diff --git a/lib/DataHarmonizer.js b/lib/DataHarmonizer.js
index ab398aae..e269dcb2 100644
--- a/lib/DataHarmonizer.js
+++ b/lib/DataHarmonizer.js
@@ -1528,12 +1528,14 @@ class DataHarmonizer {
* @param {String} prefix of export format to access in .exportField dictionary.
*/
getTransformedField(headerName, value, field, prefix) {
+ const self = this;
if (field.sources) {
// iterate thru and will return the first match found in field.sources
for (const source_index in field.sources) {
const term =
- DataHarmonizer.schema.enums[field.sources[source_index]]
- .permissible_values[value];
+ self.schema.enums[field.sources[source_index]].permissible_values[
+ value
+ ];
// Looking for term.exportField['GRDI'] for example:
if (term && term.exportField && prefix in term.exportField) {
// Here mapping involves a value substitution
diff --git a/web/templates/menu.json b/web/templates/menu.json
index faa74e88..602b714c 100644
--- a/web/templates/menu.json
+++ b/web/templates/menu.json
@@ -46,4 +46,4 @@
"display": true
}
}
-}
+}
\ No newline at end of file
diff --git a/web/templates/monkeypox/export.js b/web/templates/monkeypox/export.js
index c550c1ab..0e8a402e 100644
--- a/web/templates/monkeypox/export.js
+++ b/web/templates/monkeypox/export.js
@@ -263,7 +263,7 @@ export default {
['PH_SEQUENCING_CENTRE', []],
- ['PH_SEQUENCING_SUBMITTER', []],
+ ['PH_SEQUENCE_SUBMITTER', []],
['HC_COLLECT_DATE', []],
['HC_TEXT2', []],
diff --git a/web/templates/monkeypox/schema.json b/web/templates/monkeypox/schema.json
index 1f403f94..8d1b39d0 100644
--- a/web/templates/monkeypox/schema.json
+++ b/web/templates/monkeypox/schema.json
@@ -2,7 +2,7 @@
"name": "Monkeypox",
"description": "",
"id": "https://example.com/monkeypox",
- "version": "1.1.0",
+ "version": "3.3.1",
"prefixes": {
"linkml": {
"prefix_prefix": "linkml",
@@ -132,7 +132,9 @@
"objectidentifier": {
"name": "objectidentifier",
"description": "A URI or CURIE that represents an object in the model.",
- "comments": ["Used for inheritence and type checking"],
+ "comments": [
+ "Used for inheritence and type checking"
+ ],
"base": "ElementIdentifier",
"uri": "shex:iri",
"repr": "str"
@@ -1105,6 +1107,37 @@
}
}
},
+ "environmental material international menu": {
+ "name": "environmental material international menu",
+ "from_schema": "https://example.com/monkeypox",
+ "permissible_values": {
+ "Animal carcass": {
+ "text": "Animal carcass"
+ },
+ "Bedding (Bed linen)": {
+ "text": "Bedding (Bed linen)",
+ "meaning": "GSSO:005304"
+ },
+ "Clothing": {
+ "text": "Clothing",
+ "meaning": "GSSO:003405"
+ },
+ "Drinkware": {
+ "text": "Drinkware"
+ },
+ "Tableware": {
+ "text": "Tableware"
+ },
+ "Dish": {
+ "text": "Dish",
+ "is_a": "Tableware"
+ },
+ "Utensil": {
+ "text": "Utensil",
+ "is_a": "Tableware"
+ }
+ }
+ },
"collection method menu": {
"name": "collection method menu",
"from_schema": "https://example.com/monkeypox",
@@ -1482,6 +1515,29 @@
"Human [NCBITaxon:9606]": {
"text": "Human [NCBITaxon:9606]",
"meaning": "NCBITaxon:9606"
+ },
+ "Rodent": {
+ "text": "Rodent",
+ "meaning": "NCBITaxon:9989"
+ },
+ "Mouse": {
+ "text": "Mouse",
+ "meaning": "NCBITaxon:10090",
+ "is_a": "Rodent"
+ },
+ "Prairie Dog": {
+ "text": "Prairie Dog",
+ "is_a": "Rodent"
+ },
+ "Rat": {
+ "text": "Rat",
+ "meaning": "NCBITaxon:10116",
+ "is_a": "Rodent"
+ },
+ "Squirrel": {
+ "text": "Squirrel",
+ "meaning": "FOODON:03411389",
+ "is_a": "Rodent"
}
}
},
@@ -7578,6 +7634,36 @@
"slot_uri": "GENEPIO:0001216",
"multivalued": true
},
+ "environmental material": {
+ "name": "environmental material",
+ "description": "A substance obtained from the natural or man-made environment e.g. soil, water, sewage.",
+ "title": "environmental material",
+ "comments": [
+ "Provide a descriptor if an environmental material was sampled. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value."
+ ],
+ "examples": [
+ {
+ "value": "Bed linen"
+ }
+ ],
+ "from_schema": "https://example.com/monkeypox",
+ "exact_mappings": [
+ "GISAID:Specimen source",
+ "BIOSAMPLE:isolation_source",
+ "BIOSAMPLE:environmental_material"
+ ],
+ "slot_uri": "GENEPIO:0001223",
+ "multivalued": true,
+ "recommended": true,
+ "any_of": [
+ {
+ "range": "environmental material international menu"
+ },
+ {
+ "range": "null value menu"
+ }
+ ]
+ },
"collection device": {
"name": "collection device",
"description": "The instrument or container used to collect the sample e.g. swab.",
@@ -8814,7 +8900,9 @@
}
],
"from_schema": "https://example.com/monkeypox",
- "exact_mappings": ["NML_LIMS:number of base pairs sequenced"],
+ "exact_mappings": [
+ "NML_LIMS:number of base pairs sequenced"
+ ],
"slot_uri": "GENEPIO:0001482",
"range": "integer",
"minimum_value": 0
@@ -9175,6 +9263,12 @@
},
"Monkeypox": {
"name": "Monkeypox",
+ "annotations": {
+ "version": {
+ "tag": "version",
+ "value": "3.2.1"
+ }
+ },
"description": "Canadian specification for Monkeypox clinical virus biosample data gathering",
"from_schema": "https://example.com/monkeypox",
"see_also": [
@@ -9284,7 +9378,7 @@
"exact_mappings": [
"GISAID:Submitting lab",
"CNPHI:Sequencing Centre",
- "NML_LIMS:PH_SEQUENCING_SUBMITTER",
+ "NML_LIMS:PH_SEQUENCE_SUBMITTER",
"BIOSAMPLE:sequence_submitted_by",
"VirusSeq_Portal:sequence submitted by"
],
@@ -10610,7 +10704,7 @@
"exact_mappings": [
"GISAID:Submitting lab",
"CNPHI:Sequencing Centre",
- "NML_LIMS:PH_SEQUENCING_SUBMITTER",
+ "NML_LIMS:PH_SEQUENCE_SUBMITTER",
"BIOSAMPLE:sequence_submitted_by",
"VirusSeq_Portal:sequence submitted by"
],
@@ -12388,6 +12482,12 @@
},
"Monkeypox_international": {
"name": "Monkeypox_international",
+ "annotations": {
+ "version": {
+ "tag": "version",
+ "value": "3.3.1"
+ }
+ },
"description": "International specification for Monkeypox clinical virus biosample data gathering",
"from_schema": "https://example.com/monkeypox",
"see_also": [
@@ -12684,6 +12784,11 @@
}
]
},
+ "environmental material": {
+ "name": "environmental material",
+ "rank": 32,
+ "slot_group": "Sample collection and processing"
+ },
"collection device": {
"name": "collection device",
"examples": [
@@ -12691,7 +12796,7 @@
"value": "Swab [GENEPIO:0100027]"
}
],
- "rank": 32,
+ "rank": 33,
"slot_group": "Sample collection and processing",
"recommended": true,
"any_of": [
@@ -12710,7 +12815,7 @@
"value": "Biopsy [OBI:0002650]"
}
],
- "rank": 33,
+ "rank": 34,
"slot_group": "Sample collection and processing",
"recommended": true,
"any_of": [
@@ -12729,7 +12834,7 @@
"value": "Specimens pooled [OBI:0600016]"
}
],
- "rank": 34,
+ "rank": 35,
"slot_group": "Sample collection and processing",
"any_of": [
{
@@ -12742,12 +12847,12 @@
},
"specimen processing details": {
"name": "specimen processing details",
- "rank": 35,
+ "rank": 36,
"slot_group": "Sample collection and processing"
},
"host (common name)": {
"name": "host (common name)",
- "rank": 36,
+ "rank": 37,
"slot_group": "Host Information",
"any_of": [
{
@@ -12765,7 +12870,7 @@
"value": "Homo sapiens [NCBITaxon:9606]"
}
],
- "rank": 37,
+ "rank": 38,
"slot_group": "Host Information",
"any_of": [
{
@@ -12787,7 +12892,7 @@
"GISAID:Patient status",
"BIOSAMPLE:host_health_state"
],
- "rank": 38,
+ "rank": 39,
"slot_group": "Host Information",
"any_of": [
{
@@ -12805,7 +12910,7 @@
"value": "Hospitalized [NCIT:C25179]"
}
],
- "rank": 39,
+ "rank": 40,
"slot_group": "Host Information",
"any_of": [
{
@@ -12826,7 +12931,7 @@
"exact_mappings": [
"BIOSAMPLE:host_health_outcome"
],
- "rank": 40,
+ "rank": 41,
"slot_group": "Host Information",
"any_of": [
{
@@ -12844,7 +12949,7 @@
"value": "Monkeypox [MONDO:0002594]"
}
],
- "rank": 41,
+ "rank": 42,
"slot_group": "Host Information",
"any_of": [
{
@@ -12870,7 +12975,7 @@
"NML_LIMS:host subject ID",
"BIOSAMPLE:host_subject_id"
],
- "rank": 47,
+ "rank": 48,
"slot_group": "Host Information"
},
"host age": {
@@ -12879,7 +12984,7 @@
"GISAID:Patient age",
"BIOSAMPLE:host_age"
],
- "rank": 43,
+ "rank": 44,
"slot_group": "Host Information",
"recommended": true
},
@@ -12893,7 +12998,7 @@
"exact_mappings": [
"BIOSAMPLE:host_age_unit"
],
- "rank": 44,
+ "rank": 45,
"slot_group": "Host Information",
"recommended": true,
"any_of": [
@@ -12915,7 +13020,7 @@
"exact_mappings": [
"BIOSAMPLE:host_age_bin"
],
- "rank": 45,
+ "rank": 46,
"slot_group": "Host Information",
"recommended": true,
"any_of": [
@@ -12938,7 +13043,7 @@
"GISAID:Gender",
"BIOSAMPLE:host_sex"
],
- "rank": 46,
+ "rank": 47,
"slot_group": "Host Information",
"recommended": true,
"any_of": [
@@ -12957,7 +13062,7 @@
"value": "Canada [GAZ:00002560]"
}
],
- "rank": 48,
+ "rank": 49,
"slot_group": "Host Information",
"any_of": [
{
@@ -12970,7 +13075,7 @@
},
"symptom onset date": {
"name": "symptom onset date",
- "rank": 49,
+ "rank": 50,
"slot_group": "Host Information"
},
"signs and symptoms": {
@@ -12980,7 +13085,7 @@
"value": "Lesion (Pustule) [NCIT:C78582], Swollen Lymph Nodes [HP:0002716], Myalgia (muscle pain) [HP:0003326]"
}
],
- "rank": 50,
+ "rank": 51,
"slot_group": "Host Information",
"any_of": [
{
@@ -12993,7 +13098,7 @@
},
"pre-existing conditions and risk factors": {
"name": "pre-existing conditions and risk factors",
- "rank": 51,
+ "rank": 52,
"slot_group": "Host Information",
"any_of": [
{
@@ -13011,7 +13116,7 @@
"value": "Delayed wound healing (lesion healing) [MP:0002908]"
}
],
- "rank": 52,
+ "rank": 53,
"slot_group": "Host Information",
"any_of": [
{
@@ -13024,7 +13129,7 @@
},
"antiviral therapy": {
"name": "antiviral therapy",
- "rank": 53,
+ "rank": 54,
"slot_group": "Host Information"
},
"host vaccination status": {
@@ -13034,7 +13139,7 @@
"value": "Not Vaccinated [GENEPIO:0100102]"
}
],
- "rank": 54,
+ "rank": 55,
"slot_group": "Host vaccination information",
"any_of": [
{
@@ -13047,22 +13152,22 @@
},
"number of vaccine doses received": {
"name": "number of vaccine doses received",
- "rank": 55,
+ "rank": 56,
"slot_group": "Host vaccination information"
},
"vaccination dose 1 vaccine name": {
"name": "vaccination dose 1 vaccine name",
- "rank": 56,
+ "rank": 57,
"slot_group": "Host vaccination information"
},
"vaccination dose 1 vaccination date": {
"name": "vaccination dose 1 vaccination date",
- "rank": 57,
+ "rank": 58,
"slot_group": "Host vaccination information"
},
"vaccination history": {
"name": "vaccination history",
- "rank": 58,
+ "rank": 59,
"slot_group": "Host vaccination information"
},
"location of exposure geo_loc name (country)": {
@@ -13072,7 +13177,7 @@
"value": "Canada [GAZ:00002560]"
}
],
- "rank": 59,
+ "rank": 60,
"slot_group": "Host exposure information",
"any_of": [
{
@@ -13085,7 +13190,7 @@
},
"destination of most recent travel (city)": {
"name": "destination of most recent travel (city)",
