From 73303b57d4174b58a8177f86cb2ffd79276969d7 Mon Sep 17 00:00:00 2001 From: Kevin Schaper Date: Fri, 14 Jul 2023 17:37:31 -0700 Subject: [PATCH] make has_evidence multivalued & primary_knowledge_source single valued, plus at typo fix (#226) Fixes two schema bugs affecting the evidence display --- backend/src/monarch_py/datamodels/model.py | 10 +- backend/src/monarch_py/datamodels/model.yaml | 5 +- .../solr/solr_implementation.py | 2 +- .../implementations/solr/solr_parsers.py | 2 +- .../implementations/solr/solr_query_utils.py | 24 +- .../fixtures/association_counts_response.py | 3421 ++++------------- .../tests/fixtures/association_response.py | 3419 ++++------------ backend/tests/fixtures/association_table.py | 911 ++--- .../fixtures/association_table_response.py | 893 ++--- backend/tests/fixtures/associations.py | 3379 ++++------------ backend/tests/fixtures/autocomplete.py | 2 +- .../tests/fixtures/autocomplete_response.py | 4 +- backend/tests/fixtures/histopheno_response.py | 4 +- backend/tests/fixtures/node.py | 21 +- backend/tests/fixtures/search.py | 2 +- backend/tests/fixtures/search_response.py | 2 +- frontend/fixtures/association-table.json | 909 +++-- frontend/fixtures/associations.json | 3399 ++++------------ frontend/fixtures/autocomplete.json | 2 +- frontend/fixtures/node.json | 21 +- frontend/fixtures/search.json | 2 +- frontend/src/api/model.ts | 10 +- 22 files changed, 4384 insertions(+), 12060 deletions(-) diff --git a/backend/src/monarch_py/datamodels/model.py b/backend/src/monarch_py/datamodels/model.py index 37d886eac..8e138878d 100644 --- a/backend/src/monarch_py/datamodels/model.py +++ b/backend/src/monarch_py/datamodels/model.py @@ -74,7 +74,7 @@ class Association(ConfiguredBaseModel): default_factory=list, description="""Field containing object name and the names of all of it's ancestors""", ) - primary_knowledge_source: Optional[List[str]] = Field(default_factory=list) + primary_knowledge_source: Optional[str] = Field(None) aggregator_knowledge_source: Optional[List[str]] = Field(default_factory=list) category: Optional[str] = Field(None) negated: Optional[bool] = Field(None) @@ -82,7 +82,7 @@ class Association(ConfiguredBaseModel): publications: Optional[List[str]] = Field(default_factory=list) qualifiers: Optional[List[str]] = Field(default_factory=list) frequency_qualifier: Optional[str] = Field(None) - has_evidence: Optional[str] = Field(None) + has_evidence: Optional[List[str]] = Field(default_factory=list) onset_qualifier: Optional[str] = Field(None) sex_qualifier: Optional[str] = Field(None) stage_qualifier: Optional[str] = Field(None) @@ -218,7 +218,7 @@ class DirectionalAssociation(Association): default_factory=list, description="""Field containing object name and the names of all of it's ancestors""", ) - primary_knowledge_source: Optional[List[str]] = Field(default_factory=list) + primary_knowledge_source: Optional[str] = Field(None) aggregator_knowledge_source: Optional[List[str]] = Field(default_factory=list) category: Optional[str] = Field(None) negated: Optional[bool] = Field(None) @@ -226,7 +226,7 @@ class DirectionalAssociation(Association): publications: Optional[List[str]] = Field(default_factory=list) qualifiers: Optional[List[str]] = Field(default_factory=list) frequency_qualifier: Optional[str] = Field(None) - has_evidence: Optional[str] = Field(None) + has_evidence: Optional[List[str]] = Field(default_factory=list) onset_qualifier: Optional[str] = Field(None) sex_qualifier: Optional[str] = Field(None) stage_qualifier: Optional[str] = Field(None) @@ -352,7 +352,7 @@ class HistoBin(FacetValue): class Node(Entity): """ - UI conatiner class extending Entity with additional information + UI container class extending Entity with additional information """ in_taxon: Optional[str] = Field(None, description="""The biolink taxon that the entity is in the closure of.""") diff --git a/backend/src/monarch_py/datamodels/model.yaml b/backend/src/monarch_py/datamodels/model.yaml index 0d855d519..24bdf6918 100644 --- a/backend/src/monarch_py/datamodels/model.yaml +++ b/backend/src/monarch_py/datamodels/model.yaml @@ -185,7 +185,7 @@ classes: slots: - id Node: - description: UI conatiner class extending Entity with additional information + description: UI container class extending Entity with additional information is_a: Entity slots: - in_taxon @@ -280,6 +280,7 @@ slots: description: The long form name of an entity range: string has_evidence: + multivalued: true range: string highlight: description: matching text snippet containing html tags @@ -340,7 +341,7 @@ slots: range: string required: true primary_knowledge_source: - multivalued: true + range: string provided_by: range: string publications: diff --git a/backend/src/monarch_py/implementations/solr/solr_implementation.py b/backend/src/monarch_py/implementations/solr/solr_implementation.py index d96fb6658..02c8bd2a4 100644 --- a/backend/src/monarch_py/implementations/solr/solr_implementation.py +++ b/backend/src/monarch_py/implementations/solr/solr_implementation.py @@ -29,10 +29,10 @@ from monarch_py.implementations.solr.solr_query_utils import ( build_association_counts_query, build_association_query, + build_association_table_query, build_autocomplete_query, build_histopheno_query, build_search_query, - build_association_table_query, ) from monarch_py.interfaces.association_interface import AssociationInterface from monarch_py.interfaces.entity_interface import EntityInterface diff --git a/backend/src/monarch_py/implementations/solr/solr_parsers.py b/backend/src/monarch_py/implementations/solr/solr_parsers.py index 9834f4749..a0df8e965 100644 --- a/backend/src/monarch_py/implementations/solr/solr_parsers.py +++ b/backend/src/monarch_py/implementations/solr/solr_parsers.py @@ -7,6 +7,7 @@ AssociationCountList, AssociationDirectionEnum, AssociationResults, + AssociationTableResults, DirectionalAssociation, Entity, FacetField, @@ -15,7 +16,6 @@ HistoPheno, SearchResult, SearchResults, - AssociationTableResults, ) from monarch_py.datamodels.solr import HistoPhenoKeys, SolrQueryResult from monarch_py.utils.association_type_utils import get_association_type_mapping_by_query_string diff --git a/backend/src/monarch_py/implementations/solr/solr_query_utils.py b/backend/src/monarch_py/implementations/solr/solr_query_utils.py index cebe85a2a..2ee954c3e 100644 --- a/backend/src/monarch_py/implementations/solr/solr_query_utils.py +++ b/backend/src/monarch_py/implementations/solr/solr_query_utils.py @@ -59,7 +59,7 @@ def build_association_query( query.q = f"*{q}*" query.query_fields = "subject subject_label predicate object object_label" if sort: - query.sort = ', '.join(sort) + query.sort = ", ".join(sort) if facet_fields: query.facet_fields = facet_fields if facet_queries: @@ -67,18 +67,17 @@ def build_association_query( return query -def build_association_table_query(entity: str, - category: str, - q: str = None, - offset: int = 0, - limit: int = 5, - sort: List[str] = None) -> SolrQuery: +def build_association_table_query( + entity: str, category: str, q: str = None, offset: int = 0, limit: int = 5, sort: List[str] = None +) -> SolrQuery: if sort is None: - sort = ['evidence_count desc', - 'subject_label asc', - 'predicate asc', - 'object_label asc', - 'primary_knowledge_source asc'] + sort = [ + "evidence_count desc", + "subject_label asc", + "predicate asc", + "object_label asc", + "primary_knowledge_source asc", + ] query = build_association_query( entity=[entity], @@ -90,6 +89,7 @@ def build_association_table_query(entity: str, ) return query + def build_association_counts_query(entity: str) -> SolrQuery: subject_query = f'AND (subject:"{entity}" OR subject_closure:"{entity}")' object_query = f'AND (object:"{entity}" OR object_closure:"{entity}")' diff --git a/backend/tests/fixtures/association_counts_response.py b/backend/tests/fixtures/association_counts_response.py index 8da688ba0..b28771ede 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": 3, + "QTime": 2, "params": { "facet.query": [ '(category:"biolink:DiseaseToPhenotypicFeatureAssociation") AND (subject:"MONDO:0020121" OR subject_closure:"MONDO:0020121")', @@ -40,39 +40,32 @@ def association_counts_response(): }, }, "response": { - "num_found": 4811, + "num_found": 4806, "start": 0, "docs": [ { - "id": "uuid:1be81e3c-1e4f-11ee-871a-692638b4c502", - "original_subject": "OMIM:619478", - "predicate": "biolink:has_phenotype", - "category": "biolink:DiseaseToPhenotypicFeatureAssociation", + "id": "uuid:c2a45bf5-212f-11ee-873a-cd90a19c4085", + "original_subject": "OMIM:158800", + "predicate": "biolink:has_mode_of_inheritance", + "category": "biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation", "aggregator_knowledge_source": ["infores:monarchinitiative"], - "has_evidence": "ECO:0000269", - "primary_knowledge_source": ["infores:hpo-annotations"], - "provided_by": "hpoa_disease_phenotype_edges", - "publications": ["PMID:27153398"], - "subject": "MONDO:0030355", - "object": "HP:0003484", + "has_evidence": ["ECO:0000304"], + "primary_knowledge_source": "infores:hpo-annotations", + "provided_by": "hpoa_disease_mode_of_inheritance_edges", + "publications": ["OMIM:158800"], + "subject": "MONDO:0008028", + "object": "HP:0000006", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ "MONDO:0000001", - "MONDO:0030355", - "MONDO:0019303", - "MONDO:0100167", "MONDO:0005071", "MONDO:0020121", + "MONDO:0008028", "MONDO:0700223", - "MONDO:0001347", - "MONDO:0020573", "BFO:0000002", "BFO:0000017", "BFO:0000020", - "MONDO:0016106", - "MONDO:0042489", - "MONDO:0100137", "BFO:0000016", "MONDO:0020120", "MONDO:0019056", @@ -80,7 +73,6 @@ def association_counts_response(): "MONDO:0005218", "MONDO:0005336", "MONDO:0002081", - "MONDO:0021147", "OGMS:0000031", "MONDO:0003847", "MONDO:0003939", @@ -88,193 +80,64 @@ def association_counts_response(): ], "subject_closure_label": [ "disease or disorder", - "facioscapulohumeral muscular dystrophy", "musculoskeletal system disorder", "hereditary disease", "muscle tissue disorder", "nervous system disorder", "obsolete muscular disorder", "myopathy", - "progressive muscular dystrophy", + "muscular dystrophy, Barnes type", "neuromuscular disease", - "premature aging syndrome", "skeletal muscle disorder", "muscular dystrophy", - "inherited disease susceptibility", - "disorder of development or morphogenesis", - "facioscapulohumeral muscular dystrophy 4, digenic", - "disease susceptibility", - "telomere syndrome", - "pulmonary disease, chronic obstructive, susceptibility to", "human disease or disorder", "hereditary skeletal muscle disorder", ], - "subject_label": "facioscapulohumeral muscular dystrophy 4, digenic", + "subject_label": "muscular dystrophy, Barnes type", "object_namespace": "HP", - "object_category": "biolink:PhenotypicQuality", + "object_category": "biolink:GeneticInheritance", "object_closure": [ "HP:0000001", - "UPHENO:0002649", - "UPHENO:0082875", - "UPHENO:0075696", - "UPHENO:0002320", - "UPHENO:0001001", - "HP:0003325", - "HP:0003484", - "UPHENO:0080563", - "HP:0009127", - "UPHENO:0001005", - "HP:0011805", - "UPHENO:0001002", - "HP:0001324", - "HP:0003690", - "HP:0000118", - "BFO:0000002", - "HP:0001446", - "HP:0002817", - "BFO:0000020", - "UPHENO:0080555", - "HP:0003011", - "UPHENO:0002816", - "UPHENO:0002332", - "UPHENO:0080556", - "UPHENO:0081581", - "HP:0033127", - "UPHENO:0001003", - "UPHENO:0002536", - "UPHENO:0076692", - "UPHENO:0002647", - "UPHENO:0076710", - "HP:0040064", - "BFO:0000001", - "HP:0011804", - "PATO:0000001", - "UPHENO:0002880", - "UPHENO:0002830", - "BFO:0000001", - "BFO:0000002", - "BFO:0000004", - "BFO:0000040", - "UBERON:0001062", - "CARO:0000000", - "UBERON:0000465", - "PR:000050567", - "RO:0002577", - "UBERON:0001015", - "UBERON:0000383", - "CARO:0000006", - "UBERON:0006058", - "UBERON:0010538", - "UBERON:0005090", - "UBERON:0000061", - "UBERON:0004708", - "UBERON:0007271", - "UBERON:0014793", - "CARO:0000003", - "UBERON:0001460", - "UBERON:0002529", - "UBERON:0001630", - "UBERON:0010000", - "UBERON:0000467", - "UBERON:0015212", - "UBERON:0004710", - "UBERON:0002101", - "UBERON:0004480", - "UBERON:0007269", - "UBERON:0010708", - "UBERON:0008785", - "UBERON:0000468", - "UBERON:0000475", - "UBERON:0000062", - "UBERON:0011216", - "UBERON:0010707", - "UBERON:0002102", - "UBERON:0004481", - "UBERON:0000153", - "UBERON:0000026", - "UBERON:0010758", + "HP:0000006", + "HP:0000005", + "HP:0034345", ], "object_closure_label": [ "All (HPO)", - "Phenotypic abnormality (HPO)", - "Muscle weakness (HPO)", - "Abnormality of the musculature of the upper limbs (HPO)", - "Abnormality of the upper limb (HPO)", - "Abnormality of the musculature (HPO)", - "Limb-girdle muscle weakness (HPO)", - "Upper limb muscle weakness (HPO)", - "Limb muscle weakness (HPO)", - "Abnormality of the musculature of the limbs (HPO)", - "Abnormal muscle physiology (HPO)", - "Abnormal skeletal muscle morphology (HPO)", - "Abnormality of the musculoskeletal system (HPO)", - "Abnormality of limbs (HPO)", - "appendage", - "anatomical structure", - "organ", - "anterior region of body", - "musculature of body", - "material anatomical entity", - "anatomical system", - "multicellular organism", - "organism subdivision", - "musculature", - "anatomical entity", - "arm", - "muscle organ", - "limb", - "forelimb", - "limb segment", - "musculature of limb", - "musculature of upper limb", - "paired limb/fin", - "pectoral appendage", - "muscle structure", - "multi-limb segment region", - "pectoral appendage musculature", - "appendage musculature", - "upper limb segment", - "multicellular anatomical structure", - "paired limb/fin segment", - "appendage girdle complex", - "pectoral complex", - "subdivision of organism along appendicular axis", - "organ system subdivision", - "musculature of pectoral complex", - "lateral structure", - ], - "object_label": "Upper limb muscle weakness (HPO)", - "evidence_count": 0, + "Mode of inheritance (HPO)", + "Autosomal dominant inheritance (HPO)", + "Mendelian inheritance", + ], + "object_label": "Autosomal dominant inheritance (HPO)", + "evidence_count": 4, }, { - "id": "uuid:1fd70821-1e4f-11ee-871a-692638b4c502", - "original_subject": "OMIM:616812", - "predicate": "biolink:has_phenotype", - "category": "biolink:DiseaseToPhenotypicFeatureAssociation", + "id": "uuid:c304bcf2-212f-11ee-873a-cd90a19c4085", + "original_subject": "OMIM:158900", + "predicate": "biolink:has_mode_of_inheritance", + "category": "biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation", "aggregator_knowledge_source": ["infores:monarchinitiative"], - "has_evidence": "ECO:0000269", - "primary_knowledge_source": ["infores:hpo-annotations"], - "provided_by": "hpoa_disease_phenotype_edges", - "publications": ["PMID:26642364"], - "subject": "MONDO:0014782", - "object": "HP:0003546", + "has_evidence": ["ECO:0000501"], + "primary_knowledge_source": "infores:hpo-annotations", + "provided_by": "hpoa_disease_mode_of_inheritance_edges", + "publications": ["OMIM:158900"], + "subject": "MONDO:0008030", + "object": "HP:0000006", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ + "MONDO:0008030", "MONDO:0000001", - "MONDO:0016971", - "MONDO:0000429", - "MONDO:0100167", + "MONDO:0019303", "MONDO:0005071", "MONDO:0020121", "MONDO:0700223", - "MONDO:0020573", + "MONDO:0001347", "BFO:0000002", "BFO:0000017", "BFO:0000020", - "MONDO:0006025", "MONDO:0016106", - "MONDO:0042489", + "MONDO:0100137", "BFO:0000016", "MONDO:0020120", "MONDO:0019056", @@ -282,354 +145,172 @@ def association_counts_response(): "MONDO:0005218", "MONDO:0005336", "MONDO:0002081", + "MONDO:0021147", "OGMS:0000031", "MONDO:0003847", - "MONDO:0014782", "MONDO:0003939", "BFO:0000001", - "MONDO:0015152", ], "subject_closure_label": [ "disease or disorder", - "autosomal genetic disease", + "facioscapulohumeral muscular dystrophy", "musculoskeletal system disorder", "hereditary disease", "muscle tissue disorder", "nervous system disorder", "obsolete muscular disorder", "myopathy", - "autosomal recessive disease", - "autosomal recessive limb-girdle muscular dystrophy type 2X", - "autosomal recessive limb-girdle muscular dystrophy", + "facioscapulohumeral muscular dystrophy 1", "progressive muscular dystrophy", - "limb-girdle muscular dystrophy", "neuromuscular disease", + "premature aging syndrome", "skeletal muscle disorder", "muscular dystrophy", - "inherited disease susceptibility", - "disease susceptibility", - "pulmonary disease, chronic obstructive, susceptibility to", + "disorder of development or morphogenesis", + "telomere syndrome", "human disease or disorder", "hereditary skeletal muscle disorder", ], - "subject_label": "autosomal recessive limb-girdle muscular dystrophy type 2X", + "subject_label": "facioscapulohumeral muscular dystrophy 1", "object_namespace": "HP", - "object_category": "biolink:PhenotypicQuality", + "object_category": "biolink:GeneticInheritance", "object_closure": [ "HP:0000001", - "UPHENO:0082875", - "UPHENO:0075696", - "UPHENO:0002320", - "UPHENO:0001001", - "UPHENO:0001005", - "UPHENO:0001002", - "HP:0004302", - "HP:0000118", - "BFO:0000002", - "BFO:0000020", - "HP:0003011", - "UPHENO:0002816", - "HP:0003546", - "UPHENO:0002332", - "HP:0033127", - "UPHENO:0001003", - "UPHENO:0002536", - "BFO:0000001", - "HP:0011804", - "PATO:0000001", - "BFO:0000001", - "BFO:0000002", - "BFO:0000004", - "BFO:0000040", - "UBERON:0001062", - "CARO:0000000", - "UBERON:0000465", - "UBERON:0001015", - "UBERON:0000383", - "UBERON:0005090", - "UBERON:0000061", - "UBERON:0001630", - "UBERON:0010000", - "UBERON:0000467", - "UBERON:0000468", - "UBERON:0000062", - "UBERON:0011216", + "HP:0000006", + "HP:0000005", + "HP:0034345", ], "object_closure_label": [ "All (HPO)", - "Phenotypic abnormality (HPO)", - "Abnormality of the musculature (HPO)", - "Exercise intolerance (HPO)", - "Functional motor deficit (HPO)", - "Abnormal muscle physiology (HPO)", - "Abnormality of the musculoskeletal system (HPO)", - "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", - ], - "object_label": "Exercise intolerance (HPO)", - "evidence_count": 0, + "Mode of inheritance (HPO)", + "Autosomal dominant inheritance (HPO)", + "Mendelian inheritance", + ], + "object_label": "Autosomal dominant inheritance (HPO)", + "evidence_count": 4, }, { - "id": "uuid:1e041fb7-1e4f-11ee-871a-692638b4c502", - "original_subject": "OMIM:158900", - "predicate": "biolink:has_phenotype", - "category": "biolink:DiseaseToPhenotypicFeatureAssociation", + "id": "uuid:c3cdad58-212f-11ee-873a-cd90a19c4085", + "original_subject": "OMIM:159050", + "predicate": "biolink:has_mode_of_inheritance", + "category": "biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation", "aggregator_knowledge_source": ["infores:monarchinitiative"], - "has_evidence": "ECO:0000304", - "primary_knowledge_source": ["infores:hpo-annotations"], - "provided_by": "hpoa_disease_phenotype_edges", - "publications": ["OMIM:158900"], - "subject": "MONDO:0008030", - "object": "HP:0003547", + "has_evidence": ["ECO:0000501"], + "primary_knowledge_source": "infores:hpo-annotations", + "provided_by": "hpoa_disease_mode_of_inheritance_edges", + "publications": ["OMIM:159050"], + "subject": "MONDO:0008034", + "object": "HP:0000006", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ - "MONDO:0008030", + "MONDO:0004994", "MONDO:0000001", - "MONDO:0019303", - "MONDO:0100167", + "MONDO:0008034", "MONDO:0005071", + "MONDO:0016147", + "MONDO:0005267", "MONDO:0020121", + "MONDO:0004995", "MONDO:0700223", - "MONDO:0001347", - "MONDO:0020573", "BFO:0000002", "BFO:0000017", "BFO:0000020", + "MONDO:0010542", "MONDO:0016106", - "MONDO:0042489", - "MONDO:0100137", + "MONDO:0015470", + "MONDO:0005217", + "MONDO:0016899", "BFO:0000016", "MONDO:0020120", "MONDO:0019056", + "MONDO:0016139", "MONDO:0700096", + "MONDO:0000591", "MONDO:0005218", "MONDO:0005336", "MONDO:0002081", - "MONDO:0021147", + "MONDO:0016333", "OGMS:0000031", + "MONDO:0005021", "MONDO:0003847", "MONDO:0003939", "BFO:0000001", + "MONDO:0010311", ], "subject_closure_label": [ "disease or disorder", - "facioscapulohumeral muscular dystrophy", + "intrinsic cardiomyopathy", "musculoskeletal system disorder", "hereditary disease", "muscle tissue disorder", + "cardiomyopathy", + "cardiovascular disorder", + "dilated cardiomyopathy", "nervous system disorder", + "familial cardiomyopathy", "obsolete muscular disorder", + "heart disorder", "myopathy", - "facioscapulohumeral muscular dystrophy 1", + "muscular dystrophy, pseudohypertrophic, with Internalized capillaries", + "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", - "premature aging syndrome", "skeletal muscle disorder", "muscular dystrophy", - "inherited disease susceptibility", - "disorder of development or morphogenesis", - "disease susceptibility", - "telomere syndrome", - "pulmonary disease, chronic obstructive, susceptibility to", "human disease or disorder", "hereditary skeletal muscle disorder", ], - "subject_label": "facioscapulohumeral muscular dystrophy 1", + "subject_label": "muscular dystrophy, pseudohypertrophic, with Internalized capillaries", "object_namespace": "HP", - "object_category": "biolink:PhenotypicQuality", + "object_category": "biolink:GeneticInheritance", "object_closure": [ "HP:0000001", - "UPHENO:0002649", - "UPHENO:0082875", - "UPHENO:0075696", - "UPHENO:0002320", - "UPHENO:0001001", - "HP:0003325", - "UPHENO:0080565", - "HP:0009127", - "UPHENO:0001005", - "HP:0011805", - "UPHENO:0001002", - "HP:0001324", - "HP:0000118", - "BFO:0000002", - "HP:0001435", - "HP:0001446", - "HP:0002817", - "BFO:0000020", - "UPHENO:0080555", - "HP:0003011", - "UPHENO:0002816", - "UPHENO:0002332", - "UPHENO:0080556", - "UPHENO:0002982", - "UPHENO:0081581", - "HP:0003547", - "HP:0033127", - "UPHENO:0001003", - "UPHENO:0002536", - "UPHENO:0076692", - "UPHENO:0002647", - "UPHENO:0076710", - "HP:0040064", - "BFO:0000001", - "HP:0011804", - "PATO:0000001", - "UPHENO:0002880", - "UPHENO:0002830", - "BFO:0000001", - "BFO:0000002", - "BFO:0000004", - "BFO:0000040", - "UBERON:0001062", - "CARO:0000000", - "UBERON:0000465", - "PR:000050567", - "RO:0002577", - "UBERON:0001015", - "UBERON:0000383", - "CARO:0000006", - "UBERON:0006058", - "UBERON:0010538", - "UBERON:0018254", - "UBERON:0005090", - "UBERON:0000061", - "UBERON:0004708", - "UBERON:0007271", - "UBERON:0014793", - "CARO:0000003", - "UBERON:0001460", - "UBERON:0002529", - "UBERON:0001630", - "UBERON:0010000", - "UBERON:0000467", - "UBERON:0015212", - "UBERON:0004710", - "UBERON:0002101", - "UBERON:0004480", - "UBERON:0007269", - "UBERON:0004471", - "UBERON:0007823", - "UBERON:0010708", - "UBERON:0008785", - "UBERON:0014892", - "UBERON:0000468", - "UBERON:0000475", - "UBERON:0000062", - "UBERON:0011216", - "UBERON:0001421", - "UBERON:0010707", - "UBERON:0002102", - "UBERON:0004481", - "UBERON:0010891", - "UBERON:0000153", - "UBERON:0000026", - "UBERON:0010758", - "UBERON:0008196", + "HP:0000006", + "HP:0000005", + "HP:0034345", ], "object_closure_label": [ "All (HPO)", - "Phenotypic abnormality (HPO)", - "Muscle weakness (HPO)", - "Abnormality of the shoulder girdle musculature (HPO)", - "Abnormality of the musculature of the upper limbs (HPO)", - "Abnormality of the upper limb (HPO)", - "Abnormality of the musculature (HPO)", - "Limb-girdle muscle weakness (HPO)", - "Shoulder girdle muscle weakness (HPO)", - "Abnormality of the musculature of the limbs (HPO)", - "Abnormal muscle physiology (HPO)", - "Abnormal skeletal muscle morphology (HPO)", - "Abnormality of the musculoskeletal system (HPO)", - "Abnormality of limbs (HPO)", - "appendage", - "anatomical structure", - "organ", - "anterior region of body", - "musculature of body", - "material anatomical entity", - "anatomical system", - "multicellular organism", - "organism subdivision", - "musculature", - "anatomical entity", - "pectoral girdle region", - "arm", - "muscle organ", - "limb", - "forelimb", - "limb segment", - "musculature of pectoral girdle", - "musculature of limb", - "musculature of upper limb", - "paired limb/fin", - "pectoral appendage", - "muscle structure", - "multi-limb segment region", - "pectoral appendage musculature", - "appendage musculature", - "appendage girdle region", - "muscle of pectoral girdle", - "upper limb segment", - "multicellular anatomical structure", - "paired limb/fin segment", - "appendage girdle complex", - "pectoral complex", - "subdivision of organism along appendicular axis", - "pectoral complex muscle", - "organ system subdivision", - "musculature of pectoral complex", - "skeletal muscle organ", - "lateral structure", - "skeletal musculature", - ], - "object_label": "Shoulder girdle muscle weakness (HPO)", - "evidence_count": 0, + "Mode of inheritance (HPO)", + "Autosomal dominant inheritance (HPO)", + "Mendelian inheritance", + ], + "object_label": "Autosomal dominant inheritance (HPO)", + "evidence_count": 4, }, { - "id": "uuid:1ae78897-1e4f-11ee-871a-692638b4c502", - "original_subject": "OMIM:254110", - "predicate": "biolink:has_phenotype", - "category": "biolink:DiseaseToPhenotypicFeatureAssociation", + "id": "uuid:c3367408-212f-11ee-873a-cd90a19c4085", + "original_subject": "OMIM:160300", + "predicate": "biolink:has_mode_of_inheritance", + "category": "biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation", "aggregator_knowledge_source": ["infores:monarchinitiative"], - "has_evidence": "ECO:0000501", - "primary_knowledge_source": ["infores:hpo-annotations"], - "provided_by": "hpoa_disease_phenotype_edges", - "publications": ["OMIM:254110"], - "subject": "MONDO:0009683", - "object": "HP:0003547", + "has_evidence": ["ECO:0000304"], + "primary_knowledge_source": "infores:hpo-annotations", + "provided_by": "hpoa_disease_mode_of_inheritance_edges", + "publications": ["OMIM:160300"], + "subject": "MONDO:0008049", + "object": "HP:0000006", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ "MONDO:0000001", - "MONDO:0016971", - "MONDO:0000429", - "MONDO:0100167", "MONDO:0005071", "MONDO:0020121", "MONDO:0700223", - "MONDO:0020573", "BFO:0000002", "BFO:0000017", + "MONDO:0008049", "BFO:0000020", - "MONDO:0006025", - "MONDO:0016106", - "MONDO:0042489", "BFO:0000016", "MONDO:0020120", "MONDO:0019056", - "MONDO:0016139", "MONDO:0700096", "MONDO:0005218", "MONDO:0005336", @@ -638,216 +319,71 @@ def association_counts_response(): "MONDO:0003847", "MONDO:0003939", "BFO:0000001", - "MONDO:0015152", - "MONDO:0016153", - "MONDO:0009683", + "MONDO:0018949", ], "subject_closure_label": [ "disease or disorder", - "autosomal genetic disease", "musculoskeletal system disorder", "hereditary disease", "muscle tissue disorder", "nervous system disorder", "obsolete muscular 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", + "myopathy, distal, infantile-onset", + "distal myopathy", "neuromuscular disease", "skeletal muscle disorder", "muscular dystrophy", - "inherited disease susceptibility", - "disease susceptibility", - "pulmonary disease, chronic obstructive, susceptibility to", "human disease or disorder", "hereditary skeletal muscle disorder", ], - "subject_label": "autosomal recessive limb-girdle muscular dystrophy type 2H", + "subject_label": "myopathy, distal, infantile-onset", "object_namespace": "HP", - "object_category": "biolink:PhenotypicQuality", + "object_category": "biolink:GeneticInheritance", "object_closure": [ "HP:0000001", - "UPHENO:0002649", - "UPHENO:0082875", - "UPHENO:0075696", - "UPHENO:0002320", - "UPHENO:0001001", - "HP:0003325", - "UPHENO:0080565", - "HP:0009127", - "UPHENO:0001005", - "HP:0011805", - "UPHENO:0001002", - "HP:0001324", - "HP:0000118", - "BFO:0000002", - "HP:0001435", - "HP:0001446", - "HP:0002817", - "BFO:0000020", - "UPHENO:0080555", - "HP:0003011", - "UPHENO:0002816", - "UPHENO:0002332", - "UPHENO:0080556", - "UPHENO:0002982", - "UPHENO:0081581", - "HP:0003547", - "HP:0033127", - "UPHENO:0001003", - "UPHENO:0002536", - "UPHENO:0076692", - "UPHENO:0002647", - "UPHENO:0076710", - "HP:0040064", - "BFO:0000001", - "HP:0011804", - "PATO:0000001", - "UPHENO:0002880", - "UPHENO:0002830", - "BFO:0000001", - "BFO:0000002", - "BFO:0000004", - "BFO:0000040", - "UBERON:0001062", - "CARO:0000000", - "UBERON:0000465", - "PR:000050567", - "RO:0002577", - "UBERON:0001015", - "UBERON:0000383", - "CARO:0000006", - "UBERON:0006058", - "UBERON:0010538", - "UBERON:0018254", - "UBERON:0005090", - "UBERON:0000061", - "UBERON:0004708", - "UBERON:0007271", - "UBERON:0014793", - "CARO:0000003", - "UBERON:0001460", - "UBERON:0002529", - "UBERON:0001630", - "UBERON:0010000", - "UBERON:0000467", - "UBERON:0015212", - "UBERON:0004710", - "UBERON:0002101", - "UBERON:0004480", - "UBERON:0007269", - "UBERON:0004471", - "UBERON:0007823", - "UBERON:0010708", - "UBERON:0008785", - "UBERON:0014892", - "UBERON:0000468", - "UBERON:0000475", - "UBERON:0000062", - "UBERON:0011216", - "UBERON:0001421", - "UBERON:0010707", - "UBERON:0002102", - "UBERON:0004481", - "UBERON:0010891", - "UBERON:0000153", - "UBERON:0000026", - "UBERON:0010758", - "UBERON:0008196", + "HP:0000006", + "HP:0000005", + "HP:0034345", ], "object_closure_label": [ "All (HPO)", - "Phenotypic abnormality (HPO)", - "Muscle weakness (HPO)", - "Abnormality of the shoulder girdle musculature (HPO)", - "Abnormality of the musculature of the upper limbs (HPO)", - "Abnormality of the upper limb (HPO)", - "Abnormality of the musculature (HPO)", - "Limb-girdle muscle weakness (HPO)", - "Shoulder girdle muscle weakness (HPO)", - "Abnormality of the musculature of the limbs (HPO)", - "Abnormal muscle physiology (HPO)", - "Abnormal skeletal muscle morphology (HPO)", - "Abnormality of the musculoskeletal system (HPO)", - "Abnormality of limbs (HPO)", - "appendage", - "anatomical structure", - "organ", - "anterior region of body", - "musculature of body", - "material anatomical entity", - "anatomical system", - "multicellular organism", - "organism subdivision", - "musculature", - "anatomical entity", - "pectoral girdle region", - "arm", - "muscle organ", - "limb", - "forelimb", - "limb segment", - "musculature of pectoral girdle", - "musculature of limb", - "musculature of upper limb", - "paired limb/fin", - "pectoral appendage", - "muscle structure", - "multi-limb segment region", - "pectoral appendage musculature", - "appendage musculature", - "appendage girdle region", - "muscle of pectoral girdle", - "upper limb segment", - "multicellular anatomical structure", - "paired limb/fin segment", - "appendage girdle complex", - "pectoral complex", - "subdivision of organism along appendicular axis", - "pectoral complex muscle", - "organ system subdivision", - "musculature of pectoral complex", - "skeletal muscle organ", - "lateral structure", - "skeletal musculature", - ], - "object_label": "Shoulder girdle muscle weakness (HPO)", - "evidence_count": 0, + "Mode of inheritance (HPO)", + "Autosomal dominant inheritance (HPO)", + "Mendelian inheritance", + ], + "object_label": "Autosomal dominant inheritance (HPO)", + "evidence_count": 4, }, { - "id": "uuid:1e041dff-1e4f-11ee-871a-692638b4c502", - "original_subject": "OMIM:310095", - "predicate": "biolink:has_phenotype", - "category": "biolink:DiseaseToPhenotypicFeatureAssociation", + "id": "uuid:c39b4534-212f-11ee-873a-cd90a19c4085", + "original_subject": "OMIM:160500", + "predicate": "biolink:has_mode_of_inheritance", + "category": "biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation", "aggregator_knowledge_source": ["infores:monarchinitiative"], - "has_evidence": "ECO:0000501", - "primary_knowledge_source": ["infores:hpo-annotations"], - "provided_by": "hpoa_disease_phenotype_edges", - "publications": ["OMIM:310095"], - "subject": "MONDO:0010678", - "object": "HP:0003547", + "has_evidence": ["ECO:0000269"], + "primary_knowledge_source": "infores:hpo-annotations", + "provided_by": "hpoa_disease_mode_of_inheritance_edges", + "publications": ["PMID:15322983"], + "subject": "MONDO:0008050", + "object": "HP:0000006", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ "MONDO:0000001", - "MONDO:0100167", "MONDO:0005071", "MONDO:0020121", - "MONDO:0010678", "MONDO:0700223", - "MONDO:0020573", "BFO:0000002", + "MONDO:0019952", "BFO:0000017", "BFO:0000020", - "MONDO:0042489", + "MONDO:0008050", + "MONDO:0016195", "BFO:0000016", "MONDO:0020120", "MONDO:0019056", + "MONDO:0016139", "MONDO:0700096", "MONDO:0005218", "MONDO:0005336", @@ -856,657 +392,257 @@ def association_counts_response(): "MONDO:0003847", "MONDO:0003939", "BFO:0000001", + "MONDO:0002320", + "MONDO:0018949", ], "subject_closure_label": [ "disease or disorder", "musculoskeletal system disorder", + "congenital nervous system disorder", "hereditary disease", "muscle tissue disorder", "nervous system disorder", "obsolete muscular disorder", "myopathy", - "muscular dystrophy, progressive Pectorodorsal", + "MYH7-related skeletal myopathy", + "qualitative or quantitative protein defects in neuromuscular diseases", + "qualitative or quantitative defects of beta-myosin heavy chain (MYH7)", + "distal myopathy", "neuromuscular disease", + "congenital myopathy", "skeletal muscle disorder", "muscular dystrophy", - "inherited disease susceptibility", - "disease susceptibility", - "pulmonary disease, chronic obstructive, susceptibility to", "human disease or disorder", "hereditary skeletal muscle disorder", ], - "subject_label": "muscular dystrophy, progressive Pectorodorsal", + "subject_label": "MYH7-related skeletal myopathy", "object_namespace": "HP", - "object_category": "biolink:PhenotypicQuality", + "object_category": "biolink:GeneticInheritance", "object_closure": [ "HP:0000001", - "UPHENO:0002649", - "UPHENO:0082875", - "UPHENO:0075696", - "UPHENO:0002320", - "UPHENO:0001001", - "HP:0003325", - "UPHENO:0080565", - "HP:0009127", - "UPHENO:0001005", - "HP:0011805", - "UPHENO:0001002", - "HP:0001324", - "HP:0000118", - "BFO:0000002", - "HP:0001435", - "HP:0001446", - "HP:0002817", - "BFO:0000020", - "UPHENO:0080555", - "HP:0003011", - "UPHENO:0002816", - "UPHENO:0002332", - "UPHENO:0080556", - "UPHENO:0002982", - "UPHENO:0081581", - "HP:0003547", - "HP:0033127", - "UPHENO:0001003", - "UPHENO:0002536", - "UPHENO:0076692", - "UPHENO:0002647", - "UPHENO:0076710", - "HP:0040064", - "BFO:0000001", - "HP:0011804", - "PATO:0000001", - "UPHENO:0002880", - "UPHENO:0002830", - "BFO:0000001", - "BFO:0000002", - "BFO:0000004", - "BFO:0000040", - "UBERON:0001062", - "CARO:0000000", - "UBERON:0000465", - "PR:000050567", - "RO:0002577", - "UBERON:0001015", - "UBERON:0000383", - "CARO:0000006", - "UBERON:0006058", - "UBERON:0010538", - "UBERON:0018254", - "UBERON:0005090", - "UBERON:0000061", - "UBERON:0004708", - "UBERON:0007271", - "UBERON:0014793", - "CARO:0000003", - "UBERON:0001460", - "UBERON:0002529", - "UBERON:0001630", - "UBERON:0010000", - "UBERON:0000467", - "UBERON:0015212", - "UBERON:0004710", - "UBERON:0002101", - "UBERON:0004480", - "UBERON:0007269", - "UBERON:0004471", - "UBERON:0007823", - "UBERON:0010708", - "UBERON:0008785", - "UBERON:0014892", - "UBERON:0000468", - "UBERON:0000475", - "UBERON:0000062", - "UBERON:0011216", - "UBERON:0001421", - "UBERON:0010707", - "UBERON:0002102", - "UBERON:0004481", - "UBERON:0010891", - "UBERON:0000153", - "UBERON:0000026", - "UBERON:0010758", - "UBERON:0008196", + "HP:0000006", + "HP:0000005", + "HP:0034345", ], "object_closure_label": [ "All (HPO)", - "Phenotypic abnormality (HPO)", - "Muscle weakness (HPO)", - "Abnormality of the shoulder girdle musculature (HPO)", - "Abnormality of the musculature of the upper limbs (HPO)", - "Abnormality of the upper limb (HPO)", - "Abnormality of the musculature (HPO)", - "Limb-girdle muscle weakness (HPO)", - "Shoulder girdle muscle weakness (HPO)", - "Abnormality of the musculature of the limbs (HPO)", - "Abnormal muscle physiology (HPO)", - "Abnormal skeletal muscle morphology (HPO)", - "Abnormality of the musculoskeletal system (HPO)", - "Abnormality of limbs (HPO)", - "appendage", - "anatomical structure", - "organ", - "anterior region of body", - "musculature of body", - "material anatomical entity", - "anatomical system", - "multicellular organism", - "organism subdivision", - "musculature", - "anatomical entity", - "pectoral girdle region", - "arm", - "muscle organ", - "limb", - "forelimb", - "limb segment", - "musculature of pectoral girdle", - "musculature of limb", - "musculature of upper limb", - "paired limb/fin", - "pectoral appendage", - "muscle structure", - "multi-limb segment region", - "pectoral appendage musculature", - "appendage musculature", - "appendage girdle region", - "muscle of pectoral girdle", - "upper limb segment", - "multicellular anatomical structure", - "paired limb/fin segment", - "appendage girdle complex", - "pectoral complex", - "subdivision of organism along appendicular axis", - "pectoral complex muscle", - "organ system subdivision", - "musculature of pectoral complex", - "skeletal muscle organ", - "lateral structure", - "skeletal musculature", - ], - "object_label": "Shoulder girdle muscle weakness (HPO)", - "evidence_count": 0, + "Mode of inheritance (HPO)", + "Autosomal dominant inheritance (HPO)", + "Mendelian inheritance", + ], + "object_label": "Autosomal dominant inheritance (HPO)", + "evidence_count": 4, }, { - "id": "uuid:22fcfea0-1e4f-11ee-871a-692638b4c502", - "original_subject": "OMIM:603689", - "predicate": "biolink:has_phenotype", - "category": "biolink:DiseaseToPhenotypicFeatureAssociation", + "id": "uuid:c2d3e237-212f-11ee-873a-cd90a19c4085", + "original_subject": "OMIM:160900", + "predicate": "biolink:has_mode_of_inheritance", + "category": "biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation", "aggregator_knowledge_source": ["infores:monarchinitiative"], - "has_evidence": "ECO:0000501", - "primary_knowledge_source": ["infores:hpo-annotations"], - "provided_by": "hpoa_disease_phenotype_edges", - "publications": ["OMIM:603689"], - "subject": "MONDO:0011362", - "object": "HP:0003547", + "has_evidence": ["ECO:0000501"], + "primary_knowledge_source": "infores:hpo-annotations", + "provided_by": "hpoa_disease_mode_of_inheritance_edges", + "publications": ["OMIM:160900"], + "subject": "MONDO:0008056", + "object": "HP:0000006", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ + "MONDO:0004994", + "MONDO:0020158", "MONDO:0000001", - "MONDO:0016112", - "MONDO:0000429", - "MONDO:0100167", + "MONDO:0016107", "MONDO:0005071", + "MONDO:0005267", "MONDO:0020121", - "MONDO:0100175", + "MONDO:0005045", + "MONDO:0004995", "MONDO:0700223", - "MONDO:0020573", "BFO:0000002", - "MONDO:0019952", "BFO:0000017", "BFO:0000020", "MONDO:0016106", - "MONDO:0042489", - "MONDO:0016191", + "MONDO:0005217", + "MONDO:0024573", + "MONDO:0003382", "BFO:0000016", "MONDO:0020120", "MONDO:0019056", - "MONDO:0100494", - "MONDO:0016139", + "MONDO:0008056", "MONDO:0700096", + "MONDO:0000591", + "MONDO:0024458", "MONDO:0005218", "MONDO:0005336", "MONDO:0002081", - "MONDO:0000426", - "MONDO:0011362", + "MONDO:0002254", "OGMS:0000031", "MONDO:0003847", "MONDO:0003939", + "MONDO:0002022", + "MONDO:0016120", "BFO:0000001", - "MONDO:0002320", - "MONDO:0016108", - "MONDO:0018949", + "MONDO:0000462", + "MONDO:0005328", ], "subject_closure_label": [ "disease or disorder", - "autosomal dominant disease", - "autosomal genetic disease", + "eye adnexa disorder", + "intrinsic cardiomyopathy", + "disorder of orbital region", "musculoskeletal system disorder", - "congenital nervous system disorder", + "syndromic disease", + "eyelid disorder", "hereditary disease", "muscle tissue disorder", + "cardiomyopathy", + "cardiovascular disorder", + "hypertrophic cardiomyopathy", "nervous system disorder", + "familial cardiomyopathy", "obsolete muscular disorder", + "heart disorder", + "eye disorder", "myopathy", - "myopathy, myofibrillar, 9, with early respiratory failure", + "myotonic dystrophy type 1", "progressive muscular dystrophy", - "autosomal dominant distal myopathy", - "hereditary inclusion-body myopathy", - "qualitative or quantitative protein defects in neuromuscular diseases", - "qualitative or quantitative defects of titin", - "distal myopathy", + "myotonic dystrophy", + "myotonic syndrome", "neuromuscular disease", - "congenital myopathy", "skeletal muscle disorder", "muscular dystrophy", - "inherited disease susceptibility", - "disease susceptibility", - "pulmonary disease, chronic obstructive, susceptibility to", - "TTN-related myopathy", - "autosomal dominant titinopathy", + "eyelids malposition disorder", + "disorder of visual system", + "familial hypertrophic cardiomyopathy", "human disease or disorder", "hereditary skeletal muscle disorder", ], - "subject_label": "myopathy, myofibrillar, 9, with early respiratory failure", + "subject_label": "myotonic dystrophy type 1", "object_namespace": "HP", - "object_category": "biolink:PhenotypicQuality", + "object_category": "biolink:GeneticInheritance", "object_closure": [ "HP:0000001", - "UPHENO:0002649", - "UPHENO:0082875", - "UPHENO:0075696", - "UPHENO:0002320", - "UPHENO:0001001", - "HP:0003325", - "UPHENO:0080565", - "HP:0009127", - "UPHENO:0001005", - "HP:0011805", - "UPHENO:0001002", - "HP:0001324", - "HP:0000118", - "BFO:0000002", - "HP:0001435", - "HP:0001446", - "HP:0002817", - "BFO:0000020", - "UPHENO:0080555", - "HP:0003011", - "UPHENO:0002816", - "UPHENO:0002332", - "UPHENO:0080556", - "UPHENO:0002982", - "UPHENO:0081581", - "HP:0003547", - "HP:0033127", - "UPHENO:0001003", - "UPHENO:0002536", - "UPHENO:0076692", - "UPHENO:0002647", - "UPHENO:0076710", - "HP:0040064", - "BFO:0000001", - "HP:0011804", - "PATO:0000001", - "UPHENO:0002880", - "UPHENO:0002830", - "BFO:0000001", - "BFO:0000002", - "BFO:0000004", - "BFO:0000040", - "UBERON:0001062", - "CARO:0000000", - "UBERON:0000465", - "PR:000050567", - "RO:0002577", - "UBERON:0001015", - "UBERON:0000383", - "CARO:0000006", - "UBERON:0006058", - "UBERON:0010538", - "UBERON:0018254", - "UBERON:0005090", - "UBERON:0000061", - "UBERON:0004708", - "UBERON:0007271", - "UBERON:0014793", - "CARO:0000003", - "UBERON:0001460", - "UBERON:0002529", - "UBERON:0001630", - "UBERON:0010000", - "UBERON:0000467", - "UBERON:0015212", - "UBERON:0004710", - "UBERON:0002101", - "UBERON:0004480", - "UBERON:0007269", - "UBERON:0004471", - "UBERON:0007823", - "UBERON:0010708", - "UBERON:0008785", - "UBERON:0014892", - "UBERON:0000468", - "UBERON:0000475", - "UBERON:0000062", - "UBERON:0011216", - "UBERON:0001421", - "UBERON:0010707", - "UBERON:0002102", - "UBERON:0004481", - "UBERON:0010891", - "UBERON:0000153", - "UBERON:0000026", - "UBERON:0010758", - "UBERON:0008196", + "HP:0000006", + "HP:0000005", + "HP:0034345", ], "object_closure_label": [ "All (HPO)", - "Phenotypic abnormality (HPO)", - "Muscle weakness (HPO)", - "Abnormality of the shoulder girdle musculature (HPO)", - "Abnormality of the musculature of the upper limbs (HPO)", - "Abnormality of the upper limb (HPO)", - "Abnormality of the musculature (HPO)", - "Limb-girdle muscle weakness (HPO)", - "Shoulder girdle muscle weakness (HPO)", - "Abnormality of the musculature of the limbs (HPO)", - "Abnormal muscle physiology (HPO)", - "Abnormal skeletal muscle morphology (HPO)", - "Abnormality of the musculoskeletal system (HPO)", - "Abnormality of limbs (HPO)", - "appendage", - "anatomical structure", - "organ", - "anterior region of body", - "musculature of body", - "material anatomical entity", - "anatomical system", - "multicellular organism", - "organism subdivision", - "musculature", - "anatomical entity", - "pectoral girdle region", - "arm", - "muscle organ", - "limb", - "forelimb", - "limb segment", - "musculature of pectoral girdle", - "musculature of limb", - "musculature of upper limb", - "paired limb/fin", - "pectoral appendage", - "muscle structure", - "multi-limb segment region", - "pectoral appendage musculature", - "appendage musculature", - "appendage girdle region", - "muscle of pectoral girdle", - "upper limb segment", - "multicellular anatomical structure", - "paired limb/fin segment", - "appendage girdle complex", - "pectoral complex", - "subdivision of organism along appendicular axis", - "pectoral complex muscle", - "organ system subdivision", - "musculature of pectoral complex", - "skeletal muscle organ", - "lateral structure", - "skeletal musculature", - ], - "object_label": "Shoulder girdle muscle weakness (HPO)", - "evidence_count": 0, + "Mode of inheritance (HPO)", + "Autosomal dominant inheritance (HPO)", + "Mendelian inheritance", + ], + "object_label": "Autosomal dominant inheritance (HPO)", + "evidence_count": 4, }, { - "id": "uuid:215b1fa4-1e4f-11ee-871a-692638b4c502", - "original_subject": "OMIM:604801", - "predicate": "biolink:has_phenotype", - "category": "biolink:DiseaseToPhenotypicFeatureAssociation", + "id": "uuid:c400607b-212f-11ee-873a-cd90a19c4085", + "original_subject": "OMIM:164300", + "predicate": "biolink:has_mode_of_inheritance", + "category": "biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation", "aggregator_knowledge_source": ["infores:monarchinitiative"], - "has_evidence": "ECO:0000501", - "primary_knowledge_source": ["infores:hpo-annotations"], - "provided_by": "hpoa_disease_phenotype_edges", - "publications": ["OMIM:604801"], - "subject": "MONDO:0011486", - "object": "HP:0003547", + "has_evidence": ["ECO:0000269"], + "primary_knowledge_source": "infores:hpo-annotations", + "provided_by": "hpoa_disease_mode_of_inheritance_edges", + "publications": ["PMID:9462747"], + "subject": "MONDO:0008116", + "object": "HP:0000006", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ + "MONDO:0020158", "MONDO:0000001", - "MONDO:0100167", "MONDO:0005071", "MONDO:0020121", "MONDO:0700223", - "MONDO:0020573", + "MONDO:0004746", "BFO:0000002", "BFO:0000017", "BFO:0000020", - "MONDO:0042489", + "MONDO:0016106", + "MONDO:0003382", "BFO:0000016", "MONDO:0020120", "MONDO:0019056", - "MONDO:0011486", "MONDO:0700096", + "MONDO:0024458", "MONDO:0005218", "MONDO:0005336", "MONDO:0002081", + "MONDO:0008116", "OGMS:0000031", "MONDO:0003847", "MONDO:0003939", + "MONDO:0002022", "BFO:0000001", - "MONDO:0002320", - "MONDO:0019950", + "MONDO:0000462", + "MONDO:0005328", ], "subject_closure_label": [ "disease or disorder", + "eye adnexa disorder", + "disorder of orbital region", "musculoskeletal system disorder", - "congenital nervous system disorder", + "eyelid disorder", "hereditary disease", "muscle tissue disorder", + "myopathy of extraocular muscle", "nervous system disorder", "obsolete muscular disorder", + "eye disorder", "myopathy", - "congenital muscular dystrophy 1B", + "oculopharyngeal muscular dystrophy", + "progressive muscular dystrophy", "neuromuscular disease", - "congenital muscular dystrophy", "skeletal muscle disorder", "muscular dystrophy", - "inherited disease susceptibility", - "disease susceptibility", - "pulmonary disease, chronic obstructive, susceptibility to", + "eyelids malposition disorder", + "disorder of visual system", "human disease or disorder", "hereditary skeletal muscle disorder", ], - "subject_label": "congenital muscular dystrophy 1B", + "subject_label": "oculopharyngeal muscular dystrophy", "object_namespace": "HP", - "object_category": "biolink:PhenotypicQuality", + "object_category": "biolink:GeneticInheritance", "object_closure": [ "HP:0000001", - "UPHENO:0002649", - "UPHENO:0082875", - "UPHENO:0075696", - "UPHENO:0002320", - "UPHENO:0001001", - "HP:0003325", - "UPHENO:0080565", - "HP:0009127", - "UPHENO:0001005", - "HP:0011805", - "UPHENO:0001002", - "HP:0001324", - "HP:0000118", - "BFO:0000002", - "HP:0001435", - "HP:0001446", - "HP:0002817", - "BFO:0000020", - "UPHENO:0080555", - "HP:0003011", - "UPHENO:0002816", - "UPHENO:0002332", - "UPHENO:0080556", - "UPHENO:0002982", - "UPHENO:0081581", - "HP:0003547", - "HP:0033127", - "UPHENO:0001003", - "UPHENO:0002536", - "UPHENO:0076692", - "UPHENO:0002647", - "UPHENO:0076710", - "HP:0040064", - "BFO:0000001", - "HP:0011804", - "PATO:0000001", - "UPHENO:0002880", - "UPHENO:0002830", - "BFO:0000001", - "BFO:0000002", - "BFO:0000004", - "BFO:0000040", - "UBERON:0001062", - "CARO:0000000", - "UBERON:0000465", - "PR:000050567", - "RO:0002577", - "UBERON:0001015", - "UBERON:0000383", - "CARO:0000006", - "UBERON:0006058", - "UBERON:0010538", - "UBERON:0018254", - "UBERON:0005090", - "UBERON:0000061", - "UBERON:0004708", - "UBERON:0007271", - "UBERON:0014793", - "CARO:0000003", - "UBERON:0001460", - "UBERON:0002529", - "UBERON:0001630", - "UBERON:0010000", - "UBERON:0000467", - "UBERON:0015212", - "UBERON:0004710", - "UBERON:0002101", - "UBERON:0004480", - "UBERON:0007269", - "UBERON:0004471", - "UBERON:0007823", - "UBERON:0010708", - "UBERON:0008785", - "UBERON:0014892", - "UBERON:0000468", - "UBERON:0000475", - "UBERON:0000062", - "UBERON:0011216", - "UBERON:0001421", - "UBERON:0010707", - "UBERON:0002102", - "UBERON:0004481", - "UBERON:0010891", - "UBERON:0000153", - "UBERON:0000026", - "UBERON:0010758", - "UBERON:0008196", + "HP:0000006", + "HP:0000005", + "HP:0034345", ], "object_closure_label": [ "All (HPO)", - "Phenotypic abnormality (HPO)", - "Muscle weakness (HPO)", - "Abnormality of the shoulder girdle musculature (HPO)", - "Abnormality of the musculature of the upper limbs (HPO)", - "Abnormality of the upper limb (HPO)", - "Abnormality of the musculature (HPO)", - "Limb-girdle muscle weakness (HPO)", - "Shoulder girdle muscle weakness (HPO)", - "Abnormality of the musculature of the limbs (HPO)", - "Abnormal muscle physiology (HPO)", - "Abnormal skeletal muscle morphology (HPO)", - "Abnormality of the musculoskeletal system (HPO)", - "Abnormality of limbs (HPO)", - "appendage", - "anatomical structure", - "organ", - "anterior region of body", - "musculature of body", - "material anatomical entity", - "anatomical system", - "multicellular organism", - "organism subdivision", - "musculature", - "anatomical entity", - "pectoral girdle region", - "arm", - "muscle organ", - "limb", - "forelimb", - "limb segment", - "musculature of pectoral girdle", - "musculature of limb", - "musculature of upper limb", - "paired limb/fin", - "pectoral appendage", - "muscle structure", - "multi-limb segment region", - "pectoral appendage musculature", - "appendage musculature", - "appendage girdle region", - "muscle of pectoral girdle", - "upper limb segment", - "multicellular anatomical structure", - "paired limb/fin segment", - "appendage girdle complex", - "pectoral complex", - "subdivision of organism along appendicular axis", - "pectoral complex muscle", - "organ system subdivision", - "musculature of pectoral complex", - "skeletal muscle organ", - "lateral structure", - "skeletal musculature", - ], - "object_label": "Shoulder girdle muscle weakness (HPO)", - "evidence_count": 0, + "Mode of inheritance (HPO)", + "Autosomal dominant inheritance (HPO)", + "Mendelian inheritance", + ], + "object_label": "Autosomal dominant inheritance (HPO)", + "evidence_count": 4, }, { - "id": "uuid:19006798-1e4f-11ee-871a-692638b4c502", - "original_subject": "OMIM:607155", - "predicate": "biolink:has_phenotype", - "category": "biolink:DiseaseToPhenotypicFeatureAssociation", + "id": "uuid:c3cdaddf-212f-11ee-873a-cd90a19c4085", + "original_subject": "OMIM:254090", + "predicate": "biolink:has_mode_of_inheritance", + "category": "biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation", "aggregator_knowledge_source": ["infores:monarchinitiative"], - "has_evidence": "ECO:0000501", - "primary_knowledge_source": ["infores:hpo-annotations"], - "provided_by": "hpoa_disease_phenotype_edges", - "publications": ["OMIM:607155"], - "subject": "MONDO:0011787", - "object": "HP:0003547", + "has_evidence": ["ECO:0000501"], + "primary_knowledge_source": "infores:hpo-annotations", + "provided_by": "hpoa_disease_mode_of_inheritance_edges", + "publications": ["OMIM:254090"], + "subject": "MONDO:0009681", + "object": "HP:0000006", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ - "MONDO:0018282", "MONDO:0000001", - "MONDO:0016971", - "MONDO:0017741", - "MONDO:0000429", - "MONDO:0045010", - "MONDO:0100167", "MONDO:0005071", "MONDO:0020121", "MONDO:0700223", - "MONDO:0011787", - "MONDO:0024322", - "MONDO:0020573", "BFO:0000002", + "MONDO:0019952", "BFO:0000017", "BFO:0000020", - "MONDO:0006025", - "MONDO:0016106", - "MONDO:0016157", - "MONDO:0042489", - "MONDO:0017745", + "MONDO:0100225", "BFO:0000016", "MONDO:0020120", "MONDO:0019056", @@ -1515,1173 +651,530 @@ def association_counts_response(): "MONDO:0005218", "MONDO:0005336", "MONDO:0002081", - "MONDO:0016156", + "MONDO:0009681", "OGMS:0000031", "MONDO:0003847", "MONDO:0003939", - "MONDO:0015286", "BFO:0000001", - "MONDO:0015152", "MONDO:0002320", - "MONDO:0019052", - "MONDO:0005066", - "MONDO:0016155", - "MONDO:0700066", + "MONDO:0000355", + "MONDO:0019950", ], "subject_closure_label": [ "disease or disorder", - "autosomal genetic disease", + "Ullrich congenital muscular dystrophy", "musculoskeletal system disorder", "congenital nervous system disorder", "hereditary disease", "muscle tissue disorder", - "metabolic disease", "nervous system disorder", "obsolete muscular disorder", "myopathy", - "autosomal recessive disease", - "autosomal recessive limb-girdle muscular dystrophy type 2I", - "autosomal recessive limb-girdle muscular dystrophy", - "congenital disorder of glycosylation", - "progressive muscular dystrophy", + "Ullrich congenital muscular dystrophy 1", "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", - "limb-girdle muscular dystrophy", - "disorder of protein O-glycosylation", - "disorder of O-mannosylglycan synthesis", - "qualitative or quantitative defects of alpha-dystroglycan", - "inborn errors of metabolism", "neuromuscular disease", + "congenital muscular dystrophy", + "congenital myopathy", "skeletal muscle disorder", "muscular dystrophy", - "inherited disease susceptibility", - "disorder of glycosylation", - "disease susceptibility", - "glycoprotein metabolism disease", - "pulmonary disease, chronic obstructive, susceptibility to", - "myopathy caused by variation in FKRP", + "collagen 6-related myopathy", "human disease or disorder", "hereditary skeletal muscle disorder", ], - "subject_label": "autosomal recessive limb-girdle muscular dystrophy type 2I", + "subject_label": "Ullrich congenital muscular dystrophy 1", "object_namespace": "HP", - "object_category": "biolink:PhenotypicQuality", + "object_category": "biolink:GeneticInheritance", "object_closure": [ "HP:0000001", - "UPHENO:0002649", - "UPHENO:0082875", - "UPHENO:0075696", - "UPHENO:0002320", - "UPHENO:0001001", - "HP:0003325", - "UPHENO:0080565", - "HP:0009127", - "UPHENO:0001005", - "HP:0011805", - "UPHENO:0001002", - "HP:0001324", - "HP:0000118", - "BFO:0000002", - "HP:0001435", - "HP:0001446", - "HP:0002817", - "BFO:0000020", - "UPHENO:0080555", - "HP:0003011", - "UPHENO:0002816", - "UPHENO:0002332", - "UPHENO:0080556", - "UPHENO:0002982", - "UPHENO:0081581", - "HP:0003547", - "HP:0033127", - "UPHENO:0001003", - "UPHENO:0002536", - "UPHENO:0076692", - "UPHENO:0002647", - "UPHENO:0076710", - "HP:0040064", - "BFO:0000001", - "HP:0011804", - "PATO:0000001", - "UPHENO:0002880", - "UPHENO:0002830", - "BFO:0000001", - "BFO:0000002", - "BFO:0000004", - "BFO:0000040", - "UBERON:0001062", - "CARO:0000000", - "UBERON:0000465", - "PR:000050567", - "RO:0002577", - "UBERON:0001015", - "UBERON:0000383", - "CARO:0000006", - "UBERON:0006058", - "UBERON:0010538", - "UBERON:0018254", - "UBERON:0005090", - "UBERON:0000061", - "UBERON:0004708", - "UBERON:0007271", - "UBERON:0014793", - "CARO:0000003", - "UBERON:0001460", - "UBERON:0002529", - "UBERON:0001630", - "UBERON:0010000", - "UBERON:0000467", - "UBERON:0015212", - "UBERON:0004710", - "UBERON:0002101", - "UBERON:0004480", - "UBERON:0007269", - "UBERON:0004471", - "UBERON:0007823", - "UBERON:0010708", - "UBERON:0008785", - "UBERON:0014892", - "UBERON:0000468", - "UBERON:0000475", - "UBERON:0000062", - "UBERON:0011216", - "UBERON:0001421", - "UBERON:0010707", - "UBERON:0002102", - "UBERON:0004481", - "UBERON:0010891", - "UBERON:0000153", - "UBERON:0000026", - "UBERON:0010758", - "UBERON:0008196", + "HP:0000006", + "HP:0000005", + "HP:0034345", ], "object_closure_label": [ "All (HPO)", - "Phenotypic abnormality (HPO)", - "Muscle weakness (HPO)", - "Abnormality of the shoulder girdle musculature (HPO)", - "Abnormality of the musculature of the upper limbs (HPO)", - "Abnormality of the upper limb (HPO)", - "Abnormality of the musculature (HPO)", - "Limb-girdle muscle weakness (HPO)", - "Shoulder girdle muscle weakness (HPO)", - "Abnormality of the musculature of the limbs (HPO)", - "Abnormal muscle physiology (HPO)", - "Abnormal skeletal muscle morphology (HPO)", - "Abnormality of the musculoskeletal system (HPO)", - "Abnormality of limbs (HPO)", - "appendage", - "anatomical structure", - "organ", - "anterior region of body", - "musculature of body", - "material anatomical entity", - "anatomical system", - "multicellular organism", - "organism subdivision", - "musculature", - "anatomical entity", - "pectoral girdle region", - "arm", - "muscle organ", - "limb", - "forelimb", - "limb segment", - "musculature of pectoral girdle", - "musculature of limb", - "musculature of upper limb", - "paired limb/fin", - "pectoral appendage", - "muscle structure", - "multi-limb segment region", - "pectoral appendage musculature", - "appendage musculature", - "appendage girdle region", - "muscle of pectoral girdle", - "upper limb segment", - "multicellular anatomical structure", - "paired limb/fin segment", - "appendage girdle complex", - "pectoral complex", - "subdivision of organism along appendicular axis", - "pectoral complex muscle", - "organ system subdivision", - "musculature of pectoral complex", - "skeletal muscle organ", - "lateral structure", - "skeletal musculature", - ], - "object_label": "Shoulder girdle muscle weakness (HPO)", - "evidence_count": 0, + "Mode of inheritance (HPO)", + "Autosomal dominant inheritance (HPO)", + "Mendelian inheritance", + ], + "object_label": "Autosomal dominant inheritance (HPO)", + "evidence_count": 4, }, { - "id": "uuid:21f7e3e1-1e4f-11ee-871a-692638b4c502", - "original_subject": "OMIM:609115", - "predicate": "biolink:has_phenotype", - "category": "biolink:DiseaseToPhenotypicFeatureAssociation", + "id": "uuid:c275a020-212f-11ee-873a-cd90a19c4085", + "original_subject": "OMIM:309950", + "predicate": "biolink:has_mode_of_inheritance", + "category": "biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation", "aggregator_knowledge_source": ["infores:monarchinitiative"], - "has_evidence": "ECO:0000501", - "primary_knowledge_source": ["infores:hpo-annotations"], - "provided_by": "hpoa_disease_phenotype_edges", - "publications": ["OMIM:609115"], - "subject": "MONDO:0012193", - "object": "HP:0003547", + "has_evidence": ["ECO:0000304"], + "primary_knowledge_source": "infores:hpo-annotations", + "provided_by": "hpoa_disease_mode_of_inheritance_edges", + "publications": ["OMIM:309950"], + "subject": "MONDO:0010676", + "object": "HP:0000006", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ "MONDO:0000001", - "MONDO:0016971", - "MONDO:0000429", - "MONDO:0100167", "MONDO:0005071", "MONDO:0020121", "MONDO:0700223", - "MONDO:0020573", "BFO:0000002", "BFO:0000017", "BFO:0000020", - "MONDO:0016106", - "MONDO:0042489", "BFO:0000016", "MONDO:0020120", "MONDO:0019056", - "MONDO:0015151", "MONDO:0700096", "MONDO:0005218", "MONDO:0005336", "MONDO:0002081", - "MONDO:0012193", - "MONDO:0000426", "OGMS:0000031", "MONDO:0003847", "MONDO:0003939", "BFO:0000001", + "MONDO:0010676", ], "subject_closure_label": [ "disease or disorder", - "autosomal dominant disease", - "autosomal genetic disease", "musculoskeletal system disorder", "hereditary disease", "muscle tissue disorder", "nervous system disorder", "obsolete muscular disorder", "myopathy", - "autosomal dominant limb-girdle muscular dystrophy type 1G", - "muscular dystrophy, limb-girdle, autosomal dominant", - "progressive muscular dystrophy", - "limb-girdle muscular dystrophy", + "muscular dystrophy, Hemizygous lethal type", "neuromuscular disease", "skeletal muscle disorder", "muscular dystrophy", - "inherited disease susceptibility", - "disease susceptibility", - "pulmonary disease, chronic obstructive, susceptibility to", "human disease or disorder", "hereditary skeletal muscle disorder", ], - "subject_label": "autosomal dominant limb-girdle muscular dystrophy type 1G", + "subject_label": "muscular dystrophy, Hemizygous lethal type", "object_namespace": "HP", - "object_category": "biolink:PhenotypicQuality", + "object_category": "biolink:GeneticInheritance", "object_closure": [ "HP:0000001", - "UPHENO:0002649", - "UPHENO:0082875", - "UPHENO:0075696", - "UPHENO:0002320", - "UPHENO:0001001", - "HP:0003325", - "UPHENO:0080565", - "HP:0009127", - "UPHENO:0001005", - "HP:0011805", - "UPHENO:0001002", - "HP:0001324", - "HP:0000118", - "BFO:0000002", - "HP:0001435", - "HP:0001446", - "HP:0002817", - "BFO:0000020", - "UPHENO:0080555", - "HP:0003011", - "UPHENO:0002816", - "UPHENO:0002332", - "UPHENO:0080556", - "UPHENO:0002982", - "UPHENO:0081581", - "HP:0003547", - "HP:0033127", - "UPHENO:0001003", - 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"subject_label": "autosomal recessive limb-girdle muscular dystrophy type 2B", + "subject_label": "myotonic dystrophy type 2", "object_namespace": "HP", - "object_category": "biolink:PhenotypicQuality", + "object_category": "biolink:GeneticInheritance", "object_closure": [ "HP:0000001", - "UPHENO:0082875", - "UPHENO:0075696", - "UPHENO:0002320", - "UPHENO:0001001", - "HP:0003551", - "UPHENO:0001005", - "UPHENO:0001002", - "HP:0004302", - "HP:0000118", - "BFO:0000002", - "BFO:0000020", - "HP:0003011", - "UPHENO:0002816", - "UPHENO:0002332", - "HP:0033127", - "UPHENO:0001003", - "UPHENO:0002536", - "BFO:0000001", - "HP:0011804", - "PATO:0000001", - "BFO:0000001", - "BFO:0000002", - "BFO:0000004", - "BFO:0000040", - "UBERON:0001062", - "CARO:0000000", - "UBERON:0000465", - "UBERON:0001015", - "UBERON:0000383", - "UBERON:0005090", - "UBERON:0000061", - "UBERON:0001630", - "UBERON:0010000", - "UBERON:0000467", - "UBERON:0000468", - "UBERON:0000062", - "UBERON:0011216", + "HP:0000006", + "HP:0000005", + "HP:0034345", ], "object_closure_label": [ "All (HPO)", - "Phenotypic abnormality (HPO)", - "Abnormality of the musculature (HPO)", - "Difficulty climbing stairs (HPO)", - "Functional motor deficit (HPO)", - "Abnormal muscle physiology (HPO)", - "Abnormality of the musculoskeletal system (HPO)", - "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", - ], - "object_label": "Difficulty climbing stairs (HPO)", - "evidence_count": 0, + "Mode of inheritance (HPO)", + "Autosomal dominant inheritance (HPO)", + "Mendelian inheritance", + ], + "object_label": "Autosomal dominant inheritance (HPO)", + "evidence_count": 4, }, { - "id": "uuid:1c34b3dd-1e4f-11ee-871a-692638b4c502", - "original_subject": "OMIM:310440", - "predicate": "biolink:has_phenotype", - "category": "biolink:DiseaseToPhenotypicFeatureAssociation", + "id": "uuid:c3cdac2c-212f-11ee-873a-cd90a19c4085", + "original_subject": "OMIM:603689", + "predicate": "biolink:has_mode_of_inheritance", + "category": "biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation", "aggregator_knowledge_source": ["infores:monarchinitiative"], - "has_evidence": "ECO:0000501", - "primary_knowledge_source": ["infores:hpo-annotations"], - "provided_by": "hpoa_disease_phenotype_edges", - "publications": ["OMIM:310440"], - "subject": "MONDO:0010684", - "object": "HP:0003551", + "has_evidence": ["ECO:0000269"], + "primary_knowledge_source": "infores:hpo-annotations", + "provided_by": "hpoa_disease_mode_of_inheritance_edges", + "publications": ["PMID:22577215"], + "subject": "MONDO:0011362", + "object": "HP:0000006", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ "MONDO:0000001", "MONDO:0016112", - "MONDO:0010684", - "MONDO:0100167", + "MONDO:0000429", "MONDO:0005071", "MONDO:0020121", + "MONDO:0100175", "MONDO:0700223", - "MONDO:0020573", "BFO:0000002", + "MONDO:0019952", "BFO:0000017", "BFO:0000020", "MONDO:0016106", - "MONDO:0042489", + "MONDO:0016191", "BFO:0000016", "MONDO:0020120", "MONDO:0019056", + "MONDO:0100494", + "MONDO:0016139", "MONDO:0700096", "MONDO:0005218", "MONDO:0005336", "MONDO:0002081", + "MONDO:0000426", + "MONDO:0011362", "OGMS:0000031", "MONDO:0003847", "MONDO:0003939", "BFO:0000001", + "MONDO:0002320", + "MONDO:0016108", + "MONDO:0018949", ], "subject_closure_label": [ "disease or disorder", + "autosomal dominant disease", + "autosomal genetic disease", "musculoskeletal system disorder", + "congenital nervous system disorder", "hereditary disease", "muscle tissue disorder", "nervous system disorder", "obsolete muscular disorder", "myopathy", - "X-linked myopathy with excessive autophagy", + "myopathy, myofibrillar, 9, with early respiratory failure", "progressive muscular dystrophy", + "autosomal dominant distal myopathy", "hereditary inclusion-body myopathy", + "qualitative or quantitative protein defects in neuromuscular diseases", + "qualitative or quantitative defects of titin", + "distal myopathy", "neuromuscular disease", + "congenital myopathy", "skeletal muscle disorder", "muscular dystrophy", - "inherited disease susceptibility", - "disease susceptibility", - "pulmonary disease, chronic obstructive, susceptibility to", + "TTN-related myopathy", + "autosomal dominant titinopathy", "human disease or disorder", "hereditary skeletal muscle disorder", ], - "subject_label": "X-linked myopathy with excessive autophagy", + "subject_label": "myopathy, myofibrillar, 9, with early respiratory failure", "object_namespace": "HP", - "object_category": "biolink:PhenotypicQuality", + "object_category": "biolink:GeneticInheritance", "object_closure": [ "HP:0000001", - "UPHENO:0082875", - "UPHENO:0075696", - "UPHENO:0002320", - "UPHENO:0001001", - "HP:0003551", - "UPHENO:0001005", - "UPHENO:0001002", - "HP:0004302", - "HP:0000118", - "BFO:0000002", - "BFO:0000020", - "HP:0003011", - "UPHENO:0002816", - "UPHENO:0002332", - "HP:0033127", - "UPHENO:0001003", - "UPHENO:0002536", - "BFO:0000001", - "HP:0011804", - "PATO:0000001", - "BFO:0000001", - "BFO:0000002", - "BFO:0000004", - "BFO:0000040", - "UBERON:0001062", - "CARO:0000000", - "UBERON:0000465", - "UBERON:0001015", - "UBERON:0000383", - "UBERON:0005090", - "UBERON:0000061", - "UBERON:0001630", - "UBERON:0010000", - "UBERON:0000467", - "UBERON:0000468", - "UBERON:0000062", - "UBERON:0011216", + "HP:0000006", + "HP:0000005", + "HP:0034345", ], "object_closure_label": [ "All (HPO)", - "Phenotypic abnormality (HPO)", - "Abnormality of the musculature (HPO)", - "Difficulty climbing stairs (HPO)", - "Functional motor deficit (HPO)", - "Abnormal muscle physiology (HPO)", - "Abnormality of the musculoskeletal system (HPO)", - "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", - ], - "object_label": "Difficulty climbing stairs (HPO)", - "evidence_count": 0, + "Mode of inheritance (HPO)", + "Autosomal dominant inheritance (HPO)", + "Mendelian inheritance", + ], + "object_label": "Autosomal dominant inheritance (HPO)", + "evidence_count": 4, }, { - "id": "uuid:1e9fbb79-1e4f-11ee-871a-692638b4c502", - "original_subject": "OMIM:601954", - "predicate": "biolink:has_phenotype", - "category": "biolink:DiseaseToPhenotypicFeatureAssociation", + "id": "uuid:c3cdadba-212f-11ee-873a-cd90a19c4085", + "original_subject": "OMIM:604454", + "predicate": "biolink:has_mode_of_inheritance", + "category": "biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation", "aggregator_knowledge_source": ["infores:monarchinitiative"], - "has_evidence": "ECO:0000501", - "primary_knowledge_source": ["infores:hpo-annotations"], - "provided_by": "hpoa_disease_phenotype_edges", - "publications": ["OMIM:601954"], - "subject": "MONDO:0011170", - "object": "HP:0003551", + "has_evidence": ["ECO:0000269"], + "primary_knowledge_source": "infores:hpo-annotations", + "provided_by": "hpoa_disease_mode_of_inheritance_edges", + "publications": ["PMID:23348830"], + "subject": "MONDO:0011466", + "object": "HP:0000006", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ "MONDO:0000001", - "MONDO:0016971", + "MONDO:0011466", "MONDO:0000429", - "MONDO:0100167", "MONDO:0005071", "MONDO:0020121", "MONDO:0700223", - "MONDO:0020573", "BFO:0000002", "BFO:0000017", "BFO:0000020", - "MONDO:0006025", - "MONDO:0016106", - "MONDO:0042489", "BFO:0000016", "MONDO:0020120", "MONDO:0019056", - "MONDO:0016139", "MONDO:0700096", - "MONDO:0011170", "MONDO:0005218", "MONDO:0005336", "MONDO:0002081", + "MONDO:0000426", "OGMS:0000031", - "MONDO:0016192", "MONDO:0003847", "MONDO:0003939", "BFO:0000001", - "MONDO:0015152", + "MONDO:0016108", + "MONDO:0018949", ], "subject_closure_label": [ "disease or disorder", + "autosomal dominant disease", "autosomal genetic disease", "musculoskeletal system disorder", "hereditary disease", @@ -2689,974 +1182,560 @@ def association_counts_response(): "nervous system disorder", "obsolete muscular disorder", "myopathy", - "autosomal recessive disease", - "autosomal recessive limb-girdle muscular dystrophy type 2G", - "autosomal recessive limb-girdle muscular dystrophy", - "progressive muscular dystrophy", - "qualitative or quantitative protein defects in neuromuscular diseases", - "qualitative or quantitative defects of telethonin", - "limb-girdle muscular dystrophy", + "distal myopathy, Welander type", + "autosomal dominant distal myopathy", + "distal myopathy", "neuromuscular disease", "skeletal muscle disorder", "muscular dystrophy", - "inherited disease susceptibility", - "disease susceptibility", - "pulmonary disease, chronic obstructive, susceptibility to", "human disease or disorder", "hereditary skeletal muscle disorder", ], - "subject_label": "autosomal recessive limb-girdle muscular dystrophy type 2G", + "subject_label": "distal myopathy, Welander type", "object_namespace": "HP", - "object_category": "biolink:PhenotypicQuality", + "object_category": "biolink:GeneticInheritance", "object_closure": [ "HP:0000001", - "UPHENO:0082875", - "UPHENO:0075696", - "UPHENO:0002320", - "UPHENO:0001001", - "HP:0003551", - "UPHENO:0001005", - "UPHENO:0001002", - "HP:0004302", - "HP:0000118", - "BFO:0000002", - "BFO:0000020", - "HP:0003011", - "UPHENO:0002816", - "UPHENO:0002332", - "HP:0033127", - "UPHENO:0001003", - "UPHENO:0002536", - "BFO:0000001", - "HP:0011804", - "PATO:0000001", - "BFO:0000001", - "BFO:0000002", - "BFO:0000004", - "BFO:0000040", - "UBERON:0001062", - "CARO:0000000", - "UBERON:0000465", - "UBERON:0001015", - "UBERON:0000383", - "UBERON:0005090", - "UBERON:0000061", - "UBERON:0001630", - "UBERON:0010000", - "UBERON:0000467", - "UBERON:0000468", - "UBERON:0000062", - "UBERON:0011216", + "HP:0000006", + "HP:0000005", + "HP:0034345", ], "object_closure_label": [ "All (HPO)", - "Phenotypic abnormality (HPO)", - "Abnormality of the musculature (HPO)", - "Difficulty climbing stairs (HPO)", - "Functional motor deficit (HPO)", - "Abnormal muscle physiology (HPO)", - "Abnormality of the musculoskeletal system (HPO)", - "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", - ], - "object_label": "Difficulty climbing stairs (HPO)", - "evidence_count": 0, + "Mode of inheritance (HPO)", + "Autosomal dominant inheritance (HPO)", + "Mendelian inheritance", + ], + "object_label": "Autosomal dominant inheritance (HPO)", + "evidence_count": 4, }, { - "id": "uuid:1bce01b5-1e4f-11ee-871a-692638b4c502", - "original_subject": "OMIM:606612", - "predicate": "biolink:has_phenotype", - "category": "biolink:DiseaseToPhenotypicFeatureAssociation", + "id": "uuid:c367df64-212f-11ee-873a-cd90a19c4085", + "original_subject": "OMIM:608423", + "predicate": "biolink:has_mode_of_inheritance", + "category": "biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation", "aggregator_knowledge_source": ["infores:monarchinitiative"], - "has_evidence": "ECO:0000269", - "primary_knowledge_source": ["infores:hpo-annotations"], - "provided_by": "hpoa_disease_phenotype_edges", - "publications": ["PMID:11592034"], - "subject": "MONDO:0011688", - "object": "HP:0003551", + "has_evidence": ["ECO:0000269"], + "primary_knowledge_source": "infores:hpo-annotations", + "provided_by": "hpoa_disease_mode_of_inheritance_edges", + "publications": ["PMID:23543484"], + "subject": "MONDO:0012034", + "object": "HP:0000006", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ - "MONDO:0018282", "MONDO:0000001", - "MONDO:0017741", - "MONDO:0018276", - "MONDO:0045010", - "MONDO:0100167", + "MONDO:0016971", + "MONDO:0000429", "MONDO:0005071", "MONDO:0020121", - "MONDO:0000172", "MONDO:0700223", - "MONDO:0024322", - "MONDO:0020573", + "MONDO:0012034", "BFO:0000002", "BFO:0000017", "BFO:0000020", - "MONDO:0016157", - "MONDO:0042489", + "MONDO:0016106", "BFO:0000016", "MONDO:0020120", "MONDO:0019056", - "MONDO:0016139", + "MONDO:0015151", "MONDO:0700096", "MONDO:0005218", "MONDO:0005336", "MONDO:0002081", + "MONDO:0000426", "OGMS:0000031", "MONDO:0003847", "MONDO:0003939", - "MONDO:0015286", "BFO:0000001", - "MONDO:0002320", - "MONDO:0019052", - "MONDO:0005066", - "MONDO:0019950", - "MONDO:0016155", - "MONDO:0011688", - "MONDO:0700066", ], "subject_closure_label": [ "disease or disorder", - "muscular dystrophy-dystroglycanopathy, type B", + "autosomal dominant disease", + "autosomal genetic disease", "musculoskeletal system disorder", - "congenital nervous system disorder", "hereditary disease", "muscle tissue disorder", - "metabolic disease", "nervous system disorder", "obsolete muscular disorder", "myopathy", - "muscular dystrophy-dystroglycanopathy type B5", - "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", - "qualitative or quantitative defects of fukutin", - "disorder of protein O-glycosylation", - "muscular dystrophy-dystroglycanopathy", - "qualitative or quantitative defects of alpha-dystroglycan", - "inborn errors of metabolism", + "autosomal dominant limb-girdle muscular dystrophy type 1F", + "muscular dystrophy, limb-girdle, autosomal dominant", + "progressive muscular dystrophy", + "limb-girdle muscular dystrophy", "neuromuscular disease", - "congenital muscular dystrophy", "skeletal muscle disorder", "muscular dystrophy", - "inherited disease susceptibility", - "disorder of glycosylation", - "disease susceptibility", - "glycoprotein metabolism disease", - "pulmonary disease, chronic obstructive, susceptibility to", - "myopathy caused by variation in FKRP", "human disease or disorder", "hereditary skeletal muscle disorder", ], - "subject_label": "muscular dystrophy-dystroglycanopathy type B5", + "subject_label": "autosomal dominant limb-girdle muscular dystrophy type 1F", "object_namespace": "HP", - "object_category": "biolink:PhenotypicQuality", + "object_category": "biolink:GeneticInheritance", "object_closure": [ "HP:0000001", - "UPHENO:0082875", - "UPHENO:0075696", - "UPHENO:0002320", - "UPHENO:0001001", - "HP:0003551", - "UPHENO:0001005", - "UPHENO:0001002", - "HP:0004302", - "HP:0000118", - "BFO:0000002", - "BFO:0000020", - "HP:0003011", - "UPHENO:0002816", - "UPHENO:0002332", - "HP:0033127", - "UPHENO:0001003", - "UPHENO:0002536", - "BFO:0000001", - "HP:0011804", - "PATO:0000001", - "BFO:0000001", - "BFO:0000002", - "BFO:0000004", - "BFO:0000040", - "UBERON:0001062", - "CARO:0000000", - "UBERON:0000465", - "UBERON:0001015", - "UBERON:0000383", - "UBERON:0005090", - "UBERON:0000061", - "UBERON:0001630", - "UBERON:0010000", - "UBERON:0000467", - "UBERON:0000468", - "UBERON:0000062", - "UBERON:0011216", + "HP:0000006", + "HP:0000005", + "HP:0034345", ], "object_closure_label": [ "All (HPO)", - "Phenotypic abnormality (HPO)", - "Abnormality of the musculature (HPO)", - "Difficulty climbing stairs (HPO)", - "Functional motor deficit (HPO)", - "Abnormal muscle physiology (HPO)", - "Abnormality of the musculoskeletal system (HPO)", - "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", - ], - "object_label": "Difficulty climbing stairs (HPO)", - "evidence_count": 0, + "Mode of inheritance (HPO)", + "Autosomal dominant inheritance (HPO)", + "Mendelian inheritance", + ], + "object_label": "Autosomal dominant inheritance (HPO)", + "evidence_count": 4, }, { - "id": "uuid:19006790-1e4f-11ee-871a-692638b4c502", - "original_subject": "OMIM:607155", - "predicate": "biolink:has_phenotype", - "category": "biolink:DiseaseToPhenotypicFeatureAssociation", + "id": "uuid:c3367251-212f-11ee-873a-cd90a19c4085", + "original_subject": "OMIM:608810", + "predicate": "biolink:has_mode_of_inheritance", + "category": "biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation", "aggregator_knowledge_source": ["infores:monarchinitiative"], - "has_evidence": "ECO:0000501", - "primary_knowledge_source": ["infores:hpo-annotations"], - "provided_by": "hpoa_disease_phenotype_edges", - "publications": ["OMIM:607155"], - "subject": "MONDO:0011787", - "object": "HP:0003551", + "has_evidence": ["ECO:0000269"], + "primary_knowledge_source": "infores:hpo-annotations", + "provided_by": "hpoa_disease_mode_of_inheritance_edges", + "publications": ["PMID:14681890"], + "subject": "MONDO:0012130", + "object": "HP:0000006", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ - "MONDO:0018282", "MONDO:0000001", - "MONDO:0016971", - "MONDO:0017741", + "MONDO:0016186", "MONDO:0000429", - "MONDO:0045010", - "MONDO:0100167", "MONDO:0005071", "MONDO:0020121", + "MONDO:0018943", "MONDO:0700223", - "MONDO:0011787", - "MONDO:0024322", - "MONDO:0020573", "BFO:0000002", + "MONDO:0019952", "BFO:0000017", "BFO:0000020", - "MONDO:0006025", - "MONDO:0016106", - "MONDO:0016157", - "MONDO:0042489", - "MONDO:0017745", + "MONDO:0020343", "BFO:0000016", "MONDO:0020120", "MONDO:0019056", "MONDO:0016139", "MONDO:0700096", + "MONDO:0002921", "MONDO:0005218", "MONDO:0005336", "MONDO:0002081", - "MONDO:0016156", + "MONDO:0012130", + "MONDO:0000426", "OGMS:0000031", "MONDO:0003847", "MONDO:0003939", - "MONDO:0015286", "BFO:0000001", - "MONDO:0015152", "MONDO:0002320", - "MONDO:0019052", - "MONDO:0005066", - "MONDO:0016155", - "MONDO:0700066", + "MONDO:0016188", + "MONDO:0016108", + "MONDO:0018949", ], "subject_closure_label": [ "disease or disorder", + "autosomal dominant disease", "autosomal genetic disease", "musculoskeletal system disorder", "congenital nervous system disorder", + "congenital structural myopathy", "hereditary disease", "muscle tissue disorder", - "metabolic disease", "nervous system disorder", "obsolete muscular disorder", "myopathy", - "autosomal recessive disease", - "autosomal recessive limb-girdle muscular dystrophy type 2I", - "autosomal recessive limb-girdle muscular dystrophy", - "congenital disorder of glycosylation", - "progressive muscular dystrophy", + "myofibrillar myopathy 2", + "autosomal dominant distal myopathy", "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", - "limb-girdle muscular dystrophy", - "disorder of protein O-glycosylation", - "disorder of O-mannosylglycan synthesis", - "qualitative or quantitative defects of alpha-dystroglycan", - "inborn errors of metabolism", + "qualitative or quantitative defects of myofibrillar proteins", + "qualitative or quantitative defects of alphaB-cristallin", + "myofibrillar myopathy", + "distal myopathy", "neuromuscular disease", + "congenital myopathy", "skeletal muscle disorder", "muscular dystrophy", - "inherited disease susceptibility", - "disorder of glycosylation", - "disease susceptibility", - "glycoprotein metabolism disease", - "pulmonary disease, chronic obstructive, susceptibility to", - "myopathy caused by variation in FKRP", + "alpha-crystallinopathy", "human disease or disorder", "hereditary skeletal muscle disorder", ], - "subject_label": "autosomal recessive limb-girdle muscular dystrophy type 2I", + "subject_label": "myofibrillar myopathy 2", "object_namespace": "HP", - "object_category": "biolink:PhenotypicQuality", + "object_category": "biolink:GeneticInheritance", "object_closure": [ "HP:0000001", - "UPHENO:0082875", - "UPHENO:0075696", - "UPHENO:0002320", - "UPHENO:0001001", - "HP:0003551", - "UPHENO:0001005", - "UPHENO:0001002", - "HP:0004302", - "HP:0000118", - "BFO:0000002", - "BFO:0000020", - "HP:0003011", - "UPHENO:0002816", - "UPHENO:0002332", - "HP:0033127", - "UPHENO:0001003", - "UPHENO:0002536", - "BFO:0000001", - "HP:0011804", - "PATO:0000001", - "BFO:0000001", - "BFO:0000002", - "BFO:0000004", - "BFO:0000040", - "UBERON:0001062", - "CARO:0000000", - "UBERON:0000465", - "UBERON:0001015", - "UBERON:0000383", - "UBERON:0005090", - "UBERON:0000061", - "UBERON:0001630", - "UBERON:0010000", - "UBERON:0000467", - "UBERON:0000468", - "UBERON:0000062", - "UBERON:0011216", + "HP:0000006", + "HP:0000005", + "HP:0034345", ], "object_closure_label": [ "All (HPO)", - "Phenotypic abnormality (HPO)", - "Abnormality of the musculature (HPO)", - "Difficulty climbing stairs (HPO)", - "Functional motor deficit (HPO)", - "Abnormal muscle physiology (HPO)", - "Abnormality of the musculoskeletal system (HPO)", - "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", - ], - "object_label": "Difficulty climbing stairs (HPO)", - "evidence_count": 0, + "Mode of inheritance (HPO)", + "Autosomal dominant inheritance (HPO)", + "Mendelian inheritance", + ], + "object_label": "Autosomal dominant inheritance (HPO)", + "evidence_count": 4, }, { - 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"publications": ["OMIM:254130"], - "subject": "MONDO:0024545", - "object": "HP:0003551", + "has_evidence": ["ECO:0000501"], + "primary_knowledge_source": "infores:hpo-annotations", + "provided_by": "hpoa_disease_mode_of_inheritance_edges", + "publications": ["OMIM:609452"], + "subject": "MONDO:0012277", + "object": "HP:0000006", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ "MONDO:0000001", + "MONDO:0016186", "MONDO:0000429", - "MONDO:0016145", - "MONDO:0100167", "MONDO:0005071", "MONDO:0020121", + "MONDO:0018943", "MONDO:0700223", - "MONDO:0020573", "BFO:0000002", + "MONDO:0019952", + "MONDO:0016190", "BFO:0000017", "BFO:0000020", - "MONDO:0006025", - "MONDO:0042489", "BFO:0000016", "MONDO:0020120", "MONDO:0019056", "MONDO:0016139", "MONDO:0700096", - "MONDO:0009685", + "MONDO:0002921", "MONDO:0005218", "MONDO:0005336", "MONDO:0002081", - "MONDO:0016109", + "MONDO:0000426", "OGMS:0000031", "MONDO:0003847", "MONDO:0003939", + "MONDO:0012277", "BFO:0000001", - 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"Miyoshi muscular dystrophy 1", - "disease susceptibility", - "pulmonary disease, chronic obstructive, susceptibility to", "human disease or disorder", "hereditary skeletal muscle disorder", ], - "subject_label": "Miyoshi muscular dystrophy 1", + "subject_label": "myofibrillar myopathy 4", "object_namespace": "HP", - "object_category": "biolink:PhenotypicQuality", + "object_category": "biolink:GeneticInheritance", "object_closure": [ "HP:0000001", - "UPHENO:0082875", - "UPHENO:0075696", - "UPHENO:0002320", - "UPHENO:0001001", - "HP:0003551", - "UPHENO:0001005", - "UPHENO:0001002", - "HP:0004302", - "HP:0000118", - "BFO:0000002", - "BFO:0000020", - "HP:0003011", - "UPHENO:0002816", - "UPHENO:0002332", - "HP:0033127", - "UPHENO:0001003", - "UPHENO:0002536", - "BFO:0000001", - "HP:0011804", - "PATO:0000001", - "BFO:0000001", - "BFO:0000002", - "BFO:0000004", - "BFO:0000040", - "UBERON:0001062", - "CARO:0000000", - "UBERON:0000465", - "UBERON:0001015", - "UBERON:0000383", - "UBERON:0005090", - "UBERON:0000061", - "UBERON:0001630", - "UBERON:0010000", - "UBERON:0000467", - "UBERON:0000468", - "UBERON:0000062", - "UBERON:0011216", + "HP:0000006", + "HP:0000005", + "HP:0034345", ], "object_closure_label": [ "All (HPO)", - "Phenotypic abnormality (HPO)", - "Abnormality of the musculature (HPO)", - "Difficulty climbing stairs (HPO)", - "Functional motor deficit (HPO)", - "Abnormal muscle physiology (HPO)", - "Abnormality of the musculoskeletal system (HPO)", - "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", - ], - "object_label": "Difficulty climbing stairs (HPO)", - "evidence_count": 0, + "Mode of inheritance (HPO)", + "Autosomal dominant inheritance (HPO)", + "Mendelian inheritance", + ], + "object_label": "Autosomal dominant inheritance (HPO)", + "evidence_count": 4, }, ], }, diff --git a/backend/tests/fixtures/association_response.py b/backend/tests/fixtures/association_response.py index 251204707..6a8c4839e 100644 --- a/backend/tests/fixtures/association_response.py +++ b/backend/tests/fixtures/association_response.py @@ -18,39 +18,32 @@ def association_response(): }, }, "response": { - "num_found": 4811, + "num_found": 4806, "start": 0, "docs": [ { - "id": "uuid:1be81e3c-1e4f-11ee-871a-692638b4c502", - "original_subject": "OMIM:619478", - "predicate": "biolink:has_phenotype", - "category": "biolink:DiseaseToPhenotypicFeatureAssociation", + "id": "uuid:c2a45bf5-212f-11ee-873a-cd90a19c4085", + "original_subject": "OMIM:158800", + "predicate": "biolink:has_mode_of_inheritance", + "category": "biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation", "aggregator_knowledge_source": ["infores:monarchinitiative"], - "has_evidence": "ECO:0000269", - "primary_knowledge_source": ["infores:hpo-annotations"], - "provided_by": "hpoa_disease_phenotype_edges", - "publications": ["PMID:27153398"], - "subject": "MONDO:0030355", - "object": "HP:0003484", + "has_evidence": ["ECO:0000304"], + "primary_knowledge_source": "infores:hpo-annotations", + "provided_by": "hpoa_disease_mode_of_inheritance_edges", + "publications": ["OMIM:158800"], + "subject": "MONDO:0008028", + "object": "HP:0000006", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ "MONDO:0000001", - "MONDO:0030355", - "MONDO:0019303", - "MONDO:0100167", "MONDO:0005071", "MONDO:0020121", + "MONDO:0008028", "MONDO:0700223", - "MONDO:0001347", - "MONDO:0020573", "BFO:0000002", "BFO:0000017", "BFO:0000020", - "MONDO:0016106", - "MONDO:0042489", - "MONDO:0100137", "BFO:0000016", "MONDO:0020120", "MONDO:0019056", @@ -58,7 +51,6 @@ def association_response(): "MONDO:0005218", "MONDO:0005336", "MONDO:0002081", - "MONDO:0021147", "OGMS:0000031", "MONDO:0003847", "MONDO:0003939", @@ -66,193 +58,64 @@ def association_response(): ], "subject_closure_label": [ "disease or disorder", - "facioscapulohumeral muscular dystrophy", "musculoskeletal system disorder", "hereditary disease", "muscle tissue disorder", "nervous system disorder", "obsolete muscular disorder", "myopathy", - "progressive muscular dystrophy", + "muscular dystrophy, Barnes type", "neuromuscular disease", - "premature aging syndrome", "skeletal muscle disorder", "muscular dystrophy", - "inherited disease susceptibility", - "disorder of development or morphogenesis", - "facioscapulohumeral muscular dystrophy 4, digenic", - "disease susceptibility", - "telomere syndrome", - "pulmonary disease, chronic obstructive, susceptibility to", "human disease or disorder", "hereditary skeletal muscle disorder", ], - "subject_label": "facioscapulohumeral muscular dystrophy 4, digenic", + "subject_label": "muscular dystrophy, Barnes type", "object_namespace": "HP", - "object_category": "biolink:PhenotypicQuality", + "object_category": "biolink:GeneticInheritance", "object_closure": [ "HP:0000001", - "UPHENO:0002649", - "UPHENO:0082875", - "UPHENO:0075696", - "UPHENO:0002320", - "UPHENO:0001001", - "HP:0003325", - "HP:0003484", - "UPHENO:0080563", - "HP:0009127", - "UPHENO:0001005", - "HP:0011805", - "UPHENO:0001002", - "HP:0001324", - "HP:0003690", - "HP:0000118", - "BFO:0000002", - "HP:0001446", - "HP:0002817", - "BFO:0000020", - "UPHENO:0080555", - "HP:0003011", - "UPHENO:0002816", - "UPHENO:0002332", - "UPHENO:0080556", - "UPHENO:0081581", - "HP:0033127", - "UPHENO:0001003", - "UPHENO:0002536", - "UPHENO:0076692", - "UPHENO:0002647", - "UPHENO:0076710", - "HP:0040064", - "BFO:0000001", - "HP:0011804", - "PATO:0000001", - "UPHENO:0002880", - "UPHENO:0002830", - "BFO:0000001", - "BFO:0000002", - "BFO:0000004", - "BFO:0000040", - "UBERON:0001062", - "CARO:0000000", - "UBERON:0000465", - "PR:000050567", - "RO:0002577", - "UBERON:0001015", - "UBERON:0000383", - "CARO:0000006", - "UBERON:0006058", - "UBERON:0010538", - "UBERON:0005090", - "UBERON:0000061", - "UBERON:0004708", - "UBERON:0007271", - "UBERON:0014793", - "CARO:0000003", - "UBERON:0001460", - "UBERON:0002529", - "UBERON:0001630", - "UBERON:0010000", - "UBERON:0000467", - "UBERON:0015212", - "UBERON:0004710", - "UBERON:0002101", - "UBERON:0004480", - "UBERON:0007269", - "UBERON:0010708", - "UBERON:0008785", - "UBERON:0000468", - "UBERON:0000475", - "UBERON:0000062", - "UBERON:0011216", - "UBERON:0010707", - "UBERON:0002102", - "UBERON:0004481", - "UBERON:0000153", - "UBERON:0000026", - "UBERON:0010758", + "HP:0000006", + "HP:0000005", + "HP:0034345", ], "object_closure_label": [ "All (HPO)", - "Phenotypic abnormality (HPO)", - "Muscle weakness (HPO)", - "Abnormality of the musculature of the upper limbs (HPO)", - "Abnormality of the upper limb (HPO)", - "Abnormality of the musculature (HPO)", - "Limb-girdle muscle weakness (HPO)", - "Upper limb muscle weakness (HPO)", - "Limb muscle weakness (HPO)", - "Abnormality of the musculature of the limbs (HPO)", - "Abnormal muscle physiology (HPO)", - "Abnormal skeletal muscle morphology (HPO)", - "Abnormality of the musculoskeletal system (HPO)", - "Abnormality of limbs (HPO)", - "appendage", - "anatomical structure", - "organ", - "anterior region of body", - "musculature of body", - "material anatomical entity", - "anatomical system", - "multicellular organism", - "organism subdivision", - "musculature", - "anatomical entity", - "arm", - "muscle organ", - "limb", - "forelimb", - "limb segment", - "musculature of limb", - "musculature of upper limb", - "paired limb/fin", - "pectoral appendage", - "muscle structure", - "multi-limb segment region", - "pectoral appendage musculature", - "appendage musculature", - "upper limb segment", - "multicellular anatomical structure", - "paired limb/fin segment", - "appendage girdle complex", - "pectoral complex", - "subdivision of organism along appendicular axis", - "organ system subdivision", - "musculature of pectoral complex", - "lateral structure", - ], - "object_label": "Upper limb muscle weakness (HPO)", - "evidence_count": 0, + "Mode of inheritance (HPO)", + "Autosomal dominant inheritance (HPO)", + "Mendelian inheritance", + ], + "object_label": "Autosomal dominant inheritance (HPO)", + "evidence_count": 4, }, { - "id": "uuid:1fd70821-1e4f-11ee-871a-692638b4c502", - "original_subject": "OMIM:616812", - "predicate": "biolink:has_phenotype", - "category": "biolink:DiseaseToPhenotypicFeatureAssociation", + "id": "uuid:c304bcf2-212f-11ee-873a-cd90a19c4085", + "original_subject": "OMIM:158900", + "predicate": "biolink:has_mode_of_inheritance", + "category": "biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation", "aggregator_knowledge_source": ["infores:monarchinitiative"], - "has_evidence": "ECO:0000269", - "primary_knowledge_source": ["infores:hpo-annotations"], - "provided_by": "hpoa_disease_phenotype_edges", - "publications": ["PMID:26642364"], - "subject": "MONDO:0014782", - "object": "HP:0003546", + "has_evidence": ["ECO:0000501"], + "primary_knowledge_source": "infores:hpo-annotations", + "provided_by": "hpoa_disease_mode_of_inheritance_edges", + "publications": ["OMIM:158900"], + "subject": "MONDO:0008030", + "object": "HP:0000006", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ + "MONDO:0008030", "MONDO:0000001", - "MONDO:0016971", - "MONDO:0000429", - "MONDO:0100167", + "MONDO:0019303", "MONDO:0005071", "MONDO:0020121", "MONDO:0700223", - "MONDO:0020573", + "MONDO:0001347", "BFO:0000002", "BFO:0000017", "BFO:0000020", - "MONDO:0006025", "MONDO:0016106", - "MONDO:0042489", + "MONDO:0100137", "BFO:0000016", "MONDO:0020120", "MONDO:0019056", @@ -260,354 +123,172 @@ def association_response(): "MONDO:0005218", "MONDO:0005336", "MONDO:0002081", + "MONDO:0021147", "OGMS:0000031", "MONDO:0003847", - "MONDO:0014782", "MONDO:0003939", "BFO:0000001", - "MONDO:0015152", ], "subject_closure_label": [ "disease or disorder", - "autosomal genetic disease", + "facioscapulohumeral muscular dystrophy", "musculoskeletal system disorder", "hereditary disease", "muscle tissue disorder", "nervous system disorder", "obsolete muscular disorder", "myopathy", - "autosomal recessive disease", - "autosomal recessive limb-girdle muscular dystrophy type 2X", - "autosomal recessive limb-girdle muscular dystrophy", + "facioscapulohumeral muscular dystrophy 1", "progressive muscular dystrophy", - "limb-girdle muscular dystrophy", "neuromuscular disease", + "premature aging syndrome", "skeletal muscle disorder", "muscular dystrophy", - "inherited disease susceptibility", - "disease susceptibility", - "pulmonary disease, chronic obstructive, susceptibility to", + "disorder of development or morphogenesis", + "telomere syndrome", "human disease or disorder", "hereditary skeletal muscle disorder", ], - "subject_label": "autosomal recessive limb-girdle muscular dystrophy type 2X", + "subject_label": "facioscapulohumeral muscular dystrophy 1", "object_namespace": "HP", - "object_category": "biolink:PhenotypicQuality", + "object_category": "biolink:GeneticInheritance", "object_closure": [ "HP:0000001", - "UPHENO:0082875", - "UPHENO:0075696", - "UPHENO:0002320", - "UPHENO:0001001", - "UPHENO:0001005", - "UPHENO:0001002", - "HP:0004302", - "HP:0000118", - "BFO:0000002", - "BFO:0000020", - "HP:0003011", - "UPHENO:0002816", - "HP:0003546", - "UPHENO:0002332", - "HP:0033127", - "UPHENO:0001003", - "UPHENO:0002536", - "BFO:0000001", - "HP:0011804", - "PATO:0000001", - "BFO:0000001", - "BFO:0000002", - "BFO:0000004", - "BFO:0000040", - "UBERON:0001062", - "CARO:0000000", - "UBERON:0000465", - "UBERON:0001015", - "UBERON:0000383", - "UBERON:0005090", - "UBERON:0000061", - "UBERON:0001630", - "UBERON:0010000", - "UBERON:0000467", - "UBERON:0000468", - "UBERON:0000062", - "UBERON:0011216", + "HP:0000006", + "HP:0000005", + "HP:0034345", ], "object_closure_label": [ "All (HPO)", - "Phenotypic abnormality (HPO)", - "Abnormality of the musculature (HPO)", - "Exercise intolerance (HPO)", - "Functional motor deficit (HPO)", - "Abnormal muscle physiology (HPO)", - "Abnormality of the musculoskeletal system (HPO)", - "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", - ], - "object_label": "Exercise intolerance (HPO)", - "evidence_count": 0, + "Mode of inheritance (HPO)", + "Autosomal dominant inheritance (HPO)", + "Mendelian inheritance", + ], + "object_label": "Autosomal dominant inheritance (HPO)", + "evidence_count": 4, }, { - "id": "uuid:1e041fb7-1e4f-11ee-871a-692638b4c502", - "original_subject": "OMIM:158900", - "predicate": "biolink:has_phenotype", - "category": "biolink:DiseaseToPhenotypicFeatureAssociation", + "id": "uuid:c3cdad58-212f-11ee-873a-cd90a19c4085", + "original_subject": "OMIM:159050", + "predicate": "biolink:has_mode_of_inheritance", + "category": "biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation", "aggregator_knowledge_source": ["infores:monarchinitiative"], - "has_evidence": "ECO:0000304", - "primary_knowledge_source": ["infores:hpo-annotations"], - "provided_by": "hpoa_disease_phenotype_edges", - "publications": ["OMIM:158900"], - "subject": "MONDO:0008030", - "object": "HP:0003547", + "has_evidence": ["ECO:0000501"], + "primary_knowledge_source": "infores:hpo-annotations", + "provided_by": "hpoa_disease_mode_of_inheritance_edges", + "publications": ["OMIM:159050"], + "subject": "MONDO:0008034", + "object": "HP:0000006", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ - "MONDO:0008030", + "MONDO:0004994", "MONDO:0000001", - "MONDO:0019303", - "MONDO:0100167", + "MONDO:0008034", "MONDO:0005071", + "MONDO:0016147", + "MONDO:0005267", "MONDO:0020121", + "MONDO:0004995", "MONDO:0700223", - "MONDO:0001347", - "MONDO:0020573", "BFO:0000002", "BFO:0000017", "BFO:0000020", + "MONDO:0010542", "MONDO:0016106", - "MONDO:0042489", - "MONDO:0100137", + "MONDO:0015470", + "MONDO:0005217", + "MONDO:0016899", "BFO:0000016", "MONDO:0020120", "MONDO:0019056", + "MONDO:0016139", "MONDO:0700096", + "MONDO:0000591", "MONDO:0005218", "MONDO:0005336", "MONDO:0002081", - "MONDO:0021147", + "MONDO:0016333", "OGMS:0000031", + "MONDO:0005021", "MONDO:0003847", "MONDO:0003939", "BFO:0000001", + "MONDO:0010311", ], "subject_closure_label": [ "disease or disorder", - "facioscapulohumeral muscular dystrophy", + "intrinsic cardiomyopathy", "musculoskeletal system disorder", "hereditary disease", "muscle tissue disorder", + "cardiomyopathy", + "cardiovascular disorder", + "dilated cardiomyopathy", "nervous system disorder", + "familial cardiomyopathy", "obsolete muscular disorder", + "heart disorder", "myopathy", - "facioscapulohumeral muscular dystrophy 1", + "muscular dystrophy, pseudohypertrophic, with Internalized capillaries", + "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", - "premature aging syndrome", "skeletal muscle disorder", "muscular dystrophy", - "inherited disease susceptibility", - "disorder of development or morphogenesis", - "disease susceptibility", - "telomere syndrome", - "pulmonary disease, chronic obstructive, susceptibility to", "human disease or disorder", "hereditary skeletal muscle disorder", ], - "subject_label": "facioscapulohumeral muscular dystrophy 1", + "subject_label": "muscular dystrophy, pseudohypertrophic, with Internalized capillaries", "object_namespace": "HP", - "object_category": "biolink:PhenotypicQuality", + "object_category": "biolink:GeneticInheritance", "object_closure": [ "HP:0000001", - "UPHENO:0002649", - "UPHENO:0082875", - "UPHENO:0075696", - "UPHENO:0002320", - "UPHENO:0001001", - "HP:0003325", - "UPHENO:0080565", - "HP:0009127", - "UPHENO:0001005", - "HP:0011805", - "UPHENO:0001002", - "HP:0001324", - "HP:0000118", - "BFO:0000002", - "HP:0001435", - "HP:0001446", - "HP:0002817", - "BFO:0000020", - "UPHENO:0080555", - "HP:0003011", - "UPHENO:0002816", - "UPHENO:0002332", - "UPHENO:0080556", - "UPHENO:0002982", - "UPHENO:0081581", - "HP:0003547", - "HP:0033127", - "UPHENO:0001003", - "UPHENO:0002536", - "UPHENO:0076692", - "UPHENO:0002647", - "UPHENO:0076710", - "HP:0040064", - "BFO:0000001", - "HP:0011804", - "PATO:0000001", - "UPHENO:0002880", - "UPHENO:0002830", - "BFO:0000001", - "BFO:0000002", - "BFO:0000004", - "BFO:0000040", - "UBERON:0001062", - "CARO:0000000", - "UBERON:0000465", - "PR:000050567", - "RO:0002577", - "UBERON:0001015", - "UBERON:0000383", - "CARO:0000006", - "UBERON:0006058", - "UBERON:0010538", - "UBERON:0018254", - "UBERON:0005090", - "UBERON:0000061", - "UBERON:0004708", - "UBERON:0007271", - "UBERON:0014793", - "CARO:0000003", - "UBERON:0001460", - "UBERON:0002529", - "UBERON:0001630", - "UBERON:0010000", - "UBERON:0000467", - "UBERON:0015212", - "UBERON:0004710", - "UBERON:0002101", - "UBERON:0004480", - "UBERON:0007269", - "UBERON:0004471", - "UBERON:0007823", - "UBERON:0010708", - "UBERON:0008785", - "UBERON:0014892", - "UBERON:0000468", - "UBERON:0000475", - "UBERON:0000062", - "UBERON:0011216", - "UBERON:0001421", - "UBERON:0010707", - "UBERON:0002102", - "UBERON:0004481", - "UBERON:0010891", - "UBERON:0000153", - "UBERON:0000026", - "UBERON:0010758", - "UBERON:0008196", + "HP:0000006", + "HP:0000005", + "HP:0034345", ], "object_closure_label": [ "All (HPO)", - "Phenotypic abnormality (HPO)", - "Muscle weakness (HPO)", - "Abnormality of the shoulder girdle musculature (HPO)", - "Abnormality of the musculature of the upper limbs (HPO)", - "Abnormality of the upper limb (HPO)", - "Abnormality of the musculature (HPO)", - "Limb-girdle muscle weakness (HPO)", - "Shoulder girdle muscle weakness (HPO)", - "Abnormality of the musculature of the limbs (HPO)", - "Abnormal muscle physiology (HPO)", - "Abnormal skeletal muscle morphology (HPO)", - "Abnormality of the musculoskeletal system (HPO)", - "Abnormality of limbs (HPO)", - "appendage", - "anatomical structure", - "organ", - "anterior region of body", - "musculature of body", - "material anatomical entity", - "anatomical system", - "multicellular organism", - "organism subdivision", - "musculature", - "anatomical entity", - "pectoral girdle region", - "arm", - "muscle organ", - "limb", - "forelimb", - "limb segment", - "musculature of pectoral girdle", - "musculature of limb", - "musculature of upper limb", - "paired limb/fin", - "pectoral appendage", - "muscle structure", - "multi-limb segment region", - "pectoral appendage musculature", - "appendage musculature", - "appendage girdle region", - "muscle of pectoral girdle", - "upper limb segment", - "multicellular anatomical structure", - "paired limb/fin segment", - "appendage girdle complex", - "pectoral complex", - "subdivision of organism along appendicular axis", - "pectoral complex muscle", - "organ system subdivision", - "musculature of pectoral complex", - "skeletal muscle organ", - "lateral structure", - "skeletal musculature", - ], - "object_label": "Shoulder girdle muscle weakness (HPO)", - "evidence_count": 0, + "Mode of inheritance (HPO)", + "Autosomal dominant inheritance (HPO)", + "Mendelian inheritance", + ], + "object_label": "Autosomal dominant inheritance (HPO)", + "evidence_count": 4, }, { - "id": "uuid:1ae78897-1e4f-11ee-871a-692638b4c502", - "original_subject": "OMIM:254110", - "predicate": "biolink:has_phenotype", - "category": "biolink:DiseaseToPhenotypicFeatureAssociation", + "id": "uuid:c3367408-212f-11ee-873a-cd90a19c4085", + "original_subject": "OMIM:160300", + "predicate": "biolink:has_mode_of_inheritance", + "category": "biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation", "aggregator_knowledge_source": ["infores:monarchinitiative"], - "has_evidence": "ECO:0000501", - "primary_knowledge_source": ["infores:hpo-annotations"], - "provided_by": "hpoa_disease_phenotype_edges", - "publications": ["OMIM:254110"], - "subject": "MONDO:0009683", - "object": "HP:0003547", + "has_evidence": ["ECO:0000304"], + "primary_knowledge_source": "infores:hpo-annotations", + "provided_by": "hpoa_disease_mode_of_inheritance_edges", + "publications": ["OMIM:160300"], + "subject": "MONDO:0008049", + "object": "HP:0000006", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ "MONDO:0000001", - "MONDO:0016971", - "MONDO:0000429", - "MONDO:0100167", "MONDO:0005071", "MONDO:0020121", "MONDO:0700223", - "MONDO:0020573", "BFO:0000002", "BFO:0000017", + "MONDO:0008049", "BFO:0000020", - "MONDO:0006025", - "MONDO:0016106", - "MONDO:0042489", "BFO:0000016", "MONDO:0020120", "MONDO:0019056", - "MONDO:0016139", "MONDO:0700096", "MONDO:0005218", "MONDO:0005336", @@ -616,216 +297,71 @@ def association_response(): "MONDO:0003847", "MONDO:0003939", "BFO:0000001", - "MONDO:0015152", - "MONDO:0016153", - "MONDO:0009683", + "MONDO:0018949", ], "subject_closure_label": [ "disease or disorder", - "autosomal genetic disease", "musculoskeletal system disorder", "hereditary disease", "muscle tissue disorder", "nervous system disorder", "obsolete muscular 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", + "myopathy, distal, infantile-onset", + "distal myopathy", "neuromuscular disease", "skeletal muscle disorder", "muscular dystrophy", - "inherited disease susceptibility", - "disease susceptibility", - "pulmonary disease, chronic obstructive, susceptibility to", "human disease or disorder", "hereditary skeletal muscle disorder", ], - "subject_label": "autosomal recessive limb-girdle muscular dystrophy type 2H", + "subject_label": "myopathy, distal, infantile-onset", "object_namespace": "HP", - "object_category": "biolink:PhenotypicQuality", + "object_category": "biolink:GeneticInheritance", "object_closure": [ "HP:0000001", - "UPHENO:0002649", - "UPHENO:0082875", - "UPHENO:0075696", - "UPHENO:0002320", - "UPHENO:0001001", - "HP:0003325", - "UPHENO:0080565", - "HP:0009127", - "UPHENO:0001005", - "HP:0011805", - "UPHENO:0001002", - "HP:0001324", - "HP:0000118", - "BFO:0000002", - "HP:0001435", - "HP:0001446", - "HP:0002817", - "BFO:0000020", - "UPHENO:0080555", - "HP:0003011", - "UPHENO:0002816", - "UPHENO:0002332", - "UPHENO:0080556", - "UPHENO:0002982", - "UPHENO:0081581", - "HP:0003547", - "HP:0033127", - "UPHENO:0001003", - "UPHENO:0002536", - "UPHENO:0076692", - "UPHENO:0002647", - "UPHENO:0076710", - "HP:0040064", - "BFO:0000001", - "HP:0011804", - "PATO:0000001", - "UPHENO:0002880", - "UPHENO:0002830", - "BFO:0000001", - "BFO:0000002", - "BFO:0000004", - "BFO:0000040", - "UBERON:0001062", - "CARO:0000000", - "UBERON:0000465", - "PR:000050567", - "RO:0002577", - "UBERON:0001015", - "UBERON:0000383", - "CARO:0000006", - "UBERON:0006058", - "UBERON:0010538", - "UBERON:0018254", - "UBERON:0005090", - "UBERON:0000061", - "UBERON:0004708", - "UBERON:0007271", - "UBERON:0014793", - "CARO:0000003", - "UBERON:0001460", - "UBERON:0002529", - "UBERON:0001630", - "UBERON:0010000", - "UBERON:0000467", - "UBERON:0015212", - "UBERON:0004710", - "UBERON:0002101", - "UBERON:0004480", - "UBERON:0007269", - "UBERON:0004471", - "UBERON:0007823", - "UBERON:0010708", - "UBERON:0008785", - "UBERON:0014892", - "UBERON:0000468", - "UBERON:0000475", - "UBERON:0000062", - "UBERON:0011216", - "UBERON:0001421", - "UBERON:0010707", - "UBERON:0002102", - "UBERON:0004481", - "UBERON:0010891", - "UBERON:0000153", - "UBERON:0000026", - "UBERON:0010758", - "UBERON:0008196", + "HP:0000006", + "HP:0000005", + "HP:0034345", ], "object_closure_label": [ "All (HPO)", - "Phenotypic abnormality (HPO)", - "Muscle weakness (HPO)", - "Abnormality of the shoulder girdle musculature (HPO)", - "Abnormality of the musculature of the upper limbs (HPO)", - "Abnormality of the upper limb (HPO)", - "Abnormality of the musculature (HPO)", - "Limb-girdle muscle weakness (HPO)", - "Shoulder girdle muscle weakness (HPO)", - "Abnormality of the musculature of the limbs (HPO)", - "Abnormal muscle physiology (HPO)", - "Abnormal skeletal muscle morphology (HPO)", - "Abnormality of the musculoskeletal system (HPO)", - "Abnormality of limbs (HPO)", - "appendage", - "anatomical structure", - "organ", - "anterior region of body", - "musculature of body", - "material anatomical entity", - "anatomical system", - "multicellular organism", - "organism subdivision", - "musculature", - "anatomical entity", - "pectoral girdle region", - "arm", - "muscle organ", - "limb", - "forelimb", - "limb segment", - "musculature of pectoral girdle", - "musculature of limb", - "musculature of upper limb", - "paired limb/fin", - "pectoral appendage", - "muscle structure", - "multi-limb segment region", - "pectoral appendage musculature", - "appendage musculature", - "appendage girdle region", - "muscle of pectoral girdle", - "upper limb segment", - "multicellular anatomical structure", - "paired limb/fin segment", - "appendage girdle complex", - "pectoral complex", - "subdivision of organism along appendicular axis", - "pectoral complex muscle", - "organ system subdivision", - "musculature of pectoral complex", - "skeletal muscle organ", - "lateral structure", - "skeletal musculature", - ], - "object_label": "Shoulder girdle muscle weakness (HPO)", - "evidence_count": 0, + "Mode of inheritance (HPO)", + "Autosomal dominant inheritance (HPO)", + "Mendelian inheritance", + ], + "object_label": "Autosomal dominant inheritance (HPO)", + "evidence_count": 4, }, { - "id": "uuid:1e041dff-1e4f-11ee-871a-692638b4c502", - "original_subject": "OMIM:310095", - "predicate": "biolink:has_phenotype", - "category": "biolink:DiseaseToPhenotypicFeatureAssociation", + "id": "uuid:c39b4534-212f-11ee-873a-cd90a19c4085", + "original_subject": "OMIM:160500", + "predicate": "biolink:has_mode_of_inheritance", + "category": "biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation", "aggregator_knowledge_source": ["infores:monarchinitiative"], - "has_evidence": "ECO:0000501", - "primary_knowledge_source": ["infores:hpo-annotations"], - "provided_by": "hpoa_disease_phenotype_edges", - "publications": ["OMIM:310095"], - "subject": "MONDO:0010678", - "object": "HP:0003547", + "has_evidence": ["ECO:0000269"], + "primary_knowledge_source": "infores:hpo-annotations", + "provided_by": "hpoa_disease_mode_of_inheritance_edges", + "publications": ["PMID:15322983"], + "subject": "MONDO:0008050", + "object": "HP:0000006", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ "MONDO:0000001", - "MONDO:0100167", "MONDO:0005071", "MONDO:0020121", - "MONDO:0010678", "MONDO:0700223", - "MONDO:0020573", "BFO:0000002", + "MONDO:0019952", "BFO:0000017", "BFO:0000020", - "MONDO:0042489", + "MONDO:0008050", + "MONDO:0016195", "BFO:0000016", "MONDO:0020120", "MONDO:0019056", + "MONDO:0016139", "MONDO:0700096", "MONDO:0005218", "MONDO:0005336", @@ -834,657 +370,257 @@ def association_response(): "MONDO:0003847", "MONDO:0003939", "BFO:0000001", + "MONDO:0002320", + "MONDO:0018949", ], "subject_closure_label": [ "disease or disorder", "musculoskeletal system disorder", + "congenital nervous system disorder", "hereditary disease", "muscle tissue disorder", "nervous system disorder", "obsolete muscular disorder", "myopathy", - "muscular dystrophy, progressive Pectorodorsal", + "MYH7-related skeletal myopathy", + "qualitative or quantitative protein defects in neuromuscular diseases", + "qualitative or quantitative defects of beta-myosin heavy chain (MYH7)", + "distal myopathy", "neuromuscular disease", + "congenital myopathy", "skeletal muscle disorder", "muscular dystrophy", - "inherited disease susceptibility", - "disease susceptibility", - "pulmonary disease, chronic obstructive, susceptibility to", "human disease or disorder", "hereditary skeletal muscle disorder", ], - "subject_label": "muscular dystrophy, progressive Pectorodorsal", + "subject_label": "MYH7-related skeletal myopathy", "object_namespace": "HP", - "object_category": "biolink:PhenotypicQuality", + "object_category": "biolink:GeneticInheritance", "object_closure": [ "HP:0000001", - "UPHENO:0002649", - "UPHENO:0082875", - "UPHENO:0075696", - "UPHENO:0002320", - "UPHENO:0001001", - "HP:0003325", - "UPHENO:0080565", - "HP:0009127", - "UPHENO:0001005", - "HP:0011805", - "UPHENO:0001002", - "HP:0001324", - "HP:0000118", - "BFO:0000002", - "HP:0001435", - "HP:0001446", - "HP:0002817", - "BFO:0000020", - "UPHENO:0080555", - "HP:0003011", - "UPHENO:0002816", - "UPHENO:0002332", - "UPHENO:0080556", - "UPHENO:0002982", - "UPHENO:0081581", - "HP:0003547", - "HP:0033127", - "UPHENO:0001003", - "UPHENO:0002536", - 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"congenital muscular dystrophy", "skeletal muscle disorder", "muscular dystrophy", - "inherited disease susceptibility", - "disease susceptibility", - "pulmonary disease, chronic obstructive, susceptibility to", + "eyelids malposition disorder", + "disorder of visual system", "human disease or disorder", "hereditary skeletal muscle disorder", ], - "subject_label": "congenital muscular dystrophy 1B", + "subject_label": "oculopharyngeal muscular dystrophy", "object_namespace": "HP", - "object_category": "biolink:PhenotypicQuality", + "object_category": "biolink:GeneticInheritance", "object_closure": [ "HP:0000001", - "UPHENO:0002649", - "UPHENO:0082875", - "UPHENO:0075696", - "UPHENO:0002320", - "UPHENO:0001001", - "HP:0003325", - "UPHENO:0080565", - "HP:0009127", - "UPHENO:0001005", - "HP:0011805", - "UPHENO:0001002", - "HP:0001324", - "HP:0000118", - "BFO:0000002", - "HP:0001435", - "HP:0001446", - "HP:0002817", - "BFO:0000020", - "UPHENO:0080555", - "HP:0003011", - "UPHENO:0002816", - 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"musculature of body", - "material anatomical entity", - "anatomical system", - "multicellular organism", - "organism subdivision", - "musculature", - "anatomical entity", - "pectoral girdle region", - "arm", - "muscle organ", - "limb", - "forelimb", - "limb segment", - "musculature of pectoral girdle", - "musculature of limb", - "musculature of upper limb", - "paired limb/fin", - "pectoral appendage", - "muscle structure", - "multi-limb segment region", - "pectoral appendage musculature", - "appendage musculature", - "appendage girdle region", - "muscle of pectoral girdle", - "upper limb segment", - "multicellular anatomical structure", - "paired limb/fin segment", - "appendage girdle complex", - "pectoral complex", - "subdivision of organism along appendicular axis", - "pectoral complex muscle", - "organ system subdivision", - "musculature of pectoral complex", - "skeletal muscle organ", - "lateral structure", - "skeletal musculature", - ], - "object_label": "Shoulder girdle muscle weakness (HPO)", - "evidence_count": 0, + "Mode of inheritance (HPO)", + "Autosomal dominant inheritance (HPO)", + "Mendelian inheritance", + ], + "object_label": "Autosomal dominant inheritance (HPO)", + "evidence_count": 4, }, { - "id": "uuid:19006798-1e4f-11ee-871a-692638b4c502", - "original_subject": "OMIM:607155", - "predicate": "biolink:has_phenotype", - "category": "biolink:DiseaseToPhenotypicFeatureAssociation", + "id": "uuid:c3cdaddf-212f-11ee-873a-cd90a19c4085", + "original_subject": "OMIM:254090", + "predicate": "biolink:has_mode_of_inheritance", + "category": "biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation", "aggregator_knowledge_source": ["infores:monarchinitiative"], - "has_evidence": "ECO:0000501", - "primary_knowledge_source": ["infores:hpo-annotations"], - "provided_by": "hpoa_disease_phenotype_edges", - "publications": ["OMIM:607155"], - "subject": "MONDO:0011787", - "object": "HP:0003547", + "has_evidence": ["ECO:0000501"], + "primary_knowledge_source": "infores:hpo-annotations", + "provided_by": "hpoa_disease_mode_of_inheritance_edges", + "publications": ["OMIM:254090"], + "subject": "MONDO:0009681", + "object": "HP:0000006", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ - "MONDO:0018282", "MONDO:0000001", - "MONDO:0016971", - "MONDO:0017741", - "MONDO:0000429", - "MONDO:0045010", - "MONDO:0100167", "MONDO:0005071", "MONDO:0020121", "MONDO:0700223", - "MONDO:0011787", - "MONDO:0024322", - "MONDO:0020573", "BFO:0000002", + "MONDO:0019952", "BFO:0000017", "BFO:0000020", - "MONDO:0006025", - "MONDO:0016106", - "MONDO:0016157", - "MONDO:0042489", - "MONDO:0017745", + "MONDO:0100225", "BFO:0000016", "MONDO:0020120", "MONDO:0019056", @@ -1493,1173 +629,530 @@ def association_response(): "MONDO:0005218", "MONDO:0005336", "MONDO:0002081", - "MONDO:0016156", + "MONDO:0009681", "OGMS:0000031", "MONDO:0003847", "MONDO:0003939", - "MONDO:0015286", "BFO:0000001", - "MONDO:0015152", "MONDO:0002320", - "MONDO:0019052", - "MONDO:0005066", - "MONDO:0016155", - "MONDO:0700066", + "MONDO:0000355", + "MONDO:0019950", ], "subject_closure_label": [ "disease or disorder", - "autosomal genetic disease", + "Ullrich congenital muscular dystrophy", "musculoskeletal system disorder", "congenital nervous system disorder", "hereditary disease", "muscle tissue disorder", - "metabolic disease", "nervous system disorder", "obsolete muscular disorder", "myopathy", - "autosomal recessive disease", - "autosomal recessive limb-girdle muscular dystrophy type 2I", - "autosomal recessive limb-girdle muscular dystrophy", - "congenital disorder of glycosylation", - "progressive muscular dystrophy", + "Ullrich congenital muscular dystrophy 1", "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", - "limb-girdle muscular dystrophy", - "disorder of protein O-glycosylation", - "disorder of O-mannosylglycan synthesis", - "qualitative or quantitative defects of alpha-dystroglycan", - "inborn errors of metabolism", "neuromuscular disease", + "congenital muscular dystrophy", + "congenital myopathy", "skeletal muscle disorder", "muscular dystrophy", - "inherited disease susceptibility", - "disorder of glycosylation", - "disease susceptibility", - "glycoprotein metabolism disease", - "pulmonary disease, chronic obstructive, susceptibility to", - "myopathy caused by variation in FKRP", + "collagen 6-related myopathy", "human disease or disorder", "hereditary skeletal muscle disorder", ], - "subject_label": "autosomal recessive limb-girdle muscular dystrophy type 2I", + "subject_label": "Ullrich congenital muscular dystrophy 1", "object_namespace": "HP", - "object_category": "biolink:PhenotypicQuality", + "object_category": "biolink:GeneticInheritance", "object_closure": [ "HP:0000001", - "UPHENO:0002649", - "UPHENO:0082875", - "UPHENO:0075696", - "UPHENO:0002320", - "UPHENO:0001001", - "HP:0003325", - "UPHENO:0080565", - "HP:0009127", - "UPHENO:0001005", - "HP:0011805", - "UPHENO:0001002", - "HP:0001324", - "HP:0000118", - "BFO:0000002", - "HP:0001435", - "HP:0001446", - "HP:0002817", - "BFO:0000020", - "UPHENO:0080555", - "HP:0003011", - "UPHENO:0002816", - "UPHENO:0002332", - 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"inherited disease susceptibility", - "disease susceptibility", - "pulmonary disease, chronic obstructive, susceptibility to", "human disease or disorder", "hereditary skeletal muscle disorder", ], - "subject_label": "autosomal dominant limb-girdle muscular dystrophy type 1G", + "subject_label": "muscular dystrophy, Hemizygous lethal type", "object_namespace": "HP", - "object_category": "biolink:PhenotypicQuality", + "object_category": "biolink:GeneticInheritance", "object_closure": [ "HP:0000001", - "UPHENO:0002649", - "UPHENO:0082875", - "UPHENO:0075696", - "UPHENO:0002320", - "UPHENO:0001001", - "HP:0003325", - "UPHENO:0080565", - "HP:0009127", - "UPHENO:0001005", - "HP:0011805", - "UPHENO:0001002", - "HP:0001324", - "HP:0000118", - "BFO:0000002", - "HP:0001435", - "HP:0001446", - "HP:0002817", - "BFO:0000020", - "UPHENO:0080555", - "HP:0003011", - "UPHENO:0002816", - "UPHENO:0002332", - "UPHENO:0080556", - "UPHENO:0002982", - "UPHENO:0081581", - "HP:0003547", - "HP:0033127", - "UPHENO:0001003", - 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"MONDO:0016971", "MONDO:0000429", - "MONDO:0100167", "MONDO:0005071", "MONDO:0020121", + "MONDO:0100175", "MONDO:0700223", - "MONDO:0020573", "BFO:0000002", + "MONDO:0019952", "BFO:0000017", "BFO:0000020", - "MONDO:0006025", - "MONDO:0016106", - "MONDO:0042489", + "MONDO:0016191", "BFO:0000016", - "MONDO:0012652", "MONDO:0020120", "MONDO:0019056", + "MONDO:0100494", + "MONDO:0016139", "MONDO:0700096", "MONDO:0005218", "MONDO:0005336", "MONDO:0002081", + "MONDO:0000426", "OGMS:0000031", "MONDO:0003847", "MONDO:0003939", "BFO:0000001", - "MONDO:0015152", + "MONDO:0002320", + "MONDO:0016108", + "MONDO:0018949", ], "subject_closure_label": [ "disease or disorder", + "autosomal dominant disease", "autosomal genetic disease", "musculoskeletal system disorder", + "congenital nervous system disorder", "hereditary disease", "muscle tissue disorder", "nervous system disorder", "obsolete muscular disorder", "myopathy", - "autosomal recessive disease", - "autosomal recessive limb-girdle muscular dystrophy type 2L", - 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"MONDO:0016192", "MONDO:0003847", "MONDO:0003939", "BFO:0000001", - "MONDO:0015152", + "MONDO:0016108", + "MONDO:0018949", ], "subject_closure_label": [ "disease or disorder", + "autosomal dominant disease", "autosomal genetic disease", "musculoskeletal system disorder", "hereditary disease", @@ -2667,974 +1160,560 @@ def association_response(): "nervous system disorder", "obsolete muscular disorder", "myopathy", - "autosomal recessive disease", - "autosomal recessive limb-girdle muscular dystrophy type 2G", - "autosomal recessive limb-girdle muscular dystrophy", - "progressive muscular dystrophy", - "qualitative or quantitative protein defects in neuromuscular diseases", - "qualitative or quantitative defects of telethonin", - "limb-girdle muscular dystrophy", + "distal myopathy, Welander type", + "autosomal dominant distal myopathy", + "distal myopathy", "neuromuscular disease", "skeletal muscle disorder", "muscular dystrophy", - "inherited disease susceptibility", - "disease susceptibility", - "pulmonary disease, chronic obstructive, susceptibility to", "human disease or disorder", "hereditary skeletal muscle disorder", ], - "subject_label": "autosomal recessive limb-girdle muscular dystrophy type 2G", + "subject_label": "distal myopathy, Welander type", "object_namespace": "HP", - "object_category": "biolink:PhenotypicQuality", + "object_category": "biolink:GeneticInheritance", "object_closure": [ "HP:0000001", - "UPHENO:0082875", - "UPHENO:0075696", - "UPHENO:0002320", - "UPHENO:0001001", - "HP:0003551", - "UPHENO:0001005", - "UPHENO:0001002", - "HP:0004302", - "HP:0000118", - "BFO:0000002", - "BFO:0000020", - "HP:0003011", - "UPHENO:0002816", - "UPHENO:0002332", - "HP:0033127", - "UPHENO:0001003", - "UPHENO:0002536", - "BFO:0000001", - "HP:0011804", - "PATO:0000001", - "BFO:0000001", - "BFO:0000002", - "BFO:0000004", - "BFO:0000040", - "UBERON:0001062", - "CARO:0000000", - "UBERON:0000465", - "UBERON:0001015", - "UBERON:0000383", - "UBERON:0005090", - "UBERON:0000061", - "UBERON:0001630", - "UBERON:0010000", - "UBERON:0000467", - "UBERON:0000468", - "UBERON:0000062", - "UBERON:0011216", + "HP:0000006", + "HP:0000005", + "HP:0034345", ], "object_closure_label": [ "All (HPO)", - "Phenotypic abnormality (HPO)", - "Abnormality of the musculature (HPO)", - "Difficulty climbing stairs (HPO)", - "Functional motor deficit (HPO)", - "Abnormal muscle physiology (HPO)", - "Abnormality of the musculoskeletal system (HPO)", - "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", - ], - "object_label": "Difficulty climbing stairs (HPO)", - "evidence_count": 0, + "Mode of inheritance (HPO)", + "Autosomal dominant inheritance (HPO)", + "Mendelian inheritance", + ], + "object_label": "Autosomal dominant inheritance (HPO)", + "evidence_count": 4, }, { - "id": "uuid:1bce01b5-1e4f-11ee-871a-692638b4c502", - "original_subject": "OMIM:606612", - "predicate": "biolink:has_phenotype", - "category": "biolink:DiseaseToPhenotypicFeatureAssociation", + "id": "uuid:c367df64-212f-11ee-873a-cd90a19c4085", + "original_subject": "OMIM:608423", + "predicate": "biolink:has_mode_of_inheritance", + "category": "biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation", "aggregator_knowledge_source": ["infores:monarchinitiative"], - "has_evidence": "ECO:0000269", - "primary_knowledge_source": ["infores:hpo-annotations"], - "provided_by": "hpoa_disease_phenotype_edges", - "publications": ["PMID:11592034"], - "subject": "MONDO:0011688", - "object": "HP:0003551", + "has_evidence": ["ECO:0000269"], + "primary_knowledge_source": "infores:hpo-annotations", + "provided_by": "hpoa_disease_mode_of_inheritance_edges", + "publications": ["PMID:23543484"], + "subject": "MONDO:0012034", + "object": "HP:0000006", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ - "MONDO:0018282", "MONDO:0000001", - "MONDO:0017741", - "MONDO:0018276", - "MONDO:0045010", - "MONDO:0100167", + "MONDO:0016971", + "MONDO:0000429", "MONDO:0005071", "MONDO:0020121", - "MONDO:0000172", "MONDO:0700223", - "MONDO:0024322", - "MONDO:0020573", + "MONDO:0012034", "BFO:0000002", "BFO:0000017", "BFO:0000020", - "MONDO:0016157", - "MONDO:0042489", + "MONDO:0016106", "BFO:0000016", "MONDO:0020120", "MONDO:0019056", - "MONDO:0016139", + "MONDO:0015151", "MONDO:0700096", "MONDO:0005218", "MONDO:0005336", "MONDO:0002081", + "MONDO:0000426", "OGMS:0000031", "MONDO:0003847", "MONDO:0003939", - "MONDO:0015286", "BFO:0000001", - "MONDO:0002320", - "MONDO:0019052", - "MONDO:0005066", - "MONDO:0019950", - "MONDO:0016155", - "MONDO:0011688", - "MONDO:0700066", ], "subject_closure_label": [ "disease or disorder", - "muscular dystrophy-dystroglycanopathy, type B", + "autosomal dominant disease", + "autosomal genetic disease", "musculoskeletal system disorder", - "congenital nervous system disorder", "hereditary disease", "muscle tissue disorder", - "metabolic disease", "nervous system disorder", "obsolete muscular disorder", "myopathy", - "muscular dystrophy-dystroglycanopathy type B5", - "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", - "qualitative or quantitative defects of fukutin", - "disorder of protein O-glycosylation", - "muscular dystrophy-dystroglycanopathy", - "qualitative or quantitative defects of alpha-dystroglycan", - "inborn errors of metabolism", + "autosomal dominant limb-girdle muscular dystrophy type 1F", + "muscular dystrophy, limb-girdle, autosomal dominant", + "progressive muscular dystrophy", + "limb-girdle muscular dystrophy", "neuromuscular disease", - "congenital muscular dystrophy", "skeletal muscle disorder", "muscular dystrophy", - "inherited disease susceptibility", - "disorder of glycosylation", - "disease susceptibility", - "glycoprotein metabolism disease", - "pulmonary disease, chronic obstructive, susceptibility to", - "myopathy caused by variation in FKRP", "human disease or disorder", "hereditary skeletal muscle disorder", ], - "subject_label": "muscular dystrophy-dystroglycanopathy type B5", + "subject_label": "autosomal dominant limb-girdle muscular dystrophy type 1F", "object_namespace": "HP", - "object_category": "biolink:PhenotypicQuality", + "object_category": "biolink:GeneticInheritance", "object_closure": [ "HP:0000001", - "UPHENO:0082875", - "UPHENO:0075696", - "UPHENO:0002320", - "UPHENO:0001001", - "HP:0003551", - "UPHENO:0001005", - "UPHENO:0001002", - "HP:0004302", - "HP:0000118", - "BFO:0000002", - "BFO:0000020", - "HP:0003011", - "UPHENO:0002816", - "UPHENO:0002332", - "HP:0033127", - "UPHENO:0001003", - "UPHENO:0002536", - "BFO:0000001", - "HP:0011804", - "PATO:0000001", - "BFO:0000001", - "BFO:0000002", - "BFO:0000004", - "BFO:0000040", - "UBERON:0001062", - "CARO:0000000", - "UBERON:0000465", - "UBERON:0001015", - "UBERON:0000383", - "UBERON:0005090", - "UBERON:0000061", - "UBERON:0001630", - "UBERON:0010000", - "UBERON:0000467", - "UBERON:0000468", - "UBERON:0000062", - "UBERON:0011216", + "HP:0000006", + "HP:0000005", + "HP:0034345", ], "object_closure_label": [ "All (HPO)", - "Phenotypic abnormality (HPO)", - "Abnormality of the musculature (HPO)", - "Difficulty climbing stairs (HPO)", - "Functional motor deficit (HPO)", - "Abnormal muscle physiology (HPO)", - "Abnormality of the musculoskeletal system (HPO)", - "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", - ], - "object_label": "Difficulty climbing stairs (HPO)", - "evidence_count": 0, + "Mode of inheritance (HPO)", + "Autosomal dominant inheritance (HPO)", + "Mendelian inheritance", + ], + "object_label": "Autosomal dominant inheritance (HPO)", + "evidence_count": 4, }, { - "id": "uuid:19006790-1e4f-11ee-871a-692638b4c502", - "original_subject": "OMIM:607155", - "predicate": "biolink:has_phenotype", - "category": "biolink:DiseaseToPhenotypicFeatureAssociation", + "id": "uuid:c3367251-212f-11ee-873a-cd90a19c4085", + "original_subject": "OMIM:608810", + "predicate": "biolink:has_mode_of_inheritance", + "category": "biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation", "aggregator_knowledge_source": ["infores:monarchinitiative"], - "has_evidence": "ECO:0000501", - "primary_knowledge_source": ["infores:hpo-annotations"], - "provided_by": "hpoa_disease_phenotype_edges", - "publications": ["OMIM:607155"], - "subject": "MONDO:0011787", - "object": "HP:0003551", + "has_evidence": ["ECO:0000269"], + "primary_knowledge_source": "infores:hpo-annotations", + "provided_by": "hpoa_disease_mode_of_inheritance_edges", + "publications": ["PMID:14681890"], + "subject": "MONDO:0012130", + "object": "HP:0000006", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ - "MONDO:0018282", "MONDO:0000001", - "MONDO:0016971", - "MONDO:0017741", + "MONDO:0016186", "MONDO:0000429", - "MONDO:0045010", - "MONDO:0100167", "MONDO:0005071", "MONDO:0020121", + "MONDO:0018943", "MONDO:0700223", - "MONDO:0011787", - "MONDO:0024322", - "MONDO:0020573", "BFO:0000002", + "MONDO:0019952", "BFO:0000017", "BFO:0000020", - "MONDO:0006025", - "MONDO:0016106", - "MONDO:0016157", - "MONDO:0042489", - "MONDO:0017745", + "MONDO:0020343", "BFO:0000016", "MONDO:0020120", "MONDO:0019056", "MONDO:0016139", "MONDO:0700096", + "MONDO:0002921", "MONDO:0005218", "MONDO:0005336", "MONDO:0002081", - "MONDO:0016156", + "MONDO:0012130", + "MONDO:0000426", "OGMS:0000031", "MONDO:0003847", "MONDO:0003939", - "MONDO:0015286", "BFO:0000001", - "MONDO:0015152", "MONDO:0002320", - "MONDO:0019052", - "MONDO:0005066", - "MONDO:0016155", - "MONDO:0700066", + "MONDO:0016188", + "MONDO:0016108", + "MONDO:0018949", ], "subject_closure_label": [ "disease or disorder", + "autosomal dominant disease", "autosomal genetic disease", "musculoskeletal system disorder", "congenital nervous system disorder", + "congenital structural myopathy", "hereditary disease", "muscle tissue disorder", - "metabolic disease", "nervous system disorder", "obsolete muscular disorder", "myopathy", - "autosomal recessive disease", - "autosomal recessive limb-girdle muscular dystrophy type 2I", - "autosomal recessive limb-girdle muscular dystrophy", - "congenital disorder of glycosylation", - "progressive muscular dystrophy", + "myofibrillar myopathy 2", + "autosomal dominant distal myopathy", "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", - "limb-girdle muscular dystrophy", - "disorder of protein O-glycosylation", - "disorder of O-mannosylglycan synthesis", - "qualitative or quantitative defects of alpha-dystroglycan", - "inborn errors of metabolism", + "qualitative or quantitative defects of myofibrillar proteins", + "qualitative or quantitative defects of alphaB-cristallin", + "myofibrillar myopathy", + "distal myopathy", "neuromuscular disease", + "congenital myopathy", "skeletal muscle disorder", "muscular dystrophy", - "inherited disease susceptibility", - "disorder of glycosylation", - "disease susceptibility", - "glycoprotein metabolism disease", - "pulmonary disease, chronic obstructive, susceptibility to", - "myopathy caused by variation in FKRP", + "alpha-crystallinopathy", "human disease or disorder", "hereditary skeletal muscle disorder", ], - "subject_label": "autosomal recessive limb-girdle muscular dystrophy type 2I", + "subject_label": "myofibrillar myopathy 2", "object_namespace": "HP", - "object_category": "biolink:PhenotypicQuality", + "object_category": "biolink:GeneticInheritance", "object_closure": [ "HP:0000001", - "UPHENO:0082875", - "UPHENO:0075696", - "UPHENO:0002320", - "UPHENO:0001001", - "HP:0003551", - "UPHENO:0001005", - "UPHENO:0001002", - "HP:0004302", - "HP:0000118", - "BFO:0000002", - "BFO:0000020", - "HP:0003011", - "UPHENO:0002816", - "UPHENO:0002332", - "HP:0033127", - "UPHENO:0001003", - "UPHENO:0002536", - "BFO:0000001", - "HP:0011804", - "PATO:0000001", - "BFO:0000001", - "BFO:0000002", - "BFO:0000004", - "BFO:0000040", - "UBERON:0001062", - "CARO:0000000", - "UBERON:0000465", - "UBERON:0001015", - "UBERON:0000383", - "UBERON:0005090", - "UBERON:0000061", - "UBERON:0001630", - "UBERON:0010000", - "UBERON:0000467", - "UBERON:0000468", - "UBERON:0000062", - "UBERON:0011216", + "HP:0000006", + "HP:0000005", + "HP:0034345", ], "object_closure_label": [ "All (HPO)", - "Phenotypic abnormality (HPO)", - "Abnormality of the musculature (HPO)", - "Difficulty climbing stairs (HPO)", - "Functional motor deficit (HPO)", - "Abnormal muscle physiology (HPO)", - "Abnormality of the musculoskeletal system (HPO)", - "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", - ], - "object_label": "Difficulty climbing stairs (HPO)", - "evidence_count": 0, + "Mode of inheritance (HPO)", + "Autosomal dominant inheritance (HPO)", + "Mendelian inheritance", + ], + "object_label": "Autosomal dominant inheritance (HPO)", + "evidence_count": 4, }, { - "id": "uuid:1c016617-1e4f-11ee-871a-692638b4c502", - "original_subject": "OMIM:613157", - "predicate": "biolink:has_phenotype", - "category": "biolink:DiseaseToPhenotypicFeatureAssociation", + "id": "uuid:c39b463c-212f-11ee-873a-cd90a19c4085", + "original_subject": "OMIM:609115", + "predicate": "biolink:has_mode_of_inheritance", + "category": "biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation", "aggregator_knowledge_source": ["infores:monarchinitiative"], - "has_evidence": "ECO:0000304", - "primary_knowledge_source": ["infores:hpo-annotations"], - "provided_by": "hpoa_disease_phenotype_edges", - "publications": ["OMIM:613157"], - "subject": "MONDO:0013161", - "object": "HP:0003551", + "has_evidence": ["ECO:0000269"], + "primary_knowledge_source": "infores:hpo-annotations", + "provided_by": "hpoa_disease_mode_of_inheritance_edges", + "publications": ["PMID:24647604"], + "subject": "MONDO:0012193", + "object": "HP:0000006", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ - "MONDO:0018282", "MONDO:0000001", - "MONDO:0016182", "MONDO:0016971", - "MONDO:0017741", "MONDO:0000429", - "MONDO:0018276", - "MONDO:0045010", - "MONDO:0100167", "MONDO:0005071", "MONDO:0020121", - "MONDO:0700068", "MONDO:0700223", - "MONDO:0024322", - "MONDO:0020573", "BFO:0000002", "BFO:0000017", "BFO:0000020", - "MONDO:0013161", - "MONDO:0006025", "MONDO:0016106", - "MONDO:0042489", - "MONDO:0017745", "BFO:0000016", "MONDO:0020120", "MONDO:0019056", - "MONDO:0016139", + "MONDO:0015151", "MONDO:0700096", "MONDO:0005218", "MONDO:0005336", "MONDO:0002081", + "MONDO:0012193", + "MONDO:0000426", "OGMS:0000031", "MONDO:0003847", "MONDO:0003939", - "MONDO:0015286", "BFO:0000001", - "MONDO:0015152", - "MONDO:0002320", - "MONDO:0019052", - "MONDO:0005066", - "MONDO:0000173", - "MONDO:0019950", - "MONDO:0016155", ], "subject_closure_label": [ "disease or disorder", - "muscular dystrophy-dystroglycanopathy, type C", + "autosomal dominant disease", "autosomal genetic disease", "musculoskeletal system disorder", - "congenital nervous system disorder", "hereditary disease", "muscle tissue disorder", - "metabolic disease", "nervous system disorder", "obsolete muscular disorder", "myopathy", - "autosomal recessive disease", - "autosomal recessive limb-girdle muscular dystrophy type 2O", - "autosomal recessive limb-girdle muscular dystrophy", - "congenital disorder of glycosylation", + "autosomal dominant limb-girdle muscular dystrophy type 1G", + "muscular dystrophy, limb-girdle, autosomal dominant", "progressive muscular dystrophy", - "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 protein O-mannose beta1, 2N-acetylglucosaminyltransferase", "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", "skeletal muscle disorder", "muscular dystrophy", - "inherited disease susceptibility", - "disorder of glycosylation", - "disease susceptibility", - "glycoprotein metabolism disease", - "pulmonary disease, chronic obstructive, susceptibility to", - "myopathy caused by variation in POMGNT1", "human disease or disorder", "hereditary skeletal muscle disorder", ], - "subject_label": "autosomal recessive limb-girdle muscular dystrophy type 2O", + "subject_label": "autosomal dominant limb-girdle muscular dystrophy type 1G", "object_namespace": "HP", - "object_category": "biolink:PhenotypicQuality", + "object_category": "biolink:GeneticInheritance", "object_closure": [ "HP:0000001", - "UPHENO:0082875", - "UPHENO:0075696", - "UPHENO:0002320", - "UPHENO:0001001", - "HP:0003551", - "UPHENO:0001005", - "UPHENO:0001002", - "HP:0004302", - "HP:0000118", - "BFO:0000002", - "BFO:0000020", - "HP:0003011", - "UPHENO:0002816", - "UPHENO:0002332", - "HP:0033127", - "UPHENO:0001003", - "UPHENO:0002536", - "BFO:0000001", - "HP:0011804", - "PATO:0000001", - "BFO:0000001", - "BFO:0000002", - "BFO:0000004", - "BFO:0000040", - "UBERON:0001062", - "CARO:0000000", - "UBERON:0000465", - "UBERON:0001015", - "UBERON:0000383", - "UBERON:0005090", - "UBERON:0000061", - "UBERON:0001630", - "UBERON:0010000", - "UBERON:0000467", - "UBERON:0000468", - "UBERON:0000062", - "UBERON:0011216", + "HP:0000006", + "HP:0000005", + "HP:0034345", ], "object_closure_label": [ "All (HPO)", - "Phenotypic abnormality (HPO)", - "Abnormality of the musculature (HPO)", - "Difficulty climbing stairs (HPO)", - "Functional motor deficit (HPO)", - "Abnormal muscle physiology (HPO)", - "Abnormality of the musculoskeletal system (HPO)", - "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", - ], - "object_label": "Difficulty climbing stairs (HPO)", - "evidence_count": 0, + "Mode of inheritance (HPO)", + "Autosomal dominant inheritance (HPO)", + "Mendelian inheritance", + ], + "object_label": "Autosomal dominant inheritance (HPO)", + "evidence_count": 4, }, { - "id": "uuid:1b1ad451-1e4f-11ee-871a-692638b4c502", - "original_subject": "OMIM:613319", - "predicate": "biolink:has_phenotype", - "category": "biolink:DiseaseToPhenotypicFeatureAssociation", + "id": "uuid:c4006058-212f-11ee-873a-cd90a19c4085", + "original_subject": "OMIM:609200", + "predicate": "biolink:has_mode_of_inheritance", + "category": "biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation", "aggregator_knowledge_source": ["infores:monarchinitiative"], - "has_evidence": "ECO:0000269", - "primary_knowledge_source": ["infores:hpo-annotations"], - "provided_by": "hpoa_disease_phenotype_edges", - "publications": ["PMID:20096397"], - "subject": "MONDO:0013222", - "object": "HP:0003551", + "has_evidence": ["ECO:0000501"], + "primary_knowledge_source": "infores:hpo-annotations", + "provided_by": "hpoa_disease_mode_of_inheritance_edges", + "publications": ["OMIM:609200"], + "subject": "MONDO:0012215", + "object": "HP:0000006", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ - "MONDO:0013222", + "MONDO:0012215", "MONDO:0000001", + "MONDO:0016971", "MONDO:0000429", - "MONDO:0100167", "MONDO:0005071", "MONDO:0020121", + "MONDO:0018943", "MONDO:0700223", - "MONDO:0020573", + "MONDO:0016201", "BFO:0000002", + "MONDO:0019952", "BFO:0000017", "BFO:0000020", - "MONDO:0006025", - "MONDO:0042489", + "MONDO:0016106", "BFO:0000016", "MONDO:0020120", "MONDO:0019056", + "MONDO:0016139", + "MONDO:0015151", "MONDO:0700096", - "MONDO:0009685", + "MONDO:0002921", "MONDO:0005218", "MONDO:0005336", "MONDO:0002081", - "MONDO:0016109", + "MONDO:0000426", "OGMS:0000031", "MONDO:0003847", "MONDO:0003939", "BFO:0000001", + "MONDO:0002320", + "MONDO:0016108", "MONDO:0018949", ], "subject_closure_label": [ "disease or disorder", + "autosomal dominant disease", "autosomal genetic disease", "musculoskeletal system disorder", + "congenital nervous system disorder", + "congenital structural myopathy", "hereditary disease", "muscle tissue disorder", "nervous system disorder", "obsolete muscular disorder", "myopathy", - "autosomal recessive disease", - "Miyoshi myopathy", - "Miyoshi muscular dystrophy 3", - "autosomal recessive distal myopathy", + "myofibrillar myopathy 3", + "muscular dystrophy, limb-girdle, autosomal dominant", + "progressive muscular dystrophy", + "autosomal dominant distal myopathy", + "qualitative or quantitative protein defects in neuromuscular diseases", + "qualitative or quantitative defects of myotilin", + "limb-girdle muscular dystrophy", + "myofibrillar myopathy", "distal myopathy", "neuromuscular disease", + "congenital myopathy", "skeletal muscle disorder", "muscular dystrophy", - "inherited disease susceptibility", - "disease susceptibility", - "pulmonary disease, chronic obstructive, susceptibility to", "human disease or disorder", "hereditary skeletal muscle disorder", ], - "subject_label": "Miyoshi muscular dystrophy 3", + "subject_label": "myofibrillar myopathy 3", "object_namespace": "HP", - "object_category": "biolink:PhenotypicQuality", + "object_category": "biolink:GeneticInheritance", "object_closure": [ "HP:0000001", - "UPHENO:0082875", - "UPHENO:0075696", - "UPHENO:0002320", - "UPHENO:0001001", - "HP:0003551", - "UPHENO:0001005", - "UPHENO:0001002", - "HP:0004302", - "HP:0000118", - "BFO:0000002", - "BFO:0000020", - "HP:0003011", - "UPHENO:0002816", - "UPHENO:0002332", - "HP:0033127", - "UPHENO:0001003", - "UPHENO:0002536", - "BFO:0000001", - "HP:0011804", - "PATO:0000001", - "BFO:0000001", - "BFO:0000002", - "BFO:0000004", - "BFO:0000040", - "UBERON:0001062", - "CARO:0000000", - "UBERON:0000465", - "UBERON:0001015", - "UBERON:0000383", - "UBERON:0005090", - "UBERON:0000061", - "UBERON:0001630", - "UBERON:0010000", - "UBERON:0000467", - "UBERON:0000468", - "UBERON:0000062", - "UBERON:0011216", + "HP:0000006", + "HP:0000005", + "HP:0034345", ], "object_closure_label": [ "All (HPO)", - "Phenotypic abnormality (HPO)", - "Abnormality of the musculature (HPO)", - "Difficulty climbing stairs (HPO)", - "Functional motor deficit (HPO)", - "Abnormal muscle physiology (HPO)", - "Abnormality of the musculoskeletal system (HPO)", - "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", - ], - "object_label": "Difficulty climbing stairs (HPO)", - "evidence_count": 0, + "Mode of inheritance (HPO)", + "Autosomal dominant inheritance (HPO)", + "Mendelian inheritance", + ], + "object_label": "Autosomal dominant inheritance (HPO)", + "evidence_count": 4, }, { - "id": "uuid:1a0255cd-1e4f-11ee-871a-692638b4c502", - "original_subject": "OMIM:613723", - "predicate": "biolink:has_phenotype", - "category": "biolink:DiseaseToPhenotypicFeatureAssociation", + "id": "uuid:c275a325-212f-11ee-873a-cd90a19c4085", + "original_subject": "OMIM:609384", + "predicate": "biolink:has_mode_of_inheritance", + "category": "biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation", "aggregator_knowledge_source": ["infores:monarchinitiative"], - "has_evidence": "ECO:0000269", - "primary_knowledge_source": ["infores:hpo-annotations"], - "provided_by": "hpoa_disease_phenotype_edges", - "publications": ["PMID:21109228"], - "subject": "MONDO:0013390", - "object": "HP:0003551", + "has_evidence": ["ECO:0000501"], + "primary_knowledge_source": "infores:hpo-annotations", + "provided_by": "hpoa_disease_mode_of_inheritance_edges", + "publications": ["OMIM:609384"], + "subject": "MONDO:0012262", + "object": "HP:0000006", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ - "MONDO:0013390", + "MONDO:0020158", "MONDO:0000001", - "MONDO:0016198", - "MONDO:0016971", - "MONDO:0000429", - "MONDO:0100167", + "MONDO:0007614", "MONDO:0005071", "MONDO:0020121", "MONDO:0700223", - "MONDO:0020573", + "MONDO:0004746", "BFO:0000002", + "MONDO:0012262", + "MONDO:0957003", "BFO:0000017", "BFO:0000020", - "MONDO:0006025", "MONDO:0016106", - "MONDO:0042489", + "MONDO:0003382", "BFO:0000016", "MONDO:0020120", "MONDO:0019056", - "MONDO:0016139", + "MONDO:0003569", "MONDO:0700096", + "MONDO:0001584", + "MONDO:0024458", "MONDO:0005218", "MONDO:0005336", "MONDO:0002081", "OGMS:0000031", "MONDO:0003847", "MONDO:0003939", + "MONDO:0002022", + "MONDO:0015368", "BFO:0000001", - "MONDO:0015152", + "MONDO:0002320", + "MONDO:0000462", + "MONDO:0005328", ], "subject_closure_label": [ "disease or disorder", - "autosomal genetic disease", + "eye adnexa disorder", + "ocular motility disease", + "disorder of orbital region", "musculoskeletal system disorder", + "congenital nervous system disorder", + "eyelid disorder", + "cranial nerve neuropathy", "hereditary disease", "muscle tissue disorder", + "myopathy of extraocular muscle", "nervous system disorder", "obsolete muscular disorder", + "eye disorder", "myopathy", - "autosomal recessive disease", - "autosomal recessive limb-girdle muscular dystrophy type 2Q", - "autosomal recessive limb-girdle muscular dystrophy", + "congenital fibrosis of extraocular muscles", + "fibrosis of extraocular muscles, congenital, 3c", + "neuro-ophthalmological disease", "progressive muscular dystrophy", - "qualitative or quantitative protein defects in neuromuscular diseases", - "qualitative or quantitative defects of plectin", - "limb-girdle muscular dystrophy", "neuromuscular disease", "skeletal muscle disorder", "muscular dystrophy", - "inherited disease susceptibility", - "disease susceptibility", - "pulmonary disease, chronic obstructive, susceptibility to", + "eyelids malposition disorder", + "disorder of visual system", "human disease or disorder", "hereditary skeletal muscle disorder", + "hereditary neuro-ophthalmological disease", ], - "subject_label": "autosomal recessive limb-girdle muscular dystrophy type 2Q", + "subject_label": "fibrosis of extraocular muscles, congenital, 3c", "object_namespace": "HP", - "object_category": "biolink:PhenotypicQuality", + "object_category": "biolink:GeneticInheritance", "object_closure": [ "HP:0000001", - "UPHENO:0082875", - "UPHENO:0075696", - "UPHENO:0002320", - "UPHENO:0001001", - "HP:0003551", - "UPHENO:0001005", - "UPHENO:0001002", - "HP:0004302", - "HP:0000118", - "BFO:0000002", - "BFO:0000020", - "HP:0003011", - "UPHENO:0002816", - "UPHENO:0002332", - "HP:0033127", - "UPHENO:0001003", - "UPHENO:0002536", - "BFO:0000001", - "HP:0011804", - "PATO:0000001", - "BFO:0000001", - "BFO:0000002", - "BFO:0000004", - "BFO:0000040", - "UBERON:0001062", - "CARO:0000000", - "UBERON:0000465", - "UBERON:0001015", - "UBERON:0000383", - "UBERON:0005090", - "UBERON:0000061", - "UBERON:0001630", - "UBERON:0010000", - "UBERON:0000467", - "UBERON:0000468", - "UBERON:0000062", - "UBERON:0011216", + "HP:0000006", + "HP:0000005", + "HP:0034345", ], "object_closure_label": [ "All (HPO)", - "Phenotypic abnormality (HPO)", - "Abnormality of the musculature (HPO)", - "Difficulty climbing stairs (HPO)", - "Functional motor deficit (HPO)", - "Abnormal muscle physiology (HPO)", - "Abnormality of the musculoskeletal system (HPO)", - "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", - ], - "object_label": "Difficulty climbing stairs (HPO)", - "evidence_count": 0, + "Mode of inheritance (HPO)", + "Autosomal dominant inheritance (HPO)", + "Mendelian inheritance", + ], + "object_label": "Autosomal dominant inheritance (HPO)", + "evidence_count": 4, }, { - "id": "uuid:24d370c2-1e4f-11ee-871a-692638b4c502", - "original_subject": "OMIM:254130", - "predicate": "biolink:has_phenotype", - "category": "biolink:DiseaseToPhenotypicFeatureAssociation", + "id": "uuid:c304ba49-212f-11ee-873a-cd90a19c4085", + "original_subject": "OMIM:609452", + "predicate": "biolink:has_mode_of_inheritance", + "category": "biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation", "aggregator_knowledge_source": ["infores:monarchinitiative"], - "has_evidence": "ECO:0000304", - "primary_knowledge_source": ["infores:hpo-annotations"], - "provided_by": "hpoa_disease_phenotype_edges", - "publications": ["OMIM:254130"], - "subject": "MONDO:0024545", - "object": "HP:0003551", + "has_evidence": ["ECO:0000501"], + "primary_knowledge_source": "infores:hpo-annotations", + "provided_by": "hpoa_disease_mode_of_inheritance_edges", + "publications": ["OMIM:609452"], + "subject": "MONDO:0012277", + "object": "HP:0000006", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ "MONDO:0000001", + "MONDO:0016186", "MONDO:0000429", - "MONDO:0016145", - "MONDO:0100167", "MONDO:0005071", "MONDO:0020121", + "MONDO:0018943", "MONDO:0700223", - "MONDO:0020573", "BFO:0000002", + "MONDO:0019952", + "MONDO:0016190", "BFO:0000017", "BFO:0000020", - "MONDO:0006025", - "MONDO:0042489", "BFO:0000016", "MONDO:0020120", "MONDO:0019056", "MONDO:0016139", "MONDO:0700096", - "MONDO:0009685", + "MONDO:0002921", "MONDO:0005218", "MONDO:0005336", "MONDO:0002081", - "MONDO:0016109", + "MONDO:0000426", "OGMS:0000031", "MONDO:0003847", "MONDO:0003939", + "MONDO:0012277", "BFO:0000001", - "MONDO:0024545", + "MONDO:0002320", + "MONDO:0016108", "MONDO:0018949", ], "subject_closure_label": [ "disease or disorder", + "autosomal dominant disease", "autosomal genetic disease", "musculoskeletal system disorder", + "congenital nervous system disorder", + "congenital structural myopathy", "hereditary disease", "muscle tissue disorder", "nervous system disorder", "obsolete muscular disorder", "myopathy", - "autosomal recessive disease", - "Miyoshi myopathy", - "autosomal recessive distal myopathy", + "myofibrillar myopathy 4", + "autosomal dominant distal myopathy", "qualitative or quantitative protein defects in neuromuscular diseases", - "qualitative or quantitative defects of dysferlin", + "qualitative or quantitative defects of myofibrillar proteins", + "qualitative or quantitative defects of protein ZASP", + "myofibrillar myopathy", "distal myopathy", "neuromuscular disease", + "congenital myopathy", "skeletal muscle disorder", "muscular dystrophy", - "inherited disease susceptibility", - "Miyoshi muscular dystrophy 1", - "disease susceptibility", - "pulmonary disease, chronic obstructive, susceptibility to", "human disease or disorder", "hereditary skeletal muscle disorder", ], - "subject_label": "Miyoshi muscular dystrophy 1", + "subject_label": "myofibrillar myopathy 4", "object_namespace": "HP", - "object_category": "biolink:PhenotypicQuality", + "object_category": "biolink:GeneticInheritance", "object_closure": [ "HP:0000001", - "UPHENO:0082875", - "UPHENO:0075696", - "UPHENO:0002320", - "UPHENO:0001001", - "HP:0003551", - "UPHENO:0001005", - "UPHENO:0001002", - "HP:0004302", - "HP:0000118", - "BFO:0000002", - "BFO:0000020", - "HP:0003011", - "UPHENO:0002816", - "UPHENO:0002332", - "HP:0033127", - "UPHENO:0001003", - "UPHENO:0002536", - "BFO:0000001", - "HP:0011804", - "PATO:0000001", - "BFO:0000001", - "BFO:0000002", - "BFO:0000004", - "BFO:0000040", - "UBERON:0001062", - "CARO:0000000", - "UBERON:0000465", - "UBERON:0001015", - "UBERON:0000383", - "UBERON:0005090", - "UBERON:0000061", - "UBERON:0001630", - "UBERON:0010000", - "UBERON:0000467", - "UBERON:0000468", - "UBERON:0000062", - "UBERON:0011216", + "HP:0000006", + "HP:0000005", + "HP:0034345", ], "object_closure_label": [ "All (HPO)", - "Phenotypic abnormality (HPO)", - "Abnormality of the musculature (HPO)", - "Difficulty climbing stairs (HPO)", - "Functional motor deficit (HPO)", - "Abnormal muscle physiology (HPO)", - "Abnormality of the musculoskeletal system (HPO)", - "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", - ], - "object_label": "Difficulty climbing stairs (HPO)", - "evidence_count": 0, + "Mode of inheritance (HPO)", + "Autosomal dominant inheritance (HPO)", + "Mendelian inheritance", + ], + "object_label": "Autosomal dominant inheritance (HPO)", + "evidence_count": 4, }, ], }, diff --git a/backend/tests/fixtures/association_table.py b/backend/tests/fixtures/association_table.py index b2bbeae76..3b833e0fd 100644 --- a/backend/tests/fixtures/association_table.py +++ b/backend/tests/fixtures/association_table.py @@ -9,82 +9,68 @@ def association_table(): "total": 4011, "items": [ { - "id": "uuid:2211b990-1e4f-11ee-871a-692638b4c502", - "subject": "MONDO:0010311", - "original_subject": "OMIM:300376", + "id": "uuid:632c5b16-212f-11ee-873a-cd90a19c4085", + "subject": "MONDO:0020793", + "original_subject": "OMIM:164310", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ - "MONDO:0004994", + "MONDO:0020158", "MONDO:0000001", - "MONDO:0100167", "MONDO:0005071", - "MONDO:0016147", - "MONDO:0005267", + "MONDO:0025193", "MONDO:0020121", - "MONDO:0004995", "MONDO:0700223", - "MONDO:0020573", "BFO:0000002", + "MONDO:0020793", "BFO:0000017", "BFO:0000020", - "MONDO:0010542", "MONDO:0016106", - "MONDO:0015470", - "MONDO:0005217", - "MONDO:0016899", - "MONDO:0042489", + "MONDO:0003382", "BFO:0000016", "MONDO:0020120", "MONDO:0019056", - "MONDO:0016139", "MONDO:0700096", - "MONDO:0000591", + "MONDO:0024458", "MONDO:0005218", "MONDO:0005336", "MONDO:0002081", - "MONDO:0016333", "OGMS:0000031", - "MONDO:0005021", "MONDO:0003847", "MONDO:0003939", + "MONDO:0002022", "BFO:0000001", - "MONDO:0010311", + "MONDO:0000462", + "MONDO:0005328", + "MONDO:0018949", ], - "subject_label": "Becker muscular dystrophy", + "subject_label": "oculopharyngodistal myopathy 1", "subject_closure_label": [ "disease or disorder", - "intrinsic cardiomyopathy", + "eye adnexa disorder", + "disorder of orbital region", "musculoskeletal system disorder", + "eyelid disorder", "hereditary disease", "muscle tissue disorder", - "cardiomyopathy", - "cardiovascular disorder", - "dilated cardiomyopathy", "nervous system disorder", - "familial cardiomyopathy", "obsolete muscular disorder", - "heart disorder", + "eye 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", + "distal myopathy", "neuromuscular disease", "skeletal muscle disorder", "muscular dystrophy", - "inherited disease susceptibility", - "disease susceptibility", - "pulmonary disease, chronic obstructive, susceptibility to", + "eyelids malposition disorder", + "oculopharyngodistal myopathy 1", + "disorder of visual system", + "oculopharyngodistal myopathy", "human disease or disorder", "hereditary skeletal muscle disorder", ], "predicate": "biolink:has_phenotype", - "object": "HP:0003115", + "object": "HP:0002460", "original_object": None, "object_namespace": "HP", "object_category": "biolink:PhenotypicQuality", @@ -92,76 +78,93 @@ def association_table(): "HP:0000001", "UPHENO:0082875", "UPHENO:0075696", + "UPHENO:0002320", "UPHENO:0001001", - "HP:0030956", - "HP:0001626", - "HP:0003115", - "UPHENO:0080362", "UPHENO:0001005", - "HP:0500015", "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", - "HP:0011025", + "HP:0002460", "BFO:0000001", + "HP:0011804", "PATO:0000001", - "UPHENO:0002406", + "CARO:0000000", "BFO:0000001", + "UBERON:0000383", + "UBERON:0001015", + "UBERON:0005090", "BFO:0000002", + "UBERON:0001630", "BFO:0000004", "BFO:0000040", "UBERON:0001062", - "CARO:0000000", "UBERON:0000465", - "PR:000050567", - "UBERON:0004535", "UBERON:0000061", "UBERON:0010000", "UBERON:0000467", "UBERON:0000468", - "UBERON:0001009", + "UBERON:0000062", + "UBERON:0011216", ], - "object_label": "Abnormal EKG (HPO)", + "object_label": "Distal muscle weakness (HPO)", "object_closure_label": [ "All (HPO)", "Phenotypic abnormality (HPO)", - "Abnormality of the cardiovascular system (HPO)", - "Abnormal EKG (HPO)", - "Abnormal cardiovascular system physiology (HPO)", - "Abnormality of cardiovascular system electrophysiology (HPO)", - "Abnormal cardiac test (HPO)", + "Muscle weakness (HPO)", + "Distal muscle weakness (HPO)", + "Abnormality of the musculature (HPO)", + "Abnormal muscle physiology (HPO)", + "Abnormality of the musculoskeletal system (HPO)", "anatomical structure", + "organ", + "musculature of body", "material anatomical entity", "anatomical system", "multicellular organism", - "circulatory system", + "musculature", "anatomical entity", - "cardiovascular system", + "muscle organ", + "muscle structure", "multicellular anatomical structure", + "organ system subdivision", ], - "primary_knowledge_source": ["infores:hpo-annotations"], + "primary_knowledge_source": "infores:hpo-annotations", "aggregator_knowledge_source": ["infores:monarchinitiative"], "category": "biolink:DiseaseToPhenotypicFeatureAssociation", "negated": None, "provided_by": "hpoa_disease_phenotype_edges", - "publications": ["OMIM:300376"], + "publications": ["PMID:21242490", "PMID:32493488", "PMID:31332380"], "qualifiers": [], - "frequency_qualifier": None, - "has_evidence": "ECO:0000501", + "frequency_qualifier": "HP:0040282", + "has_evidence": ["ECO:0000269"], "onset_qualifier": None, "sex_qualifier": None, "stage_qualifier": None, - "evidence_count": 0, + "evidence_count": 6, "pathway": None, - "frequency_qualifier_label": None, - "frequency_qualifier_namespace": None, - "frequency_qualifier_category": None, - "frequency_qualifier_closure": [], - "frequency_qualifier_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)", + ], "onset_qualifier_label": None, "onset_qualifier_namespace": None, "onset_qualifier_category": None, @@ -180,191 +183,208 @@ def