used in determining total organic carbon", + "type": [ + "string", + "null" + ] + }, + "tot_org_carb": { + "description": "Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "turbidity": { + "description": "Measure of the amount of cloudiness or haziness in water caused by individual particles", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "water_cont_soil_meth": { + "description": "Reference or method used in determining the water content of soil", + "type": [ + "string", + "null" + ] + }, + "water_content": { + "description": "Water content measurement", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)?%? \\S.+$", + "type": [ + "string", + "null" + ] + }, + "watering_regm": { + "description": "Information about treatment involving an exposure to watering frequencies, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens", + "type": [ + "string", + "null" + ] + } + }, + "required": [ + "collection_date", + "depth", + "elev", + "env_broad_scale", + "env_local_scale", + "env_medium", + "geo_loc_name", + "lat_lon", + "samp_store_temp", + "analysis_type", + "samp_name" + ], + "title": "SedimentInterface", + "type": "object" + }, + "SedimentTypeEnum": { + "description": "", + "enum": [ + "biogenous", + "cosmogenous", + "hydrogenous", + "lithogenous" + ], + "title": "SedimentTypeEnum", + "type": "string" + }, + "ShadingDeviceCondEnum": { + "description": "", + "enum": [ + "damaged", + "needs repair", + "new", + "rupture", + "visible wear" + ], + "title": "ShadingDeviceCondEnum", + "type": "string" + }, + "ShadingDeviceTypeEnum": { + "description": "", + "enum": [ + "bahama shutters", + "exterior roll blind", + "gambrel awning", + "hood awning", + "porchroller awning", + "sarasota shutters", + "slatted aluminum", + "solid aluminum awning", + "sun screen", + "tree", + "trellis", + "venetian awning" + ], + "title": "ShadingDeviceTypeEnum", + "type": "string" + }, + "SoilHorizonEnum": { + "description": "", + "enum": [ + "O horizon", + "A horizon", + "E horizon", + "B horizon", + "C horizon", + "R layer", + "Permafrost", + "M horizon" + ], + "title": "SoilHorizonEnum", + "type": "string" + }, + "SoilInterface": { + "additionalProperties": false, + "description": "soil dh_interface", + "properties": { + "agrochem_addition": { + "description": "Addition of fertilizers, pesticides, etc. - amount and time of applications", + "pattern": ".*", + "type": [ + "string", + "null" + ] + }, + "air_temp_regm": { + "description": "Information about treatment involving an exposure to varying temperatures; should include the temperature, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include different temperature regimens", + "type": [ + "string", + "null" + ] + }, + "al_sat": { + "description": "The relative abundance of aluminum in the sample", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "al_sat_meth": { + "description": "Reference or method used in determining Aluminum saturation", + "type": [ + "string", + "null" + ] + }, + "ammonium_nitrogen": { + "description": "Concentration of ammonium nitrogen in the sample", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "analysis_type": { + "description": "Select all the data types associated or available for this biosample", + "items": { + "$ref": "#/$defs/AnalysisTypeEnum" + }, + "type": "array" + }, + "annual_precpt": { + "description": "The average of all annual precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or Isohyetal maps.", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "annual_temp": { + "description": "Mean annual temperature", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "biotic_regm": { + "description": "Information about treatment(s) involving use of biotic factors, such as bacteria, viruses or fungi.", + "type": [ + "string", + "null" + ] + }, + "biotic_relationship": { + "$ref": "#/$defs/BioticRelationshipEnum", + "description": "Description of relationship(s) between the subject organism and other organism(s) it is associated with. E.g., parasite on species X; mutualist with species Y. The target organism is the subject of the relationship, and the other organism(s) is the object" + }, + "bulk_elect_conductivity": { + "description": "Electrical conductivity is a measure of the ability to carry electric current, which is mostly dictated by the chemistry of and amount of water.", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "carb_nitro_ratio": { + "description": "Ratio of amount or concentrations of carbon to nitrogen", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "number", + "null" + ] + }, + "chem_administration": { + "description": "List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi", + "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\];([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", + "type": [ + "string", + "null" + ] + }, + "climate_environment": { + "description": "Treatment involving an exposure to a particular climate; treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple climates", + "type": [ + "string", + "null" + ] + }, + "collection_date": { + "description": "The date of sampling", + "pattern": "^[12]\\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\\d|3[01]))?)?$", + "type": "string" + }, + "collection_date_inc": { + "description": "Date the incubation was harvested/collected/ended. Only relevant for incubation samples.", + "pattern": "^[12]\\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\\d|3[01]))?)?$", + "type": [ + "string", + "null" + ] + }, + "collection_time": { + "description": "The time of sampling, either as an instance (single point) or interval.", + "pattern": "^([01]?\\d|2[0-3]|24(?=:00?:00?$)):([0-5]\\d)(:([0-5]\\d))?$", + "type": [ + "string", + "null" + ] + }, + "collection_time_inc": { + "description": "Time the incubation was harvested/collected/ended. Only relevant for incubation samples.", + "pattern": "^([01]?\\d|2[0-3]|24(?=:00?:00?$)):([0-5]\\d)(:([0-5]\\d))?$", + "type": [ + "string", + "null" + ] + }, + "crop_rotation": { + "description": "Whether or not crop is rotated, and if yes, rotation schedule", + "type": [ + "string", + "null" + ] + }, + "cur_land_use": { + "$ref": "#/$defs/CurLandUseEnum", + "description": "Present state of sample site" + }, + "cur_vegetation": { + "description": "Vegetation classification from one or more standard classification systems, or agricultural crop", + "type": [ + "string", + "null" + ] + }, + "cur_vegetation_meth": { + "description": "Reference or method used in vegetation classification", + "type": [ + "string", + "null" + ] + }, + "depth": { + "description": "The vertical distance below local surface, e.g. for sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples.", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)?\\s*-\\s*[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)?$", + "type": "string" + }, + "drainage_class": { + "$ref": "#/$defs/DrainageClassEnum", + "description": "Drainage classification from a standard system such as the USDA system" + }, + "ecosystem": { + "$ref": "#/$defs/EcosystemForSoilEnum", + "description": "An ecosystem is a combination of a physical environment (abiotic factors) and all the organisms (biotic factors) that interact with this environment. Ecosystem is in position 1/5 in a GOLD path." + }, + "ecosystem_category": { + "$ref": "#/$defs/EcosystemCategoryForSoilEnum", + "description": "Ecosystem categories represent divisions within the ecosystem based on specific characteristics of the environment from where an organism or sample is isolated. Ecosystem category is in position 2/5 in a GOLD path." + }, + "ecosystem_subtype": { + "$ref": "#/$defs/EcosystemSubtypeForSoilEnum", + "description": "Ecosystem subtypes represent further subdivision of Ecosystem types into more distinct subtypes. Ecosystem subtype is in position 4/5 in a GOLD path." + }, + "ecosystem_type": { + "$ref": "#/$defs/EcosystemTypeForSoilEnum", + "description": "Ecosystem types represent things having common characteristics within the Ecosystem Category. These common characteristics based grouping is still broad but specific to the characteristics of a given environment. Ecosystem type is in position 3/5 in a GOLD path." + }, + "elev": { + "description": "Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit.", + "type": "number" + }, + "env_broad_scale": { + "anyOf": [ + { + "$ref": "#/$defs/EnvBroadScaleSoilEnum" + }, + { + "type": "string" + } + ], + "description": "In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO's biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html", + "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$", + "type": "string" + }, + "env_local_scale": { + "anyOf": [ + { + "$ref": "#/$defs/EnvLocalScaleSoilEnum" + }, + { + "type": "string" + } + ], + "description": "Report the entity or entities which are in the sample or specimen\u2019s local vicinity and which you believe have significant causal influences on your sample or specimen. We recommend using EnvO terms which are of smaller spatial grain than your entry for env_broad_scale. Terms, such as anatomical sites, from other OBO Library ontologies which interoperate with EnvO (e.g. UBERON) are accepted in this field. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS.", + "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$", + "type": "string" + }, + "env_medium": { + "anyOf": [ + { + "$ref": "#/$defs/EnvMediumSoilEnum" + }, + { + "type": "string" + } + ], + "description": "Report the environmental material(s) immediately surrounding the sample or specimen at the time of sampling. We recommend using subclasses of 'environmental material' (http://purl.obolibrary.org/obo/ENVO_00010483). EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS . Terms from other OBO ontologies are permissible as long as they reference mass/volume nouns (e.g. air, water, blood) and not discrete, countable entities (e.g. a tree, a leaf, a table top).", + "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$", + "type": "string" + }, + "experimental_factor": { + "description": "Experimental factors are essentially the variable aspects of an experiment design which can be used to describe an experiment, or set of experiments, in an increasingly detailed manner. This field accepts ontology terms from Experimental Factor Ontology (EFO) and/or Ontology for Biomedical Investigations (OBI). For a browser of EFO (v 2.95) terms, please see http://purl.bioontology.org/ontology/EFO; for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI", + "type": [ + "string", + "null" + ] + }, + "experimental_factor_other": { + "description": "Other details about your sample that you feel can't be accurately represented in the available columns.", + "type": [ + "string", + "null" + ] + }, + "extreme_event": { + "description": "Unusual physical events that may have affected microbial populations", + "type": [ + "string", + "null" + ] + }, + "fao_class": { + "$ref": "#/$defs/FaoClassEnum", + "description": "Soil classification from the FAO World Reference Database for Soil Resources. The list can be found at http://www.fao.org/nr/land/sols/soil/wrb-soil-maps/reference-groups" + }, + "filter_method": { + "description": "Type of filter used or how the sample was filtered", + "type": [ + "string", + "null" + ] + }, + "fire": { + "description": "Historical and/or physical evidence of fire", + "pattern": "^[12]\\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\\d|3[01]))?)?(\\s+to\\s+[12]\\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\\d|3[01]))?)?)?$", + "type": [ + "string", + "null" + ] + }, + "flooding": { + "description": "Historical and/or physical evidence of flooding", + "type": [ + "string", + "null" + ] + }, + "gaseous_environment": { + "description": "Use of conditions with differing gaseous environments; should include the name of gaseous compound, amount administered, treatment duration, interval and total experimental duration; can include multiple gaseous environment regimens", + "type": [ + "string", + "null" + ] + }, + "geo_loc_name": { + "description": "The geographical origin of the sample as defined by the country or sea name followed by specific region name.", + "pattern": "^[^:, ][^:]*: [^:, ][^,]*, [^:, ].*$", + "type": "string" + }, + "growth_facil": { + "$ref": "#/$defs/GrowthFacilEnum", + "description": "Type of facility/location where the sample was harvested; controlled vocabulary: growth chamber, open top chamber, glasshouse, experimental garden, field." + }, + "heavy_metals": { + "description": "Heavy metals present in the sample and their concentrations.", + "pattern": "^([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+\\|)*([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+)$", + "type": [ + "string", + "null" + ] + }, + "heavy_metals_meth": { + "description": "Reference or method used in determining heavy metals", + "type": [ + "string", + "null" + ] + }, + "horizon_meth": { + "description": "Reference or method used in determining the horizon", + "type": [ + "string", + "null" + ] + }, + "humidity_regm": { + "description": "Information about treatment involving an exposure to varying degree of humidity; information about treatment involving use of growth hormones; should include amount of humidity administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens", + "type": [ + "string", + "null" + ] + }, + "infiltrations": { + "description": "The amount of time it takes to complete each infiltration activity", + "pattern": "^(?:(?:[0-9]|[1-9][0-9]|9[0-9]|0[0-9]|0[0-5][0-9]):[0-5][0-9]:[0-5][0-9])(?:;(?:[0-9]|[1-9][0-9]|9[0-9]|0[0-9]|0[0-5][0-9]):[0-5][0-9]:[0-5][0-9])*$", + "type": [ + "string", + "null" + ] + }, + "isotope_exposure": { + "description": "List isotope exposure or addition applied to your sample.", + "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]; ([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", + "type": [ + "string", + "null" + ] + }, + "lat_lon": { + "description": "The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system", + "pattern": "^[-+]?([1-8]?\\d(\\.\\d{1,8})?|90(\\.0{1,8})?)\\s[-+]?(180(\\.0{1,8})?|((1[0-7]\\d)|([1-9]?\\d))(\\.\\d{1,8})?)$", + "type": "string" + }, + "lbc_thirty": { + "description": "lime buffer capacity, determined after 30 minute incubation", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "lbceq": { + "description": "lime buffer capacity, determined at equilibrium after 5 day incubation", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "light_regm": { + "description": "Information about treatment(s) involving exposure to light, including both light intensity and quality.", + "pattern": "^\\S+.*\\S+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? \\S+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? \\S+$", + "type": [ + "string", + "null" + ] + }, + "link_addit_analys": { + "description": "Link to additional analysis results performed on the sample", + "type": [ + "string", + "null" + ] + }, + "link_class_info": { + "description": "Link to digitized soil maps or other soil classification information", + "type": [ + "string", + "null" + ] + }, + "link_climate_info": { + "description": "Link to climate resource", + "type": [ + "string", + "null" + ] + }, + "local_class": { + "description": "Soil classification based on local soil classification system", + "type": [ + "string", + "null" + ] + }, + "local_class_meth": { + "description": "Reference or method used in determining the local soil classification", + "type": [ + "string", + "null" + ] + }, + "manganese": { + "description": "Concentration of manganese in the sample", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "micro_biomass_c_meth": { + "description": "Reference or method used in determining microbial biomass carbon", + "type": [ + "string", + "null" + ] + }, + "micro_biomass_meth": { + "description": "Reference or method used in determining microbial biomass", + "type": [ + "string", + "null" + ] + }, + "micro_biomass_n_meth": { + "description": "Reference or method used in determining microbial biomass nitrogen", + "type": [ + "string", + "null" + ] + }, + "microbial_biomass": { + "description": "The part of the organic matter in the soil that constitutes living microorganisms smaller than 5-10 micrometer. If you keep this, you would need to have correction factors used for conversion to the final units", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "microbial_biomass_c": { + "description": "The part of the organic matter in the soil that constitutes living microorganisms smaller than 5-10 micrometer.", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? \\S+$", + "type": [ + "string", + "null" + ] + }, + "microbial_biomass_n": { + "description": "The part of the organic matter in the soil that constitutes living microorganisms smaller than 5-10 micrometer.", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? \\S+$", + "type": [ + "string", + "null" + ] + }, + "misc_param": { + "description": "Any other measurement performed or parameter collected, that is not listed here", + "pattern": "^([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+\\|)*([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+)$", + "type": [ + "string", + "null" + ] + }, + "nitrate_nitrogen": { + "description": "Concentration of nitrate nitrogen in the sample", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "nitrite_nitrogen": { + "description": "Concentration of nitrite nitrogen in the sample", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "non_microb_biomass": { + "description": "Amount of biomass; should include the name for the part of biomass measured, e.g.insect, plant, total. Can include multiple measurements separated by ;", + "pattern": "^[^;\\t\\r\\x0A\\|]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A\\|]+$", + "type": [ + "string", + "null" + ] + }, + "non_microb_biomass_method": { + "description": "Reference or method used in determining biomass", + "type": [ + "string", + "null" + ] + }, + "org_matter": { + "description": "Concentration of organic matter", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "org_nitro": { + "description": "Concentration of organic nitrogen", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "org_nitro_method": { + "description": "Method used for obtaining organic nitrogen", + "type": [ + "string", + "null" + ] + }, + "other_treatment": { + "description": "Other treatments applied to your samples that are not applicable to the provided fields", + "type": [ + "string", + "null" + ] + }, + "oxy_stat_samp": { + "$ref": "#/$defs/OxyStatSampEnum", + "description": "Oxygenation status of sample" + }, + "ph": { + "description": "pH measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid", + "maximum": 14, + "minimum": 0, + "type": [ + "number", + "null" + ] + }, + "ph_meth": { + "description": "Reference or method used in determining ph", + "type": [ + "string", + "null" + ] + }, + "phosphate": { + "description": "Concentration of phosphate", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "prev_land_use_meth": { + "description": "Reference or method used in determining previous land use and dates", + "type": [ + "string", + "null" + ] + }, + "previous_land_use": { + "description": "Previous land use and dates", + "pattern": "^\\S+.