- "rank": 60,
+ "rank": 61,
"slot_group": "Host exposure information"
},
"destination of most recent travel (state/province/territory)": {
@@ -13098,7 +13203,7 @@
"value": "California"
}
],
- "rank": 61,
+ "rank": 62,
"slot_group": "Host exposure information",
"range": "WhitespaceMinimizedString"
},
@@ -13109,7 +13214,7 @@
"value": "United Kingdom [GAZ:00002637]"
}
],
- "rank": 62,
+ "rank": 63,
"slot_group": "Host exposure information",
"any_of": [
{
@@ -13122,17 +13227,17 @@
},
"most recent travel departure date": {
"name": "most recent travel departure date",
- "rank": 63,
+ "rank": 64,
"slot_group": "Host exposure information"
},
"most recent travel return date": {
"name": "most recent travel return date",
- "rank": 64,
+ "rank": 65,
"slot_group": "Host exposure information"
},
"travel history": {
"name": "travel history",
- "rank": 65,
+ "rank": 66,
"slot_group": "Host exposure information"
},
"exposure event": {
@@ -13142,7 +13247,7 @@
"value": "Party [PCO:0000035]"
}
],
- "rank": 66,
+ "rank": 67,
"slot_group": "Host exposure information",
"any_of": [
{
@@ -13160,7 +13265,7 @@
"value": "Contact with infected individual [GENEPIO:0100357]"
}
],
- "rank": 67,
+ "rank": 68,
"slot_group": "Host exposure information",
"any_of": [
{
@@ -13178,7 +13283,7 @@
"value": "Acquaintance of case [GENEPIO:0100266]"
}
],
- "rank": 68,
+ "rank": 69,
"slot_group": "Host exposure information",
"range": "host role international menu"
},
@@ -13189,13 +13294,13 @@
"value": "Healthcare Setting [GENEPIO:0100201]"
}
],
- "rank": 69,
+ "rank": 70,
"slot_group": "Host exposure information",
"range": "exposure setting international menu"
},
"exposure details": {
"name": "exposure details",
- "rank": 70,
+ "rank": 71,
"slot_group": "Host exposure information"
},
"prior Monkeypox infection": {
@@ -13205,7 +13310,7 @@
"value": "Prior infection [GENEPIO:0100037]"
}
],
- "rank": 71,
+ "rank": 72,
"slot_group": "Host reinfection information",
"any_of": [
{
@@ -13218,7 +13323,7 @@
},
"prior Monkeypox infection date": {
"name": "prior Monkeypox infection date",
- "rank": 72,
+ "rank": 73,
"slot_group": "Host reinfection information"
},
"prior Monkeypox antiviral treatment": {
@@ -13228,7 +13333,7 @@
"value": "Prior antiviral treatment [GENEPIO:0100037]"
}
],
- "rank": 73,
+ "rank": 74,
"slot_group": "Host reinfection information",
"any_of": [
{
@@ -13241,7 +13346,7 @@
},
"prior antiviral treatment during prior Monkeypox infection": {
"name": "prior antiviral treatment during prior Monkeypox infection",
- "rank": 74,
+ "rank": 75,
"slot_group": "Host reinfection information"
},
"purpose of sequencing": {
@@ -13251,7 +13356,7 @@
"value": "Baseline surveillance (random sampling) [GENEPIO:0100005]"
}
],
- "rank": 75,
+ "rank": 76,
"slot_group": "Sequencing",
"any_of": [
{
@@ -13264,27 +13369,27 @@
},
"purpose of sequencing details": {
"name": "purpose of sequencing details",
- "rank": 76,
+ "rank": 77,
"slot_group": "Sequencing"
},
"sequencing date": {
"name": "sequencing date",
- "rank": 77,
+ "rank": 78,
"slot_group": "Sequencing"
},
"library ID": {
"name": "library ID",
- "rank": 78,
+ "rank": 79,
"slot_group": "Sequencing"
},
"amplicon size": {
"name": "amplicon size",
- "rank": 79,
+ "rank": 80,
"slot_group": "Sequencing"
},
"library preparation kit": {
"name": "library preparation kit",
- "rank": 80,
+ "rank": 81,
"slot_group": "Sequencing"
},
"sequencing instrument": {
@@ -13294,7 +13399,7 @@
"value": "Oxford Nanopore MinION [GENEPIO:0100142]"
}
],
- "rank": 81,
+ "rank": 82,
"slot_group": "Sequencing",
"any_of": [
{
@@ -13307,117 +13412,117 @@
},
"sequencing protocol": {
"name": "sequencing protocol",
- "rank": 82,
+ "rank": 83,
"slot_group": "Sequencing"
},
"sequencing kit number": {
"name": "sequencing kit number",
- "rank": 83,
+ "rank": 84,
"slot_group": "Sequencing"
},
"amplicon pcr primer scheme": {
"name": "amplicon pcr primer scheme",
- "rank": 84,
+ "rank": 85,
"slot_group": "Sequencing"
},
"raw sequence data processing method": {
"name": "raw sequence data processing method",
- "rank": 85,
+ "rank": 86,
"slot_group": "Bioinformatics and QC metrics"
},
"dehosting method": {
"name": "dehosting method",
- "rank": 86,
+ "rank": 87,
"slot_group": "Bioinformatics and QC metrics"
},
"consensus sequence name": {
"name": "consensus sequence name",
- "rank": 87,
+ "rank": 88,
"slot_group": "Bioinformatics and QC metrics"
},
"consensus sequence filename": {
"name": "consensus sequence filename",
- "rank": 88,
+ "rank": 89,
"slot_group": "Bioinformatics and QC metrics"
},
"consensus sequence filepath": {
"name": "consensus sequence filepath",
- "rank": 89,
+ "rank": 90,
"slot_group": "Bioinformatics and QC metrics"
},
"consensus sequence software name": {
"name": "consensus sequence software name",
- "rank": 90,
+ "rank": 91,
"slot_group": "Bioinformatics and QC metrics"
},
"consensus sequence software version": {
"name": "consensus sequence software version",
- "rank": 91,
+ "rank": 92,
"slot_group": "Bioinformatics and QC metrics"
},
"breadth of coverage value": {
"name": "breadth of coverage value",
- "rank": 92,
+ "rank": 93,
"slot_group": "Bioinformatics and QC metrics"
},
"depth of coverage value": {
"name": "depth of coverage value",
- "rank": 93,
+ "rank": 94,
"slot_group": "Bioinformatics and QC metrics"
},
"depth of coverage threshold": {
"name": "depth of coverage threshold",
- "rank": 94,
+ "rank": 95,
"slot_group": "Bioinformatics and QC metrics"
},
"r1 fastq filename": {
"name": "r1 fastq filename",
- "rank": 95,
+ "rank": 96,
"slot_group": "Bioinformatics and QC metrics"
},
"r2 fastq filename": {
"name": "r2 fastq filename",
- "rank": 96,
+ "rank": 97,
"slot_group": "Bioinformatics and QC metrics"
},
"r1 fastq filepath": {
"name": "r1 fastq filepath",
- "rank": 97,
+ "rank": 98,
"slot_group": "Bioinformatics and QC metrics"
},
"r2 fastq filepath": {
"name": "r2 fastq filepath",
- "rank": 98,
+ "rank": 99,
"slot_group": "Bioinformatics and QC metrics"
},
"fast5 filename": {
"name": "fast5 filename",
- "rank": 99,
+ "rank": 100,
"slot_group": "Bioinformatics and QC metrics"
},
"fast5 filepath": {
"name": "fast5 filepath",
- "rank": 100,
+ "rank": 101,
"slot_group": "Bioinformatics and QC metrics"
},
"number of base pairs sequenced": {
"name": "number of base pairs sequenced",
- "rank": 101,
+ "rank": 102,
"slot_group": "Bioinformatics and QC metrics"
},
"consensus genome length": {
"name": "consensus genome length",
- "rank": 102,
+ "rank": 103,
"slot_group": "Bioinformatics and QC metrics"
},
"reference genome accession": {
"name": "reference genome accession",
- "rank": 103,
+ "rank": 104,
"slot_group": "Bioinformatics and QC metrics"
},
"bioinformatics protocol": {
"name": "bioinformatics protocol",
- "rank": 104,
+ "rank": 105,
"slot_group": "Bioinformatics and QC metrics"
},
"gene name 1": {
@@ -13425,7 +13530,7 @@
"comments": [
"Provide the full name of the gene used in the test. The gene symbol (short form of gene name) can also be provided. Standardized gene names and symbols can be found in the Gene Ontology using this look-up service: https://bit.ly/2Sq1LbI"
],
- "rank": 105,
+ "rank": 106,
"slot_group": "Pathogen diagnostic testing",
"any_of": [
{
@@ -13438,7 +13543,7 @@
},
"diagnostic pcr Ct value 1": {
"name": "diagnostic pcr Ct value 1",
- "rank": 106,
+ "rank": 107,
"slot_group": "Pathogen diagnostic testing"
},
"gene name 2": {
@@ -13446,7 +13551,7 @@
"comments": [
"Provide the full name of another gene used in an RT-PCR test. The gene symbol (short form of gene name) can also be provided. Standardized gene names and symbols can be found in the Gene Ontology using this look-up service: https://bit.ly/2Sq1LbI"
],
- "rank": 107,
+ "rank": 108,
"slot_group": "Pathogen diagnostic testing",
"any_of": [
{
@@ -13459,7 +13564,7 @@
},
"diagnostic pcr Ct value 2": {
"name": "diagnostic pcr Ct value 2",
- "rank": 108,
+ "rank": 109,
"slot_group": "Pathogen diagnostic testing"
},
"gene name 3": {
@@ -13467,7 +13572,7 @@
"comments": [
"Provide the full name of another gene used in an RT-PCR test. The gene symbol (short form of gene name) can also be provided. Standardized gene names and symbols can be found in the Gene Ontology using this look-up service: https://bit.ly/2Sq1LbI"
],
- "rank": 109,
+ "rank": 110,
"slot_group": "Pathogen diagnostic testing",
"any_of": [
{
@@ -13480,17 +13585,17 @@
},
"diagnostic pcr Ct value 3": {
"name": "diagnostic pcr Ct value 3",
- "rank": 110,
+ "rank": 111,
"slot_group": "Pathogen diagnostic testing"
},
"authors": {
"name": "authors",
- "rank": 111,
+ "rank": 112,
"slot_group": "Contributor acknowledgement"
},
"DataHarmonizer provenance": {
"name": "DataHarmonizer provenance",
- "rank": 112,
+ "rank": 113,
"slot_group": "Contributor acknowledgement"
}
},
@@ -14020,6 +14125,19 @@
}
]
},
+ "environmental material": {
+ "name": "environmental material",
+ "description": "A substance obtained from the natural or man-made environment e.g. soil, water, sewage.",
+ "title": "environmental material",
+ "from_schema": "https://example.com/monkeypox",
+ "rank": 32,
+ "slot_uri": "GENEPIO:0001223",
+ "multivalued": true,
+ "alias": "environmental_material",
+ "owner": "Monkeypox_international",
+ "slot_group": "Sample collection and processing",
+ "recommended": true
+ },
"collection device": {
"name": "collection device",
"description": "The instrument or container used to collect the sample e.g. swab.",
@@ -14030,7 +14148,7 @@
}
],
"from_schema": "https://example.com/monkeypox",
- "rank": 32,
+ "rank": 33,
"slot_uri": "GENEPIO:0001234",
"multivalued": true,
"alias": "collection_device",
@@ -14056,7 +14174,7 @@
}
],
"from_schema": "https://example.com/monkeypox",
- "rank": 33,
+ "rank": 34,
"slot_uri": "GENEPIO:0001241",
"multivalued": true,
"alias": "collection_method",
@@ -14082,7 +14200,7 @@
}
],
"from_schema": "https://example.com/monkeypox",
- "rank": 34,
+ "rank": 35,
"slot_uri": "GENEPIO:0001253",
"multivalued": true,
"alias": "specimen_processing",
@@ -14102,7 +14220,7 @@
"description": "Detailed information regarding the processing applied to a sample during or after receiving the sample.",
"title": "specimen processing details",
"from_schema": "https://example.com/monkeypox",
- "rank": 35,
+ "rank": 36,
"slot_uri": "GENEPIO:0100311",
"alias": "specimen_processing_details",
"owner": "Monkeypox_international",
@@ -14114,7 +14232,7 @@
"description": "The commonly used name of the host.",
"title": "host (common name)",
"from_schema": "https://example.com/monkeypox",
- "rank": 36,
+ "rank": 37,
"slot_uri": "GENEPIO:0001386",
"alias": "host_(common_name)",
"owner": "Monkeypox_international",
@@ -14138,7 +14256,7 @@
}
],
