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index 1ba854e6c..dff0a1d47 100644 --- a/backend/pyproject.toml +++ b/backend/pyproject.toml @@ -20,7 +20,7 @@ python = "^3.9" pydantic = "^1.10.2" curies = "<1" linkml = "^1.6.1" -prefixmaps = "^0.1.6" +prefixmaps = "^0.1.7" requests = "^2.28.1" typer = "^0.7.0" diff --git a/backend/src/monarch_py/datamodels/model.py b/backend/src/monarch_py/datamodels/model.py index 92e3f332e..ce8d75fcc 100644 --- a/backend/src/monarch_py/datamodels/model.py +++ b/backend/src/monarch_py/datamodels/model.py @@ -90,6 +90,10 @@ class Association(ConfiguredBaseModel): default_factory=list, description="""List of ExpandedCuries with id and url for evidence""", ) + grouping_key: Optional[str] = Field( + None, + description="""A concatenation of fields used to group associations with the same essential/defining properties""", + ) provided_by: Optional[str] = Field(None) provided_by_link: Optional[ExpandedCurie] = Field( None, @@ -105,6 +109,19 @@ class Association(ConfiguredBaseModel): onset_qualifier: Optional[str] = Field(None) sex_qualifier: Optional[str] = Field(None) stage_qualifier: Optional[str] = Field(None) + qualifiers_label: Optional[str] = Field(None, description="""The name of the frequency_qualifier entity""") + qualifiers_namespace: Optional[str] = Field( + None, description="""The namespace/prefix of the frequency_qualifier entity""" + ) + qualifiers_category: Optional[str] = Field(None, description="""The category of the frequency_qualifier entity""") + qualifiers_closure: Optional[List[str]] = Field( + default_factory=list, + description="""Field containing frequency_qualifier id and the ids of all of it's ancestors""", + ) + qualifiers_closure_label: Optional[List[str]] = Field( + default_factory=list, + description="""Field containing frequency_qualifier name and the names of all of it's ancestors""", + ) frequency_qualifier_label: Optional[str] = Field(None, description="""The name of the frequency_qualifier entity""") frequency_qualifier_namespace: Optional[str] = Field( None, description="""The namespace/prefix of the frequency_qualifier entity""" @@ -250,6 +267,10 @@ class DirectionalAssociation(Association): default_factory=list, description="""List of ExpandedCuries with id and url for evidence""", ) + grouping_key: Optional[str] = Field( + None, + description="""A concatenation of fields used to group associations with the same essential/defining properties""", + ) provided_by: Optional[str] = Field(None) provided_by_link: Optional[ExpandedCurie] = Field( None, @@ -265,6 +286,19 @@ class DirectionalAssociation(Association): onset_qualifier: Optional[str] = Field(None) sex_qualifier: Optional[str] = Field(None) stage_qualifier: Optional[str] = Field(None) + qualifiers_label: Optional[str] = Field(None, description="""The name of the frequency_qualifier entity""") + qualifiers_namespace: Optional[str] = Field( + None, description="""The namespace/prefix of the frequency_qualifier entity""" + ) + qualifiers_category: Optional[str] = Field(None, description="""The category of the frequency_qualifier entity""") + qualifiers_closure: Optional[List[str]] = Field( + default_factory=list, + description="""Field containing frequency_qualifier id and the ids of all of it's ancestors""", + ) + qualifiers_closure_label: Optional[List[str]] = Field( + default_factory=list, + description="""Field containing frequency_qualifier name and the names of all of it's ancestors""", + ) frequency_qualifier_label: Optional[str] = Field(None, description="""The name of the frequency_qualifier entity""") frequency_qualifier_namespace: Optional[str] = Field( None, description="""The namespace/prefix of the frequency_qualifier entity""" @@ -349,6 +383,7 @@ class Entity(ConfiguredBaseModel): ) symbol: Optional[str] = Field(None) synonym: Optional[List[str]] = Field(default_factory=list) + uri: Optional[str] = Field(None, description="""The URI of the entity""") class FacetValue(ConfiguredBaseModel): @@ -394,10 +429,10 @@ class Mapping(ConfiguredBaseModel): A minimal class to hold a SSSOM mapping """ - subject_id: str = Field(..., description="""The first of the two entities being compared""") + subject_id: str = Field(...) subject_label: Optional[str] = Field(None, description="""The name of the subject entity""") predicate_id: str = Field(...) - object_id: Optional[str] = Field(None, description="""The second of the two entities being compared""") + object_id: str = Field(...) object_label: Optional[str] = Field(None, description="""The name of the object entity""") mapping_justification: Optional[str] = Field(None) @@ -439,6 +474,7 @@ class Node(Entity): provided_by: Optional[str] = Field(None) symbol: Optional[str] = Field(None) synonym: Optional[List[str]] = Field(default_factory=list) + uri: Optional[str] = Field(None, description="""The URI of the entity""") class NodeHierarchy(ConfiguredBaseModel): @@ -530,6 +566,7 @@ class SearchResult(Entity): ) symbol: Optional[str] = Field(None) synonym: Optional[List[str]] = Field(default_factory=list) + uri: Optional[str] = Field(None, description="""The URI of the entity""") class SearchResults(Results): @@ -564,10 +601,10 @@ class TermPairwiseSimilarity(PairwiseSimilarity): A simple pairwise similarity between two atomic concepts/terms """ - subject_id: str = Field(..., description="""The first of the two entities being compared""") + subject_id: str = Field(...) subject_label: Optional[str] = Field(None, description="""The name of the subject entity""") subject_source: Optional[str] = Field(None, description="""the source for the first entity""") - object_id: Optional[str] = Field(None, description="""The second of the two entities being compared""") + object_id: str = Field(...) object_label: Optional[str] = Field(None, description="""The name of the object entity""") object_source: Optional[str] = Field(None, description="""the source for the second entity""") ancestor_id: Optional[str] = Field( diff --git a/backend/src/monarch_py/datamodels/model.yaml b/backend/src/monarch_py/datamodels/model.yaml index 60902c9f9..b28bfaebe 100644 --- a/backend/src/monarch_py/datamodels/model.yaml +++ b/backend/src/monarch_py/datamodels/model.yaml @@ -53,6 +53,7 @@ classes: - evidence_count - has_evidence - has_evidence_links + - grouping_key - provided_by - provided_by_link - publications @@ -172,6 +173,7 @@ classes: - in_taxon_label - symbol - synonym + - uri EntityResults: is_a: Results slots: @@ -456,6 +458,8 @@ slots: xref: multivalued: true range: string + uri: + description: The URI of the entity url: range: string subject_label: @@ -496,6 +500,24 @@ slots: is_a: in_taxon object_taxon_label: is_a: in_taxon_label + + # this whole block will be renamed to qualifer_ after we bring in the next biolink model release + qualifiers_label: + is_a: name + description: The name of the frequency_qualifier entity + qualifiers_namespace: + range: string + description: The namespace/prefix of the frequency_qualifier entity + qualifiers_category: + is_a: category + description: The category of the frequency_qualifier entity + qualifiers_closure: + multivalued: true + description: Field containing frequency_qualifier id and the ids of all of it's ancestors + qualifiers_closure_label: + multivalued: true + description: Field containing frequency_qualifier name and the names of all of it's ancestors + frequency_qualifier_label: is_a: name description: The name of the frequency_qualifier entity @@ -557,12 +579,16 @@ slots: multivalued: true description: Field containing stage_qualifier name and the names of all of it's ancestors # sssom slots - # subject_id already exists in similarity.yaml + subject_id: + range: string + required: true # subject label is already included in this schema predicate_id: - range: string - required: true - # object_id already exists in similarity.yaml + range: string + required: true + object_id: + range: string + required: true # object label is already included in this schema mapping_justification: range: string diff --git a/backend/src/monarch_py/datamodels/similarity.yaml b/backend/src/monarch_py/datamodels/similarity.yaml index 79f759334..7aae6ba36 100644 --- a/backend/src/monarch_py/datamodels/similarity.yaml +++ b/backend/src/monarch_py/datamodels/similarity.yaml @@ -95,11 +95,11 @@ types: minimum_value: 0 slots: - subject_id: - slot_uri: sssom:subject_id - required: true - range: uriorcurie - description: The first of the two entities being compared +# subject_id: +# slot_uri: sssom:subject_id +# required: true +# range: uriorcurie +# description: The first of the two entities being compared # Excluded, since it conflicts with subject_label from this schema # subject_label: # slot_uri: sssom:subject_label @@ -107,10 +107,10 @@ slots: subject_source: slot_uri: sssom:subject_source description: the source for the first entity - object_id: - slot_uri: sssom:object_id - range: uriorcurie - description: The second of the two entities being compared +# object_id: +# slot_uri: sssom:object_id +# range: uriorcurie +# description: The second of the two entities being compared # Excluded, since it conflicts with object_label from this schema # object_label: # slot_uri: sssom:object_label diff --git a/backend/src/monarch_py/implementations/solr/solr_parsers.py b/backend/src/monarch_py/implementations/solr/solr_parsers.py index e1c2ce5fe..5c79e230d 100644 --- a/backend/src/monarch_py/implementations/solr/solr_parsers.py +++ b/backend/src/monarch_py/implementations/solr/solr_parsers.py @@ -21,6 +21,7 @@ ) from monarch_py.datamodels.solr import HistoPhenoKeys, SolrQueryResult from monarch_py.utils.association_type_utils import get_association_type_mapping_by_query_string +from monarch_py.utils.entity_utils import get_uri from monarch_py.utils.utils import get_links_for_field, get_provided_by_link #################### @@ -85,6 +86,7 @@ def parse_association_counts(query_result: SolrQueryResult, entity: str) -> Asso def parse_entity(solr_document: Dict) -> Entity: try: entity = Entity(**solr_document) + entity.uri = get_uri(entity.id) except ValidationError: logger.error(f"Validation error for {solr_document}") raise diff --git a/backend/src/monarch_py/implementations/sql/sql_implementation.py b/backend/src/monarch_py/implementations/sql/sql_implementation.py index 0aa6f98df..c61dc594d 100644 --- a/backend/src/monarch_py/implementations/sql/sql_implementation.py +++ b/backend/src/monarch_py/implementations/sql/sql_implementation.py @@ -3,11 +3,13 @@ import pystow from loguru import logger +from pydantic import ValidationError + from monarch_py.datamodels.model import Association, AssociationResults, Entity, Node, NodeHierarchy from monarch_py.interfaces.association_interface import AssociationInterface from monarch_py.interfaces.entity_interface import EntityInterface +from monarch_py.utils.entity_utils import get_uri from monarch_py.utils.utils import SQL_DATA_URL, dict_factory -from pydantic import ValidationError monarchstow = pystow.module("monarch") @@ -49,6 +51,7 @@ def get_entity(self, id: str, update: bool = False, extra: bool = False) -> Enti "in_taxon": sql_data["in_taxon"], "symbol": sql_data["symbol"], "synonym": sql_data["synonym"].split("|"), + "uri": get_uri(sql_data["id"]), } try: results["source"] = sql_data["source"] diff --git a/backend/src/monarch_py/utils/entity_utils.py b/backend/src/monarch_py/utils/entity_utils.py new file mode 100644 index 000000000..97056219a --- /dev/null +++ b/backend/src/monarch_py/utils/entity_utils.py @@ -0,0 +1,6 @@ +from monarch_py.service.curie_service import CurieService + + +def get_uri(id: str) -> str: + """Returns the URI for the given CURIE.""" + return CurieService().expand(id) diff --git a/backend/tests/fixtures/association_counts_response.py b/backend/tests/fixtures/association_counts_response.py index 0933a7019..1faefaec8 100644 --- a/backend/tests/fixtures/association_counts_response.py +++ b/backend/tests/fixtures/association_counts_response.py @@ -5,7 +5,7 @@ def association_counts_response(): return { "responseHeader": { - "QTime": 1, + "QTime": 4, "params": { "facet.query": [ '(category:"biolink:DiseaseToPhenotypicFeatureAssociation") AND (subject:"MONDO:0020121" OR subject_closure:"MONDO:0020121")', @@ -44,3784 +44,4218 @@ def association_counts_response(): }, }, "response": { - "num_found": 4835, + "num_found": 4838, "start": 0, "docs": [ { - "id": "uuid:8a89d08e-5d8c-11ee-9b27-2b20ed86a9d9", - "original_subject": "OMIM:602541", + "id": "uuid:c9c8bf2f-7529-11ee-b012-cbd37f5c3759", + "original_subject": "OMIM:160500", "predicate": "biolink:has_phenotype", "category": "biolink:DiseaseToPhenotypicFeatureAssociation", "aggregator_knowledge_source": ["infores:monarchinitiative"], "primary_knowledge_source": "infores:hpo-annotations", "provided_by": "hpoa_disease_to_phenotype_edges", - "publications": ["OMIM:602541"], - "has_evidence": ["ECO:0000304"], - "subject": "MONDO:0011246", - "object": "HP:0008064", - "subject_namespace": "MONDO", + "publications": ["PMID:17548557"], + "frequency_qualifier": "HP:0040280", + "has_evidence": ["ECO:0000269"], + "subject": "MONDO:0008050", + "object": "HP:0011399", + "subject_label": "MYH7-related skeletal myopathy", "subject_category": "biolink:Disease", + "subject_namespace": "MONDO", "subject_closure": [ - "MONDO:0000001", + "BFO:0000002", + "MONDO:0016195", + "MONDO:0005336", + "MONDO:0018949", "MONDO:0005071", + "MONDO:0008050", + "BFO:0000016", + "MONDO:0016139", + "OGMS:0000031", + "MONDO:0003847", + "BFO:0000001", "MONDO:0020121", - "MONDO:0700223", - "BFO:0000002", - "MONDO:0018117", + "MONDO:0019952", "BFO:0000017", "BFO:0000020", - "MONDO:0002525", - "BFO:0000016", "MONDO:0020120", "MONDO:0019056", + "MONDO:0000001", + "MONDO:0700223", "MONDO:0700096", - "MONDO:0005336", "MONDO:0002081", - "OGMS:0000031", - "MONDO:0003847", "MONDO:0003939", - "BFO:0000001", "MONDO:0002320", - "MONDO:0019052", - 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+ "HP:0003693", + "UPHENO:0002816", + "HP:0011399", + "UPHENO:0081581", + "HP:0033127", + "UPHENO:0019778", + "UPHENO:0002647", + "UPHENO:0013920", + "UPHENO:0002830", + "UBERON:0001062", + "UBERON:0000465", + "RO:0002577", + "UBERON:0000061", + "UBERON:0015212", + "UBERON:0000475", + "UBERON:0000062", + "UBERON:0000383", + "UBERON:0001015", + "UBERON:0000978", + "UBERON:0007270", + "UBERON:0004480", + "UBERON:0003663", + "UBERON:0014795", + "UBERON:0008230", ], "object_closure_label": [ - "entity", - "entity", - "continuant", - "continuant", - "independent continuant", - "specifically dependent continuant", - "material entity", "All (HPO)", + "abnormal musculature of lower limb", + "Abnormality of the lower limb (HPO)", + "decreased size of the anatomical entity", + "Phenotypic abnormality", "Phenotypic abnormality (HPO)", - "Abnormality of the skin (HPO)", - "Thickened skin (HPO)", - "Abnormality of the integument (HPO)", - "Ichthyosis (HPO)", - "Abnormality of skin morphology 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"decreased size of the anatomical entity in the independent continuant", + "continuant", "protein-containing material entity", - "anatomical structure", - "organ", - "material anatomical entity", - "anatomical system", - "multicellular organism", - "anatomical entity", - "skin of body", - "integument", - "integumental system", - "ectoderm-derived structure", - "multicellular anatomical structure", - "organ system subdivision", + "hindlimb", + "appendage girdle complex", + "appendage", + "subdivision of organism along appendicular axis", + "flexor muscle", + "limb muscle", + "pelvic complex muscle", + "paired limb/fin segment", + "musculature of lower limb", + "muscle of leg", + "lower limb segment", + "zeugopod", + "Lower limb amyotrophy (HPO)", "phenotype", - "Phenotypic abnormality", - "phenotype by ontology source", "abnormal phenotype by ontology source", - "increased size of the anatomical entity", - "abnormal anatomical entity", - "abnormal integument", - "abnormal skin of body", - "abnormal anatomical entity morphology in the independent continuant", - "abnormal anatomical entity morphology", - "increased thickness of the anatomical entity", - "increased thickness of the skin of body", - "increased thickness of the anatomical entity in independent continuant", - "increased size of the anatomical entity in independent continuant", + "Abnormality of the musculature of the limbs (HPO)", + "musculature of lower limb atrophy", "abnormal size of anatomical entity", + "abnormal muscle organ morphology", + "abnormal muscle organ morphology", + "entity", + "anatomical entity", + "anatomical structure", + "muscle structure", + "skeletal musculature", + "organism subdivision", + "organ", + "muscle organ", + "musculature of body", + "musculature", + "leg", + "pelvic appendage musculature", + "musculature of limb", + "hindlimb muscle", + "pelvic appendage muscle", + "tibialis", + "abnormal anatomical entity", + "Abnormality of the calf (HPO)", + "anatomical entity atrophy", + "Skeletal muscle atrophy (HPO)", + "abnormal hindlimb zeugopod", + "Abnormality of the calf musculature (HPO)", + "continuant", + "Distal lower limb amyotrophy (HPO)", + "specifically dependent continuant", + "Abnormality of the musculature (HPO)", "abnormal anatomical entity", "abnormal anatomical entity morphology", - "abnormal skin of body morphology", - "abnormal skin of body morphology in the independent continuant", - "abnormal multicellular organism morphology", + "abnormal anatomical entity morphology", + "abnormal leg", + "entity", + "muscle organ atrophy", + "abnormal limb", + "material entity", + "limb", + "pelvic appendage", + "multicellular anatomical structure", + "anatomical system", + "multicellular organism", + "organ system subdivision", + "posterior region of body", + "skeletal muscle organ", + "multi-limb segment region", + "limb segment", + "musculature of hindlimb zeugopod", ], - "object_label": "Ichthyosis (HPO)", - "evidence_count": 4, + "frequency_qualifier_label": "Obligate (HPO)", + "frequency_qualifier_category": "biolink:PhenotypicFeature", + "frequency_qualifier_namespace": "HP", + "frequency_qualifier_closure": ["HP:0000001", "HP:0040280", "HP:0040279"], + "frequency_qualifier_closure_label": ["All (HPO)", "Obligate (HPO)", "Frequency (HPO)"], + "evidence_count": 2, + "grouping_key": "MONDO:0008050🍪🍪biolink:has_phenotype🍪HP:0011399", }, { - "id": "uuid:898aa71d-5d8c-11ee-9b27-2b20ed86a9d9", - "original_subject": "OMIM:609115", + "id": "uuid:c9c8bf30-7529-11ee-b012-cbd37f5c3759", + "original_subject": "OMIM:160500", "predicate": "biolink:has_phenotype", "category": "biolink:DiseaseToPhenotypicFeatureAssociation", "aggregator_knowledge_source": ["infores:monarchinitiative"], "primary_knowledge_source": "infores:hpo-annotations", "provided_by": "hpoa_disease_to_phenotype_edges", - "publications": ["OMIM:609115"], - "has_evidence": ["ECO:0000501"], - "subject": "MONDO:0012193", - "object": "HP:0008116", - 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"MONDO:0002320", ], "subject_closure_label": [ - "entity", - "continuant", + "muscular dystrophy", + "human disease", + "musculoskeletal system disorder", + "disease", + "muscle tissue disorder", + "congenital nervous system disorder", + "hereditary skeletal muscle disorder", + "MYH7-related skeletal myopathy", "disposition", - "realizable entity", - "specifically dependent continuant", + "qualitative or quantitative protein defects in neuromuscular diseases", + "distal myopathy", "disease", - "autosomal dominant disease", - "autosomal genetic disease", - "musculoskeletal system disorder", + "continuant", + "qualitative or quantitative defects of beta-myosin heavy chain (MYH7)", + "myopathy", "hereditary disease", - "muscle tissue disorder", "nervous system disorder", - "myopathy", - "autosomal dominant limb-girdle muscular dystrophy type 1G", - "muscular dystrophy, limb-girdle, autosomal dominant", - "progressive muscular dystrophy", - "limb-girdle muscular dystrophy", - "neuromuscular disease", + "congenital myopathy", + "realizable entity", + "specifically dependent continuant", "skeletal muscle disorder", - "muscular dystrophy", - "human disease", - "hereditary skeletal muscle disorder", - "disease", + "neuromuscular disease", + "entity", ], - "subject_label": "autosomal dominant limb-girdle muscular dystrophy type 1G", - "object_namespace": "HP", + "object_label": "Left atrial enlargement (HPO)", "object_category": "biolink:PhenotypicFeature", + "object_namespace": "HP", "object_closure": [ - "HP:0000001", - "UPHENO:0002644", - "HP:0008116", - "HP:0002814", - "UPHENO:0001001", - "HP:0001436", "UPHENO:0001005", - "HP:0009127", - "HP:0011805", - "UPHENO:0001002", - "HP:0000118", "BFO:0000002", - "UPHENO:0002653", + "UPHENO:0075195", + "UPHENO:0020584", + "UPHENO:0076692", + "BFO:0000004", + "UBERON:0004535", + "UBERON:0011676", + "UBERON:0013701", + "UBERON:0002081", + "UBERON:0000915", + "UBERON:0002100", + "UBERON:0005181", + "UBERON:0002075", + 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+ "UBERON:0015410", + "UPHENO:0001001", + "UPHENO:0001002", + "UPHENO:0015324", + "HP:0025579", + "UPHENO:0001072", + "UPHENO:0081581", + "HP:0005120", + "UPHENO:0015329", + "BFO:0000002", + "UBERON:0001062", "RO:0002577", - "UBERON:0004708", "UBERON:0000061", - "UBERON:0002101", - "UBERON:0004709", "UBERON:0015212", + "UBERON:0010314", "UBERON:0010000", - "UBERON:0000467", - "UBERON:0005090", - "UBERON:0002103", - "UBERON:0010707", "UBERON:0000475", "UBERON:0000062", - "UBERON:0000468", - "UBERON:0011216", - "UBERON:0001630", - "UBERON:0010709", - "UBERON:0000154", - "UBERON:0000026", - "UBERON:0010758", - "UBERON:0000383", - "UBERON:0001015", - "UBERON:0006058", - "UBERON:0007271", - "UBERON:0014792", - "UBERON:0010538", - "UBERON:0000978", - "UBERON:0007270", - "UBERON:0004480", - "UBERON:0002529", - "UBERON:0004482", - "UBERON:0008784", - "UBERON:0002470", - "UBERON:0004488", - "UBERON:0002387", + "UBERON:0005178", + "UBERON:0007100", ], "object_closure_label": [ - "entity", - "entity", - "continuant", - "continuant", - "independent continuant", - "specifically dependent continuant", - "material entity", "All (HPO)", + "abnormal cardiac atrium morphology", + "abnormal cardiovascular system", + "increased size of the anatomical entity in independent continuant", "Phenotypic abnormality (HPO)", - "Abnormality of the foot musculature (HPO)", - "Abnormality of the musculature of the lower limbs (HPO)", - "Abnormality of the lower limb (HPO)", - "Abnormality of the musculature (HPO)", - "Flexion limitation of toes (HPO)", - "Abnormality of the musculature of the limbs (HPO)", - "Abnormal skeletal muscle morphology (HPO)", - "Abnormality of the musculoskeletal system (HPO)", - "Abnormality of limbs (HPO)", + "abnormal anatomical entity morphology in the heart", + "Abnormal left atrium morphology (HPO)", + "increased size of the anatomical entity", + "abnormal multicellular organism morphology", + "Abnormal cardiac atrium morphology (HPO)", "quality", - "protein-containing material entity", + "independent continuant", "system", - "appendage", - "anatomical structure", - "organ", - "posterior region of body", - "musculature of body", - "material anatomical entity", - "anatomical system", - "multicellular organism", - "organism subdivision", - "leg", - "musculature", - "anatomical entity", - "muscle organ", - "limb", - "hindlimb", - "pes", - "autopod region", - "limb segment", - "musculature of limb", - "musculature of lower limb", - "musculature of pes", - "paired limb/fin", - "pelvic appendage", - "muscle structure", - "multi-limb segment region", - "pelvic appendage musculature", - "appendage musculature", - "lower limb segment", - "multicellular anatomical structure", - "paired limb/fin segment", - "appendage girdle complex", - "pelvic complex", - "subdivision of organism along appendicular axis", - "organ system subdivision", - "musculature of pelvic complex", + "cardiovascular system", "lateral structure", - "phenotype", + "structure with developmental contribution from neural crest", + "multicellular anatomical structure", + "left cardiac atrium", + "Abnormality of the cardiovascular system (HPO)", "Phenotypic abnormality", + "Abnormal heart morphology (HPO)", + "specifically dependent continuant", + "abnormal left cardiac atrium morphology", + "abnormal cardiovascular system morphology", + "abnormal anatomical entity morphology in the independent continuant", + "increased size of the left cardiac atrium", "phenotype by ontology source", + "abnormal heart morphology", + "protein-containing material entity", + "material anatomical entity", + "left cardiac chamber", + "heart", + "subdivision of trunk", + "body proper", + "trunk region element", + "compound organ", + "heart plus pericardium", + "phenotype", "abnormal phenotype by ontology source", + "continuant", + "abnormal size of anatomical entity", + "entity", + "anatomical entity", + "anatomical structure", + "mesoderm-derived structure", + "organism subdivision", + "organ", + "circulatory system", + "cardiac chamber", + "thoracic cavity element", + "primary circulatory organ", + "abnormal anatomical entity", + "abnormal cardiac atrium morphology in the heart", + "Abnormality of cardiovascular system morphology (HPO)", + "Left atrial enlargement (HPO)", "abnormal anatomical entity", - "abnormal musculature of lower limb", - "abnormal musculature of limb", - "abnormal musculature of pes", - "abnormal musculature", - "abnormal limb", - "abnormal leg", "abnormal anatomical entity morphology", - "abnormal muscle organ morphology", - "abnormal multicellular organism morphology", + "abnormal anatomical entity morphology", + "entity", + "abnormal cardiac atrium morphology in the independent continuant", + "continuant", + "material entity", + "anatomical system", + "multicellular organism", + "organ part", + "subdivision of organism along main body axis", + "main body axis", + "cardiac atrium", + "thoracic segment of trunk", + "trunk", + "thoracic segment organ", + "viscus", + "circulatory organ", ], - "object_label": "Flexion limitation of toes (HPO)", - "evidence_count": 4, + "frequency_qualifier_label": "Obligate (HPO)", + "frequency_qualifier_category": "biolink:PhenotypicFeature", + "frequency_qualifier_namespace": "HP", + "frequency_qualifier_closure": ["HP:0000001", "HP:0040280", "HP:0040279"], + "frequency_qualifier_closure_label": ["All (HPO)", "Obligate (HPO)", "Frequency (HPO)"], + "evidence_count": 2, + "grouping_key": "MONDO:0008050🍪🍪biolink:has_phenotype🍪HP:0031295", }, { - "id": "uuid:87cb3e81-5d8c-11ee-9b27-2b20ed86a9d9", - "original_subject": "OMIM:609500", + "id": "uuid:c9c8bf31-7529-11ee-b012-cbd37f5c3759", + "original_subject": "OMIM:160500", "predicate": "biolink:has_phenotype", "category": "biolink:DiseaseToPhenotypicFeatureAssociation", "aggregator_knowledge_source": ["infores:monarchinitiative"], "primary_knowledge_source": "infores:hpo-annotations", "provided_by": 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"anatomical entity", + "anatomical structure", + "muscle structure", + "skeletal musculature", + "mesoderm-derived structure", + "organism subdivision", + "organ", + "muscle organ", + "gustatory system", + "cranial muscle", + "musculature of body", + "musculature", + "peripheral nervous system", + "skeletal musculature of head", + "musculature of face", "abnormal anatomical entity", - "abnormal voluntary movement behavior", - "abnormal behavior process", - "abnormal voluntary movement behavior", - "changed biological_process rate", - "abnormal behavior process", + "Abnormality of head or neck (HPO)", + "abnormal craniocervical region", + "Abnormal cranial nerve morphology (HPO)", + "Muscle weakness (HPO)", + "Weakness of facial musculature (HPO)", + "Abnormal peripheral nervous system morphology (HPO)", + "paralysed anatomical entity", + "Abnormality of the musculature (HPO)", "abnormality of anatomical entity physiology", + "abnormality of cranial nerve physiology", + "abnormal 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"object_label": "Loss of ambulation (HPO)", "object_category": "biolink:PhenotypicFeature", + "object_namespace": "HP", "object_closure": [ - "HP:0000001", "UPHENO:0082875", - "UPHENO:0075696", - "UPHENO:0078622", - "UPHENO:0049586", - "UPHENO:0080377", - "UPHENO:0001001", - "UPHENO:0052915", "UPHENO:0049622", - "UPHENO:0080585", - "HP:0001265", - "HP:0100022", "UPHENO:0001005", - "HP:0031826", - "UPHENO:0001002", - "HP:0000118", "BFO:0000002", - "UPHENO:0052178", + "HP:0002540", + "UPHENO:0050606", + "HP:0001288", + "HP:0012638", + "BFO:0000015", + "UBERON:0000061", + "GO:0050882", + "NBO:0000338", + "GO:0050905", + "UBERON:0001016", + "HP:0000001", + "UPHENO:0001001", + "UPHENO:0080585", + "HP:0000118", "BFO:0000020", "UPHENO:0002433", - "UPHENO:0050613", - "UPHENO:0005625", - "UPHENO:0050079", - "UPHENO:0005433", - "UPHENO:0002332", - "UPHENO:0050606", - "HP:0001315", - "HP:0000707", "UPHENO:0001003", - "UPHENO:0002536", "HP:0000708", - "UPHENO:0079826", - "UPHENO:0004523", 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"nervous system disorder", - "retinal disorder", - "eye disorder", - "myopathy", - "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A5", - "congenital disorder of glycosylation", - "developmental anomaly of metabolic origin", - "qualitative or quantitative protein defects in neuromuscular diseases", - "qualitative or quantitative defects of protein involved in O-glycosylation of alpha-dystroglycan", - "qualitative or quantitative defects of FKRP", - "qualitative or quantitative defects of fukutin", - "qualitative or quantitative defects of protein O-mannose beta1, 2N-acetylglucosaminyltransferase", - "qualitative or quantitative defects of protein O-mannosyltransferase 1", - "qualitative or quantitative defects of protein O-mannosyltransferase 2", - "disorder of protein O-glycosylation", - "disorder of O-mannosylglycan synthesis", - "muscular dystrophy-dystroglycanopathy", - "qualitative or quantitative defects of alpha-dystroglycan", - 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source", - "abnormality of anatomical entity physiology", - "abnormality of nervous system physiology", - "abnormal anatomical entity", - "abnormal nervous system", - "decreased biological_process", - "decreased reflex", - "abnormal response to stimulus", - "abnormal biological_process", - "abnormal behavior", - "abnormal response to external stimulus", - "abnormal voluntary musculoskeletal movement", - "abnormal musculoskeletal movement", - "decreased qualitatively biological_process", - "decreased qualitatively response to stimulus", + "specifically dependent continuant", + "Abnormal muscle physiology (HPO)", + "entity", + "anatomical entity", + "muscle structure", + "organ", + "muscle organ", + "musculature of body", + "musculature", "abnormal anatomical entity", - "abnormal voluntary movement behavior", - "abnormal behavior process", - "abnormal voluntary movement behavior", - "changed biological_process rate", - "abnormal behavior process", + "Muscle weakness (HPO)", + "Abnormality of the musculature (HPO)", "abnormality of anatomical entity physiology", + "phenotype by ontology source", + "abnormal anatomical entity", + "anatomical system", + "multicellular organism", + "organ system subdivision", ], - "object_label": "Hyporeflexia (HPO)", - "evidence_count": 4, + "evidence_count": 2, + "grouping_key": "MONDO:0008050🍪🍪biolink:has_phenotype🍪HP:0002460", }, { - "id": "uuid:840c1951-5d8c-11ee-9b27-2b20ed86a9d9", - "original_subject": "OMIM:613530", + "id": "uuid:c9c8bf32-7529-11ee-b012-cbd37f5c3759", + "original_subject": "OMIM:160500", "predicate": "biolink:has_phenotype", "category": "biolink:DiseaseToPhenotypicFeatureAssociation", "aggregator_knowledge_source": ["infores:monarchinitiative"], "primary_knowledge_source": "infores:hpo-annotations", "provided_by": "hpoa_disease_to_phenotype_edges", - "publications": ["OMIM:613530"], - "has_evidence": ["ECO:0000304"], - "subject": "MONDO:0013297", - "object": "HP:0001265", - "subject_namespace": "MONDO", + "publications": ["OMIM:160500"], + "has_evidence": ["ECO:0000501"], + "subject": "MONDO:0008050", + "object": "HP:0003805", + "subject_label": "MYH7-related skeletal myopathy", "subject_category": "biolink:Disease", + "subject_namespace": "MONDO", "subject_closure": [ - "MONDO:0000001", - "MONDO:0016971", - "MONDO:0000429", + "BFO:0000002", + "MONDO:0016195", + "MONDO:0005336", + "MONDO:0018949", "MONDO:0005071", + "MONDO:0008050", + "BFO:0000016", + "MONDO:0016139", + "OGMS:0000031", + "MONDO:0003847", + "BFO:0000001", "MONDO:0020121", - "MONDO:0700223", - "BFO:0000002", + "MONDO:0019952", "BFO:0000017", "BFO:0000020", - "MONDO:0016106", - "BFO:0000016", "MONDO:0020120", "MONDO:0019056", - "MONDO:0015151", + "MONDO:0000001", + "MONDO:0700223", "MONDO:0700096", - "MONDO:0005336", "MONDO:0002081", - "MONDO:0000426", - "OGMS:0000031", - "MONDO:0003847", "MONDO:0003939", - "BFO:0000001", - "MONDO:0013297", + "MONDO:0002320", ], "subject_closure_label": [ - "entity", - "continuant", + "muscular dystrophy", + "human disease", + "musculoskeletal system disorder", + "disease", + "muscle tissue disorder", + "congenital nervous system disorder", + "hereditary skeletal muscle disorder", + "MYH7-related skeletal myopathy", "disposition", - "realizable entity", - "specifically dependent continuant", + "qualitative or quantitative protein defects in neuromuscular diseases", + "distal myopathy", "disease", - "autosomal dominant disease", - "autosomal genetic disease", - "musculoskeletal system disorder", + "continuant", + "qualitative or quantitative defects of beta-myosin heavy chain (MYH7)", + "myopathy", "hereditary disease", - "muscle tissue disorder", "nervous system disorder", - "myopathy", - "autosomal dominant limb-girdle muscular dystrophy type 1H", - "muscular dystrophy, limb-girdle, autosomal dominant", - "progressive muscular dystrophy", - "limb-girdle muscular dystrophy", - "neuromuscular disease", + "congenital myopathy", + "realizable entity", + "specifically dependent continuant", "skeletal muscle disorder", - "muscular dystrophy", - "human disease", - "hereditary skeletal muscle disorder", - "disease", + "neuromuscular disease", + "entity", ], - "subject_label": "autosomal dominant limb-girdle muscular dystrophy type 1H", - "object_namespace": "HP", + "object_label": "Rimmed vacuoles (HPO)", "object_category": "biolink:PhenotypicFeature", + "object_namespace": "HP", "object_closure": [ + "BFO:0000002", + "BFO:0000020", + "UPHENO:0076692", + "BFO:0000001", + "BFO:0000004", + "CL:0000255", + "UBERON:0014892", + "UBERON:0002036", "HP:0000001", - "UPHENO:0082875", - "UPHENO:0075696", - "UPHENO:0078622", - "UPHENO:0049586", - "UPHENO:0080377", + "HP:0004303", "UPHENO:0001001", - "UPHENO:0052915", - "UPHENO:0049622", - "UPHENO:0080585", - "HP:0001265", - "HP:0100022", - "UPHENO:0001005", - "HP:0031826", "UPHENO:0001002", "HP:0000118", - "BFO:0000002", - "UPHENO:0052178", - "BFO:0000020", - "UPHENO:0002433", - "UPHENO:0050613", - "UPHENO:0005625", - "UPHENO:0050079", - "UPHENO:0005433", - "UPHENO:0002332", - "UPHENO:0050606", - "HP:0001315", - "HP:0000707", "UPHENO:0001003", - "UPHENO:0002536", - "HP:0000708", - "UPHENO:0079826", - "UPHENO:0004523", - "HP:0011446", - "UPHENO:0079833", - "UPHENO:0049587", - "BFO:0000001", + "UPHENO:0076710", "PATO:0000001", - "HP:0012638", "BFO:0000001", - "BFO:0000003", - "BFO:0000002", - "BFO:0000015", - "BFO:0000004", - "GO:0008150", "BFO:0000040", + "UBERON:0000467", + "CL:0000000", + "UBERON:0000468", + "UBERON:0011216", + "CL:0000548", + "UBERON:0001134", + "HP:0003011", + "UPHENO:0002536", + "HP:0003805", + "UBERON:0005090", + "UBERON:0018254", + "UBERON:0004120", + "UBERON:0000479", + "CL:0000003", + "UBERON:0001630", + "UBERON:0002385", + "CL:0000188", + "UPHENO:0001005", + "HP:0011805", + "HP:0025354", + "UPHENO:0002816", + "UPHENO:0081581", + "HP:0033127", + "BFO:0000002", "UBERON:0001062", - "GO:0050896", - "GO:0032501", "UBERON:0000465", - "GO:0009605", - "GO:0050879", - "GO:0007610", - "GO:0003008", + "RO:0002577", "UBERON:0000061", - "GO:0060004", - "GO:0050881", - "NBO:0000313", - "GO:0050877", "UBERON:0010000", - "UBERON:0000467", - "GO:0050882", - "NBO:0000338", - "GO:0050905", - "UBERON:0000468", - "UBERON:0001016", - "NBO:0000403", - "NBO:0000001", - "NBO:0000388", - "NBO:0000389", + "UBERON:0000062", + "UBERON:0000383", + "UBERON:0001015", + "CL:0002371", ], "object_closure_label": [ - "entity", - "entity", - "continuant", - "continuant", - "independent continuant", - "specifically dependent continuant", - "material entity", "All (HPO)", + "Abnormal muscle fiber morphology (HPO)", + "Phenotypic abnormality", "Phenotypic abnormality (HPO)", - "Abnormality of the nervous system (HPO)", - "Behavioral abnormality (HPO)", - "Hyporeflexia (HPO)", - "Reduced tendon reflexes (HPO)", - "Abnormality of higher mental function (HPO)", - "Abnormal nervous system physiology (HPO)", - "Abnormal reflex (HPO)", - "Abnormality of movement (HPO)", + "Abnormal cellular phenotype (HPO)", + "abnormal musculature", + "abnormal multicellular organism morphology", + "Abnormality of the musculoskeletal system (HPO)", "quality", - "anatomical structure", + "independent continuant", "material anatomical entity", - "anatomical system", - "multicellular organism", - "nervous system", - "anatomical entity", + "system", "multicellular anatomical structure", "phenotype", - "Phenotypic abnormality", - "phenotype by ontology source", "abnormal phenotype by ontology source", - "abnormality of anatomical entity physiology", - "abnormality of nervous system physiology", - "abnormal anatomical entity", - "abnormal nervous system", - "decreased biological_process", - "decreased reflex", - "abnormal response to stimulus", - "abnormal biological_process", - "abnormal behavior", - "abnormal response to external stimulus", - "abnormal voluntary musculoskeletal movement", - "abnormal musculoskeletal movement", - "decreased qualitatively biological_process", - "decreased qualitatively response to stimulus", + "Abnormal skeletal muscle morphology (HPO)", + "phenotype by ontology source", + "tissue", + "animal cell", + "skeletal muscle tissue", + "cell of skeletal muscle", + "continuant", + "specifically dependent continuant", + "abnormal muscle organ morphology", + "Rimmed vacuoles (HPO)", + "entity", + "anatomical entity", + "anatomical structure", + "muscle structure", + "skeletal musculature", + "mesoderm-derived structure", + "organ", + "native cell", + "muscle organ", + "muscle tissue", + "musculature of body", + "musculature", + "somatic cell", + "Abnormality of the musculature (HPO)", "abnormal anatomical entity", - "abnormal voluntary movement behavior", - "abnormal behavior process", - "abnormal voluntary movement behavior", - "changed biological_process rate", - "abnormal behavior process", - "abnormality of anatomical entity physiology", + "abnormal anatomical entity morphology", + "entity", + "continuant", + "material entity", + "anatomical system", + "cell", + "multicellular organism", + "organ system subdivision", + "eukaryotic cell", + "skeletal muscle organ", + "striated muscle tissue", ], - "object_label": "Hyporeflexia (HPO)", - "evidence_count": 4, + "evidence_count": 2, + "grouping_key": "MONDO:0008050🍪🍪biolink:has_phenotype🍪HP:0003805", }, ], }, diff --git a/backend/tests/fixtures/association_response.py b/backend/tests/fixtures/association_response.py index c1f1bf61a..e36c7afcd 100644 --- a/backend/tests/fixtures/association_response.py +++ b/backend/tests/fixtures/association_response.py @@ -5,7 +5,7 @@ def association_response(): return { "responseHeader": { - "QTime": 0, + "QTime": 1, "params": { "mm": "100%", "q": "*:*", @@ -18,3784 +18,4218 @@ def association_response(): }, }, "response": { - "num_found": 4835, + "num_found": 4838, "start": 0, "docs": [ { - "id": "uuid:8a89d08e-5d8c-11ee-9b27-2b20ed86a9d9", - "original_subject": "OMIM:602541", + "id": "uuid:c9c8bf2f-7529-11ee-b012-cbd37f5c3759", + "original_subject": "OMIM:160500", "predicate": "biolink:has_phenotype", "category": "biolink:DiseaseToPhenotypicFeatureAssociation", "aggregator_knowledge_source": ["infores:monarchinitiative"], "primary_knowledge_source": "infores:hpo-annotations", "provided_by": "hpoa_disease_to_phenotype_edges", - "publications": ["OMIM:602541"], - "has_evidence": ["ECO:0000304"], - "subject": "MONDO:0011246", - "object": "HP:0008064", - "subject_namespace": "MONDO", + "publications": ["PMID:17548557"], + "frequency_qualifier": "HP:0040280", + "has_evidence": ["ECO:0000269"], + "subject": "MONDO:0008050", + "object": "HP:0011399", + "subject_label": "MYH7-related skeletal myopathy", "subject_category": "biolink:Disease", + "subject_namespace": "MONDO", "subject_closure": [ - "MONDO:0000001", + "BFO:0000002", + "MONDO:0016195", + "MONDO:0005336", + "MONDO:0018949", "MONDO:0005071", + "MONDO:0008050", + "BFO:0000016", + "MONDO:0016139", + "OGMS:0000031", + "MONDO:0003847", + "BFO:0000001", "MONDO:0020121", - "MONDO:0700223", - "BFO:0000002", - "MONDO:0018117", + "MONDO:0019952", "BFO:0000017", "BFO:0000020", - "MONDO:0002525", - "BFO:0000016", "MONDO:0020120", "MONDO:0019056", + "MONDO:0000001", + "MONDO:0700223", "MONDO:0700096", - "MONDO:0005336", "MONDO:0002081", - "OGMS:0000031", - "MONDO:0003847", "MONDO:0003939", - "BFO:0000001", "MONDO:0002320", - "MONDO:0019052", - "MONDO:0005066", - "MONDO:0019950", - "MONDO:0011246", ], "subject_closure_label": [ - "entity", - "continuant", - "disposition", - "realizable entity", - "specifically dependent continuant", - "disease", + "muscular dystrophy", + "human disease", "musculoskeletal system disorder", + "disease", + "muscle tissue disorder", "congenital nervous system disorder", - "inherited lipid metabolism disorder", + "hereditary skeletal muscle disorder", + "MYH7-related skeletal myopathy", + "disposition", + "qualitative or quantitative protein defects in neuromuscular diseases", + "distal myopathy", + "disease", + "continuant", + "qualitative or quantitative defects of beta-myosin heavy chain (MYH7)", + "myopathy", "hereditary disease", - "muscle tissue disorder", - "metabolic disease", "nervous system disorder", - "myopathy", - "megaconial type congenital muscular dystrophy", - "disorder of phospholipids, sphingolipids and fatty acids biosynthesis", - "inborn errors of metabolism", - "neuromuscular disease", - "congenital muscular dystrophy", + "congenital myopathy", + "realizable entity", + "specifically dependent continuant", "skeletal muscle disorder", - "muscular dystrophy", - "human disease", - "hereditary skeletal muscle disorder", - "disease", + "neuromuscular disease", + "entity", ], - "subject_label": "megaconial type congenital muscular dystrophy", - "object_namespace": "HP", + "object_label": "Tibialis atrophy (HPO)", "object_category": "biolink:PhenotypicFeature", + "object_namespace": "HP", "object_closure": [ - "HP:0000001", - "UPHENO:0047821", - "UPHENO:0075696", - "UPHENO:0001001", - "UPHENO:0081431", - "UPHENO:0003811", - "UPHENO:0065599", - "UPHENO:0048320", + "UPHENO:0014121", + "HP:0002814", + "UPHENO:0068971", "UPHENO:0001005", - "HP:0001072", + "HP:0009127", + "UPHENO:0014120", + "UPHENO:0075195", + "HP:0030236", + "UPHENO:0020584", + "UPHENO:0076692", + "UPHENO:0003070", + "PATO:0000001", + "UPHENO:0012541", + "BFO:0000004", + "UBERON:0004708", + "UBERON:0000154", + "UBERON:0014892", + "UBERON:0006058", + "UBERON:0002529", + "UBERON:0006067", + "HP:0000001", + "UPHENO:0002644", + "UPHENO:0013936", + "HP:0003202", + "UPHENO:0075952", "UPHENO:0001002", "HP:0000118", - "BFO:0000002", - "HP:0011368", - "HP:0011121", - "UPHENO:0076739", - "BFO:0000020", - "HP:0008064", - "UPHENO:0075195", - "UPHENO:0002635", "UPHENO:0015280", - "UPHENO:0001072", - "UPHENO:0081581", "UPHENO:0001003", - "UPHENO:0002536", - "UPHENO:0047979", - "UPHENO:0020584", - "UPHENO:0076692", + "UPHENO:0076710", "BFO:0000001", - "HP:0000951", - "PATO:0000001", - "HP:0001574", "BFO:0000001", - "BFO:0000003", - "BFO:0000002", - "BFO:0000015", - "BFO:0000004", - "GO:0008150", "BFO:0000040", - "UBERON:0001062", - "GO:0009987", - "GO:0032501", - "GO:0032502", - "PR:000050567", - "UBERON:0000465", - "GO:0048869", - "GO:0031424", - "GO:0048856", - "UBERON:0002416", - "UBERON:0002199", - "UBERON:0002097", - "UBERON:0000061", - "GO:0030154", - "GO:0009888", - "GO:0048513", - "UBERON:0004121", "UBERON:0010000", "UBERON:0000467", - "GO:0030855", - "GO:0060429", - "GO:0008544", - "GO:0043588", - "UBERON:0000062", "UBERON:0000468", "UBERON:0011216", - "GO:0009913", - "GO:0030216", + "UBERON:0010709", + "UBERON:0000366", + "UBERON:0003661", + "UBERON:0010890", + "UBERON:0010538", + "UBERON:0004466", + "UBERON:0004256", + "UBERON:0003823", + "UPHENO:0075696", + "HP:0002981", + "HP:0003797", + "UPHENO:0014111", + "HP:0001430", + "BFO:0000002", + "HP:0008944", + "BFO:0000020", + "HP:0003011", + "UPHENO:0002536", + "HP:0001437", + "UPHENO:0078056", + "HP:0040064", + "BFO:0000002", + "PR:000050567", + "UBERON:0002101", + "UBERON:0004709", + "UBERON:0005090", + "UBERON:0018254", + "UBERON:0002103", + "UBERON:0010707", + "UBERON:0001630", + "UBERON:0000026", + "UBERON:0010758", + "UBERON:0007271", + "UBERON:0014792", + "UBERON:0004482", + "UBERON:0001383", + "UBERON:0008784", + "UBERON:0002471", + "HP:0007210", + "UPHENO:0001001", + "UPHENO:0075777", + "HP:0011805", + "HP:0003693", + "UPHENO:0002816", + "HP:0011399", + "UPHENO:0081581", + "HP:0033127", + "UPHENO:0019778", + "UPHENO:0002647", + "UPHENO:0013920", + "UPHENO:0002830", + "UBERON:0001062", + "UBERON:0000465", + "RO:0002577", + "UBERON:0000061", + "UBERON:0015212", + "UBERON:0000475", + "UBERON:0000062", + "UBERON:0000383", + "UBERON:0001015", + "UBERON:0000978", + "UBERON:0007270", + "UBERON:0004480", + "UBERON:0003663", + "UBERON:0014795", + "UBERON:0008230", ], "object_closure_label": [ - "entity", - "entity", - "continuant", - "continuant", - "independent continuant", - "specifically dependent continuant", - "material entity", "All (HPO)", + "abnormal musculature of lower limb", + "Abnormality of the lower limb (HPO)", + "decreased size of the anatomical entity", + "Phenotypic abnormality", "Phenotypic abnormality (HPO)", - "Abnormality of the skin (HPO)", - "Thickened skin (HPO)", - "Abnormality of the integument (HPO)", - "Ichthyosis (HPO)", - "Abnormality of skin morphology (HPO)", - "Epidermal thickening (HPO)", + "Distal amyotrophy (HPO)", + "abnormal musculature", + "Tibialis atrophy (HPO)", + "abnormal multicellular organism morphology", + "Abnormality of the musculoskeletal system (HPO)", + "abnormal musculature of limb", + "independent continuant", + "material anatomical entity", + "system", + "paired limb/fin", + "lateral structure", + "pelvic complex", + "appendage musculature", + "musculature of pelvic complex", + "musculature of leg", + "hindlimb zeugopod muscle", + "hindlimb zeugopod", + "musculature of limb atrophy", + "Limb-girdle muscle atrophy (HPO)", + "skeletal musculature atrophy", + "abnormal hindlimb zeugopod muscle", + "Abnormal skeletal muscle morphology (HPO)", + "abnormal anatomical entity morphology in the independent continuant", + "phenotype by ontology source", + "Abnormality of muscle size (HPO)", + "Abnormality of the musculature of the lower limbs (HPO)", + "tibialis atrophy", + "Abnormality of limbs (HPO)", "quality", + "decreased size of the anatomical entity in the independent continuant", + "continuant", "protein-containing material entity", - "anatomical structure", - "organ", - "material anatomical entity", - "anatomical system", - "multicellular organism", - "anatomical entity", - "skin of body", - "integument", - "integumental system", - "ectoderm-derived structure", - "multicellular anatomical structure", - "organ system subdivision", + "hindlimb", + "appendage girdle complex", + "appendage", + "subdivision of organism along appendicular axis", + "flexor muscle", + "limb muscle", + "pelvic complex muscle", + "paired limb/fin segment", + "musculature of lower limb", + "muscle of leg", + "lower limb segment", + "zeugopod", + "Lower limb amyotrophy (HPO)", "phenotype", - "Phenotypic abnormality", - "phenotype by ontology source", "abnormal phenotype by ontology source", - "increased size of the anatomical entity", - "abnormal anatomical entity", - "abnormal integument", - "abnormal skin of body", - "abnormal anatomical entity morphology in the independent continuant", - "abnormal anatomical entity morphology", - "increased thickness of the anatomical entity", - "increased thickness of the skin of body", - "increased thickness of the anatomical entity in independent continuant", - "increased size of the anatomical entity in independent continuant", + "Abnormality of the musculature of the limbs (HPO)", + "musculature of lower limb atrophy", "abnormal size of anatomical entity", + "abnormal muscle organ morphology", + "abnormal muscle organ morphology", + "entity", + "anatomical entity", + "anatomical structure", + "muscle structure", + "skeletal musculature", + "organism subdivision", + "organ", + "muscle organ", + "musculature of body", + "musculature", + "leg", + "pelvic appendage musculature", + "musculature of limb", + "hindlimb muscle", + "pelvic appendage muscle", + "tibialis", + "abnormal anatomical entity", + "Abnormality of the calf (HPO)", + "anatomical entity atrophy", + "Skeletal muscle atrophy (HPO)", + "abnormal hindlimb zeugopod", + "Abnormality of the calf musculature (HPO)", + "continuant", + "Distal lower limb amyotrophy (HPO)", + "specifically dependent continuant", + "Abnormality of the musculature (HPO)", "abnormal anatomical entity", "abnormal anatomical entity morphology", - "abnormal skin of body morphology", - "abnormal skin of body morphology in the independent continuant", - "abnormal multicellular organism morphology", + "abnormal anatomical entity morphology", + "abnormal leg", + "entity", + "muscle organ atrophy", + "abnormal limb", + "material entity", + "limb", + "pelvic appendage", + "multicellular anatomical structure", + "anatomical system", + "multicellular organism", + "organ system subdivision", + "posterior region of body", + "skeletal muscle organ", + "multi-limb segment region", + "limb segment", + "musculature of hindlimb zeugopod", ], - "object_label": "Ichthyosis (HPO)", - "evidence_count": 4, + "frequency_qualifier_label": "Obligate (HPO)", + "frequency_qualifier_category": "biolink:PhenotypicFeature", + "frequency_qualifier_namespace": "HP", + "frequency_qualifier_closure": ["HP:0000001", "HP:0040280", "HP:0040279"], + "frequency_qualifier_closure_label": ["All (HPO)", "Obligate (HPO)", "Frequency (HPO)"], + "evidence_count": 2, + "grouping_key": "MONDO:0008050🍪🍪biolink:has_phenotype🍪HP:0011399", }, { - "id": "uuid:898aa71d-5d8c-11ee-9b27-2b20ed86a9d9", - "original_subject": "OMIM:609115", + "id": "uuid:c9c8bf30-7529-11ee-b012-cbd37f5c3759", + "original_subject": "OMIM:160500", "predicate": "biolink:has_phenotype", "category": "biolink:DiseaseToPhenotypicFeatureAssociation", "aggregator_knowledge_source": ["infores:monarchinitiative"], "primary_knowledge_source": "infores:hpo-annotations", "provided_by": "hpoa_disease_to_phenotype_edges", - "publications": ["OMIM:609115"], - "has_evidence": ["ECO:0000501"], - "subject": "MONDO:0012193", - "object": "HP:0008116", - "subject_namespace": "MONDO", + "publications": ["PMID:17548557"], + "frequency_qualifier": "HP:0040280", + "has_evidence": ["ECO:0000269"], + "subject": "MONDO:0008050", + "object": "HP:0031295", + "subject_label": "MYH7-related skeletal myopathy", "subject_category": "biolink:Disease", + "subject_namespace": "MONDO", "subject_closure": [ - "MONDO:0000001", - "MONDO:0016971", - "MONDO:0000429", + "BFO:0000002", + "MONDO:0016195", + "MONDO:0005336", + "MONDO:0018949", "MONDO:0005071", + "MONDO:0008050", + "BFO:0000016", + "MONDO:0016139", + "OGMS:0000031", + "MONDO:0003847", + "BFO:0000001", "MONDO:0020121", - "MONDO:0700223", - "BFO:0000002", + "MONDO:0019952", "BFO:0000017", "BFO:0000020", - "MONDO:0016106", - "BFO:0000016", "MONDO:0020120", "MONDO:0019056", - "MONDO:0015151", + "MONDO:0000001", + "MONDO:0700223", "MONDO:0700096", - "MONDO:0005336", "MONDO:0002081", - "MONDO:0012193", - "MONDO:0000426", - "OGMS:0000031", - "MONDO:0003847", "MONDO:0003939", - "BFO:0000001", + "MONDO:0002320", ], "subject_closure_label": [ - "entity", - "continuant", + "muscular dystrophy", + "human disease", + "musculoskeletal system disorder", + "disease", + "muscle tissue disorder", + "congenital nervous system disorder", + "hereditary skeletal muscle disorder", + "MYH7-related skeletal myopathy", "disposition", - "realizable entity", - "specifically dependent continuant", + "qualitative or quantitative protein defects in neuromuscular diseases", + "distal myopathy", "disease", - "autosomal dominant disease", - "autosomal genetic disease", - "musculoskeletal system disorder", + "continuant", + "qualitative or quantitative defects of beta-myosin heavy chain (MYH7)", + "myopathy", "hereditary disease", - "muscle tissue disorder", "nervous system disorder", - "myopathy", - "autosomal dominant limb-girdle muscular dystrophy type 1G", - "muscular dystrophy, limb-girdle, autosomal dominant", - "progressive muscular dystrophy", - "limb-girdle muscular dystrophy", - "neuromuscular disease", + "congenital myopathy", + "realizable entity", + "specifically dependent continuant", "skeletal muscle disorder", - "muscular dystrophy", - "human disease", - "hereditary skeletal muscle disorder", - "disease", + "neuromuscular disease", + "entity", ], - "subject_label": "autosomal dominant limb-girdle muscular dystrophy type 1G", - "object_namespace": "HP", + "object_label": "Left atrial enlargement (HPO)", "object_category": "biolink:PhenotypicFeature", + "object_namespace": "HP", "object_closure": [ - "HP:0000001", - "UPHENO:0002644", - "HP:0008116", - "HP:0002814", - "UPHENO:0001001", - "HP:0001436", "UPHENO:0001005", - "HP:0009127", - "HP:0011805", - "UPHENO:0001002", - "HP:0000118", "BFO:0000002", - "UPHENO:0002653", + "UPHENO:0075195", + "UPHENO:0020584", + "UPHENO:0076692", + "BFO:0000004", + "UBERON:0004535", + "UBERON:0011676", + "UBERON:0013701", + "UBERON:0002081", + "UBERON:0000915", + "UBERON:0002100", + "UBERON:0005181", + "UBERON:0002075", + "UBERON:0015228", + "HP:0000001", + "UPHENO:0019897", + "HP:0030680", + "HP:0000118", + "HP:0001627", "BFO:0000020", - "HP:0003011", - "UPHENO:0002816", - "UPHENO:0081581", - "HP:0033127", + "UPHENO:0019919", + "UPHENO:0076776", + "UPHENO:0015280", + "UPHENO:0001020", "UPHENO:0001003", - "UPHENO:0002536", - "HP:0001437", - "UPHENO:0076692", - "UPHENO:0003070", - "UPHENO:0002647", - "UPHENO:0076710", - "HP:0040064", "BFO:0000001", "PATO:0000001", - "UPHENO:0002830", "BFO:0000001", - "BFO:0000002", - "BFO:0000004", "BFO:0000040", - "UBERON:0001062", + "UBERON:0000467", + "UBERON:0000468", + "UBERON:0000064", + "UBERON:0002079", + "UPHENO:0075696", + "UPHENO:0015303", + "HP:0001626", + "UPHENO:0080362", + "UPHENO:0065599", + "HP:0031295", + "UPHENO:0002536", + "UPHENO:0076810", "PR:000050567", "UBERON:0000465", + "UBERON:0004120", + "UBERON:0035553", + "UBERON:0000948", + "UBERON:0001009", + "UBERON:0004151", + "UBERON:0009569", + "UBERON:0013702", + "UBERON:0005177", + "UBERON:0003103", + "UBERON:0015410", + "UPHENO:0001001", + "UPHENO:0001002", + "UPHENO:0015324", + "HP:0025579", + "UPHENO:0001072", + "UPHENO:0081581", + "HP:0005120", + "UPHENO:0015329", + "BFO:0000002", + "UBERON:0001062", "RO:0002577", - "UBERON:0004708", "UBERON:0000061", - "UBERON:0002101", - "UBERON:0004709", "UBERON:0015212", + "UBERON:0010314", "UBERON:0010000", - "UBERON:0000467", - "UBERON:0005090", - "UBERON:0002103", - "UBERON:0010707", "UBERON:0000475", "UBERON:0000062", - "UBERON:0000468", - "UBERON:0011216", - "UBERON:0001630", - "UBERON:0010709", - "UBERON:0000154", - 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musculature of the limbs (HPO)", - "Abnormal skeletal muscle morphology (HPO)", - "Abnormality of the musculoskeletal system (HPO)", - "Abnormality of limbs (HPO)", + "abnormal anatomical entity morphology in the heart", + "Abnormal left atrium morphology (HPO)", + "increased size of the anatomical entity", + "abnormal multicellular organism morphology", + "Abnormal cardiac atrium morphology (HPO)", "quality", - "protein-containing material entity", + "independent continuant", "system", - "appendage", - "anatomical structure", - "organ", - "posterior region of body", - "musculature of body", - "material anatomical entity", - "anatomical system", - "multicellular organism", - "organism subdivision", - "leg", - "musculature", - "anatomical entity", - "muscle organ", - "limb", - "hindlimb", - "pes", - "autopod region", - "limb segment", - "musculature of limb", - "musculature of lower limb", - "musculature of pes", - "paired limb/fin", - "pelvic appendage", - "muscle structure", - "multi-limb segment region", - "pelvic appendage musculature", - "appendage musculature", - "lower limb segment", - "multicellular anatomical structure", - "paired limb/fin segment", - "appendage girdle complex", - "pelvic complex", - "subdivision of organism along appendicular axis", - "organ system subdivision", - "musculature of pelvic complex", + "cardiovascular system", "lateral structure", - "phenotype", + "structure with developmental contribution from neural crest", + "multicellular anatomical structure", + "left cardiac atrium", + "Abnormality of the cardiovascular system (HPO)", "Phenotypic abnormality", + "Abnormal heart morphology (HPO)", + "specifically dependent continuant", + "abnormal left cardiac atrium morphology", + "abnormal cardiovascular system morphology", + "abnormal anatomical entity morphology in the independent continuant", + "increased size of the left cardiac atrium", "phenotype by ontology source", + "abnormal heart morphology", + "protein-containing material entity", + "material anatomical entity", + "left cardiac chamber", + "heart", + "subdivision of trunk", + "body proper", + "trunk region element", + "compound organ", + "heart plus pericardium", + "phenotype", "abnormal phenotype by ontology source", + "continuant", + "abnormal size of anatomical entity", + "entity", + "anatomical entity", + "anatomical structure", + "mesoderm-derived structure", + "organism subdivision", + "organ", + "circulatory system", + "cardiac chamber", + "thoracic cavity element", + "primary circulatory organ", + "abnormal anatomical entity", + "abnormal cardiac atrium morphology in the heart", + "Abnormality of cardiovascular system morphology (HPO)", + "Left atrial enlargement (HPO)", "abnormal anatomical entity", - "abnormal musculature of lower limb", - "abnormal musculature of limb", - "abnormal musculature of pes", - "abnormal musculature", - "abnormal limb", - "abnormal leg", "abnormal anatomical entity morphology", - "abnormal muscle organ morphology", - "abnormal multicellular organism morphology", + "abnormal anatomical entity morphology", + "entity", + "abnormal cardiac atrium morphology in the independent continuant", + "continuant", + "material entity", + "anatomical system", + "multicellular organism", + "organ part", + "subdivision of organism along main body axis", + "main body axis", + "cardiac atrium", + "thoracic segment of trunk", + "trunk", + "thoracic segment organ", + "viscus", + "circulatory organ", ], - "object_label": "Flexion limitation of toes (HPO)", - "evidence_count": 4, + "frequency_qualifier_label": "Obligate (HPO)", + "frequency_qualifier_category": "biolink:PhenotypicFeature", + "frequency_qualifier_namespace": "HP", + "frequency_qualifier_closure": ["HP:0000001", "HP:0040280", "HP:0040279"], + "frequency_qualifier_closure_label": ["All (HPO)", "Obligate (HPO)", "Frequency (HPO)"], + "evidence_count": 2, + "grouping_key": "MONDO:0008050🍪🍪biolink:has_phenotype🍪HP:0031295", }, { - "id": 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abnormality (HPO)", - "quality", - "anatomical structure", + "Abnormality of the curvature of the vertebral column (HPO)", + "abnormal multicellular organism morphology", + "Abnormality of the musculoskeletal system (HPO)", + "Hyperlordosis (HPO)", + "abnormal postcranial axial skeleton morphology", + "independent continuant", "material anatomical entity", - "anatomical system", - "multicellular organism", - "nervous system", - "anatomical entity", "multicellular anatomical structure", - "phenotype", + "musculoskeletal system", + "abdominal segment of trunk", + "axial skeletal system", + "subdivision of vertebral column", + "postcranial axial skeletal system", + "postcranial axial skeleton", + "axial skeleton plus cranial skeleton", + "vertebral column", + "Abnormal skeletal morphology (HPO)", "Phenotypic abnormality", + "continuant", + "specifically dependent continuant", + "Abnormality of the vertebral column (HPO)", + "abnormal anatomical entity morphology in the independent continuant", + "abnormal skeletal system", "phenotype by ontology source", + "quality", + "continuant", + "subdivision of trunk", + "body proper", + "subdivision of skeletal system", + "phenotype", "abnormal phenotype by ontology source", - "abnormality of anatomical entity physiology", - "abnormality of nervous system physiology", + "Abnormal axial skeleton morphology (HPO)", + "abnormal vertebral column", + "Lumbar hyperlordosis (HPO)", + "entity", + "anatomical entity", + "anatomical structure", + "anatomical collection", + "skeleton", + "organism subdivision", + "subdivision of skeleton", + "skeletal system", + "lumbar region of vertebral column", "abnormal anatomical entity", - "abnormal nervous system", + "abnormal skeletal system morphology", + "Abnormality of the skeletal system (HPO)", "abnormal anatomical entity", - "abnormality of anatomical entity physiology", + "abnormal anatomical entity morphology", + "abnormal anatomical entity morphology", + "entity", + "material entity", + "anatomical system", + "multicellular organism", + "organ system subdivision", + "subdivision of organism along main body axis", + "dorsum", + "main body axis", + "trunk", + "lower back", ], - "object_label": "Global developmental delay (HPO)", - "evidence_count": 4, + "frequency_qualifier_label": "Obligate (HPO)", + "frequency_qualifier_category": "biolink:PhenotypicFeature", + "frequency_qualifier_namespace": "HP", + "frequency_qualifier_closure": ["HP:0000001", "HP:0040280", "HP:0040279"], + "frequency_qualifier_closure_label": ["All (HPO)", "Obligate (HPO)", "Frequency (HPO)"], + "evidence_count": 2, + "grouping_key": "MONDO:0008050🍪🍪biolink:has_phenotype🍪HP:0002938", }, { - "id": "uuid:85cb9d22-5d8c-11ee-9b27-2b20ed86a9d9", - "original_subject": "OMIM:613155", + "id": "uuid:c9c8bf38-7529-11ee-b012-cbd37f5c3759", + "original_subject": "OMIM:160500", "predicate": "biolink:has_phenotype", "category": "biolink:DiseaseToPhenotypicFeatureAssociation", 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"distal myopathy", + "disease", + "continuant", + "qualitative or quantitative defects of beta-myosin heavy chain (MYH7)", + "myopathy", "hereditary disease", - "muscle tissue disorder", - "metabolic disease", "nervous system disorder", - "myopathy", - "muscular dystrophy-dystroglycanopathy (congenital with intellectual disability), type B1", - "congenital disorder of glycosylation", - "qualitative or quantitative protein defects in neuromuscular diseases", - "qualitative or quantitative defects of protein involved in O-glycosylation of alpha-dystroglycan", - "disorder of protein O-glycosylation", - "muscular dystrophy-dystroglycanopathy", - "qualitative or quantitative defects of alpha-dystroglycan", - "inborn errors of metabolism", - "neuromuscular disease", - "congenital muscular dystrophy", + "congenital myopathy", + "realizable entity", + "specifically dependent continuant", "skeletal muscle disorder", - "muscular dystrophy", - "disorder of glycosylation", - "glycoprotein metabolism disease", - "myopathy caused by variation in POMT1", - "human disease", - "hereditary skeletal muscle disorder", - "disease", + "neuromuscular disease", + "entity", ], - "subject_label": "muscular dystrophy-dystroglycanopathy (congenital with intellectual disability), type B1", - "object_namespace": "HP", + "object_label": "Hyporeflexia (HPO)", "object_category": "biolink:PhenotypicFeature", + "object_namespace": "HP", "object_closure": [ - "HP:0000001", "UPHENO:0082875", - "UPHENO:0075696", - "UPHENO:0001001", + "UPHENO:0049622", "UPHENO:0001005", + "BFO:0000020", + "UPHENO:0050606", + "HP:0012638", + "BFO:0000015", + "BFO:0000004", + "GO:0050882", + "NBO:0000338", + "GO:0050905", + "UBERON:0001016", + "HP:0000001", + "UPHENO:0001001", + "UPHENO:0080585", + "HP:0001265", + "HP:0031826", "UPHENO:0001002", "HP:0000118", - "BFO:0000002", - "HP:0012759", - "BFO:0000020", + "UPHENO:0052178", "UPHENO:0002433", - "HP:0001263", - "UPHENO:0002332", - "HP:0000707", + "HP:0001315", 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alpha-dystroglycan", - "disorder of protein O-glycosylation", - "muscular dystrophy-dystroglycanopathy", - "qualitative or quantitative defects of alpha-dystroglycan", - "inborn errors of metabolism", - "neuromuscular disease", - "congenital muscular dystrophy", + "congenital myopathy", + "realizable entity", + "specifically dependent continuant", "skeletal muscle disorder", - "muscular dystrophy", - "disorder of glycosylation", - "glycoprotein metabolism disease", - "myopathy caused by variation in POMT2", - "human disease", - "hereditary skeletal muscle disorder", - "disease", + "neuromuscular disease", + "entity", ], - "subject_label": "muscular dystrophy-dystroglycanopathy (congenital with intellectual disability), type B2", - "object_namespace": "HP", + "object_label": "Toe extensor amyotrophy (HPO)", "object_category": "biolink:PhenotypicFeature", + "object_namespace": "HP", "object_closure": [ + "HP:0002814", + "HP:0009127", + "UPHENO:0076692", + "UPHENO:0003070", + "PATO:0000001", + "BFO:0000004", + "UBERON:0004708", + "UBERON:0000154", + "UBERON:0006058", + "UBERON:0002529", + "UBERON:0002387", "HP:0000001", - "UPHENO:0082875", - "UPHENO:0075696", - "UPHENO:0078622", - "UPHENO:0049586", - "UPHENO:0080377", + "UPHENO:0002644", "UPHENO:0001001", - "UPHENO:0052915", - "UPHENO:0049622", - "UPHENO:0080585", - "HP:0001265", - "HP:0100022", - "UPHENO:0001005", - "HP:0031826", "UPHENO:0001002", "HP:0000118", - "BFO:0000002", - "UPHENO:0052178", "BFO:0000020", - "UPHENO:0002433", - "UPHENO:0050613", - "UPHENO:0005625", - "UPHENO:0050079", - "UPHENO:0005433", - "UPHENO:0002332", - "UPHENO:0050606", - "HP:0001315", - "HP:0000707", "UPHENO:0001003", - "UPHENO:0002536", - "HP:0000708", - "UPHENO:0079826", - "UPHENO:0004523", - "HP:0011446", - "UPHENO:0079833", - "UPHENO:0049587", - "BFO:0000001", - "PATO:0000001", - "HP:0012638", + "UPHENO:0076710", + "HP:0011916", "BFO:0000001", - "BFO:0000003", - "BFO:0000002", - "BFO:0000015", - "BFO:0000004", - "GO:0008150", "BFO:0000040", "UBERON:0001062", - "GO:0050896", - "GO:0032501", - "UBERON:0000465", - "GO:0009605", - "GO:0050879", - "GO:0007610", - "GO:0003008", - "UBERON:0000061", - "GO:0060004", - "GO:0050881", - "NBO:0000313", - "GO:0050877", "UBERON:0010000", "UBERON:0000467", - "GO:0050882", - "NBO:0000338", - "GO:0050905", "UBERON:0000468", - "UBERON:0001016", - "NBO:0000403", - "NBO:0000001", - "NBO:0000388", - "NBO:0000389", + "UBERON:0011216", + "UBERON:0010709", + "UBERON:0010538", + "UBERON:0004488", + "HP:0001436", + "UPHENO:0002653", + "HP:0003011", + "UPHENO:0002536", + "HP:0001437", + "HP:0040064", + "BFO:0000002", + "PR:000050567", + "UBERON:0000465", + "UBERON:0002101", + "UBERON:0004709", + "UBERON:0005090", + "UBERON:0002103", + "UBERON:0010707", + "UBERON:0001630", + "UBERON:0000026", + "UBERON:0010758", + "UBERON:0007271", + "UBERON:0014792", + "UBERON:0004482", + "UBERON:0008784", + "UBERON:0002470", + "UPHENO:0001005", + "HP:0011805", + "BFO:0000002", + "UPHENO:0002816", + "UPHENO:0081581", + "HP:0033127", + "UPHENO:0002647", + "BFO:0000001", + "UPHENO:0002830", + "RO:0002577", + "UBERON:0000061", + "UBERON:0015212", + "UBERON:0000475", + "UBERON:0000062", + "UBERON:0000383", + "UBERON:0001015", + "UBERON:0000978", + "UBERON:0007270", + "UBERON:0004480", ], "object_closure_label": [ + "All (HPO)", + "abnormal musculature of lower limb", + "Abnormality of the lower limb (HPO)", + "Phenotypic abnormality", + "Phenotypic abnormality (HPO)", + "abnormal musculature", + "abnormal multicellular organism morphology", + "Abnormality of the musculoskeletal system (HPO)", + "abnormal musculature of limb", "entity", - "entity", - "continuant", - "continuant", "independent continuant", + "system", + "paired limb/fin", + "lateral structure", + "pelvic complex", + "appendage musculature", + "musculature of pelvic complex", + "musculature of pes", + "phenotype", + "Abnormality of the foot musculature (HPO)", + "abnormal phenotype by ontology source", + "Abnormal skeletal muscle morphology (HPO)", + "continuant", "specifically dependent continuant", + "phenotype by ontology source", + "Abnormality of the musculature of the lower limbs (HPO)", + "Abnormality of limbs (HPO)", + "quality", + "continuant", + "protein-containing material entity", + "material anatomical entity", + "hindlimb", + "appendage girdle complex", + "appendage", + "subdivision of organism along appendicular axis", + "paired limb/fin segment", + "musculature of lower limb", + "lower limb segment", + "autopod region", + "Abnormality of the musculature of the limbs (HPO)", + "abnormal muscle organ morphology", + "Toe extensor amyotrophy (HPO)", + "entity", + "anatomical structure", + "muscle structure", + "organism subdivision", + "organ", + "muscle organ", + "musculature of body", + "musculature", + "leg", + "pelvic appendage musculature", + "musculature of limb", + "abnormal musculature of pes", + "Abnormality of the musculature (HPO)", + "abnormal anatomical entity", + "abnormal anatomical entity morphology", + "abnormal leg", + "abnormal limb", "material entity", + "anatomical entity", + "limb", + "pelvic appendage", + "multicellular anatomical structure", + "anatomical system", + "multicellular organism", + "organ system subdivision", + "posterior region of body", + "multi-limb segment region", + "limb segment", + "pes", + ], + "evidence_count": 2, + "grouping_key": "MONDO:0008050🍪🍪biolink:has_phenotype🍪HP:0011916", + }, + { + "id": "uuid:c9c8bf2e-7529-11ee-b012-cbd37f5c3759", + "original_subject": "OMIM:160500", + "predicate": "biolink:has_phenotype", + "category": "biolink:DiseaseToPhenotypicFeatureAssociation", + "aggregator_knowledge_source": ["infores:monarchinitiative"], + "primary_knowledge_source": "infores:hpo-annotations", + "provided_by": "hpoa_disease_to_phenotype_edges", + "publications": ["OMIM:160500"], + "has_evidence": ["ECO:0000304"], + "subject": "MONDO:0008050", + "object": "HP:0002460", + "subject_label": "MYH7-related skeletal myopathy", + "subject_category": "biolink:Disease", + "subject_namespace": "MONDO", + "subject_closure": [ + "BFO:0000002", + "MONDO:0016195", + "MONDO:0005336", + "MONDO:0018949", + "MONDO:0005071", + "MONDO:0008050", + "BFO:0000016", + "MONDO:0016139", + "OGMS:0000031", + "MONDO:0003847", + "BFO:0000001", + "MONDO:0020121", + "MONDO:0019952", + "BFO:0000017", + "BFO:0000020", + "MONDO:0020120", + "MONDO:0019056", + "MONDO:0000001", + "MONDO:0700223", + "MONDO:0700096", + "MONDO:0002081", + "MONDO:0003939", + "MONDO:0002320", + ], + "subject_closure_label": [ + "muscular dystrophy", + "human disease", + "musculoskeletal system disorder", + "disease", + "muscle tissue disorder", + "congenital nervous system disorder", + "hereditary skeletal muscle disorder", + "MYH7-related skeletal myopathy", + "disposition", + "qualitative or quantitative protein defects in neuromuscular diseases", + "distal myopathy", + "disease", + "continuant", + "qualitative or quantitative defects of beta-myosin heavy chain (MYH7)", + "myopathy", + "hereditary disease", + "nervous system disorder", + "congenital myopathy", + "realizable entity", + "specifically dependent continuant", + "skeletal muscle disorder", + "neuromuscular disease", + "entity", + ], + "object_label": "Distal muscle weakness (HPO)", + "object_category": "biolink:PhenotypicFeature", + "object_namespace": "HP", + "object_closure": [ + "UPHENO:0082875", + "UPHENO:0002320", + "UPHENO:0001005", + "BFO:0000020", + "PATO:0000001", + "BFO:0000004", + "UBERON:0000061", + "HP:0000001", + "UPHENO:0001001", + "HP:0000118", + "BFO:0000001", + "UBERON:0000467", + "UBERON:0000468", + "UBERON:0011216", + "UPHENO:0075696", + "HP:0001324", + "HP:0003011", + "UPHENO:0002332", + "UPHENO:0001003", + "UPHENO:0002536", + "HP:0002460", + "HP:0011804", + "BFO:0000002", + "BFO:0000040", + "UBERON:0005090", + "UBERON:0001630", + "UPHENO:0001002", + "BFO:0000002", + "UPHENO:0080555", + "UPHENO:0002816", + "UPHENO:0080556", + "HP:0033127", + "BFO:0000001", + "UBERON:0001062", + "UBERON:0000465", + "UBERON:0010000", + "UBERON:0000062", + "UBERON:0000383", + "UBERON:0001015", + ], + "object_closure_label": [ "All (HPO)", + "abnormality of muscle organ physiology", "Phenotypic abnormality (HPO)", - "Abnormality of the nervous system (HPO)", - "Behavioral abnormality (HPO)", - "Hyporeflexia (HPO)", - "Reduced tendon reflexes (HPO)", - "Abnormality of higher mental function (HPO)", - "Abnormal nervous system physiology (HPO)", - "Abnormal reflex (HPO)", - "Abnormality of movement (HPO)", - "quality", - "anatomical structure", + "decreased anatomical entity strength", + "abnormal musculature", + "decreased muscle organ strength", + "Abnormality of the musculoskeletal system (HPO)", + "entity", + "independent continuant", "material anatomical entity", - "anatomical system", - "multicellular organism", - "nervous system", - "anatomical entity", + "anatomical structure", "multicellular anatomical structure", + "abnormality of anatomical entity physiology", "phenotype", "Phenotypic abnormality", - "phenotype by ontology source", + "continuant", + "Distal muscle weakness (HPO)", + "quality", + "continuant", + "material entity", "abnormal phenotype by ontology source", - "abnormality of anatomical entity physiology", - "abnormality of nervous system physiology", - "abnormal anatomical entity", - "abnormal nervous system", - "decreased biological_process", - "decreased reflex", - "abnormal response to stimulus", - "abnormal biological_process", - "abnormal behavior", - "abnormal response to external stimulus", - "abnormal voluntary musculoskeletal movement", - "abnormal musculoskeletal movement", - "decreased qualitatively biological_process", - "decreased qualitatively response to stimulus", + "specifically dependent continuant", + "Abnormal muscle physiology (HPO)", + "entity", + "anatomical entity", + "muscle structure", + "organ", + "muscle organ", + "musculature of body", + "musculature", "abnormal anatomical entity", - "abnormal voluntary movement behavior", - "abnormal behavior process", - "abnormal voluntary movement behavior", - "changed biological_process rate", - "abnormal behavior process", + "Muscle weakness (HPO)", + "Abnormality of the musculature (HPO)", "abnormality of anatomical entity physiology", + "phenotype by ontology source", + "abnormal anatomical entity", + "anatomical system", + "multicellular organism", + "organ system subdivision", ], - "object_label": "Hyporeflexia (HPO)", - "evidence_count": 4, + "evidence_count": 2, + "grouping_key": "MONDO:0008050🍪🍪biolink:has_phenotype🍪HP:0002460", }, { - "id": "uuid:840c1951-5d8c-11ee-9b27-2b20ed86a9d9", - "original_subject": "OMIM:613530", + "id": "uuid:c9c8bf32-7529-11ee-b012-cbd37f5c3759", + "original_subject": "OMIM:160500", "predicate": "biolink:has_phenotype", "category": "biolink:DiseaseToPhenotypicFeatureAssociation", "aggregator_knowledge_source": ["infores:monarchinitiative"], "primary_knowledge_source": "infores:hpo-annotations", "provided_by": "hpoa_disease_to_phenotype_edges", - "publications": ["OMIM:613530"], - "has_evidence": ["ECO:0000304"], - "subject": "MONDO:0013297", - "object": "HP:0001265", - "subject_namespace": "MONDO", + "publications": ["OMIM:160500"], + "has_evidence": ["ECO:0000501"], + "subject": "MONDO:0008050", + "object": "HP:0003805", + "subject_label": "MYH7-related skeletal myopathy", "subject_category": "biolink:Disease", + "subject_namespace": "MONDO", "subject_closure": [ - "MONDO:0000001", - "MONDO:0016971", - "MONDO:0000429", + "BFO:0000002", + "MONDO:0016195", + "MONDO:0005336", + "MONDO:0018949", "MONDO:0005071", + "MONDO:0008050", + "BFO:0000016", + "MONDO:0016139", + "OGMS:0000031", + "MONDO:0003847", + "BFO:0000001", "MONDO:0020121", - "MONDO:0700223", - "BFO:0000002", + "MONDO:0019952", "BFO:0000017", "BFO:0000020", - "MONDO:0016106", - "BFO:0000016", "MONDO:0020120", "MONDO:0019056", - "MONDO:0015151", + "MONDO:0000001", + "MONDO:0700223", "MONDO:0700096", - "MONDO:0005336", "MONDO:0002081", - "MONDO:0000426", - "OGMS:0000031", - "MONDO:0003847", "MONDO:0003939", - "BFO:0000001", - "MONDO:0013297", + "MONDO:0002320", ], "subject_closure_label": [ - "entity", - "continuant", + "muscular dystrophy", + "human disease", + "musculoskeletal system disorder", + "disease", + "muscle tissue disorder", + "congenital nervous system disorder", + "hereditary skeletal muscle disorder", + "MYH7-related skeletal myopathy", "disposition", - "realizable entity", - "specifically dependent continuant", + "qualitative or quantitative protein defects in neuromuscular diseases", + "distal myopathy", "disease", - "autosomal dominant disease", - "autosomal genetic disease", - "musculoskeletal system disorder", + "continuant", + "qualitative or quantitative defects of beta-myosin heavy chain (MYH7)", + "myopathy", "hereditary disease", - "muscle tissue disorder", "nervous system disorder", - "myopathy", - "autosomal dominant limb-girdle muscular dystrophy type 1H", - "muscular dystrophy, limb-girdle, autosomal dominant", - "progressive muscular dystrophy", - "limb-girdle muscular dystrophy", - "neuromuscular disease", + "congenital myopathy", + "realizable entity", + "specifically dependent continuant", "skeletal muscle disorder", - "muscular dystrophy", - "human disease", - "hereditary skeletal muscle disorder", - "disease", + "neuromuscular disease", + "entity", ], - "subject_label": "autosomal dominant limb-girdle muscular dystrophy type 1H", - "object_namespace": "HP", + "object_label": "Rimmed vacuoles (HPO)", "object_category": "biolink:PhenotypicFeature", + "object_namespace": "HP", "object_closure": [ + "BFO:0000002", + "BFO:0000020", + "UPHENO:0076692", + "BFO:0000001", + "BFO:0000004", + "CL:0000255", + "UBERON:0014892", + "UBERON:0002036", "HP:0000001", - "UPHENO:0082875", - "UPHENO:0075696", - "UPHENO:0078622", - "UPHENO:0049586", - "UPHENO:0080377", + "HP:0004303", "UPHENO:0001001", - "UPHENO:0052915", - "UPHENO:0049622", - "UPHENO:0080585", - "HP:0001265", - "HP:0100022", - "UPHENO:0001005", - "HP:0031826", "UPHENO:0001002", "HP:0000118", - "BFO:0000002", - "UPHENO:0052178", - "BFO:0000020", - "UPHENO:0002433", - "UPHENO:0050613", - "UPHENO:0005625", - "UPHENO:0050079", - "UPHENO:0005433", - "UPHENO:0002332", - "UPHENO:0050606", - "HP:0001315", - "HP:0000707", "UPHENO:0001003", - "UPHENO:0002536", - "HP:0000708", - "UPHENO:0079826", - "UPHENO:0004523", - "HP:0011446", - "UPHENO:0079833", - "UPHENO:0049587", - "BFO:0000001", + "UPHENO:0076710", "PATO:0000001", - "HP:0012638", "BFO:0000001", - "BFO:0000003", - "BFO:0000002", - "BFO:0000015", - "BFO:0000004", - "GO:0008150", "BFO:0000040", + "UBERON:0000467", + "CL:0000000", + "UBERON:0000468", + "UBERON:0011216", + "CL:0000548", + "UBERON:0001134", + "HP:0003011", + "UPHENO:0002536", + "HP:0003805", + "UBERON:0005090", + "UBERON:0018254", + "UBERON:0004120", + "UBERON:0000479", + "CL:0000003", + "UBERON:0001630", + "UBERON:0002385", + "CL:0000188", + "UPHENO:0001005", + "HP:0011805", + "HP:0025354", + "UPHENO:0002816", + "UPHENO:0081581", + "HP:0033127", + "BFO:0000002", "UBERON:0001062", - "GO:0050896", - "GO:0032501", "UBERON:0000465", - "GO:0009605", - "GO:0050879", - "GO:0007610", - "GO:0003008", + "RO:0002577", "UBERON:0000061", - "GO:0060004", - "GO:0050881", - "NBO:0000313", - "GO:0050877", "UBERON:0010000", - "UBERON:0000467", - "GO:0050882", - "NBO:0000338", - "GO:0050905", - "UBERON:0000468", - "UBERON:0001016", - "NBO:0000403", - "NBO:0000001", - "NBO:0000388", - "NBO:0000389", + "UBERON:0000062", + "UBERON:0000383", + "UBERON:0001015", + "CL:0002371", ], "object_closure_label": [ - "entity", - "entity", - "continuant", - "continuant", - "independent continuant", - "specifically dependent continuant", - "material entity", "All (HPO)", + "Abnormal muscle fiber morphology (HPO)", + "Phenotypic abnormality", "Phenotypic abnormality (HPO)", - "Abnormality of the nervous system (HPO)", - "Behavioral abnormality (HPO)", - "Hyporeflexia (HPO)", - "Reduced tendon reflexes (HPO)", - "Abnormality of higher mental function (HPO)", - "Abnormal nervous system physiology (HPO)", - "Abnormal reflex (HPO)", - "Abnormality of movement (HPO)", + "Abnormal cellular phenotype (HPO)", + "abnormal musculature", + "abnormal multicellular organism morphology", + "Abnormality of the musculoskeletal system (HPO)", "quality", - "anatomical structure", + "independent continuant", "material anatomical entity", - "anatomical system", - "multicellular organism", - "nervous system", - "anatomical entity", + "system", "multicellular anatomical structure", "phenotype", - "Phenotypic abnormality", - "phenotype by ontology source", "abnormal phenotype by ontology source", - "abnormality of anatomical entity physiology", - "abnormality of nervous system physiology", - "abnormal anatomical entity", - "abnormal nervous system", - "decreased biological_process", - "decreased reflex", - "abnormal response to stimulus", - "abnormal biological_process", - "abnormal behavior", - "abnormal response to external stimulus", - "abnormal voluntary musculoskeletal movement", - "abnormal musculoskeletal movement", - "decreased qualitatively biological_process", - "decreased qualitatively response to stimulus", + "Abnormal skeletal muscle morphology (HPO)", + "phenotype by ontology source", + "tissue", + "animal cell", + "skeletal muscle tissue", + "cell of skeletal muscle", + "continuant", + "specifically dependent continuant", + "abnormal muscle organ morphology", + "Rimmed vacuoles (HPO)", + "entity", + "anatomical entity", + "anatomical structure", + "muscle structure", + "skeletal musculature", + "mesoderm-derived structure", + "organ", + "native cell", + "muscle organ", + "muscle tissue", + "musculature of body", + "musculature", + "somatic cell", + "Abnormality of the musculature (HPO)", "abnormal anatomical entity", - "abnormal voluntary movement behavior", - "abnormal behavior process", - "abnormal voluntary movement behavior", - "changed biological_process rate", - "abnormal behavior process", - "abnormality of anatomical entity physiology", + "abnormal anatomical entity morphology", + "entity", + "continuant", + "material entity", + "anatomical system", + "cell", + "multicellular organism", + "organ system subdivision", + "eukaryotic cell", + "skeletal muscle organ", + "striated muscle tissue", ], - "object_label": "Hyporeflexia (HPO)", - "evidence_count": 4, + "evidence_count": 