*\\S+;([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", + "type": [ + "string", + "null" + ] + }, + "profile_position": { + "$ref": "#/$defs/ProfilePositionEnum", + "description": "Cross-sectional position in the hillslope where sample was collected.sample area position in relation to surrounding areas" + }, + "salinity": { + "description": "The total concentration of all dissolved salts in a liquid or solid sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater.", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "salinity_meth": { + "description": "Reference or method used in determining salinity", + "type": [ + "string", + "null" + ] + }, + "samp_collec_device": { + "description": "The device used to collect an environmental sample. This field accepts terms listed under environmental sampling device (http://purl.obolibrary.org/obo/ENVO). This field also accepts terms listed under specimen collection device (http://purl.obolibrary.org/obo/GENEPIO_0002094).", + "type": [ + "string", + "null" + ] + }, + "samp_collec_method": { + "description": "The method employed for collecting the sample.", + "type": [ + "string", + "null" + ] + }, + "samp_mat_process": { + "description": "A brief description of any processing applied to the sample during or after retrieving the sample from environment, or a link to the relevant protocol(s) performed.", + "type": [ + "string", + "null" + ] + }, + "samp_name": { + "description": "A local identifier or name that for the material sample collected. Refers to the original material collected or to any derived sub-samples.", + "type": "string" + }, + "samp_size": { + "description": "The total amount or size (volume (ml), mass (g) or area (m2) ) of sample collected.", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? \\S+$", + "type": [ + "string", + "null" + ] + }, + "samp_store_temp": { + "description": "Temperature at which the sample was stored (degrees are assumed)", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": "string" + }, + "sample_link": { + "description": "A unique identifier to assign parent-child, subsample, or sibling samples. This is relevant when a sample or other material was used to generate the new sample.", + "pattern": "[^\\:\\n\\r]+\\:[^\\:\\n\\r]+", + "type": [ + "string", + "null" + ] + }, + "season_precpt": { + "description": "The average of all seasonal precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or Isohyetal maps.", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "season_temp": { + "description": "Mean seasonal temperature", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "sieving": { + "description": "Collection design of pooled samples and/or sieve size and amount of sample sieved", + "type": [ + "string", + "null" + ] + }, + "size_frac_low": { + "description": "Refers to the mesh/pore size used to pre-filter/pre-sort the sample. Materials larger than the size threshold are excluded from the sample", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "size_frac_up": { + "description": "Refers to the mesh/pore size used to retain the sample. Materials smaller than the size threshold are excluded from the sample", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "slope_aspect": { + "description": "The direction a slope faces. While looking down a slope use a compass to record the direction you are facing (direction or degrees). - This measure provides an indication of sun and wind exposure that will influence soil temperature and evapotranspiration.", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "slope_gradient": { + "description": "Commonly called 'slope'. The angle between ground surface and a horizontal line (in percent). This is the direction that overland water would flow. This measure is usually taken with a hand level meter or clinometer", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "soil_horizon": { + "$ref": "#/$defs/SoilHorizonEnum", + "description": "Specific layer in the land area which measures parallel to the soil surface and possesses physical characteristics which differ from the layers above and beneath" + }, + "soil_text_measure": { + "description": "The relative proportion of different grain sizes of mineral particles in a soil, as described using a standard system; express as % sand (50 um to 2 mm), silt (2 um to 50 um), and clay (<2 um) with textural name (e.g., silty clay loam) optional.", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "soil_texture_meth": { + "description": "Reference or method used in determining soil texture", + "type": [ + "string", + "null" + ] + }, + "soil_type": { + "description": "Description of the soil type or classification. This field accepts terms under soil (http://purl.obolibrary.org/obo/ENVO_00001998). Multiple terms can be separated by pipes.", + "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$", + "type": [ + "string", + "null" + ] + }, + "soil_type_meth": { + "description": "Reference or method used in determining soil series name or other lower-level classification", + "type": [ + "string", + "null" + ] + }, + "source_mat_id": { + "description": "A globally unique identifier assigned to the biological sample.", + "pattern": "[^\\:\\n\\r]+\\:[^\\:\\n\\r]+", + "type": [ + "string", + "null" + ] + }, + "specific_ecosystem": { + "$ref": "#/$defs/SpecificEcosystemForSoilEnum", + "description": "Specific ecosystems represent specific features of the environment like aphotic zone in an ocean or gastric mucosa within a host digestive system. Specific ecosystem is in position 5/5 in a GOLD path." + }, + "start_date_inc": { + "description": "Date the incubation was started. Only relevant for incubation samples.", + "pattern": "^[12]\\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\\d|3[01]))?)?$", + "type": [ + "string", + "null" + ] + }, + "start_time_inc": { + "description": "Time the incubation was started. Only relevant for incubation samples.", + "pattern": "^([01]?\\d|2[0-3]|24(?=:00?:00?$)):([0-5]\\d)(:([0-5]\\d))?$", + "type": [ + "string", + "null" + ] + }, + "store_cond": { + "$ref": "#/$defs/StoreCondEnum", + "description": "Explain how the soil sample is stored (fresh/frozen/other)." + }, + "temp": { + "description": "Temperature of the sample at the time of sampling.", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "tillage": { + "description": "Note method(s) used for tilling", + "items": { + "$ref": "#/$defs/TillageEnum" + }, + "type": [ + "array", + "null" + ] + }, + "tot_carb": { + "description": "Total carbon content", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "tot_nitro_cont_meth": { + "description": "Reference or method used in determining the total nitrogen", + "type": [ + "string", + "null" + ] + }, + "tot_nitro_content": { + "description": "Total nitrogen content of the sample", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "tot_org_c_meth": { + "description": "Reference or method used in determining total organic carbon", + "type": [ + "string", + "null" + ] + }, + "tot_org_carb": { + "description": "Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "tot_phosp": { + "description": "Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "water_cont_soil_meth": { + "description": "Reference or method used in determining the water content of soil", + "type": [ + "string", + "null" + ] + }, + "water_content": { + "description": "Water content measurement", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)?%? \\S.+$", + "type": [ + "string", + "null" + ] + }, + "watering_regm": { + "description": "Information about treatment involving an exposure to watering frequencies, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens", + "type": [ + "string", + "null" + ] + }, + "zinc": { + "description": "Concentration of zinc in the sample", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + } + }, + "required": [ + "collection_date", + "depth", + "elev", + "env_broad_scale", + "env_local_scale", + "env_medium", + "geo_loc_name", + "growth_facil", + "lat_lon", + "samp_store_temp", + "store_cond", + "analysis_type", + "samp_name" + ], + "title": "SoilInterface", + "type": "object" + }, + "SpecificEcosystemEnum": { + "description": "", + "enum": [ + "A horizon/Topsoil", + "Abdomen", + "Abdomen nodes", + "Abomasum", + "Abscess", + "Abscess: Furuncle/Boil", + "Abscess: Pilonidal sinus", + "Abyssal plane", + "Abyssopelagic/Abyssal zone", + "Acid Mine Drainage", + "Acid mine drainage", + "Acid sulfate soil", + "Acid-saline drainage", + "Acidic", + "Acidic spring", + "Acne vulgaris", + "Actinic keratosis", + "Activated sludge", + "Adenoid/Pharyngeal", + "Adjacent soil", + "Adrenal glands", + "Agricultural land", + "Agricultural soil", + "Air sacs", + "Air-breathing organ", + "Algal bloom", + "Alkaline", + "Alkaline spring", + "Alpine", + "Alveoli", + "Amniotic fluid", + "Amniotic sac", + "Anaerobic", + "Anal canal", + "Anal canal mucosa", + "Anammox", + "Anorectal abscess", + "Anoxic zone", + "Anterior", + "Anterior chamber", + "Anterior fornix", + "Anterior nares", + "Aphotic zone", + "Appendix", + "Appendix abscess", + "Aquifer", + "Arm nodes", + "Armpit nodes", + "Arterial", + "Articular cartilage", + "Asbestos", + "Ascending colon", + "Athalassic", + "Athlete's foot", + "Atria", + "Attached/Keratinized gingiva", + "Aural", + "Auricle/Pinna", + "Axilla/Armpit", + "B horizon/Subsoil", + "Bark", + "Bartholin abscess", + "Basal cell carcinoma", + "Bathypelagic/Bathyal zone", + "Beach/Shore", + "Beaker's/Popliteal cyst", + "Beef chop", + "Beehive: Brood combs", + "Beehive: Cerumen", + "Beehive: Honey", + "Beehive: Pollen", + "Beehive: Royal jelly", + "Bench surface", + "Benthic", + "Bile", + "Bile ducts", + "Bile ducts: Bile", + "Biofilm", + "Biofilter", + "Biofouling", + "Biological", + "Biomass", + "Bioreactor", + "Black smokers", + "Bladder", + "Bladder stones", + "Bog", + "Bone", + "Bone marrow", + "Boreal forest", + "Bowens disease/Squamous cell carcinoma in situ", + "Breast abscess", + "Breast cancer", + "Breast cancer: Ductal", + "Breast cancer: Lobular", + "Breast cyst", + "Brine", + "Bronchial epithelial cells", + "Bronchioles", + "Buccal cavity", + "Buccal mucosa", + "Buffy coat", + "Bulk soil", + "C horizon/Substratum", + "C1/Glandular saccules", + "C2", + "C3", + "Caeca", + "Caeca: Bacteriome", + "Carbonate", + "Carcinosarcoma", + "Cardiac skeleton", + "Cardiac stomach", + "Cast", + "Catarrh", + "Cave lake", + "Cave microbial mat", + "Cave pool", + "Cave pool sediment", + "Cave stream", + "Cave stream sediment", + "Cave water", + "Ceca", + "Cecotropes/Night fecs", + "Cecum", + "Cecum/Intestinal cecum", + "Cellulitis", + "Cerebrospinal fluid", + "Cerumen/Earwax", + "Cervical", + "Cervical cancer", + "Cervical/Neck nodes", + "Cervix", + "Cheese", + "Chloraminated", + "Chlorinated", + "Chorionic villi", + "Chyme", + "Cibarium/Preoral cavity", + "Clasper", + "Cloaca", + "Co-culture", + "Coal core", + "Coal slurry", + "Coalbed methane well water", + "Coalbed water", + "Cold methane seep", + "Colon", + "Colon cancer", + "Colon mucosa", + "Colonic", + "Colorectal polyps", + "Colostrum", + "Commercial compost", + "Common warts", + "Compact bone", + "Concrete surface", + "Contaminated", + "Cooked blood", + "Coprolite", + "Coral reef", + "Cornea", + "Cover soil", + "Creek", + "Crop", + "Crop content", + "Crop milk", + "Crustal Fluids", + "Cryoconite", + "Cryoconite hole", + "Cud", + "Cutaneous leishmaniasis", + "Cuticle", + "Cyanobacterial aggregates", + "Cyanobacterial bloom", + "Deglaciated soil", + "Delivery networks", + "Dental abscess", + "Dental calculus", + "Dental plaque", + "Dentin", + "Dermal papilla", + "Dermatitis", + "Dermis", + "Descending colon", + "Desert", + "Diabetic foot ulcer (DFU)", + "Diffuse flow", + "Diffuse large B-cell lymphoma", + "Digestate", + "Digital dermatitis", + "Discharge", + "Drainage pipe biofilm", + "Drilled well/Borehole", + "Driven well", + "Dry permafrost", + "Dug well", + "Duodenal ulcer", + "Duodenum", + "E horizon/Subsurface", + "Ear canal", + "Ear discharge", + "Eczema", + "Effluent", + "Effusion", + "Eggs", + "Elastic", + "Empyema", + "Empyema drain", + "Endometrial/Uterine", + "Endometrium", + "Endophytes", + "Endosphere", + "Epibionts", + "Epicuticular wax", + "Epidermal mucus", + "Epidermis", + "Epilimnion", + "Epilimnion/Euphotic zone", + "Epipelagic/Euphotic zone", + "Epiphytes", + "Epithelium", + "Erythrocytes", + "Esophageal ulcer", + "Esophagus", + "Estuarine sediment", + "Estuary", + "Estuary: Microbial mat", + "Estuary: Sediment", + "Eustachian tube", + "Eutric", + "External surfaces", + "Extracellular", + "Extracellular symbionts", + "Fabric", + "Farm", + "Feathers", + "Fecal", + "Fen", + "Fibrocartilage", + "Filiform warts", + "Filter chamber", + "Filtered water", + "Fin", + "Flat warts", + "Floor", + "Floor sediment", + "Flow back/Produced fluids", + "Fluvial sediment", + "Forefield soil", + "Forelegs", + "Forest", + "Forest Soil", + "Forest soil", + "Forestomach", + "Formation fluid", + "Frass", + "Freshwater", + "Freshwater marsh", + "Frozen shrimp", + "Fungus garden/Fungus gallery", + "Gall bladder", + "Gallbladder", + "Gallbladder stones", + "Gallbladder: Bile", + "Gametophytes", + "Gaster", + "Gastric caeca", + "Gastric carcinoma", + "Gastric mucosa", + "Gastric ulcer", + "Genital herpes", + "Genital region", + "Genital ulcer", + "Genital warts", + "Gibber plain", + "Gills", + "Gingiva", + "Gingival crevice/sulcus", + "Gingival crevicular fluids", + "Gingival sulcus", + "Gizzard", + "Glacial lake", + "Glacial till/moraine", + "Glacier", + "Glacier forefield", + "Glacier meltwater", + "Glacier stream", + "Glacier terminus", + "Glandular stomach", + "Gonopodium", + "Granular sludge", + "Grasslands", + "Green roof", + "Groin", + "Groin nodes", + "Hadopelagic zone/Ocean trenches", + "Hair", + "Hair follicle", + "Hair roots", + "Hair shaft", + "Hard palate", + "Head", + "Head nodes", + "Heart valve", + "Heart wall", + "Hepatic caecum", + "Hepatic cysts", + "Hepatic flexure", + "Hepatopancreas", + "Hepatopancreas/Digestive gland/Hepatic cecum", + "Heroin", + "Herpes zoster/Shingles", + "Hind legs", + "Honeydew", + "Humus", + "Hyaline", + "Hydrocarbon", + "Hydrothermal plume", + "Hypodermis/Subcutis", + "Hypolimnion", + "Hypolimnion/Profundal zone", + "Hypophysis/Pituitary gland", + "Ice", + "Ice accretions", + "Ice core", + "Ileostomy effluent", + "Ileum", + "Ileum-cecum", + "Inferior lobe", + "Inner", + "Insect burrows", + "Intertidal zone", + "Intestinal mucosa", + "Intestine", + "Intestine: Digesta", + "Intracellular", + "Intraocular fluid/Aqueous humor", + "Introitus", + "Jejunum", + "Keratoacanthoma", + "Kidney abscess", + "Kidney stones", + "Kitchen sink", + "Lacrimal canaliculus", + "Lacrimal fluids", + "Lacrimal glands", + "Lacrimal sac", + "Lake biofilm", + "Large intestine", + "Large intestine content", + "Laryngopharyngeal", + "Laryngopharynx", + "Lateral fornices", + "Leaf lesion", + "Leaf nodule", + "Leaf surface", + "Leaf surface biofilm", + "Leaves", + "Leg nodes", + "Lens", + "Lesion", + "Lesion site", + "Liftoff microbial mat", + "Lignite", + "Limnetic zone", + "Lingual", + "Liquid manure", + "Littoral zone", + "Liver", + "Long bone", + "Low gastrointestinal tract", + "Lower digestive tract", + "Lumen", + "Lungs", + "Lymphoblastic lymphoma", + "Lymphoid follicles", + "Malignant ascites", + "Mangrove area", + "Mangrove sediment", + "Mangrove soil", + "Mangrove swamp", + "Mantle fluid", + "Marsh", + "Mature compost", + "Meadow", + "Meat trim", + "Meconium", + "Meibum", + "Melt pond", + "Meltwater", + "Mesopelagic/Twilight zone", + "Metal surface", + "Metalimnion/Thermocline", + "Microbial mat", + "Microbial mats", + "Microbialites", + "Microfouling/Biofilm", + "Middle lobe", + "Midpoint", + "Milk", + "Mine", + "Mine drainage", + "Mine pit pond", + "Mine water", + "Mineral soil", + "Mineral soil core", + "Mire", + "Mixed segment", + "Mouth ulcer", + "Mouthparts", + "Mucilage", + "Mucosa", + "Mucus", + "Multiple myeloma", + "Municipal and sewage", + "Muscle abscess", + "Muscle tissue", + "Mycosis fungoides/Cutaneous T-cell lymphoma", + "Myocardial abscess", + "Nasal", + "Nasal discharge", + "Nasal mucosa", + "Nasolacrimal canal", + "Nasopharynx", + "Neck", + "Necrotizing lesion", + "Nectar", + "Neritic zone/Coastal water", + "Nest dump", + "Neutral", + "Nose follicle", + "O horizen/Organic layer", + "O horizon/Organic", + "O horizon/Organic layer", + "Oceanic crust", + "Ocular surface", + "Oil sludge", + "Oil-contaminated", + "Oil-contaminated sediment", + "Olfactory mucosa", + "Omasum", + "Optical Lens", + "Oral cavity cancer", + "Oral fluids", + "Oral herpes", + "Oral mucosa", + "Orchard soil", + "Organic layer", + "Oropharynx", + "Osseous tissue", + "Outer", + "Ovarian", + "Ovarian cancer", + "Ovarian cyst", + "P1 segment", + "P3 segment", + "P4 segment", + "P5 segment", + "PBMC", + "Palatine/Faucial", + "Paleofeces", + "Palsa", + "Pancreatic duct", + "Paper", + "Papillate region", + "Paranasal sinuses", + "Paranasal sinuses: Catarrh", + "Paranasal sinuses: Ethmoiddal", + "Paranasal sinuses: Frontal", + "Paranasal