"from_schema": "https://example.com/monkeypox",
- "rank": 37,
+ "rank": 38,
"slot_uri": "GENEPIO:0001387",
"alias": "host_(scientific_name)",
"owner": "Monkeypox_international",
@@ -14167,7 +14285,7 @@
"GISAID:Patient status",
"BIOSAMPLE:host_health_state"
],
- "rank": 38,
+ "rank": 39,
"slot_uri": "GENEPIO:0001388",
"alias": "host_health_state",
"owner": "Monkeypox_international",
@@ -14191,7 +14309,7 @@
}
],
"from_schema": "https://example.com/monkeypox",
- "rank": 39,
+ "rank": 40,
"slot_uri": "GENEPIO:0001389",
"alias": "host_health_status_details",
"owner": "Monkeypox_international",
@@ -14218,7 +14336,7 @@
"exact_mappings": [
"BIOSAMPLE:host_health_outcome"
],
- "rank": 40,
+ "rank": 41,
"slot_uri": "GENEPIO:0001389",
"alias": "host_health_outcome",
"owner": "Monkeypox_international",
@@ -14242,7 +14360,7 @@
}
],
"from_schema": "https://example.com/monkeypox",
- "rank": 41,
+ "rank": 42,
"slot_uri": "GENEPIO:0001391",
"alias": "host_disease",
"owner": "Monkeypox_international",
@@ -14274,7 +14392,7 @@
"NML_LIMS:host subject ID",
"BIOSAMPLE:host_subject_id"
],
- "rank": 47,
+ "rank": 48,
"slot_uri": "GENEPIO:0001398",
"alias": "host_subject_ID",
"owner": "Monkeypox_international",
@@ -14290,7 +14408,7 @@
"GISAID:Patient age",
"BIOSAMPLE:host_age"
],
- "rank": 43,
+ "rank": 44,
"slot_uri": "GENEPIO:0001392",
"alias": "host_age",
"owner": "Monkeypox_international",
@@ -14312,7 +14430,7 @@
"exact_mappings": [
"BIOSAMPLE:host_age_unit"
],
- "rank": 44,
+ "rank": 45,
"slot_uri": "GENEPIO:0001393",
"alias": "host_age_unit",
"owner": "Monkeypox_international",
@@ -14340,7 +14458,7 @@
"exact_mappings": [
"BIOSAMPLE:host_age_bin"
],
- "rank": 45,
+ "rank": 46,
"slot_uri": "GENEPIO:0001394",
"alias": "host_age_bin",
"owner": "Monkeypox_international",
@@ -14369,7 +14487,7 @@
"GISAID:Gender",
"BIOSAMPLE:host_sex"
],
- "rank": 46,
+ "rank": 47,
"slot_uri": "GENEPIO:0001395",
"alias": "host_gender",
"owner": "Monkeypox_international",
@@ -14399,7 +14517,7 @@
}
],
"from_schema": "https://example.com/monkeypox",
- "rank": 48,
+ "rank": 49,
"slot_uri": "GENEPIO:0001396",
"alias": "host_residence_geo_loc_name_(country)",
"owner": "Monkeypox_international",
@@ -14418,7 +14536,7 @@
"description": "The date on which the symptoms began or were first noted.",
"title": "symptom onset date",
"from_schema": "https://example.com/monkeypox",
- "rank": 49,
+ "rank": 50,
"slot_uri": "GENEPIO:0001399",
"alias": "symptom_onset_date",
"owner": "Monkeypox_international",
@@ -14434,7 +14552,7 @@
}
],
"from_schema": "https://example.com/monkeypox",
- "rank": 50,
+ "rank": 51,
"slot_uri": "GENEPIO:0001400",
"multivalued": true,
"alias": "signs_and_symptoms",
@@ -14454,7 +14572,7 @@
"description": "Patient pre-existing conditions and risk factors. Pre-existing condition: A medical condition that existed prior to the current infection. Risk Factor: A variable associated with an increased risk of disease or infection.",
"title": "pre-existing conditions and risk factors",
"from_schema": "https://example.com/monkeypox",
- "rank": 51,
+ "rank": 52,
"slot_uri": "GENEPIO:0001401",
"multivalued": true,
"alias": "pre_existing_conditions_and_risk_factors",
@@ -14479,7 +14597,7 @@
}
],
"from_schema": "https://example.com/monkeypox",
- "rank": 52,
+ "rank": 53,
"slot_uri": "GENEPIO:0001402",
"multivalued": true,
"alias": "complications",
@@ -14499,7 +14617,7 @@
"description": "Treatment of viral infections with agents that prevent viral replication in infected cells without impairing the host cell function.",
"title": "antiviral therapy",
"from_schema": "https://example.com/monkeypox",
- "rank": 53,
+ "rank": 54,
"slot_uri": "NCIT:C16119",
"alias": "antiviral_therapy",
"owner": "Monkeypox_international",
@@ -14516,7 +14634,7 @@
}
],
"from_schema": "https://example.com/monkeypox",
- "rank": 54,
+ "rank": 55,
"slot_uri": "GENEPIO:0001404",
"alias": "host_vaccination_status",
"owner": "Monkeypox_international",
@@ -14535,7 +14653,7 @@
"description": "The number of doses of the vaccine recived by the host.",
"title": "number of vaccine doses received",
"from_schema": "https://example.com/monkeypox",
- "rank": 55,
+ "rank": 56,
"slot_uri": "GENEPIO:0001406",
"alias": "number_of_vaccine_doses_received",
"owner": "Monkeypox_international",
@@ -14547,7 +14665,7 @@
"description": "The name of the vaccine administered as the first dose of a vaccine regimen.",
"title": "vaccination dose 1 vaccine name",
"from_schema": "https://example.com/monkeypox",
- "rank": 56,
+ "rank": 57,
"slot_uri": "GENEPIO:0100313",
"alias": "vaccination_dose_1_vaccine_name",
"owner": "Monkeypox_international",
@@ -14558,7 +14676,7 @@
"description": "The date the first dose of a vaccine was administered.",
"title": "vaccination dose 1 vaccination date",
"from_schema": "https://example.com/monkeypox",
- "rank": 57,
+ "rank": 58,
"slot_uri": "GENEPIO:0100314",
"alias": "vaccination_dose_1_vaccination_date",
"owner": "Monkeypox_international",
@@ -14569,7 +14687,7 @@
"description": "A description of the vaccines received and the administration dates of a series of vaccinations against a specific disease or a set of diseases.",
"title": "vaccination history",
"from_schema": "https://example.com/monkeypox",
- "rank": 58,
+ "rank": 59,
"slot_uri": "GENEPIO:0100321",
"alias": "vaccination_history",
"owner": "Monkeypox_international",
@@ -14586,7 +14704,7 @@
}
],
"from_schema": "https://example.com/monkeypox",
- "rank": 59,
+ "rank": 60,
"slot_uri": "GENEPIO:0001410",
"alias": "location_of_exposure_geo_loc_name_(country)",
"owner": "Monkeypox_international",
@@ -14605,7 +14723,7 @@
"description": "The name of the city that was the destination of most recent travel.",
"title": "destination of most recent travel (city)",
"from_schema": "https://example.com/monkeypox",
- "rank": 60,
+ "rank": 61,
"slot_uri": "GENEPIO:0001411",
"alias": "destination_of_most_recent_travel_(city)",
"owner": "Monkeypox_international",
@@ -14625,7 +14743,7 @@
}
],
"from_schema": "https://example.com/monkeypox",
- "rank": 61,
+ "rank": 62,
"slot_uri": "GENEPIO:0001412",
"alias": "destination_of_most_recent_travel_(state/province/territory)",
"owner": "Monkeypox_international",
@@ -14642,7 +14760,7 @@
}
],
"from_schema": "https://example.com/monkeypox",
- "rank": 62,
+ "rank": 63,
"slot_uri": "GENEPIO:0001413",
"alias": "destination_of_most_recent_travel_(country)",
"owner": "Monkeypox_international",
@@ -14661,7 +14779,7 @@
"description": "The date of a person's most recent departure from their primary residence (at that time) on a journey to one or more other locations.",
"title": "most recent travel departure date",
"from_schema": "https://example.com/monkeypox",
- "rank": 63,
+ "rank": 64,
"slot_uri": "GENEPIO:0001414",
"alias": "most_recent_travel_departure_date",
"owner": "Monkeypox_international",
@@ -14672,7 +14790,7 @@
"description": "The date of a person's most recent return to some residence from a journey originating at that residence.",
"title": "most recent travel return date",
"from_schema": "https://example.com/monkeypox",
- "rank": 64,
+ "rank": 65,
"slot_uri": "GENEPIO:0001415",
"alias": "most_recent_travel_return_date",
"owner": "Monkeypox_international",
@@ -14683,7 +14801,7 @@
"description": "Travel history in last six months.",
"title": "travel history",
"from_schema": "https://example.com/monkeypox",
- "rank": 65,
+ "rank": 66,
"slot_uri": "GENEPIO:0001416",
"alias": "travel_history",
"owner": "Monkeypox_international",
@@ -14700,7 +14818,7 @@
}
],
"from_schema": "https://example.com/monkeypox",
- "rank": 66,
+ "rank": 67,
"slot_uri": "GENEPIO:0001417",
"alias": "exposure_event",
"owner": "Monkeypox_international",
@@ -14724,7 +14842,7 @@
}
],
"from_schema": "https://example.com/monkeypox",
- "rank": 67,
+ "rank": 68,
"slot_uri": "GENEPIO:0001418",
"alias": "exposure_contact_level",
"owner": "Monkeypox_international",
@@ -14748,7 +14866,7 @@
}
],
"from_schema": "https://example.com/monkeypox",
- "rank": 68,
+ "rank": 69,
"slot_uri": "GENEPIO:0001419",
"multivalued": true,
"alias": "host_role",
@@ -14766,7 +14884,7 @@
}
],
"from_schema": "https://example.com/monkeypox",
- "rank": 69,
+ "rank": 70,
"slot_uri": "GENEPIO:0001428",
"multivalued": true,
"alias": "exposure_setting",
@@ -14779,7 +14897,7 @@
"description": "Additional host exposure information.",
"title": "exposure details",
"from_schema": "https://example.com/monkeypox",
- "rank": 70,
+ "rank": 71,
"slot_uri": "GENEPIO:0001431",
"alias": "exposure_details",
"owner": "Monkeypox_international",
@@ -14796,7 +14914,7 @@
}
],
"from_schema": "https://example.com/monkeypox",
- "rank": 71,
+ "rank": 72,
"slot_uri": "GENEPIO:0100532",
"alias": "prior_Monkeypox_infection",
"owner": "Monkeypox_international",
@@ -14815,7 +14933,7 @@
"description": "The date of diagnosis of the prior Monkeypox infection.",
"title": "prior Monkeypox infection date",
"from_schema": "https://example.com/monkeypox",
- "rank": 72,
+ "rank": 73,
"slot_uri": "GENEPIO:0100533",
"alias": "prior_Monkeypox_infection_date",
"owner": "Monkeypox_international",
@@ -14831,7 +14949,7 @@
}
],
"from_schema": "https://example.com/monkeypox",
- "rank": 73,
+ "rank": 74,
"slot_uri": "GENEPIO:0100534",
"alias": "prior_Monkeypox_antiviral_treatment",
"owner": "Monkeypox_international",
@@ -14850,7 +14968,7 @@
"description": "Antiviral treatment for any infection during the prior Moneypox infection period.",
"title": "prior antiviral treatment during prior Monkeypox infection",
"from_schema": "https://example.com/monkeypox",
- "rank": 74,
+ "rank": 75,
"slot_uri": "GENEPIO:0100535",
"alias": "prior_antiviral_treatment_during_prior_Monkeypox_infection",
"owner": "Monkeypox_international",
@@ -14867,7 +14985,7 @@
}
],
"from_schema": "https://example.com/monkeypox",
- "rank": 75,
+ "rank": 76,
"slot_uri": "GENEPIO:0001445",
"multivalued": true,
"alias": "purpose_of_sequencing",
@@ -14888,7 +15006,7 @@
"description": "The description of why the sample was sequenced providing specific details.",
"title": "purpose of sequencing details",
"from_schema": "https://example.com/monkeypox",
- "rank": 76,
+ "rank": 77,
"slot_uri": "GENEPIO:0001446",
"alias": "purpose_of_sequencing_details",
"owner": "Monkeypox_international",
@@ -14900,7 +15018,7 @@
"description": "The date the sample was sequenced.",
"title": "sequencing date",
"from_schema": "https://example.com/monkeypox",
- "rank": 77,
+ "rank": 78,
"slot_uri": "GENEPIO:0001447",
"alias": "sequencing_date",
"owner": "Monkeypox_international",
@@ -14911,7 +15029,7 @@
"description": "The user-specified identifier for the library prepared for sequencing.",
"title": "library ID",