association_table(): "direction": "outgoing", }, { - "id": "uuid:29eadc82-1e4f-11ee-871a-692638b4c502", - "subject": "MONDO:0010311", - "original_subject": "Orphanet:98895", + "id": "uuid:632c5b27-212f-11ee-873a-cd90a19c4085", + "subject": "MONDO:0020793", + "original_subject": "OMIM:164310", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ - "MONDO:0004994", + "MONDO:0020158", "MONDO:0000001", - "MONDO:0100167", "MONDO:0005071", - "MONDO:0016147", - "MONDO:0005267", + "MONDO:0025193", "MONDO:0020121", - "MONDO:0004995", "MONDO:0700223", - "MONDO:0020573", "BFO:0000002", + "MONDO:0020793", "BFO:0000017", "BFO:0000020", - "MONDO:0010542", "MONDO:0016106", - "MONDO:0015470", - "MONDO:0005217", - "MONDO:0016899", - "MONDO:0042489", + "MONDO:0003382", "BFO:0000016", "MONDO:0020120", "MONDO:0019056", - "MONDO:0016139", "MONDO:0700096", - "MONDO:0000591", + "MONDO:0024458", "MONDO:0005218", "MONDO:0005336", "MONDO:0002081", - "MONDO:0016333", "OGMS:0000031", - "MONDO:0005021", "MONDO:0003847", "MONDO:0003939", + "MONDO:0002022", "BFO:0000001", - "MONDO:0010311", + "MONDO:0000462", + "MONDO:0005328", + "MONDO:0018949", ], - "subject_label": "Becker muscular dystrophy", + "subject_label": "oculopharyngodistal myopathy 1", "subject_closure_label": [ "disease or disorder", - "intrinsic cardiomyopathy", + "eye adnexa disorder", + "disorder of orbital region", "musculoskeletal system disorder", + "eyelid disorder", "hereditary disease", "muscle tissue disorder", - "cardiomyopathy", - "cardiovascular disorder", - "dilated cardiomyopathy", "nervous system disorder", - "familial cardiomyopathy", "obsolete muscular disorder", - "heart disorder", + "eye 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", + "distal myopathy", "neuromuscular disease", "skeletal muscle disorder", "muscular dystrophy", - "inherited disease susceptibility", - "disease susceptibility", - "pulmonary disease, chronic obstructive, susceptibility to", + "eyelids malposition disorder", + "oculopharyngodistal myopathy 1", + "disorder of visual system", + "oculopharyngodistal myopathy", "human disease or disorder", "hereditary skeletal muscle disorder", ], "predicate": "biolink:has_phenotype", - "object": "HP:0012086", + "object": "HP:0002015", "original_object": None, "object_namespace": "HP", "object_category": "biolink:PhenotypicQuality", "object_closure": [ "HP:0000001", "UPHENO:0082875", - "UPHENO:0002832", "UPHENO:0075696", - "UPHENO:0080210", + "HP:0011024", "UPHENO:0001001", - "HP:0012086", + "UPHENO:0002443", + "UPHENO:0002471", + "HP:0025270", + "HP:0012719", "UPHENO:0001005", + "UPHENO:0002833", + "HP:0002015", "UPHENO:0001002", - "UPHENO:0083447", + "UPHENO:0002725", "HP:0000118", "BFO:0000002", - "UPHENO:0080216", "BFO:0000020", - "HP:0011277", + "UPHENO:0002433", + "HP:0025032", "UPHENO:0002332", - "HP:0000079", - "UPHENO:0015280", - "UPHENO:0081581", + "HP:0000707", "UPHENO:0001003", "UPHENO:0002536", - "UPHENO:0083450", - "HP:0001939", - "UPHENO:0020584", - "UPHENO:0076692", - "HP:0000119", + "UPHENO:0004523", "BFO:0000001", - "HP:0003110", - "UPHENO:0002642", - "UPHENO:0002442", - "HP:0033072", "PATO:0000001", + "HP:0025031", + "UPHENO:0002474", + "HP:0012638", + "CARO:0000000", + "CARO:0000003", "BFO:0000001", - "BFO:0000003", + "UBERON:0004921", + "UBERON:0001555", + "UBERON:0001016", + "UBERON:0000915", "BFO:0000002", - "BFO:0000015", + "UBERON:0004908", + "UBERON:0001043", "BFO:0000004", - "GO:0008150", "BFO:0000040", "UBERON:0001062", - "CARO:0000000", - "GO:0008152", - "GO:0042592", + "RO:0002577", "UBERON:0000465", - "UBERON:0004122", "UBERON:0000061", - "UBERON:0000463", "UBERON:0010000", "UBERON:0000467", - "UBERON:0000174", "UBERON:0000468", - "UBERON:8450002", - "UBERON:0001088", - "UBERON:0001008", + "UBERON:0000475", + "UBERON:0000064", + "UBERON:0000062", + "UBERON:0004111", + "UBERON:0005409", + "UBERON:0001007", + "UBERON:0011676", + "UBERON:0013701", + "UBERON:0009569", + "UBERON:0013702", + "UBERON:0013522", + "UBERON:0013765", + "UBERON:0005177", + "UBERON:0000025", + "UBERON:0002100", + "UBERON:0005181", + "UBERON:0002075", + "UBERON:0005178", ], - "object_label": "Abnormal urinary color (HPO)", + "object_label": "Dysphagia (HPO)", "object_closure_label": [ "All (HPO)", - "Abnormality of the urinary system (HPO)", "Phenotypic abnormality (HPO)", - "Abnormality of the genitourinary system (HPO)", - "Abnormality of metabolism/homeostasis (HPO)", - "Abnormality of urine homeostasis (HPO)", - "Abnormality of the urinary system physiology (HPO)", - "Abnormal urinary color (HPO)", - "Abnormal macroscopic urine appearance (HPO)", + "Abnormality of the nervous system (HPO)", + "Dysphagia (HPO)", + "Abnormality of the gastrointestinal tract (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)", + "tube", "anatomical structure", - "excreta", - "organism substance", + "organ", + "organ part", "material anatomical entity", "anatomical system", "multicellular organism", - "renal system", + "organism subdivision", + "thoracic segment of trunk", + "digestive system", + "nervous system", + "esophagus", "anatomical entity", - "urine", - "genitourinary system", + "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", - "excretory system", + "subdivision of organism along main body axis", + "subdivision of tube", + "main body axis", + "body proper", + "digestive system element", ], - "primary_knowledge_source": ["infores:hpo-annotations"], + "primary_knowledge_source": "infores:hpo-annotations", "aggregator_knowledge_source": ["infores:monarchinitiative"], "category": "biolink:DiseaseToPhenotypicFeatureAssociation", "negated": None, "provided_by": "hpoa_disease_phenotype_edges", - "publications": ["orphanet:98895"], + "publications": ["PMID:21242490", "PMID:32493488", "PMID:31332380"], "qualifiers": [], - "frequency_qualifier": "HP:0040281", - "has_evidence": "ECO:0000304", + "frequency_qualifier": "HP:0040282", + "has_evidence": ["ECO:0000269"], "onset_qualifier": None, "sex_qualifier": None, "stage_qualifier": None, - "evidence_count": 0, + "evidence_count": 6, "pathway": None, - "frequency_qualifier_label": "Very frequent (HPO)", + "frequency_qualifier_label": "Frequent (HPO)", "frequency_qualifier_namespace": "HP", "frequency_qualifier_category": "biolink:PhenotypicFeature", "frequency_qualifier_closure": [ "HP:0000001", + "HP:0040282", "HP:0040279", - "HP:0040281", ], "frequency_qualifier_closure_label": [ "All (HPO)", "Frequency (HPO)", - "Very frequent (HPO)", + "Frequent (HPO)", ], "onset_qualifier_label": None, "onset_qualifier_namespace": None, @@ -384,186 +404,272 @@ def association_table(): "direction": "outgoing", }, { - "id": "uuid:29eadc85-1e4f-11ee-871a-692638b4c502", - "subject": "MONDO:0010311", - "original_subject": "Orphanet:98895", + "id": "uuid:5d7fc2a1-212f-11ee-873a-cd90a19c4085", + "subject": "MONDO:0013049", + "original_subject": "OMIM:612937", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ "MONDO:0004994", "MONDO:0000001", - "MONDO:0100167", + "MONDO:0018276", "MONDO:0005071", - "MONDO:0016147", "MONDO:0005267", + "MONDO:0013049", "MONDO:0020121", "MONDO:0004995", "MONDO:0700223", - "MONDO:0020573", + "MONDO:0024322", "BFO:0000002", "BFO:0000017", "BFO:0000020", - "MONDO:0010542", - "MONDO:0016106", - "MONDO:0015470", "MONDO:0005217", - "MONDO:0016899", - "MONDO:0042489", "BFO:0000016", "MONDO:0020120", "MONDO:0019056", - "MONDO:0016139", "MONDO:0700096", "MONDO:0000591", "MONDO:0005218", "MONDO:0005336", "MONDO:0002081", "MONDO:0016333", + "MONDO:0017749", "OGMS:0000031", "MONDO:0005021", "MONDO:0003847", "MONDO:0003939", + "MONDO:0015286", "BFO:0000001", - "MONDO:0010311", + "MONDO:0002320", + "MONDO:0019052", + "MONDO:0005500", + "MONDO:0005066", + "MONDO:0019950", ], - "subject_label": "Becker muscular dystrophy", + "subject_label": "DPM3-congenital disorder of glycosylation", "subject_closure_label": [ "disease or disorder", "intrinsic cardiomyopathy", "musculoskeletal system disorder", + "congenital nervous system disorder", "hereditary disease", "muscle tissue disorder", "cardiomyopathy", "cardiovascular disorder", "dilated cardiomyopathy", + "metabolic disease", "nervous system disorder", "familial cardiomyopathy", "obsolete muscular disorder", "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", + "congenital disorder of glycosylation type I", + "DPM3-congenital disorder of glycosylation", + "congenital disorder of glycosylation", "familial dilated cardiomyopathy", - "Duchenne and Becker muscular dystrophy", + "disorder of multiple glycosylation", + "muscular dystrophy-dystroglycanopathy", + "inborn errors of metabolism", "neuromuscular disease", + "congenital muscular dystrophy", "skeletal muscle disorder", "muscular dystrophy", - "inherited disease susceptibility", - "disease susceptibility", - "pulmonary disease, chronic obstructive, susceptibility to", + "disorder of glycosylation", "human disease or disorder", "hereditary skeletal muscle disorder", ], "predicate": "biolink:has_phenotype", - "object": "HP:0002814", + "object": "HP:0003236", "original_object": None, "object_namespace": "HP", "object_category": "biolink:PhenotypicQuality", "object_closure": [ "HP:0000001", - "HP:0002814", + "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", - "UPHENO:0003070", - "HP:0040064", + "HP:0001939", + "HP:0500165", + "UPHENO:0081547", + "UPHENO:0077826", + "HP:0032180", "BFO:0000001", + "HP:0002086", + "HP:0003236", "PATO:0000001", - "UPHENO:0002830", + "HP:0002795", + "HP:0012415", + "UPHENO:0051612", + "UPHENO:0051804", + "CARO:0000000", "BFO:0000001", + "UBERON:0004120", + "UBERON:0000178", + "BFO:0000003", "BFO:0000002", + "UBERON:0002390", + "BFO:0000015", "BFO:0000004", + "GO:0008150", "BFO:0000040", "UBERON:0001062", - "CARO:0000000", - "UBERON:0000465", + "GO:0008152", + "GO:0005575", "PR:000050567", - "RO:0002577", - "CARO:0000006", - "UBERON:0006058", - "UBERON:0010538", + "CHEBI:24431", + "UBERON:0000465", + "GO:0032991", + "CHEBI:23367", "UBERON:0000061", - "UBERON:0004708", - "CARO:0000003", - "UBERON:0000978", - "UBERON:0002529", + "UBERON:0000463", + "GO:1902494", + "CHEBI:36357", + "CHEBI:33579", "UBERON:0010000", - "UBERON:0015212", - "UBERON:0002101", - "UBERON:0004709", - "UBERON:0010709", - "UBERON:0008784", + "UBERON:0000467", + "UBERON:0006314", + "GO:1990234", + "CHEBI:33839", + "CHEBI:33675", + "CHEBI:138675", "UBERON:0000468", - "UBERON:0000475", - "UBERON:0010707", - "UBERON:0002103", - "UBERON:0000154", - "UBERON:0000026", - "UBERON:0010758", + "UBERON:0001004", + "UBERON:0002193", + "UBERON:0000179", + "GO:0061695", + "CHEBI:16670", + "CHEBI:33302", + "CHEBI:33582", + "CHEBI:33304", + "GO:0002185", + "CHEBI:15841", + "CHEBI:51143", + "CHEBI:50860", + "CHEBI:25806", + "CHEBI:36962", + "CHEBI:16541", + "CHEBI:35352", + "CHEBI:32988", + "CHEBI:33285", + "CHEBI:36963", + "CHEBI:50047", + "CHEBI:37622", + "CHEBI:33256", ], - "object_label": "Abnormality of the lower limb (HPO)", + "object_label": "Elevated circulating creatine kinase concentration (HPO)", "object_closure_label": [ + "gas molecular entity", + "polypeptide", + "protein polypeptide chain", + "peptide", + "molecular entity", + "chemical entity", + "oxygen molecular entity", + "amide", + "primary amide", + "heteroorganic entity", + "pnictogen molecular entity", + "chalcogen molecular entity", + "main group molecular entity", + "carbon group molecular entity", + "p-block molecular entity", + "macromolecule", + "organonitrogen compound", + "polyatomic entity", + "organochalcogen compound", + "organooxygen compound", + "carboxamide", + "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 the lower limb (HPO)", - "Abnormality of limbs (HPO)", - "appendage", + "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)", + "Abnormal circulating metabolite concentration (HPO)", + "Abnormal circulating creatine kinase concentration (HPO)", + "Abnormal blood oxygen level (HPO)", "anatomical structure", - "posterior region of body", + "blood", + "haemolymphatic fluid", + "organism substance", "material anatomical entity", + "anatomical system", "multicellular organism", - "organism subdivision", - "leg", + "respiratory system", "anatomical entity", - "limb", - "hindlimb", - "limb segment", - "paired limb/fin", - "pelvic appendage", - "multi-limb segment region", - "lower limb segment", + "hemolymphoid system", + "hematopoietic system", + "mesoderm-derived structure", + "bodily fluid", "multicellular anatomical structure", - "paired limb/fin segment", - "appendage girdle complex", - "pelvic complex", - "subdivision of organism along appendicular axis", - "lateral structure", ], - "primary_knowledge_source": ["infores:hpo-annotations"], + "primary_knowledge_source": "infores:hpo-annotations", "aggregator_knowledge_source": ["infores:monarchinitiative"], "category": "biolink:DiseaseToPhenotypicFeatureAssociation", "negated": None, "provided_by": "hpoa_disease_phenotype_edges", - "publications": ["orphanet:98895"], + "publications": ["PMID:19576565", "PMID:28803818"], "qualifiers": [], - "frequency_qualifier": "HP:0040282", - "has_evidence": "ECO:0000304", + "frequency_qualifier": "HP:0040280", + "has_evidence": ["ECO:0000269"], "onset_qualifier": None, "sex_qualifier": None, "stage_qualifier": None, - "evidence_count": 0, + "evidence_count": 5, "pathway": None, - "frequency_qualifier_label": "Frequent (HPO)", + "frequency_qualifier_label": "Obligate (HPO)", "frequency_qualifier_namespace": "HP", "frequency_qualifier_category": "biolink:PhenotypicFeature", "frequency_qualifier_closure": [ "HP:0000001", - "HP:0040282", "HP:0040279", + "HP:0040280", ], "frequency_qualifier_closure_label": [ "All (HPO)", "Frequency (HPO)", - "Frequent (HPO)", + "Obligate (HPO)", ], "onset_qualifier_label": None, "onset_qualifier_namespace": None, @@ -583,166 +689,162 @@ def association_table(): "direction": "outgoing", }, { - "id": "uuid:2211b994-1e4f-11ee-871a-692638b4c502", - "subject": "MONDO:0010311", - "original_subject": "OMIM:300376", + "id": "uuid:64b6842f-212f-11ee-873a-cd90a19c4085", + "subject": "MONDO:0009681", + "original_subject": "OMIM:254090", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ - "MONDO:0004994", "MONDO:0000001", - "MONDO:0100167", "MONDO:0005071", - "MONDO:0016147", - "MONDO:0005267", "MONDO:0020121", - "MONDO:0004995", "MONDO:0700223", - "MONDO:0020573", "BFO:0000002", + "MONDO:0019952", "BFO:0000017", "BFO:0000020", - "MONDO:0010542", - "MONDO:0016106", - "MONDO:0015470", - "MONDO:0005217", - "MONDO:0016899", - "MONDO:0042489", + "MONDO:0100225", "BFO:0000016", "MONDO:0020120", "MONDO:0019056", "MONDO:0016139", "MONDO:0700096", - "MONDO:0000591", "MONDO:0005218", "MONDO:0005336", "MONDO:0002081", - "MONDO:0016333", + "MONDO:0009681", "OGMS:0000031", - "MONDO:0005021", "MONDO:0003847", "MONDO:0003939", "BFO:0000001", - "MONDO:0010311", + "MONDO:0002320", + "MONDO:0000355", + "MONDO:0019950", ], - "subject_label": "Becker muscular dystrophy", + "subject_label": "Ullrich congenital muscular dystrophy 1", "subject_closure_label": [ "disease or disorder", - "intrinsic cardiomyopathy", + "Ullrich congenital muscular dystrophy", "musculoskeletal system disorder", + "congenital nervous system disorder", "hereditary disease", "muscle tissue disorder", - "cardiomyopathy", - "cardiovascular disorder", - "dilated cardiomyopathy", "nervous system disorder", - "familial cardiomyopathy", "obsolete muscular disorder", - "heart disorder", "myopathy", - "Becker muscular dystrophy", - "dilated cardiomyopathy 3B", - "familial isolated dilated cardiomyopathy", - "progressive muscular dystrophy", + "Ullrich congenital muscular dystrophy 1", "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 muscular dystrophy", + "congenital myopathy", "skeletal muscle disorder", "muscular dystrophy", - "inherited disease susceptibility", - "disease susceptibility", - "pulmonary disease, chronic obstructive, susceptibility to", + "collagen 6-related myopathy", "human disease or disorder", "hereditary skeletal muscle disorder", ], "predicate": "biolink:has_phenotype", - "object": "HP:0011675", + "object": "HP:0020152", "original_object": None, "object_namespace": "HP", "object_category": "biolink:PhenotypicQuality", "object_closure": [ "HP:0000001", + "HP:0020152", "UPHENO:0082875", + "HP:0001388", "UPHENO:0075696", "UPHENO:0001001", - "HP:0030956", - "HP:0001626", - "UPHENO:0080362", + "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", - "HP:0011025", + "UPHENO:0081440", "BFO:0000001", - "HP:0011675", "PATO:0000001", - "UPHENO:0002406", + "HP:0011843", + "CARO:0000000", "BFO:0000001", - "BFO:0000003", + "UBERON:0002204", "BFO:0000002", - "BFO:0000015", "BFO:0000004", - "GO:0008150", "BFO:0000040", "UBERON:0001062", - "CARO:0000000", - "GO:0032501", "UBERON:0000465", - "PR:000050567", - "UBERON:0004535", - "GO:0003008", "UBERON:0000061", - "GO:0003013", + "UBERON:0034925", "UBERON:0010000", "UBERON:0000467", - "GO:0003015", - "GO:0008015", + "UBERON:0004770", "UBERON:0000468", - "UBERON:0001009", - "GO:0060047", + "UBERON:0011216", + "UBERON:0034921", + "UBERON:0001434", + "UBERON:0004905", + "UBERON:0000982", ], - "object_label": "Arrhythmia (HPO)", + "object_label": "Distal joint laxity (HPO)", "object_closure_label": [ "All (HPO)", "Phenotypic abnormality (HPO)", - "Abnormality of the cardiovascular system (HPO)", - "Abnormal cardiovascular system physiology (HPO)", - "Arrhythmia (HPO)", - "Abnormality of cardiovascular system electrophysiology (HPO)", + "Abnormality of the skeletal system (HPO)", + "Joint laxity (HPO)", + "Abnormality of joint mobility (HPO)", + "Abnormality of musculoskeletal physiology (HPO)", + "Distal joint laxity (HPO)", + "Abnormality of the musculoskeletal system (HPO)", + "Abnormal joint physiology", "anatomical structure", "material anatomical entity", "anatomical system", "multicellular organism", - "circulatory system", + "skeletal joint", "anatomical entity", - "cardiovascular system", + "skeletal system", + "musculoskeletal system", + "articular system", + "articulation", "multicellular anatomical structure", + "organ system subdivision", + "multi organ part structure", + "anatomical collection", ], - "primary_knowledge_source": ["infores:hpo-annotations"], + "primary_knowledge_source": "infores:hpo-annotations", "aggregator_knowledge_source": ["infores:monarchinitiative"], "category": "biolink:DiseaseToPhenotypicFeatureAssociation", "negated": None, "provided_by": "hpoa_disease_phenotype_edges", - "publications": ["OMIM:300376"], + "publications": ["PMID:16258657", "OMIM:254090"], "qualifiers": [], - "frequency_qualifier": None, - "has_evidence": "ECO:0000304", + "frequency_qualifier": "HP:0040280", + "has_evidence": ["ECO:0000269"], "onset_qualifier": None, "sex_qualifier": None, "stage_qualifier": None, - "evidence_count": 0, + "evidence_count": 5, "pathway": None, - "frequency_qualifier_label": None, - "frequency_qualifier_namespace": None, - "frequency_qualifier_category": None, - "frequency_qualifier_closure": [], - "frequency_qualifier_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)", + ], "onset_qualifier_label": None, "onset_qualifier_namespace": None, "onset_qualifier_category": None, @@ -761,251 +863,158 @@ def association_table(): "direction": "outgoing", }, { - "id": "uuid:2211b991-1e4f-11ee-871a-692638b4c502", - "subject": "MONDO:0010311", - "original_subject": "OMIM:300376", + "id": "uuid:628f3d98-212f-11ee-873a-cd90a19c4085", + "subject": "MONDO:0009676", + "original_subject": "OMIM:253601", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ - "MONDO:0004994", "MONDO:0000001", - "MONDO:0100167", + "MONDO:0016971", + "MONDO:0000429", + "MONDO:0016145", "MONDO:0005071", - "MONDO:0016147", - "MONDO:0005267", "MONDO:0020121", - "MONDO:0004995", "MONDO:0700223", - "MONDO:0020573", "BFO:0000002", "BFO:0000017", "BFO:0000020", - "MONDO:0010542", + "MONDO:0006025", "MONDO:0016106", - "MONDO:0015470", - "MONDO:0005217", - "MONDO:0016899", - "MONDO:0042489", "BFO:0000016", "MONDO:0020120", "MONDO:0019056", "MONDO:0016139", "MONDO:0700096", - "MONDO:0000591", "MONDO:0005218", "MONDO:0005336", "MONDO:0002081", - "MONDO:0016333", + "MONDO:0009676", "OGMS:0000031", - "MONDO:0005021", "MONDO:0003847", "MONDO:0003939", "BFO:0000001", - "MONDO:0010311", + "MONDO:0015152", ], - "subject_label": "Becker muscular dystrophy", + "subject_label": "autosomal recessive limb-girdle muscular dystrophy type 2B", "subject_closure_label": [ "disease or disorder", - "intrinsic cardiomyopathy", + "autosomal genetic disease", "musculoskeletal system disorder", "hereditary disease", "muscle tissue disorder", - "cardiomyopathy", - "cardiovascular disorder", - "dilated cardiomyopathy", "nervous system disorder", - "familial cardiomyopathy", "obsolete muscular disorder", - "heart disorder", "myopathy", - "Becker muscular dystrophy", - "dilated cardiomyopathy 3B", - "familial isolated dilated cardiomyopathy", + "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 dystrophin", - "familial dilated cardiomyopathy", - "Duchenne and Becker muscular dystrophy", + "qualitative or quantitative defects of dysferlin", + "limb-girdle muscular dystrophy", "neuromuscular disease", "skeletal muscle disorder", "muscular dystrophy", - "inherited disease susceptibility", - "disease susceptibility", - "pulmonary disease, chronic obstructive, susceptibility to", "human disease or disorder", "hereditary skeletal muscle disorder", ], "predicate": "biolink:has_phenotype", - "object": "HP:0003707", + "object": "HP:0003701", "original_object": None, "object_namespace": "HP", "object_category": "biolink:PhenotypicQuality", "object_closure": [ "HP:0000001", - "UPHENO:0002644", - "HP:0002981", - "HP:0002814", + "UPHENO:0082875", + "UPHENO:0075696", + "UPHENO:0002320", "UPHENO:0001001", - "UPHENO:0075952", - "HP:0003707", - "HP:0009127", "UPHENO:0001005", - "UPHENO:0075777", - "HP:0011805", + "HP:0003701", "UPHENO:0001002", - "HP:0001430", + "HP:0001324", "HP:0000118", "BFO:0000002", "BFO:0000020", + "UPHENO:0080555", "HP:0003011", "UPHENO:0002816", - "UPHENO:0081581", + "UPHENO:0002332", + "UPHENO:0080556", "HP:0033127", "UPHENO:0001003", "UPHENO:0002536", - "HP:0001437", - "UPHENO:0076692", - "UPHENO:0003070", - "UPHENO:0002647", - "UPHENO:0076710", - "HP:0040064", "BFO:0000001", + "HP:0011804", "PATO:0000001", - "UPHENO:0002830", + "CARO:0000000", "BFO:0000001", + "UBERON:0000383", + "UBERON:0001015", + "UBERON:0005090", "BFO:0000002", + "UBERON:0001630", "BFO:0000004", "BFO:0000040", "UBERON:0001062", - "CARO:0000000", "UBERON:0000465", - "PR:000050567", - "RO:0002577", - "UBERON:0001015", - "UBERON:0000383", - "CARO:0000006", - "UBERON:0006058", - "UBERON:0010538", - "UBERON:0018254", - "UBERON:0005090", "UBERON:0000061", - "UBERON:0004708", - "UBERON:0007271", - "UBERON:0014792", - "CARO:0000003", - "UBERON:0000978", - "UBERON:0002529", - "UBERON:0001630", "UBERON:0010000", "UBERON:0000467", - "UBERON:0015212", - "UBERON:0002101", - "UBERON:0004709", - "UBERON:0007270", - "UBERON:0004480", - "UBERON:0010709", - "UBERON:0002471", - "UBERON:0008784", - "UBERON:0014892", "UBERON:0000468", - "UBERON:0000475", "UBERON:0000062", "UBERON:0011216", - "UBERON:0010707", - "UBERON:0002103", - "UBERON:0004482", - "UBERON:0003823", - "UBERON:0003661", - "UBERON:0010890", - "UBERON:0000154", - "UBERON:0000026", - "UBERON:0010758", - "UBERON:0004466", - "UBERON:0003663", - "UBERON:0014795", - "UBERON:0006067", - "UBERON:0001383", - "UBERON:0004256", ], - "object_label": "Calf muscle pseudohypertrophy (HPO)", + "object_label": "Proximal muscle weakness (HPO)", "object_closure_label": [ "All (HPO)", "Phenotypic abnormality (HPO)", - "Abnormality of the calf musculature (HPO)", - "Abnormality of the musculature of the lower limbs (HPO)", - "Abnormality of the lower limb (HPO)", - "Abnormality of the calf (HPO)", + "Muscle weakness (HPO)", "Abnormality of the musculature (HPO)", - "Calf muscle pseudohypertrophy (HPO)", - "Abnormality of the musculature of the limbs (HPO)", - "Abnormal skeletal muscle morphology (HPO)", + "Proximal muscle weakness (HPO)", + "Abnormal muscle physiology (HPO)", "Abnormality of the musculoskeletal system (HPO)", - "Abnormality of limbs (HPO)", - "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 of leg", "muscle organ", - "limb", - "hindlimb", - "zeugopod", - "limb segment", - "limb muscle", - "hindlimb muscle", - "hindlimb zeugopod", - "hindlimb zeugopod muscle", - "musculature of leg", - "musculature of limb", - "musculature of lower limb", - "paired limb/fin", - "pelvic appendage", "muscle structure", - "multi-limb segment region", - "musculature of hindlimb zeugopod", - "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", - "pelvic complex muscle", "organ system subdivision", - "musculature of pelvic complex", - "pelvic appendage muscle", - "skeletal muscle organ", - "lateral structure", - "skeletal musculature", ], - "primary_knowledge_source": ["infores:hpo-annotations"], + "primary_knowledge_source": "infores:hpo-annotations", "aggregator_knowledge_source": ["infores:monarchinitiative"], "category": "biolink:DiseaseToPhenotypicFeatureAssociation", "negated": None, "provided_by": "hpoa_disease_phenotype_edges", - "publications": ["OMIM:300376"], + "publications": ["PMID:9731527", "PMID:9009996"], "qualifiers": [], - "frequency_qualifier": None, - "has_evidence": "ECO:0000304", + "frequency_qualifier": "HP:0040280", + "has_evidence": ["ECO:0000269"], "onset_qualifier": None, "sex_qualifier": None, "stage_qualifier": None, - "evidence_count": 0, + "evidence_count": 5, "pathway": None, - "frequency_qualifier_label": None, - "frequency_qualifier_namespace": None, - "frequency_qualifier_category": None, - "frequency_qualifier_closure": [], - "frequency_qualifier_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)", + ], "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 976bc27c4..2f748c5e7 100644 --- a/backend/tests/fixtures/association_table_response.py +++ b/backend/tests/fixtures/association_table_response.py @@ -26,886 +26,913 @@ def association_table_response(): "start": 0, "docs": [ { - "id": "uuid:2211b990-1e4f-11ee-871a-692638b4c502", - "original_subject": "OMIM:300376", + "id": "uuid:632c5b16-212f-11ee-873a-cd90a19c4085", + "original_subject": "OMIM:164310", "predicate": "biolink:has_phenotype", "category": "biolink:DiseaseToPhenotypicFeatureAssociation", "aggregator_knowledge_source": ["infores:monarchinitiative"], - "has_evidence": "ECO:0000501", - "primary_knowledge_source": ["infores:hpo-annotations"], + "has_evidence": ["ECO:0000269"], + "primary_knowledge_source": "infores:hpo-annotations", "provided_by": "hpoa_disease_phenotype_edges", - "publications": ["OMIM:300376"], - "subject": "MONDO:0010311", - "object": "HP:0003115", + "publications": ["PMID:21242490", "PMID:32493488", "PMID:31332380"], + "frequency_qualifier": "HP:0040282", + "subject": "MONDO:0020793", + "object": "HP:0002460", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ - "MONDO:0004994", + "MONDO:0020158", "MONDO:0000001", - "MONDO:0100167", "MONDO:0005071", - "MONDO:0016147", - "MONDO:0005267", + "MONDO:0025193", "MONDO:0020121", - "MONDO:0004995", "MONDO:0700223", - "MONDO:0020573", "BFO:0000002", + "MONDO:0020793", "BFO:0000017", "BFO:0000020", - "MONDO:0010542", "MONDO:0016106", - "MONDO:0015470", - "MONDO:0005217", - "MONDO:0016899", - "MONDO:0042489", + "MONDO:0003382", "BFO:0000016", "MONDO:0020120", "MONDO:0019056", - "MONDO:0016139", "MONDO:0700096", - "MONDO:0000591", + "MONDO:0024458", "MONDO:0005218", "MONDO:0005336", "MONDO:0002081", - "MONDO:0016333", "OGMS:0000031", - "MONDO:0005021", "MONDO:0003847", "MONDO:0003939", + "MONDO:0002022", "BFO:0000001", - "MONDO:0010311", + "MONDO:0000462", + "MONDO:0005328", + "MONDO:0018949", ], "subject_closure_label": [ "disease or disorder", - "intrinsic cardiomyopathy", + "eye adnexa disorder", + "disorder of orbital region", "musculoskeletal system disorder", + "eyelid disorder", "hereditary disease", "muscle tissue disorder", - "cardiomyopathy", - "cardiovascular disorder", - "dilated cardiomyopathy", "nervous system disorder", - "familial cardiomyopathy", "obsolete muscular disorder", - "heart disorder", + "eye 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", + "distal myopathy", "neuromuscular disease", "skeletal muscle disorder", "muscular dystrophy", - "inherited disease susceptibility", - "disease susceptibility", - "pulmonary disease, chronic obstructive, susceptibility to", + "eyelids malposition disorder", + "oculopharyngodistal myopathy 1", + "disorder of visual system", + "oculopharyngodistal myopathy", "human disease or disorder", "hereditary skeletal muscle disorder", ], - "subject_label": "Becker muscular dystrophy", + "subject_label": "oculopharyngodistal myopathy 1", "object_namespace": "HP", "object_category": "biolink:PhenotypicQuality", "object_closure": [ "HP:0000001", "UPHENO:0082875", "UPHENO:0075696", + "UPHENO:0002320", "UPHENO:0001001", - "HP:0030956", - "HP:0001626", - "HP:0003115", - "UPHENO:0080362", "UPHENO:0001005", - "HP:0500015", "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", - "HP:0011025", + "HP:0002460", "BFO:0000001", + "HP:0011804", "PATO:0000001", - "UPHENO:0002406", + "CARO:0000000", "BFO:0000001", + "UBERON:0000383", + "UBERON:0001015", + "UBERON:0005090", "BFO:0000002", + "UBERON:0001630", "BFO:0000004", "BFO:0000040", "UBERON:0001062", - "CARO:0000000", "UBERON:0000465", - "PR:000050567", - "UBERON:0004535", "UBERON:0000061", "UBERON:0010000", "UBERON:0000467", "UBERON:0000468", - "UBERON:0001009", + "UBERON:0000062", + "UBERON:0011216", ], "object_closure_label": [ "All (HPO)", "Phenotypic abnormality (HPO)", - "Abnormality of the cardiovascular system (HPO)", - "Abnormal EKG (HPO)", - "Abnormal cardiovascular system physiology (HPO)", - "Abnormality of cardiovascular system electrophysiology (HPO)", - "Abnormal cardiac test (HPO)", + "Muscle weakness (HPO)", + "Distal muscle weakness (HPO)", + "Abnormality of the musculature (HPO)", + "Abnormal muscle physiology (HPO)", + "Abnormality of the musculoskeletal system (HPO)", "anatomical structure", + "organ", + "musculature of body", "material anatomical entity", "anatomical system", "multicellular organism", - "circulatory system", + "musculature", "anatomical entity", - "cardiovascular system", + "muscle organ", + "muscle structure", "multicellular anatomical structure", + "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)", ], - "object_label": "Abnormal EKG (HPO)", - "evidence_count": 0, + "frequency_qualifier_label": "Frequent (HPO)", + "evidence_count": 6, }, { - "id": "uuid:29eadc82-1e4f-11ee-871a-692638b4c502", - "original_subject": "Orphanet:98895", + "id": "uuid:632c5b27-212f-11ee-873a-cd90a19c4085", + "original_subject": "OMIM:164310", "predicate": "biolink:has_phenotype", "category": "biolink:DiseaseToPhenotypicFeatureAssociation", "aggregator_knowledge_source": ["infores:monarchinitiative"], - "has_evidence": "ECO:0000304", - "primary_knowledge_source": ["infores:hpo-annotations"], + "has_evidence": ["ECO:0000269"], + "primary_knowledge_source": "infores:hpo-annotations", "provided_by": "hpoa_disease_phenotype_edges", - "publications": ["orphanet:98895"], - "frequency_qualifier": "HP:0040281", - "subject": "MONDO:0010311", - "object": "HP:0012086", + "publications": ["PMID:21242490", "PMID:32493488", "PMID:31332380"], + "frequency_qualifier": "HP:0040282", + "subject": "MONDO:0020793", + "object": "HP:0002015", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ - "MONDO:0004994", + "MONDO:0020158", "MONDO:0000001", - "MONDO:0100167", "MONDO:0005071", - "MONDO:0016147", - "MONDO:0005267", + "MONDO:0025193", "MONDO:0020121", - "MONDO:0004995", "MONDO:0700223", - "MONDO:0020573", "BFO:0000002", + "MONDO:0020793", "BFO:0000017", "BFO:0000020", - "MONDO:0010542", "MONDO:0016106", - "MONDO:0015470", - "MONDO:0005217", - "MONDO:0016899", - "MONDO:0042489", + "MONDO:0003382", "BFO:0000016", "MONDO:0020120", "MONDO:0019056", - "MONDO:0016139", "MONDO:0700096", - "MONDO:0000591", + "MONDO:0024458", "MONDO:0005218", "MONDO:0005336", "MONDO:0002081", - "MONDO:0016333", "OGMS:0000031", - "MONDO:0005021", "MONDO:0003847", "MONDO:0003939", + "MONDO:0002022", "BFO:0000001", - "MONDO:0010311", + "MONDO:0000462", + "MONDO:0005328", + "MONDO:0018949", ], "subject_closure_label": [ "disease or disorder", - "intrinsic cardiomyopathy", + "eye adnexa disorder", + "disorder of orbital region", "musculoskeletal system disorder", + "eyelid disorder", "hereditary disease", "muscle tissue disorder", - "cardiomyopathy", - "cardiovascular disorder", - "dilated cardiomyopathy", "nervous system disorder", - "familial cardiomyopathy", "obsolete muscular disorder", - "heart disorder", + "eye 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", + "distal myopathy", "neuromuscular disease", "skeletal muscle disorder", "muscular dystrophy", - "inherited disease susceptibility", - "disease susceptibility", - "pulmonary disease, chronic obstructive, susceptibility to", + "eyelids malposition disorder", + "oculopharyngodistal myopathy 1", + "disorder of visual system", + "oculopharyngodistal myopathy", "human disease or disorder", "hereditary skeletal muscle disorder", ], - "subject_label": "Becker muscular dystrophy", + "subject_label": "oculopharyngodistal myopathy 1", "object_namespace": "HP", "object_category": "biolink:PhenotypicQuality", "object_closure": [ "HP:0000001", "UPHENO:0082875", - "UPHENO:0002832", "UPHENO:0075696", - "UPHENO:0080210", + "HP:0011024", "UPHENO:0001001", - "HP:0012086", + "UPHENO:0002443", + "UPHENO:0002471", + "HP:0025270", + "HP:0012719", "UPHENO:0001005", + "UPHENO:0002833", + "HP:0002015", "UPHENO:0001002", - "UPHENO:0083447", + "UPHENO:0002725", "HP:0000118", "BFO:0000002", - "UPHENO:0080216", "BFO:0000020", - "HP:0011277", + "UPHENO:0002433", + "HP:0025032", "UPHENO:0002332", - "HP:0000079", - "UPHENO:0015280", - "UPHENO:0081581", + "HP:0000707", "UPHENO:0001003", "UPHENO:0002536", - "UPHENO:0083450", - "HP:0001939", - "UPHENO:0020584", - "UPHENO:0076692", - "HP:0000119", + "UPHENO:0004523", "BFO:0000001", - "HP:0003110", - "UPHENO:0002642", - "UPHENO:0002442", - "HP:0033072", "PATO:0000001", + "HP:0025031", + "UPHENO:0002474", + "HP:0012638", + "CARO:0000000", + "CARO:0000003", "BFO:0000001", - "BFO:0000003", + "UBERON:0004921", + "UBERON:0001555", + "UBERON:0001016", + "UBERON:0000915", "BFO:0000002", - "BFO:0000015", + "UBERON:0004908", + "UBERON:0001043", "BFO:0000004", - "GO:0008150", "BFO:0000040", "UBERON:0001062", - "CARO:0000000", - "GO:0008152", - "GO:0042592", + "RO:0002577", "UBERON:0000465", - "UBERON:0004122", "UBERON:0000061", - "UBERON:0000463", "UBERON:0010000", "UBERON:0000467", - "UBERON:0000174", "UBERON:0000468", - "UBERON:8450002", - "UBERON:0001088", - "UBERON:0001008", + "UBERON:0000475", + "UBERON:0000064", + "UBERON:0000062", + "UBERON:0004111", + "UBERON:0005409", + "UBERON:0001007", + "UBERON:0011676", + "UBERON:0013701", + "UBERON:0009569", + "UBERON:0013702", + "UBERON:0013522", + "UBERON:0013765", + "UBERON:0005177", + "UBERON:0000025", + "UBERON:0002100", + "UBERON:0005181", + "UBERON:0002075", + "UBERON:0005178", ], "object_closure_label": [ "All (HPO)", - "Abnormality of the urinary system (HPO)", "Phenotypic abnormality (HPO)", - "Abnormality of the genitourinary system (HPO)", - "Abnormality of metabolism/homeostasis (HPO)", - "Abnormality of urine homeostasis (HPO)", - "Abnormality of the urinary system physiology (HPO)", - "Abnormal urinary color (HPO)", - "Abnormal macroscopic urine appearance (HPO)", + "Abnormality of the nervous system (HPO)", + "Dysphagia (HPO)", + "Abnormality of the gastrointestinal tract (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)", + "tube", "anatomical structure", - "excreta", - "organism substance", + "organ", + "organ part", "material anatomical entity", "anatomical system", "multicellular organism", - "renal system", + "organism subdivision", + "thoracic segment of trunk", + "digestive system", + "nervous system", + "esophagus", "anatomical entity", - "urine", - "genitourinary system", + "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", - "excretory system", + "subdivision of organism along main body axis", + "subdivision of tube", + "main body axis", + "body proper", + "digestive system element", ], - "object_label": "Abnormal urinary color (HPO)", + "object_label": "Dysphagia (HPO)", "frequency_qualifier_namespace": "HP", "frequency_qualifier_category": "biolink:PhenotypicFeature", "frequency_qualifier_closure": [ "HP:0000001", + "HP:0040282", "HP:0040279", - "HP:0040281", ], "frequency_qualifier_closure_label": [ "All (HPO)", "Frequency (HPO)", - "Very frequent (HPO)", + "Frequent (HPO)", ], - "frequency_qualifier_label": "Very frequent (HPO)", - "evidence_count": 0, + "frequency_qualifier_label": "Frequent (HPO)", + "evidence_count": 6, }, { - "id": "uuid:29eadc85-1e4f-11ee-871a-692638b4c502", - "original_subject": "Orphanet:98895", + "id": "uuid:5d7fc2a1-212f-11ee-873a-cd90a19c4085", + "original_subject": "OMIM:612937", "predicate": "biolink:has_phenotype", "category": "biolink:DiseaseToPhenotypicFeatureAssociation", "aggregator_knowledge_source": ["infores:monarchinitiative"], - "has_evidence": "ECO:0000304", - "primary_knowledge_source": ["infores:hpo-annotations"], + "has_evidence": ["ECO:0000269"], + "primary_knowledge_source": "infores:hpo-annotations", "provided_by": "hpoa_disease_phenotype_edges", - "publications": ["orphanet:98895"], - "frequency_qualifier": "HP:0040282", - "subject": "MONDO:0010311", - "object": "HP:0002814", + "publications": ["PMID:19576565", "PMID:28803818"], + "frequency_qualifier": "HP:0040280", + "subject": "MONDO:0013049", + "object": "HP:0003236", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ "MONDO:0004994", "MONDO:0000001", - "MONDO:0100167", + "MONDO:0018276", "MONDO:0005071", - "MONDO:0016147", "MONDO:0005267", + "MONDO:0013049", "MONDO:0020121", "MONDO:0004995", "MONDO:0700223", - "MONDO:0020573", + "MONDO:0024322", "BFO:0000002", "BFO:0000017", "BFO:0000020", - "MONDO:0010542", - "MONDO:0016106", - "MONDO:0015470", "MONDO:0005217", - "MONDO:0016899", - "MONDO:0042489", "BFO:0000016", "MONDO:0020120", "MONDO:0019056", - "MONDO:0016139", "MONDO:0700096", "MONDO:0000591", "MONDO:0005218", "MONDO:0005336", "MONDO:0002081", "MONDO:0016333", + "MONDO:0017749", "OGMS:0000031", "MONDO:0005021", "MONDO:0003847", "MONDO:0003939", + "MONDO:0015286", "BFO:0000001", - "MONDO:0010311", + "MONDO:0002320", + "MONDO:0019052", + "MONDO:0005500", + "MONDO:0005066", + "MONDO:0019950", ], "subject_closure_label": [ "disease or disorder", "intrinsic cardiomyopathy", "musculoskeletal system disorder", + "congenital nervous system disorder", "hereditary disease", "muscle tissue disorder", "cardiomyopathy", "cardiovascular disorder", "dilated cardiomyopathy", + "metabolic disease", "nervous system disorder", "familial cardiomyopathy", "obsolete muscular disorder", "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", + "congenital disorder of glycosylation type I", + "DPM3-congenital disorder of glycosylation", + "congenital disorder of glycosylation", "familial dilated cardiomyopathy", - "Duchenne and Becker muscular dystrophy", + "disorder of multiple glycosylation", + "muscular dystrophy-dystroglycanopathy", + "inborn errors of metabolism", "neuromuscular disease", + "congenital muscular dystrophy", "skeletal muscle disorder", "muscular dystrophy", - "inherited disease susceptibility", - "disease susceptibility", - "pulmonary disease, chronic obstructive, susceptibility to", + "disorder of glycosylation", "human disease or disorder", "hereditary skeletal muscle disorder", ], - "subject_label": "Becker muscular dystrophy", + "subject_label": "DPM3-congenital disorder of glycosylation", "object_namespace": "HP", "object_category": "biolink:PhenotypicQuality", "object_closure": [ "HP:0000001", - "HP:0002814", + "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", - "UPHENO:0003070", - "HP:0040064", + "HP:0001939", + "HP:0500165", + "UPHENO:0081547", + "UPHENO:0077826", + "HP:0032180", "BFO:0000001", + "HP:0002086", + "HP:0003236", "PATO:0000001", - "UPHENO:0002830", + "HP:0002795", + "HP:0012415", + "UPHENO:0051612", + "UPHENO:0051804", + "CARO:0000000", "BFO:0000001", + "UBERON:0004120", + "UBERON:0000178", + "BFO:0000003", "BFO:0000002", + "UBERON:0002390", + "BFO:0000015", "BFO:0000004", + "GO:0008150", "BFO:0000040", "UBERON:0001062", - "CARO:0000000", - "UBERON:0000465", + "GO:0008152", + "GO:0005575", "PR:000050567", - "RO:0002577", - "CARO:0000006", - "UBERON:0006058", - "UBERON:0010538", + "CHEBI:24431", + "UBERON:0000465", + "GO:0032991", + "CHEBI:23367", "UBERON:0000061", - "UBERON:0004708", - "CARO:0000003", - "UBERON:0000978", - "UBERON:0002529", + "UBERON:0000463", + "GO:1902494", + "CHEBI:36357", + "CHEBI:33579", "UBERON:0010000", - "UBERON:0015212", - "UBERON:0002101", - "UBERON:0004709", - "UBERON:0010709", - "UBERON:0008784", + "UBERON:0000467", + "UBERON:0006314", + "GO:1990234", + "CHEBI:33839", + "CHEBI:33675", + "CHEBI:138675", "UBERON:0000468", - "UBERON:0000475", - "UBERON:0010707", - "UBERON:0002103", - "UBERON:0000154", - "UBERON:0000026", - "UBERON:0010758", + "UBERON:0001004", + "UBERON:0002193", + "UBERON:0000179", + "GO:0061695", + "CHEBI:16670", + "CHEBI:33302", + "CHEBI:33582", + "CHEBI:33304", + "GO:0002185", + "CHEBI:15841", + "CHEBI:51143", + "CHEBI:50860", + "CHEBI:25806", + "CHEBI:36962", + "CHEBI:16541", + "CHEBI:35352", + "CHEBI:32988", + "CHEBI:33285", + "CHEBI:36963", + "CHEBI:50047", + "CHEBI:37622", + "CHEBI:33256", ], "object_closure_label": [ + "gas molecular entity", + "polypeptide", + "protein polypeptide chain", + "peptide", + "molecular entity", + "chemical entity", + "oxygen molecular entity", + "amide", + "primary amide", + "heteroorganic entity", + "pnictogen molecular entity", + "chalcogen molecular entity", + "main group molecular entity", + "carbon group molecular entity", + "p-block molecular entity", + "macromolecule", + "organonitrogen compound", + "polyatomic entity", + "organochalcogen compound", + "organooxygen compound", + "carboxamide", + "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 the lower limb (HPO)", - "Abnormality of limbs (HPO)", - "appendage", + "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)", + "Abnormal circulating metabolite concentration (HPO)", + "Abnormal circulating creatine kinase concentration (HPO)", + "Abnormal blood oxygen level (HPO)", "anatomical structure", - "posterior region of body", + "blood", + "haemolymphatic fluid", + "organism substance", "material anatomical entity", + "anatomical system", "multicellular organism", - "organism subdivision", - "leg", + "respiratory system", "anatomical entity", - "limb", - "hindlimb", - "limb segment", - "paired limb/fin", - "pelvic appendage", - "multi-limb segment region", - "lower limb segment", + "hemolymphoid system", + "hematopoietic system", + "mesoderm-derived structure", + "bodily fluid", "multicellular anatomical structure", - "paired limb/fin segment", - "appendage girdle complex", - "pelvic complex", - "subdivision of organism along appendicular axis", - "lateral structure", ], - "object_label": "Abnormality of the lower limb (HPO)", + "object_label": "Elevated circulating creatine kinase concentration (HPO)", "frequency_qualifier_namespace": "HP", "frequency_qualifier_category": "biolink:PhenotypicFeature", "frequency_qualifier_closure": [ "HP:0000001", - "HP:0040282", "HP:0040279", + "HP:0040280", ], "frequency_qualifier_closure_label": [ "All (HPO)", "Frequency (HPO)", - "Frequent (HPO)", + "Obligate (HPO)", ], - "frequency_qualifier_label": "Frequent (HPO)", - "evidence_count": 0, + "frequency_qualifier_label": "Obligate (HPO)", + "evidence_count": 5, }, { - "id": "uuid:2211b994-1e4f-11ee-871a-692638b4c502", - "original_subject": "OMIM:300376", + "id": "uuid:64b6842f-212f-11ee-873a-cd90a19c4085", + "original_subject": "OMIM:254090", "predicate": "biolink:has_phenotype", "category": "biolink:DiseaseToPhenotypicFeatureAssociation", "aggregator_knowledge_source": ["infores:monarchinitiative"], - "has_evidence": "ECO:0000304", - "primary_knowledge_source": ["infores:hpo-annotations"], + "has_evidence": ["ECO:0000269"], + "primary_knowledge_source": "infores:hpo-annotations", "provided_by": "hpoa_disease_phenotype_edges", - "publications": ["OMIM:300376"], - "subject": "MONDO:0010311", - "object": "HP:0011675", + "publications": ["PMID:16258657", "OMIM:254090"], + "frequency_qualifier": "HP:0040280", + "subject": "MONDO:0009681", + "object": "HP:0020152", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ - "MONDO:0004994", "MONDO:0000001", - "MONDO:0100167", "MONDO:0005071", - "MONDO:0016147", - "MONDO:0005267", "MONDO:0020121", - "MONDO:0004995", "MONDO:0700223", - "MONDO:0020573", "BFO:0000002", + "MONDO:0019952", "BFO:0000017", "BFO:0000020", - "MONDO:0010542", - "MONDO:0016106", - "MONDO:0015470", - "MONDO:0005217", - "MONDO:0016899", - "MONDO:0042489", + "MONDO:0100225", "BFO:0000016", "MONDO:0020120", "MONDO:0019056", "MONDO:0016139", "MONDO:0700096", - "MONDO:0000591", "MONDO:0005218", "MONDO:0005336", "MONDO:0002081", - "MONDO:0016333", + "MONDO:0009681", "OGMS:0000031", - "MONDO:0005021", "MONDO:0003847", "MONDO:0003939", "BFO:0000001", - "MONDO:0010311", + "MONDO:0002320", + "MONDO:0000355", + "MONDO:0019950", ], "subject_closure_label": [ "disease or disorder", - "intrinsic cardiomyopathy", + "Ullrich congenital muscular dystrophy", "musculoskeletal system disorder", + "congenital nervous system disorder", "hereditary disease", "muscle tissue disorder", - "cardiomyopathy", - "cardiovascular disorder", - "dilated cardiomyopathy", "nervous system disorder", - "familial cardiomyopathy", "obsolete muscular disorder", - "heart disorder", "myopathy", - "Becker muscular dystrophy", - "dilated cardiomyopathy 3B", - "familial isolated dilated cardiomyopathy", - "progressive muscular dystrophy", + "Ullrich congenital muscular dystrophy 1", "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 muscular dystrophy", + "congenital myopathy", "skeletal muscle disorder", "muscular dystrophy", - "inherited disease susceptibility", - "disease susceptibility", - "pulmonary disease, chronic obstructive, susceptibility to", + "collagen 6-related myopathy", "human disease or disorder", "hereditary skeletal muscle disorder", ], - "subject_label": "Becker muscular dystrophy", + "subject_label": "Ullrich congenital muscular dystrophy 1", "object_namespace": "HP", "object_category": "biolink:PhenotypicQuality", "object_closure": [ "HP:0000001", + "HP:0020152", "UPHENO:0082875", + "HP:0001388", "UPHENO:0075696", "UPHENO:0001001", - "HP:0030956", - "HP:0001626", - "UPHENO:0080362", + "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", - "HP:0011025", + "UPHENO:0081440", "BFO:0000001", - "HP:0011675", "PATO:0000001", - "UPHENO:0002406", + "HP:0011843", + "CARO:0000000", "BFO:0000001", - "BFO:0000003", + "UBERON:0002204", "BFO:0000002", - "BFO:0000015", "BFO:0000004", - "GO:0008150", "BFO:0000040", "UBERON:0001062", - "CARO:0000000", - "GO:0032501", "UBERON:0000465", - "PR:000050567", - "UBERON:0004535", - "GO:0003008", "UBERON:0000061", - "GO:0003013", + "UBERON:0034925", "UBERON:0010000", "UBERON:0000467", - "GO:0003015", - "GO:0008015", + "UBERON:0004770", "UBERON:0000468", - "UBERON:0001009", - "GO:0060047", + "UBERON:0011216", + "UBERON:0034921", + "UBERON:0001434", + "UBERON:0004905", + "UBERON:0000982", ], "object_closure_label": [ "All (HPO)", "Phenotypic abnormality (HPO)", - "Abnormality of the cardiovascular system (HPO)", - "Abnormal cardiovascular system physiology (HPO)", - "Arrhythmia (HPO)", - "Abnormality of cardiovascular system electrophysiology (HPO)", + "Abnormality of the skeletal system (HPO)", + "Joint laxity (HPO)", + "Abnormality of joint mobility (HPO)", + "Abnormality of musculoskeletal physiology (HPO)", + "Distal joint laxity (HPO)", + "Abnormality of the musculoskeletal system (HPO)", + "Abnormal joint physiology", "anatomical structure", "material anatomical entity", "anatomical system", "multicellular organism", - "circulatory system", + "skeletal joint", "anatomical entity", - "cardiovascular system", + "skeletal system", + "musculoskeletal system", + "articular system", + "articulation", "multicellular anatomical structure", + "organ system subdivision", + "multi organ part structure", + "anatomical collection", + ], + "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)", ], - "object_label": "Arrhythmia (HPO)", - "evidence_count": 0, + "frequency_qualifier_label": "Obligate (HPO)", + "evidence_count": 5, }, { - "id": "uuid:2211b991-1e4f-11ee-871a-692638b4c502", - "original_subject": "OMIM:300376", + "id": "uuid:628f3d98-212f-11ee-873a-cd90a19c4085", + "original_subject": "OMIM:253601", "predicate": "biolink:has_phenotype", "category": "biolink:DiseaseToPhenotypicFeatureAssociation", "aggregator_knowledge_source": ["infores:monarchinitiative"], - "has_evidence": "ECO:0000304", - "primary_knowledge_source": ["infores:hpo-annotations"], + "has_evidence": ["ECO:0000269"], + "primary_knowledge_source": "infores:hpo-annotations", "provided_by": "hpoa_disease_phenotype_edges", - "publications": ["OMIM:300376"], - "subject": "MONDO:0010311", - "object": "HP:0003707", + "publications": ["PMID:9731527", "PMID:9009996"], + "frequency_qualifier": "HP:0040280", + "subject": "MONDO:0009676", + "object": "HP:0003701", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ - "MONDO:0004994", "MONDO:0000001", - "MONDO:0100167", + "MONDO:0016971", + "MONDO:0000429", + "MONDO:0016145", "MONDO:0005071", - "MONDO:0016147", - "MONDO:0005267", "MONDO:0020121", - "MONDO:0004995", "MONDO:0700223", - "MONDO:0020573", "BFO:0000002", "BFO:0000017", "BFO:0000020", - "MONDO:0010542", + "MONDO:0006025", "MONDO:0016106", - "MONDO:0015470", - "MONDO:0005217", - "MONDO:0016899", - "MONDO:0042489", "BFO:0000016", "MONDO:0020120", "MONDO:0019056", "MONDO:0016139", "MONDO:0700096", - "MONDO:0000591", "MONDO:0005218", "MONDO:0005336", "MONDO:0002081", - "MONDO:0016333", + "MONDO:0009676", "OGMS:0000031", - "MONDO:0005021", "MONDO:0003847", "MONDO:0003939", "BFO:0000001", - "MONDO:0010311", + "MONDO:0015152", ], "subject_closure_label": [ "disease or disorder", - "intrinsic cardiomyopathy", + "autosomal genetic disease", "musculoskeletal system disorder", "hereditary disease", "muscle tissue disorder", - "cardiomyopathy", - "cardiovascular disorder", - "dilated cardiomyopathy", "nervous system disorder", - "familial cardiomyopathy", "obsolete muscular disorder", - "heart disorder", "myopathy", - "Becker muscular dystrophy", - "dilated cardiomyopathy 3B", - "familial isolated dilated cardiomyopathy", + "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 dystrophin", - "familial dilated cardiomyopathy", - "Duchenne and Becker muscular dystrophy", + "qualitative or quantitative defects of dysferlin", + "limb-girdle muscular dystrophy", "neuromuscular disease", "skeletal muscle disorder", "muscular dystrophy", - "inherited disease susceptibility", - "disease susceptibility", - "pulmonary disease, chronic obstructive, susceptibility to", "human disease or disorder", "hereditary skeletal muscle disorder", ], - "subject_label": "Becker muscular dystrophy", + "subject_label": "autosomal recessive limb-girdle muscular dystrophy type 2B", "object_namespace": "HP", "object_category": "biolink:PhenotypicQuality", "object_closure": [ "HP:0000001", - "UPHENO:0002644", - "HP:0002981", - "HP:0002814", + "UPHENO:0082875", + "UPHENO:0075696", + "UPHENO:0002320", "UPHENO:0001001", - "UPHENO:0075952", - "HP:0003707", - "HP:0009127", "UPHENO:0001005", - "UPHENO:0075777", - "HP:0011805", + "HP:0003701", "UPHENO:0001002", - "HP:0001430", + "HP:0001324", "HP:0000118", "BFO:0000002", "BFO:0000020", + "UPHENO:0080555", "HP:0003011", "UPHENO:0002816", - "UPHENO:0081581", + "UPHENO:0002332", + "UPHENO:0080556", "HP:0033127", "UPHENO:0001003", "UPHENO:0002536", - "HP:0001437", - "UPHENO:0076692", - "UPHENO:0003070", - "UPHENO:0002647", - "UPHENO:0076710", - "HP:0040064", "BFO:0000001", + "HP:0011804", "PATO:0000001", - "UPHENO:0002830", + "CARO:0000000", "BFO:0000001", + "UBERON:0000383", + "UBERON:0001015", + "UBERON:0005090", "BFO:0000002", + "UBERON:0001630", "BFO:0000004", "BFO:0000040", "UBERON:0001062", - "CARO:0000000", "UBERON:0000465", - "PR:000050567", - "RO:0002577", - "UBERON:0001015", - "UBERON:0000383", - "CARO:0000006", - "UBERON:0006058", - "UBERON:0010538", - "UBERON:0018254", - "UBERON:0005090", "UBERON:0000061", - "UBERON:0004708", - "UBERON:0007271", - "UBERON:0014792", - "CARO:0000003", - "UBERON:0000978", - "UBERON:0002529", - "UBERON:0001630", "UBERON:0010000", "UBERON:0000467", - "UBERON:0015212", - "UBERON:0002101", - "UBERON:0004709", - "UBERON:0007270", - "UBERON:0004480", - "UBERON:0010709", - "UBERON:0002471", - "UBERON:0008784", - "UBERON:0014892", "UBERON:0000468", - "UBERON:0000475", "UBERON:0000062", "UBERON:0011216", - "UBERON:0010707", - "UBERON:0002103", - "UBERON:0004482", - "UBERON:0003823", - "UBERON:0003661", - "UBERON:0010890", - "UBERON:0000154", - "UBERON:0000026", - "UBERON:0010758", - "UBERON:0004466", - "UBERON:0003663", - "UBERON:0014795", - "UBERON:0006067", - "UBERON:0001383", - "UBERON:0004256", ], "object_closure_label": [ "All (HPO)", "Phenotypic abnormality (HPO)", - "Abnormality of the calf musculature (HPO)", - "Abnormality of the musculature of the lower limbs (HPO)", - "Abnormality of the lower limb (HPO)", - "Abnormality of the calf (HPO)", + "Muscle weakness (HPO)", "Abnormality of the musculature (HPO)", - "Calf muscle pseudohypertrophy (HPO)", - "Abnormality of the musculature of the limbs (HPO)", - "Abnormal skeletal muscle morphology (HPO)", + "Proximal muscle weakness (HPO)", + "Abnormal muscle physiology (HPO)", "Abnormality of the musculoskeletal system (HPO)", - "Abnormality of limbs (HPO)", - "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 of leg", "muscle organ", - "limb", - "hindlimb", - "zeugopod", - "limb segment", - "limb muscle", - "hindlimb muscle", - "hindlimb zeugopod", - "hindlimb zeugopod muscle", - "musculature of leg", - "musculature of limb", - "musculature of lower limb", - "paired limb/fin", - "pelvic appendage", "muscle structure", - "multi-limb segment region", - "musculature of hindlimb zeugopod", - "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", - "pelvic complex muscle", "organ system subdivision", - "musculature of pelvic complex", - "pelvic appendage muscle", - "skeletal muscle organ", - "lateral structure", - "skeletal musculature", ], - "object_label": "Calf muscle pseudohypertrophy (HPO)", - "evidence_count": 0, + "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, }, ], }, diff --git a/backend/tests/fixtures/associations.py b/backend/tests/fixtures/associations.py index 31be3df0d..5efdeaf68 100644 --- a/backend/tests/fixtures/associations.py +++ b/backend/tests/fixtures/associations.py @@ -6,30 +6,23 @@ def associations(): return { "limit": 20, "offset": 0, - "total": 4811, + "total": 4806, "items": [ { - "id": "uuid:1be81e3c-1e4f-11ee-871a-692638b4c502", - "subject": "MONDO:0030355", - "original_subject": "OMIM:619478", + "id": "uuid:c2a45bf5-212f-11ee-873a-cd90a19c4085", + "subject": "MONDO:0008028", + "original_subject": "OMIM:158800", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ "MONDO:0000001", - "MONDO:0030355", - "MONDO:0019303", - "MONDO:0100167", "MONDO:0005071", "MONDO:0020121", + "MONDO:0008028", "MONDO:0700223", - "MONDO:0001347", - "MONDO:0020573", "BFO:0000002", "BFO:0000017", "BFO:0000020", - "MONDO:0016106", - "MONDO:0042489", - "MONDO:0100137", "BFO:0000016", "MONDO:0020120", "MONDO:0019056", @@ -37,186 +30,58 @@ def associations(): "MONDO:0005218", "MONDO:0005336", "MONDO:0002081", - "MONDO:0021147", "OGMS:0000031", "MONDO:0003847", "MONDO:0003939", "BFO:0000001", ], - "subject_label": "facioscapulohumeral muscular dystrophy 4, digenic", + "subject_label": "muscular dystrophy, Barnes type", "subject_closure_label": [ "disease or disorder", - "facioscapulohumeral muscular dystrophy", "musculoskeletal system disorder", "hereditary disease", "muscle tissue disorder", "nervous system disorder", "obsolete muscular disorder", "myopathy", - "progressive muscular dystrophy", + "muscular dystrophy, Barnes type", "neuromuscular disease", - "premature aging syndrome", "skeletal muscle disorder", "muscular dystrophy", - "inherited disease susceptibility", - "disorder of development or morphogenesis", - "facioscapulohumeral muscular dystrophy 4, digenic", - "disease susceptibility", - "telomere syndrome", - "pulmonary disease, chronic obstructive, susceptibility to", "human disease or disorder", "hereditary skeletal muscle disorder", ], - "predicate": "biolink:has_phenotype", - "object": "HP:0003484", + "predicate": "biolink:has_mode_of_inheritance", + "object": "HP:0000006", "original_object": None, "object_namespace": "HP", - "object_category": "biolink:PhenotypicQuality", + "object_category": "biolink:GeneticInheritance", "object_closure": [ "HP:0000001", - "UPHENO:0002649", - "UPHENO:0082875", - "UPHENO:0075696", - "UPHENO:0002320", - "UPHENO:0001001", - "HP:0003325", - "HP:0003484", - "UPHENO:0080563", - "HP:0009127", - "UPHENO:0001005", - "HP:0011805", - "UPHENO:0001002", - "HP:0001324", - "HP:0003690", - "HP:0000118", - "BFO:0000002", - "HP:0001446", - "HP:0002817", - "BFO:0000020", - "UPHENO:0080555", - "HP:0003011", - "UPHENO:0002816", - "UPHENO:0002332", - "UPHENO:0080556", - "UPHENO:0081581", - "HP:0033127", - "UPHENO:0001003", - "UPHENO:0002536", - "UPHENO:0076692", - "UPHENO:0002647", - "UPHENO:0076710", - "HP:0040064", - "BFO:0000001", - "HP:0011804", - "PATO:0000001", - "UPHENO:0002880", - "UPHENO:0002830", - "BFO:0000001", - "BFO:0000002", - "BFO:0000004", - "BFO:0000040", - "UBERON:0001062", - "CARO:0000000", - "UBERON:0000465", - "PR:000050567", - "RO:0002577", - "UBERON:0001015", - "UBERON:0000383", - "CARO:0000006", - "UBERON:0006058", - "UBERON:0010538", - "UBERON:0005090", - "UBERON:0000061", - "UBERON:0004708", - "UBERON:0007271", - "UBERON:0014793", - "CARO:0000003", - "UBERON:0001460", - "UBERON:0002529", - "UBERON:0001630", - "UBERON:0010000", - "UBERON:0000467", - "UBERON:0015212", - "UBERON:0004710", - "UBERON:0002101", - "UBERON:0004480", - "UBERON:0007269", - "UBERON:0010708", - "UBERON:0008785", - "UBERON:0000468", - "UBERON:0000475", - "UBERON:0000062", - "UBERON:0011216", - "UBERON:0010707", - "UBERON:0002102", - "UBERON:0004481", - "UBERON:0000153", - "UBERON:0000026", - "UBERON:0010758", + "HP:0000006", + "HP:0000005", + "HP:0034345", ], - "object_label": "Upper limb muscle weakness (HPO)", + "object_label": "Autosomal dominant inheritance (HPO)", "object_closure_label": [ "All (HPO)", - "Phenotypic abnormality (HPO)", - "Muscle weakness (HPO)", - "Abnormality of the musculature of the upper limbs (HPO)", - "Abnormality of the upper limb (HPO)", - "Abnormality of the musculature (HPO)", - "Limb-girdle muscle weakness (HPO)", - "Upper limb muscle weakness (HPO)", - "Limb muscle weakness (HPO)", - "Abnormality of the musculature of the limbs (HPO)", - "Abnormal muscle physiology (HPO)", - "Abnormal skeletal muscle morphology (HPO)", - "Abnormality of the musculoskeletal system (HPO)", - "Abnormality of limbs (HPO)", - "appendage", - "anatomical structure", - "organ", - "anterior region of body", - "musculature of body", - "material anatomical entity", - "anatomical system", - "multicellular organism", - "organism subdivision", - "musculature", - "anatomical entity", - "arm", - "muscle organ", - "limb", - "forelimb", - "limb segment", - "musculature of limb", - "musculature of upper limb", - "paired limb/fin", - "pectoral appendage", - "muscle structure", - "multi-limb segment region", - "pectoral appendage musculature", - "appendage musculature", - "upper limb segment", - "multicellular anatomical structure", - "paired limb/fin segment", - "appendage girdle complex", - "pectoral complex", - "subdivision of organism along appendicular axis", - "organ system subdivision", - "musculature of pectoral complex", - "lateral structure", + "Mode of inheritance (HPO)", + "Autosomal dominant inheritance (HPO)", + "Mendelian inheritance", ], - "primary_knowledge_source": ["infores:hpo-annotations"], + "primary_knowledge_source": "infores:hpo-annotations", "aggregator_knowledge_source": ["infores:monarchinitiative"], - "category": "biolink:DiseaseToPhenotypicFeatureAssociation", + "category": "biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation", "negated": None, - "provided_by": "hpoa_disease_phenotype_edges", - "publications": ["PMID:27153398"], + "provided_by": "hpoa_disease_mode_of_inheritance_edges", + "publications": ["OMIM:158800"], "qualifiers": [], "frequency_qualifier": None, - "has_evidence": "ECO:0000269", + "has_evidence": ["ECO:0000304"], "onset_qualifier": None, "sex_qualifier": None, "stage_qualifier": None, - "evidence_count": 0, + "evidence_count": 4, "pathway": None, "frequency_qualifier_label": None, "frequency_qualifier_namespace": None, @@ -240,26 +105,24 @@ def associations(): "stage_qualifier_closure_label": [], }, { - "id": "uuid:1fd70821-1e4f-11ee-871a-692638b4c502", - "subject": "MONDO:0014782", - "original_subject": "OMIM:616812", + "id": "uuid:c304bcf2-212f-11ee-873a-cd90a19c4085", + "subject": "MONDO:0008030", + "original_subject": "OMIM:158900", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ + "MONDO:0008030", "MONDO:0000001", - "MONDO:0016971", - "MONDO:0000429", - "MONDO:0100167", + "MONDO:0019303", "MONDO:0005071", "MONDO:0020121", "MONDO:0700223", - "MONDO:0020573", + "MONDO:0001347", "BFO:0000002", "BFO:0000017", "BFO:0000020", - "MONDO:0006025", "MONDO:0016106", - "MONDO:0042489", + "MONDO:0100137", "BFO:0000016", "MONDO:0020120", "MONDO:0019056", @@ -267,117 +130,64 @@ def associations(): "MONDO:0005218", "MONDO:0005336", "MONDO:0002081", + "MONDO:0021147", "OGMS:0000031", "MONDO:0003847", - "MONDO:0014782", "MONDO:0003939", "BFO:0000001", - "MONDO:0015152", ], - "subject_label": "autosomal recessive limb-girdle muscular dystrophy type 2X", + "subject_label": "facioscapulohumeral muscular dystrophy 1", "subject_closure_label": [ "disease or disorder", - "autosomal genetic disease", + "facioscapulohumeral muscular dystrophy", "musculoskeletal system disorder", "hereditary disease", "muscle tissue disorder", "nervous system disorder", "obsolete muscular disorder", "myopathy", - "autosomal recessive disease", - "autosomal recessive limb-girdle muscular dystrophy type 2X", - "autosomal recessive limb-girdle muscular dystrophy", + "facioscapulohumeral muscular dystrophy 1", "progressive muscular dystrophy", - "limb-girdle muscular dystrophy", "neuromuscular disease", + "premature aging syndrome", "skeletal muscle disorder", "muscular dystrophy", - "inherited disease susceptibility", - "disease susceptibility", - "pulmonary disease, chronic obstructive, susceptibility to", + "disorder of development or morphogenesis", + "telomere syndrome", "human disease or disorder", "hereditary skeletal muscle disorder", ], - "predicate": "biolink:has_phenotype", - "object": "HP:0003546", + "predicate": "biolink:has_mode_of_inheritance", + "object": "HP:0000006", "original_object": None, "object_namespace": "HP", - "object_category": "biolink:PhenotypicQuality", + "object_category": "biolink:GeneticInheritance", "object_closure": [ "HP:0000001", - "UPHENO:0082875", - "UPHENO:0075696", - "UPHENO:0002320", - "UPHENO:0001001", - "UPHENO:0001005", - "UPHENO:0001002", - "HP:0004302", - "HP:0000118", - "BFO:0000002", - "BFO:0000020", - "HP:0003011", - "UPHENO:0002816", - "HP:0003546", - "UPHENO:0002332", - "HP:0033127", - "UPHENO:0001003", - "UPHENO:0002536", - "BFO:0000001", - "HP:0011804", - "PATO:0000001", - "BFO:0000001", - "BFO:0000002", - "BFO:0000004", - "BFO:0000040", - "UBERON:0001062", - "CARO:0000000", - "UBERON:0000465", - "UBERON:0001015", - "UBERON:0000383", - "UBERON:0005090", - "UBERON:0000061", - "UBERON:0001630", - "UBERON:0010000", - "UBERON:0000467", - "UBERON:0000468", - "UBERON:0000062", - "UBERON:0011216", + "HP:0000006", + "HP:0000005", + "HP:0034345", ], - "object_label": "Exercise intolerance (HPO)", + "object_label": "Autosomal dominant inheritance (HPO)", "object_closure_label": [ "All (HPO)", - "Phenotypic abnormality (HPO)", - "Abnormality of the musculature (HPO)", - "Exercise intolerance (HPO)", - "Functional motor deficit (HPO)", - "Abnormal muscle physiology (HPO)", - "Abnormality of the musculoskeletal system (HPO)", - "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", + "Mode of inheritance (HPO)", + "Autosomal dominant inheritance (HPO)", + "Mendelian inheritance", ], - "primary_knowledge_source": ["infores:hpo-annotations"], + "primary_knowledge_source": "infores:hpo-annotations", "aggregator_knowledge_source": ["infores:monarchinitiative"], - "category": "biolink:DiseaseToPhenotypicFeatureAssociation", + "category": "biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation", "negated": None, - "provided_by": "hpoa_disease_phenotype_edges", - "publications": ["PMID:26642364"], + "provided_by": "hpoa_disease_mode_of_inheritance_edges", + "publications": ["OMIM:158900"], "qualifiers": [], "frequency_qualifier": None, - "has_evidence": "ECO:0000269", + "has_evidence": ["ECO:0000501"], "onset_qualifier": None, "sex_qualifier": None, "stage_qualifier": None, - "evidence_count": 0, + "evidence_count": 4, "pathway": None, "frequency_qualifier_label": None, "frequency_qualifier_namespace": None, @@ -401,229 +211,107 @@ def associations(): "stage_qualifier_closure_label": [], }, { - "id": "uuid:1e041fb7-1e4f-11ee-871a-692638b4c502", - "subject": "MONDO:0008030", - "original_subject": "OMIM:158900", + "id": "uuid:c3cdad58-212f-11ee-873a-cd90a19c4085", + "subject": "MONDO:0008034", + "original_subject": "OMIM:159050", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ - "MONDO:0008030", + "MONDO:0004994", "MONDO:0000001", - "MONDO:0019303", - "MONDO:0100167", + "MONDO:0008034", "MONDO:0005071", + "MONDO:0016147", + "MONDO:0005267", "MONDO:0020121", + "MONDO:0004995", "MONDO:0700223", - "MONDO:0001347", - "MONDO:0020573", "BFO:0000002", "BFO:0000017", "BFO:0000020", + "MONDO:0010542", "MONDO:0016106", - "MONDO:0042489", - "MONDO:0100137", + "MONDO:0015470", + "MONDO:0005217", + "MONDO:0016899", "BFO:0000016", "MONDO:0020120", "MONDO:0019056", + "MONDO:0016139", "MONDO:0700096", + "MONDO:0000591", "MONDO:0005218", "MONDO:0005336", "MONDO:0002081", - "MONDO:0021147", + "MONDO:0016333", "OGMS:0000031", + "MONDO:0005021", "MONDO:0003847", "MONDO:0003939", "BFO:0000001", + "MONDO:0010311", ], - "subject_label": "facioscapulohumeral muscular dystrophy 1", + "subject_label": "muscular dystrophy, pseudohypertrophic, with Internalized capillaries", "subject_closure_label": [ "disease or disorder", - "facioscapulohumeral muscular dystrophy", + "intrinsic cardiomyopathy", "musculoskeletal system disorder", "hereditary disease", "muscle tissue disorder", + "cardiomyopathy", + "cardiovascular disorder", + "dilated cardiomyopathy", "nervous system disorder", + "familial cardiomyopathy", "obsolete muscular disorder", + "heart disorder", "myopathy", - "facioscapulohumeral muscular dystrophy 1", + "muscular dystrophy, pseudohypertrophic, with Internalized capillaries", + "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", - "premature aging syndrome", "skeletal muscle disorder", "muscular dystrophy", - "inherited disease susceptibility", - "disorder of development or morphogenesis", - "disease susceptibility", - "telomere syndrome", - "pulmonary disease, chronic obstructive, susceptibility to", "human disease or disorder", "hereditary skeletal muscle disorder", ], - "predicate": "biolink:has_phenotype", - "object": "HP:0003547", + "predicate": "biolink:has_mode_of_inheritance", + "object": "HP:0000006", "original_object": None, "object_namespace": "HP", - "object_category": "biolink:PhenotypicQuality", + "object_category": "biolink:GeneticInheritance", "object_closure": [ "HP:0000001", - "UPHENO:0002649", - "UPHENO:0082875", - "UPHENO:0075696", - "UPHENO:0002320", - "UPHENO:0001001", - "HP:0003325", - "UPHENO:0080565", - "HP:0009127", - "UPHENO:0001005", - "HP:0011805", - "UPHENO:0001002", - "HP:0001324", - "HP:0000118", - "BFO:0000002", - "HP:0001435", - "HP:0001446", - "HP:0002817", - "BFO:0000020", - "UPHENO:0080555", - "HP:0003011", - "UPHENO:0002816", - "UPHENO:0002332", - "UPHENO:0080556", - "UPHENO:0002982", - "UPHENO:0081581", - "HP:0003547", - "HP:0033127", - "UPHENO:0001003", - "UPHENO:0002536", - "UPHENO:0076692", - "UPHENO:0002647", - "UPHENO:0076710", - "HP:0040064", - "BFO:0000001", - "HP:0011804", - "PATO:0000001", - "UPHENO:0002880", - "UPHENO:0002830", - "BFO:0000001", - "BFO:0000002", - "BFO:0000004", - "BFO:0000040", - "UBERON:0001062", - "CARO:0000000", - "UBERON:0000465", - "PR:000050567", - "RO:0002577", - "UBERON:0001015", - "UBERON:0000383", - "CARO:0000006", - "UBERON:0006058", - "UBERON:0010538", - "UBERON:0018254", - "UBERON:0005090", - "UBERON:0000061", - "UBERON:0004708", - "UBERON:0007271", - "UBERON:0014793", - "CARO:0000003", - "UBERON:0001460", - "UBERON:0002529", - "UBERON:0001630", - "UBERON:0010000", - "UBERON:0000467", - "UBERON:0015212", - "UBERON:0004710", - "UBERON:0002101", - "UBERON:0004480", - "UBERON:0007269", - "UBERON:0004471", - "UBERON:0007823", - "UBERON:0010708", - "UBERON:0008785", - "UBERON:0014892", - "UBERON:0000468", - "UBERON:0000475", - "UBERON:0000062", - "UBERON:0011216", - "UBERON:0001421", - "UBERON:0010707", - "UBERON:0002102", - "UBERON:0004481", - "UBERON:0010891", - "UBERON:0000153", - "UBERON:0000026", - "UBERON:0010758", - "UBERON:0008196", + "HP:0000006", + "HP:0000005", + "HP:0034345", ], - "object_label": "Shoulder girdle muscle weakness (HPO)", + "object_label": "Autosomal dominant inheritance (HPO)", "object_closure_label": [ "All (HPO)", - "Phenotypic abnormality (HPO)", - "Muscle weakness (HPO)", - "Abnormality of the shoulder girdle musculature (HPO)", - "Abnormality of the musculature of the upper limbs (HPO)", - "Abnormality of the upper limb (HPO)", - "Abnormality of the musculature (HPO)", - "Limb-girdle muscle weakness (HPO)", - "Shoulder girdle muscle weakness (HPO)", - "Abnormality of the musculature of the limbs (HPO)", - "Abnormal muscle physiology (HPO)", - "Abnormal skeletal muscle morphology (HPO)", - "Abnormality of the musculoskeletal system (HPO)", - "Abnormality of limbs (HPO)", - "appendage", - "anatomical structure", - "organ", - "anterior region of body", - "musculature of body", - "material anatomical entity", - "anatomical system", - "multicellular organism", - "organism subdivision", - "musculature", - "anatomical entity", - "pectoral girdle region", - "arm", - "muscle organ", - "limb", - "forelimb", - "limb segment", - "musculature of pectoral girdle", - "musculature of limb", - "musculature of upper limb", - "paired limb/fin", - "pectoral appendage", - "muscle structure", - "multi-limb segment region", - "pectoral appendage musculature", - "appendage musculature", - "appendage girdle region", - "muscle of pectoral girdle", - "upper limb segment", - "multicellular anatomical structure", - "paired limb/fin segment", - "appendage girdle complex", - "pectoral complex", - "subdivision of organism along appendicular axis", - "pectoral complex muscle", - "organ system subdivision", - "musculature of pectoral complex", - "skeletal muscle organ", - "lateral structure", - "skeletal musculature", + "Mode of inheritance (HPO)", + "Autosomal dominant inheritance (HPO)", + "Mendelian inheritance", ], - "primary_knowledge_source": ["infores:hpo-annotations"], + "primary_knowledge_source": "infores:hpo-annotations", "aggregator_knowledge_source": ["infores:monarchinitiative"], - "category": "biolink:DiseaseToPhenotypicFeatureAssociation", + "category": "biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation", "negated": None, - "provided_by": "hpoa_disease_phenotype_edges", - "publications": ["OMIM:158900"], + "provided_by": "hpoa_disease_mode_of_inheritance_edges", + "publications": ["OMIM:159050"], "qualifiers": [], "frequency_qualifier": None, - "has_evidence": "ECO:0000304", + "has_evidence": ["ECO:0000501"], "onset_qualifier": None, "sex_qualifier": None, "stage_qualifier": None, - "evidence_count": 0, + "evidence_count": 4, "pathway": None, "frequency_qualifier_label": None, "frequency_qualifier_namespace": None, @@ -647,30 +335,23 @@ def associations(): "stage_qualifier_closure_label": [], }, { - "id": "uuid:1ae78897-1e4f-11ee-871a-692638b4c502", - "subject": "MONDO:0009683", - "original_subject": "OMIM:254110", + "id": "uuid:c3367408-212f-11ee-873a-cd90a19c4085", + "subject": "MONDO:0008049", + "original_subject": "OMIM:160300", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ "MONDO:0000001", - "MONDO:0016971", - "MONDO:0000429", - "MONDO:0100167", "MONDO:0005071", "MONDO:0020121", "MONDO:0700223", - "MONDO:0020573", "BFO:0000002", "BFO:0000017", + "MONDO:0008049", "BFO:0000020", - "MONDO:0006025", - "MONDO:0016106", - "MONDO:0042489", "BFO:0000016", "MONDO:0020120", "MONDO:0019056", - "MONDO:0016139", "MONDO:0700096", "MONDO:0005218", "MONDO:0005336", @@ -679,201 +360,56 @@ def associations(): "MONDO:0003847", "MONDO:0003939", "BFO:0000001", - "MONDO:0015152", - "MONDO:0016153", - "MONDO:0009683", + "MONDO:0018949", ], - "subject_label": "autosomal recessive limb-girdle muscular dystrophy type 2H", + "subject_label": "myopathy, distal, infantile-onset", "subject_closure_label": [ "disease or disorder", - "autosomal genetic disease", "musculoskeletal system disorder", "hereditary disease", "muscle tissue disorder", "nervous system disorder", "obsolete muscular 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", + "myopathy, distal, infantile-onset", + "distal myopathy", "neuromuscular disease", "skeletal muscle disorder", "muscular dystrophy", - "inherited disease susceptibility", - "disease susceptibility", - "pulmonary disease, chronic obstructive, susceptibility to", "human disease or disorder", "hereditary skeletal muscle disorder", ], - "predicate": "biolink:has_phenotype", - "object": "HP:0003547", + "predicate": "biolink:has_mode_of_inheritance", + "object": "HP:0000006", "original_object": None, "object_namespace": "HP", - "object_category": "biolink:PhenotypicQuality", + "object_category": "biolink:GeneticInheritance", "object_closure": [ "HP:0000001", - "UPHENO:0002649", - "UPHENO:0082875", - "UPHENO:0075696", - "UPHENO:0002320", - "UPHENO:0001001", - "HP:0003325", - "UPHENO:0080565", - "HP:0009127", - "UPHENO:0001005", - "HP:0011805", - "UPHENO:0001002", - "HP:0001324", - "HP:0000118", - "BFO:0000002", - "HP:0001435", - "HP:0001446", - "HP:0002817", - "BFO:0000020", - "UPHENO:0080555", - "HP:0003011", - "UPHENO:0002816", - "UPHENO:0002332", - "UPHENO:0080556", - "UPHENO:0002982", - "UPHENO:0081581", - "HP:0003547", - "HP:0033127", - "UPHENO:0001003", - "UPHENO:0002536", - "UPHENO:0076692", - "UPHENO:0002647", - "UPHENO:0076710", - "HP:0040064", - "BFO:0000001", - "HP:0011804", - "PATO:0000001", - "UPHENO:0002880", - "UPHENO:0002830", - "BFO:0000001", - "BFO:0000002", - "BFO:0000004", - "BFO:0000040", - "UBERON:0001062", - "CARO:0000000", - "UBERON:0000465", - "PR:000050567", - "RO:0002577", - "UBERON:0001015", - "UBERON:0000383", - "CARO:0000006", - "UBERON:0006058", - "UBERON:0010538", - "UBERON:0018254", - "UBERON:0005090", - "UBERON:0000061", - "UBERON:0004708", - "UBERON:0007271", - "UBERON:0014793", - "CARO:0000003", - "UBERON:0001460", - "UBERON:0002529", - "UBERON:0001630", - "UBERON:0010000", - "UBERON:0000467", - "UBERON:0015212", - "UBERON:0004710", - "UBERON:0002101", - "UBERON:0004480", - "UBERON:0007269", - "UBERON:0004471", - "UBERON:0007823", - "UBERON:0010708", - "UBERON:0008785", - "UBERON:0014892", - "UBERON:0000468", - "UBERON:0000475", - "UBERON:0000062", - "UBERON:0011216", - "UBERON:0001421", - "UBERON:0010707", - "UBERON:0002102", - "UBERON:0004481", - "UBERON:0010891", - "UBERON:0000153", - "UBERON:0000026", - "UBERON:0010758", - "UBERON:0008196", + "HP:0000006", + "HP:0000005", + "HP:0034345", ], - "object_label": "Shoulder girdle muscle weakness (HPO)", + "object_label": "Autosomal dominant inheritance (HPO)", "object_closure_label": [ "All (HPO)", - "Phenotypic abnormality (HPO)", - "Muscle weakness (HPO)", - "Abnormality of the shoulder girdle musculature (HPO)", - "Abnormality of the musculature of the upper limbs (HPO)", - "Abnormality of the upper limb (HPO)", - "Abnormality of the musculature (HPO)", - "Limb-girdle muscle weakness (HPO)", - "Shoulder girdle muscle weakness (HPO)", - "Abnormality of the musculature of the limbs (HPO)", - "Abnormal muscle physiology (HPO)", - "Abnormal skeletal muscle morphology (HPO)", - "Abnormality of the musculoskeletal system (HPO)", - "Abnormality of limbs (HPO)", - "appendage", - "anatomical structure", - "organ", - "anterior region of body", - "musculature of body", - "material anatomical entity", - "anatomical system", - "multicellular organism", - "organism subdivision", - "musculature", - "anatomical entity", - "pectoral girdle region", - "arm", - "muscle organ", - "limb", - "forelimb", - "limb segment", - "musculature of pectoral girdle", - "musculature of limb", - "musculature of upper limb", - "paired limb/fin", - "pectoral appendage", - "muscle structure", - "multi-limb segment region", - "pectoral appendage musculature", - "appendage musculature", - "appendage girdle region", - "muscle of pectoral girdle", - "upper limb segment", - "multicellular anatomical structure", - "paired limb/fin segment", - "appendage girdle complex", - "pectoral complex", - "subdivision of organism along appendicular axis", - "pectoral complex muscle", - "organ system subdivision", - "musculature of pectoral complex", - "skeletal muscle organ", - "lateral structure", - "skeletal musculature", + "Mode of inheritance (HPO)", + "Autosomal dominant inheritance (HPO)", + "Mendelian inheritance", ], - "primary_knowledge_source": ["infores:hpo-annotations"], + "primary_knowledge_source": "infores:hpo-annotations", "aggregator_knowledge_source": ["infores:monarchinitiative"], - "category": "biolink:DiseaseToPhenotypicFeatureAssociation", + "category": "biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation", "negated": None, - "provided_by": "hpoa_disease_phenotype_edges", - "publications": ["OMIM:254110"], + "provided_by": "hpoa_disease_mode_of_inheritance_edges", + "publications": ["OMIM:160300"], "qualifiers": [], "frequency_qualifier": None, - "has_evidence": "ECO:0000501", + "has_evidence": ["ECO:0000304"], "onset_qualifier": None, "sex_qualifier": None, "stage_qualifier": None, - "evidence_count": 0, + "evidence_count": 4, "pathway": None, "frequency_qualifier_label": None, "frequency_qualifier_namespace": None, @@ -897,26 +433,26 @@ def associations(): "stage_qualifier_closure_label": [], }, { - "id": "uuid:1e041dff-1e4f-11ee-871a-692638b4c502", - "subject": "MONDO:0010678", - "original_subject": "OMIM:310095", + "id": "uuid:c39b4534-212f-11ee-873a-cd90a19c4085", + "subject": "MONDO:0008050", + "original_subject": "OMIM:160500", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ "MONDO:0000001", - "MONDO:0100167", "MONDO:0005071", "MONDO:0020121", - "MONDO:0010678", "MONDO:0700223", - "MONDO:0020573", "BFO:0000002", + "MONDO:0019952", "BFO:0000017", "BFO:0000020", - "MONDO:0042489", + "MONDO:0008050", + "MONDO:0016195", "BFO:0000016", "MONDO:0020120", "MONDO:0019056", + "MONDO:0016139", "MONDO:0700096", "MONDO:0005218", "MONDO:0005336", @@ -925,191 +461,61 @@ def associations(): "MONDO:0003847", "MONDO:0003939", "BFO:0000001", + "MONDO:0002320", + "MONDO:0018949", ], - "subject_label": "muscular dystrophy, progressive Pectorodorsal", + "subject_label": "MYH7-related skeletal myopathy", "subject_closure_label": [ "disease or disorder", "musculoskeletal system disorder", + "congenital nervous system disorder", "hereditary disease", "muscle tissue disorder", "nervous system disorder", "obsolete muscular disorder", "myopathy", - "muscular dystrophy, progressive Pectorodorsal", + "MYH7-related skeletal myopathy", + "qualitative or quantitative protein defects in neuromuscular diseases", + "qualitative or quantitative defects of beta-myosin heavy chain (MYH7)", + "distal myopathy", "neuromuscular disease", + "congenital myopathy", "skeletal muscle disorder", "muscular dystrophy", - "inherited disease susceptibility", - "disease susceptibility", - "pulmonary disease, chronic obstructive, susceptibility to", "human disease or disorder", "hereditary skeletal muscle disorder", ], - "predicate": "biolink:has_phenotype", - "object": "HP:0003547", + "predicate": "biolink:has_mode_of_inheritance", + "object": "HP:0000006", "original_object": None, "object_namespace": "HP", - "object_category": "biolink:PhenotypicQuality", + "object_category": "biolink:GeneticInheritance", "object_closure": [ "HP:0000001", - "UPHENO:0002649", - "UPHENO:0082875", - "UPHENO:0075696", - "UPHENO:0002320", - "UPHENO:0001001", - "HP:0003325", - "UPHENO:0080565", - "HP:0009127", - "UPHENO:0001005", - "HP:0011805", - "UPHENO:0001002", - "HP:0001324", - "HP:0000118", - "BFO:0000002", - "HP:0001435", - "HP:0001446", - "HP:0002817", - "BFO:0000020", - "UPHENO:0080555", - "HP:0003011", - "UPHENO:0002816", - "UPHENO:0002332", - "UPHENO:0080556", - "UPHENO:0002982", - "UPHENO:0081581", - "HP:0003547", - "HP:0033127", - "UPHENO:0001003", - "UPHENO:0002536", - "UPHENO:0076692", - "UPHENO:0002647", - "UPHENO:0076710", - "HP:0040064", - "BFO:0000001", - "HP:0011804", - "PATO:0000001", - "UPHENO:0002880", - "UPHENO:0002830", - "BFO:0000001", - "BFO:0000002", - "BFO:0000004", - "BFO:0000040", - "UBERON:0001062", - "CARO:0000000", - "UBERON:0000465", - "PR:000050567", - "RO:0002577", - "UBERON:0001015", - "UBERON:0000383", - "CARO:0000006", - "UBERON:0006058", - "UBERON:0010538", - "UBERON:0018254", - "UBERON:0005090", - "UBERON:0000061", - "UBERON:0004708", - "UBERON:0007271", - "UBERON:0014793", - "CARO:0000003", - "UBERON:0001460", - "UBERON:0002529", - "UBERON:0001630", - "UBERON:0010000", - "UBERON:0000467", - "UBERON:0015212", - "UBERON:0004710", - "UBERON:0002101", - "UBERON:0004480", - "UBERON:0007269", - "UBERON:0004471", - "UBERON:0007823", - "UBERON:0010708", - "UBERON:0008785", - "UBERON:0014892", - "UBERON:0000468", - "UBERON:0000475", - "UBERON:0000062", - "UBERON:0011216", - "UBERON:0001421", - "UBERON:0010707", - "UBERON:0002102", - "UBERON:0004481", - "UBERON:0010891", - "UBERON:0000153", - "UBERON:0000026", - "UBERON:0010758", - "UBERON:0008196", + "HP:0000006", + "HP:0000005", + "HP:0034345", ], - "object_label": "Shoulder girdle muscle weakness (HPO)", + "object_label": "Autosomal dominant inheritance (HPO)", "object_closure_label": [ "All (HPO)", - "Phenotypic abnormality (HPO)", - "Muscle weakness (HPO)", - "Abnormality of the shoulder girdle musculature (HPO)", - "Abnormality of the musculature of the upper limbs (HPO)", - "Abnormality of the upper limb (HPO)", - "Abnormality of the musculature (HPO)", - "Limb-girdle muscle weakness (HPO)", - "Shoulder girdle muscle weakness (HPO)", - "Abnormality of the musculature of the limbs (HPO)", - "Abnormal muscle physiology (HPO)", - "Abnormal skeletal muscle morphology (HPO)", - "Abnormality of the musculoskeletal system (HPO)", - "Abnormality of limbs (HPO)", - "appendage", - "anatomical structure", - "organ", - "anterior region of body", - "musculature of body", - "material anatomical entity", - "anatomical system", - "multicellular organism", - "organism subdivision", - "musculature", - "anatomical entity", - "pectoral girdle region", - "arm", - "muscle organ", - "limb", - "forelimb", - "limb segment", - "musculature of pectoral girdle", - "musculature of limb", - "musculature of upper limb", - "paired limb/fin", - "pectoral appendage", - "muscle structure", - "multi-limb segment region", - "pectoral appendage musculature", - "appendage musculature", - "appendage girdle region", - "muscle of pectoral girdle", - "upper limb segment", - "multicellular anatomical structure", - "paired limb/fin segment", - "appendage girdle complex", - "pectoral complex", - "subdivision of organism along appendicular axis", - "pectoral complex muscle", - "organ system subdivision", - "musculature of pectoral complex", - "skeletal muscle organ", - "lateral structure", - "skeletal musculature", + "Mode of inheritance (HPO)", + "Autosomal dominant inheritance (HPO)", + "Mendelian inheritance", ], - "primary_knowledge_source": ["infores:hpo-annotations"], + "primary_knowledge_source": "infores:hpo-annotations", "aggregator_knowledge_source": ["infores:monarchinitiative"], - "category": "biolink:DiseaseToPhenotypicFeatureAssociation", + "category": "biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation", "negated": None, - "provided_by": "hpoa_disease_phenotype_edges", - "publications": ["OMIM:310095"], + "provided_by": "hpoa_disease_mode_of_inheritance_edges", + "publications": ["PMID:15322983"], "qualifiers": [], "frequency_qualifier": None, - "has_evidence": "ECO:0000501", + "has_evidence": ["ECO:0000269"], "onset_qualifier": None, "sex_qualifier": None, "stage_qualifier": None, - "evidence_count": 0, + "evidence_count": 4, "pathway": None, "frequency_qualifier_label": None, "frequency_qualifier_namespace": None, @@ -1133,243 +539,113 @@ def associations(): "stage_qualifier_closure_label": [], }, { - "id": "uuid:22fcfea0-1e4f-11ee-871a-692638b4c502", - "subject": "MONDO:0011362", - "original_subject": "OMIM:603689", + "id": "uuid:c2d3e237-212f-11ee-873a-cd90a19c4085", + "subject": "MONDO:0008056", + "original_subject": "OMIM:160900", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ + "MONDO:0004994", + "MONDO:0020158", "MONDO:0000001", - "MONDO:0016112", - "MONDO:0000429", - "MONDO:0100167", + "MONDO:0016107", "MONDO:0005071", + "MONDO:0005267", "MONDO:0020121", - "MONDO:0100175", + "MONDO:0005045", + "MONDO:0004995", "MONDO:0700223", - "MONDO:0020573", "BFO:0000002", - "MONDO:0019952", "BFO:0000017", "BFO:0000020", "MONDO:0016106", - "MONDO:0042489", - "MONDO:0016191", + "MONDO:0005217", + "MONDO:0024573", + "MONDO:0003382", "BFO:0000016", "MONDO:0020120", "MONDO:0019056", - "MONDO:0100494", - "MONDO:0016139", + "MONDO:0008056", "MONDO:0700096", + "MONDO:0000591", + "MONDO:0024458", "MONDO:0005218", "MONDO:0005336", "MONDO:0002081", - "MONDO:0000426", - "MONDO:0011362", + "MONDO:0002254", "OGMS:0000031", "MONDO:0003847", "MONDO:0003939", + "MONDO:0002022", + "MONDO:0016120", "BFO:0000001", - "MONDO:0002320", - "MONDO:0016108", - "MONDO:0018949", + "MONDO:0000462", + "MONDO:0005328", ], - "subject_label": "myopathy, myofibrillar, 9, with early respiratory failure", + "subject_label": "myotonic dystrophy type 1", "subject_closure_label": [ "disease or disorder", - "autosomal dominant disease", - "autosomal genetic disease", + "eye adnexa disorder", + "intrinsic cardiomyopathy", + "disorder of orbital region", "musculoskeletal system disorder", - "congenital nervous system disorder", + "syndromic disease", + "eyelid disorder", "hereditary disease", "muscle tissue disorder", + "cardiomyopathy", + "cardiovascular disorder", + "hypertrophic cardiomyopathy", "nervous system disorder", + "familial cardiomyopathy", "obsolete muscular disorder", + "heart disorder", + "eye disorder", "myopathy", - "myopathy, myofibrillar, 9, with early respiratory failure", + "myotonic dystrophy type 1", "progressive muscular dystrophy", - "autosomal dominant distal myopathy", - "hereditary inclusion-body myopathy", - "qualitative or quantitative protein defects in neuromuscular diseases", - "qualitative or quantitative defects of titin", - "distal myopathy", + "myotonic dystrophy", + "myotonic syndrome", "neuromuscular disease", - "congenital myopathy", "skeletal muscle disorder", "muscular dystrophy", - "inherited disease susceptibility", - "disease susceptibility", - "pulmonary disease, chronic obstructive, susceptibility to", - "TTN-related myopathy", - "autosomal dominant titinopathy", + "eyelids malposition disorder", + "disorder of visual system", + "familial hypertrophic cardiomyopathy", "human disease or disorder", "hereditary skeletal muscle disorder", ], - "predicate": "biolink:has_phenotype", - "object": "HP:0003547", + "predicate": "biolink:has_mode_of_inheritance", + "object": "HP:0000006", "original_object": None, "object_namespace": "HP", - "object_category": "biolink:PhenotypicQuality", + "object_category": "biolink:GeneticInheritance", "object_closure": [ "HP:0000001", - "UPHENO:0002649", - "UPHENO:0082875", - "UPHENO:0075696", - "UPHENO:0002320", - "UPHENO:0001001", - "HP:0003325", - "UPHENO:0080565", - "HP:0009127", - "UPHENO:0001005", - "HP:0011805", - "UPHENO:0001002", - "HP:0001324", - "HP:0000118", - "BFO:0000002", - "HP:0001435", - "HP:0001446", - "HP:0002817", - "BFO:0000020", - "UPHENO:0080555", - "HP:0003011", - "UPHENO:0002816", - "UPHENO:0002332", - "UPHENO:0080556", - "UPHENO:0002982", - "UPHENO:0081581", - "HP:0003547", - "HP:0033127", - "UPHENO:0001003", - "UPHENO:0002536", - "UPHENO:0076692", - "UPHENO:0002647", - "UPHENO:0076710", - "HP:0040064", - "BFO:0000001", - "HP:0011804", - "PATO:0000001", - "UPHENO:0002880", - "UPHENO:0002830", - "BFO:0000001", - "BFO:0000002", - "BFO:0000004", - "BFO:0000040", - "UBERON:0001062", - "CARO:0000000", - "UBERON:0000465", - "PR:000050567", - "RO:0002577", - "UBERON:0001015", - "UBERON:0000383", - "CARO:0000006", - "UBERON:0006058", - "UBERON:0010538", - "UBERON:0018254", - "UBERON:0005090", - "UBERON:0000061", - "UBERON:0004708", - "UBERON:0007271", - "UBERON:0014793", - "CARO:0000003", - "UBERON:0001460", - "UBERON:0002529", - "UBERON:0001630", - "UBERON:0010000", - "UBERON:0000467", - "UBERON:0015212", - "UBERON:0004710", - "UBERON:0002101", - "UBERON:0004480", - "UBERON:0007269", - "UBERON:0004471", - "UBERON:0007823", - "UBERON:0010708", - "UBERON:0008785", - "UBERON:0014892", - "UBERON:0000468", - "UBERON:0000475", - "UBERON:0000062", - "UBERON:0011216", - "UBERON:0001421", - "UBERON:0010707", - "UBERON:0002102", - "UBERON:0004481", - "UBERON:0010891", - "UBERON:0000153", - "UBERON:0000026", - "UBERON:0010758", - "UBERON:0008196", + "HP:0000006", + "HP:0000005", + "HP:0034345", ], - "object_label": "Shoulder girdle muscle weakness (HPO)", + "object_label": "Autosomal dominant inheritance (HPO)", "object_closure_label": [ "All (HPO)", - "Phenotypic abnormality (HPO)", - "Muscle weakness (HPO)", - "Abnormality of the shoulder girdle musculature (HPO)", - "Abnormality of the musculature of the upper limbs (HPO)", - "Abnormality of the upper limb (HPO)", - "Abnormality of the musculature (HPO)", - "Limb-girdle muscle weakness (HPO)", - "Shoulder girdle muscle weakness (HPO)", - "Abnormality of the musculature of the limbs (HPO)", - "Abnormal muscle physiology (HPO)", - "Abnormal skeletal muscle morphology (HPO)", - "Abnormality of the musculoskeletal system (HPO)", - "Abnormality of limbs (HPO)", - "appendage", - "anatomical structure", - "organ", - "anterior region of body", - "musculature of body", - "material anatomical entity", - "anatomical system", - "multicellular organism", - "organism subdivision", - "musculature", - "anatomical entity", - "pectoral girdle region", - "arm", - "muscle organ", - "limb", - "forelimb", - "limb segment", - "musculature of pectoral girdle", - "musculature of limb", - "musculature of upper limb", - "paired limb/fin", - "pectoral appendage", - "muscle structure", - "multi-limb segment region", - "pectoral appendage musculature", - "appendage musculature", - "appendage girdle region", - "muscle of pectoral girdle", - "upper limb segment", - "multicellular anatomical structure", - "paired limb/fin segment", - "appendage girdle complex", - "pectoral complex", - "subdivision of organism along appendicular axis", - "pectoral complex muscle", - "organ system subdivision", - "musculature of pectoral complex", - "skeletal muscle organ", - "lateral structure", - "skeletal musculature", + "Mode of inheritance (HPO)", + "Autosomal dominant inheritance (HPO)", + "Mendelian inheritance", ], - "primary_knowledge_source": ["infores:hpo-annotations"], + "primary_knowledge_source": "infores:hpo-annotations", "aggregator_knowledge_source": ["infores:monarchinitiative"], - "category": "biolink:DiseaseToPhenotypicFeatureAssociation", + "category": "biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation", "negated": None, - "provided_by": "hpoa_disease_phenotype_edges", - "publications": ["OMIM:603689"], + "provided_by": "hpoa_disease_mode_of_inheritance_edges", + "publications": ["OMIM:160900"], "qualifiers": [], "frequency_qualifier": None, - "has_evidence": "ECO:0000501", + "has_evidence": ["ECO:0000501"], "onset_qualifier": None, "sex_qualifier": None, "stage_qualifier": None, - "evidence_count": 0, + "evidence_count": 4, "pathway": None, "frequency_qualifier_label": None, "frequency_qualifier_namespace": None, @@ -1393,223 +669,95 @@ def associations(): "stage_qualifier_closure_label": [], }, { - "id": "uuid:215b1fa4-1e4f-11ee-871a-692638b4c502", - "subject": "MONDO:0011486", - "original_subject": "OMIM:604801", + "id": "uuid:c400607b-212f-11ee-873a-cd90a19c4085", + "subject": "MONDO:0008116", + "original_subject": "OMIM:164300", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ + "MONDO:0020158", "MONDO:0000001", - "MONDO:0100167", "MONDO:0005071", "MONDO:0020121", "MONDO:0700223", - "MONDO:0020573", + "MONDO:0004746", "BFO:0000002", "BFO:0000017", "BFO:0000020", - "MONDO:0042489", + "MONDO:0016106", + "MONDO:0003382", "BFO:0000016", "MONDO:0020120", "MONDO:0019056", - "MONDO:0011486", "MONDO:0700096", + "MONDO:0024458", "MONDO:0005218", "MONDO:0005336", "MONDO:0002081", + "MONDO:0008116", "OGMS:0000031", "MONDO:0003847", "MONDO:0003939", + "MONDO:0002022", "BFO:0000001", - "MONDO:0002320", - "MONDO:0019950", + "MONDO:0000462", + "MONDO:0005328", ], - "subject_label": "congenital muscular dystrophy 1B", + "subject_label": "oculopharyngeal muscular dystrophy", "subject_closure_label": [ "disease or disorder", + "eye adnexa disorder", + "disorder of orbital region", "musculoskeletal system disorder", - "congenital nervous system disorder", + "eyelid disorder", "hereditary disease", "muscle tissue disorder", + "myopathy of extraocular muscle", "nervous system disorder", "obsolete muscular disorder", + "eye disorder", "myopathy", - "congenital muscular dystrophy 1B", + "oculopharyngeal muscular dystrophy", + "progressive muscular dystrophy", "neuromuscular disease", - "congenital muscular dystrophy", "skeletal muscle disorder", "muscular dystrophy", - "inherited disease susceptibility", - "disease susceptibility", - "pulmonary disease, chronic obstructive, susceptibility to", + "eyelids malposition disorder", + "disorder of visual system", "human disease or disorder", "hereditary skeletal muscle disorder", ], - "predicate": "biolink:has_phenotype", - "object": "HP:0003547", + "predicate": "biolink:has_mode_of_inheritance", + "object": "HP:0000006", "original_object": None, "object_namespace": "HP", - "object_category": "biolink:PhenotypicQuality", + "object_category": "biolink:GeneticInheritance", "object_closure": [ "HP:0000001", - "UPHENO:0002649", - "UPHENO:0082875", - "UPHENO:0075696", - "UPHENO:0002320", - "UPHENO:0001001", - "HP:0003325", - "UPHENO:0080565", - "HP:0009127", - "UPHENO:0001005", - "HP:0011805", - "UPHENO:0001002", - "HP:0001324", - "HP:0000118", - "BFO:0000002", - "HP:0001435", - "HP:0001446", - "HP:0002817", - "BFO:0000020", - "UPHENO:0080555", - "HP:0003011", - "UPHENO:0002816", - "UPHENO:0002332", - "UPHENO:0080556", - "UPHENO:0002982", - "UPHENO:0081581", - "HP:0003547", - "HP:0033127", - "UPHENO:0001003", - "UPHENO:0002536", - "UPHENO:0076692", - "UPHENO:0002647", - "UPHENO:0076710", - "HP:0040064", - "BFO:0000001", - "HP:0011804", - "PATO:0000001", - "UPHENO:0002880", - "UPHENO:0002830", - "BFO:0000001", - "BFO:0000002", - "BFO:0000004", - "BFO:0000040", - "UBERON:0001062", - "CARO:0000000", - "UBERON:0000465", - "PR:000050567", - "RO:0002577", - "UBERON:0001015", - "UBERON:0000383", - "CARO:0000006", - "UBERON:0006058", - "UBERON:0010538", - "UBERON:0018254", - "UBERON:0005090", - "UBERON:0000061", - "UBERON:0004708", - "UBERON:0007271", - "UBERON:0014793", - "CARO:0000003", - "UBERON:0001460", - "UBERON:0002529", - "UBERON:0001630", - "UBERON:0010000", - "UBERON:0000467", - "UBERON:0015212", - "UBERON:0004710", - "UBERON:0002101", - "UBERON:0004480", - "UBERON:0007269", - "UBERON:0004471", - "UBERON:0007823", - "UBERON:0010708", - "UBERON:0008785", - "UBERON:0014892", - "UBERON:0000468", - "UBERON:0000475", - "UBERON:0000062", - "UBERON:0011216", - "UBERON:0001421", - "UBERON:0010707", - "UBERON:0002102", - "UBERON:0004481", - "UBERON:0010891", - "UBERON:0000153", - "UBERON:0000026", - "UBERON:0010758", - "UBERON:0008196", + "HP:0000006", + "HP:0000005", + "HP:0034345", ], - "object_label": "Shoulder girdle muscle weakness (HPO)", + "object_label": "Autosomal dominant inheritance (HPO)", "object_closure_label": [ "All (HPO)", - "Phenotypic abnormality (HPO)", - "Muscle weakness (HPO)", - "Abnormality of the shoulder girdle musculature (HPO)", - "Abnormality of the musculature of the upper limbs (HPO)", - "Abnormality of the upper limb (HPO)", - "Abnormality of the musculature (HPO)", - "Limb-girdle muscle weakness (HPO)", - "Shoulder girdle muscle weakness (HPO)", - "Abnormality of the musculature of the limbs (HPO)", - "Abnormal muscle physiology (HPO)", - "Abnormal skeletal muscle morphology (HPO)", - "Abnormality of the musculoskeletal system (HPO)", - "Abnormality of limbs (HPO)", - "appendage", - "anatomical structure", - "organ", - "anterior region of body", - "musculature of body", - "material anatomical entity", - "anatomical system", - "multicellular organism", - "organism subdivision", - "musculature", - "anatomical entity", - "pectoral girdle region", - "arm", - "muscle organ", - "limb", - "forelimb", - "limb segment", - "musculature of pectoral girdle", - "musculature of limb", - "musculature of upper limb", - "paired limb/fin", - "pectoral appendage", - "muscle structure", - "multi-limb segment region", - "pectoral appendage musculature", - "appendage musculature", - "appendage girdle region", - "muscle of pectoral girdle", - "upper limb segment", - "multicellular anatomical structure", - "paired limb/fin segment", - "appendage girdle complex", - "pectoral complex", - "subdivision of organism along appendicular axis", - "pectoral complex muscle", - "organ system subdivision", - "musculature of pectoral complex", - "skeletal muscle organ", - "lateral structure", - "skeletal musculature", + "Mode of inheritance (HPO)", + "Autosomal dominant inheritance (HPO)", + "Mendelian inheritance", ], - "primary_knowledge_source": ["infores:hpo-annotations"], + "primary_knowledge_source": "infores:hpo-annotations", "aggregator_knowledge_source": ["infores:monarchinitiative"], - "category": "biolink:DiseaseToPhenotypicFeatureAssociation", + "category": "biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation", "negated": None, - "provided_by": "hpoa_disease_phenotype_edges", - "publications": ["OMIM:604801"], + "provided_by": "hpoa_disease_mode_of_inheritance_edges", + "publications": ["PMID:9462747"], "qualifiers": [], "frequency_qualifier": None, - "has_evidence": "ECO:0000501", + "has_evidence": ["ECO:0000269"], "onset_qualifier": None, "sex_qualifier": None, "stage_qualifier": None, - "evidence_count": 0, + "evidence_count": 4, "pathway": None, "frequency_qualifier_label": None, "frequency_qualifier_namespace": None, @@ -1633,33 +781,21 @@ def associations(): "stage_qualifier_closure_label": [], }, { - "id": "uuid:19006798-1e4f-11ee-871a-692638b4c502", - "subject": "MONDO:0011787", - "original_subject": "OMIM:607155", + "id": "uuid:c3cdaddf-212f-11ee-873a-cd90a19c4085", + "subject": "MONDO:0009681", + "original_subject": "OMIM:254090", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ - "MONDO:0018282", "MONDO:0000001", - "MONDO:0016971", - "MONDO:0017741", - "MONDO:0000429", - "MONDO:0045010", - "MONDO:0100167", "MONDO:0005071", "MONDO:0020121", "MONDO:0700223", - "MONDO:0011787", - "MONDO:0024322", - "MONDO:0020573", "BFO:0000002", + "MONDO:0019952", "BFO:0000017", "BFO:0000020", - "MONDO:0006025", - "MONDO:0016106", - "MONDO:0016157", - "MONDO:0042489", - "MONDO:0017745", + "MONDO:0100225", "BFO:0000016", "MONDO:0020120", "MONDO:0019056", @@ -1668,222 +804,68 @@ def associations(): "MONDO:0005218", "MONDO:0005336", "MONDO:0002081", - "MONDO:0016156", + "MONDO:0009681", "OGMS:0000031", "MONDO:0003847", "MONDO:0003939", - "MONDO:0015286", "BFO:0000001", - "MONDO:0015152", "MONDO:0002320", - "MONDO:0019052", - "MONDO:0005066", - "MONDO:0016155", - "MONDO:0700066", + "MONDO:0000355", + "MONDO:0019950", ], - "subject_label": "autosomal recessive limb-girdle muscular dystrophy type 2I", + "subject_label": "Ullrich congenital muscular dystrophy 1", "subject_closure_label": [ "disease or disorder", - "autosomal genetic disease", + "Ullrich congenital muscular dystrophy", "musculoskeletal system disorder", "congenital nervous system disorder", "hereditary disease", "muscle tissue disorder", - "metabolic disease", "nervous system disorder", "obsolete muscular disorder", "myopathy", - "autosomal recessive disease", - "autosomal recessive limb-girdle muscular dystrophy type 2I", - "autosomal recessive limb-girdle muscular dystrophy", - "congenital disorder of glycosylation", - "progressive muscular dystrophy", + "Ullrich congenital muscular dystrophy 1", "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", - "limb-girdle muscular dystrophy", - "disorder of protein O-glycosylation", - "disorder of O-mannosylglycan synthesis", - "qualitative or quantitative defects of alpha-dystroglycan", - "inborn errors of metabolism", "neuromuscular disease", + "congenital muscular dystrophy", + "congenital myopathy", "skeletal muscle disorder", "muscular dystrophy", - "inherited disease susceptibility", - "disorder of glycosylation", - "disease susceptibility", - "glycoprotein metabolism disease", - "pulmonary disease, chronic obstructive, susceptibility to", - "myopathy caused by variation in FKRP", + "collagen 6-related myopathy", "human disease or disorder", "hereditary skeletal muscle disorder", ], - "predicate": "biolink:has_phenotype", - "object": "HP:0003547", + "predicate": "biolink:has_mode_of_inheritance", + "object": "HP:0000006", "original_object": None, "object_namespace": "HP", - "object_category": "biolink:PhenotypicQuality", + "object_category": "biolink:GeneticInheritance", "object_closure": [ "HP:0000001", - "UPHENO:0002649", - "UPHENO:0082875", - "UPHENO:0075696", - "UPHENO:0002320", - "UPHENO:0001001", - "HP:0003325", - "UPHENO:0080565", - "HP:0009127", - "UPHENO:0001005", - "HP:0011805", - "UPHENO:0001002", - "HP:0001324", - "HP:0000118", - "BFO:0000002", - "HP:0001435", - "HP:0001446", - "HP:0002817", - "BFO:0000020", - "UPHENO:0080555", - "HP:0003011", - "UPHENO:0002816", - "UPHENO:0002332", - "UPHENO:0080556", - "UPHENO:0002982", - "UPHENO:0081581", - "HP:0003547", - "HP:0033127", - "UPHENO:0001003", - "UPHENO:0002536", - "UPHENO:0076692", - "UPHENO:0002647", - "UPHENO:0076710", - "HP:0040064", - "BFO:0000001", - "HP:0011804", - "PATO:0000001", - "UPHENO:0002880", - "UPHENO:0002830", - "BFO:0000001", - "BFO:0000002", - "BFO:0000004", - "BFO:0000040", - "UBERON:0001062", - "CARO:0000000", - "UBERON:0000465", - "PR:000050567", - "RO:0002577", - "UBERON:0001015", - "UBERON:0000383", - "CARO:0000006", - "UBERON:0006058", - "UBERON:0010538", - "UBERON:0018254", - "UBERON:0005090", - "UBERON:0000061", - "UBERON:0004708", - "UBERON:0007271", - "UBERON:0014793", - "CARO:0000003", - "UBERON:0001460", - "UBERON:0002529", - "UBERON:0001630", - "UBERON:0010000", - "UBERON:0000467", - "UBERON:0015212", - "UBERON:0004710", - "UBERON:0002101", - "UBERON:0004480", - "UBERON:0007269", - "UBERON:0004471", - "UBERON:0007823", - "UBERON:0010708", - "UBERON:0008785", - "UBERON:0014892", - "UBERON:0000468", - "UBERON:0000475", - "UBERON:0000062", - "UBERON:0011216", - "UBERON:0001421", - "UBERON:0010707", - "UBERON:0002102", - "UBERON:0004481", - "UBERON:0010891", - "UBERON:0000153", - "UBERON:0000026", - "UBERON:0010758", - "UBERON:0008196", + "HP:0000006", + "HP:0000005", + "HP:0034345", ], - "object_label": "Shoulder girdle muscle weakness (HPO)", + "object_label": "Autosomal dominant inheritance (HPO)", "object_closure_label": [ "All (HPO)", - "Phenotypic abnormality (HPO)", - "Muscle weakness (HPO)", - "Abnormality of the shoulder girdle musculature (HPO)", - "Abnormality of the musculature of the upper limbs (HPO)", - "Abnormality of the upper limb (HPO)", - "Abnormality of the musculature (HPO)", - "Limb-girdle muscle weakness (HPO)", - "Shoulder girdle muscle weakness (HPO)", - "Abnormality of the musculature of the limbs (HPO)", - "Abnormal muscle physiology (HPO)", - "Abnormal skeletal muscle morphology (HPO)", - "Abnormality of the musculoskeletal system (HPO)", - "Abnormality of limbs (HPO)", - "appendage", - "anatomical structure", - "organ", - "anterior region of body", - "musculature of body", - "material anatomical entity", - "anatomical system", - "multicellular organism", - "organism subdivision", - "musculature", - "anatomical entity", - "pectoral girdle region", - "arm", - "muscle organ", - "limb", - "forelimb", - "limb segment", - "musculature of pectoral girdle", - "musculature of limb", - "musculature of upper limb", - "paired limb/fin", - "pectoral appendage", - "muscle structure", - "multi-limb segment region", - "pectoral appendage musculature", - "appendage musculature", - "appendage girdle region", - "muscle of pectoral girdle", - "upper limb segment", - "multicellular anatomical structure", - "paired limb/fin segment", - "appendage girdle complex", - "pectoral complex", - "subdivision of organism along appendicular axis", - "pectoral complex muscle", - "organ system subdivision", - "musculature of pectoral complex", - "skeletal muscle organ", - "lateral structure", - "skeletal musculature", + "Mode of inheritance (HPO)", + "Autosomal dominant inheritance (HPO)", + "Mendelian inheritance", ], - "primary_knowledge_source": ["infores:hpo-annotations"], + "primary_knowledge_source": "infores:hpo-annotations", "aggregator_knowledge_source": ["infores:monarchinitiative"], - "category": "biolink:DiseaseToPhenotypicFeatureAssociation", + "category": "biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation", "negated": None, - "provided_by": "hpoa_disease_phenotype_edges", - "publications": ["OMIM:607155"], + "provided_by": "hpoa_disease_mode_of_inheritance_edges", + "publications": ["OMIM:254090"], "qualifiers": [], "frequency_qualifier": None, - "has_evidence": "ECO:0000501", + "has_evidence": ["ECO:0000501"], "onset_qualifier": None, "sex_qualifier": None, "stage_qualifier": None, - "evidence_count": 0, + "evidence_count": 4, "pathway": None, "frequency_qualifier_label": None, "frequency_qualifier_namespace": None, @@ -1907,229 +889,79 @@ def associations(): "stage_qualifier_closure_label": [], }, { - "id": "uuid:21f7e3e1-1e4f-11ee-871a-692638b4c502", - "subject": "MONDO:0012193", - "original_subject": "OMIM:609115", + "id": "uuid:c275a020-212f-11ee-873a-cd90a19c4085", + "subject": "MONDO:0010676", + "original_subject": "OMIM:309950", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ "MONDO:0000001", - "MONDO:0016971", - "MONDO:0000429", - "MONDO:0100167", "MONDO:0005071", "MONDO:0020121", "MONDO:0700223", - "MONDO:0020573", "BFO:0000002", "BFO:0000017", "BFO:0000020", - "MONDO:0016106", - "MONDO:0042489", "BFO:0000016", "MONDO:0020120", "MONDO:0019056", - "MONDO:0015151", "MONDO:0700096", "MONDO:0005218", "MONDO:0005336", "MONDO:0002081", - "MONDO:0012193", - "MONDO:0000426", "OGMS:0000031", "MONDO:0003847", "MONDO:0003939", "BFO:0000001", + "MONDO:0010676", ], - "subject_label": "autosomal dominant limb-girdle muscular dystrophy type 1G", + "subject_label": "muscular dystrophy, Hemizygous lethal type", "subject_closure_label": [ "disease or disorder", - "autosomal dominant disease", - "autosomal genetic disease", "musculoskeletal system disorder", "hereditary disease", "muscle tissue disorder", "nervous system disorder", "obsolete muscular disorder", "myopathy", - "autosomal dominant limb-girdle muscular dystrophy type 1G", - "muscular dystrophy, limb-girdle, autosomal dominant", - "progressive muscular dystrophy", - "limb-girdle muscular dystrophy", + "muscular dystrophy, Hemizygous lethal type", "neuromuscular disease", "skeletal muscle disorder", "muscular dystrophy", - "inherited disease susceptibility", - "disease susceptibility", - "pulmonary disease, chronic obstructive, susceptibility to", "human disease or disorder", "hereditary skeletal muscle disorder", ], - "predicate": "biolink:has_phenotype", - "object": "HP:0003547", + "predicate": "biolink:has_mode_of_inheritance", + "object": "HP:0000006", "original_object": None, "object_namespace": "HP", - "object_category": "biolink:PhenotypicQuality", + "object_category": "biolink:GeneticInheritance", "object_closure": [ "HP:0000001", - "UPHENO:0002649", - "UPHENO:0082875", - "UPHENO:0075696", - "UPHENO:0002320", - "UPHENO:0001001", - "HP:0003325", - "UPHENO:0080565", - "HP:0009127", - "UPHENO:0001005", - "HP:0011805", - "UPHENO:0001002", - "HP:0001324", - "HP:0000118", - "BFO:0000002", - "HP:0001435", - "HP:0001446", - "HP:0002817", - "BFO:0000020", - "UPHENO:0080555", - "HP:0003011", - "UPHENO:0002816", - "UPHENO:0002332", - "UPHENO:0080556", - "UPHENO:0002982", - "UPHENO:0081581", - "HP:0003547", - "HP:0033127", - "UPHENO:0001003", - "UPHENO:0002536", - "UPHENO:0076692", - "UPHENO:0002647", - "UPHENO:0076710", - "HP:0040064", - "BFO:0000001", - "HP:0011804", - "PATO:0000001", - "UPHENO:0002880", - "UPHENO:0002830", - "BFO:0000001", - "BFO:0000002", - "BFO:0000004", - "BFO:0000040", - "UBERON:0001062", - "CARO:0000000", - "UBERON:0000465", - "PR:000050567", - "RO:0002577", - "UBERON:0001015", - "UBERON:0000383", - "CARO:0000006", - "UBERON:0006058", - "UBERON:0010538", - "UBERON:0018254", - "UBERON:0005090", - "UBERON:0000061", - "UBERON:0004708", - "UBERON:0007271", - "UBERON:0014793", - "CARO:0000003", - "UBERON:0001460", - "UBERON:0002529", - "UBERON:0001630", - "UBERON:0010000", - "UBERON:0000467", - "UBERON:0015212", - "UBERON:0004710", - "UBERON:0002101", - "UBERON:0004480", - "UBERON:0007269", - "UBERON:0004471", - "UBERON:0007823", - "UBERON:0010708", - "UBERON:0008785", - "UBERON:0014892", - "UBERON:0000468", - "UBERON:0000475", - "UBERON:0000062", - "UBERON:0011216", - "UBERON:0001421", - "UBERON:0010707", - "UBERON:0002102", - "UBERON:0004481", - "UBERON:0010891", - "UBERON:0000153", - "UBERON:0000026", - "UBERON:0010758", - "UBERON:0008196", + "HP:0000006", + "HP:0000005", + "HP:0034345", ], - "object_label": "Shoulder girdle muscle weakness (HPO)", + "object_label": "Autosomal dominant inheritance (HPO)", "object_closure_label": [ "All (HPO)", - "Phenotypic abnormality (HPO)", - "Muscle weakness (HPO)", - "Abnormality of the shoulder girdle musculature (HPO)", - "Abnormality of the musculature of the upper limbs (HPO)", - "Abnormality of the upper limb (HPO)", - "Abnormality of the musculature (HPO)", - "Limb-girdle muscle weakness (HPO)", - "Shoulder girdle muscle weakness (HPO)", - "Abnormality of the musculature of the limbs (HPO)", - "Abnormal muscle physiology (HPO)", - "Abnormal skeletal muscle morphology (HPO)", - "Abnormality of the musculoskeletal system (HPO)", - "Abnormality of limbs (HPO)", - "appendage", - "anatomical structure", - "organ", - "anterior region of body", - "musculature of body", - "material anatomical entity", - "anatomical system", - "multicellular organism", - "organism subdivision", - "musculature", - "anatomical entity", - "pectoral girdle region", - "arm", - "muscle organ", - "limb", - "forelimb", - "limb segment", - "musculature of pectoral girdle", - "musculature of limb", - "musculature of upper limb", - "paired limb/fin", - "pectoral appendage", - "muscle structure", - "multi-limb segment region", - "pectoral appendage musculature", - "appendage musculature", - "appendage girdle region", - "muscle of pectoral girdle", - "upper limb segment", - "multicellular anatomical structure", - "paired limb/fin segment", - "appendage girdle complex", - "pectoral complex", - "subdivision of organism along appendicular axis", - "pectoral complex muscle", - "organ system subdivision", - "musculature of pectoral complex", - "skeletal muscle organ", - "lateral structure", - "skeletal musculature", + "Mode of inheritance (HPO)", + "Autosomal dominant inheritance (HPO)", + "Mendelian inheritance", ], - "primary_knowledge_source": ["infores:hpo-annotations"], + "primary_knowledge_source": "infores:hpo-annotations", "aggregator_knowledge_source": ["infores:monarchinitiative"], - "category": "biolink:DiseaseToPhenotypicFeatureAssociation", + "category": "biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation", "negated": None, - "provided_by": "hpoa_disease_phenotype_edges", - "publications": ["OMIM:609115"], + "provided_by": "hpoa_disease_mode_of_inheritance_edges", + "publications": ["OMIM:309950"], "qualifiers": [], "frequency_qualifier": None, - "has_evidence": "ECO:0000501", + "has_evidence": ["ECO:0000304"], "onset_qualifier": None, "sex_qualifier": None, "stage_qualifier": None, - "evidence_count": 0, + "evidence_count": 4, "pathway": None, "frequency_qualifier_label": None, "frequency_qualifier_namespace": None, @@ -2153,229 +985,99 @@ def associations(): "stage_qualifier_closure_label": [], }, { - "id": "uuid:23648587-1e4f-11ee-871a-692638b4c502", - "subject": "MONDO:0012652", - "original_subject": "OMIM:611307", + "id": "uuid:c336741f-212f-11ee-873a-cd90a19c4085", + "subject": "MONDO:0010870", + "original_subject": "OMIM:600334", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ + "MONDO:0010870", "MONDO:0000001", - "MONDO:0016971", "MONDO:0000429", - "MONDO:0100167", "MONDO:0005071", "MONDO:0020121", + "MONDO:0100175", "MONDO:0700223", - "MONDO:0020573", "BFO:0000002", + "MONDO:0019952", "BFO:0000017", "BFO:0000020", - "MONDO:0006025", - "MONDO:0016106", - "MONDO:0042489", + "MONDO:0016191", "BFO:0000016", - "MONDO:0012652", "MONDO:0020120", "MONDO:0019056", + "MONDO:0100494", + "MONDO:0016139", "MONDO:0700096", "MONDO:0005218", "MONDO:0005336", "MONDO:0002081", + "MONDO:0000426", "OGMS:0000031", "MONDO:0003847", "MONDO:0003939", "BFO:0000001", - "MONDO:0015152", + "MONDO:0002320", + "MONDO:0016108", + "MONDO:0018949", ], - "subject_label": "autosomal recessive limb-girdle muscular dystrophy type 2L", + "subject_label": "tibial muscular dystrophy", "subject_closure_label": [ "disease or disorder", + "autosomal dominant disease", "autosomal genetic disease", "musculoskeletal system disorder", + "congenital nervous system disorder", "hereditary disease", "muscle tissue disorder", "nervous system disorder", "obsolete muscular disorder", "myopathy", - "autosomal recessive disease", - "autosomal recessive limb-girdle muscular dystrophy type 2L", - "autosomal recessive limb-girdle muscular dystrophy", - "progressive muscular dystrophy", - "limb-girdle muscular dystrophy", + "tibial muscular dystrophy", + "autosomal dominant distal myopathy", + "qualitative or quantitative protein defects in neuromuscular diseases", + "qualitative or quantitative defects of titin", + "distal myopathy", "neuromuscular disease", + "congenital myopathy", "skeletal muscle disorder", "muscular dystrophy", - "inherited disease susceptibility", - "disease susceptibility", - "pulmonary disease, chronic obstructive, susceptibility to", + "TTN-related myopathy", + "autosomal dominant titinopathy", "human disease or disorder", "hereditary skeletal muscle disorder", ], - "predicate": "biolink:has_phenotype", - "object": "HP:0003547", + "predicate": "biolink:has_mode_of_inheritance", + "object": "HP:0000006", "original_object": None, "object_namespace": "HP", - "object_category": "biolink:PhenotypicQuality", + "object_category": "biolink:GeneticInheritance", "object_closure": [ "HP:0000001", - "UPHENO:0002649", - "UPHENO:0082875", - "UPHENO:0075696", - "UPHENO:0002320", - "UPHENO:0001001", - "HP:0003325", - "UPHENO:0080565", - "HP:0009127", - "UPHENO:0001005", - "HP:0011805", - "UPHENO:0001002", - "HP:0001324", - "HP:0000118", - "BFO:0000002", - "HP:0001435", - "HP:0001446", - "HP:0002817", - "BFO:0000020", - "UPHENO:0080555", - "HP:0003011", - "UPHENO:0002816", - "UPHENO:0002332", - "UPHENO:0080556", - "UPHENO:0002982", - "UPHENO:0081581", - "HP:0003547", - "HP:0033127", - "UPHENO:0001003", - "UPHENO:0002536", - "UPHENO:0076692", - "UPHENO:0002647", - "UPHENO:0076710", - "HP:0040064", - "BFO:0000001", - "HP:0011804", - "PATO:0000001", - "UPHENO:0002880", - "UPHENO:0002830", - "BFO:0000001", - "BFO:0000002", - "BFO:0000004", - "BFO:0000040", - "UBERON:0001062", - "CARO:0000000", - "UBERON:0000465", - "PR:000050567", - "RO:0002577", - "UBERON:0001015", - "UBERON:0000383", - "CARO:0000006", - "UBERON:0006058", - "UBERON:0010538", - "UBERON:0018254", - "UBERON:0005090", - "UBERON:0000061", - "UBERON:0004708", - "UBERON:0007271", - "UBERON:0014793", - "CARO:0000003", - "UBERON:0001460", - "UBERON:0002529", - "UBERON:0001630", - "UBERON:0010000", - "UBERON:0000467", - "UBERON:0015212", - "UBERON:0004710", - "UBERON:0002101", - "UBERON:0004480", - "UBERON:0007269", - "UBERON:0004471", - "UBERON:0007823", - "UBERON:0010708", - "UBERON:0008785", - "UBERON:0014892", - "UBERON:0000468", - "UBERON:0000475", - "UBERON:0000062", - "UBERON:0011216", - "UBERON:0001421", - "UBERON:0010707", - "UBERON:0002102", - "UBERON:0004481", - "UBERON:0010891", - "UBERON:0000153", - "UBERON:0000026", - "UBERON:0010758", - "UBERON:0008196", + "HP:0000006", + "HP:0000005", + "HP:0034345", ], - "object_label": "Shoulder girdle muscle weakness (HPO)", + "object_label": "Autosomal dominant inheritance (HPO)", "object_closure_label": [ "All (HPO)", - "Phenotypic abnormality (HPO)", - "Muscle weakness (HPO)", - "Abnormality of the shoulder girdle musculature (HPO)", - "Abnormality of the musculature of the upper limbs (HPO)", - "Abnormality of the upper limb (HPO)", - "Abnormality of the musculature (HPO)", - "Limb-girdle muscle weakness (HPO)", - "Shoulder girdle muscle weakness (HPO)", - "Abnormality of the musculature of the limbs (HPO)", - "Abnormal muscle physiology (HPO)", - "Abnormal skeletal muscle morphology (HPO)", - "Abnormality of the musculoskeletal system (HPO)", - "Abnormality of limbs (HPO)", - "appendage", - "anatomical structure", - "organ", - "anterior region of body", - "musculature of body", - "material anatomical entity", - "anatomical system", - "multicellular organism", - "organism subdivision", - "musculature", - "anatomical entity", - "pectoral girdle region", - "arm", - "muscle organ", - "limb", - "forelimb", - "limb segment", - "musculature of pectoral girdle", - "musculature of limb", - "musculature of upper limb", - "paired limb/fin", - "pectoral appendage", - "muscle structure", - "multi-limb segment region", - "pectoral appendage musculature", - "appendage musculature", - "appendage girdle region", - "muscle of pectoral girdle", - "upper limb segment", - "multicellular anatomical structure", - "paired limb/fin segment", - "appendage girdle complex", - "pectoral complex", - "subdivision of organism along appendicular axis", - "pectoral complex muscle", - "organ system subdivision", - "musculature of pectoral complex", - "skeletal muscle organ", - "lateral structure", - "skeletal musculature", + "Mode of inheritance (HPO)", + "Autosomal dominant inheritance (HPO)", + "Mendelian inheritance", ], - "primary_knowledge_source": ["infores:hpo-annotations"], + "primary_knowledge_source": "infores:hpo-annotations", "aggregator_knowledge_source": ["infores:monarchinitiative"], - "category": "biolink:DiseaseToPhenotypicFeatureAssociation", + "category": "biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation", "negated": None, - "provided_by": "hpoa_disease_phenotype_edges", - "publications": ["OMIM:611307"], + "provided_by": "hpoa_disease_mode_of_inheritance_edges", + "publications": ["OMIM:600334"], "qualifiers": [], "frequency_qualifier": None, - "has_evidence": "ECO:0000501", + "has_evidence": ["ECO:0000501"], "onset_qualifier": None, "sex_qualifier": None, "stage_qualifier": None, - "evidence_count": 0, + "evidence_count": 4, "pathway": None, "frequency_qualifier_label": None, "frequency_qualifier_namespace": None, @@ -2399,229 +1101,109 @@ def associations(): "stage_qualifier_closure_label": [], }, { - "id": "uuid:24013b92-1e4f-11ee-871a-692638b4c502", - "subject": "MONDO:0021018", - "original_subject": "OMIM:603511", + "id": "uuid:c275a16e-212f-11ee-873a-cd90a19c4085", + "subject": "MONDO:0010912", + "original_subject": "OMIM:600638", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ + "MONDO:0020158", "MONDO:0000001", - "MONDO:0021018", - "MONDO:0016971", - "MONDO:0000429", - "MONDO:0100167", + "MONDO:0007614", "MONDO:0005071", "MONDO:0020121", "MONDO:0700223", - "MONDO:0020573", + "MONDO:0004746", "BFO:0000002", + "MONDO:0957003", "BFO:0000017", "BFO:0000020", "MONDO:0016106", - "MONDO:0042489", + "MONDO:0003382", "BFO:0000016", "MONDO:0020120", "MONDO:0019056", - "MONDO:0015151", + "MONDO:0003569", "MONDO:0700096", + "MONDO:0001584", + "MONDO:0024458", "MONDO:0005218", "MONDO:0005336", "MONDO:0002081", - "MONDO:0000426", + "MONDO:0100153", "OGMS:0000031", "MONDO:0003847", + "MONDO:0100154", "MONDO:0003939", + "MONDO:0002022", + "MONDO:0015368", "BFO:0000001", + "MONDO:0000462", + "MONDO:0005328", + "MONDO:0010912", ], - "subject_label": "autosomal dominant limb-girdle muscular dystrophy type 1D (DNAJB6)", + "subject_label": "fibrosis of extraocular muscles, congenital, 3A, with or without extraocular involvement", "subject_closure_label": [ "disease or disorder", - "autosomal dominant disease", - "autosomal genetic disease", + "eye adnexa disorder", + "ocular motility disease", + "disorder of orbital region", "musculoskeletal system disorder", + "eyelid disorder", + "cranial nerve neuropathy", "hereditary disease", "muscle tissue disorder", + "myopathy of extraocular muscle", "nervous system disorder", "obsolete muscular disorder", + "eye disorder", "myopathy", - "muscular dystrophy, limb-girdle, autosomal dominant", + "congenital fibrosis of extraocular muscles", + "fibrosis of extraocular muscles, congenital, 3A, with or without extraocular involvement", + "neuro-ophthalmological disease", "progressive muscular dystrophy", - "limb-girdle muscular dystrophy", "neuromuscular disease", "skeletal muscle disorder", "muscular dystrophy", - "inherited disease susceptibility", - "autosomal dominant limb-girdle muscular dystrophy type 1D (DNAJB6)", - "disease susceptibility", - "pulmonary disease, chronic obstructive, susceptibility to", + "eyelids malposition disorder", + "disorder of visual system", + "tubulinopathy", + "TUBB3-related tubulinopathy", "human disease or disorder", "hereditary skeletal muscle disorder", + "hereditary neuro-ophthalmological disease", ], - "predicate": "biolink:has_phenotype", - "object": "HP:0003547", + "predicate": "biolink:has_mode_of_inheritance", + "object": "HP:0000006", "original_object": None, "object_namespace": "HP", - "object_category": "biolink:PhenotypicQuality", + "object_category": "biolink:GeneticInheritance", "object_closure": [ "HP:0000001", - "UPHENO:0002649", - "UPHENO:0082875", - "UPHENO:0075696", - "UPHENO:0002320", - "UPHENO:0001001", - "HP:0003325", - "UPHENO:0080565", - "HP:0009127", - "UPHENO:0001005", - "HP:0011805", - "UPHENO:0001002", - "HP:0001324", - "HP:0000118", - "BFO:0000002", - "HP:0001435", - "HP:0001446", - "HP:0002817", - "BFO:0000020", - "UPHENO:0080555", - "HP:0003011", - "UPHENO:0002816", - "UPHENO:0002332", - "UPHENO:0080556", - "UPHENO:0002982", - "UPHENO:0081581", - "HP:0003547", - "HP:0033127", - "UPHENO:0001003", - "UPHENO:0002536", - "UPHENO:0076692", - "UPHENO:0002647", - "UPHENO:0076710", - "HP:0040064", - "BFO:0000001", - "HP:0011804", - "PATO:0000001", - "UPHENO:0002880", - "UPHENO:0002830", - "BFO:0000001", - "BFO:0000002", - "BFO:0000004", - "BFO:0000040", - "UBERON:0001062", - "CARO:0000000", - "UBERON:0000465", - "PR:000050567", - "RO:0002577", - "UBERON:0001015", - "UBERON:0000383", - "CARO:0000006", - "UBERON:0006058", - "UBERON:0010538", - "UBERON:0018254", - "UBERON:0005090", - "UBERON:0000061", - "UBERON:0004708", - "UBERON:0007271", - "UBERON:0014793", - "CARO:0000003", - "UBERON:0001460", - "UBERON:0002529", - "UBERON:0001630", - "UBERON:0010000", - "UBERON:0000467", - "UBERON:0015212", - "UBERON:0004710", - "UBERON:0002101", - "UBERON:0004480", - "UBERON:0007269", - "UBERON:0004471", - "UBERON:0007823", - "UBERON:0010708", - "UBERON:0008785", - "UBERON:0014892", - "UBERON:0000468", - "UBERON:0000475", - "UBERON:0000062", - "UBERON:0011216", - "UBERON:0001421", - "UBERON:0010707", - "UBERON:0002102", - "UBERON:0004481", - "UBERON:0010891", - "UBERON:0000153", - "UBERON:0000026", - "UBERON:0010758", - "UBERON:0008196", + "HP:0000006", + "HP:0000005", + "HP:0034345", ], - "object_label": "Shoulder girdle muscle weakness (HPO)", + "object_label": "Autosomal dominant inheritance (HPO)", "object_closure_label": [ "All (HPO)", - "Phenotypic abnormality (HPO)", - "Muscle weakness (HPO)", - "Abnormality of the shoulder girdle musculature (HPO)", - "Abnormality of the musculature of the upper limbs (HPO)", - "Abnormality of the upper limb (HPO)", - "Abnormality of the musculature (HPO)", - "Limb-girdle muscle weakness (HPO)", - "Shoulder girdle muscle weakness (HPO)", - "Abnormality of the musculature of the limbs (HPO)", - "Abnormal muscle physiology (HPO)", - "Abnormal skeletal muscle morphology (HPO)", - "Abnormality of the musculoskeletal system (HPO)", - "Abnormality of limbs (HPO)", - "appendage", - "anatomical structure", - "organ", - "anterior region of body", - "musculature of body", - "material anatomical entity", - "anatomical system", - "multicellular organism", - "organism subdivision", - "musculature", - "anatomical entity", - "pectoral girdle region", - "arm", - "muscle organ", - "limb", - "forelimb", - "limb segment", - "musculature of pectoral girdle", - "musculature of limb", - "musculature of upper limb", - "paired limb/fin", - "pectoral appendage", - "muscle structure", - "multi-limb segment region", - "pectoral appendage musculature", - "appendage musculature", - "appendage girdle region", - "muscle of pectoral girdle", - "upper limb segment", - "multicellular anatomical structure", - "paired limb/fin segment", - "appendage girdle complex", - "pectoral complex", - "subdivision of organism along appendicular axis", - "pectoral complex muscle", - "organ system subdivision", - "musculature of pectoral complex", - "skeletal muscle organ", - "lateral structure", - "skeletal musculature", + "Mode of inheritance (HPO)", + "Autosomal dominant inheritance (HPO)", + "Mendelian inheritance", ], - "primary_knowledge_source": ["infores:hpo-annotations"], + "primary_knowledge_source": "infores:hpo-annotations", "aggregator_knowledge_source": ["infores:monarchinitiative"], - "category": "biolink:DiseaseToPhenotypicFeatureAssociation", + "category": "biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation", "negated": None, - "provided_by": "hpoa_disease_phenotype_edges", - "publications": ["PMID:22334415"], + "provided_by": "hpoa_disease_mode_of_inheritance_edges", + "publications": ["PMID:20074521"], "qualifiers": [], "frequency_qualifier": None, - "has_evidence": "ECO:0000269", + "has_evidence": ["ECO:0000269"], "onset_qualifier": None, "sex_qualifier": None, "stage_qualifier": None, - "evidence_count": 0, + "evidence_count": 4, "pathway": None, "frequency_qualifier_label": None, "frequency_qualifier_namespace": None, @@ -2645,148 +1227,99 @@ def associations(): "stage_qualifier_closure_label": [], }, { - "id": "uuid:218f00ed-1e4f-11ee-871a-692638b4c502", - "subject": "MONDO:0009676", - "original_subject": "OMIM:253601", + "id": "uuid:c367df60-212f-11ee-873a-cd90a19c4085", + "subject": "MONDO:0011266", + "original_subject": "OMIM:602668", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ + "MONDO:0020158", "MONDO:0000001", - "MONDO:0016971", - "MONDO:0000429", - "MONDO:0016145", - "MONDO:0100167", + "MONDO:0016107", "MONDO:0005071", "MONDO:0020121", "MONDO:0700223", - "MONDO:0020573", "BFO:0000002", "BFO:0000017", "BFO:0000020", - "MONDO:0006025", "MONDO:0016106", - "MONDO:0042489", + "MONDO:0003382", "BFO:0000016", "MONDO:0020120", "MONDO:0019056", - "MONDO:0016139", "MONDO:0700096", + "MONDO:0024458", "MONDO:0005218", "MONDO:0005336", "MONDO:0002081", - "MONDO:0009676", + "MONDO:0002254", + "MONDO:0011266", "OGMS:0000031", "MONDO:0003847", "MONDO:0003939", + "MONDO:0002022", + "MONDO:0016120", "BFO:0000001", - "MONDO:0015152", + "MONDO:0000462", + "MONDO:0005328", ], - "subject_label": "autosomal recessive limb-girdle muscular dystrophy type 2B", + "subject_label": "myotonic dystrophy type 2", "subject_closure_label": [ "disease or disorder", - "autosomal genetic disease", + "eye adnexa disorder", + "disorder of orbital region", "musculoskeletal system disorder", + "syndromic disease", + "eyelid disorder", "hereditary disease", "muscle tissue disorder", "nervous system disorder", "obsolete muscular disorder", + "eye disorder", "myopathy", - "autosomal recessive disease", - "autosomal recessive limb-girdle muscular dystrophy type 2B", - "autosomal recessive limb-girdle muscular dystrophy", + "myotonic dystrophy type 2", "progressive muscular dystrophy", - "qualitative or quantitative protein defects in neuromuscular diseases", - "qualitative or quantitative defects of dysferlin", - "limb-girdle muscular dystrophy", + "myotonic dystrophy", + "myotonic syndrome", "neuromuscular disease", "skeletal muscle disorder", "muscular dystrophy", - "inherited disease susceptibility", - "disease susceptibility", - "pulmonary disease, chronic obstructive, susceptibility to", + "eyelids malposition disorder", + "disorder of visual system", "human disease or disorder", "hereditary skeletal muscle disorder", ], - "predicate": "biolink:has_phenotype", - "object": "HP:0003551", + "predicate": "biolink:has_mode_of_inheritance", + "object": "HP:0000006", "original_object": None, "object_namespace": "HP", - "object_category": "biolink:PhenotypicQuality", + "object_category": "biolink:GeneticInheritance", "object_closure": [ "HP:0000001", - "UPHENO:0082875", - "UPHENO:0075696", - "UPHENO:0002320", - "UPHENO:0001001", - "HP:0003551", - "UPHENO:0001005", - "UPHENO:0001002", - "HP:0004302", - "HP:0000118", - "BFO:0000002", - "BFO:0000020", - "HP:0003011", - "UPHENO:0002816", - "UPHENO:0002332", - "HP:0033127", - "UPHENO:0001003", - "UPHENO:0002536", - "BFO:0000001", - "HP:0011804", - "PATO:0000001", - "BFO:0000001", - "BFO:0000002", - "BFO:0000004", - "BFO:0000040", - "UBERON:0001062", - "CARO:0000000", - "UBERON:0000465", - "UBERON:0001015", - "UBERON:0000383", - "UBERON:0005090", - "UBERON:0000061", - "UBERON:0001630", - "UBERON:0010000", - "UBERON:0000467", - "UBERON:0000468", - "UBERON:0000062", - "UBERON:0011216", + "HP:0000006", + "HP:0000005", + "HP:0034345", ], - "object_label": "Difficulty climbing stairs (HPO)", + "object_label": "Autosomal dominant inheritance (HPO)", "object_closure_label": [ "All (HPO)", - "Phenotypic abnormality (HPO)", - "Abnormality of the musculature (HPO)", - "Difficulty climbing stairs (HPO)", - "Functional motor deficit (HPO)", - "Abnormal muscle physiology (HPO)", - "Abnormality of the musculoskeletal system (HPO)", - "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", + "Mode of inheritance (HPO)", + "Autosomal dominant inheritance (HPO)", + "Mendelian inheritance", ], - "primary_knowledge_source": ["infores:hpo-annotations"], + "primary_knowledge_source": "infores:hpo-annotations", "aggregator_knowledge_source": ["infores:monarchinitiative"], - "category": "biolink:DiseaseToPhenotypicFeatureAssociation", + "category": "biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation", "negated": None, - "provided_by": "hpoa_disease_phenotype_edges", - "publications": ["OMIM:253601"], + "provided_by": "hpoa_disease_mode_of_inheritance_edges", + "publications": ["PMID:11486088"], "qualifiers": [], "frequency_qualifier": None, - "has_evidence": "ECO:0000501", + "has_evidence": ["ECO:0000269"], "onset_qualifier": None, "sex_qualifier": None, "stage_qualifier": None, - "evidence_count": 0, + "evidence_count": 4, "pathway": None, "frequency_qualifier_label": None, "frequency_qualifier_namespace": None, @@ -2810,138 +1343,103 @@ def associations(): "stage_qualifier_closure_label": [], }, { - "id": "uuid:1c34b3dd-1e4f-11ee-871a-692638b4c502", - "subject": "MONDO:0010684", - "original_subject": "OMIM:310440", + "id": "uuid:c3cdac2c-212f-11ee-873a-cd90a19c4085", + "subject": "MONDO:0011362", + "original_subject": "OMIM:603689", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ "MONDO:0000001", "MONDO:0016112", - "MONDO:0010684", - "MONDO:0100167", + "MONDO:0000429", "MONDO:0005071", "MONDO:0020121", + "MONDO:0100175", "MONDO:0700223", - "MONDO:0020573", "BFO:0000002", + "MONDO:0019952", "BFO:0000017", "BFO:0000020", "MONDO:0016106", - "MONDO:0042489", + "MONDO:0016191", "BFO:0000016", "MONDO:0020120", "MONDO:0019056", + "MONDO:0100494", + "MONDO:0016139", "MONDO:0700096", "MONDO:0005218", "MONDO:0005336", "MONDO:0002081", + "MONDO:0000426", + "MONDO:0011362", "OGMS:0000031", "MONDO:0003847", "MONDO:0003939", "BFO:0000001", + "MONDO:0002320", + "MONDO:0016108", + "MONDO:0018949", ], - "subject_label": "X-linked myopathy with excessive autophagy", + "subject_label": "myopathy, myofibrillar, 9, with early respiratory failure", "subject_closure_label": [ "disease or disorder", + "autosomal dominant disease", + "autosomal genetic disease", "musculoskeletal system disorder", + "congenital nervous system disorder", "hereditary disease", "muscle tissue disorder", "nervous system disorder", "obsolete muscular disorder", "myopathy", - "X-linked myopathy with excessive autophagy", + "myopathy, myofibrillar, 9, with early respiratory failure", "progressive muscular dystrophy", + "autosomal dominant distal myopathy", "hereditary inclusion-body myopathy", + "qualitative or quantitative protein defects in neuromuscular diseases", + "qualitative or quantitative defects of titin", + "distal myopathy", "neuromuscular disease", + "congenital myopathy", "skeletal muscle disorder", "muscular dystrophy", - "inherited disease susceptibility", - "disease susceptibility", - "pulmonary disease, chronic obstructive, susceptibility to", + "TTN-related myopathy", + "autosomal dominant titinopathy", "human disease or disorder", "hereditary skeletal muscle disorder", ], - "predicate": "biolink:has_phenotype", - "object": "HP:0003551", + "predicate": "biolink:has_mode_of_inheritance", + "object": "HP:0000006", "original_object": None, "object_namespace": "HP", - "object_category": "biolink:PhenotypicQuality", + "object_category": "biolink:GeneticInheritance", "object_closure": [ "HP:0000001", - "UPHENO:0082875", - "UPHENO:0075696", - "UPHENO:0002320", - "UPHENO:0001001", - "HP:0003551", - "UPHENO:0001005", - "UPHENO:0001002", - "HP:0004302", - "HP:0000118", - "BFO:0000002", - "BFO:0000020", - "HP:0003011", - "UPHENO:0002816", - "UPHENO:0002332", - "HP:0033127", - "UPHENO:0001003", - "UPHENO:0002536", - "BFO:0000001", - "HP:0011804", - "PATO:0000001", - "BFO:0000001", - "BFO:0000002", - "BFO:0000004", - "BFO:0000040", - "UBERON:0001062", - "CARO:0000000", - "UBERON:0000465", - "UBERON:0001015", - "UBERON:0000383", - "UBERON:0005090", - "UBERON:0000061", - "UBERON:0001630", - "UBERON:0010000", - "UBERON:0000467", - "UBERON:0000468", - "UBERON:0000062", - "UBERON:0011216", + "HP:0000006", + "HP:0000005", + "HP:0034345", ], - "object_label": "Difficulty climbing stairs (HPO)", + "object_label": "Autosomal dominant inheritance (HPO)", "object_closure_label": [ "All (HPO)", - "Phenotypic abnormality (HPO)", - "Abnormality of the musculature (HPO)", - "Difficulty climbing stairs (HPO)", - "Functional motor deficit (HPO)", - "Abnormal muscle physiology (HPO)", - "Abnormality of the musculoskeletal system (HPO)", - "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", + "Mode of inheritance (HPO)", + "Autosomal dominant inheritance (HPO)", + "Mendelian inheritance", ], - "primary_knowledge_source": ["infores:hpo-annotations"], + "primary_knowledge_source": "infores:hpo-annotations", "aggregator_knowledge_source": ["infores:monarchinitiative"], - "category": "biolink:DiseaseToPhenotypicFeatureAssociation", + "category": "biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation", "negated": None, - "provided_by": "hpoa_disease_phenotype_edges", - "publications": ["OMIM:310440"], + "provided_by": "hpoa_disease_mode_of_inheritance_edges", + "publications": ["PMID:22577215"], "qualifiers": [], "frequency_qualifier": None, - "has_evidence": "ECO:0000501", + "has_evidence": ["ECO:0000269"], "onset_qualifier": None, "sex_qualifier": None, "stage_qualifier": None, - "evidence_count": 0, + "evidence_count": 4, "pathway": None, "frequency_qualifier_label": None, "frequency_qualifier_namespace": None, @@ -2965,45 +1463,40 @@ def associations(): "stage_qualifier_closure_label": [], }, { - "id": "uuid:1e9fbb79-1e4f-11ee-871a-692638b4c502", - "subject": "MONDO:0011170", - "original_subject": "OMIM:601954", + "id": "uuid:c3cdadba-212f-11ee-873a-cd90a19c4085", + "subject": "MONDO:0011466", + "original_subject": "OMIM:604454", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ "MONDO:0000001", - "MONDO:0016971", + "MONDO:0011466", "MONDO:0000429", - "MONDO:0100167", "MONDO:0005071", "MONDO:0020121", "MONDO:0700223", - "MONDO:0020573", "BFO:0000002", "BFO:0000017", "BFO:0000020", - "MONDO:0006025", - "MONDO:0016106", - "MONDO:0042489", "BFO:0000016", "MONDO:0020120", "MONDO:0019056", - "MONDO:0016139", "MONDO:0700096", - "MONDO:0011170", "MONDO:0005218", "MONDO:0005336", "MONDO:0002081", + "MONDO:0000426", "OGMS:0000031", - "MONDO:0016192", "MONDO:0003847", "MONDO:0003939", "BFO:0000001", - "MONDO:0015152", + "MONDO:0016108", + "MONDO:0018949", ], - "subject_label": "autosomal recessive limb-girdle muscular dystrophy type 2G", + "subject_label": "distal myopathy, Welander type", "subject_closure_label": [ "disease or disorder", + "autosomal dominant disease", "autosomal genetic disease", "musculoskeletal system disorder", "hereditary disease", @@ -3011,102 +1504,46 @@ def associations(): "nervous system disorder", "obsolete muscular disorder", "myopathy", - "autosomal recessive disease", - "autosomal recessive limb-girdle muscular dystrophy type 2G", - "autosomal recessive limb-girdle muscular dystrophy", - "progressive muscular dystrophy", - "qualitative or quantitative protein defects in neuromuscular diseases", - "qualitative or quantitative defects of telethonin", - "limb-girdle muscular dystrophy", + "distal myopathy, Welander type", + "autosomal dominant distal myopathy", + "distal myopathy", "neuromuscular disease", "skeletal muscle disorder", "muscular dystrophy", - "inherited disease susceptibility", - "disease susceptibility", - "pulmonary disease, chronic obstructive, susceptibility to", "human disease or disorder", "hereditary skeletal muscle disorder", ], - "predicate": "biolink:has_phenotype", - "object": "HP:0003551", + "predicate": "biolink:has_mode_of_inheritance", + "object": "HP:0000006", "original_object": None, "object_namespace": "HP", - "object_category": "biolink:PhenotypicQuality", + "object_category": "biolink:GeneticInheritance", "object_closure": [ "HP:0000001", - "UPHENO:0082875", - "UPHENO:0075696", - "UPHENO:0002320", - "UPHENO:0001001", - "HP:0003551", - "UPHENO:0001005", - "UPHENO:0001002", - "HP:0004302", - "HP:0000118", - "BFO:0000002", - "BFO:0000020", - "HP:0003011", - "UPHENO:0002816", - "UPHENO:0002332", - "HP:0033127", - "UPHENO:0001003", - "UPHENO:0002536", - "BFO:0000001", - "HP:0011804", - "PATO:0000001", - "BFO:0000001", - "BFO:0000002", - "BFO:0000004", - "BFO:0000040", - "UBERON:0001062", - "CARO:0000000", - "UBERON:0000465", - "UBERON:0001015", - "UBERON:0000383", - "UBERON:0005090", - "UBERON:0000061", - "UBERON:0001630", - "UBERON:0010000", - "UBERON:0000467", - "UBERON:0000468", - "UBERON:0000062", - "UBERON:0011216", + "HP:0000006", + "HP:0000005", + "HP:0034345", ], - "object_label": "Difficulty climbing stairs (HPO)", + "object_label": "Autosomal dominant inheritance (HPO)", "object_closure_label": [ "All (HPO)", - "Phenotypic abnormality (HPO)", - "Abnormality of the musculature (HPO)", - "Difficulty climbing stairs (HPO)", - "Functional motor deficit (HPO)", - "Abnormal muscle physiology (HPO)", - "Abnormality of the musculoskeletal system (HPO)", - "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", + "Mode of inheritance (HPO)", + "Autosomal dominant inheritance (HPO)", + "Mendelian inheritance", ], - "primary_knowledge_source": ["infores:hpo-annotations"], + "primary_knowledge_source": "infores:hpo-annotations", "aggregator_knowledge_source": ["infores:monarchinitiative"], - "category": "biolink:DiseaseToPhenotypicFeatureAssociation", + "category": "biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation", "negated": None, - "provided_by": "hpoa_disease_phenotype_edges", - "publications": ["OMIM:601954"], + "provided_by": "hpoa_disease_mode_of_inheritance_edges", + "publications": ["PMID:23348830"], "qualifiers": [], "frequency_qualifier": None, - "has_evidence": "ECO:0000501", + "has_evidence": ["ECO:0000269"], "onset_qualifier": None, "sex_qualifier": None, "stage_qualifier": None, - "evidence_count": 0, + "evidence_count": 4, "pathway": None, "frequency_qualifier_label": None, "frequency_qualifier_namespace": None, @@ -3130,164 +1567,89 @@ def associations(): "stage_qualifier_closure_label": [], }, { - "id": "uuid:1bce01b5-1e4f-11ee-871a-692638b4c502", - "subject": "MONDO:0011688", - "original_subject": "OMIM:606612", + "id": "uuid:c367df64-212f-11ee-873a-cd90a19c4085", + "subject": "MONDO:0012034", + "original_subject": "OMIM:608423", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ - "MONDO:0018282", "MONDO:0000001", - "MONDO:0017741", - "MONDO:0018276", - "MONDO:0045010", - "MONDO:0100167", + "MONDO:0016971", + "MONDO:0000429", "MONDO:0005071", "MONDO:0020121", - "MONDO:0000172", "MONDO:0700223", - "MONDO:0024322", - "MONDO:0020573", + "MONDO:0012034", "BFO:0000002", "BFO:0000017", "BFO:0000020", - "MONDO:0016157", - "MONDO:0042489", + "MONDO:0016106", "BFO:0000016", "MONDO:0020120", "MONDO:0019056", - "MONDO:0016139", + "MONDO:0015151", "MONDO:0700096", "MONDO:0005218", "MONDO:0005336", "MONDO:0002081", + "MONDO:0000426", "OGMS:0000031", "MONDO:0003847", "MONDO:0003939", - "MONDO:0015286", "BFO:0000001", - "MONDO:0002320", - "MONDO:0019052", - "MONDO:0005066", - "MONDO:0019950", - "MONDO:0016155", - "MONDO:0011688", - "MONDO:0700066", ], - "subject_label": "muscular dystrophy-dystroglycanopathy type B5", + "subject_label": "autosomal dominant limb-girdle muscular dystrophy type 1F", "subject_closure_label": [ "disease or disorder", - "muscular dystrophy-dystroglycanopathy, type B", + "autosomal dominant disease", + "autosomal genetic disease", "musculoskeletal system disorder", - "congenital nervous system disorder", "hereditary disease", "muscle tissue disorder", - "metabolic disease", "nervous system disorder", "obsolete muscular disorder", "myopathy", - "muscular dystrophy-dystroglycanopathy type B5", - "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", - "qualitative or quantitative defects of fukutin", - "disorder of protein O-glycosylation", - "muscular dystrophy-dystroglycanopathy", - "qualitative or quantitative defects of alpha-dystroglycan", - "inborn errors of metabolism", + "autosomal dominant limb-girdle muscular dystrophy type 1F", + "muscular dystrophy, limb-girdle, autosomal dominant", + "progressive muscular dystrophy", + "limb-girdle muscular dystrophy", "neuromuscular disease", - "congenital muscular dystrophy", "skeletal muscle disorder", "muscular dystrophy", - "inherited disease susceptibility", - "disorder of glycosylation", - "disease susceptibility", - "glycoprotein metabolism disease", - "pulmonary disease, chronic obstructive, susceptibility to", - "myopathy caused by variation in FKRP", "human disease or disorder", "hereditary skeletal muscle disorder", ], - "predicate": "biolink:has_phenotype", - "object": "HP:0003551", + "predicate": "biolink:has_mode_of_inheritance", + "object": "HP:0000006", "original_object": None, "object_namespace": "HP", - "object_category": "biolink:PhenotypicQuality", + "object_category": "biolink:GeneticInheritance", "object_closure": [ "HP:0000001", - "UPHENO:0082875", - "UPHENO:0075696", - "UPHENO:0002320", - "UPHENO:0001001", - "HP:0003551", - "UPHENO:0001005", - "UPHENO:0001002", - "HP:0004302", - "HP:0000118", - "BFO:0000002", - "BFO:0000020", - "HP:0003011", - "UPHENO:0002816", - "UPHENO:0002332", - "HP:0033127", - "UPHENO:0001003", - "UPHENO:0002536", - "BFO:0000001", - "HP:0011804", - "PATO:0000001", - "BFO:0000001", - "BFO:0000002", - "BFO:0000004", - "BFO:0000040", - "UBERON:0001062", - "CARO:0000000", - "UBERON:0000465", - "UBERON:0001015", - "UBERON:0000383", - "UBERON:0005090", - "UBERON:0000061", - "UBERON:0001630", - "UBERON:0010000", - "UBERON:0000467", - "UBERON:0000468", - "UBERON:0000062", - "UBERON:0011216", + "HP:0000006", + "HP:0000005", + "HP:0034345", ], - "object_label": "Difficulty climbing stairs (HPO)", + "object_label": "Autosomal dominant inheritance (HPO)", "object_closure_label": [ "All (HPO)", - "Phenotypic abnormality (HPO)", - "Abnormality of the musculature (HPO)", - "Difficulty climbing stairs (HPO)", - "Functional motor deficit (HPO)", - "Abnormal muscle physiology (HPO)", - "Abnormality of the musculoskeletal system (HPO)", - "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", + "Mode of inheritance (HPO)", + "Autosomal dominant inheritance (HPO)", + "Mendelian inheritance", ], - "primary_knowledge_source": ["infores:hpo-annotations"], + "primary_knowledge_source": "infores:hpo-annotations", "aggregator_knowledge_source": ["infores:monarchinitiative"], - "category": "biolink:DiseaseToPhenotypicFeatureAssociation", + "category": "biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation", "negated": None, - "provided_by": "hpoa_disease_phenotype_edges", - "publications": ["PMID:11592034"], + "provided_by": "hpoa_disease_mode_of_inheritance_edges", + "publications": ["PMID:23543484"], "qualifiers": [], "frequency_qualifier": None, - "has_evidence": "ECO:0000269", + "has_evidence": ["ECO:0000269"], "onset_qualifier": None, "sex_qualifier": None, "stage_qualifier": None, - "evidence_count": 0, + "evidence_count": 4, "pathway": None, "frequency_qualifier_label": None, "frequency_qualifier_namespace": None, @@ -3311,172 +1673,103 @@ def associations(): "stage_qualifier_closure_label": [], }, { - "id": "uuid:19006790-1e4f-11ee-871a-692638b4c502", - "subject": "MONDO:0011787", - "original_subject": "OMIM:607155", + "id": "uuid:c3367251-212f-11ee-873a-cd90a19c4085", + "subject": "MONDO:0012130", + "original_subject": "OMIM:608810", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ - "MONDO:0018282", "MONDO:0000001", - "MONDO:0016971", - "MONDO:0017741", + "MONDO:0016186", "MONDO:0000429", - "MONDO:0045010", - "MONDO:0100167", "MONDO:0005071", "MONDO:0020121", + "MONDO:0018943", "MONDO:0700223", - "MONDO:0011787", - "MONDO:0024322", - "MONDO:0020573", "BFO:0000002", + "MONDO:0019952", "BFO:0000017", "BFO:0000020", - "MONDO:0006025", - "MONDO:0016106", - "MONDO:0016157", - "MONDO:0042489", - "MONDO:0017745", + "MONDO:0020343", "BFO:0000016", "MONDO:0020120", "MONDO:0019056", "MONDO:0016139", "MONDO:0700096", + "MONDO:0002921", "MONDO:0005218", "MONDO:0005336", "MONDO:0002081", - "MONDO:0016156", + "MONDO:0012130", + "MONDO:0000426", "OGMS:0000031", "MONDO:0003847", "MONDO:0003939", - "MONDO:0015286", "BFO:0000001", - "MONDO:0015152", "MONDO:0002320", - "MONDO:0019052", - "MONDO:0005066", - "MONDO:0016155", - "MONDO:0700066", + "MONDO:0016188", + "MONDO:0016108", + "MONDO:0018949", ], - "subject_label": "autosomal recessive limb-girdle muscular dystrophy type 2I", + "subject_label": "myofibrillar myopathy 2", "subject_closure_label": [ "disease or disorder", + "autosomal dominant disease", "autosomal genetic disease", "musculoskeletal system disorder", "congenital nervous system disorder", + "congenital structural myopathy", "hereditary disease", "muscle tissue disorder", - "metabolic disease", "nervous system disorder", "obsolete muscular disorder", "myopathy", - "autosomal recessive disease", - "autosomal recessive limb-girdle muscular dystrophy type 2I", - "autosomal recessive limb-girdle muscular dystrophy", - "congenital disorder of glycosylation", - "progressive muscular dystrophy", + "myofibrillar myopathy 2", + "autosomal dominant distal myopathy", "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", - "limb-girdle muscular dystrophy", - "disorder of protein O-glycosylation", - "disorder of O-mannosylglycan synthesis", - "qualitative or quantitative defects of alpha-dystroglycan", - "inborn errors of metabolism", + "qualitative or quantitative defects of myofibrillar proteins", + "qualitative or quantitative defects of alphaB-cristallin", + "myofibrillar myopathy", + "distal myopathy", "neuromuscular disease", + "congenital myopathy", "skeletal muscle disorder", "muscular dystrophy", - "inherited disease susceptibility", - "disorder of glycosylation", - "disease susceptibility", - "glycoprotein metabolism disease", - "pulmonary disease, chronic obstructive, susceptibility to", - "myopathy caused by variation in FKRP", + "alpha-crystallinopathy", "human disease or disorder", "hereditary skeletal muscle disorder", ], - "predicate": "biolink:has_phenotype", - "object": "HP:0003551", + "predicate": "biolink:has_mode_of_inheritance", + "object": "HP:0000006", "original_object": None, "object_namespace": "HP", - "object_category": "biolink:PhenotypicQuality", + "object_category": "biolink:GeneticInheritance", "object_closure": [ "HP:0000001", - "UPHENO:0082875", - "UPHENO:0075696", - "UPHENO:0002320", - "UPHENO:0001001", - "HP:0003551", - "UPHENO:0001005", - "UPHENO:0001002", - "HP:0004302", - "HP:0000118", - "BFO:0000002", - "BFO:0000020", - "HP:0003011", - "UPHENO:0002816", - "UPHENO:0002332", - "HP:0033127", - "UPHENO:0001003", - "UPHENO:0002536", - "BFO:0000001", - "HP:0011804", - "PATO:0000001", - "BFO:0000001", - "BFO:0000002", - "BFO:0000004", - "BFO:0000040", - "UBERON:0001062", - "CARO:0000000", - "UBERON:0000465", - "UBERON:0001015", - "UBERON:0000383", - "UBERON:0005090", - "UBERON:0000061", - "UBERON:0001630", - "UBERON:0010000", - "UBERON:0000467", - "UBERON:0000468", - "UBERON:0000062", - "UBERON:0011216", + "HP:0000006", + "HP:0000005", + "HP:0034345", ], - "object_label": "Difficulty climbing stairs (HPO)", + "object_label": "Autosomal dominant inheritance (HPO)", "object_closure_label": [ "All (HPO)", - "Phenotypic abnormality (HPO)", - "Abnormality of the musculature (HPO)", - "Difficulty climbing stairs (HPO)", - "Functional motor deficit (HPO)", - "Abnormal muscle physiology (HPO)", - "Abnormality of the musculoskeletal system (HPO)", - "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", + "Mode of inheritance (HPO)", + "Autosomal dominant inheritance (HPO)", + "Mendelian inheritance", ], - "primary_knowledge_source": ["infores:hpo-annotations"], + "primary_knowledge_source": "infores:hpo-annotations", "aggregator_knowledge_source": ["infores:monarchinitiative"], - "category": "biolink:DiseaseToPhenotypicFeatureAssociation", + "category": "biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation", "negated": None, - "provided_by": "hpoa_disease_phenotype_edges", - "publications": ["OMIM:607155"], + "provided_by": "hpoa_disease_mode_of_inheritance_edges", + "publications": ["PMID:14681890"], "qualifiers": [], "frequency_qualifier": None, - "has_evidence": "ECO:0000501", + "has_evidence": ["ECO:0000269"], "onset_qualifier": None, "sex_qualifier": None, "stage_qualifier": None, - "evidence_count": 0, + "evidence_count": 4, "pathway": None, "frequency_qualifier_label": None, "frequency_qualifier_namespace": None, @@ -3500,176 +1793,89 @@ def associations(): "stage_qualifier_closure_label": [], }, { - "id": "uuid:1c016617-1e4f-11ee-871a-692638b4c502", - "subject": "MONDO:0013161", - "original_subject": "OMIM:613157", + "id": "uuid:c39b463c-212f-11ee-873a-cd90a19c4085", + "subject": "MONDO:0012193", + "original_subject": "OMIM:609115", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ - "MONDO:0018282", "MONDO:0000001", - "MONDO:0016182", "MONDO:0016971", - "MONDO:0017741", "MONDO:0000429", - "MONDO:0018276", - "MONDO:0045010", - "MONDO:0100167", "MONDO:0005071", "MONDO:0020121", - "MONDO:0700068", "MONDO:0700223", - "MONDO:0024322", - "MONDO:0020573", "BFO:0000002", "BFO:0000017", "BFO:0000020", - "MONDO:0013161", - "MONDO:0006025", "MONDO:0016106", - "MONDO:0042489", - "MONDO:0017745", "BFO:0000016", "MONDO:0020120", "MONDO:0019056", - "MONDO:0016139", + "MONDO:0015151", "MONDO:0700096", "MONDO:0005218", "MONDO:0005336", "MONDO:0002081", + "MONDO:0012193", + "MONDO:0000426", "OGMS:0000031", "MONDO:0003847", "MONDO:0003939", - "MONDO:0015286", "BFO:0000001", - "MONDO:0015152", - "MONDO:0002320", - "MONDO:0019052", - "MONDO:0005066", - "MONDO:0000173", - "MONDO:0019950", - "MONDO:0016155", ], - "subject_label": "autosomal recessive limb-girdle muscular dystrophy type 2O", + "subject_label": "autosomal dominant limb-girdle muscular dystrophy type 1G", "subject_closure_label": [ "disease or disorder", - "muscular dystrophy-dystroglycanopathy, type C", + "autosomal dominant disease", "autosomal genetic disease", "musculoskeletal system disorder", - "congenital nervous system disorder", "hereditary disease", "muscle tissue disorder", - "metabolic disease", "nervous system disorder", "obsolete muscular disorder", "myopathy", - "autosomal recessive disease", - "autosomal recessive limb-girdle muscular dystrophy type 2O", - "autosomal recessive limb-girdle muscular dystrophy", - "congenital disorder of glycosylation", + "autosomal dominant limb-girdle muscular dystrophy type 1G", + "muscular dystrophy, limb-girdle, autosomal dominant", "progressive muscular dystrophy", - "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 protein O-mannose beta1, 2N-acetylglucosaminyltransferase", "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", "skeletal muscle disorder", "muscular dystrophy", - "inherited disease susceptibility", - "disorder of glycosylation", - "disease susceptibility", - "glycoprotein metabolism disease", - "pulmonary disease, chronic