sinuses: Maxillary", + "Paranasal sinuses: Sphenoidal", + "Parathyroid", + "Parotid abscess", + "Pasture", + "Paunch/P3 segment", + "Paw pad", + "Peat", + "Peat permafrost", + "Penis", + "Penis: Glans", + "Penis: Urethra opening", + "Perineum", + "Periodontal pockets", + "Peripheral blood mononuclear cells", + "Periphyton", + "Peritonsillar abscess", + "Permafrost", + "Pesticide", + "Petroleum sludge", + "Photic zone", + "Physical", + "Phytoplankton bloom", + "Pineal gland/Epiphysis cerebri", + "Pink", + "Pitcher", + "Pitcher fluid", + "Placenta", + "Plankton", + "Plantar warts", + "Plasma", + "Plastic", + "Plastic debries", + "Plastic surface", + "Pleural effusion", + "Pleural fluid", + "Podotheca", + "Pollen", + "Pond scum", + "Pooled tissues", + "Porewater", + "Posterior fornix", + "Posterior nares", + "Poultry litter bioaerosol", + "Poultry processing wastewater", + "Primary", + "Produced water", + "Produced water/Flow back", + "Propleura", + "Prostate fluid", + "Prothorax", + "Proventriculus", + "Proventriculus/Gizzard", + "Proximal colon", + "Psoriasis lesion", + "Pulmonary fluid", + "Pyloric stomach", + "Pyrite containing", + "Reclaimed", + "Rectal mucosa", + "Rectum", + "Red", + "Reef zone", + "Regurgitated nectar", + "Renal cyst", + "Reticulum", + "Retroauricular crease", + "Retropharyngeal", + "Rhamphotheca", + "Rhinarium", + "Rhizoids", + "Right", + "Riparian soil", + "River biofilm", + "Rock", + "Rock core/Sediment", + "Rocks", + "Room surface", + "Rosacea", + "Royal jelly", + "Rumen", + "Rumen fluid", + "Rumen mucosa", + "Rumen: Caudodorsal blind sac", + "Rumen: Caudoventral blind sac", + "Rumen: Cranial sac", + "Rumen: Dorsal sac", + "Rumen: Ventral sac", + "Runoff", + "Sabkha", + "Sabkha sediment", + "Sacciform", + "Saline", + "Saline spring", + "Saline spring sediment", + "Saline water", + "Saliva", + "Salivary glands", + "Salivary glands: Parotid glands", + "Salt crust", + "Salt flat/Salt pan", + "Salt flat/Salt pan sediment", + "Salt marsh", + "Salt marsh sediment", + "Salt pond", + "Salt pond sediment", + "Sandstone", + "Saprolite", + "Scales", + "Scalp", + "Scalp: Dandruff", + "Scalp: Non-dandruff", + "Scrotum/Scrotal sac", + "Scull: Ethmoid", + "Sea ice", + "Sea-ice brine", + "Seagrass bed", + "Seagrass bed sediment", + "Seat surface", + "Sebum", + "Secondary", + "Sediment", + "Sediment core", + "Sediment\u2013water interface", + "Seminal fluid", + "Seminal glands fluid", + "Septum", + "Serum", + "Seta", + "Setae", + "Shale carbon reservoir", + "Shoots", + "Short bone", + "Shrubland", + "Sieved", + "Sigmoid colon", + "Sinus cyst", + "Siphon", + "Skin", + "Skin surface", + "Skin tissue", + "Skull", + "Sludge", + "Small intestine", + "Small intestine content", + "Small intestine mucosa", + "Snow", + "Soft tissues", + "Soft tissues: Muscles", + "Soil", + "Solar solterns", + "Solar solterns sediment", + "Sonicate fluid", + "Speleothems", + "Sperm", + "Spider web", + "Splenic aspirate", + "Splenic flexure", + "Spongy bone", + "Sporangium", + "Spores", + "Sporophytes", + "Spring", + "Spring sediment", + "Squamous cell carcinoma", + "Stolon", + "Stomach", + "Stomach content", + "Stomach: Cardiac", + "Stomach: Fundic", + "Stomach: Pyloric", + "Stone surface", + "Stromatolites", + "Stye", + "Subcutaneous fat", + "Subgingival plaque", + "Subterranean estuary", + "Subtidal zone", + "Subtidal zone sediment", + "Sugarcane filter cake", + "Superior lobe", + "Supragingival plaque", + "Supratidal zone", + "Surface", + "Swamp", + "Sweat", + "Synovial fluid", + "Synovium", + "Synovium/Synovial membrane", + "Syrinx", + "Tears", + "Teeth", + "Tertiary", + "Testicle/Testes", + "Testicle/Testes: Sperm", + "Testicular cancer", + "Testicular non-seminoma", + "Testicular seminoma", + "Thalassic", + "Thallus/Plant body", + "Thermokarst pond", + "Thoracic", + "Thoracic segments", + "Thorax", + "Thorax drainage", + "Thorax nodes", + "Thrombolites", + "Thymus", + "Thyroid", + "Tidal flats", + "Tissue", + "Tissue-engineered", + "Tongue", + "Tongue dorsum", + "Tooth", + "Tooth: Cementum", + "Tooth: Dental pulp", + "Tooth: Dentin", + "Tooth: Enamel", + "Transverse colon", + "Trees stand", + "Tricuspid valve", + "Tropical rainforest", + "Truffle orchard", + "Tubal", + "Tubeworm bush", + "Tubiform", + "Udder", + "Udder dermatitis", + "Ulcer", + "Umbilical cord", + "Umbilical cord blood", + "Umbilicus", + "Unchlorinated", + "Unclassified", + "Unspecified tissue", + "Untreated", + "Upland zone", + "Uranium contaminated", + "Urban floodwater", + "Urothelial carcinoma/Transitional cell carcinoma (TCC)", + "Venous", + "Ventricle", + "Vertebra", + "Viscera", + "Visceral fat", + "Vitreous humor", + "Wall biofilm", + "Wall surface", + "Wastewater", + "Well", + "Well biofilm", + "Well sediment", + "Wetland zone", + "Whale fall", + "Wheat straw", + "White", + "White smokers", + "Whole blood", + "Whole body", + "Wood decay", + "Wood fall", + "Wood/Secondary xylem", + "Woodchip biofilm", + "Wooden surface", + "Xylem vessels" + ], + "title": "SpecificEcosystemEnum", + "type": "string" + }, + "SpecificEcosystemForSoilEnum": { + "description": "", + "enum": [ + "A horizon/Topsoil", + "Acid sulfate soil", + "Agricultural land", + "Agricultural soil", + "Alpine", + "B horizon/Subsoil", + "Biological", + "Bog", + "Boreal forest", + "Bulk soil", + "C horizon/Substratum", + "Contaminated", + "Cover soil", + "Creek", + "Cryoconite", + "Deglaciated soil", + "Desert", + "Dry permafrost", + "E horizon/Subsurface", + "Eutric", + "Farm", + "Fen", + "Fluvial sediment", + "Forefield soil", + "Forest", + "Forest Soil", + "Forest soil", + "Freshwater marsh", + "Gibber plain", + "Glacial till/moraine", + "Glacier forefield", + "Glacier terminus", + "Grasslands", + "Green roof", + "Humus", + "Lignite", + "Meadow", + "Mine", + "Mine drainage", + "Mineral soil", + "Mineral soil core", + "Mire", + "O horizen/Organic layer", + "O horizon/Organic", + "O horizon/Organic layer", + "Oil-contaminated", + "Orchard soil", + "Organic layer", + "Palsa", + "Pasture", + "Peat", + "Peat permafrost", + "Permafrost", + "Pesticide", + "Physical", + "Reclaimed", + "Riparian soil", + "Salt marsh", + "Saprolite", + "Sediment", + "Shrubland", + "Thermokarst pond", + "Trees stand", + "Tropical rainforest", + "Truffle orchard", + "Unclassified", + "Upland zone", + "Uranium contaminated", + "Wetland zone" + ], + "title": "SpecificEcosystemForSoilEnum", + "type": "string" + }, + "SpecificEnum": { + "description": "", + "enum": [ + "operation", + "as built", + "construction", + "bid", + "design", + "photos" + ], + "title": "SpecificEnum", + "type": "string" + }, + "SrDepEnvEnum": { + "description": "", + "enum": [ + "Lacustine", + "Fluvioldeltaic", + "Fluviomarine", + "Marine", + "other" + ], + "title": "SrDepEnvEnum", + "type": "string" + }, + "SrGeolAgeEnum": { + "description": "", + "enum": [ + "Archean", + "Cambrian", + "Carboniferous", + "Cenozoic", + "Cretaceous", + "Devonian", + "Jurassic", + "Mesozoic", + "Neogene", + "Ordovician", + "Paleogene", + "Paleozoic", + "Permian", + "Precambrian", + "Proterozoic", + "Silurian", + "Triassic", + "other" + ], + "title": "SrGeolAgeEnum", + "type": "string" + }, + "SrKerogTypeEnum": { + "description": "", + "enum": [ + "Type I", + "Type II", + "Type III", + "Type IV", + "other" + ], + "title": "SrKerogTypeEnum", + "type": "string" + }, + "SrLithologyEnum": { + "description": "", + "enum": [ + "Clastic", + "Carbonate", + "Coal", + "Biosilicieous", + "other" + ], + "title": "SrLithologyEnum", + "type": "string" + }, + "StoreCondEnum": { + "description": "", + "enum": [ + "fresh", + "frozen", + "lyophilized", + "other" + ], + "title": "StoreCondEnum", + "type": "string" + }, + "SubstructureTypeEnum": { + "description": "", + "enum": [ + "crawlspace", + "slab on grade", + "basement" + ], + "title": "SubstructureTypeEnum", + "type": "string" + }, + "SurfAirContEnum": { + "description": "", + "enum": [ + "dust", + "organic matter", + "particulate matter", + "volatile organic compounds", + "biological contaminants", + "radon", + "nutrients", + "biocides" + ], + "title": "SurfAirContEnum", + "type": "string" + }, + "SurfMaterialEnum": { + "description": "", + "enum": [ + "adobe", + "carpet", + "cinder blocks", + "concrete", + "hay bales", + "glass", + "metal", + "paint", + "plastic", + "stainless steel", + "stone", + "stucco", + "tile", + "vinyl", + "wood" + ], + "title": "SurfMaterialEnum", + "type": "string" + }, + "TidalStageEnum": { + "description": "", + "enum": [ + "low tide", + "ebb tide", + "flood tide", + "high tide" + ], + "title": "TidalStageEnum", + "type": "string" + }, + "TillageEnum": { + "description": "", + "enum": [ + "drill", + "cutting disc", + "ridge till", + "strip tillage", + "zonal tillage", + "chisel", + "tined", + "mouldboard", + "disc plough" + ], + "title": "TillageEnum", + "type": "string" + }, + "TrainLineEnum": { + "description": "", + "enum": [ + "red", + "green", + "orange" + ], + "title": "TrainLineEnum", + "type": "string" + }, + "TrainStatLocEnum": { + "description": "", + "enum": [ + "south station above ground", + "south station underground", + "south station amtrak", + "forest hills", + "riverside" + ], + "title": "TrainStatLocEnum", + "type": "string" + }, + "TrainStopLocEnum": { + "description": "", + "enum": [ + "end", + "mid", + "downtown" + ], + "title": "TrainStopLocEnum", + "type": "string" + }, + "VisMediaEnum": { + "description": "", + "enum": [ + "photos", + "videos", + "commonly of the building", + "site context (adjacent buildings, vegetation, terrain, streets)", + "interiors", + "equipment", + "3D scans" + ], + "title": "VisMediaEnum", + "type": "string" + }, + "WallConstTypeEnum": { + "description": "", + "enum": [ + "frame construction", + "joisted masonry", + "light noncombustible", + "masonry noncombustible", + "modified fire resistive", + "fire resistive" + ], + "title": "WallConstTypeEnum", + "type": "string" + }, + "WallFinishMatEnum": { + "description": "", + "enum": [ + "plaster", + "gypsum plaster", + "veneer plaster", + "gypsum board", + "tile", + "terrazzo", + "stone facing", + "acoustical treatment", + "wood", + "metal", + "masonry" + ], + "title": "WallFinishMatEnum", + "type": "string" + }, + "WallLocEnum": { + "description": "", + "enum": [ + "north", + "south", + "east", + "west" + ], + "title": "WallLocEnum", + "type": "string" + }, + "WallSurfTreatmentEnum": { + "description": "", + "enum": [ + "painted", + "wall paper", + "no treatment", + "paneling", + "stucco", + "fabric" + ], + "title": "WallSurfTreatmentEnum", + "type": "string" + }, + "WallTextureEnum": { + "description": "", + "enum": [ + "crows feet", + "crows-foot stomp", + "", + "double skip", + "hawk and trowel", + "knockdown", + "popcorn", + "orange peel", + "rosebud stomp", + "Santa-Fe texture", + "skip trowel", + "smooth", + "stomp knockdown", + "swirl" + ], + "title": "WallTextureEnum", + "type": "string" + }, + "WastewaterSludgeInterface": { + "additionalProperties": false, + "description": "wastewater_sludge dh_interface", + "properties": { + "alkalinity": { + "description": "Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "analysis_type": { + "description": "Select all the data types associated or available for this biosample", + "items": { + "$ref": "#/$defs/AnalysisTypeEnum" + }, + "type": "array" + }, + "biochem_oxygen_dem": { + "description": "Amount of dissolved oxygen needed by aerobic biological organisms in a body of water to break down organic material present in a given water sample at certain temperature over a specific time period", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "chem_administration": { + "description": "List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi", + "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\];([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", + "type": [ + "string", + "null" + ] + }, + "chem_oxygen_dem": { + "description": "A measure of the capacity of water to consume oxygen during the decomposition of organic matter and the oxidation of inorganic chemicals such as ammonia and nitrite", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "collection_date": { + "description": "The date of sampling", + "pattern": "^[12]\\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\\d|3[01]))?)?$", + "type": "string" + }, + "depth": { + "description": "The vertical distance below local surface, e.g. for sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples.", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)?(\\s*-\\s*[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)?)?$", + "type": [ + "string", + "null" + ] + }, + "ecosystem": { + "$ref": "#/$defs/EcosystemEnum", + "description": "An ecosystem is a combination of a physical environment (abiotic factors) and all the organisms (biotic factors) that interact with this environment. Ecosystem is in position 1/5 in a GOLD path." + }, + "ecosystem_category": { + "$ref": "#/$defs/EcosystemCategoryEnum", + "description": "Ecosystem categories represent divisions within the ecosystem based on specific characteristics of the environment from where an organism or sample is isolated. Ecosystem category is in position 2/5 in a GOLD path." + }, + "ecosystem_subtype": { + "$ref": "#/$defs/EcosystemSubtypeEnum", + "description": "Ecosystem subtypes represent further subdivision of Ecosystem types into more distinct subtypes. Ecosystem subtype is in position 4/5 in a GOLD path." + }, + "ecosystem_type": { + "$ref": "#/$defs/EcosystemTypeEnum", + "description": "Ecosystem types represent things having common characteristics within the Ecosystem Category. These common characteristics based grouping is still broad but specific to the characteristics of a given environment. Ecosystem type is in position 3/5 in a GOLD path." + }, + "efficiency_percent": { + "description": "Percentage of volatile solids removed from the anaerobic digestor", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "elev": { + "description": "Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit.", + "type": "number" + }, + "emulsions": { + "description": "Amount or concentration of substances such as paints, adhesives, mayonnaise, hair colorants, emulsified oils, etc.; can include multiple emulsion types", + "pattern": "^([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+\\|)*([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+)$", + "type": [ + "string", + "null" + ] + }, + "env_broad_scale": { + "description": "In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO's biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html", + "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$", + "type": "string" + }, + "env_local_scale": { + "description": "Report the entity or entities which are in the sample or specimen\u2019s local vicinity and which you believe have significant causal influences on your sample or specimen. We recommend using EnvO terms which are of smaller spatial grain than your entry for env_broad_scale. Terms, such as anatomical sites, from other OBO Library ontologies which interoperate with EnvO (e.g. UBERON) are accepted in this field. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS.", + "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$", + "type": "string" + }, + "env_medium": { + "description": "Report the environmental material(s) immediately surrounding the sample or specimen at the time of sampling. We recommend using subclasses of 'environmental material' (http://purl.obolibrary.org/obo/ENVO_00010483). EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS . Terms from other OBO ontologies are permissible as long as they reference mass/volume nouns (e.g. air, water, blood) and not discrete, countable entities (e.g. a tree, a leaf, a table top).", + "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$", + "type": "string" + }, + "experimental_factor": { + "description": "Experimental factors are essentially the variable aspects of an experiment design which can be used to describe an experiment, or set of experiments, in an increasingly detailed manner. This field accepts ontology terms from Experimental Factor Ontology (EFO) and/or Ontology for Biomedical Investigations (OBI). For a browser of EFO (v 2.95) terms, please see http://purl.bioontology.org/ontology/EFO; for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI", + "type": [ + "string", + "null" + ] + }, + "gaseous_substances": { + "description": "Amount or concentration of substances such as hydrogen sulfide, carbon dioxide, methane, etc.; can include multiple substances", + "pattern": "^([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+\\|)*([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+)$", + "type": [ + "string", + "null" + ] + }, + "geo_loc_name": { + "description": "The geographical origin of the sample as defined by the country or sea name followed by specific region name.", + "pattern": "^[^:, ][^:]*: [^:, ][^,]*, [^:, ].*$", + "type": "string" + }, + "indust_eff_percent": { + "description": "Percentage of industrial effluents received by wastewater treatment plant", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "inorg_particles": { + "description": "Concentration of particles such as sand, grit, metal particles, ceramics, etc.; can include multiple particles", + "pattern": "^([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+\\|)*([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+)$", + "type": [ + "string", + "null" + ] + }, + "lat_lon": { + "description": "The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system", + "pattern": "^[-+]?([1-8]?\\d(\\.\\d{1,8})?|90(\\.0{1,8})?)\\s[-+]?(180(\\.0{1,8})?|((1[0-7]\\d)|([1-9]?\\d))(\\.\\d{1,8})?)$", + "type": "string" + }, + "misc_param": { + "description": "Any other measurement performed or parameter collected, that is not listed here", + "pattern": "^([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+\\|)*([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+)$", + "type": [ + "string", + "null" + ] + }, + "nitrate": { + "description": "Concentration of nitrate in the sample", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "org_particles": { + "description": "Concentration of particles such as faeces, hairs, food, vomit, paper fibers, plant material, humus, etc.", + "pattern": "^([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+\\|)*([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+)$", + "type": [ + "string", + "null" + ] + }, + "organism_count": { + "description": "Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr)", + "pattern": "^([-+]?