"from_schema": "https://example.com/monkeypox",
- "rank": 78,
+ "rank": 79,
"slot_uri": "GENEPIO:0001448",
"alias": "library_ID",
"owner": "Monkeypox_international",
@@ -14924,7 +15042,7 @@
"description": "The length of the amplicon generated by PCR amplification.",
"title": "amplicon size",
"from_schema": "https://example.com/monkeypox",
- "rank": 79,
+ "rank": 80,
"slot_uri": "GENEPIO:0001449",
"alias": "amplicon_size",
"owner": "Monkeypox_international",
@@ -14936,7 +15054,7 @@
"description": "The name of the DNA library preparation kit used to generate the library being sequenced.",
"title": "library preparation kit",
"from_schema": "https://example.com/monkeypox",
- "rank": 80,
+ "rank": 81,
"slot_uri": "GENEPIO:0001450",
"alias": "library_preparation_kit",
"owner": "Monkeypox_international",
@@ -14953,7 +15071,7 @@
}
],
"from_schema": "https://example.com/monkeypox",
- "rank": 81,
+ "rank": 82,
"slot_uri": "GENEPIO:0001452",
"multivalued": true,
"alias": "sequencing_instrument",
@@ -14974,7 +15092,7 @@
"description": "The protocol used to generate the sequence.",
"title": "sequencing protocol",
"from_schema": "https://example.com/monkeypox",
- "rank": 82,
+ "rank": 83,
"slot_uri": "GENEPIO:0001454",
"alias": "sequencing_protocol",
"owner": "Monkeypox_international",
@@ -14986,7 +15104,7 @@
"description": "The manufacturer's kit number.",
"title": "sequencing kit number",
"from_schema": "https://example.com/monkeypox",
- "rank": 83,
+ "rank": 84,
"slot_uri": "GENEPIO:0001455",
"alias": "sequencing_kit_number",
"owner": "Monkeypox_international",
@@ -14998,7 +15116,7 @@
"description": "The specifications of the primers (primer sequences, binding positions, fragment size generated etc) used to generate the amplicons to be sequenced.",
"title": "amplicon pcr primer scheme",
"from_schema": "https://example.com/monkeypox",
- "rank": 84,
+ "rank": 85,
"slot_uri": "GENEPIO:0001456",
"alias": "amplicon_pcr_primer_scheme",
"owner": "Monkeypox_international",
@@ -15010,7 +15128,7 @@
"description": "The names of the software and version number used for raw data processing such as removing barcodes, adapter trimming, filtering etc.",
"title": "raw sequence data processing method",
"from_schema": "https://example.com/monkeypox",
- "rank": 85,
+ "rank": 86,
"slot_uri": "GENEPIO:0001458",
"alias": "raw_sequence_data_processing_method",
"owner": "Monkeypox_international",
@@ -15022,7 +15140,7 @@
"description": "The method used to remove host reads from the pathogen sequence.",
"title": "dehosting method",
"from_schema": "https://example.com/monkeypox",
- "rank": 86,
+ "rank": 87,
"slot_uri": "GENEPIO:0001459",
"alias": "dehosting_method",
"owner": "Monkeypox_international",
@@ -15034,7 +15152,7 @@
"description": "The name of the consensus sequence.",
"title": "consensus sequence name",
"from_schema": "https://example.com/monkeypox",
- "rank": 87,
+ "rank": 88,
"slot_uri": "GENEPIO:0001460",
"alias": "consensus_sequence_name",
"owner": "Monkeypox_international",
@@ -15046,7 +15164,7 @@
"description": "The name of the consensus sequence file.",
"title": "consensus sequence filename",
"from_schema": "https://example.com/monkeypox",
- "rank": 88,
+ "rank": 89,
"slot_uri": "GENEPIO:0001461",
"alias": "consensus_sequence_filename",
"owner": "Monkeypox_international",
@@ -15058,7 +15176,7 @@
"description": "The filepath of the consesnsus sequence file.",
"title": "consensus sequence filepath",
"from_schema": "https://example.com/monkeypox",
- "rank": 89,
+ "rank": 90,
"slot_uri": "GENEPIO:0001462",
"alias": "consensus_sequence_filepath",
"owner": "Monkeypox_international",
@@ -15070,7 +15188,7 @@
"description": "The name of software used to generate the consensus sequence.",
"title": "consensus sequence software name",
"from_schema": "https://example.com/monkeypox",
- "rank": 90,
+ "rank": 91,
"slot_uri": "GENEPIO:0001463",
"alias": "consensus_sequence_software_name",
"owner": "Monkeypox_international",
@@ -15083,7 +15201,7 @@
"description": "The version of the software used to generate the consensus sequence.",
"title": "consensus sequence software version",
"from_schema": "https://example.com/monkeypox",
- "rank": 91,
+ "rank": 92,
"slot_uri": "GENEPIO:0001469",
"alias": "consensus_sequence_software_version",
"owner": "Monkeypox_international",
@@ -15096,7 +15214,7 @@
"description": "The percentage of the reference genome covered by the sequenced data, to a prescribed depth.",
"title": "breadth of coverage value",
"from_schema": "https://example.com/monkeypox",
- "rank": 92,
+ "rank": 93,
"slot_uri": "GENEPIO:0001472",
"alias": "breadth_of_coverage_value",
"owner": "Monkeypox_international",
@@ -15108,7 +15226,7 @@
"description": "The average number of reads representing a given nucleotide in the reconstructed sequence.",
"title": "depth of coverage value",
"from_schema": "https://example.com/monkeypox",
- "rank": 93,
+ "rank": 94,
"slot_uri": "GENEPIO:0001474",
"alias": "depth_of_coverage_value",
"owner": "Monkeypox_international",
@@ -15120,7 +15238,7 @@
"description": "The threshold used as a cut-off for the depth of coverage.",
"title": "depth of coverage threshold",
"from_schema": "https://example.com/monkeypox",
- "rank": 94,
+ "rank": 95,
"slot_uri": "GENEPIO:0001475",
"alias": "depth_of_coverage_threshold",
"owner": "Monkeypox_international",
@@ -15132,7 +15250,7 @@
"description": "The user-specified filename of the r1 FASTQ file.",
"title": "r1 fastq filename",
"from_schema": "https://example.com/monkeypox",
- "rank": 95,
+ "rank": 96,
"slot_uri": "GENEPIO:0001476",
"alias": "r1_fastq_filename",
"owner": "Monkeypox_international",
@@ -15145,7 +15263,7 @@
"description": "The user-specified filename of the r2 FASTQ file.",
"title": "r2 fastq filename",
"from_schema": "https://example.com/monkeypox",
- "rank": 96,
+ "rank": 97,
"slot_uri": "GENEPIO:0001477",
"alias": "r2_fastq_filename",
"owner": "Monkeypox_international",
@@ -15158,7 +15276,7 @@
"description": "The location of the r1 FASTQ file within a user's file system.",
"title": "r1 fastq filepath",
"from_schema": "https://example.com/monkeypox",
- "rank": 97,
+ "rank": 98,
"slot_uri": "GENEPIO:0001478",
"alias": "r1_fastq_filepath",
"owner": "Monkeypox_international",
@@ -15170,7 +15288,7 @@
"description": "The location of the r2 FASTQ file within a user's file system.",
"title": "r2 fastq filepath",
"from_schema": "https://example.com/monkeypox",
- "rank": 98,
+ "rank": 99,
"slot_uri": "GENEPIO:0001479",
"alias": "r2_fastq_filepath",
"owner": "Monkeypox_international",
@@ -15182,7 +15300,7 @@
"description": "The user-specified filename of the FAST5 file.",
"title": "fast5 filename",
"from_schema": "https://example.com/monkeypox",
- "rank": 99,
+ "rank": 100,
"slot_uri": "GENEPIO:0001480",
"alias": "fast5_filename",
"owner": "Monkeypox_international",
@@ -15194,7 +15312,7 @@
"description": "The location of the FAST5 file within a user's file system.",
"title": "fast5 filepath",
"from_schema": "https://example.com/monkeypox",
- "rank": 100,
+ "rank": 101,
"slot_uri": "GENEPIO:0001481",
"alias": "fast5_filepath",
"owner": "Monkeypox_international",
@@ -15206,7 +15324,7 @@
"description": "The number of total base pairs generated by the sequencing process.",
"title": "number of base pairs sequenced",
"from_schema": "https://example.com/monkeypox",
- "rank": 101,
+ "rank": 102,
"slot_uri": "GENEPIO:0001482",
"alias": "number_of_base_pairs_sequenced",
"owner": "Monkeypox_international",
@@ -15219,7 +15337,7 @@
"description": "Size of the reconstructed genome described as the number of base pairs.",
"title": "consensus genome length",
"from_schema": "https://example.com/monkeypox",
- "rank": 102,
+ "rank": 103,
"slot_uri": "GENEPIO:0001483",
"alias": "consensus_genome_length",
"owner": "Monkeypox_international",
@@ -15232,7 +15350,7 @@
"description": "A persistent, unique identifier of a genome database entry.",
"title": "reference genome accession",
"from_schema": "https://example.com/monkeypox",
- "rank": 103,
+ "rank": 104,
"slot_uri": "GENEPIO:0001485",
"alias": "reference_genome_accession",
"owner": "Monkeypox_international",
@@ -15244,7 +15362,7 @@
"description": "A description of the overall bioinformatics strategy used.",
"title": "bioinformatics protocol",
"from_schema": "https://example.com/monkeypox",
- "rank": 104,
+ "rank": 105,
"slot_uri": "GENEPIO:0001489",
"alias": "bioinformatics_protocol",
"owner": "Monkeypox_international",
@@ -15259,7 +15377,7 @@
"Provide the full name of the gene used in the test. The gene symbol (short form of gene name) can also be provided. Standardized gene names and symbols can be found in the Gene Ontology using this look-up service: https://bit.ly/2Sq1LbI"
],
"from_schema": "https://example.com/monkeypox",
- "rank": 105,
+ "rank": 106,
"slot_uri": "GENEPIO:0001507",
"alias": "gene_name_1",
"owner": "Monkeypox_international",
@@ -15278,7 +15396,7 @@
"description": "The Ct value result from a diagnostic SARS-CoV-2 RT-PCR test.",
"title": "diagnostic pcr Ct value 1",
"from_schema": "https://example.com/monkeypox",
- "rank": 106,
+ "rank": 107,
"slot_uri": "GENEPIO:0001509",
"alias": "diagnostic_pcr_Ct_value_1",
"owner": "Monkeypox_international",
@@ -15292,7 +15410,7 @@
"Provide the full name of another gene used in an RT-PCR test. The gene symbol (short form of gene name) can also be provided. Standardized gene names and symbols can be found in the Gene Ontology using this look-up service: https://bit.ly/2Sq1LbI"
],
"from_schema": "https://example.com/monkeypox",
- "rank": 107,
+ "rank": 108,
"slot_uri": "GENEPIO:0001510",
"alias": "gene_name_2",
"owner": "Monkeypox_international",
@@ -15311,7 +15429,7 @@
"description": "The Ct value result from a diagnostic SARS-CoV-2 RT-PCR test.",
"title": "diagnostic pcr Ct value 2",
"from_schema": "https://example.com/monkeypox",
- "rank": 108,
+ "rank": 109,
"slot_uri": "GENEPIO:0001512",
"alias": "diagnostic_pcr_Ct_value_2",
"owner": "Monkeypox_international",
@@ -15325,7 +15443,7 @@
"Provide the full name of another gene used in an RT-PCR test. The gene symbol (short form of gene name) can also be provided. Standardized gene names and symbols can be found in the Gene Ontology using this look-up service: https://bit.ly/2Sq1LbI"
],
"from_schema": "https://example.com/monkeypox",
- "rank": 109,
+ "rank": 110,
"slot_uri": "GENEPIO:0001513",
"alias": "gene_name_3",
"owner": "Monkeypox_international",
@@ -15344,7 +15462,7 @@
"description": "The Ct value result from a diagnostic SARS-CoV-2 RT-PCR test.",
"title": "diagnostic pcr Ct value 3",
"from_schema": "https://example.com/monkeypox",
- "rank": 110,
+ "rank": 111,