2, + "grouping_key": "MONDO:0008050🍪🍪biolink:has_phenotype🍪HP:0003805", }, ], }, diff --git a/backend/tests/fixtures/association_table.py b/backend/tests/fixtures/association_table.py index fc50030b7..327680630 100644 --- a/backend/tests/fixtures/association_table.py +++ b/backend/tests/fixtures/association_table.py @@ -9,70 +9,70 @@ def association_table(): "total": 4027, "items": [ { - "id": "uuid:89aa7b9b-5d8c-11ee-9b27-2b20ed86a9d9", + "id": "uuid:ca3946de-7529-11ee-b012-cbd37f5c3759", "category": "biolink:DiseaseToPhenotypicFeatureAssociation", "subject": "MONDO:0020793", "original_subject": "OMIM:164310", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ - "MONDO:0020158", - "MONDO:0000001", + "BFO:0000002", + "BFO:0000020", + "MONDO:0024458", + "MONDO:0005336", + "MONDO:0018949", "MONDO:0005071", + "MONDO:0003382", + "BFO:0000016", + "OGMS:0000031", + "MONDO:0003847", + "BFO:0000001", "MONDO:0025193", "MONDO:0020121", - "MONDO:0700223", - "BFO:0000002", "MONDO:0020793", "BFO:0000017", - "BFO:0000020", - "MONDO:0016106", - "MONDO:0003382", - "BFO:0000016", "MONDO:0020120", "MONDO:0019056", + "MONDO:0000462", + "MONDO:0020158", + "MONDO:0000001", + "MONDO:0700223", + "MONDO:0016106", "MONDO:0700096", - "MONDO:0024458", - "MONDO:0005336", "MONDO:0002081", - "OGMS:0000031", - "MONDO:0003847", "MONDO:0003939", "MONDO:0002022", - "BFO:0000001", - "MONDO:0000462", "MONDO:0005328", - "MONDO:0018949", ], "subject_label": "oculopharyngodistal myopathy 1", "subject_closure_label": [ - "entity", - "continuant", - "disposition", - "realizable entity", - "specifically dependent continuant", + "oculopharyngodistal myopathy", + "muscular dystrophy", + "progressive muscular dystrophy", + "human disease", + "musculoskeletal system disorder", "disease", - "eye adnexa disorder", + "muscle tissue disorder", "disorder of orbital region", - "musculoskeletal system disorder", + "hereditary skeletal muscle disorder", "eyelid disorder", - "hereditary disease", - "muscle tissue disorder", - "nervous system disorder", - "eye disorder", - "myopathy", - "progressive muscular dystrophy", + "disposition", "distal myopathy", - "neuromuscular disease", - "skeletal muscle disorder", - "muscular dystrophy", "eyelids malposition disorder", - "oculopharyngodistal myopathy 1", - "disorder of visual system", - "oculopharyngodistal myopathy", - "human disease", - "hereditary skeletal muscle disorder", "disease", + "continuant", + "specifically dependent continuant", + "disorder of visual system", + "myopathy", + "hereditary disease", + "eye adnexa disorder", + "nervous system disorder", + "oculopharyngodistal myopathy 1", + "realizable entity", + "skeletal muscle disorder", + "neuromuscular disease", + "entity", + "eye disorder", ], "subject_taxon": None, "subject_taxon_label": None, @@ -82,87 +82,87 @@ def association_table(): "object_namespace": "HP", "object_category": "biolink:PhenotypicFeature", "object_closure": [ - "HP:0000001", "UPHENO:0082875", - "UPHENO:0075696", "UPHENO:0002320", - "UPHENO:0001001", "UPHENO:0001005", - "UPHENO:0001002", - "HP:0001324", - "HP:0000118", - "BFO:0000002", "BFO:0000020", - "UPHENO:0080555", + "PATO:0000001", + "BFO:0000004", + "UBERON:0000061", + "HP:0000001", + "UPHENO:0001001", + "HP:0000118", + "BFO:0000001", + "UBERON:0000467", + "UBERON:0000468", + "UBERON:0011216", + "UPHENO:0075696", + "HP:0001324", "HP:0003011", - "UPHENO:0002816", "UPHENO:0002332", - "UPHENO:0080556", - "HP:0033127", "UPHENO:0001003", "UPHENO:0002536", "HP:0002460", - "BFO:0000001", "HP:0011804", - "PATO:0000001", - "BFO:0000001", "BFO:0000002", - "BFO:0000004", "BFO:0000040", + "UBERON:0005090", + "UBERON:0001630", + "UPHENO:0001002", + "BFO:0000002", + "UPHENO:0080555", + "UPHENO:0002816", + "UPHENO:0080556", + "HP:0033127", + "BFO:0000001", "UBERON:0001062", "UBERON:0000465", - "UBERON:0000061", "UBERON:0010000", - "UBERON:0000467", - "UBERON:0005090", "UBERON:0000062", - "UBERON:0000468", - "UBERON:0011216", - "UBERON:0001630", "UBERON:0000383", "UBERON:0001015", ], "object_label": "Distal muscle weakness (HPO)", "object_closure_label": [ - "entity", - "entity", - "continuant", - "continuant", - "independent continuant", - "specifically dependent continuant", - "material entity", "All (HPO)", + "abnormality of muscle organ physiology", "Phenotypic abnormality (HPO)", - "Muscle weakness (HPO)", - "Distal muscle weakness (HPO)", - "Abnormality of the musculature (HPO)", - "Abnormal muscle physiology (HPO)", + "decreased anatomical entity strength", + "abnormal musculature", + "decreased muscle organ strength", "Abnormality of the musculoskeletal system (HPO)", - "quality", - "anatomical structure", - "organ", - "musculature of body", + "entity", + "independent continuant", "material anatomical entity", - "anatomical system", - "multicellular organism", - "musculature", - "anatomical entity", - "muscle organ", - "muscle structure", + "anatomical structure", "multicellular anatomical structure", - "organ system subdivision", + "abnormality of anatomical entity physiology", "phenotype", "Phenotypic abnormality", - "phenotype by ontology source", + "continuant", + "Distal muscle weakness (HPO)", + "quality", + "continuant", + "material entity", "abnormal phenotype by ontology source", - "abnormality of muscle organ physiology", - "abnormality of anatomical entity physiology", - "abnormal anatomical entity", - "abnormal musculature", + "specifically dependent continuant", + "Abnormal muscle physiology (HPO)", + "entity", + "anatomical entity", + "muscle structure", + "organ", + "muscle organ", + "musculature of body", + "musculature", "abnormal anatomical entity", - "decreased anatomical entity strength", - "decreased muscle organ strength", + "Muscle weakness (HPO)", + "Abnormality of the musculature (HPO)", "abnormality of anatomical entity physiology", + "phenotype by ontology source", + "abnormal anatomical entity", + "anatomical system", + "multicellular organism", + "organ system subdivision", ], "object_taxon": None, "object_taxon_label": None, @@ -170,9 +170,10 @@ def association_table(): "aggregator_knowledge_source": ["infores:monarchinitiative"], "negated": None, "pathway": None, - "evidence_count": 6, + "evidence_count": 4, "has_evidence": ["ECO:0000269"], "has_evidence_links": [{"id": "ECO:0000269", "url": "http://purl.obolibrary.org/obo/ECO_0000269"}], + "grouping_key": "MONDO:0020793🍪🍪biolink:has_phenotype🍪HP:0002460", "provided_by": "hpoa_disease_to_phenotype_edges", "provided_by_link": { "id": "hpoa_disease_to_phenotype", @@ -189,11 +190,16 @@ def association_table(): "onset_qualifier": None, "sex_qualifier": None, "stage_qualifier": None, + "qualifiers_label": None, + "qualifiers_namespace": None, + "qualifiers_category": None, + "qualifiers_closure": [], + "qualifiers_closure_label": [], "frequency_qualifier_label": "Frequent (HPO)", "frequency_qualifier_namespace": "HP", "frequency_qualifier_category": "biolink:PhenotypicFeature", - "frequency_qualifier_closure": ["HP:0000001", "HP:0040282", "HP:0040279"], - "frequency_qualifier_closure_label": ["All (HPO)", "Frequency (HPO)", "Frequent (HPO)"], + "frequency_qualifier_closure": ["HP:0040282", "HP:0000001", "HP:0040279"], + "frequency_qualifier_closure_label": ["All (HPO)", "Frequent (HPO)", "Frequency (HPO)"], "onset_qualifier_label": None, "onset_qualifier_namespace": None, "onset_qualifier_category": None, @@ -212,70 +218,70 @@ def association_table(): "direction": "outgoing", }, { - "id": "uuid:89aa7bac-5d8c-11ee-9b27-2b20ed86a9d9", + "id": "uuid:ca3946ef-7529-11ee-b012-cbd37f5c3759", "category": "biolink:DiseaseToPhenotypicFeatureAssociation", "subject": "MONDO:0020793", "original_subject": "OMIM:164310", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ - "MONDO:0020158", - "MONDO:0000001", + "BFO:0000002", + "BFO:0000020", + "MONDO:0024458", + "MONDO:0005336", + "MONDO:0018949", "MONDO:0005071", + "MONDO:0003382", + "BFO:0000016", + "OGMS:0000031", + "MONDO:0003847", + "BFO:0000001", "MONDO:0025193", "MONDO:0020121", - "MONDO:0700223", - "BFO:0000002", "MONDO:0020793", "BFO:0000017", - "BFO:0000020", - "MONDO:0016106", - "MONDO:0003382", - "BFO:0000016", "MONDO:0020120", "MONDO:0019056", + "MONDO:0000462", + "MONDO:0020158", + "MONDO:0000001", + "MONDO:0700223", + "MONDO:0016106", "MONDO:0700096", - "MONDO:0024458", - "MONDO:0005336", "MONDO:0002081", - "OGMS:0000031", - "MONDO:0003847", "MONDO:0003939", "MONDO:0002022", - "BFO:0000001", - "MONDO:0000462", "MONDO:0005328", - "MONDO:0018949", ], "subject_label": "oculopharyngodistal myopathy 1", "subject_closure_label": [ - "entity", - "continuant", - "disposition", - "realizable entity", - "specifically dependent continuant", + "oculopharyngodistal myopathy", + "muscular dystrophy", + "progressive muscular dystrophy", + "human disease", + "musculoskeletal system disorder", "disease", - "eye adnexa disorder", + "muscle tissue disorder", "disorder of orbital region", - "musculoskeletal system disorder", + "hereditary skeletal muscle disorder", "eyelid disorder", - "hereditary disease", - "muscle tissue disorder", - "nervous system disorder", - "eye disorder", - "myopathy", - "progressive muscular dystrophy", + "disposition", "distal myopathy", - "neuromuscular disease", - "skeletal muscle disorder", - "muscular dystrophy", "eyelids malposition disorder", - "oculopharyngodistal myopathy 1", - "disorder of visual system", - "oculopharyngodistal myopathy", - "human disease", - "hereditary skeletal muscle disorder", "disease", + "continuant", + "specifically dependent continuant", + "disorder of visual system", + "myopathy", + "hereditary disease", + "eye adnexa disorder", + "nervous system disorder", + "oculopharyngodistal myopathy 1", + "realizable entity", + "skeletal muscle disorder", + "neuromuscular disease", + "entity", + "eye disorder", ], "subject_taxon": None, "subject_taxon_label": None, @@ -285,141 +291,141 @@ def association_table(): "object_namespace": "HP", "object_category": "biolink:PhenotypicFeature", "object_closure": [ - "HP:0000001", "UPHENO:0082875", - "UPHENO:0075696", - "HP:0011024", - "UPHENO:0001001", - "UPHENO:0002443", "UPHENO:0002471", "HP:0025270", - "HP:0012719", "UPHENO:0001005", - "UPHENO:0002833", - "HP:0002015", - "UPHENO:0001002", - "UPHENO:0002725", - "HP:0000118", "BFO:0000002", "BFO:0000020", - "UPHENO:0002433", - "HP:0025032", - "UPHENO:0002332", "HP:0002664", - "HP:0000707", "HP:0011793", - "UPHENO:0001003", - "UPHENO:0002536", - "UPHENO:0004523", - "BFO:0000001", "PATO:0000001", - "HP:0025031", "UPHENO:0002474", "HP:0012638", - "BFO:0000001", - "BFO:0000002", "BFO:0000004", - "BFO:0000040", - "UBERON:0001062", - "UBERON:0000465", - "RO:0002577", "UBERON:0000061", + "UBERON:0001007", + "UBERON:0001016", + "UBERON:0011676", + "UBERON:0013701", + "UBERON:0000915", + "UBERON:0001043", + "UBERON:0002100", + "UBERON:0005181", + "UBERON:0002075", + "HP:0000001", + "UPHENO:0001001", + "HP:0000118", + "UPHENO:0002433", + "UPHENO:0001003", + "BFO:0000001", + "BFO:0000001", + "BFO:0000040", "UBERON:0010000", "UBERON:0000467", - "UBERON:0000475", - "UBERON:0000062", "UBERON:0004111", "UBERON:0000468", "UBERON:0000064", - "UBERON:0001007", - "UBERON:0001016", + "UPHENO:0075696", + "HP:0011024", + "UPHENO:0002443", + "HP:0012719", + "UPHENO:0002725", + "HP:0025032", + "UPHENO:0002332", + "UPHENO:0002536", + "UPHENO:0004523", + "BFO:0000002", + "UBERON:0000465", "UBERON:0005409", - "UBERON:0011676", - "UBERON:0013701", "UBERON:0009569", "UBERON:0013702", "UBERON:0013765", "UBERON:0005177", "UBERON:0000025", - "UBERON:0013522", - "UBERON:0000915", - "UBERON:0001043", - "UBERON:0002100", - "UBERON:0005181", - "UBERON:0002075", "UBERON:0001555", "UBERON:0004921", + "UPHENO:0002833", + "HP:0002015", + "UPHENO:0001002", + "HP:0000707", + "HP:0025031", + "UBERON:0001062", + "RO:0002577", + "UBERON:0000475", + "UBERON:0000062", + "UBERON:0013522", "UBERON:0005178", "UBERON:0004908", ], "object_label": "Dysphagia (HPO)", "object_closure_label": [ - "entity", - "entity", - "continuant", - "continuant", - "independent continuant", - "specifically dependent continuant", - "material entity", "All (HPO)", + "abnormality of alimentary part of gastrointestinal system physiology", + "Abnormal esophagus physiology (HPO)", + "Functional abnormality of the gastrointestinal tract (HPO)", "Phenotypic abnormality (HPO)", "Abnormality of the nervous system (HPO)", - "Dysphagia (HPO)", - "Neoplasm (HPO)", - "Abnormality of the gastrointestinal tract (HPO)", - "Neoplasm by anatomical site (HPO)", - "Abnormal nervous system physiology (HPO)", - "Functional abnormality of the gastrointestinal tract (HPO)", - "Abnormality of the digestive system (HPO)", - "Abnormality of digestive system physiology (HPO)", - "Abnormal esophagus physiology (HPO)", - "quality", + "independent continuant", "system", - "tube", "anatomical structure", - "organ", - "organ part", - "material anatomical entity", - "anatomical system", - "multicellular organism", - "organism subdivision", - "thoracic segment of trunk", "digestive system", "nervous system", - "esophagus", - "anatomical entity", "digestive tract", - "viscus", - "trunk", - "anatomical conduit", - "upper digestive tract", "subdivision of digestive tract", - "trunk region element", - "thoracic cavity element", - "thoracic segment organ", - "alimentary part of gastrointestinal system", - "subdivision of trunk", - "multicellular anatomical structure", - "subdivision of organism along main body axis", - "subdivision of tube", - "main body axis", - "body proper", - "digestive system element", + "abnormality of anatomical entity physiology", "phenotype", + "abnormality of digestive system physiology", + "abnormal digestive system", + "Dysphagia (HPO)", "Phenotypic abnormality", - "phenotype by ontology source", - "abnormal phenotype by ontology source", - "abnormality of anatomical entity physiology", "abnormality of nervous system physiology", - "abnormality of digestive system physiology", - "abnormality of alimentary part of gastrointestinal system physiology", + "phenotype by ontology source", + "abnormal nervous system", + "quality", "abnormality of esophagus physiology", + "Abnormal nervous system physiology (HPO)", + "continuant", + "material anatomical entity", + "subdivision of trunk", + "body proper", + "digestive system element", + "trunk region element", + "tube", + "abnormal phenotype by ontology source", + "continuant", + "specifically dependent continuant", + "Neoplasm (HPO)", + "Neoplasm by anatomical site (HPO)", + "entity", + "anatomical entity", + "organism subdivision", + "organ", + "alimentary part of gastrointestinal system", + "subdivision of tube", + "thoracic cavity element", + "upper digestive tract", "abnormal anatomical entity", + "Abnormality of the gastrointestinal tract (HPO)", "abnormal alimentary part of gastrointestinal system", - "abnormal digestive system", - "abnormal nervous system", - "abnormal anatomical entity", + "Abnormality of digestive system physiology (HPO)", "abnormality of anatomical entity physiology", + "abnormal anatomical entity", + "entity", + "Abnormality of the digestive system (HPO)", + "material entity", + "multicellular anatomical structure", + "anatomical system", + "anatomical conduit", + "multicellular organism", + "organ part", + "subdivision of organism along main body axis", + "main body axis", + "thoracic segment of trunk", + "esophagus", + "trunk", + "thoracic segment organ", + "viscus", ], "object_taxon": None, "object_taxon_label": None, @@ -427,9 +433,10 @@ def association_table(): "aggregator_knowledge_source": ["infores:monarchinitiative"], "negated": None, "pathway": None, - "evidence_count": 6, + "evidence_count": 4, "has_evidence": ["ECO:0000269"], "has_evidence_links": [{"id": "ECO:0000269", "url": "http://purl.obolibrary.org/obo/ECO_0000269"}], + "grouping_key": "MONDO:0020793🍪🍪biolink:has_phenotype🍪HP:0002015", "provided_by": "hpoa_disease_to_phenotype_edges", "provided_by_link": { "id": "hpoa_disease_to_phenotype", @@ -446,11 +453,16 @@ def association_table(): "onset_qualifier": None, "sex_qualifier": None, "stage_qualifier": None, + "qualifiers_label": None, + "qualifiers_namespace": None, + "qualifiers_category": None, + "qualifiers_closure": [], + "qualifiers_closure_label": [], "frequency_qualifier_label": "Frequent (HPO)", "frequency_qualifier_namespace": "HP", "frequency_qualifier_category": "biolink:PhenotypicFeature", - "frequency_qualifier_closure": ["HP:0000001", "HP:0040282", "HP:0040279"], - "frequency_qualifier_closure_label": ["All (HPO)", "Frequency (HPO)", "Frequent (HPO)"], + "frequency_qualifier_closure": ["HP:0040282", "HP:0000001", "HP:0040279"], + "frequency_qualifier_closure_label": ["All (HPO)", "Frequent (HPO)", "Frequency (HPO)"], "onset_qualifier_label": None, "onset_qualifier_namespace": None, "onset_qualifier_category": None, @@ -469,84 +481,84 @@ def association_table(): "direction": "outgoing", }, { - "id": "uuid:862bc0d4-5d8c-11ee-9b27-2b20ed86a9d9", + "id": "uuid:c6b3613a-7529-11ee-b012-cbd37f5c3759", "category": "biolink:DiseaseToPhenotypicFeatureAssociation", "subject": "MONDO:0013049", "original_subject": "OMIM:612937", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ + "BFO:0000002", + "BFO:0000020", + "MONDO:0005336", + "MONDO:0005021", "MONDO:0004994", - "MONDO:0000001", "MONDO:0018276", "MONDO:0005071", "MONDO:0005267", - "MONDO:0013049", + "BFO:0000016", + "MONDO:0016333", + "MONDO:0017749", + "OGMS:0000031", + "MONDO:0003847", + "BFO:0000001", "MONDO:0020121", "MONDO:0004995", - "MONDO:0700223", - "MONDO:0024322", - "BFO:0000002", "BFO:0000017", - "BFO:0000020", "MONDO:0005217", - "BFO:0000016", "MONDO:0020120", "MONDO:0019056", + "MONDO:0015286", + "MONDO:0019052", + "MONDO:0005500", + "MONDO:0005066", + "MONDO:0000001", + "MONDO:0013049", + "MONDO:0700223", + "MONDO:0024322", "MONDO:0700096", "MONDO:0000591", - "MONDO:0005336", "MONDO:0002081", - "MONDO:0016333", - "MONDO:0017749", - "OGMS:0000031", - "MONDO:0005021", - "MONDO:0003847", "MONDO:0003939", - "MONDO:0015286", - "BFO:0000001", "MONDO:0002320", - "MONDO:0019052", - "MONDO:0005500", - "MONDO:0005066", "MONDO:0019950", ], "subject_label": "DPM3-congenital disorder of glycosylation", "subject_closure_label": [ - "entity", - "continuant", - "disposition", - "realizable entity", - "specifically dependent continuant", - "disease", + "cardiomyopathy", + "muscular dystrophy", + "cardiovascular disorder", + "human disease", "intrinsic cardiomyopathy", "musculoskeletal system disorder", + "disorder of multiple glycosylation", + "disease", + "muscle tissue disorder", "congenital nervous system disorder", + "hereditary skeletal muscle disorder", + "disorder of glycosylation", + "disposition", + "congenital disorder of glycosylation", + "disease", + "DPM3-congenital disorder of glycosylation", + "continuant", + "specifically dependent continuant", + "myopathy", + "familial dilated cardiomyopathy", "hereditary disease", - "muscle tissue disorder", - "cardiomyopathy", - "cardiovascular disorder", - "dilated cardiomyopathy", + "inborn errors of metabolism", + "congenital disorder of glycosylation type I", "metabolic disease", + "muscular dystrophy-dystroglycanopathy", "nervous system disorder", - "familial cardiomyopathy", "heart disorder", - "myopathy", - "congenital disorder of glycosylation type I", - "DPM3-congenital disorder of glycosylation", - "congenital disorder of glycosylation", - "familial dilated cardiomyopathy", - "disorder of multiple glycosylation", - "muscular dystrophy-dystroglycanopathy", - "inborn errors of metabolism", + "realizable entity", + "familial cardiomyopathy", + "skeletal muscle disorder", "neuromuscular disease", + "dilated cardiomyopathy", + "entity", "congenital muscular dystrophy", - "skeletal muscle disorder", - "muscular dystrophy", - "disorder of glycosylation", - "human disease", - "hereditary skeletal muscle disorder", - "disease", ], "subject_taxon": None, "subject_taxon_label": None, @@ -556,199 +568,203 @@ def association_table(): "object_namespace": "HP", "object_category": "biolink:PhenotypicFeature", "object_closure": [ - "HP:0000001", - "HP:0011021", - "HP:0004364", "UPHENO:0082875", - "UPHENO:0075696", - "UPHENO:0077817", - "UPHENO:0076289", - "UPHENO:0002448", - "UPHENO:0001001", "UPHENO:0051763", - "UPHENO:0004536", - "UPHENO:0051668", "UPHENO:0001005", + "BFO:0000020", + "UPHENO:0077820", + "BFO:0000001", + "UPHENO:0051804", + "BFO:0000015", + "BFO:0000004", + "GO:0032991", + "CHEBI:23367", + "UBERON:0000178", + "GO:1990234", + "CHEBI:33839", + "CHEBI:33675", + "UBERON:0001004", + "HP:0000001", + "HP:0011021", + "UPHENO:0001001", "UPHENO:0001002", "UPHENO:0077825", "HP:0000118", - "BFO:0000002", "HP:0001871", - "UPHENO:0077821", - "BFO:0000020", - "UPHENO:0046284", - "UPHENO:0077829", - "UPHENO:0004459", - "UPHENO:0002332", "UPHENO:0051801", - "HP:0010876", - "UPHENO:0077820", - "UPHENO:0076286", - "HP:0040081", "UPHENO:0001003", - "UPHENO:0002536", "HP:0001939", - "HP:0500165", - "UPHENO:0081547", - "UPHENO:0077826", "HP:0032180", - "BFO:0000001", - "HP:0002086", - "HP:0003236", "PATO:0000001", "HP:0002795", - "HP:0012415", - "UPHENO:0051612", - "UPHENO:0051804", "BFO:0000001", + "BFO:0000040", + "GO:0008152", + "UBERON:0000467", + "UBERON:0000468", + "GO:0061695", + "CHEBI:16670", + "CHEBI:33302", + "CHEBI:33304", + "CHEBI:33582", + "GO:0002185", + "CHEBI:15841", + "CHEBI:51143", + "CHEBI:25806", + "CHEBI:36962", + "CHEBI:50860", + "UPHENO:0075696", + "UPHENO:0077817", + "UPHENO:0076289", + "BFO:0000002", + "UPHENO:0077821", + "UPHENO:0004459", + "UPHENO:0002332", + "UPHENO:0002536", + "HP:0500165", + "HP:0002086", + "HP:0003236", "BFO:0000003", "BFO:0000002", - "BFO:0000015", - "BFO:0000004", "GO:0008150", - "BFO:0000040", - "UBERON:0001062", - "GO:0008152", "GO:0005575", "CHEBI:24431", "PR:000050567", "UBERON:0000465", - "GO:0032991", - "CHEBI:23367", - "UBERON:0000178", - "UBERON:0000061", - "UBERON:0000463", "GO:1902494", "CHEBI:36357", "CHEBI:33579", - "UBERON:0010000", - "UBERON:0000467", "UBERON:0004120", "UBERON:0006314", - "GO:1990234", - "CHEBI:33839", - "CHEBI:33675", "CHEBI:138675", - "UBERON:0000468", - "UBERON:0001004", "UBERON:0002193", "UBERON:0002390", "UBERON:0000179", - "GO:0061695", - "CHEBI:16670", - "CHEBI:33302", - "CHEBI:33304", - "CHEBI:33582", - "GO:0002185", - "CHEBI:15841", - "CHEBI:51143", - "CHEBI:25806", - "CHEBI:36962", - "CHEBI:50860", "CHEBI:16541", "CHEBI:35352", "CHEBI:32988", - "CHEBI:36963", - "CHEBI:33285", "CHEBI:50047", "CHEBI:37622", "CHEBI:33256", + "HP:0004364", + "UPHENO:0002448", + "UPHENO:0004536", + "UPHENO:0051668", + "UPHENO:0046284", + "UPHENO:0077829", + "HP:0010876", + "UPHENO:0076286", + "HP:0040081", + "UPHENO:0081547", + "UPHENO:0077826", + "HP:0012415", + "UPHENO:0051612", + "UBERON:0001062", + "UBERON:0000061", + "UBERON:0000463", + "UBERON:0010000", + "CHEBI:36963", + "CHEBI:33285", ], "object_label": "Elevated circulating creatine kinase concentration (HPO)", "object_closure_label": [ - "entity", - "entity", - "continuant", - "continuant", + "All (HPO)", + "Abnormality of circulating enzyme level (HPO)", + "abnormal multicellular organism chemical entity level", + "Phenotypic abnormality", + "abnormal blood gas molecular entity level", + "Phenotypic abnormality (HPO)", + "abnormal chemical entity level", + "abnormal independent continuant oxygen molecular entity level", + "Abnormal circulating protein concentration (HPO)", + "abnormal role blood level", + "Abnormal circulating creatine kinase concentration (HPO)", + "Abnormality of metabolism/homeostasis (HPO)", + "abnormal role bodily fluid level", + "abnormal blood nitrogen molecular entity level", + "quality", + "Abnormal respiratory system physiology (HPO)", + "process", "independent continuant", - "specifically dependent continuant", - "material entity", - "gas molecular entity", - "polypeptide", - "protein polypeptide chain", - "peptide", + "protein-containing complex", "molecular entity", - "chemical entity", - "oxygen molecular entity", - "amide", - "primary amide", - "heteroorganic entity", + "blood", + "multicellular anatomical structure", + "respiratory system", + "transferase complex, transferring phosphorus-containing groups", + "peptide", "pnictogen molecular entity", "chalcogen molecular entity", - "main group molecular entity", "carbon group molecular entity", - "p-block molecular entity", - "macromolecule", + "protein polypeptide chain", "organonitrogen compound", - "polyatomic entity", + "amide", + "abnormality of anatomical entity physiology", + "phenotype", + "Abnormality of blood and blood-forming tissues (HPO)", + "abnormal independent continuant protein polypeptide chain level", + "phenotype by ontology source", + "Abnormal blood oxygen level (HPO)", + "abnormal blood chemical entity level", + "occurrent", + "continuant", + "biological_process", + "cellular_component", + "chemical entity", + "protein-containing material entity", + "material anatomical entity", + "gas molecular entity", + "creatine kinase complex", + "polypeptide", + "nitrogen molecular entity", + "oxygen molecular entity", "organochalcogen compound", - "organooxygen compound", + "organic molecular entity", "carboxamide", + "primary amide", "organic amino compound", - "organic molecular entity", - "nitrogen molecular entity", - "creatine kinase complex", - "cellular_component", - "protein-containing complex", - "transferase complex, transferring phosphorus-containing groups", - "catalytic complex", - "transferase complex", - "All (HPO)", - "Phenotypic abnormality (HPO)", - "Abnormality of blood and blood-forming tissues (HPO)", - "Abnormality of metabolism/homeostasis (HPO)", - "Abnormality of the respiratory system (HPO)", - "Abnormal respiratory system physiology (HPO)", - "Elevated circulating creatine kinase concentration (HPO)", "Abnormal circulating nitrogen compound concentration (HPO)", - "Abnormal circulating protein concentration (HPO)", - "Abnormality of circulating enzyme level (HPO)", - "Abnormal blood gas level (HPO)", + "abnormality of respiratory system physiology", + "abnormal respiratory system", + "abnormal independent continuant chemical entity level", + "abnormal phenotype by ontology source", + "specifically dependent continuant", + "abnormal independent continuant gas molecular entity level", "Abnormal circulating metabolite concentration (HPO)", - "Abnormal circulating creatine kinase concentration (HPO)", - "Abnormal blood oxygen level (HPO)", - "quality", - "protein-containing material entity", + "Abnormality of the respiratory system (HPO)", + "Elevated circulating creatine kinase concentration (HPO)", + "entity", + "anatomical entity", "anatomical structure", - "blood", - "haemolymphatic fluid", "organism substance", - "material anatomical entity", - "anatomical system", - "multicellular organism", - "respiratory system", - "anatomical entity", - "hemolymphoid system", - "hematopoietic system", "mesoderm-derived structure", "bodily fluid", - "multicellular anatomical structure", - "phenotype", - "Phenotypic abnormality", - "phenotype by ontology source", - "abnormal phenotype by ontology source", - "abnormality of anatomical entity physiology", - "abnormality of respiratory system physiology", - "abnormal anatomical entity", - "abnormal hematopoietic system", - "abnormal respiratory system", - "abnormal chemical entity level", - "abnormal blood protein polypeptide chain level", - "abnormal independent continuant chemical entity level", - "abnormal multicellular organism chemical entity level", - "abnormal independent continuant protein polypeptide chain level", - "abnormal blood chemical entity level", + "hemolymphoid system", + "hematopoietic system", + "haemolymphatic fluid", + "organooxygen compound", + "heteroorganic entity", "abnormal anatomical entity", - "abnormal role blood level", - "abnormal role independent continuant level", "abnormal blood oxygen molecular entity level", - "abnormal independent continuant gas molecular entity level", + "abnormal role independent continuant level", + "continuant", "abnormal independent continuant nitrogen molecular entity level", - "abnormal blood gas molecular entity level", - "abnormal blood nitrogen molecular entity level", - "abnormal independent continuant oxygen molecular entity level", - "abnormal role bodily fluid level", + "abnormal hematopoietic system", "abnormality of anatomical entity physiology", + "abnormal anatomical entity", + "entity", + "Abnormal blood gas level (HPO)", + "abnormal blood protein polypeptide chain level", + "material entity", + "metabolic process", + "catalytic complex", + "polyatomic entity", + "main group molecular entity", + "anatomical system", + "transferase complex", + "macromolecule", + "p-block molecular entity", + "multicellular organism", ], "object_taxon": None, "object_taxon_label": None, @@ -756,9 +772,10 @@ def association_table(): "aggregator_knowledge_source": ["infores:monarchinitiative"], "negated": None, "pathway": None, - "evidence_count": 5, + "evidence_count": 3, "has_evidence": ["ECO:0000269"], "has_evidence_links": [{"id": "ECO:0000269", "url": "http://purl.obolibrary.org/obo/ECO_0000269"}], + "grouping_key": "MONDO:0013049🍪🍪biolink:has_phenotype🍪HP:0003236", "provided_by": "hpoa_disease_to_phenotype_edges", "provided_by_link": { "id": "hpoa_disease_to_phenotype", @@ -774,11 +791,16 @@ def association_table(): "onset_qualifier": None, "sex_qualifier": None, "stage_qualifier": None, + "qualifiers_label": None, + "qualifiers_namespace": None, + "qualifiers_category": None, + "qualifiers_closure": [], + "qualifiers_closure_label": [], "frequency_qualifier_label": "Obligate (HPO)", "frequency_qualifier_namespace": "HP", "frequency_qualifier_category": "biolink:PhenotypicFeature", - "frequency_qualifier_closure": ["HP:0000001", "HP:0040279", "HP:0040280"], - "frequency_qualifier_closure_label": ["All (HPO)", "Frequency (HPO)", "Obligate (HPO)"], + "frequency_qualifier_closure": ["HP:0000001", "HP:0040280", "HP:0040279"], + "frequency_qualifier_closure_label": ["All (HPO)", "Obligate (HPO)", "Frequency (HPO)"], "onset_qualifier_label": None, "onset_qualifier_namespace": None, "onset_qualifier_category": None, @@ -797,64 +819,64 @@ def association_table(): "direction": "outgoing", }, { - "id": "uuid:8a99d6f0-5d8c-11ee-9b27-2b20ed86a9d9", + "id": "uuid:cb2a2f47-7529-11ee-b012-cbd37f5c3759", "category": "biolink:DiseaseToPhenotypicFeatureAssociation", "subject": "MONDO:0009681", "original_subject": "OMIM:254090", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ - "MONDO:0000001", + "BFO:0000020", + "MONDO:0005336", "MONDO:0005071", + "BFO:0000016", + "MONDO:0016139", + "OGMS:0000031", + "MONDO:0003847", + "BFO:0000001", "MONDO:0020121", - "MONDO:0700223", - "BFO:0000002", "MONDO:0019952", "BFO:0000017", "MONDO:0100225", - "BFO:0000020", - "BFO:0000016", "MONDO:0020120", "MONDO:0019056", - "MONDO:0016139", + "MONDO:0009681", + "MONDO:0000355", + "MONDO:0000001", + "MONDO:0700223", + "BFO:0000002", "MONDO:0700096", - "MONDO:0005336", "MONDO:0002081", - "MONDO:0009681", - "OGMS:0000031", - "MONDO:0003847", "MONDO:0003939", - "BFO:0000001", "MONDO:0002320", - "MONDO:0000355", "MONDO:0019950", ], "subject_label": "Ullrich congenital muscular dystrophy 1", "subject_closure_label": [ - "entity", + "muscular dystrophy", + "human disease", + "musculoskeletal system disorder", + "disease", + "muscle tissue disorder", + "congenital nervous system disorder", + "hereditary skeletal muscle disorder", "continuant", "disposition", - "realizable entity", - "specifically dependent continuant", + "qualitative or quantitative protein defects in neuromuscular diseases", + "Ullrich congenital muscular dystrophy 1", "disease", - "Ullrich congenital muscular dystrophy", - "musculoskeletal system disorder", - "congenital nervous system disorder", + "specifically dependent continuant", + "myopathy", "hereditary disease", - "muscle tissue disorder", + "Ullrich congenital muscular dystrophy", "nervous system disorder", - "myopathy", - "Ullrich congenital muscular dystrophy 1", - "qualitative or quantitative protein defects in neuromuscular diseases", - "neuromuscular disease", - "congenital muscular dystrophy", "congenital myopathy", - "skeletal muscle disorder", - "muscular dystrophy", + "realizable entity", "collagen 6-related myopathy", - "human disease", - "hereditary skeletal muscle disorder", - "disease", + "skeletal muscle disorder", + "neuromuscular disease", + "entity", + "congenital muscular dystrophy", ], "subject_taxon": None, "subject_taxon_label": None, @@ -864,91 +886,91 @@ def association_table(): "object_namespace": "HP", "object_category": "biolink:PhenotypicFeature", "object_closure": [ - "HP:0000001", - "HP:0020152", "UPHENO:0082875", "HP:0001388", - "UPHENO:0075696", - "UPHENO:0001001", - "HP:0011729", "UPHENO:0001005", + "BFO:0000002", + "BFO:0000020", + "PATO:0000001", + "HP:0011843", + "BFO:0000004", + "UBERON:0002204", + "HP:0000001", + "HP:0020152", + "UPHENO:0001001", "UPHENO:0001002", + "HP:0000118", + "UPHENO:0002964", + "BFO:0000001", + "BFO:0000001", + "BFO:0000040", + "UBERON:0000467", + "UBERON:0000468", + "UBERON:0011216", + "UBERON:0034921", + "UPHENO:0075696", + "HP:0011729", "HP:0034430", "HP:0000924", - "HP:0000118", - "BFO:0000002", - "BFO:0000020", "UPHENO:0002332", - "UPHENO:0002964", - "HP:0033127", "UPHENO:0001003", "UPHENO:0002536", - "UPHENO:0081440", - "BFO:0000001", - "PATO:0000001", - "HP:0011843", - "BFO:0000001", "BFO:0000002", - "BFO:0000004", - "BFO:0000040", - "UBERON:0001062", "UBERON:0000465", + "UBERON:0004770", + "UBERON:0000982", + "HP:0033127", + "UPHENO:0081440", + "UBERON:0001062", "UBERON:0000061", "UBERON:0034925", "UBERON:0010000", - "UBERON:0000467", - "UBERON:0004770", - "UBERON:0000468", - "UBERON:0011216", - "UBERON:0034921", - "UBERON:0002204", "UBERON:0004905", "UBERON:0001434", - "UBERON:0000982", ], "object_label": "Distal joint laxity (HPO)", "object_closure_label": [ - "entity", - "entity", - "continuant", - "continuant", - "independent continuant", - "specifically dependent continuant", - "material entity", "All (HPO)", + "Distal joint laxity (HPO)", + "Phenotypic abnormality", "Phenotypic abnormality (HPO)", - "Abnormality of the skeletal system (HPO)", + "Abnormality of the musculoskeletal system (HPO)", + "abnormality of musculoskeletal system physiology", + "independent continuant", + "multicellular anatomical structure", + "musculoskeletal system", + "skeletal joint", + "abnormality of anatomical entity physiology", "Joint laxity (HPO)", + "phenotype", "Abnormality of joint mobility (HPO)", - "Abnormality of musculoskeletal physiology (HPO)", - "Distal joint laxity (HPO)", - "Abnormality of the musculoskeletal system (HPO)", - "Abnormal joint physiology", + "abnormal skeletal system", "quality", - "anatomical structure", + "Abnormality of musculoskeletal physiology (HPO)", + "continuant", "material anatomical entity", - "anatomical system", - "multicellular organism", - "skeletal joint", + "abnormal phenotype by ontology source", + "continuant", + "specifically dependent continuant", + "entity", "anatomical entity", - "skeletal system", - "musculoskeletal system", + "anatomical structure", + "anatomical collection", "articular system", "articulation", - "multicellular anatomical structure", - "organ system subdivision", - "multi organ part structure", - "anatomical collection", - "phenotype", - "Phenotypic abnormality", - "phenotype by ontology source", - "abnormal phenotype by ontology source", - "abnormality of anatomical entity physiology", - "abnormal anatomical entity", - "abnormal skeletal system", + "skeletal system", "abnormal anatomical entity", - "abnormality of musculoskeletal system physiology", + "Abnormal joint physiology", + "Abnormality of the skeletal system (HPO)", "abnormality of anatomical entity physiology", + "phenotype by ontology source", + "abnormal anatomical entity", + "entity", + "material entity", + "anatomical system", + "multicellular organism", + "organ system subdivision", + "multi organ part structure", ], "object_taxon": None, "object_taxon_label": None, @@ -956,9 +978,10 @@ def association_table(): "aggregator_knowledge_source": ["infores:monarchinitiative"], "negated": None, "pathway": None, - "evidence_count": 5, + "evidence_count": 3, "has_evidence": ["ECO:0000269"], "has_evidence_links": [{"id": "ECO:0000269", "url": "http://purl.obolibrary.org/obo/ECO_0000269"}], + "grouping_key": "MONDO:0009681🍪🍪biolink:has_phenotype🍪HP:0020152", "provided_by": "hpoa_disease_to_phenotype_edges", "provided_by_link": { "id": "hpoa_disease_to_phenotype", @@ -974,11 +997,16 @@ def association_table(): "onset_qualifier": None, "sex_qualifier": None, "stage_qualifier": None, + "qualifiers_label": None, + "qualifiers_namespace": None, + "qualifiers_category": None, + "qualifiers_closure": [], + "qualifiers_closure_label": [], "frequency_qualifier_label": "Obligate (HPO)", "frequency_qualifier_namespace": "HP", "frequency_qualifier_category": "biolink:PhenotypicFeature", - "frequency_qualifier_closure": ["HP:0000001", "HP:0040279", "HP:0040280"], - "frequency_qualifier_closure_label": ["All (HPO)", "Frequency (HPO)", "Obligate (HPO)"], + "frequency_qualifier_closure": ["HP:0000001", "HP:0040280", "HP:0040279"], + "frequency_qualifier_closure_label": ["All (HPO)", "Obligate (HPO)", "Frequency (HPO)"], "onset_qualifier_label": None, "onset_qualifier_namespace": None, "onset_qualifier_category": None, @@ -997,66 +1025,66 @@ def association_table(): "direction": "outgoing", }, { - "id": "uuid:894ab8ce-5d8c-11ee-9b27-2b20ed86a9d9", + "id": "uuid:c9d8bdf9-7529-11ee-b012-cbd37f5c3759", "category": "biolink:DiseaseToPhenotypicFeatureAssociation", "subject": "MONDO:0009676", "original_subject": "OMIM:253601", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ - "MONDO:0000001", "MONDO:0016971", - "MONDO:0000429", - "MONDO:0016145", - "MONDO:0005071", - "MONDO:0020121", - "MONDO:0700223", "BFO:0000002", - "BFO:0000017", "BFO:0000020", + "MONDO:0005336", + "MONDO:0009676", + "MONDO:0015152", + "MONDO:0000429", + "MONDO:0005071", "MONDO:0006025", - "MONDO:0016106", "BFO:0000016", + "MONDO:0016139", + "OGMS:0000031", + "MONDO:0003847", + "BFO:0000001", + "MONDO:0016145", + "MONDO:0020121", + "BFO:0000017", "MONDO:0020120", "MONDO:0019056", - "MONDO:0016139", + "MONDO:0000001", + "MONDO:0700223", + "MONDO:0016106", "MONDO:0700096", - "MONDO:0005336", "MONDO:0002081", - "MONDO:0009676", - "OGMS:0000031", - "MONDO:0003847", "MONDO:0003939", - "MONDO:0015152", - "BFO:0000001", ], "subject_label": "autosomal recessive limb-girdle muscular dystrophy type 2B", "subject_closure_label": [ - "entity", - "continuant", - "disposition", - "realizable entity", - "specifically dependent continuant", - "disease", - "autosomal genetic disease", - "musculoskeletal system disorder", - "hereditary disease", - "muscle tissue disorder", - "nervous system disorder", - "myopathy", - "autosomal recessive disease", - "autosomal recessive limb-girdle muscular dystrophy type 2B", - "autosomal recessive limb-girdle muscular dystrophy", - "progressive muscular dystrophy", - "qualitative or quantitative protein defects in neuromuscular diseases", - "qualitative or quantitative defects of dysferlin", "limb-girdle muscular dystrophy", - "neuromuscular disease", - "skeletal muscle disorder", "muscular dystrophy", + "progressive muscular dystrophy", "human disease", + "musculoskeletal system disorder", + "disease", + "muscle tissue disorder", + "qualitative or quantitative defects of dysferlin", "hereditary skeletal muscle disorder", + "autosomal recessive disease", + "disposition", + "qualitative or quantitative protein defects in neuromuscular diseases", + "autosomal recessive limb-girdle muscular dystrophy type 2B", "disease", + "continuant", + "specifically dependent continuant", + "myopathy", + "hereditary disease", + "autosomal genetic disease", + "nervous system disorder", + "realizable entity", + "skeletal muscle disorder", + "neuromuscular disease", + "autosomal recessive limb-girdle muscular dystrophy", + "entity", ], "subject_taxon": None, "subject_taxon_label": None, @@ -1066,87 +1094,87 @@ def association_table(): "object_namespace": "HP", "object_category": "biolink:PhenotypicFeature", "object_closure": [ - "HP:0000001", "UPHENO:0082875", - "UPHENO:0075696", "UPHENO:0002320", + "BFO:0000002", + "BFO:0000004", + "UBERON:0000061", + "HP:0000001", "UPHENO:0001001", - "UPHENO:0001005", - "HP:0003701", "UPHENO:0001002", - "HP:0001324", "HP:0000118", - "BFO:0000002", "BFO:0000020", - "UPHENO:0080555", - "HP:0003011", - "UPHENO:0002816", - "UPHENO:0002332", - "UPHENO:0080556", - "HP:0033127", "UPHENO:0001003", - "UPHENO:0002536", "BFO:0000001", - "HP:0011804", "PATO:0000001", "BFO:0000001", - "BFO:0000002", - "BFO:0000004", "BFO:0000040", "UBERON:0001062", - "UBERON:0000465", - "UBERON:0000061", - "UBERON:0010000", "UBERON:0000467", - "UBERON:0005090", - "UBERON:0000062", "UBERON:0000468", "UBERON:0011216", + "UPHENO:0075696", + "HP:0001324", + "HP:0003011", + "UPHENO:0002332", + "UPHENO:0002536", + "HP:0011804", + "BFO:0000002", + "UBERON:0000465", + "UBERON:0005090", "UBERON:0001630", + "UPHENO:0001005", + "HP:0003701", + "UPHENO:0080555", + "UPHENO:0002816", + "UPHENO:0080556", + "HP:0033127", + "UBERON:0010000", + "UBERON:0000062", "UBERON:0000383", "UBERON:0001015", ], "object_label": "Proximal muscle weakness (HPO)", "object_closure_label": [ - "entity", - "entity", - "continuant", - "continuant", - "independent continuant", - "specifically dependent continuant", - "material entity", "All (HPO)", + "abnormality of muscle organ physiology", + "Phenotypic abnormality", "Phenotypic abnormality (HPO)", - "Muscle weakness (HPO)", - "Abnormality of the musculature (HPO)", - "Proximal muscle weakness (HPO)", - "Abnormal muscle physiology (HPO)", + "decreased anatomical entity strength", + "abnormal musculature", + "decreased muscle organ strength", "Abnormality of the musculoskeletal system (HPO)", "quality", + "independent continuant", "anatomical structure", - "organ", - "musculature of body", - "material anatomical entity", - "anatomical system", - "multicellular organism", - "musculature", - "anatomical entity", - "muscle organ", - "muscle structure", "multicellular anatomical structure", - "organ system subdivision", + "abnormality of anatomical entity physiology", "phenotype", - "Phenotypic abnormality", - "phenotype by ontology source", "abnormal phenotype by ontology source", - "abnormality of muscle organ physiology", - "abnormality of anatomical entity physiology", - "abnormal anatomical entity", - "abnormal musculature", + "Proximal muscle weakness (HPO)", + "specifically dependent continuant", + "phenotype by ontology source", + "continuant", + "material anatomical entity", + "continuant", + "Abnormal muscle physiology (HPO)", + "entity", + "muscle structure", + "organ", + "muscle organ", + "musculature of body", + "musculature", "abnormal anatomical entity", - "decreased anatomical entity strength", - "decreased muscle organ strength", + "Muscle weakness (HPO)", + "Abnormality of the musculature (HPO)", "abnormality of anatomical entity physiology", + "abnormal anatomical entity", + "entity", + "material entity", + "anatomical entity", + "anatomical system", + "multicellular organism", + "organ system subdivision", ], "object_taxon": None, "object_taxon_label": None, @@ -1154,9 +1182,10 @@ def association_table(): "aggregator_knowledge_source": ["infores:monarchinitiative"], "negated": None, "pathway": None, - "evidence_count": 5, + "evidence_count": 3, "has_evidence": ["ECO:0000269"], "has_evidence_links": [{"id": "ECO:0000269", "url": "http://purl.obolibrary.org/obo/ECO_0000269"}], + "grouping_key": "MONDO:0009676🍪🍪biolink:has_phenotype🍪HP:0003701", "provided_by": "hpoa_disease_to_phenotype_edges", "provided_by_link": { "id": "hpoa_disease_to_phenotype", @@ -1172,11 +1201,16 @@ def association_table(): "onset_qualifier": None, "sex_qualifier": None, "stage_qualifier": None, + "qualifiers_label": None, + "qualifiers_namespace": None, + "qualifiers_category": None, + "qualifiers_closure": [], + "qualifiers_closure_label": [], "frequency_qualifier_label": "Obligate (HPO)", "frequency_qualifier_namespace": "HP", "frequency_qualifier_category": "biolink:PhenotypicFeature", - "frequency_qualifier_closure": ["HP:0000001", "HP:0040279", "HP:0040280"], - "frequency_qualifier_closure_label": ["All (HPO)", "Frequency (HPO)", "Obligate (HPO)"], + "frequency_qualifier_closure": ["HP:0000001", "HP:0040280", "HP:0040279"], + "frequency_qualifier_closure_label": ["All (HPO)", "Obligate (HPO)", "Frequency (HPO)"], "onset_qualifier_label": None, "onset_qualifier_namespace": None, "onset_qualifier_category": None, diff --git a/backend/tests/fixtures/association_table_response.py b/backend/tests/fixtures/association_table_response.py index 8c2cbc808..fe4da13e9 100644 --- a/backend/tests/fixtures/association_table_response.py +++ b/backend/tests/fixtures/association_table_response.py @@ -5,7 +5,7 @@ def association_table_response(): return { "responseHeader": { - "QTime": 0, + "QTime": 1, "params": { "mm": "100%", "q": "*:*", @@ -26,7 +26,7 @@ def association_table_response(): "start": 0, "docs": [ { - "id": "uuid:89aa7b9b-5d8c-11ee-9b27-2b20ed86a9d9", + "id": "uuid:ca3946de-7529-11ee-b012-cbd37f5c3759", "original_subject": "OMIM:164310", "predicate": "biolink:has_phenotype", "category": "biolink:DiseaseToPhenotypicFeatureAssociation", @@ -38,161 +38,162 @@ def association_table_response(): "has_evidence": ["ECO:0000269"], "subject": "MONDO:0020793", "object": "HP:0002460", - "subject_namespace": "MONDO", + "subject_label": "oculopharyngodistal myopathy 1", "subject_category": "biolink:Disease", + "subject_namespace": "MONDO", "subject_closure": [ - "MONDO:0020158", - "MONDO:0000001", + "BFO:0000002", + "BFO:0000020", + "MONDO:0024458", + "MONDO:0005336", + "MONDO:0018949", "MONDO:0005071", + "MONDO:0003382", + "BFO:0000016", + "OGMS:0000031", + "MONDO:0003847", + "BFO:0000001", "MONDO:0025193", "MONDO:0020121", - "MONDO:0700223", - "BFO:0000002", "MONDO:0020793", "BFO:0000017", - "BFO:0000020", - "MONDO:0016106", - "MONDO:0003382", - "BFO:0000016", "MONDO:0020120", "MONDO:0019056", + "MONDO:0000462", + "MONDO:0020158", + "MONDO:0000001", + "MONDO:0700223", + "MONDO:0016106", "MONDO:0700096", - "MONDO:0024458", - "MONDO:0005336", "MONDO:0002081", - "OGMS:0000031", - "MONDO:0003847", "MONDO:0003939", "MONDO:0002022", - "BFO:0000001", - "MONDO:0000462", "MONDO:0005328", - "MONDO:0018949", ], "subject_closure_label": [ - "entity", - "continuant", - "disposition", - "realizable entity", - "specifically dependent continuant", + "oculopharyngodistal myopathy", + "muscular dystrophy", + "progressive muscular dystrophy", + "human disease", + "musculoskeletal system disorder", "disease", - "eye adnexa disorder", + "muscle tissue disorder", "disorder of orbital region", - "musculoskeletal system disorder", + "hereditary skeletal muscle disorder", "eyelid disorder", - "hereditary disease", - "muscle tissue disorder", - "nervous system disorder", - "eye disorder", - "myopathy", - "progressive muscular dystrophy", + "disposition", "distal myopathy", - "neuromuscular disease", - "skeletal muscle disorder", - "muscular dystrophy", "eyelids malposition disorder", - "oculopharyngodistal myopathy 1", - "disorder of visual system", - "oculopharyngodistal myopathy", - "human disease", - "hereditary skeletal muscle disorder", "disease", + "continuant", + "specifically dependent continuant", + "disorder of visual system", + "myopathy", + "hereditary disease", + "eye adnexa disorder", + "nervous system disorder", + "oculopharyngodistal myopathy 1", + "realizable entity", + "skeletal muscle disorder", + "neuromuscular disease", + "entity", + "eye disorder", ], - "subject_label": "oculopharyngodistal myopathy 1", - "object_namespace": "HP", + "object_label": "Distal muscle weakness (HPO)", "object_category": "biolink:PhenotypicFeature", + "object_namespace": "HP", "object_closure": [ - "HP:0000001", "UPHENO:0082875", - "UPHENO:0075696", "UPHENO:0002320", - "UPHENO:0001001", "UPHENO:0001005", - "UPHENO:0001002", - "HP:0001324", - "HP:0000118", - "BFO:0000002", "BFO:0000020", - "UPHENO:0080555", + "PATO:0000001", + "BFO:0000004", + "UBERON:0000061", + "HP:0000001", + "UPHENO:0001001", + "HP:0000118", + "BFO:0000001", + "UBERON:0000467", + "UBERON:0000468", + "UBERON:0011216", + "UPHENO:0075696", + "HP:0001324", "HP:0003011", - "UPHENO:0002816", "UPHENO:0002332", - "UPHENO:0080556", - "HP:0033127", "UPHENO:0001003", "UPHENO:0002536", "HP:0002460", - "BFO:0000001", "HP:0011804", - "PATO:0000001", - "BFO:0000001", "BFO:0000002", - "BFO:0000004", "BFO:0000040", + "UBERON:0005090", + "UBERON:0001630", + "UPHENO:0001002", + "BFO:0000002", + "UPHENO:0080555", + "UPHENO:0002816", + "UPHENO:0080556", + "HP:0033127", + "BFO:0000001", "UBERON:0001062", "UBERON:0000465", - "UBERON:0000061", "UBERON:0010000", - "UBERON:0000467", - "UBERON:0005090", "UBERON:0000062", - "UBERON:0000468", - "UBERON:0011216", - "UBERON:0001630", "UBERON:0000383", "UBERON:0001015", ], "object_closure_label": [ - "entity", - "entity", - "continuant", - "continuant", - "independent continuant", - "specifically dependent continuant", - "material entity", "All (HPO)", + "abnormality of muscle organ physiology", "Phenotypic abnormality (HPO)", - "Muscle weakness (HPO)", - "Distal muscle weakness (HPO)", - "Abnormality of the musculature (HPO)", - "Abnormal muscle physiology (HPO)", + "decreased anatomical entity strength", + "abnormal musculature", + "decreased muscle organ strength", "Abnormality of the musculoskeletal system (HPO)", - "quality", - "anatomical structure", - "organ", - "musculature of body", + "entity", + "independent continuant", "material anatomical entity", - "anatomical system", - "multicellular organism", - "musculature", - "anatomical entity", - "muscle organ", - "muscle structure", + "anatomical structure", "multicellular anatomical structure", - "organ system subdivision", + "abnormality of anatomical entity physiology", "phenotype", "Phenotypic abnormality", - "phenotype by ontology source", + "continuant", + "Distal muscle weakness (HPO)", + "quality", + "continuant", + "material entity", "abnormal phenotype by ontology source", - "abnormality of muscle organ physiology", - "abnormality of anatomical entity physiology", - "abnormal anatomical entity", - "abnormal musculature", + "specifically dependent continuant", + "Abnormal muscle physiology (HPO)", + "entity", + "anatomical entity", + "muscle structure", + "organ", + "muscle organ", + "musculature of body", + "musculature", "abnormal anatomical entity", - "decreased anatomical entity strength", - "decreased muscle organ strength", + "Muscle weakness (HPO)", + "Abnormality of the musculature (HPO)", "abnormality of anatomical entity physiology", + "phenotype by ontology source", + "abnormal anatomical entity", + "anatomical system", + "multicellular organism", + "organ system subdivision", ], - "object_label": "Distal muscle weakness (HPO)", - "frequency_qualifier_namespace": "HP", - "frequency_qualifier_category": "biolink:PhenotypicFeature", - "frequency_qualifier_closure": ["HP:0000001", "HP:0040282", "HP:0040279"], - "frequency_qualifier_closure_label": ["All (HPO)", "Frequency (HPO)", "Frequent (HPO)"], "frequency_qualifier_label": "Frequent (HPO)", - "evidence_count": 6, + "frequency_qualifier_category": "biolink:PhenotypicFeature", + "frequency_qualifier_namespace": "HP", + "frequency_qualifier_closure": ["HP:0040282", "HP:0000001", "HP:0040279"], + "frequency_qualifier_closure_label": ["All (HPO)", "Frequent (HPO)", "Frequency (HPO)"], + "evidence_count": 4, + "grouping_key": "MONDO:0020793🍪🍪biolink:has_phenotype🍪HP:0002460", }, { - "id": "uuid:89aa7bac-5d8c-11ee-9b27-2b20ed86a9d9", + "id": "uuid:ca3946ef-7529-11ee-b012-cbd37f5c3759", "original_subject": "OMIM:164310", "predicate": "biolink:has_phenotype", "category": "biolink:DiseaseToPhenotypicFeatureAssociation", @@ -204,215 +205,216 @@ def association_table_response(): "has_evidence": ["ECO:0000269"], "subject": "MONDO:0020793", "object": "HP:0002015", - "subject_namespace": "MONDO", + "subject_label": "oculopharyngodistal myopathy 1", "subject_category": "biolink:Disease", + "subject_namespace": "MONDO", "subject_closure": [ - "MONDO:0020158", - "MONDO:0000001", + "BFO:0000002", + "BFO:0000020", + "MONDO:0024458", + "MONDO:0005336", + "MONDO:0018949", "MONDO:0005071", + "MONDO:0003382", + "BFO:0000016", + "OGMS:0000031", + "MONDO:0003847", + "BFO:0000001", "MONDO:0025193", "MONDO:0020121", - "MONDO:0700223", - "BFO:0000002", "MONDO:0020793", "BFO:0000017", - "BFO:0000020", - "MONDO:0016106", - "MONDO:0003382", - "BFO:0000016", "MONDO:0020120", "MONDO:0019056", + "MONDO:0000462", + "MONDO:0020158", + "MONDO:0000001", + "MONDO:0700223", + "MONDO:0016106", "MONDO:0700096", - "MONDO:0024458", - "MONDO:0005336", "MONDO:0002081", - "OGMS:0000031", - "MONDO:0003847", "MONDO:0003939", "MONDO:0002022", - "BFO:0000001", - "MONDO:0000462", "MONDO:0005328", - "MONDO:0018949", ], "subject_closure_label": [ - "entity", - "continuant", - "disposition", - "realizable entity", - "specifically dependent continuant", + "oculopharyngodistal myopathy", + "muscular dystrophy", + "progressive muscular dystrophy", + "human disease", + "musculoskeletal system disorder", "disease", - "eye adnexa disorder", + "muscle tissue disorder", "disorder of orbital region", - "musculoskeletal system disorder", + "hereditary skeletal muscle disorder", "eyelid disorder", - "hereditary disease", - "muscle tissue disorder", - "nervous system disorder", - "eye disorder", - "myopathy", - "progressive muscular dystrophy", + "disposition", "distal myopathy", - "neuromuscular disease", - "skeletal muscle disorder", - "muscular dystrophy", "eyelids malposition disorder", - "oculopharyngodistal myopathy 1", - "disorder of visual system", - "oculopharyngodistal myopathy", - "human disease", - "hereditary skeletal muscle disorder", "disease", - ], - "subject_label": "oculopharyngodistal myopathy 1", - "object_namespace": "HP", - "object_category": "biolink:PhenotypicFeature", - "object_closure": [ - "HP:0000001", - "UPHENO:0082875", - "UPHENO:0075696", - "HP:0011024", - "UPHENO:0001001", - "UPHENO:0002443", + "continuant", + "specifically dependent continuant", + "disorder of visual system", + "myopathy", + "hereditary disease", + "eye adnexa disorder", + "nervous system disorder", + "oculopharyngodistal myopathy 1", + "realizable entity", + "skeletal muscle disorder", + "neuromuscular disease", + "entity", + "eye disorder", + ], + "object_label": "Dysphagia (HPO)", + "object_category": "biolink:PhenotypicFeature", + "object_namespace": "HP", + "object_closure": [ + "UPHENO:0082875", "UPHENO:0002471", "HP:0025270", - "HP:0012719", "UPHENO:0001005", - "UPHENO:0002833", - "HP:0002015", - "UPHENO:0001002", - "UPHENO:0002725", - "HP:0000118", "BFO:0000002", "BFO:0000020", - "UPHENO:0002433", - "HP:0025032", - "UPHENO:0002332", "HP:0002664", - "HP:0000707", "HP:0011793", - "UPHENO:0001003", - "UPHENO:0002536", - "UPHENO:0004523", - "BFO:0000001", "PATO:0000001", - "HP:0025031", "UPHENO:0002474", "HP:0012638", - "BFO:0000001", - "BFO:0000002", "BFO:0000004", - "BFO:0000040", - "UBERON:0001062", - "UBERON:0000465", - "RO:0002577", "UBERON:0000061", + "UBERON:0001007", + "UBERON:0001016", + "UBERON:0011676", + "UBERON:0013701", + "UBERON:0000915", + "UBERON:0001043", + "UBERON:0002100", + "UBERON:0005181", + "UBERON:0002075", + "HP:0000001", + "UPHENO:0001001", + "HP:0000118", + "UPHENO:0002433", + "UPHENO:0001003", + "BFO:0000001", + "BFO:0000001", + "BFO:0000040", "UBERON:0010000", "UBERON:0000467", - "UBERON:0000475", - "UBERON:0000062", "UBERON:0004111", "UBERON:0000468", "UBERON:0000064", - "UBERON:0001007", - "UBERON:0001016", + "UPHENO:0075696", + "HP:0011024", + "UPHENO:0002443", + "HP:0012719", + "UPHENO:0002725", + "HP:0025032", + "UPHENO:0002332", + "UPHENO:0002536", + "UPHENO:0004523", + "BFO:0000002", + "UBERON:0000465", "UBERON:0005409", - "UBERON:0011676", - "UBERON:0013701", "UBERON:0009569", "UBERON:0013702", "UBERON:0013765", "UBERON:0005177", "UBERON:0000025", - "UBERON:0013522", - "UBERON:0000915", - "UBERON:0001043", - "UBERON:0002100", - "UBERON:0005181", - "UBERON:0002075", "UBERON:0001555", "UBERON:0004921", + "UPHENO:0002833", + "HP:0002015", + "UPHENO:0001002", + "HP:0000707", + "HP:0025031", + "UBERON:0001062", + "RO:0002577", + "UBERON:0000475", + "UBERON:0000062", + "UBERON:0013522", "UBERON:0005178", "UBERON:0004908", ], "object_closure_label": [ - "entity", - "entity", - "continuant", - "continuant", - "independent continuant", - "specifically dependent continuant", - "material entity", "All (HPO)", + "abnormality of alimentary part of gastrointestinal system physiology", + "Abnormal esophagus physiology (HPO)", + "Functional abnormality of the gastrointestinal tract (HPO)", "Phenotypic abnormality (HPO)", "Abnormality of the nervous system (HPO)", - "Dysphagia (HPO)", - "Neoplasm (HPO)", - "Abnormality of the gastrointestinal tract (HPO)", - "Neoplasm by anatomical site (HPO)", - "Abnormal nervous system physiology (HPO)", - "Functional abnormality of the gastrointestinal tract (HPO)", - "Abnormality of the digestive system (HPO)", - "Abnormality of digestive system physiology (HPO)", - "Abnormal esophagus physiology (HPO)", - "quality", + "independent continuant", "system", - "tube", "anatomical structure", - "organ", - "organ part", - "material anatomical entity", - "anatomical system", - "multicellular organism", - "organism subdivision", - "thoracic segment of trunk", "digestive system", "nervous system", - "esophagus", - "anatomical entity", "digestive tract", - "viscus", - "trunk", - "anatomical conduit", - "upper digestive tract", "subdivision of digestive tract", - "trunk region element", - "thoracic cavity element", - "thoracic segment organ", - "alimentary part of gastrointestinal system", - "subdivision of trunk", - "multicellular anatomical structure", - "subdivision of organism along main body axis", - "subdivision of tube", - "main body axis", - "body proper", - "digestive system element", + "abnormality of anatomical entity physiology", "phenotype", + "abnormality of digestive system physiology", + "abnormal digestive system", + "Dysphagia (HPO)", "Phenotypic abnormality", - "phenotype by ontology source", - "abnormal phenotype by ontology source", - "abnormality of anatomical entity physiology", "abnormality of nervous system physiology", - "abnormality of digestive system physiology", - "abnormality of alimentary part of gastrointestinal system physiology", + "phenotype by ontology source", + "abnormal nervous system", + "quality", "abnormality of esophagus physiology", + "Abnormal nervous system physiology (HPO)", + "continuant", + "material anatomical entity", + "subdivision of trunk", + "body proper", + "digestive system element", + "trunk region element", + "tube", + "abnormal phenotype by ontology source", + "continuant", + "specifically dependent continuant", + "Neoplasm (HPO)", + "Neoplasm by anatomical site (HPO)", + "entity", + "anatomical entity", + "organism subdivision", + "organ", + "alimentary part of gastrointestinal system", + "subdivision of tube", + "thoracic cavity element", + "upper digestive tract", "abnormal anatomical entity", + "Abnormality of the gastrointestinal tract (HPO)", "abnormal alimentary part of gastrointestinal system", - "abnormal digestive system", - "abnormal nervous system", - "abnormal anatomical entity", + "Abnormality of digestive system physiology (HPO)", "abnormality of anatomical entity physiology", + "abnormal anatomical entity", + "entity", + "Abnormality of the digestive system (HPO)", + "material entity", + "multicellular anatomical structure", + "anatomical system", + "anatomical conduit", + "multicellular organism", + "organ part", + "subdivision of organism along main body axis", + "main body axis", + "thoracic segment of trunk", + "esophagus", + "trunk", + "thoracic segment organ", + "viscus", ], - "object_label": "Dysphagia (HPO)", - "frequency_qualifier_namespace": "HP", - "frequency_qualifier_category": "biolink:PhenotypicFeature", - "frequency_qualifier_closure": ["HP:0000001", "HP:0040282", "HP:0040279"], - "frequency_qualifier_closure_label": ["All (HPO)", "Frequency (HPO)", "Frequent (HPO)"], "frequency_qualifier_label": "Frequent (HPO)", - "evidence_count": 6, + "frequency_qualifier_category": "biolink:PhenotypicFeature", + "frequency_qualifier_namespace": "HP", + "frequency_qualifier_closure": ["HP:0040282", "HP:0000001", "HP:0040279"], + "frequency_qualifier_closure_label": ["All (HPO)", "Frequent (HPO)", "Frequency (HPO)"], + "evidence_count": 4, + "grouping_key": "MONDO:0020793🍪🍪biolink:has_phenotype🍪HP:0002015", }, { - "id": "uuid:862bc0d4-5d8c-11ee-9b27-2b20ed86a9d9", + "id": "uuid:c6b3613a-7529-11ee-b012-cbd37f5c3759", "original_subject": "OMIM:612937", "predicate": "biolink:has_phenotype", "category": "biolink:DiseaseToPhenotypicFeatureAssociation", @@ -424,287 +426,292 @@ def association_table_response(): "has_evidence": ["ECO:0000269"], "subject": "MONDO:0013049", "object": "HP:0003236", - "subject_namespace": "MONDO", + "subject_label": "DPM3-congenital disorder of glycosylation", "subject_category": "biolink:Disease", + "subject_namespace": "MONDO", "subject_closure": [ + "BFO:0000002", + "BFO:0000020", + "MONDO:0005336", + "MONDO:0005021", "MONDO:0004994", - "MONDO:0000001", "MONDO:0018276", "MONDO:0005071", "MONDO:0005267", - "MONDO:0013049", + "BFO:0000016", + "MONDO:0016333", + "MONDO:0017749", + "OGMS:0000031", + "MONDO:0003847", + "BFO:0000001", "MONDO:0020121", "MONDO:0004995", - "MONDO:0700223", - "MONDO:0024322", - "BFO:0000002", "BFO:0000017", - "BFO:0000020", "MONDO:0005217", - "BFO:0000016", "MONDO:0020120", "MONDO:0019056", + "MONDO:0015286", + "MONDO:0019052", + "MONDO:0005500", + "MONDO:0005066", + "MONDO:0000001", + "MONDO:0013049", + "MONDO:0700223", + "MONDO:0024322", "MONDO:0700096", "MONDO:0000591", - "MONDO:0005336", "MONDO:0002081", - "MONDO:0016333", - "MONDO:0017749", - "OGMS:0000031", - "MONDO:0005021", - "MONDO:0003847", "MONDO:0003939", - "MONDO:0015286", - "BFO:0000001", "MONDO:0002320", - "MONDO:0019052", - "MONDO:0005500", - "MONDO:0005066", "MONDO:0019950", ], "subject_closure_label": [ - "entity", - "continuant", - "disposition", - "realizable entity", - "specifically dependent continuant", - "disease", + "cardiomyopathy", + "muscular dystrophy", + "cardiovascular disorder", + "human disease", "intrinsic cardiomyopathy", "musculoskeletal system disorder", - "congenital nervous system disorder", - "hereditary disease", + "disorder of multiple glycosylation", + "disease", "muscle tissue disorder", - "cardiomyopathy", - "cardiovascular disorder", - "dilated cardiomyopathy", - "metabolic disease", - "nervous system disorder", - "familial cardiomyopathy", - "heart disorder", - "myopathy", - "congenital disorder of glycosylation type I", - "DPM3-congenital disorder of glycosylation", + "congenital nervous system disorder", + "hereditary skeletal muscle disorder", + "disorder of glycosylation", + "disposition", "congenital disorder of glycosylation", + "disease", + "DPM3-congenital disorder of glycosylation", + "continuant", + "specifically dependent continuant", + "myopathy", "familial dilated cardiomyopathy", - "disorder of multiple glycosylation", - "muscular dystrophy-dystroglycanopathy", + "hereditary disease", "inborn errors of metabolism", + "congenital disorder of glycosylation type I", + "metabolic disease", + "muscular dystrophy-dystroglycanopathy", + "nervous system disorder", + "heart disorder", + "realizable entity", + "familial cardiomyopathy", + "skeletal muscle disorder", "neuromuscular disease", + "dilated cardiomyopathy", + "entity", "congenital muscular dystrophy", - "skeletal muscle disorder", - "muscular dystrophy", - "disorder of glycosylation", - "human disease", - "hereditary skeletal muscle disorder", - "disease", ], - "subject_label": "DPM3-congenital disorder of glycosylation", - "object_namespace": "HP", + "object_label": "Elevated circulating creatine kinase concentration (HPO)", "object_category": "biolink:PhenotypicFeature", + "object_namespace": "HP", "object_closure": [ - "HP:0000001", - "HP:0011021", - "HP:0004364", "UPHENO:0082875", - "UPHENO:0075696", - "UPHENO:0077817", - "UPHENO:0076289", - "UPHENO:0002448", - "UPHENO:0001001", "UPHENO:0051763", - "UPHENO:0004536", - "UPHENO:0051668", "UPHENO:0001005", + "BFO:0000020", + "UPHENO:0077820", + "BFO:0000001", + "UPHENO:0051804", + "BFO:0000015", + "BFO:0000004", + "GO:0032991", + "CHEBI:23367", + "UBERON:0000178", + "GO:1990234", + "CHEBI:33839", + "CHEBI:33675", + "UBERON:0001004", + "HP:0000001", + "HP:0011021", + "UPHENO:0001001", "UPHENO:0001002", "UPHENO:0077825", "HP:0000118", - "BFO:0000002", "HP:0001871", - "UPHENO:0077821", - "BFO:0000020", - "UPHENO:0046284", - "UPHENO:0077829", - "UPHENO:0004459", - "UPHENO:0002332", "UPHENO:0051801", - "HP:0010876", - "UPHENO:0077820", - "UPHENO:0076286", - "HP:0040081", "UPHENO:0001003", - "UPHENO:0002536", "HP:0001939", - "HP:0500165", - "UPHENO:0081547", - "UPHENO:0077826", "HP:0032180", - "BFO:0000001", - "HP:0002086", - "HP:0003236", "PATO:0000001", "HP:0002795", - "HP:0012415", - "UPHENO:0051612", - "UPHENO:0051804", "BFO:0000001", + "BFO:0000040", + "GO:0008152", + "UBERON:0000467", + "UBERON:0000468", + "GO:0061695", + "CHEBI:16670", + "CHEBI:33302", + "CHEBI:33304", + "CHEBI:33582", + "GO:0002185", + "CHEBI:15841", + "CHEBI:51143", + "CHEBI:25806", + "CHEBI:36962", + "CHEBI:50860", + "UPHENO:0075696", + "UPHENO:0077817", + "UPHENO:0076289", + "BFO:0000002", + "UPHENO:0077821", + "UPHENO:0004459", + "UPHENO:0002332", + "UPHENO:0002536", + "HP:0500165", + "HP:0002086", + "HP:0003236", "BFO:0000003", "BFO:0000002", - "BFO:0000015", - "BFO:0000004", "GO:0008150", - "BFO:0000040", - "UBERON:0001062", - "GO:0008152", "GO:0005575", "CHEBI:24431", "PR:000050567", "UBERON:0000465", - "GO:0032991", - "CHEBI:23367", - "UBERON:0000178", - "UBERON:0000061", - "UBERON:0000463", "GO:1902494", "CHEBI:36357", "CHEBI:33579", - "UBERON:0010000", - "UBERON:0000467", "UBERON:0004120", "UBERON:0006314", - "GO:1990234", - "CHEBI:33839", - "CHEBI:33675", "CHEBI:138675", - "UBERON:0000468", - "UBERON:0001004", "UBERON:0002193", "UBERON:0002390", "UBERON:0000179", - "GO:0061695", - "CHEBI:16670", - "CHEBI:33302", - "CHEBI:33304", - "CHEBI:33582", - "GO:0002185", - "CHEBI:15841", - "CHEBI:51143", - "CHEBI:25806", - "CHEBI:36962", - "CHEBI:50860", "CHEBI:16541", "CHEBI:35352", "CHEBI:32988", - "CHEBI:36963", - "CHEBI:33285", "CHEBI:50047", "CHEBI:37622", "CHEBI:33256", + "HP:0004364", + "UPHENO:0002448", + "UPHENO:0004536", + "UPHENO:0051668", + "UPHENO:0046284", + "UPHENO:0077829", + "HP:0010876", + "UPHENO:0076286", + "HP:0040081", + "UPHENO:0081547", + "UPHENO:0077826", + "HP:0012415", + "UPHENO:0051612", + "UBERON:0001062", + "UBERON:0000061", + "UBERON:0000463", + "UBERON:0010000", + "CHEBI:36963", + "CHEBI:33285", ], "object_closure_label": [ - "entity", - "entity", - "continuant", - "continuant", + "All (HPO)", + "Abnormality of circulating enzyme level (HPO)", + "abnormal multicellular organism chemical entity level", + "Phenotypic abnormality", + "abnormal blood gas molecular entity level", + "Phenotypic abnormality (HPO)", + "abnormal chemical entity level", + "abnormal independent continuant oxygen molecular entity level", + "Abnormal circulating protein concentration (HPO)", + "abnormal role blood level", + "Abnormal circulating creatine kinase concentration (HPO)", + "Abnormality of metabolism/homeostasis (HPO)", + "abnormal role bodily fluid level", + "abnormal blood nitrogen molecular entity level", + "quality", + "Abnormal respiratory system physiology (HPO)", + "process", "independent continuant", - "specifically dependent continuant", - "material entity", - "gas molecular entity", - "polypeptide", - "protein polypeptide chain", - "peptide", + "protein-containing complex", "molecular entity", - "chemical entity", - "oxygen molecular entity", - "amide", - "primary amide", - "heteroorganic entity", + "blood", + "multicellular anatomical structure", + "respiratory system", + "transferase complex, transferring phosphorus-containing groups", + "peptide", "pnictogen molecular entity", "chalcogen molecular entity", - "main group molecular entity", "carbon group molecular entity", - "p-block molecular entity", - "macromolecule", + "protein polypeptide chain", "organonitrogen compound", - "polyatomic entity", + "amide", + "abnormality of anatomical entity physiology", + "phenotype", + "Abnormality of blood and blood-forming tissues (HPO)", + "abnormal independent continuant protein polypeptide chain level", + "phenotype by ontology source", + "Abnormal blood oxygen level (HPO)", + "abnormal blood chemical entity level", + "occurrent", + "continuant", + "biological_process", + "cellular_component", + "chemical entity", + "protein-containing material entity", + "material anatomical entity", + "gas molecular entity", + "creatine kinase complex", + "polypeptide", + "nitrogen molecular entity", + "oxygen molecular entity", "organochalcogen compound", - "organooxygen compound", + "organic molecular entity", "carboxamide", + "primary amide", "organic amino compound", - "organic molecular entity", - "nitrogen molecular entity", - "creatine kinase complex", - "cellular_component", - "protein-containing complex", - "transferase complex, transferring phosphorus-containing groups", - "catalytic complex", - "transferase complex", - "All (HPO)", - "Phenotypic abnormality (HPO)", - "Abnormality of blood and blood-forming tissues (HPO)", - "Abnormality of metabolism/homeostasis (HPO)", - "Abnormality of the respiratory system (HPO)", - "Abnormal respiratory system physiology (HPO)", - "Elevated circulating creatine kinase concentration (HPO)", "Abnormal circulating nitrogen compound concentration (HPO)", - "Abnormal circulating protein concentration (HPO)", - "Abnormality of circulating enzyme level (HPO)", - "Abnormal blood gas level (HPO)", + "abnormality of respiratory system physiology", + "abnormal respiratory system", + "abnormal independent continuant chemical entity level", + "abnormal phenotype by ontology source", + "specifically dependent continuant", + "abnormal independent continuant gas molecular entity level", "Abnormal circulating metabolite concentration (HPO)", - "Abnormal circulating creatine kinase concentration (HPO)", - "Abnormal blood oxygen level (HPO)", - "quality", - "protein-containing material entity", + "Abnormality of the respiratory system (HPO)", + "Elevated circulating creatine kinase concentration (HPO)", + "entity", + "anatomical entity", "anatomical structure", - "blood", - "haemolymphatic fluid", "organism substance", - "material anatomical entity", - "anatomical system", - "multicellular organism", - "respiratory system", - "anatomical entity", - "hemolymphoid system", - "hematopoietic system", "mesoderm-derived structure", "bodily fluid", - "multicellular anatomical structure", - "phenotype", - "Phenotypic abnormality", - "phenotype by ontology source", - "abnormal phenotype by ontology source", - "abnormality of anatomical entity physiology", - "abnormality of respiratory system physiology", - "abnormal anatomical entity", - "abnormal hematopoietic system", - "abnormal respiratory system", - "abnormal chemical entity level", - "abnormal blood protein polypeptide chain level", - "abnormal independent continuant chemical entity level", - "abnormal multicellular organism chemical entity level", - "abnormal independent continuant protein polypeptide chain level", - "abnormal blood chemical entity level", + "hemolymphoid system", + "hematopoietic system", + "haemolymphatic fluid", + "organooxygen compound", + "heteroorganic entity", "abnormal anatomical entity", - "abnormal role blood level", - "abnormal role independent continuant level", "abnormal blood oxygen molecular entity level", - "abnormal independent continuant gas molecular entity level", + "abnormal role independent continuant level", + "continuant", "abnormal independent continuant nitrogen molecular entity level", - "abnormal blood gas molecular entity level", - "abnormal blood nitrogen molecular entity level", - "abnormal independent continuant oxygen molecular entity level", - "abnormal role bodily fluid level", + "abnormal hematopoietic system", "abnormality of anatomical entity physiology", + "abnormal anatomical entity", + "entity", + "Abnormal blood gas level (HPO)", + "abnormal blood protein polypeptide chain level", + "material entity", + "metabolic process", + "catalytic complex", + "polyatomic entity", + "main group molecular entity", + "anatomical system", + "transferase complex", + "macromolecule", + "p-block molecular entity", + "multicellular organism", ], - "object_label": "Elevated circulating creatine kinase concentration (HPO)", - "frequency_qualifier_namespace": "HP", - "frequency_qualifier_category": "biolink:PhenotypicFeature", - "frequency_qualifier_closure": ["HP:0000001", "HP:0040279", "HP:0040280"], - "frequency_qualifier_closure_label": ["All (HPO)", "Frequency (HPO)", "Obligate (HPO)"], "frequency_qualifier_label": "Obligate (HPO)", - "evidence_count": 5, + "frequency_qualifier_category": "biolink:PhenotypicFeature", + "frequency_qualifier_namespace": "HP", + "frequency_qualifier_closure": ["HP:0000001", "HP:0040280", "HP:0040279"], + "frequency_qualifier_closure_label": ["All (HPO)", "Obligate (HPO)", "Frequency (HPO)"], + "evidence_count": 3, + "grouping_key": "MONDO:0013049🍪🍪biolink:has_phenotype🍪HP:0003236", }, { - "id": "uuid:8a99d6f0-5d8c-11ee-9b27-2b20ed86a9d9", + "id": "uuid:cb2a2f47-7529-11ee-b012-cbd37f5c3759", "original_subject": "OMIM:254090", "predicate": "biolink:has_phenotype", "category": "biolink:DiseaseToPhenotypicFeatureAssociation", @@ -716,159 +723,160 @@ def association_table_response(): "has_evidence": ["ECO:0000269"], "subject": "MONDO:0009681", "object": "HP:0020152", - "subject_namespace": "MONDO", + "subject_label": "Ullrich congenital muscular dystrophy 1", "subject_category": "biolink:Disease", + "subject_namespace": "MONDO", "subject_closure": [ - "MONDO:0000001", + "BFO:0000020", + "MONDO:0005336", "MONDO:0005071", + "BFO:0000016", + "MONDO:0016139", + "OGMS:0000031", + "MONDO:0003847", + "BFO:0000001", "MONDO:0020121", - "MONDO:0700223", - "BFO:0000002", "MONDO:0019952", "BFO:0000017", "MONDO:0100225", - "BFO:0000020", - "BFO:0000016", "MONDO:0020120", "MONDO:0019056", - "MONDO:0016139", + "MONDO:0009681", + "MONDO:0000355", + "MONDO:0000001", + "MONDO:0700223", + "BFO:0000002", "MONDO:0700096", - "MONDO:0005336", "MONDO:0002081", - "MONDO:0009681", - "OGMS:0000031", - "MONDO:0003847", "MONDO:0003939", - "BFO:0000001", "MONDO:0002320", - "MONDO:0000355", "MONDO:0019950", ], "subject_closure_label": [ - "entity", + "muscular dystrophy", + "human disease", + "musculoskeletal system disorder", + "disease", + "muscle tissue disorder", + "congenital nervous system disorder", + "hereditary skeletal muscle disorder", "continuant", "disposition", - "realizable entity", - "specifically dependent continuant", + "qualitative or quantitative protein defects in neuromuscular diseases", + "Ullrich congenital muscular dystrophy 1", "disease", - "Ullrich congenital muscular dystrophy", - "musculoskeletal system disorder", - "congenital nervous system disorder", + "specifically dependent continuant", + "myopathy", "hereditary disease", - "muscle tissue disorder", + "Ullrich congenital muscular dystrophy", "nervous system disorder", - "myopathy", - "Ullrich congenital muscular dystrophy 1", - "qualitative or quantitative protein defects in neuromuscular diseases", - "neuromuscular disease", - "congenital muscular dystrophy", "congenital myopathy", - "skeletal muscle disorder", - "muscular dystrophy", + "realizable entity", "collagen 6-related myopathy", - "human disease", - "hereditary skeletal muscle disorder", - "disease", + "skeletal muscle disorder", + "neuromuscular disease", + "entity", + "congenital muscular dystrophy", ], - "subject_label": "Ullrich congenital muscular dystrophy 1", - "object_namespace": "HP", + "object_label": "Distal joint laxity (HPO)", "object_category": "biolink:PhenotypicFeature", + "object_namespace": "HP", "object_closure": [ - "HP:0000001", - "HP:0020152", "UPHENO:0082875", "HP:0001388", - "UPHENO:0075696", - "UPHENO:0001001", - "HP:0011729", "UPHENO:0001005", + "BFO:0000002", + "BFO:0000020", + "PATO:0000001", + "HP:0011843", + "BFO:0000004", + "UBERON:0002204", + "HP:0000001", + "HP:0020152", + "UPHENO:0001001", "UPHENO:0001002", + "HP:0000118", + "UPHENO:0002964", + "BFO:0000001", + "BFO:0000001", + "BFO:0000040", + "UBERON:0000467", + "UBERON:0000468", + "UBERON:0011216", + "UBERON:0034921", + "UPHENO:0075696", + "HP:0011729", "HP:0034430", "HP:0000924", - "HP:0000118", - "BFO:0000002", - "BFO:0000020", "UPHENO:0002332", - "UPHENO:0002964", - "HP:0033127", "UPHENO:0001003", "UPHENO:0002536", - "UPHENO:0081440", - "BFO:0000001", - "PATO:0000001", - "HP:0011843", - "BFO:0000001", "BFO:0000002", - "BFO:0000004", - "BFO:0000040", + "UBERON:0000465", + "UBERON:0004770", + "UBERON:0000982", + "HP:0033127", + "UPHENO:0081440", "UBERON:0001062", - "UBERON:0000465", "UBERON:0000061", "UBERON:0034925", "UBERON:0010000", - "UBERON:0000467", - "UBERON:0004770", - "UBERON:0000468", - "UBERON:0011216", - "UBERON:0034921", - "UBERON:0002204", "UBERON:0004905", "UBERON:0001434", - "UBERON:0000982", ], "object_closure_label": [ - "entity", - "entity", - "continuant", - "continuant", - "independent continuant", - "specifically dependent continuant", - "material entity", "All (HPO)", + "Distal joint laxity (HPO)", + "Phenotypic abnormality", "Phenotypic abnormality (HPO)", - "Abnormality of the skeletal system (HPO)", + "Abnormality of the musculoskeletal system (HPO)", + "abnormality of musculoskeletal system physiology", + "independent continuant", + "multicellular anatomical structure", + "musculoskeletal system", + "skeletal joint", + "abnormality of anatomical entity physiology", "Joint laxity (HPO)", + "phenotype", "Abnormality of joint mobility (HPO)", - "Abnormality of musculoskeletal physiology (HPO)", - "Distal joint laxity (HPO)", - "Abnormality of the musculoskeletal system (HPO)", - "Abnormal joint physiology", + "abnormal skeletal system", "quality", - "anatomical structure", + "Abnormality of musculoskeletal physiology (HPO)", + "continuant", "material anatomical entity", - "anatomical system", - "multicellular organism", - "skeletal joint", + "abnormal phenotype by ontology source", + "continuant", + "specifically dependent continuant", + "entity", "anatomical entity", - "skeletal system", - "musculoskeletal system", + "anatomical structure", + "anatomical collection", "articular system", "articulation", - "multicellular anatomical structure", - "organ system subdivision", - "multi organ part structure", - "anatomical collection", - "phenotype", - "Phenotypic abnormality", - "phenotype by ontology source", - "abnormal phenotype by ontology source", - "abnormality of anatomical entity physiology", - "abnormal anatomical entity", - "abnormal skeletal system", + "skeletal system", "abnormal anatomical entity", - "abnormality of musculoskeletal system physiology", + "Abnormal joint physiology", + "Abnormality of the skeletal system (HPO)", "abnormality of anatomical entity physiology", + "phenotype by ontology source", + "abnormal anatomical entity", + "entity", + "material entity", + "anatomical system", + "multicellular organism", + "organ system subdivision", + "multi organ part structure", ], - "object_label": "Distal joint laxity (HPO)", - "frequency_qualifier_namespace": "HP", - "frequency_qualifier_category": "biolink:PhenotypicFeature", - "frequency_qualifier_closure": ["HP:0000001", "HP:0040279", "HP:0040280"], - "frequency_qualifier_closure_label": ["All (HPO)", "Frequency (HPO)", "Obligate (HPO)"], "frequency_qualifier_label": "Obligate (HPO)", - "evidence_count": 5, + "frequency_qualifier_category": "biolink:PhenotypicFeature", + "frequency_qualifier_namespace": "HP", + "frequency_qualifier_closure": ["HP:0000001", "HP:0040280", "HP:0040279"], + "frequency_qualifier_closure_label": ["All (HPO)", "Obligate (HPO)", "Frequency (HPO)"], + "evidence_count": 3, + "grouping_key": "MONDO:0009681🍪🍪biolink:has_phenotype🍪HP:0020152", }, { - "id": "uuid:894ab8ce-5d8c-11ee-9b27-2b20ed86a9d9", + "id": "uuid:c9d8bdf9-7529-11ee-b012-cbd37f5c3759", "original_subject": "OMIM:253601", "predicate": "biolink:has_phenotype", "category": "biolink:DiseaseToPhenotypicFeatureAssociation", @@ -880,154 +888,155 @@ def association_table_response(): "has_evidence": ["ECO:0000269"], "subject": "MONDO:0009676", "object": "HP:0003701", - "subject_namespace": "MONDO", + "subject_label": "autosomal recessive limb-girdle muscular dystrophy type 2B", "subject_category": "biolink:Disease", + "subject_namespace": "MONDO", "subject_closure": [ - "MONDO:0000001", "MONDO:0016971", - "MONDO:0000429", - "MONDO:0016145", - "MONDO:0005071", - "MONDO:0020121", - "MONDO:0700223", "BFO:0000002", - "BFO:0000017", "BFO:0000020", + "MONDO:0005336", + "MONDO:0009676", + "MONDO:0015152", + "MONDO:0000429", + "MONDO:0005071", "MONDO:0006025", - "MONDO:0016106", "BFO:0000016", + "MONDO:0016139", + "OGMS:0000031", + "MONDO:0003847", + "BFO:0000001", + "MONDO:0016145", + "MONDO:0020121", + "BFO:0000017", "MONDO:0020120", "MONDO:0019056", - "MONDO:0016139", + "MONDO:0000001", + "MONDO:0700223", + "MONDO:0016106", "MONDO:0700096", - "MONDO:0005336", "MONDO:0002081", - "MONDO:0009676", - "OGMS:0000031", - "MONDO:0003847", "MONDO:0003939", - "MONDO:0015152", - "BFO:0000001", ], "subject_closure_label": [ - "entity", - "continuant", - "disposition", - "realizable entity", - "specifically dependent continuant", - "disease", - "autosomal genetic disease", - "musculoskeletal system disorder", - "hereditary disease", - "muscle tissue disorder", - "nervous system disorder", - "myopathy", - "autosomal recessive disease", - "autosomal recessive limb-girdle muscular dystrophy type 2B", - "autosomal recessive limb-girdle muscular dystrophy", - "progressive muscular dystrophy", - "qualitative or quantitative protein defects in neuromuscular diseases", - "qualitative or quantitative defects of dysferlin", "limb-girdle muscular dystrophy", - "neuromuscular disease", - "skeletal muscle disorder", "muscular dystrophy", + "progressive muscular dystrophy", "human disease", + "musculoskeletal system disorder", + "disease", + "muscle tissue disorder", + "qualitative or quantitative defects of dysferlin", "hereditary skeletal muscle disorder", + "autosomal recessive disease", + "disposition", + "qualitative or quantitative protein defects in neuromuscular diseases", + "autosomal recessive limb-girdle muscular dystrophy type 2B", "disease", + "continuant", + "specifically dependent continuant", + "myopathy", + "hereditary disease", + "autosomal genetic disease", + "nervous system disorder", + "realizable entity", + "skeletal muscle disorder", + "neuromuscular disease", + "autosomal recessive limb-girdle muscular dystrophy", + "entity", ], - "subject_label": "autosomal recessive limb-girdle muscular dystrophy type 