From 8b38a7a497ef7825741bae9bc34a06ddc344ac74 Mon Sep 17 00:00:00 2001 From: Kevin Schaper Date: Tue, 18 Jul 2023 09:45:25 -0700 Subject: [PATCH] Add taxon & taxon label fields for subject & object (#228) Adds subject_taxon, subject_taxon_label, object_taxon, object_taxon_label fields --- backend/pyproject.toml | 2 +- backend/src/monarch_py/datamodels/model.py | 8 + backend/src/monarch_py/datamodels/model.yaml | 12 + backend/tests/fixtures/association_counts.py | 6 +- .../fixtures/association_counts_response.py | 3042 ++++++++++++---- .../tests/fixtures/association_response.py | 3034 ++++++++++++---- backend/tests/fixtures/association_table.py | 457 ++- .../fixtures/association_table_response.py | 439 ++- backend/tests/fixtures/associations.py | 3154 ++++++++++++---- backend/tests/fixtures/histopheno.py | 38 +- backend/tests/fixtures/histopheno_response.py | 42 +- backend/tests/fixtures/node.py | 18 +- backend/tests/fixtures/search_response.py | 2 +- frontend/fixtures/association-counts.json | 6 +- frontend/fixtures/association-table.json | 473 ++- frontend/fixtures/associations.json | 3214 +++++++++++++---- frontend/fixtures/histopheno.json | 46 +- frontend/fixtures/node.json | 18 +- frontend/src/api/model.ts | 8 + 19 files changed, 10466 insertions(+), 3553 deletions(-) diff --git a/backend/pyproject.toml b/backend/pyproject.toml index e48676ef9..f0ea9ca32 100644 --- a/backend/pyproject.toml +++ b/backend/pyproject.toml @@ -1,6 +1,6 @@ [tool.poetry] name = "monarch-py" -version = "0.13.4" +version = "0.13.5" description = "Python package for interacting with Monarch Initiative knowledge graph" authors = [ "glass-ships ", diff --git a/backend/src/monarch_py/datamodels/model.py b/backend/src/monarch_py/datamodels/model.py index 8e138878d..3242c7b1f 100644 --- a/backend/src/monarch_py/datamodels/model.py +++ b/backend/src/monarch_py/datamodels/model.py @@ -60,6 +60,8 @@ class Association(ConfiguredBaseModel): default_factory=list, description="""Field containing subject name and the names of all of it's ancestors""", ) + subject_taxon: Optional[str] = Field(None) + subject_taxon_label: Optional[str] = Field(None) predicate: str = Field(...) object: str = Field(...) original_object: Optional[str] = Field(None) @@ -74,6 +76,8 @@ class Association(ConfiguredBaseModel): default_factory=list, description="""Field containing object name and the names of all of it's ancestors""", ) + object_taxon: Optional[str] = Field(None) + object_taxon_label: Optional[str] = Field(None) primary_knowledge_source: Optional[str] = Field(None) aggregator_knowledge_source: Optional[List[str]] = Field(default_factory=list) category: Optional[str] = Field(None) @@ -204,6 +208,8 @@ class DirectionalAssociation(Association): default_factory=list, description="""Field containing subject name and the names of all of it's ancestors""", ) + subject_taxon: Optional[str] = Field(None) + subject_taxon_label: Optional[str] = Field(None) predicate: str = Field(...) object: str = Field(...) original_object: Optional[str] = Field(None) @@ -218,6 +224,8 @@ class DirectionalAssociation(Association): default_factory=list, description="""Field containing object name and the names of all of it's ancestors""", ) + object_taxon: Optional[str] = Field(None) + object_taxon_label: Optional[str] = Field(None) primary_knowledge_source: Optional[str] = Field(None) aggregator_knowledge_source: Optional[List[str]] = Field(default_factory=list) category: Optional[str] = Field(None) diff --git a/backend/src/monarch_py/datamodels/model.yaml b/backend/src/monarch_py/datamodels/model.yaml index 24bdf6918..cf0edc72f 100644 --- a/backend/src/monarch_py/datamodels/model.yaml +++ b/backend/src/monarch_py/datamodels/model.yaml @@ -34,6 +34,8 @@ classes: - subject_closure - subject_label - subject_closure_label + - subject_taxon + - subject_taxon_label - predicate - object - original_object @@ -42,6 +44,8 @@ classes: - object_closure - object_label - object_closure_label + - object_taxon + - object_taxon_label - primary_knowledge_source - aggregator_knowledge_source - category @@ -401,6 +405,10 @@ slots: subject_closure_label: multivalued: true description: Field containing subject name and the names of all of it's ancestors + subject_taxon: + is_a: in_taxon + subject_taxon_label: + is_a: in_taxon_label object_label: is_a: name description: The name of the object entity @@ -416,6 +424,10 @@ slots: object_closure_label: multivalued: true description: Field containing object name and the names of all of it's ancestors + object_taxon: + is_a: in_taxon + object_taxon_label: + is_a: in_taxon_label frequency_qualifier_label: is_a: name description: The name of the frequency_qualifier entity diff --git a/backend/tests/fixtures/association_counts.py b/backend/tests/fixtures/association_counts.py index 79467b039..551876496 100644 --- a/backend/tests/fixtures/association_counts.py +++ b/backend/tests/fixtures/association_counts.py @@ -7,17 +7,17 @@ def association_counts(): "items": [ { "label": "Phenotypes", - "count": 4011, + "count": 4312, "category": "biolink:DiseaseToPhenotypicFeatureAssociation", }, { "label": "Causal Genes", - "count": 121, + "count": 123, "category": "biolink:CausalGeneToDiseaseAssociation", }, { "label": "Correlated Genes", - "count": 147, + "count": 149, "category": "biolink:CorrelatedGeneToDiseaseAssociation", }, ] diff --git a/backend/tests/fixtures/association_counts_response.py b/backend/tests/fixtures/association_counts_response.py index b28771ede..9ba55ea41 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": 2, + "QTime": 1, "params": { "facet.query": [ '(category:"biolink:DiseaseToPhenotypicFeatureAssociation") AND (subject:"MONDO:0020121" OR subject_closure:"MONDO:0020121")', @@ -40,35 +40,37 @@ def association_counts_response(): }, }, "response": { - "num_found": 4806, + "num_found": 5124, "start": 0, "docs": [ { - "id": "uuid:c2a45bf5-212f-11ee-873a-cd90a19c4085", - "original_subject": "OMIM:158800", - "predicate": "biolink:has_mode_of_inheritance", - "category": "biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation", + "id": "uuid:628f39f7-212f-11ee-873a-cd90a19c4085", + "original_subject": "OMIM:160500", + "predicate": "biolink:has_phenotype", + "category": "biolink:DiseaseToPhenotypicFeatureAssociation", "aggregator_knowledge_source": ["infores:monarchinitiative"], "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", + "provided_by": "hpoa_disease_phenotype_edges", + "publications": ["OMIM:160500"], + "subject": "MONDO:0008050", + "object": "HP:0003803", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ "MONDO:0000001", "MONDO:0005071", "MONDO:0020121", - "MONDO:0008028", - "MONDO:0700223", "BFO:0000002", + "MONDO:0019952", "BFO:0000017", "BFO:0000020", + "MONDO:0008050", + "MONDO:0016195", "BFO:0000016", "MONDO:0020120", "MONDO:0019056", + "MONDO:0016139", "MONDO:0700096", "MONDO:0005218", "MONDO:0005336", @@ -77,326 +79,606 @@ 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, Barnes type", + "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", "human disease or disorder", - "hereditary skeletal muscle disorder", ], - "subject_label": "muscular dystrophy, Barnes type", + "subject_label": "MYH7-related skeletal myopathy", "object_namespace": "HP", - "object_category": "biolink:GeneticInheritance", + "object_category": "biolink:PhenotypicQuality", "object_closure": [ "HP:0000001", - "HP:0000006", - "HP:0000005", - "HP:0034345", + "HP:0004303", + "UPHENO:0001001", + "HP:0003803", + "HP:0033684", + "UPHENO:0001005", + "HP:0011805", + "UPHENO:0001002", + "HP:0000118", + "BFO:0000002", + "HP:0025354", + "BFO:0000020", + "HP:0003011", + "UPHENO:0002816", + "UPHENO:0081581", + "HP:0033127", + "UPHENO:0001003", + "UPHENO:0002536", + "UPHENO:0076692", + "UPHENO:0076710", + "BFO:0000001", + "PATO:0000001", + "BFO:0000001", + "BFO:0000002", + "BFO:0000004", + "BFO:0000040", + "UBERON:0001062", + "CARO:0000000", + "CL:0000000", + "UBERON:0000465", + "UBERON:0000383", + "UBERON:0001015", + "UBERON:0018254", + "UBERON:0005090", + "UBERON:0004120", + "CL:0000003", + "UBERON:0000061", + "UBERON:0001630", + "UBERON:0002385", + "CL:0002371", + "UBERON:0010000", + "UBERON:0000467", + "UBERON:0014892", + "UBERON:0002036", + "CL:0000188", + "UBERON:0000479", + "UBERON:0000468", + "UBERON:0000062", + "UBERON:0011216", + "UBERON:0001134", ], "object_closure_label": [ "All (HPO)", - "Mode of inheritance (HPO)", - "Autosomal dominant inheritance (HPO)", - "Mendelian inheritance", - ], - "object_label": "Autosomal dominant inheritance (HPO)", + "Phenotypic abnormality (HPO)", + "Abnormality of the musculature (HPO)", + "Type 1 muscle fiber predominance (HPO)", + "Abnormal muscle fiber morphology (HPO)", + "Abnormal skeletal muscle morphology (HPO)", + "Abnormal cellular phenotype (HPO)", + "Abnormality of the musculoskeletal system (HPO)", + "Abnormal muscle fiber-type distribution (HPO)", + "anatomical structure", + "organ", + "musculature of body", + "material anatomical entity", + "anatomical system", + "multicellular organism", + "tissue", + "musculature", + "anatomical entity", + "skeletal muscle tissue", + "muscle organ", + "striated muscle tissue", + "muscle tissue", + "mesoderm-derived structure", + "muscle structure", + "multicellular anatomical structure", + "organ system subdivision", + "skeletal muscle organ", + "skeletal musculature", + ], + "object_label": "Type 1 muscle fiber predominance (HPO)", "evidence_count": 4, }, { - "id": "uuid:c304bcf2-212f-11ee-873a-cd90a19c4085", - "original_subject": "OMIM:158900", - "predicate": "biolink:has_mode_of_inheritance", - "category": "biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation", + "id": "uuid:64b68436-212f-11ee-873a-cd90a19c4085", + "original_subject": "OMIM:254090", + "predicate": "biolink:has_phenotype", + "category": "biolink:DiseaseToPhenotypicFeatureAssociation", "aggregator_knowledge_source": ["infores:monarchinitiative"], "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", + "provided_by": "hpoa_disease_phenotype_edges", + "publications": ["OMIM:254090"], + "subject": "MONDO:0009681", + "object": "HP:0003803", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ - "MONDO:0008030", "MONDO:0000001", - "MONDO:0019303", "MONDO:0005071", "MONDO:0020121", - "MONDO:0700223", - "MONDO:0001347", "BFO:0000002", "BFO:0000017", "BFO:0000020", - "MONDO:0016106", - "MONDO:0100137", + "MONDO:0100225", "BFO:0000016", "MONDO:0020120", "MONDO:0019056", + "MONDO:0016139", "MONDO:0700096", "MONDO:0005218", "MONDO:0005336", "MONDO:0002081", - "MONDO:0021147", + "MONDO:0009681", "OGMS:0000031", "MONDO:0003847", "MONDO:0003939", "BFO:0000001", + "MONDO:0002320", + "MONDO:0000355", + "MONDO:0019950", ], "subject_closure_label": [ "disease or disorder", - "facioscapulohumeral muscular dystrophy", + "Ullrich congenital muscular dystrophy", "musculoskeletal system disorder", + "congenital nervous system disorder", "hereditary disease", "muscle tissue disorder", "nervous system disorder", "obsolete muscular disorder", "myopathy", - "facioscapulohumeral muscular dystrophy 1", - "progressive muscular dystrophy", + "Ullrich congenital muscular dystrophy 1", + "qualitative or quantitative protein defects in neuromuscular diseases", "neuromuscular disease", - "premature aging syndrome", + "congenital muscular dystrophy", "skeletal muscle disorder", "muscular dystrophy", - "disorder of development or morphogenesis", - "telomere syndrome", + "collagen 6-related myopathy", "human disease or disorder", - "hereditary skeletal muscle disorder", ], - "subject_label": "facioscapulohumeral muscular dystrophy 1", + "subject_label": "Ullrich congenital muscular dystrophy 1", "object_namespace": "HP", - "object_category": "biolink:GeneticInheritance", + "object_category": "biolink:PhenotypicQuality", "object_closure": [ "HP:0000001", - "HP:0000006", - "HP:0000005", - "HP:0034345", + "HP:0004303", + "UPHENO:0001001", + "HP:0003803", + "HP:0033684", + "UPHENO:0001005", + "HP:0011805", + "UPHENO:0001002", + "HP:0000118", + "BFO:0000002", + "HP:0025354", + "BFO:0000020", + "HP:0003011", + "UPHENO:0002816", + "UPHENO:0081581", + "HP:0033127", + "UPHENO:0001003", + "UPHENO:0002536", + "UPHENO:0076692", + "UPHENO:0076710", + "BFO:0000001", + "PATO:0000001", + "BFO:0000001", + "BFO:0000002", + "BFO:0000004", + "BFO:0000040", + "UBERON:0001062", + "CARO:0000000", + "CL:0000000", + "UBERON:0000465", + "UBERON:0000383", + "UBERON:0001015", + "UBERON:0018254", + "UBERON:0005090", + "UBERON:0004120", + "CL:0000003", + "UBERON:0000061", + "UBERON:0001630", + "UBERON:0002385", + "CL:0002371", + "UBERON:0010000", + "UBERON:0000467", + "UBERON:0014892", + "UBERON:0002036", + "CL:0000188", + "UBERON:0000479", + "UBERON:0000468", + "UBERON:0000062", + "UBERON:0011216", + "UBERON:0001134", ], "object_closure_label": [ "All (HPO)", - "Mode of inheritance (HPO)", - "Autosomal dominant inheritance (HPO)", - "Mendelian inheritance", - ], - "object_label": "Autosomal dominant inheritance (HPO)", + "Phenotypic abnormality (HPO)", + "Abnormality of the musculature (HPO)", + "Type 1 muscle fiber predominance (HPO)", + "Abnormal muscle fiber morphology (HPO)", + "Abnormal skeletal muscle morphology (HPO)", + "Abnormal cellular phenotype (HPO)", + "Abnormality of the musculoskeletal system (HPO)", + "Abnormal muscle fiber-type distribution (HPO)", + "anatomical structure", + "organ", + "musculature of body", + "material anatomical entity", + "anatomical system", + "multicellular organism", + "tissue", + "musculature", + "anatomical entity", + "skeletal muscle tissue", + "muscle organ", + "striated muscle tissue", + "muscle tissue", + "mesoderm-derived structure", + "muscle structure", + "multicellular anatomical structure", + "organ system subdivision", + "skeletal muscle organ", + "skeletal musculature", + ], + "object_label": "Type 1 muscle fiber predominance (HPO)", "evidence_count": 4, }, { - "id": "uuid:c3cdad58-212f-11ee-873a-cd90a19c4085", - "original_subject": "OMIM:159050", - "predicate": "biolink:has_mode_of_inheritance", - "category": "biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation", + "id": "uuid:628f39f6-212f-11ee-873a-cd90a19c4085", + "original_subject": "OMIM:160500", + "predicate": "biolink:has_phenotype", + "category": "biolink:DiseaseToPhenotypicFeatureAssociation", "aggregator_knowledge_source": ["infores:monarchinitiative"], "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", + "provided_by": "hpoa_disease_phenotype_edges", + "publications": ["OMIM:160500"], + "subject": "MONDO:0008050", + "object": "HP:0003805", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ - "MONDO:0004994", "MONDO:0000001", - "MONDO:0008034", "MONDO:0005071", - "MONDO:0016147", - "MONDO:0005267", "MONDO:0020121", - "MONDO:0004995", - "MONDO:0700223", "BFO:0000002", + "MONDO:0019952", "BFO:0000017", "BFO:0000020", - "MONDO:0010542", - "MONDO:0016106", - "MONDO:0015470", - "MONDO:0005217", - "MONDO:0016899", + "MONDO:0008050", + "MONDO:0016195", "BFO:0000016", "MONDO:0020120", "MONDO:0019056", "MONDO:0016139", "MONDO:0700096", - "MONDO:0000591", "MONDO:0005218", "MONDO:0005336", "MONDO:0002081", - "MONDO:0016333", "OGMS:0000031", - "MONDO:0005021", "MONDO:0003847", "MONDO:0003939", "BFO:0000001", - "MONDO:0010311", + "MONDO:0002320", + "MONDO:0018949", ], "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", "nervous system disorder", - "familial cardiomyopathy", "obsolete muscular disorder", - "heart disorder", "myopathy", - "muscular dystrophy, pseudohypertrophic, with Internalized capillaries", - "Becker muscular dystrophy", - "dilated cardiomyopathy 3B", - "familial isolated dilated cardiomyopathy", - "progressive muscular dystrophy", + "MYH7-related skeletal myopathy", "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 beta-myosin heavy chain (MYH7)", + "distal myopathy", "neuromuscular disease", + "congenital myopathy", "skeletal muscle disorder", "muscular dystrophy", "human disease or disorder", - "hereditary skeletal muscle disorder", ], - "subject_label": "muscular dystrophy, pseudohypertrophic, with Internalized capillaries", + "subject_label": "MYH7-related skeletal myopathy", "object_namespace": "HP", - "object_category": "biolink:GeneticInheritance", + "object_category": "biolink:PhenotypicQuality", "object_closure": [ "HP:0000001", - "HP:0000006", - "HP:0000005", - "HP:0034345", + "HP:0004303", + "UPHENO:0001001", + "UPHENO:0001005", + "HP:0011805", + "UPHENO:0001002", + "HP:0000118", + "BFO:0000002", + "HP:0025354", + "BFO:0000020", + "HP:0003011", + "UPHENO:0002816", + "UPHENO:0081581", + "HP:0033127", + "UPHENO:0001003", + "UPHENO:0002536", + "UPHENO:0076692", + "UPHENO:0076710", + "BFO:0000001", + "HP:0003805", + "PATO:0000001", + "BFO:0000001", + "BFO:0000002", + "BFO:0000004", + "BFO:0000040", + "UBERON:0001062", + "CARO:0000000", + "CL:0000000", + "UBERON:0000465", + "UBERON:0000383", + "UBERON:0001015", + "UBERON:0018254", + "UBERON:0005090", + "UBERON:0004120", + "CL:0000003", + "UBERON:0000061", + "UBERON:0001630", + "UBERON:0002385", + "CL:0002371", + "UBERON:0010000", + "UBERON:0000467", + "UBERON:0014892", + "UBERON:0002036", + "CL:0000188", + "UBERON:0000479", + "UBERON:0000468", + "UBERON:0000062", + "UBERON:0011216", + "UBERON:0001134", ], "object_closure_label": [ "All (HPO)", - "Mode of inheritance (HPO)", - "Autosomal dominant inheritance (HPO)", - "Mendelian inheritance", - ], - "object_label": "Autosomal dominant inheritance (HPO)", + "Phenotypic abnormality (HPO)", + "Abnormality of the musculature (HPO)", + "Rimmed vacuoles (HPO)", + "Abnormal muscle fiber morphology (HPO)", + "Abnormal skeletal muscle morphology (HPO)", + "Abnormal cellular phenotype (HPO)", + "Abnormality of the musculoskeletal system (HPO)", + "anatomical structure", + "organ", + "musculature of body", + "material anatomical entity", + "anatomical system", + "multicellular organism", + "tissue", + "musculature", + "anatomical entity", + "skeletal muscle tissue", + "muscle organ", + "striated muscle tissue", + "muscle tissue", + "mesoderm-derived structure", + "muscle structure", + "multicellular anatomical structure", + "organ system subdivision", + "skeletal muscle organ", + "skeletal musculature", + ], + "object_label": "Rimmed vacuoles (HPO)", "evidence_count": 4, }, { - "id": "uuid:c3367408-212f-11ee-873a-cd90a19c4085", - "original_subject": "OMIM:160300", - "predicate": "biolink:has_mode_of_inheritance", - "category": "biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation", + "id": "uuid:5ebb4d1e-212f-11ee-873a-cd90a19c4085", + "original_subject": "OMIM:300696", + "predicate": "biolink:has_phenotype", + "category": "biolink:DiseaseToPhenotypicFeatureAssociation", "aggregator_knowledge_source": ["infores:monarchinitiative"], - "has_evidence": ["ECO:0000304"], + "has_evidence": ["ECO:0000501"], "primary_knowledge_source": "infores:hpo-annotations", - "provided_by": "hpoa_disease_mode_of_inheritance_edges", - "publications": ["OMIM:160300"], - "subject": "MONDO:0008049", - "object": "HP:0000006", + "provided_by": "hpoa_disease_phenotype_edges", + "publications": ["OMIM:300696"], + "subject": "MONDO:0010401", + "object": "HP:0003805", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ + "MONDO:0004994", "MONDO:0000001", "MONDO:0005071", + "MONDO:0005267", "MONDO:0020121", - "MONDO:0700223", + "MONDO:0004995", "BFO:0000002", + "MONDO:0010401", "BFO:0000017", - "MONDO:0008049", "BFO:0000020", + "MONDO:0016106", + "MONDO:0005217", "BFO:0000016", "MONDO:0020120", "MONDO:0019056", "MONDO:0700096", + "MONDO:0000591", "MONDO:0005218", "MONDO:0005336", "MONDO:0002081", + "MONDO:0016333", + "MONDO:0016830", "OGMS:0000031", + "MONDO:0005021", "MONDO:0003847", "MONDO:0003939", "BFO:0000001", - "MONDO:0018949", ], "subject_closure_label": [ "disease or disorder", + "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", - "myopathy, distal, infantile-onset", - "distal myopathy", + "X-linked myopathy with postural muscle atrophy", + "progressive muscular dystrophy", + "familial dilated cardiomyopathy", + "Emery-Dreifuss muscular dystrophy", "neuromuscular disease", "skeletal muscle disorder", "muscular dystrophy", "human disease or disorder", - "hereditary skeletal muscle disorder", ], - "subject_label": "myopathy, distal, infantile-onset", + "subject_label": "X-linked myopathy with postural muscle atrophy", "object_namespace": "HP", - "object_category": "biolink:GeneticInheritance", + "object_category": "biolink:PhenotypicQuality", "object_closure": [ "HP:0000001", - "HP:0000006", - "HP:0000005", - "HP:0034345", + "HP:0004303", + "UPHENO:0001001", + "UPHENO:0001005", + "HP:0011805", + "UPHENO:0001002", + "HP:0000118", + "BFO:0000002", + "HP:0025354", + "BFO:0000020", + "HP:0003011", + "UPHENO:0002816", + "UPHENO:0081581", + "HP:0033127", + "UPHENO:0001003", + "UPHENO:0002536", + "UPHENO:0076692", + "UPHENO:0076710", + "BFO:0000001", + "HP:0003805", + "PATO:0000001", + "BFO:0000001", + "BFO:0000002", + "BFO:0000004", + "BFO:0000040", + "UBERON:0001062", + "CARO:0000000", + "CL:0000000", + "UBERON:0000465", + "UBERON:0000383", + "UBERON:0001015", + "UBERON:0018254", + "UBERON:0005090", + "UBERON:0004120", + "CL:0000003", + "UBERON:0000061", + "UBERON:0001630", + "UBERON:0002385", + "CL:0002371", + "UBERON:0010000", + "UBERON:0000467", + "UBERON:0014892", + "UBERON:0002036", + "CL:0000188", + "UBERON:0000479", + "UBERON:0000468", + "UBERON:0000062", + "UBERON:0011216", + "UBERON:0001134", ], "object_closure_label": [ "All (HPO)", - "Mode of inheritance (HPO)", - "Autosomal dominant inheritance (HPO)", - "Mendelian inheritance", - ], - "object_label": "Autosomal dominant inheritance (HPO)", + "Phenotypic abnormality (HPO)", + "Abnormality of the musculature (HPO)", + "Rimmed vacuoles (HPO)", + "Abnormal muscle fiber morphology (HPO)", + "Abnormal skeletal muscle morphology (HPO)", + "Abnormal cellular phenotype (HPO)", + "Abnormality of the musculoskeletal system (HPO)", + "anatomical structure", + "organ", + "musculature of body", + "material anatomical entity", + "anatomical system", + "multicellular organism", + "tissue", + "musculature", + "anatomical entity", + "skeletal muscle tissue", + "muscle organ", + "striated muscle tissue", + "muscle tissue", + "mesoderm-derived structure", + "muscle structure", + "multicellular anatomical structure", + "organ system subdivision", + "skeletal muscle organ", + "skeletal musculature", + ], + "object_label": "Rimmed vacuoles (HPO)", "evidence_count": 4, }, { - "id": "uuid:c39b4534-212f-11ee-873a-cd90a19c4085", - "original_subject": "OMIM:160500", - "predicate": "biolink:has_mode_of_inheritance", - "category": "biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation", + "id": "uuid:607e98ad-212f-11ee-873a-cd90a19c4085", + "original_subject": "OMIM:600334", + "predicate": "biolink:has_phenotype", + "category": "biolink:DiseaseToPhenotypicFeatureAssociation", "aggregator_knowledge_source": ["infores:monarchinitiative"], - "has_evidence": ["ECO:0000269"], + "has_evidence": ["ECO:0000304"], "primary_knowledge_source": "infores:hpo-annotations", - "provided_by": "hpoa_disease_mode_of_inheritance_edges", - "publications": ["PMID:15322983"], - "subject": "MONDO:0008050", - "object": "HP:0000006", + "provided_by": "hpoa_disease_phenotype_edges", + "publications": ["OMIM:600334"], + "subject": "MONDO:0010870", + "object": "HP:0003805", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ + "MONDO:0010870", "MONDO:0000001", + "MONDO:0000429", "MONDO:0005071", "MONDO:0020121", - "MONDO:0700223", + "MONDO:0100175", "BFO:0000002", "MONDO:0019952", "BFO:0000017", "BFO:0000020", - "MONDO:0008050", - "MONDO:0016195", + "MONDO:0016191", "BFO:0000016", "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: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", @@ -404,401 +686,760 @@ def association_counts_response(): "nervous system disorder", "obsolete muscular disorder", "myopathy", - "MYH7-related skeletal myopathy", + "tibial muscular dystrophy", + "autosomal dominant distal myopathy", "qualitative or quantitative protein defects in neuromuscular diseases", - "qualitative or quantitative defects of beta-myosin heavy chain (MYH7)", + "qualitative or quantitative defects of titin", "distal myopathy", "neuromuscular disease", "congenital myopathy", "skeletal muscle disorder", "muscular dystrophy", + "TTN-related myopathy", + "autosomal dominant titinopathy", "human disease or disorder", - "hereditary skeletal muscle disorder", ], - "subject_label": "MYH7-related skeletal myopathy", + "subject_label": "tibial muscular dystrophy", "object_namespace": "HP", - "object_category": "biolink:GeneticInheritance", + "object_category": "biolink:PhenotypicQuality", "object_closure": [ "HP:0000001", - "HP:0000006", - "HP:0000005", - "HP:0034345", + "HP:0004303", + "UPHENO:0001001", + "UPHENO:0001005", + "HP:0011805", + "UPHENO:0001002", + "HP:0000118", + "BFO:0000002", + "HP:0025354", + "BFO:0000020", + "HP:0003011", + "UPHENO:0002816", + "UPHENO:0081581", + "HP:0033127", + "UPHENO:0001003", + "UPHENO:0002536", + "UPHENO:0076692", + "UPHENO:0076710", + "BFO:0000001", + "HP:0003805", + "PATO:0000001", + "BFO:0000001", + "BFO:0000002", + "BFO:0000004", + "BFO:0000040", + "UBERON:0001062", + "CARO:0000000", + "CL:0000000", + "UBERON:0000465", + "UBERON:0000383", + "UBERON:0001015", + "UBERON:0018254", + "UBERON:0005090", + "UBERON:0004120", + "CL:0000003", + "UBERON:0000061", + "UBERON:0001630", + "UBERON:0002385", + "CL:0002371", + "UBERON:0010000", + "UBERON:0000467", + "UBERON:0014892", + "UBERON:0002036", + "CL:0000188", + "UBERON:0000479", + "UBERON:0000468", + "UBERON:0000062", + "UBERON:0011216", + "UBERON:0001134", ], "object_closure_label": [ "All (HPO)", - "Mode of inheritance (HPO)", - "Autosomal dominant inheritance (HPO)", - "Mendelian inheritance", - ], - "object_label": "Autosomal dominant inheritance (HPO)", + "Phenotypic abnormality (HPO)", + "Abnormality of the musculature (HPO)", + "Rimmed vacuoles (HPO)", + "Abnormal muscle fiber morphology (HPO)", + "Abnormal skeletal muscle morphology (HPO)", + "Abnormal cellular phenotype (HPO)", + "Abnormality of the musculoskeletal system (HPO)", + "anatomical structure", + "organ", + "musculature of body", + "material anatomical entity", + "anatomical system", + "multicellular organism", + "tissue", + "musculature", + "anatomical entity", + "skeletal muscle tissue", + "muscle organ", + "striated muscle tissue", + "muscle tissue", + "mesoderm-derived structure", + "muscle structure", + "multicellular anatomical structure", + "organ system subdivision", + "skeletal muscle organ", + "skeletal musculature", + ], + "object_label": "Rimmed vacuoles (HPO)", "evidence_count": 4, }, { - "id": "uuid:c2d3e237-212f-11ee-873a-cd90a19c4085", - "original_subject": "OMIM:160900", - "predicate": "biolink:has_mode_of_inheritance", - "category": "biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation", + "id": "uuid:5f90dae3-212f-11ee-873a-cd90a19c4085", + "original_subject": "OMIM:601954", + "predicate": "biolink:has_phenotype", + "category": "biolink:DiseaseToPhenotypicFeatureAssociation", "aggregator_knowledge_source": ["infores:monarchinitiative"], "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", + "provided_by": "hpoa_disease_phenotype_edges", + "publications": ["OMIM:601954"], + "subject": "MONDO:0011170", + "object": "HP:0003805", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ - "MONDO:0004994", - "MONDO:0020158", "MONDO:0000001", - "MONDO:0016107", + "MONDO:0016971", + "MONDO:0000429", "MONDO:0005071", - "MONDO:0005267", "MONDO:0020121", - "MONDO:0005045", - "MONDO:0004995", - "MONDO:0700223", "BFO:0000002", "BFO:0000017", "BFO:0000020", + "MONDO:0006025", "MONDO:0016106", - "MONDO:0005217", - "MONDO:0024573", - "MONDO:0003382", "BFO:0000016", "MONDO:0020120", "MONDO:0019056", - "MONDO:0008056", + "MONDO:0016139", "MONDO:0700096", - "MONDO:0000591", - "MONDO:0024458", + "MONDO:0011170", "MONDO:0005218", "MONDO:0005336", "MONDO:0002081", - "MONDO:0002254", "OGMS:0000031", + "MONDO:0016192", "MONDO:0003847", "MONDO:0003939", - "MONDO:0002022", - "MONDO:0016120", "BFO:0000001", - "MONDO:0000462", - "MONDO:0005328", + "MONDO:0015152", ], "subject_closure_label": [ "disease or disorder", - "eye adnexa disorder", - "intrinsic cardiomyopathy", - "disorder of orbital region", + "autosomal genetic disease", "musculoskeletal 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", - "myotonic dystrophy type 1", + "autosomal recessive disease", + "autosomal recessive limb-girdle muscular dystrophy type 2G", + "autosomal recessive limb-girdle muscular dystrophy", "progressive muscular dystrophy", - "myotonic dystrophy", - "myotonic syndrome", + "qualitative or quantitative protein defects in neuromuscular diseases", + "qualitative or quantitative defects of telethonin", + "limb-girdle muscular dystrophy", "neuromuscular disease", "skeletal muscle disorder", "muscular dystrophy", - "eyelids malposition disorder", - "disorder of visual system", - "familial hypertrophic cardiomyopathy", "human disease or disorder", - "hereditary skeletal muscle disorder", ], - "subject_label": "myotonic dystrophy type 1", + "subject_label": "autosomal recessive limb-girdle muscular dystrophy type 2G", "object_namespace": "HP", - "object_category": "biolink:GeneticInheritance", + "object_category": "biolink:PhenotypicQuality", "object_closure": [ "HP:0000001", - "HP:0000006", - "HP:0000005", - "HP:0034345", + "HP:0004303", + "UPHENO:0001001", + "UPHENO:0001005", + "HP:0011805", + "UPHENO:0001002", + "HP:0000118", + "BFO:0000002", + "HP:0025354", + "BFO:0000020", + "HP:0003011", + "UPHENO:0002816", + "UPHENO:0081581", + "HP:0033127", + "UPHENO:0001003", + "UPHENO:0002536", + "UPHENO:0076692", + "UPHENO:0076710", + "BFO:0000001", + "HP:0003805", + "PATO:0000001", + "BFO:0000001", + "BFO:0000002", + "BFO:0000004", + "BFO:0000040", + "UBERON:0001062", + "CARO:0000000", + "CL:0000000", + "UBERON:0000465", + "UBERON:0000383", + "UBERON:0001015", + "UBERON:0018254", + "UBERON:0005090", + "UBERON:0004120", + "CL:0000003", + "UBERON:0000061", + "UBERON:0001630", + "UBERON:0002385", + "CL:0002371", + "UBERON:0010000", + "UBERON:0000467", + "UBERON:0014892", + "UBERON:0002036", + "CL:0000188", + "UBERON:0000479", + "UBERON:0000468", + "UBERON:0000062", + "UBERON:0011216", + "UBERON:0001134", ], "object_closure_label": [ "All (HPO)", - "Mode of inheritance (HPO)", - "Autosomal dominant inheritance (HPO)", - "Mendelian inheritance", - ], - "object_label": "Autosomal dominant inheritance (HPO)", + "Phenotypic abnormality (HPO)", + "Abnormality of the musculature (HPO)", + "Rimmed vacuoles (HPO)", + "Abnormal muscle fiber morphology (HPO)", + "Abnormal skeletal muscle morphology (HPO)", + "Abnormal cellular phenotype (HPO)", + "Abnormality of the musculoskeletal system (HPO)", + "anatomical structure", + "organ", + "musculature