"slot_uri": "GENEPIO:0001515",
"alias": "diagnostic_pcr_Ct_value_3",
"owner": "Monkeypox_international",
@@ -15355,7 +15473,7 @@
"description": "Names of individuals contributing to the processes of sample collection, sequence generation, analysis, and data submission.",
"title": "authors",
"from_schema": "https://example.com/monkeypox",
- "rank": 111,
+ "rank": 112,
"slot_uri": "GENEPIO:0001517",
"alias": "authors",
"owner": "Monkeypox_international",
@@ -15368,7 +15486,7 @@
"description": "The DataHarmonizer software version provenance.",
"title": "DataHarmonizer provenance",
"from_schema": "https://example.com/monkeypox",
- "rank": 112,
+ "rank": 113,
"slot_uri": "GENEPIO:0001518",
"alias": "DataHarmonizer_provenance",
"owner": "Monkeypox_international",
@@ -15394,4 +15512,4 @@
}
},
"@type": "SchemaDefinition"
-}
+}
\ No newline at end of file
diff --git a/web/templates/monkeypox/schema.yaml b/web/templates/monkeypox/schema.yaml
index 25c98a7d..6c7d414a 100644
--- a/web/templates/monkeypox/schema.yaml
+++ b/web/templates/monkeypox/schema.yaml
@@ -1,9 +1,9 @@
id: https://example.com/monkeypox
name: Monkeypox
-version: 1.1.0
+version: 3.3.1
description: ''
imports:
- - linkml:types
+- linkml:types
prefixes:
linkml: https://w3id.org/linkml/
GENEPIO: http://purl.obolibrary.org/obo/GENEPIO_
@@ -14,11 +14,12 @@ classes:
from_schema: https://example.com/Monkeypox
Monkeypox:
name: Monkeypox
- description:
- Canadian specification for Monkeypox clinical virus biosample data
+ description: Canadian specification for Monkeypox clinical virus biosample data
gathering
is_a: dh_interface
see_also: template/monkeypox/SOP_Monkeypox.pdf
+ annotations:
+ version: 3.2.1
slots:
- specimen collector sample ID
- Related specimen primary ID
@@ -202,7 +203,7 @@ classes:
exact_mappings:
- GISAID:Submitting lab
- CNPHI:Sequencing Centre
- - NML_LIMS:PH_SEQUENCING_SUBMITTER
+ - NML_LIMS:PH_SEQUENCE_SUBMITTER
- BIOSAMPLE:sequence_submitted_by
- VirusSeq_Portal:sequence submitted by
sequence submitter contact email:
@@ -781,6 +782,8 @@ classes:
data gathering
is_a: dh_interface
see_also: template/monkeypox/SOP_Monkeypox_international.pdf
+ annotations:
+ version: 3.3.1
slots:
- specimen collector sample ID
- case ID
@@ -813,6 +816,7 @@ classes:
- anatomical material
- anatomical part
- body product
+ - environmental material
- collection device
- collection method
- specimen processing
@@ -1049,9 +1053,12 @@ classes:
any_of:
- range: body product international menu
- range: null value menu
- collection device:
+ environmental material:
rank: 32
slot_group: Sample collection and processing
+ collection device:
+ rank: 33
+ slot_group: Sample collection and processing
recommended: true
examples:
- value: Swab [GENEPIO:0100027]
@@ -1059,7 +1066,7 @@ classes:
- range: collection device international menu
- range: null value menu
collection method:
- rank: 33
+ rank: 34
slot_group: Sample collection and processing
recommended: true
examples:
@@ -1068,7 +1075,7 @@ classes:
- range: collection method international menu
- range: null value menu
specimen processing:
- rank: 34
+ rank: 35
slot_group: Sample collection and processing
examples:
- value: Specimens pooled [OBI:0600016]
@@ -1076,16 +1083,16 @@ classes:
- range: specimen processing international menu
- range: null value menu
specimen processing details:
- rank: 35
+ rank: 36
slot_group: Sample collection and processing
host (common name):
- rank: 36
+ rank: 37
slot_group: Host Information
any_of:
- range: host (common name) international menu
- range: null value menu
host (scientific name):
- rank: 37
+ rank: 38
slot_group: Host Information
examples:
- value: Homo sapiens [NCBITaxon:9606]
@@ -1093,7 +1100,7 @@ classes:
- range: host (scientific name) international menu
- range: null value menu
host health state:
- rank: 38
+ rank: 39
slot_group: Host Information
examples:
- value: Asymptomatic [NCIT:C3833]
@@ -1104,7 +1111,7 @@ classes:
- GISAID:Patient status
- BIOSAMPLE:host_health_state
host health status details:
- rank: 39
+ rank: 40
slot_group: Host Information
examples:
- value: Hospitalized [NCIT:C25179]
@@ -1112,7 +1119,7 @@ classes:
- range: host health status details international menu
- range: null value menu
host health outcome:
- rank: 40
+ rank: 41
slot_group: Host Information
examples:
- value: Recovered [NCIT:C49498]
@@ -1122,7 +1129,7 @@ classes:
exact_mappings:
- BIOSAMPLE:host_health_outcome
host disease:
- rank: 41
+ rank: 42
slot_group: Host Information
examples:
- value: Monkeypox [MONDO:0002594]
@@ -1130,7 +1137,7 @@ classes:
- range: host disease international menu
- range: null value menu
host subject ID:
- rank: 47
+ rank: 48
slot_group: Host Information
description: 'A unique identifier by which each host can be referred to e.g.
#131'
@@ -1141,14 +1148,14 @@ classes:
- NML_LIMS:host subject ID
- BIOSAMPLE:host_subject_id
host age:
- rank: 43
+ rank: 44
slot_group: Host Information
recommended: true
exact_mappings:
- GISAID:Patient age
- BIOSAMPLE:host_age
host age unit:
- rank: 44
+ rank: 45
slot_group: Host Information
recommended: true
examples:
@@ -1159,7 +1166,7 @@ classes:
exact_mappings:
- BIOSAMPLE:host_age_unit
host age bin:
- rank: 45
+ rank: 46
slot_group: Host Information
recommended: true
examples:
@@ -1170,7 +1177,7 @@ classes:
exact_mappings:
- BIOSAMPLE:host_age_bin
host gender:
- rank: 46
+ rank: 47
slot_group: Host Information
recommended: true
examples:
@@ -1182,7 +1189,7 @@ classes:
- GISAID:Gender
- BIOSAMPLE:host_sex
host residence geo_loc name (country):
- rank: 48
+ rank: 49
slot_group: Host Information
examples:
- value: Canada [GAZ:00002560]
@@ -1190,10 +1197,10 @@ classes:
- range: geo_loc_name (country) international menu
- range: null value menu
symptom onset date:
- rank: 49
+ rank: 50
slot_group: Host Information
signs and symptoms:
- rank: 50
+ rank: 51
slot_group: Host Information
examples:
- value: Lesion (Pustule) [NCIT:C78582], Swollen Lymph Nodes [HP:0002716],
@@ -1202,13 +1209,13 @@ classes:
- range: signs and symptoms international menu
- range: null value menu
pre-existing conditions and risk factors:
- rank: 51
+ rank: 52
slot_group: Host Information
any_of:
- range: pre-existing conditions and risk factors international menu
- range: null value menu
complications:
- rank: 52
+ rank: 53
slot_group: Host Information
examples:
- value: Delayed wound healing (lesion healing) [MP:0002908]
@@ -1216,10 +1223,10 @@ classes:
- range: complications international menu
- range: null value menu
antiviral therapy:
- rank: 53
+ rank: 54
slot_group: Host Information
host vaccination status:
- rank: 54
+ rank: 55
slot_group: Host vaccination information
examples:
- value: Not Vaccinated [GENEPIO:0100102]
@@ -1227,19 +1234,19 @@ classes:
- range: host vaccination status international menu
- range: null value menu
number of vaccine doses received:
- rank: 55
+ rank: 56
slot_group: Host vaccination information
vaccination dose 1 vaccine name:
- rank: 56
+ rank: 57
slot_group: Host vaccination information
vaccination dose 1 vaccination date:
- rank: 57
+ rank: 58
slot_group: Host vaccination information
vaccination history:
- rank: 58
+ rank: 59
slot_group: Host vaccination information
location of exposure geo_loc name (country):
- rank: 59
+ rank: 60
slot_group: Host exposure information
examples:
- value: Canada [GAZ:00002560]
@@ -1247,10 +1254,10 @@ classes:
- range: geo_loc_name (country) international menu
- range: null value menu
destination of most recent travel (city):
- rank: 60
+ rank: 61
slot_group: Host exposure information
destination of most recent travel (state/province/territory):
- rank: 61
+ rank: 62
slot_group: Host exposure information
range: WhitespaceMinimizedString
comments: 'Provide the name of the state/province/territory that the host
@@ -1259,7 +1266,7 @@ classes:
examples:
- value: California
destination of most recent travel (country):
- rank: 62
+ rank: 63
slot_group: Host exposure information
examples:
- value: United Kingdom [GAZ:00002637]
@@ -1267,16 +1274,16 @@ classes:
- range: geo_loc_name (country) international menu
- range: null value menu
most recent travel departure date:
- rank: 63
+ rank: 64
slot_group: Host exposure information
most recent travel return date:
- rank: 64
+ rank: 65
slot_group: Host exposure information
travel history:
- rank: 65
+ rank: 66
slot_group: Host exposure information
exposure event:
- rank: 66
+ rank: 67
slot_group: Host exposure information
examples:
- value: Party [PCO:0000035]
@@ -1284,7 +1291,7 @@ classes:
- range: exposure event international menu
- range: null value menu
exposure contact level:
- rank: 67
+ rank: 68
slot_group: Host exposure information
examples:
- value: Contact with infected individual [GENEPIO:0100357]
@@ -1292,22 +1299,22 @@ classes:
- range: exposure contact level international menu
- range: null value menu
host role:
- rank: 68
+ rank: 69
slot_group: Host exposure information
range: host role international menu
examples:
- value: Acquaintance of case [GENEPIO:0100266]
exposure setting:
- rank: 69
+ rank: 70
slot_group: Host exposure information
range: exposure setting international menu
examples:
- value: Healthcare Setting [GENEPIO:0100201]
exposure details:
- rank: 70
+ rank: 71
slot_group: Host exposure information
prior Monkeypox infection:
- rank: 71
+ rank: 72
slot_group: Host reinfection information
examples:
- value: Prior infection [GENEPIO:0100037]
@@ -1315,10 +1322,10 @@ classes:
- range: prior Monkeypox infection international menu
- range: null value menu
prior Monkeypox infection date:
- rank: 72
+ rank: 73
slot_group: Host reinfection information
prior Monkeypox antiviral treatment:
- rank: 73
+ rank: 74
slot_group: Host reinfection information
examples:
- value: Prior antiviral treatment [GENEPIO:0100037]
@@ -1326,10 +1333,10 @@ classes:
- range: prior Monkeypox antiviral treatment international menu
- range: null value menu
prior antiviral treatment during prior Monkeypox infection:
- rank: 74
+ rank: 75
slot_group: Host reinfection information
purpose of sequencing:
- rank: 75
+ rank: 76
slot_group: Sequencing
examples:
- value: Baseline surveillance (random sampling) [GENEPIO:0100005]
@@ -1337,22 +1344,22 @@ classes:
- range: purpose of sequencing international menu
- range: null value menu
purpose of sequencing details:
- rank: 76
+ rank: 77
slot_group: Sequencing
sequencing date:
- rank: 77
+ rank: 78
slot_group: Sequencing
library ID:
- rank: 78
+ rank: 79
slot_group: Sequencing
amplicon size:
- rank: 79
+ rank: 80
slot_group: Sequencing
library preparation kit:
- rank: 80
+ rank: 81
slot_group: Sequencing
sequencing instrument:
- rank: 81
+ rank: 82