2B", - "object_namespace": "HP", + "object_label": "Proximal muscle weakness (HPO)", "object_category": "biolink:PhenotypicFeature", + "object_namespace": "HP", "object_closure": [ - "HP:0000001", "UPHENO:0082875", - "UPHENO:0075696", "UPHENO:0002320", + "BFO:0000002", + "BFO:0000004", + "UBERON:0000061", + "HP:0000001", "UPHENO:0001001", - "UPHENO:0001005", - "HP:0003701", "UPHENO:0001002", - "HP:0001324", "HP:0000118", - "BFO:0000002", "BFO:0000020", - "UPHENO:0080555", - "HP:0003011", - "UPHENO:0002816", - "UPHENO:0002332", - "UPHENO:0080556", - "HP:0033127", "UPHENO:0001003", - "UPHENO:0002536", "BFO:0000001", - "HP:0011804", "PATO:0000001", "BFO:0000001", - "BFO:0000002", - "BFO:0000004", "BFO:0000040", "UBERON:0001062", - "UBERON:0000465", - "UBERON:0000061", - "UBERON:0010000", "UBERON:0000467", - "UBERON:0005090", - "UBERON:0000062", "UBERON:0000468", "UBERON:0011216", + "UPHENO:0075696", + "HP:0001324", + "HP:0003011", + "UPHENO:0002332", + "UPHENO:0002536", + "HP:0011804", + "BFO:0000002", + "UBERON:0000465", + "UBERON:0005090", "UBERON:0001630", + "UPHENO:0001005", + "HP:0003701", + "UPHENO:0080555", + "UPHENO:0002816", + "UPHENO:0080556", + "HP:0033127", + "UBERON:0010000", + "UBERON:0000062", "UBERON:0000383", "UBERON:0001015", ], "object_closure_label": [ - "entity", - "entity", - "continuant", - "continuant", - "independent continuant", - "specifically dependent continuant", - "material entity", "All (HPO)", + "abnormality of muscle organ physiology", + "Phenotypic abnormality", "Phenotypic abnormality (HPO)", - "Muscle weakness (HPO)", - "Abnormality of the musculature (HPO)", - "Proximal muscle weakness (HPO)", - "Abnormal muscle physiology (HPO)", + "decreased anatomical entity strength", + "abnormal musculature", + "decreased muscle organ strength", "Abnormality of the musculoskeletal system (HPO)", "quality", + "independent continuant", "anatomical structure", - "organ", - "musculature of body", - "material anatomical entity", - "anatomical system", - "multicellular organism", - "musculature", - "anatomical entity", - "muscle organ", - "muscle structure", "multicellular anatomical structure", - "organ system subdivision", + "abnormality of anatomical entity physiology", "phenotype", - "Phenotypic abnormality", - "phenotype by ontology source", "abnormal phenotype by ontology source", - "abnormality of muscle organ physiology", - "abnormality of anatomical entity physiology", - "abnormal anatomical entity", - "abnormal musculature", + "Proximal muscle weakness (HPO)", + "specifically dependent continuant", + "phenotype by ontology source", + "continuant", + "material anatomical entity", + "continuant", + "Abnormal muscle physiology (HPO)", + "entity", + "muscle structure", + "organ", + "muscle organ", + "musculature of body", + "musculature", "abnormal anatomical entity", - "decreased anatomical entity strength", - "decreased muscle organ strength", + "Muscle weakness (HPO)", + "Abnormality of the musculature (HPO)", "abnormality of anatomical entity physiology", + "abnormal anatomical entity", + "entity", + "material entity", + "anatomical entity", + "anatomical system", + "multicellular organism", + "organ system subdivision", ], - "object_label": "Proximal muscle weakness (HPO)", - "frequency_qualifier_namespace": "HP", - "frequency_qualifier_category": "biolink:PhenotypicFeature", - "frequency_qualifier_closure": ["HP:0000001", "HP:0040279", "HP:0040280"], - "frequency_qualifier_closure_label": ["All (HPO)", "Frequency (HPO)", "Obligate (HPO)"], "frequency_qualifier_label": "Obligate (HPO)", - "evidence_count": 5, + "frequency_qualifier_category": "biolink:PhenotypicFeature", + "frequency_qualifier_namespace": "HP", + "frequency_qualifier_closure": ["HP:0000001", "HP:0040280", "HP:0040279"], + "frequency_qualifier_closure_label": ["All (HPO)", "Obligate (HPO)", "Frequency (HPO)"], + "evidence_count": 3, + "grouping_key": "MONDO:0009676🍪🍪biolink:has_phenotype🍪HP:0003701", }, ], }, diff --git a/backend/tests/fixtures/associations.py b/backend/tests/fixtures/associations.py index 571a93b9d..b85ec11ce 100644 --- a/backend/tests/fixtures/associations.py +++ b/backend/tests/fixtures/associations.py @@ -6,195 +6,283 @@ def associations(): return { "limit": 20, "offset": 0, - "total": 4835, + "total": 4838, "items": [ { - "id": "uuid:8a89d08e-5d8c-11ee-9b27-2b20ed86a9d9", + "id": "uuid:c9c8bf2f-7529-11ee-b012-cbd37f5c3759", "category": "biolink:DiseaseToPhenotypicFeatureAssociation", - "subject": "MONDO:0011246", - "original_subject": "OMIM:602541", + "subject": "MONDO:0008050", + "original_subject": "OMIM:160500", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ - "MONDO:0000001", + "BFO:0000002", + "MONDO:0016195", + "MONDO:0005336", + "MONDO:0018949", "MONDO:0005071", + "MONDO:0008050", + "BFO:0000016", + "MONDO:0016139", + "OGMS:0000031", + "MONDO:0003847", + "BFO:0000001", "MONDO:0020121", - "MONDO:0700223", - "BFO:0000002", - "MONDO:0018117", + "MONDO:0019952", "BFO:0000017", "BFO:0000020", - "MONDO:0002525", - "BFO:0000016", "MONDO:0020120", "MONDO:0019056", + "MONDO:0000001", + "MONDO:0700223", "MONDO:0700096", - "MONDO:0005336", "MONDO:0002081", - "OGMS:0000031", - "MONDO:0003847", "MONDO:0003939", - "BFO:0000001", "MONDO:0002320", - "MONDO:0019052", - "MONDO:0005066", - "MONDO:0019950", - "MONDO:0011246", ], - "subject_label": "megaconial type congenital muscular dystrophy", + "subject_label": "MYH7-related skeletal myopathy", "subject_closure_label": [ - "entity", - "continuant", - "disposition", - "realizable entity", - "specifically dependent continuant", - "disease", + "muscular dystrophy", + "human disease", "musculoskeletal system disorder", + "disease", + "muscle tissue disorder", "congenital nervous system disorder", - "inherited lipid metabolism disorder", + "hereditary skeletal muscle disorder", + "MYH7-related skeletal myopathy", + "disposition", + "qualitative or quantitative protein defects in neuromuscular diseases", + "distal myopathy", + "disease", + "continuant", + "qualitative or quantitative defects of beta-myosin heavy chain (MYH7)", + "myopathy", "hereditary disease", - "muscle tissue disorder", - "metabolic disease", "nervous system disorder", - "myopathy", - "megaconial type congenital muscular dystrophy", - "disorder of phospholipids, sphingolipids and fatty acids biosynthesis", - "inborn errors of metabolism", - "neuromuscular disease", - "congenital muscular dystrophy", + "congenital myopathy", + "realizable entity", + "specifically dependent continuant", "skeletal muscle disorder", - "muscular dystrophy", - "human disease", - "hereditary skeletal muscle disorder", - "disease", + "neuromuscular disease", + "entity", ], "subject_taxon": None, "subject_taxon_label": None, "predicate": "biolink:has_phenotype", - "object": "HP:0008064", + "object": "HP:0011399", "original_object": None, "object_namespace": "HP", "object_category": "biolink:PhenotypicFeature", "object_closure": [ - "HP:0000001", - "UPHENO:0047821", - "UPHENO:0075696", - "UPHENO:0001001", - "UPHENO:0081431", - "UPHENO:0003811", - "UPHENO:0065599", - "UPHENO:0048320", + "UPHENO:0014121", + "HP:0002814", + "UPHENO:0068971", "UPHENO:0001005", - "HP:0001072", + "HP:0009127", + "UPHENO:0014120", + "UPHENO:0075195", + "HP:0030236", + "UPHENO:0020584", + "UPHENO:0076692", + "UPHENO:0003070", + "PATO:0000001", + "UPHENO:0012541", + "BFO:0000004", + "UBERON:0004708", + "UBERON:0000154", + "UBERON:0014892", + "UBERON:0006058", + "UBERON:0002529", + "UBERON:0006067", + "HP:0000001", + "UPHENO:0002644", + "UPHENO:0013936", + "HP:0003202", + "UPHENO:0075952", "UPHENO:0001002", "HP:0000118", - "BFO:0000002", - "HP:0011368", - "HP:0011121", - "UPHENO:0076739", - "BFO:0000020", - "HP:0008064", - "UPHENO:0075195", - "UPHENO:0002635", "UPHENO:0015280", - "UPHENO:0001072", - "UPHENO:0081581", "UPHENO:0001003", - "UPHENO:0002536", - "UPHENO:0047979", - "UPHENO:0020584", - "UPHENO:0076692", + "UPHENO:0076710", "BFO:0000001", - "HP:0000951", - "PATO:0000001", - "HP:0001574", "BFO:0000001", - "BFO:0000003", - "BFO:0000002", - "BFO:0000015", - "BFO:0000004", - "GO:0008150", "BFO:0000040", - "UBERON:0001062", - "GO:0009987", - "GO:0032501", - "GO:0032502", - "PR:000050567", - "UBERON:0000465", - "GO:0048869", - "GO:0031424", - "GO:0048856", - "UBERON:0002416", - "UBERON:0002199", - "UBERON:0002097", - "UBERON:0000061", - "GO:0030154", - "GO:0009888", - "GO:0048513", - "UBERON:0004121", "UBERON:0010000", "UBERON:0000467", - "GO:0030855", - "GO:0060429", - "GO:0008544", - "GO:0043588", - "UBERON:0000062", "UBERON:0000468", "UBERON:0011216", - "GO:0009913", - "GO:0030216", + "UBERON:0010709", + "UBERON:0000366", + "UBERON:0003661", + "UBERON:0010890", + "UBERON:0010538", + "UBERON:0004466", + "UBERON:0004256", + "UBERON:0003823", + "UPHENO:0075696", + "HP:0002981", + "HP:0003797", + "UPHENO:0014111", + "HP:0001430", + "BFO:0000002", + "HP:0008944", + "BFO:0000020", + "HP:0003011", + "UPHENO:0002536", + "HP:0001437", + "UPHENO:0078056", + "HP:0040064", + "BFO:0000002", + "PR:000050567", + "UBERON:0002101", + "UBERON:0004709", + "UBERON:0005090", + "UBERON:0018254", + "UBERON:0002103", + "UBERON:0010707", + "UBERON:0001630", + "UBERON:0000026", + "UBERON:0010758", + "UBERON:0007271", + "UBERON:0014792", + "UBERON:0004482", + "UBERON:0001383", + "UBERON:0008784", + "UBERON:0002471", + "HP:0007210", + "UPHENO:0001001", + "UPHENO:0075777", + "HP:0011805", + "HP:0003693", + "UPHENO:0002816", + "HP:0011399", + "UPHENO:0081581", + "HP:0033127", + "UPHENO:0019778", + "UPHENO:0002647", + "UPHENO:0013920", + "UPHENO:0002830", + "UBERON:0001062", + "UBERON:0000465", + "RO:0002577", + "UBERON:0000061", + "UBERON:0015212", + "UBERON:0000475", + "UBERON:0000062", + "UBERON:0000383", + "UBERON:0001015", + "UBERON:0000978", + "UBERON:0007270", + "UBERON:0004480", + "UBERON:0003663", + "UBERON:0014795", + "UBERON:0008230", ], - "object_label": "Ichthyosis (HPO)", + "object_label": "Tibialis atrophy (HPO)", "object_closure_label": [ - "entity", - "entity", - "continuant", - "continuant", - "independent continuant", - "specifically dependent continuant", - "material entity", "All (HPO)", + "abnormal musculature of lower limb", + "Abnormality of the lower limb (HPO)", + "decreased size of the anatomical entity", + "Phenotypic abnormality", "Phenotypic abnormality (HPO)", - "Abnormality of the skin (HPO)", - "Thickened skin (HPO)", - "Abnormality of the integument (HPO)", - "Ichthyosis (HPO)", - "Abnormality of skin morphology (HPO)", - "Epidermal thickening (HPO)", + "Distal amyotrophy (HPO)", + "abnormal musculature", + "Tibialis atrophy (HPO)", + "abnormal multicellular organism morphology", + "Abnormality of the musculoskeletal system (HPO)", + "abnormal musculature of limb", + "independent continuant", + "material anatomical entity", + "system", + "paired limb/fin", + "lateral structure", + "pelvic complex", + "appendage musculature", + "musculature of pelvic complex", + "musculature of leg", + "hindlimb zeugopod muscle", + "hindlimb zeugopod", + "musculature of limb atrophy", + "Limb-girdle muscle atrophy (HPO)", + "skeletal musculature atrophy", + "abnormal hindlimb zeugopod muscle", + "Abnormal skeletal muscle morphology (HPO)", + "abnormal anatomical entity morphology in the independent continuant", + "phenotype by ontology source", + "Abnormality of muscle size (HPO)", + "Abnormality of the musculature of the lower limbs (HPO)", + "tibialis atrophy", + "Abnormality of limbs (HPO)", "quality", + "decreased size of the anatomical entity in the independent continuant", + "continuant", "protein-containing material entity", - "anatomical structure", - "organ", - "material anatomical entity", - "anatomical system", - "multicellular organism", - "anatomical entity", - "skin of body", - "integument", - "integumental system", - "ectoderm-derived structure", - "multicellular anatomical structure", - "organ system subdivision", + "hindlimb", + "appendage girdle complex", + "appendage", + "subdivision of organism along appendicular axis", + "flexor muscle", + "limb muscle", + "pelvic complex muscle", + "paired limb/fin segment", + "musculature of lower limb", + "muscle of leg", + "lower limb segment", + "zeugopod", + "Lower limb amyotrophy (HPO)", "phenotype", - "Phenotypic abnormality", - "phenotype by ontology source", "abnormal phenotype by ontology source", - "increased size of the anatomical entity", - "abnormal anatomical entity", - "abnormal integument", - "abnormal skin of body", - "abnormal anatomical entity morphology in the independent continuant", - "abnormal anatomical entity morphology", - "increased thickness of the anatomical entity", - "increased thickness of the skin of body", - "increased thickness of the anatomical entity in independent continuant", - "increased size of the anatomical entity in independent continuant", + "Abnormality of the musculature of the limbs (HPO)", + "musculature of lower limb atrophy", "abnormal size of anatomical entity", + "abnormal muscle organ morphology", + "abnormal muscle organ morphology", + "entity", + "anatomical entity", + "anatomical structure", + "muscle structure", + "skeletal musculature", + "organism subdivision", + "organ", + "muscle organ", + "musculature of body", + "musculature", + "leg", + "pelvic appendage musculature", + "musculature of limb", + "hindlimb muscle", + "pelvic appendage muscle", + "tibialis", + "abnormal anatomical entity", + "Abnormality of the calf (HPO)", + "anatomical entity atrophy", + "Skeletal muscle atrophy (HPO)", + "abnormal hindlimb zeugopod", + "Abnormality of the calf musculature (HPO)", + "continuant", + "Distal lower limb amyotrophy (HPO)", + "specifically dependent continuant", + "Abnormality of the musculature (HPO)", "abnormal anatomical entity", "abnormal anatomical entity morphology", - "abnormal skin of body morphology", - "abnormal skin of body morphology in the independent continuant", - "abnormal multicellular organism morphology", + "abnormal anatomical entity morphology", + "abnormal leg", + "entity", + "muscle organ atrophy", + "abnormal limb", + "material entity", + "limb", + "pelvic appendage", + "multicellular anatomical structure", + "anatomical system", + "multicellular organism", + "organ system subdivision", + "posterior region of body", + "skeletal muscle organ", + "multi-limb segment region", + "limb segment", + "musculature of hindlimb zeugopod", ], "object_taxon": None, "object_taxon_label": None, @@ -202,26 +290,32 @@ def associations(): "aggregator_knowledge_source": ["infores:monarchinitiative"], "negated": None, "pathway": None, - "evidence_count": 4, - "has_evidence": ["ECO:0000304"], - "has_evidence_links": [{"id": "ECO:0000304", "url": "http://purl.obolibrary.org/obo/ECO_0000304"}], + "evidence_count": 2, + "has_evidence": ["ECO:0000269"], + "has_evidence_links": [{"id": "ECO:0000269", "url": "http://purl.obolibrary.org/obo/ECO_0000269"}], + "grouping_key": "MONDO:0008050🍪🍪biolink:has_phenotype🍪HP:0011399", "provided_by": "hpoa_disease_to_phenotype_edges", "provided_by_link": { "id": "hpoa_disease_to_phenotype", "url": "https://monarch-initiative.github.io/monarch-ingest/Sources/hpoa/#disease_to_phenotype", }, - "publications": ["OMIM:602541"], - "publications_links": [{"id": "OMIM:602541", "url": "http://identifiers.org/mim/602541"}], + "publications": ["PMID:17548557"], + "publications_links": [{"id": "PMID:17548557", "url": "http://identifiers.org/pubmed/17548557"}], "qualifiers": [], - "frequency_qualifier": None, + "frequency_qualifier": "HP:0040280", "onset_qualifier": None, "sex_qualifier": None, "stage_qualifier": None, - "frequency_qualifier_label": None, - "frequency_qualifier_namespace": None, - "frequency_qualifier_category": None, - "frequency_qualifier_closure": [], - "frequency_qualifier_closure_label": [], + "qualifiers_label": None, + "qualifiers_namespace": None, + "qualifiers_category": None, + "qualifiers_closure": [], + "qualifiers_closure_label": [], + "frequency_qualifier_label": "Obligate (HPO)", + "frequency_qualifier_namespace": "HP", + "frequency_qualifier_category": "biolink:PhenotypicFeature", + "frequency_qualifier_closure": ["HP:0000001", "HP:0040280", "HP:0040279"], + "frequency_qualifier_closure_label": ["All (HPO)", "Obligate (HPO)", "Frequency (HPO)"], "onset_qualifier_label": None, "onset_qualifier_namespace": None, "onset_qualifier_category": None, @@ -239,216 +333,220 @@ def associations(): "stage_qualifier_closure_label": [], }, { - "id": "uuid:898aa71d-5d8c-11ee-9b27-2b20ed86a9d9", + "id": "uuid:c9c8bf30-7529-11ee-b012-cbd37f5c3759", "category": "biolink:DiseaseToPhenotypicFeatureAssociation", - "subject": "MONDO:0012193", - "original_subject": "OMIM:609115", + "subject": "MONDO:0008050", + "original_subject": "OMIM:160500", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ - "MONDO:0000001", - "MONDO:0016971", - "MONDO:0000429", + "BFO:0000002", + "MONDO:0016195", + "MONDO:0005336", + "MONDO:0018949", "MONDO:0005071", + "MONDO:0008050", + "BFO:0000016", + "MONDO:0016139", + "OGMS:0000031", + "MONDO:0003847", + "BFO:0000001", "MONDO:0020121", - "MONDO:0700223", - "BFO:0000002", + "MONDO:0019952", "BFO:0000017", "BFO:0000020", - "MONDO:0016106", - "BFO:0000016", "MONDO:0020120", "MONDO:0019056", - "MONDO:0015151", + "MONDO:0000001", + "MONDO:0700223", "MONDO:0700096", - "MONDO:0005336", "MONDO:0002081", - "MONDO:0012193", - "MONDO:0000426", - "OGMS:0000031", - "MONDO:0003847", "MONDO:0003939", - "BFO:0000001", + "MONDO:0002320", ], - "subject_label": "autosomal dominant limb-girdle muscular dystrophy type 1G", + "subject_label": "MYH7-related skeletal myopathy", "subject_closure_label": [ - "entity", - "continuant", + "muscular dystrophy", + "human disease", + "musculoskeletal system disorder", + "disease", + "muscle tissue disorder", + "congenital nervous system disorder", + "hereditary skeletal muscle disorder", + "MYH7-related skeletal myopathy", "disposition", - "realizable entity", - "specifically dependent continuant", + "qualitative or quantitative protein defects in neuromuscular diseases", + "distal myopathy", "disease", - "autosomal dominant disease", - "autosomal genetic disease", - "musculoskeletal system disorder", + "continuant", + "qualitative or quantitative defects of beta-myosin heavy chain (MYH7)", + "myopathy", "hereditary disease", - "muscle tissue disorder", "nervous system disorder", - "myopathy", - "autosomal dominant limb-girdle muscular dystrophy type 1G", - "muscular dystrophy, limb-girdle, autosomal dominant", - "progressive muscular dystrophy", - "limb-girdle muscular dystrophy", - "neuromuscular disease", + "congenital myopathy", + "realizable entity", + "specifically dependent continuant", "skeletal muscle disorder", - "muscular dystrophy", - "human disease", - "hereditary skeletal muscle disorder", - "disease", + "neuromuscular disease", + "entity", ], "subject_taxon": None, "subject_taxon_label": None, "predicate": "biolink:has_phenotype", - "object": "HP:0008116", + "object": "HP:0031295", "original_object": None, "object_namespace": "HP", "object_category": "biolink:PhenotypicFeature", "object_closure": [ - "HP:0000001", - "UPHENO:0002644", - "HP:0008116", - "HP:0002814", - "UPHENO:0001001", - "HP:0001436", "UPHENO:0001005", - "HP:0009127", - "HP:0011805", - "UPHENO:0001002", - "HP:0000118", "BFO:0000002", - "UPHENO:0002653", + "UPHENO:0075195", + "UPHENO:0020584", + "UPHENO:0076692", + "BFO:0000004", + "UBERON:0004535", + "UBERON:0011676", + "UBERON:0013701", + "UBERON:0002081", + "UBERON:0000915", + "UBERON:0002100", + "UBERON:0005181", + "UBERON:0002075", + "UBERON:0015228", + "HP:0000001", + "UPHENO:0019897", + "HP:0030680", + "HP:0000118", + "HP:0001627", "BFO:0000020", - "HP:0003011", - "UPHENO:0002816", - "UPHENO:0081581", - "HP:0033127", + "UPHENO:0019919", + "UPHENO:0076776", + "UPHENO:0015280", + "UPHENO:0001020", "UPHENO:0001003", - "UPHENO:0002536", - "HP:0001437", - "UPHENO:0076692", - "UPHENO:0003070", - "UPHENO:0002647", - "UPHENO:0076710", - "HP:0040064", "BFO:0000001", "PATO:0000001", - "UPHENO:0002830", "BFO:0000001", - "BFO:0000002", - "BFO:0000004", "BFO:0000040", - "UBERON:0001062", + "UBERON:0000467", + "UBERON:0000468", + "UBERON:0000064", + "UBERON:0002079", + "UPHENO:0075696", + "UPHENO:0015303", + "HP:0001626", + "UPHENO:0080362", + "UPHENO:0065599", + "HP:0031295", + "UPHENO:0002536", + "UPHENO:0076810", "PR:000050567", "UBERON:0000465", + "UBERON:0004120", + "UBERON:0035553", + "UBERON:0000948", + "UBERON:0001009", + "UBERON:0004151", + "UBERON:0009569", + "UBERON:0013702", + "UBERON:0005177", + "UBERON:0003103", + "UBERON:0015410", + "UPHENO:0001001", + "UPHENO:0001002", + "UPHENO:0015324", + "HP:0025579", + "UPHENO:0001072", + "UPHENO:0081581", + "HP:0005120", + "UPHENO:0015329", + "BFO:0000002", + "UBERON:0001062", "RO:0002577", - "UBERON:0004708", "UBERON:0000061", - "UBERON:0002101", - "UBERON:0004709", "UBERON:0015212", + "UBERON:0010314", "UBERON:0010000", - "UBERON:0000467", - "UBERON:0005090", - "UBERON:0002103", - "UBERON:0010707", "UBERON:0000475", "UBERON:0000062", - "UBERON:0000468", - "UBERON:0011216", - "UBERON:0001630", - "UBERON:0010709", - "UBERON:0000154", - "UBERON:0000026", - "UBERON:0010758", - "UBERON:0000383", - "UBERON:0001015", - "UBERON:0006058", - "UBERON:0007271", - "UBERON:0014792", - "UBERON:0010538", - "UBERON:0000978", - "UBERON:0007270", - "UBERON:0004480", - "UBERON:0002529", - "UBERON:0004482", - "UBERON:0008784", - "UBERON:0002470", - "UBERON:0004488", - "UBERON:0002387", + "UBERON:0005178", + "UBERON:0007100", ], - "object_label": "Flexion limitation of toes (HPO)", + "object_label": "Left atrial enlargement (HPO)", "object_closure_label": [ - "entity", - "entity", - "continuant", - "continuant", - "independent continuant", - "specifically dependent continuant", - "material entity", "All (HPO)", + "abnormal cardiac atrium morphology", + "abnormal cardiovascular system", + "increased size of the anatomical entity in independent continuant", "Phenotypic abnormality (HPO)", - "Abnormality of the foot musculature (HPO)", - "Abnormality of the musculature of the lower limbs (HPO)", - "Abnormality of the lower limb (HPO)", - "Abnormality of the musculature (HPO)", - "Flexion limitation of toes (HPO)", - "Abnormality of the musculature of the limbs (HPO)", - "Abnormal skeletal muscle morphology (HPO)", - "Abnormality of the musculoskeletal system (HPO)", - "Abnormality of limbs (HPO)", + "abnormal anatomical entity morphology in the heart", + "Abnormal left atrium morphology (HPO)", + "increased size of the anatomical entity", + "abnormal multicellular organism morphology", + "Abnormal cardiac atrium morphology (HPO)", "quality", - "protein-containing material entity", + "independent continuant", "system", - "appendage", - "anatomical structure", - "organ", - "posterior region of body", - "musculature of body", - "material anatomical entity", - "anatomical system", - "multicellular organism", - "organism subdivision", - "leg", - "musculature", - "anatomical entity", - "muscle organ", - "limb", - "hindlimb", - "pes", - "autopod region", - "limb segment", - "musculature of limb", - "musculature of lower limb", - "musculature of pes", - "paired limb/fin", - "pelvic appendage", - "muscle structure", - "multi-limb segment region", - "pelvic appendage musculature", - "appendage musculature", - "lower limb segment", - "multicellular anatomical structure", - "paired limb/fin segment", - "appendage girdle complex", - "pelvic complex", - "subdivision of organism along appendicular axis", - "organ system subdivision", - "musculature of pelvic complex", + "cardiovascular system", "lateral structure", - "phenotype", + "structure with developmental contribution from neural crest", + "multicellular anatomical structure", + "left cardiac atrium", + "Abnormality of the cardiovascular system (HPO)", "Phenotypic abnormality", + "Abnormal heart morphology (HPO)", + "specifically dependent continuant", + "abnormal left cardiac atrium morphology", + "abnormal cardiovascular system morphology", + "abnormal anatomical entity morphology in the independent continuant", + "increased size of the left cardiac atrium", "phenotype by ontology source", + "abnormal heart morphology", + "protein-containing material entity", + "material anatomical entity", + "left cardiac chamber", + "heart", + "subdivision of trunk", + "body proper", + "trunk region element", + "compound organ", + "heart plus pericardium", + "phenotype", "abnormal phenotype by ontology source", + "continuant", + "abnormal size of anatomical entity", + "entity", + "anatomical entity", + "anatomical structure", + "mesoderm-derived structure", + "organism subdivision", + "organ", + "circulatory system", + "cardiac chamber", + "thoracic cavity element", + "primary circulatory organ", + "abnormal anatomical entity", + "abnormal cardiac atrium morphology in the heart", + "Abnormality of cardiovascular system morphology (HPO)", + "Left atrial enlargement (HPO)", "abnormal anatomical entity", - "abnormal musculature of lower limb", - "abnormal musculature of limb", - "abnormal musculature of pes", - "abnormal musculature", - "abnormal limb", - "abnormal leg", "abnormal anatomical entity morphology", - "abnormal muscle organ morphology", - "abnormal multicellular organism morphology", + "abnormal anatomical entity morphology", + "entity", + "abnormal cardiac atrium morphology in the independent continuant", + "continuant", + "material entity", + "anatomical system", + "multicellular organism", + "organ part", + "subdivision of organism along main body axis", + "main body axis", + "cardiac atrium", + "thoracic segment of trunk", + "trunk", + "thoracic segment organ", + "viscus", + "circulatory organ", ], "object_taxon": None, "object_taxon_label": None, @@ -456,26 +554,32 @@ def associations(): "aggregator_knowledge_source": ["infores:monarchinitiative"], "negated": None, "pathway": None, - "evidence_count": 4, - "has_evidence": ["ECO:0000501"], - "has_evidence_links": [{"id": "ECO:0000501", "url": "http://purl.obolibrary.org/obo/ECO_0000501"}], + "evidence_count": 2, + "has_evidence": ["ECO:0000269"], + "has_evidence_links": [{"id": "ECO:0000269", "url": "http://purl.obolibrary.org/obo/ECO_0000269"}], + "grouping_key": "MONDO:0008050🍪🍪biolink:has_phenotype🍪HP:0031295", "provided_by": "hpoa_disease_to_phenotype_edges", "provided_by_link": { "id": "hpoa_disease_to_phenotype", "url": "https://monarch-initiative.github.io/monarch-ingest/Sources/hpoa/#disease_to_phenotype", }, - "publications": ["OMIM:609115"], - "publications_links": [{"id": "OMIM:609115", "url": "http://identifiers.org/mim/609115"}], + "publications": ["PMID:17548557"], + "publications_links": [{"id": "PMID:17548557", "url": "http://identifiers.org/pubmed/17548557"}], "qualifiers": [], - "frequency_qualifier": None, + "frequency_qualifier": "HP:0040280", "onset_qualifier": None, "sex_qualifier": None, "stage_qualifier": None, - "frequency_qualifier_label": None, - "frequency_qualifier_namespace": None, - "frequency_qualifier_category": None, - "frequency_qualifier_closure": [], - "frequency_qualifier_closure_label": [], + "qualifiers_label": None, + "qualifiers_namespace": None, + "qualifiers_category": None, + "qualifiers_closure": [], + "qualifiers_closure_label": [], + "frequency_qualifier_label": "Obligate (HPO)", + "frequency_qualifier_namespace": "HP", + "frequency_qualifier_category": "biolink:PhenotypicFeature", + "frequency_qualifier_closure": ["HP:0000001", "HP:0040280", "HP:0040279"], + "frequency_qualifier_closure_label": ["All (HPO)", "Obligate (HPO)", "Frequency (HPO)"], "onset_qualifier_label": None, "onset_qualifier_namespace": None, "onset_qualifier_category": None, @@ -493,134 +597,196 @@ def associations(): "stage_qualifier_closure_label": [], }, { - "id": "uuid:87cb3e81-5d8c-11ee-9b27-2b20ed86a9d9", + "id": "uuid:c9c8bf31-7529-11ee-b012-cbd37f5c3759", "category": "biolink:DiseaseToPhenotypicFeatureAssociation", - "subject": "MONDO:0012286", - "original_subject": "OMIM:609500", + "subject": "MONDO:0008050", + "original_subject": "OMIM:160500", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ - "MONDO:0000001", - "MONDO:0016112", - "MONDO:0010684", + "BFO:0000002", + "MONDO:0016195", + "MONDO:0005336", + "MONDO:0018949", "MONDO:0005071", + "MONDO:0008050", + "BFO:0000016", + "MONDO:0016139", + "OGMS:0000031", + "MONDO:0003847", + "BFO:0000001", "MONDO:0020121", - "MONDO:0700223", - "BFO:0000002", - "MONDO:0012286", + "MONDO:0019952", "BFO:0000017", "BFO:0000020", - "MONDO:0016106", - "BFO:0000016", "MONDO:0020120", "MONDO:0019056", + "MONDO:0000001", + "MONDO:0700223", "MONDO:0700096", - "MONDO:0005336", "MONDO:0002081", - "OGMS:0000031", - "MONDO:0003847", "MONDO:0003939", - "BFO:0000001", + "MONDO:0002320", ], - "subject_label": "myopathy, autophagic vacuolar, infantile-onset", + "subject_label": "MYH7-related skeletal myopathy", "subject_closure_label": [ - "entity", - "continuant", + "muscular dystrophy", + "human disease", + "musculoskeletal system disorder", + "disease", + "muscle tissue disorder", + "congenital nervous system disorder", + "hereditary skeletal muscle disorder", + "MYH7-related skeletal myopathy", "disposition", - "realizable entity", - "specifically dependent continuant", + "qualitative or quantitative protein defects in neuromuscular diseases", + "distal myopathy", "disease", - "musculoskeletal system disorder", + "continuant", + "qualitative or quantitative defects of beta-myosin heavy chain (MYH7)", + "myopathy", "hereditary disease", - "muscle tissue disorder", "nervous system disorder", - "myopathy", - "X-linked myopathy with excessive autophagy", - "myopathy, autophagic vacuolar, infantile-onset", - "progressive muscular dystrophy", - "hereditary inclusion-body myopathy", - "neuromuscular disease", + "congenital myopathy", + "realizable entity", + "specifically dependent continuant", "skeletal muscle disorder", - "muscular dystrophy", - "human disease", - "hereditary skeletal muscle disorder", - "disease", + "neuromuscular disease", + "entity", ], "subject_taxon": None, "subject_taxon_label": None, "predicate": "biolink:has_phenotype", - "object": "HP:0001263", + "object": "HP:0002938", "original_object": None, "object_namespace": "HP", "object_category": "biolink:PhenotypicFeature", "object_closure": [ - "HP:0000001", - "UPHENO:0082875", - "UPHENO:0075696", - "UPHENO:0001001", "UPHENO:0001005", - "UPHENO:0001002", + "HP:0009121", + "UPHENO:0020584", + "UPHENO:0076692", + "BFO:0000001", + "PATO:0000001", + "BFO:0000004", + "UBERON:0002204", + "UBERON:0011676", + "UBERON:0001137", + "UBERON:0013701", + "UBERON:0002100", + "UBERON:0005462", + "HP:0000001", + "UPHENO:0076703", "HP:0000118", - "BFO:0000002", - "HP:0012759", "BFO:0000020", - "UPHENO:0002433", - "HP:0001263", - "UPHENO:0002332", - "HP:0000707", + "HP:0000925", + "UPHENO:0015280", + "UPHENO:0002964", "UPHENO:0001003", - "UPHENO:0002536", - "HP:0012758", - "UPHENO:0004523", - "BFO:0000001", - "PATO:0000001", - "HP:0012638", + "HP:0003307", + "UPHENO:0022529", "BFO:0000001", - "BFO:0000002", - "BFO:0000004", "BFO:0000040", - "UBERON:0001062", - "UBERON:0000465", - "UBERON:0000061", - "UBERON:0010000", "UBERON:0000467", "UBERON:0000468", - "UBERON:0001016", - ], - "object_label": "Global developmental delay (HPO)", - "object_closure_label": [ - "entity", - "entity", - "continuant", - "continuant", - "independent continuant", - "specifically dependent continuant", - "material entity", + "UBERON:0011216", + "UPHENO:0075696", + "HP:0000924", + "UPHENO:0002536", + "BFO:0000002", + "UBERON:0004288", + "UBERON:0009569", + "UBERON:0013702", + "UBERON:0000075", + "UBERON:0002417", + "UBERON:0011137", + "UBERON:0006077", + "UBERON:0011138", + "UBERON:0002090", + "UBERON:0005944", + "UBERON:0001130", + "UPHENO:0001001", + "HP:0011842", + "UPHENO:0001002", + "BFO:0000002", + "HP:0010674", + "UPHENO:0081581", + "HP:0033127", + "UPHENO:0002813", + "HP:0002938", + "UBERON:0001062", + "UBERON:0000465", + "UBERON:0000061", + "UBERON:0034925", + "UBERON:0010000", + "UBERON:0000475", + "UBERON:0010912", + "UBERON:0001434", + "UBERON:0006074", + ], + "object_label": "Lumbar hyperlordosis (HPO)", + "object_closure_label": [ "All (HPO)", "Phenotypic abnormality (HPO)", - "Abnormality of the nervous system (HPO)", - "Global developmental delay (HPO)", - "Abnormal nervous system physiology (HPO)", - "Neurodevelopmental delay (HPO)", - "Neurodevelopmental abnormality (HPO)", - "quality", - "anatomical structure", + "Abnormality of the curvature of the vertebral column (HPO)", + "abnormal multicellular organism morphology", + "Abnormality of the musculoskeletal system (HPO)", + "Hyperlordosis (HPO)", + "abnormal postcranial axial skeleton morphology", + "independent continuant", "material anatomical entity", - "anatomical system", - "multicellular organism", - "nervous system", - "anatomical entity", "multicellular anatomical structure", - "phenotype", + "musculoskeletal system", + "abdominal segment of trunk", + "axial skeletal system", + "subdivision of vertebral column", + "postcranial axial skeletal system", + "postcranial axial skeleton", + "axial skeleton plus cranial skeleton", + "vertebral column", + "Abnormal skeletal morphology (HPO)", "Phenotypic abnormality", + "continuant", + "specifically dependent continuant", + "Abnormality of the vertebral column (HPO)", + "abnormal anatomical entity morphology in the independent continuant", + "abnormal skeletal system", "phenotype by ontology source", + "quality", + "continuant", + "subdivision of trunk", + "body proper", + "subdivision of skeletal system", + "phenotype", "abnormal phenotype by ontology source", - "abnormality of anatomical entity physiology", - "abnormality of nervous system physiology", + "Abnormal axial skeleton morphology (HPO)", + "abnormal vertebral column", + "Lumbar hyperlordosis (HPO)", + "entity", + "anatomical entity", + "anatomical structure", + "anatomical collection", + "skeleton", + "organism subdivision", + "subdivision of skeleton", + "skeletal system", + "lumbar region of vertebral column", "abnormal anatomical entity", - "abnormal nervous system", + "abnormal skeletal system morphology", + "Abnormality of the skeletal system (HPO)", "abnormal anatomical entity", - "abnormality of anatomical entity physiology", + "abnormal anatomical entity morphology", + "abnormal anatomical entity morphology", + "entity", + "material entity", + "anatomical system", + "multicellular organism", + "organ system subdivision", + "subdivision of organism along main body axis", + "dorsum", + "main body axis", + "trunk", + "lower back", ], "object_taxon": None, "object_taxon_label": None, @@ -628,26 +794,32 @@ def associations(): "aggregator_knowledge_source": ["infores:monarchinitiative"], "negated": None, "pathway": None, - "evidence_count": 4, - "has_evidence": ["ECO:0000304"], - "has_evidence_links": [{"id": "ECO:0000304", "url": "http://purl.obolibrary.org/obo/ECO_0000304"}], + "evidence_count": 2, + "has_evidence": ["ECO:0000269"], + "has_evidence_links": [{"id": "ECO:0000269", "url": "http://purl.obolibrary.org/obo/ECO_0000269"}], + "grouping_key": "MONDO:0008050🍪🍪biolink:has_phenotype🍪HP:0002938", "provided_by": "hpoa_disease_to_phenotype_edges", "provided_by_link": { "id": "hpoa_disease_to_phenotype", "url": "https://monarch-initiative.github.io/monarch-ingest/Sources/hpoa/#disease_to_phenotype", }, - "publications": ["OMIM:609500"], - "publications_links": [{"id": "OMIM:609500", "url": "http://identifiers.org/mim/609500"}], + "publications": ["PMID:17548557"], + "publications_links": [{"id": "PMID:17548557", "url": "http://identifiers.org/pubmed/17548557"}], "qualifiers": [], - "frequency_qualifier": None, + "frequency_qualifier": "HP:0040280", "onset_qualifier": None, "sex_qualifier": None, "stage_qualifier": None, - "frequency_qualifier_label": None, - "frequency_qualifier_namespace": None, - "frequency_qualifier_category": None, - "frequency_qualifier_closure": [], - "frequency_qualifier_closure_label": [], + "qualifiers_label": None, + "qualifiers_namespace": None, + "qualifiers_category": None, + "qualifiers_closure": [], + "qualifiers_closure_label": [], + "frequency_qualifier_label": "Obligate (HPO)", + "frequency_qualifier_namespace": "HP", + "frequency_qualifier_category": "biolink:PhenotypicFeature", + "frequency_qualifier_closure": ["HP:0000001", "HP:0040280", "HP:0040279"], + "frequency_qualifier_closure_label": ["All (HPO)", "Obligate (HPO)", "Frequency (HPO)"], "onset_qualifier_label": None, "onset_qualifier_namespace": None, "onset_qualifier_category": None, @@ -665,156 +837,214 @@ def associations(): "stage_qualifier_closure_label": [], }, { - "id": "uuid:85cb9d22-5d8c-11ee-9b27-2b20ed86a9d9", + "id": "uuid:c9c8bf38-7529-11ee-b012-cbd37f5c3759", "category": "biolink:DiseaseToPhenotypicFeatureAssociation", - "subject": "MONDO:0013159", - "original_subject": "OMIM:613155", + "subject": "MONDO:0008050", + "original_subject": "OMIM:160500", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ - "MONDO:0018282", - "MONDO:0000001", - "MONDO:0017741", - "MONDO:0018276", - "MONDO:0045010", + "BFO:0000002", + "MONDO:0016195", + "MONDO:0005336", + "MONDO:0018949", "MONDO:0005071", + "MONDO:0008050", + "BFO:0000016", + "MONDO:0016139", + "OGMS:0000031", + "MONDO:0003847", + "BFO:0000001", "MONDO:0020121", - "MONDO:0000172", - "MONDO:0700223", - "MONDO:0013159", - "MONDO:0024322", - "BFO:0000002", + "MONDO:0019952", "BFO:0000017", "BFO:0000020", - "BFO:0000016", "MONDO:0020120", "MONDO:0019056", - "MONDO:0016139", + "MONDO:0000001", + "MONDO:0700223", "MONDO:0700096", - "MONDO:0005336", "MONDO:0002081", - "OGMS:0000031", - "MONDO:0003847", - "MONDO:0700070", "MONDO:0003939", - "MONDO:0015286", - "BFO:0000001", "MONDO:0002320", - "MONDO:0019052", - "MONDO:0005066", - "MONDO:0019950", - "MONDO:0016155", ], - "subject_label": "muscular dystrophy-dystroglycanopathy (congenital with intellectual disability), type B1", + "subject_label": "MYH7-related skeletal myopathy", "subject_closure_label": [ - "entity", - "continuant", - "disposition", - "realizable entity", - "specifically dependent continuant", - "disease", - "muscular dystrophy-dystroglycanopathy, type B", + "muscular dystrophy", + "human disease", "musculoskeletal system disorder", + "disease", + "muscle tissue disorder", "congenital nervous system disorder", + "hereditary skeletal muscle disorder", + "MYH7-related skeletal myopathy", + "disposition", + "qualitative or quantitative protein defects in neuromuscular diseases", + "distal myopathy", + "disease", + "continuant", + "qualitative or quantitative defects of beta-myosin heavy chain (MYH7)", + "myopathy", "hereditary disease", - "muscle tissue disorder", - "metabolic disease", "nervous system disorder", - "myopathy", - "muscular dystrophy-dystroglycanopathy (congenital with intellectual disability), type B1", - "congenital disorder of glycosylation", - "qualitative or quantitative protein defects in neuromuscular diseases", - "qualitative or quantitative defects of protein involved in O-glycosylation of alpha-dystroglycan", - "disorder of protein O-glycosylation", - "muscular dystrophy-dystroglycanopathy", - "qualitative or quantitative defects of alpha-dystroglycan", - "inborn errors of metabolism", - "neuromuscular disease", - "congenital muscular dystrophy", + "congenital myopathy", + "realizable entity", + "specifically dependent continuant", "skeletal muscle disorder", - "muscular dystrophy", - "disorder of glycosylation", - "glycoprotein metabolism disease", - "myopathy caused by variation in POMT1", - "human disease", - "hereditary skeletal muscle disorder", - "disease", + "neuromuscular disease", + "entity", ], "subject_taxon": None, "subject_taxon_label": None, "predicate": "biolink:has_phenotype", - "object": "HP:0001263", + "object": "HP:0001265", "original_object": None, "object_namespace": "HP", "object_category": "biolink:PhenotypicFeature", "object_closure": [ - "HP:0000001", "UPHENO:0082875", - "UPHENO:0075696", - "UPHENO:0001001", + "UPHENO:0049622", "UPHENO:0001005", + "BFO:0000020", + "UPHENO:0050606", + "HP:0012638", + "BFO:0000015", + "BFO:0000004", + "GO:0050882", + "NBO:0000338", + "GO:0050905", + "UBERON:0001016", + "HP:0000001", + "UPHENO:0001001", + "UPHENO:0080585", + "HP:0001265", + "HP:0031826", "UPHENO:0001002", "HP:0000118", - "BFO:0000002", - "HP:0012759", - "BFO:0000020", + "UPHENO:0052178", "UPHENO:0002433", - "HP:0001263", - "UPHENO:0002332", - "HP:0000707", + "HP:0001315", "UPHENO:0001003", - "UPHENO:0002536", - "HP:0012758", - "UPHENO:0004523", - "BFO:0000001", + "HP:0000708", + "HP:0011446", "PATO:0000001", - "HP:0012638", "BFO:0000001", - "BFO:0000002", - "BFO:0000004", "BFO:0000040", "UBERON:0001062", + "GO:0050896", + "GO:0032501", + "GO:0060004", + "GO:0050881", + "NBO:0000313", + "GO:0050877", + "UBERON:0000467", + "UBERON:0000468", + "NBO:0000403", + "NBO:0000001", + "NBO:0000388", + "UPHENO:0075696", + "UPHENO:0078622", + "UPHENO:0049586", + "UPHENO:0080377", + "HP:0100022", + "UPHENO:0050613", + "UPHENO:0005433", + "UPHENO:0002332", + "UPHENO:0002536", + "UPHENO:0079826", + "UPHENO:0004523", + "UPHENO:0049587", + "BFO:0000003", + "BFO:0000002", + "GO:0008150", + "GO:0009605", + "GO:0050879", + "GO:0007610", + "GO:0003008", + "NBO:0000389", + "UPHENO:0052915", + "BFO:0000002", + "UPHENO:0005625", + "UPHENO:0050079", + "HP:0000707", + "UPHENO:0079833", + "BFO:0000001", "UBERON:0000465", "UBERON:0000061", "UBERON:0010000", - "UBERON:0000467", - "UBERON:0000468", - "UBERON:0001016", ], - "object_label": "Global developmental delay (HPO)", + "object_label": "Hyporeflexia (HPO)", "object_closure_label": [ - "entity", - "entity", - "continuant", - "continuant", - "independent continuant", - "specifically dependent continuant", - "material entity", "All (HPO)", + "abnormal behavior", + "Abnormality of movement (HPO)", + "Phenotypic abnormality", "Phenotypic abnormality (HPO)", + "decreased reflex", + "abnormal response to external stimulus", "Abnormality of the nervous system (HPO)", - "Global developmental delay (HPO)", - "Abnormal nervous system physiology (HPO)", - "Neurodevelopmental delay (HPO)", - "Neurodevelopmental abnormality (HPO)", + "Behavioral abnormality (HPO)", + "Abnormality of higher mental function (HPO)", + "abnormal voluntary movement behavior", + "entity", "quality", - "anatomical structure", + "process", + "independent continuant", "material anatomical entity", - "anatomical system", - "multicellular organism", - "nervous system", - "anatomical entity", "multicellular anatomical structure", - "phenotype", - "Phenotypic abnormality", - "phenotype by ontology source", - "abnormal phenotype by ontology source", + "nervous system", + "voluntary movement behavior", + "body part movement", + "reflexive behavior", "abnormality of anatomical entity physiology", + "phenotype", + "continuant", + "decreased qualitatively biological_process", "abnormality of nervous system physiology", - "abnormal anatomical entity", + "Reduced tendon reflexes (HPO)", + "phenotype by ontology source", + "abnormal behavior process", "abnormal nervous system", + "abnormal biological_process", + "Abnormal nervous system physiology (HPO)", + "occurrent", + "continuant", + "biological_process", + "response to external stimulus", + "multicellular organismal movement", + "behavior", + "system process", + "reflex", + "musculoskeletal movement", + "behavior process", + "nervous system process", + "involuntary movement behavior", + "decreased qualitatively response to stimulus", + "abnormal phenotype by ontology source", + "specifically dependent continuant", + "abnormal voluntary musculoskeletal movement", + "entity", + "anatomical structure", "abnormal anatomical entity", + "abnormal voluntary movement behavior", + "changed biological_process rate", + "abnormal response to stimulus", + "abnormal behavior process", + "Hyporeflexia (HPO)", + "Abnormal reflex (HPO)", + "abnormal musculoskeletal movement", + "decreased biological_process", "abnormality of anatomical entity physiology", + "abnormal anatomical entity", + "material entity", + "anatomical entity", + "response to stimulus", + "multicellular organismal process", + "anatomical system", + "voluntary musculoskeletal movement", + "kinesthetic behavior", + "neuromuscular process", + "multicellular organism", ], "object_taxon": None, "object_taxon_label": None, @@ -822,26 +1052,32 @@ def associations(): "aggregator_knowledge_source": ["infores:monarchinitiative"], "negated": None, "pathway": None, - "evidence_count": 4, - "has_evidence": ["ECO:0000304"], - "has_evidence_links": [{"id": "ECO:0000304", "url": "http://purl.obolibrary.org/obo/ECO_0000304"}], + "evidence_count": 2, + "has_evidence": ["ECO:0000269"], + "has_evidence_links": [{"id": "ECO:0000269", "url": "http://purl.obolibrary.org/obo/ECO_0000269"}], + "grouping_key": "MONDO:0008050🍪🍪biolink:has_phenotype🍪HP:0001265", "provided_by": "hpoa_disease_to_phenotype_edges", "provided_by_link": { "id": "hpoa_disease_to_phenotype", "url": "https://monarch-initiative.github.io/monarch-ingest/Sources/hpoa/#disease_to_phenotype", }, - "publications": ["OMIM:613155"], - "publications_links": [{"id": "OMIM:613155", "url": "http://identifiers.org/mim/613155"}], + "publications": ["PMID:17548557"], + "publications_links": [{"id": "PMID:17548557", "url": "http://identifiers.org/pubmed/17548557"}], "qualifiers": [], - "frequency_qualifier": None, + "frequency_qualifier": "HP:0040280", "onset_qualifier": None, "sex_qualifier": None, "stage_qualifier": None, - "frequency_qualifier_label": None, - "frequency_qualifier_namespace": None, - "frequency_qualifier_category": None, - "frequency_qualifier_closure": [], - "frequency_qualifier_closure_label": [], + "qualifiers_label": None, + "qualifiers_namespace": None, + "qualifiers_category": None, + "qualifiers_closure": [], + "qualifiers_closure_label": [], + "frequency_qualifier_label": "Obligate (HPO)", + "frequency_qualifier_namespace": "HP", + "frequency_qualifier_category": "biolink:PhenotypicFeature", + "frequency_qualifier_closure": ["HP:0000001", "HP:0040280", "HP:0040279"], + "frequency_qualifier_closure_label": ["All (HPO)", "Obligate (HPO)", "Frequency (HPO)"], "onset_qualifier_label": None, "onset_qualifier_namespace": None, "onset_qualifier_category": None, @@ -859,200 +1095,228 @@ def associations(): "stage_qualifier_closure_label": [], }, { - "id": "uuid:875b0482-5d8c-11ee-9b27-2b20ed86a9d9", + "id": "uuid:c9c8bf3f-7529-11ee-b012-cbd37f5c3759", "category": "biolink:DiseaseToPhenotypicFeatureAssociation", - "subject": "MONDO:0013904", - "original_subject": "OMIM:614830", + "subject": "MONDO:0008050", + "original_subject": "OMIM:160500", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ - "MONDO:0018282", - "MONDO:0000001", - "MONDO:0016182", - "MONDO:0017741", - "MONDO:0018276", - "MONDO:0045010", + "BFO:0000002", + "MONDO:0016195", + "MONDO:0005336", + "MONDO:0018949", "MONDO:0005071", + "MONDO:0008050", + "BFO:0000016", + "MONDO:0016139", + "OGMS:0000031", + "MONDO:0003847", + "BFO:0000001", "MONDO:0020121", - "MONDO:0700068", - "MONDO:0700223", - "MONDO:0700075", - "MONDO:0024322", - "MONDO:0005283", - "MONDO:0020238", - "BFO:0000002", - "MONDO:0016185", - "MONDO:0000171", + "MONDO:0019952", "BFO:0000017", - "MONDO:0018869", "BFO:0000020", - "MONDO:0016157", - "MONDO:0017745", - "BFO:0000016", "MONDO:0020120", - "MONDO:0700069", "MONDO:0019056", - "MONDO:0016139", + "MONDO:0000001", + "MONDO:0700223", "MONDO:0700096", - "MONDO:0018838", - "MONDO:0024458", - "MONDO:0005336", "MONDO:0002081", - "MONDO:0016184", - "MONDO:0016156", - "MONDO:0020246", - "MONDO:0021147", - "MONDO:0013904", - "MONDO:0044137", - "MONDO:0019755", - "OGMS:0000031", - "MONDO:0015327", - "MONDO:0003847", "MONDO:0003939", - "MONDO:0002022", - "MONDO:0015286", - "BFO:0000001", "MONDO:0002320", - "MONDO:0019052", - "MONDO:0020247", - "MONDO:0005066", - "MONDO:0005328", - "MONDO:0019950", - "MONDO:0016155", - "MONDO:0700066", ], - "subject_label": "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type a, 8", + "subject_label": "MYH7-related skeletal myopathy", "subject_closure_label": [ - "entity", - "continuant", - "disposition", - "realizable entity", - "specifically dependent continuant", - "disease", - "muscular dystrophy-dystroglycanopathy, type A", - "disorder of orbital region", + "muscular dystrophy", + "human disease", "musculoskeletal system disorder", + "disease", + "muscle tissue disorder", "congenital nervous system disorder", + "hereditary skeletal muscle disorder", + "MYH7-related skeletal myopathy", + "disposition", + "qualitative or quantitative protein defects in neuromuscular diseases", + "distal myopathy", + "disease", + "continuant", + "qualitative or quantitative defects of beta-myosin heavy chain (MYH7)", + "myopathy", "hereditary disease", - "muscle tissue disorder", - "metabolic disease", "nervous system disorder", - "retinal disorder", - "eye disorder", - "myopathy", - "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type a, 8", - "congenital disorder of glycosylation", - "developmental anomaly of metabolic origin", - "qualitative or quantitative protein defects in neuromuscular diseases", - "qualitative or quantitative defects of protein involved in O-glycosylation of alpha-dystroglycan", - "qualitative or quantitative defects of FKRP", - "qualitative or quantitative defects of fukutin", - "qualitative or quantitative defects of protein O-mannose beta1, 2N-acetylglucosaminyltransferase", - "qualitative or quantitative defects of protein O-mannosyltransferase 1", - "qualitative or quantitative defects of protein O-mannosyltransferase 2", - "disorder of protein O-glycosylation", - "disorder of O-mannosylglycan synthesis", - "muscular dystrophy-dystroglycanopathy", - "qualitative or quantitative defects of alpha-dystroglycan", - "lissencephaly spectrum disorders", - "cobblestone lissencephaly", - "inborn errors of metabolism", - "neuromuscular disease", - "developmental defect during embryogenesis", - "congenital muscular dystrophy", + "congenital myopathy", + "realizable entity", + "specifically dependent continuant", "skeletal muscle disorder", - "muscular dystrophy", - "inherited vitreous-retinal disease", - "inherited vitreoretinopathy", - "congenital vitreoretinal dysplasia", - "disorder of development or morphogenesis", - "disorder of glycosylation", - "disorder of visual system", - "vitreous body disorder", - "glycoprotein metabolism disease", - "myopathy caused by variation in FKRP", - "myopathy caused by variation in POMGNT1", - "myopathy caused by variation in POMGNT2", - "congenital muscular dystrophy caused by variation in POMGNT2", - "human disease", - "hereditary skeletal muscle disorder", - "disease", + "neuromuscular disease", + "entity", ], "subject_taxon": None, "subject_taxon_label": None, "predicate": "biolink:has_phenotype", - "object": "HP:0001263", + "object": "HP:0009053", "original_object": None, "object_namespace": "HP", "object_category": "biolink:PhenotypicFeature", "object_closure": [ - "HP:0000001", "UPHENO:0082875", - "UPHENO:0075696", - "UPHENO:0001001", + "UPHENO:0002320", + "HP:0002814", "UPHENO:0001005", - "UPHENO:0001002", + "HP:0009127", + "UPHENO:0076692", + "UPHENO:0003070", + "BFO:0000004", + "UBERON:0004708", + "UBERON:0000154", + "UBERON:0000026", + "UBERON:0014892", + "UBERON:0006058", + "UBERON:0002529", + "HP:0000001", "HP:0000118", "BFO:0000002", - "HP:0012759", "BFO:0000020", - "UPHENO:0002433", - "HP:0001263", - "UPHENO:0002332", - "HP:0000707", - "UPHENO:0001003", - "UPHENO:0002536", - "HP:0012758", - "UPHENO:0004523", + "UPHENO:0076710", "BFO:0000001", "PATO:0000001", - "HP:0012638", "BFO:0000001", - "BFO:0000002", - "BFO:0000004", "BFO:0000040", - "UBERON:0001062", + "UBERON:0000467", + "UBERON:0000468", + "UBERON:0011216", + "UBERON:0010709", + "UBERON:0010890", + "UBERON:0010538", + "UPHENO:0075696", + "UPHENO:0080575", + "HP:0001324", + "HP:0003690", + "HP:0003011", + "UPHENO:0002332", + "UPHENO:0001003", + "UPHENO:0002536", + "HP:0002460", + "HP:0040064", + "HP:0009053", + "HP:0011804", + "PR:000050567", "UBERON:0000465", + "UBERON:0002101", + "UBERON:0004709", + "UBERON:0005090", + "UBERON:0018254", + "UBERON:0002103", + "UBERON:0010707", + "UBERON:0001630", + "UBERON:0010758", + "UBERON:0007271", + "UBERON:0014792", + "UBERON:0008784", + "HP:0007340", + "UPHENO:0001001", + "HP:0011805", + "UPHENO:0001002", + "UPHENO:0080555", + "UPHENO:0002816", + "UPHENO:0080556", + "UPHENO:0081581", + "HP:0033127", + "UPHENO:0002647", + "UPHENO:0002830", + "BFO:0000002", + "UBERON:0001062", + "RO:0002577", "UBERON:0000061", + "UBERON:0015212", "UBERON:0010000", - "UBERON:0000467", - "UBERON:0000468", - "UBERON:0001016", + "UBERON:0000475", + "UBERON:0000062", + "UBERON:0000383", + "UBERON:0001015", + "UBERON:0000978", + "UBERON:0004480", ], - "object_label": "Global developmental delay (HPO)", + "object_label": "Distal lower limb muscle weakness (HPO)", "object_closure_label": [ - "entity", - "entity", - "continuant", - "continuant", - "independent continuant", - "specifically dependent continuant", - "material entity", "All (HPO)", + "abnormality of muscle organ physiology", + "Abnormality of the lower limb (HPO)", "Phenotypic abnormality (HPO)", - "Abnormality of the nervous system (HPO)", - "Global developmental delay (HPO)", - "Abnormal nervous system physiology (HPO)", - "Neurodevelopmental delay (HPO)", - "Neurodevelopmental abnormality (HPO)", + "continuant", + "decreased anatomical entity strength", + "abnormal musculature", + "decreased muscle organ strength", + "abnormal multicellular organism morphology", + "Abnormality of the musculoskeletal system (HPO)", + "abnormal musculature of limb", "quality", - "anatomical structure", - "material anatomical entity", - "anatomical system", - "multicellular organism", - "nervous system", - "anatomical entity", + "independent continuant", + "system", + "paired limb/fin", + "lateral structure", "multicellular anatomical structure", - "phenotype", + "pelvic complex", + "appendage musculature", + "musculature of pelvic complex", + "abnormality of anatomical entity physiology", + "Abnormal skeletal muscle morphology (HPO)", "Phenotypic abnormality", - "phenotype by ontology source", + "specifically dependent continuant", + "Distal muscle weakness (HPO)", + "Abnormality of limbs (HPO)", + "Distal lower limb muscle weakness (HPO)", + "protein-containing material entity", + "material anatomical entity", + "hindlimb", + "appendage girdle complex", + "subdivision of organism along appendicular axis", + "pelvic complex muscle", + "paired limb/fin segment", + "lower limb segment", + "Lower limb muscle weakness (HPO)", + "phenotype", "abnormal phenotype by ontology source", - "abnormality of anatomical entity physiology", - "abnormality of nervous system physiology", - "abnormal anatomical entity", - "abnormal nervous system", + "Abnormality of the musculature of the limbs (HPO)", + "abnormal muscle organ morphology", + "Abnormal muscle physiology (HPO)", + "entity", + "anatomical entity", + "anatomical structure", + "muscle structure", + "skeletal musculature", + "organism subdivision", + "organ", + "muscle organ", + "musculature of body", + "musculature", + "leg", + "musculature of limb", "abnormal anatomical entity", + "decreased pelvic complex muscle strength", + "Muscle weakness (HPO)", + "Limb muscle weakness (HPO)", + "Abnormality of the musculature (HPO)", "abnormality of anatomical entity physiology", + "phenotype by ontology source", + "abnormal anatomical entity", + "abnormal anatomical entity morphology", + "abnormal leg", + "entity", + "abnormal limb", + "continuant", + "material entity", + "limb", + "pelvic appendage", + "anatomical system", + "multicellular organism", + "organ system subdivision", + "posterior region of body", + "appendage", + "skeletal muscle organ", + "multi-limb segment region", + "limb segment", ], "object_taxon": None, "object_taxon_label": None, @@ -1060,26 +1324,32 @@ def associations(): "aggregator_knowledge_source": ["infores:monarchinitiative"], "negated": None, "pathway": None, - "evidence_count": 4, + "evidence_count": 2, "has_evidence": ["ECO:0000269"], "has_evidence_links": [{"id": "ECO:0000269", "url": "http://purl.obolibrary.org/obo/ECO_0000269"}], + "grouping_key": "MONDO:0008050🍪🍪biolink:has_phenotype🍪HP:0009053", "provided_by": "hpoa_disease_to_phenotype_edges", "provided_by_link": { "id": "hpoa_disease_to_phenotype", "url": "https://monarch-initiative.github.io/monarch-ingest/Sources/hpoa/#disease_to_phenotype", }, - "publications": ["PMID:22958903"], - "publications_links": [{"id": "PMID:22958903", "url": "http://identifiers.org/pubmed/22958903"}], + "publications": ["PMID:17548557"], + "publications_links": [{"id": "PMID:17548557", "url": "http://identifiers.org/pubmed/17548557"}], "qualifiers": [], - "frequency_qualifier": None, + "frequency_qualifier": "HP:0040280", "onset_qualifier": None, "sex_qualifier": None, "stage_qualifier": None, - "frequency_qualifier_label": None, - "frequency_qualifier_namespace": None, - "frequency_qualifier_category": None, - "frequency_qualifier_closure": [], - "frequency_qualifier_closure_label": [], + "qualifiers_label": None, + "qualifiers_namespace": None, + "qualifiers_category": None, + "qualifiers_closure": [], + "qualifiers_closure_label": [], + "frequency_qualifier_label": "Obligate (HPO)", + "frequency_qualifier_namespace": "HP", + "frequency_qualifier_category": "biolink:PhenotypicFeature", + "frequency_qualifier_closure": ["HP:0000001", "HP:0040280", "HP:0040279"], + "frequency_qualifier_closure_label": ["All (HPO)", "Obligate (HPO)", "Frequency (HPO)"], "onset_qualifier_label": None, "onset_qualifier_namespace": None, "onset_qualifier_category": None, @@ -1097,146 +1367,222 @@ def associations(): "stage_qualifier_closure_label": [], }, { - "id": "uuid:85eb98e5-5d8c-11ee-9b27-2b20ed86a9d9", + "id": "uuid:c9c8bf41-7529-11ee-b012-cbd37f5c3759", "category": "biolink:DiseaseToPhenotypicFeatureAssociation", - "subject": "MONDO:0014023", - "original_subject": "OMIM:615042", + "subject": "MONDO:0008050", + "original_subject": "OMIM:160500", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ - "MONDO:0000001", - "MONDO:0018276", + "BFO:0000002", + "MONDO:0016195", + "MONDO:0005336", + "MONDO:0018949", "MONDO:0005071", + "MONDO:0008050", + "BFO:0000016", + "MONDO:0016139", + "OGMS:0000031", + "MONDO:0003847", + "BFO:0000001", "MONDO:0020121", - "MONDO:0700223", - "MONDO:0024322", - "BFO:0000002", + "MONDO:0019952", "BFO:0000017", "BFO:0000020", - "BFO:0000016", "MONDO:0020120", "MONDO:0019056", - "MONDO:0014023", + "MONDO:0000001", + "MONDO:0700223", "MONDO:0700096", - "MONDO:0005336", "MONDO:0002081", - "MONDO:0017749", - "OGMS:0000031", - "MONDO:0003847", "MONDO:0003939", - "MONDO:0015286", - "BFO:0000001", "MONDO:0002320", - "MONDO:0019052", - "MONDO:0005500", - "MONDO:0005066", - "MONDO:0019950", ], - "subject_label": "congenital muscular dystrophy with intellectual disability and severe epilepsy", + "subject_label": "MYH7-related skeletal myopathy", "subject_closure_label": [ - "entity", - "continuant", - "disposition", - "realizable entity", - "specifically dependent continuant", - "disease", + "muscular dystrophy", + "human disease", "musculoskeletal system disorder", + "disease", + "muscle tissue disorder", "congenital nervous system disorder", + "hereditary skeletal muscle disorder", + "MYH7-related skeletal myopathy", + "disposition", + "qualitative or quantitative protein defects in neuromuscular diseases", + "distal myopathy", + "disease", + "continuant", + "qualitative or quantitative defects of beta-myosin heavy chain (MYH7)", + "myopathy", "hereditary disease", - "muscle tissue disorder", - "metabolic disease", "nervous system disorder", - "myopathy", - "congenital disorder of glycosylation type I", - "congenital muscular dystrophy with intellectual disability and severe epilepsy", - "congenital disorder of glycosylation", - "disorder of multiple glycosylation", - "muscular dystrophy-dystroglycanopathy", - "inborn errors of metabolism", - "neuromuscular disease", - "congenital muscular dystrophy", + "congenital myopathy", + "realizable entity", + "specifically dependent continuant", "skeletal muscle disorder", - "muscular dystrophy", - "disorder of glycosylation", - "human disease", - "hereditary skeletal muscle disorder", - "disease", + "neuromuscular disease", + "entity", ], "subject_taxon": None, "subject_taxon_label": None, "predicate": "biolink:has_phenotype", - "object": "HP:0001263", + "object": "HP:0009077", "original_object": None, "object_namespace": "HP", "object_category": "biolink:PhenotypicFeature", "object_closure": [ + "HP:0009127", + "BFO:0000002", + "UPHENO:0002655", + "UPHENO:0076692", + "BFO:0000001", + "PATO:0000001", + "BFO:0000004", + "UBERON:0004708", + "UBERON:0000061", + "UBERON:0000153", + "UBERON:0000026", + "UBERON:0006058", + "UBERON:0002529", + "UBERON:0002398", "HP:0000001", - "UPHENO:0082875", - "UPHENO:0075696", + "UPHENO:0002649", "UPHENO:0001001", - "UPHENO:0001005", "UPHENO:0001002", "HP:0000118", - "BFO:0000002", - "HP:0012759", + "HP:0001446", "BFO:0000020", - "UPHENO:0002433", - "HP:0001263", - "UPHENO:0002332", - "HP:0000707", - "UPHENO:0001003", - "UPHENO:0002536", - "HP:0012758", - "UPHENO:0004523", - "BFO:0000001", - "PATO:0000001", - "HP:0012638", + "UPHENO:0002708", + "HP:0009077", + "UPHENO:0076710", "BFO:0000001", - "BFO:0000002", - "BFO:0000004", "BFO:0000040", - "UBERON:0001062", - "UBERON:0000465", - "UBERON:0000061", - "UBERON:0010000", "UBERON:0000467", "UBERON:0000468", - "UBERON:0001016", + "UBERON:0011216", + "UBERON:0010708", + "UBERON:0010538", + "UBERON:0004489", + "HP:0001421", + "HP:0030237", + "HP:0002817", + "HP:0003011", + "UPHENO:0002536", + "HP:0040064", + "BFO:0000002", + "PR:000050567", + "UBERON:0000465", + "UBERON:0002101", + "UBERON:0004710", + "UBERON:0005090", + "UBERON:0002102", + "UBERON:0010707", + "UBERON:0001630", + "UBERON:0010758", + "UBERON:0007271", + "UBERON:0014793", + "UBERON:0004481", + "UBERON:0002470", + "UBERON:0008785", + "UPHENO:0001005", + "HP:0001155", + "HP:0011805", + "UPHENO:0002816", + "UPHENO:0081581", + "HP:0033127", + "UPHENO:0001003", + "UPHENO:0002647", + "UPHENO:0002880", + "UPHENO:0002830", + "UBERON:0001062", + "RO:0002577", + "UBERON:0015212", + "UBERON:0010000", + "UBERON:0000475", + "UBERON:0000062", + "UBERON:0000383", + "UBERON:0001015", + "UBERON:0001460", + "UBERON:0004480", + "UBERON:0007269", ], - "object_label": "Global developmental delay (HPO)", + "object_label": "Weakness of long finger extensor muscles (HPO)", "object_closure_label": [ - "entity", - "entity", - "continuant", - "continuant", - "independent continuant", - "specifically dependent continuant", - "material entity", "All (HPO)", + "abnormal musculature of upper limb", + "Phenotypic abnormality", "Phenotypic abnormality (HPO)", - "Abnormality of the nervous system (HPO)", - "Global developmental delay (HPO)", - "Abnormal nervous system physiology (HPO)", - "Neurodevelopmental delay (HPO)", - "Neurodevelopmental abnormality (HPO)", - "quality", + "abnormal musculature", + "abnormal multicellular organism morphology", + "Abnormality of the musculoskeletal system (HPO)", + "phenotype by ontology source", + "abnormal musculature of limb", + "independent continuant", + "system", + "paired limb/fin", "anatomical structure", - "material anatomical entity", - "anatomical system", - "multicellular organism", - "nervous system", - "anatomical entity", + "lateral structure", "multicellular anatomical structure", + "pectoral complex", + "appendage musculature", + "musculature of pectoral complex", + "musculature of manus", "phenotype", - "Phenotypic abnormality", - "phenotype by ontology source", + "Abnormality of the musculature of the hand (HPO)", "abnormal phenotype by ontology source", - "abnormality of anatomical entity physiology", - "abnormality of nervous system physiology", - "abnormal anatomical entity", - "abnormal nervous system", + "Abnormality of the hand (HPO)", + "Abnormal skeletal muscle morphology (HPO)", + "Abnormality of the musculature of the upper limbs (HPO)", + "specifically dependent continuant", + "abnormal manus", + "Abnormality of limbs (HPO)", + "quality", + "continuant", + "protein-containing material entity", + "material anatomical entity", + "forelimb", + "appendage girdle complex", + "subdivision of organism along appendicular axis", + "paired limb/fin segment", + "musculature of upper limb", + "autopod region", + "upper limb segment", + "Abnormality of the musculature of the limbs (HPO)", + "continuant", + "abnormal musculature of manus", + "Weakness of long finger extensor muscles (HPO)", + "abnormal muscle organ morphology", + "entity", + "anatomical entity", + "muscle structure", + "organism subdivision", + "organ", + "muscle organ", + "musculature of body", + "musculature", + "arm", + "musculature of limb", + "pectoral appendage musculature", + "Hand muscle weakness (HPO)", + "Abnormality of the upper limb (HPO)", + "Abnormality of the musculature (HPO)", "abnormal anatomical entity", - "abnormality of anatomical entity physiology", + "abnormal anatomical entity morphology", + "entity", + "abnormal arm", + "abnormal limb", + "material entity", + "limb", + "pectoral appendage", + "anatomical system", + "multicellular organism", + "organ system subdivision", + "anterior region of body", + "appendage", + "multi-limb segment region", + "limb segment", + "manus", ], "object_taxon": None, "object_taxon_label": None, @@ -1244,26 +1590,32 @@ def associations(): "aggregator_knowledge_source": ["infores:monarchinitiative"], "negated": None, "pathway": None, - "evidence_count": 4, - "has_evidence": ["ECO:0000304"], - "has_evidence_links": [{"id": "ECO:0000304", "url": "http://purl.obolibrary.org/obo/ECO_0000304"}], + "evidence_count": 2, + "has_evidence": ["ECO:0000269"], + "has_evidence_links": [{"id": "ECO:0000269", "url": "http://purl.obolibrary.org/obo/ECO_0000269"}], + "grouping_key": "MONDO:0008050🍪🍪biolink:has_phenotype🍪HP:0009077", "provided_by": "hpoa_disease_to_phenotype_edges", "provided_by_link": { "id": "hpoa_disease_to_phenotype", "url": "https://monarch-initiative.github.io/monarch-ingest/Sources/hpoa/#disease_to_phenotype", }, - "publications": ["PMID:19901254"], - "publications_links": [{"id": "PMID:19901254", "url": "http://identifiers.org/pubmed/19901254"}], + "publications": ["PMID:17548557"], + "publications_links": [{"id": "PMID:17548557", "url": "http://identifiers.org/pubmed/17548557"}], "qualifiers": [], - "frequency_qualifier": None, + "frequency_qualifier": "HP:0040280", "onset_qualifier": None, "sex_qualifier": None, "stage_qualifier": None, - "frequency_qualifier_label": None, - "frequency_qualifier_namespace": None, - "frequency_qualifier_category": None, - "frequency_qualifier_closure": [], - "frequency_qualifier_closure_label": [], + "qualifiers_label": None, + "qualifiers_namespace": None, + "qualifiers_category": None, + "qualifiers_closure": [], + "qualifiers_closure_label": [], + "frequency_qualifier_label": "Obligate (HPO)", + "frequency_qualifier_namespace": "HP", + "frequency_qualifier_category": "biolink:PhenotypicFeature", + "frequency_qualifier_closure": ["HP:0000001", "HP:0040280", "HP:0040279"], + "frequency_qualifier_closure_label": ["All (HPO)", "Obligate (HPO)", "Frequency (HPO)"], "onset_qualifier_label": None, "onset_qualifier_namespace": None, "onset_qualifier_category": None, @@ -1281,196 +1633,190 @@ def associations(): "stage_qualifier_closure_label": [], }, { - "id": "uuid:87eb5818-5d8c-11ee-9b27-2b20ed86a9d9", + "id": "uuid:c9c8bf42-7529-11ee-b012-cbd37f5c3759", "category": "biolink:DiseaseToPhenotypicFeatureAssociation", - "subject": "MONDO:0014101", - "original_subject": "OMIM:615249", + "subject": "MONDO:0008050", + "original_subject": "OMIM:160500", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ - "MONDO:0018282", - "MONDO:0000001", - "MONDO:0016182", - "MONDO:0017741", - "MONDO:0018276", - "MONDO:0045010", + "BFO:0000002", + "MONDO:0016195", + "MONDO:0005336", + "MONDO:0018949", "MONDO:0005071", + "MONDO:0008050", + "BFO:0000016", + "MONDO:0016139", + "OGMS:0000031", + "MONDO:0003847", + "BFO:0000001", "MONDO:0020121", - "MONDO:0700068", - "MONDO:0700223", - "MONDO:0024322", - "MONDO:0005283", - "MONDO:0020238", - "BFO:0000002", - "MONDO:0014101", - "MONDO:0016185", - "MONDO:0000171", + "MONDO:0019952", "BFO:0000017", - "MONDO:0018869", "BFO:0000020", - "MONDO:0016157", - "MONDO:0017745", - "BFO:0000016", "MONDO:0020120", "MONDO:0019056", - "MONDO:0016139", + "MONDO:0000001", + "MONDO:0700223", "MONDO:0700096", - "MONDO:0018838", - "MONDO:0024458", - "MONDO:0005336", "MONDO:0002081", - "MONDO:0016184", - "MONDO:0016156", - "MONDO:0020246", - "MONDO:0021147", - "MONDO:0044137", - "MONDO:0019755", - "OGMS:0000031", - "MONDO:0015327", - "MONDO:0003847", "MONDO:0003939", - "MONDO:0002022", - "MONDO:0015286", - "BFO:0000001", "MONDO:0002320", - "MONDO:0019052", - "MONDO:0020247", - "MONDO:0005066", - "MONDO:0005328", - "MONDO:0019950", - "MONDO:0016155", - "MONDO:0700066", ], - "subject_label": "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type a, 12", + "subject_label": "MYH7-related skeletal myopathy", "subject_closure_label": [ - "entity", - "continuant", - "disposition", - "realizable entity", - "specifically dependent continuant", - "disease", - "muscular dystrophy-dystroglycanopathy, type A", - "disorder of orbital region", + "muscular dystrophy", + "human disease", "musculoskeletal system disorder", + "disease", + "muscle tissue disorder", "congenital nervous system disorder", + "hereditary skeletal muscle disorder", + "MYH7-related skeletal myopathy", + "disposition", + "qualitative or quantitative protein defects in neuromuscular diseases", + "distal myopathy", + "disease", + "continuant", + "qualitative or quantitative defects of beta-myosin heavy chain (MYH7)", + "myopathy", "hereditary disease", - "muscle tissue disorder", - "metabolic disease", "nervous system disorder", - "retinal disorder", - "eye disorder", - "myopathy", - "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type a, 12", - "congenital disorder of glycosylation", - "developmental anomaly of metabolic origin", - "qualitative or quantitative protein defects in neuromuscular diseases", - "qualitative or quantitative defects of protein involved in O-glycosylation of alpha-dystroglycan", - "qualitative or quantitative defects of FKRP", - "qualitative or quantitative defects of fukutin", - "qualitative or quantitative defects of protein O-mannose beta1, 2N-acetylglucosaminyltransferase", - "qualitative or quantitative defects of protein O-mannosyltransferase 1", - "qualitative or quantitative defects of protein O-mannosyltransferase 2", - "disorder of protein O-glycosylation", - "disorder of O-mannosylglycan synthesis", - "muscular dystrophy-dystroglycanopathy", - "qualitative or quantitative defects of alpha-dystroglycan", - "lissencephaly spectrum disorders", - "cobblestone lissencephaly", - "inborn errors of metabolism", - "neuromuscular disease", - "developmental defect during embryogenesis", - "congenital muscular dystrophy", + "congenital myopathy", + "realizable entity", + "specifically dependent continuant", "skeletal muscle disorder", - "muscular dystrophy", - "inherited vitreous-retinal disease", - "inherited vitreoretinopathy", - "congenital vitreoretinal dysplasia", - "disorder of development or morphogenesis", - "disorder of glycosylation", - "disorder of visual system", - "vitreous body disorder", - "glycoprotein metabolism disease", - "myopathy caused by variation in FKRP", - "myopathy caused by variation in POMGNT1", - "human disease", - "hereditary skeletal muscle disorder", - "disease", + "neuromuscular disease", + "entity", ], "subject_taxon": None, "subject_taxon_label": None, "predicate": "biolink:has_phenotype", - "object": "HP:0001263", + "object": "HP:0030051", "original_object": None, "object_namespace": "HP", "object_category": "biolink:PhenotypicFeature", "object_closure": [ - "HP:0000001", "UPHENO:0082875", - "UPHENO:0075696", - "UPHENO:0001001", + "UPHENO:0049622", "UPHENO:0001005", + "BFO:0000002", + "UPHENO:0050606", + "HP:0001288", + "HP:0012638", + "BFO:0000015", + "BFO:0000004", + "GO:0050882", + "NBO:0000338", + "GO:0050905", + "UBERON:0001016", + "HP:0000001", + "UPHENO:0001001", + "UPHENO:0080585", "UPHENO:0001002", "HP:0000118", - "BFO:0000002", - "HP:0012759", "BFO:0000020", "UPHENO:0002433", - "HP:0001263", - "UPHENO:0002332", - "HP:0000707", "UPHENO:0001003", - "UPHENO:0002536", - "HP:0012758", - "UPHENO:0004523", + "HP:0000708", + "HP:0011446", "BFO:0000001", "PATO:0000001", - "HP:0012638", "BFO:0000001", - "BFO:0000002", - "BFO:0000004", "BFO:0000040", - "UBERON:0001062", - "UBERON:0000465", - "UBERON:0000061", + "GO:0032501", + "GO:0050881", + "NBO:0000313", + "GO:0050877", "UBERON:0010000", "UBERON:0000467", "UBERON:0000468", - "UBERON:0001016", + "NBO:0000403", + "NBO:0000001", + "UPHENO:0075696", + "UPHENO:0078622", + "UPHENO:0049586", + "HP:0100022", + "UPHENO:0050613", + "UPHENO:0002332", + "UPHENO:0002536", + "UPHENO:0079826", + "UPHENO:0004523", + "UPHENO:0049587", + "BFO:0000003", + "GO:0008150", + "GO:0050879", + "GO:0007610", + "GO:0003008", + "HP:0030051", + "HP:0000707", + "UPHENO:0079833", + "BFO:0000002", + "UBERON:0001062", + "UBERON:0000465", + "UBERON:0000061", ], - "object_label": "Global developmental delay (HPO)", + "object_label": "Tip-toe gait (HPO)", "object_closure_label": [ - "entity", - "entity", - "continuant", - "continuant", - "independent continuant", - "specifically dependent continuant", - "material entity", "All (HPO)", + "abnormal behavior", + "Abnormality of movement (HPO)", + "Phenotypic abnormality", "Phenotypic abnormality (HPO)", + "Tip-toe gait (HPO)", "Abnormality of the nervous system (HPO)", - "Global developmental delay (HPO)", - "Abnormal nervous system physiology (HPO)", - "Neurodevelopmental delay (HPO)", - "Neurodevelopmental abnormality (HPO)", + "Behavioral abnormality (HPO)", + "Abnormality of higher mental function (HPO)", + "abnormal voluntary movement behavior", "quality", - "anatomical structure", + "process", + "independent continuant", "material anatomical entity", - "anatomical system", - "multicellular organism", "nervous system", - "anatomical entity", - "multicellular anatomical structure", + "voluntary movement behavior", + "body part movement", + "abnormality of anatomical entity physiology", "phenotype", - "Phenotypic abnormality", + "specifically dependent continuant", + "abnormality of nervous system physiology", "phenotype by ontology source", + "Gait disturbance (HPO)", + "abnormal behavior process", + "abnormal nervous system", + "abnormal biological_process", + "Abnormal nervous system physiology (HPO)", + "occurrent", + "biological_process", + "multicellular organismal movement", + "behavior", + "system process", + "musculoskeletal movement", + "behavior process", + "nervous system process", "abnormal phenotype by ontology source", - "abnormality of anatomical entity physiology", - "abnormality of nervous system physiology", - "abnormal anatomical entity", - "abnormal nervous system", + "continuant", + "abnormal voluntary musculoskeletal movement", + "entity", + "anatomical entity", + "anatomical structure", "abnormal anatomical entity", + "abnormal voluntary movement behavior", + "abnormal response to stimulus", + "abnormal behavior process", + "abnormal musculoskeletal movement", "abnormality of anatomical entity physiology", + "abnormal anatomical entity", + "entity", + "continuant", + "material entity", + "multicellular organismal process", + "multicellular anatomical structure", + "anatomical system", + "voluntary musculoskeletal movement", + "kinesthetic behavior", + "neuromuscular process", + "multicellular organism", ], "object_taxon": None, "object_taxon_label": None, @@ -1478,26 +1824,32 @@ def associations(): "aggregator_knowledge_source": ["infores:monarchinitiative"], "negated": None, "pathway": None, - "evidence_count": 4, - "has_evidence": ["ECO:0000304"], - "has_evidence_links": [{"id": "ECO:0000304", "url": "http://purl.obolibrary.org/obo/ECO_0000304"}], + "evidence_count": 2, + "has_evidence": ["ECO:0000269"], + "has_evidence_links": [{"id": "ECO:0000269", "url": "http://purl.obolibrary.org/obo/ECO_0000269"}], + "grouping_key": "MONDO:0008050🍪🍪biolink:has_phenotype🍪HP:0030051", "provided_by": "hpoa_disease_to_phenotype_edges", "provided_by_link": { "id": "hpoa_disease_to_phenotype", "url": "https://monarch-initiative.github.io/monarch-ingest/Sources/hpoa/#disease_to_phenotype", }, - "publications": ["OMIM:615249"], - "publications_links": [{"id": "OMIM:615249", "url": "http://identifiers.org/mim/615249"}], + "publications": ["PMID:17548557"], + "publications_links": [{"id": "PMID:17548557", "url": "http://identifiers.org/pubmed/17548557"}], "qualifiers": [], - "frequency_qualifier": None, + "frequency_qualifier": "HP:0040280", "onset_qualifier": None, "sex_qualifier": None, "stage_qualifier": None, - "frequency_qualifier_label": None, - "frequency_qualifier_namespace": None, - "frequency_qualifier_category": None, - "frequency_qualifier_closure": [], - "frequency_qualifier_closure_label": [], + "qualifiers_label": None, + "qualifiers_namespace": None, + "qualifiers_category": None, + "qualifiers_closure": [], + "qualifiers_closure_label": [], + "frequency_qualifier_label": "Obligate (HPO)", + "frequency_qualifier_namespace": "HP", + "frequency_qualifier_category": "biolink:PhenotypicFeature", + "frequency_qualifier_closure": ["HP:0000001", "HP:0040280", "HP:0040279"], + "frequency_qualifier_closure_label": ["All (HPO)", "Obligate (HPO)", "Frequency (HPO)"], "onset_qualifier_label": None, "onset_qualifier_namespace": None, "onset_qualifier_category": None, @@ -1515,196 +1867,206 @@ def associations(): "stage_qualifier_closure_label": [], }, { - "id": "uuid:86cb89df-5d8c-11ee-9b27-2b20ed86a9d9", + "id": "uuid:c9c8bfed-7529-11ee-b012-cbd37f5c3759", "category": "biolink:DiseaseToPhenotypicFeatureAssociation", - "subject": "MONDO:0014120", - "original_subject": "OMIM:615287", + "subject": "MONDO:0009675", + "original_subject": "OMIM:253600", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ - "MONDO:0018282", - "MONDO:0000001", - "MONDO:0016182", - "MONDO:0017741", - "MONDO:0014120", - "MONDO:0018276", - "MONDO:0045010", + "MONDO:0016971", + "MONDO:0005336", + "MONDO:0015152", + "MONDO:0000429", "MONDO:0005071", + "MONDO:0006025", + "BFO:0000016", + "MONDO:0016139", + "OGMS:0000031", + "BFO:0000001", "MONDO:0020121", - "MONDO:0700068", - "MONDO:0700223", - "MONDO:0024322", - "MONDO:0005283", - "MONDO:0020238", - "BFO:0000002", - "MONDO:0016185", - "MONDO:0000171", "BFO:0000017", - "MONDO:0018869", "BFO:0000020", - "MONDO:0016157", - "MONDO:0017745", - "BFO:0000016", + "MONDO:0009675", "MONDO:0020120", + "MONDO:0016152", "MONDO:0019056", - "MONDO:0016139", + "MONDO:0000001", + "MONDO:0700223", + "BFO:0000002", + "MONDO:0016106", "MONDO:0700096", - "MONDO:0018838", - "MONDO:0024458", - "MONDO:0005336", "MONDO:0002081", - "MONDO:0016184", - "MONDO:0016156", - "MONDO:0020246", - "MONDO:0021147", - "MONDO:0044137", - "MONDO:0019755", - "OGMS:0000031", - "MONDO:0015327", "MONDO:0003847", "MONDO:0003939", - "MONDO:0002022", - "MONDO:0015286", - "BFO:0000001", - "MONDO:0002320", - "MONDO:0019052", - "MONDO:0020247", - "MONDO:0005066", - "MONDO:0005328", - "MONDO:0019950", - "MONDO:0016155", - "MONDO:0700066", ], - "subject_label": "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A13", + "subject_label": "autosomal recessive limb-girdle muscular dystrophy type 2A", "subject_closure_label": [ - "entity", - "continuant", - "disposition", - "realizable entity", - "specifically dependent continuant", - "disease", - "muscular dystrophy-dystroglycanopathy, type A", - "disorder of orbital region", + "limb-girdle muscular dystrophy", + "muscular dystrophy", + "progressive muscular dystrophy", + "human disease", "musculoskeletal system disorder", - "congenital nervous system disorder", + "disease", "hereditary disease", "muscle tissue disorder", - "metabolic disease", - "nervous system disorder", - "retinal disorder", - "eye disorder", - "myopathy", - "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A13", - "congenital disorder of glycosylation", - "developmental anomaly of metabolic origin", - "qualitative or quantitative protein defects in neuromuscular diseases", - "qualitative or quantitative defects of protein involved in O-glycosylation of alpha-dystroglycan", - "qualitative or quantitative defects of FKRP", - "qualitative or quantitative defects of fukutin", - "qualitative or quantitative defects of protein O-mannose beta1, 2N-acetylglucosaminyltransferase", - "qualitative or quantitative defects of protein O-mannosyltransferase 1", - "qualitative or quantitative defects of protein O-mannosyltransferase 2", - "disorder of protein O-glycosylation", - "disorder of O-mannosylglycan synthesis", - "muscular dystrophy-dystroglycanopathy", - "qualitative or quantitative defects of alpha-dystroglycan", - "lissencephaly spectrum disorders", - "cobblestone lissencephaly", - "inborn errors of metabolism", - "neuromuscular disease", - "developmental defect during embryogenesis", - "congenital muscular dystrophy", - "skeletal muscle disorder", - "muscular dystrophy", - "inherited vitreous-retinal disease", - "inherited vitreoretinopathy", - "congenital vitreoretinal dysplasia", - "disorder of development or morphogenesis", - "disorder of glycosylation", - "disorder of visual system", - "vitreous body disorder", - "glycoprotein metabolism disease", - "myopathy caused by variation in FKRP", - "myopathy caused by variation in POMGNT1", - "human disease", "hereditary skeletal muscle disorder", + "continuant", + "autosomal recessive disease", + "disposition", + "qualitative or quantitative protein defects in neuromuscular diseases", "disease", + "myopathy", + "autosomal genetic disease", + "nervous system disorder", + "realizable entity", + "specifically dependent continuant", + "autosomal recessive limb-girdle muscular dystrophy type 2A", + "skeletal muscle disorder", + "qualitative or quantitative defects of calpain", + "neuromuscular disease", + "autosomal recessive limb-girdle muscular dystrophy", + "entity", ], "subject_taxon": None, "subject_taxon_label": None, "predicate": "biolink:has_phenotype", - "object": "HP:0001263", + "object": "HP:0001880", "original_object": None, "object_namespace": "HP", "object_category": "biolink:PhenotypicFeature", "object_closure": [ - "HP:0000001", - "UPHENO:0082875", - "UPHENO:0075696", - "UPHENO:0001001", + "HP:0001879", "UPHENO:0001005", - "UPHENO:0001002", - "HP:0000118", "BFO:0000002", - "HP:0012759", "BFO:0000020", - "UPHENO:0002433", - "HP:0001263", - "UPHENO:0002332", - "HP:0000707", + "HP:0002715", + "HP:0001911", + "HP:0001880", + "BFO:0000004", + "UBERON:0000178", + "CL:0000094", + "CL:0002242", + "CL:0000255", + "CL:0000219", + "HP:0000001", + "HP:0032309", + "HP:0010974", + "HP:0000118", + "HP:0001871", + "HP:0020064", "UPHENO:0001003", "UPHENO:0002536", - "HP:0012758", - "UPHENO:0004523", "BFO:0000001", "PATO:0000001", - "HP:0012638", "BFO:0000001", + "UBERON:0000467", + "CL:0000000", + "UBERON:0000468", + "CL:0000738", + "CL:0000548", + "CL:0000763", + "CL:0000081", + "UPHENO:0002948", + "UPHENO:0001002", + "HP:0025461", + "HP:0001881", + "HP:0020047", + "UPHENO:0004459", + "HP:0032251", "BFO:0000002", - "BFO:0000004", "BFO:0000040", - "UBERON:0001062", + "PR:000050567", "UBERON:0000465", + "CL:0000771", + "UBERON:0004120", + "UBERON:0006314", + "UBERON:0015203", + "CL:0000003", + "UBERON:0002193", + "UBERON:0002390", + "UBERON:0000179", + "UBERON:0002405", + "CL:0000988", + "HP:0011893", + "UPHENO:0001001", + "HP:0025354", + "HP:0001974", + "HP:0010987", + "UBERON:0001062", "UBERON:0000061", + "UBERON:0000463", + "UBERON:0034923", "UBERON:0010000", - "UBERON:0000467", - "UBERON:0000468", - "UBERON:0001016", + "CL:0000766", + "CL:0002371", ], - "object_label": "Global