obstructive, susceptibility to", - "myopathy caused by variation in POMGNT1", "human disease or disorder", "hereditary skeletal muscle disorder", ], - "predicate": "biolink:has_phenotype", - "object": "HP:0003551", + "predicate": "biolink:has_mode_of_inheritance", + "object": "HP:0000006", "original_object": None, "object_namespace": "HP", - "object_category": "biolink:PhenotypicQuality", + "object_category": "biolink:GeneticInheritance", "object_closure": [ "HP:0000001", - "UPHENO:0082875", - "UPHENO:0075696", - "UPHENO:0002320", - "UPHENO:0001001", - "HP:0003551", - "UPHENO:0001005", - "UPHENO:0001002", - "HP:0004302", - "HP:0000118", - "BFO:0000002", - "BFO:0000020", - "HP:0003011", - "UPHENO:0002816", - "UPHENO:0002332", - "HP:0033127", - "UPHENO:0001003", - "UPHENO:0002536", - "BFO:0000001", - "HP:0011804", - "PATO:0000001", - "BFO:0000001", - "BFO:0000002", - "BFO:0000004", - "BFO:0000040", - "UBERON:0001062", - "CARO:0000000", - "UBERON:0000465", - "UBERON:0001015", - "UBERON:0000383", - "UBERON:0005090", - "UBERON:0000061", - "UBERON:0001630", - "UBERON:0010000", - "UBERON:0000467", - "UBERON:0000468", - "UBERON:0000062", - "UBERON:0011216", + "HP:0000006", + "HP:0000005", + "HP:0034345", ], - "object_label": "Difficulty climbing stairs (HPO)", + "object_label": "Autosomal dominant inheritance (HPO)", "object_closure_label": [ "All (HPO)", - "Phenotypic abnormality (HPO)", - "Abnormality of the musculature (HPO)", - "Difficulty climbing stairs (HPO)", - "Functional motor deficit (HPO)", - "Abnormal muscle physiology (HPO)", - "Abnormality of the musculoskeletal system (HPO)", - "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", + "Mode of inheritance (HPO)", + "Autosomal dominant inheritance (HPO)", + "Mendelian inheritance", ], - "primary_knowledge_source": ["infores:hpo-annotations"], + "primary_knowledge_source": "infores:hpo-annotations", "aggregator_knowledge_source": ["infores:monarchinitiative"], - "category": "biolink:DiseaseToPhenotypicFeatureAssociation", + "category": "biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation", "negated": None, - "provided_by": "hpoa_disease_phenotype_edges", - "publications": ["OMIM:613157"], + "provided_by": "hpoa_disease_mode_of_inheritance_edges", + "publications": ["PMID:24647604"], "qualifiers": [], "frequency_qualifier": None, - "has_evidence": "ECO:0000304", + "has_evidence": ["ECO:0000269"], "onset_qualifier": None, "sex_qualifier": None, "stage_qualifier": None, - "evidence_count": 0, + "evidence_count": 4, "pathway": None, "frequency_qualifier_label": None, "frequency_qualifier_namespace": None, @@ -3693,144 +1899,105 @@ def associations(): "stage_qualifier_closure_label": [], }, { - "id": "uuid:1b1ad451-1e4f-11ee-871a-692638b4c502", - "subject": "MONDO:0013222", - "original_subject": "OMIM:613319", + "id": "uuid:c4006058-212f-11ee-873a-cd90a19c4085", + "subject": "MONDO:0012215", + "original_subject": "OMIM:609200", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ - "MONDO:0013222", + "MONDO:0012215", "MONDO:0000001", + "MONDO:0016971", "MONDO:0000429", - "MONDO:0100167", "MONDO:0005071", "MONDO:0020121", + "MONDO:0018943", "MONDO:0700223", - "MONDO:0020573", + "MONDO:0016201", "BFO:0000002", + "MONDO:0019952", "BFO:0000017", "BFO:0000020", - "MONDO:0006025", - "MONDO:0042489", + "MONDO:0016106", "BFO:0000016", "MONDO:0020120", "MONDO:0019056", + "MONDO:0016139", + "MONDO:0015151", "MONDO:0700096", - "MONDO:0009685", + "MONDO:0002921", "MONDO:0005218", "MONDO:0005336", "MONDO:0002081", - "MONDO:0016109", + "MONDO:0000426", "OGMS:0000031", "MONDO:0003847", "MONDO:0003939", "BFO:0000001", + "MONDO:0002320", + "MONDO:0016108", "MONDO:0018949", ], - "subject_label": "Miyoshi muscular dystrophy 3", + "subject_label": "myofibrillar myopathy 3", "subject_closure_label": [ "disease or disorder", + "autosomal dominant disease", "autosomal genetic disease", "musculoskeletal system disorder", + "congenital nervous system disorder", + "congenital structural myopathy", "hereditary disease", "muscle tissue disorder", "nervous system disorder", "obsolete muscular disorder", "myopathy", - "autosomal recessive disease", - "Miyoshi myopathy", - "Miyoshi muscular dystrophy 3", - "autosomal recessive distal myopathy", + "myofibrillar myopathy 3", + "muscular dystrophy, limb-girdle, autosomal dominant", + "progressive muscular dystrophy", + "autosomal dominant distal myopathy", + "qualitative or quantitative protein defects in neuromuscular diseases", + "qualitative or quantitative defects of myotilin", + "limb-girdle muscular dystrophy", + "myofibrillar myopathy", "distal myopathy", "neuromuscular disease", + "congenital myopathy", "skeletal muscle disorder", "muscular dystrophy", - "inherited disease susceptibility", - "disease susceptibility", - "pulmonary disease, chronic obstructive, susceptibility to", "human disease or disorder", "hereditary skeletal muscle disorder", ], - "predicate": "biolink:has_phenotype", - "object": "HP:0003551", + "predicate": "biolink:has_mode_of_inheritance", + "object": "HP:0000006", "original_object": None, "object_namespace": "HP", - "object_category": "biolink:PhenotypicQuality", + "object_category": "biolink:GeneticInheritance", "object_closure": [ "HP:0000001", - "UPHENO:0082875", - "UPHENO:0075696", - "UPHENO:0002320", - "UPHENO:0001001", - "HP:0003551", - "UPHENO:0001005", - "UPHENO:0001002", - "HP:0004302", - "HP:0000118", - "BFO:0000002", - "BFO:0000020", - "HP:0003011", - "UPHENO:0002816", - "UPHENO:0002332", - "HP:0033127", - "UPHENO:0001003", - "UPHENO:0002536", - "BFO:0000001", - "HP:0011804", - "PATO:0000001", - "BFO:0000001", - "BFO:0000002", - "BFO:0000004", - "BFO:0000040", - "UBERON:0001062", - "CARO:0000000", - "UBERON:0000465", - "UBERON:0001015", - "UBERON:0000383", - "UBERON:0005090", - "UBERON:0000061", - "UBERON:0001630", - "UBERON:0010000", - "UBERON:0000467", - "UBERON:0000468", - "UBERON:0000062", - "UBERON:0011216", + "HP:0000006", + "HP:0000005", + "HP:0034345", ], - "object_label": "Difficulty climbing stairs (HPO)", + "object_label": "Autosomal dominant inheritance (HPO)", "object_closure_label": [ "All (HPO)", - "Phenotypic abnormality (HPO)", - "Abnormality of the musculature (HPO)", - "Difficulty climbing stairs (HPO)", - "Functional motor deficit (HPO)", - "Abnormal muscle physiology (HPO)", - "Abnormality of the musculoskeletal system (HPO)", - "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", + "Mode of inheritance (HPO)", + "Autosomal dominant inheritance (HPO)", + "Mendelian inheritance", ], - "primary_knowledge_source": ["infores:hpo-annotations"], + "primary_knowledge_source": "infores:hpo-annotations", "aggregator_knowledge_source": ["infores:monarchinitiative"], - "category": "biolink:DiseaseToPhenotypicFeatureAssociation", + "category": "biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation", "negated": None, - "provided_by": "hpoa_disease_phenotype_edges", - "publications": ["PMID:20096397"], + "provided_by": "hpoa_disease_mode_of_inheritance_edges", + "publications": ["OMIM:609200"], "qualifiers": [], "frequency_qualifier": None, - "has_evidence": "ECO:0000269", + "has_evidence": ["ECO:0000501"], "onset_qualifier": None, "sex_qualifier": None, "stage_qualifier": None, - "evidence_count": 0, + "evidence_count": 4, "pathway": None, "frequency_qualifier_label": None, "frequency_qualifier_namespace": None, @@ -3854,148 +2021,107 @@ def associations(): "stage_qualifier_closure_label": [], }, { - "id": "uuid:1a0255cd-1e4f-11ee-871a-692638b4c502", - "subject": "MONDO:0013390", - "original_subject": "OMIM:613723", + "id": "uuid:c275a325-212f-11ee-873a-cd90a19c4085", + "subject": "MONDO:0012262", + "original_subject": "OMIM:609384", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ - "MONDO:0013390", + "MONDO:0020158", "MONDO:0000001", - "MONDO:0016198", - "MONDO:0016971", - "MONDO:0000429", - "MONDO:0100167", + "MONDO:0007614", "MONDO:0005071", "MONDO:0020121", "MONDO:0700223", - "MONDO:0020573", + "MONDO:0004746", "BFO:0000002", + "MONDO:0012262", + "MONDO:0957003", "BFO:0000017", "BFO:0000020", - "MONDO:0006025", "MONDO:0016106", - "MONDO:0042489", + "MONDO:0003382", "BFO:0000016", "MONDO:0020120", "MONDO:0019056", - "MONDO:0016139", + "MONDO:0003569", "MONDO:0700096", + "MONDO:0001584", + "MONDO:0024458", "MONDO:0005218", "MONDO:0005336", "MONDO:0002081", "OGMS:0000031", "MONDO:0003847", "MONDO:0003939", + "MONDO:0002022", + "MONDO:0015368", "BFO:0000001", - "MONDO:0015152", + "MONDO:0002320", + "MONDO:0000462", + "MONDO:0005328", ], - "subject_label": "autosomal recessive limb-girdle muscular dystrophy type 2Q", + "subject_label": "fibrosis of extraocular muscles, congenital, 3c", "subject_closure_label": [ "disease or disorder", - "autosomal genetic disease", + "eye adnexa disorder", + "ocular motility disease", + "disorder of orbital region", "musculoskeletal system disorder", + "congenital nervous system disorder", + "eyelid disorder", + "cranial nerve neuropathy", "hereditary disease", "muscle tissue disorder", + "myopathy of extraocular muscle", "nervous system disorder", "obsolete muscular disorder", + "eye disorder", "myopathy", - "autosomal recessive disease", - "autosomal recessive limb-girdle muscular dystrophy type 2Q", - "autosomal recessive limb-girdle muscular dystrophy", + "congenital fibrosis of extraocular muscles", + "fibrosis of extraocular muscles, congenital, 3c", + "neuro-ophthalmological disease", "progressive muscular dystrophy", - "qualitative or quantitative protein defects in neuromuscular diseases", - "qualitative or quantitative defects of plectin", - "limb-girdle muscular dystrophy", "neuromuscular disease", "skeletal muscle disorder", "muscular dystrophy", - "inherited disease susceptibility", - "disease susceptibility", - "pulmonary disease, chronic obstructive, susceptibility to", + "eyelids malposition disorder", + "disorder of visual system", "human disease or disorder", "hereditary skeletal muscle disorder", + "hereditary neuro-ophthalmological disease", ], - "predicate": "biolink:has_phenotype", - "object": "HP:0003551", + "predicate": "biolink:has_mode_of_inheritance", + "object": "HP:0000006", "original_object": None, "object_namespace": "HP", - "object_category": "biolink:PhenotypicQuality", + "object_category": "biolink:GeneticInheritance", "object_closure": [ "HP:0000001", - "UPHENO:0082875", - "UPHENO:0075696", - "UPHENO:0002320", - "UPHENO:0001001", - "HP:0003551", - "UPHENO:0001005", - "UPHENO:0001002", - "HP:0004302", - "HP:0000118", - "BFO:0000002", - "BFO:0000020", - "HP:0003011", - "UPHENO:0002816", - "UPHENO:0002332", - "HP:0033127", - "UPHENO:0001003", - "UPHENO:0002536", - "BFO:0000001", - "HP:0011804", - "PATO:0000001", - "BFO:0000001", - "BFO:0000002", - "BFO:0000004", - "BFO:0000040", - "UBERON:0001062", - "CARO:0000000", - "UBERON:0000465", - "UBERON:0001015", - "UBERON:0000383", - "UBERON:0005090", - "UBERON:0000061", - "UBERON:0001630", - "UBERON:0010000", - "UBERON:0000467", - "UBERON:0000468", - "UBERON:0000062", - "UBERON:0011216", + "HP:0000006", + "HP:0000005", + "HP:0034345", ], - "object_label": "Difficulty climbing stairs (HPO)", + "object_label": "Autosomal dominant inheritance (HPO)", "object_closure_label": [ "All (HPO)", - "Phenotypic abnormality (HPO)", - "Abnormality of the musculature (HPO)", - "Difficulty climbing stairs (HPO)", - "Functional motor deficit (HPO)", - "Abnormal muscle physiology (HPO)", - "Abnormality of the musculoskeletal system (HPO)", - "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", + "Mode of inheritance (HPO)", + "Autosomal dominant inheritance (HPO)", + "Mendelian inheritance", ], - "primary_knowledge_source": ["infores:hpo-annotations"], + "primary_knowledge_source": "infores:hpo-annotations", "aggregator_knowledge_source": ["infores:monarchinitiative"], - "category": "biolink:DiseaseToPhenotypicFeatureAssociation", + "category": "biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation", "negated": None, - "provided_by": "hpoa_disease_phenotype_edges", - "publications": ["PMID:21109228"], + "provided_by": "hpoa_disease_mode_of_inheritance_edges", + "publications": ["OMIM:609384"], "qualifiers": [], "frequency_qualifier": None, - "has_evidence": "ECO:0000269", + "has_evidence": ["ECO:0000501"], "onset_qualifier": None, "sex_qualifier": None, "stage_qualifier": None, - "evidence_count": 0, + "evidence_count": 4, "pathway": None, "frequency_qualifier_label": None, "frequency_qualifier_namespace": None, @@ -4019,148 +2145,101 @@ def associations(): "stage_qualifier_closure_label": [], }, { - "id": "uuid:24d370c2-1e4f-11ee-871a-692638b4c502", - "subject": "MONDO:0024545", - "original_subject": "OMIM:254130", + "id": "uuid:c304ba49-212f-11ee-873a-cd90a19c4085", + "subject": "MONDO:0012277", + "original_subject": "OMIM:609452", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ "MONDO:0000001", + "MONDO:0016186", "MONDO:0000429", - "MONDO:0016145", - "MONDO:0100167", "MONDO:0005071", "MONDO:0020121", + "MONDO:0018943", "MONDO:0700223", - "MONDO:0020573", "BFO:0000002", + "MONDO:0019952", + "MONDO:0016190", "BFO:0000017", "BFO:0000020", - "MONDO:0006025", - "MONDO:0042489", "BFO:0000016", "MONDO:0020120", "MONDO:0019056", "MONDO:0016139", "MONDO:0700096", - "MONDO:0009685", + "MONDO:0002921", "MONDO:0005218", "MONDO:0005336", "MONDO:0002081", - "MONDO:0016109", + "MONDO:0000426", "OGMS:0000031", "MONDO:0003847", "MONDO:0003939", + "MONDO:0012277", "BFO:0000001", - "MONDO:0024545", + "MONDO:0002320", + "MONDO:0016108", "MONDO:0018949", ], - "subject_label": "Miyoshi muscular dystrophy 1", + "subject_label": "myofibrillar myopathy 4", "subject_closure_label": [ "disease or disorder", + "autosomal dominant disease", "autosomal genetic disease", "musculoskeletal system disorder", + "congenital nervous system disorder", + "congenital structural myopathy", "hereditary disease", "muscle tissue disorder", "nervous system disorder", "obsolete muscular disorder", "myopathy", - "autosomal recessive disease", - "Miyoshi myopathy", - "autosomal recessive distal myopathy", + "myofibrillar myopathy 4", + "autosomal dominant distal myopathy", "qualitative or quantitative protein defects in neuromuscular diseases", - "qualitative or quantitative defects of dysferlin", + "qualitative or quantitative defects of myofibrillar proteins", + "qualitative or quantitative defects of protein ZASP", + "myofibrillar myopathy", "distal myopathy", "neuromuscular disease", + "congenital myopathy", "skeletal muscle disorder", "muscular dystrophy", - "inherited disease susceptibility", - "Miyoshi muscular dystrophy 1", - "disease susceptibility", - "pulmonary disease, chronic obstructive, susceptibility to", "human disease or disorder", "hereditary skeletal muscle disorder", ], - "predicate": "biolink:has_phenotype", - "object": "HP:0003551", + "predicate": "biolink:has_mode_of_inheritance", + "object": "HP:0000006", "original_object": None, "object_namespace": "HP", - "object_category": "biolink:PhenotypicQuality", + "object_category": "biolink:GeneticInheritance", "object_closure": [ "HP:0000001", - "UPHENO:0082875", - "UPHENO:0075696", - "UPHENO:0002320", - "UPHENO:0001001", - "HP:0003551", - "UPHENO:0001005", - "UPHENO:0001002", - "HP:0004302", - "HP:0000118", - "BFO:0000002", - "BFO:0000020", - "HP:0003011", - "UPHENO:0002816", - "UPHENO:0002332", - "HP:0033127", - "UPHENO:0001003", - "UPHENO:0002536", - "BFO:0000001", - "HP:0011804", - "PATO:0000001", - "BFO:0000001", - "BFO:0000002", - "BFO:0000004", - "BFO:0000040", - "UBERON:0001062", - "CARO:0000000", - "UBERON:0000465", - "UBERON:0001015", - "UBERON:0000383", - "UBERON:0005090", - "UBERON:0000061", - "UBERON:0001630", - "UBERON:0010000", - "UBERON:0000467", - "UBERON:0000468", - "UBERON:0000062", - "UBERON:0011216", + "HP:0000006", + "HP:0000005", + "HP:0034345", ], - "object_label": "Difficulty climbing stairs (HPO)", + "object_label": "Autosomal dominant inheritance (HPO)", "object_closure_label": [ "All (HPO)", - "Phenotypic abnormality (HPO)", - "Abnormality of the musculature (HPO)", - "Difficulty climbing stairs (HPO)", - "Functional motor deficit (HPO)", - "Abnormal muscle physiology (HPO)", - "Abnormality of the musculoskeletal system (HPO)", - "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", + "Mode of inheritance (HPO)", + "Autosomal dominant inheritance (HPO)", + "Mendelian inheritance", ], - "primary_knowledge_source": ["infores:hpo-annotations"], + "primary_knowledge_source": "infores:hpo-annotations", "aggregator_knowledge_source": ["infores:monarchinitiative"], - "category": "biolink:DiseaseToPhenotypicFeatureAssociation", + "category": "biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation", "negated": None, - "provided_by": "hpoa_disease_phenotype_edges", - "publications": ["OMIM:254130"], + "provided_by": "hpoa_disease_mode_of_inheritance_edges", + "publications": ["OMIM:609452"], "qualifiers": [], "frequency_qualifier": None, - "has_evidence": "ECO:0000304", + "has_evidence": ["ECO:0000501"], "onset_qualifier": None, "sex_qualifier": None, "stage_qualifier": None, - "evidence_count": 0, + "evidence_count": 4, "pathway": None, "frequency_qualifier_label": None, "frequency_qualifier_namespace": None, diff --git a/backend/tests/fixtures/autocomplete.py b/backend/tests/fixtures/autocomplete.py index 8afb89bf6..5fa3a7a77 100644 --- a/backend/tests/fixtures/autocomplete.py +++ b/backend/tests/fixtures/autocomplete.py @@ -6,7 +6,7 @@ def autocomplete(): return { "limit": 10, "offset": 0, - "total": 193, + "total": 195, "items": [ { "id": "MONDO:0001083", diff --git a/backend/tests/fixtures/autocomplete_response.py b/backend/tests/fixtures/autocomplete_response.py index 822db39b8..d531011c3 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": 1, + "QTime": 0, "params": { "mm": "100%", "q": "fanc", @@ -19,7 +19,7 @@ def autocomplete_response(): }, }, "response": { - "num_found": 193, + "num_found": 195, "start": 1, "docs": [ { diff --git a/backend/tests/fixtures/histopheno_response.py b/backend/tests/fixtures/histopheno_response.py index 22f33edc9..37f8ec838 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": 6, + "QTime": 2, "params": { "facet.query": [ 'object_closure:"HP:0000924"', @@ -39,7 +39,7 @@ def histopheno_response(): "facet": "true", }, }, - "response": {"num_found": 4542, "start": 0, "docs": []}, + "response": {"num_found": 4538, "start": 0, "docs": []}, "facet_counts": { "facet_fields": {}, "facet_queries": { diff --git a/backend/tests/fixtures/node.py b/backend/tests/fixtures/node.py index 1e2a3768a..4314d12a2 100644 --- a/backend/tests/fixtures/node.py +++ b/backend/tests/fixtures/node.py @@ -46,19 +46,6 @@ def node(): ], "node_hierarchy": { "super_classes": [ - { - "id": "MONDO:0005336", - "category": "biolink:Disease", - "name": "myopathy", - "full_name": None, - "description": None, - "xref": [], - "provided_by": None, - "in_taxon": None, - "in_taxon_label": None, - "symbol": None, - "synonym": [], - }, { "id": "MONDO:0019056", "category": "biolink:Disease", @@ -73,9 +60,9 @@ def node(): "synonym": [], }, { - "id": "MONDO:0100167", + "id": "MONDO:0700223", "category": "biolink:Disease", - "name": "pulmonary disease, chronic obstructive, susceptibility to", + "name": "hereditary skeletal muscle disorder", "full_name": None, "description": None, "xref": [], @@ -86,9 +73,9 @@ def node(): "synonym": [], }, { - "id": "MONDO:0700223", + "id": "MONDO:0005336", "category": "biolink:Disease", - "name": "hereditary skeletal muscle disorder", + "name": "myopathy", "full_name": None, "description": None, "xref": [], diff --git a/backend/tests/fixtures/search.py b/backend/tests/fixtures/search.py index 2c99e14b3..4c585d6e5 100644 --- a/backend/tests/fixtures/search.py +++ b/backend/tests/fixtures/search.py @@ -6,7 +6,7 @@ def search(): return { "limit": 20, "offset": 0, - "total": 92, + "total": 93, "items": [ { "id": "MONDO:0019391", diff --git a/backend/tests/fixtures/search_response.py b/backend/tests/fixtures/search_response.py index f0c6266b2..1cc7ba67f 100644 --- a/backend/tests/fixtures/search_response.py +++ b/backend/tests/fixtures/search_response.py @@ -20,7 +20,7 @@ def search_response(): }, }, "response": { - "num_found": 92, + "num_found": 93, "start": 0, "docs": [ { diff --git a/frontend/fixtures/association-table.json b/frontend/fixtures/association-table.json index d9ea419cf..e5fd56c8d 100644 --- a/frontend/fixtures/association-table.json +++ b/frontend/fixtures/association-table.json @@ -4,82 +4,68 @@ "total": 4011, "items": [ { - "id": "uuid:2211b990-1e4f-11ee-871a-692638b4c502", - "subject": "MONDO:0010311", - "original_subject": "OMIM:300376", + "id": "uuid:632c5b16-212f-11ee-873a-cd90a19c4085", + "subject": "MONDO:0020793", + "original_subject": "OMIM:164310", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ - "MONDO:0004994", + "MONDO:0020158", "MONDO:0000001", - "MONDO:0100167", "MONDO:0005071", - "MONDO:0016147", - "MONDO:0005267", + "MONDO:0025193", "MONDO:0020121", - "MONDO:0004995", "MONDO:0700223", - "MONDO:0020573", "BFO:0000002", + "MONDO:0020793", "BFO:0000017", "BFO:0000020", - "MONDO:0010542", "MONDO:0016106", - "MONDO:0015470", - "MONDO:0005217", - "MONDO:0016899", - "MONDO:0042489", + "MONDO:0003382", "BFO:0000016", "MONDO:0020120", "MONDO:0019056", - "MONDO:0016139", "MONDO:0700096", - "MONDO:0000591", + "MONDO:0024458", "MONDO:0005218", "MONDO:0005336", "MONDO:0002081", - "MONDO:0016333", "OGMS:0000031", - "MONDO:0005021", "MONDO:0003847", "MONDO:0003939", + "MONDO:0002022", "BFO:0000001", - "MONDO:0010311" + "MONDO:0000462", + "MONDO:0005328", + "MONDO:0018949" ], - "subject_label": "Becker muscular dystrophy", + "subject_label": "oculopharyngodistal myopathy 1", "subject_closure_label": [ "disease or disorder", - "intrinsic cardiomyopathy", + "eye adnexa disorder", + "disorder of orbital region", "musculoskeletal system disorder", + "eyelid disorder", "hereditary disease", "muscle tissue disorder", - "cardiomyopathy", - "cardiovascular disorder", - "dilated cardiomyopathy", "nervous system disorder", - "familial cardiomyopathy", "obsolete muscular disorder", - "heart disorder", + "eye 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", + "distal myopathy", "neuromuscular disease", "skeletal muscle disorder", "muscular dystrophy", - "inherited disease susceptibility", - "disease susceptibility", - "pulmonary disease, chronic obstructive, susceptibility to", + "eyelids malposition disorder", + "oculopharyngodistal myopathy 1", + "disorder of visual system", + "oculopharyngodistal myopathy", "human disease or disorder", "hereditary skeletal muscle disorder" ], "predicate": "biolink:has_phenotype", - "object": "HP:0003115", + "object": "HP:0002460", "original_object": null, "object_namespace": "HP", "object_category": "biolink:PhenotypicQuality", @@ -87,76 +73,89 @@ "HP:0000001", "UPHENO:0082875", "UPHENO:0075696", + "UPHENO:0002320", "UPHENO:0001001", - "HP:0030956", - "HP:0001626", - "HP:0003115", - "UPHENO:0080362", "UPHENO:0001005", - "HP:0500015", "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", - "HP:0011025", + "HP:0002460", "BFO:0000001", + "HP:0011804", "PATO:0000001", - "UPHENO:0002406", + "CARO:0000000", "BFO:0000001", + "UBERON:0000383", + "UBERON:0001015", + "UBERON:0005090", "BFO:0000002", + "UBERON:0001630", "BFO:0000004", "BFO:0000040", "UBERON:0001062", - "CARO:0000000", "UBERON:0000465", - "PR:000050567", - "UBERON:0004535", "UBERON:0000061", "UBERON:0010000", "UBERON:0000467", "UBERON:0000468", - "UBERON:0001009" + "UBERON:0000062", + "UBERON:0011216" ], - "object_label": "Abnormal EKG (HPO)", + "object_label": "Distal muscle weakness (HPO)", "object_closure_label": [ "All (HPO)", "Phenotypic abnormality (HPO)", - "Abnormality of the cardiovascular system (HPO)", - "Abnormal EKG (HPO)", - "Abnormal cardiovascular system physiology (HPO)", - "Abnormality of cardiovascular system electrophysiology (HPO)", - "Abnormal cardiac test (HPO)", + "Muscle weakness (HPO)", + "Distal muscle weakness (HPO)", + "Abnormality of the musculature (HPO)", + "Abnormal muscle physiology (HPO)", + "Abnormality of the musculoskeletal system (HPO)", "anatomical structure", + "organ", + "musculature of body", "material anatomical entity", "anatomical system", "multicellular organism", - "circulatory system", + "musculature", "anatomical entity", - "cardiovascular system", - "multicellular anatomical structure" + "muscle organ", + "muscle structure", + "multicellular anatomical structure", + "organ system subdivision" ], - "primary_knowledge_source": ["infores:hpo-annotations"], + "primary_knowledge_source": "infores:hpo-annotations", "aggregator_knowledge_source": ["infores:monarchinitiative"], "category": "biolink:DiseaseToPhenotypicFeatureAssociation", "negated": null, "provided_by": "hpoa_disease_phenotype_edges", - "publications": ["OMIM:300376"], + "publications": ["PMID:21242490", "PMID:32493488", "PMID:31332380"], "qualifiers": [], - "frequency_qualifier": null, - "has_evidence": "ECO:0000501", + "frequency_qualifier": "HP:0040282", + "has_evidence": ["ECO:0000269"], "onset_qualifier": null, "sex_qualifier": null, "stage_qualifier": null, - "evidence_count": 0, + "evidence_count": 6, "pathway": null, - "frequency_qualifier_label": null, - "frequency_qualifier_namespace": null, - "frequency_qualifier_category": null, - "frequency_qualifier_closure": [], - "frequency_qualifier_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)" + ], "onset_qualifier_label": null, "onset_qualifier_namespace": null, "onset_qualifier_category": null, @@ -175,187 +174,204 @@ "direction": "outgoing" }, { - "id": "uuid:29eadc82-1e4f-11ee-871a-692638b4c502", - "subject": "MONDO:0010311", - "original_subject": "Orphanet:98895", + "id": "uuid:632c5b27-212f-11ee-873a-cd90a19c4085", + "subject": "MONDO:0020793", + "original_subject": "OMIM:164310", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ - "MONDO:0004994", + "MONDO:0020158", "MONDO:0000001", - "MONDO:0100167", "MONDO:0005071", - "MONDO:0016147", - "MONDO:0005267", + "MONDO:0025193", "MONDO:0020121", - "MONDO:0004995", "MONDO:0700223", - "MONDO:0020573", "BFO:0000002", + "MONDO:0020793", "BFO:0000017", "BFO:0000020", - "MONDO:0010542", "MONDO:0016106", - "MONDO:0015470", - "MONDO:0005217", - "MONDO:0016899", - "MONDO:0042489", + "MONDO:0003382", "BFO:0000016", "MONDO:0020120", "MONDO:0019056", - "MONDO:0016139", "MONDO:0700096", - "MONDO:0000591", + "MONDO:0024458", "MONDO:0005218", "MONDO:0005336", "MONDO:0002081", - "MONDO:0016333", "OGMS:0000031", - "MONDO:0005021", "MONDO:0003847", "MONDO:0003939", + "MONDO:0002022", "BFO:0000001", - "MONDO:0010311" + "MONDO:0000462", + "MONDO:0005328", + "MONDO:0018949" ], - "subject_label": "Becker muscular dystrophy", + "subject_label": "oculopharyngodistal myopathy 1", "subject_closure_label": [ "disease or disorder", - "intrinsic cardiomyopathy", + "eye adnexa disorder", + "disorder of orbital region", "musculoskeletal system disorder", + "eyelid disorder", "hereditary disease", "muscle tissue disorder", - "cardiomyopathy", - "cardiovascular disorder", - "dilated cardiomyopathy", "nervous system disorder", - "familial cardiomyopathy", "obsolete muscular disorder", - "heart disorder", + "eye 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", + "distal myopathy", "neuromuscular disease", "skeletal muscle disorder", "muscular dystrophy", - "inherited disease susceptibility", - "disease susceptibility", - "pulmonary disease, chronic obstructive, susceptibility to", + "eyelids malposition disorder", + "oculopharyngodistal myopathy 1", + "disorder of visual system", + "oculopharyngodistal myopathy", "human disease or disorder", "hereditary skeletal muscle disorder" ], "predicate": "biolink:has_phenotype", - "object": "HP:0012086", + "object": "HP:0002015", "original_object": null, "object_namespace": "HP", "object_category": "biolink:PhenotypicQuality", "object_closure": [ "HP:0000001", "UPHENO:0082875", - "UPHENO:0002832", "UPHENO:0075696", - "UPHENO:0080210", + "HP:0011024", "UPHENO:0001001", - "HP:0012086", + "UPHENO:0002443", + "UPHENO:0002471", + "HP:0025270", + "HP:0012719", "UPHENO:0001005", + "UPHENO:0002833", + "HP:0002015", "UPHENO:0001002", - "UPHENO:0083447", + "UPHENO:0002725", "HP:0000118", "BFO:0000002", - "UPHENO:0080216", "BFO:0000020", - "HP:0011277", + "UPHENO:0002433", + "HP:0025032", "UPHENO:0002332", - "HP:0000079", - "UPHENO:0015280", - "UPHENO:0081581", + "HP:0000707", "UPHENO:0001003", "UPHENO:0002536", - "UPHENO:0083450", - "HP:0001939", - "UPHENO:0020584", - "UPHENO:0076692", - "HP:0000119", + "UPHENO:0004523", "BFO:0000001", - "HP:0003110", - "UPHENO:0002642", - "UPHENO:0002442", - "HP:0033072", "PATO:0000001", + "HP:0025031", + "UPHENO:0002474", + "HP:0012638", + "CARO:0000000", + "CARO:0000003", "BFO:0000001", - "BFO:0000003", + "UBERON:0004921", + "UBERON:0001555", + "UBERON:0001016", + "UBERON:0000915", "BFO:0000002", - "BFO:0000015", + "UBERON:0004908", + "UBERON:0001043", "BFO:0000004", - "GO:0008150", "BFO:0000040", "UBERON:0001062", - "CARO:0000000", - "GO:0008152", - "GO:0042592", + "RO:0002577", "UBERON:0000465", - "UBERON:0004122", "UBERON:0000061", - "UBERON:0000463", "UBERON:0010000", "UBERON:0000467", - "UBERON:0000174", "UBERON:0000468", - "UBERON:8450002", - "UBERON:0001088", - "UBERON:0001008" + "UBERON:0000475", + "UBERON:0000064", + "UBERON:0000062", + "UBERON:0004111", + "UBERON:0005409", + "UBERON:0001007", + "UBERON:0011676", + "UBERON:0013701", + "UBERON:0009569", + "UBERON:0013702", + "UBERON:0013522", + "UBERON:0013765", + "UBERON:0005177", + "UBERON:0000025", + "UBERON:0002100", + "UBERON:0005181", + "UBERON:0002075", + "UBERON:0005178" ], - "object_label": "Abnormal urinary color (HPO)", + "object_label": "Dysphagia (HPO)", "object_closure_label": [ "All (HPO)", - "Abnormality of the urinary system (HPO)", "Phenotypic abnormality (HPO)", - "Abnormality of the genitourinary system (HPO)", - "Abnormality of metabolism/homeostasis (HPO)", - "Abnormality of urine homeostasis (HPO)", - "Abnormality of the urinary system physiology (HPO)", - "Abnormal urinary color (HPO)", - "Abnormal macroscopic urine appearance (HPO)", + "Abnormality of the nervous system (HPO)", + "Dysphagia (HPO)", + "Abnormality of the gastrointestinal tract (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)", + "tube", "anatomical structure", - "excreta", - "organism substance", + "organ", + "organ part", "material anatomical entity", "anatomical system", "multicellular organism", - "renal system", + "organism subdivision", + "thoracic segment of trunk", + "digestive system", + "nervous system", + "esophagus", "anatomical entity", - "urine", - "genitourinary system", + "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", - "excretory system" + "subdivision of organism along main body axis", + "subdivision of tube", + "main body axis", + "body proper", + "digestive system element" ], - "primary_knowledge_source": ["infores:hpo-annotations"], + "primary_knowledge_source": "infores:hpo-annotations", "aggregator_knowledge_source": ["infores:monarchinitiative"], "category": "biolink:DiseaseToPhenotypicFeatureAssociation", "negated": null, "provided_by": "hpoa_disease_phenotype_edges", - "publications": ["orphanet:98895"], + "publications": ["PMID:21242490", "PMID:32493488", "PMID:31332380"], "qualifiers": [], - "frequency_qualifier": "HP:0040281", - "has_evidence": "ECO:0000304", + "frequency_qualifier": "HP:0040282", + "has_evidence": ["ECO:0000269"], "onset_qualifier": null, "sex_qualifier": null, "stage_qualifier": null, - "evidence_count": 0, + "evidence_count": 6, "pathway": null, - "frequency_qualifier_label": "Very frequent (HPO)", + "frequency_qualifier_label": "Frequent (HPO)", "frequency_qualifier_namespace": "HP", "frequency_qualifier_category": "biolink:PhenotypicFeature", - "frequency_qualifier_closure": ["HP:0000001", "HP:0040279", "HP:0040281"], + "frequency_qualifier_closure": ["HP:0000001", "HP:0040282", "HP:0040279"], "frequency_qualifier_closure_label": [ "All (HPO)", "Frequency (HPO)", - "Very frequent (HPO)" + "Frequent (HPO)" ], "onset_qualifier_label": null, "onset_qualifier_namespace": null, @@ -375,182 +391,268 @@ "direction": "outgoing" }, { - "id": "uuid:29eadc85-1e4f-11ee-871a-692638b4c502", - "subject": "MONDO:0010311", - "original_subject": "Orphanet:98895", + "id": "uuid:5d7fc2a1-212f-11ee-873a-cd90a19c4085", + "subject": "MONDO:0013049", + "original_subject": "OMIM:612937", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ "MONDO:0004994", "MONDO:0000001", - "MONDO:0100167", + "MONDO:0018276", "MONDO:0005071", - "MONDO:0016147", "MONDO:0005267", + "MONDO:0013049", "MONDO:0020121", "MONDO:0004995", "MONDO:0700223", - "MONDO:0020573", + "MONDO:0024322", "BFO:0000002", "BFO:0000017", "BFO:0000020", - "MONDO:0010542", - "MONDO:0016106", - "MONDO:0015470", "MONDO:0005217", - "MONDO:0016899", - "MONDO:0042489", "BFO:0000016", "MONDO:0020120", "MONDO:0019056", - "MONDO:0016139", "MONDO:0700096", "MONDO:0000591", "MONDO:0005218", "MONDO:0005336", "MONDO:0002081", "MONDO:0016333", + "MONDO:0017749", "OGMS:0000031", "MONDO:0005021", "MONDO:0003847", "MONDO:0003939", + "MONDO:0015286", "BFO:0000001", - "MONDO:0010311" + "MONDO:0002320", + "MONDO:0019052", + "MONDO:0005500", + "MONDO:0005066", + "MONDO:0019950" ], - "subject_label": "Becker muscular dystrophy", + "subject_label": "DPM3-congenital disorder of glycosylation", "subject_closure_label": [ "disease or disorder", "intrinsic cardiomyopathy", "musculoskeletal system disorder", + "congenital nervous system disorder", "hereditary disease", "muscle tissue disorder", "cardiomyopathy", "cardiovascular disorder", "dilated cardiomyopathy", + "metabolic disease", "nervous system disorder", "familial cardiomyopathy", "obsolete muscular disorder", "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", + "congenital disorder of glycosylation type I", + "DPM3-congenital disorder of glycosylation", + "congenital disorder of glycosylation", "familial dilated cardiomyopathy", - "Duchenne and Becker muscular dystrophy", + "disorder of multiple glycosylation", + "muscular dystrophy-dystroglycanopathy", + "inborn errors of metabolism", "neuromuscular disease", + "congenital muscular dystrophy", "skeletal muscle disorder", "muscular dystrophy", - "inherited disease susceptibility", - "disease susceptibility", - "pulmonary disease, chronic obstructive, susceptibility to", + "disorder of glycosylation", "human disease or disorder", "hereditary skeletal muscle disorder" ], "predicate": "biolink:has_phenotype", - "object": "HP:0002814", + "object": "HP:0003236", "original_object": null, "object_namespace": "HP", "object_category": "biolink:PhenotypicQuality", "object_closure": [ "HP:0000001", - "HP:0002814", + "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", - "UPHENO:0003070", - "HP:0040064", + "HP:0001939", + "HP:0500165", + "UPHENO:0081547", + "UPHENO:0077826", + "HP:0032180", "BFO:0000001", + "HP:0002086", + "HP:0003236", "PATO:0000001", - "UPHENO:0002830", + "HP:0002795", + "HP:0012415", + "UPHENO:0051612", + "UPHENO:0051804", + "CARO:0000000", "BFO:0000001", + "UBERON:0004120", + "UBERON:0000178", + "BFO:0000003", "BFO:0000002", + "UBERON:0002390", + "BFO:0000015", "BFO:0000004", + "GO:0008150", "BFO:0000040", "UBERON:0001062", - "CARO:0000000", - "UBERON:0000465", + "GO:0008152", + "GO:0005575", "PR:000050567", - "RO:0002577", - "CARO:0000006", - "UBERON:0006058", - "UBERON:0010538", + "CHEBI:24431", + "UBERON:0000465", + "GO:0032991", + "CHEBI:23367", "UBERON:0000061", - "UBERON:0004708", - "CARO:0000003", - "UBERON:0000978", - "UBERON:0002529", + "UBERON:0000463", + "GO:1902494", + "CHEBI:36357", + "CHEBI:33579", "UBERON:0010000", - "UBERON:0015212", - "UBERON:0002101", - "UBERON:0004709", - "UBERON:0010709", - "UBERON:0008784", + "UBERON:0000467", + "UBERON:0006314", + "GO:1990234", + "CHEBI:33839", + "CHEBI:33675", + "CHEBI:138675", "UBERON:0000468", - "UBERON:0000475", - "UBERON:0010707", - "UBERON:0002103", - "UBERON:0000154", - "UBERON:0000026", - "UBERON:0010758" + "UBERON:0001004", + "UBERON:0002193", + "UBERON:0000179", + "GO:0061695", + "CHEBI:16670", + "CHEBI:33302", + "CHEBI:33582", + "CHEBI:33304", + "GO:0002185", + "CHEBI:15841", + "CHEBI:51143", + "CHEBI:50860", + "CHEBI:25806", + "CHEBI:36962", + "CHEBI:16541", + "CHEBI:35352", + "CHEBI:32988", + "CHEBI:33285", + "CHEBI:36963", + "CHEBI:50047", + "CHEBI:37622", + "CHEBI:33256" ], - "object_label": "Abnormality of the lower limb (HPO)", + "object_label": "Elevated circulating creatine kinase concentration (HPO)", "object_closure_label": [ + "gas molecular entity", + "polypeptide", + "protein polypeptide chain", + "peptide", + "molecular entity", + "chemical entity", + "oxygen molecular entity", + "amide", + "primary amide", + "heteroorganic entity", + "pnictogen molecular entity", + "chalcogen molecular entity", + "main group molecular entity", + "carbon group molecular entity", + "p-block molecular entity", + "macromolecule", + "organonitrogen compound", + "polyatomic entity", + "organochalcogen compound", + "organooxygen compound", + "carboxamide", + "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 the lower limb (HPO)", - "Abnormality of limbs (HPO)", - "appendage", + "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)", + "Abnormal circulating metabolite concentration (HPO)", + "Abnormal circulating creatine kinase concentration (HPO)", + "Abnormal blood oxygen level (HPO)", "anatomical structure", - "posterior region of body", + "blood", + "haemolymphatic fluid", + "organism substance", "material anatomical entity", + "anatomical system", "multicellular organism", - "organism subdivision", - "leg", + "respiratory system", "anatomical entity", - "limb", - "hindlimb", - "limb segment", - "paired limb/fin", - "pelvic appendage", - "multi-limb segment region", - "lower limb segment", - "multicellular anatomical structure", - "paired limb/fin segment", - "appendage girdle complex", - "pelvic complex", - "subdivision of organism along appendicular axis", - "lateral structure" + "hemolymphoid system", + "hematopoietic system", + "mesoderm-derived structure", + "bodily fluid", + "multicellular anatomical structure" ], - "primary_knowledge_source": ["infores:hpo-annotations"], + "primary_knowledge_source": "infores:hpo-annotations", "aggregator_knowledge_source": ["infores:monarchinitiative"], "category": "biolink:DiseaseToPhenotypicFeatureAssociation", "negated": null, "provided_by": "hpoa_disease_phenotype_edges", - "publications": ["orphanet:98895"], + "publications": ["PMID:19576565", "PMID:28803818"], "qualifiers": [], - "frequency_qualifier": "HP:0040282", - "has_evidence": "ECO:0000304", + "frequency_qualifier": "HP:0040280", + "has_evidence": ["ECO:0000269"], "onset_qualifier": null, "sex_qualifier": null, "stage_qualifier": null, - "evidence_count": 0, + "evidence_count": 5, "pathway": null, - "frequency_qualifier_label": "Frequent (HPO)", + "frequency_qualifier_label": "Obligate (HPO)", "frequency_qualifier_namespace": "HP", "frequency_qualifier_category": "biolink:PhenotypicFeature", - "frequency_qualifier_closure": ["HP:0000001", "HP:0040282", "HP:0040279"], + "frequency_qualifier_closure": ["HP:0000001", "HP:0040279", "HP:0040280"], "frequency_qualifier_closure_label": [ "All (HPO)", "Frequency (HPO)", - "Frequent (HPO)" + "Obligate (HPO)" ], "onset_qualifier_label": null, "onset_qualifier_namespace": null, @@ -570,166 +672,158 @@ "direction": "outgoing" }, { - "id": "uuid:2211b994-1e4f-11ee-871a-692638b4c502", - "subject": "MONDO:0010311", - "original_subject": "OMIM:300376", + "id": "uuid:64b6842f-212f-11ee-873a-cd90a19c4085", + "subject": "MONDO:0009681", + "original_subject": "OMIM:254090", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ - "MONDO:0004994", "MONDO:0000001", - "MONDO:0100167", "MONDO:0005071", - "MONDO:0016147", - "MONDO:0005267", "MONDO:0020121", - "MONDO:0004995", "MONDO:0700223", - "MONDO:0020573", "BFO:0000002", + "MONDO:0019952", "BFO:0000017", "BFO:0000020", - "MONDO:0010542", - "MONDO:0016106", - "MONDO:0015470", - "MONDO:0005217", - "MONDO:0016899", - "MONDO:0042489", + "MONDO:0100225", "BFO:0000016", "MONDO:0020120", "MONDO:0019056", "MONDO:0016139", "MONDO:0700096", - "MONDO:0000591", "MONDO:0005218", "MONDO:0005336", "MONDO:0002081", - "MONDO:0016333", + "MONDO:0009681", "OGMS:0000031", - "MONDO:0005021", "MONDO:0003847", "MONDO:0003939", "BFO:0000001", - "MONDO:0010311" + "MONDO:0002320", + "MONDO:0000355", + "MONDO:0019950" ], - "subject_label": "Becker muscular dystrophy", + "subject_label": "Ullrich congenital muscular dystrophy 1", "subject_closure_label": [ "disease or disorder", - "intrinsic cardiomyopathy", + "Ullrich congenital muscular dystrophy", "musculoskeletal system disorder", + "congenital nervous system disorder", "hereditary disease", "muscle tissue disorder", - "cardiomyopathy", - "cardiovascular disorder", - "dilated cardiomyopathy", "nervous system disorder", - "familial cardiomyopathy", "obsolete muscular disorder", - "heart disorder", "myopathy", - "Becker muscular dystrophy", - "dilated cardiomyopathy 3B", - "familial isolated dilated cardiomyopathy", - "progressive muscular dystrophy", + "Ullrich congenital muscular dystrophy 1", "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 muscular dystrophy", + "congenital myopathy", "skeletal muscle disorder", "muscular dystrophy", - "inherited disease susceptibility", - "disease susceptibility", - "pulmonary disease, chronic obstructive, susceptibility to", + "collagen 6-related myopathy", "human disease or disorder", "hereditary skeletal muscle disorder" ], "predicate": "biolink:has_phenotype", - "object": "HP:0011675", + "object": "HP:0020152", "original_object": null, "object_namespace": "HP", "object_category": "biolink:PhenotypicQuality", "object_closure": [ "HP:0000001", + "HP:0020152", "UPHENO:0082875", + "HP:0001388", "UPHENO:0075696", "UPHENO:0001001", - "HP:0030956", - "HP:0001626", - "UPHENO:0080362", + "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", - "HP:0011025", + "UPHENO:0081440", "BFO:0000001", - "HP:0011675", "PATO:0000001", - "UPHENO:0002406", + "HP:0011843", + "CARO:0000000", "BFO:0000001", - "BFO:0000003", + "UBERON:0002204", "BFO:0000002", - "BFO:0000015", "BFO:0000004", - "GO:0008150", "BFO:0000040", "UBERON:0001062", - "CARO:0000000", - "GO:0032501", "UBERON:0000465", - "PR:000050567", - "UBERON:0004535", - "GO:0003008", "UBERON:0000061", - "GO:0003013", + "UBERON:0034925", "UBERON:0010000", "UBERON:0000467", - "GO:0003015", - "GO:0008015", + "UBERON:0004770", "UBERON:0000468", - "UBERON:0001009", - "GO:0060047" + "UBERON:0011216", + "UBERON:0034921", + "UBERON:0001434", + "UBERON:0004905", + "UBERON:0000982" ], - "object_label": "Arrhythmia (HPO)", + "object_label": "Distal joint laxity (HPO)", "object_closure_label": [ "All (HPO)", "Phenotypic abnormality (HPO)", - "Abnormality of the cardiovascular system (HPO)", - "Abnormal cardiovascular system physiology (HPO)", - "Arrhythmia (HPO)", - "Abnormality of cardiovascular system electrophysiology (HPO)", + "Abnormality of the skeletal system (HPO)", + "Joint laxity (HPO)", + "Abnormality of joint mobility (HPO)", + "Abnormality of musculoskeletal physiology (HPO)", + "Distal joint laxity (HPO)", + "Abnormality of the musculoskeletal system (HPO)", + "Abnormal joint physiology", "anatomical structure", "material anatomical entity", "anatomical system", "multicellular organism", - "circulatory system", + "skeletal joint", "anatomical entity", - "cardiovascular system", - "multicellular anatomical structure" + "skeletal system", + "musculoskeletal system", + "articular system", + "articulation", + "multicellular anatomical structure", + "organ system subdivision", + "multi organ part structure", + "anatomical collection" ], - "primary_knowledge_source": ["infores:hpo-annotations"], + "primary_knowledge_source": "infores:hpo-annotations", "aggregator_knowledge_source": ["infores:monarchinitiative"], "category": "biolink:DiseaseToPhenotypicFeatureAssociation", "negated": null, "provided_by": "hpoa_disease_phenotype_edges", - "publications": ["OMIM:300376"], + "publications": ["PMID:16258657", "OMIM:254090"], "qualifiers": [], - "frequency_qualifier": null, - "has_evidence": "ECO:0000304", + "frequency_qualifier": "HP:0040280", + "has_evidence": ["ECO:0000269"], "onset_qualifier": null, "sex_qualifier": null, "stage_qualifier": null, - "evidence_count": 0, + "evidence_count": 5, "pathway": null, - "frequency_qualifier_label": null, - "frequency_qualifier_namespace": null, - "frequency_qualifier_category": null, - "frequency_qualifier_closure": [], - "frequency_qualifier_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)" + ], "onset_qualifier_label": null, "onset_qualifier_namespace": null, "onset_qualifier_category": null, @@ -748,251 +842,154 @@ "direction": "outgoing" }, { - "id": "uuid:2211b991-1e4f-11ee-871a-692638b4c502", - "subject": "MONDO:0010311", - "original_subject": "OMIM:300376", + "id": "uuid:628f3d98-212f-11ee-873a-cd90a19c4085", + "subject": "MONDO:0009676", + "original_subject": "OMIM:253601", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ - "MONDO:0004994", "MONDO:0000001", - "MONDO:0100167", + "MONDO:0016971", + "MONDO:0000429", + "MONDO:0016145", "MONDO:0005071", - "MONDO:0016147", - "MONDO:0005267", "MONDO:0020121", - "MONDO:0004995", "MONDO:0700223", - "MONDO:0020573", "BFO:0000002", "BFO:0000017", "BFO:0000020", - "MONDO:0010542", + "MONDO:0006025", "MONDO:0016106", - "MONDO:0015470", - "MONDO:0005217", - "MONDO:0016899", - "MONDO:0042489", "BFO:0000016", "MONDO:0020120", "MONDO:0019056", "MONDO:0016139", "MONDO:0700096", - "MONDO:0000591", "MONDO:0005218", "MONDO:0005336", "MONDO:0002081", - "MONDO:0016333", + "MONDO:0009676", "OGMS:0000031", - "MONDO:0005021", "MONDO:0003847", "MONDO:0003939", "BFO:0000001", - "MONDO:0010311" + "MONDO:0015152" ], - "subject_label": "Becker muscular dystrophy", + "subject_label": "autosomal recessive limb-girdle muscular dystrophy type 2B", "subject_closure_label": [ "disease or disorder", - "intrinsic cardiomyopathy", + "autosomal genetic disease", "musculoskeletal system disorder", "hereditary disease", "muscle tissue disorder", - "cardiomyopathy", - "cardiovascular disorder", - "dilated cardiomyopathy", "nervous system disorder", - "familial cardiomyopathy", "obsolete muscular disorder", - "heart disorder", "myopathy", - "Becker muscular dystrophy", - "dilated cardiomyopathy 3B", - "familial isolated dilated cardiomyopathy", + "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 dystrophin", - "familial dilated cardiomyopathy", - "Duchenne and Becker muscular dystrophy", + "qualitative or quantitative defects of dysferlin", + "limb-girdle muscular dystrophy", "neuromuscular disease", "skeletal muscle disorder", "muscular dystrophy", - "inherited disease susceptibility", - "disease susceptibility", - "pulmonary disease, chronic obstructive, susceptibility to", "human disease or disorder", "hereditary skeletal muscle disorder" ], "predicate": "biolink:has_phenotype", - "object": "HP:0003707", + "object": "HP:0003701", "original_object": null, "object_namespace": "HP", "object_category": "biolink:PhenotypicQuality", "object_closure": [ "HP:0000001", - "UPHENO:0002644", - "HP:0002981", - "HP:0002814", + "UPHENO:0082875", + "UPHENO:0075696", + "UPHENO:0002320", "UPHENO:0001001", - "UPHENO:0075952", - "HP:0003707", - "HP:0009127", "UPHENO:0001005", - "UPHENO:0075777", - "HP:0011805", + "HP:0003701", "UPHENO:0001002", - "HP:0001430", + "HP:0001324", "HP:0000118", "BFO:0000002", "BFO:0000020", + "UPHENO:0080555", "HP:0003011", "UPHENO:0002816", - "UPHENO:0081581", + "UPHENO:0002332", + "UPHENO:0080556", "HP:0033127", "UPHENO:0001003", "UPHENO:0002536", - "HP:0001437", - "UPHENO:0076692", - "UPHENO:0003070", - "UPHENO:0002647", - "UPHENO:0076710", - "HP:0040064", "BFO:0000001", + "HP:0011804", "PATO:0000001", - "UPHENO:0002830", + "CARO:0000000", "BFO:0000001", + "UBERON:0000383", + "UBERON:0001015", + "UBERON:0005090", "BFO:0000002", + "UBERON:0001630", "BFO:0000004", "BFO:0000040", "UBERON:0001062", - "CARO:0000000", "UBERON:0000465", - "PR:000050567", - "RO:0002577", - "UBERON:0001015", - "UBERON:0000383", - "CARO:0000006", - "UBERON:0006058", - "UBERON:0010538", - "UBERON:0018254", - "UBERON:0005090", "UBERON:0000061", - "UBERON:0004708", - "UBERON:0007271", - "UBERON:0014792", - "CARO:0000003", - "UBERON:0000978", - "UBERON:0002529", - "UBERON:0001630", "UBERON:0010000", "UBERON:0000467", - "UBERON:0015212", - "UBERON:0002101", - "UBERON:0004709", - "UBERON:0007270", - "UBERON:0004480", - "UBERON:0010709", - "UBERON:0002471", - "UBERON:0008784", - "UBERON:0014892", "UBERON:0000468", - "UBERON:0000475", "UBERON:0000062", - "UBERON:0011216", - "UBERON:0010707", - "UBERON:0002103", - "UBERON:0004482", - "UBERON:0003823", - "UBERON:0003661", - "UBERON:0010890", - "UBERON:0000154", - "UBERON:0000026", - "UBERON:0010758", - "UBERON:0004466", - "UBERON:0003663", - "UBERON:0014795", - "UBERON:0006067", - "UBERON:0001383", - "UBERON:0004256" + "UBERON:0011216" ], - "object_label": "Calf muscle pseudohypertrophy (HPO)", + "object_label": "Proximal muscle weakness (HPO)", "object_closure_label": [ "All (HPO)", "Phenotypic abnormality (HPO)", - "Abnormality of the calf musculature (HPO)", - "Abnormality of the musculature of the lower limbs (HPO)", - "Abnormality of the lower limb (HPO)", - "Abnormality of the calf (HPO)", + "Muscle weakness (HPO)", "Abnormality of the musculature (HPO)", - "Calf muscle pseudohypertrophy (HPO)", - "Abnormality of the musculature of the limbs (HPO)", - "Abnormal skeletal muscle morphology (HPO)", + "Proximal muscle weakness (HPO)", + "Abnormal muscle physiology (HPO)", "Abnormality of the musculoskeletal system (HPO)", - "Abnormality of limbs (HPO)", - "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 of leg", "muscle organ", - "limb", - "hindlimb", - "zeugopod", - "limb segment", - "limb muscle", - "hindlimb muscle", - "hindlimb zeugopod", - "hindlimb zeugopod muscle", - "musculature of leg", - "musculature of limb", - "musculature of lower limb", - "paired limb/fin", - "pelvic appendage", "muscle structure", - "multi-limb segment region", - "musculature of hindlimb zeugopod", - "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", - "pelvic complex muscle", - "organ system subdivision", - "musculature of pelvic complex", - "pelvic appendage muscle", - "skeletal muscle organ", - "lateral structure", - "skeletal musculature" + "organ system subdivision" ], - "primary_knowledge_source": ["infores:hpo-annotations"], + "primary_knowledge_source": "infores:hpo-annotations", "aggregator_knowledge_source": ["infores:monarchinitiative"], "category": "biolink:DiseaseToPhenotypicFeatureAssociation", "negated": null, "provided_by": "hpoa_disease_phenotype_edges", - "publications": ["OMIM:300376"], + "publications": ["PMID:9731527", "PMID:9009996"], "qualifiers": [], - "frequency_qualifier": null, - "has_evidence": "ECO:0000304", + "frequency_qualifier": "HP:0040280", + "has_evidence": ["ECO:0000269"], "onset_qualifier": null, "sex_qualifier": null, "stage_qualifier": null, - "evidence_count": 0, + "evidence_count": 5, "pathway": null, - "frequency_qualifier_label": null, - "frequency_qualifier_namespace": null, - "frequency_qualifier_category": null, - "frequency_qualifier_closure": [], - "frequency_qualifier_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)" + ], "onset_qualifier_label": null, "onset_qualifier_namespace": null, "onset_qualifier_category": null, diff --git a/frontend/fixtures/associations.json b/frontend/fixtures/associations.json