slot_group: Sequencing
examples:
- value: Oxford Nanopore MinION [GENEPIO:0100142]
@@ -1360,76 +1367,76 @@ classes:
- range: sequencing instrument international menu
- range: null value menu
sequencing protocol:
- rank: 82
+ rank: 83
slot_group: Sequencing
sequencing kit number:
- rank: 83
+ rank: 84
slot_group: Sequencing
amplicon pcr primer scheme:
- rank: 84
+ rank: 85
slot_group: Sequencing
raw sequence data processing method:
- rank: 85
+ rank: 86
slot_group: Bioinformatics and QC metrics
dehosting method:
- rank: 86
+ rank: 87
slot_group: Bioinformatics and QC metrics
consensus sequence name:
- rank: 87
+ rank: 88
slot_group: Bioinformatics and QC metrics
consensus sequence filename:
- rank: 88
+ rank: 89
slot_group: Bioinformatics and QC metrics
consensus sequence filepath:
- rank: 89
+ rank: 90
slot_group: Bioinformatics and QC metrics
consensus sequence software name:
- rank: 90
+ rank: 91
slot_group: Bioinformatics and QC metrics
consensus sequence software version:
- rank: 91
+ rank: 92
slot_group: Bioinformatics and QC metrics
breadth of coverage value:
- rank: 92
+ rank: 93
slot_group: Bioinformatics and QC metrics
depth of coverage value:
- rank: 93
+ rank: 94
slot_group: Bioinformatics and QC metrics
depth of coverage threshold:
- rank: 94
+ rank: 95
slot_group: Bioinformatics and QC metrics
r1 fastq filename:
- rank: 95
+ rank: 96
slot_group: Bioinformatics and QC metrics
r2 fastq filename:
- rank: 96
+ rank: 97
slot_group: Bioinformatics and QC metrics
r1 fastq filepath:
- rank: 97
+ rank: 98
slot_group: Bioinformatics and QC metrics
r2 fastq filepath:
- rank: 98
+ rank: 99
slot_group: Bioinformatics and QC metrics
fast5 filename:
- rank: 99
+ rank: 100
slot_group: Bioinformatics and QC metrics
fast5 filepath:
- rank: 100
+ rank: 101
slot_group: Bioinformatics and QC metrics
number of base pairs sequenced:
- rank: 101
+ rank: 102
slot_group: Bioinformatics and QC metrics
consensus genome length:
- rank: 102
+ rank: 103
slot_group: Bioinformatics and QC metrics
reference genome accession:
- rank: 103
+ rank: 104
slot_group: Bioinformatics and QC metrics
bioinformatics protocol:
- rank: 104
+ rank: 105
slot_group: Bioinformatics and QC metrics
gene name 1:
- rank: 105
+ rank: 106
slot_group: Pathogen diagnostic testing
comments: 'Provide the full name of the gene used in the test. The gene symbol
(short form of gene name) can also be provided. Standardized gene names
@@ -1439,10 +1446,10 @@ classes:
- range: WhitespaceMinimizedString
- range: null value menu
diagnostic pcr Ct value 1:
- rank: 106
+ rank: 107
slot_group: Pathogen diagnostic testing
gene name 2:
- rank: 107
+ rank: 108
slot_group: Pathogen diagnostic testing
comments: 'Provide the full name of another gene used in an RT-PCR test. The
gene symbol (short form of gene name) can also be provided. Standardized
@@ -1452,10 +1459,10 @@ classes:
- range: WhitespaceMinimizedString
- range: null value menu
diagnostic pcr Ct value 2:
- rank: 108
+ rank: 109
slot_group: Pathogen diagnostic testing
gene name 3:
- rank: 109
+ rank: 110
slot_group: Pathogen diagnostic testing
comments: 'Provide the full name of another gene used in an RT-PCR test. The
gene symbol (short form of gene name) can also be provided. Standardized
@@ -1465,13 +1472,13 @@ classes:
- range: WhitespaceMinimizedString
- range: null value menu
diagnostic pcr Ct value 3:
- rank: 110
+ rank: 111
slot_group: Pathogen diagnostic testing
authors:
- rank: 111
+ rank: 112
slot_group: Contributor acknowledgement
DataHarmonizer provenance:
- rank: 112
+ rank: 113
slot_group: Contributor acknowledgement
slots:
specimen collector sample ID:
@@ -1775,28 +1782,27 @@ slots:
name: sample collection date precision
title: sample collection date precision
description: The precision to which the "sample collection date" was provided.
- comments:
- Provide the precision of granularity to the "day", "month", or "year"
+ comments: Provide the precision of granularity to the "day", "month", or "year"
for the date provided in the "sample collection date" field. The "sample collection
date" will be truncated to the precision specified upon export; "day" for "YYYY-MM-DD",
"month" for "YYYY-MM", or "year" for "YYYY".
examples:
- - value: year
+ - value: year
slot_uri: GENEPIO:0001177
any_of:
- - range: sample collection date precision menu
- - range: null value menu
+ - range: sample collection date precision menu
+ - range: null value menu
required: true
exact_mappings:
- - CNPHI:Precision of date collected
- - NML_LIMS:HC_TEXT2
+ - CNPHI:Precision of date collected
+ - NML_LIMS:HC_TEXT2
sample received date:
name: sample received date
title: sample received date
description: The date on which the sample was received.
comments: ISO 8601 standard "YYYY-MM-DD".
examples:
- - value: '2020-03-20'
+ - value: '2020-03-20'
slot_uri: GENEPIO:0001179
any_of:
- range: date
@@ -1805,7 +1811,7 @@ slots:
- '>=2019-10-01'
- <={today}
exact_mappings:
- - NML_LIMS:sample received date
+ - NML_LIMS:sample received date
geo_loc_name (country):
name: geo_loc_name (country)
title: geo_loc_name (country)
@@ -1814,17 +1820,17 @@ slots:
slot_uri: GENEPIO:0001181
required: true
exact_mappings:
- - GISAID:Location
- - CNPHI:Patient Country
- - NML_LIMS:HC_COUNTRY
- - BIOSAMPLE:geo_loc_name
- - VirusSeq_Portal:geo_loc_name (country)
+ - GISAID:Location
+ - CNPHI:Patient Country
+ - NML_LIMS:HC_COUNTRY
+ - BIOSAMPLE:geo_loc_name
+ - VirusSeq_Portal:geo_loc_name (country)
geo_loc_name (state/province/territory):
name: geo_loc_name (state/province/territory)
title: geo_loc_name (state/province/territory)
description: The state/province/territory where the sample was collected.
examples:
- - value: Saskatchewan
+ - value: Saskatchewan
slot_uri: GENEPIO:0001185
required: true
exact_mappings:
@@ -1869,178 +1875,185 @@ slots:
slot_uri: GENEPIO:0001191
required: true
exact_mappings:
- - CNPHI:Pathogen
- - NML_LIMS:HC_CURRENT_ID
- - BIOSAMPLE:organism
- - VirusSeq_Portal:organism
+ - CNPHI:Pathogen
+ - NML_LIMS:HC_CURRENT_ID
+ - BIOSAMPLE:organism
+ - VirusSeq_Portal:organism
isolate:
name: isolate
title: isolate
description: Identifier of the specific isolate.
any_of:
- - range: WhitespaceMinimizedString
- - range: null value menu
+ - range: WhitespaceMinimizedString
+ - range: null value menu
required: true
purpose of sampling:
name: purpose of sampling
title: purpose of sampling
description: The reason that the sample was collected.
- comments:
- As all samples are taken for diagnostic purposes, "Diagnostic Testing"
+ comments: As all samples are taken for diagnostic purposes, "Diagnostic Testing"
should be chosen from the picklist at this time. The reason why a sample was
originally collected may differ from the reason why it was selected for sequencing,
which should be indicated in the "purpose of sequencing" field.
slot_uri: GENEPIO:0001198
required: true
exact_mappings:
- - CNPHI:Reason for Sampling
- - NML_LIMS:HC_SAMPLE_CATEGORY
- - BIOSAMPLE:purpose_of_sampling
- - VirusSeq_Portal:purpose of sampling
+ - CNPHI:Reason for Sampling
+ - NML_LIMS:HC_SAMPLE_CATEGORY
+ - BIOSAMPLE:purpose_of_sampling
+ - VirusSeq_Portal:purpose of sampling
purpose of sampling details:
name: purpose of sampling details
title: purpose of sampling details
- description:
- The description of why the sample was collected, providing specific
+ description: The description of why the sample was collected, providing specific
details.
- comments:
- Provide an expanded description of why the sample was collected using
+ comments: Provide an expanded description of why the sample was collected using
free text. The description may include the importance of the sample for a particular
public health investigation/surveillance activity/research question. If details
are not available, provide a null value.
examples:
- - value: Symptomology and history suggested Monkeypox diagnosis.
+ - value: Symptomology and history suggested Monkeypox diagnosis.
slot_uri: GENEPIO:0001200
any_of:
- - range: WhitespaceMinimizedString
- - range: null value menu
+ - range: WhitespaceMinimizedString
+ - range: null value menu
required: true
exact_mappings:
- - CNPHI:Details on the Reason for Sampling
- - NML_LIMS:PH_SAMPLING_DETAILS
- - BIOSAMPLE:description
- - VirusSeq_Portal:purpose of sampling details
+ - CNPHI:Details on the Reason for Sampling
+ - NML_LIMS:PH_SAMPLING_DETAILS
+ - BIOSAMPLE:description
+ - VirusSeq_Portal:purpose of sampling details
NML submitted specimen type:
name: NML submitted specimen type
title: NML submitted specimen type
- description:
- The type of specimen submitted to the National Microbiology Laboratory
+ description: The type of specimen submitted to the National Microbiology Laboratory
(NML) for testing.
- comments:
- "This information is required for upload through the CNPHI LaSER system.\
+ comments: "This information is required for upload through the CNPHI LaSER system.\
\ Select the specimen type from the pick list provided. If sequence data is\
\ being submitted rather than a specimen for testing, select \u201CNot Applicable\u201D\
."
examples:
- - value: Nucleic Acid
+ - value: Nucleic Acid
slot_uri: GENEPIO:0001204
range: NML submitted specimen type menu
required: true
exact_mappings:
- - CNPHI:Specimen Type
- - NML_LIMS:PH_SPECIMEN_TYPE
+ - CNPHI:Specimen Type
+ - NML_LIMS:PH_SPECIMEN_TYPE
Related specimen relationship type:
name: Related specimen relationship type
title: Related specimen relationship type
- description:
- The relationship of the current specimen to the specimen/sample previously
+ description: The relationship of the current specimen to the specimen/sample previously
submitted to the repository.
- comments:
- Provide the tag that describes how the previous sample is related to
+ comments: Provide the tag that describes how the previous sample is related to
the current sample being submitted from the pick list provided, so that the
samples can be linked and tracked in the system.
examples:
- - value: Previously Submitted
+ - value: Previously Submitted
slot_uri: GENEPIO:0001209
any_of:
- range: Related specimen relationship type menu
- range: null value menu
exact_mappings:
- - CNPHI:Related Specimen ID
- - CNPHI:Related Specimen Relationship Type
- - NML_LIMS:PH_RELATED_RELATIONSHIP_TYPE
+ - CNPHI:Related Specimen ID
+ - CNPHI:Related Specimen Relationship Type
+ - NML_LIMS:PH_RELATED_RELATIONSHIP_TYPE
anatomical material:
name: anatomical material
title: anatomical material
- description:
- A substance obtained from an anatomical part of an organism e.g.
+ description: A substance obtained from an anatomical part of an organism e.g.
tissue, blood.