developmental delay (HPO)", + "object_label": "Eosinophilia (HPO)", "object_closure_label": [ - "entity", - "entity", - "continuant", - "continuant", - "independent continuant", - "specifically dependent continuant", - "material entity", "All (HPO)", + "Abnormal eosinophil morphology (HPO)", + "Abnormal myeloid leukocyte morphology (HPO)", "Phenotypic abnormality (HPO)", - "Abnormality of the nervous system (HPO)", - "Global developmental delay (HPO)", - "Abnormal nervous system physiology (HPO)", - "Neurodevelopmental delay (HPO)", - "Neurodevelopmental abnormality (HPO)", + "Abnormal cellular phenotype (HPO)", + "Leukocytosis (HPO)", + "Abnormal cellular immune system morphology (HPO)", "quality", - "anatomical structure", - "material anatomical entity", - "anatomical system", - "multicellular organism", - "nervous system", - "anatomical entity", + "independent continuant", + "blood", + "granulocyte", "multicellular anatomical structure", - "phenotype", - "Phenotypic abnormality", + "myeloid cell", + "blood cell", + "Abnormality of blood and blood-forming tissues (HPO)", + "Abnormal eosinophil count (HPO)", "phenotype by ontology source", + "continuant", + "material entity", + "protein-containing material entity", + "material anatomical entity", + "leukocyte", + "animal cell", + "hematopoietic cell", + "Abnormal leukocyte count (HPO)", + "phenotype", "abnormal phenotype by ontology source", - "abnormality of anatomical entity physiology", - "abnormality of nervous system physiology", - "abnormal anatomical entity", - "abnormal nervous system", + "continuant", + "specifically dependent continuant", + "Abnormality of the immune system (HPO)", + "Abnormal granulocyte morphology (HPO)", + "Eosinophilia (HPO)", "abnormal anatomical entity", - "abnormality of anatomical entity physiology", + "Abnormal immune system morphology (HPO)", + "entity", + "anatomical entity", + "anatomical structure", + "organism substance", + "disconnected anatomical group", + "mesoderm-derived structure", + "bodily fluid", + "non-connected functional system", + "native cell", + "hemolymphoid system", + "hematopoietic system", + "haemolymphatic fluid", + "immune system", + "myeloid leukocyte", + "somatic cell", + "abnormal immune system", + "Abnormal granulocyte count (HPO)", + "Phenotypic abnormality", + "Abnormal cell morphology (HPO)", + "Abnormal leukocyte morphology (HPO)", + "Abnormal myeloid cell morphology (HPO)", + "abnormal hematopoietic system", + "entity", + "eosinophil", + "anatomical system", + "cell", + "multicellular organism", + "nucleate cell", + "eukaryotic cell", + "motile cell", ], "object_taxon": None, "object_taxon_label": None, @@ -1712,26 +2074,32 @@ def associations(): "aggregator_knowledge_source": ["infores:monarchinitiative"], "negated": None, "pathway": None, - "evidence_count": 4, - "has_evidence": ["ECO:0000304"], - "has_evidence_links": [{"id": "ECO:0000304", "url": "http://purl.obolibrary.org/obo/ECO_0000304"}], + "evidence_count": 2, + "has_evidence": ["ECO:0000269"], + "has_evidence_links": [{"id": "ECO:0000269", "url": "http://purl.obolibrary.org/obo/ECO_0000269"}], + "grouping_key": "MONDO:0009675🍪🍪biolink:has_phenotype🍪HP:0001880", "provided_by": "hpoa_disease_to_phenotype_edges", "provided_by_link": { "id": "hpoa_disease_to_phenotype", "url": "https://monarch-initiative.github.io/monarch-ingest/Sources/hpoa/#disease_to_phenotype", }, - "publications": ["OMIM:615287"], - "publications_links": [{"id": "OMIM:615287", "url": "http://identifiers.org/mim/615287"}], + "publications": ["PMID:16607617"], + "publications_links": [{"id": "PMID:16607617", "url": "http://identifiers.org/pubmed/16607617"}], "qualifiers": [], - "frequency_qualifier": None, + "frequency_qualifier": "HP:0040282", "onset_qualifier": None, "sex_qualifier": None, "stage_qualifier": None, - "frequency_qualifier_label": None, - "frequency_qualifier_namespace": None, - "frequency_qualifier_category": None, - "frequency_qualifier_closure": [], - "frequency_qualifier_closure_label": [], + "qualifiers_label": None, + "qualifiers_namespace": None, + "qualifiers_category": None, + "qualifiers_closure": [], + "qualifiers_closure_label": [], + "frequency_qualifier_label": "Frequent (HPO)", + "frequency_qualifier_namespace": "HP", + "frequency_qualifier_category": "biolink:PhenotypicFeature", + "frequency_qualifier_closure": ["HP:0040282", "HP:0000001", "HP:0040279"], + "frequency_qualifier_closure_label": ["All (HPO)", "Frequent (HPO)", "Frequency (HPO)"], "onset_qualifier_label": None, "onset_qualifier_namespace": None, "onset_qualifier_category": None, @@ -1749,200 +2117,144 @@ def associations(): "stage_qualifier_closure_label": [], }, { - "id": "uuid:852ba5be-5d8c-11ee-9b27-2b20ed86a9d9", + "id": "uuid:c9c8bfee-7529-11ee-b012-cbd37f5c3759", "category": "biolink:DiseaseToPhenotypicFeatureAssociation", - "subject": "MONDO:0014140", - "original_subject": "OMIM:615350", + "subject": "MONDO:0009675", + "original_subject": "OMIM:253600", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ - "MONDO:0700084", - "MONDO:0018282", - "MONDO:0000001", - "MONDO:0016182", - "MONDO:0017741", - "MONDO:0018276", - "MONDO:0045010", + "MONDO:0016971", + "MONDO:0005336", + "MONDO:0015152", + "MONDO:0000429", "MONDO:0005071", + "MONDO:0006025", + "BFO:0000016", + "MONDO:0016139", + "OGMS:0000031", + "BFO:0000001", "MONDO:0020121", - "MONDO:0700068", - "MONDO:0700223", - "MONDO:0024322", - "MONDO:0005283", - "MONDO:0020238", - "BFO:0000002", - "MONDO:0016185", - "MONDO:0000171", "BFO:0000017", - "MONDO:0018869", "BFO:0000020", - "MONDO:0016157", - "MONDO:0017745", - "BFO:0000016", + "MONDO:0009675", "MONDO:0020120", + "MONDO:0016152", "MONDO:0019056", - "MONDO:0016139", + "MONDO:0000001", + "MONDO:0700223", + "BFO:0000002", + "MONDO:0016106", "MONDO:0700096", - "MONDO:0018838", - "MONDO:0024458", - "MONDO:0005336", "MONDO:0002081", - "MONDO:0016184", - "MONDO:0016156", - "MONDO:0018939", - "MONDO:0020246", - "MONDO:0021147", - "MONDO:0014140", - "MONDO:0044137", - "MONDO:0019755", - "OGMS:0000031", - "MONDO:0015327", "MONDO:0003847", "MONDO:0003939", - "MONDO:0002022", - "MONDO:0015286", - "BFO:0000001", - "MONDO:0002320", - "MONDO:0019052", - "MONDO:0020247", - "MONDO:0005066", - "MONDO:0005328", - "MONDO:0019950", - "MONDO:0016155", - "MONDO:0700066", ], - "subject_label": "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A14", + "subject_label": "autosomal recessive limb-girdle muscular dystrophy type 2A", "subject_closure_label": [ - "entity", - "continuant", - "disposition", - "realizable entity", - "specifically dependent continuant", - "disease", - "muscular dystrophy-dystroglycanopathy, type A", - "disorder of orbital region", + "limb-girdle muscular dystrophy", + "muscular dystrophy", + "progressive muscular dystrophy", + "human disease", "musculoskeletal system disorder", - "congenital nervous system disorder", + "disease", "hereditary disease", "muscle tissue disorder", - "metabolic disease", - "nervous system disorder", - "retinal disorder", - "eye disorder", - "myopathy", - "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A14", - "congenital disorder of glycosylation", - "developmental anomaly of metabolic origin", - "qualitative or quantitative protein defects in neuromuscular diseases", - "qualitative or quantitative defects of protein involved in O-glycosylation of alpha-dystroglycan", - "qualitative or quantitative defects of FKRP", - "qualitative or quantitative defects of fukutin", - "qualitative or quantitative defects of protein O-mannose beta1, 2N-acetylglucosaminyltransferase", - "qualitative or quantitative defects of protein O-mannosyltransferase 1", - "qualitative or quantitative defects of protein O-mannosyltransferase 2", - "disorder of protein O-glycosylation", - "disorder of O-mannosylglycan synthesis", - "muscular dystrophy-dystroglycanopathy", - "qualitative or quantitative defects of alpha-dystroglycan", - "lissencephaly spectrum disorders", - "cobblestone lissencephaly", - "muscle-eye-brain disease", - "inborn errors of metabolism", - "neuromuscular disease", - "developmental defect during embryogenesis", - "congenital muscular dystrophy", - "skeletal muscle disorder", - "muscular dystrophy", - "inherited vitreous-retinal disease", - "inherited vitreoretinopathy", - "congenital vitreoretinal dysplasia", - "disorder of development or morphogenesis", - "disorder of glycosylation", - "disorder of visual system", - "vitreous body disorder", - "glycoprotein metabolism disease", - "myopathy caused by variation in FKRP", - "myopathy caused by variation in POMGNT1", - "myopathy caused by variation in GMPPB", - "human disease", "hereditary skeletal muscle disorder", + "continuant", + "autosomal recessive disease", + "disposition", + "qualitative or quantitative protein defects in neuromuscular diseases", "disease", + "myopathy", + "autosomal genetic disease", + "nervous system disorder", + "realizable entity", + "specifically dependent continuant", + "autosomal recessive limb-girdle muscular dystrophy type 2A", + "skeletal muscle disorder", + "qualitative or quantitative defects of calpain", + "neuromuscular disease", + "autosomal recessive limb-girdle muscular dystrophy", + "entity", ], "subject_taxon": None, "subject_taxon_label": None, "predicate": "biolink:has_phenotype", - "object": "HP:0001263", + "object": "HP:0002312", "original_object": None, "object_namespace": "HP", "object_category": "biolink:PhenotypicFeature", "object_closure": [ - "HP:0000001", "UPHENO:0082875", - "UPHENO:0075696", - "UPHENO:0001001", "UPHENO:0001005", - "UPHENO:0001002", + "HP:0012638", + "BFO:0000004", + "UBERON:0000061", + "UBERON:0001016", + "HP:0000001", "HP:0000118", - "BFO:0000002", - "HP:0012759", "BFO:0000020", "UPHENO:0002433", - "HP:0001263", - "UPHENO:0002332", - "HP:0000707", "UPHENO:0001003", - "UPHENO:0002536", - "HP:0012758", - "UPHENO:0004523", - "BFO:0000001", "PATO:0000001", - "HP:0012638", "BFO:0000001", - "BFO:0000002", - "BFO:0000004", "BFO:0000040", - "UBERON:0001062", - "UBERON:0000465", - "UBERON:0000061", - "UBERON:0010000", "UBERON:0000467", "UBERON:0000468", - "UBERON:0001016", + "UPHENO:0075696", + "HP:0011442", + "UPHENO:0001002", + "UPHENO:0002332", + "UPHENO:0002536", + "UPHENO:0004523", + "HP:0002312", + "HP:0011443", + "BFO:0000002", + "UBERON:0000465", + "UPHENO:0001001", + "BFO:0000002", + "HP:0000707", + "HP:0002311", + "BFO:0000001", + "UBERON:0001062", + "UBERON:0010000", ], - "object_label": "Global developmental delay (HPO)", + "object_label": "Clumsiness (HPO)", "object_closure_label": [ - "entity", - "entity", - "continuant", - "continuant", - "independent continuant", - "specifically dependent continuant", - "material entity", "All (HPO)", + "Abnormal central motor function (HPO)", "Phenotypic abnormality (HPO)", "Abnormality of the nervous system (HPO)", - "Global developmental delay (HPO)", - "Abnormal nervous system physiology (HPO)", - "Neurodevelopmental delay (HPO)", - "Neurodevelopmental abnormality (HPO)", + "entity", "quality", + "independent continuant", "anatomical structure", - "material anatomical entity", - "anatomical system", - "multicellular organism", - "nervous system", - "anatomical entity", "multicellular anatomical structure", - "phenotype", - "Phenotypic abnormality", - "phenotype by ontology source", - "abnormal phenotype by ontology source", + "nervous system", "abnormality of anatomical entity physiology", + "continuant", + "specifically dependent continuant", "abnormality of nervous system physiology", - "abnormal anatomical entity", + "phenotype by ontology source", "abnormal nervous system", + "Clumsiness (HPO)", + "Abnormal nervous system physiology (HPO)", + "continuant", + "material anatomical entity", + "phenotype", + "abnormal phenotype by ontology source", + "Incoordination (HPO)", + "Abnormality of coordination (HPO)", + "entity", + "anatomical entity", "abnormal anatomical entity", + "Phenotypic abnormality", "abnormality of anatomical entity physiology", + "abnormal anatomical entity", + "material entity", + "anatomical system", + "multicellular organism", ], "object_taxon": None, "object_taxon_label": None, @@ -1950,26 +2262,32 @@ def associations(): "aggregator_knowledge_source": ["infores:monarchinitiative"], "negated": None, "pathway": None, - "evidence_count": 4, + "evidence_count": 2, "has_evidence": ["ECO:0000269"], "has_evidence_links": [{"id": "ECO:0000269", "url": "http://purl.obolibrary.org/obo/ECO_0000269"}], + "grouping_key": "MONDO:0009675🍪🍪biolink:has_phenotype🍪HP:0002312", "provided_by": "hpoa_disease_to_phenotype_edges", "provided_by_link": { "id": "hpoa_disease_to_phenotype", "url": "https://monarch-initiative.github.io/monarch-ingest/Sources/hpoa/#disease_to_phenotype", }, - "publications": ["PMID:23768512"], - "publications_links": [{"id": "PMID:23768512", "url": "http://identifiers.org/pubmed/23768512"}], + "publications": ["PMID:16607617"], + "publications_links": [{"id": "PMID:16607617", "url": "http://identifiers.org/pubmed/16607617"}], "qualifiers": [], - "frequency_qualifier": None, + "frequency_qualifier": "HP:0040282", "onset_qualifier": None, "sex_qualifier": None, "stage_qualifier": None, - "frequency_qualifier_label": None, - "frequency_qualifier_namespace": None, - "frequency_qualifier_category": None, - "frequency_qualifier_closure": [], - "frequency_qualifier_closure_label": [], + "qualifiers_label": None, + "qualifiers_namespace": None, + "qualifiers_category": None, + "qualifiers_closure": [], + "qualifiers_closure_label": [], + "frequency_qualifier_label": "Frequent (HPO)", + "frequency_qualifier_namespace": "HP", + "frequency_qualifier_category": "biolink:PhenotypicFeature", + "frequency_qualifier_closure": ["HP:0040282", "HP:0000001", "HP:0040279"], + "frequency_qualifier_closure_label": ["All (HPO)", "Frequent (HPO)", "Frequency (HPO)"], "onset_qualifier_label": None, "onset_qualifier_namespace": None, "onset_qualifier_category": None, @@ -1987,156 +2305,148 @@ def associations(): "stage_qualifier_closure_label": [], }, { - "id": "uuid:850bd377-5d8c-11ee-9b27-2b20ed86a9d9", + "id": "uuid:c9c8bff4-7529-11ee-b012-cbd37f5c3759", "category": "biolink:DiseaseToPhenotypicFeatureAssociation", - "subject": "MONDO:0014141", - "original_subject": "OMIM:615351", + "subject": "MONDO:0009675", + "original_subject": "OMIM:253600", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ - "MONDO:0700084", - "MONDO:0018282", - "MONDO:0000001", - "MONDO:0017741", - "MONDO:0018276", - "MONDO:0045010", + "MONDO:0016971", + "MONDO:0005336", + "MONDO:0015152", + "MONDO:0000429", "MONDO:0005071", + "MONDO:0006025", + "BFO:0000016", + "MONDO:0016139", + "OGMS:0000031", + "BFO:0000001", "MONDO:0020121", - "MONDO:0000172", - "MONDO:0700223", - "MONDO:0024322", - "BFO:0000002", "BFO:0000017", - "MONDO:0014141", "BFO:0000020", - "BFO:0000016", + "MONDO:0009675", "MONDO:0020120", + "MONDO:0016152", "MONDO:0019056", - "MONDO:0016139", + "MONDO:0000001", + "MONDO:0700223", + "BFO:0000002", + "MONDO:0016106", "MONDO:0700096", - "MONDO:0005336", "MONDO:0002081", - "OGMS:0000031", "MONDO:0003847", "MONDO:0003939", - "MONDO:0015286", - "BFO:0000001", - "MONDO:0002320", - "MONDO:0019052", - "MONDO:0005066", - "MONDO:0019950", - "MONDO:0016155", ], - "subject_label": "muscular dystrophy-dystroglycanopathy (congenital with intellectual disability), type B14", + "subject_label": "autosomal recessive limb-girdle muscular dystrophy type 2A", "subject_closure_label": [ - "entity", - "continuant", - "disposition", - "realizable entity", - "specifically dependent continuant", - "disease", - "muscular dystrophy-dystroglycanopathy, type B", + "limb-girdle muscular dystrophy", + "muscular dystrophy", + "progressive muscular dystrophy", + "human disease", "musculoskeletal system disorder", - "congenital nervous system disorder", + "disease", "hereditary disease", "muscle tissue disorder", - "metabolic disease", - "nervous system disorder", - "myopathy", - "muscular dystrophy-dystroglycanopathy (congenital with intellectual disability), type B14", - "congenital disorder of glycosylation", - "qualitative or quantitative protein defects in neuromuscular diseases", - "qualitative or quantitative defects of protein involved in O-glycosylation of alpha-dystroglycan", - "disorder of protein O-glycosylation", - "muscular dystrophy-dystroglycanopathy", - "qualitative or quantitative defects of alpha-dystroglycan", - "inborn errors of metabolism", - "neuromuscular disease", - "congenital muscular dystrophy", - "skeletal muscle disorder", - "muscular dystrophy", - "disorder of glycosylation", - "glycoprotein metabolism disease", - "myopathy caused by variation in GMPPB", - "human disease", "hereditary skeletal muscle disorder", + "continuant", + "autosomal recessive disease", + "disposition", + "qualitative or quantitative protein defects in neuromuscular diseases", "disease", + "myopathy", + "autosomal genetic disease", + "nervous system disorder", + "realizable entity", + "specifically dependent continuant", + "autosomal recessive limb-girdle muscular dystrophy type 2A", + "skeletal muscle disorder", + "qualitative or quantitative defects of calpain", + "neuromuscular disease", + "autosomal recessive limb-girdle muscular dystrophy", + "entity", ], "subject_taxon": None, "subject_taxon_label": None, "predicate": "biolink:has_phenotype", - "object": "HP:0001263", + "object": "HP:0032019", "original_object": None, "object_namespace": "HP", "object_category": "biolink:PhenotypicFeature", "object_closure": [ - "HP:0000001", - "UPHENO:0082875", - "UPHENO:0075696", - "UPHENO:0001001", "UPHENO:0001005", - "UPHENO:0001002", - "HP:0000118", "BFO:0000002", - "HP:0012759", "BFO:0000020", - "UPHENO:0002433", - "HP:0001263", - "UPHENO:0002332", - "HP:0000707", + "UPHENO:0076692", + "PATO:0000001", + "BFO:0000004", + "UBERON:0000061", + "HP:0000001", + "UPHENO:0001001", + "HP:0000118", + "HP:0032019", "UPHENO:0001003", - "UPHENO:0002536", - "HP:0012758", - "UPHENO:0004523", + "UPHENO:0076710", "BFO:0000001", - "PATO:0000001", - "HP:0012638", "BFO:0000001", - "BFO:0000002", - "BFO:0000004", "BFO:0000040", - "UBERON:0001062", - "UBERON:0000465", - "UBERON:0000061", - "UBERON:0010000", "UBERON:0000467", "UBERON:0000468", - "UBERON:0001016", + "UBERON:0011216", + "HP:0003011", + "UPHENO:0002536", + "BFO:0000002", + "UBERON:0000465", + "UBERON:0005090", + "UBERON:0001630", + "HP:0011805", + "UPHENO:0001002", + "UPHENO:0002816", + "UPHENO:0081581", + "HP:0033127", + "UBERON:0001062", + "UBERON:0010000", + "UBERON:0000062", + "UBERON:0000383", + "UBERON:0001015", ], - "object_label": "Global developmental delay (HPO)", + "object_label": "Muscle eosinophilia (HPO)", "object_closure_label": [ - "entity", - "entity", - "continuant", - "continuant", - "independent continuant", - "specifically dependent continuant", - "material entity", "All (HPO)", "Phenotypic abnormality (HPO)", - "Abnormality of the nervous system (HPO)", - "Global developmental delay (HPO)", - "Abnormal nervous system physiology (HPO)", - "Neurodevelopmental delay (HPO)", - "Neurodevelopmental abnormality (HPO)", - "quality", + "abnormal musculature", + "abnormal multicellular organism morphology", + "Abnormality of the musculoskeletal system (HPO)", + "independent continuant", "anatomical structure", - "material anatomical entity", - "anatomical system", - "multicellular organism", - "nervous system", - "anatomical entity", "multicellular anatomical structure", "phenotype", + "Abnormal skeletal muscle morphology (HPO)", "Phenotypic abnormality", + "Muscle eosinophilia (HPO)", "phenotype by ontology source", + "quality", + "continuant", + "material anatomical entity", "abnormal phenotype by ontology source", - "abnormality of anatomical entity physiology", - "abnormality of nervous system physiology", - "abnormal anatomical entity", - "abnormal nervous system", + "continuant", + "specifically dependent continuant", + "abnormal muscle organ morphology", + "entity", + "anatomical entity", + "muscle structure", + "organ", + "muscle organ", + "musculature of body", + "musculature", + "Abnormality of the musculature (HPO)", "abnormal anatomical entity", - "abnormality of anatomical entity physiology", + "abnormal anatomical entity morphology", + "entity", + "material entity", + "anatomical system", + "multicellular organism", + "organ system subdivision", ], "object_taxon": None, "object_taxon_label": None, @@ -2144,26 +2454,32 @@ def associations(): "aggregator_knowledge_source": ["infores:monarchinitiative"], "negated": None, "pathway": None, - "evidence_count": 4, + "evidence_count": 2, "has_evidence": ["ECO:0000269"], "has_evidence_links": [{"id": "ECO:0000269", "url": "http://purl.obolibrary.org/obo/ECO_0000269"}], + "grouping_key": "MONDO:0009675🍪🍪biolink:has_phenotype🍪HP:0032019", "provided_by": "hpoa_disease_to_phenotype_edges", "provided_by_link": { "id": "hpoa_disease_to_phenotype", "url": "https://monarch-initiative.github.io/monarch-ingest/Sources/hpoa/#disease_to_phenotype", }, - "publications": ["PMID:23768512"], - "publications_links": [{"id": "PMID:23768512", "url": "http://identifiers.org/pubmed/23768512"}], + "publications": ["PMID:16607617"], + "publications_links": [{"id": "PMID:16607617", "url": "http://identifiers.org/pubmed/16607617"}], "qualifiers": [], - "frequency_qualifier": None, + "frequency_qualifier": "HP:0040280", "onset_qualifier": None, "sex_qualifier": None, "stage_qualifier": None, - "frequency_qualifier_label": None, - "frequency_qualifier_namespace": None, - "frequency_qualifier_category": None, - "frequency_qualifier_closure": [], - "frequency_qualifier_closure_label": [], + "qualifiers_label": None, + "qualifiers_namespace": None, + "qualifiers_category": None, + "qualifiers_closure": [], + "qualifiers_closure_label": [], + "frequency_qualifier_label": "Obligate (HPO)", + "frequency_qualifier_namespace": "HP", + "frequency_qualifier_category": "biolink:PhenotypicFeature", + "frequency_qualifier_closure": ["HP:0000001", "HP:0040280", "HP:0040279"], + "frequency_qualifier_closure_label": ["All (HPO)", "Obligate (HPO)", "Frequency (HPO)"], "onset_qualifier_label": None, "onset_qualifier_namespace": None, "onset_qualifier_category": None, @@ -2181,142 +2497,206 @@ def associations(): "stage_qualifier_closure_label": [], }, { - "id": "uuid:842bf67e-5d8c-11ee-9b27-2b20ed86a9d9", + "id": "uuid:c9c8bff5-7529-11ee-b012-cbd37f5c3759", "category": "biolink:DiseaseToPhenotypicFeatureAssociation", - "subject": "MONDO:0014144", - "original_subject": "OMIM:615356", + "subject": "MONDO:0009675", + "original_subject": "OMIM:253600", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ - "MONDO:0000001", "MONDO:0016971", + "MONDO:0005336", + "MONDO:0015152", "MONDO:0000429", - "MONDO:0014144", "MONDO:0005071", + "MONDO:0006025", + "BFO:0000016", + "MONDO:0016139", + "OGMS:0000031", + "BFO:0000001", "MONDO:0020121", - "MONDO:0700223", - "BFO:0000002", - "MONDO:0005395", "BFO:0000017", "BFO:0000020", - "MONDO:0006025", - "MONDO:0016106", - "BFO:0000016", + "MONDO:0009675", "MONDO:0020120", + "MONDO:0016152", "MONDO:0019056", + "MONDO:0000001", + "MONDO:0700223", + "BFO:0000002", + "MONDO:0016106", "MONDO:0700096", - "MONDO:0005336", "MONDO:0002081", - "MONDO:0018243", - "OGMS:0000031", "MONDO:0003847", "MONDO:0003939", - "MONDO:0015152", - "BFO:0000001", ], - "subject_label": "autosomal recessive limb-girdle muscular dystrophy type R18", + "subject_label": "autosomal recessive limb-girdle muscular dystrophy type 2A", "subject_closure_label": [ - "entity", + "limb-girdle muscular dystrophy", + "muscular dystrophy", + "progressive muscular dystrophy", + "human disease", + "musculoskeletal system disorder", + "disease", + "hereditary disease", + "muscle tissue disorder", + "hereditary skeletal muscle disorder", "continuant", + "autosomal recessive disease", "disposition", - "realizable entity", - "specifically dependent continuant", + "qualitative or quantitative protein defects in neuromuscular diseases", "disease", + "myopathy", "autosomal genetic disease", - "musculoskeletal system disorder", - "hereditary disease", - "muscle tissue disorder", "nervous system disorder", - "myopathy", - "movement disorder", - "autosomal recessive disease", - "autosomal recessive limb-girdle muscular dystrophy type R18", - "autosomal recessive limb-girdle muscular dystrophy", - "progressive muscular dystrophy", - "limb-girdle muscular dystrophy", - "intellectual disability-hyperkinetic movement-truncal ataxia syndrome", - "neuromuscular disease", + "realizable entity", + "specifically dependent continuant", + "autosomal recessive limb-girdle muscular dystrophy type 2A", "skeletal muscle disorder", - "muscular dystrophy", - "human disease", - "hereditary skeletal muscle disorder", - "disease", + "qualitative or quantitative defects of calpain", + "neuromuscular disease", + "autosomal recessive limb-girdle muscular dystrophy", + "entity", ], "subject_taxon": None, "subject_taxon_label": None, "predicate": "biolink:has_phenotype", - "object": "HP:0001263", + "object": "HP:0007340", "original_object": None, "object_namespace": "HP", "object_category": "biolink:PhenotypicFeature", "object_closure": [ - "HP:0000001", "UPHENO:0082875", - "UPHENO:0075696", - "UPHENO:0001001", + "UPHENO:0002320", "UPHENO:0001005", - "UPHENO:0001002", - "HP:0000118", - "BFO:0000002", - "HP:0012759", + "HP:0009127", "BFO:0000020", - "UPHENO:0002433", - "HP:0001263", - "UPHENO:0002332", - "HP:0000707", - "UPHENO:0001003", - "UPHENO:0002536", - "HP:0012758", - "UPHENO:0004523", - "BFO:0000001", - "PATO:0000001", - "HP:0012638", + "UPHENO:0076692", "BFO:0000001", - "BFO:0000002", "BFO:0000004", - "BFO:0000040", - "UBERON:0001062", - "UBERON:0000465", + "UBERON:0004708", "UBERON:0000061", - "UBERON:0010000", + "UBERON:0000026", + "UBERON:0014892", + "HP:0000001", + "UPHENO:0001001", + "UPHENO:0001002", + "HP:0000118", + "UPHENO:0076710", + "PATO:0000001", + "BFO:0000001", + "BFO:0000040", + "UBERON:0001062", "UBERON:0000467", "UBERON:0000468", - "UBERON:0001016", + "UBERON:0011216", + "UBERON:0010709", + "UBERON:0010890", + "UPHENO:0075696", + "UPHENO:0080575", + "HP:0001324", + "HP:0003690", + "HP:0003011", + "UPHENO:0002332", + "UPHENO:0001003", + "UPHENO:0002536", + "HP:0040064", + "HP:0011804", + "BFO:0000002", + "PR:000050567", + "UBERON:0002101", + "UBERON:0005090", + "UBERON:0018254", + "UBERON:0010707", + "UBERON:0001630", + "UBERON:0007271", + "UBERON:0014792", + "HP:0007340", + "HP:0011805", + "BFO:0000002", + "UPHENO:0080555", + "UPHENO:0002816", + "UPHENO:0080556", + "UPHENO:0081581", + "HP:0033127", + "UPHENO:0002647", + "UPHENO:0002830", + "UBERON:0000465", + "RO:0002577", + "UBERON:0015212", + "UBERON:0010000", + "UBERON:0000475", + "UBERON:0000062", + "UBERON:0000383", + "UBERON:0001015", + "UBERON:0004480", ], - "object_label": "Global developmental delay (HPO)", + "object_label": "Lower limb muscle weakness (HPO)", "object_closure_label": [ - "entity", - "entity", - "continuant", - "continuant", - "independent continuant", - "specifically dependent continuant", - "material entity", "All (HPO)", + "abnormality of muscle organ physiology", + "Phenotypic abnormality", "Phenotypic abnormality (HPO)", - "Abnormality of the nervous system (HPO)", - "Global developmental delay (HPO)", - "Abnormal nervous system physiology (HPO)", - "Neurodevelopmental delay (HPO)", - "Neurodevelopmental abnormality (HPO)", + "decreased anatomical entity strength", + "abnormal musculature", + "decreased muscle organ strength", + "abnormal multicellular organism morphology", + "Abnormality of the musculoskeletal system (HPO)", + "abnormal musculature of limb", "quality", - "anatomical structure", + "independent continuant", "material anatomical entity", - "anatomical system", - "multicellular organism", - "nervous system", - "anatomical entity", + "system", + "paired limb/fin", + "anatomical structure", + "lateral structure", "multicellular anatomical structure", + "pelvic complex", + "appendage musculature", + "musculature of pelvic complex", + "abnormality of anatomical entity physiology", "phenotype", - "Phenotypic abnormality", - "phenotype by ontology source", + "Abnormal skeletal muscle morphology (HPO)", + "continuant", + "Abnormality of limbs (HPO)", + "continuant", + "protein-containing material entity", + "appendage girdle complex", + "pelvic complex muscle", + "Lower limb muscle weakness (HPO)", "abnormal phenotype by ontology source", - "abnormality of anatomical entity physiology", - "abnormality of nervous system physiology", - "abnormal anatomical entity", - "abnormal nervous system", + "Abnormality of the musculature of the limbs (HPO)", + "specifically dependent continuant", + "abnormal muscle organ morphology", + "Abnormal muscle physiology (HPO)", + "entity", + "muscle structure", + "skeletal musculature", + "organism subdivision", + "organ", + "muscle organ", + "musculature of body", + "musculature", + "musculature of limb", "abnormal anatomical entity", + "decreased pelvic complex muscle strength", + "Muscle weakness (HPO)", + "Limb muscle weakness (HPO)", + "Abnormality of the musculature (HPO)", "abnormality of anatomical entity physiology", + "phenotype by ontology source", + "abnormal anatomical entity", + "abnormal anatomical entity morphology", + "entity", + "abnormal limb", + "material entity", + "anatomical entity", + "limb", + "anatomical system", + "multicellular organism", + "organ system subdivision", + "appendage", + "skeletal muscle organ", ], "object_taxon": None, "object_taxon_label": None, @@ -2324,26 +2704,32 @@ def associations(): "aggregator_knowledge_source": ["infores:monarchinitiative"], "negated": None, "pathway": None, - "evidence_count": 4, - "has_evidence": ["ECO:0000304"], - "has_evidence_links": [{"id": "ECO:0000304", "url": "http://purl.obolibrary.org/obo/ECO_0000304"}], + "evidence_count": 2, + "has_evidence": ["ECO:0000269"], + "has_evidence_links": [{"id": "ECO:0000269", "url": "http://purl.obolibrary.org/obo/ECO_0000269"}], + "grouping_key": "MONDO:0009675🍪🍪biolink:has_phenotype🍪HP:0007340", "provided_by": "hpoa_disease_to_phenotype_edges", "provided_by_link": { "id": "hpoa_disease_to_phenotype", "url": "https://monarch-initiative.github.io/monarch-ingest/Sources/hpoa/#disease_to_phenotype", }, - "publications": ["OMIM:615356"], - "publications_links": [{"id": "OMIM:615356", "url": "http://identifiers.org/mim/615356"}], + "publications": ["PMID:16607617"], + "publications_links": [{"id": "PMID:16607617", "url": "http://identifiers.org/pubmed/16607617"}], "qualifiers": [], - "frequency_qualifier": None, + "frequency_qualifier": "HP:0040282", "onset_qualifier": None, "sex_qualifier": None, "stage_qualifier": None, - "frequency_qualifier_label": None, - "frequency_qualifier_namespace": None, - "frequency_qualifier_category": None, - "frequency_qualifier_closure": [], - "frequency_qualifier_closure_label": [], + "qualifiers_label": None, + "qualifiers_namespace": None, + "qualifiers_category": None, + "qualifiers_closure": [], + "qualifiers_closure_label": [], + "frequency_qualifier_label": "Frequent (HPO)", + "frequency_qualifier_namespace": "HP", + "frequency_qualifier_category": "biolink:PhenotypicFeature", + "frequency_qualifier_closure": ["HP:0040282", "HP:0000001", "HP:0040279"], + "frequency_qualifier_closure_label": ["All (HPO)", "Frequent (HPO)", "Frequency (HPO)"], "onset_qualifier_label": None, "onset_qualifier_namespace": None, "onset_qualifier_category": None, @@ -2361,132 +2747,156 @@ def associations(): "stage_qualifier_closure_label": [], }, { - "id": "uuid:8a99d59c-5d8c-11ee-9b27-2b20ed86a9d9", + "id": "uuid:c9d8bdf9-7529-11ee-b012-cbd37f5c3759", "category": "biolink:DiseaseToPhenotypicFeatureAssociation", - "subject": "MONDO:0024607", - "original_subject": "OMIM:617404", + "subject": "MONDO:0009676", + "original_subject": "OMIM:253601", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ - "MONDO:0000001", - "MONDO:0024607", - "MONDO:0005071", - "MONDO:0020121", - "MONDO:0700223", + "MONDO:0016971", "BFO:0000002", - "BFO:0000017", "BFO:0000020", + "MONDO:0005336", + "MONDO:0009676", + "MONDO:0015152", + "MONDO:0000429", + "MONDO:0005071", + "MONDO:0006025", "BFO:0000016", + "MONDO:0016139", + "OGMS:0000031", + "MONDO:0003847", + "BFO:0000001", + "MONDO:0016145", + "MONDO:0020121", + "BFO:0000017", "MONDO:0020120", "MONDO:0019056", + "MONDO:0000001", + "MONDO:0700223", + "MONDO:0016106", "MONDO:0700096", - "MONDO:0005336", "MONDO:0002081", - "OGMS:0000031", - "MONDO:0003847", "MONDO:0003939", - "BFO:0000001", - "MONDO:0002320", - "MONDO:0019950", ], - "subject_label": "congenital muscular dystrophy with cataracts and intellectual disability", + "subject_label": "autosomal recessive limb-girdle muscular dystrophy type 2B", "subject_closure_label": [ - "entity", - "continuant", + "limb-girdle muscular dystrophy", + "muscular dystrophy", + "progressive muscular dystrophy", + "human disease", + "musculoskeletal system disorder", + "disease", + "muscle tissue disorder", + "qualitative or quantitative defects of dysferlin", + "hereditary skeletal muscle disorder", + "autosomal recessive disease", "disposition", - "realizable entity", - "specifically dependent continuant", + "qualitative or quantitative protein defects in neuromuscular diseases", + "autosomal recessive limb-girdle muscular dystrophy type 2B", "disease", - "musculoskeletal system disorder", - "congenital nervous system disorder", + "continuant", + "specifically dependent continuant", + "myopathy", "hereditary disease", - "muscle tissue disorder", + "autosomal genetic disease", "nervous system disorder", - "myopathy", - "neuromuscular disease", - "congenital muscular dystrophy", + "realizable entity", "skeletal muscle disorder", - "muscular dystrophy", - "congenital muscular dystrophy with cataracts and intellectual disability", - "human disease", - "hereditary skeletal muscle disorder", - "disease", + "neuromuscular disease", + "autosomal recessive limb-girdle muscular dystrophy", + "entity", ], "subject_taxon": None, "subject_taxon_label": None, "predicate": "biolink:has_phenotype", - "object": "HP:0001263", + "object": "HP:0003701", "original_object": None, "object_namespace": "HP", "object_category": "biolink:PhenotypicFeature", "object_closure": [ - "HP:0000001", "UPHENO:0082875", - "UPHENO:0075696", + "UPHENO:0002320", + "BFO:0000002", + "BFO:0000004", + "UBERON:0000061", + "HP:0000001", "UPHENO:0001001", - "UPHENO:0001005", "UPHENO:0001002", "HP:0000118", - "BFO:0000002", - "HP:0012759", "BFO:0000020", - "UPHENO:0002433", - "HP:0001263", - "UPHENO:0002332", - "HP:0000707", "UPHENO:0001003", - "UPHENO:0002536", - "HP:0012758", - "UPHENO:0004523", "BFO:0000001", "PATO:0000001", - "HP:0012638", "BFO:0000001", - "BFO:0000002", - "BFO:0000004", "BFO:0000040", "UBERON:0001062", - "UBERON:0000465", - "UBERON:0000061", - "UBERON:0010000", "UBERON:0000467", "UBERON:0000468", - "UBERON:0001016", + "UBERON:0011216", + "UPHENO:0075696", + "HP:0001324", + "HP:0003011", + "UPHENO:0002332", + "UPHENO:0002536", + "HP:0011804", + "BFO:0000002", + "UBERON:0000465", + "UBERON:0005090", + "UBERON:0001630", + "UPHENO:0001005", + "HP:0003701", + "UPHENO:0080555", + "UPHENO:0002816", + "UPHENO:0080556", + "HP:0033127", + "UBERON:0010000", + "UBERON:0000062", + "UBERON:0000383", + "UBERON:0001015", ], - "object_label": "Global developmental delay (HPO)", + "object_label": "Proximal muscle weakness (HPO)", "object_closure_label": [ - "entity", - "entity", - "continuant", - "continuant", - "independent continuant", - "specifically dependent continuant", - "material entity", "All (HPO)", + "abnormality of muscle organ physiology", + "Phenotypic abnormality", "Phenotypic abnormality (HPO)", - "Abnormality of the nervous system (HPO)", - "Global developmental delay (HPO)", - "Abnormal nervous system physiology (HPO)", - "Neurodevelopmental delay (HPO)", - "Neurodevelopmental abnormality (HPO)", + "decreased anatomical entity strength", + "abnormal musculature", + "decreased muscle organ strength", + "Abnormality of the musculoskeletal system (HPO)", "quality", + "independent continuant", "anatomical structure", - "material anatomical entity", - "anatomical system", - "multicellular organism", - "nervous system", - "anatomical entity", "multicellular anatomical structure", + "abnormality of anatomical entity physiology", "phenotype", - "Phenotypic abnormality", - "phenotype by ontology source", "abnormal phenotype by ontology source", - "abnormality of anatomical entity physiology", - "abnormality of nervous system physiology", - "abnormal anatomical entity", - "abnormal nervous system", + "Proximal muscle weakness (HPO)", + "specifically dependent continuant", + "phenotype by ontology source", + "continuant", + "material anatomical entity", + "continuant", + "Abnormal muscle physiology (HPO)", + "entity", + "muscle structure", + "organ", + "muscle organ", + "musculature of body", + "musculature", "abnormal anatomical entity", + "Muscle weakness (HPO)", + "Abnormality of the musculature (HPO)", "abnormality of anatomical entity physiology", + "abnormal anatomical entity", + "entity", + "material entity", + "anatomical entity", + "anatomical system", + "multicellular organism", + "organ system subdivision", ], "object_taxon": None, "object_taxon_label": None, @@ -2494,26 +2904,35 @@ def associations(): "aggregator_knowledge_source": ["infores:monarchinitiative"], "negated": None, "pathway": None, - "evidence_count": 4, - "has_evidence": ["ECO:0000304"], - "has_evidence_links": [{"id": "ECO:0000304", "url": "http://purl.obolibrary.org/obo/ECO_0000304"}], + "evidence_count": 3, + "has_evidence": ["ECO:0000269"], + "has_evidence_links": [{"id": "ECO:0000269", "url": "http://purl.obolibrary.org/obo/ECO_0000269"}], + "grouping_key": "MONDO:0009676🍪🍪biolink:has_phenotype🍪HP:0003701", "provided_by": "hpoa_disease_to_phenotype_edges", "provided_by_link": { "id": "hpoa_disease_to_phenotype", "url": "https://monarch-initiative.github.io/monarch-ingest/Sources/hpoa/#disease_to_phenotype", }, - "publications": ["OMIM:617404"], - "publications_links": [{"id": "OMIM:617404", "url": "http://identifiers.org/mim/617404"}], + "publications": ["PMID:9731527", "PMID:9009996"], + "publications_links": [ + {"id": "PMID:9731527", "url": "http://identifiers.org/pubmed/9731527"}, + {"id": "PMID:9009996", "url": "http://identifiers.org/pubmed/9009996"}, + ], "qualifiers": [], - "frequency_qualifier": None, + "frequency_qualifier": "HP:0040280", "onset_qualifier": None, "sex_qualifier": None, "stage_qualifier": None, - "frequency_qualifier_label": None, - "frequency_qualifier_namespace": None, - "frequency_qualifier_category": None, - "frequency_qualifier_closure": [], - "frequency_qualifier_closure_label": [], + "qualifiers_label": None, + "qualifiers_namespace": None, + "qualifiers_category": None, + "qualifiers_closure": [], + "qualifiers_closure_label": [], + "frequency_qualifier_label": "Obligate (HPO)", + "frequency_qualifier_namespace": "HP", + "frequency_qualifier_category": "biolink:PhenotypicFeature", + "frequency_qualifier_closure": ["HP:0000001", "HP:0040280", "HP:0040279"], + "frequency_qualifier_closure_label": ["All (HPO)", "Obligate (HPO)", "Frequency (HPO)"], "onset_qualifier_label": None, "onset_qualifier_namespace": None, "onset_qualifier_category": None, @@ -2531,198 +2950,152 @@ def associations(): "stage_qualifier_closure_label": [], }, { - "id": "uuid:851bc9ee-5d8c-11ee-9b27-2b20ed86a9d9", + "id": "uuid:c9c8bf35-7529-11ee-b012-cbd37f5c3759", "category": "biolink:DiseaseToPhenotypicFeatureAssociation", - "subject": "MONDO:0009683", - "original_subject": "OMIM:254110", + "subject": "MONDO:0008050", + "original_subject": "OMIM:160500", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ - "MONDO:0000001", - "MONDO:0016971", - "MONDO:0000429", + "BFO:0000002", + "MONDO:0016195", + "MONDO:0005336", + "MONDO:0018949", "MONDO:0005071", + "MONDO:0008050", + "BFO:0000016", + "MONDO:0016139", + "OGMS:0000031", + "MONDO:0003847", + "BFO:0000001", "MONDO:0020121", - "MONDO:0700223", - "BFO:0000002", + "MONDO:0019952", "BFO:0000017", "BFO:0000020", - "MONDO:0006025", - "MONDO:0016106", - "BFO:0000016", "MONDO:0020120", "MONDO:0019056", - "MONDO:0016139", + "MONDO:0000001", + "MONDO:0700223", "MONDO:0700096", - "MONDO:0005336", "MONDO:0002081", - "OGMS:0000031", - "MONDO:0003847", "MONDO:0003939", - "MONDO:0015152", - "BFO:0000001", - "MONDO:0016153", - "MONDO:0009683", + "MONDO:0002320", ], - "subject_label": "autosomal recessive limb-girdle muscular dystrophy type 2H", + "subject_label": "MYH7-related skeletal myopathy", "subject_closure_label": [ - "entity", - "continuant", + "muscular dystrophy", + "human disease", + "musculoskeletal system disorder", + "disease", + "muscle tissue disorder", + "congenital nervous system disorder", + "hereditary skeletal muscle disorder", + "MYH7-related skeletal myopathy", "disposition", - "realizable entity", - "specifically dependent continuant", + "qualitative or quantitative protein defects in neuromuscular diseases", + "distal myopathy", "disease", - "autosomal genetic disease", - "musculoskeletal system disorder", + "continuant", + "qualitative or quantitative defects of beta-myosin heavy chain (MYH7)", + "myopathy", "hereditary disease", - "muscle tissue disorder", "nervous system disorder", - "myopathy", - "autosomal recessive disease", - "autosomal recessive limb-girdle muscular dystrophy type 2H", - "autosomal recessive limb-girdle muscular dystrophy", - "progressive muscular dystrophy", - "qualitative or quantitative protein defects in neuromuscular diseases", - "qualitative or quantitative defects of TRIM32", - "limb-girdle muscular dystrophy", - "neuromuscular disease", + "congenital myopathy", + "realizable entity", + "specifically dependent continuant", "skeletal muscle disorder", - "muscular dystrophy", - "human disease", - "hereditary skeletal muscle disorder", - "disease", + "neuromuscular disease", + "entity", ], "subject_taxon": None, "subject_taxon_label": None, "predicate": "biolink:has_phenotype", - "object": "HP:0001265", + "object": "HP:0003701", "original_object": None, "object_namespace": "HP", "object_category": "biolink:PhenotypicFeature", "object_closure": [ - "HP:0000001", "UPHENO:0082875", - "UPHENO:0075696", - "UPHENO:0078622", - "UPHENO:0049586", - "UPHENO:0080377", + "UPHENO:0002320", + "BFO:0000002", + "BFO:0000004", + "UBERON:0000061", + "HP:0000001", "UPHENO:0001001", - "UPHENO:0052915", - "UPHENO:0049622", - "UPHENO:0080585", - "HP:0001265", - "HP:0100022", - "UPHENO:0001005", - "HP:0031826", "UPHENO:0001002", "HP:0000118", - "BFO:0000002", - "UPHENO:0052178", "BFO:0000020", - "UPHENO:0002433", - "UPHENO:0050613", - "UPHENO:0005625", - "UPHENO:0050079", - "UPHENO:0005433", - "UPHENO:0002332", - "UPHENO:0050606", - "HP:0001315", - "HP:0000707", "UPHENO:0001003", - "UPHENO:0002536", - "HP:0000708", - "UPHENO:0079826", - "UPHENO:0004523", - "HP:0011446", - "UPHENO:0079833", - "UPHENO:0049587", "BFO:0000001", "PATO:0000001", - "HP:0012638", "BFO:0000001", - "BFO:0000003", - "BFO:0000002", - "BFO:0000015", - "BFO:0000004", - "GO:0008150", "BFO:0000040", "UBERON:0001062", - "GO:0050896", - "GO:0032501", - "UBERON:0000465", - "GO:0009605", - "GO:0050879", - "GO:0007610", - "GO:0003008", - "UBERON:0000061", - "GO:0060004", - "GO:0050881", - "NBO:0000313", - "GO:0050877", - "UBERON:0010000", "UBERON:0000467", - "GO:0050882", - "NBO:0000338", - "GO:0050905", "UBERON:0000468", - "UBERON:0001016", - "NBO:0000403", - "NBO:0000001", - "NBO:0000388", - "NBO:0000389", + "UBERON:0011216", + "UPHENO:0075696", + "HP:0001324", + "HP:0003011", + "UPHENO:0002332", + "UPHENO:0002536", + "HP:0011804", + "BFO:0000002", + "UBERON:0000465", + "UBERON:0005090", + "UBERON:0001630", + "UPHENO:0001005", + "HP:0003701", + "UPHENO:0080555", + "UPHENO:0002816", + "UPHENO:0080556", + "HP:0033127", + "UBERON:0010000", + "UBERON:0000062", + "UBERON:0000383", + "UBERON:0001015", ], - "object_label": "Hyporeflexia (HPO)", + "object_label": "Proximal muscle weakness (HPO)", "object_closure_label": [ - "entity", - "entity", - "continuant", - "continuant", - "independent continuant", - "specifically dependent continuant", - "material entity", "All (HPO)", + "abnormality of muscle organ physiology", + "Phenotypic abnormality", "Phenotypic abnormality (HPO)", - "Abnormality of the nervous system (HPO)", - "Behavioral abnormality (HPO)", - "Hyporeflexia (HPO)", - "Reduced tendon reflexes (HPO)", - "Abnormality of higher mental function (HPO)", - "Abnormal nervous system physiology (HPO)", - "Abnormal reflex (HPO)", - "Abnormality of movement (HPO)", + "decreased anatomical entity strength", + "abnormal musculature", + "decreased muscle organ strength", + "Abnormality of the musculoskeletal system (HPO)", "quality", + "independent continuant", "anatomical structure", - "material anatomical entity", - "anatomical system", - "multicellular organism", - "nervous system", - "anatomical entity", "multicellular anatomical structure", + "abnormality of anatomical entity physiology", "phenotype", - "Phenotypic abnormality", - "phenotype by ontology source", "abnormal phenotype by ontology source", - "abnormality of anatomical entity physiology", - "abnormality of nervous system physiology", - "abnormal anatomical entity", - "abnormal nervous system", - "decreased biological_process", - "decreased reflex", - "abnormal response to stimulus", - "abnormal biological_process", - "abnormal behavior", - "abnormal response to external stimulus", - "abnormal voluntary musculoskeletal movement", - "abnormal musculoskeletal movement", - "decreased qualitatively biological_process", - "decreased qualitatively response to stimulus", + "Proximal muscle weakness (HPO)", + "specifically dependent continuant", + "phenotype by ontology source", + "continuant", + "material anatomical entity", + "continuant", + "Abnormal muscle physiology (HPO)", + "entity", + "muscle structure", + "organ", + "muscle organ", + "musculature of body", + "musculature", "abnormal anatomical entity", - "abnormal voluntary movement behavior", - "abnormal behavior process", - "abnormal voluntary movement behavior", - "changed biological_process rate", - "abnormal behavior process", + "Muscle weakness (HPO)", + "Abnormality of the musculature (HPO)", "abnormality of anatomical entity physiology", + "abnormal anatomical entity", + "entity", + "material entity", + "anatomical entity", + "anatomical system", + "multicellular organism", + "organ system subdivision", ], "object_taxon": None, "object_taxon_label": None, @@ -2730,26 +3103,32 @@ def associations(): "aggregator_knowledge_source": ["infores:monarchinitiative"], "negated": None, "pathway": None, - "evidence_count": 4, - "has_evidence": ["ECO:0000501"], - "has_evidence_links": [{"id": "ECO:0000501", "url": "http://purl.obolibrary.org/obo/ECO_0000501"}], + "evidence_count": 2, + "has_evidence": ["ECO:0000304"], + "has_evidence_links": [{"id": "ECO:0000304", "url": "http://purl.obolibrary.org/obo/ECO_0000304"}], + "grouping_key": "MONDO:0008050🍪🍪biolink:has_phenotype🍪HP:0003701", "provided_by": "hpoa_disease_to_phenotype_edges", "provided_by_link": { "id": "hpoa_disease_to_phenotype", "url": "https://monarch-initiative.github.io/monarch-ingest/Sources/hpoa/#disease_to_phenotype", }, - "publications": ["OMIM:254110"], - "publications_links": [{"id": "OMIM:254110", "url": "http://identifiers.org/mim/254110"}], + "publications": ["OMIM:160500"], + "publications_links": [{"id": "OMIM:160500", "url": "http://identifiers.org/mim/160500"}], "qualifiers": [], - "frequency_qualifier": None, + "frequency_qualifier": "HP:0040283", "onset_qualifier": None, "sex_qualifier": None, "stage_qualifier": None, - "frequency_qualifier_label": None, - "frequency_qualifier_namespace": None, - "frequency_qualifier_category": None, - "frequency_qualifier_closure": [], - "frequency_qualifier_closure_label": [], + "qualifiers_label": None, + "qualifiers_namespace": None, + "qualifiers_category": None, + "qualifiers_closure": [], + "qualifiers_closure_label": [], + "frequency_qualifier_label": "Occasional (HPO)", + "frequency_qualifier_namespace": "HP", + "frequency_qualifier_category": "biolink:PhenotypicFeature", + "frequency_qualifier_closure": ["HP:0000001", "HP:0040283", "HP:0040279"], + "frequency_qualifier_closure_label": ["All (HPO)", "Occasional (HPO)", "Frequency (HPO)"], "onset_qualifier_label": None, "onset_qualifier_namespace": None, "onset_qualifier_category": None, @@ -2767,210 +3146,212 @@ def associations(): "stage_qualifier_closure_label": [], }, { - "id": "uuid:899a8f89-5d8c-11ee-9b27-2b20ed86a9d9", + "id": "uuid:c9c8bf37-7529-11ee-b012-cbd37f5c3759", "category": "biolink:DiseaseToPhenotypicFeatureAssociation", - "subject": "MONDO:0010311", - "original_subject": "OMIM:300376", + "subject": "MONDO:0008050", + "original_subject": "OMIM:160500", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ - "MONDO:0004994", - "MONDO:0000001", + "BFO:0000002", + "MONDO:0016195", + "MONDO:0005336", + "MONDO:0018949", "MONDO:0005071", - "MONDO:0016147", - "MONDO:0005267", + "MONDO:0008050", + "BFO:0000016", + "MONDO:0016139", + "OGMS:0000031", + "MONDO:0003847", + "BFO:0000001", "MONDO:0020121", - "MONDO:0004995", - "MONDO:0700223", - "BFO:0000002", + "MONDO:0019952", "BFO:0000017", - "MONDO:0010542", "BFO:0000020", - "MONDO:0016106", - "MONDO:0015470", - "MONDO:0005217", - "MONDO:0016899", - "BFO:0000016", "MONDO:0020120", "MONDO:0019056", - "MONDO:0016139", + "MONDO:0000001", + "MONDO:0700223", "MONDO:0700096", - "MONDO:0000591", - "MONDO:0005336", "MONDO:0002081", - "MONDO:0016333", - "OGMS:0000031", - "MONDO:0005021", - "MONDO:0003847", "MONDO:0003939", - "BFO:0000001", - "MONDO:0010311", + "MONDO:0002320", ], - "subject_label": "Becker muscular dystrophy", + "subject_label": "MYH7-related skeletal myopathy", "subject_closure_label": [ - "entity", - "continuant", + "muscular dystrophy", + "human disease", + "musculoskeletal system disorder", + "disease", + "muscle tissue disorder", + "congenital nervous system disorder", + "hereditary skeletal muscle disorder", + "MYH7-related skeletal myopathy", "disposition", - "realizable entity", - "specifically dependent continuant", + "qualitative or quantitative protein defects in neuromuscular diseases", + "distal myopathy", "disease", - "intrinsic cardiomyopathy", - "musculoskeletal system disorder", + "continuant", + "qualitative or quantitative defects of beta-myosin heavy chain (MYH7)", + "myopathy", "hereditary disease", - "muscle tissue disorder", - "cardiomyopathy", - "cardiovascular disorder", - "dilated cardiomyopathy", "nervous system disorder", - "familial cardiomyopathy", - "heart disorder", - "myopathy", - "Becker muscular dystrophy", - "dilated cardiomyopathy 3B", - "familial isolated dilated cardiomyopathy", - "progressive muscular dystrophy", - "qualitative or quantitative protein defects in neuromuscular diseases", - "qualitative or quantitative defects of dystrophin", - "familial dilated cardiomyopathy", - "Duchenne and Becker muscular dystrophy", - "neuromuscular disease", + "congenital myopathy", + "realizable entity", + "specifically dependent continuant", "skeletal muscle disorder", - "muscular dystrophy", - "human disease", - "hereditary skeletal muscle disorder", - "disease", + "neuromuscular disease", + "entity", ], "subject_taxon": None, "subject_taxon_label": None, "predicate": "biolink:has_phenotype", - "object": "HP:0001265", + "object": "HP:0001644", "original_object": None, "object_namespace": "HP", "object_category": "biolink:PhenotypicFeature", "object_closure": [ - "HP:0000001", "UPHENO:0082875", - "UPHENO:0075696", - "UPHENO:0078622", - "UPHENO:0049586", - "UPHENO:0080377", - "UPHENO:0001001", - "UPHENO:0052915", - "UPHENO:0049622", - "UPHENO:0080585", - "HP:0001265", - "HP:0100022", + "HP:0001637", "UPHENO:0001005", - "HP:0031826", + "BFO:0000020", + "UPHENO:0077800", + "UPHENO:0066927", + "UPHENO:0076692", + "PATO:0000001", + "BFO:0000004", + "UBERON:0004535", + "UBERON:0011676", + "UBERON:0013701", + "UBERON:0002349", + "UBERON:0000915", + "UBERON:0002100", + "UBERON:0005181", + "UBERON:0002075", + "UBERON:0015228", + "HP:0000001", + "UPHENO:0001001", + "HP:0001644", + "HP:0030680", "UPHENO:0001002", "HP:0000118", - "BFO:0000002", - "UPHENO:0052178", - "BFO:0000020", - "UPHENO:0002433", - "UPHENO:0050613", - "UPHENO:0005625", - "UPHENO:0050079", - "UPHENO:0005433", - "UPHENO:0002332", - "UPHENO:0050606", - "HP:0001315", - "HP:0000707", + "HP:0001627", + "UPHENO:0076776", "UPHENO:0001003", - "UPHENO:0002536", - "HP:0000708", - "UPHENO:0079826", - "UPHENO:0004523", - "HP:0011446", - "UPHENO:0079833", - "UPHENO:0049587", + "UPHENO:0024906", "BFO:0000001", - "PATO:0000001", - "HP:0012638", "BFO:0000001", - "BFO:0000003", - "BFO:0000002", - "BFO:0000015", - "BFO:0000004", - "GO:0008150", "BFO:0000040", - "UBERON:0001062", - "GO:0050896", - "GO:0032501", - "UBERON:0000465", - "GO:0009605", - "GO:0050879", - "GO:0007610", - "GO:0003008", - "UBERON:0000061", - "GO:0060004", - "GO:0050881", - "NBO:0000313", - "GO:0050877", "UBERON:0010000", "UBERON:0000467", - "GO:0050882", - "NBO:0000338", - "GO:0050905", "UBERON:0000468", - "UBERON:0001016", - "NBO:0000403", - "NBO:0000001", - "NBO:0000388", - "NBO:0000389", + "UBERON:0011216", + "UBERON:0000064", + "UPHENO:0075696", + "HP:0001626", + "UPHENO:0080362", + "HP:0001638", + "BFO:0000002", + "UPHENO:0002332", + "UPHENO:0002536", + "UPHENO:0076810", + "BFO:0000002", + "PR:000050567", + "UBERON:0004120", + "UBERON:0000948", + "UBERON:0001009", + "UBERON:0005983", + "UBERON:0009569", + "UBERON:0013702", + "UBERON:0005177", + "UBERON:0003103", + "UBERON:0018260", + "UBERON:0015410", + "UPHENO:0076781", + "UPHENO:0081581", + "UBERON:0001062", + "UBERON:0000465", + "UBERON:0000061", + "UBERON:0010314", + "UBERON:0000475", + "UBERON:0000062", + "UBERON:0000383", + "UBERON:0000060", + "UBERON:0004923", + "UBERON:0005178", + "UBERON:0007100", ], - "object_label": "Hyporeflexia (HPO)", + "object_label": "Dilated cardiomyopathy (HPO)", "object_closure_label": [ - "entity", - "entity", - "continuant", - "continuant", - "independent continuant", - "specifically dependent continuant", - "material entity", "All (HPO)", + "abnormal cardiovascular system", + "Cardiomyopathy (HPO)", + "Phenotypic abnormality", "Phenotypic abnormality (HPO)", - "Abnormality of the nervous system (HPO)", - "Behavioral abnormality (HPO)", - "Hyporeflexia (HPO)", - "Reduced tendon reflexes (HPO)", - "Abnormality of higher mental function (HPO)", - "Abnormal nervous system physiology (HPO)", - "Abnormal reflex (HPO)", - "Abnormality of movement (HPO)", - "quality", - "anatomical structure", + "abnormal myocardium morphology", + "abnormal multicellular organism morphology", + "independent continuant", "material anatomical entity", - "anatomical system", - "multicellular organism", - "nervous system", - "anatomical entity", - "multicellular anatomical structure", + "cardiovascular system", + "structure with developmental contribution from neural crest", + "layer of muscle tissue", + "abnormality of anatomical entity physiology", + "Abnormal myocardium morphology (HPO)", "phenotype", - "Phenotypic abnormality", + "Abnormality of the cardiovascular system (HPO)", + "Abnormal heart morphology (HPO)", + "abnormal cardiovascular system morphology", "phenotype by ontology source", + "abnormally decreased functionality of the anatomical entity", + "abnormal heart morphology", + "quality", + "continuant", + "protein-containing material entity", + "heart", + "subdivision of trunk", + "body proper", + "trunk region element", + "compound organ", + "heart plus pericardium", "abnormal phenotype by ontology source", - "abnormality of anatomical entity physiology", - "abnormality of nervous system physiology", - "abnormal anatomical entity", - "abnormal nervous system", - "decreased biological_process", - "decreased reflex", - "abnormal response to stimulus", - "abnormal biological_process", - "abnormal behavior", - "abnormal response to external stimulus", - "abnormal voluntary musculoskeletal movement", - "abnormal musculoskeletal movement", - "decreased qualitatively biological_process", - "decreased qualitatively response to stimulus", + "specifically dependent continuant", + "abnormally decreased functionality of the myocardium", + "anatomical entity dysfunction in independent continuant", + "entity", + "anatomical entity", + "anatomical structure", + "mesoderm-derived structure", + "organism subdivision", + "organ", + "circulatory system", + "heart layer", + "musculature of body", + "anatomical wall", + "organ component layer", + "thoracic cavity element", + "primary circulatory organ", "abnormal anatomical entity", - "abnormal voluntary movement behavior", - "abnormal behavior process", - "abnormal voluntary movement behavior", - "changed biological_process rate", - "abnormal behavior process", + "Dilated cardiomyopathy (HPO)", + "Abnormality of cardiovascular system morphology (HPO)", + "continuant", "abnormality of anatomical entity physiology", + "abnormal anatomical entity", + "abnormal anatomical entity morphology", + "entity", + "material entity", + "multicellular anatomical structure", + "anatomical system", + "multicellular organism", + "organ system subdivision", + "organ part", + "subdivision of organism along main body axis", + "main body axis", + "myocardium", + "thoracic segment of trunk", + "trunk", + "thoracic segment organ", + "viscus", + "circulatory organ", ], "object_taxon": None, "object_taxon_label": None, @@ -2978,26 +3359,32 @@ def associations(): "aggregator_knowledge_source": ["infores:monarchinitiative"], "negated": None, "pathway": None, - "evidence_count": 4, + "evidence_count": 2, "has_evidence": ["ECO:0000304"], "has_evidence_links": [{"id": "ECO:0000304", "url": "http://purl.obolibrary.org/obo/ECO_0000304"}], + "grouping_key": "MONDO:0008050🍪🍪biolink:has_phenotype🍪HP:0001644", "provided_by": "hpoa_disease_to_phenotype_edges", "provided_by_link": { "id": "hpoa_disease_to_phenotype", "url": "https://monarch-initiative.github.io/monarch-ingest/Sources/hpoa/#disease_to_phenotype", }, - "publications": ["OMIM:300376"], - "publications_links": [{"id": "OMIM:300376", "url": "http://identifiers.org/mim/300376"}], + "publications": ["OMIM:160500"], + "publications_links": [{"id": "OMIM:160500", "url": "http://identifiers.org/mim/160500"}], "qualifiers": [], - "frequency_qualifier": None, + "frequency_qualifier": "HP:0040283", "onset_qualifier": None, "sex_qualifier": None, "stage_qualifier": None, - "frequency_qualifier_label": None, - "frequency_qualifier_namespace": None, - "frequency_qualifier_category": None, - "frequency_qualifier_closure": [], - "frequency_qualifier_closure_label": [], + "qualifiers_label": None, + "qualifiers_namespace": None, + "qualifiers_category": None, + "qualifiers_closure": [], + "qualifiers_closure_label": [], + "frequency_qualifier_label": "Occasional (HPO)", + "frequency_qualifier_namespace": "HP", + "frequency_qualifier_category": "biolink:PhenotypicFeature", + "frequency_qualifier_closure": ["HP:0000001", "HP:0040283", "HP:0040279"], + "frequency_qualifier_closure_label": ["All (HPO)", "Occasional (HPO)", "Frequency (HPO)"], "onset_qualifier_label": None, "onset_qualifier_namespace": None, "onset_qualifier_category": None, @@ -3015,210 +3402,292 @@ def associations(): "stage_qualifier_closure_label": [], }, { - "id": "uuid:8aea255f-5d8c-11ee-9b27-2b20ed86a9d9", + "id": "uuid:c9c8bff0-7529-11ee-b012-cbd37f5c3759", "category": "biolink:DiseaseToPhenotypicFeatureAssociation", - "subject": "MONDO:0010679", - "original_subject": "OMIM:310200", + "subject": "MONDO:0009675", + "original_subject": "OMIM:253600", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ - "MONDO:0004994", - "MONDO:0000001", - "MONDO:0010679", + "MONDO:0016971", + "MONDO:0005336", + "MONDO:0015152", + "MONDO:0000429", "MONDO:0005071", - "MONDO:0016147", - "MONDO:0005267", + "MONDO:0006025", + "BFO:0000016", + "MONDO:0016139", + "OGMS:0000031", + "BFO:0000001", "MONDO:0020121", - "MONDO:0004995", - "MONDO:0700223", - "BFO:0000002", "BFO:0000017", - "MONDO:0010542", "BFO:0000020", - "MONDO:0016106", - "MONDO:0015470", - "MONDO:0005217", - "MONDO:0016899", - "BFO:0000016", + "MONDO:0009675", "MONDO:0020120", + "MONDO:0016152", "MONDO:0019056", - "MONDO:0016139", + "MONDO:0000001", + "MONDO:0700223", + "BFO:0000002", + "MONDO:0016106", "MONDO:0700096", - "MONDO:0000591", - "MONDO:0005336", "MONDO:0002081", - "MONDO:0016333", - "OGMS:0000031", - "MONDO:0005021", "MONDO:0003847", "MONDO:0003939", - "BFO:0000001", ], - "subject_label": "Duchenne muscular dystrophy", + "subject_label": "autosomal recessive limb-girdle muscular dystrophy type 2A", "subject_closure_label": [ - "entity", - "continuant", - "disposition", - "realizable entity", - "specifically dependent continuant", - "disease", - "intrinsic cardiomyopathy", + "limb-girdle muscular dystrophy", + "muscular dystrophy", + "progressive muscular dystrophy", + "human disease", "musculoskeletal system disorder", + "disease", "hereditary disease", "muscle tissue disorder", - "cardiomyopathy", - "cardiovascular disorder", - "dilated cardiomyopathy", - "nervous system disorder", - "familial cardiomyopathy", - "heart disorder", - "myopathy", - "dilated cardiomyopathy 3B", - "Duchenne muscular dystrophy", - "familial isolated dilated cardiomyopathy", - "progressive muscular dystrophy", - "qualitative or quantitative protein defects in neuromuscular diseases", - "qualitative or quantitative defects of dystrophin", - "familial dilated cardiomyopathy", - "Duchenne and Becker muscular dystrophy", - "neuromuscular disease", - "skeletal muscle disorder", - "muscular dystrophy", - "human disease", "hereditary skeletal muscle disorder", + "continuant", + "autosomal recessive disease", + "disposition", + "qualitative or quantitative protein defects in neuromuscular diseases", "disease", + "myopathy", + "autosomal genetic disease", + "nervous system disorder", + "realizable entity", + "specifically dependent continuant", + "autosomal recessive limb-girdle muscular dystrophy type 2A", + "skeletal muscle disorder", + "qualitative or quantitative defects of calpain", + "neuromuscular disease", + "autosomal recessive limb-girdle muscular dystrophy", + "entity", ], "subject_taxon": None, "subject_taxon_label": None, "predicate": "biolink:has_phenotype", - "object": "HP:0001265", + "object": "HP:0010628", "original_object": None, "object_namespace": "HP", "object_category": "biolink:PhenotypicFeature", "object_closure": [ - "HP:0000001", "UPHENO:0082875", - "UPHENO:0075696", - "UPHENO:0078622", - "UPHENO:0049586", - "UPHENO:0080377", - "UPHENO:0001001", - "UPHENO:0052915", - "UPHENO:0049622", - "UPHENO:0080585", - "HP:0001265", - "HP:0100022", - "UPHENO:0001005", - "HP:0031826", + "UPHENO:0076772", + "UPHENO:0002320", + "UPHENO:0005116", + "HP:0031910", + "HP:0011799", + "HP:0410008", + "UPHENO:0076692", + "BFO:0000001", + "PATO:0000001", + "HP:0012638", + "BFO:0000004", + "UBERON:0001016", + "UBERON:0001021", + "UBERON:0000153", + "UBERON:0011676", + "UBERON:0013701", + "UBERON:0014892", + "UBERON:0015789", + "UBERON:0011779", + "UBERON:0000033", + "HP:0000001", + "HP:0000152", + "UPHENO:0002764", "UPHENO:0001002", "HP:0000118", - "BFO:0000002", - "UPHENO:0052178", "BFO:0000020", "UPHENO:0002433", - "UPHENO:0050613", - "UPHENO:0005625", - "UPHENO:0050079", - "UPHENO:0005433", - "UPHENO:0002332", - "UPHENO:0050606", - "HP:0001315", - "HP:0000707", + "HP:0000234", + "HP:0000271", + "HP:0010827", "UPHENO:0001003", - "UPHENO:0002536", - "HP:0000708", - "UPHENO:0079826", - "UPHENO:0004523", - "HP:0011446", - "UPHENO:0079833", - "UPHENO:0049587", - "BFO:0000001", - "PATO:0000001", - "HP:0012638", + "HP:0012639", + "UPHENO:0076710", + "UPHENO:0002908", "BFO:0000001", - "BFO:0000003", - "BFO:0000002", - "BFO:0000015", - "BFO:0000004", - "GO:0008150", "BFO:0000040", - "UBERON:0001062", - "GO:0050896", - "GO:0032501", + "UBERON:0000467", + "UBERON:0000468", + "UBERON:0011216", + "UBERON:0001785", + "UBERON:0010959", + "UBERON:0001577", + "UPHENO:0075696", + "HP:0045010", + "UPHENO:0002844", + "HP:0001291", + "HP:0001324", + "HP:0030319", + "HP:0000759", + "UPHENO:0081700", + "HP:0003011", + "UPHENO:0002332", + "UPHENO:0078730", + "UPHENO:0002536", + "UPHENO:0081709", + "HP:0000301", + "UPHENO:0004523", + "UPHENO:0004508", + "HP:0011804", + "BFO:0000002", "UBERON:0000465", - "GO:0009605", - "GO:0050879", - "GO:0007610", - "GO:0003008", + "UBERON:0005090", + "UBERON:0018254", + "UBERON:0004120", + "UBERON:0034713", + "UBERON:0001647", + "UBERON:0000122", + "UBERON:0001630", + "UBERON:0001033", + "UBERON:0002376", + "UBERON:0007811", + "UBERON:0001444", + "UBERON:0013702", + "UBERON:0001456", + "UBERON:0008229", + "UBERON:0013700", + "UPHENO:0001001", + "UPHENO:0002910", + "HP:0010628", + "UPHENO:0001005", + "HP:0011805", + "BFO:0000002", + "UPHENO:0076722", + "UPHENO:0080555", + "UPHENO:0003587", + "UPHENO:0002816", + "UPHENO:0080556", + "HP:0000707", + "HP:0006824", + "UPHENO:0081581", + "HP:0033127", + "UPHENO:0076702", + "UBERON:0001062", + "RO:0002577", "UBERON:0000061", - "GO:0060004", - "GO:0050881", - "NBO:0000313", - "GO:0050877", + "UBERON:0015212", + "UBERON:0010314", + "UBERON:0005162", "UBERON:0010000", - "UBERON:0000467", - "GO:0050882", - "NBO:0000338", - "GO:0050905", - "UBERON:0000468", - "UBERON:0001016", - "NBO:0000403", - "NBO:0000001", - "NBO:0000388", - "NBO:0000389", + "UBERON:0000475", + "UBERON:0000062", + "UBERON:0000383", + "UBERON:0001015", + "UBERON:0000010", + "UBERON:0004461", + "UBERON:0004473", ], - "object_label": "Hyporeflexia (HPO)", + "object_label": "Facial palsy (HPO)", "object_closure_label": [ - "entity", - "entity", - "continuant", - "continuant", - "independent continuant", - "specifically dependent continuant", - "material entity", "All (HPO)", + "abnormality of muscle organ physiology", + "abnormal peripheral nervous system", + "Abnormal cranial nerve physiology (HPO)", + "Abnormality of facial soft tissue (HPO)", + "abnormal head", + "Phenotypic abnormality", "Phenotypic abnormality (HPO)", + "abnormal peripheral nervous system morphology", + "decreased anatomical entity strength", + "abnormal facial nerve", + "abnormal musculature", + "decreased muscle organ strength", "Abnormality of the nervous system (HPO)", - "Behavioral abnormality (HPO)", - "Hyporeflexia (HPO)", - "Reduced tendon reflexes (HPO)", - "Abnormality of higher mental function (HPO)", - "Abnormal nervous system physiology (HPO)", - "Abnormal reflex (HPO)", - "Abnormality of movement (HPO)", - "quality", - "anatomical structure", - "material anatomical entity", - "anatomical system", - "multicellular organism", - "nervous system", - "anatomical entity", + "Cranial nerve paralysis (HPO)", + "abnormal multicellular organism morphology", + "Abnormality of the musculoskeletal system (HPO)", + "Abnormal nervous system morphology (HPO)", + "abnormal facial muscle", + "independent continuant", + "system", + "lateral structure", + "structure with developmental contribution from neural crest", + "multi cell part structure", "multicellular anatomical structure", - "phenotype", - "Phenotypic abnormality", - "phenotype by ontology source", - "abnormal phenotype by ontology source", + "nervous system", + "cranial nerve", + "face", + "craniocervical region musculature", + "axial musculature", "abnormality of anatomical entity physiology", + "abnormal cranial nerve morphology", + "Abnormality of peripheral nerves (HPO)", + "Facial palsy (HPO)", + "abnormal phenotype by ontology source", + "Abnormal skeletal muscle morphology (HPO)", + "continuant", + "specifically dependent continuant", "abnormality of nervous system physiology", - "abnormal anatomical entity", + "Abnormality of the head (HPO)", + "Abnormality of the face (HPO)", + "Abnormality of the seventh cranial nerve (HPO)", + "phenotype by ontology source", + "Abnormality of the peripheral nervous system (HPO)", + "paralysed cranial nerve", + "Abnormality of facial musculature (HPO)", "abnormal nervous system", - "decreased biological_process", - "decreased reflex", - "abnormal response to stimulus", - "abnormal biological_process", - "abnormal behavior", - "abnormal response to external stimulus", - "abnormal voluntary musculoskeletal movement", - "abnormal musculoskeletal movement", - "decreased qualitatively biological_process", - "decreased qualitatively response to stimulus", + "abnormal nerve", + "quality", + "Abnormal nervous system physiology (HPO)", + "continuant", + "material anatomical entity", + "cranial neuron projection bundle", + "facial nerve", + "neuron projection bundle", + "craniocervical region", + "subdivision of head", + "body proper", + "craniocervical muscle", + "facial muscle", + "phenotype", + "abnormal face", + "abnormal muscle organ morphology", + "Abnormal muscle physiology (HPO)", + "entity", + "anatomical entity", + "anatomical structure", + "muscle structure", + "skeletal musculature", + "mesoderm-derived structure", + "organism subdivision", + "organ", + "muscle organ", + "gustatory system", + "cranial muscle", + "musculature of body", + "musculature", + "peripheral nervous system", + "skeletal musculature of head", + "musculature of face", "abnormal anatomical entity", - "abnormal voluntary movement behavior", - "abnormal behavior process", - "abnormal voluntary movement behavior", - "changed biological_process rate", - "abnormal behavior process", + "Abnormality of head or neck (HPO)", + "abnormal craniocervical region", + "Abnormal cranial nerve morphology (HPO)", + "Muscle weakness (HPO)", + "Weakness of facial musculature (HPO)", + "Abnormal peripheral nervous system morphology (HPO)", + "paralysed anatomical entity", + "Abnormality of the musculature (HPO)", "abnormality of anatomical entity physiology", + "abnormality of cranial nerve physiology", + "abnormal anatomical entity", + "abnormal anatomical entity morphology", + "entity", + "abnormal nervous system morphology", + "material entity", + "anatomical system", + "multicellular organism", + "organ system subdivision", + "nerve", + "anterior region of body", + "subdivision of organism along main body axis", + "main body axis", + "skeletal muscle organ", + "cranial or facial muscle", + "nerve of head region", + "head", ], "object_taxon": None, "object_taxon_label": None, @@ -3226,26 +3695,32 @@ def associations(): "aggregator_knowledge_source": ["infores:monarchinitiative"], "negated": None, "pathway": None, - "evidence_count": 4, - "has_evidence": ["ECO:0000501"], - "has_evidence_links": [{"id": "ECO:0000501", "url": "http://purl.obolibrary.org/obo/ECO_0000501"}], + "evidence_count": 2, + "has_evidence": ["ECO:0000304"], + "has_evidence_links": [{"id": "ECO:0000304", "url": "http://purl.obolibrary.org/obo/ECO_0000304"}], + "grouping_key": "MONDO:0009675🍪🍪biolink:has_phenotype🍪HP:0010628", "provided_by": "hpoa_disease_to_phenotype_edges", "provided_by_link": { "id": "hpoa_disease_to_phenotype", "url": "https://monarch-initiative.github.io/monarch-ingest/Sources/hpoa/#disease_to_phenotype", }, - "publications": ["OMIM:310200"], - "publications_links": [{"id": "OMIM:310200", "url": "http://identifiers.org/mim/310200"}], + "publications": ["OMIM:253600"], + "publications_links": [{"id": "OMIM:253600", "url": "http://identifiers.org/mim/253600"}], "qualifiers": [], - "frequency_qualifier": None, + "frequency_qualifier": "HP:0040283", "onset_qualifier": None, "sex_qualifier": None, "stage_qualifier": None, - "frequency_qualifier_label": None, - "frequency_qualifier_namespace": None, - "frequency_qualifier_category": None, - "frequency_qualifier_closure": [], - "frequency_qualifier_closure_label": [], + "qualifiers_label": None, + "qualifiers_namespace": None, + "qualifiers_category": None, + "qualifiers_closure": [], + "qualifiers_closure_label": [], + "frequency_qualifier_label": "Occasional (HPO)", + "frequency_qualifier_namespace": "HP", + "frequency_qualifier_category": "biolink:PhenotypicFeature", + "frequency_qualifier_closure": ["HP:0000001", "HP:0040283", "HP:0040279"], + "frequency_qualifier_closure_label": ["All (HPO)", "Occasional (HPO)", "Frequency (HPO)"], "onset_qualifier_label": None, "onset_qualifier_namespace": None, "onset_qualifier_category": None, @@ -3263,194 +3738,196 @@ def associations(): "stage_qualifier_closure_label": [], }, { - "id": "uuid:898aa716-5d8c-11ee-9b27-2b20ed86a9d9", + "id": "uuid:c9d8bdf7-7529-11ee-b012-cbd37f5c3759", "category": "biolink:DiseaseToPhenotypicFeatureAssociation", - "subject": "MONDO:0012193", - "original_subject": "OMIM:609115", + "subject": "MONDO:0009676", + "original_subject": "OMIM:253601", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ - "MONDO:0000001", "MONDO:0016971", + "BFO:0000002", + "BFO:0000020", + "MONDO:0005336", + "MONDO:0009676", + "MONDO:0015152", "MONDO:0000429", "MONDO:0005071", + "MONDO:0006025", + "BFO:0000016", + "MONDO:0016139", + "OGMS:0000031", + "MONDO:0003847", + "BFO:0000001", + "MONDO:0016145", "MONDO:0020121", - "MONDO:0700223", - "BFO:0000002", "BFO:0000017", - "BFO:0000020", - "MONDO:0016106", - "BFO:0000016", "MONDO:0020120", "MONDO:0019056", - "MONDO:0015151", + "MONDO:0000001", + "MONDO:0700223", + "MONDO:0016106", "MONDO:0700096", - "MONDO:0005336", "MONDO:0002081", - "MONDO:0012193", - "MONDO:0000426", - "OGMS:0000031", - "MONDO:0003847", "MONDO:0003939", - "BFO:0000001", ], - "subject_label": "autosomal dominant limb-girdle muscular dystrophy type 1G", + "subject_label": "autosomal recessive limb-girdle muscular dystrophy type 2B", "subject_closure_label": [ - "entity", - "continuant", - "disposition", - "realizable entity", - "specifically dependent continuant", - "disease", - "autosomal dominant disease", - "autosomal genetic disease", - "musculoskeletal system disorder", - "hereditary disease", - "muscle tissue disorder", - "nervous system disorder", - "myopathy", - "autosomal dominant limb-girdle muscular dystrophy type 1G", - "muscular dystrophy, limb-girdle, autosomal dominant", - "progressive muscular dystrophy", "limb-girdle muscular dystrophy", - "neuromuscular disease", - "skeletal muscle disorder", "muscular dystrophy", + "progressive muscular dystrophy", "human disease", + "musculoskeletal system disorder", + "disease", + "muscle tissue disorder", + "qualitative or quantitative defects of dysferlin", "hereditary skeletal muscle disorder", + "autosomal recessive disease", + "disposition", + "qualitative or quantitative protein defects in neuromuscular diseases", + "autosomal recessive limb-girdle muscular dystrophy type 2B", "disease", + "continuant", + "specifically dependent continuant", + "myopathy", + "hereditary disease", + "autosomal genetic disease", + "nervous system disorder", + "realizable entity", + "skeletal muscle disorder", + "neuromuscular disease", + "autosomal recessive limb-girdle muscular dystrophy", + "entity", ], "subject_taxon": None, "subject_taxon_label": None, "predicate": "biolink:has_phenotype", - "object": "HP:0001265", + "object": "HP:0002505", "original_object": None, "object_namespace": "HP", "object_category": "biolink:PhenotypicFeature", "object_closure": [ - "HP:0000001", "UPHENO:0082875", - "UPHENO:0075696", - "UPHENO:0078622", - "UPHENO:0049586", - "UPHENO:0080377", - "UPHENO:0001001", - "UPHENO:0052915", "UPHENO:0049622", - "UPHENO:0080585", - "HP:0001265", - "HP:0100022", "UPHENO:0001005", - "HP:0031826", - "UPHENO:0001002", - "HP:0000118", "BFO:0000002", - "UPHENO:0052178", + "HP:0002540", + "UPHENO:0050606", + "HP:0001288", + "HP:0012638", + "BFO:0000015", + "UBERON:0000061", + "GO:0050882", + "NBO:0000338", + "GO:0050905", + "UBERON:0001016", + "HP:0000001", + "UPHENO:0001001", + "UPHENO:0080585", + "HP:0000118", "BFO:0000020", "UPHENO:0002433", - "UPHENO:0050613", - "UPHENO:0005625", - "UPHENO:0050079", - "UPHENO:0005433", - "UPHENO:0002332", - "UPHENO:0050606", - "HP:0001315", - "HP:0000707", "UPHENO:0001003", - "UPHENO:0002536", "HP:0000708", - "UPHENO:0079826", - "UPHENO:0004523", "HP:0011446", - "UPHENO:0079833", - "UPHENO:0049587", "BFO:0000001", "PATO:0000001", - "HP:0012638", "BFO:0000001", - "BFO:0000003", - "BFO:0000002", - "BFO:0000015", "BFO:0000004", - "GO:0008150", - "BFO:0000040", - "UBERON:0001062", - "GO:0050896", "GO:0032501", - "UBERON:0000465", - "GO:0009605", - "GO:0050879", - "GO:0007610", - "GO:0003008", - "UBERON:0000061", - "GO:0060004", "GO:0050881", "NBO:0000313", "GO:0050877", - "UBERON:0010000", "UBERON:0000467", - "GO:0050882", - "NBO:0000338", - "GO:0050905", "UBERON:0000468", - "UBERON:0001016", "NBO:0000403", "NBO:0000001", - "NBO:0000388", - "NBO:0000389", + "UPHENO:0075696", + "UPHENO:0078622", + "HP:0002505", + "UPHENO:0049586", + "HP:0100022", + "UPHENO:0001002", + "UPHENO:0050613", + "UPHENO:0002332", + "UPHENO:0002536", + "UPHENO:0079826", + "UPHENO:0004523", + "UPHENO:0049587", + "BFO:0000003", + "BFO:0000002", + "GO:0008150", + "BFO:0000040", + "GO:0050879", + "GO:0007610", + "GO:0003008", + "HP:0000707", + "UPHENO:0079833", + "UBERON:0001062", + "UBERON:0000465", + "UBERON:0010000", ], - "object_label": "Hyporeflexia (HPO)", + "object_label": "Loss of ambulation (HPO)", "object_closure_label": [ - "entity", - "entity", - "continuant", - "continuant", - "independent continuant", - "specifically dependent continuant", - "material entity", "All (HPO)", + "abnormal behavior", + "Abnormality of movement (HPO)", "Phenotypic abnormality (HPO)", "Abnormality of the nervous system (HPO)", "Behavioral abnormality (HPO)", - "Hyporeflexia (HPO)", - "Reduced tendon reflexes (HPO)", "Abnormality of higher mental function (HPO)", - "Abnormal nervous system physiology (HPO)", - "Abnormal reflex (HPO)", - "Abnormality of movement (HPO)", + "abnormal voluntary movement behavior", "quality", - "anatomical structure", + "process", "material anatomical entity", - "anatomical system", - "multicellular organism", - "nervous system", - "anatomical entity", + "anatomical structure", "multicellular anatomical structure", - "phenotype", - "Phenotypic abnormality", - "phenotype by ontology source", - "abnormal phenotype by ontology source", + "nervous system", + "voluntary movement behavior", + "body part movement", "abnormality of anatomical entity physiology", + "phenotype", + "specifically dependent continuant", "abnormality of nervous system physiology", - "abnormal anatomical entity", + "phenotype by ontology source", + "Gait disturbance (HPO)", + "abnormal behavior process", "abnormal nervous system", - "decreased biological_process", - "decreased reflex", - "abnormal response to stimulus", "abnormal biological_process", - "abnormal behavior", - "abnormal response to external stimulus", + "Abnormal nervous system physiology (HPO)", + "occurrent", + "continuant", + "biological_process", + "material entity", + "multicellular organismal movement", + "behavior", + "system process", + "musculoskeletal movement", + "behavior process", + "nervous system process", + "abnormal phenotype by ontology source", + "continuant", + "Inability to walk (HPO)", "abnormal voluntary musculoskeletal movement", - "abnormal musculoskeletal movement", - "decreased qualitatively biological_process", - "decreased qualitatively response to stimulus", + "entity", + "independent continuant", + "anatomical entity", "abnormal anatomical entity", "abnormal voluntary movement behavior", + "Loss of ambulation (HPO)", + "abnormal response to stimulus", "abnormal behavior process", - "abnormal voluntary movement behavior", - "changed biological_process rate", - "abnormal behavior process", + "Phenotypic abnormality", + "abnormal musculoskeletal movement", "abnormality of anatomical entity physiology", + "abnormal anatomical entity", + "entity", + "multicellular organismal process", + "anatomical system", + "voluntary musculoskeletal movement", + "kinesthetic behavior", + "neuromuscular process", + "multicellular organism", ], "object_taxon": None, "object_taxon_label": None, @@ -3458,26 +3935,32 @@ def associations(): "aggregator_knowledge_source": ["infores:monarchinitiative"], "negated": None, "pathway": None, - "evidence_count": 4, - "has_evidence": ["ECO:0000501"], - "has_evidence_links": [{"id": "ECO:0000501", "url": "http://purl.obolibrary.org/obo/ECO_0000501"}], + "evidence_count": 2, + "has_evidence": ["ECO:0000269"], + "has_evidence_links": [{"id": "ECO:0000269", "url": "http://purl.obolibrary.org/obo/ECO_0000269"}], + "grouping_key": "MONDO:0009676🍪🍪biolink:has_phenotype🍪HP:0002505", "provided_by": "hpoa_disease_to_phenotype_edges", "provided_by_link": { "id": "hpoa_disease_to_phenotype", "url": "https://monarch-initiative.github.io/monarch-ingest/Sources/hpoa/#disease_to_phenotype", }, - "publications": ["OMIM:609115"], - "publications_links": [{"id": "OMIM:609115", "url": "http://identifiers.org/mim/609115"}], + "publications": ["PMID:9731527"], + "publications_links": [{"id": "PMID:9731527", "url": "http://identifiers.org/pubmed/9731527"}], "qualifiers": [], - "frequency_qualifier": None, + "frequency_qualifier": "HP:0040283", "onset_qualifier": None, "sex_qualifier": None, "stage_qualifier": None, - "frequency_qualifier_label": None, - "frequency_qualifier_namespace": None, - "frequency_qualifier_category": None, - "frequency_qualifier_closure": [], - "frequency_qualifier_closure_label": [], + "qualifiers_label": None, + "qualifiers_namespace": None, + "qualifiers_category": None, + "qualifiers_closure": [], + "qualifiers_closure_label": [], + "frequency_qualifier_label": "Occasional (HPO)", + "frequency_qualifier_namespace": "HP", + "frequency_qualifier_category": "biolink:PhenotypicFeature", + "frequency_qualifier_closure": ["HP:0000001", "HP:0040283", "HP:0040279"], + "frequency_qualifier_closure_label": ["All (HPO)", "Occasional (HPO)", "Frequency (HPO)"], "onset_qualifier_label": None, "onset_qualifier_namespace": None, "onset_qualifier_category": None, @@ -3495,238 +3978,288 @@ def associations(): "stage_qualifier_closure_label": [], }, { - "id": "uuid:880b4cc5-5d8c-11ee-9b27-2b20ed86a9d9", + "id": "uuid:c9c8bf2b-7529-11ee-b012-cbd37f5c3759", "category": "biolink:DiseaseToPhenotypicFeatureAssociation", - "subject": "MONDO:0012699", - "original_subject": "OMIM:611588", + "subject": "MONDO:0008050", + "original_subject": "OMIM:160500", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ - "MONDO:0700067", - "MONDO:0004994", - "MONDO:0018282", - "MONDO:0000001", - "MONDO:0016971", - "MONDO:0017741", - "MONDO:0000429", - "MONDO:0018276", - "MONDO:0045010", + "BFO:0000002", + "MONDO:0016195", + "MONDO:0005336", + "MONDO:0018949", "MONDO:0005071", - "MONDO:0005267", + "MONDO:0008050", + "BFO:0000016", + "MONDO:0016139", + "OGMS:0000031", + "MONDO:0003847", + "BFO:0000001", "MONDO:0020121", - "MONDO:0004995", - "MONDO:0700223", - "MONDO:0024322", - "BFO:0000002", + "MONDO:0019952", "BFO:0000017", "BFO:0000020", - "MONDO:0006025", - "MONDO:0016106", - "MONDO:0005217", - "MONDO:0017745", - "BFO:0000016", "MONDO:0020120", "MONDO:0019056", - "MONDO:0016139", + "MONDO:0000001", + "MONDO:0700223", "MONDO:0700096", - "MONDO:0000591", - "MONDO:0005336", "MONDO:0002081", - "MONDO:0016333", - "OGMS:0000031", - "MONDO:0005021", - "MONDO:0003847", "MONDO:0003939", - "MONDO:0012699", - "MONDO:0015286", - "MONDO:0015152", - "BFO:0000001", "MONDO:0002320", - "MONDO:0019052", - "MONDO:0005066", - "MONDO:0000173", - "MONDO:0019950", - "MONDO:0016155", ], - "subject_label": "autosomal recessive limb-girdle muscular dystrophy type 2M", + "subject_label": "MYH7-related skeletal myopathy", "subject_closure_label": [ - "entity", - "continuant", - "disposition", - "realizable entity", - "specifically dependent continuant", - "disease", - "muscular dystrophy-dystroglycanopathy, type C", - "autosomal genetic disease", - "intrinsic cardiomyopathy", + "muscular dystrophy", + "human disease", "musculoskeletal system disorder", + "disease", + "muscle tissue disorder", "congenital nervous system disorder", + "hereditary skeletal muscle disorder", + "MYH7-related skeletal myopathy", + "disposition", + "qualitative or quantitative protein defects in neuromuscular diseases", + "distal myopathy", + "disease", + "continuant", + "qualitative or quantitative defects of beta-myosin heavy chain (MYH7)", + "myopathy", "hereditary disease", - "muscle tissue disorder", - "cardiomyopathy", - "cardiovascular disorder", - "dilated cardiomyopathy", - "metabolic disease", "nervous system disorder", - "familial cardiomyopathy", - "heart disorder", - "myopathy", - "autosomal recessive disease", - "autosomal recessive limb-girdle muscular dystrophy type 2M", - "autosomal recessive limb-girdle muscular dystrophy", - "congenital disorder of glycosylation", - "progressive muscular dystrophy", - "qualitative or quantitative protein defects in neuromuscular diseases", - "qualitative or quantitative defects of protein involved in O-glycosylation of alpha-dystroglycan", - "familial dilated cardiomyopathy", - "limb-girdle muscular dystrophy", - "disorder of protein O-glycosylation", - "disorder of O-mannosylglycan synthesis", - "muscular dystrophy-dystroglycanopathy", - "qualitative or quantitative defects of alpha-dystroglycan", - "inborn errors of metabolism", - "neuromuscular disease", - "congenital muscular dystrophy", + "congenital myopathy", + "realizable entity", + "specifically dependent continuant", "skeletal muscle disorder", - "muscular dystrophy", - "disorder of glycosylation", - "glycoprotein metabolism disease", - "myopathy caused by variation in FKTN", - "human disease", - "hereditary skeletal muscle disorder", - "disease", + "neuromuscular disease", + "entity", ], "subject_taxon": None, "subject_taxon_label": None, "predicate": "biolink:has_phenotype", - "object": "HP:0001265", + "object": "HP:0010628", "original_object": None, "object_namespace": "HP", "object_category": "biolink:PhenotypicFeature", "object_closure": [ - "HP:0000001", "UPHENO:0082875", - "UPHENO:0075696", - "UPHENO:0078622", - "UPHENO:0049586", - "UPHENO:0080377", - "UPHENO:0001001", - "UPHENO:0052915", - "UPHENO:0049622", - "UPHENO:0080585", - "HP:0001265", - "HP:0100022", - "UPHENO:0001005", - "HP:0031826", + "UPHENO:0076772", + "UPHENO:0002320", + "UPHENO:0005116", + "HP:0031910", + "HP:0011799", + "HP:0410008", + "UPHENO:0076692", + "BFO:0000001", + "PATO:0000001", + "HP:0012638", + "BFO:0000004", + "UBERON:0001016", + "UBERON:0001021", + "UBERON:0000153", + "UBERON:0011676", + "UBERON:0013701", + "UBERON:0014892", + "UBERON:0015789", + "UBERON:0011779", + "UBERON:0000033", + "HP:0000001", + "HP:0000152", + "UPHENO:0002764", "UPHENO:0001002", "HP:0000118", - "BFO:0000002", - "UPHENO:0052178", "BFO:0000020", "UPHENO:0002433", - "UPHENO:0050613", - "UPHENO:0005625", - "UPHENO:0050079", - "UPHENO:0005433", - "UPHENO:0002332", - "UPHENO:0050606", - "HP:0001315", - "HP:0000707", + "HP:0000234", + "HP:0000271", + "HP:0010827", "UPHENO:0001003", + "HP:0012639", + "UPHENO:0076710", + "UPHENO:0002908", + "BFO:0000001", + "BFO:0000040", + "UBERON:0000467", + "UBERON:0000468", + "UBERON:0011216", + "UBERON:0001785", + "UBERON:0010959", + "UBERON:0001577", + "UPHENO:0075696", + "HP:0045010", + "UPHENO:0002844", + "HP:0001291", + "HP:0001324", + "HP:0030319", + "HP:0000759", + "UPHENO:0081700", + "HP:0003011", + "UPHENO:0002332", + "UPHENO:0078730", "UPHENO:0002536", - "HP:0000708", - "UPHENO:0079826", + "UPHENO:0081709", + "HP:0000301", "UPHENO:0004523", - "HP:0011446", - "UPHENO:0079833", - "UPHENO:0049587", - "BFO:0000001", - "PATO:0000001", - "HP:0012638", - "BFO:0000001", - "BFO:0000003", + "UPHENO:0004508", + "HP:0011804", "BFO:0000002", - "BFO:0000015", - "BFO:0000004", - "GO:0008150", - "BFO:0000040", - "UBERON:0001062", - "GO:0050896", - "GO:0032501", "UBERON:0000465", - "GO:0009605", - "GO:0050879", - "GO:0007610", - "GO:0003008", + "UBERON:0005090", + "UBERON:0018254", + "UBERON:0004120", + "UBERON:0034713", + "UBERON:0001647", + "UBERON:0000122", + "UBERON:0001630", + "UBERON:0001033", + "UBERON:0002376", + "UBERON:0007811", + "UBERON:0001444", + "UBERON:0013702", + "UBERON:0001456", + "UBERON:0008229", + "UBERON:0013700", + "UPHENO:0001001", + "UPHENO:0002910", + "HP:0010628", + "UPHENO:0001005", + "HP:0011805", + "BFO:0000002", + "UPHENO:0076722", + "UPHENO:0080555", + "UPHENO:0003587", + "UPHENO:0002816", + "UPHENO:0080556", + "HP:0000707", + "HP:0006824", + "UPHENO:0081581", + "HP:0033127", + "UPHENO:0076702", + "UBERON:0001062", + "RO:0002577", "UBERON:0000061", - "GO:0060004", - "GO:0050881", - "NBO:0000313", - "GO:0050877", + "UBERON:0015212", + "UBERON:0010314", + "UBERON:0005162", "UBERON:0010000", - "UBERON:0000467", - "GO:0050882", - "NBO:0000338", - "GO:0050905", - "UBERON:0000468", - "UBERON:0001016", - "NBO:0000403", - "NBO:0000001", - "NBO:0000388", - "NBO:0000389", + "UBERON:0000475", + "UBERON:0000062", + "UBERON:0000383", + "UBERON:0001015", + "UBERON:0000010", + "UBERON:0004461", + "UBERON:0004473", ], - "object_label": "Hyporeflexia (HPO)", + "object_label": "Facial palsy (HPO)", "object_closure_label": [ - "entity", - "entity", - "continuant", - "continuant", - "independent continuant", - "specifically dependent continuant", - "material entity", "All (HPO)", + "abnormality of muscle organ physiology", + "abnormal peripheral nervous system", + "Abnormal cranial nerve physiology (HPO)", + "Abnormality of facial soft tissue (HPO)", + "abnormal head", + "Phenotypic abnormality", "Phenotypic abnormality (HPO)", + "abnormal peripheral nervous system morphology", + "decreased anatomical entity strength", + "abnormal facial nerve", + "abnormal musculature", + "decreased muscle organ strength", "Abnormality of the nervous system (HPO)", - "Behavioral abnormality (HPO)", - "Hyporeflexia (HPO)", - "Reduced tendon reflexes (HPO)", - "Abnormality of higher mental function (HPO)", - "Abnormal nervous system physiology (HPO)", - "Abnormal reflex (HPO)", - "Abnormality of movement (HPO)", - "quality", - "anatomical structure", - "material anatomical entity", - "anatomical system", - "multicellular organism", - "nervous system", - "anatomical entity", + "Cranial nerve paralysis (HPO)", + "abnormal multicellular organism morphology", + "Abnormality of the musculoskeletal system (HPO)", + "Abnormal nervous system morphology (HPO)", + "abnormal facial muscle", + "independent continuant", + "system", + "lateral structure", + "structure with developmental contribution from neural crest", + "multi cell part structure", "multicellular anatomical structure", - "phenotype", - "Phenotypic abnormality", - "phenotype by ontology source", - "abnormal phenotype by ontology source", + "nervous system", + "cranial nerve", + "face", + "craniocervical region musculature", + "axial musculature", "abnormality of anatomical entity physiology", + "abnormal cranial nerve morphology", + "Abnormality of peripheral nerves (HPO)", + "Facial palsy (HPO)", + "abnormal phenotype by ontology source", + "Abnormal skeletal muscle morphology (HPO)", + "continuant", + "specifically dependent continuant", "abnormality of nervous system physiology", - "abnormal anatomical entity", + "Abnormality of the head (HPO)", + "Abnormality of the face (HPO)", + "Abnormality of the seventh cranial nerve (HPO)", + "phenotype by ontology source", + "Abnormality of the peripheral nervous system (HPO)", + "paralysed cranial nerve", + "Abnormality of facial musculature (HPO)", "abnormal nervous system", - "decreased biological_process", - "decreased reflex", - "abnormal response to stimulus", - "abnormal biological_process", - "abnormal behavior", - "abnormal response to external stimulus", - "abnormal voluntary musculoskeletal movement", - "abnormal musculoskeletal movement", - "decreased qualitatively biological_process", - "decreased qualitatively response to stimulus", + "abnormal nerve", + "quality", + "Abnormal nervous system physiology (HPO)", + "continuant", + "material anatomical entity", + "cranial neuron projection bundle", + "facial nerve", + "neuron projection bundle", + "craniocervical region", + "subdivision of head", + "body proper", + "craniocervical muscle", + "facial muscle", + "phenotype", + "abnormal face", + "abnormal muscle organ morphology", + "Abnormal muscle physiology (HPO)", + "entity", + "anatomical entity", + "anatomical structure", + "muscle structure", + "skeletal musculature", + "mesoderm-derived structure", + "organism subdivision", + "organ", + "muscle organ", + "gustatory system", + "cranial muscle", + "musculature of body", + "musculature", + "peripheral nervous system", + "skeletal musculature of head", + "musculature of face", "abnormal anatomical entity", - "abnormal voluntary movement behavior", - "abnormal behavior process", - "abnormal voluntary movement behavior", - "changed biological_process rate", - "abnormal behavior process", + "Abnormality of head or neck (HPO)", + "abnormal craniocervical region", + "Abnormal cranial nerve morphology (HPO)", + "Muscle weakness (HPO)", + "Weakness of facial musculature (HPO)", + "Abnormal peripheral nervous system morphology (HPO)", + "paralysed anatomical entity", + "Abnormality of the musculature (HPO)", "abnormality of anatomical entity physiology", + "abnormality of cranial nerve physiology", + "abnormal anatomical entity", + "abnormal anatomical entity morphology", + "entity", + "abnormal nervous system morphology", + "material entity", + "anatomical system", + "multicellular organism", + "organ system subdivision", + "nerve", + "anterior region of body", + "subdivision of organism along main body axis", + "main body axis", + "skeletal muscle organ", + "cranial or facial muscle", + "nerve of head region", + "head", ], "object_taxon": None, "object_taxon_label": None, @@ -3734,21 +4267,27 @@ def associations(): "aggregator_knowledge_source": ["infores:monarchinitiative"], "negated": None, "pathway": None, - "evidence_count": 4, - "has_evidence": ["ECO:0000501"], - "has_evidence_links": [{"id": "ECO:0000501", "url": "http://purl.obolibrary.org/obo/ECO_0000501"}], + "evidence_count": 2, + "has_evidence": ["ECO:0000304"], + "has_evidence_links": [{"id": "ECO:0000304", "url": "http://purl.obolibrary.org/obo/ECO_0000304"}], + "grouping_key": "MONDO:0008050🍪🍪biolink:has_phenotype🍪HP:0010628", "provided_by": "hpoa_disease_to_phenotype_edges", "provided_by_link": { "id": "hpoa_disease_to_phenotype", "url": "https://monarch-initiative.github.io/monarch-ingest/Sources/hpoa/#disease_to_phenotype", }, - "publications": ["OMIM:611588"], - "publications_links": [{"id": "OMIM:611588", "url": "http://identifiers.org/mim/611588"}], + "publications": ["OMIM:160500"], + "publications_links": [{"id": "OMIM:160500", "url": "http://identifiers.org/mim/160500"}], "qualifiers": [], "frequency_qualifier": None, "onset_qualifier": None, "sex_qualifier": None, "stage_qualifier": None, + "qualifiers_label": None, + "qualifiers_namespace": None, + "qualifiers_category": None, + "qualifiers_closure": [], + "qualifiers_closure_label": [], "frequency_qualifier_label": None, "frequency_qualifier_namespace": None, "frequency_qualifier_category": None, @@ -3771,254 +4310,216 @@ def associations(): "stage_qualifier_closure_label": [], }, { - "id": "uuid:86db7919-5d8c-11ee-9b27-2b20ed86a9d9", + "id": "uuid:c9c8bf2d-7529-11ee-b012-cbd37f5c3759", "category": "biolink:DiseaseToPhenotypicFeatureAssociation", - "subject": "MONDO:0013157", - "original_subject": "OMIM:613153", + "subject": "MONDO:0008050", + "original_subject": "OMIM:160500", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ - "MONDO:0018282", - "MONDO:0000001", - "MONDO:0016182", - "MONDO:0017741", - "MONDO:0018276", - "MONDO:0045010", + "BFO:0000002", + "MONDO:0016195", + "MONDO:0005336", + "MONDO:0018949", "MONDO:0005071", + "MONDO:0008050", + "BFO:0000016", + "MONDO:0016139", + "OGMS:0000031", + "MONDO:0003847", + "BFO:0000001", "MONDO:0020121", - "MONDO:0700068", - "MONDO:0700223", - "MONDO:0024322", - "MONDO:0005283", - "MONDO:0020238", - "BFO:0000002", - "MONDO:0016185", - "MONDO:0000171", + "MONDO:0019952", "BFO:0000017", - "MONDO:0018869", "BFO:0000020", - "MONDO:0016157", - "MONDO:0017745", - "BFO:0000016", "MONDO:0020120", "MONDO:0019056", - "MONDO:0016139", + "MONDO:0000001", + "MONDO:0700223", "MONDO:0700096", - "MONDO:0018838", - "MONDO:0024458", - "MONDO:0005336", "MONDO:0002081", - "MONDO:0016184", - "MONDO:0016156", - "MONDO:0018939", - "MONDO:0020246", - "MONDO:0021147", - "MONDO:0044137", - "MONDO:0019755", - "OGMS:0000031", - "MONDO:0015327", - "MONDO:0003847", "MONDO:0003939", - "MONDO:0002022", - "MONDO:0015286", - "BFO:0000001", "MONDO:0002320", - "MONDO:0013157", - "MONDO:0019052", - "MONDO:0020247", - "MONDO:0005066", - "MONDO:0005328", - "MONDO:0019950", - "MONDO:0016155", - "MONDO:0700066", ], - "subject_label": "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A5", + "subject_label": "MYH7-related skeletal myopathy", "subject_closure_label": [ - "entity", - "continuant", - "disposition", - "realizable entity", - "specifically dependent continuant", - "disease", - "muscular dystrophy-dystroglycanopathy, type A", - "disorder of orbital region", + "muscular dystrophy", + "human disease", "musculoskeletal system disorder", + "disease", + "muscle tissue disorder", "congenital nervous system disorder", + "hereditary skeletal muscle disorder", + "MYH7-related skeletal myopathy", + "disposition", + "qualitative or quantitative protein defects in neuromuscular diseases", + "distal myopathy", + "disease", + "continuant", + "qualitative or quantitative defects of beta-myosin heavy chain (MYH7)", + "myopathy", "hereditary disease", - "muscle tissue disorder", - "metabolic disease", "nervous system disorder", - "retinal disorder", - "eye disorder", - "myopathy", - "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A5", - "congenital disorder of glycosylation", - "developmental anomaly of metabolic origin", - "qualitative or quantitative protein defects in neuromuscular diseases", - "qualitative or quantitative defects of protein involved in O-glycosylation of alpha-dystroglycan", - "qualitative or quantitative defects of FKRP", - "qualitative or quantitative defects of fukutin", - "qualitative or quantitative defects of protein O-mannose beta1, 2N-acetylglucosaminyltransferase", - "qualitative or quantitative defects of protein O-mannosyltransferase 1", - "qualitative or quantitative defects of protein O-mannosyltransferase 2", - "disorder of protein O-glycosylation", - "disorder of O-mannosylglycan synthesis", - "muscular dystrophy-dystroglycanopathy", - "qualitative or quantitative defects of alpha-dystroglycan", - "lissencephaly spectrum disorders", - "cobblestone lissencephaly", - "muscle-eye-brain disease", - "inborn errors of metabolism", - "neuromuscular disease", - "developmental defect during embryogenesis", - "congenital muscular dystrophy", + "congenital myopathy", + "realizable entity", + "specifically dependent continuant", "skeletal muscle disorder", - "muscular dystrophy", - "inherited vitreous-retinal disease", - "inherited vitreoretinopathy", - "congenital vitreoretinal dysplasia", - "disorder of development or morphogenesis", - "disorder of glycosylation", - "disorder of visual system", - "vitreous body disorder", - "glycoprotein metabolism disease", - "myopathy caused by variation in FKRP", - "myopathy caused by variation in POMGNT1", - "human disease", - "hereditary skeletal muscle disorder", - "disease", + "neuromuscular disease", + "entity", ], "subject_taxon": None, "subject_taxon_label": None, "predicate": "biolink:has_phenotype", - "object": "HP:0001265", + "object": "HP:0011916", "original_object": None, "object_namespace": "HP", "object_category": "biolink:PhenotypicFeature", "object_closure": [ + "HP:0002814", + "HP:0009127", + "UPHENO:0076692", + "UPHENO:0003070", + "PATO:0000001", + "BFO:0000004", + "UBERON:0004708", + "UBERON:0000154", + "UBERON:0006058", + "UBERON:0002529", + "UBERON:0002387", "HP:0000001", - "UPHENO:0082875", - "UPHENO:0075696", - "UPHENO:0078622", - "UPHENO:0049586", - "UPHENO:0080377", + "UPHENO:0002644", "UPHENO:0001001", - "UPHENO:0052915", - "UPHENO:0049622", - "UPHENO:0080585", - "HP:0001265", - "HP:0100022", - "UPHENO:0001005", - "HP:0031826", "UPHENO:0001002", "HP:0000118", - "BFO:0000002", - "UPHENO:0052178", "BFO:0000020", - "UPHENO:0002433", - "UPHENO:0050613", - "UPHENO:0005625", - "UPHENO:0050079", - "UPHENO:0005433", - "UPHENO:0002332", - "UPHENO:0050606", - "HP:0001315", - "HP:0000707", "UPHENO:0001003", - "UPHENO:0002536", - "HP:0000708", - "UPHENO:0079826", - "UPHENO:0004523", - "HP:0011446", - "UPHENO:0079833", - "UPHENO:0049587", - "BFO:0000001", - "PATO:0000001", - "HP:0012638", + "UPHENO:0076710", + "HP:0011916", "BFO:0000001", - "BFO:0000003", - "BFO:0000002", - "BFO:0000015", - "BFO:0000004", - "GO:0008150", "BFO:0000040", "UBERON:0001062", - "GO:0050896", - "GO:0032501", - "UBERON:0000465", - "GO:0009605", - "GO:0050879", - "GO:0007610", - "GO:0003008", - "UBERON:0000061", - "GO:0060004", - "GO:0050881", - "NBO:0000313", - "GO:0050877", "UBERON:0010000", "UBERON:0000467", - "GO:0050882", - "NBO:0000338", - "GO:0050905", "UBERON:0000468", - "UBERON:0001016", - "NBO:0000403", - "NBO:0000001", - "NBO:0000388", - "NBO:0000389", + "UBERON:0011216", + "UBERON:0010709", + "UBERON:0010538", + "UBERON:0004488", + "HP:0001436", + "UPHENO:0002653", + "HP:0003011", + "UPHENO:0002536", + "HP:0001437", + "HP:0040064", + "BFO:0000002", + "PR:000050567", + "UBERON:0000465", + "UBERON:0002101", + "UBERON:0004709", + "UBERON:0005090", + "UBERON:0002103", + "UBERON:0010707", + "UBERON:0001630", + "UBERON:0000026", + "UBERON:0010758", + "UBERON:0007271", + "UBERON:0014792", + "UBERON:0004482", + "UBERON:0008784", + "UBERON:0002470", + "UPHENO:0001005", + "HP:0011805", + "BFO:0000002", + "UPHENO:0002816", + "UPHENO:0081581", + "HP:0033127", + "UPHENO:0002647", + "BFO:0000001", + "UPHENO:0002830", + "RO:0002577", + "UBERON:0000061", + "UBERON:0015212", + "UBERON:0000475", + "UBERON:0000062", + "UBERON:0000383", + "UBERON:0001015", + "UBERON:0000978", + "UBERON:0007270", + "UBERON:0004480", ], - "object_label": "Hyporeflexia (HPO)", + "object_label": "Toe extensor amyotrophy (HPO)", "object_closure_label": [ + "All (HPO)", + "abnormal musculature of lower limb", + "Abnormality of the lower limb (HPO)", + "Phenotypic abnormality", + "Phenotypic abnormality (HPO)", + "abnormal musculature", + "abnormal multicellular organism morphology", + "Abnormality of the musculoskeletal system (HPO)", + "abnormal musculature of limb", "entity", - "entity", - "continuant", - "continuant", "independent continuant", + "system", + "paired limb/fin", + "lateral structure", + "pelvic complex", + "appendage musculature", + "musculature of pelvic complex", + "musculature of pes", + "phenotype", + "Abnormality of the foot musculature (HPO)", + "abnormal phenotype by ontology source", + "Abnormal skeletal muscle morphology (HPO)", + "continuant", "specifically dependent continuant", - "material entity", - "All (HPO)", - "Phenotypic abnormality (HPO)", - "Abnormality of the nervous system (HPO)", - "Behavioral abnormality (HPO)", - "Hyporeflexia (HPO)", - "Reduced tendon reflexes (HPO)", - "Abnormality of higher mental function (HPO)", - "Abnormal nervous system physiology (HPO)", - "Abnormal reflex (HPO)", - "Abnormality of movement (HPO)", + "phenotype by ontology source", + "Abnormality of the musculature of the lower limbs (HPO)", + "Abnormality of limbs (HPO)", "quality", - "anatomical structure", + "continuant", + "protein-containing material entity", "material anatomical entity", - "anatomical system", - "multicellular organism", - "nervous system", + "hindlimb", + "appendage girdle complex", + "appendage", + "subdivision of organism along appendicular axis", + "paired limb/fin segment", + "musculature of lower limb", + "lower limb segment", + "autopod region", + "Abnormality of the musculature of the limbs (HPO)", + "abnormal muscle organ morphology", + "Toe extensor amyotrophy (HPO)", + "entity", + "anatomical structure", + "muscle structure", + "organism subdivision", + "organ", + "muscle organ", + "musculature of body", + "musculature", + "leg", + "pelvic appendage musculature", + "musculature of limb", + "abnormal musculature of pes", + "Abnormality of the musculature (HPO)", + "abnormal anatomical entity", + "abnormal anatomical entity morphology", + "abnormal leg", + "abnormal limb", + "material entity", "anatomical entity", + "limb", + "pelvic appendage", "multicellular anatomical structure", - "phenotype", - "Phenotypic abnormality", - "phenotype by ontology source", - "abnormal phenotype by ontology source", - "abnormality of anatomical entity physiology", - "abnormality of nervous system physiology", - "abnormal anatomical entity", - "abnormal nervous system", - "decreased biological_process", - "decreased reflex", - "abnormal response to stimulus", - "abnormal biological_process", - "abnormal behavior", - "abnormal response to external stimulus", - "abnormal voluntary musculoskeletal movement", - "abnormal musculoskeletal movement", - "decreased qualitatively biological_process", - "decreased qualitatively response to stimulus", - "abnormal anatomical entity", - "abnormal voluntary movement behavior", - "abnormal behavior process", - "abnormal voluntary movement behavior", - "changed biological_process rate", - "abnormal behavior process", - "abnormality of anatomical entity physiology", + "anatomical system", + "multicellular organism", + "organ system subdivision", + "posterior region of body", + "multi-limb segment region", + "limb segment", + "pes", ], "object_taxon": None, "object_taxon_label": None, @@ -4026,21 +4527,27 @@ def associations(): "aggregator_knowledge_source": ["infores:monarchinitiative"], "negated": None, "pathway": None, - "evidence_count": 4, + "evidence_count": 2, "has_evidence": ["ECO:0000304"], "has_evidence_links": [{"id": "ECO:0000304", "url": "http://purl.obolibrary.org/obo/ECO_0000304"}], + "grouping_key": "MONDO:0008050🍪🍪biolink:has_phenotype🍪HP:0011916", "provided_by": "hpoa_disease_to_phenotype_edges", "provided_by_link": { "id": "hpoa_disease_to_phenotype", "url": "https://monarch-initiative.github.io/monarch-ingest/Sources/hpoa/#disease_to_phenotype", }, - "publications": ["OMIM:613153"], - "publications_links": [{"id": "OMIM:613153", "url": "http://identifiers.org/mim/613153"}], + "publications": ["OMIM:160500"], + "publications_links": [{"id": "OMIM:160500", "url": "http://identifiers.org/mim/160500"}], "qualifiers": [], "frequency_qualifier": None, "onset_qualifier": None, "sex_qualifier": None, "stage_qualifier": None, + "qualifiers_label": None, + "qualifiers_namespace": None, + "qualifiers_category": None, + "qualifiers_closure": [], + "qualifiers_closure_label": [], "frequency_qualifier_label": None, "frequency_qualifier_namespace": None, "frequency_qualifier_category": None, @@ -4063,212 +4570,152 @@ def associations(): "stage_qualifier_closure_label": [], }, { - "id": "uuid:864bb8df-5d8c-11ee-9b27-2b20ed86a9d9", + "id": "uuid:c9c8bf2e-7529-11ee-b012-cbd37f5c3759", "category": "biolink:DiseaseToPhenotypicFeatureAssociation", - "subject": "MONDO:0013160", - "original_subject": "OMIM:613156", + "subject": "MONDO:0008050", + "original_subject": "OMIM:160500", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ - "MONDO:0018282", - "MONDO:0000001", - "MONDO:0017741", - "MONDO:0018276", - "MONDO:0045010", + "BFO:0000002", + "MONDO:0016195", + "MONDO:0005336", + "MONDO:0018949", "MONDO:0005071", + "MONDO:0008050", + "BFO:0000016", + "MONDO:0016139", + "OGMS:0000031", + "MONDO:0003847", + "BFO:0000001", "MONDO:0020121", - "MONDO:0000172", - "MONDO:0700223", - "MONDO:0024322", - "BFO:0000002", + "MONDO:0019952", "BFO:0000017", "BFO:0000020", - "MONDO:0013160", - "MONDO:0700071", - "BFO:0000016", "MONDO:0020120", "MONDO:0019056", - "MONDO:0016139", + "MONDO:0000001", + "MONDO:0700223", "MONDO:0700096", - "MONDO:0005336", "MONDO:0002081", - "OGMS:0000031", - "MONDO:0003847", "MONDO:0003939", - "MONDO:0015286", - "BFO:0000001", "MONDO:0002320", - "MONDO:0019052", - "MONDO:0005066", - "MONDO:0019950", - "MONDO:0016155", ], - "subject_label": "muscular dystrophy-dystroglycanopathy (congenital with intellectual disability), type B2", + "subject_label": "MYH7-related skeletal myopathy", "subject_closure_label": [ - "entity", - "continuant", - "disposition", - "realizable entity", - "specifically dependent continuant", - "disease", - "muscular dystrophy-dystroglycanopathy, type B", + "muscular dystrophy", + "human disease", "musculoskeletal system disorder", + "disease", + "muscle tissue disorder", "congenital nervous system disorder", + "hereditary skeletal muscle disorder", + "MYH7-related skeletal myopathy", + "disposition", + "qualitative or quantitative protein defects in neuromuscular diseases", + "distal myopathy", + "disease", + "continuant", + "qualitative or quantitative defects of beta-myosin heavy chain (MYH7)", + "myopathy", "hereditary disease", - "muscle tissue disorder", - "metabolic disease", "nervous system disorder", - "myopathy", - "muscular dystrophy-dystroglycanopathy (congenital with intellectual disability), type B2", - "congenital disorder of glycosylation", - "qualitative or quantitative protein defects in neuromuscular diseases", - "qualitative or quantitative defects of protein involved in O-glycosylation of alpha-dystroglycan", - "disorder of protein O-glycosylation", - "muscular dystrophy-dystroglycanopathy", - "qualitative or quantitative defects of alpha-dystroglycan", - "inborn errors of metabolism", - "neuromuscular disease", - "congenital muscular dystrophy", + "congenital myopathy", + "realizable entity", + "specifically dependent continuant", "skeletal muscle disorder", - "muscular dystrophy", - "disorder of glycosylation", - "glycoprotein metabolism disease", - "myopathy caused by variation in POMT2", - "human disease", - "hereditary skeletal muscle disorder", - "disease", + "neuromuscular disease", + "entity", ], "subject_taxon": None, "subject_taxon_label": None, "predicate": "biolink:has_phenotype", - "object": "HP:0001265", + "object": "HP:0002460", "original_object": None, "object_namespace": "HP", "object_category": "biolink:PhenotypicFeature", "object_closure": [ - "HP:0000001", "UPHENO:0082875", - "UPHENO:0075696", - "UPHENO:0078622", - "UPHENO:0049586", - "UPHENO:0080377", - "UPHENO:0001001", - "UPHENO:0052915", - "UPHENO:0049622", - "UPHENO:0080585", - "HP:0001265", - "HP:0100022", + "UPHENO:0002320", "UPHENO:0001005", - "HP:0031826", - "UPHENO:0001002", - "HP:0000118", - "BFO:0000002", - "UPHENO:0052178", "BFO:0000020", - "UPHENO:0002433", - "UPHENO:0050613", - "UPHENO:0005625", - "UPHENO:0050079", - "UPHENO:0005433", + "PATO:0000001", + "BFO:0000004", + "UBERON:0000061", + "HP:0000001", + "UPHENO:0001001", + "HP:0000118", + "BFO:0000001", + "UBERON:0000467", + "UBERON:0000468", + "UBERON:0011216", + "UPHENO:0075696", + "HP:0001324", + "HP:0003011", "UPHENO:0002332", - "UPHENO:0050606", - "HP:0001315", - "HP:0000707", "UPHENO:0001003", "UPHENO:0002536", - "HP:0000708", - "UPHENO:0079826", - "UPHENO:0004523", - "HP:0011446", - "UPHENO:0079833", - "UPHENO:0049587", - "BFO:0000001", - "PATO:0000001", - "HP:0012638", - "BFO:0000001", - "BFO:0000003", + "HP:0002460", + "HP:0011804", "BFO:0000002", - "BFO:0000015", - "BFO:0000004", - "GO:0008150", "BFO:0000040", + "UBERON:0005090", + "UBERON:0001630", + "UPHENO:0001002", + "BFO:0000002", + "UPHENO:0080555", + "UPHENO:0002816", + "UPHENO:0080556", + "HP:0033127", + "BFO:0000001", "UBERON:0001062", - "GO:0050896", - "GO:0032501", "UBERON:0000465", - "GO:0009605", - "GO:0050879", - "GO:0007610", - "GO:0003008", - "UBERON:0000061", - "GO:0060004", - "GO:0050881", - "NBO:0000313", - "GO:0050877", "UBERON:0010000", - "UBERON:0000467", - "GO:0050882", - "NBO:0000338", - "GO:0050905", - "UBERON:0000468", - "UBERON:0001016", - "NBO:0000403", - "NBO:0000001", - "NBO:0000388", - "NBO:0000389", + "UBERON:0000062", + "UBERON:0000383", + "UBERON:0001015", ], - "object_label": "Hyporeflexia (HPO)", + "object_label": "Distal muscle weakness (HPO)", "object_closure_label": [ - "entity", - "entity", - "continuant", - "continuant", - "independent continuant", - "specifically dependent continuant", - "material entity", - "All (HPO)", - "Phenotypic abnormality (HPO)", - "Abnormality of the nervous system (HPO)", - "Behavioral abnormality (HPO)", - "Hyporeflexia (HPO)", - "Reduced tendon reflexes (HPO)", - "Abnormality of higher mental function (HPO)", - "Abnormal nervous system physiology (HPO)", - "Abnormal reflex (HPO)", - "Abnormality of movement (HPO)", - "quality", - "anatomical structure", + "All (HPO)", + "abnormality of muscle organ physiology", + "Phenotypic abnormality (HPO)", + "decreased anatomical entity strength", + "abnormal musculature", + "decreased muscle organ strength", + "Abnormality of the musculoskeletal system (HPO)", + "entity", + "independent continuant", "material anatomical entity", - "anatomical system", - "multicellular organism", - "nervous system", - "anatomical entity", + "anatomical structure", "multicellular anatomical structure", + "abnormality of anatomical entity physiology", "phenotype", "Phenotypic abnormality", - "phenotype by ontology source", + "continuant", + "Distal muscle weakness (HPO)", + "quality", + "continuant", + "material entity", "abnormal phenotype by ontology source", - "abnormality of anatomical entity physiology", - "abnormality of nervous system physiology", - "abnormal anatomical entity", - "abnormal nervous system", - "decreased biological_process", - "decreased reflex", - "abnormal response to stimulus", - "abnormal biological_process", - "abnormal behavior", - "abnormal response to external stimulus", - "abnormal voluntary musculoskeletal movement", - "abnormal musculoskeletal movement", - "decreased qualitatively biological_process", - "decreased qualitatively response to stimulus", + "specifically dependent continuant", + "Abnormal muscle physiology (HPO)", + "entity", + "anatomical entity", + "muscle structure", + "organ", + "muscle organ", + "musculature of body", + "musculature", "abnormal anatomical entity", - "abnormal voluntary movement behavior", - "abnormal behavior process", - "abnormal voluntary movement behavior", - "changed biological_process rate", - "abnormal behavior process", + "Muscle weakness (HPO)", + "Abnormality of the musculature (HPO)", "abnormality of anatomical entity physiology", + "phenotype by ontology source", + "abnormal anatomical entity", + "anatomical system", + "multicellular organism", + "organ system subdivision", ], "object_taxon": None, "object_taxon_label": None, @@ -4276,21 +4723,27 @@ def associations(): "aggregator_knowledge_source": ["infores:monarchinitiative"], "negated": None, "pathway": None, - "evidence_count": 4, + "evidence_count": 2, "has_evidence": ["ECO:0000304"], "has_evidence_links": [{"id": "ECO:0000304", "url": "http://purl.obolibrary.org/obo/ECO_0000304"}], + "grouping_key": "MONDO:0008050🍪🍪biolink:has_phenotype🍪HP:0002460", "provided_by": "hpoa_disease_to_phenotype_edges", "provided_by_link": { "id": "hpoa_disease_to_phenotype", "url": "https://monarch-initiative.github.io/monarch-ingest/Sources/hpoa/#disease_to_phenotype", }, - "publications": ["OMIM:613156"], - "publications_links": [{"id": "OMIM:613156", "url": "http://identifiers.org/mim/613156"}], + "publications": ["OMIM:160500"], + "publications_links": [{"id": "OMIM:160500", "url": "http://identifiers.org/mim/160500"}], "qualifiers": [], "frequency_qualifier": None, "onset_qualifier": None, "sex_qualifier": None, "stage_qualifier": None, + "qualifiers_label": None, + "qualifiers_namespace": None, + "qualifiers_category": None, + "qualifiers_closure": [], + "qualifiers_closure_label": [], "frequency_qualifier_label": None, "frequency_qualifier_namespace": None, "frequency_qualifier_category": None, @@ -4313,194 +4766,176 @@ def associations(): "stage_qualifier_closure_label": [], }, { - "id": "uuid:840c1951-5d8c-11ee-9b27-2b20ed86a9d9", + "id": "uuid:c9c8bf32-7529-11ee-b012-cbd37f5c3759", "category": "biolink:DiseaseToPhenotypicFeatureAssociation", - "subject": "MONDO:0013297", - "original_subject": "OMIM:613530", + "subject": "MONDO:0008050", + "original_subject": "OMIM:160500", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ - "MONDO:0000001", - "MONDO:0016971", - "MONDO:0000429", + "BFO:0000002", + "MONDO:0016195", + "MONDO:0005336", + "MONDO:0018949", "MONDO:0005071", + "MONDO:0008050", + "BFO:0000016", + "MONDO:0016139", + "OGMS:0000031", + "MONDO:0003847", + "BFO:0000001", "MONDO:0020121", - "MONDO:0700223", - "BFO:0000002", + "MONDO:0019952", "BFO:0000017", "BFO:0000020", - "MONDO:0016106", - "BFO:0000016", "MONDO:0020120", "MONDO:0019056", - "MONDO:0015151", + "MONDO:0000001", + "MONDO:0700223", "MONDO:0700096", - "MONDO:0005336", "MONDO:0002081", - "MONDO:0000426", - "OGMS:0000031", - "MONDO:0003847", "MONDO:0003939", - "BFO:0000001", - "MONDO:0013297", + "MONDO:0002320", ], - "subject_label": "autosomal dominant limb-girdle muscular dystrophy type 1H", + "subject_label": "MYH7-related skeletal myopathy", "subject_closure_label": [ - "entity", - "continuant", + "muscular dystrophy", + "human disease", + "musculoskeletal system disorder", + "disease", + "muscle tissue disorder", + "congenital nervous system disorder", + "hereditary skeletal muscle disorder", + "MYH7-related skeletal myopathy", "disposition", - "realizable entity", - "specifically dependent continuant", + "qualitative or quantitative protein defects in neuromuscular diseases", + "distal myopathy", "disease", - "autosomal dominant disease", - "autosomal genetic disease", - "musculoskeletal system disorder", + "continuant", + "qualitative or quantitative defects of beta-myosin heavy chain (MYH7)", + "myopathy", "hereditary disease", - "muscle tissue disorder", "nervous system disorder", - "myopathy", - "autosomal dominant limb-girdle muscular dystrophy type 1H", - "muscular dystrophy, limb-girdle, autosomal dominant", - "progressive muscular dystrophy", - "limb-girdle muscular dystrophy", - "neuromuscular disease", + "congenital myopathy", + "realizable entity", + "specifically dependent continuant", "skeletal muscle disorder", - "muscular dystrophy", - "human disease", - "hereditary skeletal muscle disorder", - "disease", + "neuromuscular disease", + "entity", ], "subject_taxon": None, "subject_taxon_label": None, "predicate": "biolink:has_phenotype", - "object": "HP:0001265", + "object": "HP:0003805", "original_object": None, "object_namespace": "HP", "object_category": "biolink:PhenotypicFeature", "object_closure": [ + "BFO:0000002", + "BFO:0000020", + "UPHENO:0076692", + "BFO:0000001", + "BFO:0000004", + "CL:0000255", + "UBERON:0014892", + "UBERON:0002036", "HP:0000001", - "UPHENO:0082875", - "UPHENO:0075696", - "UPHENO:0078622", - "UPHENO:0049586", - "UPHENO:0080377", + "HP:0004303", "UPHENO:0001001", - "UPHENO:0052915", - "UPHENO:0049622", - "UPHENO:0080585", - "HP:0001265", - "HP:0100022", - "UPHENO:0001005", - "HP:0031826", "UPHENO:0001002", "HP:0000118", - "BFO:0000002", - "UPHENO:0052178", - "BFO:0000020", - "UPHENO:0002433", - "UPHENO:0050613", - "UPHENO:0005625", - "UPHENO:0050079", - "UPHENO:0005433", - "UPHENO:0002332", - "UPHENO:0050606", - "HP:0001315", - "HP:0000707", "UPHENO:0001003", - "UPHENO:0002536", - "HP:0000708", - "UPHENO:0079826", - "UPHENO:0004523", - "HP:0011446", - "UPHENO:0079833", - "UPHENO:0049587", - "BFO:0000001", + "UPHENO:0076710", "PATO:0000001", - "HP:0012638", "BFO:0000001", - "BFO:0000003", - "BFO:0000002", - "BFO:0000015", - "BFO:0000004", - "GO:0008150", "BFO:0000040", + "UBERON:0000467", + "CL:0000000", + "UBERON:0000468", + "UBERON:0011216", + "CL:0000548", + "UBERON:0001134", + "HP:0003011", + "UPHENO:0002536", + "HP:0003805", + "UBERON:0005090", + "UBERON:0018254", + "UBERON:0004120", + "UBERON:0000479", + "CL:0000003", + "UBERON:0001630", + "UBERON:0002385", + "CL:0000188", + "UPHENO:0001005", + "HP:0011805", + "HP:0025354", + "UPHENO:0002816", + "UPHENO:0081581", + "HP:0033127", + "BFO:0000002", "UBERON:0001062", - "GO:0050896", - "GO:0032501", "UBERON:0000465", - "GO:0009605", - "GO:0050879", - "GO:0007610", - "GO:0003008", + "RO:0002577", "UBERON:0000061", - "GO:0060004", - "GO:0050881", - "NBO:0000313", - "GO:0050877", "UBERON:0010000", - "UBERON:0000467", - "GO:0050882", - "NBO:0000338", - "GO:0050905", - "UBERON:0000468", - "UBERON:0001016", - "NBO:0000403", - "NBO:0000001", - "NBO:0000388", - "NBO:0000389", + "UBERON:0000062", + "UBERON:0000383", + "UBERON:0001015", + "CL:0002371", ], - "object_label": "Hyporeflexia (HPO)", + "object_label": "Rimmed vacuoles (HPO)", "object_closure_label": [ - "entity", - "entity", - "continuant", - "continuant", - "independent continuant", - "specifically dependent continuant", - "material entity", "All (HPO)", + "Abnormal muscle fiber morphology (HPO)", + "Phenotypic abnormality", "Phenotypic abnormality (HPO)", - "Abnormality of the nervous system (HPO)", - "Behavioral abnormality (HPO)", - "Hyporeflexia (HPO)", - "Reduced tendon reflexes (HPO)", - "Abnormality of higher mental function (HPO)", - "Abnormal nervous system physiology (HPO)", - "Abnormal reflex (HPO)", - "Abnormality of movement (HPO)", + "Abnormal cellular phenotype (HPO)", + "abnormal musculature", + "abnormal multicellular organism morphology", + "Abnormality of the musculoskeletal system (HPO)", "quality", - "anatomical structure", + "independent continuant", "material anatomical entity", - "anatomical system", - "multicellular organism", - "nervous system", - "anatomical entity", + "system", "multicellular anatomical structure", "phenotype", - "Phenotypic abnormality", - "phenotype by ontology source", "abnormal phenotype by ontology source", - "abnormality of anatomical entity physiology", - "abnormality of nervous system physiology", - "abnormal anatomical entity", - "abnormal nervous system", - "decreased biological_process", - "decreased reflex", - "abnormal response to stimulus", - "abnormal biological_process", - "abnormal behavior", - "abnormal response to external stimulus", - "abnormal voluntary musculoskeletal movement", - "abnormal musculoskeletal movement", - "decreased qualitatively biological_process", - "decreased qualitatively response to stimulus", + "Abnormal skeletal muscle morphology (HPO)", + "phenotype by ontology source", + "tissue", + "animal cell", + "skeletal muscle tissue", + "cell of skeletal muscle", + "continuant", + "specifically dependent continuant", + "abnormal muscle organ morphology", + "Rimmed vacuoles (HPO)", + "entity", + "anatomical entity", + "anatomical structure", + "muscle structure", + "skeletal musculature", + "mesoderm-derived structure", + "organ", + "native cell", + "muscle organ", + "muscle tissue", + "musculature of body", + "musculature", + "somatic cell", + "Abnormality of the musculature (HPO)", "abnormal anatomical entity", - "abnormal voluntary movement behavior", - "abnormal behavior process", - "abnormal voluntary movement behavior", - "changed biological_process rate", - "abnormal behavior process", - "abnormality of anatomical entity physiology", + "abnormal anatomical entity morphology", + "entity", + "continuant", + "material entity", + "anatomical system", + "cell", + "multicellular organism", + "organ system subdivision", + "eukaryotic cell", + "skeletal muscle organ", + "striated muscle tissue", ], "object_taxon": None, "object_taxon_label": None, @@ -4508,21 +4943,27 @@ def associations(): "aggregator_knowledge_source": ["infores:monarchinitiative"], "negated": None, "pathway": None, - "evidence_count": 4, - "has_evidence": ["ECO:0000304"], - "has_evidence_links": [{"id": "ECO:0000304", "url": "http://purl.obolibrary.org/obo/ECO_0000304"}], + "evidence_count": 2, + "has_evidence": ["ECO:0000501"], + "has_evidence_links": [{"id": "ECO:0000501", "url": "http://purl.obolibrary.org/obo/ECO_0000501"}], + "grouping_key": "MONDO:0008050🍪🍪biolink:has_phenotype🍪HP:0003805", "provided_by": "hpoa_disease_to_phenotype_edges", "provided_by_link": { "id": "hpoa_disease_to_phenotype", "url": "https://monarch-initiative.github.io/monarch-ingest/Sources/hpoa/#disease_to_phenotype", }, - "publications": ["OMIM:613530"], - "publications_links": [{"id": "OMIM:613530", "url": "http://identifiers.org/mim/613530"}], + "publications": ["OMIM:160500"], + "publications_links": [{"id": "OMIM:160500", "url": "http://identifiers.org/mim/160500"}], "qualifiers": [], "frequency_qualifier": None, "onset_qualifier": None, "sex_qualifier": None, "stage_qualifier": None, + "qualifiers_label": None, + "qualifiers_namespace": None, + "qualifiers_category": None, + "qualifiers_closure": [], + "qualifiers_closure_label": [], "frequency_qualifier_label": None, "frequency_qualifier_namespace": None, "frequency_qualifier_category": None, diff --git a/backend/tests/fixtures/autocomplete.py b/backend/tests/fixtures/autocomplete.py index 816f70ecf..fc911209d 100644 --- a/backend/tests/fixtures/autocomplete.py +++ b/backend/tests/fixtures/autocomplete.py @@ -33,6 +33,7 @@ def autocomplete(): "infantile nephropathic cystinosis", "toni-debre-Fanconi syndrome", ], + "uri": None, "highlight": None, "score": None, }, @@ -60,6 +61,7 @@ def autocomplete(): "Fanconi anemia complementation group type A", "Fanconi anemia, complementation group A", ], + "uri": None, "highlight": None, "score": None, }, @@ -84,6 +86,7 @@ def autocomplete(): "Fanconi anemia complementation group type L", "Fanconi anemia, complementation group L", ], + "uri": None, "highlight": None, "score": None, }, @@ -108,6 +111,7 @@ def autocomplete(): "Fanconi anemia, complementation group E", "face", ], + "uri": None, "highlight": None, "score": None, }, @@ -134,6 +138,7 @@ def autocomplete(): "primary Fanconi renotubular syndrome", "renal Fanconi syndrome", ], + "uri": None, "highlight": None, "score": None, }, @@ -157,6 +162,7 @@ def autocomplete(): "pancytopenia, congenital", "primary erythroid hypoplasia", ], + "uri": None, "highlight": None, "score": None, }, @@ -181,6 +187,7 @@ def autocomplete(): "RAD51C Fanconi anemia", "Rad51C Fanconi anemia", ], + "uri": None, "highlight": None, "score": None, }, @@ -205,6 +212,7 @@ def autocomplete(): "SLX4 Fanconi anemia", "Slx4 Fanconi anemia", ], + "uri": None, "highlight": None, "score": None, }, @@ -229,21 +237,7 @@ def autocomplete(): "Fanconi anemia, complementation GROUP V", "MAD2L2 Fanconi anemia", ], - "highlight": None, - "score": None, - }, - { - "id": "MONDO:0100136", - "category": "biolink:Disease", - "name": "obsolete Fanconia anemia complementation group M", - "full_name": None, - "description": "OBSOLETE Any Fanconi anemia in which the cause of the disease is a mutation in the FANCM gene.", - "xref": [], - "provided_by": "phenio_nodes", - "in_taxon": None, - "in_taxon_label": None, - "symbol": None, - "synonym": ["FANCM Fanconi anemia", "Fanconi anemia caused by mutation in FANCM"], + "uri": None, "highlight": None, "score": None, }, @@ -270,6 +264,7 @@ def autocomplete(): "Fanconi pancytopenia type 2", "Fanconi pancytopenia, type 2", ], + "uri": None, "highlight": None, "score": None, }, @@ -293,6 +288,7 @@ def autocomplete(): "Fanconi anemia, complementation group N", "PALB2 Fanconi anemia", ], + "uri": None, "highlight": None, "score": None, }, @@ -316,6 +312,7 @@ def autocomplete(): "Fanconi anemia, complementation GROUP R", "RAD51 Fanconi anemia", ], + "uri": None, "highlight": None, "score": None, }, @@ -339,6 +336,23 @@ def autocomplete(): "Fanconi anemia, complementation GROUP U", "XRCC2 Fanconi anemia", ], + "uri": None, + "highlight": None, + "score": None, + }, + { + "id": "MONDO:0100136", + "category": "biolink:Disease", + "name": "obsolete Fanconia anemia complementation group M", + "full_name": None, + "description": "OBSOLETE Any Fanconi anemia in which the cause of the disease is a mutation in the FANCM gene.", + "xref": [], + "provided_by": "phenio_nodes", + "in_taxon": None, + "in_taxon_label": None, + "symbol": None, + "synonym": ["FANCM Fanconi anemia", "Fanconi anemia caused by mutation in FANCM"], + "uri": None, "highlight": None, "score": None, }, @@ -365,6 +379,7 @@ def autocomplete(): "Fanconi pancytopenia, type 3", "facc", ], + "uri": None, "highlight": None, "score": None, }, @@ -390,6 +405,7 @@ def autocomplete(): "Fanconi pancytopenia type 4", "Fanconi pancytopenia, type 4", ], + "uri": None, "highlight": None, "score": None, }, @@ -412,6 +428,7 @@ def autocomplete(): "Fanconi anemia complementation group type I", "Fanconi anemia, complementation group I", ], + "uri": None, "highlight": None, "score": None, }, @@ -434,6 +451,7 @@ def autocomplete(): "Fanconi anemia complementation group type Q", "Fanconi anemia, complementation group Q", ], + "uri": None, "highlight": None, "score": None, }, @@ -456,6 +474,7 @@ def autocomplete(): "Fanconi anemia, complementation group T", "UBE2T Fanconi anemia", ], + "uri": None, "highlight": None, "score": None, }, @@ -477,6 +496,7 @@ def autocomplete(): "Fanconi anemia complementation group type F", "Fanconi anemia, complementation group F", ], + "uri": None, "highlight": None, "score": None, }, diff --git a/backend/tests/fixtures/autocomplete_response.py b/backend/tests/fixtures/autocomplete_response.py index 97c726c11..abdee91f4 100644 --- a/backend/tests/fixtures/autocomplete_response.py +++ b/backend/tests/fixtures/autocomplete_response.py @@ -5,7 +5,7 @@ def autocomplete_response(): return { "responseHeader": { - "QTime": 0, + "QTime": 1, "params": { "mm": "100%", "q": "fanc", @@ -182,14 +182,6 @@ def autocomplete_response(): ], "description": "Any Fanconi anemia in which the cause of the disease is a mutation in the MAD2L2 gene.", }, - { - "id": "MONDO:0100136", - "category": "biolink:Disease", - "name": "obsolete Fanconia anemia complementation group M", - "provided_by": "phenio_nodes", - "synonym": ["FANCM Fanconi anemia", "Fanconi anemia caused by mutation in FANCM"], - "description": "OBSOLETE Any Fanconi anemia in which the cause of the disease is a mutation in the FANCM gene.", - }, { "id": "MONDO:0010351", "category": "biolink:Disease", @@ -257,6 +249,14 @@ def autocomplete_response(): ], "description": "Any Fanconi anemia in which the cause of the disease is a mutation in the XRCC2 gene.", }, + { + "id": "MONDO:0100136", + "category": "biolink:Disease", + "name": "obsolete Fanconia anemia complementation group M", + "provided_by": "phenio_nodes", + "synonym": ["FANCM Fanconi anemia", "Fanconi anemia caused by mutation in FANCM"], + "description": "OBSOLETE Any Fanconi anemia in which the cause of the disease is a mutation in the FANCM gene.", + }, { "id": "MONDO:0009213", "category": "biolink:Disease", diff --git a/backend/tests/fixtures/entity.py b/backend/tests/fixtures/entity.py index 79b9e8340..c53c3edf6 100644 --- a/backend/tests/fixtures/entity.py +++ b/backend/tests/fixtures/entity.py @@ -15,4 +15,5 @@ def entity(): "in_taxon_label": None, "symbol": None, "synonym": [], + "uri": "http://purl.obolibrary.org/obo/MONDO_0020121", } diff --git a/backend/tests/fixtures/histopheno_response.py b/backend/tests/fixtures/histopheno_response.py index 2ebdf4537..bfee7c9f2 100644 --- a/backend/tests/fixtures/histopheno_response.py +++ b/backend/tests/fixtures/histopheno_response.py @@ -5,7 +5,7 @@ def histopheno_response(): return { "responseHeader": { - "QTime": 1, + "QTime": 6, "params": { "facet.query": [ 'object_closure:"HP:0000924"', @@ -39,7 +39,7 @@ def histopheno_response(): "facet": "true", }, }, - "response": {"num_found": 4560, "start": 0, "docs": []}, + "response": {"num_found": 4563, "start": 0, "docs": []}, "facet_counts": { "facet_fields": {}, "facet_queries": { diff --git a/backend/tests/fixtures/node.py b/backend/tests/fixtures/node.py index 7021054cc..a25b43ff0 100644 --- a/backend/tests/fixtures/node.py +++ b/backend/tests/fixtures/node.py @@ -15,6 +15,7 @@ def node(): "in_taxon_label": None, "symbol": None, "synonym": [], + "uri": None, "inheritance": None, "causal_gene": [], "causes_disease": [], @@ -31,9 +32,9 @@ def node(): "node_hierarchy": { "super_classes": [ { - "id": "MONDO:0005336", + "id": "MONDO:0019056", "category": "biolink:Disease", - "name": "myopathy", + "name": "neuromuscular disease", "full_name": None, "description": None, "xref": [], @@ -42,6 +43,7 @@ def node(): "in_taxon_label": None, "symbol": None, "synonym": [], + "uri": None, }, { "id": "MONDO:0700223", @@ -55,11 +57,12 @@ def node(): "in_taxon_label": None, "symbol": None, "synonym": [], + "uri": None, }, { - "id": "MONDO:0019056", + "id": "MONDO:0005336", "category": "biolink:Disease", - "name": "neuromuscular disease", + "name": "myopathy", "full_name": None, "description": None, "xref": [], @@ -68,13 +71,14 @@ def node(): "in_taxon_label": None, "symbol": None, "synonym": [], + "uri": None, }, ], "sub_classes": [ { - "id": "MONDO:0008028", + "id": "MONDO:0018949", "category": "biolink:Disease", - "name": "muscular dystrophy, Barnes type", + "name": "distal myopathy", "full_name": None, "description": None, "xref": [], @@ -83,11 +87,12 @@ def node(): "in_taxon_label": None, "symbol": None, "synonym": [], + "uri": None, }, { - "id": "MONDO:0010675", + "id": "MONDO:0019950", "category": "biolink:Disease", - "name": "muscular dystrophy, cardiac type", + "name": "congenital muscular dystrophy", "full_name": None, "description": None, "xref": [], @@ -96,11 +101,12 @@ def node(): "in_taxon_label": None, "symbol": None, "synonym": [], + "uri": None, }, { - "id": "MONDO:0010676", + "id": "MONDO:0023204", "category": "biolink:Disease", - "name": "muscular dystrophy, Hemizygous lethal type", + "name": "Fukuda-Miyanomae-Nakata syndrome", "full_name": None, "description": None, "xref": [], @@ -109,11 +115,12 @@ def node(): "in_taxon_label": None, "symbol": None, "synonym": [], + "uri": None, }, { - "id": "MONDO:0010677", + "id": "MONDO:0100228", "category": "biolink:Disease", - "name": "muscular dystrophy, Mabry type", + "name": "LAMA2-related muscular dystrophy", "full_name": None, "description": None, "xref": [], @@ -122,11 +129,12 @@ def node(): "in_taxon_label": None, "symbol": None, "synonym": [], + "uri": None, }, { - "id": "MONDO:0010678", + "id": "MONDO:0008028", "category": "biolink:Disease", - "name": "muscular dystrophy, progressive Pectorodorsal", + "name": "muscular dystrophy, Barnes type", "full_name": None, "description": None, "xref": [], @@ -135,11 +143,12 @@ def node(): "in_taxon_label": None, "symbol": None, "synonym": [], + "uri": None, }, { - "id": "MONDO:0016106", + "id": "MONDO:0010675", "category": "biolink:Disease", - "name": "progressive muscular dystrophy", + "name": "muscular dystrophy, cardiac type", "full_name": None, "description": None, "xref": [], @@ -148,11 +157,12 @@ def node(): "in_taxon_label": None, "symbol": None, "synonym": [], + "uri": None, }, { - "id": "MONDO:0018949", + "id": "MONDO:0010676", "category": "biolink:Disease", - "name": "distal myopathy", + "name": "muscular dystrophy, Hemizygous lethal type", "full_name": None, "description": None, "xref": [], @@ -161,11 +171,12 @@ def node(): "in_taxon_label": None, "symbol": None, "synonym": [], + "uri": None, }, { - "id": "MONDO:0019950", + "id": "MONDO:0010677", "category": "biolink:Disease", - "name": "congenital muscular dystrophy", + "name": "muscular dystrophy, Mabry type", "full_name": None, "description": None, "xref": [], @@ -174,11 +185,12 @@ def node(): "in_taxon_label": None, "symbol": None, "synonym": [], + "uri": None, }, { - "id": "MONDO:0023204", + "id": "MONDO:0010678", "category": "biolink:Disease", - "name": "Fukuda-Miyanomae-Nakata syndrome", + "name": "muscular dystrophy, progressive Pectorodorsal", "full_name": None, "description": None, "xref": [], @@ -187,11 +199,12 @@ def node(): "in_taxon_label": None, "symbol": None, "synonym": [], + "uri": None, }, { - "id": "MONDO:0100228", + "id": "MONDO:0016106", "category": "biolink:Disease", - "name": "LAMA2-related muscular dystrophy", + "name": "progressive muscular dystrophy", "full_name": None, "description": None, "xref": [], @@ -200,6 +213,7 @@ def node(): "in_taxon_label": None, "symbol": None, "synonym": [], + "uri": None, }, ], }, diff --git a/backend/tests/fixtures/phenotype_explorer_compare.py b/backend/tests/fixtures/phenotype_explorer_compare.py index 6046d629d..660f9f571 100644 --- a/backend/tests/fixtures/phenotype_explorer_compare.py +++ b/backend/tests/fixtures/phenotype_explorer_compare.py @@ -15,7 +15,7 @@ def phenotype_explorer_compare(): "match_source_label": "no abnormal phenotype detected (MPO)", "match_target": "HP:0004325", "match_target_label": "Decreased body weight (HPO)", - "score": 1.5616002210519475, + "score": 1.4431977534690428, "match_subsumer": None, "match_subsumer_label": None, "similarity": { @@ -30,11 +30,11 @@ def phenotype_explorer_compare(): "ancestor_source": None, "object_information_content": None, "subject_information_content": None, - "ancestor_information_content": 1.5616002210519475, + "ancestor_information_content": 1.4431977534690428, "jaccard_similarity": 0.16216216216216217, "cosine_similarity": None, "dice_similarity": None, - "phenodigm_score": 0.5032220864376823, + "phenodigm_score": 0.48376861011243283, }, }, "MP:0010771": { @@ -42,7 +42,7 @@ def phenotype_explorer_compare(): "match_source_label": "integument phenotype (MPO)", "match_target": "HP:0004325", "match_target_label": "Decreased body weight (HPO)", - "score": 2.2728188647181566, + "score": 1.4431977534690428, "match_subsumer": None, "match_subsumer_label": None, "similarity": { @@ -52,16 +52,16 @@ def phenotype_explorer_compare(): "object_id": "HP:0004325", "object_label": None, "object_source": None, - "ancestor_id": "UBERON:0000468", + "ancestor_id": "UPHENO:0001003", "ancestor_label": "", "ancestor_source": None, "object_information_content": None, "subject_information_content": None, - "ancestor_information_content": 2.2728188647181566, - "jaccard_similarity": 0.325, + "ancestor_information_content": 1.4431977534690428, + "jaccard_similarity": 0.3333333333333333, "cosine_similarity": None, "dice_similarity": None, - "phenodigm_score": 0.8594568814276845, + "phenodigm_score": 0.6935891563620457, }, }, }, @@ -71,7 +71,7 @@ def phenotype_explorer_compare(): "match_source_label": "Decreased body weight (HPO)", "match_target": "MP:0010771", "match_target_label": "integument phenotype (MPO)", - "score": 2.2728188647181566, + "score": 1.4431977534690428, "match_subsumer": None, "match_subsumer_label": None, "similarity": { @@ -81,20 +81,20 @@ def phenotype_explorer_compare(): "object_id": "MP:0010771", "object_label": None, "object_source": None, - "ancestor_id": "UBERON:0000468", + "ancestor_id": "UPHENO:0001003", "ancestor_label": "", "ancestor_source": None, "object_information_content": None, "subject_information_content": None, - "ancestor_information_content": 2.2728188647181566, - "jaccard_similarity": 0.325, + "ancestor_information_content": 1.4431977534690428, + "jaccard_similarity": 0.3333333333333333, "cosine_similarity": None, "dice_similarity": None, - "phenodigm_score": 0.8594568814276845, + "phenodigm_score": 0.6935891563620457, }, } }, - "average_score": 2.0950142038016044, - "best_score": 2.2728188647181566, + "average_score": 1.4431977534690428, + "best_score": 1.4431977534690428, "metric": "ancestor_information_content", } diff --git a/backend/tests/fixtures/search.py b/backend/tests/fixtures/search.py index 1adca2437..ada436fc0 100644 --- a/backend/tests/fixtures/search.py +++ b/backend/tests/fixtures/search.py @@ -28,6 +28,7 @@ def search(): "pancytopenia, congenital", "primary erythroid hypoplasia", ], + "uri": None, "highlight": None, "score": None, }, @@ -56,6 +57,7 @@ def search(): "infantile nephropathic cystinosis", "toni-debre-Fanconi syndrome", ], + "uri": None, "highlight": None, "score": None, }, @@ -71,6 +73,7 @@ def search(): "in_taxon_label": None, "symbol": None, "synonym": ["FRTS1", "Fanconi renotubular syndrome 1", "primary Fanconi renotubular syndrome"], + "uri": None, "highlight": None, "score": None, }, @@ -86,6 +89,7 @@ def search(): "in_taxon_label": None, "symbol": None, "synonym": ["Fanconi-like syndrome"], + "uri": None, "highlight": None, "score": None, }, @@ -101,6 +105,7 @@ def search(): "in_taxon_label": None, "symbol": None, "synonym": ["adult Fanconi syndrome", "adult Fanconi's syndrome"], + "uri": None, "highlight": None, "score": None, }, @@ -116,6 +121,7 @@ def search(): "in_taxon_label": None, "symbol": None, "synonym": ["acquired Fanconi syndrome"], + "uri": None, "highlight": None, "score": None, }, @@ -131,6 +137,7 @@ def search(): "in_taxon_label": None, "symbol": None, "synonym": [], + "uri": None, "highlight": None, "score": None, }, @@ -152,6 +159,7 @@ def search(): "Fanconi syndrome caused by mutation in SLC34A1", "SLC34A1 Fanconi syndrome", ], + "uri": None, "highlight": None, "score": None, }, @@ -173,6 +181,7 @@ def search(): "Fanconi renotubular syndrome type 3", "Fanconi syndrome caused by mutation in EHHADH", ], + "uri": None, "highlight": None, "score": None, }, @@ -199,6 +208,7 @@ def search(): "primary Fanconi renotubular syndrome", "renal Fanconi syndrome", ], + "uri": None, "highlight": None, "score": None, }, @@ -219,6 +229,7 @@ def search(): "Fanconi Renotubular Syndrome, Acadian Variant", "Fanconi renotubular syndrome 5", ], + "uri": None, "highlight": None, "score": None, }, @@ -234,6 +245,7 @@ def search(): "in_taxon_label": None, "symbol": None, "synonym": ["hereditary Fanconi renotubular syndrome"], + "uri": None, "highlight": None, "score": None, }, @@ -260,6 +272,7 @@ def search(): "Fanconi pancytopenia, type 3", "facc", ], + "uri": None, "highlight": None, "score": None, }, @@ -285,6 +298,7 @@ def search(): "Fanconi pancytopenia type 4", "Fanconi pancytopenia, type 4", ], + "uri": None, "highlight": None, "score": None, }, @@ -312,6 +326,7 @@ def search(): "Fanconi anemia complementation group type A", "Fanconi anemia, complementation group A", ], + "uri": None, "highlight": None, "score": None, }, @@ -338,6 +353,7 @@ def search(): "Fanconi pancytopenia type 2", "Fanconi pancytopenia, type 2", ], + "uri": None, "highlight": None, "score": None, }, @@ -362,6 +378,7 @@ def search(): "Fanconi anemia, complementation group E", "face", ], + "uri": None, "highlight": None, "score": None, }, @@ -383,6 +400,7 @@ def search(): "Fanconi anemia complementation group type F", "Fanconi anemia, complementation group F", ], + "uri": None, "highlight": None, "score": None, }, @@ -405,6 +423,7 @@ def search(): "Fanconi anemia, complementation group D1", "inherited cancer-predisposing syndrome due to biallelic BRCA2 mutations", ], + "uri": None, "highlight": None, "score": None, }, @@ -427,6 +446,7 @@ def search(): "Fanconi anemia complementation group type I", "Fanconi anemia, complementation group I", ], + "uri": None, "highlight": None, "score": None, }, diff --git a/backend/tests/fixtures/search_response.py b/backend/tests/fixtures/search_response.py index bed27890b..f1dab08ed 100644 --- a/backend/tests/fixtures/search_response.py +++ b/backend/tests/fixtures/search_response.py @@ -5,7 +5,7 @@ def search_response(): return { "responseHeader": { - "QTime": 0, + "QTime": 3, "params": { "mm": "100%", "q": "fanconi", diff --git a/docs/Usage/CLI.md b/docs/Usage/CLI.md index 417f53dab..aebcdc956 100644 --- a/docs/Usage/CLI.md +++ b/docs/Usage/CLI.md @@ -21,8 +21,10 @@ $ monarch [OPTIONS] COMMAND [ARGS]... * `association-table` * `associations`: Paginate through associations * `autocomplete`: Return entity autcomplete matches for a... +* `compare`: Compare two entities using semantic... * `entity`: Retrieve an entity by ID * `histopheno`: Retrieve the histopheno data for an entity... +* `multi-entity-associations`: Paginate through associations for multiple... * `schema`: Print the linkml schema for the data model * `search`: Search for entities * `solr` @@ -112,7 +114,7 @@ $ monarch associations [OPTIONS] * `-l, --limit INTEGER`: The number of associations to return [default: 20] * `--offset INTEGER`: The offset of the first association to be retrieved [default: 0] * `-f, --format TEXT`: The format of the output (json, yaml, tsv, table) [default: json] -* `-o, --output TEXT`: The path to the output file +* `-O, --output TEXT`: The path to the output file * `--help`: Show this message and exit. ## `monarch autocomplete` @@ -140,6 +142,27 @@ $ monarch autocomplete [OPTIONS] [Q] * `-o, --output TEXT`: The path to the output file * `--help`: Show this message and exit. +## `monarch compare` + +Compare two entities using semantic similarity via OAK + +**Usage**: + +```console +$ monarch compare [OPTIONS] SUBJECTS OBJECTS +``` + +**Arguments**: + +* `SUBJECTS`: Comma separated list of subjects to compare [required] +* `OBJECTS`: Comma separated list of objects to compare [required] + +**Options**: + +* `-f, --format TEXT`: The format of the output (json, yaml, tsv, table) [default: json] +* `-o, --output TEXT`: The path to the output file +* `--help`: Show this message and exit. + ## `monarch entity` Retrieve an entity by ID @@ -193,6 +216,34 @@ $ monarch histopheno [OPTIONS] [SUBJECT] * `-o, --output TEXT`: The path to the output file * `--help`: Show this message and exit. +## `monarch multi-entity-associations` + +Paginate through associations for multiple entities + +Args: + entity: A comma-separated list of entities + counterpart_category: A comma-separated list of counterpart categories + limit: The number of associations to return + offset: The offset of the first association to be retrieved + fmt: The format of the output (json, yaml, tsv, table) + output: The path to the output file (stdout if not specified) + +**Usage**: + +```console +$ monarch multi-entity-associations [OPTIONS] +``` + +**Options**: + +* `-e, --entity TEXT`: Comma-separated list of entities +* `-c, --counterpart-category TEXT` +* `-l, --limit INTEGER`: [default: 20] +* `--offset INTEGER`: [default: 0] +* `-f, --format TEXT`: The format of the output (json, yaml, tsv, table) [default: json] +* `-o, --output TEXT`: The path to the output file +* `--help`: Show this message and exit. + ## `monarch schema` Print the linkml schema for the data model @@ -214,7 +265,7 @@ Search for entities Args: q: The query string to search for category: The category of the entity - taxon: The taxon of the entity + in_taxon_label: The taxon label to filter by limit: The number of entities to return offset: The offset of the first entity to be retrieved fmt: The format of the output (json, yaml, tsv, table) @@ -230,7 +281,7 @@ $ monarch search [OPTIONS] * `-q, --query TEXT` * `-c, --category TEXT` -* `-t, --in-taxon TEXT` +* `-t, --in-taxon-label TEXT` * `-ff, --facet-fields TEXT` * `--facet-queries TEXT` * `-l, --limit INTEGER`: [default: 20] @@ -262,6 +313,7 @@ $ monarch solr [OPTIONS] COMMAND [ARGS]... * `download`: Download the Monarch Solr KG. * `entity`: Retrieve an entity by ID * `histopheno`: Retrieve the histopheno associations for a... +* `multi-entity-associations`: Paginate through associations for multiple... * `search`: Search for entities * `start`: Starts a local Solr container. * `status`: Checks the status of the local Solr... @@ -275,7 +327,6 @@ Args: entity (str): The entity to get association counts for Optional Args: - update (bool): Whether to re-download the Monarch KG. Default False fmt (str): The format of the output (json, yaml, tsv, table). Default JSON output (str): The path to the output file. Default stdout @@ -430,7 +481,6 @@ Args: subject (str): The subject of the association Optional Args: - update (bool): Whether to re-download the Monarch KG. Default False fmt (str): The format of the output (json, yaml, tsv, table). Default JSON output (str): The path to the output file. Default stdout @@ -450,6 +500,34 @@ $ monarch solr histopheno [OPTIONS] [SUBJECT] * `-o, --output TEXT`: The path to the output file * `--help`: Show this message and exit. +### `monarch solr multi-entity-associations` + +Paginate through associations for multiple entities + +Args: + entity: A comma-separated list of entities + counterpart_category: A comma-separated list of counterpart categories + limit: The number of associations to return + offset: The offset of the first association to be retrieved + fmt: The format of the output (json, yaml, tsv, table) + output: The path to the output file (stdout if not specified) + +**Usage**: + +```console +$ monarch solr multi-entity-associations [OPTIONS] +``` + +**Options**: + +* `-e, --entity TEXT`: Entity ID to get associations for +* `-c, --counterpart-category TEXT`: Counterpart category to get associations for +* `-l, --limit INTEGER`: [default: 20] +* `--offset INTEGER`: [default: 0] +* `-f, --format TEXT`: The format of the output (json, yaml, tsv, table) [default: json] +* `-o, --output TEXT`: The path to the output file +* `--help`: Show this message and exit. + ### `monarch solr search` Search for entities @@ -457,7 +535,7 @@ Search for entities Optional Args: q: The query string to search for category: The category of the entity - taxon: The taxon of the entity + in_taxon_label: The taxon label to filter on facet_fields: The fields to facet on facet_queries: The queries to facet on limit: The number of entities to return @@ -475,7 +553,7 @@ $ monarch solr search [OPTIONS] * `-q, --query TEXT` * `-c, --category TEXT` -* `-t, --in-taxon TEXT` +* `-t, --in-taxon-label TEXT` * `-ff, --facet-fields TEXT` * `--facet-queries TEXT` * `-l, --limit INTEGER`: [default: 20] diff --git a/frontend/e2e/phenotype-explorer.test.ts b/frontend/e2e/phenotype-explorer.test.ts index 4b1128926..cf0221b66 100644 --- a/frontend/e2e/phenotype-explorer.test.ts +++ b/frontend/e2e/phenotype-explorer.test.ts @@ -69,7 +69,7 @@ test("Phenotype set vs gene/disease works", async ({ page }) => { .first() .click(); - /** paste specific dummy phenotypes */ + /** paste specific fake phenotypes */ await paste(page.locator("input"), "HP:0004970,HP:0004933,HP:0004927"); /** run analysis, and look for expected results */ @@ -87,7 +87,7 @@ test("Phenotype set vs phenotype set works", async ({ page }) => { await page.goto("/explore#phenotype-explorer"); - /** paste specific dummy phenotypes */ + /** paste specific fake phenotypes */ await paste( page.locator("input").first(), "HP:0004970,HP:0004933,HP:0004927", diff --git a/frontend/e2e/search.test.ts b/frontend/e2e/search.test.ts index 0802f2638..8fdeb7282 100644 --- a/frontend/e2e/search.test.ts +++ b/frontend/e2e/search.test.ts @@ -21,61 +21,59 @@ test("Redirects to explore page from home page", async ({ page }) => { test("Recent/frequent results show", async ({ page }) => { await page.goto("/explore"); - /** dummy searches */ - const searches = [ - "abc def", - "123", - "123", - "abc def", - "123", - "123", - "abc def", + const nodes = [ + "MONDO:0007523", + "HP:0003179", + "HP:0003179", + "MONDO:0007523", + "HP:0003179", + "HP:0003179", + "MONDO:0007523", + "HP:0100775", ]; - /** go through dummy searches */ - for (const search of searches) { - await page.locator("input").fill(search); - /** dispatch textbox change event which triggers search and records it */ - await page.locator("input").dispatchEvent("change"); - /** wait for results */ - await expect(page.locator("p.description").first()).toBeVisible(); - await page.locator(".textbox button").click(); + for (const node of nodes) { + await page.goto("/" + node); + await expect(page.locator("#overview")).toBeVisible(); } - /** go to node page, which should also get added to search history */ - await page.goto("/MONDO:12345"); - /** wait for page to load */ - await expect(page.locator("#overview")).toBeVisible(); await page.goto("/explore"); - - /** focus search box to show list of results */ await page.locator("input").focus(); + const options = page.locator("[role='option']"); /** recent */ - const options = page.locator("[role='option']"); await expect( options .nth(0) - .getByText(/muscular dystrophy/i) + .getByText(/Dural ectasia/i) .first(), ).toBeVisible(); await expect( options .nth(1) - .getByText(/abc def/i) + .getByText(/Ehlers-Danlos syndrome, hypermobility/i) + .first(), + ).toBeVisible(); + await expect( + options + .nth(2) + .getByText(/Protrusio acetabuli/i) .first(), ).toBeVisible(); - await expect(options.nth(2).getByText(/123/).first()).toBeVisible(); /** frequent */ await expect( - page.locator("[role='option']").nth(3).getByText(/123/).first(), + page + .locator("[role='option']") + .nth(3) + .getByText(/Protrusio acetabuli/i) + .first(), ).toBeVisible(); await expect( page .locator("[role='option']") .nth(4) - .getByText(/abc def/) + .getByText(/Ehlers-Danlos syndrome, hypermobility/i) .first(), ).toBeVisible(); }); diff --git a/frontend/fixtures/association-counts.json b/frontend/fixtures/association-counts.json new file mode 100644 index 000000000..207c58a9c --- /dev/null +++ b/frontend/fixtures/association-counts.json @@ -0,0 +1,19 @@ +{ + "items": [ + { + "label": "Phenotypes", + "count": 4027, + "category": "biolink:DiseaseToPhenotypicFeatureAssociation" + }, + { + "label": "Causal Genes", + "count": 124, + "category": "biolink:CausalGeneToDiseaseAssociation" + }, + { + "label": "Correlated Genes", + "count": 151, + "category": "biolink:CorrelatedGeneToDiseaseAssociation" + } + ] +} diff --git a/frontend/fixtures/association-table.json b/frontend/fixtures/association-table.json index 3cabd27d9..b312b5bd0 100644 --- a/frontend/fixtures/association-table.json +++ b/frontend/fixtures/association-table.json @@ -4,70 +4,70 @@ "total": 4027, "items": [ { - "id": "uuid:89aa7b9b-5d8c-11ee-9b27-2b20ed86a9d9", + "id": "uuid:ca3946de-7529-11ee-b012-cbd37f5c3759", "category": "biolink:DiseaseToPhenotypicFeatureAssociation", "subject": "MONDO:0020793", "original_subject": "OMIM:164310", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ - "MONDO:0020158", - "MONDO:0000001", + "BFO:0000002", + "BFO:0000020", + "MONDO:0024458", + "MONDO:0005336", + "MONDO:0018949", "MONDO:0005071", + "MONDO:0003382", + "BFO:0000016", + "OGMS:0000031", + "MONDO:0003847", + "BFO:0000001", "MONDO:0025193", "MONDO:0020121", - "MONDO:0700223", - "BFO:0000002", "MONDO:0020793", "BFO:0000017", - "BFO:0000020", - "MONDO:0016106", - "MONDO:0003382", - "BFO:0000016", "MONDO:0020120", "MONDO:0019056", + "MONDO:0000462", + "MONDO:0020158", + "MONDO:0000001", + "MONDO:0700223", + "MONDO:0016106", "MONDO:0700096", - "MONDO:0024458", - "MONDO:0005336", "MONDO:0002081", - "OGMS:0000031", - "MONDO:0003847", "MONDO:0003939", "MONDO:0002022", - "BFO:0000001", - "MONDO:0000462", - "MONDO:0005328", - "MONDO:0018949" + "MONDO:0005328" ], "subject_label": "oculopharyngodistal myopathy 1", "subject_closure_label": [ - "entity", - "continuant", - "disposition", - "realizable entity", - "specifically dependent continuant", + "oculopharyngodistal myopathy", + "muscular dystrophy", + "progressive muscular dystrophy", + "human disease", + "musculoskeletal system disorder", "disease", - "eye adnexa disorder", + "muscle tissue disorder", "disorder of orbital region", - "musculoskeletal system disorder", + "hereditary skeletal muscle disorder", "eyelid disorder", - "hereditary disease", - "muscle tissue disorder", - "nervous system disorder", - "eye disorder", - "myopathy", - "progressive muscular dystrophy", + "disposition", "distal myopathy", - "neuromuscular disease", - "skeletal muscle disorder", - "muscular dystrophy", "eyelids malposition disorder", - "oculopharyngodistal myopathy 1", + "disease", + "continuant", + "specifically dependent continuant", "disorder of visual system", - "oculopharyngodistal myopathy", - "human disease", - "hereditary skeletal muscle disorder", - "disease" + "myopathy", + "hereditary disease", + "eye adnexa disorder", + "nervous system disorder", + "oculopharyngodistal myopathy 1", + "realizable entity", + "skeletal muscle disorder", + "neuromuscular disease", + "entity", + "eye disorder" ], "subject_taxon": null, "subject_taxon_label": null, @@ -77,87 +77,87 @@ "object_namespace": "HP", "object_category": "biolink:PhenotypicFeature", "object_closure": [ - "HP:0000001", "UPHENO:0082875", - "UPHENO:0075696", "UPHENO:0002320", - "UPHENO:0001001", "UPHENO:0001005", - "UPHENO:0001002", - "HP:0001324", - "HP:0000118", - "BFO:0000002", "BFO:0000020", - "UPHENO:0080555", + "PATO:0000001", + "BFO:0000004", + "UBERON:0000061", + "HP:0000001", + "UPHENO:0001001", + "HP:0000118", + "BFO:0000001", + "UBERON:0000467", + "UBERON:0000468", + "UBERON:0011216", + "UPHENO:0075696", + "HP:0001324", "HP:0003011", - "UPHENO:0002816", "UPHENO:0002332", - "UPHENO:0080556", - "HP:0033127", "UPHENO:0001003", "UPHENO:0002536", "HP:0002460", - "BFO:0000001", "HP:0011804", - "PATO:0000001", - "BFO:0000001", "BFO:0000002", - "BFO:0000004", "BFO:0000040", + "UBERON:0005090", + "UBERON:0001630", + "UPHENO:0001002", + "BFO:0000002", + "UPHENO:0080555", + "UPHENO:0002816", + "UPHENO:0080556", + "HP:0033127", + "BFO:0000001", "UBERON:0001062", "UBERON:0000465", - "UBERON:0000061", "UBERON:0010000", - "UBERON:0000467", - "UBERON:0005090", "UBERON:0000062", - "UBERON:0000468", - "UBERON:0011216", - "UBERON:0001630", "UBERON:0000383", "UBERON:0001015" ], "object_label": "Distal muscle weakness (HPO)", "object_closure_label": [ - "entity", - "entity", - "continuant", - "continuant", - "independent continuant", - "specifically dependent continuant", - "material entity", "All (HPO)", + "abnormality of muscle organ physiology", "Phenotypic abnormality (HPO)", - "Muscle weakness (HPO)", - "Distal muscle weakness (HPO)", - "Abnormality of the musculature (HPO)", - "Abnormal muscle physiology (HPO)", + "decreased anatomical entity strength", + "abnormal musculature", + "decreased muscle organ strength", "Abnormality of the musculoskeletal system (HPO)", - "quality", - "anatomical structure", - "organ", - "musculature of body", + "entity", + "independent continuant", "material anatomical entity", - "anatomical system", - "multicellular organism", - "musculature", - "anatomical entity", - "muscle organ", - "muscle structure", + "anatomical structure", "multicellular anatomical structure", - "organ system subdivision", + "abnormality of anatomical entity physiology", "phenotype", "Phenotypic abnormality", - "phenotype by ontology source", + "continuant", + "Distal muscle weakness (HPO)", + "quality", + "continuant", + "material entity", "abnormal phenotype by ontology source", - "abnormality of muscle organ physiology", - "abnormality of anatomical entity physiology", + "specifically dependent continuant", + "Abnormal muscle physiology (HPO)", + "entity", + "anatomical entity", + "muscle structure", + "organ", + "muscle organ", + "musculature of body", + "musculature", "abnormal anatomical entity", - "abnormal musculature", + "Muscle weakness (HPO)", + "Abnormality of the musculature (HPO)", + "abnormality of anatomical entity physiology", + "phenotype by ontology source", "abnormal anatomical entity", - "decreased anatomical entity strength", - "decreased muscle organ strength", - "abnormality of anatomical entity physiology" + "anatomical system", + "multicellular organism", + "organ system subdivision" ], "object_taxon": null, "object_taxon_label": null, @@ -165,7 +165,7 @@ "aggregator_knowledge_source": ["infores:monarchinitiative"], "negated": null, "pathway": null, - "evidence_count": 6, + "evidence_count": 4, "has_evidence": ["ECO:0000269"], "has_evidence_links": [ { @@ -173,6 +173,7 @@ "url": "http://purl.obolibrary.org/obo/ECO_0000269" } ], + "grouping_key": "MONDO:0020793\ud83c\udf6a\ud83c\udf6abiolink:has_phenotype\ud83c\udf6aHP:0002460", "provided_by": "hpoa_disease_to_phenotype_edges", "provided_by_link": { "id": "hpoa_disease_to_phenotype", @@ -198,14 +199,19 @@ "onset_qualifier": null, "sex_qualifier": null, "stage_qualifier": null, + "qualifiers_label": null, + "qualifiers_namespace": null, + "qualifiers_category": null, + "qualifiers_closure": [], + "qualifiers_closure_label": [], "frequency_qualifier_label": "Frequent (HPO)", "frequency_qualifier_namespace": "HP", "frequency_qualifier_category": "biolink:PhenotypicFeature", - "frequency_qualifier_closure": ["HP:0000001", "HP:0040282", "HP:0040279"], + "frequency_qualifier_closure": ["HP:0040282", "HP:0000001", "HP:0040279"], "frequency_qualifier_closure_label": [ "All (HPO)", - "Frequency (HPO)", - "Frequent (HPO)" + "Frequent (HPO)", + "Frequency (HPO)" ], "onset_qualifier_label": null, "onset_qualifier_namespace": null, @@ -225,70 +231,70 @@ "direction": "outgoing" }, { - "id": "uuid:89aa7bac-5d8c-11ee-9b27-2b20ed86a9d9", + "id": "uuid:ca3946ef-7529-11ee-b012-cbd37f5c3759", "category": "biolink:DiseaseToPhenotypicFeatureAssociation", "subject": "MONDO:0020793", "original_subject": "OMIM:164310", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ - "MONDO:0020158", - "MONDO:0000001", + "BFO:0000002", + "BFO:0000020", + "MONDO:0024458", + "MONDO:0005336", + "MONDO:0018949", "MONDO:0005071", + "MONDO:0003382", + "BFO:0000016", + "OGMS:0000031", + "MONDO:0003847", + "BFO:0000001", "MONDO:0025193", "MONDO:0020121", - "MONDO:0700223", - "BFO:0000002", "MONDO:0020793", "BFO:0000017", - "BFO:0000020", - "MONDO:0016106", - "MONDO:0003382", - "BFO:0000016", "MONDO:0020120", "MONDO:0019056", + "MONDO:0000462", + "MONDO:0020158", + "MONDO:0000001", + "MONDO:0700223", + "MONDO:0016106", "MONDO:0700096", - "MONDO:0024458", - "MONDO:0005336", "MONDO:0002081", - "OGMS:0000031", - "MONDO:0003847", "MONDO:0003939", "MONDO:0002022", - "BFO:0000001", - "MONDO:0000462", - "MONDO:0005328", - "MONDO:0018949" + "MONDO:0005328" ], "subject_label": "oculopharyngodistal myopathy 1", "subject_closure_label": [ - "entity", - "continuant", - "disposition", - "realizable entity", - "specifically dependent continuant", + "oculopharyngodistal myopathy", + "muscular dystrophy", + "progressive muscular dystrophy", + "human disease", + "musculoskeletal system disorder", "disease", - "eye adnexa disorder", + "muscle tissue disorder", "disorder of orbital region", - "musculoskeletal system disorder", + "hereditary skeletal muscle disorder", "eyelid disorder", - "hereditary disease", - "muscle tissue disorder", - "nervous system disorder", - "eye disorder", - "myopathy", - "progressive muscular dystrophy", + "disposition", "distal myopathy", - "neuromuscular disease", - "skeletal muscle disorder", - "muscular dystrophy", "eyelids malposition disorder", - "oculopharyngodistal myopathy 1", + "disease", + "continuant", + "specifically dependent continuant", "disorder of visual system", - "oculopharyngodistal myopathy", - "human disease", - "hereditary skeletal muscle disorder", - "disease" + "myopathy", + "hereditary disease", + "eye adnexa disorder", + "nervous system disorder", + "oculopharyngodistal myopathy 1", + "realizable entity", + "skeletal muscle disorder", + "neuromuscular disease", + "entity", + "eye disorder" ], "subject_taxon": null, "subject_taxon_label": null, @@ -298,141 +304,141 @@ "object_namespace": "HP", "object_category": "biolink:PhenotypicFeature", "object_closure": [ - "HP:0000001", "UPHENO:0082875", - "UPHENO:0075696", - "HP:0011024", - "UPHENO:0001001", - "UPHENO:0002443", "UPHENO:0002471", "HP:0025270", - "HP:0012719", "UPHENO:0001005", - "UPHENO:0002833", - "HP:0002015", - "UPHENO:0001002", - "UPHENO:0002725", - "HP:0000118", "BFO:0000002", "BFO:0000020", - "UPHENO:0002433", - "HP:0025032", - "UPHENO:0002332", "HP:0002664", - "HP:0000707", "HP:0011793", - "UPHENO:0001003", - "UPHENO:0002536", - "UPHENO:0004523", - "BFO:0000001", "PATO:0000001", - "HP:0025031", "UPHENO:0002474", "HP:0012638", - "BFO:0000001", - "BFO:0000002", "BFO:0000004", - "BFO:0000040", - "UBERON:0001062", - "UBERON:0000465", - "RO:0002577", "UBERON:0000061", + "UBERON:0001007", + "UBERON:0001016", + "UBERON:0011676", + "UBERON:0013701", + "UBERON:0000915", + "UBERON:0001043", + "UBERON:0002100", + "UBERON:0005181", + "UBERON:0002075", + "HP:0000001", + "UPHENO:0001001", + "HP:0000118", + "UPHENO:0002433", + "UPHENO:0001003", + "BFO:0000001", + "BFO:0000001", + "BFO:0000040", "UBERON:0010000", "UBERON:0000467", - "UBERON:0000475", - "UBERON:0000062", "UBERON:0004111", "UBERON:0000468", "UBERON:0000064", - "UBERON:0001007", - "UBERON:0001016", + "UPHENO:0075696", + "HP:0011024", + "UPHENO:0002443", + "HP:0012719", + "UPHENO:0002725", + "HP:0025032", + "UPHENO:0002332", + "UPHENO:0002536", + "UPHENO:0004523", + "BFO:0000002", + "UBERON:0000465", "UBERON:0005409", - "UBERON:0011676", - "UBERON:0013701", "UBERON:0009569", "UBERON:0013702", "UBERON:0013765", "UBERON:0005177", "UBERON:0000025", - "UBERON:0013522", - "UBERON:0000915", - "UBERON:0001043", - "UBERON:0002100", - "UBERON:0005181", - "UBERON:0002075", "UBERON:0001555", "UBERON:0004921", + "UPHENO:0002833", + "HP:0002015", + "UPHENO:0001002", + "HP:0000707", + "HP:0025031", + "UBERON:0001062", + "RO:0002577", + "UBERON:0000475", + "UBERON:0000062", + "UBERON:0013522", "UBERON:0005178", "UBERON:0004908" ], "object_label": "Dysphagia (HPO)", "object_closure_label": [ - "entity", - "entity", - "continuant", - "continuant", - "independent continuant", - "specifically dependent continuant", - "material entity", "All (HPO)", + "abnormality of alimentary part of gastrointestinal system physiology", + "Abnormal esophagus physiology (HPO)", + "Functional abnormality of the gastrointestinal tract (HPO)", "Phenotypic abnormality (HPO)", "Abnormality of the nervous system (HPO)", - "Dysphagia (HPO)", - "Neoplasm (HPO)", - "Abnormality of the gastrointestinal tract (HPO)", - "Neoplasm by anatomical site (HPO)", - "Abnormal nervous system physiology (HPO)", - "Functional abnormality of the gastrointestinal tract (HPO)", - "Abnormality of the digestive system (HPO)", - "Abnormality of digestive system physiology (HPO)", - "Abnormal esophagus physiology (HPO)", - "quality", + "independent continuant", "system", - "tube", "anatomical structure", - "organ", - "organ part", - "material anatomical entity", - "anatomical system", - "multicellular organism", - "organism subdivision", - "thoracic segment of trunk", "digestive system", "nervous system", - "esophagus", - "anatomical entity", "digestive