index 0f6dc35f1..2a0b320b3 100644 --- a/frontend/fixtures/associations.json +++ b/frontend/fixtures/associations.json @@ -1,30 +1,23 @@ { "limit": 20, "offset": 0, - "total": 4811, + "total": 4806, "items": [ { - "id": "uuid:1be81e3c-1e4f-11ee-871a-692638b4c502", - "subject": "MONDO:0030355", - "original_subject": "OMIM:619478", + "id": "uuid:c2a45bf5-212f-11ee-873a-cd90a19c4085", + "subject": "MONDO:0008028", + "original_subject": "OMIM:158800", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ "MONDO:0000001", - "MONDO:0030355", - "MONDO:0019303", - "MONDO:0100167", "MONDO:0005071", "MONDO:0020121", + "MONDO:0008028", "MONDO:0700223", - "MONDO:0001347", - "MONDO:0020573", "BFO:0000002", "BFO:0000017", "BFO:0000020", - "MONDO:0016106", - "MONDO:0042489", - "MONDO:0100137", "BFO:0000016", "MONDO:0020120", "MONDO:0019056", @@ -32,186 +25,58 @@ "MONDO:0005218", "MONDO:0005336", "MONDO:0002081", - "MONDO:0021147", "OGMS:0000031", "MONDO:0003847", "MONDO:0003939", "BFO:0000001" ], - "subject_label": "facioscapulohumeral muscular dystrophy 4, digenic", + "subject_label": "muscular dystrophy, Barnes type", "subject_closure_label": [ "disease or disorder", - "facioscapulohumeral muscular dystrophy", "musculoskeletal system disorder", "hereditary disease", "muscle tissue disorder", "nervous system disorder", "obsolete muscular disorder", "myopathy", - "progressive muscular dystrophy", + "muscular dystrophy, Barnes type", "neuromuscular disease", - "premature aging syndrome", "skeletal muscle disorder", "muscular dystrophy", - "inherited disease susceptibility", - "disorder of development or morphogenesis", - "facioscapulohumeral muscular dystrophy 4, digenic", - "disease susceptibility", - "telomere syndrome", - "pulmonary disease, chronic obstructive, susceptibility to", "human disease or disorder", "hereditary skeletal muscle disorder" ], - "predicate": "biolink:has_phenotype", - "object": "HP:0003484", + "predicate": "biolink:has_mode_of_inheritance", + "object": "HP:0000006", "original_object": null, "object_namespace": "HP", - "object_category": "biolink:PhenotypicQuality", + "object_category": "biolink:GeneticInheritance", "object_closure": [ "HP:0000001", - "UPHENO:0002649", - "UPHENO:0082875", - "UPHENO:0075696", - "UPHENO:0002320", - "UPHENO:0001001", - "HP:0003325", - "HP:0003484", - "UPHENO:0080563", - "HP:0009127", - "UPHENO:0001005", - "HP:0011805", - "UPHENO:0001002", - "HP:0001324", - "HP:0003690", - "HP:0000118", - "BFO:0000002", - "HP:0001446", - "HP:0002817", - "BFO:0000020", - "UPHENO:0080555", - "HP:0003011", - "UPHENO:0002816", - "UPHENO:0002332", - "UPHENO:0080556", - "UPHENO:0081581", - "HP:0033127", - "UPHENO:0001003", - "UPHENO:0002536", - "UPHENO:0076692", - "UPHENO:0002647", - "UPHENO:0076710", - "HP:0040064", - "BFO:0000001", - "HP:0011804", - "PATO:0000001", - "UPHENO:0002880", - "UPHENO:0002830", - "BFO:0000001", - "BFO:0000002", - "BFO:0000004", - "BFO:0000040", - "UBERON:0001062", - "CARO:0000000", - "UBERON:0000465", - "PR:000050567", - "RO:0002577", - "UBERON:0001015", - "UBERON:0000383", - "CARO:0000006", - "UBERON:0006058", - "UBERON:0010538", - "UBERON:0005090", - "UBERON:0000061", - "UBERON:0004708", - "UBERON:0007271", - "UBERON:0014793", - "CARO:0000003", - "UBERON:0001460", - "UBERON:0002529", - "UBERON:0001630", - "UBERON:0010000", - "UBERON:0000467", - "UBERON:0015212", - "UBERON:0004710", - "UBERON:0002101", - "UBERON:0004480", - "UBERON:0007269", - "UBERON:0010708", - "UBERON:0008785", - "UBERON:0000468", - "UBERON:0000475", - "UBERON:0000062", - "UBERON:0011216", - "UBERON:0010707", - "UBERON:0002102", - "UBERON:0004481", - "UBERON:0000153", - "UBERON:0000026", - "UBERON:0010758" + "HP:0000006", + "HP:0000005", + "HP:0034345" ], - "object_label": "Upper limb muscle weakness (HPO)", + "object_label": "Autosomal dominant inheritance (HPO)", "object_closure_label": [ "All (HPO)", - "Phenotypic abnormality (HPO)", - "Muscle weakness (HPO)", - "Abnormality of the musculature of the upper limbs (HPO)", - "Abnormality of the upper limb (HPO)", - "Abnormality of the musculature (HPO)", - "Limb-girdle muscle weakness (HPO)", - "Upper limb muscle weakness (HPO)", - "Limb muscle weakness (HPO)", - "Abnormality of the musculature of the limbs (HPO)", - "Abnormal muscle physiology (HPO)", - "Abnormal skeletal muscle morphology (HPO)", - "Abnormality of the musculoskeletal system (HPO)", - "Abnormality of limbs (HPO)", - "appendage", - "anatomical structure", - "organ", - "anterior region of body", - "musculature of body", - "material anatomical entity", - "anatomical system", - "multicellular organism", - "organism subdivision", - "musculature", - "anatomical entity", - "arm", - "muscle organ", - "limb", - "forelimb", - "limb segment", - "musculature of limb", - "musculature of upper limb", - "paired limb/fin", - "pectoral appendage", - "muscle structure", - "multi-limb segment region", - "pectoral appendage musculature", - "appendage musculature", - "upper limb segment", - "multicellular anatomical structure", - "paired limb/fin segment", - "appendage girdle complex", - "pectoral complex", - "subdivision of organism along appendicular axis", - "organ system subdivision", - "musculature of pectoral complex", - "lateral structure" + "Mode of inheritance (HPO)", + "Autosomal dominant inheritance (HPO)", + "Mendelian inheritance" ], - "primary_knowledge_source": ["infores:hpo-annotations"], + "primary_knowledge_source": "infores:hpo-annotations", "aggregator_knowledge_source": ["infores:monarchinitiative"], - "category": "biolink:DiseaseToPhenotypicFeatureAssociation", + "category": "biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation", "negated": null, - "provided_by": "hpoa_disease_phenotype_edges", - "publications": ["PMID:27153398"], + "provided_by": "hpoa_disease_mode_of_inheritance_edges", + "publications": ["OMIM:158800"], "qualifiers": [], "frequency_qualifier": null, - "has_evidence": "ECO:0000269", + "has_evidence": ["ECO:0000304"], "onset_qualifier": null, "sex_qualifier": null, "stage_qualifier": null, - "evidence_count": 0, + "evidence_count": 4, "pathway": null, "frequency_qualifier_label": null, "frequency_qualifier_namespace": null, @@ -235,26 +100,24 @@ "stage_qualifier_closure_label": [] }, { - "id": "uuid:1fd70821-1e4f-11ee-871a-692638b4c502", - "subject": "MONDO:0014782", - "original_subject": "OMIM:616812", + "id": "uuid:c304bcf2-212f-11ee-873a-cd90a19c4085", + "subject": "MONDO:0008030", + "original_subject": "OMIM:158900", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ + "MONDO:0008030", "MONDO:0000001", - "MONDO:0016971", - "MONDO:0000429", - "MONDO:0100167", + "MONDO:0019303", "MONDO:0005071", "MONDO:0020121", "MONDO:0700223", - "MONDO:0020573", + "MONDO:0001347", "BFO:0000002", "BFO:0000017", "BFO:0000020", - "MONDO:0006025", "MONDO:0016106", - "MONDO:0042489", + "MONDO:0100137", "BFO:0000016", "MONDO:0020120", "MONDO:0019056", @@ -262,117 +125,64 @@ "MONDO:0005218", "MONDO:0005336", "MONDO:0002081", + "MONDO:0021147", "OGMS:0000031", "MONDO:0003847", - "MONDO:0014782", "MONDO:0003939", - "BFO:0000001", - "MONDO:0015152" + "BFO:0000001" ], - "subject_label": "autosomal recessive limb-girdle muscular dystrophy type 2X", + "subject_label": "facioscapulohumeral muscular dystrophy 1", "subject_closure_label": [ "disease or disorder", - "autosomal genetic disease", + "facioscapulohumeral muscular dystrophy", "musculoskeletal system disorder", "hereditary disease", "muscle tissue disorder", "nervous system disorder", "obsolete muscular disorder", "myopathy", - "autosomal recessive disease", - "autosomal recessive limb-girdle muscular dystrophy type 2X", - "autosomal recessive limb-girdle muscular dystrophy", + "facioscapulohumeral muscular dystrophy 1", "progressive muscular dystrophy", - "limb-girdle muscular dystrophy", "neuromuscular disease", + "premature aging syndrome", "skeletal muscle disorder", "muscular dystrophy", - "inherited disease susceptibility", - "disease susceptibility", - "pulmonary disease, chronic obstructive, susceptibility to", + "disorder of development or morphogenesis", + "telomere syndrome", "human disease or disorder", "hereditary skeletal muscle disorder" ], - "predicate": "biolink:has_phenotype", - "object": "HP:0003546", + "predicate": "biolink:has_mode_of_inheritance", + "object": "HP:0000006", "original_object": null, "object_namespace": "HP", - "object_category": "biolink:PhenotypicQuality", + "object_category": "biolink:GeneticInheritance", "object_closure": [ "HP:0000001", - "UPHENO:0082875", - "UPHENO:0075696", - "UPHENO:0002320", - "UPHENO:0001001", - "UPHENO:0001005", - "UPHENO:0001002", - "HP:0004302", - "HP:0000118", - "BFO:0000002", - "BFO:0000020", - "HP:0003011", - "UPHENO:0002816", - "HP:0003546", - "UPHENO:0002332", - "HP:0033127", - "UPHENO:0001003", - "UPHENO:0002536", - "BFO:0000001", - "HP:0011804", - "PATO:0000001", - "BFO:0000001", - "BFO:0000002", - "BFO:0000004", - "BFO:0000040", - "UBERON:0001062", - "CARO:0000000", - "UBERON:0000465", - "UBERON:0001015", - "UBERON:0000383", - "UBERON:0005090", - "UBERON:0000061", - "UBERON:0001630", - "UBERON:0010000", - "UBERON:0000467", - "UBERON:0000468", - "UBERON:0000062", - "UBERON:0011216" + "HP:0000006", + "HP:0000005", + "HP:0034345" ], - "object_label": "Exercise intolerance (HPO)", + "object_label": "Autosomal dominant inheritance (HPO)", "object_closure_label": [ "All (HPO)", - "Phenotypic abnormality (HPO)", - "Abnormality of the musculature (HPO)", - "Exercise intolerance (HPO)", - "Functional motor deficit (HPO)", - "Abnormal muscle physiology (HPO)", - "Abnormality of the musculoskeletal system (HPO)", - "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" + "Mode of inheritance (HPO)", + "Autosomal dominant inheritance (HPO)", + "Mendelian inheritance" ], - "primary_knowledge_source": ["infores:hpo-annotations"], + "primary_knowledge_source": "infores:hpo-annotations", "aggregator_knowledge_source": ["infores:monarchinitiative"], - "category": "biolink:DiseaseToPhenotypicFeatureAssociation", + "category": "biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation", "negated": null, - "provided_by": "hpoa_disease_phenotype_edges", - "publications": ["PMID:26642364"], + "provided_by": "hpoa_disease_mode_of_inheritance_edges", + "publications": ["OMIM:158900"], "qualifiers": [], "frequency_qualifier": null, - "has_evidence": "ECO:0000269", + "has_evidence": ["ECO:0000501"], "onset_qualifier": null, "sex_qualifier": null, "stage_qualifier": null, - "evidence_count": 0, + "evidence_count": 4, "pathway": null, "frequency_qualifier_label": null, "frequency_qualifier_namespace": null, @@ -396,229 +206,107 @@ "stage_qualifier_closure_label": [] }, { - "id": "uuid:1e041fb7-1e4f-11ee-871a-692638b4c502", - "subject": "MONDO:0008030", - "original_subject": "OMIM:158900", + "id": "uuid:c3cdad58-212f-11ee-873a-cd90a19c4085", + "subject": "MONDO:0008034", + "original_subject": "OMIM:159050", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ - "MONDO:0008030", + "MONDO:0004994", "MONDO:0000001", - "MONDO:0019303", - "MONDO:0100167", + "MONDO:0008034", "MONDO:0005071", + "MONDO:0016147", + "MONDO:0005267", "MONDO:0020121", + "MONDO:0004995", "MONDO:0700223", - "MONDO:0001347", - "MONDO:0020573", "BFO:0000002", "BFO:0000017", "BFO:0000020", + "MONDO:0010542", "MONDO:0016106", - "MONDO:0042489", - "MONDO:0100137", + "MONDO:0015470", + "MONDO:0005217", + "MONDO:0016899", "BFO:0000016", "MONDO:0020120", "MONDO:0019056", + "MONDO:0016139", "MONDO:0700096", + "MONDO:0000591", "MONDO:0005218", "MONDO:0005336", "MONDO:0002081", - "MONDO:0021147", + "MONDO:0016333", "OGMS:0000031", + "MONDO:0005021", "MONDO:0003847", "MONDO:0003939", - "BFO:0000001" + "BFO:0000001", + "MONDO:0010311" ], - "subject_label": "facioscapulohumeral muscular dystrophy 1", + "subject_label": "muscular dystrophy, pseudohypertrophic, with Internalized capillaries", "subject_closure_label": [ "disease or disorder", - "facioscapulohumeral muscular dystrophy", + "intrinsic cardiomyopathy", "musculoskeletal system disorder", "hereditary disease", "muscle tissue disorder", + "cardiomyopathy", + "cardiovascular disorder", + "dilated cardiomyopathy", "nervous system disorder", + "familial cardiomyopathy", "obsolete muscular disorder", + "heart disorder", "myopathy", - "facioscapulohumeral muscular dystrophy 1", + "muscular dystrophy, pseudohypertrophic, with Internalized capillaries", + "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", - "premature aging syndrome", "skeletal muscle disorder", "muscular dystrophy", - "inherited disease susceptibility", - "disorder of development or morphogenesis", - "disease susceptibility", - "telomere syndrome", - "pulmonary disease, chronic obstructive, susceptibility to", "human disease or disorder", "hereditary skeletal muscle disorder" ], - "predicate": "biolink:has_phenotype", - "object": "HP:0003547", + "predicate": "biolink:has_mode_of_inheritance", + "object": "HP:0000006", "original_object": null, "object_namespace": "HP", - "object_category": "biolink:PhenotypicQuality", + "object_category": "biolink:GeneticInheritance", "object_closure": [ "HP:0000001", - "UPHENO:0002649", - "UPHENO:0082875", - "UPHENO:0075696", - "UPHENO:0002320", - "UPHENO:0001001", - "HP:0003325", - "UPHENO:0080565", - "HP:0009127", - "UPHENO:0001005", - "HP:0011805", - "UPHENO:0001002", - "HP:0001324", - "HP:0000118", - "BFO:0000002", - "HP:0001435", - "HP:0001446", - "HP:0002817", - "BFO:0000020", - "UPHENO:0080555", - "HP:0003011", - "UPHENO:0002816", - "UPHENO:0002332", - "UPHENO:0080556", - "UPHENO:0002982", - "UPHENO:0081581", - "HP:0003547", - "HP:0033127", - "UPHENO:0001003", - "UPHENO:0002536", - "UPHENO:0076692", - "UPHENO:0002647", - "UPHENO:0076710", - "HP:0040064", - "BFO:0000001", - "HP:0011804", - "PATO:0000001", - "UPHENO:0002880", - "UPHENO:0002830", - "BFO:0000001", - "BFO:0000002", - "BFO:0000004", - "BFO:0000040", - "UBERON:0001062", - "CARO:0000000", - "UBERON:0000465", - "PR:000050567", - "RO:0002577", - "UBERON:0001015", - "UBERON:0000383", - "CARO:0000006", - "UBERON:0006058", - "UBERON:0010538", - "UBERON:0018254", - "UBERON:0005090", - "UBERON:0000061", - "UBERON:0004708", - "UBERON:0007271", - "UBERON:0014793", - "CARO:0000003", - "UBERON:0001460", - "UBERON:0002529", - "UBERON:0001630", - "UBERON:0010000", - "UBERON:0000467", - "UBERON:0015212", - "UBERON:0004710", - "UBERON:0002101", - "UBERON:0004480", - "UBERON:0007269", - "UBERON:0004471", - "UBERON:0007823", - "UBERON:0010708", - "UBERON:0008785", - "UBERON:0014892", - "UBERON:0000468", - "UBERON:0000475", - "UBERON:0000062", - "UBERON:0011216", - "UBERON:0001421", - "UBERON:0010707", - "UBERON:0002102", - "UBERON:0004481", - "UBERON:0010891", - "UBERON:0000153", - "UBERON:0000026", - "UBERON:0010758", - "UBERON:0008196" + "HP:0000006", + "HP:0000005", + "HP:0034345" ], - "object_label": "Shoulder girdle muscle weakness (HPO)", + "object_label": "Autosomal dominant inheritance (HPO)", "object_closure_label": [ "All (HPO)", - "Phenotypic abnormality (HPO)", - "Muscle weakness (HPO)", - "Abnormality of the shoulder girdle musculature (HPO)", - "Abnormality of the musculature of the upper limbs (HPO)", - "Abnormality of the upper limb (HPO)", - "Abnormality of the musculature (HPO)", - "Limb-girdle muscle weakness (HPO)", - "Shoulder girdle muscle weakness (HPO)", - "Abnormality of the musculature of the limbs (HPO)", - "Abnormal muscle physiology (HPO)", - "Abnormal skeletal muscle morphology (HPO)", - "Abnormality of the musculoskeletal system (HPO)", - "Abnormality of limbs (HPO)", - "appendage", - "anatomical structure", - "organ", - "anterior region of body", - "musculature of body", - "material anatomical entity", - "anatomical system", - "multicellular organism", - "organism subdivision", - "musculature", - "anatomical entity", - "pectoral girdle region", - "arm", - "muscle organ", - "limb", - "forelimb", - "limb segment", - "musculature of pectoral girdle", - "musculature of limb", - "musculature of upper limb", - "paired limb/fin", - "pectoral appendage", - "muscle structure", - "multi-limb segment region", - "pectoral appendage musculature", - "appendage musculature", - "appendage girdle region", - "muscle of pectoral girdle", - "upper limb segment", - "multicellular anatomical structure", - "paired limb/fin segment", - "appendage girdle complex", - "pectoral complex", - "subdivision of organism along appendicular axis", - "pectoral complex muscle", - "organ system subdivision", - "musculature of pectoral complex", - "skeletal muscle organ", - "lateral structure", - "skeletal musculature" + "Mode of inheritance (HPO)", + "Autosomal dominant inheritance (HPO)", + "Mendelian inheritance" ], - "primary_knowledge_source": ["infores:hpo-annotations"], + "primary_knowledge_source": "infores:hpo-annotations", "aggregator_knowledge_source": ["infores:monarchinitiative"], - "category": "biolink:DiseaseToPhenotypicFeatureAssociation", + "category": "biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation", "negated": null, - "provided_by": "hpoa_disease_phenotype_edges", - "publications": ["OMIM:158900"], + "provided_by": "hpoa_disease_mode_of_inheritance_edges", + "publications": ["OMIM:159050"], "qualifiers": [], "frequency_qualifier": null, - "has_evidence": "ECO:0000304", + "has_evidence": ["ECO:0000501"], "onset_qualifier": null, "sex_qualifier": null, "stage_qualifier": null, - "evidence_count": 0, + "evidence_count": 4, "pathway": null, "frequency_qualifier_label": null, "frequency_qualifier_namespace": null, @@ -642,30 +330,23 @@ "stage_qualifier_closure_label": [] }, { - "id": "uuid:1ae78897-1e4f-11ee-871a-692638b4c502", - "subject": "MONDO:0009683", - "original_subject": "OMIM:254110", + "id": "uuid:c3367408-212f-11ee-873a-cd90a19c4085", + "subject": "MONDO:0008049", + "original_subject": "OMIM:160300", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ "MONDO:0000001", - "MONDO:0016971", - "MONDO:0000429", - "MONDO:0100167", "MONDO:0005071", "MONDO:0020121", "MONDO:0700223", - "MONDO:0020573", "BFO:0000002", "BFO:0000017", + "MONDO:0008049", "BFO:0000020", - "MONDO:0006025", - "MONDO:0016106", - "MONDO:0042489", "BFO:0000016", "MONDO:0020120", "MONDO:0019056", - "MONDO:0016139", "MONDO:0700096", "MONDO:0005218", "MONDO:0005336", @@ -674,201 +355,56 @@ "MONDO:0003847", "MONDO:0003939", "BFO:0000001", - "MONDO:0015152", - "MONDO:0016153", - "MONDO:0009683" + "MONDO:0018949" ], - "subject_label": "autosomal recessive limb-girdle muscular dystrophy type 2H", + "subject_label": "myopathy, distal, infantile-onset", "subject_closure_label": [ "disease or disorder", - "autosomal genetic disease", "musculoskeletal system disorder", "hereditary disease", "muscle tissue disorder", "nervous system disorder", "obsolete muscular 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", + "myopathy, distal, infantile-onset", + "distal myopathy", "neuromuscular disease", "skeletal muscle disorder", "muscular dystrophy", - "inherited disease susceptibility", - "disease susceptibility", - "pulmonary disease, chronic obstructive, susceptibility to", "human disease or disorder", "hereditary skeletal muscle disorder" ], - "predicate": "biolink:has_phenotype", - "object": "HP:0003547", + "predicate": "biolink:has_mode_of_inheritance", + "object": "HP:0000006", "original_object": null, "object_namespace": "HP", - "object_category": "biolink:PhenotypicQuality", + "object_category": "biolink:GeneticInheritance", "object_closure": [ "HP:0000001", - "UPHENO:0002649", - "UPHENO:0082875", - "UPHENO:0075696", - "UPHENO:0002320", - "UPHENO:0001001", - "HP:0003325", - "UPHENO:0080565", - "HP:0009127", - "UPHENO:0001005", - "HP:0011805", - "UPHENO:0001002", - "HP:0001324", - "HP:0000118", - "BFO:0000002", - "HP:0001435", - "HP:0001446", - "HP:0002817", - "BFO:0000020", - "UPHENO:0080555", - "HP:0003011", - "UPHENO:0002816", - "UPHENO:0002332", - "UPHENO:0080556", - "UPHENO:0002982", - "UPHENO:0081581", - "HP:0003547", - "HP:0033127", - "UPHENO:0001003", - "UPHENO:0002536", - "UPHENO:0076692", - "UPHENO:0002647", - "UPHENO:0076710", - "HP:0040064", - "BFO:0000001", - "HP:0011804", - "PATO:0000001", - "UPHENO:0002880", - "UPHENO:0002830", - "BFO:0000001", - "BFO:0000002", - "BFO:0000004", - "BFO:0000040", - "UBERON:0001062", - "CARO:0000000", - "UBERON:0000465", - "PR:000050567", - "RO:0002577", - "UBERON:0001015", - 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"Muscle weakness (HPO)", - "Abnormality of the shoulder girdle musculature (HPO)", - "Abnormality of the musculature of the upper limbs (HPO)", - "Abnormality of the upper limb (HPO)", - "Abnormality of the musculature (HPO)", - "Limb-girdle muscle weakness (HPO)", - "Shoulder girdle muscle weakness (HPO)", - "Abnormality of the musculature of the limbs (HPO)", - "Abnormal muscle physiology (HPO)", - "Abnormal skeletal muscle morphology (HPO)", - "Abnormality of the musculoskeletal system (HPO)", - "Abnormality of limbs (HPO)", - "appendage", - "anatomical structure", - "organ", - "anterior region of body", - "musculature of body", - "material anatomical entity", - "anatomical system", - "multicellular organism", - "organism subdivision", - "musculature", - "anatomical entity", - "pectoral girdle region", - "arm", - "muscle organ", - "limb", - "forelimb", - "limb segment", - "musculature of pectoral girdle", - "musculature of limb", - "musculature of upper limb", - "paired limb/fin", - 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"provided_by": "hpoa_disease_phenotype_edges", - "publications": ["OMIM:254110"], + "provided_by": "hpoa_disease_mode_of_inheritance_edges", + "publications": ["OMIM:160300"], "qualifiers": [], "frequency_qualifier": null, - "has_evidence": "ECO:0000501", + "has_evidence": ["ECO:0000304"], "onset_qualifier": null, "sex_qualifier": null, "stage_qualifier": null, - "evidence_count": 0, + "evidence_count": 4, "pathway": null, "frequency_qualifier_label": null, "frequency_qualifier_namespace": null, @@ -892,26 +428,26 @@ "stage_qualifier_closure_label": [] }, { - "id": "uuid:1e041dff-1e4f-11ee-871a-692638b4c502", - "subject": "MONDO:0010678", - "original_subject": "OMIM:310095", + "id": "uuid:c39b4534-212f-11ee-873a-cd90a19c4085", + "subject": "MONDO:0008050", + "original_subject": "OMIM:160500", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ "MONDO:0000001", - "MONDO:0100167", "MONDO:0005071", "MONDO:0020121", - "MONDO:0010678", "MONDO:0700223", - "MONDO:0020573", "BFO:0000002", + "MONDO:0019952", "BFO:0000017", "BFO:0000020", - "MONDO:0042489", + "MONDO:0008050", + "MONDO:0016195", "BFO:0000016", "MONDO:0020120", "MONDO:0019056", + "MONDO:0016139", "MONDO:0700096", "MONDO:0005218", "MONDO:0005336", @@ -919,192 +455,62 @@ "OGMS:0000031", "MONDO:0003847", "MONDO:0003939", - "BFO:0000001" + "BFO:0000001", + "MONDO:0002320", + "MONDO:0018949" ], - "subject_label": "muscular dystrophy, progressive Pectorodorsal", + "subject_label": "MYH7-related skeletal myopathy", "subject_closure_label": [ "disease or disorder", "musculoskeletal system disorder", + "congenital nervous system disorder", "hereditary disease", "muscle tissue disorder", "nervous system disorder", "obsolete muscular disorder", "myopathy", - "muscular dystrophy, progressive Pectorodorsal", + "MYH7-related skeletal myopathy", + "qualitative or quantitative protein defects in neuromuscular diseases", + "qualitative or quantitative defects of beta-myosin heavy chain (MYH7)", + "distal myopathy", "neuromuscular disease", + "congenital myopathy", "skeletal muscle disorder", "muscular dystrophy", - "inherited disease susceptibility", - "disease susceptibility", - "pulmonary disease, chronic obstructive, susceptibility to", "human disease or disorder", "hereditary skeletal muscle disorder" ], - "predicate": "biolink:has_phenotype", - "object": "HP:0003547", + "predicate": "biolink:has_mode_of_inheritance", + "object": "HP:0000006", "original_object": null, "object_namespace": "HP", - "object_category": "biolink:PhenotypicQuality", + "object_category": "biolink:GeneticInheritance", "object_closure": [ "HP:0000001", - "UPHENO:0002649", - "UPHENO:0082875", - "UPHENO:0075696", - "UPHENO:0002320", - "UPHENO:0001001", - "HP:0003325", - "UPHENO:0080565", - "HP:0009127", - "UPHENO:0001005", - "HP:0011805", - "UPHENO:0001002", - "HP:0001324", - "HP:0000118", - "BFO:0000002", - "HP:0001435", - "HP:0001446", - "HP:0002817", - "BFO:0000020", - "UPHENO:0080555", - "HP:0003011", - "UPHENO:0002816", - "UPHENO:0002332", - "UPHENO:0080556", - "UPHENO:0002982", - "UPHENO:0081581", - "HP:0003547", - 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"inherited disease susceptibility", - "disease susceptibility", - "pulmonary disease, chronic obstructive, susceptibility to", - "TTN-related myopathy", - "autosomal dominant titinopathy", + "eyelids malposition disorder", + "disorder of visual system", + "familial hypertrophic cardiomyopathy", "human disease or disorder", "hereditary skeletal muscle disorder" ], - "predicate": "biolink:has_phenotype", - "object": "HP:0003547", + "predicate": "biolink:has_mode_of_inheritance", + "object": "HP:0000006", "original_object": null, "object_namespace": "HP", - "object_category": "biolink:PhenotypicQuality", + "object_category": "biolink:GeneticInheritance", "object_closure": [ "HP:0000001", - "UPHENO:0002649", - "UPHENO:0082875", - "UPHENO:0075696", - "UPHENO:0002320", - "UPHENO:0001001", - "HP:0003325", - "UPHENO:0080565", - "HP:0009127", - "UPHENO:0001005", - "HP:0011805", - "UPHENO:0001002", - "HP:0001324", - "HP:0000118", - "BFO:0000002", - "HP:0001435", - "HP:0001446", - "HP:0002817", - 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"musculature of pectoral complex", - "skeletal muscle organ", - "lateral structure", - "skeletal musculature" + "Mode of inheritance (HPO)", + "Autosomal dominant inheritance (HPO)", + "Mendelian inheritance" ], - "primary_knowledge_source": ["infores:hpo-annotations"], + "primary_knowledge_source": "infores:hpo-annotations", "aggregator_knowledge_source": ["infores:monarchinitiative"], - "category": "biolink:DiseaseToPhenotypicFeatureAssociation", + "category": "biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation", "negated": null, - "provided_by": "hpoa_disease_phenotype_edges", - "publications": ["OMIM:603689"], + "provided_by": "hpoa_disease_mode_of_inheritance_edges", + "publications": ["OMIM:160900"], "qualifiers": [], "frequency_qualifier": null, - "has_evidence": "ECO:0000501", + "has_evidence": ["ECO:0000501"], "onset_qualifier": null, "sex_qualifier": null, "stage_qualifier": null, - "evidence_count": 0, + "evidence_count": 4, "pathway": null, "frequency_qualifier_label": null, "frequency_qualifier_namespace": null, @@ -1388,223 +664,95 @@ "stage_qualifier_closure_label": [] }, { - "id": "uuid:215b1fa4-1e4f-11ee-871a-692638b4c502", - "subject": "MONDO:0011486", - "original_subject": "OMIM:604801", + "id": "uuid:c400607b-212f-11ee-873a-cd90a19c4085", + "subject": "MONDO:0008116", + "original_subject": "OMIM:164300", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ + "MONDO:0020158", "MONDO:0000001", - "MONDO:0100167", "MONDO:0005071", "MONDO:0020121", "MONDO:0700223", - "MONDO:0020573", + "MONDO:0004746", "BFO:0000002", "BFO:0000017", "BFO:0000020", - "MONDO:0042489", + "MONDO:0016106", + "MONDO:0003382", "BFO:0000016", "MONDO:0020120", "MONDO:0019056", - "MONDO:0011486", "MONDO:0700096", + "MONDO:0024458", "MONDO:0005218", "MONDO:0005336", "MONDO:0002081", + "MONDO:0008116", "OGMS:0000031", "MONDO:0003847", "MONDO:0003939", + "MONDO:0002022", "BFO:0000001", - "MONDO:0002320", - "MONDO:0019950" + "MONDO:0000462", + "MONDO:0005328" ], - "subject_label": "congenital muscular dystrophy 1B", + "subject_label": "oculopharyngeal muscular dystrophy", "subject_closure_label": [ "disease or disorder", + "eye adnexa disorder", + "disorder of orbital region", "musculoskeletal system disorder", - "congenital nervous system disorder", + "eyelid disorder", "hereditary disease", "muscle tissue disorder", + "myopathy of extraocular muscle", "nervous system disorder", "obsolete muscular disorder", + "eye disorder", "myopathy", - "congenital muscular dystrophy 1B", + "oculopharyngeal muscular dystrophy", + "progressive muscular dystrophy", "neuromuscular disease", - "congenital muscular dystrophy", "skeletal muscle disorder", "muscular dystrophy", - "inherited disease susceptibility", - "disease susceptibility", - "pulmonary disease, chronic obstructive, susceptibility to", + "eyelids malposition disorder", + "disorder of visual system", "human disease or disorder", "hereditary skeletal muscle disorder" ], - "predicate": "biolink:has_phenotype", - "object": "HP:0003547", + "predicate": "biolink:has_mode_of_inheritance", + "object": "HP:0000006", "original_object": null, "object_namespace": "HP", - "object_category": "biolink:PhenotypicQuality", + "object_category": "biolink:GeneticInheritance", "object_closure": [ "HP:0000001", - 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"Abnormality of the upper limb (HPO)", - "Abnormality of the musculature (HPO)", - "Limb-girdle muscle weakness (HPO)", - "Shoulder girdle muscle weakness (HPO)", - "Abnormality of the musculature of the limbs (HPO)", - "Abnormal muscle physiology (HPO)", - "Abnormal skeletal muscle morphology (HPO)", - "Abnormality of the musculoskeletal system (HPO)", - "Abnormality of limbs (HPO)", - "appendage", - "anatomical structure", - "organ", - "anterior region of body", - "musculature of body", - "material anatomical entity", - "anatomical system", - "multicellular organism", - "organism subdivision", - "musculature", - "anatomical entity", - "pectoral girdle region", - "arm", - "muscle organ", - "limb", - "forelimb", - "limb segment", - "musculature of pectoral girdle", - "musculature of limb", - "musculature of upper limb", - "paired limb/fin", - "pectoral appendage", - "muscle structure", - "multi-limb segment region", - "pectoral appendage musculature", - "appendage musculature", - "appendage girdle region", - "muscle of pectoral girdle", - "upper limb segment", - "multicellular anatomical structure", - "paired limb/fin segment", - "appendage girdle complex", - "pectoral complex", - "subdivision of organism along appendicular axis", - "pectoral complex muscle", - "organ system subdivision", - "musculature of pectoral complex", - "skeletal muscle organ", - "lateral structure", - "skeletal musculature" + "Mode of inheritance (HPO)", + "Autosomal dominant inheritance (HPO)", + "Mendelian inheritance" ], - "primary_knowledge_source": ["infores:hpo-annotations"], + "primary_knowledge_source": "infores:hpo-annotations", "aggregator_knowledge_source": ["infores:monarchinitiative"], - "category": "biolink:DiseaseToPhenotypicFeatureAssociation", + "category": "biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation", "negated": null, - "provided_by": "hpoa_disease_phenotype_edges", - "publications": ["OMIM:604801"], + "provided_by": "hpoa_disease_mode_of_inheritance_edges", + "publications": ["PMID:9462747"], "qualifiers": [], "frequency_qualifier": null, - "has_evidence": "ECO:0000501", + "has_evidence": ["ECO:0000269"], "onset_qualifier": null, "sex_qualifier": null, "stage_qualifier": null, - "evidence_count": 0, + "evidence_count": 4, "pathway": null, "frequency_qualifier_label": null, "frequency_qualifier_namespace": null, @@ -1628,33 +776,21 @@ "stage_qualifier_closure_label": [] }, { - "id": "uuid:19006798-1e4f-11ee-871a-692638b4c502", - "subject": "MONDO:0011787", - "original_subject": "OMIM:607155", + "id": "uuid:c3cdaddf-212f-11ee-873a-cd90a19c4085", + "subject": "MONDO:0009681", + "original_subject": "OMIM:254090", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ - "MONDO:0018282", "MONDO:0000001", - "MONDO:0016971", - "MONDO:0017741", - "MONDO:0000429", - "MONDO:0045010", - "MONDO:0100167", "MONDO:0005071", "MONDO:0020121", "MONDO:0700223", - "MONDO:0011787", - "MONDO:0024322", - "MONDO:0020573", "BFO:0000002", + "MONDO:0019952", "BFO:0000017", "BFO:0000020", - "MONDO:0006025", - "MONDO:0016106", - "MONDO:0016157", - "MONDO:0042489", - "MONDO:0017745", + "MONDO:0100225", "BFO:0000016", "MONDO:0020120", "MONDO:0019056", @@ -1663,222 +799,68 @@ "MONDO:0005218", "MONDO:0005336", "MONDO:0002081", - "MONDO:0016156", + "MONDO:0009681", "OGMS:0000031", "MONDO:0003847", "MONDO:0003939", - "MONDO:0015286", "BFO:0000001", - "MONDO:0015152", "MONDO:0002320", - "MONDO:0019052", - "MONDO:0005066", - "MONDO:0016155", - "MONDO:0700066" + "MONDO:0000355", + "MONDO:0019950" ], - "subject_label": "autosomal recessive limb-girdle muscular dystrophy type 2I", + "subject_label": "Ullrich congenital muscular dystrophy 1", "subject_closure_label": [ "disease or disorder", - "autosomal genetic disease", + "Ullrich congenital muscular dystrophy", "musculoskeletal system disorder", "congenital nervous system disorder", "hereditary disease", "muscle tissue disorder", - "metabolic disease", "nervous system disorder", "obsolete muscular disorder", "myopathy", - "autosomal recessive disease", - "autosomal recessive limb-girdle muscular dystrophy type 2I", - "autosomal recessive limb-girdle muscular dystrophy", - "congenital disorder of glycosylation", - "progressive muscular dystrophy", + "Ullrich congenital muscular dystrophy 1", "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", - "limb-girdle muscular dystrophy", - "disorder of protein O-glycosylation", - "disorder of O-mannosylglycan synthesis", - "qualitative or quantitative defects of alpha-dystroglycan", - "inborn errors of metabolism", "neuromuscular disease", + "congenital muscular dystrophy", + "congenital myopathy", "skeletal muscle disorder", "muscular dystrophy", - "inherited disease susceptibility", - "disorder of glycosylation", - "disease susceptibility", - "glycoprotein metabolism disease", - "pulmonary disease, chronic obstructive, susceptibility to", - "myopathy caused by variation in FKRP", + "collagen 6-related myopathy", "human disease or disorder", "hereditary skeletal muscle disorder" ], - "predicate": "biolink:has_phenotype", - "object": "HP:0003547", + "predicate": "biolink:has_mode_of_inheritance", + "object": "HP:0000006", "original_object": null, "object_namespace": "HP", - "object_category": "biolink:PhenotypicQuality", + "object_category": "biolink:GeneticInheritance", "object_closure": [ "HP:0000001", - "UPHENO:0002649", - "UPHENO:0082875", - "UPHENO:0075696", - "UPHENO:0002320", - "UPHENO:0001001", - "HP:0003325", - "UPHENO:0080565", - "HP:0009127", - "UPHENO:0001005", - "HP:0011805", - "UPHENO:0001002", - "HP:0001324", - "HP:0000118", - "BFO:0000002", - "HP:0001435", - "HP:0001446", - "HP:0002817", - "BFO:0000020", - "UPHENO:0080555", - "HP:0003011", - "UPHENO:0002816", - "UPHENO:0002332", - "UPHENO:0080556", - "UPHENO:0002982", - "UPHENO:0081581", - "HP:0003547", - "HP:0033127", - "UPHENO:0001003", - "UPHENO:0002536", - 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"primary_knowledge_source": ["infores:hpo-annotations"], + "primary_knowledge_source": "infores:hpo-annotations", "aggregator_knowledge_source": ["infores:monarchinitiative"], - "category": "biolink:DiseaseToPhenotypicFeatureAssociation", + "category": "biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation", "negated": null, - "provided_by": "hpoa_disease_phenotype_edges", - "publications": ["OMIM:310440"], + "provided_by": "hpoa_disease_mode_of_inheritance_edges", + "publications": ["PMID:22577215"], "qualifiers": [], "frequency_qualifier": null, - "has_evidence": "ECO:0000501", + "has_evidence": ["ECO:0000269"], "onset_qualifier": null, "sex_qualifier": null, "stage_qualifier": null, - "evidence_count": 0, + "evidence_count": 4, "pathway": null, "frequency_qualifier_label": null, "frequency_qualifier_namespace": null, @@ -2960,45 +1458,40 @@ "stage_qualifier_closure_label": [] }, { - "id": "uuid:1e9fbb79-1e4f-11ee-871a-692638b4c502", - "subject": "MONDO:0011170", - "original_subject": "OMIM:601954", + "id": "uuid:c3cdadba-212f-11ee-873a-cd90a19c4085", + "subject": "MONDO:0011466", + "original_subject": "OMIM:604454", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ "MONDO:0000001", - "MONDO:0016971", + "MONDO:0011466", "MONDO:0000429", - "MONDO:0100167", "MONDO:0005071", "MONDO:0020121", "MONDO:0700223", - "MONDO:0020573", "BFO:0000002", "BFO:0000017", "BFO:0000020", - "MONDO:0006025", - "MONDO:0016106", - "MONDO:0042489", "BFO:0000016", "MONDO:0020120", "MONDO:0019056", - "MONDO:0016139", "MONDO:0700096", - "MONDO:0011170", "MONDO:0005218", "MONDO:0005336", "MONDO:0002081", + "MONDO:0000426", "OGMS:0000031", - "MONDO:0016192", "MONDO:0003847", "MONDO:0003939", "BFO:0000001", - "MONDO:0015152" + "MONDO:0016108", + "MONDO:0018949" ], - "subject_label": "autosomal recessive limb-girdle muscular dystrophy type 2G", + "subject_label": "distal myopathy, Welander type", "subject_closure_label": [ "disease or disorder", + "autosomal dominant disease", "autosomal genetic disease", "musculoskeletal system disorder", "hereditary disease", @@ -3006,102 +1499,46 @@ "nervous system disorder", "obsolete muscular disorder", "myopathy", - "autosomal recessive disease", - "autosomal recessive limb-girdle muscular dystrophy type 2G", - 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"Functional motor deficit (HPO)", - "Abnormal muscle physiology (HPO)", - "Abnormality of the musculoskeletal system (HPO)", - "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" + "Mode of inheritance (HPO)", + "Autosomal dominant inheritance (HPO)", + "Mendelian inheritance" ], - "primary_knowledge_source": ["infores:hpo-annotations"], + "primary_knowledge_source": "infores:hpo-annotations", "aggregator_knowledge_source": ["infores:monarchinitiative"], - "category": "biolink:DiseaseToPhenotypicFeatureAssociation", + "category": "biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation", "negated": null, - "provided_by": "hpoa_disease_phenotype_edges", - "publications": ["PMID:20096397"], + "provided_by": "hpoa_disease_mode_of_inheritance_edges", + "publications": ["OMIM:609200"], "qualifiers": [], "frequency_qualifier": null, - "has_evidence": "ECO:0000269", + "has_evidence": ["ECO:0000501"], "onset_qualifier": null, "sex_qualifier": null, "stage_qualifier": null, - "evidence_count": 0, + "evidence_count": 4, "pathway": null, "frequency_qualifier_label": null, "frequency_qualifier_namespace": null, @@ -3849,148 +2016,107 @@ "stage_qualifier_closure_label": [] }, { - "id": "uuid:1a0255cd-1e4f-11ee-871a-692638b4c502", - "subject": "MONDO:0013390", - "original_subject": "OMIM:613723", + "id": "uuid:c275a325-212f-11ee-873a-cd90a19c4085", + "subject": "MONDO:0012262", + "original_subject": "OMIM:609384", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ - "MONDO:0013390", + "MONDO:0020158", "MONDO:0000001", - "MONDO:0016198", - "MONDO:0016971", - "MONDO:0000429", - "MONDO:0100167", + "MONDO:0007614", "MONDO:0005071", "MONDO:0020121", "MONDO:0700223", - "MONDO:0020573", + "MONDO:0004746", "BFO:0000002", + "MONDO:0012262", + "MONDO:0957003", "BFO:0000017", "BFO:0000020", - "MONDO:0006025", "MONDO:0016106", - "MONDO:0042489", + "MONDO:0003382", "BFO:0000016", "MONDO:0020120", "MONDO:0019056", - "MONDO:0016139", + "MONDO:0003569", "MONDO:0700096", + "MONDO:0001584", + "MONDO:0024458", "MONDO:0005218", "MONDO:0005336", "MONDO:0002081", "OGMS:0000031", "MONDO:0003847", "MONDO:0003939", + "MONDO:0002022", + "MONDO:0015368", "BFO:0000001", - "MONDO:0015152" + "MONDO:0002320", + "MONDO:0000462", + "MONDO:0005328" ], - "subject_label": "autosomal recessive limb-girdle muscular dystrophy type 2Q", + "subject_label": "fibrosis of extraocular muscles, congenital, 3c", "subject_closure_label": [ "disease or disorder", - "autosomal genetic disease", + "eye adnexa disorder", + "ocular motility disease", + "disorder of orbital region", "musculoskeletal system disorder", + "congenital nervous system disorder", + "eyelid disorder", + "cranial nerve neuropathy", "hereditary disease", "muscle tissue disorder", + "myopathy of extraocular muscle", "nervous system disorder", "obsolete muscular disorder", + "eye disorder", "myopathy", - "autosomal recessive disease", - "autosomal recessive limb-girdle muscular dystrophy type 2Q", - "autosomal recessive limb-girdle muscular dystrophy", + "congenital fibrosis of extraocular muscles", + "fibrosis of extraocular muscles, congenital, 3c", + "neuro-ophthalmological disease", "progressive muscular dystrophy", - "qualitative or quantitative protein defects in neuromuscular diseases", - "qualitative or quantitative defects of plectin", - "limb-girdle muscular dystrophy", "neuromuscular disease", "skeletal muscle disorder", "muscular dystrophy", - "inherited disease susceptibility", - "disease susceptibility", - "pulmonary disease, chronic obstructive, susceptibility to", + "eyelids malposition disorder", + "disorder of visual system", "human disease or disorder", - "hereditary skeletal muscle disorder" + "hereditary skeletal muscle disorder", + "hereditary neuro-ophthalmological disease" ], - "predicate": "biolink:has_phenotype", - "object": "HP:0003551", + "predicate": "biolink:has_mode_of_inheritance", + "object": "HP:0000006", "original_object": null, "object_namespace": "HP", - "object_category": "biolink:PhenotypicQuality", + "object_category": "biolink:GeneticInheritance", "object_closure": [ "HP:0000001", - "UPHENO:0082875", - "UPHENO:0075696", - "UPHENO:0002320", - "UPHENO:0001001", - "HP:0003551", - "UPHENO:0001005", - "UPHENO:0001002", - "HP:0004302", - "HP:0000118", - "BFO:0000002", - "BFO:0000020", - "HP:0003011", - "UPHENO:0002816", - "UPHENO:0002332", - "HP:0033127", - "UPHENO:0001003", - "UPHENO:0002536", - "BFO:0000001", - "HP:0011804", - "PATO:0000001", - "BFO:0000001", - "BFO:0000002", - "BFO:0000004", - "BFO:0000040", - "UBERON:0001062", - "CARO:0000000", - "UBERON:0000465", - "UBERON:0001015", - "UBERON:0000383", - "UBERON:0005090", - "UBERON:0000061", - "UBERON:0001630", - "UBERON:0010000", - "UBERON:0000467", - "UBERON:0000468", - "UBERON:0000062", - "UBERON:0011216" + "HP:0000006", + "HP:0000005", + "HP:0034345" ], - "object_label": "Difficulty climbing stairs (HPO)", + "object_label": "Autosomal dominant inheritance (HPO)", "object_closure_label": [ "All (HPO)", - "Phenotypic abnormality (HPO)", - "Abnormality of the musculature (HPO)", - "Difficulty climbing stairs (HPO)", - "Functional motor deficit (HPO)", - "Abnormal muscle physiology (HPO)", - "Abnormality of the musculoskeletal system (HPO)", - "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" + "Mode of inheritance (HPO)", + "Autosomal dominant inheritance (HPO)", + "Mendelian inheritance" ], - "primary_knowledge_source": ["infores:hpo-annotations"], + "primary_knowledge_source": "infores:hpo-annotations", "aggregator_knowledge_source": ["infores:monarchinitiative"], - "category": "biolink:DiseaseToPhenotypicFeatureAssociation", + "category": "biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation", "negated": null, - "provided_by": "hpoa_disease_phenotype_edges", - "publications": ["PMID:21109228"], + "provided_by": "hpoa_disease_mode_of_inheritance_edges", + "publications": ["OMIM:609384"], "qualifiers": [], "frequency_qualifier": null, - "has_evidence": "ECO:0000269", + "has_evidence": ["ECO:0000501"], "onset_qualifier": null, "sex_qualifier": null, "stage_qualifier": null, - "evidence_count": 0, + "evidence_count": 4, "pathway": null, "frequency_qualifier_label": null, "frequency_qualifier_namespace": null, @@ -4014,148 +2140,101 @@ "stage_qualifier_closure_label": [] }, { - "id": "uuid:24d370c2-1e4f-11ee-871a-692638b4c502", - "subject": "MONDO:0024545", - "original_subject": "OMIM:254130", + "id": "uuid:c304ba49-212f-11ee-873a-cd90a19c4085", + "subject": "MONDO:0012277", + "original_subject": "OMIM:609452", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ "MONDO:0000001", + "MONDO:0016186", "MONDO:0000429", - "MONDO:0016145", - "MONDO:0100167", "MONDO:0005071", "MONDO:0020121", + "MONDO:0018943", "MONDO:0700223", - "MONDO:0020573", "BFO:0000002", + "MONDO:0019952", + "MONDO:0016190", "BFO:0000017", "BFO:0000020", - "MONDO:0006025", - "MONDO:0042489", "BFO:0000016", "MONDO:0020120", "MONDO:0019056", "MONDO:0016139", "MONDO:0700096", - "MONDO:0009685", + "MONDO:0002921", "MONDO:0005218", "MONDO:0005336", "MONDO:0002081", - "MONDO:0016109", + "MONDO:0000426", "OGMS:0000031", "MONDO:0003847", "MONDO:0003939", + "MONDO:0012277", "BFO:0000001", - "MONDO:0024545", + "MONDO:0002320", + "MONDO:0016108", "MONDO:0018949" ], - "subject_label": "Miyoshi muscular dystrophy 1", + "subject_label": "myofibrillar myopathy 4", "subject_closure_label": [ "disease or disorder", + "autosomal dominant disease", "autosomal genetic disease", "musculoskeletal system disorder", + "congenital nervous system disorder", + "congenital structural myopathy", "hereditary disease", "muscle tissue disorder", "nervous system disorder", "obsolete muscular disorder", "myopathy", - "autosomal recessive disease", - "Miyoshi myopathy", - "autosomal recessive distal myopathy", + "myofibrillar myopathy 4", + "autosomal dominant distal myopathy", "qualitative or quantitative protein defects in neuromuscular diseases", - "qualitative or quantitative defects of dysferlin", + "qualitative or quantitative defects of myofibrillar proteins", + "qualitative or quantitative defects of protein ZASP", + "myofibrillar myopathy", "distal myopathy", "neuromuscular disease", + "congenital myopathy", "skeletal muscle disorder", "muscular dystrophy", - "inherited disease susceptibility", - "Miyoshi muscular dystrophy 1", - "disease susceptibility", - "pulmonary disease, chronic obstructive, susceptibility to", "human disease or disorder", "hereditary skeletal muscle disorder" ], - "predicate": "biolink:has_phenotype", - "object": "HP:0003551", + "predicate": "biolink:has_mode_of_inheritance", + "object": "HP:0000006", "original_object": null, "object_namespace": "HP", - "object_category": "biolink:PhenotypicQuality", + "object_category": "biolink:GeneticInheritance", "object_closure": [ "HP:0000001", - "UPHENO:0082875", - "UPHENO:0075696", - "UPHENO:0002320", - "UPHENO:0001001", - "HP:0003551", - "UPHENO:0001005", - "UPHENO:0001002", - "HP:0004302", - "HP:0000118", - "BFO:0000002", - "BFO:0000020", - "HP:0003011", - "UPHENO:0002816", - "UPHENO:0002332", - "HP:0033127", - "UPHENO:0001003", - "UPHENO:0002536", - "BFO:0000001", - "HP:0011804", - "PATO:0000001", - "BFO:0000001", - "BFO:0000002", - "BFO:0000004", - "BFO:0000040", - "UBERON:0001062", - "CARO:0000000", - "UBERON:0000465", - "UBERON:0001015", - "UBERON:0000383", - "UBERON:0005090", - "UBERON:0000061", - "UBERON:0001630", - "UBERON:0010000", - "UBERON:0000467", - "UBERON:0000468", - "UBERON:0000062", - "UBERON:0011216" + "HP:0000006", + "HP:0000005", + "HP:0034345" ], - "object_label": "Difficulty climbing stairs (HPO)", + "object_label": "Autosomal dominant inheritance (HPO)", "object_closure_label": [ "All (HPO)", - "Phenotypic abnormality (HPO)", - "Abnormality of the musculature (HPO)", - "Difficulty climbing stairs (HPO)", - "Functional motor deficit (HPO)", - "Abnormal muscle physiology (HPO)", - "Abnormality of the musculoskeletal system (HPO)", - "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" + "Mode of inheritance (HPO)", + "Autosomal dominant inheritance (HPO)", + "Mendelian inheritance" ], - "primary_knowledge_source": ["infores:hpo-annotations"], + "primary_knowledge_source": "infores:hpo-annotations", "aggregator_knowledge_source": ["infores:monarchinitiative"], - "category": "biolink:DiseaseToPhenotypicFeatureAssociation", + "category": "biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation", "negated": null, - "provided_by": "hpoa_disease_phenotype_edges", - "publications": ["OMIM:254130"], + "provided_by": "hpoa_disease_mode_of_inheritance_edges", + "publications": ["OMIM:609452"], "qualifiers": [], "frequency_qualifier": null, - "has_evidence": "ECO:0000304", + "has_evidence": ["ECO:0000501"], "onset_qualifier": null, "sex_qualifier": null, "stage_qualifier": null, - "evidence_count": 0, + "evidence_count": 4, "pathway": null, "frequency_qualifier_label": null, "frequency_qualifier_namespace": null, diff --git a/frontend/fixtures/autocomplete.json b/frontend/fixtures/autocomplete.json index f34ce696e..a179eb30d 100644 --- a/frontend/fixtures/autocomplete.json +++ b/frontend/fixtures/autocomplete.json @@ -1,7 +1,7 @@ { "limit": 10, "offset": 0, - "total": 193, + "total": 195, "items": [ { "id": "MONDO:0001083", diff --git a/frontend/fixtures/node.json b/frontend/fixtures/node.json index 8528dc4b3..2275f533c 100644 --- a/frontend/fixtures/node.json +++ b/frontend/fixtures/node.json @@ -41,19 +41,6 @@ ], "node_hierarchy": { "super_classes": [ - { - "id": "MONDO:0005336", - "category": "biolink:Disease", - "name": "myopathy", - "full_name": null, - "description": null, - "xref": [], - "provided_by": null, - "in_taxon": null, - "in_taxon_label": null, - "symbol": null, - "synonym": [] - }, { "id": "MONDO:0019056", "category": "biolink:Disease", @@ -68,9 +55,9 @@ "synonym": [] }, { - "id": "MONDO:0100167", + "id": "MONDO:0700223", "category": "biolink:Disease", - "name": "pulmonary disease, chronic obstructive, susceptibility to", + "name": "hereditary skeletal muscle disorder", "full_name": null, "description": null, "xref": [], @@ -81,9 +68,9 @@ "synonym": [] }, { - "id": "MONDO:0700223", + "id": "MONDO:0005336", "category": "biolink:Disease", - "name": "hereditary skeletal muscle disorder", + "name": "myopathy", "full_name": null, "description": null, "xref": [], diff --git a/frontend/fixtures/search.json b/frontend/fixtures/search.json index c241ddee2..1aa63d692 100644 --- a/frontend/fixtures/search.json +++ b/frontend/fixtures/search.json @@ -1,7 +1,7 @@ { "limit": 20, "offset": 0, - "total": 92, + "total": 93, "items": [ { "id": "MONDO:0019391", diff --git a/frontend/src/api/model.ts b/frontend/src/api/model.ts index 8017b8afc..709d5ee0b 100644 --- a/frontend/src/api/model.ts +++ b/frontend/src/api/model.ts @@ -45,7 +45,7 @@ export interface Association { object_label?: string, /** Field containing object name and the names of all of it's ancestors */ object_closure_label?: string[], - primary_knowledge_source?: string[], + primary_knowledge_source?: string, aggregator_knowledge_source?: string[], category?: string, negated?: boolean, @@ -53,7 +53,7 @@ export interface Association { publications?: string[], qualifiers?: string[], frequency_qualifier?: string, - has_evidence?: string, + has_evidence?: string[], onset_qualifier?: string, sex_qualifier?: string, stage_qualifier?: string, @@ -182,7 +182,7 @@ export interface DirectionalAssociation extends Association { object_label?: string, /** Field containing object name and the names of all of it's ancestors */ object_closure_label?: string[], - primary_knowledge_source?: string[], + primary_knowledge_source?: string, aggregator_knowledge_source?: string[], category?: string, negated?: boolean, @@ -190,7 +190,7 @@ export interface DirectionalAssociation extends Association { publications?: string[], qualifiers?: string[], frequency_qualifier?: string, - has_evidence?: string, + has_evidence?: string[], onset_qualifier?: string, sex_qualifier?: string, stage_qualifier?: string, @@ -294,7 +294,7 @@ export interface HistoBin extends FacetValue { count?: number, }; /** - * UI conatiner class extending Entity with additional information + * UI container class extending Entity with additional information */ export interface Node extends Entity { /** The biolink taxon that the entity is in the closure of. */