of body", + "material anatomical entity", + "anatomical system", + "multicellular organism", + "tissue", + "musculature", + "anatomical entity", + "skeletal muscle tissue", + "muscle organ", + "striated muscle tissue", + "muscle tissue", + "mesoderm-derived structure", + "muscle structure", + "multicellular anatomical structure", + "organ system subdivision", + "skeletal muscle organ", + "skeletal musculature", + ], + "object_label": "Rimmed vacuoles (HPO)", "evidence_count": 4, }, { - "id": "uuid:c400607b-212f-11ee-873a-cd90a19c4085", - "original_subject": "OMIM:164300", - "predicate": "biolink:has_mode_of_inheritance", - "category": "biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation", + "id": "uuid:63fd8f8b-212f-11ee-873a-cd90a19c4085", + "original_subject": "OMIM:603689", + "predicate": "biolink:has_phenotype", + "category": "biolink:DiseaseToPhenotypicFeatureAssociation", "aggregator_knowledge_source": ["infores:monarchinitiative"], "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", + "provided_by": "hpoa_disease_phenotype_edges", + "publications": ["PMID:22577215"], + "subject": "MONDO:0011362", + "object": "HP:0003805", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ - "MONDO:0020158", "MONDO:0000001", + "MONDO:0016112", + "MONDO:0000429", "MONDO:0005071", "MONDO:0020121", - "MONDO:0700223", - "MONDO:0004746", + "MONDO:0100175", "BFO:0000002", + "MONDO:0019952", "BFO:0000017", "BFO:0000020", "MONDO:0016106", - "MONDO:0003382", + "MONDO:0016191", "BFO:0000016", "MONDO:0020120", "MONDO:0019056", + "MONDO:0100494", + "MONDO:0016139", "MONDO:0700096", - "MONDO:0024458", "MONDO:0005218", "MONDO:0005336", "MONDO:0002081", - "MONDO:0008116", + "MONDO:0000426", + "MONDO:0011362", "OGMS:0000031", "MONDO:0003847", "MONDO:0003939", - "MONDO:0002022", "BFO:0000001", - "MONDO:0000462", - "MONDO:0005328", + "MONDO:0002320", + "MONDO:0016108", + "MONDO:0018949", ], "subject_closure_label": [ "disease or disorder", - "eye adnexa disorder", - "disorder of orbital region", + "autosomal dominant disease", + "autosomal genetic disease", "musculoskeletal system disorder", - "eyelid disorder", + "congenital nervous system disorder", "hereditary disease", "muscle tissue disorder", - "myopathy of extraocular muscle", "nervous system disorder", "obsolete muscular disorder", - "eye disorder", "myopathy", - "oculopharyngeal muscular dystrophy", + "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", - "eyelids malposition disorder", - "disorder of visual system", + "TTN-related myopathy", + "autosomal dominant titinopathy", "human disease or disorder", - "hereditary skeletal muscle disorder", ], - "subject_label": "oculopharyngeal muscular dystrophy", + "subject_label": "myopathy, myofibrillar, 9, with early respiratory failure", "object_namespace": "HP", - "object_category": "biolink:GeneticInheritance", + "object_category": "biolink:PhenotypicQuality", "object_closure": [ "HP:0000001", - "HP:0000006", - "HP:0000005", - "HP:0034345", + "HP:0004303", + "UPHENO:0001001", + "UPHENO:0001005", + "HP:0011805", + "UPHENO:0001002", + "HP:0000118", + "BFO:0000002", + "HP:0025354", + "BFO:0000020", + "HP:0003011", + "UPHENO:0002816", + "UPHENO:0081581", + "HP:0033127", + "UPHENO:0001003", + "UPHENO:0002536", + "UPHENO:0076692", + "UPHENO:0076710", + "BFO:0000001", + "HP:0003805", + "PATO:0000001", + "BFO:0000001", + "BFO:0000002", + "BFO:0000004", + "BFO:0000040", + "UBERON:0001062", + "CARO:0000000", + "CL:0000000", + "UBERON:0000465", + "UBERON:0000383", + "UBERON:0001015", + "UBERON:0018254", + "UBERON:0005090", + "UBERON:0004120", + "CL:0000003", + "UBERON:0000061", + "UBERON:0001630", + "UBERON:0002385", + "CL:0002371", + "UBERON:0010000", + "UBERON:0000467", + "UBERON:0014892", + "UBERON:0002036", + "CL:0000188", + "UBERON:0000479", + "UBERON:0000468", + "UBERON:0000062", + "UBERON:0011216", + "UBERON:0001134", ], "object_closure_label": [ "All (HPO)", - "Mode of inheritance (HPO)", - "Autosomal dominant inheritance (HPO)", - "Mendelian inheritance", - ], - "object_label": "Autosomal dominant inheritance (HPO)", + "Phenotypic abnormality (HPO)", + "Abnormality of the musculature (HPO)", + "Rimmed vacuoles (HPO)", + "Abnormal muscle fiber morphology (HPO)", + "Abnormal skeletal muscle morphology (HPO)", + "Abnormal cellular phenotype (HPO)", + "Abnormality of the musculoskeletal system (HPO)", + "anatomical structure", + "organ", + "musculature of body", + "material anatomical entity", + "anatomical system", + "multicellular organism", + "tissue", + "musculature", + "anatomical entity", + "skeletal muscle tissue", + "muscle organ", + "striated muscle tissue", + "muscle tissue", + "mesoderm-derived structure", + "muscle structure", + "multicellular anatomical structure", + "organ system subdivision", + "skeletal muscle organ", + "skeletal musculature", + ], + "object_label": "Rimmed vacuoles (HPO)", "evidence_count": 4, }, { - "id": "uuid:c3cdaddf-212f-11ee-873a-cd90a19c4085", - "original_subject": "OMIM:254090", - "predicate": "biolink:has_mode_of_inheritance", - "category": "biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation", + "id": "uuid:649c482d-212f-11ee-873a-cd90a19c4085", + "original_subject": "OMIM:604454", + "predicate": "biolink:has_phenotype", + "category": "biolink:DiseaseToPhenotypicFeatureAssociation", "aggregator_knowledge_source": ["infores:monarchinitiative"], - "has_evidence": ["ECO:0000501"], + "has_evidence": ["ECO:0000269"], "primary_knowledge_source": "infores:hpo-annotations", - "provided_by": "hpoa_disease_mode_of_inheritance_edges", - "publications": ["OMIM:254090"], - "subject": "MONDO:0009681", - "object": "HP:0000006", + "provided_by": "hpoa_disease_phenotype_edges", + "publications": ["PMID:23348830"], + "subject": "MONDO:0011466", + "object": "HP:0003805", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ "MONDO:0000001", + "MONDO:0011466", + "MONDO:0000429", "MONDO:0005071", "MONDO:0020121", - "MONDO:0700223", "BFO:0000002", - "MONDO:0019952", "BFO:0000017", "BFO:0000020", - "MONDO:0100225", "BFO:0000016", "MONDO:0020120", "MONDO:0019056", - "MONDO:0016139", "MONDO:0700096", "MONDO:0005218", "MONDO:0005336", "MONDO:0002081", - "MONDO:0009681", + "MONDO:0000426", "OGMS:0000031", "MONDO:0003847", "MONDO:0003939", "BFO:0000001", - "MONDO:0002320", - "MONDO:0000355", - "MONDO:0019950", + "MONDO:0016108", + "MONDO:0018949", ], "subject_closure_label": [ "disease or disorder", - "Ullrich congenital muscular dystrophy", + "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", - "Ullrich congenital muscular dystrophy 1", - "qualitative or quantitative protein defects in neuromuscular diseases", + "distal myopathy, Welander type", + "autosomal dominant distal myopathy", + "distal myopathy", "neuromuscular disease", - "congenital muscular dystrophy", - "congenital myopathy", "skeletal muscle disorder", "muscular dystrophy", - "collagen 6-related myopathy", "human disease or disorder", - "hereditary skeletal muscle disorder", ], - "subject_label": "Ullrich congenital muscular dystrophy 1", + "subject_label": "distal myopathy, Welander type", "object_namespace": "HP", - "object_category": "biolink:GeneticInheritance", + "object_category": "biolink:PhenotypicQuality", "object_closure": [ "HP:0000001", - "HP:0000006", - "HP:0000005", - "HP:0034345", + "HP:0004303", + "UPHENO:0001001", + "UPHENO:0001005", + "HP:0011805", + "UPHENO:0001002", + "HP:0000118", + "BFO:0000002", + "HP:0025354", + "BFO:0000020", + "HP:0003011", + "UPHENO:0002816", + "UPHENO:0081581", + "HP:0033127", + "UPHENO:0001003", + "UPHENO:0002536", + "UPHENO:0076692", + "UPHENO:0076710", + "BFO:0000001", + "HP:0003805", + "PATO:0000001", + "BFO:0000001", + "BFO:0000002", + "BFO:0000004", + "BFO:0000040", + "UBERON:0001062", + "CARO:0000000", + "CL:0000000", + "UBERON:0000465", + "UBERON:0000383", + "UBERON:0001015", + "UBERON:0018254", + "UBERON:0005090", + "UBERON:0004120", + "CL:0000003", + "UBERON:0000061", + "UBERON:0001630", + "UBERON:0002385", + "CL:0002371", + "UBERON:0010000", + "UBERON:0000467", + "UBERON:0014892", + "UBERON:0002036", + "CL:0000188", + "UBERON:0000479", + "UBERON:0000468", + "UBERON:0000062", + "UBERON:0011216", + "UBERON:0001134", ], "object_closure_label": [ "All (HPO)", - "Mode of inheritance (HPO)", - "Autosomal dominant inheritance (HPO)", - "Mendelian inheritance", - ], - "object_label": "Autosomal dominant inheritance (HPO)", + "Phenotypic abnormality (HPO)", + "Abnormality of the musculature (HPO)", + "Rimmed vacuoles (HPO)", + "Abnormal muscle fiber morphology (HPO)", + "Abnormal skeletal muscle morphology (HPO)", + "Abnormal cellular phenotype (HPO)", + "Abnormality of the musculoskeletal system (HPO)", + "anatomical structure", + "organ", + "musculature of body", + "material anatomical entity", + "anatomical system", + "multicellular organism", + "tissue", + "musculature", + "anatomical entity", + "skeletal muscle tissue", + "muscle organ", + "striated muscle tissue", + "muscle tissue", + "mesoderm-derived structure", + "muscle structure", + "multicellular anatomical structure", + "organ system subdivision", + "skeletal muscle organ", + "skeletal musculature", + ], + "object_label": "Rimmed vacuoles (HPO)", "evidence_count": 4, }, { - "id": "uuid:c275a020-212f-11ee-873a-cd90a19c4085", - 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"MONDO:0700223", + "MONDO:0021166", + "MONDO:0024322", "BFO:0000002", + "MONDO:0016200", "BFO:0000017", "BFO:0000020", + "MONDO:0100241", + "MONDO:0006025", + "MONDO:0007827", + "MONDO:0011603", "BFO:0000016", "MONDO:0020120", "MONDO:0019056", + "MONDO:0016139", "MONDO:0700096", "MONDO:0005218", "MONDO:0005336", + "MONDO:0009332", "MONDO:0002081", + "MONDO:0021167", + "MONDO:0016109", + "MONDO:0018795", + "MONDO:0017749", + "MONDO:0002049", "OGMS:0000031", "MONDO:0003847", "MONDO:0003939", + "MONDO:0015286", "BFO:0000001", - "MONDO:0010676", + "MONDO:0002320", + "MONDO:0019052", + "MONDO:0005066", + "MONDO:0018949", ], "subject_closure_label": [ "disease or disorder", + "autosomal genetic disease", + "thrombocytopenia", "musculoskeletal system disorder", + "blood platelet disease", + "congenital nervous system disorder", "hereditary disease", "muscle tissue disorder", + "metabolic disease", "nervous system disorder", "obsolete muscular disorder", "myopathy", - "muscular dystrophy, Hemizygous lethal type", + "hematologic disorder", + "autosomal recessive disease", + "inclusion body myositis", + "congenital hematological disorder", + "GNE myopathy", + "congenital disorder of glycosylation", + "autosomal recessive distal myopathy", + "hereditary inclusion-body myopathy", + "qualitative or quantitative protein defects in neuromuscular diseases", + "qualitative or quantitative defects of glucosamine (UDP-N-acetyl)-2-epimerase/N-acetylmannosamine kinase", + "disorder of multiple glycosylation", + "syndromic constitutional thrombocytopenia", + "distal myopathy", + "inborn errors of metabolism", "neuromuscular disease", "skeletal muscle disorder", "muscular dystrophy", + "inflammatory disease", + "myositis disease", + "disorder of glycosylation", + "inherited thrombocytopenia", "human disease or disorder", - "hereditary skeletal muscle disorder", ], - "subject_label": "muscular dystrophy, Hemizygous lethal type", + "subject_label": "GNE myopathy", "object_namespace": "HP", - "object_category": "biolink:GeneticInheritance", + "object_category": "biolink:PhenotypicQuality", "object_closure": [ "HP:0000001", - "HP:0000006", - "HP:0000005", - "HP:0034345", + "HP:0004303", + "UPHENO:0001001", + "UPHENO:0001005", + "HP:0011805", + "UPHENO:0001002", + "HP:0000118", + "BFO:0000002", + "HP:0025354", + "BFO:0000020", + "HP:0003011", + "UPHENO:0002816", + "UPHENO:0081581", + "HP:0033127", + "UPHENO:0001003", + "UPHENO:0002536", + "UPHENO:0076692", + "UPHENO:0076710", + "BFO:0000001", + "HP:0003805", + "PATO:0000001", + "BFO:0000001", + "BFO:0000002", + "BFO:0000004", + "BFO:0000040", + "UBERON:0001062", + "CARO:0000000", + "CL:0000000", + "UBERON:0000465", + "UBERON:0000383", + "UBERON:0001015", + "UBERON:0018254", + "UBERON:0005090", + "UBERON:0004120", + "CL:0000003", + "UBERON:0000061", + "UBERON:0001630", + "UBERON:0002385", + "CL:0002371", + "UBERON:0010000", + "UBERON:0000467", + "UBERON:0014892", + "UBERON:0002036", + "CL:0000188", + "UBERON:0000479", + "UBERON:0000468", + "UBERON:0000062", + "UBERON:0011216", + "UBERON:0001134", ], "object_closure_label": [ "All (HPO)", - "Mode of inheritance (HPO)", - "Autosomal dominant inheritance (HPO)", - "Mendelian inheritance", - ], - "object_label": "Autosomal dominant inheritance (HPO)", + "Phenotypic abnormality (HPO)", + "Abnormality of the musculature (HPO)", + "Rimmed vacuoles (HPO)", + "Abnormal muscle fiber morphology (HPO)", + "Abnormal skeletal muscle morphology (HPO)", + "Abnormal cellular phenotype (HPO)", + "Abnormality of the musculoskeletal system (HPO)", + "anatomical structure", + "organ", + "musculature of body", + "material anatomical entity", + "anatomical system", + "multicellular organism", + "tissue", + "musculature", + "anatomical entity", + "skeletal muscle tissue", + "muscle organ", + "striated muscle tissue", + "muscle tissue", + "mesoderm-derived structure", + "muscle structure", + "multicellular anatomical structure", + "organ system subdivision", + "skeletal muscle organ", + "skeletal musculature", + ], + "object_label": "Rimmed vacuoles (HPO)", "evidence_count": 4, }, { - "id": "uuid:c336741f-212f-11ee-873a-cd90a19c4085", - "original_subject": "OMIM:600334", - "predicate": "biolink:has_mode_of_inheritance", - "category": "biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation", + "id": "uuid:60cdba46-212f-11ee-873a-cd90a19c4085", + "original_subject": "OMIM:608423", + "predicate": "biolink:has_phenotype", + "category": "biolink:DiseaseToPhenotypicFeatureAssociation", "aggregator_knowledge_source": ["infores:monarchinitiative"], - "has_evidence": ["ECO:0000501"], + "has_evidence": ["ECO:0000269"], "primary_knowledge_source": "infores:hpo-annotations", - "provided_by": "hpoa_disease_mode_of_inheritance_edges", - "publications": ["OMIM:600334"], - "subject": "MONDO:0010870", - "object": "HP:0000006", + "provided_by": "hpoa_disease_phenotype_edges", + "publications": ["PMID:23543484"], + "subject": "MONDO:0012034", + "object": "HP:0003805", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ - "MONDO:0010870", "MONDO:0000001", + "MONDO:0016971", "MONDO:0000429", "MONDO:0005071", "MONDO:0020121", - "MONDO:0100175", - "MONDO:0700223", + "MONDO:0012034", "BFO:0000002", - "MONDO:0019952", "BFO:0000017", "BFO:0000020", - "MONDO:0016191", + "MONDO:0016106", "BFO:0000016", "MONDO:0020120", "MONDO:0019056", - "MONDO:0100494", - "MONDO:0016139", + "MONDO:0015151", "MONDO:0700096", "MONDO:0005218", "MONDO:0005336", @@ -808,933 +1449,1832 @@ def association_counts_response(): "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", - "tibial muscular dystrophy", - "autosomal dominant distal myopathy", - "qualitative or quantitative protein defects in neuromuscular diseases", - "qualitative or quantitative defects of titin", - "distal myopathy", + "autosomal dominant limb-girdle muscular dystrophy type 1F", + "muscular dystrophy, limb-girdle, autosomal dominant", + "progressive muscular dystrophy", + "limb-girdle muscular dystrophy", "neuromuscular disease", - "congenital myopathy", "skeletal muscle disorder", "muscular dystrophy", - "TTN-related myopathy", - "autosomal dominant titinopathy", "human disease or disorder", - "hereditary skeletal muscle disorder", ], - "subject_label": "tibial muscular dystrophy", + "subject_label": "autosomal dominant limb-girdle muscular dystrophy type 1F", "object_namespace": "HP", - "object_category": "biolink:GeneticInheritance", + "object_category": "biolink:PhenotypicQuality", "object_closure": [ "HP:0000001", - "HP:0000006", - "HP:0000005", - "HP:0034345", + "HP:0004303", + "UPHENO:0001001", + "UPHENO:0001005", + "HP:0011805", + "UPHENO:0001002", + "HP:0000118", + "BFO:0000002", + "HP:0025354", + "BFO:0000020", + "HP:0003011", + "UPHENO:0002816", + "UPHENO:0081581", + "HP:0033127", + "UPHENO:0001003", + "UPHENO:0002536", + "UPHENO:0076692", + "UPHENO:0076710", + "BFO:0000001", + "HP:0003805", + "PATO:0000001", + "BFO:0000001", + "BFO:0000002", + "BFO:0000004", + "BFO:0000040", + "UBERON:0001062", + "CARO:0000000", + "CL:0000000", + "UBERON:0000465", + "UBERON:0000383", + "UBERON:0001015", + "UBERON:0018254", + "UBERON:0005090", + "UBERON:0004120", + "CL:0000003", + "UBERON:0000061", + "UBERON:0001630", + "UBERON:0002385", + "CL:0002371", + "UBERON:0010000", + "UBERON:0000467", + "UBERON:0014892", + "UBERON:0002036", + "CL:0000188", + "UBERON:0000479", + "UBERON:0000468", + "UBERON:0000062", + "UBERON:0011216", + "UBERON:0001134", ], "object_closure_label": [ "All (HPO)", - "Mode of inheritance (HPO)", - "Autosomal dominant inheritance (HPO)", - "Mendelian inheritance", - ], - "object_label": "Autosomal dominant inheritance (HPO)", + "Phenotypic abnormality (HPO)", + "Abnormality of the musculature (HPO)", + "Rimmed vacuoles (HPO)", + "Abnormal muscle fiber morphology (HPO)", + "Abnormal skeletal muscle morphology (HPO)", + "Abnormal cellular phenotype (HPO)", + "Abnormality of the musculoskeletal system (HPO)", + "anatomical structure", + "organ", + "musculature of body", + "material anatomical entity", + "anatomical system", + "multicellular organism", + "tissue", + "musculature", + "anatomical entity", + "skeletal muscle tissue", + "muscle organ", + "striated muscle tissue", + "muscle tissue", + "mesoderm-derived structure", + "muscle structure", + "multicellular anatomical structure", + "organ system subdivision", + "skeletal muscle organ", + "skeletal musculature", + ], + "object_label": "Rimmed vacuoles (HPO)", "evidence_count": 4, }, { - "id": "uuid:c275a16e-212f-11ee-873a-cd90a19c4085", - "original_subject": "OMIM:600638", - "predicate": "biolink:has_mode_of_inheritance", - "category": "biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation", + "id": "uuid:62f7ecd4-212f-11ee-873a-cd90a19c4085", + "original_subject": "OMIM:609115", + "predicate": "biolink:has_phenotype", + "category": "biolink:DiseaseToPhenotypicFeatureAssociation", "aggregator_knowledge_source": ["infores:monarchinitiative"], - "has_evidence": ["ECO:0000269"], + "has_evidence": ["ECO:0000304"], "primary_knowledge_source": "infores:hpo-annotations", - "provided_by": "hpoa_disease_mode_of_inheritance_edges", - "publications": ["PMID:20074521"], - "subject": "MONDO:0010912", - "object": "HP:0000006", + "provided_by": "hpoa_disease_phenotype_edges", + "publications": ["OMIM:609115"], + "subject": "MONDO:0012193", + "object": "HP:0003805", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ - "MONDO:0020158", "MONDO:0000001", - "MONDO:0007614", + "MONDO:0016971", + "MONDO:0000429", "MONDO:0005071", "MONDO:0020121", - "MONDO:0700223", - "MONDO:0004746", "BFO:0000002", - "MONDO:0957003", "BFO:0000017", "BFO:0000020", "MONDO:0016106", - "MONDO:0003382", "BFO:0000016", "MONDO:0020120", "MONDO:0019056", - "MONDO:0003569", + "MONDO:0015151", "MONDO:0700096", - "MONDO:0001584", - "MONDO:0024458", "MONDO:0005218", "MONDO:0005336", "MONDO:0002081", - "MONDO:0100153", + "MONDO:0012193", + "MONDO:0000426", "OGMS:0000031", "MONDO:0003847", - "MONDO:0100154", "MONDO:0003939", - "MONDO:0002022", - "MONDO:0015368", "BFO:0000001", - "MONDO:0000462", - "MONDO:0005328", - "MONDO:0010912", ], "subject_closure_label": [ "disease or disorder", - "eye adnexa disorder", - "ocular motility disease", - "disorder of orbital region", + "autosomal dominant disease", + "autosomal genetic disease", "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", - "congenital fibrosis of extraocular muscles", - "fibrosis of extraocular muscles, congenital, 3A, with or without extraocular involvement", - "neuro-ophthalmological disease", + "autosomal dominant limb-girdle muscular dystrophy type 1G", + "muscular dystrophy, limb-girdle, autosomal dominant", "progressive muscular dystrophy", + "limb-girdle muscular dystrophy", "neuromuscular disease", "skeletal muscle disorder", "muscular dystrophy", - "eyelids malposition disorder", - "disorder of visual system", - "tubulinopathy", - "TUBB3-related tubulinopathy", "human disease or disorder", - "hereditary skeletal muscle disorder", - "hereditary neuro-ophthalmological disease", ], - "subject_label": "fibrosis of extraocular muscles, congenital, 3A, with or without extraocular involvement", + "subject_label": "autosomal dominant limb-girdle muscular dystrophy type 1G", "object_namespace": "HP", - "object_category": "biolink:GeneticInheritance", + "object_category": "biolink:PhenotypicQuality", "object_closure": [ "HP:0000001", - "HP:0000006", - "HP:0000005", - "HP:0034345", + "HP:0004303", + "UPHENO:0001001", + "UPHENO:0001005", + "HP:0011805", + "UPHENO:0001002", + "HP:0000118", + "BFO:0000002", + "HP:0025354", + "BFO:0000020", + "HP:0003011", + "UPHENO:0002816", + "UPHENO:0081581", + "HP:0033127", + "UPHENO:0001003", + "UPHENO:0002536", + "UPHENO:0076692", + "UPHENO:0076710", + "BFO:0000001", + "HP:0003805", + "PATO:0000001", + "BFO:0000001", + "BFO:0000002", + "BFO:0000004", + "BFO:0000040", + "UBERON:0001062", + "CARO:0000000", + "CL:0000000", + "UBERON:0000465", + "UBERON:0000383", + "UBERON:0001015", + "UBERON:0018254", + "UBERON:0005090", + "UBERON:0004120", + "CL:0000003", + "UBERON:0000061", + "UBERON:0001630", + "UBERON:0002385", + "CL:0002371", + "UBERON:0010000", + "UBERON:0000467", + "UBERON:0014892", + "UBERON:0002036", + "CL:0000188", + "UBERON:0000479", + "UBERON:0000468", + "UBERON:0000062", + "UBERON:0011216", + "UBERON:0001134", ], "object_closure_label": [ "All (HPO)", - "Mode of inheritance (HPO)", - "Autosomal dominant inheritance (HPO)", - "Mendelian inheritance", - ], - "object_label": "Autosomal dominant inheritance (HPO)", + "Phenotypic abnormality (HPO)", + "Abnormality of the musculature (HPO)", + "Rimmed vacuoles (HPO)", + "Abnormal muscle fiber morphology (HPO)", + "Abnormal skeletal muscle morphology (HPO)", + "Abnormal cellular phenotype (HPO)", + "Abnormality of the musculoskeletal system (HPO)", + "anatomical structure", + "organ", + "musculature of body", + "material anatomical entity", + "anatomical system", + "multicellular organism", + "tissue", + "musculature", + "anatomical entity", + "skeletal muscle tissue", + "muscle organ", + "striated muscle tissue", + "muscle tissue", + "mesoderm-derived structure", + "muscle structure", + "multicellular anatomical structure", + "organ system subdivision", + "skeletal muscle organ", + "skeletal musculature", + ], + "object_label": "Rimmed vacuoles (HPO)", "evidence_count": 4, }, { - "id": "uuid:c367df60-212f-11ee-873a-cd90a19c4085", - 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"Mode of inheritance (HPO)", - "Autosomal dominant inheritance (HPO)", - "Mendelian inheritance", - ], - "object_label": "Autosomal dominant inheritance (HPO)", + "Phenotypic abnormality (HPO)", + "Abnormality of head or neck (HPO)", + "Abnormality of the head (HPO)", + "Abnormality of the skin (HPO)", + "Atypical scarring of skin (HPO)", + "Abnormality of the integument (HPO)", + "Abnormal hair morphology (HPO)", + "Alopecia (HPO)", + "Abnormal scalp morphology (HPO)", + "Alopecia of scalp (HPO)", + "Abnormality of connective tissue (HPO)", + "Scarring alopecia of scalp (HPO)", + "Abnormality of skin morphology (HPO)", + "Abnormality of skin adnexa morphology (HPO)", + "Localized skin lesion (HPO)", + "Abnormal hair quantity (HPO)", + "Abnormality of the musculoskeletal system (HPO)", + "Abnormality of the scalp hair (HPO)", + "Scarring (HPO)", + "cutaneous appendage", + "head", + "anatomical structure", + "organ", + "organ subunit", + "organ part", + "anterior region of body", + "scalp", + "material anatomical entity", + "anatomical system", + "multicellular organism", + "organism subdivision", + "tissue", + "epithelium", + "skin epidermis", + "strand of hair", + "anatomical entity", + "skin of body", + "integument", + "connective tissue", + "integumental system", + "surface structure", + "ectoderm-derived structure", + "anatomical projection", + "integumentary adnexa", + "outer epithelium", + "craniocervical region", + "multicellular anatomical structure", + "structure with developmental contribution from neural crest", + "ecto-epithelium", + "organ system subdivision", + "subdivision of organism along main body axis", + "pilosebaceous unit", + "main body axis", + "body proper", + "integumentary projection", + "hair of head", + "morphological feature", + "multi organ part structure", + "external integument structure", + ], + "object_label": "Scarring alopecia of scalp (HPO)", "evidence_count": 4, }, { - "id": "uuid:c304ba49-212f-11ee-873a-cd90a19c4085", - "original_subject": "OMIM:609452", - "predicate": "biolink:has_mode_of_inheritance", - "category": "biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation", + "id": "uuid:62c348df-212f-11ee-873a-cd90a19c4085", + "original_subject": "OMIM:310300", + "predicate": "biolink:has_phenotype", + "category": "biolink:DiseaseToPhenotypicFeatureAssociation", "aggregator_knowledge_source": ["infores:monarchinitiative"], "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", + "provided_by": "hpoa_disease_phenotype_edges", + "publications": ["OMIM:310300"], + "subject": "MONDO:0010680", + "object": "HP:0004631", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ + "MONDO:0004994", "MONDO:0000001", - "MONDO:0016186", - "MONDO:0000429", + "MONDO:0010680", "MONDO:0005071", + "MONDO:0005267", "MONDO:0020121", - "MONDO:0018943", - "MONDO:0700223", + "MONDO:0004995", + "MONDO:0016196", "BFO:0000002", - "MONDO:0019952", - "MONDO:0016190", "BFO:0000017", "BFO:0000020", + "MONDO:0016106", + "MONDO:0005217", "BFO:0000016", "MONDO:0020120", "MONDO:0019056", "MONDO:0016139", "MONDO:0700096", - "MONDO:0002921", + "MONDO:0000591", "MONDO:0005218", "MONDO:0005336", "MONDO:0002081", - "MONDO:0000426", + "MONDO:0016333", + "MONDO:0016830", "OGMS:0000031", + "MONDO:0000425", + "MONDO:0005021", + "MONDO:0021106", "MONDO:0003847", "MONDO:0003939", - "MONDO:0012277", "BFO:0000001", - "MONDO:0002320", - "MONDO:0016108", - "MONDO:0018949", + "MONDO:0020606", ], "subject_closure_label": [ "disease or disorder", - "autosomal dominant disease", - "autosomal genetic disease", + "X-linked disease", + "intrinsic cardiomyopathy", "musculoskeletal system disorder", - "congenital nervous system disorder", - "congenital structural myopathy", "hereditary disease", "muscle tissue disorder", + "cardiomyopathy", + "cardiovascular disorder", + "dilated cardiomyopathy", "nervous system disorder", + "familial cardiomyopathy", "obsolete muscular disorder", + "heart disorder", "myopathy", - "myofibrillar myopathy 4", - "autosomal dominant distal myopathy", + "X-linked Emery-Dreifuss muscular dystrophy", + "progressive muscular dystrophy", "qualitative or quantitative protein defects in neuromuscular diseases", - "qualitative or quantitative defects of myofibrillar proteins", - "qualitative or quantitative defects of protein ZASP", - "myofibrillar myopathy", - "distal myopathy", + "qualitative or quantitative defects of emerin", + "familial dilated cardiomyopathy", + "Emery-Dreifuss muscular dystrophy", "neuromuscular disease", - "congenital myopathy", "skeletal muscle disorder", "muscular dystrophy", + "sex-linked disease", + "laminopathy", "human disease or disorder", - "hereditary skeletal muscle disorder", ], - "subject_label": "myofibrillar myopathy 4", + "subject_label": "X-linked Emery-Dreifuss muscular dystrophy", "object_namespace": "HP", - "object_category": "biolink:GeneticInheritance", + "object_category": "biolink:PhenotypicQuality", "object_closure": [ "HP:0000001", - "HP:0000006", - "HP:0000005", - "HP:0034345", + "UPHENO:0082875", + "UPHENO:0046505", + "UPHENO:0075696", + "UPHENO:0068971", + "UPHENO:0001001", + "HP:0001371", + "HP:0003549", + "HP:0011729", + "UPHENO:0076703", + "HP:0100261", + "UPHENO:0001005", + "HP:0011842", + "HP:0011805", + "UPHENO:0001002", + "HP:0004631", + "HP:0034430", + "HP:0000924", + "HP:0000118", + "BFO:0000002", + "HP:0034392", + "UPHENO:0021425", + "BFO:0000020", + "UPHENO:0075195", + "HP:0003011", + "UPHENO:0002816", + "UPHENO:0002332", + "UPHENO:0015280", + "UPHENO:0002964", + "UPHENO:0081581", + "HP:0033127", + "UPHENO:0001003", + "UPHENO:0002536", + "UPHENO:0046759", + "UPHENO:0020584", + "UPHENO:0031839", + "UPHENO:0076692", + "UPHENO:0081440", + "UPHENO:0076710", + "UPHENO:0002712", + "BFO:0000001", + "PATO:0000001", + "UPHENO:0012541", + "HP:0011843", + "BFO:0000001", + "BFO:0000002", + "BFO:0000004", + "BFO:0000040", + "UBERON:0001062", + "CARO:0000000", + "UBERON:0000465", + "UBERON:0000383", + "UBERON:0001015", + "UBERON:0007845", + "UBERON:0002204", + "UBERON:0005090", + "UBERON:0000061", + "UBERON:0034925", + "UBERON:0007846", + "UBERON:0001630", + "UBERON:0010000", + "UBERON:0000467", + "UBERON:0004770", + "UBERON:0000043", + "UBERON:0000479", + "UBERON:0000468", + "UBERON:0000062", + "UBERON:0011216", + "UBERON:0034921", + "UBERON:0002384", + "UBERON:0004905", + "UBERON:0001434", + "UBERON:0011823", + "UBERON:0000982", ], "object_closure_label": [ "All (HPO)", - "Mode of inheritance (HPO)", - "Autosomal dominant inheritance (HPO)", - "Mendelian inheritance", - ], - "object_label": "Autosomal dominant inheritance (HPO)", + "Phenotypic abnormality (HPO)", + "Abnormality of the skeletal system (HPO)", + "Flexion contracture (HPO)", + "Abnormality of the musculature (HPO)", + "Abnormality of connective tissue (HPO)", + "Decreased cervical spine flexion due to contractures of posterior cervical muscles (HPO)", + "Abnormality of joint mobility (HPO)", + "Abnormal skeletal muscle morphology (HPO)", + "Abnormal skeletal morphology (HPO)", + "Abnormality of musculoskeletal physiology (HPO)", + "Abnormality of the musculoskeletal system (HPO)", + "Joint contracture", + "Abnormal joint physiology", + "Abnormal tendon morphology (HPO)", + "tendon", + "anatomical structure", + "organ", + "musculature of body", + "material anatomical entity", + "anatomical system", + "multicellular organism", + "tissue", + "skeletal joint", + "musculature", + "anatomical entity", + "skeletal system", + "muscle organ", + "musculoskeletal system", + "connective tissue", + "articular system", + "articulation", + "muscle structure", + "regular connective tissue", + "dense regular connective tissue", + "multicellular anatomical structure", + "organ system subdivision", + "dense connective tissue", + "multi organ part structure", + "anatomical collection", + ], + "object_label": "Decreased cervical spine flexion due to contractures of posterior cervical muscles (HPO)", "evidence_count": 4, }, ], @@ -1742,7 +3282,7 @@ def association_counts_response(): "facet_counts": { "facet_fields": {}, "facet_queries": { - '(category:"biolink:DiseaseToPhenotypicFeatureAssociation") AND (subject:"MONDO:0020121" OR subject_closure:"MONDO:0020121")': 4011, + '(category:"biolink:DiseaseToPhenotypicFeatureAssociation") AND (subject:"MONDO:0020121" OR subject_closure:"MONDO:0020121")': 4312, '(category:"biolink:GeneToPhenotypicFeatureAssociation") AND (subject:"MONDO:0020121" OR subject_closure:"MONDO:0020121")': 0, '(category:"biolink:PairwiseGeneToGeneInteraction") AND (subject:"MONDO:0020121" OR subject_closure:"MONDO:0020121")': 0, '(category:"biolink:GeneToPathwayAssociation") AND (subject:"MONDO:0020121" OR subject_closure:"MONDO:0020121")': 0, @@ -1760,8 +3300,8 @@ def association_counts_response(): '(category:"biolink:GeneToGeneHomologyAssociation") AND (object:"MONDO:0020121" OR object_closure:"MONDO:0020121")': 0, '(category:"biolink:ChemicalToPathwayAssociation") AND (object:"MONDO:0020121" OR object_closure:"MONDO:0020121")': 0, '(category:"biolink:MacromolecularMachineToMolecularActivityAssociation") AND (object:"MONDO:0020121" OR object_closure:"MONDO:0020121")': 0, - '(category:"biolink:CausalGeneToDiseaseAssociation") AND (object:"MONDO:0020121" OR object_closure:"MONDO:0020121")': 121, - '(category:"biolink:CorrelatedGeneToDiseaseAssociation") AND (object:"MONDO:0020121" OR object_closure:"MONDO:0020121")': 147, + '(category:"biolink:CausalGeneToDiseaseAssociation") AND (object:"MONDO:0020121" OR object_closure:"MONDO:0020121")': 123, + '(category:"biolink:CorrelatedGeneToDiseaseAssociation") AND (object:"MONDO:0020121" OR object_closure:"MONDO:0020121")': 149, }, }, } diff --git a/backend/tests/fixtures/association_response.py b/backend/tests/fixtures/association_response.py index 6a8c4839e..7dbe1b6a9 100644 --- a/backend/tests/fixtures/association_response.py +++ b/backend/tests/fixtures/association_response.py @@ -18,35 +18,37 @@ def association_response(): }, }, "response": { - "num_found": 4806, + "num_found": 5124, "start": 0, "docs": [ { - "id": "uuid:c2a45bf5-212f-11ee-873a-cd90a19c4085", - "original_subject": "OMIM:158800", - "predicate": "biolink:has_mode_of_inheritance", - "category": "biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation", + "id": "uuid:628f39f7-212f-11ee-873a-cd90a19c4085", + "original_subject": "OMIM:160500", + "predicate": "biolink:has_phenotype", + "category": "biolink:DiseaseToPhenotypicFeatureAssociation", "aggregator_knowledge_source": ["infores:monarchinitiative"], "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", + "provided_by": "hpoa_disease_phenotype_edges", + "publications": ["OMIM:160500"], + "subject": "MONDO:0008050", + "object": "HP:0003803", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ "MONDO:0000001", "MONDO:0005071", "MONDO:0020121", - "MONDO:0008028", - "MONDO:0700223", "BFO:0000002", + "MONDO:0019952", "BFO:0000017", "BFO:0000020", + "MONDO:0008050", + "MONDO:0016195", "BFO:0000016", "MONDO:0020120", "MONDO:0019056", + "MONDO:0016139", "MONDO:0700096", "MONDO:0005218", "MONDO:0005336", @@ -55,326 +57,606 @@ 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, Barnes type", + "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", "human disease or disorder", - "hereditary skeletal muscle disorder", ], - "subject_label": "muscular dystrophy, Barnes type", + "subject_label": "MYH7-related skeletal myopathy", "object_namespace": "HP", - "object_category": "biolink:GeneticInheritance", + "object_category": "biolink:PhenotypicQuality", "object_closure": [ "HP:0000001", - "HP:0000006", - "HP:0000005", - "HP:0034345", + "HP:0004303", + "UPHENO:0001001", + "HP:0003803", + "HP:0033684", + "UPHENO:0001005", + "HP:0011805", + "UPHENO:0001002", + "HP:0000118", + "BFO:0000002", + "HP:0025354", + "BFO:0000020", + "HP:0003011", + "UPHENO:0002816", + "UPHENO:0081581", + "HP:0033127", + "UPHENO:0001003", + "UPHENO:0002536", + "UPHENO:0076692", + "UPHENO:0076710", + "BFO:0000001", + "PATO:0000001", + "BFO:0000001", + "BFO:0000002", + "BFO:0000004", + "BFO:0000040", + "UBERON:0001062", + "CARO:0000000", + "CL:0000000", + "UBERON:0000465", + "UBERON:0000383", + "UBERON:0001015", + "UBERON:0018254", + "UBERON:0005090", + "UBERON:0004120", + "CL:0000003", + "UBERON:0000061", + "UBERON:0001630", + "UBERON:0002385", + "CL:0002371", + "UBERON:0010000", + "UBERON:0000467", + "UBERON:0014892", + "UBERON:0002036", + "CL:0000188", + "UBERON:0000479", + "UBERON:0000468", + "UBERON:0000062", + "UBERON:0011216", + "UBERON:0001134", ], "object_closure_label": [ "All (HPO)", - "Mode of inheritance (HPO)", - "Autosomal dominant inheritance (HPO)", - "Mendelian inheritance", - ], - "object_label": "Autosomal dominant inheritance (HPO)", + "Phenotypic abnormality (HPO)", + "Abnormality of the musculature (HPO)", + "Type 1 muscle fiber predominance (HPO)", + "Abnormal muscle fiber morphology (HPO)", + "Abnormal skeletal muscle morphology (HPO)", + "Abnormal cellular phenotype (HPO)", + "Abnormality of the musculoskeletal system (HPO)", + "Abnormal muscle fiber-type distribution (HPO)", + "anatomical structure", + "organ", + "musculature of body", + "material anatomical entity", + "anatomical system", + "multicellular organism", + "tissue", + "musculature", + "anatomical entity", + "skeletal muscle tissue", + "muscle organ", + "striated muscle tissue", + "muscle tissue", + "mesoderm-derived structure", + "muscle structure", + "multicellular anatomical structure", + "organ system subdivision", + "skeletal muscle organ", + "skeletal musculature", + ], + "object_label": "Type 1 muscle fiber predominance (HPO)", "evidence_count": 4, }, { - "id": "uuid:c304bcf2-212f-11ee-873a-cd90a19c4085", - "original_subject": "OMIM:158900", - "predicate": "biolink:has_mode_of_inheritance", - "category": "biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation", + "id": "uuid:64b68436-212f-11ee-873a-cd90a19c4085", + "original_subject": "OMIM:254090", + "predicate": "biolink:has_phenotype", + "category": "biolink:DiseaseToPhenotypicFeatureAssociation", "aggregator_knowledge_source": ["infores:monarchinitiative"], "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", + "provided_by": "hpoa_disease_phenotype_edges", + "publications": ["OMIM:254090"], + "subject": "MONDO:0009681", + "object": "HP:0003803", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ - "MONDO:0008030", "MONDO:0000001", - "MONDO:0019303", "MONDO:0005071", "MONDO:0020121", - "MONDO:0700223", - "MONDO:0001347", "BFO:0000002", "BFO:0000017", "BFO:0000020", - "MONDO:0016106", - "MONDO:0100137", + "MONDO:0100225", "BFO:0000016", "MONDO:0020120", "MONDO:0019056", + "MONDO:0016139", "MONDO:0700096", "MONDO:0005218", "MONDO:0005336", "MONDO:0002081", - "MONDO:0021147", + "MONDO:0009681", "OGMS:0000031", "MONDO:0003847", "MONDO:0003939", "BFO:0000001", + "MONDO:0002320", + "MONDO:0000355", + "MONDO:0019950", ], "subject_closure_label": [ "disease or disorder", - "facioscapulohumeral muscular dystrophy", + "Ullrich congenital muscular dystrophy", "musculoskeletal system disorder", + "congenital nervous system disorder", "hereditary disease", "muscle tissue disorder", "nervous system disorder", "obsolete muscular disorder", "myopathy", - "facioscapulohumeral muscular dystrophy 1", - "progressive muscular dystrophy", + "Ullrich congenital muscular dystrophy 1", + "qualitative or quantitative protein defects in neuromuscular diseases", "neuromuscular disease", - "premature aging syndrome", + "congenital muscular dystrophy", "skeletal muscle disorder", "muscular dystrophy", - "disorder of development or morphogenesis", - "telomere syndrome", + "collagen 6-related myopathy", "human disease or disorder", - "hereditary skeletal muscle disorder", ], - "subject_label": "facioscapulohumeral muscular dystrophy 1", + "subject_label": "Ullrich congenital muscular dystrophy 1", "object_namespace": "HP", - "object_category": "biolink:GeneticInheritance", + "object_category": "biolink:PhenotypicQuality", "object_closure": [ "HP:0000001", - "HP:0000006", - "HP:0000005", - "HP:0034345", + "HP:0004303", + "UPHENO:0001001", + "HP:0003803", + "HP:0033684", + "UPHENO:0001005", + "HP:0011805", + "UPHENO:0001002", + "HP:0000118", + "BFO:0000002", + "HP:0025354", + "BFO:0000020", + "HP:0003011", + "UPHENO:0002816", + "UPHENO:0081581", + "HP:0033127", + "UPHENO:0001003", + "UPHENO:0002536", + "UPHENO:0076692", + "UPHENO:0076710", + "BFO:0000001", + "PATO:0000001", + "BFO:0000001", + "BFO:0000002", + "BFO:0000004", + "BFO:0000040", + "UBERON:0001062", + "CARO:0000000", + "CL:0000000", + "UBERON:0000465", + "UBERON:0000383", + "UBERON:0001015", + "UBERON:0018254", + "UBERON:0005090", + "UBERON:0004120", + "CL:0000003", + "UBERON:0000061", + "UBERON:0001630", + "UBERON:0002385", + "CL:0002371", + "UBERON:0010000", + "UBERON:0000467", + "UBERON:0014892", + "UBERON:0002036", + "CL:0000188", + "UBERON:0000479", + "UBERON:0000468", + "UBERON:0000062", + "UBERON:0011216", + "UBERON:0001134", ], "object_closure_label": [ "All (HPO)", - "Mode of inheritance (HPO)", - "Autosomal dominant inheritance (HPO)", - "Mendelian inheritance", - ], - "object_label": "Autosomal dominant inheritance (HPO)", + "Phenotypic abnormality (HPO)", + "Abnormality of the musculature (HPO)", + "Type 1 muscle fiber predominance (HPO)", + "Abnormal muscle fiber morphology (HPO)", + "Abnormal skeletal muscle morphology (HPO)", + "Abnormal cellular phenotype (HPO)", + "Abnormality of the musculoskeletal system (HPO)", + "Abnormal muscle fiber-type distribution (HPO)", + "anatomical structure", + "organ", + "musculature of body", + "material anatomical entity", + "anatomical system", + "multicellular organism", + "tissue", + "musculature", + "anatomical entity", + "skeletal muscle tissue", + "muscle organ", + "striated muscle tissue", + "muscle tissue", + "mesoderm-derived structure", + "muscle structure", + "multicellular anatomical structure", + "organ system subdivision", + "skeletal muscle organ", + "skeletal musculature", + ], + "object_label": "Type 1 muscle fiber predominance (HPO)", "evidence_count": 4, }, { - "id": "uuid:c3cdad58-212f-11ee-873a-cd90a19c4085", - "original_subject": "OMIM:159050", - "predicate": "biolink:has_mode_of_inheritance", - "category": "biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation", + "id": "uuid:628f39f6-212f-11ee-873a-cd90a19c4085", + "original_subject": "OMIM:160500", + "predicate": "biolink:has_phenotype", + "category": "biolink:DiseaseToPhenotypicFeatureAssociation", "aggregator_knowledge_source": ["infores:monarchinitiative"], "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", + "provided_by": "hpoa_disease_phenotype_edges", + "publications": ["OMIM:160500"], + "subject": "MONDO:0008050", + "object": "HP:0003805", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ - "MONDO:0004994", "MONDO:0000001", - "MONDO:0008034", "MONDO:0005071", - "MONDO:0016147", - "MONDO:0005267", "MONDO:0020121", - "MONDO:0004995", - "MONDO:0700223", "BFO:0000002", + "MONDO:0019952", "BFO:0000017", "BFO:0000020", - "MONDO:0010542", - "MONDO:0016106", - "MONDO:0015470", - "MONDO:0005217", - "MONDO:0016899", + "MONDO:0008050", + "MONDO:0016195", "BFO:0000016", "MONDO:0020120", "MONDO:0019056", "MONDO:0016139", "MONDO:0700096", - "MONDO:0000591", "MONDO:0005218", "MONDO:0005336", "MONDO:0002081", - "MONDO:0016333", "OGMS:0000031", - "MONDO:0005021", "MONDO:0003847", "MONDO:0003939", "BFO:0000001", - "MONDO:0010311", + "MONDO:0002320", + "MONDO:0018949", ], "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", "nervous system disorder", - "familial cardiomyopathy", "obsolete muscular disorder", - "heart disorder", "myopathy", - "muscular dystrophy, pseudohypertrophic, with Internalized capillaries", - "Becker muscular dystrophy", - "dilated cardiomyopathy 3B", - "familial isolated dilated cardiomyopathy", - "progressive muscular dystrophy", + "MYH7-related skeletal myopathy", "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 beta-myosin heavy chain (MYH7)", + "distal myopathy", "neuromuscular disease", + "congenital myopathy", "skeletal muscle disorder", "muscular dystrophy", "human disease or disorder", - "hereditary skeletal muscle disorder", ], - "subject_label": "muscular dystrophy, pseudohypertrophic, with Internalized capillaries", + "subject_label": "MYH7-related skeletal myopathy", "object_namespace": "HP", - "object_category": "biolink:GeneticInheritance", + "object_category": "biolink:PhenotypicQuality", "object_closure": [ "HP:0000001", - "HP:0000006", - "HP:0000005", - "HP:0034345", + "HP:0004303", + "UPHENO:0001001", + "UPHENO:0001005", + "HP:0011805", + "UPHENO:0001002", + "HP:0000118", + "BFO:0000002", + "HP:0025354", + "BFO:0000020", + "HP:0003011", + "UPHENO:0002816", + "UPHENO:0081581", + "HP:0033127", + "UPHENO:0001003", + "UPHENO:0002536", + "UPHENO:0076692", + "UPHENO:0076710", + "BFO:0000001", + "HP:0003805", + "PATO:0000001", + "BFO:0000001", + "BFO:0000002", + "BFO:0000004", + "BFO:0000040", + "UBERON:0001062", + "CARO:0000000", + "CL:0000000", + "UBERON:0000465", + "UBERON:0000383", + "UBERON:0001015", + "UBERON:0018254", + "UBERON:0005090", + "UBERON:0004120", + "CL:0000003", + "UBERON:0000061", + "UBERON:0001630", + "UBERON:0002385", + "CL:0002371", + "UBERON:0010000", + "UBERON:0000467", + "UBERON:0014892", + "UBERON:0002036", + "CL:0000188", + "UBERON:0000479", + "UBERON:0000468", + "UBERON:0000062", + "UBERON:0011216", + "UBERON:0001134", ], "object_closure_label": [ "All (HPO)", - "Mode of inheritance (HPO)", - "Autosomal dominant inheritance (HPO)", - "Mendelian inheritance", - ], - "object_label": "Autosomal dominant inheritance (HPO)", + "Phenotypic abnormality (HPO)", + "Abnormality of the musculature (HPO)", + "Rimmed vacuoles (HPO)", + "Abnormal muscle fiber morphology (HPO)", + "Abnormal skeletal muscle morphology (HPO)", + "Abnormal cellular phenotype (HPO)", + "Abnormality of the musculoskeletal system (HPO)", + "anatomical structure", + "organ", + "musculature of body", + "material anatomical entity", + "anatomical system", + "multicellular organism", + "tissue", + "musculature", + "anatomical entity", + "skeletal muscle tissue", + "muscle organ", + "striated muscle tissue", + "muscle tissue", + "mesoderm-derived structure", + "muscle structure", + "multicellular anatomical structure", + "organ system subdivision", + "skeletal muscle organ", + "skeletal musculature", + ], + "object_label": "Rimmed vacuoles (HPO)", "evidence_count": 4, }, { - "id": "uuid:c3367408-212f-11ee-873a-cd90a19c4085", - "original_subject": "OMIM:160300", - "predicate": "biolink:has_mode_of_inheritance", - "category": "biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation", + "id": "uuid:5ebb4d1e-212f-11ee-873a-cd90a19c4085", + "original_subject": "OMIM:300696", + "predicate": "biolink:has_phenotype", + "category": "biolink:DiseaseToPhenotypicFeatureAssociation", "aggregator_knowledge_source": ["infores:monarchinitiative"], - "has_evidence": ["ECO:0000304"], + "has_evidence": ["ECO:0000501"], "primary_knowledge_source": "infores:hpo-annotations", - "provided_by": "hpoa_disease_mode_of_inheritance_edges", - "publications": ["OMIM:160300"], - "subject": "MONDO:0008049", - "object": "HP:0000006", + "provided_by": "hpoa_disease_phenotype_edges", + "publications": ["OMIM:300696"], + "subject": "MONDO:0010401", + "object": "HP:0003805", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ + "MONDO:0004994", "MONDO:0000001", "MONDO:0005071", + "MONDO:0005267", "MONDO:0020121", - "MONDO:0700223", + "MONDO:0004995", "BFO:0000002", + "MONDO:0010401", "BFO:0000017", - "MONDO:0008049", "BFO:0000020", + "MONDO:0016106", + "MONDO:0005217", "BFO:0000016", "MONDO:0020120", "MONDO:0019056", "MONDO:0700096", + "MONDO:0000591", "MONDO:0005218", "MONDO:0005336", "MONDO:0002081", + "MONDO:0016333", + "MONDO:0016830", "OGMS:0000031", + "MONDO:0005021", "MONDO:0003847", "MONDO:0003939", "BFO:0000001", - "MONDO:0018949", ], "subject_closure_label": [ "disease or disorder", + "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", - "myopathy, distal, infantile-onset", - "distal myopathy", + "X-linked myopathy with postural muscle atrophy", + "progressive muscular dystrophy", + "familial dilated cardiomyopathy", + "Emery-Dreifuss muscular dystrophy", "neuromuscular disease", "skeletal muscle disorder", "muscular dystrophy", "human disease or disorder", - "hereditary skeletal muscle disorder", ], - "subject_label": "myopathy, distal, infantile-onset", + "subject_label": "X-linked myopathy with postural muscle atrophy", "object_namespace": "HP", - "object_category": "biolink:GeneticInheritance", + "object_category": "biolink:PhenotypicQuality", "object_closure": [ "HP:0000001", - "HP:0000006", - "HP:0000005", - "HP:0034345", + "HP:0004303", + "UPHENO:0001001", + "UPHENO:0001005", + "HP:0011805", + "UPHENO:0001002", + "HP:0000118", + "BFO:0000002", + "HP:0025354", + "BFO:0000020", + "HP:0003011", + "UPHENO:0002816", + "UPHENO:0081581", + "HP:0033127", + "UPHENO:0001003", + "UPHENO:0002536", + "UPHENO:0076692", + "UPHENO:0076710", + "BFO:0000001", + "HP:0003805", + "PATO:0000001", + "BFO:0000001", + "BFO:0000002", + "BFO:0000004", + "BFO:0000040", + "UBERON:0001062", + "CARO:0000000", + "CL:0000000", + "UBERON:0000465", + "UBERON:0000383", + "UBERON:0001015", + "UBERON:0018254", + "UBERON:0005090", + "UBERON:0004120", + "CL:0000003", + "UBERON:0000061", + "UBERON:0001630", + "UBERON:0002385", + "CL:0002371", + "UBERON:0010000", + "UBERON:0000467", + "UBERON:0014892", + "UBERON:0002036", + "CL:0000188", + "UBERON:0000479", + "UBERON:0000468", + "UBERON:0000062", + "UBERON:0011216", + "UBERON:0001134", ], "object_closure_label": [ "All (HPO)", - "Mode of inheritance (HPO)", - "Autosomal dominant inheritance (HPO)", - "Mendelian inheritance", - ], - "object_label": "Autosomal dominant inheritance (HPO)", + "Phenotypic abnormality (HPO)", + "Abnormality of the musculature (HPO)", + "Rimmed vacuoles (HPO)", + "Abnormal muscle fiber morphology (HPO)", + "Abnormal skeletal muscle morphology (HPO)", + "Abnormal cellular phenotype (HPO)", + "Abnormality of the musculoskeletal system (HPO)", + "anatomical structure", + "organ", + "musculature of body", + "material anatomical entity", + "anatomical system", + "multicellular organism", + "tissue", + "musculature", + "anatomical entity", + "skeletal muscle tissue", + "muscle organ", + "striated muscle tissue", + "muscle tissue", + "mesoderm-derived structure", + "muscle structure", + "multicellular anatomical structure", + "organ system subdivision", + "skeletal muscle organ", + "skeletal musculature", + ], + "object_label": "Rimmed vacuoles (HPO)", "evidence_count": 4, }, { - "id": "uuid:c39b4534-212f-11ee-873a-cd90a19c4085", - "original_subject": "OMIM:160500", - "predicate": "biolink:has_mode_of_inheritance", - "category": "biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation", + "id": "uuid:607e98ad-212f-11ee-873a-cd90a19c4085", + "original_subject": "OMIM:600334", + "predicate": "biolink:has_phenotype", + "category": "biolink:DiseaseToPhenotypicFeatureAssociation", "aggregator_knowledge_source": ["infores:monarchinitiative"], - "has_evidence": ["ECO:0000269"], + "has_evidence": ["ECO:0000304"], "primary_knowledge_source": "infores:hpo-annotations", - "provided_by": "hpoa_disease_mode_of_inheritance_edges", - "publications": ["PMID:15322983"], - "subject": "MONDO:0008050", - "object": "HP:0000006", + "provided_by": "hpoa_disease_phenotype_edges", + "publications": ["OMIM:600334"], + "subject": "MONDO:0010870", + "object": "HP:0003805", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ + "MONDO:0010870", "MONDO:0000001", + "MONDO:0000429", "MONDO:0005071", "MONDO:0020121", - "MONDO:0700223", + "MONDO:0100175", "BFO:0000002", "MONDO:0019952", "BFO:0000017", "BFO:0000020", - "MONDO:0008050", - "MONDO:0016195", + "MONDO:0016191", "BFO:0000016", "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: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", @@ -382,401 +664,760 @@ def association_response(): "nervous system disorder", "obsolete muscular disorder", "myopathy", - "MYH7-related skeletal myopathy", + "tibial muscular dystrophy", + "autosomal dominant distal myopathy", "qualitative or quantitative protein defects in neuromuscular diseases", - "qualitative or quantitative defects of beta-myosin heavy chain (MYH7)", + "qualitative or quantitative defects of titin", "distal myopathy", "neuromuscular disease", "congenital myopathy", "skeletal muscle disorder", "muscular dystrophy", + "TTN-related myopathy", + "autosomal dominant titinopathy", "human disease or disorder", - "hereditary skeletal muscle disorder", ], - "subject_label": "MYH7-related skeletal myopathy", + "subject_label": "tibial muscular dystrophy", "object_namespace": "HP", - "object_category": "biolink:GeneticInheritance", + "object_category": "biolink:PhenotypicQuality", "object_closure": [ "HP:0000001", - "HP:0000006", - "HP:0000005", - "HP:0034345", + "HP:0004303", + "UPHENO:0001001", + "UPHENO:0001005", + "HP:0011805", + "UPHENO:0001002", + "HP:0000118", + "BFO:0000002", + "HP:0025354", + "BFO:0000020", + "HP:0003011", + "UPHENO:0002816", + "UPHENO:0081581", + "HP:0033127", + "UPHENO:0001003", + "UPHENO:0002536", + "UPHENO:0076692", + "UPHENO:0076710", + "BFO:0000001", + "HP:0003805", + "PATO:0000001", + "BFO:0000001", + "BFO:0000002", + "BFO:0000004", + "BFO:0000040", + "UBERON:0001062", + "CARO:0000000", + "CL:0000000", + "UBERON:0000465", + "UBERON:0000383", + "UBERON:0001015", + "UBERON:0018254", + "UBERON:0005090", + "UBERON:0004120", + "CL:0000003", + "UBERON:0000061", + "UBERON:0001630", + "UBERON:0002385", + "CL:0002371", + "UBERON:0010000", + "UBERON:0000467", + "UBERON:0014892", + "UBERON:0002036", + "CL:0000188", + "UBERON:0000479", + "UBERON:0000468", + "UBERON:0000062", + "UBERON:0011216", + "UBERON:0001134", ], "object_closure_label": [ "All (HPO)", - "Mode of inheritance (HPO)", - "Autosomal dominant inheritance (HPO)", - "Mendelian inheritance", - ], - "object_label": "Autosomal dominant inheritance (HPO)", + "Phenotypic abnormality (HPO)", + "Abnormality of the musculature (HPO)", + "Rimmed vacuoles (HPO)", + "Abnormal muscle fiber morphology (HPO)", + "Abnormal skeletal muscle morphology (HPO)", + "Abnormal cellular phenotype (HPO)", + "Abnormality of the musculoskeletal system (HPO)", + "anatomical structure", + "organ", + "musculature of body", + "material anatomical entity", + "anatomical system", + "multicellular organism", + "tissue", + "musculature", + "anatomical entity", + "skeletal muscle tissue", + "muscle organ", + "striated muscle tissue", + "muscle tissue", + "mesoderm-derived structure", + "muscle structure", + "multicellular anatomical structure", + "organ system subdivision", + "skeletal muscle organ", + "skeletal musculature", + ], + "object_label": "Rimmed vacuoles (HPO)", "evidence_count": 4, }, { - "id": "uuid:c2d3e237-212f-11ee-873a-cd90a19c4085", - "original_subject": "OMIM:160900", - "predicate": "biolink:has_mode_of_inheritance", - "category": "biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation", + "id": "uuid:5f90dae3-212f-11ee-873a-cd90a19c4085", + "original_subject": "OMIM:601954", + "predicate": "biolink:has_phenotype", + "category": "biolink:DiseaseToPhenotypicFeatureAssociation", "aggregator_knowledge_source": ["infores:monarchinitiative"], "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", + "provided_by": "hpoa_disease_phenotype_edges", + "publications": ["OMIM:601954"], + "subject": "MONDO:0011170", + "object": "HP:0003805", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ - "MONDO:0004994", - "MONDO:0020158", "MONDO:0000001", - "MONDO:0016107", + "MONDO:0016971", + "MONDO:0000429", "MONDO:0005071", - "MONDO:0005267", "MONDO:0020121", - "MONDO:0005045", - "MONDO:0004995", - "MONDO:0700223", "BFO:0000002", "BFO:0000017", "BFO:0000020", + "MONDO:0006025", "MONDO:0016106", - "MONDO:0005217", - "MONDO:0024573", - "MONDO:0003382", "BFO:0000016", "MONDO:0020120", "MONDO:0019056", - "MONDO:0008056", + "MONDO:0016139", "MONDO:0700096", - "MONDO:0000591", - "MONDO:0024458", + "MONDO:0011170", "MONDO:0005218", "MONDO:0005336", "MONDO:0002081", - "MONDO:0002254", "OGMS:0000031", + "MONDO:0016192", "MONDO:0003847", "MONDO:0003939", - "MONDO:0002022", - "MONDO:0016120", "BFO:0000001", - "MONDO:0000462", - "MONDO:0005328", + "MONDO:0015152", ], "subject_closure_label": [ "disease or disorder", - "eye adnexa disorder", - "intrinsic cardiomyopathy", - "disorder of orbital region", + "autosomal genetic disease", "musculoskeletal 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", - "myotonic dystrophy type 1", + "autosomal recessive disease", + "autosomal recessive limb-girdle muscular dystrophy type 2G", + "autosomal recessive limb-girdle muscular dystrophy", "progressive muscular dystrophy", - "myotonic dystrophy", - "myotonic syndrome", + "qualitative or quantitative protein defects in neuromuscular diseases", + "qualitative or quantitative defects of telethonin", + "limb-girdle muscular dystrophy", "neuromuscular disease", "skeletal muscle disorder", "muscular dystrophy", - "eyelids malposition disorder", - "disorder of visual system", - "familial hypertrophic cardiomyopathy", "human disease or disorder", - "hereditary skeletal muscle disorder", ], - "subject_label": "myotonic dystrophy type 1", + "subject_label": "autosomal recessive limb-girdle muscular dystrophy type 2G", "object_namespace": "HP", - "object_category": "biolink:GeneticInheritance", + "object_category": "biolink:PhenotypicQuality", "object_closure": [ "HP:0000001", - "HP:0000006", - "HP:0000005", - "HP:0034345", + "HP:0004303", + "UPHENO:0001001", + "UPHENO:0001005", + "HP:0011805", + "UPHENO:0001002", + "HP:0000118", + "BFO:0000002", + "HP:0025354", + "BFO:0000020", + "HP:0003011", + "UPHENO:0002816", + "UPHENO:0081581", + "HP:0033127", + "UPHENO:0001003", + "UPHENO:0002536", + "UPHENO:0076692", + "UPHENO:0076710", + "BFO:0000001", + "HP:0003805", + "PATO:0000001", + "BFO:0000001", + "BFO:0000002", + "BFO:0000004", + "BFO:0000040", + "UBERON:0001062", + "CARO:0000000", + "CL:0000000", + "UBERON:0000465", + "UBERON:0000383", + "UBERON:0001015", + "UBERON:0018254", + "UBERON:0005090", + "UBERON:0004120", + "CL:0000003", + "UBERON:0000061", + "UBERON:0001630", + "UBERON:0002385", + "CL:0002371", + "UBERON:0010000", + "UBERON:0000467", + "UBERON:0014892", + "UBERON:0002036", + "CL:0000188", + "UBERON:0000479", + "UBERON:0000468", + "UBERON:0000062", + "UBERON:0011216", + "UBERON:0001134", ], "object_closure_label": [ "All (HPO)", - "Mode of inheritance (HPO)", - "Autosomal dominant inheritance (HPO)", - "Mendelian inheritance", - ], - "object_label": "Autosomal dominant inheritance (HPO)", + "Phenotypic abnormality (HPO)", + "Abnormality of the musculature (HPO)", + "Rimmed vacuoles (HPO)", + "Abnormal muscle fiber morphology (HPO)", + "Abnormal skeletal muscle morphology (HPO)", + "Abnormal cellular phenotype (HPO)", + "Abnormality of the musculoskeletal system (HPO)", + "anatomical structure", + "organ", + "musculature of body", + "material anatomical entity", + "anatomical system", + "multicellular organism", + "tissue", + "musculature", + "anatomical entity", + "skeletal muscle tissue", + "muscle organ", + "striated muscle tissue", + "muscle tissue", + "mesoderm-derived structure", + "muscle structure", + "multicellular anatomical structure", + "organ system subdivision", + "skeletal muscle organ", + "skeletal musculature", + ], + "object_label": "Rimmed vacuoles (HPO)", "evidence_count": 4, }, { - "id": "uuid:c400607b-212f-11ee-873a-cd90a19c4085", - "original_subject": "OMIM:164300", - "predicate": "biolink:has_mode_of_inheritance", - "category": "biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation", + "id": "uuid:63fd8f8b-212f-11ee-873a-cd90a19c4085", + "original_subject": "OMIM:603689", + "predicate": "biolink:has_phenotype", + "category": "biolink:DiseaseToPhenotypicFeatureAssociation", "aggregator_knowledge_source": ["infores:monarchinitiative"], "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", + "provided_by": "hpoa_disease_phenotype_edges", + "publications": ["PMID:22577215"], + "subject": "MONDO:0011362", + "object": "HP:0003805", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ - "MONDO:0020158", "MONDO:0000001", + "MONDO:0016112", + "MONDO:0000429", "MONDO:0005071", "MONDO:0020121", - "MONDO:0700223", - "MONDO:0004746", + "MONDO:0100175", "BFO:0000002", + "MONDO:0019952", "BFO:0000017", "BFO:0000020", "MONDO:0016106", - "MONDO:0003382", + "MONDO:0016191", "BFO:0000016", "MONDO:0020120", "MONDO:0019056", + "MONDO:0100494", + "MONDO:0016139", "MONDO:0700096", - "MONDO:0024458", "MONDO:0005218", "MONDO:0005336", "MONDO:0002081", - "MONDO:0008116", + "MONDO:0000426", + "MONDO:0011362", "OGMS:0000031", "MONDO:0003847", "MONDO:0003939", - "MONDO:0002022", "BFO:0000001", - "MONDO:0000462", - "MONDO:0005328", + "MONDO:0002320", + "MONDO:0016108", + "MONDO:0018949", ], "subject_closure_label": [ "disease or disorder", - "eye adnexa disorder", - "disorder of orbital region", + "autosomal dominant disease", + "autosomal genetic disease", "musculoskeletal system disorder", - "eyelid disorder", + "congenital nervous system disorder", "hereditary disease", "muscle tissue disorder", - "myopathy of extraocular muscle", "nervous system disorder", "obsolete muscular disorder", - "eye disorder", "myopathy", - "oculopharyngeal muscular dystrophy", + "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", - "eyelids malposition disorder", - "disorder of visual system", + "TTN-related myopathy", + "autosomal dominant titinopathy", "human disease or disorder", - "hereditary skeletal muscle disorder", ], - "subject_label": "oculopharyngeal muscular dystrophy", + "subject_label": "myopathy, myofibrillar, 9, with early respiratory failure", "object_namespace": "HP", - "object_category": "biolink:GeneticInheritance", + "object_category": "biolink:PhenotypicQuality", "object_closure": [ "HP:0000001", - "HP:0000006", - "HP:0000005", - "HP:0034345", + "HP:0004303", + "UPHENO:0001001", + "UPHENO:0001005", + "HP:0011805", + "UPHENO:0001002", + "HP:0000118", + "BFO:0000002", + "HP:0025354", + "BFO:0000020", + "HP:0003011", + "UPHENO:0002816", + "UPHENO:0081581", + "HP:0033127", + "UPHENO:0001003", + "UPHENO:0002536", + "UPHENO:0076692", + "UPHENO:0076710", + "BFO:0000001", + "HP:0003805", + "PATO:0000001", + "BFO:0000001", + "BFO:0000002", + "BFO:0000004", + "BFO:0000040", + "UBERON:0001062", + "CARO:0000000", + "CL:0000000", + "UBERON:0000465", + "UBERON:0000383", + "UBERON:0001015", + "UBERON:0018254", + "UBERON:0005090", + "UBERON:0004120", + "CL:0000003", + "UBERON:0000061", + "UBERON:0001630", + "UBERON:0002385", + "CL:0002371", + "UBERON:0010000", + "UBERON:0000467", + "UBERON:0014892", + "UBERON:0002036", + "CL:0000188", + "UBERON:0000479", + "UBERON:0000468", + "UBERON:0000062", + "UBERON:0011216", + "UBERON:0001134", ], "object_closure_label": [ "All (HPO)", - "Mode of inheritance (HPO)", - "Autosomal dominant inheritance (HPO)", - "Mendelian inheritance", - ], - "object_label": "Autosomal dominant inheritance (HPO)", + "Phenotypic abnormality (HPO)", + "Abnormality of the musculature (HPO)", + "Rimmed vacuoles (HPO)", + "Abnormal muscle fiber morphology (HPO)", + "Abnormal skeletal muscle morphology (HPO)", + "Abnormal cellular phenotype (HPO)", + "Abnormality of the musculoskeletal system (HPO)", + "anatomical structure", + "organ", + "musculature of body", + "material anatomical entity", + "anatomical system", + "multicellular organism", + "tissue", + "musculature", + "anatomical entity", + "skeletal muscle tissue", + "muscle organ", + "striated muscle tissue", + "muscle tissue", + "mesoderm-derived structure", + "muscle structure", + "multicellular anatomical structure", + "organ system subdivision", + "skeletal muscle organ", + "skeletal musculature", + ], + "object_label": "Rimmed vacuoles (HPO)", "evidence_count": 4, }, { - "id": "uuid:c3cdaddf-212f-11ee-873a-cd90a19c4085", - 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"hereditary skeletal muscle disorder", ], - "subject_label": "muscular dystrophy, Hemizygous lethal type", + "subject_label": "GNE myopathy", "object_namespace": "HP", - "object_category": "biolink:GeneticInheritance", + "object_category": "biolink:PhenotypicQuality", "object_closure": [ "HP:0000001", - "HP:0000006", - "HP:0000005", - "HP:0034345", + "HP:0004303", + "UPHENO:0001001", + "UPHENO:0001005", + "HP:0011805", + "UPHENO:0001002", + "HP:0000118", + "BFO:0000002", + "HP:0025354", + "BFO:0000020", + "HP:0003011", + "UPHENO:0002816", + "UPHENO:0081581", + "HP:0033127", + "UPHENO:0001003", + "UPHENO:0002536", + "UPHENO:0076692", + "UPHENO:0076710", + "BFO:0000001", + "HP:0003805", + "PATO:0000001", + "BFO:0000001", + "BFO:0000002", + "BFO:0000004", + "BFO:0000040", + "UBERON:0001062", + "CARO:0000000", + "CL:0000000", + "UBERON:0000465", + "UBERON:0000383", + "UBERON:0001015", + "UBERON:0018254", + "UBERON:0005090", + "UBERON:0004120", + "CL:0000003", + "UBERON:0000061", + "UBERON:0001630", + "UBERON:0002385", + "CL:0002371", + "UBERON:0010000", + "UBERON:0000467", + "UBERON:0014892", + "UBERON:0002036", + "CL:0000188", + "UBERON:0000479", + "UBERON:0000468", + "UBERON:0000062", + "UBERON:0011216", + "UBERON:0001134", ], "object_closure_label": [ "All (HPO)", - "Mode of inheritance (HPO)", - "Autosomal dominant inheritance (HPO)", - "Mendelian inheritance", - ], - "object_label": "Autosomal dominant inheritance (HPO)", + "Phenotypic abnormality (HPO)", + "Abnormality of the musculature (HPO)", + "Rimmed vacuoles (HPO)", + "Abnormal muscle fiber morphology (HPO)", + "Abnormal skeletal muscle morphology (HPO)", + "Abnormal cellular phenotype (HPO)", + "Abnormality of the musculoskeletal system (HPO)", + "anatomical structure", + "organ", + "musculature of body", + "material anatomical entity", + "anatomical system", + "multicellular organism", + "tissue", + "musculature", + "anatomical entity", + "skeletal muscle tissue", + "muscle organ", + "striated muscle tissue", + "muscle tissue", + "mesoderm-derived structure", + "muscle structure", + "multicellular anatomical structure", + "organ system subdivision", + "skeletal muscle organ", + "skeletal musculature", + ], + "object_label": "Rimmed vacuoles (HPO)", "evidence_count": 4, }, { - "id": "uuid:c336741f-212f-11ee-873a-cd90a19c4085", - "original_subject": "OMIM:600334", - "predicate": "biolink:has_mode_of_inheritance", - "category": "biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation", + "id": "uuid:60cdba46-212f-11ee-873a-cd90a19c4085", + "original_subject": "OMIM:608423", + "predicate": "biolink:has_phenotype", + "category": "biolink:DiseaseToPhenotypicFeatureAssociation", "aggregator_knowledge_source": ["infores:monarchinitiative"], - "has_evidence": ["ECO:0000501"], + "has_evidence": ["ECO:0000269"], "primary_knowledge_source": "infores:hpo-annotations", - "provided_by": "hpoa_disease_mode_of_inheritance_edges", - "publications": ["OMIM:600334"], - "subject": "MONDO:0010870", - "object": "HP:0000006", + "provided_by": "hpoa_disease_phenotype_edges", + "publications": ["PMID:23543484"], + "subject": "MONDO:0012034", + "object": "HP:0003805", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ - "MONDO:0010870", "MONDO:0000001", + "MONDO:0016971", "MONDO:0000429", "MONDO:0005071", "MONDO:0020121", - "MONDO:0100175", - "MONDO:0700223", + "MONDO:0012034", "BFO:0000002", - "MONDO:0019952", "BFO:0000017", "BFO:0000020", - "MONDO:0016191", + "MONDO:0016106", "BFO:0000016", "MONDO:0020120", "MONDO:0019056", - "MONDO:0100494", - "MONDO:0016139", + "MONDO:0015151", "MONDO:0700096", "MONDO:0005218", "MONDO:0005336", @@ -786,933 +1427,1832 @@ def association_response(): "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", - "tibial muscular dystrophy", - "autosomal dominant distal myopathy", - "qualitative or quantitative protein defects in neuromuscular diseases", - "qualitative or quantitative defects of titin", - "distal myopathy", + "autosomal dominant limb-girdle muscular dystrophy type 1F", + "muscular dystrophy, limb-girdle, autosomal dominant", + "progressive muscular dystrophy", + "limb-girdle muscular dystrophy", "neuromuscular disease", - "congenital myopathy", "skeletal muscle disorder", "muscular dystrophy", - "TTN-related myopathy", - "autosomal dominant titinopathy", "human disease or disorder", - "hereditary skeletal muscle disorder", ], - "subject_label": "tibial muscular dystrophy", + "subject_label": "autosomal dominant limb-girdle muscular dystrophy type 1F", "object_namespace": "HP", - "object_category": "biolink:GeneticInheritance", + "object_category": "biolink:PhenotypicQuality", "object_closure": [ "HP:0000001", - "HP:0000006", - "HP:0000005", - "HP:0034345", + "HP:0004303", + "UPHENO:0001001", + "UPHENO:0001005", + "HP:0011805", + "UPHENO:0001002", + "HP:0000118", + "BFO:0000002", + "HP:0025354", + "BFO:0000020", + "HP:0003011", + "UPHENO:0002816", + "UPHENO:0081581", + "HP:0033127", + "UPHENO:0001003", + "UPHENO:0002536", + "UPHENO:0076692", + "UPHENO:0076710", + "BFO:0000001", + "HP:0003805", + "PATO:0000001", + "BFO:0000001", + "BFO:0000002", + "BFO:0000004", + "BFO:0000040", + "UBERON:0001062", + "CARO:0000000", + "CL:0000000", + "UBERON:0000465", + "UBERON:0000383", + "UBERON:0001015", + "UBERON:0018254", + "UBERON:0005090", + "UBERON:0004120", + "CL:0000003", + "UBERON:0000061", + "UBERON:0001630", + "UBERON:0002385", + "CL:0002371", + "UBERON:0010000", + "UBERON:0000467", + "UBERON:0014892", + "UBERON:0002036", + "CL:0000188", + "UBERON:0000479", + "UBERON:0000468", + "UBERON:0000062", + "UBERON:0011216", + "UBERON:0001134", ], "object_closure_label": [ "All (HPO)", - "Mode of inheritance (HPO)", - "Autosomal dominant inheritance (HPO)", - "Mendelian inheritance", - ], - "object_label": "Autosomal dominant inheritance (HPO)", + "Phenotypic abnormality (HPO)", + "Abnormality of the musculature (HPO)", + "Rimmed vacuoles (HPO)", + "Abnormal muscle fiber morphology (HPO)", + "Abnormal skeletal muscle morphology (HPO)", + "Abnormal cellular phenotype (HPO)", + "Abnormality of the musculoskeletal system (HPO)", + "anatomical structure", + "organ", + "musculature of body", + "material anatomical entity", + "anatomical system", + "multicellular organism", + "tissue", + "musculature", + "anatomical entity", + "skeletal muscle tissue", + "muscle organ", + "striated muscle tissue", + "muscle tissue", + "mesoderm-derived structure", + "muscle structure", + "multicellular anatomical structure", + "organ system subdivision", + "skeletal muscle organ", + "skeletal musculature", + ], + "object_label": "Rimmed vacuoles (HPO)", "evidence_count": 4, }, { - "id": "uuid:c275a16e-212f-11ee-873a-cd90a19c4085", - "original_subject": "OMIM:600638", - "predicate": "biolink:has_mode_of_inheritance", - "category": "biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation", + "id": "uuid:62f7ecd4-212f-11ee-873a-cd90a19c4085", + "original_subject": "OMIM:609115", + "predicate": "biolink:has_phenotype", + "category": "biolink:DiseaseToPhenotypicFeatureAssociation", "aggregator_knowledge_source": ["infores:monarchinitiative"], - "has_evidence": ["ECO:0000269"], + "has_evidence": ["ECO:0000304"], "primary_knowledge_source": "infores:hpo-annotations", - "provided_by": "hpoa_disease_mode_of_inheritance_edges", - "publications": ["PMID:20074521"], - "subject": "MONDO:0010912", - "object": "HP:0000006", + "provided_by": "hpoa_disease_phenotype_edges", + "publications": ["OMIM:609115"], + "subject": "MONDO:0012193", + "object": "HP:0003805", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ - "MONDO:0020158", "MONDO:0000001", - "MONDO:0007614", + "MONDO:0016971", + "MONDO:0000429", "MONDO:0005071", "MONDO:0020121", - 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"Mode of inheritance (HPO)", - "Autosomal dominant inheritance (HPO)", - "Mendelian inheritance", - ], - "object_label": "Autosomal dominant inheritance (HPO)", + "Abnormality of body height (HPO)", + "Phenotypic abnormality (HPO)", + "Growth abnormality (HPO)", + "Growth delay (HPO)", + "Short stature (HPO)", + "anatomical structure", + "material anatomical entity", + "multicellular organism", + "anatomical entity", + "multicellular anatomical structure", + ], + "object_label": "Short stature (HPO)", "evidence_count": 4, }, { - "id": "uuid:c275a325-212f-11ee-873a-cd90a19c4085", - "original_subject": "OMIM:609384", - "predicate": "biolink:has_mode_of_inheritance", - "category": "biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation", + "id": "uuid:624032b1-212f-11ee-873a-cd90a19c4085", + "original_subject": "OMIM:226670", + "predicate": "biolink:has_phenotype", + "category": "biolink:DiseaseToPhenotypicFeatureAssociation", "aggregator_knowledge_source": ["infores:monarchinitiative"], "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", + "provided_by": "hpoa_disease_phenotype_edges", + "publications": ["OMIM:226670"], + "subject": "MONDO:0009181", + "object": "HP:0004552", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ - "MONDO:0020158", "MONDO:0000001", - "MONDO:0007614", + "MONDO:0016198", + "MONDO:0016971", + "MONDO:0000429", "MONDO:0005071", "MONDO:0020121", - "MONDO:0700223", - "MONDO:0004746", "BFO:0000002", - "MONDO:0012262", - "MONDO:0957003", + "MONDO:0006617", "BFO:0000017", "BFO:0000020", + "MONDO:0017610", + "MONDO:0006025", "MONDO:0016106", - "MONDO:0003382", + "MONDO:0002051", "BFO:0000016", "MONDO:0020120", "MONDO:0019056", - "MONDO:0003569", + "MONDO:0016139", "MONDO:0700096", - "MONDO:0001584", - "MONDO:0024458", "MONDO:0005218", "MONDO:0005336", "MONDO:0002081", + "MONDO:0002254", + "MONDO:0009181", + "MONDO:0019276", + "MONDO:0005093", "OGMS:0000031", + "MONDO:0019268", "MONDO:0003847", "MONDO:0003939", - "MONDO:0002022", - "MONDO:0015368", + "MONDO:0006541", "BFO:0000001", - "MONDO:0002320", - "MONDO:0000462", - "MONDO:0005328", + "MONDO:0015152", ], "subject_closure_label": [ "disease or disorder", - "eye adnexa disorder", - "ocular motility disease", - "disorder of orbital region", + "autosomal genetic disease", + "integumentary system disorder", "musculoskeletal system disorder", - "congenital nervous system disorder", - "eyelid disorder", - "cranial nerve neuropathy", + "syndromic disease", "hereditary disease", "muscle tissue disorder", - "myopathy of extraocular muscle", "nervous system disorder", + "skin disorder", "obsolete muscular disorder", - "eye disorder", "myopathy", - "congenital fibrosis of extraocular muscles", - "fibrosis of extraocular muscles, congenital, 3c", - "neuro-ophthalmological disease", + "autosomal recessive disease", + "epidermolysis bullosa", + "vesiculobullous skin disease", + "epidermolysis bullosa simplex 5B, with muscular dystrophy", + "autosomal recessive limb-girdle muscular dystrophy", "progressive muscular dystrophy", + "qualitative or quantitative protein defects in neuromuscular diseases", + "qualitative or quantitative defects of plectin", + "limb-girdle muscular dystrophy", + "epidermolysis bullosa simplex", "neuromuscular disease", + "epidermal disease", + "inherited epidermolysis bullosa", "skeletal muscle disorder", "muscular dystrophy", - "eyelids malposition disorder", - "disorder of visual system", "human disease or disorder", - "hereditary skeletal muscle disorder", - "hereditary neuro-ophthalmological disease", ], - "subject_label": "fibrosis of extraocular muscles, congenital, 3c", + "subject_label": "epidermolysis bullosa simplex 5B, with muscular dystrophy", "object_namespace": "HP", - "object_category": "biolink:GeneticInheritance", + "object_category": "biolink:PhenotypicQuality", "object_closure": [ "HP:0000001", - "HP:0000006", - "HP:0000005", - "HP:0034345", + "HP:0001965", + "UPHENO:0011535", + "UPHENO:0075696", + "UPHENO:0001001", + "HP:0003549", + "HP:0000152", + "UPHENO:0003811", + "UPHENO:0002768", + "UPHENO:0002844", + "UPHENO:0001005", + "HP:0000987", + "UPHENO:0002764", + "UPHENO:0001002", + "HP:0000118", + "BFO:0000002", + "HP:0011355", + "UPHENO:0011498", + "HP:0011121", + "HP:0002293", + "UPHENO:0076739", + "BFO:0000020", + "HP:0100699", + "UPHENO:0003035", + "HP:0000234", + "HP:0001595", + "UPHENO:0075677", + "UPHENO:0002635", + "UPHENO:0015280", + "HP:0011362", + "UPHENO:0006910", + "UPHENO:0081581", + "HP:0033127", + "UPHENO:0001003", + "UPHENO:0002536", + "UPHENO:0020584", + "HP:0100037", + "UPHENO:0019853", + "UPHENO:0076692", + "HP:0004552", + "UPHENO:0002712", + "HP:0001596", + "BFO:0000001", + "HP:0000951", + "HP:0011138", + "PATO:0000001", + "HP:0001574", + "BFO:0000001", + "BFO:0000002", + "BFO:0000004", + "BFO:0000040", + "UBERON:0001062", + "CARO:0000000", + "UBERON:0000465", + "RO:0002577", + "UBERON:0004121", + "CARO:0000006", + "UBERON:0002416", + "UBERON:0007811", + "UBERON:0002199", + "UBERON:0000403", + "UBERON:0010314", + "UBERON:0000061", + "UBERON:0001037", + "UBERON:0002097", + "UBERON:0010371", + "CARO:0000003", + "UBERON:0011932", + "UBERON:0010000", + "UBERON:0000467", + "UBERON:0034768", + "UBERON:0003102", + "UBERON:0016446", + "UBERON:0007376", + "UBERON:0000021", + "UBERON:0000479", + "UBERON:0000468", + "UBERON:0000475", + "UBERON:0000064", + "UBERON:0000062", + "UBERON:0011216", + "UBERON:0034921", + "UBERON:0004529", + "UBERON:3000961", + "UBERON:0001003", + "UBERON:0000483", + "UBERON:0002384", + "UBERON:0000153", + "UBERON:0011676", + "UBERON:0013701", + "UBERON:0000063", + "UBERON:0013702", + "UBERON:0006003", + "UBERON:0013703", + "UBERON:0000033", ], "object_closure_label": [ "All (HPO)", - "Mode of inheritance (HPO)", - "Autosomal dominant inheritance (HPO)", - "Mendelian inheritance", - ], - "object_label": "Autosomal dominant inheritance (HPO)", + "Phenotypic abnormality (HPO)", + "Abnormality of head or neck (HPO)", + "Abnormality of the head (HPO)", + "Abnormality of the skin (HPO)", + "Atypical scarring of skin (HPO)", + "Abnormality of the integument (HPO)", + "Abnormal hair morphology (HPO)", + "Alopecia (HPO)", + "Abnormal scalp morphology (HPO)", + "Alopecia of scalp (HPO)", + "Abnormality of connective tissue (HPO)", + "Scarring alopecia of scalp (HPO)", + "Abnormality of skin morphology (HPO)", + "Abnormality of skin adnexa morphology (HPO)", + "Localized skin lesion (HPO)", + "Abnormal hair quantity (HPO)", + "Abnormality of the musculoskeletal system (HPO)", + "Abnormality of the scalp hair (HPO)", + "Scarring (HPO)", + "cutaneous appendage", + "head", + "anatomical structure", + "organ", + "organ subunit", + "organ part", + "anterior region of body", + "scalp", + "material anatomical entity", + "anatomical system", + "multicellular organism", + "organism subdivision", + "tissue", + "epithelium", + "skin epidermis", + "strand of hair", + "anatomical entity", + "skin of body", + "integument", + "connective tissue", + "integumental system", + "surface structure", + "ectoderm-derived structure", + "anatomical projection", + "integumentary adnexa", + "outer epithelium", + "craniocervical region", + "multicellular anatomical structure", + "structure with developmental contribution from neural crest", + "ecto-epithelium", + "organ system subdivision", + "subdivision of organism along main body axis", + "pilosebaceous unit", + "main body axis", + "body proper", + "integumentary projection", + "hair of head", + "morphological feature", + "multi organ part structure", + "external integument structure", + ], + "object_label": "Scarring alopecia of scalp (HPO)", "evidence_count": 4, }, { - "id": "uuid:c304ba49-212f-11ee-873a-cd90a19c4085", - "original_subject": "OMIM:609452", - "predicate": "biolink:has_mode_of_inheritance", - "category": "biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation", + "id": "uuid:62c348df-212f-11ee-873a-cd90a19c4085", + "original_subject": "OMIM:310300", + "predicate": "biolink:has_phenotype", + "category": "biolink:DiseaseToPhenotypicFeatureAssociation", "aggregator_knowledge_source": ["infores:monarchinitiative"], "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", + "provided_by": "hpoa_disease_phenotype_edges", + "publications": ["OMIM:310300"], + "subject": "MONDO:0010680", + "object": "HP:0004631", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ + "MONDO:0004994", "MONDO:0000001", - "MONDO:0016186", - "MONDO:0000429", + "MONDO:0010680", "MONDO:0005071", + "MONDO:0005267", "MONDO:0020121", - "MONDO:0018943", - "MONDO:0700223", + "MONDO:0004995", + "MONDO:0016196", "BFO:0000002", - "MONDO:0019952", - "MONDO:0016190", "BFO:0000017", "BFO:0000020", + "MONDO:0016106", + "MONDO:0005217", "BFO:0000016", "MONDO:0020120", "MONDO:0019056", "MONDO:0016139", "MONDO:0700096", - "MONDO:0002921", + "MONDO:0000591", "MONDO:0005218", "MONDO:0005336", "MONDO:0002081", - "MONDO:0000426", + "MONDO:0016333", + "MONDO:0016830", "OGMS:0000031", + "MONDO:0000425", + "MONDO:0005021", + "MONDO:0021106", "MONDO:0003847", "MONDO:0003939", - "MONDO:0012277", "BFO:0000001", - "MONDO:0002320", - "MONDO:0016108", - "MONDO:0018949", + "MONDO:0020606", ], "subject_closure_label": [ "disease or disorder", - "autosomal dominant disease", - "autosomal genetic disease", + "X-linked disease", + "intrinsic cardiomyopathy", "musculoskeletal system disorder", - "congenital nervous system disorder", - "congenital structural myopathy", "hereditary disease", "muscle tissue disorder", + "cardiomyopathy", + "cardiovascular disorder", + "dilated cardiomyopathy", "nervous system disorder", + "familial cardiomyopathy", "obsolete muscular disorder", + "heart disorder", "myopathy", - "myofibrillar myopathy 4", - "autosomal dominant distal myopathy", + "X-linked Emery-Dreifuss muscular dystrophy", + "progressive muscular dystrophy", "qualitative or quantitative protein defects in neuromuscular diseases", - "qualitative or quantitative defects of myofibrillar proteins", - "qualitative or quantitative defects of protein ZASP", - "myofibrillar myopathy", - "distal myopathy", + "qualitative or quantitative defects of emerin", + "familial dilated cardiomyopathy", + "Emery-Dreifuss muscular dystrophy", "neuromuscular disease", - "congenital myopathy", "skeletal muscle disorder", "muscular dystrophy", + "sex-linked disease", + "laminopathy", "human disease or disorder", - "hereditary skeletal muscle disorder", ], - "subject_label": "myofibrillar myopathy 4", + "subject_label": "X-linked Emery-Dreifuss muscular dystrophy", "object_namespace": "HP", - "object_category": "biolink:GeneticInheritance", + "object_category": "biolink:PhenotypicQuality", "object_closure": [ "HP:0000001", - "HP:0000006", - "HP:0000005", - "HP:0034345", + "UPHENO:0082875", + "UPHENO:0046505", + "UPHENO:0075696", + "UPHENO:0068971", + "UPHENO:0001001", + "HP:0001371", + "HP:0003549", + "HP:0011729", + "UPHENO:0076703", + "HP:0100261", + "UPHENO:0001005", + "HP:0011842", + "HP:0011805", + "UPHENO:0001002", + "HP:0004631", + "HP:0034430", + "HP:0000924", + "HP:0000118", + "BFO:0000002", + "HP:0034392", + "UPHENO:0021425", + "BFO:0000020", + "UPHENO:0075195", + "HP:0003011", + "UPHENO:0002816", + "UPHENO:0002332", + "UPHENO:0015280", + "UPHENO:0002964", + "UPHENO:0081581", + "HP:0033127", + "UPHENO:0001003", + "UPHENO:0002536", + "UPHENO:0046759", + "UPHENO:0020584", + "UPHENO:0031839", + "UPHENO:0076692", + "UPHENO:0081440", + "UPHENO:0076710", + "UPHENO:0002712", + "BFO:0000001", + "PATO:0000001", + "UPHENO:0012541", + "HP:0011843", + "BFO:0000001", + "BFO:0000002", + "BFO:0000004", + "BFO:0000040", + "UBERON:0001062", + "CARO:0000000", + "UBERON:0000465", + "UBERON:0000383", + "UBERON:0001015", + "UBERON:0007845", + "UBERON:0002204", + "UBERON:0005090", + "UBERON:0000061", + "UBERON:0034925", + "UBERON:0007846", + "UBERON:0001630", + "UBERON:0010000", + "UBERON:0000467", + "UBERON:0004770", + "UBERON:0000043", + "UBERON:0000479", + "UBERON:0000468", + "UBERON:0000062", + "UBERON:0011216", + "UBERON:0034921", + "UBERON:0002384", + "UBERON:0004905", + "UBERON:0001434", + "UBERON:0011823", + "UBERON:0000982", ], "object_closure_label": [ "All (HPO)", - "Mode of inheritance (HPO)", - "Autosomal dominant inheritance (HPO)", - "Mendelian inheritance", - ], - "object_label": "Autosomal dominant inheritance (HPO)", + "Phenotypic abnormality (HPO)", + "Abnormality of the skeletal system (HPO)", + "Flexion contracture (HPO)", + "Abnormality of the musculature (HPO)", + "Abnormality of connective tissue (HPO)", + "Decreased cervical spine flexion due to contractures of posterior cervical muscles (HPO)", + "Abnormality of joint mobility (HPO)", + "Abnormal skeletal muscle morphology (HPO)", + "Abnormal skeletal morphology (HPO)", + "Abnormality of musculoskeletal physiology (HPO)", + "Abnormality of the musculoskeletal system (HPO)", + "Joint contracture", + "Abnormal joint physiology", + "Abnormal tendon morphology (HPO)", + "tendon", + "anatomical structure", + "organ", + "musculature of body", + "material anatomical entity", + "anatomical system", + "multicellular organism", + "tissue", + "skeletal joint", + "musculature", + "anatomical entity", + "skeletal system", + "muscle organ", + "musculoskeletal system", + "connective tissue", + "articular system", + "articulation", + "muscle structure", + "regular connective tissue", + "dense regular connective tissue", + "multicellular anatomical structure", + "organ system subdivision", + "dense connective tissue", + "multi organ part structure", + "anatomical collection", + ], + "object_label": "Decreased cervical spine flexion due to contractures of posterior cervical muscles (HPO)", "evidence_count": 4, }, ], diff --git a/backend/tests/fixtures/association_table.py b/backend/tests/fixtures/association_table.py index 3b833e0fd..f901b4de9 100644 --- a/backend/tests/fixtures/association_table.py +++ b/backend/tests/fixtures/association_table.py @@ -6,7 +6,7 @@ def association_table(): return { "limit": 5, "offset": 0, - "total": 4011, + "total": 4312, "items": [ { "id": "uuid:632c5b16-212f-11ee-873a-cd90a19c4085", @@ -20,7 +20,6 @@ def association_table(): "MONDO:0005071", "MONDO:0025193", "MONDO:0020121", - "MONDO:0700223", "BFO:0000002", "MONDO:0020793", "BFO:0000017", @@ -67,8 +66,9 @@ def association_table(): "disorder of visual system", "oculopharyngodistal myopathy", "human disease or disorder", - "hereditary skeletal muscle disorder", ], + "subject_taxon": None, + "subject_taxon_label": None, "predicate": "biolink:has_phenotype", "object": "HP:0002460", "original_object": None, @@ -98,18 +98,18 @@ def association_table(): "BFO:0000001", "HP:0011804", "PATO:0000001", - "CARO:0000000", "BFO:0000001", - "UBERON:0000383", - "UBERON:0001015", - "UBERON:0005090", "BFO:0000002", - "UBERON:0001630", "BFO:0000004", "BFO:0000040", "UBERON:0001062", + "CARO:0000000", "UBERON:0000465", + "UBERON:0000383", + "UBERON:0001015", + "UBERON:0005090", "UBERON:0000061", + "UBERON:0001630", "UBERON:0010000", "UBERON:0000467", "UBERON:0000468", @@ -138,6 +138,8 @@ def association_table(): "multicellular anatomical structure", "organ system subdivision", ], + "object_taxon": None, + "object_taxon_label": None, "primary_knowledge_source": "infores:hpo-annotations", "aggregator_knowledge_source": ["infores:monarchinitiative"], "category": "biolink:DiseaseToPhenotypicFeatureAssociation", @@ -194,7 +196,6 @@ def association_table(): "MONDO:0005071", "MONDO:0025193", "MONDO:0020121", - "MONDO:0700223", "BFO:0000002", "MONDO:0020793", "BFO:0000017", @@ -241,8 +242,9 @@ def association_table(): "disorder of visual system", "oculopharyngodistal myopathy", "human disease or disorder", - "hereditary skeletal muscle disorder", ], + "subject_taxon": None, + "subject_taxon_label": None, "predicate": "biolink:has_phenotype", "object": "HP:0002015", "original_object": None, @@ -278,42 +280,43 @@ def association_table(): "HP:0025031", "UPHENO:0002474", "HP:0012638", - "CARO:0000000", - "CARO:0000003", "BFO:0000001", - "UBERON:0004921", - "UBERON:0001555", - "UBERON:0001016", - "UBERON:0000915", "BFO:0000002", - "UBERON:0004908", - "UBERON:0001043", "BFO:0000004", "BFO:0000040", "UBERON:0001062", - "RO:0002577", + "CARO:0000000", "UBERON:0000465", + "RO:0002577", + "CARO:0000006", + "UBERON:0004921", + "UBERON:0001555", + "UBERON:0001016", "UBERON:0000061", + "CARO:0000003", + "UBERON:0004908", + "UBERON:0001043", "UBERON:0010000", "UBERON:0000467", + "UBERON:0000915", "UBERON:0000468", "UBERON:0000475", "UBERON:0000064", "UBERON:0000062", "UBERON:0004111", - "UBERON:0005409", "UBERON:0001007", + "UBERON:0005409", "UBERON:0011676", "UBERON:0013701", "UBERON:0009569", - "UBERON:0013702", "UBERON:0013522", + "UBERON:0013702", "UBERON:0013765", "UBERON:0005177", "UBERON:0000025", - "UBERON:0002100", "UBERON:0005181", "UBERON:0002075", + "UBERON:0002100", "UBERON:0005178", ], "object_label": "Dysphagia (HPO)", @@ -359,6 +362,8 @@ def association_table(): "body proper", "digestive system element", ], + "object_taxon": None, + "object_taxon_label": None, "primary_knowledge_source": "infores:hpo-annotations", "aggregator_knowledge_source": ["infores:monarchinitiative"], "category": "biolink:DiseaseToPhenotypicFeatureAssociation", @@ -418,7 +423,6 @@ def association_table(): "MONDO:0013049", "MONDO:0020121", "MONDO:0004995", - "MONDO:0700223", "MONDO:0024322", "BFO:0000002", "BFO:0000017", @@ -476,8 +480,9 @@ def association_table(): "muscular dystrophy", "disorder of glycosylation", "human disease or disorder", - "hereditary skeletal muscle disorder", ], + "subject_taxon": None, + "subject_taxon_label": None, "predicate": "biolink:has_phenotype", "object": "HP:0003236", "original_object": None, @@ -528,41 +533,41 @@ def association_table(): "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", "GO:0008152", + "BFO:0000030", + "UBERON:0000465", "GO:0005575", - "PR:000050567", + "UBERON:0000178", + "UBERON:0004120", + "UBERON:0000061", + "UBERON:0000463", "CHEBI:24431", - "UBERON:0000465", "GO:0032991", + "UBERON:0002390", + "UBERON:0010000", + "UBERON:0000467", + "UBERON:0006314", "CHEBI:23367", - "UBERON:0000061", - "UBERON:0000463", "GO:1902494", + "UBERON:0000468", + "UBERON:0001004", + "UBERON:0002193", + "UBERON:0000179", "CHEBI:36357", "CHEBI:33579", - "UBERON:0010000", - "UBERON:0000467", - "UBERON:0006314", "GO:1990234", "CHEBI:33839", "CHEBI:33675", "CHEBI:138675", - "UBERON:0000468", - "UBERON:0001004", - "UBERON:0002193", - "UBERON:0000179", "GO:0061695", "CHEBI:16670", "CHEBI:33302", @@ -644,6 +649,8 @@ def association_table(): "bodily fluid", "multicellular anatomical structure", ], + "object_taxon": None, + "object_taxon_label": None, "primary_knowledge_source": "infores:hpo-annotations", "aggregator_knowledge_source": ["infores:monarchinitiative"], "category": "biolink:DiseaseToPhenotypicFeatureAssociation", @@ -689,161 +696,303 @@ def association_table(): "direction": "outgoing", }, { - "id": "uuid:64b6842f-212f-11ee-873a-cd90a19c4085", - "subject": "MONDO:0009681", - "original_subject": "OMIM:254090", + "id": "uuid:59b1387d-212f-11ee-873a-cd90a19c4085", + "subject": "MONDO:0100435", + "original_subject": "OMIM:255800", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ "MONDO:0000001", + "MONDO:0018230", + "MONDO:0016121", + "MONDO:0005381", + "MONDO:0000429", + "MONDO:0019689", "MONDO:0005071", "MONDO:0020121", - "MONDO:0700223", + "MONDO:0016151", "BFO:0000002", - "MONDO:0019952", "BFO:0000017", "BFO:0000020", - "MONDO:0100225", + "MONDO:0006025", + "MONDO:0016106", + "MONDO:0005172", "BFO:0000016", "MONDO:0020120", "MONDO:0019056", + "MONDO:0005497", "MONDO:0016139", "MONDO:0700096", "MONDO:0005218", "MONDO:0005336", + "MONDO:0016761", "MONDO:0002081", - "MONDO:0009681", + "MONDO:0002254", + "MONDO:0021147", + "MONDO:0009717", "OGMS:0000031", + "MONDO:0100435", "MONDO:0003847", "MONDO:0003939", + "MONDO:0016120", "BFO:0000001", "MONDO:0002320", - "MONDO:0000355", - "MONDO:0019950", + "MONDO:0005516", ], - "subject_label": "Ullrich congenital muscular dystrophy 1", + "subject_label": "Schwartz-Jampel syndrome type 1", "subject_closure_label": [ "disease or disorder", - "Ullrich congenital muscular dystrophy", + "autosomal genetic disease", "musculoskeletal system disorder", + "syndromic disease", "congenital nervous system disorder", "hereditary disease", "muscle tissue disorder", "nervous system disorder", + "skeletal system disorder", "obsolete muscular disorder", "myopathy", - "Ullrich congenital muscular dystrophy 1", + "bone disorder", + "bone development disease", + "osteochondrodysplasia", + "autosomal recessive disease", + "Schwartz-Jampel syndrome", + "progressive muscular dystrophy", + "myotonic syndrome", + "congenital myotonia", "qualitative or quantitative protein defects in neuromuscular diseases", + "qualitative or quantitative defects of perlecan", + "spondyloepiphyseal dysplasia", + "skeletal dysplasia", "neuromuscular disease", - "congenital muscular dystrophy", - "congenital myopathy", + "perlecan-related bone disorder", "skeletal muscle disorder", "muscular dystrophy", - "collagen 6-related myopathy", + "disorder of development or morphogenesis", + "Schwartz-Jampel syndrome type 1", "human disease or disorder", - "hereditary skeletal muscle disorder", ], + "subject_taxon": None, + "subject_taxon_label": None, "predicate": "biolink:has_phenotype", - "object": "HP:0020152", + "object": "HP:0002979", "original_object": None, "object_namespace": "HP", "object_category": "biolink:PhenotypicQuality", "object_closure": [ "HP:0000001", - "HP:0020152", - "UPHENO:0082875", - "HP:0001388", + "UPHENO:0031310", + "UPHENO:0041226", + "UPHENO:0041610", + "UPHENO:0041098", "UPHENO:0075696", + "UPHENO:0076740", + "HP:0002981", + "HP:0002814", "UPHENO:0001001", - "HP:0011729", + "UPHENO:0080300", + "UPHENO:0041573", + "UPHENO:0076703", + "UPHENO:0075952", + "UPHENO:0019749", "UPHENO:0001005", + "HP:0011314", + "UPHENO:0082449", + "HP:0011842", "UPHENO:0001002", - "HP:0034430", "HP:0000924", "HP:0000118", "BFO:0000002", + "HP:0002813", "BFO:0000020", - "UPHENO:0002332", + "UPHENO:0041536", + "UPHENO:0077858", + "UPHENO:0082467", + "UPHENO:0002896", + "UPHENO:0015280", + "UPHENO:0031193", "UPHENO:0002964", + "UPHENO:0041258", + "UPHENO:0082129", + "HP:0006487", + "UPHENO:0081581", "HP:0033127", "UPHENO:0001003", "UPHENO:0002536", - "UPHENO:0081440", + "HP:0002979", + "HP:0011844", + "UPHENO:0020041", + "UPHENO:0076727", + "UPHENO:0020584", + "UPHENO:0076692", + "UPHENO:0003070", + "UPHENO:0041591", + "HP:0040064", "BFO:0000001", "PATO:0000001", - "HP:0011843", - "CARO:0000000", + "HP:0040068", + "UPHENO:0002830", + "HP:0000940", + "UPHENO:0079873", "BFO:0000001", - "UBERON:0002204", "BFO:0000002", "BFO:0000004", "BFO:0000040", "UBERON:0001062", + "CARO:0000000", "UBERON:0000465", + "RO:0002577", + "UBERON:0001474", + "UBERON:0002204", + "CARO:0000006", + "UBERON:0006058", + "UBERON:0010712", + "UBERON:0005913", + "UBERON:0010538", + "UBERON:0004120", "UBERON:0000061", "UBERON:0034925", + "UBERON:0010740", + "UBERON:0002495", + "UBERON:0002513", + "CARO:0000003", + "UBERON:0000978", + "UBERON:0004381", + "UBERON:0005055", + "UBERON:0002529", + "UBERON:0011582", + "UBERON:0015061", + "UBERON:0004375", "UBERON:0010000", "UBERON:0000467", - "UBERON:0004770", + "UBERON:0015212", + "UBERON:0004288", + "UBERON:0002428", + "UBERON:0004708", + "UBERON:0010709", + "UBERON:0004769", + "UBERON:0008784", + "UBERON:0002471", "UBERON:0000468", + "UBERON:0000475", + "UBERON:0000064", + "UBERON:0000062", "UBERON:0011216", - "UBERON:0034921", + "UBERON:0010707", + "UBERON:0002101", + "UBERON:0004709", + "UBERON:0003823", + "UBERON:0000154", + "UBERON:0000026", + "UBERON:0010758", + "UBERON:0034944", + "UBERON:0004765", + "UBERON:0000075", + "UBERON:0010912", "UBERON:0001434", - "UBERON:0004905", - "UBERON:0000982", + "UBERON:0002103", + "UBERON:0010363", + "UBERON:0011249", + "UBERON:0002091", ], - "object_label": "Distal joint laxity (HPO)", + "object_label": "Bowing of the legs (HPO)", "object_closure_label": [ "All (HPO)", "Phenotypic abnormality (HPO)", "Abnormality of the skeletal system (HPO)", - "Joint laxity (HPO)", - "Abnormality of joint mobility (HPO)", - "Abnormality of musculoskeletal physiology (HPO)", - "Distal joint laxity (HPO)", + "Abnormal diaphysis morphology (HPO)", + "Abnormality of limb bone morphology (HPO)", + "Abnormality of the lower limb (HPO)", + "Bowing of the legs (HPO)", + "Abnormality of the calf (HPO)", + "Bowing of the long bones (HPO)", + "Abnormality of long bone morphology (HPO)", + "Abnormal skeletal morphology (HPO)", + "Abnormal appendicular skeleton morphology (HPO)", "Abnormality of the musculoskeletal system (HPO)", - "Abnormal joint physiology", + "Abnormality of limbs (HPO)", + "Abnormality of limb bone (HPO)", + "appendage", "anatomical structure", + "organ", + "organ part", + "subdivision of skeletal system", + "posterior region of body", "material anatomical entity", "anatomical system", "multicellular organism", - "skeletal joint", + "organism subdivision", + "leg", "anatomical entity", "skeletal system", + "bone element", + "appendicular skeleton", + "limb", + "hindlimb", "musculoskeletal system", - "articular system", - "articulation", + "limb bone", + "zeugopod", + "long bone", + "endochondral bone", + "limb segment", + "hindlimb zeugopod", + "mesoderm-derived structure", + "skeleton", + "bone of free limb or fin", + "skeleton of limb", + "paired limb/fin", + "pelvic appendage", + "skeletal element", + "diaphysis", + "zone of long bone", + "zone of bone organ", + "multi-limb segment region", + "lower limb segment", "multicellular anatomical structure", + "endochondral element", + "paired limb/fin segment", + "appendage girdle complex", + "pelvic complex", + "limb skeleton subdivision", + "bone of appendage girdle complex", + "subdivision of organism along appendicular axis", + "subdivision of skeleton", "organ system subdivision", - "multi organ part structure", + "appendicular skeletal system", + "paired limb/fin skeleton", + "limb endochondral element", + "lateral structure", "anatomical collection", + "zone of organ", ], + "object_taxon": None, + "object_taxon_label": None, "primary_knowledge_source": "infores:hpo-annotations", "aggregator_knowledge_source": ["infores:monarchinitiative"], "category": "biolink:DiseaseToPhenotypicFeatureAssociation", "negated": None, "provided_by": "hpoa_disease_phenotype_edges", - "publications": ["PMID:16258657", "OMIM:254090"], + "publications": ["PMID:16927315", "PMID:11941538"], "qualifiers": [], - "frequency_qualifier": "HP:0040280", + "frequency_qualifier": "HP:0040283", "has_evidence": ["ECO:0000269"], "onset_qualifier": None, "sex_qualifier": None, "stage_qualifier": None, "evidence_count": 5, "pathway": None, - "frequency_qualifier_label": "Obligate (HPO)", + "frequency_qualifier_label": "Occasional (HPO)", "frequency_qualifier_namespace": "HP", "frequency_qualifier_category": "biolink:PhenotypicFeature", "frequency_qualifier_closure": [ "HP:0000001", + "HP:0040283", "HP:0040279", - "HP:0040280", ], "frequency_qualifier_closure_label": [ "All (HPO)", "Frequency (HPO)", - "Obligate (HPO)", + "Occasional (HPO)", ], "onset_qualifier_label": None, "onset_qualifier_namespace": None, @@ -863,157 +1012,203 @@ def association_table(): "direction": "outgoing", }, { - "id": "uuid:628f3d98-212f-11ee-873a-cd90a19c4085", - "subject": "MONDO:0009676", - "original_subject": "OMIM:253601", + "id": "uuid:59b13885-212f-11ee-873a-cd90a19c4085", + "subject": "MONDO:0100435", + "original_subject": "OMIM:255800", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ "MONDO:0000001", - "MONDO:0016971", + "MONDO:0018230", + "MONDO:0016121", + "MONDO:0005381", "MONDO:0000429", - "MONDO:0016145", + "MONDO:0019689", "MONDO:0005071", "MONDO:0020121", - "MONDO:0700223", + "MONDO:0016151", "BFO:0000002", "BFO:0000017", "BFO:0000020", "MONDO:0006025", "MONDO:0016106", + "MONDO:0005172", "BFO:0000016", "MONDO:0020120", "MONDO:0019056", + "MONDO:0005497", "MONDO:0016139", "MONDO:0700096", "MONDO:0005218", "MONDO:0005336", + "MONDO:0016761", "MONDO:0002081", - "MONDO:0009676", + "MONDO:0002254", + "MONDO:0021147", + "MONDO:0009717", "OGMS:0000031", + "MONDO:0100435", "MONDO:0003847", "MONDO:0003939", + "MONDO:0016120", "BFO:0000001", - "MONDO:0015152", + "MONDO:0002320", + "MONDO:0005516", ], - "subject_label": "autosomal recessive limb-girdle muscular dystrophy type 2B", + "subject_label": "Schwartz-Jampel syndrome type 1", "subject_closure_label": [ "disease or disorder", "autosomal genetic disease", "musculoskeletal system disorder", + "syndromic disease", + "congenital nervous system disorder", "hereditary disease", "muscle tissue disorder", "nervous system disorder", + "skeletal system disorder", "obsolete muscular disorder", "myopathy", + "bone disorder", + "bone development disease", + "osteochondrodysplasia", "autosomal recessive disease", - "autosomal recessive limb-girdle muscular dystrophy type 2B", - "autosomal recessive limb-girdle muscular dystrophy", + "Schwartz-Jampel syndrome", "progressive muscular dystrophy", + "myotonic syndrome", + "congenital myotonia", "qualitative or quantitative protein defects in neuromuscular diseases", - "qualitative or quantitative defects of dysferlin", - "limb-girdle muscular dystrophy", + "qualitative or quantitative defects of perlecan", + "spondyloepiphyseal dysplasia", + "skeletal dysplasia", "neuromuscular disease", + "perlecan-related bone disorder", "skeletal muscle disorder", "muscular dystrophy", + "disorder of development or morphogenesis", + "Schwartz-Jampel syndrome type 1", "human disease or disorder", - "hereditary skeletal muscle disorder", ], + "subject_taxon": None, + "subject_taxon_label": None, "predicate": "biolink:has_phenotype", - "object": "HP:0003701", + "object": "HP:0002751", "original_object": None, "object_namespace": "HP", "object_category": "biolink:PhenotypicQuality", "object_closure": [ "HP:0000001", - "UPHENO:0082875", + "HP:0002808", "UPHENO:0075696", - "UPHENO:0002320", "UPHENO:0001001", + "UPHENO:0076703", "UPHENO:0001005", - "HP:0003701", + "HP:0011842", "UPHENO:0001002", - "HP:0001324", + "HP:0000924", "HP:0000118", "BFO:0000002", "BFO:0000020", - "UPHENO:0080555", - "HP:0003011", - "UPHENO:0002816", - "UPHENO:0002332", - "UPHENO:0080556", + "HP:0009121", + "HP:0010674", + "HP:0000925", + "UPHENO:0015280", + "UPHENO:0002964", + "UPHENO:0081581", "HP:0033127", "UPHENO:0001003", "UPHENO:0002536", + "UPHENO:0002813", + "UPHENO:0020584", + "UPHENO:0076692", + "HP:0002650", "BFO:0000001", - "HP:0011804", + "HP:0002751", "PATO:0000001", - "CARO:0000000", + "UPHENO:0022529", "BFO:0000001", - "UBERON:0000383", - "UBERON:0001015", - "UBERON:0005090", "BFO:0000002", - "UBERON:0001630", "BFO:0000004", "BFO:0000040", "UBERON:0001062", + "CARO:0000000", "UBERON:0000465", + "UBERON:0011137", + "UBERON:0002204", + "UBERON:0005944", + "UBERON:0002090", + "UBERON:0001130", + "UBERON:0011138", "UBERON:0000061", + "UBERON:0034925", "UBERON:0010000", "UBERON:0000467", + "UBERON:0004288", "UBERON:0000468", - "UBERON:0000062", "UBERON:0011216", + "UBERON:0000075", + "UBERON:0010912", + "UBERON:0001434", ], - "object_label": "Proximal muscle weakness (HPO)", + "object_label": "Kyphoscoliosis (HPO)", "object_closure_label": [ "All (HPO)", "Phenotypic abnormality (HPO)", - "Muscle weakness (HPO)", - "Abnormality of the musculature (HPO)", - "Proximal muscle weakness (HPO)", - "Abnormal muscle physiology (HPO)", + "Abnormality of the skeletal system (HPO)", + "Abnormality of the vertebral column (HPO)", + "Scoliosis (HPO)", + "Kyphoscoliosis (HPO)", + "Kyphosis (HPO)", + "Abnormal axial skeleton morphology (HPO)", + "Abnormality of the curvature of the vertebral column (HPO)", + "Abnormal skeletal morphology (HPO)", "Abnormality of the musculoskeletal system (HPO)", "anatomical structure", - "organ", - "musculature of body", + "subdivision of skeletal system", "material anatomical entity", "anatomical system", "multicellular organism", - "musculature", "anatomical entity", - "muscle organ", - "muscle structure", + "vertebral column", + "skeletal system", + "postcranial axial skeleton", + "musculoskeletal system", + "skeleton", + "axial skeleton plus cranial skeleton", "multicellular anatomical structure", + "subdivision of skeleton", + "axial skeletal system", + "postcranial axial skeletal system", "organ system subdivision", + "anatomical collection", ], + "object_taxon": None, + "object_taxon_label": None, "primary_knowledge_source": "infores:hpo-annotations", "aggregator_knowledge_source": ["infores:monarchinitiative"], "category": "biolink:DiseaseToPhenotypicFeatureAssociation", "negated": None, "provided_by": "hpoa_disease_phenotype_edges", - "publications": ["PMID:9731527", "PMID:9009996"], + "publications": ["PMID:16927315", "PMID:11941538"], "qualifiers": [], - "frequency_qualifier": "HP:0040280", + "frequency_qualifier": "HP:0040283", "has_evidence": ["ECO:0000269"], "onset_qualifier": None, "sex_qualifier": None, "stage_qualifier": None, "evidence_count": 5, "pathway": None, - "frequency_qualifier_label": "Obligate (HPO)", + "frequency_qualifier_label": "Occasional (HPO)", "frequency_qualifier_namespace": "HP", "frequency_qualifier_category": "biolink:PhenotypicFeature", "frequency_qualifier_closure": [ "HP:0000001", + "HP:0040283", "HP:0040279", - "HP:0040280", ], "frequency_qualifier_closure_label": [ "All (HPO)", "Frequency (HPO)", - "Obligate (HPO)", + "Occasional (HPO)", ], "onset_qualifier_label": None, "onset_qualifier_namespace": None, diff --git a/backend/tests/fixtures/association_table_response.py b/backend/tests/fixtures/association_table_response.py index 2f748c5e7..10cf52e4c 100644 --- a/backend/tests/fixtures/association_table_response.py +++ b/backend/tests/fixtures/association_table_response.py @@ -5,7 +5,7 @@ def association_table_response(): return { "responseHeader": { - "QTime": 1, + "QTime": 0, "params": { "mm": "100%", "q": "*:*", @@ -22,7 +22,7 @@ def association_table_response(): }, }, "response": { - "num_found": 4011, + "num_found": 4312, "start": 0, "docs": [ { @@ -46,7 +46,6 @@ def association_table_response(): "MONDO:0005071", "MONDO:0025193", "MONDO:0020121", - "MONDO:0700223", "BFO:0000002", "MONDO:0020793", "BFO:0000017", @@ -92,7 +91,6 @@ def association_table_response(): "disorder of visual system", "oculopharyngodistal myopathy", "human disease or disorder", - "hereditary skeletal muscle disorder", ], "subject_label": "oculopharyngodistal myopathy 1", "object_namespace": "HP", @@ -121,18 +119,18 @@ def association_table_response(): "BFO:0000001", "HP:0011804", "PATO:0000001", - "CARO:0000000", "BFO:0000001", - "UBERON:0000383", - "UBERON:0001015", - "UBERON:0005090", "BFO:0000002", - "UBERON:0001630", "BFO:0000004", "BFO:0000040", "UBERON:0001062", + "CARO:0000000", "UBERON:0000465", + "UBERON:0000383", + "UBERON:0001015", + "UBERON:0005090", "UBERON:0000061", + "UBERON:0001630", "UBERON:0010000", "UBERON:0000467", "UBERON:0000468", @@ -197,7 +195,6 @@ def association_table_response(): "MONDO:0005071", "MONDO:0025193", "MONDO:0020121", - "MONDO:0700223", "BFO:0000002", "MONDO:0020793", "BFO:0000017", @@ -243,7 +240,6 @@ def association_table_response(): "disorder of visual system", "oculopharyngodistal myopathy", "human disease or disorder", - "hereditary skeletal muscle disorder", ], "subject_label": "oculopharyngodistal myopathy 1", "object_namespace": "HP", @@ -278,42 +274,43 @@ def association_table_response(): "HP:0025031", "UPHENO:0002474", "HP:0012638", - "CARO:0000000", - "CARO:0000003", "BFO:0000001", - "UBERON:0004921", - "UBERON:0001555", - "UBERON:0001016", - "UBERON:0000915", "BFO:0000002", - "UBERON:0004908", - "UBERON:0001043", "BFO:0000004", "BFO:0000040", "UBERON:0001062", - "RO:0002577", + "CARO:0000000", "UBERON:0000465", + "RO:0002577", + "CARO:0000006", + "UBERON:0004921", + "UBERON:0001555", + "UBERON:0001016", "UBERON:0000061", + "CARO:0000003", + "UBERON:0004908", + "UBERON:0001043", "UBERON:0010000", "UBERON:0000467", + "UBERON:0000915", "UBERON:0000468", "UBERON:0000475", "UBERON:0000064", "UBERON:0000062", "UBERON:0004111", - "UBERON:0005409", "UBERON:0001007", + "UBERON:0005409", "UBERON:0011676", "UBERON:0013701", "UBERON:0009569", - "UBERON:0013702", "UBERON:0013522", + "UBERON:0013702", "UBERON:0013765", "UBERON:0005177", "UBERON:0000025", - "UBERON:0002100", "UBERON:0005181", "UBERON:0002075", + "UBERON:0002100", "UBERON:0005178", ], "object_closure_label": [ @@ -398,7 +395,6 @@ def association_table_response(): "MONDO:0013049", "MONDO:0020121", "MONDO:0004995", - "MONDO:0700223", "MONDO:0024322", "BFO:0000002", "BFO:0000017", @@ -455,7 +451,6 @@ def association_table_response(): "muscular dystrophy", "disorder of glycosylation", "human disease or disorder", - "hereditary skeletal muscle disorder", ], "subject_label": "DPM3-congenital disorder of glycosylation", "object_namespace": "HP", @@ -505,41 +500,41 @@ def association_table_response(): "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", "GO:0008152", + "BFO:0000030", + "UBERON:0000465", "GO:0005575", - "PR:000050567", + "UBERON:0000178", + "UBERON:0004120", + "UBERON:0000061", + "UBERON:0000463", "CHEBI:24431", - "UBERON:0000465", "GO:0032991", + "UBERON:0002390", + "UBERON:0010000", + "UBERON:0000467", + "UBERON:0006314", "CHEBI:23367", - "UBERON:0000061", - "UBERON:0000463", "GO:1902494", + "UBERON:0000468", + "UBERON:0001004", + "UBERON:0002193", + "UBERON:0000179", "CHEBI:36357", "CHEBI:33579", - "UBERON:0010000", - "UBERON:0000467", - "UBERON:0006314", "GO:1990234", "CHEBI:33839", "CHEBI:33675", "CHEBI:138675", - "UBERON:0000468", - "UBERON:0001004", - "UBERON:0002193", - "UBERON:0000179", "GO:0061695", "CHEBI:16670", "CHEBI:33302", @@ -637,301 +632,481 @@ def association_table_response(): "evidence_count": 5, }, { - "id": "uuid:64b6842f-212f-11ee-873a-cd90a19c4085", - "original_subject": "OMIM:254090", + "id": "uuid:59b1387d-212f-11ee-873a-cd90a19c4085", + "original_subject": "OMIM:255800", "predicate": "biolink:has_phenotype", "category": "biolink:DiseaseToPhenotypicFeatureAssociation", "aggregator_knowledge_source": ["infores:monarchinitiative"], "has_evidence": ["ECO:0000269"], "primary_knowledge_source": "infores:hpo-annotations", "provided_by": "hpoa_disease_phenotype_edges", - "publications": ["PMID:16258657", "OMIM:254090"], - "frequency_qualifier": "HP:0040280", - "subject": "MONDO:0009681", - "object": "HP:0020152", + "publications": ["PMID:16927315", "PMID:11941538"], + "frequency_qualifier": "HP:0040283", + "subject": "MONDO:0100435", + "object": "HP:0002979", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ "MONDO:0000001", + "MONDO:0018230", + "MONDO:0016121", + "MONDO:0005381", + "MONDO:0000429", + "MONDO:0019689", "MONDO:0005071", "MONDO:0020121", - "MONDO:0700223", + "MONDO:0016151", "BFO:0000002", - "MONDO:0019952", "BFO:0000017", "BFO:0000020", - "MONDO:0100225", + "MONDO:0006025", + "MONDO:0016106", + "MONDO:0005172", "BFO:0000016", "MONDO:0020120", "MONDO:0019056", + "MONDO:0005497", "MONDO:0016139", "MONDO:0700096", "MONDO:0005218", "MONDO:0005336", + "MONDO:0016761", "MONDO:0002081", - "MONDO:0009681", + "MONDO:0002254", + "MONDO:0021147", + "MONDO:0009717", "OGMS:0000031", + "MONDO:0100435", "MONDO:0003847", "MONDO:0003939", + "MONDO:0016120", "BFO:0000001", "MONDO:0002320", - "MONDO:0000355", - "MONDO:0019950", + "MONDO:0005516", ], "subject_closure_label": [ "disease or disorder", - "Ullrich congenital muscular dystrophy", + "autosomal genetic disease", "musculoskeletal system disorder", + "syndromic disease", "congenital nervous system disorder", "hereditary disease", "muscle tissue disorder", "nervous system disorder", + "skeletal system disorder", "obsolete muscular disorder", "myopathy", - "Ullrich congenital muscular dystrophy 1", + "bone disorder", + "bone development disease", + "osteochondrodysplasia", + "autosomal recessive disease", + "Schwartz-Jampel syndrome", + "progressive muscular dystrophy", + "myotonic syndrome", + "congenital myotonia", "qualitative or quantitative protein defects in neuromuscular diseases", + "qualitative or quantitative defects of perlecan", + "spondyloepiphyseal dysplasia", + "skeletal dysplasia", "neuromuscular disease", - "congenital muscular dystrophy", - "congenital myopathy", + "perlecan-related bone disorder", "skeletal muscle disorder", "muscular dystrophy", - "collagen 6-related myopathy", + "disorder of development or morphogenesis", + "Schwartz-Jampel syndrome type 1", "human disease or disorder", - "hereditary skeletal muscle disorder", ], - "subject_label": "Ullrich congenital muscular dystrophy 1", + "subject_label": "Schwartz-Jampel syndrome type 1", "object_namespace": "HP", "object_category": "biolink:PhenotypicQuality", "object_closure": [ "HP:0000001", - "HP:0020152", - "UPHENO:0082875", - "HP:0001388", + "UPHENO:0031310", + "UPHENO:0041226", + "UPHENO:0041610", + "UPHENO:0041098", "UPHENO:0075696", + "UPHENO:0076740", + "HP:0002981", + "HP:0002814", "UPHENO:0001001", - "HP:0011729", + "UPHENO:0080300", + "UPHENO:0041573", + "UPHENO:0076703", + "UPHENO:0075952", + "UPHENO:0019749", "UPHENO:0001005", + "HP:0011314", + "UPHENO:0082449", + "HP:0011842", "UPHENO:0001002", - "HP:0034430", "HP:0000924", "HP:0000118", "BFO:0000002", + "HP:0002813", "BFO:0000020", - "UPHENO:0002332", + "UPHENO:0041536", + "UPHENO:0077858", + "UPHENO:0082467", + "UPHENO:0002896", + "UPHENO:0015280", + "UPHENO:0031193", "UPHENO:0002964", + "UPHENO:0041258", + "UPHENO:0082129", + "HP:0006487", + "UPHENO:0081581", "HP:0033127", "UPHENO:0001003", "UPHENO:0002536", - "UPHENO:0081440", + "HP:0002979", + "HP:0011844", + "UPHENO:0020041", + "UPHENO:0076727", + "UPHENO:0020584", + "UPHENO:0076692", + "UPHENO:0003070", + "UPHENO:0041591", + "HP:0040064", "BFO:0000001", "PATO:0000001", - "HP:0011843", - "CARO:0000000", + "HP:0040068", + "UPHENO:0002830", + "HP:0000940", + "UPHENO:0079873", "BFO:0000001", - "UBERON:0002204", "BFO:0000002", "BFO:0000004", "BFO:0000040", "UBERON:0001062", + "CARO:0000000", "UBERON:0000465", + "RO:0002577", + "UBERON:0001474", + "UBERON:0002204", + "CARO:0000006", + "UBERON:0006058", + "UBERON:0010712", + "UBERON:0005913", + "UBERON:0010538", + "UBERON:0004120", "UBERON:0000061", "UBERON:0034925", + "UBERON:0010740", + "UBERON:0002495", + "UBERON:0002513", + "CARO:0000003", + "UBERON:0000978", + "UBERON:0004381", + "UBERON:0005055", + "UBERON:0002529", + "UBERON:0011582", + "UBERON:0015061", + "UBERON:0004375", "UBERON:0010000", "UBERON:0000467", - "UBERON:0004770", + "UBERON:0015212", + "UBERON:0004288", + "UBERON:0002428", + "UBERON:0004708", + "UBERON:0010709", + "UBERON:0004769", + "UBERON:0008784", + "UBERON:0002471", "UBERON:0000468", + "UBERON:0000475", + "UBERON:0000064", + "UBERON:0000062", "UBERON:0011216", - "UBERON:0034921", + "UBERON:0010707", + "UBERON:0002101", + "UBERON:0004709", + "UBERON:0003823", + "UBERON:0000154", + "UBERON:0000026", + "UBERON:0010758", + "UBERON:0034944", + "UBERON:0004765", + "UBERON:0000075", + "UBERON:0010912", "UBERON:0001434", - "UBERON:0004905", - "UBERON:0000982", + "UBERON:0002103", + "UBERON:0010363", + "UBERON:0011249", + "UBERON:0002091", ], "object_closure_label": [ "All (HPO)", "Phenotypic abnormality (HPO)", "Abnormality of the skeletal system (HPO)", - "Joint laxity (HPO)", - "Abnormality of joint mobility (HPO)", - "Abnormality of musculoskeletal physiology (HPO)", - "Distal joint laxity (HPO)", + "Abnormal diaphysis morphology (HPO)", + "Abnormality of limb bone morphology (HPO)", + "Abnormality of the lower limb (HPO)", + "Bowing of the legs (HPO)", + "Abnormality of the calf (HPO)", + "Bowing of the long bones (HPO)", + "Abnormality of long bone morphology (HPO)", + "Abnormal skeletal morphology (HPO)", + "Abnormal appendicular skeleton morphology (HPO)", "Abnormality of the musculoskeletal system (HPO)", - "Abnormal joint physiology", + "Abnormality of limbs (HPO)", + "Abnormality of limb bone (HPO)", + "appendage", "anatomical structure", + "organ", + "organ part", + "subdivision of skeletal system", + "posterior region of body", "material anatomical entity", "anatomical system", "multicellular organism", - "skeletal joint", + "organism subdivision", + "leg", "anatomical entity", "skeletal system", + "bone element", + "appendicular skeleton", + "limb", + "hindlimb", "musculoskeletal system", - "articular system", - "articulation", + "limb bone", + "zeugopod", + "long bone", + "endochondral bone", + "limb segment", + "hindlimb zeugopod", + "mesoderm-derived structure", + "skeleton", + "bone of free limb or fin", + "skeleton of limb", + "paired limb/fin", + "pelvic appendage", + "skeletal element", + "diaphysis", + "zone of long bone", + "zone of bone organ", + "multi-limb segment region", + "lower limb segment", "multicellular anatomical structure", + "endochondral element", + "paired limb/fin segment", + "appendage girdle complex", + "pelvic complex", + "limb skeleton subdivision", + "bone of appendage girdle complex", + "subdivision of organism along appendicular axis", + "subdivision of skeleton", "organ system subdivision", - "multi organ part structure", + "appendicular skeletal system", + "paired limb/fin skeleton", + "limb endochondral element", + "lateral structure", "anatomical collection", + "zone of organ", ], - "object_label": "Distal joint laxity (HPO)", + "object_label": "Bowing of the legs (HPO)", "frequency_qualifier_namespace": "HP", "frequency_qualifier_category": "biolink:PhenotypicFeature", "frequency_qualifier_closure": [ "HP:0000001", + "HP:0040283", "HP:0040279", - "HP:0040280", ], "frequency_qualifier_closure_label": [ "All (HPO)", "Frequency (HPO)", - "Obligate (HPO)", + "Occasional (HPO)", ], - "frequency_qualifier_label": "Obligate (HPO)", + "frequency_qualifier_label": "Occasional (HPO)", "evidence_count": 5, }, { - "id": "uuid:628f3d98-212f-11ee-873a-cd90a19c4085", - "original_subject": "OMIM:253601", + "id": "uuid:59b13885-212f-11ee-873a-cd90a19c4085", + "original_subject": "OMIM:255800", "predicate": "biolink:has_phenotype", "category": "biolink:DiseaseToPhenotypicFeatureAssociation", "aggregator_knowledge_source": ["infores:monarchinitiative"], "has_evidence": ["ECO:0000269"], "primary_knowledge_source": "infores:hpo-annotations", "provided_by": "hpoa_disease_phenotype_edges", - "publications": ["PMID:9731527", "PMID:9009996"], - "frequency_qualifier": "HP:0040280", - "subject": "MONDO:0009676", - "object": "HP:0003701", + "publications": ["PMID:16927315", "PMID:11941538"], + "frequency_qualifier": "HP:0040283", + "subject": "MONDO:0100435", + "object": "HP:0002751", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ "MONDO:0000001", - "MONDO:0016971", + "MONDO:0018230", + "MONDO:0016121", + "MONDO:0005381", "MONDO:0000429", - "MONDO:0016145", + "MONDO:0019689", "MONDO:0005071", "MONDO:0020121", - "MONDO:0700223", + "MONDO:0016151", "BFO:0000002", "BFO:0000017", "BFO:0000020", "MONDO:0006025", "MONDO:0016106", + "MONDO:0005172", "BFO:0000016", "MONDO:0020120", "MONDO:0019056", + "MONDO:0005497", "MONDO:0016139", "MONDO:0700096", "MONDO:0005218", "MONDO:0005336", + "MONDO:0016761", "MONDO:0002081", - "MONDO:0009676", + "MONDO:0002254", + "MONDO:0021147", + "MONDO:0009717", "OGMS:0000031", + "MONDO:0100435", "MONDO:0003847", "MONDO:0003939", + "MONDO:0016120", "BFO:0000001", - "MONDO:0015152", + "MONDO:0002320", + "MONDO:0005516", ], "subject_closure_label": [ "disease or disorder", "autosomal genetic disease", "musculoskeletal system disorder", + "syndromic disease", + "congenital nervous system disorder", "hereditary disease", "muscle tissue disorder", "nervous system disorder", + "skeletal system disorder", "obsolete muscular disorder", "myopathy", + "bone disorder", + "bone development disease", + "osteochondrodysplasia", "autosomal recessive disease", - "autosomal recessive limb-girdle muscular dystrophy type 2B", - "autosomal recessive limb-girdle muscular dystrophy", + "Schwartz-Jampel syndrome", "progressive muscular dystrophy", + "myotonic syndrome", + "congenital myotonia", "qualitative or quantitative protein defects in neuromuscular diseases", - "qualitative or quantitative defects of dysferlin", - "limb-girdle muscular dystrophy", + "qualitative or quantitative defects of perlecan", + "spondyloepiphyseal dysplasia", + "skeletal dysplasia", "neuromuscular disease", + "perlecan-related bone disorder", "skeletal muscle disorder", "muscular dystrophy", + "disorder of development or morphogenesis", + "Schwartz-Jampel syndrome type 1", "human disease or disorder", - "hereditary skeletal muscle disorder", ], - "subject_label": "autosomal recessive limb-girdle muscular dystrophy type 2B", + "subject_label": "Schwartz-Jampel syndrome type 1", "object_namespace": "HP", "object_category": "biolink:PhenotypicQuality", "object_closure": [ "HP:0000001", - "UPHENO:0082875", + "HP:0002808", "UPHENO:0075696", - "UPHENO:0002320", "UPHENO:0001001", + "UPHENO:0076703", "UPHENO:0001005", - "HP:0003701", + "HP:0011842", "UPHENO:0001002", - "HP:0001324", + "HP:0000924", "HP:0000118", "BFO:0000002", "BFO:0000020", - "UPHENO:0080555", - "HP:0003011", - "UPHENO:0002816", - "UPHENO:0002332", - "UPHENO:0080556", + "HP:0009121", + "HP:0010674", + "HP:0000925", + "UPHENO:0015280", + "UPHENO:0002964", + "UPHENO:0081581", "HP:0033127", "UPHENO:0001003", "UPHENO:0002536", + "UPHENO:0002813", + "UPHENO:0020584", + "UPHENO:0076692", + "HP:0002650", "BFO:0000001", - "HP:0011804", + "HP:0002751", "PATO:0000001", - "CARO:0000000", + "UPHENO:0022529", "BFO:0000001", - "UBERON:0000383", - "UBERON:0001015", - "UBERON:0005090", "BFO:0000002", - "UBERON:0001630", "BFO:0000004", "BFO:0000040", "UBERON:0001062", + "CARO:0000000", "UBERON:0000465", + "UBERON:0011137", + "UBERON:0002204", + "UBERON:0005944", + "UBERON:0002090", + "UBERON:0001130", + "UBERON:0011138", "UBERON:0000061", + "UBERON:0034925", "UBERON:0010000", "UBERON:0000467", + "UBERON:0004288", "UBERON:0000468", - "UBERON:0000062", "UBERON:0011216", + "UBERON:0000075", + "UBERON:0010912", + "UBERON:0001434", ], "object_closure_label": [ "All (HPO)", "Phenotypic abnormality (HPO)", - "Muscle weakness (HPO)", - "Abnormality of the musculature (HPO)", - "Proximal muscle weakness (HPO)", - "Abnormal muscle physiology (HPO)", + "Abnormality of the skeletal system (HPO)", + "Abnormality of the vertebral column (HPO)", + "Scoliosis (HPO)", + "Kyphoscoliosis (HPO)", + "Kyphosis (HPO)", + "Abnormal axial skeleton morphology (HPO)", + "Abnormality of the curvature of the vertebral column (HPO)", + "Abnormal skeletal morphology (HPO)", "Abnormality of the musculoskeletal system (HPO)", "anatomical structure", - "organ", - "musculature of body", + "subdivision of skeletal system", "material anatomical entity", "anatomical system", "multicellular organism", - "musculature", "anatomical entity", - "muscle organ", - "muscle structure", + "vertebral column", + "skeletal system", + "postcranial axial skeleton", + "musculoskeletal system", + "skeleton", + "axial skeleton plus cranial skeleton", "multicellular anatomical structure", + "subdivision of skeleton", + "axial skeletal system", + "postcranial axial skeletal system", "organ system subdivision", + "anatomical collection", ], - "object_label": "Proximal muscle weakness (HPO)", + "object_label": "Kyphoscoliosis (HPO)", "frequency_qualifier_namespace": "HP", "frequency_qualifier_category": "biolink:PhenotypicFeature", "frequency_qualifier_closure": [ "HP:0000001", + "HP:0040283", "HP:0040279", - "HP:0040280", ], "frequency_qualifier_closure_label": [ "All (HPO)", "Frequency (HPO)", - "Obligate (HPO)", + "Occasional (HPO)", ], - "frequency_qualifier_label": "Obligate (HPO)", + "frequency_qualifier_label": "Occasional (HPO)", "evidence_count": 5, }, ], diff --git a/backend/tests/fixtures/associations.py b/backend/tests/fixtures/associations.py index 5efdeaf68..3be462284 100644 --- a/backend/tests/fixtures/associations.py +++ b/backend/tests/fixtures/associations.py @@ -6,26 +6,28 @@ def associations(): return { "limit": 20, "offset": 0, - "total": 4806, + "total": 5124, "items": [ { - "id": "uuid:c2a45bf5-212f-11ee-873a-cd90a19c4085", - "subject": "MONDO:0008028", - "original_subject": "OMIM:158800", + "id": "uuid:628f39f7-212f-11ee-873a-cd90a19c4085", + "subject": "MONDO:0008050", + "original_subject": "OMIM:160500", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ "MONDO:0000001", "MONDO:0005071", "MONDO:0020121", - "MONDO:0008028", - "MONDO:0700223", "BFO:0000002", + "MONDO:0019952", "BFO:0000017", "BFO:0000020", + "MONDO:0008050", + "MONDO:0016195", "BFO:0000016", "MONDO:0020120", "MONDO:0019056", + "MONDO:0016139", "MONDO:0700096", "MONDO:0005218", "MONDO:0005336", @@ -34,47 +36,127 @@ def associations(): "MONDO:0003847", "MONDO:0003939", "BFO:0000001", + "MONDO:0002320", + "MONDO:0018949", ], - "subject_label": "muscular dystrophy, Barnes type", + "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, Barnes