tract", - "viscus", - "trunk", - "anatomical conduit", - "upper digestive tract", "subdivision of digestive tract", - "trunk region element", - "thoracic cavity element", - "thoracic segment organ", - "alimentary part of gastrointestinal system", - "subdivision of trunk", - "multicellular anatomical structure", - "subdivision of organism along main body axis", - "subdivision of tube", - "main body axis", - "body proper", - "digestive system element", + "abnormality of anatomical entity physiology", "phenotype", + "abnormality of digestive system physiology", + "abnormal digestive system", + "Dysphagia (HPO)", "Phenotypic abnormality", - "phenotype by ontology source", - "abnormal phenotype by ontology source", - "abnormality of anatomical entity physiology", "abnormality of nervous system physiology", - "abnormality of digestive system physiology", - "abnormality of alimentary part of gastrointestinal system physiology", + "phenotype by ontology source", + "abnormal nervous system", + "quality", "abnormality of esophagus physiology", + "Abnormal nervous system physiology (HPO)", + "continuant", + "material anatomical entity", + "subdivision of trunk", + "body proper", + "digestive system element", + "trunk region element", + "tube", + "abnormal phenotype by ontology source", + "continuant", + "specifically dependent continuant", + "Neoplasm (HPO)", + "Neoplasm by anatomical site (HPO)", + "entity", + "anatomical entity", + "organism subdivision", + "organ", + "alimentary part of gastrointestinal system", + "subdivision of tube", + "thoracic cavity element", + "upper digestive tract", "abnormal anatomical entity", + "Abnormality of the gastrointestinal tract (HPO)", "abnormal alimentary part of gastrointestinal system", - "abnormal digestive system", - "abnormal nervous system", + "Abnormality of digestive system physiology (HPO)", + "abnormality of anatomical entity physiology", "abnormal anatomical entity", - "abnormality of anatomical entity physiology" + "entity", + "Abnormality of the digestive system (HPO)", + "material entity", + "multicellular anatomical structure", + "anatomical system", + "anatomical conduit", + "multicellular organism", + "organ part", + "subdivision of organism along main body axis", + "main body axis", + "thoracic segment of trunk", + "esophagus", + "trunk", + "thoracic segment organ", + "viscus" ], "object_taxon": null, "object_taxon_label": null, @@ -440,7 +446,7 @@ "aggregator_knowledge_source": ["infores:monarchinitiative"], "negated": null, "pathway": null, - "evidence_count": 6, + "evidence_count": 4, "has_evidence": ["ECO:0000269"], "has_evidence_links": [ { @@ -448,6 +454,7 @@ "url": "http://purl.obolibrary.org/obo/ECO_0000269" } ], + "grouping_key": "MONDO:0020793\ud83c\udf6a\ud83c\udf6abiolink:has_phenotype\ud83c\udf6aHP:0002015", "provided_by": "hpoa_disease_to_phenotype_edges", "provided_by_link": { "id": "hpoa_disease_to_phenotype", @@ -473,14 +480,19 @@ "onset_qualifier": null, "sex_qualifier": null, "stage_qualifier": null, + "qualifiers_label": null, + "qualifiers_namespace": null, + "qualifiers_category": null, + "qualifiers_closure": [], + "qualifiers_closure_label": [], "frequency_qualifier_label": "Frequent (HPO)", "frequency_qualifier_namespace": "HP", "frequency_qualifier_category": "biolink:PhenotypicFeature", - "frequency_qualifier_closure": ["HP:0000001", "HP:0040282", "HP:0040279"], + "frequency_qualifier_closure": ["HP:0040282", "HP:0000001", "HP:0040279"], "frequency_qualifier_closure_label": [ "All (HPO)", - "Frequency (HPO)", - "Frequent (HPO)" + "Frequent (HPO)", + "Frequency (HPO)" ], "onset_qualifier_label": null, "onset_qualifier_namespace": null, @@ -500,84 +512,84 @@ "direction": "outgoing" }, { - "id": "uuid:862bc0d4-5d8c-11ee-9b27-2b20ed86a9d9", + "id": "uuid:c6b3613a-7529-11ee-b012-cbd37f5c3759", "category": "biolink:DiseaseToPhenotypicFeatureAssociation", "subject": "MONDO:0013049", "original_subject": "OMIM:612937", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ + "BFO:0000002", + "BFO:0000020", + "MONDO:0005336", + "MONDO:0005021", "MONDO:0004994", - "MONDO:0000001", "MONDO:0018276", "MONDO:0005071", "MONDO:0005267", - "MONDO:0013049", + "BFO:0000016", + "MONDO:0016333", + "MONDO:0017749", + "OGMS:0000031", + "MONDO:0003847", + "BFO:0000001", "MONDO:0020121", "MONDO:0004995", - "MONDO:0700223", - "MONDO:0024322", - "BFO:0000002", "BFO:0000017", - "BFO:0000020", "MONDO:0005217", - "BFO:0000016", "MONDO:0020120", "MONDO:0019056", + "MONDO:0015286", + "MONDO:0019052", + "MONDO:0005500", + "MONDO:0005066", + "MONDO:0000001", + "MONDO:0013049", + "MONDO:0700223", + "MONDO:0024322", "MONDO:0700096", "MONDO:0000591", - "MONDO:0005336", "MONDO:0002081", - "MONDO:0016333", - "MONDO:0017749", - "OGMS:0000031", - "MONDO:0005021", - "MONDO:0003847", "MONDO:0003939", - "MONDO:0015286", - "BFO:0000001", "MONDO:0002320", - "MONDO:0019052", - "MONDO:0005500", - "MONDO:0005066", "MONDO:0019950" ], "subject_label": "DPM3-congenital disorder of glycosylation", "subject_closure_label": [ - "entity", - "continuant", - "disposition", - "realizable entity", - "specifically dependent continuant", - "disease", + "cardiomyopathy", + "muscular dystrophy", + "cardiovascular disorder", + "human disease", "intrinsic cardiomyopathy", "musculoskeletal system disorder", + "disorder of multiple glycosylation", + "disease", + "muscle tissue disorder", "congenital nervous system disorder", + "hereditary skeletal muscle disorder", + "disorder of glycosylation", + "disposition", + "congenital disorder of glycosylation", + "disease", + "DPM3-congenital disorder of glycosylation", + "continuant", + "specifically dependent continuant", + "myopathy", + "familial dilated cardiomyopathy", "hereditary disease", - "muscle tissue disorder", - "cardiomyopathy", - "cardiovascular disorder", - "dilated cardiomyopathy", + "inborn errors of metabolism", + "congenital disorder of glycosylation type I", "metabolic disease", + "muscular dystrophy-dystroglycanopathy", "nervous system disorder", - "familial cardiomyopathy", "heart disorder", - "myopathy", - "congenital disorder of glycosylation type I", - "DPM3-congenital disorder of glycosylation", - "congenital disorder of glycosylation", - "familial dilated cardiomyopathy", - "disorder of multiple glycosylation", - "muscular dystrophy-dystroglycanopathy", - "inborn errors of metabolism", - "neuromuscular disease", - "congenital muscular dystrophy", + "realizable entity", + "familial cardiomyopathy", "skeletal muscle disorder", - "muscular dystrophy", - "disorder of glycosylation", - "human disease", - "hereditary skeletal muscle disorder", - "disease" + "neuromuscular disease", + "dilated cardiomyopathy", + "entity", + "congenital muscular dystrophy" ], "subject_taxon": null, "subject_taxon_label": null, @@ -587,84 +599,40 @@ "object_namespace": "HP", "object_category": "biolink:PhenotypicFeature", "object_closure": [ - "HP:0000001", - "HP:0011021", - "HP:0004364", "UPHENO:0082875", - "UPHENO:0075696", - "UPHENO:0077817", - "UPHENO:0076289", - "UPHENO:0002448", - "UPHENO:0001001", "UPHENO:0051763", - "UPHENO:0004536", - "UPHENO:0051668", "UPHENO:0001005", - "UPHENO:0001002", - "UPHENO:0077825", - "HP:0000118", - "BFO:0000002", - "HP:0001871", - "UPHENO:0077821", "BFO:0000020", - "UPHENO:0046284", - "UPHENO:0077829", - "UPHENO:0004459", - "UPHENO:0002332", - "UPHENO:0051801", - "HP:0010876", "UPHENO:0077820", - "UPHENO:0076286", - "HP:0040081", - "UPHENO:0001003", - "UPHENO:0002536", - "HP:0001939", - "HP:0500165", - "UPHENO:0081547", - "UPHENO:0077826", - "HP:0032180", "BFO:0000001", - "HP:0002086", - "HP:0003236", - "PATO:0000001", - "HP:0002795", - "HP:0012415", - "UPHENO:0051612", "UPHENO:0051804", - "BFO:0000001", - "BFO:0000003", - "BFO:0000002", "BFO:0000015", "BFO:0000004", - "GO:0008150", - "BFO:0000040", - "UBERON:0001062", - "GO:0008152", - "GO:0005575", - "CHEBI:24431", - "PR:000050567", - "UBERON:0000465", "GO:0032991", "CHEBI:23367", "UBERON:0000178", - "UBERON:0000061", - "UBERON:0000463", - "GO:1902494", - "CHEBI:36357", - "CHEBI:33579", - "UBERON:0010000", - "UBERON:0000467", - "UBERON:0004120", - "UBERON:0006314", "GO:1990234", "CHEBI:33839", "CHEBI:33675", - "CHEBI:138675", - "UBERON:0000468", "UBERON:0001004", - "UBERON:0002193", - "UBERON:0002390", - "UBERON:0000179", + "HP:0000001", + "HP:0011021", + "UPHENO:0001001", + "UPHENO:0001002", + "UPHENO:0077825", + "HP:0000118", + "HP:0001871", + "UPHENO:0051801", + "UPHENO:0001003", + "HP:0001939", + "HP:0032180", + "PATO:0000001", + "HP:0002795", + "BFO:0000001", + "BFO:0000040", + "GO:0008152", + "UBERON:0000467", + "UBERON:0000468", "GO:0061695", "CHEBI:16670", "CHEBI:33302", @@ -676,110 +644,158 @@ "CHEBI:25806", "CHEBI:36962", "CHEBI:50860", + "UPHENO:0075696", + "UPHENO:0077817", + "UPHENO:0076289", + "BFO:0000002", + "UPHENO:0077821", + "UPHENO:0004459", + "UPHENO:0002332", + "UPHENO:0002536", + "HP:0500165", + "HP:0002086", + "HP:0003236", + "BFO:0000003", + "BFO:0000002", + "GO:0008150", + "GO:0005575", + "CHEBI:24431", + "PR:000050567", + "UBERON:0000465", + "GO:1902494", + "CHEBI:36357", + "CHEBI:33579", + "UBERON:0004120", + "UBERON:0006314", + "CHEBI:138675", + "UBERON:0002193", + "UBERON:0002390", + "UBERON:0000179", "CHEBI:16541", "CHEBI:35352", "CHEBI:32988", - "CHEBI:36963", - "CHEBI:33285", "CHEBI:50047", "CHEBI:37622", - "CHEBI:33256" + "CHEBI:33256", + "HP:0004364", + "UPHENO:0002448", + "UPHENO:0004536", + "UPHENO:0051668", + "UPHENO:0046284", + "UPHENO:0077829", + "HP:0010876", + "UPHENO:0076286", + "HP:0040081", + "UPHENO:0081547", + "UPHENO:0077826", + "HP:0012415", + "UPHENO:0051612", + "UBERON:0001062", + "UBERON:0000061", + "UBERON:0000463", + "UBERON:0010000", + "CHEBI:36963", + "CHEBI:33285" ], "object_label": "Elevated circulating creatine kinase concentration (HPO)", "object_closure_label": [ - "entity", - "entity", - "continuant", - "continuant", + "All (HPO)", + "Abnormality of circulating enzyme level (HPO)", + "abnormal multicellular organism chemical entity level", + "Phenotypic abnormality", + "abnormal blood gas molecular entity level", + "Phenotypic abnormality (HPO)", + "abnormal chemical entity level", + "abnormal independent continuant oxygen molecular entity level", + "Abnormal circulating protein concentration (HPO)", + "abnormal role blood level", + "Abnormal circulating creatine kinase concentration (HPO)", + "Abnormality of metabolism/homeostasis (HPO)", + "abnormal role bodily fluid level", + "abnormal blood nitrogen molecular entity level", + "quality", + "Abnormal respiratory system physiology (HPO)", + "process", "independent continuant", - "specifically dependent continuant", - "material entity", - "gas molecular entity", - "polypeptide", - "protein polypeptide chain", - "peptide", + "protein-containing complex", "molecular entity", - "chemical entity", - "oxygen molecular entity", - "amide", - "primary amide", - "heteroorganic entity", + "blood", + "multicellular anatomical structure", + "respiratory system", + "transferase complex, transferring phosphorus-containing groups", + "peptide", "pnictogen molecular entity", "chalcogen molecular entity", - "main group molecular entity", "carbon group molecular entity", - "p-block molecular entity", - "macromolecule", + "protein polypeptide chain", "organonitrogen compound", - "polyatomic entity", + "amide", + "abnormality of anatomical entity physiology", + "phenotype", + "Abnormality of blood and blood-forming tissues (HPO)", + "abnormal independent continuant protein polypeptide chain level", + "phenotype by ontology source", + "Abnormal blood oxygen level (HPO)", + "abnormal blood chemical entity level", + "occurrent", + "continuant", + "biological_process", + "cellular_component", + "chemical entity", + "protein-containing material entity", + "material anatomical entity", + "gas molecular entity", + "creatine kinase complex", + "polypeptide", + "nitrogen molecular entity", + "oxygen molecular entity", "organochalcogen compound", - "organooxygen compound", + "organic molecular entity", "carboxamide", + "primary amide", "organic amino compound", - "organic molecular entity", - "nitrogen molecular entity", - "creatine kinase complex", - "cellular_component", - "protein-containing complex", - "transferase complex, transferring phosphorus-containing groups", - "catalytic complex", - "transferase complex", - "All (HPO)", - "Phenotypic abnormality (HPO)", - "Abnormality of blood and blood-forming tissues (HPO)", - "Abnormality of metabolism/homeostasis (HPO)", - "Abnormality of the respiratory system (HPO)", - "Abnormal respiratory system physiology (HPO)", - "Elevated circulating creatine kinase concentration (HPO)", "Abnormal circulating nitrogen compound concentration (HPO)", - "Abnormal circulating protein concentration (HPO)", - "Abnormality of circulating enzyme level (HPO)", - "Abnormal blood gas level (HPO)", + "abnormality of respiratory system physiology", + "abnormal respiratory system", + "abnormal independent continuant chemical entity level", + "abnormal phenotype by ontology source", + "specifically dependent continuant", + "abnormal independent continuant gas molecular entity level", "Abnormal circulating metabolite concentration (HPO)", - "Abnormal circulating creatine kinase concentration (HPO)", - "Abnormal blood oxygen level (HPO)", - "quality", - "protein-containing material entity", + "Abnormality of the respiratory system (HPO)", + "Elevated circulating creatine kinase concentration (HPO)", + "entity", + "anatomical entity", "anatomical structure", - "blood", - "haemolymphatic fluid", "organism substance", - "material anatomical entity", - "anatomical system", - "multicellular organism", - "respiratory system", - "anatomical entity", - "hemolymphoid system", - "hematopoietic system", "mesoderm-derived structure", "bodily fluid", - "multicellular anatomical structure", - "phenotype", - "Phenotypic abnormality", - "phenotype by ontology source", - "abnormal phenotype by ontology source", - "abnormality of anatomical entity physiology", - "abnormality of respiratory system physiology", - "abnormal anatomical entity", - "abnormal hematopoietic system", - "abnormal respiratory system", - "abnormal chemical entity level", - "abnormal blood protein polypeptide chain level", - "abnormal independent continuant chemical entity level", - "abnormal multicellular organism chemical entity level", - "abnormal independent continuant protein polypeptide chain level", - "abnormal blood chemical entity level", + "hemolymphoid system", + "hematopoietic system", + "haemolymphatic fluid", + "organooxygen compound", + "heteroorganic entity", "abnormal anatomical entity", - "abnormal role blood level", - "abnormal role independent continuant level", "abnormal blood oxygen molecular entity level", - "abnormal independent continuant gas molecular entity level", + "abnormal role independent continuant level", + "continuant", "abnormal independent continuant nitrogen molecular entity level", - "abnormal blood gas molecular entity level", - "abnormal blood nitrogen molecular entity level", - "abnormal independent continuant oxygen molecular entity level", - "abnormal role bodily fluid level", - "abnormality of anatomical entity physiology" + "abnormal hematopoietic system", + "abnormality of anatomical entity physiology", + "abnormal anatomical entity", + "entity", + "Abnormal blood gas level (HPO)", + "abnormal blood protein polypeptide chain level", + "material entity", + "metabolic process", + "catalytic complex", + "polyatomic entity", + "main group molecular entity", + "anatomical system", + "transferase complex", + "macromolecule", + "p-block molecular entity", + "multicellular organism" ], "object_taxon": null, "object_taxon_label": null, @@ -787,7 +803,7 @@ "aggregator_knowledge_source": ["infores:monarchinitiative"], "negated": null, "pathway": null, - "evidence_count": 5, + "evidence_count": 3, "has_evidence": ["ECO:0000269"], "has_evidence_links": [ { @@ -795,6 +811,7 @@ "url": "http://purl.obolibrary.org/obo/ECO_0000269" } ], + "grouping_key": "MONDO:0013049\ud83c\udf6a\ud83c\udf6abiolink:has_phenotype\ud83c\udf6aHP:0003236", "provided_by": "hpoa_disease_to_phenotype_edges", "provided_by_link": { "id": "hpoa_disease_to_phenotype", @@ -816,14 +833,19 @@ "onset_qualifier": null, "sex_qualifier": null, "stage_qualifier": null, + "qualifiers_label": null, + "qualifiers_namespace": null, + "qualifiers_category": null, + "qualifiers_closure": [], + "qualifiers_closure_label": [], "frequency_qualifier_label": "Obligate (HPO)", "frequency_qualifier_namespace": "HP", "frequency_qualifier_category": "biolink:PhenotypicFeature", - "frequency_qualifier_closure": ["HP:0000001", "HP:0040279", "HP:0040280"], + "frequency_qualifier_closure": ["HP:0000001", "HP:0040280", "HP:0040279"], "frequency_qualifier_closure_label": [ "All (HPO)", - "Frequency (HPO)", - "Obligate (HPO)" + "Obligate (HPO)", + "Frequency (HPO)" ], "onset_qualifier_label": null, "onset_qualifier_namespace": null, @@ -843,64 +865,64 @@ "direction": "outgoing" }, { - "id": "uuid:8a99d6f0-5d8c-11ee-9b27-2b20ed86a9d9", + "id": "uuid:cb2a2f47-7529-11ee-b012-cbd37f5c3759", "category": "biolink:DiseaseToPhenotypicFeatureAssociation", "subject": "MONDO:0009681", "original_subject": "OMIM:254090", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ - "MONDO:0000001", + "BFO:0000020", + "MONDO:0005336", "MONDO:0005071", + "BFO:0000016", + "MONDO:0016139", + "OGMS:0000031", + "MONDO:0003847", + "BFO:0000001", "MONDO:0020121", - "MONDO:0700223", - "BFO:0000002", "MONDO:0019952", "BFO:0000017", "MONDO:0100225", - "BFO:0000020", - "BFO:0000016", "MONDO:0020120", "MONDO:0019056", - "MONDO:0016139", + "MONDO:0009681", + "MONDO:0000355", + "MONDO:0000001", + "MONDO:0700223", + "BFO:0000002", "MONDO:0700096", - "MONDO:0005336", "MONDO:0002081", - "MONDO:0009681", - "OGMS:0000031", - "MONDO:0003847", "MONDO:0003939", - "BFO:0000001", "MONDO:0002320", - "MONDO:0000355", "MONDO:0019950" ], "subject_label": "Ullrich congenital muscular dystrophy 1", "subject_closure_label": [ - "entity", + "muscular dystrophy", + "human disease", + "musculoskeletal system disorder", + "disease", + "muscle tissue disorder", + "congenital nervous system disorder", + "hereditary skeletal muscle disorder", "continuant", "disposition", - "realizable entity", - "specifically dependent continuant", + "qualitative or quantitative protein defects in neuromuscular diseases", + "Ullrich congenital muscular dystrophy 1", "disease", - "Ullrich congenital muscular dystrophy", - "musculoskeletal system disorder", - "congenital nervous system disorder", + "specifically dependent continuant", + "myopathy", "hereditary disease", - "muscle tissue disorder", + "Ullrich congenital muscular dystrophy", "nervous system disorder", - "myopathy", - "Ullrich congenital muscular dystrophy 1", - "qualitative or quantitative protein defects in neuromuscular diseases", - "neuromuscular disease", - "congenital muscular dystrophy", "congenital myopathy", - "skeletal muscle disorder", - "muscular dystrophy", + "realizable entity", "collagen 6-related myopathy", - "human disease", - "hereditary skeletal muscle disorder", - "disease" + "skeletal muscle disorder", + "neuromuscular disease", + "entity", + "congenital muscular dystrophy" ], "subject_taxon": null, "subject_taxon_label": null, @@ -910,91 +932,91 @@ "object_namespace": "HP", "object_category": "biolink:PhenotypicFeature", "object_closure": [ - "HP:0000001", - "HP:0020152", "UPHENO:0082875", "HP:0001388", + "UPHENO:0001005", + "BFO:0000002", + "BFO:0000020", + "PATO:0000001", + "HP:0011843", + "BFO:0000004", + "UBERON:0002204", + "HP:0000001", + "HP:0020152", + "UPHENO:0001001", + "UPHENO:0001002", + "HP:0000118", + "UPHENO:0002964", + "BFO:0000001", + "BFO:0000001", + "BFO:0000040", + "UBERON:0000467", + "UBERON:0000468", + "UBERON:0011216", + "UBERON:0034921", "UPHENO:0075696", - "UPHENO:0001001", "HP:0011729", - "UPHENO:0001005", - "UPHENO:0001002", "HP:0034430", "HP:0000924", - "HP:0000118", - "BFO:0000002", - "BFO:0000020", "UPHENO:0002332", - "UPHENO:0002964", - "HP:0033127", "UPHENO:0001003", "UPHENO:0002536", - "UPHENO:0081440", - "BFO:0000001", - "PATO:0000001", - "HP:0011843", - "BFO:0000001", "BFO:0000002", - "BFO:0000004", - "BFO:0000040", - "UBERON:0001062", "UBERON:0000465", + "UBERON:0004770", + "UBERON:0000982", + "HP:0033127", + "UPHENO:0081440", + "UBERON:0001062", "UBERON:0000061", "UBERON:0034925", "UBERON:0010000", - "UBERON:0000467", - "UBERON:0004770", - "UBERON:0000468", - "UBERON:0011216", - "UBERON:0034921", - "UBERON:0002204", "UBERON:0004905", - "UBERON:0001434", - "UBERON:0000982" + "UBERON:0001434" ], "object_label": "Distal joint laxity (HPO)", "object_closure_label": [ - "entity", - "entity", - "continuant", - "continuant", - "independent continuant", - "specifically dependent continuant", - "material entity", "All (HPO)", + "Distal joint laxity (HPO)", + "Phenotypic abnormality", "Phenotypic abnormality (HPO)", - "Abnormality of the skeletal system (HPO)", + "Abnormality of the musculoskeletal system (HPO)", + "abnormality of musculoskeletal system physiology", + "independent continuant", + "multicellular anatomical structure", + "musculoskeletal system", + "skeletal joint", + "abnormality of anatomical entity physiology", "Joint laxity (HPO)", + "phenotype", "Abnormality of joint mobility (HPO)", - "Abnormality of musculoskeletal physiology (HPO)", - "Distal joint laxity (HPO)", - "Abnormality of the musculoskeletal system (HPO)", - "Abnormal joint physiology", + "abnormal skeletal system", "quality", - "anatomical structure", + "Abnormality of musculoskeletal physiology (HPO)", + "continuant", "material anatomical entity", - "anatomical system", - "multicellular organism", - "skeletal joint", + "abnormal phenotype by ontology source", + "continuant", + "specifically dependent continuant", + "entity", "anatomical entity", - "skeletal system", - "musculoskeletal system", + "anatomical structure", + "anatomical collection", "articular system", "articulation", - "multicellular anatomical structure", - "organ system subdivision", - "multi organ part structure", - "anatomical collection", - "phenotype", - "Phenotypic abnormality", - "phenotype by ontology source", - "abnormal phenotype by ontology source", - "abnormality of anatomical entity physiology", + "skeletal system", "abnormal anatomical entity", - "abnormal skeletal system", + "Abnormal joint physiology", + "Abnormality of the skeletal system (HPO)", + "abnormality of anatomical entity physiology", + "phenotype by ontology source", "abnormal anatomical entity", - "abnormality of musculoskeletal system physiology", - "abnormality of anatomical entity physiology" + "entity", + "material entity", + "anatomical system", + "multicellular organism", + "organ system subdivision", + "multi organ part structure" ], "object_taxon": null, "object_taxon_label": null, @@ -1002,7 +1024,7 @@ "aggregator_knowledge_source": ["infores:monarchinitiative"], "negated": null, "pathway": null, - "evidence_count": 5, + "evidence_count": 3, "has_evidence": ["ECO:0000269"], "has_evidence_links": [ { @@ -1010,6 +1032,7 @@ "url": "http://purl.obolibrary.org/obo/ECO_0000269" } ], + "grouping_key": "MONDO:0009681\ud83c\udf6a\ud83c\udf6abiolink:has_phenotype\ud83c\udf6aHP:0020152", "provided_by": "hpoa_disease_to_phenotype_edges", "provided_by_link": { "id": "hpoa_disease_to_phenotype", @@ -1031,14 +1054,19 @@ "onset_qualifier": null, "sex_qualifier": null, "stage_qualifier": null, + "qualifiers_label": null, + "qualifiers_namespace": null, + "qualifiers_category": null, + "qualifiers_closure": [], + "qualifiers_closure_label": [], "frequency_qualifier_label": "Obligate (HPO)", "frequency_qualifier_namespace": "HP", "frequency_qualifier_category": "biolink:PhenotypicFeature", - "frequency_qualifier_closure": ["HP:0000001", "HP:0040279", "HP:0040280"], + "frequency_qualifier_closure": ["HP:0000001", "HP:0040280", "HP:0040279"], "frequency_qualifier_closure_label": [ "All (HPO)", - "Frequency (HPO)", - "Obligate (HPO)" + "Obligate (HPO)", + "Frequency (HPO)" ], "onset_qualifier_label": null, "onset_qualifier_namespace": null, @@ -1058,66 +1086,66 @@ "direction": "outgoing" }, { - "id": "uuid:894ab8ce-5d8c-11ee-9b27-2b20ed86a9d9", + "id": "uuid:c9d8bdf9-7529-11ee-b012-cbd37f5c3759", "category": "biolink:DiseaseToPhenotypicFeatureAssociation", "subject": "MONDO:0009676", "original_subject": "OMIM:253601", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ - "MONDO:0000001", "MONDO:0016971", - "MONDO:0000429", - "MONDO:0016145", - "MONDO:0005071", - "MONDO:0020121", - "MONDO:0700223", "BFO:0000002", - "BFO:0000017", "BFO:0000020", + "MONDO:0005336", + "MONDO:0009676", + "MONDO:0015152", + "MONDO:0000429", + "MONDO:0005071", "MONDO:0006025", - "MONDO:0016106", "BFO:0000016", + "MONDO:0016139", + "OGMS:0000031", + "MONDO:0003847", + "BFO:0000001", + "MONDO:0016145", + "MONDO:0020121", + "BFO:0000017", "MONDO:0020120", "MONDO:0019056", - "MONDO:0016139", + "MONDO:0000001", + "MONDO:0700223", + "MONDO:0016106", "MONDO:0700096", - "MONDO:0005336", "MONDO:0002081", - "MONDO:0009676", - "OGMS:0000031", - "MONDO:0003847", - "MONDO:0003939", - "MONDO:0015152", - "BFO:0000001" + "MONDO:0003939" ], "subject_label": "autosomal recessive limb-girdle muscular dystrophy type 2B", "subject_closure_label": [ - "entity", - "continuant", - "disposition", - "realizable entity", - "specifically dependent continuant", - "disease", - "autosomal genetic disease", + "limb-girdle muscular dystrophy", + "muscular dystrophy", + "progressive muscular dystrophy", + "human disease", "musculoskeletal system disorder", - "hereditary disease", + "disease", "muscle tissue disorder", - "nervous system disorder", - "myopathy", + "qualitative or quantitative defects of dysferlin", + "hereditary skeletal muscle disorder", "autosomal recessive disease", - "autosomal recessive limb-girdle muscular dystrophy type 2B", - "autosomal recessive limb-girdle muscular dystrophy", - "progressive muscular dystrophy", + "disposition", "qualitative or quantitative protein defects in neuromuscular diseases", - "qualitative or quantitative defects of dysferlin", - "limb-girdle muscular dystrophy", - "neuromuscular disease", + "autosomal recessive limb-girdle muscular dystrophy type 2B", + "disease", + "continuant", + "specifically dependent continuant", + "myopathy", + "hereditary disease", + "autosomal genetic disease", + "nervous system disorder", + "realizable entity", "skeletal muscle disorder", - "muscular dystrophy", - "human disease", - "hereditary skeletal muscle disorder", - "disease" + "neuromuscular disease", + "autosomal recessive limb-girdle muscular dystrophy", + "entity" ], "subject_taxon": null, "subject_taxon_label": null, @@ -1127,87 +1155,87 @@ "object_namespace": "HP", "object_category": "biolink:PhenotypicFeature", "object_closure": [ - "HP:0000001", "UPHENO:0082875", - "UPHENO:0075696", "UPHENO:0002320", + "BFO:0000002", + "BFO:0000004", + "UBERON:0000061", + "HP:0000001", "UPHENO:0001001", - "UPHENO:0001005", - "HP:0003701", "UPHENO:0001002", - "HP:0001324", "HP:0000118", - "BFO:0000002", "BFO:0000020", - "UPHENO:0080555", - "HP:0003011", - "UPHENO:0002816", - "UPHENO:0002332", - "UPHENO:0080556", - "HP:0033127", "UPHENO:0001003", - "UPHENO:0002536", "BFO:0000001", - "HP:0011804", "PATO:0000001", "BFO:0000001", - "BFO:0000002", - "BFO:0000004", "BFO:0000040", "UBERON:0001062", - "UBERON:0000465", - "UBERON:0000061", - "UBERON:0010000", "UBERON:0000467", - "UBERON:0005090", - "UBERON:0000062", "UBERON:0000468", "UBERON:0011216", + "UPHENO:0075696", + "HP:0001324", + "HP:0003011", + "UPHENO:0002332", + "UPHENO:0002536", + "HP:0011804", + "BFO:0000002", + "UBERON:0000465", + "UBERON:0005090", "UBERON:0001630", + "UPHENO:0001005", + "HP:0003701", + "UPHENO:0080555", + "UPHENO:0002816", + "UPHENO:0080556", + "HP:0033127", + "UBERON:0010000", + "UBERON:0000062", "UBERON:0000383", "UBERON:0001015" ], "object_label": "Proximal muscle weakness (HPO)", "object_closure_label": [ - "entity", - "entity", - "continuant", - "continuant", - "independent continuant", - "specifically dependent continuant", - "material entity", "All (HPO)", + "abnormality of muscle organ physiology", + "Phenotypic abnormality", "Phenotypic abnormality (HPO)", - "Muscle weakness (HPO)", - "Abnormality of the musculature (HPO)", - "Proximal muscle weakness (HPO)", - "Abnormal muscle physiology (HPO)", + "decreased anatomical entity strength", + "abnormal musculature", + "decreased muscle organ strength", "Abnormality of the musculoskeletal system (HPO)", "quality", + "independent continuant", "anatomical structure", - "organ", - "musculature of body", - "material anatomical entity", - "anatomical system", - "multicellular organism", - "musculature", - "anatomical entity", - "muscle organ", - "muscle structure", "multicellular anatomical structure", - "organ system subdivision", + "abnormality of anatomical entity physiology", "phenotype", - "Phenotypic abnormality", - "phenotype by ontology source", "abnormal phenotype by ontology source", - "abnormality of muscle organ physiology", - "abnormality of anatomical entity physiology", + "Proximal muscle weakness (HPO)", + "specifically dependent continuant", + "phenotype by ontology source", + "continuant", + "material anatomical entity", + "continuant", + "Abnormal muscle physiology (HPO)", + "entity", + "muscle structure", + "organ", + "muscle organ", + "musculature of body", + "musculature", "abnormal anatomical entity", - "abnormal musculature", + "Muscle weakness (HPO)", + "Abnormality of the musculature (HPO)", + "abnormality of anatomical entity physiology", "abnormal anatomical entity", - "decreased anatomical entity strength", - "decreased muscle organ strength", - "abnormality of anatomical entity physiology" + "entity", + "material entity", + "anatomical entity", + "anatomical system", + "multicellular organism", + "organ system subdivision" ], "object_taxon": null, "object_taxon_label": null, @@ -1215,7 +1243,7 @@ "aggregator_knowledge_source": ["infores:monarchinitiative"], "negated": null, "pathway": null, - "evidence_count": 5, + "evidence_count": 3, "has_evidence": ["ECO:0000269"], "has_evidence_links": [ { @@ -1223,6 +1251,7 @@ "url": "http://purl.obolibrary.org/obo/ECO_0000269" } ], + "grouping_key": "MONDO:0009676\ud83c\udf6a\ud83c\udf6abiolink:has_phenotype\ud83c\udf6aHP:0003701", "provided_by": "hpoa_disease_to_phenotype_edges", "provided_by_link": { "id": "hpoa_disease_to_phenotype", @@ -1244,14 +1273,19 @@ "onset_qualifier": null, "sex_qualifier": null, "stage_qualifier": null, + "qualifiers_label": null, + "qualifiers_namespace": null, + "qualifiers_category": null, + "qualifiers_closure": [], + "qualifiers_closure_label": [], "frequency_qualifier_label": "Obligate (HPO)", "frequency_qualifier_namespace": "HP", "frequency_qualifier_category": "biolink:PhenotypicFeature", - "frequency_qualifier_closure": ["HP:0000001", "HP:0040279", "HP:0040280"], + "frequency_qualifier_closure": ["HP:0000001", "HP:0040280", "HP:0040279"], "frequency_qualifier_closure_label": [ "All (HPO)", - "Frequency (HPO)", - "Obligate (HPO)" + "Obligate (HPO)", + "Frequency (HPO)" ], "onset_qualifier_label": null, "onset_qualifier_namespace": null, diff --git a/frontend/fixtures/associations.json b/frontend/fixtures/associations.json index dd7998dcc..13258976e 100644 --- a/frontend/fixtures/associations.json +++ b/frontend/fixtures/associations.json @@ -1,195 +1,283 @@ { "limit": 20, "offset": 0, - "total": 4835, + "total": 4838, "items": [ { - "id": "uuid:8a89d08e-5d8c-11ee-9b27-2b20ed86a9d9", + "id": "uuid:c9c8bf2f-7529-11ee-b012-cbd37f5c3759", "category": "biolink:DiseaseToPhenotypicFeatureAssociation", - "subject": "MONDO:0011246", - "original_subject": "OMIM:602541", + "subject": "MONDO:0008050", + "original_subject": "OMIM:160500", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ - "MONDO:0000001", + "BFO:0000002", + "MONDO:0016195", + "MONDO:0005336", + "MONDO:0018949", "MONDO:0005071", + "MONDO:0008050", + "BFO:0000016", + "MONDO:0016139", + "OGMS:0000031", + "MONDO:0003847", + "BFO:0000001", "MONDO:0020121", - "MONDO:0700223", - "BFO:0000002", - "MONDO:0018117", + "MONDO:0019952", "BFO:0000017", "BFO:0000020", - "MONDO:0002525", - "BFO:0000016", "MONDO:0020120", "MONDO:0019056", + "MONDO:0000001", + "MONDO:0700223", "MONDO:0700096", - "MONDO:0005336", "MONDO:0002081", - "OGMS:0000031", - "MONDO:0003847", "MONDO:0003939", - "BFO:0000001", - "MONDO:0002320", - "MONDO:0019052", - "MONDO:0005066", - "MONDO:0019950", - "MONDO:0011246" + "MONDO:0002320" ], - "subject_label": "megaconial type congenital muscular dystrophy", + "subject_label": "MYH7-related skeletal myopathy", "subject_closure_label": [ - "entity", - "continuant", - "disposition", - "realizable entity", - "specifically dependent continuant", - "disease", + "muscular dystrophy", + "human disease", "musculoskeletal system disorder", + "disease", + "muscle tissue disorder", "congenital nervous system disorder", - "inherited lipid metabolism disorder", + "hereditary skeletal muscle disorder", + "MYH7-related skeletal myopathy", + "disposition", + "qualitative or quantitative protein defects in neuromuscular diseases", + "distal myopathy", + "disease", + "continuant", + "qualitative or quantitative defects of beta-myosin heavy chain (MYH7)", + "myopathy", "hereditary disease", - "muscle tissue disorder", - "metabolic disease", "nervous system disorder", - "myopathy", - "megaconial type congenital muscular dystrophy", - "disorder of phospholipids, sphingolipids and fatty acids biosynthesis", - "inborn errors of metabolism", - "neuromuscular disease", - "congenital muscular dystrophy", + "congenital myopathy", + "realizable entity", + "specifically dependent continuant", "skeletal muscle disorder", - "muscular dystrophy", - "human disease", - "hereditary skeletal muscle disorder", - "disease" + "neuromuscular disease", + "entity" ], "subject_taxon": null, "subject_taxon_label": null, "predicate": "biolink:has_phenotype", - "object": "HP:0008064", + "object": "HP:0011399", "original_object": null, "object_namespace": "HP", "object_category": "biolink:PhenotypicFeature", "object_closure": [ - "HP:0000001", - "UPHENO:0047821", - "UPHENO:0075696", - "UPHENO:0001001", - "UPHENO:0081431", - "UPHENO:0003811", - "UPHENO:0065599", - "UPHENO:0048320", + "UPHENO:0014121", + "HP:0002814", + "UPHENO:0068971", "UPHENO:0001005", - "HP:0001072", + "HP:0009127", + "UPHENO:0014120", + "UPHENO:0075195", + "HP:0030236", + "UPHENO:0020584", + "UPHENO:0076692", + "UPHENO:0003070", + "PATO:0000001", + "UPHENO:0012541", + "BFO:0000004", + "UBERON:0004708", + "UBERON:0000154", + "UBERON:0014892", + "UBERON:0006058", + "UBERON:0002529", + "UBERON:0006067", + "HP:0000001", + "UPHENO:0002644", + "UPHENO:0013936", + "HP:0003202", + "UPHENO:0075952", "UPHENO:0001002", "HP:0000118", - "BFO:0000002", - "HP:0011368", - "HP:0011121", - "UPHENO:0076739", - "BFO:0000020", - "HP:0008064", - "UPHENO:0075195", - "UPHENO:0002635", "UPHENO:0015280", - "UPHENO:0001072", - "UPHENO:0081581", "UPHENO:0001003", - "UPHENO:0002536", - "UPHENO:0047979", - "UPHENO:0020584", - "UPHENO:0076692", + "UPHENO:0076710", "BFO:0000001", - "HP:0000951", - "PATO:0000001", - "HP:0001574", "BFO:0000001", - "BFO:0000003", - "BFO:0000002", - "BFO:0000015", - "BFO:0000004", - "GO:0008150", "BFO:0000040", - "UBERON:0001062", - "GO:0009987", - "GO:0032501", - "GO:0032502", - "PR:000050567", - "UBERON:0000465", - "GO:0048869", - "GO:0031424", - "GO:0048856", - "UBERON:0002416", - "UBERON:0002199", - "UBERON:0002097", - "UBERON:0000061", - "GO:0030154", - "GO:0009888", - "GO:0048513", - "UBERON:0004121", "UBERON:0010000", "UBERON:0000467", - "GO:0030855", - "GO:0060429", - "GO:0008544", - "GO:0043588", - "UBERON:0000062", "UBERON:0000468", "UBERON:0011216", - "GO:0009913", - "GO:0030216" + "UBERON:0010709", + "UBERON:0000366", + "UBERON:0003661", + "UBERON:0010890", + "UBERON:0010538", + "UBERON:0004466", + "UBERON:0004256", + "UBERON:0003823", + "UPHENO:0075696", + "HP:0002981", + "HP:0003797", + "UPHENO:0014111", + "HP:0001430", + "BFO:0000002", + "HP:0008944", + "BFO:0000020", + "HP:0003011", + "UPHENO:0002536", + "HP:0001437", + "UPHENO:0078056", + "HP:0040064", + "BFO:0000002", + "PR:000050567", + "UBERON:0002101", + "UBERON:0004709", + "UBERON:0005090", + "UBERON:0018254", + "UBERON:0002103", + "UBERON:0010707", + "UBERON:0001630", + "UBERON:0000026", + "UBERON:0010758", + "UBERON:0007271", + "UBERON:0014792", + "UBERON:0004482", + "UBERON:0001383", + "UBERON:0008784", + "UBERON:0002471", + "HP:0007210", + "UPHENO:0001001", + "UPHENO:0075777", + "HP:0011805", + "HP:0003693", + "UPHENO:0002816", + "HP:0011399", + "UPHENO:0081581", + "HP:0033127", + "UPHENO:0019778", + "UPHENO:0002647", + "UPHENO:0013920", + "UPHENO:0002830", + "UBERON:0001062", + "UBERON:0000465", + "RO:0002577", + "UBERON:0000061", + "UBERON:0015212", + "UBERON:0000475", + "UBERON:0000062", + "UBERON:0000383", + "UBERON:0001015", + "UBERON:0000978", + "UBERON:0007270", + "UBERON:0004480", + "UBERON:0003663", + "UBERON:0014795", + "UBERON:0008230" ], - "object_label": "Ichthyosis (HPO)", + "object_label": "Tibialis atrophy (HPO)", "object_closure_label": [ - "entity", - "entity", - "continuant", - "continuant", - "independent continuant", - "specifically dependent continuant", - "material entity", "All (HPO)", + "abnormal musculature of lower limb", + "Abnormality of the lower limb (HPO)", + "decreased size of the anatomical entity", + "Phenotypic abnormality", "Phenotypic abnormality (HPO)", - "Abnormality of the skin (HPO)", - "Thickened skin (HPO)", - "Abnormality of the integument (HPO)", - "Ichthyosis (HPO)", - "Abnormality of skin morphology (HPO)", - "Epidermal thickening (HPO)", + "Distal amyotrophy (HPO)", + "abnormal musculature", + "Tibialis atrophy (HPO)", + "abnormal multicellular organism morphology", + "Abnormality of the musculoskeletal system (HPO)", + "abnormal musculature of limb", + "independent continuant", + "material anatomical entity", + "system", + "paired limb/fin", + "lateral structure", + "pelvic complex", + "appendage musculature", + "musculature of pelvic complex", + "musculature of leg", + "hindlimb zeugopod muscle", + "hindlimb zeugopod", + "musculature of limb atrophy", + "Limb-girdle muscle atrophy (HPO)", + "skeletal musculature atrophy", + "abnormal hindlimb zeugopod muscle", + "Abnormal skeletal muscle morphology (HPO)", + "abnormal anatomical entity morphology in the independent continuant", + "phenotype by ontology source", + "Abnormality of muscle size (HPO)", + "Abnormality of the musculature of the lower limbs (HPO)", + "tibialis atrophy", + "Abnormality of limbs (HPO)", "quality", + "decreased size of the anatomical entity in the independent continuant", + "continuant", "protein-containing material entity", - "anatomical structure", - "organ", - "material anatomical entity", - "anatomical system", - "multicellular organism", - "anatomical entity", - "skin of body", - "integument", - "integumental system", - "ectoderm-derived structure", - "multicellular anatomical structure", - "organ system subdivision", + "hindlimb", + "appendage girdle complex", + "appendage", + "subdivision of organism along appendicular axis", + "flexor muscle", + "limb muscle", + "pelvic complex muscle", + "paired limb/fin segment", + "musculature of lower limb", + "muscle of leg", + "lower limb segment", + "zeugopod", + "Lower limb amyotrophy (HPO)", "phenotype", - "Phenotypic abnormality", - "phenotype by ontology source", "abnormal phenotype by ontology source", - "increased size of the anatomical entity", - "abnormal anatomical entity", - "abnormal integument", - "abnormal skin of body", - "abnormal anatomical entity morphology in the independent continuant", - "abnormal anatomical entity morphology", - "increased thickness of the anatomical entity", - "increased thickness of the skin of body", - "increased thickness of the anatomical entity in independent continuant", - "increased size of the anatomical entity in independent continuant", + "Abnormality of the musculature of the limbs (HPO)", + "musculature of lower limb atrophy", "abnormal size of anatomical entity", + "abnormal muscle organ morphology", + "abnormal muscle organ morphology", + "entity", + "anatomical entity", + "anatomical structure", + "muscle structure", + "skeletal musculature", + "organism subdivision", + "organ", + "muscle organ", + "musculature of body", + "musculature", + "leg", + "pelvic appendage musculature", + "musculature of limb", + "hindlimb muscle", + "pelvic appendage muscle", + "tibialis", + "abnormal anatomical entity", + "Abnormality of the calf (HPO)", + "anatomical entity atrophy", + "Skeletal muscle atrophy (HPO)", + "abnormal hindlimb zeugopod", + "Abnormality of the calf musculature (HPO)", + "continuant", + "Distal lower limb amyotrophy (HPO)", + "specifically dependent continuant", + "Abnormality of the musculature (HPO)", "abnormal anatomical entity", "abnormal anatomical entity morphology", - "abnormal skin of body morphology", - "abnormal skin of body morphology in the independent continuant", - "abnormal multicellular organism morphology" + "abnormal anatomical entity morphology", + "abnormal leg", + "entity", + "muscle organ atrophy", + "abnormal limb", + "material entity", + "limb", + "pelvic appendage", + "multicellular anatomical structure", + "anatomical system", + "multicellular organism", + "organ system subdivision", + "posterior region of body", + "skeletal muscle organ", + "multi-limb segment region", + "limb segment", + "musculature of hindlimb zeugopod" ], "object_taxon": null, "object_taxon_label": null, @@ -197,36 +285,46 @@ "aggregator_knowledge_source": ["infores:monarchinitiative"], "negated": null, "pathway": null, - "evidence_count": 4, - "has_evidence": ["ECO:0000304"], + "evidence_count": 2, + "has_evidence": ["ECO:0000269"], "has_evidence_links": [ { - "id": "ECO:0000304", - "url": "http://purl.obolibrary.org/obo/ECO_0000304" + "id": "ECO:0000269", + "url": "http://purl.obolibrary.org/obo/ECO_0000269" } ], + "grouping_key": "MONDO:0008050\ud83c\udf6a\ud83c\udf6abiolink:has_phenotype\ud83c\udf6aHP:0011399", "provided_by": "hpoa_disease_to_phenotype_edges", "provided_by_link": { "id": "hpoa_disease_to_phenotype", "url": "https://monarch-initiative.github.io/monarch-ingest/Sources/hpoa/#disease_to_phenotype" }, - "publications": ["OMIM:602541"], + "publications": ["PMID:17548557"], "publications_links": [ { - "id": "OMIM:602541", - "url": "http://identifiers.org/mim/602541" + "id": "PMID:17548557", + "url": "http://identifiers.org/pubmed/17548557" } ], "qualifiers": [], - "frequency_qualifier": null, + "frequency_qualifier": "HP:0040280", "onset_qualifier": null, "sex_qualifier": null, "stage_qualifier": null, - "frequency_qualifier_label": null, - "frequency_qualifier_namespace": null, - "frequency_qualifier_category": null, - "frequency_qualifier_closure": [], - "frequency_qualifier_closure_label": [], + "qualifiers_label": null, + "qualifiers_namespace": null, + "qualifiers_category": null, + "qualifiers_closure": [], + "qualifiers_closure_label": [], + "frequency_qualifier_label": "Obligate (HPO)", + "frequency_qualifier_namespace": "HP", + "frequency_qualifier_category": "biolink:PhenotypicFeature", + "frequency_qualifier_closure": ["HP:0000001", "HP:0040280", "HP:0040279"], + "frequency_qualifier_closure_label": [ + "All (HPO)", + "Obligate (HPO)", + "Frequency (HPO)" + ], "onset_qualifier_label": null, "onset_qualifier_namespace": null, "onset_qualifier_category": null, @@ -244,216 +342,220 @@ "stage_qualifier_closure_label": [] }, { - "id": "uuid:898aa71d-5d8c-11ee-9b27-2b20ed86a9d9", + "id": "uuid:c9c8bf30-7529-11ee-b012-cbd37f5c3759", "category": "biolink:DiseaseToPhenotypicFeatureAssociation", - "subject": "MONDO:0012193", - "original_subject": "OMIM:609115", + "subject": "MONDO:0008050", + "original_subject": "OMIM:160500", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ - "MONDO:0000001", - "MONDO:0016971", - "MONDO:0000429", + "BFO:0000002", + "MONDO:0016195", + "MONDO:0005336", + "MONDO:0018949", "MONDO:0005071", + "MONDO:0008050", + "BFO:0000016", + "MONDO:0016139", + "OGMS:0000031", + "MONDO:0003847", + "BFO:0000001", "MONDO:0020121", - "MONDO:0700223", - "BFO:0000002", + "MONDO:0019952", "BFO:0000017", "BFO:0000020", - "MONDO:0016106", - "BFO:0000016", "MONDO:0020120", "MONDO:0019056", - "MONDO:0015151", + "MONDO:0000001", + "MONDO:0700223", "MONDO:0700096", - "MONDO:0005336", "MONDO:0002081", - "MONDO:0012193", - "MONDO:0000426", - "OGMS:0000031", - "MONDO:0003847", "MONDO:0003939", - "BFO:0000001" + "MONDO:0002320" ], - "subject_label": "autosomal dominant limb-girdle muscular dystrophy type 1G", + "subject_label": "MYH7-related skeletal myopathy", "subject_closure_label": [ - "entity", - "continuant", + "muscular dystrophy", + "human disease", + "musculoskeletal system disorder", + "disease", + "muscle tissue disorder", + "congenital nervous system disorder", + "hereditary skeletal muscle disorder", + "MYH7-related skeletal myopathy", "disposition", - "realizable entity", - "specifically dependent continuant", + "qualitative or quantitative protein defects in neuromuscular diseases", + "distal myopathy", "disease", - "autosomal dominant disease", - "autosomal genetic disease", - "musculoskeletal system disorder", + "continuant", + "qualitative or quantitative defects of beta-myosin heavy chain (MYH7)", + "myopathy", "hereditary disease", - "muscle tissue disorder", "nervous system disorder", - "myopathy", - "autosomal dominant limb-girdle muscular dystrophy type 1G", - "muscular dystrophy, limb-girdle, autosomal dominant", - "progressive muscular dystrophy", - "limb-girdle muscular dystrophy", - "neuromuscular disease", + "congenital myopathy", + "realizable entity", + "specifically dependent continuant", "skeletal muscle disorder", - "muscular dystrophy", - "human disease", - "hereditary skeletal muscle disorder", - "disease" + "neuromuscular disease", + "entity" ], "subject_taxon": null, "subject_taxon_label": null, "predicate": "biolink:has_phenotype", - "object": "HP:0008116", + "object": "HP:0031295", "original_object": null, "object_namespace": "HP", "object_category": "biolink:PhenotypicFeature", "object_closure": [ - "HP:0000001", - "UPHENO:0002644", - "HP:0008116", - "HP:0002814", - "UPHENO:0001001", - "HP:0001436", "UPHENO:0001005", - "HP:0009127", - "HP:0011805", - "UPHENO:0001002", - "HP:0000118", "BFO:0000002", - "UPHENO:0002653", + "UPHENO:0075195", + "UPHENO:0020584", + "UPHENO:0076692", + "BFO:0000004", + "UBERON:0004535", + "UBERON:0011676", + "UBERON:0013701", + "UBERON:0002081", + "UBERON:0000915", + "UBERON:0002100", + "UBERON:0005181", + "UBERON:0002075", + "UBERON:0015228", + "HP:0000001", + "UPHENO:0019897", + "HP:0030680", + "HP:0000118", + "HP:0001627", "BFO:0000020", - "HP:0003011", - "UPHENO:0002816", - "UPHENO:0081581", - "HP:0033127", + "UPHENO:0019919", + "UPHENO:0076776", + "UPHENO:0015280", + "UPHENO:0001020", "UPHENO:0001003", - "UPHENO:0002536", - "HP:0001437", - "UPHENO:0076692", - "UPHENO:0003070", - "UPHENO:0002647", - "UPHENO:0076710", - "HP:0040064", "BFO:0000001", "PATO:0000001", - "UPHENO:0002830", "BFO:0000001", - "BFO:0000002", - "BFO:0000004", "BFO:0000040", - "UBERON:0001062", + "UBERON:0000467", + "UBERON:0000468", + "UBERON:0000064", + "UBERON:0002079", + "UPHENO:0075696", + "UPHENO:0015303", + "HP:0001626", + "UPHENO:0080362", + "UPHENO:0065599", + "HP:0031295", + "UPHENO:0002536", + "UPHENO:0076810", "PR:000050567", "UBERON:0000465", + "UBERON:0004120", + "UBERON:0035553", + "UBERON:0000948", + "UBERON:0001009", + "UBERON:0004151", + "UBERON:0009569", + "UBERON:0013702", + "UBERON:0005177", + "UBERON:0003103", + "UBERON:0015410", + "UPHENO:0001001", + "UPHENO:0001002", + "UPHENO:0015324", + "HP:0025579", + "UPHENO:0001072", + "UPHENO:0081581", + "HP:0005120", + "UPHENO:0015329", + "BFO:0000002", + "UBERON:0001062", "RO:0002577", - "UBERON:0004708", "UBERON:0000061", - "UBERON:0002101", - "UBERON:0004709", "UBERON:0015212", + "UBERON:0010314", "UBERON:0010000", - "UBERON:0000467", - "UBERON:0005090", - "UBERON:0002103", - "UBERON:0010707", "UBERON:0000475", "UBERON:0000062", - "UBERON:0000468", - "UBERON:0011216", - "UBERON:0001630", - "UBERON:0010709", - "UBERON:0000154", - "UBERON:0000026", - "UBERON:0010758", - "UBERON:0000383", - "UBERON:0001015", - "UBERON:0006058", - "UBERON:0007271", - "UBERON:0014792", - "UBERON:0010538", - "UBERON:0000978", - "UBERON:0007270", - "UBERON:0004480", - "UBERON:0002529", - "UBERON:0004482", - "UBERON:0008784", - "UBERON:0002470", - "UBERON:0004488", - "UBERON:0002387" + "UBERON:0005178", + "UBERON:0007100" ], - "object_label": "Flexion limitation of toes (HPO)", + "object_label": "Left atrial enlargement (HPO)", "object_closure_label": [ - "entity", - "entity", - "continuant", - "continuant", - "independent continuant", - "specifically dependent continuant", - "material entity", "All (HPO)", + "abnormal cardiac atrium morphology", + "abnormal cardiovascular system", + "increased size of the anatomical entity in independent continuant", "Phenotypic abnormality (HPO)", - "Abnormality of the foot musculature (HPO)", - "Abnormality of the musculature of the lower limbs (HPO)", - "Abnormality of the lower limb (HPO)", - "Abnormality of the musculature (HPO)", - "Flexion limitation of toes (HPO)", - "Abnormality of the musculature of the limbs (HPO)", - "Abnormal skeletal muscle morphology (HPO)", - "Abnormality of the musculoskeletal system (HPO)", - "Abnormality of limbs (HPO)", + "abnormal anatomical entity morphology in the heart", + "Abnormal left atrium morphology (HPO)", + "increased size of the anatomical entity", + "abnormal multicellular organism morphology", + "Abnormal cardiac atrium morphology (HPO)", "quality", - "protein-containing material entity", + "independent continuant", "system", - "appendage", - "anatomical structure", - "organ", - "posterior region of body", - "musculature of body", - "material anatomical entity", - "anatomical system", - "multicellular organism", - "organism subdivision", - "leg", - "musculature", - "anatomical entity", - "muscle organ", - "limb", - "hindlimb", - "pes", - "autopod region", - "limb segment", - "musculature of limb", - "musculature of lower limb", - "musculature of pes", - "paired limb/fin", - "pelvic appendage", - "muscle structure", - "multi-limb segment region", - "pelvic appendage musculature", - "appendage musculature", - "lower limb segment", - "multicellular anatomical structure", - "paired limb/fin segment", - "appendage girdle complex", - "pelvic complex", - "subdivision of organism along appendicular axis", - "organ system subdivision", - "musculature of pelvic complex", + "cardiovascular system", "lateral structure", - "phenotype", + "structure with developmental contribution from neural crest", + "multicellular anatomical structure", + "left cardiac atrium", + "Abnormality of the cardiovascular system (HPO)", "Phenotypic abnormality", + "Abnormal heart morphology (HPO)", + "specifically dependent continuant", + "abnormal left cardiac atrium morphology", + "abnormal cardiovascular system morphology", + "abnormal anatomical entity morphology in the independent continuant", + "increased size of the left cardiac atrium", "phenotype by ontology source", + "abnormal heart morphology", + "protein-containing material entity", + "material anatomical entity", + "left cardiac chamber", + "heart", + "subdivision of trunk", + "body proper", + "trunk region element", + "compound organ", + "heart plus pericardium", + "phenotype", "abnormal phenotype by ontology source", + "continuant", + "abnormal size of anatomical entity", + "entity", + "anatomical entity", + "anatomical structure", + "mesoderm-derived structure", + "organism subdivision", + "organ", + "circulatory system", + "cardiac chamber", + "thoracic cavity element", + "primary circulatory organ", + "abnormal anatomical entity", + "abnormal cardiac atrium morphology in the heart", + "Abnormality of cardiovascular system morphology (HPO)", + "Left atrial enlargement (HPO)", "abnormal anatomical entity", - "abnormal musculature of lower limb", - "abnormal musculature of limb", - "abnormal musculature of pes", - "abnormal musculature", - "abnormal limb", - "abnormal leg", "abnormal anatomical entity morphology", - "abnormal muscle organ morphology", - "abnormal multicellular organism morphology" + "abnormal anatomical entity morphology", + "entity", + "abnormal cardiac atrium morphology in the independent continuant", + "continuant", + "material entity", + "anatomical system", + "multicellular organism", + "organ part", + "subdivision of organism along main body axis", + "main body axis", + "cardiac atrium", + "thoracic segment of trunk", + "trunk", + "thoracic segment organ", + "viscus", + "circulatory organ" ], "object_taxon": null, "object_taxon_label": null, @@ -461,36 +563,46 @@ "aggregator_knowledge_source": ["infores:monarchinitiative"], "negated": null, "pathway": null, - "evidence_count": 4, - "has_evidence": ["ECO:0000501"], + "evidence_count": 2, + "has_evidence": ["ECO:0000269"], "has_evidence_links": [ { - "id": "ECO:0000501", - "url": "http://purl.obolibrary.org/obo/ECO_0000501" + "id": "ECO:0000269", + "url": "http://purl.obolibrary.org/obo/ECO_0000269" } ], + "grouping_key": "MONDO:0008050\ud83c\udf6a\ud83c\udf6abiolink:has_phenotype\ud83c\udf6aHP:0031295", "provided_by": "hpoa_disease_to_phenotype_edges", "provided_by_link": { "id": "hpoa_disease_to_phenotype", "url": "https://monarch-initiative.github.io/monarch-ingest/Sources/hpoa/#disease_to_phenotype" }, - "publications": ["OMIM:609115"], + "publications": ["PMID:17548557"], "publications_links": [ { - "id": "OMIM:609115", - "url": "http://identifiers.org/mim/609115" + "id": "PMID:17548557", + "url": "http://identifiers.org/pubmed/17548557" } ], "qualifiers": [], - "frequency_qualifier": null, + "frequency_qualifier": "HP:0040280", "onset_qualifier": null, "sex_qualifier": null, "stage_qualifier": null, - "frequency_qualifier_label": null, - "frequency_qualifier_namespace": null, - "frequency_qualifier_category": null, - "frequency_qualifier_closure": [], - "frequency_qualifier_closure_label": [], + "qualifiers_label": null, + "qualifiers_namespace": null, + "qualifiers_category": null, + "qualifiers_closure": [], + "qualifiers_closure_label": [], + "frequency_qualifier_label": "Obligate (HPO)", + "frequency_qualifier_namespace": "HP", + "frequency_qualifier_category": "biolink:PhenotypicFeature", + "frequency_qualifier_closure": ["HP:0000001", "HP:0040280", "HP:0040279"], + "frequency_qualifier_closure_label": [ + "All (HPO)", + "Obligate (HPO)", + "Frequency (HPO)" + ], "onset_qualifier_label": null, "onset_qualifier_namespace": null, "onset_qualifier_category": null, @@ -508,134 +620,196 @@ "stage_qualifier_closure_label": [] }, { - "id": "uuid:87cb3e81-5d8c-11ee-9b27-2b20ed86a9d9", + "id": "uuid:c9c8bf31-7529-11ee-b012-cbd37f5c3759", "category": "biolink:DiseaseToPhenotypicFeatureAssociation", - "subject": "MONDO:0012286", - "original_subject": "OMIM:609500", + "subject": "MONDO:0008050", + "original_subject": "OMIM:160500", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ - "MONDO:0000001", - "MONDO:0016112", - "MONDO:0010684", + "BFO:0000002", + "MONDO:0016195", + "MONDO:0005336", + "MONDO:0018949", "MONDO:0005071", + "MONDO:0008050", + "BFO:0000016", + "MONDO:0016139", + "OGMS:0000031", + "MONDO:0003847", + "BFO:0000001", "MONDO:0020121", - "MONDO:0700223", - "BFO:0000002", - "MONDO:0012286", + "MONDO:0019952", "BFO:0000017", "BFO:0000020", - "MONDO:0016106", - "BFO:0000016", "MONDO:0020120", "MONDO:0019056", + "MONDO:0000001", + "MONDO:0700223", "MONDO:0700096", - "MONDO:0005336", "MONDO:0002081", - "OGMS:0000031", - "MONDO:0003847", "MONDO:0003939", - "BFO:0000001" + "MONDO:0002320" ], - "subject_label": "myopathy, autophagic vacuolar, infantile-onset", + "subject_label": "MYH7-related skeletal myopathy", "subject_closure_label": [ - "entity", - "continuant", + "muscular dystrophy", + "human disease", + "musculoskeletal system disorder", + "disease", + "muscle tissue disorder", + "congenital nervous system disorder", + "hereditary skeletal muscle disorder", + "MYH7-related skeletal myopathy", "disposition", - "realizable entity", - "specifically dependent continuant", + "qualitative or quantitative protein defects in neuromuscular diseases", + "distal myopathy", "disease", - "musculoskeletal system disorder", + "continuant", + "qualitative or quantitative defects of beta-myosin heavy chain (MYH7)", + "myopathy", "hereditary disease", - "muscle tissue disorder", "nervous system disorder", - "myopathy", - "X-linked myopathy with excessive autophagy", - "myopathy, autophagic vacuolar, infantile-onset", - "progressive muscular dystrophy", - "hereditary inclusion-body myopathy", - "neuromuscular disease", + "congenital myopathy", + "realizable entity", + "specifically dependent continuant", "skeletal muscle disorder", - "muscular dystrophy", - "human disease", - "hereditary skeletal muscle disorder", - "disease" + "neuromuscular disease", + "entity" ], "subject_taxon": null, "subject_taxon_label": null, "predicate": "biolink:has_phenotype", - "object": "HP:0001263", + "object": "HP:0002938", "original_object": null, "object_namespace": "HP", "object_category": "biolink:PhenotypicFeature", "object_closure": [ - "HP:0000001", - "UPHENO:0082875", - "UPHENO:0075696", - "UPHENO:0001001", "UPHENO:0001005", - "UPHENO:0001002", + "HP:0009121", + "UPHENO:0020584", + "UPHENO:0076692", + "BFO:0000001", + "PATO:0000001", + "BFO:0000004", + "UBERON:0002204", + "UBERON:0011676", + "UBERON:0001137", + "UBERON:0013701", + "UBERON:0002100", + "UBERON:0005462", + "HP:0000001", + "UPHENO:0076703", "HP:0000118", - "BFO:0000002", - "HP:0012759", "BFO:0000020", - "UPHENO:0002433", - "HP:0001263", - "UPHENO:0002332", - "HP:0000707", + "HP:0000925", + "UPHENO:0015280", + "UPHENO:0002964", "UPHENO:0001003", - "UPHENO:0002536", - "HP:0012758", - "UPHENO:0004523", - "BFO:0000001", - "PATO:0000001", - "HP:0012638", + "HP:0003307", + "UPHENO:0022529", "BFO:0000001", - "BFO:0000002", - "BFO:0000004", "BFO:0000040", + "UBERON:0000467", + "UBERON:0000468", + "UBERON:0011216", + "UPHENO:0075696", + "HP:0000924", + "UPHENO:0002536", + "BFO:0000002", + "UBERON:0004288", + "UBERON:0009569", + "UBERON:0013702", + "UBERON:0000075", + "UBERON:0002417", + "UBERON:0011137", + "UBERON:0006077", + "UBERON:0011138", + "UBERON:0002090", + "UBERON:0005944", + "UBERON:0001130", + "UPHENO:0001001", + "HP:0011842", + "UPHENO:0001002", + "BFO:0000002", + "HP:0010674", + "UPHENO:0081581", + "HP:0033127", + "UPHENO:0002813", + "HP:0002938", "UBERON:0001062", "UBERON:0000465", "UBERON:0000061", + "UBERON:0034925", "UBERON:0010000", - "UBERON:0000467", - "UBERON:0000468", - "UBERON:0001016" + "UBERON:0000475", + "UBERON:0010912", + "UBERON:0001434", + "UBERON:0006074" ], - "object_label": "Global developmental delay (HPO)", + "object_label": "Lumbar hyperlordosis (HPO)", "object_closure_label": [ - "entity", - "entity", - "continuant", - "continuant", - "independent continuant", - "specifically dependent continuant", - "material entity", "All (HPO)", "Phenotypic abnormality (HPO)", - "Abnormality of the nervous system (HPO)", - "Global developmental delay (HPO)", - "Abnormal nervous system physiology (HPO)", - "Neurodevelopmental delay (HPO)", - "Neurodevelopmental abnormality (HPO)", - "quality", - "anatomical structure", + "Abnormality of the curvature of the vertebral column (HPO)", + "abnormal multicellular organism morphology", + "Abnormality of the musculoskeletal system (HPO)", + "Hyperlordosis (HPO)", + "abnormal postcranial axial skeleton morphology", + "independent continuant", "material anatomical entity", - "anatomical system", - "multicellular organism", - "nervous system", - "anatomical entity", "multicellular anatomical structure", - "phenotype", + "musculoskeletal system", + "abdominal segment of trunk", + "axial skeletal system", + "subdivision of vertebral column", + "postcranial axial skeletal system", + "postcranial axial skeleton", + "axial skeleton plus cranial skeleton", + "vertebral column", + "Abnormal skeletal morphology (HPO)", "Phenotypic abnormality", + "continuant", + "specifically dependent continuant", + "Abnormality of the vertebral column (HPO)", + "abnormal anatomical entity morphology in the independent continuant", + "abnormal skeletal system", "phenotype by ontology source", + "quality", + "continuant", + "subdivision of trunk", + "body proper", + "subdivision of skeletal system", + "phenotype", "abnormal phenotype by ontology source", - "abnormality of anatomical entity physiology", - "abnormality of nervous system physiology", + "Abnormal axial skeleton morphology (HPO)", + "abnormal vertebral column", + "Lumbar hyperlordosis (HPO)", + "entity", + "anatomical entity", + "anatomical structure", + "anatomical collection", + "skeleton", + "organism subdivision", + "subdivision of skeleton", + "skeletal system", + "lumbar region of vertebral column", "abnormal anatomical entity", - "abnormal nervous system", + "abnormal skeletal system morphology", + "Abnormality of the skeletal system (HPO)", "abnormal anatomical entity", - "abnormality of anatomical entity physiology" + "abnormal anatomical entity morphology", + "abnormal anatomical entity morphology", + "entity", + "material entity", + "anatomical system", + "multicellular organism", + "organ system subdivision", + "subdivision of organism along main body axis", + "dorsum", + "main body axis", + "trunk", + "lower back" ], "object_taxon": null, "object_taxon_label": null, @@ -643,36 +817,46 @@ "aggregator_knowledge_source": ["infores:monarchinitiative"], "negated": null, "pathway": null, - "evidence_count": 4, - "has_evidence": ["ECO:0000304"], + "evidence_count": 2, + "has_evidence": ["ECO:0000269"], "has_evidence_links": [ { - "id": "ECO:0000304", - "url": "http://purl.obolibrary.org/obo/ECO_0000304" + "id": "ECO:0000269", + "url": "http://purl.obolibrary.org/obo/ECO_0000269" } ], + "grouping_key": "MONDO:0008050\ud83c\udf6a\ud83c\udf6abiolink:has_phenotype\ud83c\udf6aHP:0002938", "provided_by": "hpoa_disease_to_phenotype_edges", "provided_by_link": { "id": "hpoa_disease_to_phenotype", "url": "https://monarch-initiative.github.io/monarch-ingest/Sources/hpoa/#disease_to_phenotype" }, - "publications": ["OMIM:609500"], + "publications": ["PMID:17548557"], "publications_links": [ { - "id": "OMIM:609500", - "url": "http://identifiers.org/mim/609500" + "id": "PMID:17548557", + "url": "http://identifiers.org/pubmed/17548557" } ], "qualifiers": [], - "frequency_qualifier": null, + "frequency_qualifier": "HP:0040280", "onset_qualifier": null, "sex_qualifier": null, "stage_qualifier": null, - "frequency_qualifier_label": null, - "frequency_qualifier_namespace": null, - "frequency_qualifier_category": null, - "frequency_qualifier_closure": [], - "frequency_qualifier_closure_label": [], + "qualifiers_label": null, + "qualifiers_namespace": null, + "qualifiers_category": null, + "qualifiers_closure": [], + "qualifiers_closure_label": [], + "frequency_qualifier_label": "Obligate (HPO)", + "frequency_qualifier_namespace": "HP", + "frequency_qualifier_category": "biolink:PhenotypicFeature", + "frequency_qualifier_closure": ["HP:0000001", "HP:0040280", "HP:0040279"], + "frequency_qualifier_closure_label": [ + "All (HPO)", + "Obligate (HPO)", + "Frequency (HPO)" + ], "onset_qualifier_label": null, "onset_qualifier_namespace": null, "onset_qualifier_category": null, @@ -690,156 +874,214 @@ "stage_qualifier_closure_label": [] }, { - "id": "uuid:85cb9d22-5d8c-11ee-9b27-2b20ed86a9d9", + "id": "uuid:c9c8bf38-7529-11ee-b012-cbd37f5c3759", "category": "biolink:DiseaseToPhenotypicFeatureAssociation", - "subject": "MONDO:0013159", - "original_subject": "OMIM:613155", + "subject": "MONDO:0008050", + "original_subject": "OMIM:160500", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ - "MONDO:0018282", - "MONDO:0000001", - "MONDO:0017741", - "MONDO:0018276", - "MONDO:0045010", + "BFO:0000002", + "MONDO:0016195", + "MONDO:0005336", + "MONDO:0018949", "MONDO:0005071", + "MONDO:0008050", + "BFO:0000016", + "MONDO:0016139", + "OGMS:0000031", + "MONDO:0003847", + "BFO:0000001", "MONDO:0020121", - "MONDO:0000172", - "MONDO:0700223", - "MONDO:0013159", - "MONDO:0024322", - "BFO:0000002", + "MONDO:0019952", "BFO:0000017", "BFO:0000020", - "BFO:0000016", "MONDO:0020120", "MONDO:0019056", - "MONDO:0016139", + "MONDO:0000001", + "MONDO:0700223", "MONDO:0700096", - "MONDO:0005336", "MONDO:0002081", - "OGMS:0000031", - "MONDO:0003847", - "MONDO:0700070", "MONDO:0003939", - "MONDO:0015286", - "BFO:0000001", - "MONDO:0002320", - "MONDO:0019052", - "MONDO:0005066", - "MONDO:0019950", - "MONDO:0016155" + "MONDO:0002320" ], - "subject_label": "muscular dystrophy-dystroglycanopathy (congenital with intellectual disability), type B1", + "subject_label": "MYH7-related skeletal myopathy", "subject_closure_label": [ - "entity", - "continuant", - "disposition", - "realizable entity", - "specifically dependent continuant", - "disease", - "muscular dystrophy-dystroglycanopathy, type B", + "muscular dystrophy", + "human disease", "musculoskeletal system disorder", + "disease", + "muscle tissue disorder", "congenital nervous system disorder", + "hereditary skeletal muscle disorder", + "MYH7-related skeletal myopathy", + "disposition", + "qualitative or quantitative protein defects in neuromuscular diseases", + "distal myopathy", + "disease", + "continuant", + "qualitative or quantitative defects of beta-myosin heavy chain (MYH7)", + "myopathy", "hereditary disease", - "muscle tissue disorder", - "metabolic disease", "nervous system disorder", - "myopathy", - "muscular dystrophy-dystroglycanopathy (congenital with intellectual disability), type B1", - "congenital disorder of glycosylation", - "qualitative or quantitative protein defects in neuromuscular diseases", - "qualitative or quantitative defects of protein involved in O-glycosylation of alpha-dystroglycan", - "disorder of protein O-glycosylation", - "muscular dystrophy-dystroglycanopathy", - "qualitative or quantitative defects of alpha-dystroglycan", - "inborn errors of metabolism", - "neuromuscular disease", - "congenital muscular dystrophy", + "congenital myopathy", + "realizable entity", + "specifically dependent continuant", "skeletal muscle disorder", - "muscular dystrophy", - "disorder of glycosylation", - "glycoprotein metabolism disease", - "myopathy caused by variation in POMT1", - "human disease", - "hereditary skeletal muscle disorder", - "disease" + "neuromuscular disease", + "entity" ], "subject_taxon": null, "subject_taxon_label": null, "predicate": "biolink:has_phenotype", - "object": "HP:0001263", + "object": "HP:0001265", "original_object": null, "object_namespace": "HP", "object_category": "biolink:PhenotypicFeature", "object_closure": [ - "HP:0000001", "UPHENO:0082875", - "UPHENO:0075696", - "UPHENO:0001001", + "UPHENO:0049622", "UPHENO:0001005", + "BFO:0000020", + "UPHENO:0050606", + "HP:0012638", + "BFO:0000015", + "BFO:0000004", + "GO:0050882", + "NBO:0000338", + "GO:0050905", + "UBERON:0001016", + "HP:0000001", + "UPHENO:0001001", + "UPHENO:0080585", + "HP:0001265", + "HP:0031826", "UPHENO:0001002", "HP:0000118", - "BFO:0000002", - "HP:0012759", - "BFO:0000020", + "UPHENO:0052178", "UPHENO:0002433", - "HP:0001263", - "UPHENO:0002332", - "HP:0000707", + "HP:0001315", "UPHENO:0001003", - "UPHENO:0002536", - "HP:0012758", - "UPHENO:0004523", - "BFO:0000001", + "HP:0000708", + "HP:0011446", "PATO:0000001", - "HP:0012638", "BFO:0000001", - "BFO:0000002", - "BFO:0000004", "BFO:0000040", "UBERON:0001062", - "UBERON:0000465", - "UBERON:0000061", - "UBERON:0010000", + "GO:0050896", + "GO:0032501", + "GO:0060004", + "GO:0050881", + "NBO:0000313", + "GO:0050877", "UBERON:0000467", "UBERON:0000468", - "UBERON:0001016" + "NBO:0000403", + "NBO:0000001", + "NBO:0000388", + "UPHENO:0075696", + "UPHENO:0078622", + "UPHENO:0049586", + "UPHENO:0080377", + "HP:0100022", + "UPHENO:0050613", + "UPHENO:0005433", + "UPHENO:0002332", + "UPHENO:0002536", + "UPHENO:0079826", + "UPHENO:0004523", + "UPHENO:0049587", + "BFO:0000003", + "BFO:0000002", + "GO:0008150", + "GO:0009605", + "GO:0050879", + "GO:0007610", + "GO:0003008", + "NBO:0000389", + "UPHENO:0052915", + "BFO:0000002", + "UPHENO:0005625", + "UPHENO:0050079", + "HP:0000707", + "UPHENO:0079833", + "BFO:0000001", + "UBERON:0000465", + "UBERON:0000061", + "UBERON:0010000" ], - "object_label": "Global developmental delay (HPO)", + "object_label": "Hyporeflexia (HPO)", "object_closure_label": [ - "entity", - "entity", - "continuant", - "continuant", - "independent continuant", - "specifically dependent continuant", - "material entity", "All (HPO)", + "abnormal behavior", + "Abnormality of movement (HPO)", + "Phenotypic abnormality", "Phenotypic abnormality (HPO)", + "decreased reflex", + "abnormal response to external stimulus", "Abnormality of the nervous system (HPO)", - "Global developmental delay (HPO)", - "Abnormal nervous system physiology (HPO)", - "Neurodevelopmental delay (HPO)", - "Neurodevelopmental abnormality (HPO)", + "Behavioral abnormality (HPO)", + "Abnormality of higher mental function (HPO)", + "abnormal voluntary movement behavior", + "entity", "quality", - "anatomical structure", + "process", + "independent continuant", "material anatomical entity", - "anatomical system", - "multicellular organism", - "nervous system", - "anatomical entity", "multicellular anatomical structure", + "nervous system", + "voluntary movement behavior", + "body part movement", + "reflexive behavior", + "abnormality of anatomical entity physiology", "phenotype", - "Phenotypic abnormality", + "continuant", + "decreased qualitatively biological_process", + "abnormality of nervous system physiology", + "Reduced tendon reflexes (HPO)", "phenotype by ontology source", + "abnormal behavior process", + "abnormal nervous system", + "abnormal biological_process", + "Abnormal nervous system physiology (HPO)", + "occurrent", + "continuant", + "biological_process", + "response to external stimulus", + "multicellular organismal movement", + "behavior", + "system process", + "reflex", + "musculoskeletal movement", + "behavior process", + "nervous system process", + "involuntary movement behavior", + "decreased qualitatively response to stimulus", "abnormal phenotype by ontology source", - "abnormality of anatomical entity physiology", - "abnormality of nervous system physiology", + "specifically dependent continuant", + "abnormal voluntary musculoskeletal movement", + "entity", + "anatomical structure", "abnormal anatomical entity", - "abnormal nervous system", + "abnormal voluntary movement behavior", + "changed biological_process rate", + "abnormal response to stimulus", + "abnormal behavior process", + "Hyporeflexia (HPO)", + "Abnormal reflex (HPO)", + "abnormal musculoskeletal movement", + "decreased biological_process", + "abnormality of anatomical entity physiology", "abnormal anatomical entity", - "abnormality of anatomical entity physiology" + "material entity", + "anatomical entity", + "response to stimulus", + "multicellular organismal process", + "anatomical system", + "voluntary musculoskeletal movement", + "kinesthetic behavior", + "neuromuscular process", + "multicellular organism" ], "object_taxon": null, "object_taxon_label": null, @@ -847,36 +1089,46 @@ "aggregator_knowledge_source": ["infores:monarchinitiative"], "negated": null, "pathway": null, - "evidence_count": 4, - "has_evidence": ["ECO:0000304"], + "evidence_count": 2, + "has_evidence": ["ECO:0000269"], "has_evidence_links": [ { - "id": "ECO:0000304", - "url": "http://purl.obolibrary.org/obo/ECO_0000304" + "id": "ECO:0000269", + "url": "http://purl.obolibrary.org/obo/ECO_0000269" } ], + "grouping_key": "MONDO:0008050\ud83c\udf6a\ud83c\udf6abiolink:has_phenotype\ud83c\udf6aHP:0001265", "provided_by": "hpoa_disease_to_phenotype_edges", "provided_by_link": { "id": "hpoa_disease_to_phenotype", "url": "https://monarch-initiative.github.io/monarch-ingest/Sources/hpoa/#disease_to_phenotype" }, - "publications": ["OMIM:613155"], + "publications": ["PMID:17548557"], "publications_links": [ { - "id": "OMIM:613155", - "url": "http://identifiers.org/mim/613155" + "id": "PMID:17548557", + "url": "http://identifiers.org/pubmed/17548557" } ], "qualifiers": [], - "frequency_qualifier": null, + "frequency_qualifier": "HP:0040280", "onset_qualifier": null, "sex_qualifier": null, "stage_qualifier": null, - "frequency_qualifier_label": null, - "frequency_qualifier_namespace": null, - "frequency_qualifier_category": null, - "frequency_qualifier_closure": [], - "frequency_qualifier_closure_label": [], + "qualifiers_label": null, + "qualifiers_namespace": null, + "qualifiers_category": null, + "qualifiers_closure": [], + "qualifiers_closure_label": [], + "frequency_qualifier_label": "Obligate (HPO)", + "frequency_qualifier_namespace": "HP", + "frequency_qualifier_category": "biolink:PhenotypicFeature", + "frequency_qualifier_closure": ["HP:0000001", "HP:0040280", "HP:0040279"], + "frequency_qualifier_closure_label": [ + "All (HPO)", + "Obligate (HPO)", + "Frequency (HPO)" + ], "onset_qualifier_label": null, "onset_qualifier_namespace": null, "onset_qualifier_category": null, @@ -894,200 +1146,228 @@ "stage_qualifier_closure_label": [] }, { - "id": "uuid:875b0482-5d8c-11ee-9b27-2b20ed86a9d9", + "id": "uuid:c9c8bf3f-7529-11ee-b012-cbd37f5c3759", "category": "biolink:DiseaseToPhenotypicFeatureAssociation", - "subject": "MONDO:0013904", - "original_subject": "OMIM:614830", + "subject": "MONDO:0008050", + "original_subject": "OMIM:160500", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ - "MONDO:0018282", - "MONDO:0000001", - "MONDO:0016182", - "MONDO:0017741", - "MONDO:0018276", - "MONDO:0045010", + "BFO:0000002", + "MONDO:0016195", + "MONDO:0005336", + "MONDO:0018949", "MONDO:0005071", + "MONDO:0008050", + "BFO:0000016", + "MONDO:0016139", + "OGMS:0000031", + "MONDO:0003847", + "BFO:0000001", "MONDO:0020121", - "MONDO:0700068", - "MONDO:0700223", - "MONDO:0700075", - "MONDO:0024322", - "MONDO:0005283", - "MONDO:0020238", - "BFO:0000002", - "MONDO:0016185", - "MONDO:0000171", + "MONDO:0019952", "BFO:0000017", - "MONDO:0018869", "BFO:0000020", - "MONDO:0016157", - "MONDO:0017745", - "BFO:0000016", "MONDO:0020120", - "MONDO:0700069", "MONDO:0019056", - "MONDO:0016139", + "MONDO:0000001", + "MONDO:0700223", "MONDO:0700096", - "MONDO:0018838", - "MONDO:0024458", - "MONDO:0005336", "MONDO:0002081", - "MONDO:0016184", - "MONDO:0016156", - "MONDO:0020246", - "MONDO:0021147", - "MONDO:0013904", - "MONDO:0044137", - "MONDO:0019755", - "OGMS:0000031", - "MONDO:0015327", - "MONDO:0003847", "MONDO:0003939", - "MONDO:0002022", - "MONDO:0015286", - "BFO:0000001", - "MONDO:0002320", - "MONDO:0019052", - "MONDO:0020247", - "MONDO:0005066", - "MONDO:0005328", - "MONDO:0019950", - "MONDO:0016155", - "MONDO:0700066" - ], - "subject_label": "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type a, 8", + "MONDO:0002320" + ], + "subject_label": "MYH7-related skeletal myopathy", "subject_closure_label": [ - "entity", - "continuant", - "disposition", - "realizable entity", - "specifically dependent continuant", - "disease", - "muscular dystrophy-dystroglycanopathy, type A", - "disorder of orbital region", + "muscular dystrophy", + "human disease", "musculoskeletal system disorder", + "disease", + "muscle tissue disorder", "congenital nervous system disorder", + "hereditary skeletal muscle disorder", + "MYH7-related skeletal myopathy", + "disposition", + "qualitative or quantitative protein defects in neuromuscular diseases", + "distal myopathy", + "disease", + "continuant", + "qualitative or quantitative defects of beta-myosin heavy chain (MYH7)", + "myopathy", "hereditary disease", - "muscle tissue disorder", - "metabolic disease", "nervous system disorder", - "retinal disorder", - "eye disorder", - "myopathy", - "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type a, 8", - "congenital disorder of glycosylation", - "developmental anomaly of metabolic origin", - "qualitative or quantitative protein defects in neuromuscular diseases", - "qualitative or quantitative defects of protein involved in O-glycosylation of alpha-dystroglycan", - "qualitative or quantitative defects of FKRP", - "qualitative or quantitative defects of fukutin", - "qualitative or quantitative defects of protein O-mannose beta1, 2N-acetylglucosaminyltransferase", - "qualitative or quantitative defects of protein O-mannosyltransferase 1", - "qualitative or quantitative defects of protein O-mannosyltransferase 2", - "disorder of protein O-glycosylation", - "disorder of O-mannosylglycan synthesis", - "muscular dystrophy-dystroglycanopathy", - "qualitative or quantitative defects of alpha-dystroglycan", - "lissencephaly spectrum disorders", - "cobblestone lissencephaly", - "inborn errors of metabolism", - "neuromuscular disease", - "developmental defect during embryogenesis", - "congenital muscular dystrophy", + "congenital myopathy", + "realizable entity", + "specifically dependent continuant", "skeletal muscle disorder", - "muscular dystrophy", - "inherited vitreous-retinal disease", - "inherited vitreoretinopathy", - "congenital vitreoretinal dysplasia", - "disorder of development or morphogenesis", - "disorder of glycosylation", - "disorder of visual system", - "vitreous body disorder", - "glycoprotein metabolism disease", - "myopathy caused by variation in FKRP", - "myopathy caused by variation in POMGNT1", - "myopathy caused by variation in POMGNT2", - "congenital muscular dystrophy caused by variation in POMGNT2", - "human disease", - "hereditary skeletal muscle disorder", - "disease" + "neuromuscular disease", + "entity" ], "subject_taxon": null, "subject_taxon_label": null, "predicate": "biolink:has_phenotype", - "object": "HP:0001263", + "object": "HP:0009053", "original_object": null, "object_namespace": "HP", "object_category": "biolink:PhenotypicFeature", "object_closure": [ - "HP:0000001", "UPHENO:0082875", - "UPHENO:0075696", - "UPHENO:0001001", + "UPHENO:0002320", + "HP:0002814", "UPHENO:0001005", - "UPHENO:0001002", + "HP:0009127", + "UPHENO:0076692", + "UPHENO:0003070", + "BFO:0000004", + "UBERON:0004708", + "UBERON:0000154", + "UBERON:0000026", + "UBERON:0014892", + "UBERON:0006058", + "UBERON:0002529", + "HP:0000001", "HP:0000118", "BFO:0000002", - "HP:0012759", "BFO:0000020", - "UPHENO:0002433", - "HP:0001263", - "UPHENO:0002332", - "HP:0000707", - "UPHENO:0001003", - "UPHENO:0002536", - "HP:0012758", - "UPHENO:0004523", + "UPHENO:0076710", "BFO:0000001", "PATO:0000001", - "HP:0012638", "BFO:0000001", - "BFO:0000002", - "BFO:0000004", "BFO:0000040", - "UBERON:0001062", + "UBERON:0000467", + "UBERON:0000468", + "UBERON:0011216", + "UBERON:0010709", + "UBERON:0010890", + "UBERON:0010538", + "UPHENO:0075696", + "UPHENO:0080575", + "HP:0001324", + "HP:0003690", + "HP:0003011", + "UPHENO:0002332", + "UPHENO:0001003", + "UPHENO:0002536", + "HP:0002460", + "HP:0040064", + "HP:0009053", + "HP:0011804", + "PR:000050567", "UBERON:0000465", + "UBERON:0002101", + "UBERON:0004709", + "UBERON:0005090", + "UBERON:0018254", + "UBERON:0002103", + "UBERON:0010707", + "UBERON:0001630", + "UBERON:0010758", + "UBERON:0007271", + "UBERON:0014792", + "UBERON:0008784", + "HP:0007340", + "UPHENO:0001001", + "HP:0011805", + "UPHENO:0001002", + "UPHENO:0080555", + "UPHENO:0002816", + "UPHENO:0080556", + "UPHENO:0081581", + "HP:0033127", + "UPHENO:0002647", + "UPHENO:0002830", + "BFO:0000002", + "UBERON:0001062", + "RO:0002577", "UBERON:0000061", + "UBERON:0015212", "UBERON:0010000", - "UBERON:0000467", - "UBERON:0000468", - "UBERON:0001016" + "UBERON:0000475", + "UBERON:0000062", + "UBERON:0000383", + "UBERON:0001015", + "UBERON:0000978", + "UBERON:0004480" ], - "object_label": "Global developmental delay (HPO)", + "object_label": "Distal lower limb muscle weakness (HPO)", "object_closure_label": [ - "entity", - "entity", - "continuant", - "continuant", - "independent continuant", - "specifically dependent continuant", - "material entity", "All (HPO)", + "abnormality of muscle organ physiology", + "Abnormality of the lower limb (HPO)", "Phenotypic abnormality (HPO)", - "Abnormality of the nervous system (HPO)", - "Global developmental delay (HPO)", - "Abnormal nervous system physiology (HPO)", - "Neurodevelopmental delay (HPO)", - "Neurodevelopmental abnormality (HPO)", + "continuant", + "decreased anatomical entity strength", + "abnormal musculature", + "decreased muscle organ strength", + "abnormal multicellular organism morphology", + "Abnormality of the musculoskeletal system (HPO)", + "abnormal musculature of limb", "quality", - "anatomical structure", - "material anatomical entity", - "anatomical system", - "multicellular organism", - "nervous system", - "anatomical entity", + "independent continuant", + "system", + "paired limb/fin", + "lateral structure", "multicellular anatomical structure", - "phenotype", + "pelvic complex", + "appendage musculature", + "musculature of pelvic complex", + "abnormality of anatomical entity physiology", + "Abnormal skeletal muscle morphology (HPO)", "Phenotypic abnormality", - "phenotype by ontology source", + "specifically dependent continuant", + "Distal muscle weakness (HPO)", + "Abnormality of limbs (HPO)", + "Distal lower limb muscle weakness (HPO)", + "protein-containing material entity", + "material anatomical entity", + "hindlimb", + "appendage girdle complex", + "subdivision of organism along appendicular axis", + "pelvic complex muscle", + "paired limb/fin segment", + "lower limb segment", + "Lower limb muscle weakness (HPO)", + "phenotype", "abnormal phenotype by ontology source", - "abnormality of anatomical entity physiology", - "abnormality of nervous system physiology", + "Abnormality of the musculature of the limbs (HPO)", + "abnormal muscle organ morphology", + "Abnormal muscle physiology (HPO)", + "entity", + "anatomical entity", + "anatomical structure", + "muscle structure", + "skeletal musculature", + "organism subdivision", + "organ", + "muscle organ", + "musculature of body", + "musculature", + "leg", + "musculature of limb", "abnormal anatomical entity", - "abnormal nervous system", + "decreased pelvic complex muscle strength", + "Muscle weakness (HPO)", + "Limb muscle weakness (HPO)", + "Abnormality of the musculature (HPO)", + "abnormality of anatomical entity physiology", + "phenotype by ontology source", "abnormal anatomical entity", - "abnormality of anatomical entity physiology" + "abnormal anatomical entity morphology", + "abnormal leg", + "entity", + "abnormal limb", + "continuant", + "material entity", + "limb", + "pelvic appendage", + "anatomical system", + "multicellular organism", + "organ system subdivision", + "posterior region of body", + "appendage", + "skeletal muscle organ", + "multi-limb segment region", + "limb segment" ], "object_taxon": null, "object_taxon_label": null, @@ -1095,7 +1375,7 @@ "aggregator_knowledge_source": ["infores:monarchinitiative"], "negated": null, "pathway": null, - "evidence_count": 4, + "evidence_count": 2, "has_evidence": ["ECO:0000269"], "has_evidence_links": [ { @@ -1103,28 +1383,38 @@ "url": "http://purl.obolibrary.org/obo/ECO_0000269" } ], + "grouping_key": "MONDO:0008050\ud83c\udf6a\ud83c\udf6abiolink:has_phenotype\ud83c\udf6aHP:0009053", "provided_by": "hpoa_disease_to_phenotype_edges", "provided_by_link": { "id": "hpoa_disease_to_phenotype", "url": "https://monarch-initiative.github.io/monarch-ingest/Sources/hpoa/#disease_to_phenotype" }, - "publications": ["PMID:22958903"], + "publications": ["PMID:17548557"], "publications_links": [ { - "id": "PMID:22958903", - "url": "http://identifiers.org/pubmed/22958903" + "id": "PMID:17548557", + "url": "http://identifiers.org/pubmed/17548557" } ], "qualifiers": [], - "frequency_qualifier": null, + "frequency_qualifier": "HP:0040280", "onset_qualifier": null, "sex_qualifier": null, "stage_qualifier": null, - "frequency_qualifier_label": null, - "frequency_qualifier_namespace": null, - "frequency_qualifier_category": null, - "frequency_qualifier_closure": [], - "frequency_qualifier_closure_label": [], + "qualifiers_label": null, + "qualifiers_namespace": null, + "qualifiers_category": null, + "qualifiers_closure": [], + "qualifiers_closure_label": [], + "frequency_qualifier_label": "Obligate (HPO)", + "frequency_qualifier_namespace": "HP", + "frequency_qualifier_category": "biolink:PhenotypicFeature", + "frequency_qualifier_closure": ["HP:0000001", "HP:0040280", "HP:0040279"], + "frequency_qualifier_closure_label": [ + "All (HPO)", + "Obligate (HPO)", + "Frequency (HPO)" + ], "onset_qualifier_label": null, "onset_qualifier_namespace": null, "onset_qualifier_category": null, @@ -1142,146 +1432,222 @@ "stage_qualifier_closure_label": [] }, { - "id": "uuid:85eb98e5-5d8c-11ee-9b27-2b20ed86a9d9", + "id": "uuid:c9c8bf41-7529-11ee-b012-cbd37f5c3759", "category": "biolink:DiseaseToPhenotypicFeatureAssociation", - "subject": "MONDO:0014023", - "original_subject": "OMIM:615042", + "subject": "MONDO:0008050", + "original_subject": "OMIM:160500", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ - "MONDO:0000001", - "MONDO:0018276", + "BFO:0000002", + "MONDO:0016195", + "MONDO:0005336", + "MONDO:0018949", "MONDO:0005071", + "MONDO:0008050", + "BFO:0000016", + "MONDO:0016139", + "OGMS:0000031", + "MONDO:0003847", + "BFO:0000001", "MONDO:0020121", - "MONDO:0700223", - "MONDO:0024322", - "BFO:0000002", + "MONDO:0019952", "BFO:0000017", "BFO:0000020", - "BFO:0000016", "MONDO:0020120", "MONDO:0019056", - "MONDO:0014023", + "MONDO:0000001", + "MONDO:0700223", "MONDO:0700096", - "MONDO:0005336", "MONDO:0002081", - "MONDO:0017749", - "OGMS:0000031", - "MONDO:0003847", "MONDO:0003939", - "MONDO:0015286", - "BFO:0000001", - "MONDO:0002320", - "MONDO:0019052", - "MONDO:0005500", - "MONDO:0005066", - "MONDO:0019950" + "MONDO:0002320" ], - "subject_label": "congenital muscular dystrophy with intellectual disability and severe epilepsy", + "subject_label": "MYH7-related skeletal myopathy", "subject_closure_label": [ - "entity", - "continuant", - "disposition", - "realizable entity", - "specifically dependent continuant", - "disease", + "muscular dystrophy", + "human disease", "musculoskeletal system disorder", + "disease", + "muscle tissue disorder", "congenital nervous system disorder", + "hereditary skeletal muscle disorder", + "MYH7-related skeletal myopathy", + "disposition", + "qualitative or quantitative protein defects in neuromuscular diseases", + "distal myopathy", + "disease", + "continuant", + "qualitative or quantitative defects of beta-myosin heavy chain (MYH7)", + "myopathy", "hereditary disease", - "muscle tissue disorder", - "metabolic disease", "nervous system disorder", - "myopathy", - "congenital disorder of glycosylation type I", - "congenital muscular dystrophy with intellectual disability and severe epilepsy", - "congenital disorder of glycosylation", - "disorder of multiple glycosylation", - "muscular dystrophy-dystroglycanopathy", - "inborn errors of metabolism", - "neuromuscular disease", - "congenital muscular dystrophy", + "congenital myopathy", + "realizable entity", + "specifically dependent continuant", "skeletal muscle disorder", - "muscular dystrophy", - "disorder of glycosylation", - "human disease", - "hereditary skeletal muscle disorder", - "disease" + "neuromuscular disease", + "entity" ], "subject_taxon": null, "subject_taxon_label": null, "predicate": "biolink:has_phenotype", - "object": "HP:0001263", + "object": "HP:0009077", "original_object": null, "object_namespace": "HP", "object_category": "biolink:PhenotypicFeature", "object_closure": [ + "HP:0009127", + "BFO:0000002", + "UPHENO:0002655", + "UPHENO:0076692", + "BFO:0000001", + "PATO:0000001", + "BFO:0000004", + "UBERON:0004708", + "UBERON:0000061", + "UBERON:0000153", + "UBERON:0000026", + "UBERON:0006058", + "UBERON:0002529", + "UBERON:0002398", "HP:0000001", - "UPHENO:0082875", - "UPHENO:0075696", + "UPHENO:0002649", "UPHENO:0001001", - "UPHENO:0001005", "UPHENO:0001002", "HP:0000118", - "BFO:0000002", - "HP:0012759", + "HP:0001446", "BFO:0000020", - "UPHENO:0002433", - "HP:0001263", - "UPHENO:0002332", - "HP:0000707", - "UPHENO:0001003", - "UPHENO:0002536", - "HP:0012758", - "UPHENO:0004523", - "BFO:0000001", - "PATO:0000001", - "HP:0012638", + "UPHENO:0002708", + "HP:0009077", + "UPHENO:0076710", "BFO:0000001", - "BFO:0000002", - "BFO:0000004", "BFO:0000040", - "UBERON:0001062", - "UBERON:0000465", - "UBERON:0000061", - "UBERON:0010000", "UBERON:0000467", "UBERON:0000468", - "UBERON:0001016" - ], - "object_label": "Global developmental delay (HPO)", - "object_closure_label": [ - "entity", - "entity", - "continuant", - "continuant", - "independent continuant", - "specifically dependent continuant", - "material entity", + "UBERON:0011216", + "UBERON:0010708", + "UBERON:0010538", + "UBERON:0004489", + "HP:0001421", + "HP:0030237", + "HP:0002817", + "HP:0003011", + "UPHENO:0002536", + "HP:0040064", + "BFO:0000002", + "PR:000050567", + "UBERON:0000465", + "UBERON:0002101", + "UBERON:0004710", + "UBERON:0005090", + "UBERON:0002102", + "UBERON:0010707", + "UBERON:0001630", + "UBERON:0010758", + "UBERON:0007271", + "UBERON:0014793", + "UBERON:0004481", + "UBERON:0002470", + "UBERON:0008785", + "UPHENO:0001005", + "HP:0001155", + "HP:0011805", + "UPHENO:0002816", + "UPHENO:0081581", + "HP:0033127", + "UPHENO:0001003", + "UPHENO:0002647", + "UPHENO:0002880", + "UPHENO:0002830", + "UBERON:0001062", + "RO:0002577", + "UBERON:0015212", + "UBERON:0010000", + "UBERON:0000475", + "UBERON:0000062", + "UBERON:0000383", + "UBERON:0001015", + "UBERON:0001460", + "UBERON:0004480", + "UBERON:0007269" + ], + "object_label": "Weakness of long finger extensor muscles (HPO)", + "object_closure_label": [ "All (HPO)", + "abnormal musculature of upper limb", + "Phenotypic abnormality", "Phenotypic abnormality (HPO)", - 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"abnormality of nervous system physiology", - "abnormal anatomical entity", - "abnormal nervous system", + "Abnormality of the hand (HPO)", + "Abnormal skeletal muscle morphology (HPO)", + "Abnormality of the musculature of the upper limbs (HPO)", + "specifically dependent continuant", + "abnormal manus", + "Abnormality of limbs (HPO)", + "quality", + "continuant", + "protein-containing material entity", + "material anatomical entity", + "forelimb", + "appendage girdle complex", + "subdivision of organism along appendicular axis", + "paired limb/fin segment", + "musculature of upper limb", + "autopod region", + "upper limb segment", + "Abnormality of the musculature of the limbs (HPO)", + "continuant", + "abnormal musculature of manus", + "Weakness of long finger extensor muscles (HPO)", + "abnormal muscle organ morphology", + "entity", + "anatomical entity", + "muscle structure", + "organism subdivision", + "organ", + "muscle organ", + "musculature of body", + "musculature", + "arm", + "musculature of limb", + "pectoral appendage musculature", + "Hand muscle weakness (HPO)", + "Abnormality of the upper limb (HPO)", + "Abnormality of the musculature (HPO)", "abnormal anatomical entity", - "abnormality of anatomical entity physiology" + "abnormal anatomical entity morphology", + "entity", + "abnormal arm", + "abnormal limb", + "material entity", + "limb", + "pectoral appendage", + "anatomical system", + "multicellular organism", + "organ system subdivision", + "anterior region of body", + "appendage", + "multi-limb segment region", + "limb segment", + "manus" ], "object_taxon": null, "object_taxon_label": null, @@ -1289,36 +1655,46 @@ "aggregator_knowledge_source": ["infores:monarchinitiative"], "negated": null, "pathway": null, - "evidence_count": 4, - "has_evidence": ["ECO:0000304"], + "evidence_count": 2, + "has_evidence": ["ECO:0000269"], "has_evidence_links": [ { - "id": "ECO:0000304", - "url": "http://purl.obolibrary.org/obo/ECO_0000304" + "id": "ECO:0000269", + "url": "http://purl.obolibrary.org/obo/ECO_0000269" } ], + "grouping_key": "MONDO:0008050\ud83c\udf6a\ud83c\udf6abiolink:has_phenotype\ud83c\udf6aHP:0009077", "provided_by": "hpoa_disease_to_phenotype_edges", "provided_by_link": { "id": "hpoa_disease_to_phenotype", "url": "https://monarch-initiative.github.io/monarch-ingest/Sources/hpoa/#disease_to_phenotype" }, - "publications": ["PMID:19901254"], + "publications": ["PMID:17548557"], "publications_links": [ { - "id": "PMID:19901254", - "url": "http://identifiers.org/pubmed/19901254" + "id": "PMID:17548557", + "url": "http://identifiers.org/pubmed/17548557" } ], "qualifiers": [], - "frequency_qualifier": null, + "frequency_qualifier": "HP:0040280", "onset_qualifier": null, "sex_qualifier": null, "stage_qualifier": null, - "frequency_qualifier_label": null, - "frequency_qualifier_namespace": null, - "frequency_qualifier_category": null, - "frequency_qualifier_closure": [], - "frequency_qualifier_closure_label": [], + "qualifiers_label": null, + "qualifiers_namespace": null, + "qualifiers_category": null, + "qualifiers_closure": [], + "qualifiers_closure_label": [], + "frequency_qualifier_label": "Obligate (HPO)", + "frequency_qualifier_namespace": "HP", + "frequency_qualifier_category": "biolink:PhenotypicFeature", + "frequency_qualifier_closure": ["HP:0000001", "HP:0040280", "HP:0040279"], + "frequency_qualifier_closure_label": [ + "All (HPO)", + "Obligate (HPO)", + "Frequency (HPO)" + ], "onset_qualifier_label": null, "onset_qualifier_namespace": null, "onset_qualifier_category": null, @@ -1336,196 +1712,190 @@ "stage_qualifier_closure_label": [] }, { - "id": "uuid:87eb5818-5d8c-11ee-9b27-2b20ed86a9d9", + "id": "uuid:c9c8bf42-7529-11ee-b012-cbd37f5c3759", "category": "biolink:DiseaseToPhenotypicFeatureAssociation", - "subject": "MONDO:0014101", - "original_subject": "OMIM:615249", + "subject": "MONDO:0008050", + "original_subject": "OMIM:160500", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ - "MONDO:0018282", - "MONDO:0000001", - "MONDO:0016182", - "MONDO:0017741", - "MONDO:0018276", - "MONDO:0045010", + "BFO:0000002", + "MONDO:0016195", + "MONDO:0005336", + "MONDO:0018949", "MONDO:0005071", + "MONDO:0008050", + "BFO:0000016", + "MONDO:0016139", + "OGMS:0000031", + "MONDO:0003847", + "BFO:0000001", "MONDO:0020121", - "MONDO:0700068", - "MONDO:0700223", - "MONDO:0024322", - "MONDO:0005283", - "MONDO:0020238", - "BFO:0000002", - "MONDO:0014101", - "MONDO:0016185", - "MONDO:0000171", + "MONDO:0019952", "BFO:0000017", - "MONDO:0018869", "BFO:0000020", - "MONDO:0016157", - "MONDO:0017745", - "BFO:0000016", "MONDO:0020120", "MONDO:0019056", - "MONDO:0016139", + "MONDO:0000001", + "MONDO:0700223", "MONDO:0700096", - "MONDO:0018838", - "MONDO:0024458", - "MONDO:0005336", "MONDO:0002081", - "MONDO:0016184", - "MONDO:0016156", - "MONDO:0020246", - "MONDO:0021147", - "MONDO:0044137", - "MONDO:0019755", - "OGMS:0000031", - "MONDO:0015327", - "MONDO:0003847", "MONDO:0003939", - "MONDO:0002022", - "MONDO:0015286", - "BFO:0000001", - "MONDO:0002320", - "MONDO:0019052", - "MONDO:0020247", - "MONDO:0005066", - "MONDO:0005328", - "MONDO:0019950", - "MONDO:0016155", - "MONDO:0700066" - ], - "subject_label": "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type a, 12", + "MONDO:0002320" + ], + "subject_label": "MYH7-related skeletal myopathy", "subject_closure_label": [ - "entity", - "continuant", - "disposition", - "realizable entity", - "specifically dependent continuant", - "disease", - "muscular dystrophy-dystroglycanopathy, type A", - "disorder of orbital region", + "muscular dystrophy", + "human disease", "musculoskeletal system disorder", + "disease", + "muscle tissue disorder", "congenital nervous system disorder", + "hereditary skeletal muscle disorder", + "MYH7-related skeletal myopathy", + "disposition", + "qualitative or quantitative protein defects in neuromuscular diseases", + "distal myopathy", + "disease", + "continuant", + "qualitative or quantitative defects of beta-myosin heavy chain (MYH7)", + "myopathy", "hereditary disease", - 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"lissencephaly spectrum disorders", - "cobblestone lissencephaly", - "inborn errors of metabolism", - "neuromuscular disease", - "developmental defect during embryogenesis", - "congenital muscular dystrophy", + "congenital myopathy", + "realizable entity", + "specifically dependent continuant", "skeletal muscle disorder", - "muscular dystrophy", - "inherited vitreous-retinal disease", - "inherited vitreoretinopathy", - "congenital vitreoretinal dysplasia", - "disorder of development or morphogenesis", - "disorder of glycosylation", - "disorder of visual system", - "vitreous body disorder", - "glycoprotein metabolism disease", - "myopathy caused by variation in FKRP", - "myopathy caused by variation in POMGNT1", - "human disease", - "hereditary skeletal muscle disorder", - "disease" + "neuromuscular disease", + "entity" ], "subject_taxon": null, "subject_taxon_label": null, "predicate": "biolink:has_phenotype", - "object": "HP:0001263", + "object": "HP:0030051", "original_object": null, "object_namespace": "HP", "object_category": "biolink:PhenotypicFeature", "object_closure": [ - 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"abnormality of anatomical entity physiology" + "entity", + "continuant", + "material entity", + "multicellular organismal process", + "multicellular anatomical structure", + "anatomical system", + "voluntary musculoskeletal movement", + "kinesthetic behavior", + "neuromuscular process", + "multicellular organism" ], "object_taxon": null, "object_taxon_label": null, @@ -1533,36 +1903,46 @@ "aggregator_knowledge_source": ["infores:monarchinitiative"], "negated": null, "pathway": null, - "evidence_count": 4, - "has_evidence": ["ECO:0000304"], + "evidence_count": 2, + "has_evidence": ["ECO:0000269"], "has_evidence_links": [ { - "id": "ECO:0000304", - "url": "http://purl.obolibrary.org/obo/ECO_0000304" + "id": "ECO:0000269", + "url": "http://purl.obolibrary.org/obo/ECO_0000269" } ], + "grouping_key": "MONDO:0008050\ud83c\udf6a\ud83c\udf6abiolink:has_phenotype\ud83c\udf6aHP:0030051", "provided_by": "hpoa_disease_to_phenotype_edges", "provided_by_link": { "id": "hpoa_disease_to_phenotype", "url": "https://monarch-initiative.github.io/monarch-ingest/Sources/hpoa/#disease_to_phenotype" }, - "publications": ["OMIM:615249"], + "publications": ["PMID:17548557"], "publications_links": [ { - "id": "OMIM:615249", - "url": "http://identifiers.org/mim/615249" + "id": "PMID:17548557", + "url": "http://identifiers.org/pubmed/17548557" } ], "qualifiers": [], - "frequency_qualifier": null, + "frequency_qualifier": "HP:0040280", "onset_qualifier": null, "sex_qualifier": null, "stage_qualifier": null, - "frequency_qualifier_label": null, - "frequency_qualifier_namespace": null, - "frequency_qualifier_category": null, - "frequency_qualifier_closure": [], - "frequency_qualifier_closure_label": [], + "qualifiers_label": null, + "qualifiers_namespace": null, + "qualifiers_category": null, + "qualifiers_closure": [], + "qualifiers_closure_label": [], + "frequency_qualifier_label": "Obligate (HPO)", + "frequency_qualifier_namespace": "HP", + "frequency_qualifier_category": "biolink:PhenotypicFeature", + "frequency_qualifier_closure": ["HP:0000001", "HP:0040280", "HP:0040279"], + "frequency_qualifier_closure_label": [ + "All (HPO)", + "Obligate (HPO)", + "Frequency (HPO)" + ], "onset_qualifier_label": null, "onset_qualifier_namespace": null, "onset_qualifier_category": null, @@ -1580,196 +1960,206 @@ "stage_qualifier_closure_label": [] }, { - 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"abnormality of anatomical entity physiology", - "abnormality of nervous system physiology", - "abnormal anatomical entity", - "abnormal nervous system", + "continuant", + "specifically dependent continuant", + "Abnormality of the immune system (HPO)", + "Abnormal granulocyte morphology (HPO)", + "Eosinophilia (HPO)", "abnormal anatomical entity", - "abnormality of anatomical entity physiology" + "Abnormal immune system morphology (HPO)", + "entity", + "anatomical entity", + "anatomical structure", + "organism substance", + "disconnected anatomical group", + "mesoderm-derived structure", + "bodily fluid", + "non-connected functional system", + "native cell", + "hemolymphoid system", + "hematopoietic system", + "haemolymphatic fluid", + "immune system", + "myeloid leukocyte", + "somatic cell", + "abnormal immune system", + "Abnormal granulocyte count (HPO)", + "Phenotypic abnormality", + "Abnormal cell morphology (HPO)", + "Abnormal leukocyte morphology (HPO)", + "Abnormal myeloid cell morphology (HPO)", + "abnormal hematopoietic system", + "entity", + "eosinophil", + "anatomical system", + "cell", + "multicellular organism", + "nucleate cell", + "eukaryotic cell", + "motile cell" ], "object_taxon": null, "object_taxon_label": null, @@ -1777,36 +2167,46 @@ "aggregator_knowledge_source": ["infores:monarchinitiative"], "negated": null, "pathway": null, - 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"myopathy caused by variation in POMGNT1", - "myopathy caused by variation in GMPPB", - "human disease", - "hereditary skeletal muscle disorder", - "disease" + "qualitative or quantitative defects of calpain", + "neuromuscular disease", + "autosomal recessive limb-girdle muscular dystrophy", + "entity" ], "subject_taxon": null, "subject_taxon_label": null, "predicate": "biolink:has_phenotype", - "object": "HP:0001263", + "object": "HP:0002312", "original_object": null, "object_namespace": "HP", "object_category": "biolink:PhenotypicFeature", "object_closure": [ - "HP:0000001", "UPHENO:0082875", - "UPHENO:0075696", - "UPHENO:0001001", "UPHENO:0001005", - "UPHENO:0001002", + "HP:0012638", + "BFO:0000004", + "UBERON:0000061", + "UBERON:0001016", + "HP:0000001", "HP:0000118", - "BFO:0000002", - "HP:0012759", "BFO:0000020", "UPHENO:0002433", - "HP:0001263", - "UPHENO:0002332", - "HP:0000707", "UPHENO:0001003", - "UPHENO:0002536", - "HP:0012758", - "UPHENO:0004523", - "BFO:0000001", "PATO:0000001", - "HP:0012638", "BFO:0000001", - "BFO:0000002", - "BFO:0000004", "BFO:0000040", - "UBERON:0001062", - "UBERON:0000465", - "UBERON:0000061", - "UBERON:0010000", "UBERON:0000467", "UBERON:0000468", - "UBERON:0001016" + "UPHENO:0075696", + "HP:0011442", + "UPHENO:0001002", + "UPHENO:0002332", + "UPHENO:0002536", + "UPHENO:0004523", + "HP:0002312", + "HP:0011443", + "BFO:0000002", + "UBERON:0000465", + "UPHENO:0001001", + "BFO:0000002", + "HP:0000707", + "HP:0002311", + "BFO:0000001", + "UBERON:0001062", + "UBERON:0010000" ], - "object_label": "Global developmental delay (HPO)", + "object_label": "Clumsiness (HPO)", "object_closure_label": [ - "entity", - "entity", - "continuant", - "continuant", - "independent continuant", - "specifically dependent continuant", - "material entity", "All (HPO)", + "Abnormal central motor function (HPO)", "Phenotypic abnormality (HPO)", "Abnormality of the nervous system (HPO)", - "Global developmental delay (HPO)", - "Abnormal nervous system physiology (HPO)", - "Neurodevelopmental delay (HPO)", - "Neurodevelopmental abnormality (HPO)", + "entity", "quality", + "independent continuant", "anatomical structure", - "material anatomical entity", - "anatomical system", - "multicellular organism", - "nervous system", - "anatomical entity", "multicellular anatomical structure", - "phenotype", - "Phenotypic abnormality", - "phenotype by ontology source", - "abnormal phenotype by ontology source", + "nervous system", "abnormality of anatomical entity physiology", + "continuant", + "specifically dependent continuant", "abnormality of nervous system physiology", - "abnormal anatomical entity", + "phenotype by ontology source", "abnormal nervous system", - "abnormal anatomical entity", - "abnormality of anatomical entity physiology" - ], - "object_taxon": null, - "object_taxon_label": null, - "primary_knowledge_source": "infores:hpo-annotations", - "aggregator_knowledge_source": ["infores:monarchinitiative"], + "Clumsiness (HPO)", + "Abnormal nervous system physiology (HPO)", + "continuant", + "material anatomical entity", + "phenotype", + "abnormal phenotype by ontology source", + "Incoordination (HPO)", + "Abnormality of coordination (HPO)", + "entity", + "anatomical entity", + "abnormal anatomical entity", + "Phenotypic abnormality", + "abnormality of anatomical entity physiology", + "abnormal anatomical entity", + "material entity", + "anatomical system", + "multicellular organism" + ], + "object_taxon": null, + "object_taxon_label": null, + "primary_knowledge_source": "infores:hpo-annotations", + "aggregator_knowledge_source": ["infores:monarchinitiative"], "negated": null, "pathway": null, - "evidence_count": 4, + "evidence_count": 2, "has_evidence": ["ECO:0000269"], "has_evidence_links": [ { @@ -2033,28 +2377,38 @@ "url": "http://purl.obolibrary.org/obo/ECO_0000269" } ], + "grouping_key": "MONDO:0009675\ud83c\udf6a\ud83c\udf6abiolink:has_phenotype\ud83c\udf6aHP:0002312", "provided_by": "hpoa_disease_to_phenotype_edges", "provided_by_link": { "id": "hpoa_disease_to_phenotype", "url": "https://monarch-initiative.github.io/monarch-ingest/Sources/hpoa/#disease_to_phenotype" }, - "publications": ["PMID:23768512"], + "publications": ["PMID:16607617"], "publications_links": [ { - "id": "PMID:23768512", - "url": "http://identifiers.org/pubmed/23768512" + "id": "PMID:16607617", + "url": "http://identifiers.org/pubmed/16607617" } ], "qualifiers": [], - "frequency_qualifier": null, + "frequency_qualifier": "HP:0040282", "onset_qualifier": null, "sex_qualifier": null, "stage_qualifier": null, - "frequency_qualifier_label": null, - "frequency_qualifier_namespace": null, - "frequency_qualifier_category": null, - "frequency_qualifier_closure": [], - "frequency_qualifier_closure_label": [], + "qualifiers_label": null, + "qualifiers_namespace": null, + "qualifiers_category": null, + "qualifiers_closure": [], + "qualifiers_closure_label": [], + "frequency_qualifier_label": "Frequent (HPO)", + "frequency_qualifier_namespace": "HP", + "frequency_qualifier_category": "biolink:PhenotypicFeature", + "frequency_qualifier_closure": ["HP:0040282", "HP:0000001", "HP:0040279"], + "frequency_qualifier_closure_label": [ + "All (HPO)", + "Frequent (HPO)", + "Frequency (HPO)" + ], "onset_qualifier_label": null, "onset_qualifier_namespace": null, "onset_qualifier_category": null, @@ -2072,156 +2426,148 @@ "stage_qualifier_closure_label": [] }, { - "id": "uuid:850bd377-5d8c-11ee-9b27-2b20ed86a9d9", + "id": "uuid:c9c8bff4-7529-11ee-b012-cbd37f5c3759", "category": "biolink:DiseaseToPhenotypicFeatureAssociation", - "subject": "MONDO:0014141", - "original_subject": "OMIM:615351", + "subject": "MONDO:0009675", + "original_subject": "OMIM:253600", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ - "MONDO:0700084", - "MONDO:0018282", - "MONDO:0000001", - "MONDO:0017741", - "MONDO:0018276", - "MONDO:0045010", + "MONDO:0016971", + "MONDO:0005336", + "MONDO:0015152", + "MONDO:0000429", "MONDO:0005071", + "MONDO:0006025", + "BFO:0000016", + "MONDO:0016139", + "OGMS:0000031", + "BFO:0000001", "MONDO:0020121", - "MONDO:0000172", - "MONDO:0700223", - "MONDO:0024322", - "BFO:0000002", "BFO:0000017", - "MONDO:0014141", "BFO:0000020", - "BFO:0000016", + "MONDO:0009675", "MONDO:0020120", + "MONDO:0016152", "MONDO:0019056", - "MONDO:0016139", + "MONDO:0000001", + "MONDO:0700223", + "BFO:0000002", + "MONDO:0016106", "MONDO:0700096", - "MONDO:0005336", "MONDO:0002081", - "OGMS:0000031", "MONDO:0003847", - "MONDO:0003939", - "MONDO:0015286", - "BFO:0000001", - "MONDO:0002320", - "MONDO:0019052", - "MONDO:0005066", - "MONDO:0019950", - "MONDO:0016155" + "MONDO:0003939" ], - "subject_label": "muscular dystrophy-dystroglycanopathy (congenital with intellectual disability), type B14", + "subject_label": "autosomal recessive limb-girdle muscular dystrophy type 2A", "subject_closure_label": [ - "entity", - "continuant", - "disposition", - "realizable entity", - "specifically dependent continuant", - "disease", - "muscular dystrophy-dystroglycanopathy, type B", + "limb-girdle muscular dystrophy", + "muscular dystrophy", + "progressive muscular dystrophy", + "human disease", "musculoskeletal system disorder", - "congenital nervous system disorder", + "disease", "hereditary disease", "muscle tissue disorder", - "metabolic disease", - "nervous system disorder", - "myopathy", - "muscular dystrophy-dystroglycanopathy (congenital with intellectual disability), type B14", - "congenital disorder of glycosylation", + "hereditary skeletal muscle disorder", + "continuant", + "autosomal recessive disease", + "disposition", "qualitative or quantitative protein defects in neuromuscular diseases", - "qualitative or quantitative defects of protein involved in O-glycosylation of alpha-dystroglycan", - "disorder of protein O-glycosylation", - "muscular dystrophy-dystroglycanopathy", - "qualitative or quantitative defects of alpha-dystroglycan", - "inborn errors of metabolism", - "neuromuscular disease", - "congenital muscular dystrophy", + "disease", + "myopathy", + "autosomal genetic disease", + "nervous system disorder", + "realizable entity", + "specifically dependent continuant", + "autosomal recessive limb-girdle muscular dystrophy type 2A", "skeletal muscle disorder", - "muscular dystrophy", - "disorder of glycosylation", - "glycoprotein metabolism disease", - "myopathy caused by variation in GMPPB", - "human disease", - "hereditary skeletal muscle disorder", - "disease" + "qualitative or quantitative defects of calpain", + "neuromuscular disease", + "autosomal recessive limb-girdle muscular dystrophy", + "entity" ], "subject_taxon": null, "subject_taxon_label": null, "predicate": "biolink:has_phenotype", - "object": "HP:0001263", + "object": "HP:0032019", "original_object": null, "object_namespace": "HP", "object_category": "biolink:PhenotypicFeature", "object_closure": [ - "HP:0000001", - "UPHENO:0082875", - "UPHENO:0075696", - "UPHENO:0001001", "UPHENO:0001005", - "UPHENO:0001002", - "HP:0000118", "BFO:0000002", - "HP:0012759", "BFO:0000020", - "UPHENO:0002433", - "HP:0001263", - "UPHENO:0002332", - "HP:0000707", + "UPHENO:0076692", + "PATO:0000001", + "BFO:0000004", + "UBERON:0000061", + "HP:0000001", + "UPHENO:0001001", + "HP:0000118", + "HP:0032019", "UPHENO:0001003", - "UPHENO:0002536", - "HP:0012758", - "UPHENO:0004523", + "UPHENO:0076710", "BFO:0000001", - "PATO:0000001", - "HP:0012638", "BFO:0000001", - "BFO:0000002", - "BFO:0000004", "BFO:0000040", - "UBERON:0001062", - "UBERON:0000465", - "UBERON:0000061", - "UBERON:0010000", "UBERON:0000467", "UBERON:0000468", - "UBERON:0001016" + "UBERON:0011216", + "HP:0003011", + "UPHENO:0002536", + "BFO:0000002", + "UBERON:0000465", + "UBERON:0005090", + "UBERON:0001630", + "HP:0011805", + "UPHENO:0001002", + "UPHENO:0002816", + "UPHENO:0081581", + "HP:0033127", + "UBERON:0001062", + "UBERON:0010000", + "UBERON:0000062", + "UBERON:0000383", + "UBERON:0001015" ], - "object_label": "Global developmental delay (HPO)", + "object_label": "Muscle eosinophilia (HPO)", "object_closure_label": [ - "entity", - "entity", - "continuant", - "continuant", - "independent continuant", - "specifically dependent continuant", - "material entity", "All (HPO)", "Phenotypic abnormality (HPO)", - "Abnormality of the nervous system (HPO)", - "Global developmental delay (HPO)", - "Abnormal nervous system physiology (HPO)", - "Neurodevelopmental delay (HPO)", - "Neurodevelopmental abnormality (HPO)", - "quality", + "abnormal musculature", + "abnormal multicellular organism morphology", + "Abnormality of the musculoskeletal system (HPO)", + "independent continuant", "anatomical structure", - "material anatomical entity", - "anatomical system", - "multicellular organism", - "nervous system", - "anatomical entity", "multicellular anatomical structure", "phenotype", + "Abnormal skeletal muscle morphology (HPO)", "Phenotypic abnormality", + "Muscle eosinophilia (HPO)", "phenotype by ontology source", + "quality", + "continuant", + "material anatomical entity", "abnormal phenotype by ontology source", - "abnormality of anatomical entity physiology", - "abnormality of nervous system physiology", - "abnormal anatomical entity", - "abnormal nervous system", + "continuant", + "specifically dependent continuant", + "abnormal muscle organ morphology", + "entity", + "anatomical entity", + "muscle structure", + "organ", + "muscle organ", + "musculature of body", + "musculature", + "Abnormality of the musculature (HPO)", "abnormal anatomical entity", - "abnormality of anatomical entity physiology" + "abnormal anatomical entity morphology", + "entity", + "material entity", + "anatomical system", + "multicellular organism", + "organ system subdivision" ], "object_taxon": null, "object_taxon_label": null, @@ -2229,7 +2575,7 @@ "aggregator_knowledge_source": ["infores:monarchinitiative"], "negated": null, "pathway": null, - "evidence_count": 4, + "evidence_count": 2, "has_evidence": ["ECO:0000269"], "has_evidence_links": [ { @@ -2237,28 +2583,38 @@ "url": "http://purl.obolibrary.org/obo/ECO_0000269" } ], + "grouping_key": "MONDO:0009675\ud83c\udf6a\ud83c\udf6abiolink:has_phenotype\ud83c\udf6aHP:0032019", "provided_by": "hpoa_disease_to_phenotype_edges", "provided_by_link": { "id": "hpoa_disease_to_phenotype", "url": "https://monarch-initiative.github.io/monarch-ingest/Sources/hpoa/#disease_to_phenotype" }, - "publications": ["PMID:23768512"], + "publications": ["PMID:16607617"], "publications_links": [ { - "id": "PMID:23768512", - "url": "http://identifiers.org/pubmed/23768512" + "id": "PMID:16607617", + "url": "http://identifiers.org/pubmed/16607617" } ], "qualifiers": [], - "frequency_qualifier": null, + "frequency_qualifier": "HP:0040280", "onset_qualifier": null, "sex_qualifier": null, "stage_qualifier": null, - "frequency_qualifier_label": null, - "frequency_qualifier_namespace": null, - "frequency_qualifier_category": null, - "frequency_qualifier_closure": [], - "frequency_qualifier_closure_label": [], + "qualifiers_label": null, + "qualifiers_namespace": null, + "qualifiers_category": null, + "qualifiers_closure": [], + "qualifiers_closure_label": [], + "frequency_qualifier_label": "Obligate (HPO)", + "frequency_qualifier_namespace": "HP", + "frequency_qualifier_category": "biolink:PhenotypicFeature", + "frequency_qualifier_closure": ["HP:0000001", "HP:0040280", "HP:0040279"], + "frequency_qualifier_closure_label": [ + "All (HPO)", + "Obligate (HPO)", + "Frequency (HPO)" + ], "onset_qualifier_label": null, "onset_qualifier_namespace": null, "onset_qualifier_category": null, @@ -2276,142 +2632,206 @@ "stage_qualifier_closure_label": [] }, { - "id": "uuid:842bf67e-5d8c-11ee-9b27-2b20ed86a9d9", + "id": "uuid:c9c8bff5-7529-11ee-b012-cbd37f5c3759", "category": "biolink:DiseaseToPhenotypicFeatureAssociation", - "subject": "MONDO:0014144", - "original_subject": "OMIM:615356", + "subject": "MONDO:0009675", + "original_subject": "OMIM:253600", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ - "MONDO:0000001", "MONDO:0016971", + "MONDO:0005336", + "MONDO:0015152", "MONDO:0000429", - "MONDO:0014144", "MONDO:0005071", + "MONDO:0006025", + "BFO:0000016", + "MONDO:0016139", + "OGMS:0000031", + "BFO:0000001", "MONDO:0020121", - "MONDO:0700223", - "BFO:0000002", - "MONDO:0005395", "BFO:0000017", "BFO:0000020", - "MONDO:0006025", - "MONDO:0016106", - "BFO:0000016", + "MONDO:0009675", "MONDO:0020120", + "MONDO:0016152", "MONDO:0019056", + "MONDO:0000001", + "MONDO:0700223", + "BFO:0000002", + "MONDO:0016106", "MONDO:0700096", - "MONDO:0005336", "MONDO:0002081", - "MONDO:0018243", - "OGMS:0000031", "MONDO:0003847", - "MONDO:0003939", - "MONDO:0015152", - "BFO:0000001" + "MONDO:0003939" ], - "subject_label": "autosomal recessive limb-girdle muscular dystrophy type R18", + "subject_label": "autosomal recessive limb-girdle muscular dystrophy type 2A", "subject_closure_label": [ - "entity", + "limb-girdle muscular dystrophy", + "muscular dystrophy", + "progressive muscular dystrophy", + "human disease", + "musculoskeletal system disorder", + "disease", + "hereditary disease", + "muscle tissue disorder", + "hereditary skeletal muscle disorder", "continuant", + "autosomal recessive disease", "disposition", - "realizable entity", - "specifically dependent continuant", + "qualitative or quantitative protein defects in neuromuscular diseases", "disease", + "myopathy", "autosomal genetic disease", - "musculoskeletal system disorder", - "hereditary disease", - "muscle tissue disorder", "nervous system disorder", - "myopathy", - "movement disorder", - "autosomal recessive disease", - "autosomal recessive limb-girdle muscular dystrophy type R18", - "autosomal recessive limb-girdle muscular dystrophy", - "progressive muscular dystrophy", - "limb-girdle muscular dystrophy", - "intellectual disability-hyperkinetic movement-truncal ataxia syndrome", - "neuromuscular disease", + "realizable entity", + "specifically dependent continuant", + "autosomal recessive limb-girdle muscular dystrophy type 2A", "skeletal muscle disorder", - "muscular dystrophy", - "human disease", - "hereditary skeletal muscle disorder", - "disease" + "qualitative or quantitative defects of calpain", + "neuromuscular disease", + "autosomal recessive limb-girdle muscular dystrophy", + "entity" ], "subject_taxon": null, "subject_taxon_label": null, "predicate": "biolink:has_phenotype", - "object": "HP:0001263", + "object": "HP:0007340", "original_object": null, "object_namespace": "HP", "object_category": "biolink:PhenotypicFeature", "object_closure": [ - "HP:0000001", "UPHENO:0082875", - "UPHENO:0075696", - "UPHENO:0001001", + "UPHENO:0002320", "UPHENO:0001005", - "UPHENO:0001002", - "HP:0000118", - "BFO:0000002", - "HP:0012759", + "HP:0009127", "BFO:0000020", - "UPHENO:0002433", - "HP:0001263", - "UPHENO:0002332", - "HP:0000707", - "UPHENO:0001003", - "UPHENO:0002536", - "HP:0012758", - "UPHENO:0004523", + "UPHENO:0076692", "BFO:0000001", + "BFO:0000004", + "UBERON:0004708", + "UBERON:0000061", + "UBERON:0000026", + "UBERON:0014892", + "HP:0000001", + "UPHENO:0001001", + "UPHENO:0001002", + "HP:0000118", + "UPHENO:0076710", "PATO:0000001", - "HP:0012638", "BFO:0000001", - "BFO:0000002", - "BFO:0000004", "BFO:0000040", "UBERON:0001062", - "UBERON:0000465", - "UBERON:0000061", - "UBERON:0010000", "UBERON:0000467", "UBERON:0000468", - "UBERON:0001016" - ], - "object_label": "Global developmental delay (HPO)", - "object_closure_label": [ - "entity", - "entity", - "continuant", - "continuant", - "independent continuant", - "specifically dependent continuant", - "material entity", + "UBERON:0011216", + "UBERON:0010709", + "UBERON:0010890", + "UPHENO:0075696", + "UPHENO:0080575", + "HP:0001324", + "HP:0003690", + "HP:0003011", + "UPHENO:0002332", + "UPHENO:0001003", + "UPHENO:0002536", + "HP:0040064", + "HP:0011804", + "BFO:0000002", + "PR:000050567", + "UBERON:0002101", + "UBERON:0005090", + "UBERON:0018254", + "UBERON:0010707", + "UBERON:0001630", + "UBERON:0007271", + "UBERON:0014792", + "HP:0007340", + "HP:0011805", + "BFO:0000002", + "UPHENO:0080555", + "UPHENO:0002816", + "UPHENO:0080556", + "UPHENO:0081581", + "HP:0033127", + "UPHENO:0002647", + "UPHENO:0002830", + "UBERON:0000465", + "RO:0002577", + "UBERON:0015212", + "UBERON:0010000", + "UBERON:0000475", + "UBERON:0000062", + "UBERON:0000383", + "UBERON:0001015", + "UBERON:0004480" + ], + "object_label": "Lower limb muscle weakness (HPO)", + "object_closure_label": [ "All (HPO)", + "abnormality of muscle organ physiology", + "Phenotypic abnormality", "Phenotypic abnormality (HPO)", - "Abnormality of the nervous system (HPO)", - "Global developmental delay (HPO)", - "Abnormal nervous system physiology (HPO)", - "Neurodevelopmental delay (HPO)", - "Neurodevelopmental abnormality (HPO)", + "decreased anatomical entity strength", + "abnormal musculature", + "decreased muscle organ strength", + "abnormal multicellular organism morphology", + "Abnormality of the musculoskeletal system (HPO)", + "abnormal musculature of limb", "quality", - "anatomical structure", + "independent continuant", "material anatomical entity", - "anatomical system", - "multicellular organism", - "nervous system", - "anatomical entity", + "system", + "paired limb/fin", + "anatomical structure", + "lateral structure", "multicellular anatomical structure", + "pelvic complex", + "appendage musculature", + "musculature of pelvic complex", + "abnormality of anatomical entity physiology", "phenotype", - "Phenotypic abnormality", - "phenotype by ontology source", + "Abnormal skeletal muscle morphology (HPO)", + "continuant", + "Abnormality of limbs (HPO)", + "continuant", + "protein-containing material entity", + "appendage girdle complex", + "pelvic complex muscle", + "Lower limb muscle weakness (HPO)", "abnormal phenotype by ontology source", - "abnormality of anatomical entity physiology", - "abnormality of nervous system physiology", + "Abnormality of the musculature of the limbs (HPO)", + "specifically dependent continuant", + "abnormal muscle organ morphology", + "Abnormal muscle physiology (HPO)", + "entity", + "muscle structure", + "skeletal musculature", + "organism subdivision", + "organ", + "muscle organ", + "musculature of body", + "musculature", + "musculature of limb", "abnormal anatomical entity", - "abnormal nervous system", + "decreased pelvic complex muscle strength", + "Muscle weakness (HPO)", + "Limb muscle weakness (HPO)", + "Abnormality of the musculature (HPO)", + "abnormality of anatomical entity physiology", + "phenotype by ontology source", "abnormal anatomical entity", - "abnormality of anatomical entity physiology" + "abnormal anatomical entity morphology", + "entity", + "abnormal limb", + "material entity", + "anatomical entity", + "limb", + "anatomical system", + "multicellular organism", + "organ system subdivision", + "appendage", + "skeletal muscle organ" ], "object_taxon": null, "object_taxon_label": null, @@ -2419,36 +2839,46 @@ "aggregator_knowledge_source": ["infores:monarchinitiative"], "negated": null, "pathway": null, - "evidence_count": 4, - "has_evidence": ["ECO:0000304"], + "evidence_count": 2, + "has_evidence": ["ECO:0000269"], "has_evidence_links": [ { - "id": "ECO:0000304", - "url": "http://purl.obolibrary.org/obo/ECO_0000304" + "id": "ECO:0000269", + "url": "http://purl.obolibrary.org/obo/ECO_0000269" } ], + "grouping_key": "MONDO:0009675\ud83c\udf6a\ud83c\udf6abiolink:has_phenotype\ud83c\udf6aHP:0007340", "provided_by": "hpoa_disease_to_phenotype_edges", "provided_by_link": { "id": "hpoa_disease_to_phenotype", "url": "https://monarch-initiative.github.io/monarch-ingest/Sources/hpoa/#disease_to_phenotype" }, - "publications": ["OMIM:615356"], + "publications": ["PMID:16607617"], "publications_links": [ { - "id": "OMIM:615356", - "url": "http://identifiers.org/mim/615356" + "id": "PMID:16607617", + "url": "http://identifiers.org/pubmed/16607617" } ], "qualifiers": [], - "frequency_qualifier": null, + "frequency_qualifier": "HP:0040282", "onset_qualifier": null, "sex_qualifier": null, "stage_qualifier": null, - "frequency_qualifier_label": null, - "frequency_qualifier_namespace": null, - "frequency_qualifier_category": null, - "frequency_qualifier_closure": [], - "frequency_qualifier_closure_label": [], + "qualifiers_label": null, + "qualifiers_namespace": null, + "qualifiers_category": null, + "qualifiers_closure": [], + "qualifiers_closure_label": [], + "frequency_qualifier_label": "Frequent (HPO)", + "frequency_qualifier_namespace": "HP", + "frequency_qualifier_category": "biolink:PhenotypicFeature", + "frequency_qualifier_closure": ["HP:0040282", "HP:0000001", "HP:0040279"], + "frequency_qualifier_closure_label": [ + "All (HPO)", + "Frequent (HPO)", + "Frequency (HPO)" + ], "onset_qualifier_label": null, "onset_qualifier_namespace": null, "onset_qualifier_category": null, @@ -2466,132 +2896,156 @@ "stage_qualifier_closure_label": [] }, { - "id": "uuid:8a99d59c-5d8c-11ee-9b27-2b20ed86a9d9", + "id": "uuid:c9d8bdf9-7529-11ee-b012-cbd37f5c3759", "category": "biolink:DiseaseToPhenotypicFeatureAssociation", - "subject": "MONDO:0024607", - "original_subject": "OMIM:617404", + "subject": "MONDO:0009676", + "original_subject": "OMIM:253601", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ - "MONDO:0000001", - "MONDO:0024607", - "MONDO:0005071", - "MONDO:0020121", - "MONDO:0700223", + "MONDO:0016971", "BFO:0000002", - "BFO:0000017", "BFO:0000020", + "MONDO:0005336", + "MONDO:0009676", + "MONDO:0015152", + "MONDO:0000429", + "MONDO:0005071", + "MONDO:0006025", "BFO:0000016", + "MONDO:0016139", + "OGMS:0000031", + "MONDO:0003847", + "BFO:0000001", + "MONDO:0016145", + "MONDO:0020121", + "BFO:0000017", "MONDO:0020120", "MONDO:0019056", + "MONDO:0000001", + "MONDO:0700223", + "MONDO:0016106", "MONDO:0700096", - "MONDO:0005336", "MONDO:0002081", - "OGMS:0000031", - "MONDO:0003847", - "MONDO:0003939", - "BFO:0000001", - "MONDO:0002320", - "MONDO:0019950" + "MONDO:0003939" ], - "subject_label": "congenital muscular dystrophy with cataracts and intellectual disability", + "subject_label": "autosomal recessive limb-girdle muscular dystrophy type 2B", "subject_closure_label": [ - "entity", - "continuant", + "limb-girdle muscular dystrophy", + "muscular dystrophy", + "progressive muscular dystrophy", + "human disease", + "musculoskeletal system disorder", + "disease", + "muscle tissue disorder", + "qualitative or quantitative defects of dysferlin", + "hereditary skeletal muscle disorder", + "autosomal recessive disease", "disposition", - "realizable entity", - "specifically dependent continuant", + "qualitative or quantitative protein defects in neuromuscular diseases", + "autosomal recessive limb-girdle muscular dystrophy type 2B", "disease", - "musculoskeletal system disorder", - "congenital nervous system disorder", + "continuant", + "specifically dependent continuant", + "myopathy", "hereditary disease", - "muscle tissue disorder", + "autosomal genetic disease", "nervous system disorder", - "myopathy", - "neuromuscular disease", - "congenital muscular dystrophy", + "realizable entity", "skeletal muscle disorder", - "muscular dystrophy", - "congenital muscular dystrophy with cataracts and intellectual disability", - "human disease", - "hereditary skeletal muscle disorder", - "disease" + "neuromuscular disease", + "autosomal recessive limb-girdle muscular dystrophy", + "entity" ], "subject_taxon": null, "subject_taxon_label": null, "predicate": "biolink:has_phenotype", - "object": "HP:0001263", + "object": "HP:0003701", "original_object": null, "object_namespace": "HP", "object_category": "biolink:PhenotypicFeature", "object_closure": [ - "HP:0000001", "UPHENO:0082875", - "UPHENO:0075696", + "UPHENO:0002320", + "BFO:0000002", + "BFO:0000004", + "UBERON:0000061", + "HP:0000001", "UPHENO:0001001", - "UPHENO:0001005", "UPHENO:0001002", "HP:0000118", - "BFO:0000002", - "HP:0012759", "BFO:0000020", - "UPHENO:0002433", - "HP:0001263", - "UPHENO:0002332", - "HP:0000707", "UPHENO:0001003", - "UPHENO:0002536", - "HP:0012758", - "UPHENO:0004523", "BFO:0000001", "PATO:0000001", - "HP:0012638", "BFO:0000001", - "BFO:0000002", - "BFO:0000004", "BFO:0000040", "UBERON:0001062", - "UBERON:0000465", - "UBERON:0000061", - "UBERON:0010000", "UBERON:0000467", "UBERON:0000468", - "UBERON:0001016" + "UBERON:0011216", + "UPHENO:0075696", + "HP:0001324", + "HP:0003011", + "UPHENO:0002332", + "UPHENO:0002536", + "HP:0011804", + "BFO:0000002", + "UBERON:0000465", + "UBERON:0005090", + "UBERON:0001630", + "UPHENO:0001005", + "HP:0003701", + "UPHENO:0080555", + "UPHENO:0002816", + "UPHENO:0080556", + "HP:0033127", + "UBERON:0010000", + "UBERON:0000062", + "UBERON:0000383", + "UBERON:0001015" ], - "object_label": "Global developmental delay (HPO)", + "object_label": "Proximal muscle weakness (HPO)", "object_closure_label": [ - "entity", - "entity", - "continuant", - "continuant", - "independent continuant", - "specifically dependent continuant", - "material entity", "All (HPO)", + "abnormality of muscle organ physiology", + "Phenotypic abnormality", "Phenotypic abnormality (HPO)", - "Abnormality of the nervous system (HPO)", - "Global developmental delay (HPO)", - "Abnormal nervous system physiology (HPO)", - "Neurodevelopmental delay (HPO)", - "Neurodevelopmental abnormality (HPO)", + "decreased anatomical entity strength", + "abnormal musculature", + "decreased muscle organ strength", + "Abnormality of the musculoskeletal system (HPO)", "quality", + "independent continuant", "anatomical structure", - "material anatomical entity", - "anatomical system", - "multicellular organism", - "nervous system", - "anatomical entity", "multicellular anatomical structure", + "abnormality of anatomical entity physiology", "phenotype", - "Phenotypic abnormality", - "phenotype by ontology source", "abnormal phenotype by ontology source", - "abnormality of anatomical entity physiology", - "abnormality of nervous system physiology", + "Proximal muscle weakness (HPO)", + "specifically dependent continuant", + "phenotype by ontology source", + "continuant", + "material anatomical entity", + "continuant", + "Abnormal muscle physiology (HPO)", + "entity", + "muscle structure", + "organ", + "muscle organ", + "musculature of body", + "musculature", "abnormal anatomical entity", - "abnormal nervous system", + "Muscle weakness (HPO)", + "Abnormality of the musculature (HPO)", + "abnormality of anatomical entity physiology", "abnormal anatomical entity", - "abnormality of anatomical entity physiology" + "entity", + "material entity", + "anatomical entity", + "anatomical system", + "multicellular organism", + "organ system subdivision" ], "object_taxon": null, "object_taxon_label": null, @@ -2599,36 +3053,50 @@ "aggregator_knowledge_source": ["infores:monarchinitiative"], "negated": null, "pathway": null, - "evidence_count": 4, - "has_evidence": ["ECO:0000304"], + "evidence_count": 3, + "has_evidence": ["ECO:0000269"], "has_evidence_links": [ { - "id": "ECO:0000304", - "url": "http://purl.obolibrary.org/obo/ECO_0000304" + "id": "ECO:0000269", + "url": "http://purl.obolibrary.org/obo/ECO_0000269" } ], + "grouping_key": "MONDO:0009676\ud83c\udf6a\ud83c\udf6abiolink:has_phenotype\ud83c\udf6aHP:0003701", "provided_by": "hpoa_disease_to_phenotype_edges", "provided_by_link": { "id": "hpoa_disease_to_phenotype", "url": "https://monarch-initiative.github.io/monarch-ingest/Sources/hpoa/#disease_to_phenotype" }, - "publications": ["OMIM:617404"], + "publications": ["PMID:9731527", "PMID:9009996"], "publications_links": [ { - "id": "OMIM:617404", - "url": "http://identifiers.org/mim/617404" + "id": "PMID:9731527", + "url": "http://identifiers.org/pubmed/9731527" + }, + { + "id": "PMID:9009996", + "url": "http://identifiers.org/pubmed/9009996" } ], "qualifiers": [], - "frequency_qualifier": null, + "frequency_qualifier": "HP:0040280", "onset_qualifier": null, "sex_qualifier": null, "stage_qualifier": null, - "frequency_qualifier_label": null, - "frequency_qualifier_namespace": null, - "frequency_qualifier_category": null, - "frequency_qualifier_closure": [], - "frequency_qualifier_closure_label": [], + "qualifiers_label": null, + "qualifiers_namespace": null, + "qualifiers_category": null, + "qualifiers_closure": [], + "qualifiers_closure_label": [], + "frequency_qualifier_label": "Obligate (HPO)", + "frequency_qualifier_namespace": "HP", + "frequency_qualifier_category": "biolink:PhenotypicFeature", + "frequency_qualifier_closure": ["HP:0000001", "HP:0040280", "HP:0040279"], + "frequency_qualifier_closure_label": [ + "All (HPO)", + "Obligate (HPO)", + "Frequency (HPO)" + ], "onset_qualifier_label": null, "onset_qualifier_namespace": null, "onset_qualifier_category": null, @@ -2646,198 +3114,152 @@ "stage_qualifier_closure_label": [] }, { - "id": "uuid:851bc9ee-5d8c-11ee-9b27-2b20ed86a9d9", + "id": "uuid:c9c8bf35-7529-11ee-b012-cbd37f5c3759", "category": "biolink:DiseaseToPhenotypicFeatureAssociation", - "subject": "MONDO:0009683", - "original_subject": "OMIM:254110", + "subject": "MONDO:0008050", + "original_subject": "OMIM:160500", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ - "MONDO:0000001", - "MONDO:0016971", - "MONDO:0000429", - "MONDO:0005071", - "MONDO:0020121", - "MONDO:0700223", "BFO:0000002", + "MONDO:0016195", + "MONDO:0005336", + "MONDO:0018949", + "MONDO:0005071", + "MONDO:0008050", + "BFO:0000016", + "MONDO:0016139", + "OGMS:0000031", + "MONDO:0003847", + "BFO:0000001", + "MONDO:0020121", + "MONDO:0019952", "BFO:0000017", "BFO:0000020", - "MONDO:0006025", - "MONDO:0016106", - "BFO:0000016", "MONDO:0020120", "MONDO:0019056", - "MONDO:0016139", + "MONDO:0000001", + "MONDO:0700223", "MONDO:0700096", - "MONDO:0005336", "MONDO:0002081", - "OGMS:0000031", - "MONDO:0003847", "MONDO:0003939", - "MONDO:0015152", - "BFO:0000001", - "MONDO:0016153", - "MONDO:0009683" + "MONDO:0002320" ], - "subject_label": "autosomal recessive limb-girdle muscular dystrophy type 2H", + "subject_label": "MYH7-related skeletal myopathy", "subject_closure_label": [ - "entity", - "continuant", + "muscular dystrophy", + "human disease", + "musculoskeletal system disorder", + "disease", + "muscle tissue disorder", + "congenital nervous system disorder", + "hereditary skeletal muscle disorder", + "MYH7-related skeletal myopathy", "disposition", - "realizable entity", - "specifically dependent continuant", + "qualitative or quantitative protein defects in neuromuscular diseases", + "distal myopathy", "disease", - "autosomal genetic disease", - "musculoskeletal system disorder", + "continuant", + "qualitative or quantitative defects of beta-myosin heavy chain (MYH7)", + "myopathy", "hereditary disease", - "muscle tissue disorder", "nervous system disorder", - "myopathy", - "autosomal recessive disease", - "autosomal recessive limb-girdle muscular dystrophy type 2H", - "autosomal recessive limb-girdle muscular dystrophy", - "progressive muscular dystrophy", - "qualitative or quantitative protein defects in neuromuscular diseases", - "qualitative or quantitative defects of TRIM32", - "limb-girdle muscular dystrophy", - "neuromuscular disease", + "congenital myopathy", + "realizable entity", + "specifically dependent continuant", "skeletal muscle disorder", - "muscular dystrophy", - "human disease", - "hereditary skeletal muscle disorder", - "disease" + "neuromuscular disease", + "entity" ], "subject_taxon": null, "subject_taxon_label": null, "predicate": "biolink:has_phenotype", - "object": "HP:0001265", + "object": "HP:0003701", "original_object": null, "object_namespace": "HP", "object_category": "biolink:PhenotypicFeature", "object_closure": [ - "HP:0000001", "UPHENO:0082875", - "UPHENO:0075696", - "UPHENO:0078622", - "UPHENO:0049586", - "UPHENO:0080377", + "UPHENO:0002320", + "BFO:0000002", + "BFO:0000004", + "UBERON:0000061", + "HP:0000001", "UPHENO:0001001", - "UPHENO:0052915", - "UPHENO:0049622", - "UPHENO:0080585", - "HP:0001265", - "HP:0100022", - "UPHENO:0001005", - "HP:0031826", "UPHENO:0001002", "HP:0000118", - "BFO:0000002", - "UPHENO:0052178", "BFO:0000020", - "UPHENO:0002433", - "UPHENO:0050613", - "UPHENO:0005625", - "UPHENO:0050079", - "UPHENO:0005433", - "UPHENO:0002332", - "UPHENO:0050606", - "HP:0001315", - "HP:0000707", "UPHENO:0001003", - "UPHENO:0002536", - "HP:0000708", - "UPHENO:0079826", - "UPHENO:0004523", - "HP:0011446", - "UPHENO:0079833", - "UPHENO:0049587", "BFO:0000001", "PATO:0000001", - "HP:0012638", "BFO:0000001", - "BFO:0000003", - "BFO:0000002", - "BFO:0000015", - "BFO:0000004", - "GO:0008150", "BFO:0000040", "UBERON:0001062", - "GO:0050896", - "GO:0032501", - "UBERON:0000465", - "GO:0009605", - "GO:0050879", - "GO:0007610", - "GO:0003008", - "UBERON:0000061", - "GO:0060004", - "GO:0050881", - "NBO:0000313", - "GO:0050877", - "UBERON:0010000", "UBERON:0000467", - "GO:0050882", - "NBO:0000338", - "GO:0050905", "UBERON:0000468", - "UBERON:0001016", - "NBO:0000403", - "NBO:0000001", - "NBO:0000388", - "NBO:0000389" + "UBERON:0011216", + "UPHENO:0075696", + "HP:0001324", + "HP:0003011", + "UPHENO:0002332", + "UPHENO:0002536", + "HP:0011804", + "BFO:0000002", + "UBERON:0000465", + "UBERON:0005090", + "UBERON:0001630", + "UPHENO:0001005", + "HP:0003701", + "UPHENO:0080555", + "UPHENO:0002816", + "UPHENO:0080556", + "HP:0033127", + "UBERON:0010000", + "UBERON:0000062", + "UBERON:0000383", + "UBERON:0001015" ], - "object_label": "Hyporeflexia (HPO)", + "object_label": "Proximal muscle weakness (HPO)", "object_closure_label": [ - "entity", - "entity", - "continuant", - "continuant", - "independent continuant", - "specifically dependent continuant", - "material entity", "All (HPO)", + "abnormality of muscle organ physiology", + "Phenotypic abnormality", "Phenotypic abnormality (HPO)", - "Abnormality of the nervous system (HPO)", - "Behavioral abnormality (HPO)", - "Hyporeflexia (HPO)", - "Reduced tendon reflexes (HPO)", - "Abnormality of higher mental function (HPO)", - "Abnormal nervous system physiology (HPO)", - "Abnormal reflex (HPO)", - "Abnormality of movement (HPO)", + "decreased anatomical entity strength", + "abnormal musculature", + "decreased muscle organ strength", + "Abnormality of the musculoskeletal system (HPO)", "quality", + "independent continuant", "anatomical structure", - "material anatomical entity", - "anatomical system", - "multicellular organism", - "nervous system", - "anatomical entity", "multicellular anatomical structure", + "abnormality of anatomical entity physiology", "phenotype", - "Phenotypic abnormality", - "phenotype by ontology source", "abnormal phenotype by ontology source", - "abnormality of anatomical entity physiology", - "abnormality of nervous system physiology", + "Proximal muscle weakness (HPO)", + "specifically dependent continuant", + "phenotype by ontology source", + "continuant", + "material anatomical entity", + "continuant", + "Abnormal muscle physiology (HPO)", + "entity", + "muscle structure", + "organ", + "muscle organ", + "musculature of body", + "musculature", "abnormal anatomical entity", - "abnormal nervous system", - "decreased biological_process", - "decreased reflex", - "abnormal response to stimulus", - "abnormal biological_process", - "abnormal behavior", - "abnormal response to external stimulus", - "abnormal voluntary musculoskeletal movement", - "abnormal musculoskeletal movement", - "decreased qualitatively biological_process", - "decreased qualitatively response to stimulus", + "Muscle weakness (HPO)", + "Abnormality of the musculature (HPO)", + "abnormality of anatomical entity physiology", "abnormal anatomical entity", - "abnormal voluntary movement behavior", - "abnormal behavior process", - "abnormal voluntary movement behavior", - "changed biological_process rate", - "abnormal behavior process", - "abnormality of anatomical entity physiology" + "entity", + "material entity", + "anatomical entity", + "anatomical system", + "multicellular organism", + "organ system subdivision" ], "object_taxon": null, "object_taxon_label": null, @@ -2845,36 +3267,46 @@ "aggregator_knowledge_source": ["infores:monarchinitiative"], "negated": null, "pathway": null, - "evidence_count": 4, - "has_evidence": ["ECO:0000501"], + "evidence_count": 2, + "has_evidence": ["ECO:0000304"], "has_evidence_links": [ { - "id": "ECO:0000501", - "url": "http://purl.obolibrary.org/obo/ECO_0000501" + "id": "ECO:0000304", + "url": "http://purl.obolibrary.org/obo/ECO_0000304" } ], + "grouping_key": "MONDO:0008050\ud83c\udf6a\ud83c\udf6abiolink:has_phenotype\ud83c\udf6aHP:0003701", "provided_by": "hpoa_disease_to_phenotype_edges", "provided_by_link": { "id": "hpoa_disease_to_phenotype", "url": "https://monarch-initiative.github.io/monarch-ingest/Sources/hpoa/#disease_to_phenotype" }, - "publications": ["OMIM:254110"], + "publications": ["OMIM:160500"], "publications_links": [ { - "id": "OMIM:254110", - "url": "http://identifiers.org/mim/254110" + "id": "OMIM:160500", + "url": "http://identifiers.org/mim/160500" } ], "qualifiers": [], - "frequency_qualifier": null, + "frequency_qualifier": "HP:0040283", "onset_qualifier": null, "sex_qualifier": null, "stage_qualifier": null, - "frequency_qualifier_label": null, - "frequency_qualifier_namespace": null, - "frequency_qualifier_category": null, - "frequency_qualifier_closure": [], - "frequency_qualifier_closure_label": [], + "qualifiers_label": null, + "qualifiers_namespace": null, + "qualifiers_category": null, + "qualifiers_closure": [], + "qualifiers_closure_label": [], + "frequency_qualifier_label": "Occasional (HPO)", + "frequency_qualifier_namespace": "HP", + "frequency_qualifier_category": "biolink:PhenotypicFeature", + "frequency_qualifier_closure": ["HP:0000001", "HP:0040283", "HP:0040279"], + "frequency_qualifier_closure_label": [ + "All (HPO)", + "Occasional (HPO)", + "Frequency (HPO)" + ], "onset_qualifier_label": null, "onset_qualifier_namespace": null, "onset_qualifier_category": null, @@ -2892,210 +3324,212 @@ "stage_qualifier_closure_label": [] }, { - "id": "uuid:899a8f89-5d8c-11ee-9b27-2b20ed86a9d9", + "id": "uuid:c9c8bf37-7529-11ee-b012-cbd37f5c3759", "category": "biolink:DiseaseToPhenotypicFeatureAssociation", - "subject": "MONDO:0010311", - "original_subject": "OMIM:300376", + "subject": "MONDO:0008050", + "original_subject": "OMIM:160500", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ - "MONDO:0004994", - "MONDO:0000001", + "BFO:0000002", + "MONDO:0016195", + "MONDO:0005336", + "MONDO:0018949", "MONDO:0005071", - "MONDO:0016147", - "MONDO:0005267", + "MONDO:0008050", + "BFO:0000016", + "MONDO:0016139", + "OGMS:0000031", + "MONDO:0003847", + "BFO:0000001", "MONDO:0020121", - "MONDO:0004995", - "MONDO:0700223", - "BFO:0000002", + "MONDO:0019952", "BFO:0000017", - "MONDO:0010542", "BFO:0000020", - "MONDO:0016106", - "MONDO:0015470", - "MONDO:0005217", - "MONDO:0016899", - "BFO:0000016", "MONDO:0020120", "MONDO:0019056", - "MONDO:0016139", + "MONDO:0000001", + "MONDO:0700223", "MONDO:0700096", - "MONDO:0000591", - "MONDO:0005336", "MONDO:0002081", - "MONDO:0016333", - "OGMS:0000031", - "MONDO:0005021", - "MONDO:0003847", "MONDO:0003939", - "BFO:0000001", - "MONDO:0010311" + "MONDO:0002320" ], - "subject_label": "Becker muscular dystrophy", + "subject_label": "MYH7-related skeletal myopathy", "subject_closure_label": [ - "entity", - "continuant", + "muscular dystrophy", + "human disease", + "musculoskeletal system disorder", + "disease", + "muscle tissue disorder", + "congenital nervous system disorder", + "hereditary skeletal muscle disorder", + "MYH7-related skeletal myopathy", "disposition", - "realizable entity", - "specifically dependent continuant", + "qualitative or quantitative protein defects in neuromuscular diseases", + "distal myopathy", "disease", - "intrinsic cardiomyopathy", - "musculoskeletal system disorder", + "continuant", + "qualitative or quantitative defects of beta-myosin heavy chain (MYH7)", + "myopathy", "hereditary disease", - "muscle tissue disorder", - "cardiomyopathy", - "cardiovascular disorder", - "dilated cardiomyopathy", "nervous system disorder", - "familial cardiomyopathy", - "heart disorder", - "myopathy", - "Becker muscular dystrophy", - "dilated cardiomyopathy 3B", - "familial isolated dilated cardiomyopathy", - "progressive muscular dystrophy", - "qualitative or quantitative protein defects in neuromuscular diseases", - "qualitative or quantitative defects of dystrophin", - "familial dilated cardiomyopathy", - "Duchenne and Becker muscular dystrophy", - "neuromuscular disease", + "congenital myopathy", + "realizable entity", + "specifically dependent continuant", "skeletal muscle disorder", - "muscular dystrophy", - "human disease", - "hereditary skeletal muscle disorder", - "disease" + "neuromuscular disease", + "entity" ], "subject_taxon": null, "subject_taxon_label": null, "predicate": "biolink:has_phenotype", - "object": "HP:0001265", + "object": "HP:0001644", "original_object": null, "object_namespace": "HP", "object_category": "biolink:PhenotypicFeature", "object_closure": [ - "HP:0000001", "UPHENO:0082875", - "UPHENO:0075696", - "UPHENO:0078622", - "UPHENO:0049586", - "UPHENO:0080377", - "UPHENO:0001001", - "UPHENO:0052915", - "UPHENO:0049622", - "UPHENO:0080585", - "HP:0001265", - "HP:0100022", + "HP:0001637", "UPHENO:0001005", - "HP:0031826", + "BFO:0000020", + "UPHENO:0077800", + "UPHENO:0066927", + "UPHENO:0076692", + "PATO:0000001", + "BFO:0000004", + "UBERON:0004535", + "UBERON:0011676", + "UBERON:0013701", + "UBERON:0002349", + "UBERON:0000915", + "UBERON:0002100", + "UBERON:0005181", + "UBERON:0002075", + "UBERON:0015228", + "HP:0000001", + "UPHENO:0001001", + "HP:0001644", + "HP:0030680", "UPHENO:0001002", "HP:0000118", - "BFO:0000002", - "UPHENO:0052178", - "BFO:0000020", - "UPHENO:0002433", - "UPHENO:0050613", - "UPHENO:0005625", - "UPHENO:0050079", - "UPHENO:0005433", - "UPHENO:0002332", - "UPHENO:0050606", - "HP:0001315", - "HP:0000707", + "HP:0001627", + "UPHENO:0076776", "UPHENO:0001003", - "UPHENO:0002536", - "HP:0000708", - "UPHENO:0079826", - "UPHENO:0004523", - "HP:0011446", - "UPHENO:0079833", - "UPHENO:0049587", + "UPHENO:0024906", "BFO:0000001", - "PATO:0000001", - "HP:0012638", "BFO:0000001", - "BFO:0000003", - "BFO:0000002", - "BFO:0000015", - "BFO:0000004", - "GO:0008150", "BFO:0000040", - "UBERON:0001062", - "GO:0050896", - "GO:0032501", - "UBERON:0000465", - "GO:0009605", - "GO:0050879", - "GO:0007610", - "GO:0003008", - "UBERON:0000061", - "GO:0060004", - "GO:0050881", - "NBO:0000313", - "GO:0050877", "UBERON:0010000", "UBERON:0000467", - "GO:0050882", - "NBO:0000338", - "GO:0050905", "UBERON:0000468", - "UBERON:0001016", - "NBO:0000403", - "NBO:0000001", - "NBO:0000388", - "NBO:0000389" + "UBERON:0011216", + "UBERON:0000064", + "UPHENO:0075696", + "HP:0001626", + "UPHENO:0080362", + "HP:0001638", + "BFO:0000002", + "UPHENO:0002332", + "UPHENO:0002536", + "UPHENO:0076810", + "BFO:0000002", + "PR:000050567", + "UBERON:0004120", + "UBERON:0000948", + "UBERON:0001009", + "UBERON:0005983", + "UBERON:0009569", + "UBERON:0013702", + "UBERON:0005177", + "UBERON:0003103", + "UBERON:0018260", + "UBERON:0015410", + "UPHENO:0076781", + "UPHENO:0081581", + "UBERON:0001062", + "UBERON:0000465", + "UBERON:0000061", + "UBERON:0010314", + "UBERON:0000475", + "UBERON:0000062", + "UBERON:0000383", + "UBERON:0000060", + "UBERON:0004923", + "UBERON:0005178", + "UBERON:0007100" ], - "object_label": "Hyporeflexia (HPO)", + "object_label": "Dilated cardiomyopathy (HPO)", "object_closure_label": [ - "entity", - "entity", - "continuant", - "continuant", - "independent continuant", - "specifically dependent continuant", - "material entity", "All (HPO)", + "abnormal cardiovascular system", + "Cardiomyopathy (HPO)", + "Phenotypic abnormality", "Phenotypic abnormality (HPO)", - "Abnormality of the nervous system (HPO)", - "Behavioral abnormality (HPO)", - "Hyporeflexia (HPO)", - "Reduced tendon reflexes (HPO)", - "Abnormality of higher mental function (HPO)", - "Abnormal nervous system physiology (HPO)", - "Abnormal reflex (HPO)", - "Abnormality of movement (HPO)", - "quality", - "anatomical structure", + "abnormal myocardium morphology", + "abnormal multicellular organism morphology", + "independent continuant", "material anatomical entity", - "anatomical system", - "multicellular organism", - "nervous system", - "anatomical entity", - "multicellular anatomical structure", + "cardiovascular system", + "structure with developmental contribution from neural crest", + "layer of muscle tissue", + "abnormality of anatomical entity physiology", + "Abnormal myocardium morphology (HPO)", "phenotype", - "Phenotypic abnormality", + "Abnormality of the cardiovascular system (HPO)", + "Abnormal heart morphology (HPO)", + "abnormal cardiovascular system morphology", "phenotype by ontology source", + "abnormally decreased functionality of the anatomical entity", + "abnormal heart morphology", + "quality", + "continuant", + "protein-containing material entity", + "heart", + "subdivision of trunk", + "body proper", + "trunk region element", + "compound organ", + "heart plus pericardium", "abnormal phenotype by ontology source", - "abnormality of anatomical entity physiology", - "abnormality of nervous system physiology", + "specifically dependent continuant", + "abnormally decreased functionality of the myocardium", + "anatomical entity dysfunction in independent continuant", + "entity", + "anatomical entity", + "anatomical structure", + "mesoderm-derived structure", + "organism subdivision", + "organ", + "circulatory system", + "heart layer", + "musculature of body", + "anatomical wall", + "organ component layer", + "thoracic cavity element", + "primary circulatory organ", "abnormal anatomical entity", - "abnormal nervous system", - "decreased biological_process", - "decreased reflex", - "abnormal response to stimulus", - "abnormal biological_process", - "abnormal behavior", - "abnormal response to external stimulus", - "abnormal voluntary musculoskeletal movement", - "abnormal musculoskeletal movement", - "decreased qualitatively biological_process", - "decreased qualitatively response to stimulus", + "Dilated cardiomyopathy (HPO)", + "Abnormality of cardiovascular system morphology (HPO)", + "continuant", + "abnormality of anatomical entity physiology", "abnormal anatomical entity", - "abnormal voluntary movement behavior", - "abnormal behavior process", - "abnormal voluntary movement behavior", - "changed biological_process rate", - "abnormal behavior process", - "abnormality of anatomical entity physiology" + "abnormal anatomical entity morphology", + "entity", + "material entity", + "multicellular anatomical structure", + "anatomical system", + "multicellular organism", + "organ system subdivision", + "organ part", + "subdivision of organism along main body axis", + "main body axis", + "myocardium", + "thoracic segment of trunk", + "trunk", + "thoracic segment organ", + "viscus", + "circulatory organ" ], "object_taxon": null, "object_taxon_label": null, @@ -3103,7 +3537,7 @@ "aggregator_knowledge_source": ["infores:monarchinitiative"], "negated": null, "pathway": null, - "evidence_count": 4, + "evidence_count": 2, "has_evidence": ["ECO:0000304"], "has_evidence_links": [ { @@ -3111,28 +3545,38 @@ "url": "http://purl.obolibrary.org/obo/ECO_0000304" } ], + "grouping_key": "MONDO:0008050\ud83c\udf6a\ud83c\udf6abiolink:has_phenotype\ud83c\udf6aHP:0001644", "provided_by": "hpoa_disease_to_phenotype_edges", "provided_by_link": { "id": "hpoa_disease_to_phenotype", "url": "https://monarch-initiative.github.io/monarch-ingest/Sources/hpoa/#disease_to_phenotype" }, - "publications": ["OMIM:300376"], + "publications": ["OMIM:160500"], "publications_links": [ { - "id": "OMIM:300376", - "url": "http://identifiers.org/mim/300376" + "id": "OMIM:160500", + "url": "http://identifiers.org/mim/160500" } ], "qualifiers": [], - "frequency_qualifier": null, + "frequency_qualifier": "HP:0040283", "onset_qualifier": null, "sex_qualifier": null, "stage_qualifier": null, - "frequency_qualifier_label": null, - "frequency_qualifier_namespace": null, - "frequency_qualifier_category": null, - "frequency_qualifier_closure": [], - "frequency_qualifier_closure_label": [], + "qualifiers_label": null, + "qualifiers_namespace": null, + "qualifiers_category": null, + "qualifiers_closure": [], + "qualifiers_closure_label": [], + "frequency_qualifier_label": "Occasional (HPO)", + "frequency_qualifier_namespace": "HP", + "frequency_qualifier_category": "biolink:PhenotypicFeature", + "frequency_qualifier_closure": ["HP:0000001", "HP:0040283", "HP:0040279"], + "frequency_qualifier_closure_label": [ + "All (HPO)", + "Occasional (HPO)", + "Frequency (HPO)" + ], "onset_qualifier_label": null, "onset_qualifier_namespace": null, "onset_qualifier_category": null, @@ -3150,210 +3594,292 @@ "stage_qualifier_closure_label": [] }, { - "id": "uuid:8aea255f-5d8c-11ee-9b27-2b20ed86a9d9", + "id": "uuid:c9c8bff0-7529-11ee-b012-cbd37f5c3759", "category": "biolink:DiseaseToPhenotypicFeatureAssociation", - "subject": "MONDO:0010679", - "original_subject": "OMIM:310200", + "subject": "MONDO:0009675", + "original_subject": "OMIM:253600", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ - "MONDO:0004994", - "MONDO:0000001", - "MONDO:0010679", + "MONDO:0016971", + "MONDO:0005336", + "MONDO:0015152", + "MONDO:0000429", "MONDO:0005071", - "MONDO:0016147", - "MONDO:0005267", + "MONDO:0006025", + "BFO:0000016", + "MONDO:0016139", + "OGMS:0000031", + "BFO:0000001", "MONDO:0020121", - "MONDO:0004995", - "MONDO:0700223", - "BFO:0000002", "BFO:0000017", - "MONDO:0010542", "BFO:0000020", - "MONDO:0016106", - "MONDO:0015470", - "MONDO:0005217", - "MONDO:0016899", - "BFO:0000016", + "MONDO:0009675", "MONDO:0020120", + "MONDO:0016152", "MONDO:0019056", - "MONDO:0016139", + "MONDO:0000001", + "MONDO:0700223", + "BFO:0000002", + "MONDO:0016106", "MONDO:0700096", - "MONDO:0000591", - "MONDO:0005336", "MONDO:0002081", - "MONDO:0016333", - "OGMS:0000031", - "MONDO:0005021", "MONDO:0003847", - "MONDO:0003939", - "BFO:0000001" + "MONDO:0003939" ], - "subject_label": "Duchenne muscular dystrophy", + "subject_label": "autosomal recessive limb-girdle muscular dystrophy type 2A", "subject_closure_label": [ - "entity", - "continuant", - "disposition", - "realizable entity", - "specifically dependent continuant", - "disease", - "intrinsic cardiomyopathy", + "limb-girdle muscular dystrophy", + "muscular dystrophy", + "progressive muscular dystrophy", + "human disease", "musculoskeletal system disorder", + "disease", "hereditary disease", "muscle tissue disorder", - "cardiomyopathy", - "cardiovascular disorder", - "dilated cardiomyopathy", - "nervous system disorder", - "familial cardiomyopathy", - "heart disorder", - "myopathy", - "dilated cardiomyopathy 3B", - "Duchenne muscular dystrophy", - "familial isolated dilated cardiomyopathy", - "progressive muscular dystrophy", + "hereditary skeletal muscle disorder", + "continuant", + "autosomal recessive disease", + "disposition", "qualitative or quantitative protein defects in neuromuscular diseases", - "qualitative or quantitative defects of dystrophin", - "familial dilated cardiomyopathy", - "Duchenne and Becker muscular dystrophy", - "neuromuscular disease", + "disease", + "myopathy", + "autosomal genetic disease", + "nervous system disorder", + "realizable entity", + "specifically dependent continuant", + "autosomal recessive limb-girdle muscular dystrophy type 2A", "skeletal muscle disorder", - "muscular dystrophy", - "human disease", - "hereditary skeletal muscle disorder", - "disease" + "qualitative or quantitative defects of calpain", + "neuromuscular disease", + "autosomal recessive limb-girdle muscular dystrophy", + "entity" ], "subject_taxon": null, "subject_taxon_label": null, "predicate": "biolink:has_phenotype", - "object": "HP:0001265", + "object": "HP:0010628", "original_object": null, "object_namespace": "HP", "object_category": "biolink:PhenotypicFeature", "object_closure": [ - "HP:0000001", "UPHENO:0082875", - "UPHENO:0075696", - "UPHENO:0078622", - "UPHENO:0049586", - "UPHENO:0080377", - "UPHENO:0001001", - "UPHENO:0052915", - "UPHENO:0049622", - "UPHENO:0080585", - "HP:0001265", - "HP:0100022", - "UPHENO:0001005", - "HP:0031826", + "UPHENO:0076772", + "UPHENO:0002320", + "UPHENO:0005116", + "HP:0031910", + "HP:0011799", + "HP:0410008", + "UPHENO:0076692", + "BFO:0000001", + "PATO:0000001", + "HP:0012638", + "BFO:0000004", + "UBERON:0001016", + "UBERON:0001021", + "UBERON:0000153", + "UBERON:0011676", + "UBERON:0013701", + "UBERON:0014892", + "UBERON:0015789", + "UBERON:0011779", + "UBERON:0000033", + "HP:0000001", + "HP:0000152", + "UPHENO:0002764", "UPHENO:0001002", "HP:0000118", - "BFO:0000002", - "UPHENO:0052178", "BFO:0000020", "UPHENO:0002433", - "UPHENO:0050613", - "UPHENO:0005625", - "UPHENO:0050079", - "UPHENO:0005433", - "UPHENO:0002332", - "UPHENO:0050606", - "HP:0001315", - "HP:0000707", + "HP:0000234", + "HP:0000271", + "HP:0010827", "UPHENO:0001003", + "HP:0012639", + "UPHENO:0076710", + "UPHENO:0002908", + "BFO:0000001", + "BFO:0000040", + "UBERON:0000467", + "UBERON:0000468", + "UBERON:0011216", + "UBERON:0001785", + "UBERON:0010959", + "UBERON:0001577", + "UPHENO:0075696", + "HP:0045010", + "UPHENO:0002844", + "HP:0001291", + "HP:0001324", + "HP:0030319", + "HP:0000759", + "UPHENO:0081700", + "HP:0003011", + "UPHENO:0002332", + "UPHENO:0078730", "UPHENO:0002536", - "HP:0000708", - "UPHENO:0079826", + "UPHENO:0081709", + "HP:0000301", "UPHENO:0004523", - "HP:0011446", - "UPHENO:0079833", - "UPHENO:0049587", - "BFO:0000001", - "PATO:0000001", - "HP:0012638", - "BFO:0000001", - "BFO:0000003", + "UPHENO:0004508", + "HP:0011804", "BFO:0000002", - "BFO:0000015", - "BFO:0000004", - "GO:0008150", - "BFO:0000040", - "UBERON:0001062", - "GO:0050896", - "GO:0032501", "UBERON:0000465", - "GO:0009605", - "GO:0050879", - "GO:0007610", - "GO:0003008", + "UBERON:0005090", + "UBERON:0018254", + "UBERON:0004120", + "UBERON:0034713", + "UBERON:0001647", + "UBERON:0000122", + "UBERON:0001630", + "UBERON:0001033", + "UBERON:0002376", + "UBERON:0007811", + "UBERON:0001444", + "UBERON:0013702", + "UBERON:0001456", + "UBERON:0008229", + "UBERON:0013700", + "UPHENO:0001001", + "UPHENO:0002910", + "HP:0010628", + "UPHENO:0001005", + "HP:0011805", + "BFO:0000002", + "UPHENO:0076722", + "UPHENO:0080555", + "UPHENO:0003587", + "UPHENO:0002816", + "UPHENO:0080556", + "HP:0000707", + "HP:0006824", + "UPHENO:0081581", + "HP:0033127", + "UPHENO:0076702", + "UBERON:0001062", + "RO:0002577", "UBERON:0000061", - "GO:0060004", - "GO:0050881", - "NBO:0000313", - "GO:0050877", + "UBERON:0015212", + "UBERON:0010314", + "UBERON:0005162", "UBERON:0010000", - "UBERON:0000467", - "GO:0050882", - "NBO:0000338", - "GO:0050905", - "UBERON:0000468", - "UBERON:0001016", - "NBO:0000403", - "NBO:0000001", - "NBO:0000388", - "NBO:0000389" + "UBERON:0000475", + "UBERON:0000062", + "UBERON:0000383", + "UBERON:0001015", + "UBERON:0000010", + "UBERON:0004461", + "UBERON:0004473" ], - "object_label": "Hyporeflexia (HPO)", + "object_label": "Facial palsy (HPO)", "object_closure_label": [ - "entity", - "entity", - "continuant", - "continuant", - "independent continuant", - "specifically dependent continuant", - "material entity", "All (HPO)", + "abnormality of muscle organ physiology", + "abnormal peripheral nervous system", + "Abnormal cranial nerve physiology (HPO)", + "Abnormality of facial soft tissue (HPO)", + "abnormal head", + "Phenotypic abnormality", "Phenotypic abnormality (HPO)", + "abnormal peripheral nervous system morphology", + "decreased anatomical entity strength", + "abnormal facial nerve", + "abnormal musculature", + "decreased muscle organ strength", "Abnormality of the nervous system (HPO)", - "Behavioral abnormality (HPO)", - "Hyporeflexia (HPO)", - "Reduced tendon reflexes (HPO)", - "Abnormality of higher mental function (HPO)", - "Abnormal nervous system physiology (HPO)", - "Abnormal reflex (HPO)", - "Abnormality of movement (HPO)", - "quality", - "anatomical structure", - "material anatomical entity", - "anatomical system", - "multicellular organism", - "nervous system", - "anatomical entity", + "Cranial nerve paralysis (HPO)", + "abnormal multicellular organism morphology", + "Abnormality of the musculoskeletal system (HPO)", + "Abnormal nervous system morphology (HPO)", + "abnormal facial muscle", + "independent continuant", + "system", + "lateral structure", + "structure with developmental contribution from neural crest", + "multi cell part structure", "multicellular anatomical structure", - "phenotype", - "Phenotypic abnormality", - "phenotype by ontology source", - "abnormal phenotype by ontology source", + "nervous system", + "cranial nerve", + "face", + "craniocervical region musculature", + "axial musculature", "abnormality of anatomical entity physiology", + "abnormal cranial nerve morphology", + "Abnormality of peripheral nerves (HPO)", + "Facial palsy (HPO)", + "abnormal phenotype by ontology source", + "Abnormal skeletal muscle morphology (HPO)", + "continuant", + "specifically dependent continuant", "abnormality of nervous system physiology", - "abnormal anatomical entity", + "Abnormality of the head (HPO)", + "Abnormality of the face (HPO)", + "Abnormality of the seventh cranial nerve (HPO)", + "phenotype by ontology source", + "Abnormality of the peripheral nervous system (HPO)", + "paralysed cranial nerve", + "Abnormality of facial musculature (HPO)", "abnormal nervous system", - "decreased biological_process", - "decreased reflex", - "abnormal response to stimulus", - "abnormal biological_process", - "abnormal behavior", - "abnormal response to external stimulus", - "abnormal voluntary musculoskeletal movement", - "abnormal musculoskeletal movement", - "decreased qualitatively biological_process", - "decreased qualitatively response to stimulus", + "abnormal nerve", + "quality", + "Abnormal nervous system physiology (HPO)", + "continuant", + "material anatomical entity", + "cranial neuron projection bundle", + "facial nerve", + "neuron projection bundle", + "craniocervical region", + "subdivision of head", + "body proper", + "craniocervical muscle", + "facial muscle", + "phenotype", + "abnormal face", + "abnormal muscle organ morphology", + "Abnormal muscle physiology (HPO)", + "entity", + "anatomical entity", + "anatomical structure", + "muscle structure", + "skeletal musculature", + "mesoderm-derived structure", + "organism subdivision", + "organ", + "muscle organ", + "gustatory system", + "cranial muscle", + "musculature of body", + "musculature", + "peripheral nervous system", + "skeletal musculature of head", + "musculature of face", "abnormal anatomical entity", - "abnormal voluntary movement behavior", - "abnormal behavior process", - "abnormal voluntary movement behavior", - "changed biological_process rate", - "abnormal behavior process", - "abnormality of anatomical entity physiology" + "Abnormality of head or neck (HPO)", + "abnormal craniocervical region", + "Abnormal cranial nerve morphology (HPO)", + "Muscle weakness (HPO)", + "Weakness of facial musculature (HPO)", + "Abnormal peripheral nervous system morphology (HPO)", + "paralysed anatomical entity", + "Abnormality of the musculature (HPO)", + "abnormality of anatomical entity physiology", + "abnormality of cranial nerve physiology", + "abnormal anatomical entity", + "abnormal anatomical entity morphology", + "entity", + "abnormal nervous system morphology", + "material entity", + "anatomical system", + "multicellular organism", + "organ system subdivision", + "nerve", + "anterior region of body", + "subdivision of organism along main body axis", + "main body axis", + "skeletal muscle organ", + "cranial or facial muscle", + "nerve of head region", + "head" ], "object_taxon": null, "object_taxon_label": null, @@ -3361,36 +3887,46 @@ "aggregator_knowledge_source": ["infores:monarchinitiative"], "negated": null, "pathway": null, - "evidence_count": 4, - "has_evidence": ["ECO:0000501"], + "evidence_count": 2, + "has_evidence": ["ECO:0000304"], "has_evidence_links": [ { - "id": "ECO:0000501", - "url": "http://purl.obolibrary.org/obo/ECO_0000501" + "id": "ECO:0000304", + "url": "http://purl.obolibrary.org/obo/ECO_0000304" } ], + "grouping_key": "MONDO:0009675\ud83c\udf6a\ud83c\udf6abiolink:has_phenotype\ud83c\udf6aHP:0010628", "provided_by": "hpoa_disease_to_phenotype_edges", "provided_by_link": { "id": "hpoa_disease_to_phenotype", "url": "https://monarch-initiative.github.io/monarch-ingest/Sources/hpoa/#disease_to_phenotype" }, - "publications": ["OMIM:310200"], + "publications": ["OMIM:253600"], "publications_links": [ { - "id": "OMIM:310200", - "url": "http://identifiers.org/mim/310200" + "id": "OMIM:253600", + "url": "http://identifiers.org/mim/253600" } ], "qualifiers": [], - "frequency_qualifier": null, + "frequency_qualifier": "HP:0040283", "onset_qualifier": null, "sex_qualifier": null, "stage_qualifier": null, - "frequency_qualifier_label": null, - "frequency_qualifier_namespace": null, - "frequency_qualifier_category": null, - "frequency_qualifier_closure": [], - "frequency_qualifier_closure_label": [], + "qualifiers_label": null, + "qualifiers_namespace": null, + "qualifiers_category": null, + "qualifiers_closure": [], + "qualifiers_closure_label": [], + "frequency_qualifier_label": "Occasional (HPO)", + "frequency_qualifier_namespace": "HP", + "frequency_qualifier_category": "biolink:PhenotypicFeature", + "frequency_qualifier_closure": ["HP:0000001", "HP:0040283", "HP:0040279"], + "frequency_qualifier_closure_label": [ + "All (HPO)", + "Occasional (HPO)", + "Frequency (HPO)" + ], "onset_qualifier_label": null, "onset_qualifier_namespace": null, "onset_qualifier_category": null, @@ -3408,194 +3944,196 @@ "stage_qualifier_closure_label": [] }, { - "id": "uuid:898aa716-5d8c-11ee-9b27-2b20ed86a9d9", + "id": "uuid:c9d8bdf7-7529-11ee-b012-cbd37f5c3759", "category": "biolink:DiseaseToPhenotypicFeatureAssociation", - "subject": "MONDO:0012193", - "original_subject": "OMIM:609115", + "subject": "MONDO:0009676", + "original_subject": "OMIM:253601", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ - "MONDO:0000001", "MONDO:0016971", + "BFO:0000002", + "BFO:0000020", + "MONDO:0005336", + "MONDO:0009676", + "MONDO:0015152", "MONDO:0000429", "MONDO:0005071", + "MONDO:0006025", + "BFO:0000016", + "MONDO:0016139", + "OGMS:0000031", + "MONDO:0003847", + "BFO:0000001", + "MONDO:0016145", "MONDO:0020121", - "MONDO:0700223", - "BFO:0000002", "BFO:0000017", - "BFO:0000020", - "MONDO:0016106", - "BFO:0000016", "MONDO:0020120", "MONDO:0019056", - "MONDO:0015151", + "MONDO:0000001", + "MONDO:0700223", + "MONDO:0016106", "MONDO:0700096", - "MONDO:0005336", "MONDO:0002081", - "MONDO:0012193", - "MONDO:0000426", - "OGMS:0000031", - "MONDO:0003847", - "MONDO:0003939", - "BFO:0000001" + "MONDO:0003939" ], - "subject_label": "autosomal dominant limb-girdle muscular dystrophy type 1G", + "subject_label": "autosomal recessive limb-girdle muscular dystrophy type 2B", "subject_closure_label": [ - "entity", - "continuant", + "limb-girdle muscular dystrophy", + "muscular dystrophy", + "progressive muscular dystrophy", + "human disease", + "musculoskeletal system disorder", + "disease", + "muscle tissue disorder", + "qualitative or quantitative defects of dysferlin", + "hereditary skeletal muscle disorder", + "autosomal recessive disease", "disposition", - "realizable entity", - "specifically dependent continuant", + "qualitative or quantitative protein defects in neuromuscular diseases", + "autosomal recessive limb-girdle muscular dystrophy type 2B", "disease", - "autosomal dominant disease", - "autosomal genetic