[0-9]*\\.?[0-9]+ +\\S.*\\|)*([-+]?[0-9]*\\.?[0-9]+ +\\S.*)$", + "type": [ + "string", + "null" + ] + }, + "oxy_stat_samp": { + "$ref": "#/$defs/OxyStatSampEnum", + "description": "Oxygenation status of sample" + }, + "perturbation": { + "description": "Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types", + "type": [ + "string", + "null" + ] + }, + "ph": { + "description": "pH measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid", + "maximum": 14, + "minimum": 0, + "type": [ + "number", + "null" + ] + }, + "ph_meth": { + "description": "Reference or method used in determining ph", + "type": [ + "string", + "null" + ] + }, + "phosphate": { + "description": "Concentration of phosphate", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "pre_treatment": { + "description": "The process of pre-treatment removes materials that can be easily collected from the raw wastewater", + "type": [ + "string", + "null" + ] + }, + "primary_treatment": { + "description": "The process to produce both a generally homogeneous liquid capable of being treated biologically and a sludge that can be separately treated or processed", + "type": [ + "string", + "null" + ] + }, + "reactor_type": { + "description": "Anaerobic digesters can be designed and engineered to operate using a number of different process configurations, as batch or continuous, mesophilic, high solid or low solid, and single stage or multistage", + "type": [ + "string", + "null" + ] + }, + "salinity": { + "description": "The total concentration of all dissolved salts in a liquid or solid sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater.", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "samp_collec_device": { + "description": "The device used to collect an environmental sample. This field accepts terms listed under environmental sampling device (http://purl.obolibrary.org/obo/ENVO). This field also accepts terms listed under specimen collection device (http://purl.obolibrary.org/obo/GENEPIO_0002094).", + "type": [ + "string", + "null" + ] + }, + "samp_collec_method": { + "description": "The method employed for collecting the sample.", + "type": [ + "string", + "null" + ] + }, + "samp_mat_process": { + "description": "A brief description of any processing applied to the sample during or after retrieving the sample from environment, or a link to the relevant protocol(s) performed.", + "type": [ + "string", + "null" + ] + }, + "samp_name": { + "description": "A local identifier or name that for the material sample collected. Refers to the original material collected or to any derived sub-samples.", + "type": "string" + }, + "samp_size": { + "description": "The total amount or size (volume (ml), mass (g) or area (m2) ) of sample collected.", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? \\S+$", + "type": [ + "string", + "null" + ] + }, + "samp_store_dur": { + "description": "Duration for which the sample was stored", + "type": [ + "string", + "null" + ] + }, + "samp_store_loc": { + "description": "Location at which sample was stored, usually name of a specific freezer/room", + "type": [ + "string", + "null" + ] + }, + "samp_store_temp": { + "description": "Temperature at which the sample was stored (degrees are assumed)", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": "string" + }, + "sample_link": { + "description": "A unique identifier to assign parent-child, subsample, or sibling samples. This is relevant when a sample or other material was used to generate the new sample.", + "pattern": "[^\\:\\n\\r]+\\:[^\\:\\n\\r]+", + "type": [ + "string", + "null" + ] + }, + "secondary_treatment": { + "description": "The process for substantially degrading the biological content of the sewage", + "type": [ + "string", + "null" + ] + }, + "sewage_type": { + "description": "Type of wastewater treatment plant as municipial or industrial", + "type": [ + "string", + "null" + ] + }, + "size_frac": { + "description": "Filtering pore size used in sample preparation", + "type": [ + "string", + "null" + ] + }, + "sludge_retent_time": { + "description": "The time activated sludge remains in reactor", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "sodium": { + "description": "Sodium concentration in the sample", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "soluble_inorg_mat": { + "description": "Concentration of substances such as ammonia, road-salt, sea-salt, cyanide, hydrogen sulfide, thiocyanates, thiosulfates, etc.", + "pattern": "^([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+\\|)*([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+)$", + "type": [ + "string", + "null" + ] + }, + "soluble_org_mat": { + "description": "Concentration of substances such as urea, fruit sugars, soluble proteins, drugs, pharmaceuticals, etc.", + "pattern": "^([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+\\|)*([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+)$", + "type": [ + "string", + "null" + ] + }, + "source_mat_id": { + "description": "A globally unique identifier assigned to the biological sample.", + "pattern": "[^\\:\\n\\r]+\\:[^\\:\\n\\r]+", + "type": [ + "string", + "null" + ] + }, + "specific_ecosystem": { + "$ref": "#/$defs/SpecificEcosystemEnum", + "description": "Specific ecosystems represent specific features of the environment like aphotic zone in an ocean or gastric mucosa within a host digestive system. Specific ecosystem is in position 5/5 in a GOLD path." + }, + "suspend_solids": { + "description": "Concentration of substances including a wide variety of material, such as silt, decaying plant and animal matter; can include multiple substances", + "pattern": "^([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+\\|)*([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+)$", + "type": [ + "string", + "null" + ] + }, + "temp": { + "description": "Temperature of the sample at the time of sampling.", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "tertiary_treatment": { + "description": "The process providing a final treatment stage to raise the effluent quality before it is discharged to the receiving environment", + "type": [ + "string", + "null" + ] + }, + "tot_nitro": { + "description": "Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "tot_phosphate": { + "description": "Total amount or concentration of phosphate", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "wastewater_type": { + "description": "The origin of wastewater such as human waste, rainfall, storm drains, etc.", + "type": [ + "string", + "null" + ] + } + }, + "required": [ + "collection_date", + "elev", + "env_broad_scale", + "env_local_scale", + "env_medium", + "geo_loc_name", + "lat_lon", + "samp_store_temp", + "analysis_type", + "samp_name" + ], + "title": "WastewaterSludgeInterface", + "type": "object" + }, + "WaterFeatTypeEnum": { + "description": "", + "enum": [ + "fountain", + "pool", + "standing feature", + "stream", + "waterfall" + ], + "title": "WaterFeatTypeEnum", + "type": "string" + }, + "WaterInterface": { + "additionalProperties": false, + "description": "water dh_interface", + "properties": { + "air_temp_regm": { + "description": "Information about treatment involving an exposure to varying temperatures; should include the temperature, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include different temperature regimens", + "type": [ + "string", + "null" + ] + }, + "alkalinity": { + "description": "Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "alkalinity_method": { + "description": "Method used for alkalinity measurement", + "type": [ + "string", + "null" + ] + }, + "alkyl_diethers": { + "description": "Concentration of alkyl diethers", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "aminopept_act": { + "description": "Measurement of aminopeptidase activity", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "ammonium": { + "description": "Concentration of ammonium in the sample", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "analysis_type": { + "description": "Select all the data types associated or available for this biosample", + "items": { + "$ref": "#/$defs/AnalysisTypeEnum" + }, + "type": "array" + }, + "atmospheric_data": { + "description": "Measurement of atmospheric data; can include multiple data", + "pattern": "^([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+\\|)*([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+)$", + "type": [ + "string", + "null" + ] + }, + "bac_prod": { + "description": "Bacterial production in the water column measured by isotope uptake", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "bac_resp": { + "description": "Measurement of bacterial respiration in the water column", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "bacteria_carb_prod": { + "description": "Measurement of bacterial carbon production", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "biomass": { + "description": "Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements", + "pattern": "^([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+\\|)*([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+)$", + "type": [ + "string", + "null" + ] + }, + "biotic_regm": { + "description": "Information about treatment(s) involving use of biotic factors, such as bacteria, viruses or fungi.", + "type": [ + "string", + "null" + ] + }, + "bishomohopanol": { + "description": "Concentration of bishomohopanol", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "bromide": { + "description": "Concentration of bromide", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "calcium": { + "description": "Concentration of calcium in the sample", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "carb_nitro_ratio": { + "description": "Ratio of amount or concentrations of carbon to nitrogen", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "number", + "null" + ] + }, + "chem_administration": { + "description": "List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi", + "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\];([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", + "type": [ + "string", + "null" + ] + }, + "chloride": { + "description": "Concentration of chloride in the sample", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "chlorophyll": { + "description": "Concentration of chlorophyll", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "climate_environment": { + "description": "Treatment involving an exposure to a particular climate; treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple climates", + "type": [ + "string", + "null" + ] + }, + "collection_date": { + "description": "The date of sampling", + "pattern": "^[12]\\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\\d|3[01]))?)?$", + "type": "string" + }, + "collection_date_inc": { + "description": "Date the incubation was harvested/collected/ended. Only relevant for incubation samples.", + "pattern": "^[12]\\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\\d|3[01]))?)?$", + "type": [ + "string", + "null" + ] + }, + "collection_time": { + "description": "The time of sampling, either as an instance (single point) or interval.", + "pattern": "^([01]?\\d|2[0-3]|24(?=:00?:00?$)):([0-5]\\d)(:([0-5]\\d))?$", + "type": [ + "string", + "null" + ] + }, + "conduc": { + "description": "Electrical conductivity of water", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "density": { + "description": "Density of the sample, which is its mass per unit volume (aka volumetric mass density)", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "depth": { + "description": "The vertical distance below local surface, e.g. for sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples.", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)?(\\s*-\\s*[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)?)?$", + "type": "string" + }, + "diether_lipids": { + "description": "Concentration of diether lipids; can include multiple types of diether lipids", + "pattern": "^([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+\\|)*([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+)$", + "type": [ + "string", + "null" + ] + }, + "diss_carb_dioxide": { + "description": "Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "diss_hydrogen": { + "description": "Concentration of dissolved hydrogen", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "diss_inorg_carb": { + "description": "Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "diss_inorg_nitro": { + "description": "Concentration of dissolved inorganic nitrogen", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "diss_inorg_phosp": { + "description": "Concentration of dissolved inorganic phosphorus in the sample", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "diss_org_carb": { + "description": "Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "diss_org_nitro": { + "description": "Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "diss_oxygen": { + "description": "Concentration of dissolved oxygen", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "down_par": { + "description": "Visible waveband radiance and irradiance measurements in the water column", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "ecosystem": { + "description": "An ecosystem is a combination of a physical environment (abiotic factors) and all the organisms (biotic factors) that interact with this environment. Ecosystem is in position 1/5 in a GOLD path.", + "type": [ + "string", + "null" + ] + }, + "ecosystem_category": { + "description": "Ecosystem categories represent divisions within the ecosystem based on specific characteristics of the environment from where an organism or sample is isolated. Ecosystem category is in position 2/5 in a GOLD path.", + "type": [ + "string", + "null" + ] + }, + "ecosystem_subtype": { + "description": "Ecosystem subtypes represent further subdivision of Ecosystem types into more distinct subtypes. Ecosystem subtype is in position 4/5 in a GOLD path.", + "type": [ + "string", + "null" + ] + }, + "ecosystem_type": { + "description": "Ecosystem types represent things having common characteristics within the Ecosystem Category. These common characteristics based grouping is still broad but specific to the characteristics of a given environment. Ecosystem type is in position 3/5 in a GOLD path.", + "type": [ + "string", + "null" + ] + }, + "elev": { + "description": "Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit.", + "type": [ + "number", + "null" + ] + }, + "env_broad_scale": { + "description": "Report the major environmental system the sample or specimen came from. The system(s) identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. in the desert or a rainforest). We recommend using subclasses of EnvO\u2019s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS", + "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$", + "type": "string" + }, + "env_local_scale": { + "description": "Report the entity or entities which are in the sample or specimen\u2019s local vicinity and which you believe have significant causal influences on your sample or specimen. We recommend using EnvO terms which are of smaller spatial grain than your entry for env_broad_scale. Terms, such as anatomical sites, from other OBO Library ontologies which interoperate with EnvO (e.g. UBERON) are accepted in this field. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS.", + "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$", + "type": "string" + }, + "env_medium": { + "description": "Report the environmental material(s) immediately surrounding the sample or specimen at the time of sampling. We recommend using subclasses of 'environmental material' (http://purl.obolibrary.org/obo/ENVO_00010483). EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS . Terms from other OBO ontologies are permissible as long as they reference mass/volume nouns (e.g. air, water, blood) and not discrete, countable entities (e.g. a tree, a leaf, a table top).", + "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$", + "type": "string" + }, + "experimental_factor": { + "description": "Experimental factors are essentially the variable aspects of an experiment design which can be used to describe an experiment, or set of experiments, in an increasingly detailed manner. This field accepts ontology terms from Experimental Factor Ontology (EFO) and/or Ontology for Biomedical Investigations (OBI). For a browser of EFO (v 2.95) terms, please see http://purl.bioontology.org/ontology/EFO; for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI", + "type": [ + "string", + "null" + ] + }, + "filter_method": { + "description": "Type of filter used or how the sample was filtered", + "type": [ + "string", + "null" + ] + }, + "fluor": { + "description": "Raw or converted fluorescence of water", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "gaseous_environment": { + "description": "Use of conditions with differing gaseous environments; should include the name of gaseous compound, amount administered, treatment duration, interval and total experimental duration; can include multiple gaseous environment regimens", + "type": [ + "string", + "null" + ] + }, + "geo_loc_name": { + "description": "The geographical origin of the sample as defined by the country or sea name followed by specific region name.", + "type": "string" + }, + "glucosidase_act": { + "description": "Measurement of glucosidase activity", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "humidity_regm": { + "description": "Information about treatment involving an exposure to varying degree of humidity; information about treatment involving use of growth hormones; should include amount of humidity administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens", + "type": [ + "string", + "null" + ] + }, + "isotope_exposure": { + "description": "List isotope exposure or addition applied to your sample.", + "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]; ([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", + "type": [ + "string", + "null" + ] + }, + "lat_lon": { + "description": "The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)?