type", + "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", "human disease or disorder", - "hereditary skeletal muscle disorder", ], - "predicate": "biolink:has_mode_of_inheritance", - "object": "HP:0000006", + "subject_taxon": None, + "subject_taxon_label": None, + "predicate": "biolink:has_phenotype", + "object": "HP:0003803", "original_object": None, "object_namespace": "HP", - "object_category": "biolink:GeneticInheritance", + "object_category": "biolink:PhenotypicQuality", "object_closure": [ "HP:0000001", - "HP:0000006", - "HP:0000005", - "HP:0034345", - ], - "object_label": "Autosomal dominant inheritance (HPO)", + "HP:0004303", + "UPHENO:0001001", + "HP:0003803", + "HP:0033684", + "UPHENO:0001005", + "HP:0011805", + "UPHENO:0001002", + "HP:0000118", + "BFO:0000002", + "HP:0025354", + "BFO:0000020", + "HP:0003011", + "UPHENO:0002816", + "UPHENO:0081581", + "HP:0033127", + "UPHENO:0001003", + "UPHENO:0002536", + "UPHENO:0076692", + "UPHENO:0076710", + "BFO:0000001", + "PATO:0000001", + "BFO:0000001", + "BFO:0000002", + "BFO:0000004", + "BFO:0000040", + "UBERON:0001062", + "CARO:0000000", + "CL:0000000", + "UBERON:0000465", + "UBERON:0000383", + "UBERON:0001015", + "UBERON:0018254", + "UBERON:0005090", + "UBERON:0004120", + "CL:0000003", + "UBERON:0000061", + "UBERON:0001630", + "UBERON:0002385", + "CL:0002371", + "UBERON:0010000", + "UBERON:0000467", + "UBERON:0014892", + "UBERON:0002036", + "CL:0000188", + "UBERON:0000479", + "UBERON:0000468", + "UBERON:0000062", + "UBERON:0011216", + "UBERON:0001134", + ], + "object_label": "Type 1 muscle fiber predominance (HPO)", "object_closure_label": [ "All (HPO)", - "Mode of inheritance (HPO)", - "Autosomal dominant inheritance (HPO)", - "Mendelian inheritance", - ], + "Phenotypic abnormality (HPO)", + "Abnormality of the musculature (HPO)", + "Type 1 muscle fiber predominance (HPO)", + "Abnormal muscle fiber morphology (HPO)", + "Abnormal skeletal muscle morphology (HPO)", + "Abnormal cellular phenotype (HPO)", + "Abnormality of the musculoskeletal system (HPO)", + "Abnormal muscle fiber-type distribution (HPO)", + "anatomical structure", + "organ", + "musculature of body", + "material anatomical entity", + "anatomical system", + "multicellular organism", + "tissue", + "musculature", + "anatomical entity", + "skeletal muscle tissue", + "muscle organ", + "striated muscle tissue", + "muscle tissue", + "mesoderm-derived structure", + "muscle structure", + "multicellular anatomical structure", + "organ system subdivision", + "skeletal muscle organ", + "skeletal musculature", + ], + "object_taxon": None, + "object_taxon_label": None, "primary_knowledge_source": "infores:hpo-annotations", "aggregator_knowledge_source": ["infores:monarchinitiative"], - "category": "biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation", + "category": "biolink:DiseaseToPhenotypicFeatureAssociation", "negated": None, - "provided_by": "hpoa_disease_mode_of_inheritance_edges", - "publications": ["OMIM:158800"], + "provided_by": "hpoa_disease_phenotype_edges", + "publications": ["OMIM:160500"], "qualifiers": [], "frequency_qualifier": None, "has_evidence": ["ECO:0000304"], @@ -105,82 +187,154 @@ def associations(): "stage_qualifier_closure_label": [], }, { - "id": "uuid:c304bcf2-212f-11ee-873a-cd90a19c4085", - "subject": "MONDO:0008030", - "original_subject": "OMIM:158900", + "id": "uuid:64b68436-212f-11ee-873a-cd90a19c4085", + "subject": "MONDO:0009681", + "original_subject": "OMIM:254090", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ - "MONDO:0008030", "MONDO:0000001", - "MONDO:0019303", "MONDO:0005071", "MONDO:0020121", - "MONDO:0700223", - "MONDO:0001347", "BFO:0000002", "BFO:0000017", "BFO:0000020", - "MONDO:0016106", - "MONDO:0100137", + "MONDO:0100225", "BFO:0000016", "MONDO:0020120", "MONDO:0019056", + "MONDO:0016139", "MONDO:0700096", "MONDO:0005218", "MONDO:0005336", "MONDO:0002081", - "MONDO:0021147", + "MONDO:0009681", "OGMS:0000031", "MONDO:0003847", "MONDO:0003939", "BFO:0000001", + "MONDO:0002320", + "MONDO:0000355", + "MONDO:0019950", ], - "subject_label": "facioscapulohumeral muscular dystrophy 1", + "subject_label": "Ullrich congenital muscular dystrophy 1", "subject_closure_label": [ "disease or disorder", - "facioscapulohumeral muscular dystrophy", + "Ullrich congenital muscular dystrophy", "musculoskeletal system disorder", + "congenital nervous system disorder", "hereditary disease", "muscle tissue disorder", "nervous system disorder", "obsolete muscular disorder", "myopathy", - "facioscapulohumeral muscular dystrophy 1", - "progressive muscular dystrophy", + "Ullrich congenital muscular dystrophy 1", + "qualitative or quantitative protein defects in neuromuscular diseases", "neuromuscular disease", - "premature aging syndrome", + "congenital muscular dystrophy", "skeletal muscle disorder", "muscular dystrophy", - "disorder of development or morphogenesis", - "telomere syndrome", + "collagen 6-related myopathy", "human disease or disorder", - "hereditary skeletal muscle disorder", ], - "predicate": "biolink:has_mode_of_inheritance", - "object": "HP:0000006", + "subject_taxon": None, + "subject_taxon_label": None, + "predicate": "biolink:has_phenotype", + "object": "HP:0003803", "original_object": None, "object_namespace": "HP", - "object_category": "biolink:GeneticInheritance", + "object_category": "biolink:PhenotypicQuality", "object_closure": [ "HP:0000001", - "HP:0000006", - "HP:0000005", - "HP:0034345", - ], - "object_label": "Autosomal dominant inheritance (HPO)", + "HP:0004303", + "UPHENO:0001001", + "HP:0003803", + "HP:0033684", + "UPHENO:0001005", + "HP:0011805", + "UPHENO:0001002", + "HP:0000118", + "BFO:0000002", + "HP:0025354", + "BFO:0000020", + "HP:0003011", + "UPHENO:0002816", + "UPHENO:0081581", + "HP:0033127", + "UPHENO:0001003", + "UPHENO:0002536", + "UPHENO:0076692", + "UPHENO:0076710", + "BFO:0000001", + "PATO:0000001", + "BFO:0000001", + "BFO:0000002", + "BFO:0000004", + "BFO:0000040", + "UBERON:0001062", + "CARO:0000000", + "CL:0000000", + "UBERON:0000465", + "UBERON:0000383", + "UBERON:0001015", + "UBERON:0018254", + "UBERON:0005090", + "UBERON:0004120", + "CL:0000003", + "UBERON:0000061", + "UBERON:0001630", + "UBERON:0002385", + "CL:0002371", + "UBERON:0010000", + "UBERON:0000467", + "UBERON:0014892", + "UBERON:0002036", + "CL:0000188", + "UBERON:0000479", + "UBERON:0000468", + "UBERON:0000062", + "UBERON:0011216", + "UBERON:0001134", + ], + "object_label": "Type 1 muscle fiber predominance (HPO)", "object_closure_label": [ "All (HPO)", - "Mode of inheritance (HPO)", - "Autosomal dominant inheritance (HPO)", - "Mendelian inheritance", - ], + "Phenotypic abnormality (HPO)", + "Abnormality of the musculature (HPO)", + "Type 1 muscle fiber predominance (HPO)", + "Abnormal muscle fiber morphology (HPO)", + "Abnormal skeletal muscle morphology (HPO)", + "Abnormal cellular phenotype (HPO)", + "Abnormality of the musculoskeletal system (HPO)", + "Abnormal muscle fiber-type distribution (HPO)", + "anatomical structure", + "organ", + "musculature of body", + "material anatomical entity", + "anatomical system", + "multicellular organism", + "tissue", + "musculature", + "anatomical entity", + "skeletal muscle tissue", + "muscle organ", + "striated muscle tissue", + "muscle tissue", + "mesoderm-derived structure", + "muscle structure", + "multicellular anatomical structure", + "organ system subdivision", + "skeletal muscle organ", + "skeletal musculature", + ], + "object_taxon": None, + "object_taxon_label": None, "primary_knowledge_source": "infores:hpo-annotations", "aggregator_knowledge_source": ["infores:monarchinitiative"], - "category": "biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation", + "category": "biolink:DiseaseToPhenotypicFeatureAssociation", "negated": None, - "provided_by": "hpoa_disease_mode_of_inheritance_edges", - "publications": ["OMIM:158900"], + "provided_by": "hpoa_disease_phenotype_edges", + "publications": ["OMIM:254090"], "qualifiers": [], "frequency_qualifier": None, "has_evidence": ["ECO:0000501"], @@ -211,100 +365,152 @@ def associations(): "stage_qualifier_closure_label": [], }, { - "id": "uuid:c3cdad58-212f-11ee-873a-cd90a19c4085", - "subject": "MONDO:0008034", - "original_subject": "OMIM:159050", + "id": "uuid:628f39f6-212f-11ee-873a-cd90a19c4085", + "subject": "MONDO:0008050", + "original_subject": "OMIM:160500", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ - "MONDO:0004994", "MONDO:0000001", - "MONDO:0008034", "MONDO:0005071", - "MONDO:0016147", - "MONDO:0005267", "MONDO:0020121", - "MONDO:0004995", - "MONDO:0700223", "BFO:0000002", + "MONDO:0019952", "BFO:0000017", "BFO:0000020", - "MONDO:0010542", - "MONDO:0016106", - "MONDO:0015470", - "MONDO:0005217", - "MONDO:0016899", + "MONDO:0008050", + "MONDO:0016195", "BFO:0000016", "MONDO:0020120", "MONDO:0019056", "MONDO:0016139", "MONDO:0700096", - "MONDO:0000591", "MONDO:0005218", "MONDO:0005336", "MONDO:0002081", - "MONDO:0016333", "OGMS:0000031", - "MONDO:0005021", "MONDO:0003847", "MONDO:0003939", "BFO:0000001", - "MONDO:0010311", + "MONDO:0002320", + "MONDO:0018949", ], - "subject_label": "muscular dystrophy, pseudohypertrophic, with Internalized capillaries", + "subject_label": "MYH7-related skeletal myopathy", "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", "nervous system disorder", - "familial cardiomyopathy", "obsolete muscular disorder", - "heart disorder", "myopathy", - "muscular dystrophy, pseudohypertrophic, with Internalized capillaries", - "Becker muscular dystrophy", - "dilated cardiomyopathy 3B", - "familial isolated dilated cardiomyopathy", - "progressive muscular dystrophy", + "MYH7-related skeletal myopathy", "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 beta-myosin heavy chain (MYH7)", + "distal myopathy", "neuromuscular disease", + "congenital myopathy", "skeletal muscle disorder", "muscular dystrophy", "human disease or disorder", - "hereditary skeletal muscle disorder", ], - "predicate": "biolink:has_mode_of_inheritance", - "object": "HP:0000006", + "subject_taxon": None, + "subject_taxon_label": None, + "predicate": "biolink:has_phenotype", + "object": "HP:0003805", "original_object": None, "object_namespace": "HP", - "object_category": "biolink:GeneticInheritance", + "object_category": "biolink:PhenotypicQuality", "object_closure": [ "HP:0000001", - "HP:0000006", - "HP:0000005", - "HP:0034345", - ], - "object_label": "Autosomal dominant inheritance (HPO)", + "HP:0004303", + "UPHENO:0001001", + "UPHENO:0001005", + "HP:0011805", + "UPHENO:0001002", + "HP:0000118", + "BFO:0000002", + "HP:0025354", + "BFO:0000020", + "HP:0003011", + "UPHENO:0002816", + "UPHENO:0081581", + "HP:0033127", + "UPHENO:0001003", + "UPHENO:0002536", + "UPHENO:0076692", + "UPHENO:0076710", + "BFO:0000001", + "HP:0003805", + "PATO:0000001", + "BFO:0000001", + "BFO:0000002", + "BFO:0000004", + "BFO:0000040", + "UBERON:0001062", + "CARO:0000000", + "CL:0000000", + "UBERON:0000465", + "UBERON:0000383", + "UBERON:0001015", + "UBERON:0018254", + "UBERON:0005090", + "UBERON:0004120", + "CL:0000003", + "UBERON:0000061", + "UBERON:0001630", + "UBERON:0002385", + "CL:0002371", + "UBERON:0010000", + "UBERON:0000467", + "UBERON:0014892", + "UBERON:0002036", + "CL:0000188", + "UBERON:0000479", + "UBERON:0000468", + "UBERON:0000062", + "UBERON:0011216", + "UBERON:0001134", + ], + "object_label": "Rimmed vacuoles (HPO)", "object_closure_label": [ "All (HPO)", - "Mode of inheritance (HPO)", - "Autosomal dominant inheritance (HPO)", - "Mendelian inheritance", - ], + "Phenotypic abnormality (HPO)", + "Abnormality of the musculature (HPO)", + "Rimmed vacuoles (HPO)", + "Abnormal muscle fiber morphology (HPO)", + "Abnormal skeletal muscle morphology (HPO)", + "Abnormal cellular phenotype (HPO)", + "Abnormality of the musculoskeletal system (HPO)", + "anatomical structure", + "organ", + "musculature of body", + "material anatomical entity", + "anatomical system", + "multicellular organism", + "tissue", + "musculature", + "anatomical entity", + "skeletal muscle tissue", + "muscle organ", + "striated muscle tissue", + "muscle tissue", + "mesoderm-derived structure", + "muscle structure", + "multicellular anatomical structure", + "organ system subdivision", + "skeletal muscle organ", + "skeletal musculature", + ], + "object_taxon": None, + "object_taxon_label": None, "primary_knowledge_source": "infores:hpo-annotations", "aggregator_knowledge_source": ["infores:monarchinitiative"], - "category": "biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation", + "category": "biolink:DiseaseToPhenotypicFeatureAssociation", "negated": None, - "provided_by": "hpoa_disease_mode_of_inheritance_edges", - "publications": ["OMIM:159050"], + "provided_by": "hpoa_disease_phenotype_edges", + "publications": ["OMIM:160500"], "qualifiers": [], "frequency_qualifier": None, "has_evidence": ["ECO:0000501"], @@ -335,77 +541,163 @@ def associations(): "stage_qualifier_closure_label": [], }, { - "id": "uuid:c3367408-212f-11ee-873a-cd90a19c4085", - "subject": "MONDO:0008049", - "original_subject": "OMIM:160300", + "id": "uuid:5ebb4d1e-212f-11ee-873a-cd90a19c4085", + "subject": "MONDO:0010401", + "original_subject": "OMIM:300696", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ + "MONDO:0004994", "MONDO:0000001", "MONDO:0005071", + "MONDO:0005267", "MONDO:0020121", - "MONDO:0700223", + "MONDO:0004995", "BFO:0000002", + "MONDO:0010401", "BFO:0000017", - "MONDO:0008049", "BFO:0000020", + "MONDO:0016106", + "MONDO:0005217", "BFO:0000016", "MONDO:0020120", "MONDO:0019056", "MONDO:0700096", + "MONDO:0000591", "MONDO:0005218", "MONDO:0005336", "MONDO:0002081", + "MONDO:0016333", + "MONDO:0016830", "OGMS:0000031", + "MONDO:0005021", "MONDO:0003847", "MONDO:0003939", "BFO:0000001", - "MONDO:0018949", ], - "subject_label": "myopathy, distal, infantile-onset", + "subject_label": "X-linked myopathy with postural muscle atrophy", "subject_closure_label": [ "disease or disorder", + "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", - "myopathy, distal, infantile-onset", - "distal myopathy", + "X-linked myopathy with postural muscle atrophy", + "progressive muscular dystrophy", + "familial dilated cardiomyopathy", + "Emery-Dreifuss muscular dystrophy", "neuromuscular disease", "skeletal muscle disorder", "muscular dystrophy", "human disease or disorder", - "hereditary skeletal muscle disorder", ], - "predicate": "biolink:has_mode_of_inheritance", - "object": "HP:0000006", + "subject_taxon": None, + "subject_taxon_label": None, + "predicate": "biolink:has_phenotype", + "object": "HP:0003805", "original_object": None, "object_namespace": "HP", - "object_category": "biolink:GeneticInheritance", + "object_category": "biolink:PhenotypicQuality", "object_closure": [ "HP:0000001", - "HP:0000006", - "HP:0000005", - "HP:0034345", - ], - "object_label": "Autosomal dominant inheritance (HPO)", + "HP:0004303", + "UPHENO:0001001", + "UPHENO:0001005", + "HP:0011805", + "UPHENO:0001002", + "HP:0000118", + "BFO:0000002", + "HP:0025354", + "BFO:0000020", + "HP:0003011", + "UPHENO:0002816", + "UPHENO:0081581", + "HP:0033127", + "UPHENO:0001003", + "UPHENO:0002536", + "UPHENO:0076692", + "UPHENO:0076710", + "BFO:0000001", + "HP:0003805", + "PATO:0000001", + "BFO:0000001", + "BFO:0000002", + "BFO:0000004", + "BFO:0000040", + "UBERON:0001062", + "CARO:0000000", + "CL:0000000", + "UBERON:0000465", + "UBERON:0000383", + "UBERON:0001015", + "UBERON:0018254", + "UBERON:0005090", + "UBERON:0004120", + "CL:0000003", + "UBERON:0000061", + "UBERON:0001630", + "UBERON:0002385", + "CL:0002371", + "UBERON:0010000", + "UBERON:0000467", + "UBERON:0014892", + "UBERON:0002036", + "CL:0000188", + "UBERON:0000479", + "UBERON:0000468", + "UBERON:0000062", + "UBERON:0011216", + "UBERON:0001134", + ], + "object_label": "Rimmed vacuoles (HPO)", "object_closure_label": [ "All (HPO)", - "Mode of inheritance (HPO)", - "Autosomal dominant inheritance (HPO)", - "Mendelian inheritance", - ], + "Phenotypic abnormality (HPO)", + "Abnormality of the musculature (HPO)", + "Rimmed vacuoles (HPO)", + "Abnormal muscle fiber morphology (HPO)", + "Abnormal skeletal muscle morphology (HPO)", + "Abnormal cellular phenotype (HPO)", + "Abnormality of the musculoskeletal system (HPO)", + "anatomical structure", + "organ", + "musculature of body", + "material anatomical entity", + "anatomical system", + "multicellular organism", + "tissue", + "musculature", + "anatomical entity", + "skeletal muscle tissue", + "muscle organ", + "striated muscle tissue", + "muscle tissue", + "mesoderm-derived structure", + "muscle structure", + "multicellular anatomical structure", + "organ system subdivision", + "skeletal muscle organ", + "skeletal musculature", + ], + "object_taxon": None, + "object_taxon_label": None, "primary_knowledge_source": "infores:hpo-annotations", "aggregator_knowledge_source": ["infores:monarchinitiative"], - "category": "biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation", + "category": "biolink:DiseaseToPhenotypicFeatureAssociation", "negated": None, - "provided_by": "hpoa_disease_mode_of_inheritance_edges", - "publications": ["OMIM:160300"], + "provided_by": "hpoa_disease_phenotype_edges", + "publications": ["OMIM:300696"], "qualifiers": [], "frequency_qualifier": None, - "has_evidence": ["ECO:0000304"], + "has_evidence": ["ECO:0000501"], "onset_qualifier": None, "sex_qualifier": None, "stage_qualifier": None, @@ -433,40 +725,46 @@ def associations(): "stage_qualifier_closure_label": [], }, { - "id": "uuid:c39b4534-212f-11ee-873a-cd90a19c4085", - "subject": "MONDO:0008050", - "original_subject": "OMIM:160500", + "id": "uuid:607e98ad-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:0000429", "MONDO:0005071", "MONDO:0020121", - "MONDO:0700223", + "MONDO:0100175", "BFO:0000002", "MONDO:0019952", "BFO:0000017", "BFO:0000020", - "MONDO:0008050", - "MONDO:0016195", + "MONDO:0016191", "BFO:0000016", "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:0002320", + "MONDO:0016108", "MONDO:0018949", ], - "subject_label": "MYH7-related skeletal myopathy", + "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", @@ -474,44 +772,118 @@ def associations(): "nervous system disorder", "obsolete muscular disorder", "myopathy", - "MYH7-related skeletal myopathy", + "tibial muscular dystrophy", + "autosomal dominant distal myopathy", "qualitative or quantitative protein defects in neuromuscular diseases", - "qualitative or quantitative defects of beta-myosin heavy chain (MYH7)", + "qualitative or quantitative defects of titin", "distal myopathy", "neuromuscular disease", "congenital myopathy", "skeletal muscle disorder", "muscular dystrophy", + "TTN-related myopathy", + "autosomal dominant titinopathy", "human disease or disorder", - "hereditary skeletal muscle disorder", ], - "predicate": "biolink:has_mode_of_inheritance", - "object": "HP:0000006", + "subject_taxon": None, + "subject_taxon_label": None, + "predicate": "biolink:has_phenotype", + "object": "HP:0003805", "original_object": None, "object_namespace": "HP", - "object_category": "biolink:GeneticInheritance", + "object_category": "biolink:PhenotypicQuality", "object_closure": [ "HP:0000001", - "HP:0000006", - "HP:0000005", - "HP:0034345", - ], - "object_label": "Autosomal dominant inheritance (HPO)", + "HP:0004303", + "UPHENO:0001001", + "UPHENO:0001005", + "HP:0011805", + "UPHENO:0001002", + "HP:0000118", + "BFO:0000002", + "HP:0025354", + "BFO:0000020", + "HP:0003011", + "UPHENO:0002816", + "UPHENO:0081581", + "HP:0033127", + "UPHENO:0001003", + "UPHENO:0002536", + "UPHENO:0076692", + "UPHENO:0076710", + "BFO:0000001", + "HP:0003805", + "PATO:0000001", + "BFO:0000001", + "BFO:0000002", + "BFO:0000004", + "BFO:0000040", + "UBERON:0001062", + "CARO:0000000", + "CL:0000000", + "UBERON:0000465", + "UBERON:0000383", + "UBERON:0001015", + "UBERON:0018254", + "UBERON:0005090", + "UBERON:0004120", + "CL:0000003", + "UBERON:0000061", + "UBERON:0001630", + "UBERON:0002385", + "CL:0002371", + "UBERON:0010000", + "UBERON:0000467", + "UBERON:0014892", + "UBERON:0002036", + "CL:0000188", + "UBERON:0000479", + "UBERON:0000468", + "UBERON:0000062", + "UBERON:0011216", + "UBERON:0001134", + ], + "object_label": "Rimmed vacuoles (HPO)", "object_closure_label": [ "All (HPO)", - "Mode of inheritance (HPO)", - "Autosomal dominant inheritance (HPO)", - "Mendelian inheritance", - ], + "Phenotypic abnormality (HPO)", + "Abnormality of the musculature (HPO)", + "Rimmed vacuoles (HPO)", + "Abnormal muscle fiber morphology (HPO)", + "Abnormal skeletal muscle morphology (HPO)", + "Abnormal cellular phenotype (HPO)", + "Abnormality of the musculoskeletal system (HPO)", + "anatomical structure", + "organ", + "musculature of body", + "material anatomical entity", + "anatomical system", + "multicellular organism", + "tissue", + "musculature", + "anatomical entity", + "skeletal muscle tissue", + "muscle organ", + "striated muscle tissue", + "muscle tissue", + "mesoderm-derived structure", + "muscle structure", + "multicellular anatomical structure", + "organ system subdivision", + "skeletal muscle organ", + "skeletal musculature", + ], + "object_taxon": None, + "object_taxon_label": None, "primary_knowledge_source": "infores:hpo-annotations", "aggregator_knowledge_source": ["infores:monarchinitiative"], - "category": "biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation", + "category": "biolink:DiseaseToPhenotypicFeatureAssociation", "negated": None, - "provided_by": "hpoa_disease_mode_of_inheritance_edges", - "publications": ["PMID:15322983"], + "provided_by": "hpoa_disease_phenotype_edges", + "publications": ["OMIM:600334"], "qualifiers": [], "frequency_qualifier": None, - "has_evidence": ["ECO:0000269"], + "has_evidence": ["ECO:0000304"], "onset_qualifier": None, "sex_qualifier": None, "stage_qualifier": None, @@ -539,106 +911,156 @@ def associations(): "stage_qualifier_closure_label": [], }, { - "id": "uuid:c2d3e237-212f-11ee-873a-cd90a19c4085", - "subject": "MONDO:0008056", - "original_subject": "OMIM:160900", + "id": "uuid:5f90dae3-212f-11ee-873a-cd90a19c4085", + "subject": "MONDO:0011170", + "original_subject": "OMIM:601954", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ - "MONDO:0004994", - "MONDO:0020158", "MONDO:0000001", - "MONDO:0016107", + "MONDO:0016971", + "MONDO:0000429", "MONDO:0005071", - "MONDO:0005267", "MONDO:0020121", - "MONDO:0005045", - "MONDO:0004995", - "MONDO:0700223", "BFO:0000002", "BFO:0000017", "BFO:0000020", + "MONDO:0006025", "MONDO:0016106", - "MONDO:0005217", - "MONDO:0024573", - "MONDO:0003382", "BFO:0000016", "MONDO:0020120", "MONDO:0019056", - "MONDO:0008056", + "MONDO:0016139", "MONDO:0700096", - "MONDO:0000591", - "MONDO:0024458", + "MONDO:0011170", "MONDO:0005218", "MONDO:0005336", "MONDO:0002081", - "MONDO:0002254", "OGMS:0000031", + "MONDO:0016192", "MONDO:0003847", "MONDO:0003939", - "MONDO:0002022", - "MONDO:0016120", "BFO:0000001", - "MONDO:0000462", - "MONDO:0005328", + "MONDO:0015152", ], - "subject_label": "myotonic dystrophy type 1", + "subject_label": "autosomal recessive limb-girdle muscular dystrophy type 2G", "subject_closure_label": [ "disease or disorder", - "eye adnexa disorder", - "intrinsic cardiomyopathy", - "disorder of orbital region", + "autosomal genetic disease", "musculoskeletal 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", - "myotonic dystrophy type 1", + "autosomal recessive disease", + "autosomal recessive limb-girdle muscular dystrophy type 2G", + "autosomal recessive limb-girdle muscular dystrophy", "progressive muscular dystrophy", - "myotonic dystrophy", - "myotonic syndrome", + "qualitative or quantitative protein defects in neuromuscular diseases", + "qualitative or quantitative defects of telethonin", + "limb-girdle muscular dystrophy", "neuromuscular disease", "skeletal muscle disorder", "muscular dystrophy", - "eyelids malposition disorder", - "disorder of visual system", - "familial hypertrophic cardiomyopathy", "human disease or disorder", - "hereditary skeletal muscle disorder", ], - "predicate": "biolink:has_mode_of_inheritance", - "object": "HP:0000006", + "subject_taxon": None, + "subject_taxon_label": None, + "predicate": "biolink:has_phenotype", + "object": "HP:0003805", "original_object": None, "object_namespace": "HP", - "object_category": "biolink:GeneticInheritance", + "object_category": "biolink:PhenotypicQuality", "object_closure": [ "HP:0000001", - "HP:0000006", - "HP:0000005", - "HP:0034345", - ], - "object_label": "Autosomal dominant inheritance (HPO)", + "HP:0004303", + "UPHENO:0001001", + "UPHENO:0001005", + "HP:0011805", + "UPHENO:0001002", + "HP:0000118", + "BFO:0000002", + "HP:0025354", + "BFO:0000020", + "HP:0003011", + "UPHENO:0002816", + "UPHENO:0081581", + "HP:0033127", + "UPHENO:0001003", + "UPHENO:0002536", + "UPHENO:0076692", + "UPHENO:0076710", + "BFO:0000001", + "HP:0003805", + "PATO:0000001", + "BFO:0000001", + "BFO:0000002", + "BFO:0000004", + "BFO:0000040", + "UBERON:0001062", + "CARO:0000000", + "CL:0000000", + "UBERON:0000465", + "UBERON:0000383", + "UBERON:0001015", + "UBERON:0018254", + "UBERON:0005090", + "UBERON:0004120", + "CL:0000003", + "UBERON:0000061", + "UBERON:0001630", + "UBERON:0002385", + "CL:0002371", + "UBERON:0010000", + "UBERON:0000467", + "UBERON:0014892", + "UBERON:0002036", + "CL:0000188", + "UBERON:0000479", + "UBERON:0000468", + "UBERON:0000062", + "UBERON:0011216", + "UBERON:0001134", + ], + "object_label": "Rimmed vacuoles (HPO)", "object_closure_label": [ "All (HPO)", - "Mode of inheritance (HPO)", - "Autosomal dominant inheritance (HPO)", - "Mendelian inheritance", - ], + "Phenotypic abnormality (HPO)", + "Abnormality of the musculature (HPO)", + "Rimmed vacuoles (HPO)", + "Abnormal muscle fiber morphology (HPO)", + "Abnormal skeletal muscle morphology (HPO)", + "Abnormal cellular phenotype (HPO)", + "Abnormality of the musculoskeletal system (HPO)", + "anatomical structure", + "organ", + "musculature of body", + "material anatomical entity", + "anatomical system", + "multicellular organism", + "tissue", + "musculature", + "anatomical entity", + "skeletal muscle tissue", + "muscle organ", + "striated muscle tissue", + "muscle tissue", + "mesoderm-derived structure", + "muscle structure", + "multicellular anatomical structure", + "organ system subdivision", + "skeletal muscle organ", + "skeletal musculature", + ], + "object_taxon": None, + "object_taxon_label": None, "primary_knowledge_source": "infores:hpo-annotations", "aggregator_knowledge_source": ["infores:monarchinitiative"], - "category": "biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation", + "category": "biolink:DiseaseToPhenotypicFeatureAssociation", "negated": None, - "provided_by": "hpoa_disease_mode_of_inheritance_edges", - "publications": ["OMIM:160900"], + "provided_by": "hpoa_disease_phenotype_edges", + "publications": ["OMIM:601954"], "qualifiers": [], "frequency_qualifier": None, "has_evidence": ["ECO:0000501"], @@ -669,88 +1091,166 @@ def associations(): "stage_qualifier_closure_label": [], }, { - "id": "uuid:c400607b-212f-11ee-873a-cd90a19c4085", - "subject": "MONDO:0008116", - "original_subject": "OMIM:164300", + "id": "uuid:63fd8f8b-212f-11ee-873a-cd90a19c4085", + "subject": "MONDO:0011362", + "original_subject": "OMIM:603689", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ - "MONDO:0020158", "MONDO:0000001", + "MONDO:0016112", + "MONDO:0000429", "MONDO:0005071", "MONDO:0020121", - "MONDO:0700223", - "MONDO:0004746", + "MONDO:0100175", "BFO:0000002", + "MONDO:0019952", "BFO:0000017", "BFO:0000020", "MONDO:0016106", - "MONDO:0003382", + "MONDO:0016191", "BFO:0000016", "MONDO:0020120", "MONDO:0019056", + "MONDO:0100494", + "MONDO:0016139", "MONDO:0700096", - "MONDO:0024458", "MONDO:0005218", "MONDO:0005336", "MONDO:0002081", - "MONDO:0008116", + "MONDO:0000426", + "MONDO:0011362", "OGMS:0000031", "MONDO:0003847", "MONDO:0003939", - "MONDO:0002022", "BFO:0000001", - "MONDO:0000462", - "MONDO:0005328", + "MONDO:0002320", + "MONDO:0016108", + "MONDO:0018949", ], - "subject_label": "oculopharyngeal muscular dystrophy", + "subject_label": "myopathy, myofibrillar, 9, with early respiratory failure", "subject_closure_label": [ "disease or disorder", - "eye adnexa disorder", - "disorder of orbital region", + "autosomal dominant disease", + "autosomal genetic disease", "musculoskeletal system disorder", - "eyelid disorder", + "congenital nervous system disorder", "hereditary disease", "muscle tissue disorder", - "myopathy of extraocular muscle", "nervous system disorder", "obsolete muscular disorder", - "eye disorder", "myopathy", - "oculopharyngeal muscular dystrophy", + "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", - "eyelids malposition disorder", - "disorder of visual system", + "TTN-related myopathy", + "autosomal dominant titinopathy", "human disease or disorder", - "hereditary skeletal muscle disorder", ], - "predicate": "biolink:has_mode_of_inheritance", - "object": "HP:0000006", + "subject_taxon": None, + "subject_taxon_label": None, + "predicate": "biolink:has_phenotype", + "object": "HP:0003805", "original_object": None, "object_namespace": "HP", - "object_category": "biolink:GeneticInheritance", + "object_category": "biolink:PhenotypicQuality", "object_closure": [ "HP:0000001", - "HP:0000006", - "HP:0000005", - "HP:0034345", - ], - "object_label": "Autosomal dominant inheritance (HPO)", + "HP:0004303", + "UPHENO:0001001", + "UPHENO:0001005", + "HP:0011805", + "UPHENO:0001002", + "HP:0000118", + "BFO:0000002", + "HP:0025354", + "BFO:0000020", + "HP:0003011", + "UPHENO:0002816", + "UPHENO:0081581", + "HP:0033127", + "UPHENO:0001003", + "UPHENO:0002536", + "UPHENO:0076692", + "UPHENO:0076710", + "BFO:0000001", + "HP:0003805", + "PATO:0000001", + "BFO:0000001", + "BFO:0000002", + "BFO:0000004", + "BFO:0000040", + "UBERON:0001062", + "CARO:0000000", + "CL:0000000", + "UBERON:0000465", + "UBERON:0000383", + "UBERON:0001015", + "UBERON:0018254", + "UBERON:0005090", + "UBERON:0004120", + "CL:0000003", + "UBERON:0000061", + "UBERON:0001630", + "UBERON:0002385", + "CL:0002371", + "UBERON:0010000", + "UBERON:0000467", + "UBERON:0014892", + "UBERON:0002036", + "CL:0000188", + "UBERON:0000479", + "UBERON:0000468", + "UBERON:0000062", + "UBERON:0011216", + "UBERON:0001134", + ], + "object_label": "Rimmed vacuoles (HPO)", "object_closure_label": [ "All (HPO)", - "Mode of inheritance (HPO)", - "Autosomal dominant inheritance (HPO)", - "Mendelian inheritance", - ], + "Phenotypic abnormality (HPO)", + "Abnormality of the musculature (HPO)", + "Rimmed vacuoles (HPO)", + "Abnormal muscle fiber morphology (HPO)", + "Abnormal skeletal muscle morphology (HPO)", + "Abnormal cellular phenotype (HPO)", + "Abnormality of the musculoskeletal system (HPO)", + "anatomical structure", + "organ", + "musculature of body", + "material anatomical entity", + "anatomical