- comments:
- Provide a descriptor if an anatomical material was sampled. Use the
+ comments: Provide a descriptor if an anatomical material was sampled. Use the
picklist provided in the template. If a desired term is missing from the picklist,
contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose
a null value.
slot_uri: GENEPIO:0001211
multivalued: true
exact_mappings:
- - GISAID:Specimen source
- - CNPHI:Anatomical Material
- - NML_LIMS:PH_ISOLATION_SITE_DESC
- - BIOSAMPLE:isolation_source
- - BIOSAMPLE:anatomical_material
- - VirusSeq_Portal:anatomical material
+ - GISAID:Specimen source
+ - CNPHI:Anatomical Material
+ - NML_LIMS:PH_ISOLATION_SITE_DESC
+ - BIOSAMPLE:isolation_source
+ - BIOSAMPLE:anatomical_material
+ - VirusSeq_Portal:anatomical material
anatomical part:
name: anatomical part
title: anatomical part
description: An anatomical part of an organism e.g. oropharynx.
- comments:
- Provide a descriptor if an anatomical part was sampled. Use the picklist
+ comments: Provide a descriptor if an anatomical part was sampled. Use the picklist
provided in the template. If a desired term is missing from the picklist, contact
emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null
value.
slot_uri: GENEPIO:0001214
multivalued: true
exact_mappings:
- - GISAID:Specimen source
- - CNPHI:Anatomical Site
- - NML_LIMS:PH_ISOLATION_SITE
- - BIOSAMPLE:isolation_source
- - BIOSAMPLE:anatomical_part
- - VirusSeq_Portal:anatomical part
+ - GISAID:Specimen source
+ - CNPHI:Anatomical Site
+ - NML_LIMS:PH_ISOLATION_SITE
+ - BIOSAMPLE:isolation_source
+ - BIOSAMPLE:anatomical_part
+ - VirusSeq_Portal:anatomical part
body product:
name: body product
title: body product
- description:
- A substance excreted/secreted from an organism e.g. feces, urine,
+ description: A substance excreted/secreted from an organism e.g. feces, urine,
sweat.
- comments:
- Provide a descriptor if a body product was sampled. Use the picklist
+ comments: Provide a descriptor if a body product was sampled. Use the picklist
provided in the template. If a desired term is missing from the picklist, contact
emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null
value.
slot_uri: GENEPIO:0001216
multivalued: true
exact_mappings:
- - GISAID:Specimen source
- - CNPHI:Body Product
- - NML_LIMS:PH_SPECIMEN_SOURCE_DESC
- - BIOSAMPLE:isolation_source
- - BIOSAMPLE:body_product
- - VirusSeq_Portal:body product
+ - GISAID:Specimen source
+ - CNPHI:Body Product
+ - NML_LIMS:PH_SPECIMEN_SOURCE_DESC
+ - BIOSAMPLE:isolation_source
+ - BIOSAMPLE:body_product
+ - VirusSeq_Portal:body product
+ environmental material:
+ name: environmental material
+ title: environmental material
+ description: A substance obtained from the natural or man-made environment e.g.
+ soil, water, sewage.
+ comments: Provide a descriptor if an environmental material was sampled. Use the
+ picklist provided in the template. If a desired term is missing from the picklist,
+ contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose
+ a null value.
+ examples:
+ - value: Bed linen
+ slot_uri: GENEPIO:0001223
+ any_of:
+ - range: environmental material international menu
+ - range: null value menu
+ multivalued: true
+ recommended: true
+ exact_mappings:
+ - GISAID:Specimen source
+ - BIOSAMPLE:isolation_source
+ - BIOSAMPLE:environmental_material
collection device:
name: collection device
title: collection device
description: The instrument or container used to collect the sample e.g. swab.
- comments:
- Provide a descriptor if a device was used for sampling. Use the picklist
+ comments: Provide a descriptor if a device was used for sampling. Use the picklist
provided in the template. If a desired term is missing from the picklist, contact
emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null
value.
slot_uri: GENEPIO:0001234
multivalued: true
exact_mappings:
- - GISAID:Specimen source
- - CNPHI:Specimen Collection Matrix
- - NML_LIMS:PH_SPECIMEN_TYPE_ORIG
- - BIOSAMPLE:isolation_source
- - BIOSAMPLE:collection_device
- - VirusSeq_Portal:collection device
+ - GISAID:Specimen source
+ - CNPHI:Specimen Collection Matrix
+ - NML_LIMS:PH_SPECIMEN_TYPE_ORIG
+ - BIOSAMPLE:isolation_source
+ - BIOSAMPLE:collection_device
+ - VirusSeq_Portal:collection device
collection method:
name: collection method
title: collection method
description: The process used to collect the sample e.g. phlebotamy, necropsy.
- comments:
- Provide a descriptor if a collection method was used for sampling. Use
+ comments: Provide a descriptor if a collection method was used for sampling. Use
the picklist provided in the template. If a desired term is missing from the
picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank.
Choose a null value.
@@ -2092,8 +2105,7 @@ slots:
name: host (scientific name)
title: host (scientific name)
description: The taxonomic, or scientific name of the host.
- comments:
- Common name or scientific name are required if there was a host. Both
+ comments: Common name or scientific name are required if there was a host. Both
can be provided, if known. Use terms from the pick lists in the template. Scientific
name e.g. Homo sapiens, If the sample was environmental, put "not applicable
slot_uri: GENEPIO:0001387
@@ -2515,39 +2527,37 @@ slots:
purpose of sequencing details:
name: purpose of sequencing details
title: purpose of sequencing details
- description:
- The description of why the sample was sequenced providing specific
+ description: The description of why the sample was sequenced providing specific
details.
- comments:
- 'Provide an expanded description of why the sample was sequenced using
+ comments: 'Provide an expanded description of why the sample was sequenced using
free text. The description may include the importance of the sequences for a
particular public health investigation/surveillance activity/research question.
Suggested standardized descriotions include: Screened due to travel history,
Screened due to close contact with infected individual.'
examples:
- - value: Outbreak in MSM community
+ - value: Outbreak in MSM community
slot_uri: GENEPIO:0001446
any_of:
- - range: WhitespaceMinimizedString
- - range: null value menu
+ - range: WhitespaceMinimizedString
+ - range: null value menu
required: true
exact_mappings:
- - CNPHI:Details on the Reason for Sequencing
- - NML_LIMS:PH_REASON_FOR_SEQUENCING_DETAILS
- - VirusSeq_Portal:purpose of sequencing details
+ - CNPHI:Details on the Reason for Sequencing
+ - NML_LIMS:PH_REASON_FOR_SEQUENCING_DETAILS
+ - VirusSeq_Portal:purpose of sequencing details
sequencing date:
name: sequencing date
title: sequencing date
description: The date the sample was sequenced.
comments: ISO 8601 standard "YYYY-MM-DD".
examples:
- - value: '2020-06-22'
+ - value: '2020-06-22'
slot_uri: GENEPIO:0001447
any_of:
- range: date
- range: null value menu
todos:
- - '>={sample collection date}'
+ - '>={sample collection date}'
exact_mappings:
- NML_LIMS:PH_SEQUENCING_DATE
library ID:
@@ -2577,16 +2587,15 @@ slots:
library preparation kit:
name: library preparation kit
title: library preparation kit
- description:
- The name of the DNA library preparation kit used to generate the
+ description: The name of the DNA library preparation kit used to generate the
library being sequenced.
comments: Provide the name of the library preparation kit used.
examples:
- - value: Nextera XT
+ - value: Nextera XT
slot_uri: GENEPIO:0001450
range: WhitespaceMinimizedString
exact_mappings:
- - NML_LIMS:PH_LIBRARY_PREP_KIT
+ - NML_LIMS:PH_LIBRARY_PREP_KIT
sequencing instrument:
name: sequencing instrument
title: sequencing instrument
@@ -2596,16 +2605,15 @@ slots:
multivalued: true
required: true
exact_mappings:
- - GISAID:Sequencing technology
- - CNPHI:Sequencing Instrument
- - NML_LIMS:PH_INSTRUMENT_CGN
- - VirusSeq_Portal:sequencing instrument
+ - GISAID:Sequencing technology
+ - CNPHI:Sequencing Instrument
+ - NML_LIMS:PH_INSTRUMENT_CGN
+ - VirusSeq_Portal:sequencing instrument
sequencing protocol:
name: sequencing protocol
title: sequencing protocol
description: The protocol used to generate the sequence.
- comments:
- 'Provide a free text description of the methods and materials used to
+ comments: 'Provide a free text description of the methods and materials used to
generate the sequence. Suggested text, fill in information where indicated.:
"Viral sequencing was performed following a metagenomic shotgun sequencing approach.
Sequencing was performed using a sequencing instrument. Libraries
@@ -2646,28 +2654,25 @@ slots:
raw sequence data processing method:
name: raw sequence data processing method
title: raw sequence data processing method
- description:
- The names of the software and version number used for raw data processing
+ description: The names of the software and version number used for raw data processing
such as removing barcodes, adapter trimming, filtering etc.
- comments:
- Provide the software name followed by the version e.g. Trimmomatic v.
+ comments: Provide the software name followed by the version e.g. Trimmomatic v.
0.38, Porechop v. 0.2.3
examples:
- - value: Porechop 0.2.3
+ - value: Porechop 0.2.3
slot_uri: GENEPIO:0001458
range: WhitespaceMinimizedString
exact_mappings:
- - NML_LIMS:PH_RAW_SEQUENCE_METHOD
- - VirusSeq_Portal:raw sequence data processing method
+ - NML_LIMS:PH_RAW_SEQUENCE_METHOD
+ - VirusSeq_Portal:raw sequence data processing method
dehosting method:
name: dehosting method
title: dehosting method
description: The method used to remove host reads from the pathogen sequence.
- comments:
- Provide the name and version number of the software used to remove host
+ comments: Provide the name and version number of the software used to remove host
reads.
examples:
- - value: Nanostripper
+ - value: Nanostripper
slot_uri: GENEPIO:0001459
range: WhitespaceMinimizedString
exact_mappings:
@@ -2713,7 +2718,7 @@ slots:
description: The name of software used to generate the consensus sequence.
comments: Provide the name of the software used to generate the consensus sequence.
examples:
- - value: iVar
+ - value: iVar
slot_uri: GENEPIO:0001463
range: WhitespaceMinimizedString
required: true
@@ -2728,7 +2733,7 @@ slots:
description: The version of the software used to generate the consensus sequence.
comments: Provide the version of the software used to generate the consensus sequence.
examples:
- - value: '1.3'
+ - value: '1.3'
slot_uri: GENEPIO:0001469
range: WhitespaceMinimizedString
required: true
@@ -2740,26 +2745,24 @@ slots:
breadth of coverage value:
name: breadth of coverage value
title: breadth of coverage value
- description:
- The percentage of the reference genome covered by the sequenced data,
+ description: The percentage of the reference genome covered by the sequenced data,
to a prescribed depth.
comments: Provide value as a percent.
examples:
- - value: 95%
+ - value: 95%
slot_uri: GENEPIO:0001472
range: WhitespaceMinimizedString
exact_mappings:
- - NML_LIMS:breadth of coverage value
- - VirusSeq_Portal:breadth of coverage value
+ - NML_LIMS:breadth of coverage value
+ - VirusSeq_Portal:breadth of coverage value
depth of coverage value:
name: depth of coverage value
title: depth of coverage value
- description:
- The average number of reads representing a given nucleotide in the
+ description: The average number of reads representing a given nucleotide in the
reconstructed sequence.
comments: Provide value as a fold of coverage.
examples:
- - value: 400x
+ - value: 400x
slot_uri: GENEPIO:0001474
range: WhitespaceMinimizedString
exact_mappings:
@@ -2772,7 +2775,7 @@ slots:
description: The threshold used as a cut-off for the depth of coverage.
comments: Provide the threshold fold coverage.
examples:
- - value: 100x
+ - value: 100x
slot_uri: GENEPIO:0001475
range: WhitespaceMinimizedString
exact_mappings:
@@ -2842,7 +2845,7 @@ slots:
description: The number of total base pairs generated by the sequencing process.
comments: Provide a numerical value (no need to include units).
examples:
- - value: '2639019'
+ - value: '2639019'
slot_uri: GENEPIO:0001482
range: integer
minimum_value: '0'
@@ -2855,7 +2858,7 @@ slots:
pairs.
comments: Provide a numerical value (no need to include units).
examples:
- - value: '197063'
+ - value: '197063'
slot_uri: GENEPIO:0001483
range: integer
minimum_value: '0'
@@ -2876,8 +2879,7 @@ slots:
name: bioinformatics protocol
title: bioinformatics protocol
description: A description of the overall bioinformatics strategy used.