disease", - "musculoskeletal system disorder", + "continuant", + "specifically dependent continuant", + "myopathy", "hereditary disease", - "muscle tissue disorder", + "autosomal genetic disease", "nervous system disorder", - "myopathy", - "autosomal dominant limb-girdle muscular dystrophy type 1G", - "muscular dystrophy, limb-girdle, autosomal dominant", - "progressive muscular dystrophy", - "limb-girdle muscular dystrophy", - "neuromuscular disease", + "realizable entity", "skeletal muscle disorder", - "muscular dystrophy", - "human disease", - "hereditary skeletal muscle disorder", - "disease" + "neuromuscular disease", + "autosomal recessive limb-girdle muscular dystrophy", + "entity" ], "subject_taxon": null, "subject_taxon_label": null, "predicate": "biolink:has_phenotype", - "object": "HP:0001265", + "object": "HP:0002505", "original_object": null, "object_namespace": "HP", "object_category": "biolink:PhenotypicFeature", "object_closure": [ - "HP:0000001", "UPHENO:0082875", - "UPHENO:0075696", - "UPHENO:0078622", - "UPHENO:0049586", - "UPHENO:0080377", - "UPHENO:0001001", - "UPHENO:0052915", "UPHENO:0049622", - "UPHENO:0080585", - "HP:0001265", - "HP:0100022", "UPHENO:0001005", - "HP:0031826", - "UPHENO:0001002", - "HP:0000118", "BFO:0000002", - "UPHENO:0052178", + "HP:0002540", + "UPHENO:0050606", + "HP:0001288", + "HP:0012638", + "BFO:0000015", + "UBERON:0000061", + "GO:0050882", + "NBO:0000338", + "GO:0050905", + "UBERON:0001016", + "HP:0000001", + "UPHENO:0001001", + "UPHENO:0080585", + "HP:0000118", "BFO:0000020", "UPHENO:0002433", - "UPHENO:0050613", - "UPHENO:0005625", - "UPHENO:0050079", - "UPHENO:0005433", - "UPHENO:0002332", - "UPHENO:0050606", - "HP:0001315", - "HP:0000707", "UPHENO:0001003", - "UPHENO:0002536", "HP:0000708", - "UPHENO:0079826", - "UPHENO:0004523", "HP:0011446", - "UPHENO:0079833", - "UPHENO:0049587", "BFO:0000001", "PATO:0000001", - "HP:0012638", "BFO:0000001", - "BFO:0000003", - "BFO:0000002", - "BFO:0000015", "BFO:0000004", - "GO:0008150", - "BFO:0000040", - "UBERON:0001062", - "GO:0050896", "GO:0032501", - "UBERON:0000465", - "GO:0009605", - "GO:0050879", - "GO:0007610", - "GO:0003008", - "UBERON:0000061", - "GO:0060004", "GO:0050881", "NBO:0000313", "GO:0050877", - "UBERON:0010000", "UBERON:0000467", - "GO:0050882", - "NBO:0000338", - "GO:0050905", "UBERON:0000468", - "UBERON:0001016", "NBO:0000403", "NBO:0000001", - "NBO:0000388", - "NBO:0000389" - ], - "object_label": "Hyporeflexia (HPO)", - "object_closure_label": [ - "entity", - "entity", - "continuant", - "continuant", - "independent continuant", - "specifically dependent continuant", - "material entity", - "All (HPO)", - "Phenotypic abnormality (HPO)", - "Abnormality of the nervous system (HPO)", - "Behavioral abnormality (HPO)", - "Hyporeflexia (HPO)", - "Reduced tendon reflexes (HPO)", - "Abnormality of higher mental function (HPO)", - "Abnormal nervous system physiology (HPO)", - "Abnormal reflex (HPO)", + "UPHENO:0075696", + "UPHENO:0078622", + "HP:0002505", + "UPHENO:0049586", + "HP:0100022", + "UPHENO:0001002", + "UPHENO:0050613", + "UPHENO:0002332", + "UPHENO:0002536", + "UPHENO:0079826", + "UPHENO:0004523", + "UPHENO:0049587", + "BFO:0000003", + "BFO:0000002", + "GO:0008150", + "BFO:0000040", + "GO:0050879", + "GO:0007610", + "GO:0003008", + "HP:0000707", + "UPHENO:0079833", + "UBERON:0001062", + "UBERON:0000465", + "UBERON:0010000" + ], + "object_label": "Loss of ambulation (HPO)", + "object_closure_label": [ + "All (HPO)", + "abnormal behavior", "Abnormality of movement (HPO)", + "Phenotypic abnormality (HPO)", + "Abnormality of the nervous system (HPO)", + "Behavioral abnormality (HPO)", + "Abnormality of higher mental function (HPO)", + "abnormal voluntary movement behavior", "quality", - "anatomical structure", + "process", "material anatomical entity", - "anatomical system", - "multicellular organism", - "nervous system", - "anatomical entity", + "anatomical structure", "multicellular anatomical structure", - "phenotype", - "Phenotypic abnormality", - "phenotype by ontology source", - "abnormal phenotype by ontology source", + "nervous system", + "voluntary movement behavior", + "body part movement", "abnormality of anatomical entity physiology", + "phenotype", + "specifically dependent continuant", "abnormality of nervous system physiology", - "abnormal anatomical entity", + "phenotype by ontology source", + "Gait disturbance (HPO)", + "abnormal behavior process", "abnormal nervous system", - "decreased biological_process", - "decreased reflex", - "abnormal response to stimulus", "abnormal biological_process", - "abnormal behavior", - "abnormal response to external stimulus", + "Abnormal nervous system physiology (HPO)", + "occurrent", + "continuant", + "biological_process", + "material entity", + "multicellular organismal movement", + "behavior", + "system process", + "musculoskeletal movement", + "behavior process", + "nervous system process", + "abnormal phenotype by ontology source", + "continuant", + "Inability to walk (HPO)", "abnormal voluntary musculoskeletal movement", - "abnormal musculoskeletal movement", - "decreased qualitatively biological_process", - "decreased qualitatively response to stimulus", + "entity", + "independent continuant", + "anatomical entity", "abnormal anatomical entity", "abnormal voluntary movement behavior", + "Loss of ambulation (HPO)", + "abnormal response to stimulus", "abnormal behavior process", - "abnormal voluntary movement behavior", - "changed biological_process rate", - "abnormal behavior process", - "abnormality of anatomical entity physiology" + "Phenotypic abnormality", + "abnormal musculoskeletal movement", + "abnormality of anatomical entity physiology", + "abnormal anatomical entity", + "entity", + "multicellular organismal process", + "anatomical system", + "voluntary musculoskeletal movement", + "kinesthetic behavior", + "neuromuscular process", + "multicellular organism" ], "object_taxon": null, "object_taxon_label": null, @@ -3603,36 +4141,46 @@ "aggregator_knowledge_source": ["infores:monarchinitiative"], "negated": null, "pathway": null, - "evidence_count": 4, - "has_evidence": ["ECO:0000501"], + "evidence_count": 2, + "has_evidence": ["ECO:0000269"], "has_evidence_links": [ { - "id": "ECO:0000501", - "url": "http://purl.obolibrary.org/obo/ECO_0000501" + "id": "ECO:0000269", + "url": "http://purl.obolibrary.org/obo/ECO_0000269" } ], + "grouping_key": "MONDO:0009676\ud83c\udf6a\ud83c\udf6abiolink:has_phenotype\ud83c\udf6aHP:0002505", "provided_by": "hpoa_disease_to_phenotype_edges", "provided_by_link": { "id": "hpoa_disease_to_phenotype", "url": "https://monarch-initiative.github.io/monarch-ingest/Sources/hpoa/#disease_to_phenotype" }, - "publications": ["OMIM:609115"], + "publications": ["PMID:9731527"], "publications_links": [ { - "id": "OMIM:609115", - "url": "http://identifiers.org/mim/609115" + "id": "PMID:9731527", + "url": "http://identifiers.org/pubmed/9731527" } ], "qualifiers": [], - "frequency_qualifier": null, + "frequency_qualifier": "HP:0040283", "onset_qualifier": null, "sex_qualifier": null, "stage_qualifier": null, - "frequency_qualifier_label": null, - "frequency_qualifier_namespace": null, - "frequency_qualifier_category": null, - "frequency_qualifier_closure": [], - "frequency_qualifier_closure_label": [], + "qualifiers_label": null, + "qualifiers_namespace": null, + "qualifiers_category": null, + "qualifiers_closure": [], + "qualifiers_closure_label": [], + "frequency_qualifier_label": "Occasional (HPO)", + "frequency_qualifier_namespace": "HP", + "frequency_qualifier_category": "biolink:PhenotypicFeature", + "frequency_qualifier_closure": ["HP:0000001", "HP:0040283", "HP:0040279"], + "frequency_qualifier_closure_label": [ + "All (HPO)", + "Occasional (HPO)", + "Frequency (HPO)" + ], "onset_qualifier_label": null, "onset_qualifier_namespace": null, "onset_qualifier_category": null, @@ -3650,238 +4198,288 @@ "stage_qualifier_closure_label": [] }, { - "id": "uuid:880b4cc5-5d8c-11ee-9b27-2b20ed86a9d9", + "id": "uuid:c9c8bf2b-7529-11ee-b012-cbd37f5c3759", "category": "biolink:DiseaseToPhenotypicFeatureAssociation", - "subject": "MONDO:0012699", - "original_subject": "OMIM:611588", + "subject": "MONDO:0008050", + "original_subject": "OMIM:160500", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ - "MONDO:0700067", - "MONDO:0004994", - "MONDO:0018282", - "MONDO:0000001", - "MONDO:0016971", - "MONDO:0017741", - "MONDO:0000429", - "MONDO:0018276", - "MONDO:0045010", + "BFO:0000002", + "MONDO:0016195", + "MONDO:0005336", + "MONDO:0018949", "MONDO:0005071", - "MONDO:0005267", + "MONDO:0008050", + "BFO:0000016", + "MONDO:0016139", + "OGMS:0000031", + "MONDO:0003847", + "BFO:0000001", "MONDO:0020121", - "MONDO:0004995", - "MONDO:0700223", - "MONDO:0024322", - "BFO:0000002", + "MONDO:0019952", "BFO:0000017", "BFO:0000020", - "MONDO:0006025", - "MONDO:0016106", - "MONDO:0005217", - "MONDO:0017745", - "BFO:0000016", "MONDO:0020120", "MONDO:0019056", - "MONDO:0016139", + "MONDO:0000001", + "MONDO:0700223", "MONDO:0700096", - "MONDO:0000591", - "MONDO:0005336", "MONDO:0002081", - "MONDO:0016333", - "OGMS:0000031", - "MONDO:0005021", - "MONDO:0003847", "MONDO:0003939", - "MONDO:0012699", - "MONDO:0015286", - "MONDO:0015152", - "BFO:0000001", - "MONDO:0002320", - "MONDO:0019052", - "MONDO:0005066", - "MONDO:0000173", - "MONDO:0019950", - "MONDO:0016155" - ], - "subject_label": "autosomal recessive limb-girdle muscular dystrophy type 2M", + "MONDO:0002320" + ], + "subject_label": "MYH7-related skeletal myopathy", "subject_closure_label": [ - "entity", - "continuant", - "disposition", - "realizable entity", - "specifically dependent continuant", - "disease", - "muscular dystrophy-dystroglycanopathy, type C", - "autosomal genetic disease", - "intrinsic cardiomyopathy", + "muscular dystrophy", + "human disease", "musculoskeletal system disorder", + "disease", + "muscle tissue disorder", "congenital nervous system disorder", + "hereditary skeletal muscle disorder", + "MYH7-related skeletal myopathy", + "disposition", + "qualitative or quantitative protein defects in neuromuscular diseases", + "distal myopathy", + "disease", + "continuant", + "qualitative or quantitative defects of beta-myosin heavy chain (MYH7)", + "myopathy", "hereditary disease", - "muscle tissue disorder", - "cardiomyopathy", - "cardiovascular disorder", - "dilated cardiomyopathy", - "metabolic disease", "nervous system disorder", - "familial cardiomyopathy", - "heart disorder", - "myopathy", - "autosomal recessive disease", - "autosomal recessive limb-girdle muscular dystrophy type 2M", - "autosomal recessive limb-girdle muscular dystrophy", - "congenital disorder of glycosylation", - "progressive muscular dystrophy", - "qualitative or quantitative protein defects in neuromuscular diseases", - "qualitative or quantitative defects of protein involved in O-glycosylation of alpha-dystroglycan", - "familial dilated cardiomyopathy", - "limb-girdle muscular dystrophy", - "disorder of protein O-glycosylation", - "disorder of O-mannosylglycan synthesis", - "muscular dystrophy-dystroglycanopathy", - "qualitative or quantitative defects of alpha-dystroglycan", - "inborn errors of metabolism", - "neuromuscular disease", - "congenital muscular dystrophy", + "congenital myopathy", + "realizable entity", + "specifically dependent continuant", "skeletal muscle disorder", - "muscular dystrophy", - "disorder of glycosylation", - "glycoprotein metabolism disease", - "myopathy caused by variation in FKTN", - "human disease", - "hereditary skeletal muscle disorder", - "disease" + "neuromuscular disease", + "entity" ], "subject_taxon": null, "subject_taxon_label": null, "predicate": "biolink:has_phenotype", - "object": "HP:0001265", + "object": "HP:0010628", "original_object": null, "object_namespace": "HP", "object_category": "biolink:PhenotypicFeature", "object_closure": [ - "HP:0000001", "UPHENO:0082875", - "UPHENO:0075696", - "UPHENO:0078622", - "UPHENO:0049586", - "UPHENO:0080377", - "UPHENO:0001001", - "UPHENO:0052915", - "UPHENO:0049622", - "UPHENO:0080585", - "HP:0001265", - "HP:0100022", - "UPHENO:0001005", - "HP:0031826", + "UPHENO:0076772", + "UPHENO:0002320", + "UPHENO:0005116", + "HP:0031910", + "HP:0011799", + "HP:0410008", + "UPHENO:0076692", + "BFO:0000001", + "PATO:0000001", + "HP:0012638", + "BFO:0000004", + "UBERON:0001016", + "UBERON:0001021", + "UBERON:0000153", + "UBERON:0011676", + "UBERON:0013701", + "UBERON:0014892", + "UBERON:0015789", + "UBERON:0011779", + "UBERON:0000033", + "HP:0000001", + "HP:0000152", + "UPHENO:0002764", "UPHENO:0001002", "HP:0000118", - "BFO:0000002", - "UPHENO:0052178", "BFO:0000020", "UPHENO:0002433", - "UPHENO:0050613", - "UPHENO:0005625", - "UPHENO:0050079", - "UPHENO:0005433", - "UPHENO:0002332", - "UPHENO:0050606", - "HP:0001315", - "HP:0000707", + "HP:0000234", + "HP:0000271", + "HP:0010827", "UPHENO:0001003", + "HP:0012639", + "UPHENO:0076710", + "UPHENO:0002908", + "BFO:0000001", + "BFO:0000040", + "UBERON:0000467", + "UBERON:0000468", + "UBERON:0011216", + "UBERON:0001785", + "UBERON:0010959", + "UBERON:0001577", + "UPHENO:0075696", + "HP:0045010", + "UPHENO:0002844", + "HP:0001291", + "HP:0001324", + "HP:0030319", + "HP:0000759", + "UPHENO:0081700", + "HP:0003011", + "UPHENO:0002332", + "UPHENO:0078730", "UPHENO:0002536", - "HP:0000708", - "UPHENO:0079826", + "UPHENO:0081709", + "HP:0000301", "UPHENO:0004523", - "HP:0011446", - "UPHENO:0079833", - "UPHENO:0049587", - "BFO:0000001", - "PATO:0000001", - "HP:0012638", - "BFO:0000001", - "BFO:0000003", + "UPHENO:0004508", + "HP:0011804", "BFO:0000002", - "BFO:0000015", - "BFO:0000004", - "GO:0008150", - "BFO:0000040", - "UBERON:0001062", - "GO:0050896", - "GO:0032501", "UBERON:0000465", - "GO:0009605", - "GO:0050879", - "GO:0007610", - "GO:0003008", + "UBERON:0005090", + "UBERON:0018254", + "UBERON:0004120", + "UBERON:0034713", + "UBERON:0001647", + "UBERON:0000122", + "UBERON:0001630", + "UBERON:0001033", + "UBERON:0002376", + "UBERON:0007811", + "UBERON:0001444", + "UBERON:0013702", + "UBERON:0001456", + "UBERON:0008229", + "UBERON:0013700", + "UPHENO:0001001", + "UPHENO:0002910", + "HP:0010628", + "UPHENO:0001005", + "HP:0011805", + "BFO:0000002", + "UPHENO:0076722", + "UPHENO:0080555", + "UPHENO:0003587", + "UPHENO:0002816", + "UPHENO:0080556", + "HP:0000707", + "HP:0006824", + "UPHENO:0081581", + "HP:0033127", + "UPHENO:0076702", + "UBERON:0001062", + "RO:0002577", "UBERON:0000061", - "GO:0060004", - "GO:0050881", - "NBO:0000313", - "GO:0050877", + "UBERON:0015212", + "UBERON:0010314", + "UBERON:0005162", "UBERON:0010000", - "UBERON:0000467", - "GO:0050882", - "NBO:0000338", - "GO:0050905", - "UBERON:0000468", - "UBERON:0001016", - "NBO:0000403", - "NBO:0000001", - "NBO:0000388", - "NBO:0000389" + "UBERON:0000475", + "UBERON:0000062", + "UBERON:0000383", + "UBERON:0001015", + "UBERON:0000010", + "UBERON:0004461", + "UBERON:0004473" ], - "object_label": "Hyporeflexia (HPO)", + "object_label": "Facial palsy (HPO)", "object_closure_label": [ - "entity", - "entity", - "continuant", - "continuant", - "independent continuant", - "specifically dependent continuant", - "material entity", "All (HPO)", + "abnormality of muscle organ physiology", + "abnormal peripheral nervous system", + "Abnormal cranial nerve physiology (HPO)", + "Abnormality of facial soft tissue (HPO)", + "abnormal head", + "Phenotypic abnormality", "Phenotypic abnormality (HPO)", + "abnormal peripheral nervous system morphology", + "decreased anatomical entity strength", + "abnormal facial nerve", + "abnormal musculature", + "decreased muscle organ strength", "Abnormality of the nervous system (HPO)", - "Behavioral abnormality (HPO)", - "Hyporeflexia (HPO)", - "Reduced tendon reflexes (HPO)", - "Abnormality of higher mental function (HPO)", - "Abnormal nervous system physiology (HPO)", - "Abnormal reflex (HPO)", - "Abnormality of movement (HPO)", - "quality", - "anatomical structure", - "material anatomical entity", - "anatomical system", - "multicellular organism", - "nervous system", - "anatomical entity", + "Cranial nerve paralysis (HPO)", + "abnormal multicellular organism morphology", + "Abnormality of the musculoskeletal system (HPO)", + "Abnormal nervous system morphology (HPO)", + "abnormal facial muscle", + "independent continuant", + "system", + "lateral structure", + "structure with developmental contribution from neural crest", + "multi cell part structure", "multicellular anatomical structure", - "phenotype", - "Phenotypic abnormality", - "phenotype by ontology source", - "abnormal phenotype by ontology source", + "nervous system", + "cranial nerve", + "face", + "craniocervical region musculature", + "axial musculature", "abnormality of anatomical entity physiology", + "abnormal cranial nerve morphology", + "Abnormality of peripheral nerves (HPO)", + "Facial palsy (HPO)", + "abnormal phenotype by ontology source", + "Abnormal skeletal muscle morphology (HPO)", + "continuant", + "specifically dependent continuant", "abnormality of nervous system physiology", - "abnormal anatomical entity", + "Abnormality of the head (HPO)", + "Abnormality of the face (HPO)", + "Abnormality of the seventh cranial nerve (HPO)", + "phenotype by ontology source", + "Abnormality of the peripheral nervous system (HPO)", + "paralysed cranial nerve", + "Abnormality of facial musculature (HPO)", "abnormal nervous system", - "decreased biological_process", - "decreased reflex", - "abnormal response to stimulus", - "abnormal biological_process", - "abnormal behavior", - "abnormal response to external stimulus", - "abnormal voluntary musculoskeletal movement", - "abnormal musculoskeletal movement", - "decreased qualitatively biological_process", - "decreased qualitatively response to stimulus", + "abnormal nerve", + "quality", + "Abnormal nervous system physiology (HPO)", + "continuant", + "material anatomical entity", + "cranial neuron projection bundle", + "facial nerve", + "neuron projection bundle", + "craniocervical region", + "subdivision of head", + "body proper", + "craniocervical muscle", + "facial muscle", + "phenotype", + "abnormal face", + "abnormal muscle organ morphology", + "Abnormal muscle physiology (HPO)", + "entity", + "anatomical entity", + "anatomical structure", + "muscle structure", + "skeletal musculature", + "mesoderm-derived structure", + "organism subdivision", + "organ", + "muscle organ", + "gustatory system", + "cranial muscle", + "musculature of body", + "musculature", + "peripheral nervous system", + "skeletal musculature of head", + "musculature of face", "abnormal anatomical entity", - "abnormal voluntary movement behavior", - "abnormal behavior process", - "abnormal voluntary movement behavior", - "changed biological_process rate", - "abnormal behavior process", - "abnormality of anatomical entity physiology" + "Abnormality of head or neck (HPO)", + "abnormal craniocervical region", + "Abnormal cranial nerve morphology (HPO)", + "Muscle weakness (HPO)", + "Weakness of facial musculature (HPO)", + "Abnormal peripheral nervous system morphology (HPO)", + "paralysed anatomical entity", + "Abnormality of the musculature (HPO)", + "abnormality of anatomical entity physiology", + "abnormality of cranial nerve physiology", + "abnormal anatomical entity", + "abnormal anatomical entity morphology", + "entity", + "abnormal nervous system morphology", + "material entity", + "anatomical system", + "multicellular organism", + "organ system subdivision", + "nerve", + "anterior region of body", + "subdivision of organism along main body axis", + "main body axis", + "skeletal muscle organ", + "cranial or facial muscle", + "nerve of head region", + "head" ], "object_taxon": null, "object_taxon_label": null, @@ -3889,24 +4487,25 @@ "aggregator_knowledge_source": ["infores:monarchinitiative"], "negated": null, "pathway": null, - "evidence_count": 4, - "has_evidence": ["ECO:0000501"], + "evidence_count": 2, + "has_evidence": ["ECO:0000304"], "has_evidence_links": [ { - "id": "ECO:0000501", - "url": "http://purl.obolibrary.org/obo/ECO_0000501" + "id": "ECO:0000304", + "url": "http://purl.obolibrary.org/obo/ECO_0000304" } ], + "grouping_key": "MONDO:0008050\ud83c\udf6a\ud83c\udf6abiolink:has_phenotype\ud83c\udf6aHP:0010628", "provided_by": "hpoa_disease_to_phenotype_edges", "provided_by_link": { "id": "hpoa_disease_to_phenotype", "url": "https://monarch-initiative.github.io/monarch-ingest/Sources/hpoa/#disease_to_phenotype" }, - "publications": ["OMIM:611588"], + "publications": ["OMIM:160500"], "publications_links": [ { - "id": "OMIM:611588", - "url": "http://identifiers.org/mim/611588" + "id": "OMIM:160500", + "url": "http://identifiers.org/mim/160500" } ], "qualifiers": [], @@ -3914,6 +4513,11 @@ "onset_qualifier": null, "sex_qualifier": null, "stage_qualifier": null, + "qualifiers_label": null, + "qualifiers_namespace": null, + "qualifiers_category": null, + "qualifiers_closure": [], + "qualifiers_closure_label": [], "frequency_qualifier_label": null, "frequency_qualifier_namespace": null, "frequency_qualifier_category": null, @@ -3936,254 +4540,216 @@ "stage_qualifier_closure_label": [] }, { - "id": "uuid:86db7919-5d8c-11ee-9b27-2b20ed86a9d9", + "id": "uuid:c9c8bf2d-7529-11ee-b012-cbd37f5c3759", "category": "biolink:DiseaseToPhenotypicFeatureAssociation", - "subject": "MONDO:0013157", - "original_subject": "OMIM:613153", + "subject": "MONDO:0008050", + "original_subject": "OMIM:160500", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ - "MONDO:0018282", - "MONDO:0000001", - "MONDO:0016182", - "MONDO:0017741", - "MONDO:0018276", - "MONDO:0045010", + "BFO:0000002", + "MONDO:0016195", + "MONDO:0005336", + "MONDO:0018949", "MONDO:0005071", + "MONDO:0008050", + "BFO:0000016", + "MONDO:0016139", + "OGMS:0000031", + "MONDO:0003847", + "BFO:0000001", "MONDO:0020121", - "MONDO:0700068", - "MONDO:0700223", - "MONDO:0024322", - "MONDO:0005283", - "MONDO:0020238", - "BFO:0000002", - "MONDO:0016185", - "MONDO:0000171", + "MONDO:0019952", "BFO:0000017", - "MONDO:0018869", "BFO:0000020", - "MONDO:0016157", - "MONDO:0017745", - "BFO:0000016", "MONDO:0020120", "MONDO:0019056", - "MONDO:0016139", + "MONDO:0000001", + "MONDO:0700223", "MONDO:0700096", - "MONDO:0018838", - "MONDO:0024458", - "MONDO:0005336", "MONDO:0002081", - "MONDO:0016184", - "MONDO:0016156", - "MONDO:0018939", - "MONDO:0020246", - "MONDO:0021147", - "MONDO:0044137", - "MONDO:0019755", - "OGMS:0000031", - "MONDO:0015327", - "MONDO:0003847", "MONDO:0003939", - "MONDO:0002022", - "MONDO:0015286", - "BFO:0000001", - "MONDO:0002320", - "MONDO:0013157", - "MONDO:0019052", - "MONDO:0020247", - "MONDO:0005066", - "MONDO:0005328", - "MONDO:0019950", - "MONDO:0016155", - "MONDO:0700066" - ], - "subject_label": "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A5", + "MONDO:0002320" + ], + "subject_label": "MYH7-related skeletal myopathy", "subject_closure_label": [ - "entity", - "continuant", - "disposition", - "realizable entity", - "specifically dependent continuant", - "disease", - "muscular dystrophy-dystroglycanopathy, type A", - "disorder of orbital region", + "muscular dystrophy", + "human disease", "musculoskeletal system disorder", + "disease", + "muscle tissue disorder", "congenital nervous system disorder", + "hereditary skeletal muscle disorder", + "MYH7-related skeletal myopathy", + "disposition", + "qualitative or quantitative protein defects in neuromuscular diseases", + "distal myopathy", + "disease", + "continuant", + "qualitative or quantitative defects of beta-myosin heavy chain (MYH7)", + "myopathy", "hereditary disease", - "muscle tissue disorder", - "metabolic disease", "nervous system disorder", - "retinal disorder", - "eye disorder", - "myopathy", - "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A5", - "congenital disorder of glycosylation", - "developmental anomaly of metabolic origin", - "qualitative or quantitative protein defects in neuromuscular diseases", - "qualitative or quantitative defects of protein involved in O-glycosylation of alpha-dystroglycan", - "qualitative or quantitative defects of FKRP", - "qualitative or quantitative defects of fukutin", - "qualitative or quantitative defects of protein O-mannose beta1, 2N-acetylglucosaminyltransferase", - "qualitative or quantitative defects of protein O-mannosyltransferase 1", - "qualitative or quantitative defects of protein O-mannosyltransferase 2", - "disorder of protein O-glycosylation", - "disorder of O-mannosylglycan synthesis", - "muscular dystrophy-dystroglycanopathy", - "qualitative or quantitative defects of alpha-dystroglycan", - "lissencephaly spectrum disorders", - "cobblestone lissencephaly", - "muscle-eye-brain disease", - "inborn errors of metabolism", - "neuromuscular disease", - "developmental defect during embryogenesis", - "congenital muscular dystrophy", + "congenital myopathy", + "realizable entity", + "specifically dependent continuant", "skeletal muscle disorder", - "muscular dystrophy", - "inherited vitreous-retinal disease", - "inherited vitreoretinopathy", - "congenital vitreoretinal dysplasia", - "disorder of development or morphogenesis", - "disorder of glycosylation", - "disorder of visual system", - "vitreous body disorder", - "glycoprotein metabolism disease", - "myopathy caused by variation in FKRP", - "myopathy caused by variation in POMGNT1", - "human disease", - "hereditary skeletal muscle disorder", - "disease" + "neuromuscular disease", + "entity" ], "subject_taxon": null, "subject_taxon_label": null, "predicate": "biolink:has_phenotype", - "object": "HP:0001265", + "object": "HP:0011916", "original_object": null, "object_namespace": "HP", "object_category": "biolink:PhenotypicFeature", "object_closure": [ + "HP:0002814", + "HP:0009127", + "UPHENO:0076692", + "UPHENO:0003070", + "PATO:0000001", + "BFO:0000004", + "UBERON:0004708", + "UBERON:0000154", + "UBERON:0006058", + "UBERON:0002529", + "UBERON:0002387", "HP:0000001", - "UPHENO:0082875", - "UPHENO:0075696", - "UPHENO:0078622", - "UPHENO:0049586", - "UPHENO:0080377", + "UPHENO:0002644", "UPHENO:0001001", - "UPHENO:0052915", - "UPHENO:0049622", - "UPHENO:0080585", - "HP:0001265", - "HP:0100022", - "UPHENO:0001005", - "HP:0031826", "UPHENO:0001002", "HP:0000118", - "BFO:0000002", - "UPHENO:0052178", "BFO:0000020", - "UPHENO:0002433", - "UPHENO:0050613", - "UPHENO:0005625", - "UPHENO:0050079", - "UPHENO:0005433", - "UPHENO:0002332", - "UPHENO:0050606", - "HP:0001315", - "HP:0000707", "UPHENO:0001003", - "UPHENO:0002536", - "HP:0000708", - "UPHENO:0079826", - "UPHENO:0004523", - "HP:0011446", - "UPHENO:0079833", - "UPHENO:0049587", - "BFO:0000001", - "PATO:0000001", - "HP:0012638", + "UPHENO:0076710", + "HP:0011916", "BFO:0000001", - "BFO:0000003", - "BFO:0000002", - "BFO:0000015", - "BFO:0000004", - "GO:0008150", "BFO:0000040", "UBERON:0001062", - "GO:0050896", - "GO:0032501", - "UBERON:0000465", - "GO:0009605", - "GO:0050879", - "GO:0007610", - "GO:0003008", - "UBERON:0000061", - "GO:0060004", - "GO:0050881", - "NBO:0000313", - "GO:0050877", "UBERON:0010000", "UBERON:0000467", - "GO:0050882", - "NBO:0000338", - "GO:0050905", "UBERON:0000468", - "UBERON:0001016", - "NBO:0000403", - "NBO:0000001", - "NBO:0000388", - "NBO:0000389" + "UBERON:0011216", + "UBERON:0010709", + "UBERON:0010538", + "UBERON:0004488", + "HP:0001436", + "UPHENO:0002653", + "HP:0003011", + "UPHENO:0002536", + "HP:0001437", + "HP:0040064", + "BFO:0000002", + "PR:000050567", + "UBERON:0000465", + "UBERON:0002101", + "UBERON:0004709", + "UBERON:0005090", + "UBERON:0002103", + "UBERON:0010707", + "UBERON:0001630", + "UBERON:0000026", + "UBERON:0010758", + "UBERON:0007271", + "UBERON:0014792", + "UBERON:0004482", + "UBERON:0008784", + "UBERON:0002470", + "UPHENO:0001005", + "HP:0011805", + "BFO:0000002", + "UPHENO:0002816", + "UPHENO:0081581", + "HP:0033127", + "UPHENO:0002647", + "BFO:0000001", + "UPHENO:0002830", + "RO:0002577", + "UBERON:0000061", + "UBERON:0015212", + "UBERON:0000475", + "UBERON:0000062", + "UBERON:0000383", + "UBERON:0001015", + "UBERON:0000978", + "UBERON:0007270", + "UBERON:0004480" ], - "object_label": "Hyporeflexia (HPO)", + "object_label": "Toe extensor amyotrophy (HPO)", "object_closure_label": [ + "All (HPO)", + "abnormal musculature of lower limb", + "Abnormality of the lower limb (HPO)", + "Phenotypic abnormality", + "Phenotypic abnormality (HPO)", + "abnormal musculature", + "abnormal multicellular organism morphology", + "Abnormality of the musculoskeletal system (HPO)", + "abnormal musculature of limb", "entity", - "entity", - "continuant", - "continuant", "independent continuant", + "system", + "paired limb/fin", + "lateral structure", + "pelvic complex", + "appendage musculature", + "musculature of pelvic complex", + "musculature of pes", + "phenotype", + "Abnormality of the foot musculature (HPO)", + "abnormal phenotype by ontology source", + "Abnormal skeletal muscle morphology (HPO)", + "continuant", "specifically dependent continuant", - "material entity", - "All (HPO)", - "Phenotypic abnormality (HPO)", - "Abnormality of the nervous system (HPO)", - "Behavioral abnormality (HPO)", - "Hyporeflexia (HPO)", - "Reduced tendon reflexes (HPO)", - "Abnormality of higher mental function (HPO)", - "Abnormal nervous system physiology (HPO)", - "Abnormal reflex (HPO)", - "Abnormality of movement (HPO)", + "phenotype by ontology source", + "Abnormality of the musculature of the lower limbs (HPO)", + "Abnormality of limbs (HPO)", "quality", - "anatomical structure", + "continuant", + "protein-containing material entity", "material anatomical entity", - "anatomical system", - "multicellular organism", - "nervous system", + "hindlimb", + "appendage girdle complex", + "appendage", + "subdivision of organism along appendicular axis", + "paired limb/fin segment", + "musculature of lower limb", + "lower limb segment", + "autopod region", + "Abnormality of the musculature of the limbs (HPO)", + "abnormal muscle organ morphology", + "Toe extensor amyotrophy (HPO)", + "entity", + "anatomical structure", + "muscle structure", + "organism subdivision", + "organ", + "muscle organ", + "musculature of body", + "musculature", + "leg", + "pelvic appendage musculature", + "musculature of limb", + "abnormal musculature of pes", + "Abnormality of the musculature (HPO)", + "abnormal anatomical entity", + "abnormal anatomical entity morphology", + "abnormal leg", + "abnormal limb", + "material entity", "anatomical entity", + "limb", + "pelvic appendage", "multicellular anatomical structure", - "phenotype", - "Phenotypic abnormality", - "phenotype by ontology source", - "abnormal phenotype by ontology source", - "abnormality of anatomical entity physiology", - "abnormality of nervous system physiology", - "abnormal anatomical entity", - "abnormal nervous system", - "decreased biological_process", - "decreased reflex", - "abnormal response to stimulus", - "abnormal biological_process", - "abnormal behavior", - "abnormal response to external stimulus", - "abnormal voluntary musculoskeletal movement", - "abnormal musculoskeletal movement", - "decreased qualitatively biological_process", - "decreased qualitatively response to stimulus", - "abnormal anatomical entity", - "abnormal voluntary movement behavior", - "abnormal behavior process", - "abnormal voluntary movement behavior", - "changed biological_process rate", - "abnormal behavior process", - "abnormality of anatomical entity physiology" + "anatomical system", + "multicellular organism", + "organ system subdivision", + "posterior region of body", + "multi-limb segment region", + "limb segment", + "pes" ], "object_taxon": null, "object_taxon_label": null, @@ -4191,7 +4757,7 @@ "aggregator_knowledge_source": ["infores:monarchinitiative"], "negated": null, "pathway": null, - "evidence_count": 4, + "evidence_count": 2, "has_evidence": ["ECO:0000304"], "has_evidence_links": [ { @@ -4199,16 +4765,17 @@ "url": "http://purl.obolibrary.org/obo/ECO_0000304" } ], + "grouping_key": "MONDO:0008050\ud83c\udf6a\ud83c\udf6abiolink:has_phenotype\ud83c\udf6aHP:0011916", "provided_by": "hpoa_disease_to_phenotype_edges", "provided_by_link": { "id": "hpoa_disease_to_phenotype", "url": "https://monarch-initiative.github.io/monarch-ingest/Sources/hpoa/#disease_to_phenotype" }, - "publications": ["OMIM:613153"], + "publications": ["OMIM:160500"], "publications_links": [ { - "id": "OMIM:613153", - "url": "http://identifiers.org/mim/613153" + "id": "OMIM:160500", + "url": "http://identifiers.org/mim/160500" } ], "qualifiers": [], @@ -4216,6 +4783,11 @@ "onset_qualifier": null, "sex_qualifier": null, "stage_qualifier": null, + "qualifiers_label": null, + "qualifiers_namespace": null, + "qualifiers_category": null, + "qualifiers_closure": [], + "qualifiers_closure_label": [], "frequency_qualifier_label": null, "frequency_qualifier_namespace": null, "frequency_qualifier_category": null, @@ -4238,212 +4810,152 @@ "stage_qualifier_closure_label": [] }, { - "id": "uuid:864bb8df-5d8c-11ee-9b27-2b20ed86a9d9", + "id": "uuid:c9c8bf2e-7529-11ee-b012-cbd37f5c3759", "category": "biolink:DiseaseToPhenotypicFeatureAssociation", - "subject": "MONDO:0013160", - "original_subject": "OMIM:613156", + "subject": "MONDO:0008050", + "original_subject": "OMIM:160500", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ - "MONDO:0018282", - "MONDO:0000001", - "MONDO:0017741", - "MONDO:0018276", - "MONDO:0045010", + "BFO:0000002", + "MONDO:0016195", + "MONDO:0005336", + "MONDO:0018949", "MONDO:0005071", + "MONDO:0008050", + "BFO:0000016", + "MONDO:0016139", + "OGMS:0000031", + "MONDO:0003847", + "BFO:0000001", "MONDO:0020121", - "MONDO:0000172", - "MONDO:0700223", - "MONDO:0024322", - "BFO:0000002", + "MONDO:0019952", "BFO:0000017", "BFO:0000020", - "MONDO:0013160", - "MONDO:0700071", - "BFO:0000016", "MONDO:0020120", "MONDO:0019056", - "MONDO:0016139", + "MONDO:0000001", + "MONDO:0700223", "MONDO:0700096", - "MONDO:0005336", "MONDO:0002081", - "OGMS:0000031", - "MONDO:0003847", "MONDO:0003939", - "MONDO:0015286", - "BFO:0000001", - "MONDO:0002320", - "MONDO:0019052", - "MONDO:0005066", - "MONDO:0019950", - "MONDO:0016155" + "MONDO:0002320" ], - "subject_label": "muscular dystrophy-dystroglycanopathy (congenital with intellectual disability), type B2", + "subject_label": "MYH7-related skeletal myopathy", "subject_closure_label": [ - "entity", - "continuant", - "disposition", - "realizable entity", - "specifically dependent continuant", - "disease", - "muscular dystrophy-dystroglycanopathy, type B", + "muscular dystrophy", + "human disease", "musculoskeletal system disorder", + "disease", + "muscle tissue disorder", "congenital nervous system disorder", + "hereditary skeletal muscle disorder", + "MYH7-related skeletal myopathy", + "disposition", + "qualitative or quantitative protein defects in neuromuscular diseases", + "distal myopathy", + "disease", + "continuant", + "qualitative or quantitative defects of beta-myosin heavy chain (MYH7)", + "myopathy", "hereditary disease", - "muscle tissue disorder", - "metabolic disease", "nervous system disorder", - "myopathy", - "muscular dystrophy-dystroglycanopathy (congenital with intellectual disability), type B2", - "congenital disorder of glycosylation", - "qualitative or quantitative protein defects in neuromuscular diseases", - "qualitative or quantitative defects of protein involved in O-glycosylation of alpha-dystroglycan", - "disorder of protein O-glycosylation", - "muscular dystrophy-dystroglycanopathy", - "qualitative or quantitative defects of alpha-dystroglycan", - "inborn errors of metabolism", - "neuromuscular disease", - "congenital muscular dystrophy", + "congenital myopathy", + "realizable entity", + "specifically dependent continuant", "skeletal muscle disorder", - "muscular dystrophy", - "disorder of glycosylation", - "glycoprotein metabolism disease", - "myopathy caused by variation in POMT2", - "human disease", - "hereditary skeletal muscle disorder", - "disease" + "neuromuscular disease", + "entity" ], "subject_taxon": null, "subject_taxon_label": null, "predicate": "biolink:has_phenotype", - "object": "HP:0001265", + "object": "HP:0002460", "original_object": null, "object_namespace": "HP", "object_category": "biolink:PhenotypicFeature", "object_closure": [ - "HP:0000001", "UPHENO:0082875", - "UPHENO:0075696", - "UPHENO:0078622", - "UPHENO:0049586", - "UPHENO:0080377", - "UPHENO:0001001", - "UPHENO:0052915", - "UPHENO:0049622", - "UPHENO:0080585", - "HP:0001265", - "HP:0100022", + "UPHENO:0002320", "UPHENO:0001005", - "HP:0031826", - "UPHENO:0001002", - "HP:0000118", - "BFO:0000002", - "UPHENO:0052178", "BFO:0000020", - "UPHENO:0002433", - "UPHENO:0050613", - "UPHENO:0005625", - "UPHENO:0050079", - "UPHENO:0005433", + "PATO:0000001", + "BFO:0000004", + "UBERON:0000061", + "HP:0000001", + "UPHENO:0001001", + "HP:0000118", + "BFO:0000001", + "UBERON:0000467", + "UBERON:0000468", + "UBERON:0011216", + "UPHENO:0075696", + "HP:0001324", + "HP:0003011", "UPHENO:0002332", - "UPHENO:0050606", - "HP:0001315", - "HP:0000707", "UPHENO:0001003", "UPHENO:0002536", - "HP:0000708", - "UPHENO:0079826", - "UPHENO:0004523", - "HP:0011446", - "UPHENO:0079833", - "UPHENO:0049587", - "BFO:0000001", - "PATO:0000001", - "HP:0012638", - "BFO:0000001", - "BFO:0000003", + "HP:0002460", + "HP:0011804", "BFO:0000002", - "BFO:0000015", - "BFO:0000004", - "GO:0008150", "BFO:0000040", + "UBERON:0005090", + "UBERON:0001630", + "UPHENO:0001002", + "BFO:0000002", + "UPHENO:0080555", + "UPHENO:0002816", + "UPHENO:0080556", + "HP:0033127", + "BFO:0000001", "UBERON:0001062", - "GO:0050896", - "GO:0032501", - "UBERON:0000465", - "GO:0009605", - "GO:0050879", - "GO:0007610", - "GO:0003008", - "UBERON:0000061", - "GO:0060004", - "GO:0050881", - "NBO:0000313", - "GO:0050877", - "UBERON:0010000", - "UBERON:0000467", - "GO:0050882", - "NBO:0000338", - "GO:0050905", - "UBERON:0000468", - "UBERON:0001016", - "NBO:0000403", - "NBO:0000001", - "NBO:0000388", - "NBO:0000389" - ], - "object_label": "Hyporeflexia (HPO)", - "object_closure_label": [ - "entity", - "entity", - "continuant", - "continuant", - "independent continuant", - "specifically dependent continuant", - "material entity", - "All (HPO)", - "Phenotypic abnormality (HPO)", - "Abnormality of the nervous system (HPO)", - "Behavioral abnormality (HPO)", - "Hyporeflexia (HPO)", - "Reduced tendon reflexes (HPO)", - "Abnormality of higher mental function (HPO)", - "Abnormal nervous system physiology (HPO)", - "Abnormal reflex (HPO)", - "Abnormality of movement (HPO)", - "quality", - "anatomical structure", + "UBERON:0000465", + "UBERON:0010000", + "UBERON:0000062", + "UBERON:0000383", + "UBERON:0001015" + ], + "object_label": "Distal muscle weakness (HPO)", + "object_closure_label": [ + "All (HPO)", + "abnormality of muscle organ physiology", + "Phenotypic abnormality (HPO)", + "decreased anatomical entity strength", + "abnormal musculature", + "decreased muscle organ strength", + "Abnormality of the musculoskeletal system (HPO)", + "entity", + "independent continuant", "material anatomical entity", - "anatomical system", - "multicellular organism", - "nervous system", - "anatomical entity", + "anatomical structure", "multicellular anatomical structure", + "abnormality of anatomical entity physiology", "phenotype", "Phenotypic abnormality", - "phenotype by ontology source", + "continuant", + "Distal muscle weakness (HPO)", + "quality", + "continuant", + "material entity", "abnormal phenotype by ontology source", - "abnormality of anatomical entity physiology", - "abnormality of nervous system physiology", + "specifically dependent continuant", + "Abnormal muscle physiology (HPO)", + "entity", + "anatomical entity", + "muscle structure", + "organ", + "muscle organ", + "musculature of body", + "musculature", "abnormal anatomical entity", - "abnormal nervous system", - "decreased biological_process", - "decreased reflex", - "abnormal response to stimulus", - "abnormal biological_process", - "abnormal behavior", - "abnormal response to external stimulus", - "abnormal voluntary musculoskeletal movement", - "abnormal musculoskeletal movement", - "decreased qualitatively biological_process", - "decreased qualitatively response to stimulus", + "Muscle weakness (HPO)", + "Abnormality of the musculature (HPO)", + "abnormality of anatomical entity physiology", + "phenotype by ontology source", "abnormal anatomical entity", - "abnormal voluntary movement behavior", - "abnormal behavior process", - "abnormal voluntary movement behavior", - "changed biological_process rate", - "abnormal behavior process", - "abnormality of anatomical entity physiology" + "anatomical system", + "multicellular organism", + "organ system subdivision" ], "object_taxon": null, "object_taxon_label": null, @@ -4451,7 +4963,7 @@ "aggregator_knowledge_source": ["infores:monarchinitiative"], "negated": null, "pathway": null, - "evidence_count": 4, + "evidence_count": 2, "has_evidence": ["ECO:0000304"], "has_evidence_links": [ { @@ -4459,16 +4971,17 @@ "url": "http://purl.obolibrary.org/obo/ECO_0000304" } ], + "grouping_key": "MONDO:0008050\ud83c\udf6a\ud83c\udf6abiolink:has_phenotype\ud83c\udf6aHP:0002460", "provided_by": "hpoa_disease_to_phenotype_edges", "provided_by_link": { "id": "hpoa_disease_to_phenotype", "url": "https://monarch-initiative.github.io/monarch-ingest/Sources/hpoa/#disease_to_phenotype" }, - "publications": ["OMIM:613156"], + "publications": ["OMIM:160500"], "publications_links": [ { - "id": "OMIM:613156", - "url": "http://identifiers.org/mim/613156" + "id": "OMIM:160500", + "url": "http://identifiers.org/mim/160500" } ], "qualifiers": [], @@ -4476,6 +4989,11 @@ "onset_qualifier": null, "sex_qualifier": null, "stage_qualifier": null, + "qualifiers_label": null, + "qualifiers_namespace": null, + "qualifiers_category": null, + "qualifiers_closure": [], + "qualifiers_closure_label": [], "frequency_qualifier_label": null, "frequency_qualifier_namespace": null, "frequency_qualifier_category": null, @@ -4498,194 +5016,176 @@ "stage_qualifier_closure_label": [] }, { - "id": "uuid:840c1951-5d8c-11ee-9b27-2b20ed86a9d9", + "id": "uuid:c9c8bf32-7529-11ee-b012-cbd37f5c3759", "category": "biolink:DiseaseToPhenotypicFeatureAssociation", - "subject": "MONDO:0013297", - "original_subject": "OMIM:613530", + "subject": "MONDO:0008050", + "original_subject": "OMIM:160500", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ - "MONDO:0000001", - "MONDO:0016971", - "MONDO:0000429", + "BFO:0000002", + "MONDO:0016195", + "MONDO:0005336", + "MONDO:0018949", "MONDO:0005071", + "MONDO:0008050", + "BFO:0000016", + "MONDO:0016139", + "OGMS:0000031", + "MONDO:0003847", + "BFO:0000001", "MONDO:0020121", - "MONDO:0700223", - "BFO:0000002", + "MONDO:0019952", "BFO:0000017", "BFO:0000020", - "MONDO:0016106", - "BFO:0000016", "MONDO:0020120", "MONDO:0019056", - "MONDO:0015151", + "MONDO:0000001", + "MONDO:0700223", "MONDO:0700096", - "MONDO:0005336", "MONDO:0002081", - "MONDO:0000426", - "OGMS:0000031", - "MONDO:0003847", "MONDO:0003939", - "BFO:0000001", - "MONDO:0013297" + "MONDO:0002320" ], - "subject_label": "autosomal dominant limb-girdle muscular dystrophy type 1H", + "subject_label": "MYH7-related skeletal myopathy", "subject_closure_label": [ - "entity", - "continuant", + "muscular dystrophy", + "human disease", + "musculoskeletal system disorder", + "disease", + "muscle tissue disorder", + "congenital nervous system disorder", + "hereditary skeletal muscle disorder", + "MYH7-related skeletal myopathy", "disposition", - "realizable entity", - "specifically dependent continuant", + "qualitative or quantitative protein defects in neuromuscular diseases", + "distal myopathy", "disease", - "autosomal dominant disease", - "autosomal genetic disease", - "musculoskeletal system disorder", + "continuant", + "qualitative or quantitative defects of beta-myosin heavy chain (MYH7)", + "myopathy", "hereditary disease", - "muscle tissue disorder", "nervous system disorder", - "myopathy", - "autosomal dominant limb-girdle muscular dystrophy type 1H", - "muscular dystrophy, limb-girdle, autosomal dominant", - "progressive muscular dystrophy", - "limb-girdle muscular dystrophy", - "neuromuscular disease", + "congenital myopathy", + "realizable entity", + "specifically dependent continuant", "skeletal muscle disorder", - "muscular dystrophy", - "human disease", - "hereditary skeletal muscle disorder", - "disease" + "neuromuscular disease", + "entity" ], "subject_taxon": null, "subject_taxon_label": null, "predicate": "biolink:has_phenotype", - "object": "HP:0001265", + "object": "HP:0003805", "original_object": null, "object_namespace": "HP", "object_category": "biolink:PhenotypicFeature", "object_closure": [ + "BFO:0000002", + "BFO:0000020", + "UPHENO:0076692", + "BFO:0000001", + "BFO:0000004", + "CL:0000255", + "UBERON:0014892", + "UBERON:0002036", "HP:0000001", - "UPHENO:0082875", - "UPHENO:0075696", - "UPHENO:0078622", - "UPHENO:0049586", - "UPHENO:0080377", + "HP:0004303", "UPHENO:0001001", - "UPHENO:0052915", - "UPHENO:0049622", - "UPHENO:0080585", - "HP:0001265", - "HP:0100022", - "UPHENO:0001005", - "HP:0031826", "UPHENO:0001002", "HP:0000118", - "BFO:0000002", - "UPHENO:0052178", - "BFO:0000020", - "UPHENO:0002433", - "UPHENO:0050613", - "UPHENO:0005625", - "UPHENO:0050079", - "UPHENO:0005433", - "UPHENO:0002332", - "UPHENO:0050606", - "HP:0001315", - "HP:0000707", "UPHENO:0001003", - "UPHENO:0002536", - "HP:0000708", - "UPHENO:0079826", - "UPHENO:0004523", - "HP:0011446", - "UPHENO:0079833", - "UPHENO:0049587", - "BFO:0000001", + "UPHENO:0076710", "PATO:0000001", - "HP:0012638", "BFO:0000001", - "BFO:0000003", - "BFO:0000002", - "BFO:0000015", - "BFO:0000004", - "GO:0008150", "BFO:0000040", + "UBERON:0000467", + "CL:0000000", + "UBERON:0000468", + "UBERON:0011216", + "CL:0000548", + "UBERON:0001134", + "HP:0003011", + "UPHENO:0002536", + "HP:0003805", + "UBERON:0005090", + "UBERON:0018254", + "UBERON:0004120", + "UBERON:0000479", + "CL:0000003", + "UBERON:0001630", + "UBERON:0002385", + "CL:0000188", + "UPHENO:0001005", + "HP:0011805", + "HP:0025354", + "UPHENO:0002816", + "UPHENO:0081581", + "HP:0033127", + "BFO:0000002", "UBERON:0001062", - "GO:0050896", - "GO:0032501", "UBERON:0000465", - "GO:0009605", - "GO:0050879", - "GO:0007610", - "GO:0003008", + "RO:0002577", "UBERON:0000061", - "GO:0060004", - "GO:0050881", - "NBO:0000313", - "GO:0050877", "UBERON:0010000", - "UBERON:0000467", - "GO:0050882", - "NBO:0000338", - "GO:0050905", - "UBERON:0000468", - "UBERON:0001016", - "NBO:0000403", - "NBO:0000001", - "NBO:0000388", - "NBO:0000389" + "UBERON:0000062", + "UBERON:0000383", + "UBERON:0001015", + "CL:0002371" ], - "object_label": "Hyporeflexia (HPO)", + "object_label": "Rimmed vacuoles (HPO)", "object_closure_label": [ - "entity", - "entity", - "continuant", - "continuant", - "independent continuant", - "specifically dependent continuant", - "material entity", "All (HPO)", + "Abnormal muscle fiber morphology (HPO)", + "Phenotypic abnormality", "Phenotypic abnormality (HPO)", - "Abnormality of the nervous system (HPO)", - "Behavioral abnormality (HPO)", - "Hyporeflexia (HPO)", - "Reduced tendon reflexes (HPO)", - "Abnormality of higher mental function (HPO)", - "Abnormal nervous system physiology (HPO)", - "Abnormal reflex (HPO)", - "Abnormality of movement (HPO)", + "Abnormal cellular phenotype (HPO)", + "abnormal musculature", + "abnormal multicellular organism morphology", + "Abnormality of the musculoskeletal system (HPO)", "quality", - "anatomical structure", + "independent continuant", "material anatomical entity", - "anatomical system", - "multicellular organism", - "nervous system", - "anatomical entity", + "system", "multicellular anatomical structure", "phenotype", - "Phenotypic abnormality", - "phenotype by ontology source", "abnormal phenotype by ontology source", - "abnormality of anatomical entity physiology", - "abnormality of nervous system physiology", - "abnormal anatomical entity", - "abnormal nervous system", - "decreased biological_process", - "decreased reflex", - "abnormal response to stimulus", - "abnormal biological_process", - "abnormal behavior", - "abnormal response to external stimulus", - "abnormal voluntary musculoskeletal movement", - "abnormal musculoskeletal movement", - "decreased qualitatively biological_process", - "decreased qualitatively response to stimulus", + "Abnormal skeletal muscle morphology (HPO)", + "phenotype by ontology source", + "tissue", + "animal cell", + "skeletal muscle tissue", + "cell of skeletal muscle", + "continuant", + "specifically dependent continuant", + "abnormal muscle organ morphology", + "Rimmed vacuoles (HPO)", + "entity", + "anatomical entity", + "anatomical structure", + "muscle structure", + "skeletal musculature", + "mesoderm-derived structure", + "organ", + "native cell", + "muscle organ", + "muscle tissue", + "musculature of body", + "musculature", + "somatic cell", + "Abnormality of the musculature (HPO)", "abnormal anatomical entity", - "abnormal voluntary movement behavior", - "abnormal behavior process", - "abnormal voluntary movement behavior", - "changed biological_process rate", - "abnormal behavior process", - "abnormality of anatomical entity physiology" + "abnormal anatomical entity morphology", + "entity", + "continuant", + "material entity", + "anatomical system", + "cell", + "multicellular organism", + "organ system subdivision", + "eukaryotic cell", + "skeletal muscle organ", + "striated muscle tissue" ], "object_taxon": null, "object_taxon_label": null, @@ -4693,24 +5193,25 @@ "aggregator_knowledge_source": ["infores:monarchinitiative"], "negated": null, "pathway": null, - "evidence_count": 4, - "has_evidence": ["ECO:0000304"], + "evidence_count": 2, + "has_evidence": ["ECO:0000501"], "has_evidence_links": [ { - "id": "ECO:0000304", - "url": "http://purl.obolibrary.org/obo/ECO_0000304" + "id": "ECO:0000501", + "url": "http://purl.obolibrary.org/obo/ECO_0000501" } ], + "grouping_key": "MONDO:0008050\ud83c\udf6a\ud83c\udf6abiolink:has_phenotype\ud83c\udf6aHP:0003805", "provided_by": "hpoa_disease_to_phenotype_edges", "provided_by_link": { "id": "hpoa_disease_to_phenotype", "url": "https://monarch-initiative.github.io/monarch-ingest/Sources/hpoa/#disease_to_phenotype" }, - "publications": ["OMIM:613530"], + "publications": ["OMIM:160500"], "publications_links": [ { - "id": "OMIM:613530", - "url": "http://identifiers.org/mim/613530" + "id": "OMIM:160500", + "url": "http://identifiers.org/mim/160500" } ], "qualifiers": [], @@ -4718,6 +5219,11 @@ "onset_qualifier": null, "sex_qualifier": null, "stage_qualifier": null, + "qualifiers_label": null, + "qualifiers_namespace": null, + "qualifiers_category": null, + "qualifiers_closure": [], + "qualifiers_closure_label": [], "frequency_qualifier_label": null, "frequency_qualifier_namespace": null, "frequency_qualifier_category": null, diff --git a/frontend/fixtures/autocomplete.json b/frontend/fixtures/autocomplete.json index 6798fe2d9..bf9100203 100644 --- a/frontend/fixtures/autocomplete.json +++ b/frontend/fixtures/autocomplete.json @@ -28,6 +28,7 @@ "infantile nephropathic cystinosis", "toni-debre-Fanconi syndrome" ], + "uri": null, "highlight": null, "score": null }, @@ -55,6 +56,7 @@ "Fanconi anemia complementation group type A", "Fanconi anemia, complementation group A" ], + "uri": null, "highlight": null, "score": null }, @@ -79,6 +81,7 @@ "Fanconi anemia complementation group type L", "Fanconi anemia, complementation group L" ], + "uri": null, "highlight": null, "score": null }, @@ -103,6 +106,7 @@ "Fanconi anemia, complementation group E", "face" ], + "uri": null, "highlight": null, "score": null }, @@ -129,6 +133,7 @@ "primary Fanconi renotubular syndrome", "renal Fanconi syndrome" ], + "uri": null, "highlight": null, "score": null }, @@ -152,6 +157,7 @@ "pancytopenia, congenital", "primary erythroid hypoplasia" ], + "uri": null, "highlight": null, "score": null }, @@ -176,6 +182,7 @@ "RAD51C Fanconi anemia", "Rad51C Fanconi anemia" ], + "uri": null, "highlight": null, "score": null }, @@ -200,6 +207,7 @@ "SLX4 Fanconi anemia", "Slx4 Fanconi anemia" ], + "uri": null, "highlight": null, "score": null }, @@ -224,24 +232,7 @@ "Fanconi anemia, complementation GROUP V", "MAD2L2 Fanconi anemia" ], - "highlight": null, - "score": null - }, - { - "id": "MONDO:0100136", - "category": "biolink:Disease", - "name": "obsolete Fanconia anemia complementation group M", - "full_name": null, - "description": "OBSOLETE Any Fanconi anemia in which the cause of the disease is a mutation in the FANCM gene.", - "xref": [], - "provided_by": "phenio_nodes", - "in_taxon": null, - "in_taxon_label": null, - "symbol": null, - "synonym": [ - "FANCM Fanconi anemia", - "Fanconi anemia caused by mutation in FANCM" - ], + "uri": null, "highlight": null, "score": null }, @@ -268,6 +259,7 @@ "Fanconi pancytopenia type 2", "Fanconi pancytopenia, type 2" ], + "uri": null, "highlight": null, "score": null }, @@ -291,6 +283,7 @@ "Fanconi anemia, complementation group N", "PALB2 Fanconi anemia" ], + "uri": null, "highlight": null, "score": null }, @@ -314,6 +307,7 @@ "Fanconi anemia, complementation GROUP R", "RAD51 Fanconi anemia" ], + "uri": null, "highlight": null, "score": null }, @@ -337,6 +331,26 @@ "Fanconi anemia, complementation GROUP U", "XRCC2 Fanconi anemia" ], + "uri": null, + "highlight": null, + "score": null + }, + { + "id": "MONDO:0100136", + "category": "biolink:Disease", + "name": "obsolete Fanconia anemia complementation group M", + "full_name": null, + "description": "OBSOLETE Any Fanconi anemia in which the cause of the disease is a mutation in the FANCM gene.", + "xref": [], + "provided_by": "phenio_nodes", + "in_taxon": null, + "in_taxon_label": null, + "symbol": null, + "synonym": [ + "FANCM Fanconi anemia", + "Fanconi anemia caused by mutation in FANCM" + ], + "uri": null, "highlight": null, "score": null }, @@ -363,6 +377,7 @@ "Fanconi pancytopenia, type 3", "facc" ], + "uri": null, "highlight": null, "score": null }, @@ -388,6 +403,7 @@ "Fanconi pancytopenia type 4", "Fanconi pancytopenia, type 4" ], + "uri": null, "highlight": null, "score": null }, @@ -410,6 +426,7 @@ "Fanconi anemia complementation group type I", "Fanconi anemia, complementation group I" ], + "uri": null, "highlight": null, "score": null }, @@ -432,6 +449,7 @@ "Fanconi anemia complementation group type Q", "Fanconi anemia, complementation group Q" ], + "uri": null, "highlight": null, "score": null }, @@ -454,6 +472,7 @@ "Fanconi anemia, complementation group T", "UBE2T Fanconi anemia" ], + "uri": null, "highlight": null, "score": null }, @@ -475,6 +494,7 @@ "Fanconi anemia complementation group type F", "Fanconi anemia, complementation group F" ], + "uri": null, "highlight": null, "score": null } diff --git a/frontend/fixtures/entity.json b/frontend/fixtures/entity.json new file mode 100644 index 000000000..766f989c9 --- /dev/null +++ b/frontend/fixtures/entity.json @@ -0,0 +1,14 @@ +{ + "id": "MONDO:0020121", + "category": "biolink:Disease", + "name": "muscular dystrophy", + "full_name": null, + "description": "Muscular dystrophy (MD) refers to a group of more than 30 genetic diseases characterized by progressive weakness and degeneration of the skeletal muscles that control movement. Some forms of MD are seen in newborns, infants or children, while others have late-onset and may not appear until middle age or later. The disorders differ in terms of the distribution and extent of muscle weakness (some forms of MD also affect cardiac muscle), age of onset, rate of progression, and pattern of inheritance. The prognosis for people with MD varies according to the type and progression of the disorder. There is no specific treatment to stop or reverse any form of MD. Treatment is supportive and may include physical therapy, respiratory therapy, speech therapy, orthopedic appliances used for support, corrective orthopedic surgery, and medicationsincluding corticosteroids, anticonvulsants (seizure medications), immunosuppressants, and antibiotics. Some individuals may need assisted ventilation to treat respiratory muscle weaknessor a pacemaker for cardiac (heart)abnormalities.", + "xref": [], + "provided_by": "phenio_nodes", + "in_taxon": null, + "in_taxon_label": null, + "symbol": null, + "synonym": [], + "uri": "http://purl.obolibrary.org/obo/MONDO_0020121" +} diff --git a/frontend/fixtures/node.json b/frontend/fixtures/node.json index 70b327106..baf9051e2 100644 --- a/frontend/fixtures/node.json +++ b/frontend/fixtures/node.json @@ -10,6 +10,7 @@ "in_taxon_label": null, "symbol": null, "synonym": [], + "uri": null, "inheritance": null, "causal_gene": [], "causes_disease": [], @@ -38,9 +39,9 @@ "node_hierarchy": { "super_classes": [ { - "id": "MONDO:0005336", + "id": "MONDO:0019056", "category": "biolink:Disease", - "name": "myopathy", + "name": "neuromuscular disease", "full_name": null, "description": null, "xref": [], @@ -48,7 +49,8 @@ "in_taxon": null, "in_taxon_label": null, "symbol": null, - "synonym": [] + "synonym": [], + "uri": null }, { "id": "MONDO:0700223", @@ -61,12 +63,13 @@ "in_taxon": null, "in_taxon_label": null, "symbol": null, - "synonym": [] + "synonym": [], + "uri": null }, { - "id": "MONDO:0019056", + "id": "MONDO:0005336", "category": "biolink:Disease", - "name": "neuromuscular disease", + "name": "myopathy", "full_name": null, "description": null, "xref": [], @@ -74,14 +77,15 @@ "in_taxon": null, "in_taxon_label": null, "symbol": null, - "synonym": [] + "synonym": [], + "uri": null } ], "sub_classes": [ { - "id": "MONDO:0008028", + "id": "MONDO:0018949", "category": "biolink:Disease", - "name": "muscular dystrophy, Barnes type", + "name": "distal myopathy", "full_name": null, "description": null, "xref": [], @@ -89,12 +93,13 @@ "in_taxon": null, "in_taxon_label": null, "symbol": null, - "synonym": [] + "synonym": [], + "uri": null }, { - "id": "MONDO:0010675", + "id": "MONDO:0019950", "category": "biolink:Disease", - "name": "muscular dystrophy, cardiac type", + "name": "congenital muscular dystrophy", "full_name": null, "description": null, "xref": [], @@ -102,12 +107,13 @@ "in_taxon": null, "in_taxon_label": null, "symbol": null, - "synonym": [] + "synonym": [], + "uri": null }, { - "id": "MONDO:0010676", + "id": "MONDO:0023204", "category": "biolink:Disease", - "name": "muscular dystrophy, Hemizygous lethal type", + "name": "Fukuda-Miyanomae-Nakata syndrome", "full_name": null, "description": null, "xref": [], @@ -115,12 +121,13 @@ "in_taxon": null, "in_taxon_label": null, "symbol": null, - "synonym": [] + "synonym": [], + "uri": null }, { - "id": "MONDO:0010677", + "id": "MONDO:0100228", "category": "biolink:Disease", - "name": "muscular dystrophy, Mabry type", + "name": "LAMA2-related muscular dystrophy", "full_name": null, "description": null, "xref": [], @@ -128,12 +135,13 @@ "in_taxon": null, "in_taxon_label": null, "symbol": null, - "synonym": [] + "synonym": [], + "uri": null }, { - "id": "MONDO:0010678", + "id": "MONDO:0008028", "category": "biolink:Disease", - "name": "muscular dystrophy, progressive Pectorodorsal", + "name": "muscular dystrophy, Barnes type", "full_name": null, "description": null, "xref": [], @@ -141,12 +149,13 @@ "in_taxon": null, "in_taxon_label": null, "symbol": null, - "synonym": [] + "synonym": [], + "uri": null }, { - "id": "MONDO:0016106", + "id": "MONDO:0010675", "category": "biolink:Disease", - "name": "progressive muscular dystrophy", + "name": "muscular dystrophy, cardiac type", "full_name": null, "description": null, "xref": [], @@ -154,12 +163,13 @@ "in_taxon": null, "in_taxon_label": null, "symbol": null, - "synonym": [] + "synonym": [], + "uri": null }, { - "id": "MONDO:0018949", + "id": "MONDO:0010676", "category": "biolink:Disease", - "name": "distal myopathy", + "name": "muscular dystrophy, Hemizygous lethal type", "full_name": null, "description": null, "xref": [], @@ -167,12 +177,13 @@ "in_taxon": null, "in_taxon_label": null, "symbol": null, - "synonym": [] + "synonym": [], + "uri": null }, { - "id": "MONDO:0019950", + "id": "MONDO:0010677", "category": "biolink:Disease", - "name": "congenital muscular dystrophy", + "name": "muscular dystrophy, Mabry type", "full_name": null, "description": null, "xref": [], @@ -180,12 +191,13 @@ "in_taxon": null, "in_taxon_label": null, "symbol": null, - "synonym": [] + "synonym": [], + "uri": null }, { - "id": "MONDO:0023204", + "id": "MONDO:0010678", "category": "biolink:Disease", - "name": "Fukuda-Miyanomae-Nakata syndrome", + "name": "muscular dystrophy, progressive Pectorodorsal", "full_name": null, "description": null, "xref": [], @@ -193,12 +205,13 @@ "in_taxon": null, "in_taxon_label": null, "symbol": null, - "synonym": [] + "synonym": [], + "uri": null }, { - "id": "MONDO:0100228", + "id": "MONDO:0016106", "category": "biolink:Disease", - "name": "LAMA2-related muscular dystrophy", + "name": "progressive muscular dystrophy", "full_name": null, "description": null, "xref": [], @@ -206,7 +219,8 @@ "in_taxon": null, "in_taxon_label": null, "symbol": null, - "synonym": [] + "synonym": [], + "uri": null } ] } diff --git a/frontend/fixtures/phenotype-explorer-compare.json b/frontend/fixtures/phenotype-explorer-compare.json index 9eee78b95..47898790d 100644 --- a/frontend/fixtures/phenotype-explorer-compare.json +++ b/frontend/fixtures/phenotype-explorer-compare.json @@ -21,7 +21,7 @@ "match_source_label": "no abnormal phenotype detected (MPO)", "match_target": "HP:0004325", "match_target_label": "Decreased body weight (HPO)", - "score": 1.5616002210519475, + "score": 1.4431977534690428, "match_subsumer": null, "match_subsumer_label": null, "similarity": { @@ -36,11 +36,11 @@ "ancestor_source": null, "object_information_content": null, "subject_information_content": null, - "ancestor_information_content": 1.5616002210519475, + "ancestor_information_content": 1.4431977534690428, "jaccard_similarity": 0.16216216216216217, "cosine_similarity": null, "dice_similarity": null, - "phenodigm_score": 0.5032220864376823 + "phenodigm_score": 0.48376861011243283 } }, "MP:0010771": { @@ -48,7 +48,7 @@ "match_source_label": "integument phenotype (MPO)", "match_target": "HP:0004325", "match_target_label": "Decreased body weight (HPO)", - "score": 2.2728188647181566, + "score": 1.4431977534690428, "match_subsumer": null, "match_subsumer_label": null, "similarity": { @@ -58,16 +58,16 @@ "object_id": "HP:0004325", "object_label": null, "object_source": null, - "ancestor_id": "UBERON:0000468", + "ancestor_id": "UPHENO:0001003", "ancestor_label": "", "ancestor_source": null, "object_information_content": null, "subject_information_content": null, - "ancestor_information_content": 2.2728188647181566, - "jaccard_similarity": 0.325, + "ancestor_information_content": 1.4431977534690428, + "jaccard_similarity": 0.3333333333333333, "cosine_similarity": null, "dice_similarity": null, - "phenodigm_score": 0.8594568814276845 + "phenodigm_score": 0.6935891563620457 } } }, @@ -77,7 +77,7 @@ "match_source_label": "Decreased body weight (HPO)", "match_target": "MP:0010771", "match_target_label": "integument phenotype (MPO)", - "score": 2.2728188647181566, + "score": 1.4431977534690428, "match_subsumer": null, "match_subsumer_label": null, "similarity": { @@ -87,20 +87,20 @@ "object_id": "MP:0010771", "object_label": null, "object_source": null, - "ancestor_id": "UBERON:0000468", + "ancestor_id": "UPHENO:0001003", "ancestor_label": "", "ancestor_source": null, "object_information_content": null, "subject_information_content": null, - "ancestor_information_content": 2.2728188647181566, - "jaccard_similarity": 0.325, + "ancestor_information_content": 1.4431977534690428, + "jaccard_similarity": 0.3333333333333333, "cosine_similarity": null, "dice_similarity": null, - "phenodigm_score": 0.8594568814276845 + "phenodigm_score": 0.6935891563620457 } } }, - "average_score": 2.0950142038016044, - "best_score": 2.2728188647181566, + "average_score": 1.4431977534690428, + "best_score": 1.4431977534690428, "metric": "ancestor_information_content" } diff --git a/frontend/fixtures/search.json b/frontend/fixtures/search.json index f98914ea5..92510b879 100644 --- a/frontend/fixtures/search.json +++ b/frontend/fixtures/search.json @@ -23,6 +23,7 @@ "pancytopenia, congenital", "primary erythroid hypoplasia" ], + "uri": null, "highlight": null, "score": null }, @@ -51,6 +52,7 @@ "infantile nephropathic cystinosis", "toni-debre-Fanconi syndrome" ], + "uri": null, "highlight": null, "score": null }, @@ -70,6 +72,7 @@ "Fanconi renotubular syndrome 1", "primary Fanconi renotubular syndrome" ], + "uri": null, "highlight": null, "score": null }, @@ -85,6 +88,7 @@ "in_taxon_label": null, "symbol": null, "synonym": ["Fanconi-like syndrome"], + "uri": null, "highlight": null, "score": null }, @@ -100,6 +104,7 @@ "in_taxon_label": null, "symbol": null, "synonym": ["adult Fanconi syndrome", "adult Fanconi's syndrome"], + "uri": null, "highlight": null, "score": null }, @@ -115,6 +120,7 @@ "in_taxon_label": null, "symbol": null, "synonym": ["acquired Fanconi syndrome"], + "uri": null, "highlight": null, "score": null }, @@ -130,6 +136,7 @@ "in_taxon_label": null, "symbol": null, "synonym": [], + "uri": null, "highlight": null, "score": null }, @@ -151,6 +158,7 @@ "Fanconi syndrome caused by mutation in SLC34A1", "SLC34A1 Fanconi syndrome" ], + "uri": null, "highlight": null, "score": null }, @@ -172,6 +180,7 @@ "Fanconi renotubular syndrome type 3", "Fanconi syndrome caused by mutation in EHHADH" ], + "uri": null, "highlight": null, "score": null }, @@ -198,6 +207,7 @@ "primary Fanconi renotubular syndrome", "renal Fanconi syndrome" ], + "uri": null, "highlight": null, "score": null }, @@ -218,6 +228,7 @@ "Fanconi Renotubular Syndrome, Acadian Variant", "Fanconi renotubular syndrome 5" ], + "uri": null, "highlight": null, "score": null }, @@ -233,6 +244,7 @@ "in_taxon_label": null, "symbol": null, "synonym": ["hereditary Fanconi renotubular syndrome"], + "uri": null, "highlight": null, "score": null }, @@ -259,6 +271,7 @@ "Fanconi pancytopenia, type 3", "facc" ], + "uri": null, "highlight": null, "score": null }, @@ -284,6 +297,7 @@ "Fanconi pancytopenia type 4", "Fanconi pancytopenia, type 4" ], + "uri": null, "highlight": null, "score": null }, @@ -311,6 +325,7 @@ "Fanconi anemia complementation group type A", "Fanconi anemia, complementation group A" ], + "uri": null, "highlight": null, "score": null }, @@ -337,6 +352,7 @@ "Fanconi pancytopenia type 2", "Fanconi pancytopenia, type 2" ], + "uri": null, "highlight": null, "score": null }, @@ -361,6 +377,7 @@ "Fanconi anemia, complementation group E", "face" ], + "uri": null, "highlight": null, "score": null }, @@ -382,6 +399,7 @@ "Fanconi anemia complementation group type F", "Fanconi anemia, complementation group F" ], + "uri": null, "highlight": null, "score": null }, @@ -404,6 +422,7 @@ "Fanconi anemia, complementation group D1", "inherited cancer-predisposing syndrome due to biallelic BRCA2 mutations" ], + "uri": null, "highlight": null, "score": null }, @@ -426,6 +445,7 @@ "Fanconi anemia complementation group type I", "Fanconi anemia, complementation group I" ], + "uri": null, "highlight": null, "score": null } diff --git a/frontend/src/api/model.ts b/frontend/src/api/model.ts index 8a861812a..34b656aeb 100644 --- a/frontend/src/api/model.ts +++ b/frontend/src/api/model.ts @@ -63,6 +63,8 @@ export interface Association { has_evidence?: string[], /** List of ExpandedCuries with id and url for evidence */ has_evidence_links?: ExpandedCurie[], + /** A concatenation of fields used to group associations with the same essential/defining properties */ + grouping_key?: string, provided_by?: string, /** A link to the docs for the knowledge source that provided the node/edge. */ provided_by_link?: ExpandedCurie, @@ -75,6 +77,16 @@ export interface Association { sex_qualifier?: string, stage_qualifier?: string, /** The name of the frequency_qualifier entity */ + qualifiers_label?: string, + /** The namespace/prefix of the frequency_qualifier entity */ + qualifiers_namespace?: string, + /** The category of the frequency_qualifier entity */ + qualifiers_category?: string, + /** Field containing frequency_qualifier id and the ids of all of it's ancestors */ + qualifiers_closure?: string[], + /** Field containing frequency_qualifier name and the names of all of it's ancestors */ + qualifiers_closure_label?: string[], + /** The name of the frequency_qualifier entity */ frequency_qualifier_label?: string, /** The namespace/prefix of the frequency_qualifier entity */ frequency_qualifier_namespace?: string, @@ -223,6 +235,8 @@ export interface DirectionalAssociation extends Association { has_evidence?: string[], /** List of ExpandedCuries with id and url for evidence */ has_evidence_links?: ExpandedCurie[], + /** A concatenation of fields used to group associations with the same essential/defining properties */ + grouping_key?: string, provided_by?: string, /** A link to the docs for the knowledge source that provided the node/edge. */ provided_by_link?: ExpandedCurie, @@ -235,6 +249,16 @@ export interface DirectionalAssociation extends Association { sex_qualifier?: string, stage_qualifier?: string, /** The name of the frequency_qualifier entity */ + qualifiers_label?: string, + /** The namespace/prefix of the frequency_qualifier entity */ + qualifiers_namespace?: string, + /** The category of the frequency_qualifier entity */ + qualifiers_category?: string, + /** Field containing frequency_qualifier id and the ids of all of it's ancestors */ + qualifiers_closure?: string[], + /** Field containing frequency_qualifier name and the names of all of it's ancestors */ + qualifiers_closure_label?: string[], + /** The name of the frequency_qualifier entity */ frequency_qualifier_label?: string, /** The namespace/prefix of the frequency_qualifier entity */ frequency_qualifier_namespace?: string, @@ -300,6 +324,8 @@ export interface Entity { in_taxon_label?: string, symbol?: string, synonym?: string[], + /** The URI of the entity */ + uri?: string, }; export interface EntityResults extends Results { @@ -341,13 +367,11 @@ export interface HistoBin extends FacetValue { * A minimal class to hold a SSSOM mapping */ export interface Mapping { - /** The first of the two entities being compared */ subject_id: string, /** The name of the subject entity */ subject_label?: string, predicate_id: string, - /** The second of the two entities being compared */ - object_id?: string, + object_id: string, /** The name of the object entity */ object_label?: string, mapping_justification?: string, @@ -393,6 +417,8 @@ export interface Node extends Entity { provided_by?: string, symbol?: string, synonym?: string[], + /** The URI of the entity */ + uri?: string, }; export interface NodeHierarchy { @@ -427,6 +453,8 @@ export interface SearchResult extends Entity { in_taxon_label?: string, symbol?: string, synonym?: string[], + /** The URI of the entity */ + uri?: string, }; export interface SearchResults extends Results { @@ -452,14 +480,12 @@ export interface PairwiseSimilarity { * A simple pairwise similarity between two atomic concepts/terms */ export interface TermPairwiseSimilarity extends PairwiseSimilarity { - /** The first of the two entities being compared */ subject_id: string, /** The name of the subject entity */ subject_label?: string, /** the source for the first entity */ subject_source?: string, - /** The second of the two entities being compared */ - object_id?: string, + object_id: string, /** The name of the object entity */ object_label?: string, /** the source for the second entity */ @@ -476,12 +502,12 @@ export interface TermPairwiseSimilarity extends PairwiseSimilarity { /** The IC of the object */ ancestor_information_content?: string, /** The number of concepts in the intersection divided by the number in the union */ - jaccard_similarity?: string, + jaccard_similarity?: number, /** the dot product of two node embeddings divided by the product of their lengths */ cosine_similarity?: number, - dice_similarity?: string, + dice_similarity?: number, /** the geometric mean of the jaccard similarity and the information content */ - phenodigm_score?: string, + phenodigm_score?: number, }; /** * A simple pairwise similarity between two sets of concepts/terms diff --git a/frontend/src/api/phenotype-explorer.ts b/frontend/src/api/phenotype-explorer.ts index 54159ecd7..cffdf02c8 100644 --- a/frontend/src/api/phenotype-explorer.ts +++ b/frontend/src/api/phenotype-explorer.ts @@ -139,8 +139,13 @@ export const compareSetToSet = async ( [key: string]: { score: number; strength: number; - simInfo: Partial; - }; + } & Pick< + TermPairwiseSimilarity, + | "ancestor_id" + | "ancestor_label" + | "jaccard_similarity" + | "phenodigm_score" + >; } = {}; /** get subject matches */ @@ -162,8 +167,9 @@ export const compareSetToSet = async ( cells[col.id + row.id] = { score: match?.score || 0, strength: 0, - simInfo: pick(match?.similarity, [ + ...pick(match?.similarity, [ "ancestor_id", + "ancestor_label", "jaccard_similarity", "phenodigm_score", ]), diff --git a/frontend/src/api/search.ts b/frontend/src/api/search.ts index 0da68fdb0..70b0523c8 100644 --- a/frontend/src/api/search.ts +++ b/frontend/src/api/search.ts @@ -1,5 +1,4 @@ -import { groupBy, uniq } from "lodash"; -import type { SearchResult, SearchResults } from "@/api/model"; +import type { SearchResults } from "@/api/model"; import { apiUrl, request } from "./index"; export type Filters = { [key: string]: string[] }; @@ -21,29 +20,13 @@ export const getSearch = async ( return response; }; -type DedupedSearchResults = Omit & { - items: (SearchResult & { dupes: string[] })[]; -}; - export const getAutocomplete = async (q: string) => { const url = `${apiUrl}/autocomplete`; const response = await request(url, { q }); - const transformedResponse: DedupedSearchResults = { + const transformedResponse = { ...response, - items: Object.values( - /** consolidate items */ - groupBy( - response.items, - /** by name, case insensitively */ - (item) => item.name.toLowerCase(), - ), - ).map((dupes) => ({ - ...dupes[0], - /** keep list of duplicated names */ - /** de-dupe this list case sensitively */ - dupes: uniq(dupes.map((dupe) => dupe.name)), - })), + items: response.items.slice(0, 20), }; return transformedResponse; diff --git a/frontend/src/components/AppSelectAutocomplete.vue b/frontend/src/components/AppSelectAutocomplete.vue index d662d64ae..3036173bb 100644 --- a/frontend/src/components/AppSelectAutocomplete.vue +++ b/frontend/src/components/AppSelectAutocomplete.vue @@ -62,11 +62,14 @@ :id="`option-${id}-${index}`" :key="index" v-tooltip="option.tooltip" - :class="['option', { highlighted: index === highlighted }]" + :class="[ + 'option', + { highlighted: index === highlighted, special: option.special }, + ]" role="option" :aria-selected="true" tabindex="0" - @click.prevent="() => select(option.label)" + @click.prevent="() => select(option)" @mousedown.prevent="" @focusin="() => null" @keydown="() => null" @@ -83,9 +86,6 @@ - - -
{{ description }}
@@ -99,12 +99,16 @@ export type Option = { icon?: string; /** display label */ label: string; + /** unique id */ + id?: string; /** highlighting html */ highlight?: string; /** info col */ info?: string; /** tooltip on hover */ tooltip?: string; + /** whether option is "special" (gets styled differently) */ + special?: boolean; }; @@ -136,9 +140,9 @@ type Emits = { /** when input focused */ focus: []; /** when input value change "submitted"/"committed" by user */ - change: [string]; + change: [string | Option, string]; /** when user wants to delete an entry */ - delete: [string]; + delete: [Option]; }; const emit = defineEmits(); @@ -182,9 +186,13 @@ async function onDebounce() { await runGetResults(); } +/** ignore next child input box change event */ +let ignoreChange = false; + /** when user "commits" change to value, e.g. pressing enter, de-focusing, etc */ -function onChange(value: string) { - select(value); +async function onChange(value: string) { + if (!ignoreChange) select(value); + ignoreChange = false; } /** when user presses key in input */ @@ -210,13 +218,12 @@ async function onKeydown(event: KeyboardEvent) { /** enter key to select highlighted result */ if (event.key === "Enter" && highlighted.value >= 0) { - event.stopPropagation(); - select(results.value[highlighted.value].label); + select(results.value[highlighted.value]); } /** delete key to delete the highlighted result */ if (event.key === "Delete" && event.shiftKey) { - emit("delete", results.value[highlighted.value].label); + emit("delete", results.value[highlighted.value]); await runGetResults(); } @@ -225,9 +232,11 @@ async function onKeydown(event: KeyboardEvent) { } /** select an option */ -async function select(value: string) { - search.value = value; - emit("change", value); +async function select(value: string | Option) { + /** ignore next child input box change event triggered by enter press */ + ignoreChange = true; + emit("change", value, search.value); + search.value = typeof value === "string" ? value : value.label; close(); } @@ -345,9 +354,7 @@ watch(highlighted, () => { color: $gray; } -.description { - margin-top: 10px; - color: $dark-gray; - font-size: 0.9rem; +.special { + font-weight: 500; } diff --git a/frontend/src/components/AppTable.vue b/frontend/src/components/AppTable.vue index 78ba2092d..5645cccaf 100644 --- a/frontend/src/components/AppTable.vue +++ b/frontend/src/components/AppTable.vue @@ -468,7 +468,7 @@ watch( } &.divider { - width: 2px; + width: 2px !important; margin: 0 auto; padding: 0; background: $light-gray; diff --git a/frontend/src/components/AppTextbox.vue b/frontend/src/components/AppTextbox.vue index ac1ec0fe1..05147d129 100644 --- a/frontend/src/components/AppTextbox.vue +++ b/frontend/src/components/AppTextbox.vue @@ -80,7 +80,7 @@ type Emits = { blur: []; }; -const emit = defineEmits(); +defineEmits(); /** element reference */ const textbox = ref(); @@ -91,7 +91,7 @@ const input = ref(); function clear() { input.value.input.value = ""; input.value.input.dispatchEvent(new Event("input")); - emit("change", ""); + input.value.input.dispatchEvent(new Event("change")); } /** allow parent to access ref */ @@ -141,7 +141,6 @@ $height: 40px; justify-content: center; width: $height; height: $height; - color: $gray; } .input { diff --git a/frontend/src/components/TheHeader.vue b/frontend/src/components/TheHeader.vue index c9943f111..02a2aa4bb 100644 --- a/frontend/src/components/TheHeader.vue +++ b/frontend/src/components/TheHeader.vue @@ -242,8 +242,8 @@ $wrap: 900px; .nav { display: flex; align-items: center; - justify-content: center; - max-width: 100%; + justify-content: flex-end; + width: 100%; padding: 15px; gap: 10px; } diff --git a/frontend/src/components/ThePhenogrid.vue b/frontend/src/components/ThePhenogrid.vue index 8d8025628..fd0912ad2 100644 --- a/frontend/src/components/ThePhenogrid.vue +++ b/frontend/src/components/ThePhenogrid.vue @@ -85,21 +85,28 @@ :node="{ id: row.id, name: row.label }" :absolute="true" /> - Score + Ancestor + + Ancestor IC {{ - data.cells[col.id + row.id].score.toFixed(2) + data.cells[col.id + row.id].score.toFixed(3) + }} + Phenodigm + {{ + data.cells[col.id + row.id].phenodigm_score?.toFixed(3) + }} + Jaccard + {{ + data.cells[col.id + row.id].jaccard_similarity?.toFixed( + 3, + ) }} - @@ -146,7 +153,7 @@ :options="sortMethods" /> - + import { ref } from "vue"; -import { sortBy, startCase } from "lodash"; +import { sortBy } from "lodash"; import { hideAll } from "tippy.js"; import type { TermInfo } from "@/api/model"; import { type SetToSet } from "@/api/phenotype-explorer"; @@ -190,17 +197,21 @@ function hoverCell(colIndex: number, rowIndex: number, unset = false) { else hovered.value = { col: colIndex, row: rowIndex }; } -const flex = ref<{ element: HTMLTableElement }>(); +const flex = ref<{ element: HTMLElement }>(); const scroll = ref(); +/** set container to be full size (of contents) */ +function setFullsize(full: boolean) { + if (!flex.value?.element || !scroll.value) return; + scroll.value.classList[full ? "add" : "remove"]("full-size"); + flex.value.element.classList[full ? "add" : "remove"]("full-size"); +} + /** download grid as png */ async function download() { if (!flex.value?.element || !scroll.value) return; - /** make full size */ - scroll.value.classList.add("saving"); - flex.value.element.classList.add("saving"); - + setFullsize(true); hideAll(); /** wait for dom to update */ @@ -216,9 +227,7 @@ async function download() { snackbar("Error saving image"); } - /** reset size */ - scroll.value.classList.remove("saving"); - flex.value.element.classList.remove("saving"); + setFullsize(false); } /** options for sorting */ @@ -251,12 +260,11 @@ function copy() { - diff --git a/frontend/src/pages/explore/TabPhenotypeExplorer.vue b/frontend/src/pages/explore/TabPhenotypeExplorer.vue index 70f8d72d8..068d046cb 100644 --- a/frontend/src/pages/explore/TabPhenotypeExplorer.vue +++ b/frontend/src/pages/explore/TabPhenotypeExplorer.vue @@ -135,9 +135,8 @@ import type { Option, Options } from "@/components/AppSelectTags.vue"; import AppSelectTags from "@/components/AppSelectTags.vue"; import ThePhenogrid from "@/components/ThePhenogrid.vue"; import { snackbar } from "@/components/TheSnackbar.vue"; -import { scrollToElement } from "@/router"; +import { scrollTo } from "@/router"; import { useQuery } from "@/util/composables"; -import { waitFor } from "@/util/dom"; import { parse } from "@/util/object"; import examples from "./phenotype-explorer.json"; @@ -235,7 +234,7 @@ const { /** scroll results into view */ async function scrollToResults() { - scrollToElement(await waitFor("#results")); + scrollTo("#results"); } /** when multi select component runs spread options function */ diff --git a/frontend/src/pages/explore/TabSearch.vue b/frontend/src/pages/explore/TabSearch.vue index 83222b196..8339b78ea 100644 --- a/frontend/src/pages/explore/TabSearch.vue +++ b/frontend/src/pages/explore/TabSearch.vue @@ -108,24 +108,27 @@ @@ -429,8 +445,7 @@ watch(from, () => runGetSearch(false)); } .header-box { - width: 300px; - max-width: 100%; + width: 100%; } .header-box :deep(input) { @@ -444,7 +459,7 @@ watch(from, () => runGetSearch(false)); } .header-box :deep(.icon) { - color: currentColor; + color: currentColor !important; } diff --git a/frontend/src/pages/metadata.json b/frontend/src/pages/metadata.json index 9f6dd1f00..1655a0493 100644 --- a/frontend/src/pages/metadata.json +++ b/frontend/src/pages/metadata.json @@ -3,7 +3,7 @@ { "label": "Genes", "icon": "category-gene", - "count": 565986 + "count": 558334 }, { "label": "Phenotypes", @@ -18,29 +18,29 @@ { "label": "Total Nodes", "icon": "node", - "count": 806761 + "count": 838004 } ], "association": [ { "label": "Gene to Disease", "icon": "association-gene-to-disease", - "count": 15038 + "count": 15032 }, { "label": "Gene to Phenotype", "icon": "association-gene-to-phenotype", - "count": 832433 + "count": 882338 }, { "label": "Disease to Phenotype", "icon": "association-disease-to-phenotype", - "count": 240556 + "count": 240274 }, { "label": "Total Associations", "icon": "association", - "count": 8076791 + "count": 10049896 } ] } diff --git a/frontend/src/pages/node/PageNode.vue b/frontend/src/pages/node/PageNode.vue index 350afcd13..e7740b430 100644 --- a/frontend/src/pages/node/PageNode.vue +++ b/frontend/src/pages/node/PageNode.vue @@ -36,14 +36,13 @@