system", + "multicellular organism", + "tissue", + "musculature", + "anatomical entity", + "skeletal muscle tissue", + "muscle organ", + "striated muscle tissue", + "muscle tissue", + "mesoderm-derived structure", + "muscle structure", + "multicellular anatomical structure", + "organ system subdivision", + "skeletal muscle organ", + "skeletal musculature", + ], + "object_taxon": None, + "object_taxon_label": None, "primary_knowledge_source": "infores:hpo-annotations", "aggregator_knowledge_source": ["infores:monarchinitiative"], - "category": "biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation", + "category": "biolink:DiseaseToPhenotypicFeatureAssociation", "negated": None, - "provided_by": "hpoa_disease_mode_of_inheritance_edges", - "publications": ["PMID:9462747"], + "provided_by": "hpoa_disease_phenotype_edges", + "publications": ["PMID:22577215"], "qualifiers": [], "frequency_qualifier": None, "has_evidence": ["ECO:0000269"], @@ -781,87 +1281,153 @@ def associations(): "stage_qualifier_closure_label": [], }, { - "id": "uuid:c3cdaddf-212f-11ee-873a-cd90a19c4085", - "subject": "MONDO:0009681", - "original_subject": "OMIM:254090", + "id": "uuid:649c482d-212f-11ee-873a-cd90a19c4085", + "subject": "MONDO:0011466", + "original_subject": "OMIM:604454", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ "MONDO:0000001", + "MONDO:0011466", + "MONDO:0000429", "MONDO:0005071", "MONDO:0020121", - "MONDO:0700223", "BFO:0000002", - "MONDO:0019952", "BFO:0000017", "BFO:0000020", - "MONDO:0100225", "BFO:0000016", "MONDO:0020120", "MONDO:0019056", - "MONDO:0016139", "MONDO:0700096", "MONDO:0005218", "MONDO:0005336", "MONDO:0002081", - "MONDO:0009681", + "MONDO:0000426", "OGMS:0000031", "MONDO:0003847", "MONDO:0003939", "BFO:0000001", - "MONDO:0002320", - "MONDO:0000355", - "MONDO:0019950", + "MONDO:0016108", + "MONDO:0018949", ], - "subject_label": "Ullrich congenital muscular dystrophy 1", + "subject_label": "distal myopathy, Welander type", "subject_closure_label": [ "disease or disorder", - "Ullrich congenital muscular dystrophy", + "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", - "Ullrich congenital muscular dystrophy 1", - "qualitative or quantitative protein defects in neuromuscular diseases", + "distal myopathy, Welander type", + "autosomal dominant distal myopathy", + "distal myopathy", "neuromuscular disease", - "congenital muscular dystrophy", - "congenital myopathy", "skeletal muscle disorder", "muscular dystrophy", - "collagen 6-related myopathy", "human disease or disorder", - "hereditary skeletal muscle disorder", ], - "predicate": "biolink:has_mode_of_inheritance", - "object": "HP:0000006", + "subject_taxon": None, + "subject_taxon_label": None, + "predicate": "biolink:has_phenotype", + "object": "HP:0003805", "original_object": None, "object_namespace": "HP", - "object_category": "biolink:GeneticInheritance", + "object_category": "biolink:PhenotypicQuality", "object_closure": [ "HP:0000001", - "HP:0000006", - "HP:0000005", - "HP:0034345", - ], - "object_label": "Autosomal dominant inheritance (HPO)", + "HP:0004303", + "UPHENO:0001001", + "UPHENO:0001005", + "HP:0011805", + "UPHENO:0001002", + "HP:0000118", + "BFO:0000002", + "HP:0025354", + "BFO:0000020", + "HP:0003011", + "UPHENO:0002816", + "UPHENO:0081581", + "HP:0033127", + "UPHENO:0001003", + "UPHENO:0002536", + "UPHENO:0076692", + "UPHENO:0076710", + "BFO:0000001", + "HP:0003805", + "PATO:0000001", + "BFO:0000001", + "BFO:0000002", + "BFO:0000004", + "BFO:0000040", + "UBERON:0001062", + "CARO:0000000", + "CL:0000000", + "UBERON:0000465", + "UBERON:0000383", + "UBERON:0001015", + "UBERON:0018254", + "UBERON:0005090", + "UBERON:0004120", + "CL:0000003", + "UBERON:0000061", + "UBERON:0001630", + "UBERON:0002385", + "CL:0002371", + "UBERON:0010000", + "UBERON:0000467", + "UBERON:0014892", + "UBERON:0002036", + "CL:0000188", + "UBERON:0000479", + "UBERON:0000468", + "UBERON:0000062", + "UBERON:0011216", + "UBERON:0001134", + ], + "object_label": "Rimmed vacuoles (HPO)", "object_closure_label": [ "All (HPO)", - "Mode of inheritance (HPO)", - "Autosomal dominant inheritance (HPO)", - "Mendelian inheritance", - ], + "Phenotypic abnormality (HPO)", + "Abnormality of the musculature (HPO)", + "Rimmed vacuoles (HPO)", + "Abnormal muscle fiber morphology (HPO)", + "Abnormal skeletal muscle morphology (HPO)", + "Abnormal cellular phenotype (HPO)", + "Abnormality of the musculoskeletal system (HPO)", + "anatomical structure", + "organ", + "musculature of body", + "material anatomical entity", + "anatomical system", + "multicellular organism", + "tissue", + "musculature", + "anatomical entity", + "skeletal muscle tissue", + "muscle organ", + "striated muscle tissue", + "muscle tissue", + "mesoderm-derived structure", + "muscle structure", + "multicellular anatomical structure", + "organ system subdivision", + "skeletal muscle organ", + "skeletal musculature", + ], + "object_taxon": None, + "object_taxon_label": None, "primary_knowledge_source": "infores:hpo-annotations", "aggregator_knowledge_source": ["infores:monarchinitiative"], - "category": "biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation", + "category": "biolink:DiseaseToPhenotypicFeatureAssociation", "negated": None, - "provided_by": "hpoa_disease_mode_of_inheritance_edges", - "publications": ["OMIM:254090"], + "provided_by": "hpoa_disease_phenotype_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, @@ -889,75 +1455,189 @@ def associations(): "stage_qualifier_closure_label": [], }, { - "id": "uuid:c275a020-212f-11ee-873a-cd90a19c4085", - "subject": "MONDO:0010676", - "original_subject": "OMIM:309950", + "id": "uuid:65070139-212f-11ee-873a-cd90a19c4085", + "subject": "MONDO:0011603", + "original_subject": "OMIM:605820", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ "MONDO:0000001", + "MONDO:0002245", + "MONDO:0016112", + "MONDO:0000429", + "MONDO:0005570", "MONDO:0005071", "MONDO:0020121", - "MONDO:0700223", + "MONDO:0021166", + "MONDO:0024322", "BFO:0000002", + "MONDO:0016200", "BFO:0000017", "BFO:0000020", + "MONDO:0100241", + "MONDO:0006025", + "MONDO:0007827", + "MONDO:0011603", "BFO:0000016", "MONDO:0020120", "MONDO:0019056", + "MONDO:0016139", "MONDO:0700096", "MONDO:0005218", "MONDO:0005336", + "MONDO:0009332", "MONDO:0002081", + "MONDO:0021167", + "MONDO:0016109", + "MONDO:0018795", + "MONDO:0017749", + "MONDO:0002049", "OGMS:0000031", "MONDO:0003847", "MONDO:0003939", + "MONDO:0015286", "BFO:0000001", - "MONDO:0010676", + "MONDO:0002320", + "MONDO:0019052", + "MONDO:0005066", + "MONDO:0018949", ], - "subject_label": "muscular dystrophy, Hemizygous lethal type", + "subject_label": "GNE myopathy", "subject_closure_label": [ "disease or disorder", + "autosomal genetic disease", + "thrombocytopenia", "musculoskeletal system disorder", + "blood platelet disease", + "congenital nervous system disorder", "hereditary disease", "muscle tissue disorder", + "metabolic disease", "nervous system disorder", "obsolete muscular disorder", "myopathy", - "muscular dystrophy, Hemizygous lethal type", + "hematologic disorder", + "autosomal recessive disease", + "inclusion body myositis", + "congenital hematological disorder", + "GNE myopathy", + "congenital disorder of glycosylation", + "autosomal recessive distal myopathy", + "hereditary inclusion-body myopathy", + "qualitative or quantitative protein defects in neuromuscular diseases", + "qualitative or quantitative defects of glucosamine (UDP-N-acetyl)-2-epimerase/N-acetylmannosamine kinase", + "disorder of multiple glycosylation", + "syndromic constitutional thrombocytopenia", + "distal myopathy", + "inborn errors of metabolism", "neuromuscular disease", "skeletal muscle disorder", "muscular dystrophy", + "inflammatory disease", + "myositis disease", + "disorder of glycosylation", + "inherited thrombocytopenia", "human disease or disorder", - "hereditary skeletal muscle disorder", ], - "predicate": "biolink:has_mode_of_inheritance", - "object": "HP:0000006", + "subject_taxon": None, + "subject_taxon_label": None, + "predicate": "biolink:has_phenotype", + "object": "HP:0003805", "original_object": None, "object_namespace": "HP", - "object_category": "biolink:GeneticInheritance", + "object_category": "biolink:PhenotypicQuality", "object_closure": [ "HP:0000001", - "HP:0000006", - "HP:0000005", - "HP:0034345", - ], - "object_label": "Autosomal dominant inheritance (HPO)", + "HP:0004303", + "UPHENO:0001001", + "UPHENO:0001005", + "HP:0011805", + "UPHENO:0001002", + "HP:0000118", + "BFO:0000002", + "HP:0025354", + "BFO:0000020", + "HP:0003011", + "UPHENO:0002816", + "UPHENO:0081581", + "HP:0033127", + "UPHENO:0001003", + "UPHENO:0002536", + "UPHENO:0076692", + "UPHENO:0076710", + "BFO:0000001", + "HP:0003805", + "PATO:0000001", + "BFO:0000001", + "BFO:0000002", + "BFO:0000004", + "BFO:0000040", + "UBERON:0001062", + "CARO:0000000", + "CL:0000000", + "UBERON:0000465", + "UBERON:0000383", + "UBERON:0001015", + "UBERON:0018254", + "UBERON:0005090", + "UBERON:0004120", + "CL:0000003", + "UBERON:0000061", + "UBERON:0001630", + "UBERON:0002385", + "CL:0002371", + "UBERON:0010000", + "UBERON:0000467", + "UBERON:0014892", + "UBERON:0002036", + "CL:0000188", + "UBERON:0000479", + "UBERON:0000468", + "UBERON:0000062", + "UBERON:0011216", + "UBERON:0001134", + ], + "object_label": "Rimmed vacuoles (HPO)", "object_closure_label": [ "All (HPO)", - "Mode of inheritance (HPO)", - "Autosomal dominant inheritance (HPO)", - "Mendelian inheritance", - ], + "Phenotypic abnormality (HPO)", + "Abnormality of the musculature (HPO)", + "Rimmed vacuoles (HPO)", + "Abnormal muscle fiber morphology (HPO)", + "Abnormal skeletal muscle morphology (HPO)", + "Abnormal cellular phenotype (HPO)", + "Abnormality of the musculoskeletal system (HPO)", + "anatomical structure", + "organ", + "musculature of body", + "material anatomical entity", + "anatomical system", + "multicellular organism", + "tissue", + "musculature", + "anatomical entity", + "skeletal muscle tissue", + "muscle organ", + "striated muscle tissue", + "muscle tissue", + "mesoderm-derived structure", + "muscle structure", + "multicellular anatomical structure", + "organ system subdivision", + "skeletal muscle organ", + "skeletal musculature", + ], + "object_taxon": None, + "object_taxon_label": None, "primary_knowledge_source": "infores:hpo-annotations", "aggregator_knowledge_source": ["infores:monarchinitiative"], - "category": "biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation", + "category": "biolink:DiseaseToPhenotypicFeatureAssociation", "negated": None, - "provided_by": "hpoa_disease_mode_of_inheritance_edges", - "publications": ["OMIM:309950"], + "provided_by": "hpoa_disease_phenotype_edges", + "publications": ["PMID:12177386"], "qualifiers": [], "frequency_qualifier": None, - "has_evidence": ["ECO:0000304"], + "has_evidence": ["ECO:0000269"], "onset_qualifier": None, "sex_qualifier": None, "stage_qualifier": None, @@ -985,29 +1665,26 @@ def associations(): "stage_qualifier_closure_label": [], }, { - "id": "uuid:c336741f-212f-11ee-873a-cd90a19c4085", - "subject": "MONDO:0010870", - "original_subject": "OMIM:600334", + "id": "uuid:60cdba46-212f-11ee-873a-cd90a19c4085", + "subject": "MONDO:0012034", + "original_subject": "OMIM:608423", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ - "MONDO:0010870", "MONDO:0000001", + "MONDO:0016971", "MONDO:0000429", "MONDO:0005071", "MONDO:0020121", - "MONDO:0100175", - "MONDO:0700223", + "MONDO:0012034", "BFO:0000002", - "MONDO:0019952", "BFO:0000017", "BFO:0000020", - "MONDO:0016191", + "MONDO:0016106", "BFO:0000016", "MONDO:0020120", "MONDO:0019056", - "MONDO:0100494", - "MONDO:0016139", + "MONDO:0015151", "MONDO:0700096", "MONDO:0005218", "MONDO:0005336", @@ -1017,63 +1694,126 @@ def associations(): "MONDO:0003847", "MONDO:0003939", "BFO:0000001", - "MONDO:0002320", - "MONDO:0016108", - "MONDO:0018949", ], - "subject_label": "tibial muscular dystrophy", + "subject_label": "autosomal dominant limb-girdle muscular dystrophy type 1F", "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", - "tibial muscular dystrophy", - "autosomal dominant distal myopathy", - "qualitative or quantitative protein defects in neuromuscular diseases", - "qualitative or quantitative defects of titin", - "distal myopathy", + "autosomal dominant limb-girdle muscular dystrophy type 1F", + "muscular dystrophy, limb-girdle, autosomal dominant", + "progressive muscular dystrophy", + "limb-girdle muscular dystrophy", "neuromuscular disease", - "congenital myopathy", "skeletal muscle disorder", "muscular dystrophy", - "TTN-related myopathy", - "autosomal dominant titinopathy", "human disease or disorder", - "hereditary skeletal muscle disorder", ], - "predicate": "biolink:has_mode_of_inheritance", - "object": "HP:0000006", + "subject_taxon": None, + "subject_taxon_label": None, + "predicate": "biolink:has_phenotype", + "object": "HP:0003805", "original_object": None, "object_namespace": "HP", - "object_category": "biolink:GeneticInheritance", + "object_category": "biolink:PhenotypicQuality", "object_closure": [ "HP:0000001", - "HP:0000006", - "HP:0000005", - "HP:0034345", - ], - "object_label": "Autosomal dominant inheritance (HPO)", + "HP:0004303", + "UPHENO:0001001", + "UPHENO:0001005", + "HP:0011805", + "UPHENO:0001002", + "HP:0000118", + "BFO:0000002", + "HP:0025354", + "BFO:0000020", + "HP:0003011", + "UPHENO:0002816", + "UPHENO:0081581", + "HP:0033127", + "UPHENO:0001003", + "UPHENO:0002536", + "UPHENO:0076692", + "UPHENO:0076710", + "BFO:0000001", + "HP:0003805", + "PATO:0000001", + "BFO:0000001", + "BFO:0000002", + "BFO:0000004", + "BFO:0000040", + "UBERON:0001062", + "CARO:0000000", + "CL:0000000", + "UBERON:0000465", + "UBERON:0000383", + "UBERON:0001015", + "UBERON:0018254", + "UBERON:0005090", + "UBERON:0004120", + "CL:0000003", + "UBERON:0000061", + "UBERON:0001630", + "UBERON:0002385", + "CL:0002371", + "UBERON:0010000", + "UBERON:0000467", + "UBERON:0014892", + "UBERON:0002036", + "CL:0000188", + "UBERON:0000479", + "UBERON:0000468", + "UBERON:0000062", + "UBERON:0011216", + "UBERON:0001134", + ], + "object_label": "Rimmed vacuoles (HPO)", "object_closure_label": [ "All (HPO)", - "Mode of inheritance (HPO)", - "Autosomal dominant inheritance (HPO)", - "Mendelian inheritance", - ], + "Phenotypic abnormality (HPO)", + "Abnormality of the musculature (HPO)", + "Rimmed vacuoles (HPO)", + "Abnormal muscle fiber morphology (HPO)", + "Abnormal skeletal muscle morphology (HPO)", + "Abnormal cellular phenotype (HPO)", + "Abnormality of the musculoskeletal system (HPO)", + "anatomical structure", + "organ", + "musculature of body", + "material anatomical entity", + "anatomical system", + "multicellular organism", + "tissue", + "musculature", + "anatomical entity", + "skeletal muscle tissue", + "muscle organ", + "striated muscle tissue", + "muscle tissue", + "mesoderm-derived structure", + "muscle structure", + "multicellular anatomical structure", + "organ system subdivision", + "skeletal muscle organ", + "skeletal musculature", + ], + "object_taxon": None, + "object_taxon_label": None, "primary_knowledge_source": "infores:hpo-annotations", "aggregator_knowledge_source": ["infores:monarchinitiative"], - "category": "biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation", + "category": "biolink:DiseaseToPhenotypicFeatureAssociation", "negated": None, - "provided_by": "hpoa_disease_mode_of_inheritance_edges", - "publications": ["OMIM:600334"], + "provided_by": "hpoa_disease_phenotype_edges", + "publications": ["PMID:23543484"], "qualifiers": [], "frequency_qualifier": None, - "has_evidence": ["ECO:0000501"], + "has_evidence": ["ECO:0000269"], "onset_qualifier": None, "sex_qualifier": None, "stage_qualifier": None, @@ -1101,105 +1841,155 @@ def associations(): "stage_qualifier_closure_label": [], }, { - "id": "uuid:c275a16e-212f-11ee-873a-cd90a19c4085", - "subject": "MONDO:0010912", - "original_subject": "OMIM:600638", + "id": "uuid:62f7ecd4-212f-11ee-873a-cd90a19c4085", + "subject": "MONDO:0012193", + "original_subject": "OMIM:609115", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ - "MONDO:0020158", "MONDO:0000001", - "MONDO:0007614", + "MONDO:0016971", + "MONDO:0000429", "MONDO:0005071", "MONDO:0020121", - "MONDO:0700223", - "MONDO:0004746", "BFO:0000002", - "MONDO:0957003", "BFO:0000017", "BFO:0000020", "MONDO:0016106", - "MONDO:0003382", "BFO:0000016", "MONDO:0020120", "MONDO:0019056", - "MONDO:0003569", + "MONDO:0015151", "MONDO:0700096", - "MONDO:0001584", - "MONDO:0024458", "MONDO:0005218", "MONDO:0005336", "MONDO:0002081", - "MONDO:0100153", + "MONDO:0012193", + "MONDO:0000426", "OGMS:0000031", "MONDO:0003847", - "MONDO:0100154", "MONDO:0003939", - "MONDO:0002022", - "MONDO:0015368", "BFO:0000001", - "MONDO:0000462", - "MONDO:0005328", - "MONDO:0010912", ], - "subject_label": "fibrosis of extraocular muscles, congenital, 3A, with or without extraocular involvement", + "subject_label": "autosomal dominant limb-girdle muscular dystrophy type 1G", "subject_closure_label": [ "disease or disorder", - "eye adnexa disorder", - "ocular motility disease", - "disorder of orbital region", + "autosomal dominant disease", + "autosomal genetic disease", "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", - "congenital fibrosis of extraocular muscles", - "fibrosis of extraocular muscles, congenital, 3A, with or without extraocular involvement", - "neuro-ophthalmological disease", + "autosomal dominant limb-girdle muscular dystrophy type 1G", + "muscular dystrophy, limb-girdle, autosomal dominant", "progressive muscular dystrophy", + "limb-girdle muscular dystrophy", "neuromuscular disease", "skeletal muscle disorder", "muscular dystrophy", - "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_mode_of_inheritance", - "object": "HP:0000006", + "subject_taxon": None, + "subject_taxon_label": None, + "predicate": "biolink:has_phenotype", + "object": "HP:0003805", "original_object": None, "object_namespace": "HP", - "object_category": "biolink:GeneticInheritance", + "object_category": "biolink:PhenotypicQuality", "object_closure": [ "HP:0000001", - "HP:0000006", - "HP:0000005", - "HP:0034345", - ], - "object_label": "Autosomal dominant inheritance (HPO)", + "HP:0004303", + "UPHENO:0001001", + "UPHENO:0001005", + "HP:0011805", + "UPHENO:0001002", + "HP:0000118", + "BFO:0000002", + "HP:0025354", + "BFO:0000020", + "HP:0003011", + "UPHENO:0002816", + "UPHENO:0081581", + "HP:0033127", + "UPHENO:0001003", + "UPHENO:0002536", + "UPHENO:0076692", + "UPHENO:0076710", + "BFO:0000001", + "HP:0003805", + "PATO:0000001", + "BFO:0000001", + "BFO:0000002", + "BFO:0000004", + "BFO:0000040", + "UBERON:0001062", + "CARO:0000000", + "CL:0000000", + "UBERON:0000465", + "UBERON:0000383", + "UBERON:0001015", + "UBERON:0018254", + "UBERON:0005090", + "UBERON:0004120", + "CL:0000003", + "UBERON:0000061", + "UBERON:0001630", + "UBERON:0002385", + "CL:0002371", + "UBERON:0010000", + "UBERON:0000467", + "UBERON:0014892", + "UBERON:0002036", + "CL:0000188", + "UBERON:0000479", + "UBERON:0000468", + "UBERON:0000062", + "UBERON:0011216", + "UBERON:0001134", + ], + "object_label": "Rimmed vacuoles (HPO)", "object_closure_label": [ "All (HPO)", - "Mode of inheritance (HPO)", - "Autosomal dominant inheritance (HPO)", - "Mendelian inheritance", - ], + "Phenotypic abnormality (HPO)", + "Abnormality of the musculature (HPO)", + "Rimmed vacuoles (HPO)", + "Abnormal muscle fiber morphology (HPO)", + "Abnormal skeletal muscle morphology (HPO)", + "Abnormal cellular phenotype (HPO)", + "Abnormality of the musculoskeletal system (HPO)", + "anatomical structure", + "organ", + "musculature of body", + "material anatomical entity", + "anatomical system", + "multicellular organism", + "tissue", + "musculature", + "anatomical entity", + "skeletal muscle tissue", + "muscle organ", + "striated muscle tissue", + "muscle tissue", + "mesoderm-derived structure", + "muscle structure", + "multicellular anatomical structure", + "organ system subdivision", + "skeletal muscle organ", + "skeletal musculature", + ], + "object_taxon": None, + "object_taxon_label": None, "primary_knowledge_source": "infores:hpo-annotations", "aggregator_knowledge_source": ["infores:monarchinitiative"], - "category": "biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation", + "category": "biolink:DiseaseToPhenotypicFeatureAssociation", "negated": None, - "provided_by": "hpoa_disease_mode_of_inheritance_edges", - "publications": ["PMID:20074521"], + "provided_by": "hpoa_disease_phenotype_edges", + "publications": ["OMIM:609115"], "qualifiers": [], "frequency_qualifier": None, - "has_evidence": ["ECO:0000269"], + "has_evidence": ["ECO:0000304"], "onset_qualifier": None, "sex_qualifier": None, "stage_qualifier": None, @@ -1227,95 +2017,153 @@ def associations(): "stage_qualifier_closure_label": [], }, { - "id": "uuid:c367df60-212f-11ee-873a-cd90a19c4085", - "subject": "MONDO:0011266", - "original_subject": "OMIM:602668", + "id": "uuid:5d3057d5-212f-11ee-873a-cd90a19c4085", + "subject": "MONDO:0012410", + "original_subject": "OMIM:610099", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ - "MONDO:0020158", "MONDO:0000001", - "MONDO:0016107", + "MONDO:0000429", "MONDO:0005071", "MONDO:0020121", - "MONDO:0700223", "BFO:0000002", "BFO:0000017", "BFO:0000020", - "MONDO:0016106", - "MONDO:0003382", "BFO:0000016", "MONDO:0020120", "MONDO:0019056", "MONDO:0700096", - "MONDO:0024458", "MONDO:0005218", "MONDO:0005336", "MONDO:0002081", - "MONDO:0002254", - "MONDO:0011266", + "MONDO:0012410", + "MONDO:0000426", "OGMS:0000031", "MONDO:0003847", "MONDO:0003939", - "MONDO:0002022", - "MONDO:0016120", "BFO:0000001", - "MONDO:0000462", - "MONDO:0005328", + "MONDO:0016108", + "MONDO:0018949", ], - "subject_label": "myotonic dystrophy type 2", + "subject_label": "Finnish upper limb-onset distal myopathy", "subject_closure_label": [ "disease or disorder", - "eye adnexa disorder", - "disorder of orbital region", + "autosomal dominant disease", + "autosomal genetic disease", "musculoskeletal system disorder", - "syndromic disease", - "eyelid disorder", "hereditary disease", "muscle tissue disorder", "nervous system disorder", "obsolete muscular disorder", - "eye disorder", "myopathy", - "myotonic dystrophy type 2", - "progressive muscular dystrophy", - "myotonic dystrophy", - "myotonic syndrome", + "Finnish upper limb-onset distal myopathy", + "autosomal dominant distal myopathy", + "distal myopathy", "neuromuscular disease", "skeletal muscle disorder", "muscular dystrophy", - "eyelids malposition disorder", - "disorder of visual system", "human disease or disorder", - "hereditary skeletal muscle disorder", ], - "predicate": "biolink:has_mode_of_inheritance", - "object": "HP:0000006", + "subject_taxon": None, + "subject_taxon_label": None, + "predicate": "biolink:has_phenotype", + "object": "HP:0003805", "original_object": None, "object_namespace": "HP", - "object_category": "biolink:GeneticInheritance", + "object_category": "biolink:PhenotypicQuality", "object_closure": [ "HP:0000001", - "HP:0000006", - "HP:0000005", - "HP:0034345", - ], - "object_label": "Autosomal dominant inheritance (HPO)", + "HP:0004303", + "UPHENO:0001001", + "UPHENO:0001005", + "HP:0011805", + "UPHENO:0001002", + "HP:0000118", + "BFO:0000002", + "HP:0025354", + "BFO:0000020", + "HP:0003011", + "UPHENO:0002816", + "UPHENO:0081581", + "HP:0033127", + "UPHENO:0001003", + "UPHENO:0002536", + "UPHENO:0076692", + "UPHENO:0076710", + "BFO:0000001", + "HP:0003805", + "PATO:0000001", + "BFO:0000001", + "BFO:0000002", + "BFO:0000004", + "BFO:0000040", + "UBERON:0001062", + "CARO:0000000", + "CL:0000000", + "UBERON:0000465", + "UBERON:0000383", + "UBERON:0001015", + "UBERON:0018254", + "UBERON:0005090", + "UBERON:0004120", + "CL:0000003", + "UBERON:0000061", + "UBERON:0001630", + "UBERON:0002385", + "CL:0002371", + "UBERON:0010000", + "UBERON:0000467", + "UBERON:0014892", + "UBERON:0002036", + "CL:0000188", + "UBERON:0000479", + "UBERON:0000468", + "UBERON:0000062", + "UBERON:0011216", + "UBERON:0001134", + ], + "object_label": "Rimmed vacuoles (HPO)", "object_closure_label": [ "All (HPO)", - "Mode of inheritance (HPO)", - "Autosomal dominant inheritance (HPO)", - "Mendelian inheritance", - ], + "Phenotypic abnormality (HPO)", + "Abnormality of the musculature (HPO)", + "Rimmed vacuoles (HPO)", + "Abnormal muscle fiber morphology (HPO)", + "Abnormal skeletal muscle morphology (HPO)", + "Abnormal cellular phenotype (HPO)", + "Abnormality of the musculoskeletal system (HPO)", + "anatomical structure", + "organ", + "musculature of body", + "material anatomical entity", + "anatomical system", + "multicellular organism", + "tissue", + "musculature", + "anatomical entity", + "skeletal muscle tissue", + "muscle organ", + "striated muscle tissue", + "muscle tissue", + "mesoderm-derived structure", + "muscle structure", + "multicellular anatomical structure", + "organ system subdivision", + "skeletal muscle organ", + "skeletal musculature", + ], + "object_taxon": None, + "object_taxon_label": None, "primary_knowledge_source": "infores:hpo-annotations", "aggregator_knowledge_source": ["infores:monarchinitiative"], - "category": "biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation", + "category": "biolink:DiseaseToPhenotypicFeatureAssociation", "negated": None, - "provided_by": "hpoa_disease_mode_of_inheritance_edges", - "publications": ["PMID:11486088"], + "provided_by": "hpoa_disease_phenotype_edges", + "publications": ["OMIM:610099"], "qualifiers": [], "frequency_qualifier": None, - "has_evidence": ["ECO:0000269"], + "has_evidence": ["ECO:0000501"], "onset_qualifier": None, "sex_qualifier": None, "stage_qualifier": None, @@ -1343,96 +2191,144 @@ def associations(): "stage_qualifier_closure_label": [], }, { - "id": "uuid:c3cdac2c-212f-11ee-873a-cd90a19c4085", - "subject": "MONDO:0011362", - "original_subject": "OMIM:603689", + "id": "uuid:64816953-212f-11ee-873a-cd90a19c4085", + "subject": "MONDO:0014945", + "original_subject": "OMIM:617158", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ "MONDO:0000001", - "MONDO:0016112", - "MONDO:0000429", "MONDO:0005071", "MONDO:0020121", - "MONDO:0100175", - "MONDO:0700223", "BFO:0000002", - "MONDO:0019952", "BFO:0000017", "BFO:0000020", - "MONDO:0016106", - "MONDO:0016191", "BFO:0000016", "MONDO:0020120", + "MONDO:0014945", "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": "myopathy, myofibrillar, 9, with early respiratory failure", + "subject_label": "myopathy, distal, with rimmed vacuoles", "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", - "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", + "myopathy, distal, with rimmed vacuoles", "distal myopathy", "neuromuscular disease", - "congenital myopathy", "skeletal muscle disorder", "muscular dystrophy", - "TTN-related myopathy", - "autosomal dominant titinopathy", "human disease or disorder", - "hereditary skeletal muscle disorder", ], - "predicate": "biolink:has_mode_of_inheritance", - "object": "HP:0000006", + "subject_taxon": None, + "subject_taxon_label": None, + "predicate": "biolink:has_phenotype", + "object": "HP:0003805", "original_object": None, "object_namespace": "HP", - "object_category": "biolink:GeneticInheritance", + "object_category": "biolink:PhenotypicQuality", "object_closure": [ "HP:0000001", - "HP:0000006", - "HP:0000005", - "HP:0034345", - ], - "object_label": "Autosomal dominant inheritance (HPO)", + "HP:0004303", + "UPHENO:0001001", + "UPHENO:0001005", + "HP:0011805", + "UPHENO:0001002", + "HP:0000118", + "BFO:0000002", + "HP:0025354", + "BFO:0000020", + "HP:0003011", + "UPHENO:0002816", + "UPHENO:0081581", + "HP:0033127", + "UPHENO:0001003", + "UPHENO:0002536", + "UPHENO:0076692", + "UPHENO:0076710", + "BFO:0000001", + "HP:0003805", + "PATO:0000001", + "BFO:0000001", + "BFO:0000002", + "BFO:0000004", + "BFO:0000040", + "UBERON:0001062", + "CARO:0000000", + "CL:0000000", + "UBERON:0000465", + "UBERON:0000383", + "UBERON:0001015", + "UBERON:0018254", + "UBERON:0005090", + "UBERON:0004120", + "CL:0000003", + "UBERON:0000061", + "UBERON:0001630", + "UBERON:0002385", + "CL:0002371", + "UBERON:0010000", + "UBERON:0000467", + "UBERON:0014892", + "UBERON:0002036", + "CL:0000188", + "UBERON:0000479", + "UBERON:0000468", + "UBERON:0000062", + "UBERON:0011216", + "UBERON:0001134", + ], + "object_label": "Rimmed vacuoles (HPO)", "object_closure_label": [ "All (HPO)", - "Mode of inheritance (HPO)", - "Autosomal dominant inheritance (HPO)", - "Mendelian inheritance", - ], + "Phenotypic abnormality (HPO)", + "Abnormality of the musculature (HPO)", + "Rimmed vacuoles (HPO)", + "Abnormal muscle fiber morphology (HPO)", + "Abnormal skeletal muscle morphology (HPO)", + "Abnormal cellular phenotype (HPO)", + "Abnormality of the musculoskeletal system (HPO)", + "anatomical structure", + "organ", + "musculature of body", + "material anatomical entity", + "anatomical system", + "multicellular organism", + "tissue", + "musculature", + "anatomical entity", + "skeletal muscle tissue", + "muscle organ", + "striated muscle tissue", + "muscle tissue", + "mesoderm-derived structure", + "muscle structure", + "multicellular anatomical structure", + "organ system subdivision", + "skeletal muscle organ", + "skeletal musculature", + ], + "object_taxon": None, + "object_taxon_label": None, "primary_knowledge_source": "infores:hpo-annotations", "aggregator_knowledge_source": ["infores:monarchinitiative"], - "category": "biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation", + "category": "biolink:DiseaseToPhenotypicFeatureAssociation", "negated": None, - "provided_by": "hpoa_disease_mode_of_inheritance_edges", - "publications": ["PMID:22577215"], + "provided_by": "hpoa_disease_phenotype_edges", + "publications": ["PMID:26208961"], "qualifiers": [], "frequency_qualifier": None, "has_evidence": ["ECO:0000269"], @@ -1463,83 +2359,338 @@ def associations(): "stage_qualifier_closure_label": [], }, { - "id": "uuid:c3cdadba-212f-11ee-873a-cd90a19c4085", - "subject": "MONDO:0011466", - "original_subject": "OMIM:604454", + "id": "uuid:6481675d-212f-11ee-873a-cd90a19c4085", + "subject": "MONDO:0012270", + "original_subject": "OMIM:609428", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ + "MONDO:0020158", "MONDO:0000001", - "MONDO:0011466", - "MONDO:0000429", + "MONDO:0007614", "MONDO:0005071", "MONDO:0020121", - "MONDO:0700223", + "MONDO:0004746", "BFO:0000002", "BFO:0000017", "BFO:0000020", + "MONDO:0016106", + "MONDO:0003382", "BFO:0000016", "MONDO:0020120", "MONDO:0019056", + "MONDO:0003569", "MONDO:0700096", + "MONDO:0001584", + "MONDO:0024458", "MONDO:0005218", "MONDO:0005336", "MONDO:0002081", - "MONDO:0000426", + "MONDO:0012270", "OGMS:0000031", "MONDO:0003847", "MONDO:0003939", + "MONDO:0002022", + "MONDO:0015368", "BFO:0000001", - "MONDO:0016108", - "MONDO:0018949", + "MONDO:0000462", + "MONDO:0005328", ], - "subject_label": "distal