- comments:
- Further details regarding the methods used to process raw data, and/or
+ comments: Further details regarding the methods used to process raw data, and/or
generate assemblies, and/or generate consensus sequences can. This information
can be provided in an SOP or protocol or pipeline/workflow. Provide the name
and version number of the protocol, or a GitHub link to a pipeline or workflow.
@@ -3034,31 +3036,28 @@ slots:
authors:
name: authors
title: authors
- description:
- Names of individuals contributing to the processes of sample collection,
+ description: Names of individuals contributing to the processes of sample collection,
sequence generation, analysis, and data submission.
- comments:
- Include the first and last names of all individuals that should be attributed,
+ comments: Include the first and last names of all individuals that should be attributed,
separated by a comma.
examples:
- - value: Tejinder Singh, Fei Hu, Joe Blogs
+ - value: Tejinder Singh, Fei Hu, Joe Blogs
slot_uri: GENEPIO:0001517
range: WhitespaceMinimizedString
recommended: true
exact_mappings:
- - GISAID:Authors
- - CNPHI:Authors
- - NML_LIMS:PH_CANCOGEN_AUTHORS
+ - GISAID:Authors
+ - CNPHI:Authors
+ - NML_LIMS:PH_CANCOGEN_AUTHORS
DataHarmonizer provenance:
name: DataHarmonizer provenance
title: DataHarmonizer provenance
description: The DataHarmonizer software version provenance.
- comments:
- The current software version information will be automatically generated
+ comments: The current software version information will be automatically generated
in this field after the user utilizes the "validate" function. This information
will be generated regardless as to whether the row is valid of not.
examples:
- - value: 'DataHarmonizer provenance: v0.13.21'
+ - value: 'DataHarmonizer provenance: v0.13.21'
slot_uri: GENEPIO:0001518
range: Provenance
exact_mappings:
@@ -3791,6 +3790,27 @@ enums:
Urine [UBERON:0001088]:
text: Urine [UBERON:0001088]
meaning: UBERON:0001088
+ environmental material international menu:
+ name: environmental material international menu
+ permissible_values:
+ Animal carcass:
+ text: Animal carcass
+ Bedding (Bed linen):
+ text: Bedding (Bed linen)
+ meaning: GSSO:005304
+ Clothing:
+ text: Clothing
+ meaning: GSSO:003405
+ Drinkware:
+ text: Drinkware
+ Tableware:
+ text: Tableware
+ Dish:
+ text: Dish
+ is_a: Tableware
+ Utensil:
+ text: Utensil
+ is_a: Tableware
collection method menu:
name: collection method menu
permissible_values:
@@ -4069,6 +4089,24 @@ enums:
Human [NCBITaxon:9606]:
text: Human [NCBITaxon:9606]
meaning: NCBITaxon:9606
+ Rodent:
+ text: Rodent
+ meaning: NCBITaxon:9989
+ Mouse:
+ text: Mouse
+ meaning: NCBITaxon:10090
+ is_a: Rodent
+ Prairie Dog:
+ text: Prairie Dog
+ is_a: Rodent
+ Rat:
+ text: Rat
+ meaning: NCBITaxon:10116
+ is_a: Rodent
+ Squirrel:
+ text: Squirrel
+ meaning: FOODON:03411389
+ is_a: Rodent
host (scientific name) menu:
name: host (scientific name) menu
permissible_values:
@@ -8111,8 +8149,7 @@ types:
WhitespaceMinimizedString:
name: WhitespaceMinimizedString
typeof: string
- description:
- 'A string that has all whitespace trimmed off of beginning and end,
+ description: 'A string that has all whitespace trimmed off of beginning and end,
and all internal whitespace segments reduced to single spaces. Whitespace includes
#x9 (tab), #xA (linefeed), and #xD (carriage return).'
base: str
@@ -8120,8 +8157,7 @@ types:
Provenance:
name: Provenance
typeof: string
- description:
- A field containing a DataHarmonizer versioning marker. It is issued
+ description: A field containing a DataHarmonizer versioning marker. It is issued
by DataHarmonizer when validation is applied to a given row of data.
base: str
uri: xsd:token
diff --git a/web/templates/monkeypox/schema_core.yaml b/web/templates/monkeypox/schema_core.yaml
index d3e658d5..3b11648b 100644
--- a/web/templates/monkeypox/schema_core.yaml
+++ b/web/templates/monkeypox/schema_core.yaml
@@ -1,6 +1,6 @@
id: https://example.com/monkeypox
name: Monkeypox
-version: 1.1.0
+version: 3.3.1
description: ""
imports:
- 'linkml:types'
@@ -17,11 +17,15 @@ classes:
description: Canadian specification for Monkeypox clinical virus biosample data gathering
is_a: dh_interface
see_also: template/monkeypox/SOP_Monkeypox.pdf
+ annotations:
+ version: 3.2.1
"Monkeypox_international":
name: "Monkeypox_international"
description: International specification for Monkeypox clinical virus biosample data gathering
is_a: dh_interface
see_also: template/monkeypox/SOP_Monkeypox_international.pdf
+ annotations:
+ version: 3.3.1
slots: {}
enums: {}
types:
diff --git a/web/templates/monkeypox/schema_enums.tsv b/web/templates/monkeypox/schema_enums.tsv
index 88e14627..06bc5538 100644
--- a/web/templates/monkeypox/schema_enums.tsv
+++ b/web/templates/monkeypox/schema_enums.tsv
@@ -221,6 +221,14 @@ body product international menu UBERON:0001913 Breast Milk [UBERON:0001913]
UBERON:0001827 Tear [UBERON:0001827]
UBERON:0001088 Urine [UBERON:0001088]
+environmental material international menu Animal carcass
+ GSSO:005304 Bedding (Bed linen)
+ GSSO:003405 Clothing
+ Drinkware
+ Tableware
+ Dish
+ Utensil
+
collection method menu NCIT:C52009 Amniocentesis
NCIT:C15631 Aspiration
@@ -311,6 +319,11 @@ specimen processing international menu GENEPIO:0100039 Virus passage [GENEPIO:01
host (common name) menu NCBITaxon:9606 Human
host (common name) international menu NCBITaxon:9606 Human [NCBITaxon:9606]
+ NCBITaxon:9989 Rodent
+ NCBITaxon:10090 Mouse
+ Prairie Dog
+ NCBITaxon:10116 Rat
+ FOODON:03411389 Squirrel
host (scientific name) menu NCBITaxon:9606 Homo sapiens Human
diff --git a/web/templates/monkeypox/schema_slots.tsv b/web/templates/monkeypox/schema_slots.tsv
index d77c5b2c..146a1287 100644
--- a/web/templates/monkeypox/schema_slots.tsv
+++ b/web/templates/monkeypox/schema_slots.tsv
@@ -18,7 +18,7 @@ Monkeypox Sample collection and processing GENEPIO:0100416 sequenced by sequenc
Monkeypox_international Sample collection and processing GENEPIO:0100416 sequenced by WhitespaceMinimizedString null value menu TRUE The name of the agency that generated the sequence. The name of the agency should be written out in full, (with minor exceptions) and be consistent across multiple submissions. If submitting specimens rather than sequencing data, please put the "National Microbiology Laboratory (NML)". Public Health Ontario (PHO) sequenced_by
Monkeypox;Monkeypox_international Sample collection and processing GENEPIO:0100422 sequenced by contact email WhitespaceMinimizedString The email address of the contact responsible for follow-up regarding the sequence. The email address can represent a specific individual or lab e.g. johnnyblogs@lab.ca, or RespLab@lab.ca RespLab@lab.ca sequenced by contact email
Monkeypox;Monkeypox_international Sample collection and processing GENEPIO:0100423 sequenced by contact address WhitespaceMinimizedString The mailing address of the agency submitting the sequence. The mailing address should be in the format: Street number and name, City, Province/Territory, Postal Code, Country 123 Sunnybrooke St, Toronto, Ontario, M4P 1L6, Canada sequenced by contact address
-Monkeypox Sample collection and processing GENEPIO:0001159 sequence submitted by sequence submitted by menu null value menu TRUE The name of the agency that submitted the sequence to a database. The name of the agency should be written out in full, (with minor exceptions) and be consistent across multiple submissions. If submitting specimens rather than sequencing data, please put the "National Microbiology Laboratory (NML)". Public Health Ontario (PHO) Submitting lab Sequencing Centre PH_SEQUENCING_SUBMITTER sequence_submitted_by sequence submitted by
+Monkeypox Sample collection and processing GENEPIO:0001159 sequence submitted by sequence submitted by menu null value menu TRUE The name of the agency that submitted the sequence to a database. The name of the agency should be written out in full, (with minor exceptions) and be consistent across multiple submissions. If submitting specimens rather than sequencing data, please put the "National Microbiology Laboratory (NML)". Public Health Ontario (PHO) Submitting lab Sequencing Centre PH_SEQUENCE_SUBMITTER sequence_submitted_by sequence submitted by
Monkeypox_international Sample collection and processing GENEPIO:0001159 sequence submitted by WhitespaceMinimizedString null value menu TRUE The name of the agency that submitted the sequence to a database. The name of the agency should be written out in full, (with minor exceptions) and be consistent across multiple submissions. If submitting specimens rather than sequencing data, please put the "National Microbiology Laboratory (NML)". Public Health Ontario (PHO) Submitting lab sequence_submitted_by
Monkeypox;Monkeypox_international Sample collection and processing GENEPIO:0001165 sequence submitter contact email WhitespaceMinimizedString The email address of the agency responsible for submission of the sequence. The email address can represent a specific individual or lab e.g. johnnyblogs@lab.ca, or RespLab@lab.ca RespLab@lab.ca sequence submitter contact email
Monkeypox;Monkeypox_international Sample collection and processing GENEPIO:0001167 sequence submitter contact address WhitespaceMinimizedString The mailing address of the agency responsible for submission of the sequence. The mailing address should be in the format: Street number and name, City, Province/Territory, Postal Code, Country 123 Sunnybrooke St, Toronto, Ontario, M4P 1L6, Canada Address sequence submitter contact address
@@ -46,6 +46,7 @@ Monkeypox Sample collection and processing GENEPIO:0001214 anatomical part anat
Monkeypox_international Sample collection and processing GENEPIO:0001214 anatomical part anatomical part international menu null value menu TRUE TRUE An anatomical part of an organism e.g. oropharynx. Provide a descriptor if an anatomical part was sampled. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value. Genital area [BTO:0003358] Specimen source Anatomical Site PH_ISOLATION_SITE isolation_source;anatomical_part anatomical part
Monkeypox Sample collection and processing GENEPIO:0001216 body product body product menu null value menu TRUE TRUE A substance excreted/secreted from an organism e.g. feces, urine, sweat. Provide a descriptor if a body product was sampled. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value. Pus Specimen source Body Product PH_SPECIMEN_SOURCE_DESC isolation_source;body_product body product
Monkeypox_international Sample collection and processing GENEPIO:0001216 body product body product international menu null value menu TRUE TRUE A substance excreted/secreted from an organism e.g. feces, urine, sweat. Provide a descriptor if a body product was sampled. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value. Pus [UBERON:0000177] Specimen source Body Product PH_SPECIMEN_SOURCE_DESC isolation_source;body_product body product
+Monkeypox_international Sample collection and processing GENEPIO:0001223 environmental material environmental material international menu null value menu TRUE TRUE A substance obtained from the natural or man-made environment e.g. soil, water, sewage. Provide a descriptor if an environmental material was sampled. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value. Bed linen Specimen source isolation_source;environmental_material
Monkeypox Sample collection and processing GENEPIO:0001234 collection device collection device menu null value menu TRUE TRUE The instrument or container used to collect the sample e.g. swab. Provide a descriptor if a device was used for sampling. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value. Swab Specimen source Specimen Collection Matrix PH_SPECIMEN_TYPE_ORIG isolation_source;collection_device collection device
Monkeypox_international Sample collection and processing GENEPIO:0001234 collection device collection device international menu null value menu TRUE TRUE The instrument or container used to collect the sample e.g. swab. Provide a descriptor if a device was used for sampling. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value. Swab [GENEPIO:0100027] Specimen source Specimen Collection Matrix PH_SPECIMEN_TYPE_ORIG isolation_source;collection_device collection device
Monkeypox Sample collection and processing GENEPIO:0001241 collection method collection method menu null value menu TRUE TRUE The process used to collect the sample e.g. phlebotamy, necropsy. Provide a descriptor if a collection method was used for sampling. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value. Biopsy Specimen source Collection Method COLLECTION_METHOD isolation_source;collection_method collection method