$", + "type": [ + "string", + "null" + ] + }, + "light_intensity": { + "description": "Measurement of light intensity", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "light_regm": { + "description": "Information about treatment(s) involving exposure to light, including both light intensity and quality.", + "pattern": "^\\S+.*\\S+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? \\S+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? \\S+$", + "type": [ + "string", + "null" + ] + }, + "magnesium": { + "description": "Concentration of magnesium in the sample", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "mean_frict_vel": { + "description": "Measurement of mean friction velocity", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "mean_peak_frict_vel": { + "description": "Measurement of mean peak friction velocity", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "misc_param": { + "description": "Any other measurement performed or parameter collected, that is not listed here", + "pattern": "^([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+\\|)*([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+)$", + "type": [ + "string", + "null" + ] + }, + "n_alkanes": { + "description": "Concentration of n-alkanes; can include multiple n-alkanes", + "pattern": "^([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+\\|)*([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+)$", + "type": [ + "string", + "null" + ] + }, + "nitrate": { + "description": "Concentration of nitrate in the sample", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "nitrite": { + "description": "Concentration of nitrite in the sample", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "nitro": { + "description": "Concentration of nitrogen (total)", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "org_carb": { + "description": "Concentration of organic carbon", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "org_matter": { + "description": "Concentration of organic matter", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "org_nitro": { + "description": "Concentration of organic nitrogen", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "organism_count": { + "description": "Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr)", + "pattern": "^(\\S+.*\\S+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? \\S+.*\\S+;(qPCR|ATP|MPN|other)\\|)*(\\S+.*\\S+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? \\S+.*\\S+;(qPCR|ATP|MPN|other))$", + "type": [ + "string", + "null" + ] + }, + "oxy_stat_samp": { + "$ref": "#/$defs/OxyStatSampEnum", + "description": "Oxygenation status of sample" + }, + "part_org_carb": { + "description": "Concentration of particulate organic carbon", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "part_org_nitro": { + "description": "Concentration of particulate organic nitrogen", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "perturbation": { + "description": "Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types", + "type": [ + "string", + "null" + ] + }, + "petroleum_hydrocarb": { + "description": "Concentration of petroleum hydrocarbon", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "ph": { + "description": "Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid", + "type": [ + "number", + "null" + ] + }, + "ph_meth": { + "description": "Reference or method used in determining ph", + "type": [ + "string", + "null" + ] + }, + "phaeopigments": { + "description": "Concentration of phaeopigments; can include multiple phaeopigments", + "pattern": "^([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+\\|)*([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+)$", + "type": [ + "string", + "null" + ] + }, + "phosphate": { + "description": "Concentration of phosphate", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "phosplipid_fatt_acid": { + "description": "Concentration of phospholipid fatty acids; can include multiple values", + "pattern": "^([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+\\|)*([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+)$", + "type": [ + "string", + "null" + ] + }, + "photon_flux": { + "description": "Measurement of photon flux", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "potassium": { + "description": "Concentration of potassium in the sample", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "pressure": { + "description": "Pressure to which the sample is subject to, in atmospheres", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "primary_prod": { + "description": "Measurement of primary production, generally measured as isotope uptake", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "redox_potential": { + "description": "Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "salinity": { + "description": "The total concentration of all dissolved salts in a liquid or solid sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater.", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "salinity_meth": { + "description": "Reference or method used in determining salinity", + "type": [ + "string", + "null" + ] + }, + "samp_collec_device": { + "description": "The device used to collect an environmental sample. This field accepts terms listed under environmental sampling device (http://purl.obolibrary.org/obo/ENVO). This field also accepts terms listed under specimen collection device (http://purl.obolibrary.org/obo/GENEPIO_0002094).", + "type": [ + "string", + "null" + ] + }, + "samp_collec_method": { + "description": "The method employed for collecting the sample.", + "type": [ + "string", + "null" + ] + }, + "samp_mat_process": { + "description": "A brief description of any processing applied to the sample during or after retrieving the sample from environment, or a link to the relevant protocol(s) performed.", + "type": [ + "string", + "null" + ] + }, + "samp_name": { + "description": "A local identifier or name that for the material sample collected. Refers to the original material collected or to any derived sub-samples.", + "type": "string" + }, + "samp_size": { + "description": "The total amount or size (volume (ml), mass (g) or area (m2) ) of sample collected.", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "samp_store_dur": { + "description": "Duration for which the sample was stored", + "type": [ + "string", + "null" + ] + }, + "samp_store_loc": { + "description": "Location at which sample was stored, usually name of a specific freezer/room", + "type": [ + "string", + "null" + ] + }, + "samp_store_temp": { + "description": "Temperature at which sample was stored, e.g. -80 degree Celsius", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "sample_link": { + "description": "A unique identifier to assign parent-child, subsample, or sibling samples. This is relevant when a sample or other material was used to generate the new sample.", + "pattern": "[^\\:\\n\\r]+\\:[^\\:\\n\\r]+", + "type": [ + "string", + "null" + ] + }, + "silicate": { + "description": "Concentration of silicate", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "size_frac": { + "description": "Filtering pore size used in sample preparation", + "type": [ + "string", + "null" + ] + }, + "size_frac_low": { + "description": "Refers to the mesh/pore size used to pre-filter/pre-sort the sample. Materials larger than the size threshold are excluded from the sample", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "size_frac_up": { + "description": "Refers to the mesh/pore size used to retain the sample. Materials smaller than the size threshold are excluded from the sample", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "sodium": { + "description": "Sodium concentration in the sample", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "soluble_react_phosp": { + "description": "Concentration of soluble reactive phosphorus", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "source_mat_id": { + "description": "A globally unique identifier assigned to the biological sample.", + "pattern": "[^\\:\\n\\r]+\\:[^\\:\\n\\r]+", + "type": [ + "string", + "null" + ] + }, + "specific_ecosystem": { + "description": "Specific ecosystems represent specific features of the environment like aphotic zone in an ocean or gastric mucosa within a host digestive system. Specific ecosystem is in position 5/5 in a GOLD path.", + "type": [ + "string", + "null" + ] + }, + "start_date_inc": { + "description": "Date the incubation was started. Only relevant for incubation samples.", + "pattern": "^[12]\\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\\d|3[01]))?)?$", + "type": [ + "string", + "null" + ] + }, + "sulfate": { + "description": "Concentration of sulfate in the sample", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "sulfide": { + "description": "Concentration of sulfide in the sample", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "suspend_part_matter": { + "description": "Concentration of suspended particulate matter", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "temp": { + "description": "Temperature of the sample at the time of sampling.", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "tidal_stage": { + "$ref": "#/$defs/TidalStageEnum", + "description": "Stage of tide" + }, + "tot_depth_water_col": { + "description": "Measurement of total depth of water column", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "tot_diss_nitro": { + "description": "Total dissolved nitrogen concentration, reported as nitrogen, measured by: total dissolved nitrogen = NH4 + NO3NO2 + dissolved organic nitrogen", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "tot_inorg_nitro": { + "description": "Total inorganic nitrogen content", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "tot_nitro": { + "description": "Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "tot_part_carb": { + "description": "Total particulate carbon content", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "tot_phosp": { + "description": "Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "turbidity": { + "description": "Measure of the amount of cloudiness or haziness in water caused by individual particles", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "water_current": { + "description": "Measurement of magnitude and direction of flow within a fluid", + "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", + "type": [ + "string", + "null" + ] + }, + "watering_regm": { + "description": "Information about treatment involving an exposure to watering frequencies, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens", + "type": [ + "string", + "null" + ] + } + }, + "required": [ + "collection_date", + "depth", + "env_broad_scale", + "env_local_scale", + "env_medium", + "geo_loc_name", + "analysis_type", + "samp_name" + ], + "title": "WaterInterface", + "type": "object" + }, + "WeekdayEnum": { + "description": "", + "enum": [ + "Monday", + "Tuesday", + "Wednesday", + "Thursday", + "Friday", + "Saturday", + "Sunday" + ], + "title": "WeekdayEnum", + "type": "string" + }, + "WindowCondEnum": { + "description": "", + "enum": [ + "damaged", + "needs repair", + "new", + "rupture", + "visible wear" + ], + "title": "WindowCondEnum", + "type": "string" + }, + "WindowCoverEnum": { + "description": "", + "enum": [ + "blinds", + "curtains", + "none" + ], + "title": "WindowCoverEnum", + "type": "string" + }, + "WindowHorizPosEnum": { + "description": "", + "enum": [ + "left", + "middle", + "right" + ], + "title": "WindowHorizPosEnum", + "type": "string" + }, + "WindowLocEnum": { + "description": "", + "enum": [ + "north", + "south", + "east", + "west" + ], + "title": "WindowLocEnum", + "type": "string" + }, + "WindowMatEnum": { + "description": "", + "enum": [ + "clad", + "fiberglass", + "metal", + "vinyl", + "wood" + ], + "title": "WindowMatEnum", + "type": "string" + }, + "WindowTypeEnum": { + "description": "", + "enum": [ + "single-hung sash window", + "horizontal sash window", + "fixed window" + ], + "title": "WindowTypeEnum", + "type": "string" + }, + "WindowVertPosEnum": { + "description": "", + "enum": [ + "bottom", + "middle", + "top", + "low", + "high" + ], + "title": "WindowVertPosEnum", + "type": "string" + }, + "YesNoEnum": { + "description": "replaces DnaDnaseEnum and DnaseRnaEnum", + "enum": [ + "no", + "yes" + ], + "title": "YesNoEnum", + "type": "string" + } + }, + "$id": "https://example.com/nmdc_submission_schema", + "$schema": "https://json-schema.org/draft/2019-09/schema", + "additionalProperties": false, + "description": "represents data produced by the DataHarmonizer tabs of the submission portal", + "metamodel_version": "1.7.0", + "properties": { + "air_data": { + "description": "aggregation slot relating air data collections to a SampleData container", + "items": { + "$ref": "#/$defs/AirInterface" + }, + "type": [ + "array", + "null" + ] + }, + "biofilm_data": { + "description": "aggregation slot relating biofilm data collections to a SampleData container", + "items": { + "$ref": "#/$defs/BiofilmInterface" + }, + "type": [ + "array", + "null" + ] + }, + "built_env_data": { + "description": "aggregation slot relating built_env data collections to a SampleData container", + "items": { + "$ref": "#/$defs/BuiltEnvInterface" + }, + "type": [ + "array", + "null" + ] + }, + "emsl_data": { + "description": "aggregation slot relating emsl data collections to a SampleData container", + "items": { + "$ref": "#/$defs/EmslInterface" + }, + "type": [ + "array", + "null" + ] + }, + "host_associated_data": { + "description": "aggregation slot relating host_associated data collections to a SampleData container", + "items": { + "$ref": "#/$defs/HostAssociatedInterface" + }, + "type": [ + "array", + "null" + ] + }, + "jgi_mg_data": { + "description": "aggregation slot relating jgi_mg data collections to a SampleData container", + "items": { + "$ref": "#/$defs/JgiMgInterface" + }, + "type": [ + "array", + "null" + ] + }, + "jgi_mg_lr_data": { + "description": "aggregation slot relating jgi_mg_lr data collections to a SampleData container", + "items": { + "$ref": "#/$defs/JgiMgLrInterface" + }, + "type": [ + "array", + "null" + ] + }, + "jgi_mt_data": { + "description": "aggregation slot relating jgi_mt data collections to a SampleData container", + "items": { + "$ref": "#/$defs/JgiMtInterface" + }, + "type": [ + "array", + "null" + ] + }, + "plant_associated_data": { + "description": "aggregation slot relating plant_associated data collections to a SampleData container", + "items": { + "$ref": "#/$defs/PlantAssociatedInterface" + }, + "type": [ + "array", + "null" + ] + }, + "sediment_data": { + "description": "aggregation slot relating sediment data collections to a SampleData container", + "items": { + "$ref": "#/$defs/SedimentInterface" + }, + "type": [ + "array", + "null" + ] + }, + "soil_data": { + "description": "aggregation slot relating soil data collections to a SampleData container", + "items": { + "$ref": "#/$defs/SoilInterface" + }, + "type": [ + "array", + "null" + ] + }, + "wastewater_sludge_data": { + "description": "aggregation slot relating wastewater_sludge data collections to a SampleData container", + "items": { + "$ref": "#/$defs/WastewaterSludgeInterface" + }, + "type": [ + "array", + "null" + ] + }, + "water_data": { + "description": "aggregation slot relating water data collections to a SampleData container", + "items": { + "$ref": "#/$defs/WaterInterface" + }, + "type": [ + "array", + "null" + ] + } + }, + "title": "nmdc_submission_schema", + "type": "object", + "version": "0.0.0" +} \ No newline at end of file diff --git a/project/thirdparty/GoldEcosystemTree.json b/project/thirdparty/GoldEcosystemTree.json index 3c6d281c..50be49b5 100644 --- a/project/thirdparty/GoldEcosystemTree.json +++ b/project/thirdparty/GoldEcosystemTree.json @@ -2,7 +2,7 @@ "name": "Ecosystems", "children": [ -{"name": "Engineered", "count": "17892" , "url": "search?Biosample.Ecosystem=Engineered" , "children" : [ +{"name": "Engineered", "count": "18171" , "url": "search?Biosample.Ecosystem=Engineered" , "children" : [ {"name": "Animal feed production" , "count": "0" , "url": "search?Biosample.Ecosystem=Engineered&Biosample.Ecosystem+Category=Animal feed production" , "children" : [ {"name": "Fermentation" , "count": "0" , "url": "search?Biosample.Ecosystem=Engineered&Biosample.Ecosystem+Category=Animal feed production&Biosample.Ecosystem+Type=Fermentation" , "children" : [ {"name": "Swine waste with corn" , "count": "0" , "url": "search?Biosample.Ecosystem=Engineered&Biosample.Ecosystem+Category=Animal feed production&Biosample.Ecosystem+Type=Fermentation&Biosample.Ecosystem+Subtype=Swine waste with corn" , "children" : [ @@ -261,7 +261,7 @@ }] }, - {"name": "Bioreactor" , "count": "2235" , "url": "search?Biosample.Ecosystem=Engineered&Biosample.Ecosystem+Category=Bioreactor" , "children" : [ + {"name": "Bioreactor" , "count": "2512" , "url": "search?Biosample.Ecosystem=Engineered&Biosample.Ecosystem+Category=Bioreactor" , "children" : [ {"name": "Aerobic" , "count": "163" , "url": "search?Biosample.Ecosystem=Engineered&Biosample.Ecosystem+Category=Bioreactor&Biosample.Ecosystem+Type=Aerobic" , "children" : [ {"name": "AGS (Aerobic granular sludge)" , "count": "0" , "url": "search?Biosample.Ecosystem=Engineered&Biosample.Ecosystem+Category=Bioreactor&Biosample.Ecosystem+Type=Aerobic&Biosample.Ecosystem+Subtype=AGS (Aerobic granular sludge)" , "children" : [ {"name": "Unclassified" , "count": "0" , "url": "search?Biosample.Ecosystem=Engineered&Biosample.Ecosystem+Category=Bioreactor&Biosample.Ecosystem+Type=Aerobic&Biosample.Ecosystem+Subtype=AGS (Aerobic granular sludge)&Biosample.Specific Ecosystem=Unclassified" }] @@ -280,7 +280,7 @@ }] }, - {"name": "Anaerobic" , "count": "1687" , "url": "search?Biosample.Ecosystem=Engineered&Biosample.Ecosystem+Category=Bioreactor&Biosample.Ecosystem+Type=Anaerobic" , "children" : [ + {"name": "Anaerobic" , "count": "1964" , "url": "search?Biosample.Ecosystem=Engineered&Biosample.Ecosystem+Category=Bioreactor&Biosample.Ecosystem+Type=Anaerobic" , "children" : [ {"name": "Biofilm" , "count": "3" , "url": "search?Biosample.Ecosystem=Engineered&Biosample.Ecosystem+Category=Bioreactor&Biosample.Ecosystem+Type=Anaerobic&Biosample.Ecosystem+Subtype=Biofilm" , "children" : [ {"name": "Unclassified" , "count": "3" , "url": "search?Biosample.Ecosystem=Engineered&Biosample.Ecosystem+Category=Bioreactor&Biosample.Ecosystem+Type=Anaerobic&Biosample.Ecosystem+Subtype=Biofilm&Biosample.Specific Ecosystem=Unclassified" }] }, @@ -327,8 +327,8 @@ {"name": "Unclassified" , "count": "0" , "url": "search?Biosample.Ecosystem=Engineered&Biosample.Ecosystem+Category=Bioreactor&Biosample.Ecosystem+Type=Anaerobic&Biosample.Ecosystem+Subtype=Thermophilic digester&Biosample.Specific Ecosystem=Unclassified" }] }, - {"name": "Unclassified" , "count": "761" , "url": "search?Biosample.Ecosystem=Engineered&Biosample.Ecosystem+Category=Bioreactor&Biosample.Ecosystem+Type=Anaerobic&Biosample.Ecosystem+Subtype=Unclassified" , "children" : [ - {"name": "Unclassified" , "count": "761" , "url": "search?Biosample.Ecosystem=Engineered&Biosample.Ecosystem+Category=Bioreactor&Biosample.Ecosystem+Type=Anaerobic&Biosample.Ecosystem+Subtype=Unclassified&Biosample.Specific Ecosystem=Unclassified" }] + {"name": "Unclassified" , "count": "1038" , "url": "search?Biosample.Ecosystem=Engineered&Biosample.Ecosystem+Category=Bioreactor&Biosample.Ecosystem+Type=Anaerobic&Biosample.Ecosystem+Subtype=Unclassified" , "children" : [ + {"name": "Unclassified" , "count": "1038" , "url": "search?Biosample.Ecosystem=Engineered&Biosample.Ecosystem+Category=Bioreactor&Biosample.Ecosystem+Type=Anaerobic&Biosample.Ecosystem+Subtype=Unclassified&Biosample.Specific Ecosystem=Unclassified" }] }, {"name": "Wastewater" , "count": "0" , "url": "search?Biosample.Ecosystem=Engineered&Biosample.Ecosystem+Category=Bioreactor&Biosample.Ecosystem+Type=Anaerobic&Biosample.Ecosystem+Subtype=Wastewater" , "children" : [ @@ -1339,8 +1339,8 @@ }] }, - {"name": "Lab culture" , "count": "194" , "url": "search?Biosample.Ecosystem=Engineered&Biosample.Ecosystem+Category=Lab culture" , "children" : [ - {"name": "Culture media" , "count": "194" , "url": "search?Biosample.Ecosystem=Engineered&Biosample.Ecosystem+Category=Lab culture&Biosample.Ecosystem+Type=Culture media" , "children" : [ + {"name": "Lab culture" , "count": "196" , "url": "search?Biosample.Ecosystem=Engineered&Biosample.Ecosystem+Category=Lab culture" , "children" : [ + {"name": "Culture media" , "count": "196" , "url": "search?Biosample.Ecosystem=Engineered&Biosample.Ecosystem+Category=Lab culture&Biosample.Ecosystem+Type=Culture media" , "children" : [ {"name": "Algae" , "count": "6" , "url": "search?Biosample.Ecosystem=Engineered&Biosample.Ecosystem+Category=Lab culture&Biosample.Ecosystem+Type=Culture media&Biosample.Ecosystem+Subtype=Algae" , "children" : [ {"name": "Contaminated" , "count": "6" , "url": "search?Biosample.Ecosystem=Engineered&Biosample.Ecosystem+Category=Lab culture&Biosample.Ecosystem+Type=Culture media&Biosample.Ecosystem+Subtype=Algae&Biosample.Specific Ecosystem=Contaminated" }] }, @@ -1351,10 +1351,10 @@ {"name": "Unclassified" , "count": "2" , "url": "search?Biosample.Ecosystem=Engineered&Biosample.Ecosystem+Category=Lab culture&Biosample.Ecosystem+Type=Culture media&Biosample.Ecosystem+Subtype=Archaea&Biosample.Specific Ecosystem=Unclassified" }] }, - {"name": "Bacteria" , "count": "115" , "url": "search?Biosample.Ecosystem=Engineered&Biosample.Ecosystem+Category=Lab culture&Biosample.Ecosystem+Type=Culture media&Biosample.Ecosystem+Subtype=Bacteria" , "children" : [ + {"name": "Bacteria" , "count": "117" , "url": "search?Biosample.Ecosystem=Engineered&Biosample.Ecosystem+Category=Lab culture&Biosample.Ecosystem+Type=Culture media&Biosample.Ecosystem+Subtype=Bacteria" , "children" : [ {"name": "Co-culture" , "count": "0" , "url": "search?Biosample.Ecosystem=Engineered&Biosample.Ecosystem+Category=Lab culture&Biosample.Ecosystem+Type=Culture media&Biosample.Ecosystem+Subtype=Bacteria&Biosample.Specific Ecosystem=Co-culture" }, - {"name": "Contaminated" , "count": "6" , "url": "search?Biosample.Ecosystem=Engineered&Biosample.Ecosystem+Category=Lab culture&Biosample.Ecosystem+Type=Culture media&Biosample.Ecosystem+Subtype=Bacteria&Biosample.Specific Ecosystem=Contaminated" }, + {"name": "Contaminated" , "count": "8" , "url": "search?Biosample.Ecosystem=Engineered&Biosample.Ecosystem+Category=Lab culture&Biosample.Ecosystem+Type=Culture media&Biosample.Ecosystem+Subtype=Bacteria&Biosample.Specific Ecosystem=Contaminated" }, {"name": "Unclassified" , "count": "109" , "url": "search?Biosample.Ecosystem=Engineered&Biosample.Ecosystem+Category=Lab culture&Biosample.Ecosystem+Type=Culture media&Biosample.Ecosystem+Subtype=Bacteria&Biosample.Specific Ecosystem=Unclassified" }] }, @@ -1525,6 +1525,10 @@ {"name": "Spent mushroom substrate" , "count": "0" , "url": "search?Biosample.Ecosystem=Engineered&Biosample.Ecosystem+Category=Solid waste&Biosample.Ecosystem+Type=Agricultural waste&Biosample.Ecosystem+Subtype=Spent mushroom substrate" , "children" : [ {"name": "Unclassified" , "count": "0" , "url": "search?Biosample.Ecosystem=Engineered&Biosample.Ecosystem+Category=Solid waste&Biosample.Ecosystem+Type=Agricultural waste&Biosample.Ecosystem+Subtype=Spent mushroom substrate&Biosample.Specific Ecosystem=Unclassified" }] +}, + + {"name": "Unclassified" , "count": "0" , "url": "search?Biosample.Ecosystem=Engineered&Biosample.Ecosystem+Category=Solid waste&Biosample.Ecosystem+Type=Agricultural waste&Biosample.Ecosystem+Subtype=Unclassified" , "children" : [ + {"name": "Unclassified" , "count": "0" , "url": "search?Biosample.Ecosystem=Engineered&Biosample.Ecosystem+Category=Solid waste&Biosample.Ecosystem+Type=Agricultural waste&Biosample.Ecosystem+Subtype=Unclassified&Biosample.Specific Ecosystem=Unclassified" }] }] }, @@ -2036,7 +2040,7 @@ }] } , -{"name": "Environmental", "count": "97020" , "url": "search?Biosample.Ecosystem=Environmental" , "children" : [ +{"name": "Environmental", "count": "97038" , "url": "search?Biosample.Ecosystem=Environmental" , "children" : [ {"name": "Air" , "count": "1638" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Air" , "children" : [ {"name": "Indoor Air" , "count": "349" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Air&Biosample.Ecosystem+Type=Indoor Air" , "children" : [ {"name": "Air scrubber" , "count": "0" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Air&Biosample.Ecosystem+Type=Indoor Air&Biosample.Ecosystem+Subtype=Air scrubber" , "children" : [ @@ -2079,7 +2083,7 @@ }] }, - {"name": "Aquatic" , "count": "56103" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Aquatic" , "children" : [ + {"name": "Aquatic" , "count": "56104" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Aquatic" , "children" : [ {"name": "Acidic" , "count": "0" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Aquatic&Biosample.Ecosystem+Type=Acidic" , "children" : [ {"name": "Acidic hypersaline lake" , "count": "0" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Aquatic&Biosample.Ecosystem+Type=Acidic&Biosample.Ecosystem+Subtype=Acidic hypersaline lake" , "children" : [ {"name": "Microbial mat" , "count": "0" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Aquatic&Biosample.Ecosystem+Type=Acidic&Biosample.Ecosystem+Subtype=Acidic hypersaline lake&Biosample.Specific Ecosystem=Microbial mat" }, @@ -2206,7 +2210,7 @@ }] }, - {"name": "Freshwater" , "count": "19874" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Aquatic&Biosample.Ecosystem+Type=Freshwater" , "children" : [ + {"name": "Freshwater" , "count": "19875" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Aquatic&Biosample.Ecosystem+Type=Freshwater" , "children" : [ {"name": "Agricultural field" , "count": "1" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Aquatic&Biosample.Ecosystem+Type=Freshwater&Biosample.Ecosystem+Subtype=Agricultural field" , "children" : [ {"name": "Unclassified" , "count": "1" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Aquatic&Biosample.Ecosystem+Type=Freshwater&Biosample.Ecosystem+Subtype=Agricultural field&Biosample.Specific Ecosystem=Unclassified" }] }, @@ -2335,7 +2339,7 @@ {"name": "Unclassified" , "count": "98" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Aquatic&Biosample.Ecosystem+Type=Freshwater&Biosample.Ecosystem+Subtype=Kettle hole&Biosample.Specific Ecosystem=Unclassified" }] }, - {"name": "Lake" , "count": "9165" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Aquatic&Biosample.Ecosystem+Type=Freshwater&Biosample.Ecosystem+Subtype=Lake" , "children" : [ + {"name": "Lake" , "count": "9166" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Aquatic&Biosample.Ecosystem+Type=Freshwater&Biosample.Ecosystem+Subtype=Lake" , "children" : [ {"name": "Algal bloom" , "count": "8" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Aquatic&Biosample.Ecosystem+Type=Freshwater&Biosample.Ecosystem+Subtype=Lake&Biosample.Specific Ecosystem=Algal bloom" }, {"name": "Anoxic zone" , "count": "27" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Aquatic&Biosample.Ecosystem+Type=Freshwater&Biosample.Ecosystem+Subtype=Lake&Biosample.Specific Ecosystem=Anoxic zone" }, @@ -2362,7 +2366,7 @@ {"name": "Metalimnion/Thermocline" , "count": "0" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Aquatic&Biosample.Ecosystem+Type=Freshwater&Biosample.Ecosystem+Subtype=Lake&Biosample.Specific Ecosystem=Metalimnion/Thermocline" }, - {"name": "Microbial mats" , "count": "31" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Aquatic&Biosample.Ecosystem+Type=Freshwater&Biosample.Ecosystem+Subtype=Lake&Biosample.Specific Ecosystem=Microbial mats" }, + {"name": "Microbial mats" , "count": "32" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Aquatic&Biosample.Ecosystem+Type=Freshwater&Biosample.Ecosystem+Subtype=Lake&Biosample.Specific Ecosystem=Microbial mats" }, {"name": "Sediment" , "count": "1445" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Aquatic&Biosample.Ecosystem+Type=Freshwater&Biosample.Ecosystem+Subtype=Lake&Biosample.Specific Ecosystem=Sediment" }, @@ -3115,7 +3119,7 @@ }] }, - {"name": "Terrestrial" , "count": "39279" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Terrestrial" , "children" : [ + {"name": "Terrestrial" , "count": "39296" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Terrestrial" , "children" : [ {"name": "Agricultural field" , "count": "0" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Terrestrial&Biosample.Ecosystem+Type=Agricultural field" , "children" : [ {"name": "Unclassified" , "count": "0" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Terrestrial&Biosample.Ecosystem+Type=Agricultural field&Biosample.Ecosystem+Subtype=Unclassified" , "children" : [ {"name": "Unclassified" , "count": "0" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Terrestrial&Biosample.Ecosystem+Type=Agricultural field&Biosample.Ecosystem+Subtype=Unclassified&Biosample.Specific Ecosystem=Unclassified" }] @@ -3380,7 +3384,7 @@ }] }, - {"name": "Soil" , "count": "36245" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Terrestrial&Biosample.Ecosystem+Type=Soil" , "children" : [ + {"name": "Soil" , "count": "36262" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Terrestrial&Biosample.Ecosystem+Type=Soil" , "children" : [ {"name": "Agricultural land" , "count": "7441" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Terrestrial&Biosample.Ecosystem+Type=Soil&Biosample.Ecosystem+Subtype=Agricultural land" , "children" : [ {"name": "Bulk soil" , "count": "4306" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Terrestrial&Biosample.Ecosystem+Type=Soil&Biosample.Ecosystem+Subtype=Agricultural land&Biosample.Specific Ecosystem=Bulk soil" }, @@ -3527,12 +3531,12 @@ {"name": "Unclassified" , "count": "94" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Terrestrial&Biosample.Ecosystem+Type=Soil&Biosample.Ecosystem+Subtype=Glacier&Biosample.Specific Ecosystem=Unclassified" }] }, - {"name": "Grasslands" , "count": "3581" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Terrestrial&Biosample.Ecosystem+Type=Soil&Biosample.Ecosystem+Subtype=Grasslands" , "children" : [ + {"name": "Grasslands" , "count": "3582" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Terrestrial&Biosample.Ecosystem+Type=Soil&Biosample.Ecosystem+Subtype=Grasslands" , "children" : [ {"name": "Bulk soil" , "count": "354" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Terrestrial&Biosample.Ecosystem+Type=Soil&Biosample.Ecosystem+Subtype=Grasslands&Biosample.Specific Ecosystem=Bulk soil" }, {"name": "Pasture" , "count": "137" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Terrestrial&Biosample.Ecosystem+Type=Soil&Biosample.Ecosystem+Subtype=Grasslands&Biosample.Specific Ecosystem=Pasture" }, - {"name": "Unclassified" , "count": "3090" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Terrestrial&Biosample.Ecosystem+Type=Soil&Biosample.Ecosystem+Subtype=Grasslands&Biosample.Specific Ecosystem=Unclassified" }] + {"name": "Unclassified" , "count": "3091" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Terrestrial&Biosample.Ecosystem+Type=Soil&Biosample.Ecosystem+Subtype=Grasslands&Biosample.Specific Ecosystem=Unclassified" }] }, {"name": "Gravesite" , "count": "2" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Terrestrial&Biosample.Ecosystem+Type=Soil&Biosample.Ecosystem+Subtype=Gravesite" , "children" : [ @@ -3729,8 +3733,8 @@ {"name": "Unclassified" , "count": "1" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Terrestrial&Biosample.Ecosystem+Type=Soil&Biosample.Ecosystem+Subtype=Silt&Biosample.Specific Ecosystem=Unclassified" }] }, - {"name": "Soil crust" , "count": "339" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Terrestrial&Biosample.Ecosystem+Type=Soil&Biosample.Ecosystem+Subtype=Soil crust" , "children" : [ - {"name": "Biological" , "count": "161" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Terrestrial&Biosample.Ecosystem+Type=Soil&Biosample.Ecosystem+Subtype=Soil crust&Biosample.Specific Ecosystem=Biological" }, + {"name": "Soil crust" , "count": "340" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Terrestrial&Biosample.Ecosystem+Type=Soil&Biosample.Ecosystem+Subtype=Soil crust" , "children" : [ + {"name": "Biological" , "count": "162" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Terrestrial&Biosample.Ecosystem+Type=Soil&Biosample.Ecosystem+Subtype=Soil crust&Biosample.Specific Ecosystem=Biological" }, {"name": "Physical" , "count": "1" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Terrestrial&Biosample.Ecosystem+Type=Soil&Biosample.Ecosystem+Subtype=Soil crust&Biosample.Specific Ecosystem=Physical" }, @@ -3751,7 +3755,7 @@ {"name": "Unclassified" , "count": "1" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Terrestrial&Biosample.Ecosystem+Type=Soil&Biosample.Ecosystem+Subtype=Tailings&Biosample.Specific Ecosystem=Unclassified" }] }, - {"name": "Temperate forest" , "count": "3927" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Terrestrial&Biosample.Ecosystem+Type=Soil&Biosample.Ecosystem+Subtype=Temperate forest" , "children" : [ + {"name": "Temperate forest" , "count": "3942" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Terrestrial&Biosample.Ecosystem+Type=Soil&Biosample.Ecosystem+Subtype=Temperate forest" , "children" : [ {"name": "A horizon/Topsoil" , "count": "12" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Terrestrial&Biosample.Ecosystem+Type=Soil&Biosample.Ecosystem+Subtype=Temperate forest&Biosample.Specific Ecosystem=A horizon/Topsoil" }, {"name": "B horizon/Subsoil" , "count": "11" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Terrestrial&Biosample.Ecosystem+Type=Soil&Biosample.Ecosystem+Subtype=Temperate forest&Biosample.Specific Ecosystem=B horizon/Subsoil" }, @@ -3764,7 +3768,7 @@ {"name": "Humus" , "count": "33" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Terrestrial&Biosample.Ecosystem+Type=Soil&Biosample.Ecosystem+Subtype=Temperate forest&Biosample.Specific Ecosystem=Humus" }, - {"name": "Mineral soil" , "count": "339" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Terrestrial&Biosample.Ecosystem+Type=Soil&Biosample.Ecosystem+Subtype=Temperate forest&Biosample.Specific Ecosystem=Mineral soil" }, + {"name": "Mineral soil" , "count": "354" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Terrestrial&Biosample.Ecosystem+Type=Soil&Biosample.Ecosystem+Subtype=Temperate forest&Biosample.Specific Ecosystem=Mineral soil" }, {"name": "O horizon/Organic" , "count": "472" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Terrestrial&Biosample.Ecosystem+Type=Soil&Biosample.Ecosystem+Subtype=Temperate forest&Biosample.Specific Ecosystem=O horizon/Organic" }, diff --git a/src/nmdc_submission_schema/datamodel/nmdc_submission_schema.py b/src/nmdc_submission_schema/datamodel/nmdc_submission_schema.py index 9c87d2fe..ed7521e5 100644 --- a/src/nmdc_submission_schema/datamodel/nmdc_submission_schema.py +++ b/src/nmdc_submission_schema/datamodel/nmdc_submission_schema.py @@ -1,5 +1,5 @@ # Auto generated from nmdc_submission_schema.yaml by pythongen.py version: 0.0.1 -# Generation date: 2024-11-11T18:14:51 +# Generation date: 2024-11-14T12:57:10 # Schema: nmdc_submission_schema # # id: https://example.com/nmdc_submission_schema @@ -83,6 +83,7 @@ HMDB = CurieNamespace('HMDB', 'https://bioregistry.io/hmdb:') ISA = CurieNamespace('ISA', 'http://example.org/isa/') KEGG_COMPOUND = CurieNamespace('KEGG_COMPOUND', 'https://bioregistry.io/kegg.compound:') +KEGG_MODULE = CurieNamespace('KEGG_MODULE', 'https://bioregistry.io/kegg.module:') KEGG_ORTHOLOGY = CurieNamespace('KEGG_ORTHOLOGY', 'https://bioregistry.io/kegg.orthology:') KEGG_REACTION = CurieNamespace('KEGG_REACTION', 'https://bioregistry.io/kegg.reaction:') KEGG_PATHWAY = CurieNamespace('KEGG_PATHWAY', 'https://bioregistry.io/kegg.pathway:') @@ -182,22 +183,6 @@ class LanguageCode(str): type_model_uri = NMDC_SUB_SCHEMA.LanguageCode -class Uriorcurie(URIorCURIE): - """ a URI or a CURIE """ - type_class_uri = XSD["anyURI"] - type_class_curie = "xsd:anyURI" - type_name = "uriorcurie" - type_model_uri = NMDC_SUB_SCHEMA.Uriorcurie - - -class Float(float): - """ A real number that conforms to the xsd:float specification """ - type_class_uri = XSD["float"] - type_class_curie = "xsd:float" - type_name = "float" - type_model_uri = NMDC_SUB_SCHEMA.Float - - class Decimal(Decimal): """ A real number with arbitrary precision that conforms to the xsd:decimal specification """ type_class_uri = XSD["decimal"] @@ -206,12 +191,12 @@ class Decimal(Decimal): type_model_uri = NMDC_SUB_SCHEMA.Decimal -class String(str): - """ A character string """ - type_class_uri = XSD["string"] - type_class_curie = "xsd:string" - type_name = "string" - type_model_uri = NMDC_SUB_SCHEMA.String +class Double(float): + """ A real number that conforms to the xsd:double specification """ + type_class_uri = XSD["double"] + type_class_curie = "xsd:double" + type_name = "double" + type_model_uri = NMDC_SUB_SCHEMA.Double class Integer(int): @@ -222,12 +207,28 @@ class Integer(int): type_model_uri = NMDC_SUB_SCHEMA.Integer -class Double(float): - """ A real number that conforms to the xsd:double specification """ - type_class_uri = XSD["double"] - type_class_curie = "xsd:double" - type_name = "double" - type_model_uri = NMDC_SUB_SCHEMA.Double +class String(str): + """ A character string """ + type_class_uri = XSD["string"] + type_class_curie = "xsd:string" + type_name = "string" + type_model_uri = NMDC_SUB_SCHEMA.String + + +class Float(float): + """ A real number that conforms to the xsd:float specification """ + type_class_uri = XSD["float"] + type_class_curie = "xsd:float" + type_name = "float" + type_model_uri = NMDC_SUB_SCHEMA.Float + + +class Uriorcurie(URIorCURIE): + """ a URI or a CURIE """ + type_class_uri = XSD["anyURI"] + type_class_curie = "xsd:anyURI" + type_name = "uriorcurie" + type_model_uri = NMDC_SUB_SCHEMA.Uriorcurie class Boolean(Bool): @@ -9892,219 +9893,6 @@ class YesNoEnum(EnumDefinitionImpl): description="replaces DnaDnaseEnum and DnaseRnaEnum", ) -class EnvMediumSoilEnum(EnumDefinitionImpl): - - _defn = EnumDefinition( - name="EnvMediumSoilEnum", - ) - - @classmethod - def _addvals(cls): - setattr(cls, "pathogen-suppressive soil [ENVO:03600036]", - PermissibleValue(text="pathogen-suppressive soil [ENVO:03600036]")) - setattr(cls, "mangrove biome soil [ENVO:02000138]", - PermissibleValue(text="mangrove biome soil [ENVO:02000138]")) - setattr(cls, "surface soil [ENVO:02000059]", - PermissibleValue(text="surface soil [ENVO:02000059]")) - setattr(cls, "frost-susceptible soil [ENVO:01001638]", - PermissibleValue(text="frost-susceptible soil [ENVO:01001638]")) - setattr(cls, "bare soil [ENVO:01001616]", - PermissibleValue(text="bare soil [ENVO:01001616]")) - setattr(cls, "frozen soil [ENVO:01001526]", - PermissibleValue(text="frozen soil [ENVO:01001526]")) - setattr(cls, "__friable-frozen soil [ENVO:01001528]", - PermissibleValue(text="__friable-frozen soil [ENVO:01001528]")) - setattr(cls, "__plastic-frozen soil [ENVO:01001527]", - PermissibleValue(text="__plastic-frozen soil [ENVO:01001527]")) - setattr(cls, "__hard-frozen soil [ENVO:01001525]", - PermissibleValue(text="__hard-frozen soil [ENVO:01001525]")) - setattr(cls, "__frozen compost soil [ENVO:00005765]", - PermissibleValue(text="__frozen compost soil [ENVO:00005765]")) - setattr(cls, "__cryosol [ENVO:00002236]", - PermissibleValue(text="__cryosol [ENVO:00002236]")) - setattr(cls, "ultisol [ENVO:01001397]", - PermissibleValue(text="ultisol [ENVO:01001397]")) - setattr(cls, "__acrisol [ENVO:00002234]", - PermissibleValue(text="__acrisol [ENVO:00002234]")) - setattr(cls, "acidic soil [ENVO:01001185]", - PermissibleValue(text="acidic soil [ENVO:01001185]")) - setattr(cls, "bulk soil [ENVO:00005802]", - PermissibleValue(text="bulk soil [ENVO:00005802]")) - setattr(cls, "red soil [ENVO:00005790]", - PermissibleValue(text="red soil [ENVO:00005790]")) - setattr(cls, "upland soil [ENVO:00005786]", - PermissibleValue(text="upland soil [ENVO:00005786]")) - setattr(cls, "__mountain forest soil [ENVO:00005769]", - PermissibleValue(text="__mountain forest soil [ENVO:00005769]")) - setattr(cls, "__dune soil [ENVO:00002260]", - PermissibleValue(text="__dune soil [ENVO:00002260]")) - setattr(cls, "ornithogenic soil [ENVO:00005782]", - PermissibleValue(text="ornithogenic soil [ENVO:00005782]")) - setattr(cls, "heat stressed soil [ENVO:00005781]", - PermissibleValue(text="heat stressed soil [ENVO:00005781]")) - setattr(cls, "greenhouse soil [ENVO:00005780]", - PermissibleValue(text="greenhouse soil [ENVO:00005780]")) - setattr(cls, "tropical soil [ENVO:00005778]", - PermissibleValue(text="tropical soil [ENVO:00005778]")) - setattr(cls, "pasture soil [ENVO:00005773]", - PermissibleValue(text="pasture soil [ENVO:00005773]")) - setattr(cls, "muddy soil [ENVO:00005771]", - PermissibleValue(text="muddy soil [ENVO:00005771]")) - setattr(cls, "orchid soil [ENVO:00005768]", - PermissibleValue(text="orchid soil [ENVO:00005768]")) - setattr(cls, "manured soil [ENVO:00005767]", - PermissibleValue(text="manured soil [ENVO:00005767]")) - setattr(cls, "limed soil [ENVO:00005766]", - PermissibleValue(text="limed soil [ENVO:00005766]")) - setattr(cls, "pond soil [ENVO:00005764]", - PermissibleValue(text="pond soil [ENVO:00005764]")) - setattr(cls, "meadow soil [ENVO:00005761]", - PermissibleValue(text="meadow soil [ENVO:00005761]")) - setattr(cls, "burned soil [ENVO:00005760]", - PermissibleValue(text="burned soil [ENVO:00005760]")) - setattr(cls, "lawn soil [ENVO:00005756]", - PermissibleValue(text="lawn soil [ENVO:00005756]")) - setattr(cls, "field soil [ENVO:00005755]", - PermissibleValue(text="field soil [ENVO:00005755]")) - setattr(cls, "__paddy field soil [ENVO:00005740]", - PermissibleValue(text="__paddy field soil [ENVO:00005740]")) - setattr(cls, "____peaty paddy field soil [ENVO:00005776]", - PermissibleValue(text="____peaty paddy field soil [ENVO:00005776]")) - setattr(cls, "____alluvial paddy field soil [ENVO:00005759]", - PermissibleValue(text="____alluvial paddy field soil [ENVO:00005759]")) - setattr(cls, "fertilized soil [ENVO:00005754]", - PermissibleValue(text="fertilized soil [ENVO:00005754]")) - setattr(cls, "sawah soil [ENVO:00005752]", - PermissibleValue(text="sawah soil [ENVO:00005752]")) - setattr(cls, "jungle soil [ENVO:00005751]", - PermissibleValue(text="jungle soil [ENVO:00005751]")) - setattr(cls, "grassland soil [ENVO:00005750]", - PermissibleValue(text="grassland soil [ENVO:00005750]")) - setattr(cls, "__steppe soil [ENVO:00005777]", - PermissibleValue(text="__steppe soil [ENVO:00005777]")) - setattr(cls, "__savanna soil [ENVO:00005746]", - PermissibleValue(text="__savanna soil [ENVO:00005746]")) - setattr(cls, "farm soil [ENVO:00005749]", - PermissibleValue(text="farm soil [ENVO:00005749]")) - setattr(cls, "__rubber plantation soil [ENVO:00005788]", - PermissibleValue(text="__rubber plantation soil [ENVO:00005788]")) - setattr(cls, "__orchard soil [ENVO:00005772]", - PermissibleValue(text="__orchard soil [ENVO:00005772]")) - setattr(cls, "dry soil [ENVO:00005748]", - PermissibleValue(text="dry soil [ENVO:00005748]")) - setattr(cls, "compost soil [ENVO:00005747]", - PermissibleValue(text="compost soil [ENVO:00005747]")) - setattr(cls, "roadside soil [ENVO:00005743]", - PermissibleValue(text="roadside soil [ENVO:00005743]")) - setattr(cls, "arable soil [ENVO:00005742]", - PermissibleValue(text="arable soil [ENVO:00005742]")) - setattr(cls, "alpine soil [ENVO:00005741]", - PermissibleValue(text="alpine soil [ENVO:00005741]")) - setattr(cls, "alluvial soil [ENVO:00002871]", - PermissibleValue(text="alluvial soil [ENVO:00002871]")) - setattr(cls, "__alluvial paddy field soil [ENVO:00005759]", - PermissibleValue(text="__alluvial paddy field soil [ENVO:00005759]")) - setattr(cls, "__alluvial swamp soil [ENVO:00005758]", - PermissibleValue(text="__alluvial swamp soil [ENVO:00005758]")) - setattr(cls, "technosol [ENVO:00002275]", - PermissibleValue(text="technosol [ENVO:00002275]")) - setattr(cls, "stagnosol [ENVO:00002274]", - PermissibleValue(text="stagnosol [ENVO:00002274]")) - setattr(cls, "fluvisol [ENVO:00002273]", - PermissibleValue(text="fluvisol [ENVO:00002273]")) - setattr(cls, "garden soil [ENVO:00002263]", - PermissibleValue(text="garden soil [ENVO:00002263]")) - setattr(cls, "__vegetable garden soil [ENVO:00005779]", - PermissibleValue(text="__vegetable garden soil [ENVO:00005779]")) - setattr(cls, "__allotment garden soil [ENVO:00005744]", - PermissibleValue(text="__allotment garden soil [ENVO:00005744]")) - setattr(cls, "clay soil [ENVO:00002262]", - PermissibleValue(text="clay soil [ENVO:00002262]")) - setattr(cls, "forest soil [ENVO:00002261]", - PermissibleValue(text="forest soil [ENVO:00002261]")) - setattr(cls, "__eucalyptus forest soil [ENVO:00005787]", - PermissibleValue(text="__eucalyptus forest soil [ENVO:00005787]")) - setattr(cls, "__spruce forest soil [ENVO:00005784]", - PermissibleValue(text="__spruce forest soil [ENVO:00005784]")) - setattr(cls, "__leafy wood soil [ENVO:00005783]", - PermissibleValue(text="__leafy wood soil [ENVO:00005783]")) - setattr(cls, "__beech forest soil [ENVO:00005770]", - PermissibleValue(text="__beech forest soil [ENVO:00005770]")) - setattr(cls, "agricultural soil [ENVO:00002259]", - PermissibleValue(text="agricultural soil [ENVO:00002259]")) - setattr(cls, "__bluegrass field soil [ENVO:00005789]", - PermissibleValue(text="__bluegrass field soil [ENVO:00005789]")) - setattr(cls, "loam [ENVO:00002258]", - PermissibleValue(text="loam [ENVO:00002258]")) - setattr(cls, "__clay loam [ENVO:06105277]", - PermissibleValue(text="__clay loam [ENVO:06105277]")) - setattr(cls, "____silty clay loam [ENVO:06105278]", - PermissibleValue(text="____silty clay loam [ENVO:06105278]")) - setattr(cls, "____sandy clay loam [ENVO:06105276]", - PermissibleValue(text="____sandy clay loam [ENVO:06105276]")) - setattr(cls, "__silty loam [ENVO:06105275]", - PermissibleValue(text="__silty loam [ENVO:06105275]")) - setattr(cls, "__sandy loam [ENVO:06105274]", - PermissibleValue(text="__sandy loam [ENVO:06105274]")) - setattr(cls, "podzol [ENVO:00002257]", - PermissibleValue(text="podzol [ENVO:00002257]")) - setattr(cls, "regosol [ENVO:00002256]", - PermissibleValue(text="regosol [ENVO:00002256]")) - setattr(cls, "solonetz [ENVO:00002255]", - PermissibleValue(text="solonetz [ENVO:00002255]")) - setattr(cls, "vertisol [ENVO:00002254]", - PermissibleValue(text="vertisol [ENVO:00002254]")) - setattr(cls, "umbrisol [ENVO:00002253]", - PermissibleValue(text="umbrisol [ENVO:00002253]")) - setattr(cls, "solonchak [ENVO:00002252]", - PermissibleValue(text="solonchak [ENVO:00002252]")) - setattr(cls, "planosol [ENVO:00002251]", - PermissibleValue(text="planosol [ENVO:00002251]")) - setattr(cls, "plinthosol [ENVO:00002250]", - PermissibleValue(text="plinthosol [ENVO:00002250]")) - setattr(cls, "phaeozem [ENVO:00002249]", - PermissibleValue(text="phaeozem [ENVO:00002249]")) - setattr(cls, "luvisol [ENVO:00002248]", - PermissibleValue(text="luvisol [ENVO:00002248]")) - setattr(cls, "nitisol [ENVO:00002247]", - PermissibleValue(text="nitisol [ENVO:00002247]")) - setattr(cls, "ferralsol [ENVO:00002246]", - PermissibleValue(text="ferralsol [ENVO:00002246]")) - setattr(cls, "gypsisol [ENVO:00002245]", - PermissibleValue(text="gypsisol [ENVO:00002245]")) - setattr(cls, "gleysol [ENVO:00002244]", - PermissibleValue(text="gleysol [ENVO:00002244]")) - setattr(cls, "histosol [ENVO:00002243]", - PermissibleValue(text="histosol [ENVO:00002243]")) - setattr(cls, "__peat soil [ENVO:00005774]", - PermissibleValue(text="__peat soil [ENVO:00005774]")) - setattr(cls, "lixisol [ENVO:00002242]", - PermissibleValue(text="lixisol [ENVO:00002242]")) - setattr(cls, "leptosol [ENVO:00002241]", - PermissibleValue(text="leptosol [ENVO:00002241]")) - setattr(cls, "kastanozem [ENVO:00002240]", - PermissibleValue(text="kastanozem [ENVO:00002240]")) - setattr(cls, "calcisol [ENVO:00002239]", - PermissibleValue(text="calcisol [ENVO:00002239]")) - setattr(cls, "durisol [ENVO:00002238]", - PermissibleValue(text="durisol [ENVO:00002238]")) - setattr(cls, "chernozem [ENVO:00002237]", - PermissibleValue(text="chernozem [ENVO:00002237]")) - setattr(cls, "cambisol [ENVO:00002235]", - PermissibleValue(text="cambisol [ENVO:00002235]")) - setattr(cls, "albeluvisol [ENVO:00002233]", - PermissibleValue(text="albeluvisol [ENVO:00002233]")) - setattr(cls, "andosol [ENVO:00002232]", - PermissibleValue(text="andosol [ENVO:00002232]")) - setattr(cls, "__volcanic soil [ENVO:01001841]", - PermissibleValue(text="__volcanic soil [ENVO:01001841]")) - setattr(cls, "alisol [ENVO:00002231]", - PermissibleValue(text="alisol [ENVO:00002231]")) - setattr(cls, "anthrosol [ENVO:00002230]", - PermissibleValue(text="anthrosol [ENVO:00002230]")) - setattr(cls, "arenosol [ENVO:00002229]", - PermissibleValue(text="arenosol [ENVO:00002229]")) - class OxyStatSampEnum(EnumDefinitionImpl): aerobic = PermissibleValue(text="aerobic") @@ -15094,6 +14882,226 @@ def _addvals(cls): setattr(cls, "Wetland zone", PermissibleValue(text="Wetland zone")) +class EnvMediumWaterEnum(EnumDefinitionImpl): + + _defn = EnumDefinition( + name="EnvMediumWaterEnum", + ) + + @classmethod + def _addvals(cls): + setattr(cls, "acidic water [ENVO:01000358]", + PermissibleValue(text="acidic water [ENVO:01000358]")) + setattr(cls, "alkaline water [ENVO:01000357]", + PermissibleValue(text="alkaline water [ENVO:01000357]")) + setattr(cls, "anoxic water [ENVO:01000173]", + PermissibleValue(text="anoxic water [ENVO:01000173]")) + setattr(cls, "bacon curing brine [ENVO:00003045]", + PermissibleValue(text="bacon curing brine [ENVO:00003045]")) + setattr(cls, "ballast water [ENVO:01000872]", + PermissibleValue(text="ballast water [ENVO:01000872]")) + setattr(cls, "borax leachate [ENVO:00002142]", + PermissibleValue(text="borax leachate [ENVO:00002142]")) + setattr(cls, "brackish water [ENVO:00002019]", + PermissibleValue(text="brackish water [ENVO:00002019]")) + setattr(cls, "brine [ENVO:00003044]", + PermissibleValue(text="brine [ENVO:00003044]")) + setattr(cls, "cloud water [ENVO:03600081]", + PermissibleValue(text="cloud water [ENVO:03600081]")) + setattr(cls, "coastal sea water [ENVO:00002150]", + PermissibleValue(text="coastal sea water [ENVO:00002150]")) + setattr(cls, "cooling water [ENVO:03600002]", + PermissibleValue(text="cooling water [ENVO:03600002]")) + setattr(cls, "desalinated water [ENVO:06105269]", + PermissibleValue(text="desalinated water [ENVO:06105269]")) + setattr(cls, "distilled water [ENVO:00003065]", + PermissibleValue(text="distilled water [ENVO:00003065]")) + setattr(cls, "ditch water [ENVO:00002158]", + PermissibleValue(text="ditch water [ENVO:00002158]")) + setattr(cls, "drilling bore water [ENVO:00002159]", + PermissibleValue(text="drilling bore water [ENVO:00002159]")) + setattr(cls, "drinking water [ENVO:00003064]", + PermissibleValue(text="drinking water [ENVO:00003064]")) + setattr(cls, "estuarine water [ENVO:01000301]", + PermissibleValue(text="estuarine water [ENVO:01000301]")) + setattr(cls, "eutrophic water [ENVO:00002224]", + PermissibleValue(text="eutrophic water [ENVO:00002224]")) + setattr(cls, "fresh water [ENVO:00002011]", + PermissibleValue(text="fresh water [ENVO:00002011]")) + setattr(cls, "groundwater [ENVO:01001004]", + PermissibleValue(text="groundwater [ENVO:01001004]")) + setattr(cls, "highly saline water [ENVO:01001039]", + PermissibleValue(text="highly saline water [ENVO:01001039]")) + setattr(cls, "hydrothermal fluid [ENVO:01000134]", + PermissibleValue(text="hydrothermal fluid [ENVO:01000134]")) + setattr(cls, "hypereutrophic water [ENVO:01001018]", + PermissibleValue(text="hypereutrophic water [ENVO:01001018]")) + setattr(cls, "hypersaline water [ENVO:00002012]", + PermissibleValue(text="hypersaline water [ENVO:00002012]")) + setattr(cls, "hypoxic water [ENVO:01001064]", + PermissibleValue(text="hypoxic water [ENVO:01001064]")) + setattr(cls, "interstitial water [ENVO:03600009]", + PermissibleValue(text="interstitial water [ENVO:03600009]")) + setattr(cls, "leachate [ENVO:00002141]", + PermissibleValue(text="leachate [ENVO:00002141]")) + setattr(cls, "liquid water [ENVO:00002006]", + PermissibleValue(text="liquid water [ENVO:00002006]")) + setattr(cls, "meltwater [ENVO:01000722]", + PermissibleValue(text="meltwater [ENVO:01000722]")) + setattr(cls, "mesotrophic water [ENVO:00002225]", + PermissibleValue(text="mesotrophic water [ENVO:00002225]")) + setattr(cls, "moderately saline water [ENVO:01001038]", + PermissibleValue(text="moderately saline water [ENVO:01001038]")) + setattr(cls, "muddy water [ENVO:00005793]", + PermissibleValue(text="muddy water [ENVO:00005793]")) + setattr(cls, "oligotrophic water [ENVO:00002223]", + PermissibleValue(text="oligotrophic water [ENVO:00002223]")) + setattr(cls, "oxic water [ENVO:01001063]", + PermissibleValue(text="oxic water [ENVO:01001063]")) + setattr(cls, "pond water [ENVO:00002228]", + PermissibleValue(text="pond water [ENVO:00002228]")) + setattr(cls, "rainwater [ENVO:01000600]", + PermissibleValue(text="rainwater [ENVO:01000600]")) + setattr(cls, "rural stormwater [ENVO:01001270]", + PermissibleValue(text="rural stormwater [ENVO:01001270]")) + setattr(cls, "saline shrimp pond water [ENVO:01001257]", + PermissibleValue(text="saline shrimp pond water [ENVO:01001257]")) + setattr(cls, "saline water [ENVO:00002010]", + PermissibleValue(text="saline water [ENVO:00002010]")) + setattr(cls, "sea water [ENVO:00002149]", + PermissibleValue(text="sea water [ENVO:00002149]")) + setattr(cls, "slightly saline water [ENVO:01001037]", + PermissibleValue(text="slightly saline water [ENVO:01001037]")) + setattr(cls, "stagnant water [ENVO:03501370]", + PermissibleValue(text="stagnant water [ENVO:03501370]")) + setattr(cls, "sterile water [ENVO:00005791]", + PermissibleValue(text="sterile water [ENVO:00005791]")) + setattr(cls, "stormwater [ENVO:01001267]", + PermissibleValue(text="stormwater [ENVO:01001267]")) + setattr(cls, "subterranean lake [ENVO:02000145]", + PermissibleValue(text="subterranean lake [ENVO:02000145]")) + setattr(cls, "surface water [ENVO:00002042]", + PermissibleValue(text="surface water [ENVO:00002042]")) + setattr(cls, "tap water [ENVO:00003096]", + PermissibleValue(text="tap water [ENVO:00003096]")) + setattr(cls, "underground water [ENVO:00005792]", + PermissibleValue(text="underground water [ENVO:00005792]")) + setattr(cls, "urban stormwater [ENVO:01001268]", + PermissibleValue(text="urban stormwater [ENVO:01001268]")) + +class EnvBroadScaleSoilEnum(EnumDefinitionImpl): + + _defn = EnumDefinition( + name="EnvBroadScaleSoilEnum", + ) + + @classmethod + def _addvals(cls): + setattr(cls, "alpine tundra biome [ENVO:01001505]", + PermissibleValue(text="alpine tundra biome [ENVO:01001505]")) + setattr(cls, "anthropogenic terrestrial biome [ENVO:01000219]", + PermissibleValue(text="anthropogenic terrestrial biome [ENVO:01000219]")) + setattr(cls, "broadleaf forest biome [ENVO:01000197]", + PermissibleValue(text="broadleaf forest biome [ENVO:01000197]")) + setattr(cls, "coniferous forest biome [ENVO:01000196]", + PermissibleValue(text="coniferous forest biome [ENVO:01000196]")) + setattr(cls, "cropland biome [ENVO:01000245]", + PermissibleValue(text="cropland biome [ENVO:01000245]")) + setattr(cls, "flooded grassland biome [ENVO:01000195]", + PermissibleValue(text="flooded grassland biome [ENVO:01000195]")) + setattr(cls, "flooded savanna biome [ENVO:01000190]", + PermissibleValue(text="flooded savanna biome [ENVO:01000190]")) + setattr(cls, "forest biome [ENVO:01000174]", + PermissibleValue(text="forest biome [ENVO:01000174]")) + setattr(cls, "grassland biome [ENVO:01000177]", + PermissibleValue(text="grassland biome [ENVO:01000177]")) + setattr(cls, "mangrove biome [ENVO:01000181]", + PermissibleValue(text="mangrove biome [ENVO:01000181]")) + setattr(cls, "mediterranean forest biome [ENVO:01000199]", + PermissibleValue(text="mediterranean forest biome [ENVO:01000199]")) + setattr(cls, "mediterranean grassland biome [ENVO:01000224]", + PermissibleValue(text="mediterranean grassland biome [ENVO:01000224]")) + setattr(cls, "mediterranean savanna biome [ENVO:01000229]", + PermissibleValue(text="mediterranean savanna biome [ENVO:01000229]")) + setattr(cls, "mediterranean shrubland biome [ENVO:01000217]", + PermissibleValue(text="mediterranean shrubland biome [ENVO:01000217]")) + setattr(cls, "mediterranean woodland biome [ENVO:01000208]", + PermissibleValue(text="mediterranean woodland biome [ENVO:01000208]")) + setattr(cls, "mixed forest biome [ENVO:01000198]", + PermissibleValue(text="mixed forest biome [ENVO:01000198]")) + setattr(cls, "montane grassland biome [ENVO:01000194]", + PermissibleValue(text="montane grassland biome [ENVO:01000194]")) + setattr(cls, "montane savanna biome [ENVO:01000223]", + PermissibleValue(text="montane savanna biome [ENVO:01000223]")) + setattr(cls, "montane shrubland biome [ENVO:01000216]", + PermissibleValue(text="montane shrubland biome [ENVO:01000216]")) + setattr(cls, "rangeland biome [ENVO:01000247]", + PermissibleValue(text="rangeland biome [ENVO:01000247]")) + setattr(cls, "savanna biome [ENVO:01000178]", + PermissibleValue(text="savanna biome [ENVO:01000178]")) + setattr(cls, "shrubland biome [ENVO:01000176]", + PermissibleValue(text="shrubland biome [ENVO:01000176]")) + setattr(cls, "subpolar coniferous forest biome [ENVO:01000250]", + PermissibleValue(text="subpolar coniferous forest biome [ENVO:01000250]")) + setattr(cls, "subtropical broadleaf forest biome [ENVO:01000201]", + PermissibleValue(text="subtropical broadleaf forest biome [ENVO:01000201]")) + setattr(cls, "subtropical coniferous forest biome [ENVO:01000209]", + PermissibleValue(text="subtropical coniferous forest biome [ENVO:01000209]")) + setattr(cls, "subtropical dry broadleaf forest biome [ENVO:01000225]", + PermissibleValue(text="subtropical dry broadleaf forest biome [ENVO:01000225]")) + setattr(cls, "subtropical grassland biome [ENVO:01000191]", + PermissibleValue(text="subtropical grassland biome [ENVO:01000191]")) + setattr(cls, "subtropical moist broadleaf forest biome [ENVO:01000226]", + PermissibleValue(text="subtropical moist broadleaf forest biome [ENVO:01000226]")) + setattr(cls, "subtropical savanna biome [ENVO:01000187]", + PermissibleValue(text="subtropical savanna biome [ENVO:01000187]")) + setattr(cls, "subtropical shrubland biome [ENVO:01000213]", + PermissibleValue(text="subtropical shrubland biome [ENVO:01000213]")) + setattr(cls, "subtropical woodland biome [ENVO:01000222]", + PermissibleValue(text="subtropical woodland biome [ENVO:01000222]")) + setattr(cls, "temperate broadleaf forest biome [ENVO:01000202]", + PermissibleValue(text="temperate broadleaf forest biome [ENVO:01000202]")) + setattr(cls, "temperate coniferous forest biome [ENVO:01000211]", + PermissibleValue(text="temperate coniferous forest biome [ENVO:01000211]")) + setattr(cls, "temperate grassland biome [ENVO:01000193]", + PermissibleValue(text="temperate grassland biome [ENVO:01000193]")) + setattr(cls, "temperate mixed forest biome [ENVO:01000212]", + PermissibleValue(text="temperate mixed forest biome [ENVO:01000212]")) + setattr(cls, "temperate savanna biome [ENVO:01000189]", + PermissibleValue(text="temperate savanna biome [ENVO:01000189]")) + setattr(cls, "temperate shrubland biome [ENVO:01000215]", + PermissibleValue(text="temperate shrubland biome [ENVO:01000215]")) + setattr(cls, "temperate woodland biome [ENVO:01000221]", + PermissibleValue(text="temperate woodland biome [ENVO:01000221]")) + setattr(cls, "terrestrial biome [ENVO:00000446]", + PermissibleValue(text="terrestrial biome [ENVO:00000446]")) + setattr(cls, "tidal mangrove shrubland [ENVO:01001369]", + PermissibleValue(text="tidal mangrove shrubland [ENVO:01001369]")) + setattr(cls, "tropical broadleaf forest biome [ENVO:01000200]", + PermissibleValue(text="tropical broadleaf forest biome [ENVO:01000200]")) + setattr(cls, "tropical coniferous forest biome [ENVO:01000210]", + PermissibleValue(text="tropical coniferous forest biome [ENVO:01000210]")) + setattr(cls, "tropical dry broadleaf forest biome [ENVO:01000227]", + PermissibleValue(text="tropical dry broadleaf forest biome [ENVO:01000227]")) + setattr(cls, "tropical grassland biome [ENVO:01000192]", + PermissibleValue(text="tropical grassland biome [ENVO:01000192]")) + setattr(cls, "tropical mixed forest biome [ENVO:01001798]", + PermissibleValue(text="tropical mixed forest biome [ENVO:01001798]")) + setattr(cls, "tropical moist broadleaf forest biome [ENVO:01000228]", + PermissibleValue(text="tropical moist broadleaf forest biome [ENVO:01000228]")) + setattr(cls, "tropical savanna biome [ENVO:01000188]", + PermissibleValue(text="tropical savanna biome [ENVO:01000188]")) + setattr(cls, "tropical shrubland biome [ENVO:01000214]", + PermissibleValue(text="tropical shrubland biome [ENVO:01000214]")) + setattr(cls, "tropical woodland biome [ENVO:01000220]", + PermissibleValue(text="tropical woodland biome [ENVO:01000220]")) + setattr(cls, "tundra biome [ENVO:01000180]", + PermissibleValue(text="tundra biome [ENVO:01000180]")) + setattr(cls, "woodland biome [ENVO:01000175]", + PermissibleValue(text="woodland biome [ENVO:01000175]")) + setattr(cls, "xeric shrubland biome [ENVO:01000218]", + PermissibleValue(text="xeric shrubland biome [ENVO:01000218]")) + class EnvLocalScaleSoilEnum(EnumDefinitionImpl): _defn = EnumDefinition( @@ -15293,10 +15301,10 @@ def _addvals(cls): setattr(cls, "woodland clearing [ENVO:00000444]", PermissibleValue(text="woodland clearing [ENVO:00000444]")) -class EnvMediumScaleSoilEnum(EnumDefinitionImpl): +class EnvMediumSoilEnum(EnumDefinitionImpl): _defn = EnumDefinition( - name="EnvMediumScaleSoilEnum", + name="EnvMediumSoilEnum", ) @classmethod @@ -15474,119 +15482,6 @@ def _addvals(cls): setattr(cls, "vertisol [ENVO:00002254]", PermissibleValue(text="vertisol [ENVO:00002254]")) -class EnvBroadScaleSoilEnum(EnumDefinitionImpl): - - _defn = EnumDefinition( - name="EnvBroadScaleSoilEnum", - ) - - @classmethod - def _addvals(cls): - setattr(cls, "alpine tundra biome [ENVO:01001505]", - PermissibleValue(text="alpine tundra biome [ENVO:01001505]")) - setattr(cls, "anthropogenic terrestrial biome [ENVO:01000219]", - PermissibleValue(text="anthropogenic terrestrial biome [ENVO:01000219]")) - setattr(cls, "broadleaf forest biome [ENVO:01000197]", - PermissibleValue(text="broadleaf forest biome [ENVO:01000197]")) - setattr(cls, "coniferous forest biome [ENVO:01000196]", - PermissibleValue(text="coniferous forest biome [ENVO:01000196]")) - setattr(cls, "cropland biome [ENVO:01000245]", - PermissibleValue(text="cropland biome [ENVO:01000245]")) - setattr(cls, "flooded grassland biome [ENVO:01000195]", - PermissibleValue(text="flooded grassland biome [ENVO:01000195]")) - setattr(cls, "flooded savanna biome [ENVO:01000190]", - PermissibleValue(text="flooded savanna biome [ENVO:01000190]")) - setattr(cls, "forest biome [ENVO:01000174]", - PermissibleValue(text="forest biome [ENVO:01000174]")) - setattr(cls, "grassland biome [ENVO:01000177]", - PermissibleValue(text="grassland biome [ENVO:01000177]")) - setattr(cls, "mangrove biome [ENVO:01000181]", - PermissibleValue(text="mangrove biome [ENVO:01000181]")) - setattr(cls, "mediterranean forest biome [ENVO:01000199]", - PermissibleValue(text="mediterranean forest biome [ENVO:01000199]")) - setattr(cls, "mediterranean grassland biome [ENVO:01000224]", - PermissibleValue(text="mediterranean grassland biome [ENVO:01000224]")) - setattr(cls, "mediterranean savanna biome [ENVO:01000229]", - PermissibleValue(text="mediterranean savanna biome [ENVO:01000229]")) - setattr(cls, "mediterranean shrubland biome [ENVO:01000217]", - PermissibleValue(text="mediterranean shrubland biome [ENVO:01000217]")) - setattr(cls, "mediterranean woodland biome [ENVO:01000208]", - PermissibleValue(text="mediterranean woodland biome [ENVO:01000208]")) - setattr(cls, "mixed forest biome [ENVO:01000198]", - PermissibleValue(text="mixed forest biome [ENVO:01000198]")) - setattr(cls, "montane grassland biome [ENVO:01000194]", - PermissibleValue(text="montane grassland biome [ENVO:01000194]")) - setattr(cls, "montane savanna biome [ENVO:01000223]", - PermissibleValue(text="montane savanna biome [ENVO:01000223]")) - setattr(cls, "montane shrubland biome [ENVO:01000216]", - PermissibleValue(text="montane shrubland biome [ENVO:01000216]")) - setattr(cls, "rangeland biome [ENVO:01000247]", - PermissibleValue(text="rangeland biome [ENVO:01000247]")) - setattr(cls, "savanna biome [ENVO:01000178]", - PermissibleValue(text="savanna biome [ENVO:01000178]")) - setattr(cls, "shrubland biome [ENVO:01000176]", - PermissibleValue(text="shrubland biome [ENVO:01000176]")) - setattr(cls, "subpolar coniferous forest biome [ENVO:01000250]", - PermissibleValue(text="subpolar coniferous forest biome [ENVO:01000250]")) - setattr(cls, "subtropical broadleaf forest biome [ENVO:01000201]", - PermissibleValue(text="subtropical broadleaf forest biome [ENVO:01000201]")) - setattr(cls, "subtropical coniferous forest biome [ENVO:01000209]", - PermissibleValue(text="subtropical coniferous forest biome [ENVO:01000209]")) - setattr(cls, "subtropical dry broadleaf forest biome [ENVO:01000225]", - PermissibleValue(text="subtropical dry broadleaf forest biome [ENVO:01000225]")) - setattr(cls, "subtropical grassland biome [ENVO:01000191]", - PermissibleValue(text="subtropical grassland biome [ENVO:01000191]")) - setattr(cls, "subtropical moist broadleaf forest biome [ENVO:01000226]", - PermissibleValue(text="subtropical moist broadleaf forest biome [ENVO:01000226]")) - setattr(cls, "subtropical savanna biome [ENVO:01000187]", - PermissibleValue(text="subtropical savanna biome [ENVO:01000187]")) - setattr(cls, "subtropical shrubland biome [ENVO:01000213]", - PermissibleValue(text="subtropical shrubland biome [ENVO:01000213]")) - setattr(cls, "subtropical woodland biome [ENVO:01000222]", - PermissibleValue(text="subtropical woodland biome [ENVO:01000222]")) - setattr(cls, "temperate broadleaf forest biome [ENVO:01000202]", - PermissibleValue(text="temperate broadleaf forest biome [ENVO:01000202]")) - setattr(cls, "temperate coniferous forest biome [ENVO:01000211]", - PermissibleValue(text="temperate coniferous forest biome [ENVO:01000211]")) - setattr(cls, "temperate grassland biome [ENVO:01000193]", - PermissibleValue(text="temperate grassland biome [ENVO:01000193]")) - setattr(cls, "temperate mixed forest biome [ENVO:01000212]", - PermissibleValue(text="temperate mixed forest biome [ENVO:01000212]")) - setattr(cls, "temperate savanna biome [ENVO:01000189]", - PermissibleValue(text="temperate savanna biome [ENVO:01000189]")) - setattr(cls, "temperate shrubland biome [ENVO:01000215]", - PermissibleValue(text="temperate shrubland biome [ENVO:01000215]")) - setattr(cls, "temperate woodland biome [ENVO:01000221]", - PermissibleValue(text="temperate woodland biome [ENVO:01000221]")) - setattr(cls, "terrestrial biome [ENVO:00000446]", - PermissibleValue(text="terrestrial biome [ENVO:00000446]")) - setattr(cls, "tidal mangrove shrubland [ENVO:01001369]", - PermissibleValue(text="tidal mangrove shrubland [ENVO:01001369]")) - setattr(cls, "tropical broadleaf forest biome [ENVO:01000200]", - PermissibleValue(text="tropical broadleaf forest biome [ENVO:01000200]")) - setattr(cls, "tropical coniferous forest biome [ENVO:01000210]", - PermissibleValue(text="tropical coniferous forest biome [ENVO:01000210]")) - setattr(cls, "tropical dry broadleaf forest biome [ENVO:01000227]", - PermissibleValue(text="tropical dry broadleaf forest biome [ENVO:01000227]")) - setattr(cls, "tropical grassland biome [ENVO:01000192]", - PermissibleValue(text="tropical grassland biome [ENVO:01000192]")) - setattr(cls, "tropical mixed forest biome [ENVO:01001798]", - PermissibleValue(text="tropical mixed forest biome [ENVO:01001798]")) - setattr(cls, "tropical moist broadleaf forest biome [ENVO:01000228]", - PermissibleValue(text="tropical moist broadleaf forest biome [ENVO:01000228]")) - setattr(cls, "tropical savanna biome [ENVO:01000188]", - PermissibleValue(text="tropical savanna biome [ENVO:01000188]")) - setattr(cls, "tropical shrubland biome [ENVO:01000214]", - PermissibleValue(text="tropical shrubland biome [ENVO:01000214]")) - setattr(cls, "tropical woodland biome [ENVO:01000220]", - PermissibleValue(text="tropical woodland biome [ENVO:01000220]")) - setattr(cls, "tundra biome [ENVO:01000180]", - PermissibleValue(text="tundra biome [ENVO:01000180]")) - setattr(cls, "woodland biome [ENVO:01000175]", - PermissibleValue(text="woodland biome [ENVO:01000175]")) - setattr(cls, "xeric shrubland biome [ENVO:01000218]", - PermissibleValue(text="xeric shrubland biome [ENVO:01000218]")) - # Slots class slots: pass diff --git a/src/nmdc_submission_schema/schema/nmdc_submission_schema.yaml b/src/nmdc_submission_schema/schema/nmdc_submission_schema.yaml index 4afd09f4..43f6bb13 100644 --- a/src/nmdc_submission_schema/schema/nmdc_submission_schema.yaml +++ b/src/nmdc_submission_schema/schema/nmdc_submission_schema.yaml @@ -190,6 +190,9 @@ prefixes: kegg: prefix_prefix: kegg prefix_reference: 'https://bioregistry.io/kegg:' + KEGG.MODULE: + prefix_prefix: KEGG.MODULE + prefix_reference: 'https://bioregistry.io/kegg.module:' mgnify.proj: prefix_prefix: mgnify.proj prefix_reference: 'https://bioregistry.io/mgnify.proj:' @@ -353,28 +356,6 @@ types: from_schema: https://example.com/nmdc_submission_schema base: str uri: xsd:language - uriorcurie: - name: uriorcurie - description: a URI or a CURIE - notes: - - If you are authoring schemas in LinkML YAML, the type is referenced with the - lower case "uriorcurie". - from_schema: https://example.com/nmdc_submission_schema - base: URIorCURIE - uri: xsd:anyURI - repr: str - string: - name: string - description: A character string - notes: - - In RDF serializations, a slot with range of string is treated as a literal or - type xsd:string. If you are authoring schemas in LinkML YAML, the type is - referenced with the lower case "string". - from_schema: https://example.com/nmdc_submission_schema - exact_mappings: - - schema:Text - base: str - uri: xsd:string decimal: name: decimal description: A real number with arbitrary precision that conforms to the xsd:decimal @@ -387,17 +368,17 @@ types: - schema:Number base: Decimal uri: xsd:decimal - float: - name: float - description: A real number that conforms to the xsd:float specification + double: + name: double + description: A real number that conforms to the xsd:double specification notes: - If you are authoring schemas in LinkML YAML, the type is referenced with the - lower case "float". + lower case "double". from_schema: https://example.com/nmdc_submission_schema - exact_mappings: + close_mappings: - schema:Float base: float - uri: xsd:float + uri: xsd:double integer: name: integer description: An integer @@ -409,17 +390,39 @@ types: - schema:Integer base: int uri: xsd:integer - double: - name: double - description: A real number that conforms to the xsd:double specification + string: + name: string + description: A character string + notes: + - In RDF serializations, a slot with range of string is treated as a literal or + type xsd:string. If you are authoring schemas in LinkML YAML, the type is + referenced with the lower case "string". + from_schema: https://example.com/nmdc_submission_schema + exact_mappings: + - schema:Text + base: str + uri: xsd:string + float: + name: float + description: A real number that conforms to the xsd:float specification notes: - If you are authoring schemas in LinkML YAML, the type is referenced with the - lower case "double". + lower case "float". from_schema: https://example.com/nmdc_submission_schema - close_mappings: + exact_mappings: - schema:Float base: float - uri: xsd:double + uri: xsd:float + uriorcurie: + name: uriorcurie + description: a URI or a CURIE + notes: + - If you are authoring schemas in LinkML YAML, the type is referenced with the + lower case "uriorcurie". + from_schema: https://example.com/nmdc_submission_schema + base: URIorCURIE + uri: xsd:anyURI + repr: str boolean: name: boolean description: A binary (true or false) value