myopathy, Welander type", + "subject_label": "Tukel syndrome", "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", - "distal myopathy, Welander type", - "autosomal dominant distal myopathy", - "distal myopathy", + "congenital fibrosis of extraocular muscles", + "Tukel syndrome", + "neuro-ophthalmological disease", + "progressive muscular dystrophy", "neuromuscular disease", "skeletal muscle disorder", "muscular dystrophy", + "eyelids malposition disorder", + "disorder of visual system", "human disease or disorder", - "hereditary skeletal muscle disorder", ], - "predicate": "biolink:has_mode_of_inheritance", - "object": "HP:0000006", + "subject_taxon": None, + "subject_taxon_label": None, + "predicate": "biolink:has_phenotype", + "object": "HP:0004231", "original_object": None, "object_namespace": "HP", - "object_category": "biolink:GeneticInheritance", + "object_category": "biolink:PhenotypicQuality", "object_closure": [ "HP:0000001", - "HP:0000006", - "HP:0000005", - "HP:0034345", - ], - "object_label": "Autosomal dominant inheritance (HPO)", + "HP:0006502", + "UPHENO:0079870", + "UPHENO:0075696", + "UPHENO:0076740", + "UPHENO:0080325", + "UPHENO:0001001", + "UPHENO:0080079", + "UPHENO:0080126", + "UPHENO:0026183", + "UPHENO:0026181", + "UPHENO:0020968", + "UPHENO:0026023", + "HP:0009823", + "UPHENO:0076703", + "UPHENO:0081524", + "HP:0045060", + "UPHENO:0001005", + "HP:0009825", + "HP:0005922", + "UPHENO:0076718", + "HP:0009815", + "HP:0001155", + "HP:0011842", + "UPHENO:0002696", + "UPHENO:0001002", + "UPHENO:0076723", + "HP:0000924", + "UPHENO:0016527", + "HP:0000118", + "BFO:0000002", + "HP:0002813", + "UPHENO:0011498", + "HP:0003019", + "UPHENO:0026028", + "HP:0002817", + "HP:0005927", + "BFO:0000020", + "UPHENO:0002708", + "HP:0001367", + "UPHENO:0080173", + "UPHENO:0026001", + "UPHENO:0002896", + "HP:0001191", + "UPHENO:0026144", + "UPHENO:0015280", + "UPHENO:0002964", + "UPHENO:0002961", + "UPHENO:0081451", + "UPHENO:0006910", + "UPHENO:0008523", + "UPHENO:0081581", + "HP:0033127", + "UPHENO:0001003", + "UPHENO:0002536", + "HP:0006496", + "HP:0009115", + "HP:0011844", + "UPHENO:0026506", + "UPHENO:0076727", + "UPHENO:0020584", + "UPHENO:0076692", + "HP:0009810", + "HP:0004231", + "HP:0040064", + "BFO:0000001", + "HP:0040070", + "PATO:0000001", + "HP:0040068", + "UPHENO:0076767", + "UPHENO:0002880", + "UPHENO:0002830", + "UPHENO:0079876", + "BFO:0000001", + "BFO:0000002", + "BFO:0000004", + "BFO:0000040", + "UBERON:0001062", + "CARO:0000000", + "UBERON:0000465", + "RO:0002577", + "UBERON:0001474", + "UBERON:0002204", + "CARO:0000006", + "UBERON:0006058", + "UBERON:0010712", + "UBERON:0010538", + "UBERON:0004120", + "UBERON:0000061", + "UBERON:0034925", + "UBERON:0010740", + "UBERON:0013630", + "UBERON:0002513", + "CARO:0000003", + "UBERON:0001460", + "UBERON:0004381", + "UBERON:0009878", + "UBERON:0006717", + "UBERON:0002529", + "UBERON:0011582", + "UBERON:0015061", + "UBERON:0004375", + "UBERON:0010000", + "UBERON:0000467", + "UBERON:0015212", + "UBERON:0004288", + "UBERON:0004770", + "UBERON:0010741", + "UBERON:0003656", + "UBERON:0002428", + "UBERON:0004708", + "UBERON:0002470", + "UBERON:0010708", + "UBERON:0012475", + "UBERON:0006716", + "UBERON:0001440", + "UBERON:0009880", + "UBERON:0001442", + "UBERON:0008785", + "UBERON:0007272", + "UBERON:0015021", + "UBERON:0015063", + "UBERON:0000468", + "UBERON:0000475", + "UBERON:0000062", + "UBERON:0011216", + "UBERON:0034921", + "UBERON:0010707", + "UBERON:0008962", + "UBERON:0001435", + "UBERON:0011250", + "UBERON:0002101", + "UBERON:0004710", + "UBERON:0002398", + "UBERON:0004452", + "UBERON:0015049", + "UBERON:0000153", + "UBERON:0000026", + "UBERON:0010758", + "UBERON:0004765", + "UBERON:0000075", + "UBERON:0010912", + "UBERON:0004905", + "UBERON:0001434", + "UBERON:0005897", + "UBERON:0002102", + "UBERON:0010363", + "UBERON:0011249", + "UBERON:0000982", + "UBERON:0002091", + ], + "object_label": "Carpal bone aplasia (HPO)", "object_closure_label": [ "All (HPO)", - "Mode of inheritance (HPO)", - "Autosomal dominant inheritance (HPO)", - "Mendelian inheritance", - ], + "Phenotypic abnormality (HPO)", + "Abnormality of the skeletal system (HPO)", + "Abnormality of the hand (HPO)", + "Abnormal carpal morphology (HPO)", + "Abnormal joint morphology (HPO)", + "Abnormality of limb bone morphology (HPO)", + "Abnormality of the upper limb (HPO)", + "Abnormality of the wrist (HPO)", + "Carpal bone aplasia (HPO)", + "Abnormal hand morphology (HPO)", + "Aplasia/hypoplasia involving bones of the hand (HPO)", + "Aplasia/hypoplasia involving bones of the upper limbs (HPO)", + "Aplasia/Hypoplasia involving the carpal bones (HPO)", + "Aplasia/hypoplasia involving the skeleton (HPO)", + "Abnormality of upper limb joint (HPO)", + "Aplasia/hypoplasia of the extremities (HPO)", + "Aplasia involving bones of the upper limbs (HPO)", + "Aplasia involving bones of the extremities (HPO)", + "Abnormal skeletal morphology (HPO)", + "Abnormal appendicular skeleton morphology (HPO)", + "Abnormality of the musculoskeletal system (HPO)", + "Abnormality of limbs (HPO)", + "Abnormality of limb bone (HPO)", + "Abnormal upper limb bone morphology (HPO)", + "Aplasia/hypoplasia involving bones of the extremities (HPO)", + "appendage", + "anatomical structure", + "organ", + "subdivision of skeletal system", + "anterior region of body", + "material anatomical entity", + "anatomical system", + "multicellular organism", + "organism subdivision", + "skeletal joint", + "anatomical entity", + "skeletal system", + "carpal bone", + "forelimb skeleton", + "skeleton of manus", + "arm", + "bone element", + "appendicular skeleton", + "limb", + "forelimb", + "musculoskeletal system", + "manus", + "limb bone", + "autopod region", + "endochondral bone", + "limb segment", + "mesopodium bone", + "mesoderm-derived structure", + "skeleton", + "bone of free limb or fin", + "skeleton of limb", + "carpal region", + "paired limb/fin", + "pectoral appendage", + "skeletal element", + "articular system", + "articulation", + "manus bone", + "multi-limb segment region", + "mesopodium region", + "autopodial skeleton", + "pectoral appendage skeleton", + "upper limb segment", + "forelimb bone", + "mesopodial skeleton", + "carpal skeleton", + "multicellular anatomical structure", + "endochondral element", + "paired limb/fin segment", + "appendage girdle complex", + "pectoral complex", + "limb skeleton subdivision", + "bone of appendage girdle complex", + "bone of pectoral complex", + "subdivision of organism along appendicular axis", + "subdivision of skeleton", + "organ system subdivision", + "appendicular skeletal system", + "autopod bone", + "paired limb/fin skeleton", + "skeleton of pectoral complex", + "short bone", + "forelimb endochondral element", + "carpus endochondral element", + "limb endochondral element", + "autopod endochondral element", + "lateral structure", + "multi organ part structure", + "anatomical collection", + ], + "object_taxon": None, + "object_taxon_label": None, "primary_knowledge_source": "infores:hpo-annotations", "aggregator_knowledge_source": ["infores:monarchinitiative"], - "category": "biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation", + "category": "biolink:DiseaseToPhenotypicFeatureAssociation", "negated": None, - "provided_by": "hpoa_disease_mode_of_inheritance_edges", - "publications": ["PMID:23348830"], + "provided_by": "hpoa_disease_phenotype_edges", + "publications": ["OMIM:609428"], "qualifiers": [], "frequency_qualifier": None, - "has_evidence": ["ECO:0000269"], + "has_evidence": ["ECO:0000501"], "onset_qualifier": None, "sex_qualifier": None, "stage_qualifier": None, @@ -1567,85 +2718,156 @@ def associations(): "stage_qualifier_closure_label": [], }, { - "id": "uuid:c367df64-212f-11ee-873a-cd90a19c4085", - "subject": "MONDO:0012034", - "original_subject": "OMIM:608423", + "id": "uuid:624032ae-212f-11ee-873a-cd90a19c4085", + "subject": "MONDO:0009181", + "original_subject": "OMIM:226670", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ "MONDO:0000001", + "MONDO:0016198", "MONDO:0016971", "MONDO:0000429", "MONDO:0005071", "MONDO:0020121", - "MONDO:0700223", - "MONDO:0012034", "BFO:0000002", + "MONDO:0006617", "BFO:0000017", "BFO:0000020", + "MONDO:0017610", + "MONDO:0006025", "MONDO:0016106", + "MONDO:0002051", "BFO:0000016", "MONDO:0020120", "MONDO:0019056", - "MONDO:0015151", + "MONDO:0016139", "MONDO:0700096", "MONDO:0005218", "MONDO:0005336", "MONDO:0002081", - "MONDO:0000426", + "MONDO:0002254", + "MONDO:0009181", + "MONDO:0019276", + "MONDO:0005093", "OGMS:0000031", + "MONDO:0019268", "MONDO:0003847", "MONDO:0003939", + "MONDO:0006541", "BFO:0000001", + "MONDO:0015152", ], - "subject_label": "autosomal dominant limb-girdle muscular dystrophy type 1F", + "subject_label": "epidermolysis bullosa simplex 5B, with muscular dystrophy", "subject_closure_label": [ "disease or disorder", - "autosomal dominant disease", "autosomal genetic disease", + "integumentary system disorder", "musculoskeletal system disorder", + "syndromic disease", "hereditary disease", "muscle tissue disorder", "nervous system disorder", + "skin disorder", "obsolete muscular disorder", "myopathy", - "autosomal dominant limb-girdle muscular dystrophy type 1F", - "muscular dystrophy, limb-girdle, autosomal dominant", + "autosomal recessive disease", + "epidermolysis bullosa", + "vesiculobullous skin disease", + "epidermolysis bullosa simplex 5B, with muscular dystrophy", + "autosomal recessive limb-girdle muscular dystrophy", "progressive muscular dystrophy", + "qualitative or quantitative protein defects in neuromuscular diseases", + "qualitative or quantitative defects of plectin", "limb-girdle muscular dystrophy", + "epidermolysis bullosa simplex", "neuromuscular disease", + "epidermal disease", + "inherited epidermolysis bullosa", "skeletal muscle disorder", "muscular dystrophy", "human disease or disorder", - "hereditary skeletal muscle disorder", ], - "predicate": "biolink:has_mode_of_inheritance", - "object": "HP:0000006", + "subject_taxon": None, + "subject_taxon_label": None, + "predicate": "biolink:has_phenotype", + "object": "HP:0004322", "original_object": None, "object_namespace": "HP", - "object_category": "biolink:GeneticInheritance", + "object_category": "biolink:PhenotypicQuality", "object_closure": [ "HP:0000001", - "HP:0000006", - "HP:0000005", - "HP:0034345", - ], - "object_label": "Autosomal dominant inheritance (HPO)", + "UPHENO:0000543", + "UPHENO:0075696", + "HP:0001507", + "UPHENO:0081423", + "UPHENO:0068971", + "UPHENO:0001001", + "UPHENO:0069254", + "UPHENO:0075159", + "UPHENO:0001005", + "HP:0000002", + "UPHENO:0001002", + "UPHENO:0080351", + "HP:0000118", + "BFO:0000002", + "HP:0001510", + "BFO:0000020", + "UPHENO:0075195", + "UPHENO:0015280", + "UPHENO:0081581", + "UPHENO:0001003", + "UPHENO:0002536", + "UPHENO:0049874", + "UPHENO:0020584", + "UPHENO:0076692", + "UPHENO:0081424", + "UPHENO:0080352", + "UPHENO:0049587", + "BFO:0000001", + "HP:0004322", + "UPHENO:0000541", + "PATO:0000001", + "UPHENO:0012541", + "BFO:0000001", + "BFO:0000003", + "BFO:0000002", + "BFO:0000015", + "BFO:0000004", + "GO:0008150", + "BFO:0000040", + "UBERON:0001062", + "GO:0040007", + "UBERON:0000465", + "UBERON:0000061", + "UBERON:0010000", + "UBERON:0000468", + ], + "object_label": "Short stature (HPO)", "object_closure_label": [ "All (HPO)", - "Mode of inheritance (HPO)", - "Autosomal dominant inheritance (HPO)", - "Mendelian inheritance", - ], + "Abnormality of body height (HPO)", + "Phenotypic abnormality (HPO)", + "Growth abnormality (HPO)", + "Growth delay (HPO)", + "Short stature (HPO)", + "anatomical structure", + "material anatomical entity", + "multicellular organism", + "anatomical entity", + "multicellular anatomical structure", + ], + "object_taxon": None, + "object_taxon_label": None, "primary_knowledge_source": "infores:hpo-annotations", "aggregator_knowledge_source": ["infores:monarchinitiative"], - "category": "biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation", + "category": "biolink:DiseaseToPhenotypicFeatureAssociation", "negated": None, - "provided_by": "hpoa_disease_mode_of_inheritance_edges", - "publications": ["PMID:23543484"], + "provided_by": "hpoa_disease_phenotype_edges", + "publications": ["OMIM:226670"], "qualifiers": [], "frequency_qualifier": None, - "has_evidence": ["ECO:0000269"], + "has_evidence": ["ECO:0000501"], "onset_qualifier": None, "sex_qualifier": None, "stage_qualifier": None, @@ -1673,99 +2895,134 @@ def associations(): "stage_qualifier_closure_label": [], }, { - "id": "uuid:c3367251-212f-11ee-873a-cd90a19c4085", - "subject": "MONDO:0012130", - "original_subject": "OMIM:608810", + "id": "uuid:5ad388d6-212f-11ee-873a-cd90a19c4085", + "subject": "MONDO:0012138", + "original_subject": "OMIM:608840", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ "MONDO:0000001", - "MONDO:0016186", - "MONDO:0000429", + "MONDO:0012138", + "MONDO:0018276", "MONDO:0005071", "MONDO:0020121", - "MONDO:0018943", - "MONDO:0700223", + "MONDO:0000172", "BFO:0000002", - "MONDO:0019952", "BFO:0000017", "BFO:0000020", - "MONDO:0020343", "BFO:0000016", "MONDO:0020120", "MONDO:0019056", - "MONDO:0016139", "MONDO:0700096", - "MONDO:0002921", "MONDO:0005218", "MONDO:0005336", "MONDO:0002081", - "MONDO:0012130", - "MONDO:0000426", "OGMS:0000031", "MONDO:0003847", "MONDO:0003939", "BFO:0000001", "MONDO:0002320", - "MONDO:0016188", - "MONDO:0016108", - "MONDO:0018949", + "MONDO:0019950", ], - "subject_label": "myofibrillar myopathy 2", + "subject_label": "muscular dystrophy-dystroglycanopathy type B6", "subject_closure_label": [ "disease or disorder", - "autosomal dominant disease", - "autosomal genetic disease", + "muscular dystrophy-dystroglycanopathy, type B", "musculoskeletal system disorder", "congenital nervous system disorder", - "congenital structural myopathy", "hereditary disease", "muscle tissue disorder", "nervous system disorder", "obsolete muscular disorder", "myopathy", - "myofibrillar myopathy 2", - "autosomal dominant distal myopathy", - "qualitative or quantitative protein defects in neuromuscular diseases", - "qualitative or quantitative defects of myofibrillar proteins", - "qualitative or quantitative defects of alphaB-cristallin", - "myofibrillar myopathy", - "distal myopathy", + "muscular dystrophy-dystroglycanopathy type B6", + "muscular dystrophy-dystroglycanopathy", "neuromuscular disease", - "congenital myopathy", + "congenital muscular dystrophy", "skeletal muscle disorder", "muscular dystrophy", - "alpha-crystallinopathy", "human disease or disorder", - "hereditary skeletal muscle disorder", ], - "predicate": "biolink:has_mode_of_inheritance", - "object": "HP:0000006", + "subject_taxon": None, + "subject_taxon_label": None, + "predicate": "biolink:has_phenotype", + "object": "HP:0004322", "original_object": None, "object_namespace": "HP", - "object_category": "biolink:GeneticInheritance", + "object_category": "biolink:PhenotypicQuality", "object_closure": [ "HP:0000001", - "HP:0000006", - "HP:0000005", - "HP:0034345", - ], - "object_label": "Autosomal dominant inheritance (HPO)", + "UPHENO:0000543", + "UPHENO:0075696", + "HP:0001507", + "UPHENO:0081423", + "UPHENO:0068971", + "UPHENO:0001001", + "UPHENO:0069254", + "UPHENO:0075159", + "UPHENO:0001005", + "HP:0000002", + "UPHENO:0001002", + "UPHENO:0080351", + "HP:0000118", + "BFO:0000002", + "HP:0001510", + "BFO:0000020", + "UPHENO:0075195", + "UPHENO:0015280", + "UPHENO:0081581", + "UPHENO:0001003", + "UPHENO:0002536", + "UPHENO:0049874", + "UPHENO:0020584", + "UPHENO:0076692", + "UPHENO:0081424", + "UPHENO:0080352", + "UPHENO:0049587", + "BFO:0000001", + "HP:0004322", + "UPHENO:0000541", + "PATO:0000001", + "UPHENO:0012541", + "BFO:0000001", + "BFO:0000003", + "BFO:0000002", + "BFO:0000015", + "BFO:0000004", + "GO:0008150", + "BFO:0000040", + "UBERON:0001062", + "GO:0040007", + "UBERON:0000465", + "UBERON:0000061", + "UBERON:0010000", + "UBERON:0000468", + ], + "object_label": "Short stature (HPO)", "object_closure_label": [ "All (HPO)", - "Mode of inheritance (HPO)", - "Autosomal dominant inheritance (HPO)", - "Mendelian inheritance", - ], + "Abnormality of body height (HPO)", + "Phenotypic abnormality (HPO)", + "Growth abnormality (HPO)", + "Growth delay (HPO)", + "Short stature (HPO)", + "anatomical structure", + "material anatomical entity", + "multicellular organism", + "anatomical entity", + "multicellular anatomical structure", + ], + "object_taxon": None, + "object_taxon_label": None, "primary_knowledge_source": "infores:hpo-annotations", "aggregator_knowledge_source": ["infores:monarchinitiative"], - "category": "biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation", + "category": "biolink:DiseaseToPhenotypicFeatureAssociation", "negated": None, - "provided_by": "hpoa_disease_mode_of_inheritance_edges", - "publications": ["PMID:14681890"], + "provided_by": "hpoa_disease_phenotype_edges", + "publications": ["OMIM:608840"], "qualifiers": [], "frequency_qualifier": None, - "has_evidence": ["ECO:0000269"], + "has_evidence": ["ECO:0000501"], "onset_qualifier": None, "sex_qualifier": None, "stage_qualifier": None, @@ -1793,85 +3050,156 @@ def associations(): "stage_qualifier_closure_label": [], }, { - "id": "uuid:c39b463c-212f-11ee-873a-cd90a19c4085", - "subject": "MONDO:0012193", - "original_subject": "OMIM:609115", + "id": "uuid:5a352272-212f-11ee-873a-cd90a19c4085", + "subject": "MONDO:0014144", + "original_subject": "OMIM:615356", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ "MONDO:0000001", + "MONDO:0000508", "MONDO:0016971", + "MONDO:0005503", + "MONDO:0002025", "MONDO:0000429", + "MONDO:0014144", "MONDO:0005071", "MONDO:0020121", - "MONDO:0700223", + "MONDO:0001071", "BFO:0000002", + "MONDO:0005395", "BFO:0000017", "BFO:0000020", + "MONDO:0006025", + "MONDO:0002602", "MONDO:0016106", "BFO:0000016", "MONDO:0020120", "MONDO:0019056", - "MONDO:0015151", "MONDO:0700096", "MONDO:0005218", "MONDO:0005336", "MONDO:0002081", - "MONDO:0012193", - "MONDO:0000426", + "MONDO:0002254", + "MONDO:0018243", + "MONDO:0005084", "OGMS:0000031", "MONDO:0003847", "MONDO:0003939", "BFO:0000001", + "MONDO:0015152", + "MONDO:0005560", ], - "subject_label": "autosomal dominant limb-girdle muscular dystrophy type 1G", + "subject_label": "autosomal recessive limb-girdle muscular dystrophy type R18", "subject_closure_label": [ "disease or disorder", - "autosomal dominant disease", "autosomal genetic disease", + "syndromic intellectual disability", + "intellectual disability", + "psychiatric disorder", "musculoskeletal system disorder", + "syndromic disease", + "central nervous system disorder", "hereditary disease", "muscle tissue disorder", "nervous system disorder", + "mental disorder", "obsolete muscular disorder", "myopathy", - "autosomal dominant limb-girdle muscular dystrophy type 1G", - "muscular dystrophy, limb-girdle, autosomal dominant", + "movement disorder", + "developmental disorder of mental health", + "brain disorder", + "autosomal recessive disease", + "autosomal recessive limb-girdle muscular dystrophy type R18", + "autosomal recessive limb-girdle muscular dystrophy", "progressive muscular dystrophy", "limb-girdle muscular dystrophy", + "intellectual disability-hyperkinetic movement-truncal ataxia syndrome", "neuromuscular disease", "skeletal muscle disorder", "muscular dystrophy", "human disease or disorder", - "hereditary skeletal muscle disorder", ], - "predicate": "biolink:has_mode_of_inheritance", - "object": "HP:0000006", + "subject_taxon": None, + "subject_taxon_label": None, + "predicate": "biolink:has_phenotype", + "object": "HP:0004322", "original_object": None, "object_namespace": "HP", - "object_category": "biolink:GeneticInheritance", + "object_category": "biolink:PhenotypicQuality", "object_closure": [ "HP:0000001", - "HP:0000006", - "HP:0000005", - "HP:0034345", - ], - "object_label": "Autosomal dominant inheritance (HPO)", + "UPHENO:0000543", + "UPHENO:0075696", + "HP:0001507", + "UPHENO:0081423", + "UPHENO:0068971", + "UPHENO:0001001", + "UPHENO:0069254", + "UPHENO:0075159", + "UPHENO:0001005", + "HP:0000002", + "UPHENO:0001002", + "UPHENO:0080351", + "HP:0000118", + "BFO:0000002", + "HP:0001510", + "BFO:0000020", + "UPHENO:0075195", + "UPHENO:0015280", + "UPHENO:0081581", + "UPHENO:0001003", + "UPHENO:0002536", + "UPHENO:0049874", + "UPHENO:0020584", + "UPHENO:0076692", + "UPHENO:0081424", + "UPHENO:0080352", + "UPHENO:0049587", + "BFO:0000001", + "HP:0004322", + "UPHENO:0000541", + "PATO:0000001", + "UPHENO:0012541", + "BFO:0000001", + "BFO:0000003", + "BFO:0000002", + "BFO:0000015", + "BFO:0000004", + "GO:0008150", + "BFO:0000040", + "UBERON:0001062", + "GO:0040007", + "UBERON:0000465", + "UBERON:0000061", + "UBERON:0010000", + "UBERON:0000468", + ], + "object_label": "Short stature (HPO)", "object_closure_label": [ "All (HPO)", - "Mode of inheritance (HPO)", - "Autosomal dominant inheritance (HPO)", - "Mendelian inheritance", - ], + "Abnormality of body height (HPO)", + "Phenotypic abnormality (HPO)", + "Growth abnormality (HPO)", + "Growth delay (HPO)", + "Short stature (HPO)", + "anatomical structure", + "material anatomical entity", + "multicellular organism", + "anatomical entity", + "multicellular anatomical structure", + ], + "object_taxon": None, + "object_taxon_label": None, "primary_knowledge_source": "infores:hpo-annotations", "aggregator_knowledge_source": ["infores:monarchinitiative"], - "category": "biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation", + "category": "biolink:DiseaseToPhenotypicFeatureAssociation", "negated": None, - "provided_by": "hpoa_disease_mode_of_inheritance_edges", - "publications": ["PMID:24647604"], + "provided_by": "hpoa_disease_phenotype_edges", + "publications": ["OMIM:615356"], "qualifiers": [], "frequency_qualifier": None, - "has_evidence": ["ECO:0000269"], + "has_evidence": ["ECO:0000304"], "onset_qualifier": None, "sex_qualifier": None, "stage_qualifier": None, @@ -1899,101 +3227,128 @@ def associations(): "stage_qualifier_closure_label": [], }, { - "id": "uuid:c4006058-212f-11ee-873a-cd90a19c4085", - "subject": "MONDO:0012215", - "original_subject": "OMIM:609200", + "id": "uuid:64b682db-212f-11ee-873a-cd90a19c4085", + "subject": "MONDO:0024607", + "original_subject": "OMIM:617404", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ - "MONDO:0012215", "MONDO:0000001", - "MONDO:0016971", - "MONDO:0000429", + "MONDO:0024607", "MONDO:0005071", "MONDO:0020121", - "MONDO:0018943", - "MONDO:0700223", - "MONDO:0016201", "BFO:0000002", - "MONDO:0019952", "BFO:0000017", "BFO:0000020", - "MONDO:0016106", "BFO:0000016", "MONDO:0020120", "MONDO:0019056", - "MONDO:0016139", - "MONDO:0015151", "MONDO:0700096", - "MONDO:0002921", "MONDO:0005218", "MONDO:0005336", "MONDO:0002081", - "MONDO:0000426", "OGMS:0000031", - "MONDO:0003847", "MONDO:0003939", "BFO:0000001", "MONDO:0002320", - "MONDO:0016108", - "MONDO:0018949", + "MONDO:0019950", ], - "subject_label": "myofibrillar myopathy 3", + "subject_label": "congenital muscular dystrophy with cataracts and intellectual disability", "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", - "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", + "congenital muscular dystrophy", "skeletal muscle disorder", "muscular dystrophy", + "congenital muscular dystrophy with cataracts and intellectual disability", "human disease or disorder", - "hereditary skeletal muscle disorder", ], - "predicate": "biolink:has_mode_of_inheritance", - "object": "HP:0000006", + "subject_taxon": None, + "subject_taxon_label": None, + "predicate": "biolink:has_phenotype", + "object": "HP:0004322", "original_object": None, "object_namespace": "HP", - "object_category": "biolink:GeneticInheritance", + "object_category": "biolink:PhenotypicQuality", "object_closure": [ "HP:0000001", - "HP:0000006", - "HP:0000005", - "HP:0034345", - ], - "object_label": "Autosomal dominant inheritance (HPO)", + "UPHENO:0000543", + "UPHENO:0075696", + "HP:0001507", + "UPHENO:0081423", + "UPHENO:0068971", + "UPHENO:0001001", + "UPHENO:0069254", + "UPHENO:0075159", + "UPHENO:0001005", + "HP:0000002", + "UPHENO:0001002", + "UPHENO:0080351", + "HP:0000118", + "BFO:0000002", + "HP:0001510", + "BFO:0000020", + "UPHENO:0075195", + "UPHENO:0015280", + "UPHENO:0081581", + "UPHENO:0001003", + "UPHENO:0002536", + "UPHENO:0049874", + "UPHENO:0020584", + "UPHENO:0076692", + "UPHENO:0081424", + "UPHENO:0080352", + "UPHENO:0049587", + "BFO:0000001", + "HP:0004322", + "UPHENO:0000541", + "PATO:0000001", + "UPHENO:0012541", + "BFO:0000001", + "BFO:0000003", + "BFO:0000002", + "BFO:0000015", + "BFO:0000004", + "GO:0008150", + "BFO:0000040", + "UBERON:0001062", + "GO:0040007", + "UBERON:0000465", + "UBERON:0000061", + "UBERON:0010000", + "UBERON:0000468", + ], + "object_label": "Short stature (HPO)", "object_closure_label": [ "All (HPO)", - "Mode of inheritance (HPO)", - "Autosomal dominant inheritance (HPO)", - "Mendelian inheritance", - ], + "Abnormality of body height (HPO)", + "Phenotypic abnormality (HPO)", + "Growth abnormality (HPO)", + "Growth delay (HPO)", + "Short stature (HPO)", + "anatomical structure", + "material anatomical entity", + "multicellular organism", + "anatomical entity", + "multicellular anatomical structure", + ], + "object_taxon": None, + "object_taxon_label": None, "primary_knowledge_source": "infores:hpo-annotations", "aggregator_knowledge_source": ["infores:monarchinitiative"], - "category": "biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation", + "category": "biolink:DiseaseToPhenotypicFeatureAssociation", "negated": None, - "provided_by": "hpoa_disease_mode_of_inheritance_edges", - "publications": ["OMIM:609200"], + "provided_by": "hpoa_disease_phenotype_edges", + "publications": ["OMIM:617404"], "qualifiers": [], "frequency_qualifier": None, - "has_evidence": ["ECO:0000501"], + "has_evidence": ["ECO:0000304"], "onset_qualifier": None, "sex_qualifier": None, "stage_qualifier": None, @@ -2021,100 +3376,251 @@ def associations(): "stage_qualifier_closure_label": [], }, { - "id": "uuid:c275a325-212f-11ee-873a-cd90a19c4085", - "subject": "MONDO:0012262", - "original_subject": "OMIM:609384", + "id": "uuid:624032b1-212f-11ee-873a-cd90a19c4085", + "subject": "MONDO:0009181", + "original_subject": "OMIM:226670", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ - "MONDO:0020158", "MONDO:0000001", - "MONDO:0007614", + "MONDO:0016198", + "MONDO:0016971", + "MONDO:0000429", "MONDO:0005071", "MONDO:0020121", - "MONDO:0700223", - "MONDO:0004746", "BFO:0000002", - "MONDO:0012262", - "MONDO:0957003", + "MONDO:0006617", "BFO:0000017", "BFO:0000020", + "MONDO:0017610", + "MONDO:0006025", "MONDO:0016106", - "MONDO:0003382", + "MONDO:0002051", "BFO:0000016", "MONDO:0020120", "MONDO:0019056", - "MONDO:0003569", + "MONDO:0016139", "MONDO:0700096", - "MONDO:0001584", - "MONDO:0024458", "MONDO:0005218", "MONDO:0005336", "MONDO:0002081", + "MONDO:0002254", + "MONDO:0009181", + "MONDO:0019276", + "MONDO:0005093", "OGMS:0000031", + "MONDO:0019268", "MONDO:0003847", "MONDO:0003939", - "MONDO:0002022", - "MONDO:0015368", + "MONDO:0006541", "BFO:0000001", - "MONDO:0002320", - "MONDO:0000462", - "MONDO:0005328", + "MONDO:0015152", ], - "subject_label": "fibrosis of extraocular muscles, congenital, 3c", + "subject_label": "epidermolysis bullosa simplex 5B, with muscular dystrophy", "subject_closure_label": [ "disease or disorder", - "eye adnexa disorder", - "ocular motility disease", - "disorder of orbital region", + "autosomal genetic disease", + "integumentary system disorder", "musculoskeletal system disorder", - "congenital nervous system disorder", - "eyelid disorder", - "cranial nerve neuropathy", + "syndromic disease", "hereditary disease", "muscle tissue disorder", - "myopathy of extraocular muscle", "nervous system disorder", + "skin disorder", "obsolete muscular disorder", - "eye disorder", "myopathy", - "congenital fibrosis of extraocular muscles", - "fibrosis of extraocular muscles, congenital, 3c", - "neuro-ophthalmological disease", + "autosomal recessive disease", + "epidermolysis bullosa", + "vesiculobullous skin disease", + "epidermolysis bullosa simplex 5B, with muscular dystrophy", + "autosomal recessive limb-girdle muscular dystrophy", "progressive muscular dystrophy", + "qualitative or quantitative protein defects in neuromuscular diseases", + "qualitative or quantitative defects of plectin", + "limb-girdle muscular dystrophy", + "epidermolysis bullosa simplex", "neuromuscular disease", + "epidermal disease", + "inherited epidermolysis bullosa", "skeletal muscle disorder", "muscular dystrophy", - "eyelids malposition disorder", - "disorder of visual system", "human disease or disorder", - "hereditary skeletal muscle disorder", - "hereditary neuro-ophthalmological disease", ], - "predicate": "biolink:has_mode_of_inheritance", - "object": "HP:0000006", + "subject_taxon": None, + "subject_taxon_label": None, + "predicate": "biolink:has_phenotype", + "object": "HP:0004552", "original_object": None, "object_namespace": "HP", - "object_category": "biolink:GeneticInheritance", + "object_category": "biolink:PhenotypicQuality", "object_closure": [ "HP:0000001", - "HP:0000006", - "HP:0000005", - "HP:0034345", - ], - "object_label": "Autosomal dominant inheritance (HPO)", + "HP:0001965", + "UPHENO:0011535", + "UPHENO:0075696", + "UPHENO:0001001", + "HP:0003549", + "HP:0000152", + "UPHENO:0003811", + "UPHENO:0002768", + "UPHENO:0002844", + "UPHENO:0001005", + "HP:0000987", + "UPHENO:0002764", + "UPHENO:0001002", + "HP:0000118", + "BFO:0000002", + "HP:0011355", + "UPHENO:0011498", + "HP:0011121", + "HP:0002293", + "UPHENO:0076739", + "BFO:0000020", + "HP:0100699", + "UPHENO:0003035", + "HP:0000234", + "HP:0001595", + "UPHENO:0075677", + "UPHENO:0002635", + "UPHENO:0015280", + "HP:0011362", + "UPHENO:0006910", + "UPHENO:0081581", + "HP:0033127", + "UPHENO:0001003", + "UPHENO:0002536", + "UPHENO:0020584", + "HP:0100037", + "UPHENO:0019853", + "UPHENO:0076692", + "HP:0004552", + "UPHENO:0002712", + "HP:0001596", + "BFO:0000001", + "HP:0000951", + "HP:0011138", + "PATO:0000001", + "HP:0001574", + "BFO:0000001", + "BFO:0000002", + "BFO:0000004", + "BFO:0000040", + "UBERON:0001062", + "CARO:0000000", + "UBERON:0000465", + "RO:0002577", + "UBERON:0004121", + "CARO:0000006", + "UBERON:0002416", + "UBERON:0007811", + "UBERON:0002199", + "UBERON:0000403", + "UBERON:0010314", + "UBERON:0000061", + "UBERON:0001037", + "UBERON:0002097", + "UBERON:0010371", + "CARO:0000003", + "UBERON:0011932", + "UBERON:0010000", + "UBERON:0000467", + "UBERON:0034768", + "UBERON:0003102", + "UBERON:0016446", + "UBERON:0007376", + "UBERON:0000021", + "UBERON:0000479", + "UBERON:0000468", + "UBERON:0000475", + "UBERON:0000064", + "UBERON:0000062", + "UBERON:0011216", + "UBERON:0034921", + "UBERON:0004529", + "UBERON:3000961", + "UBERON:0001003", + "UBERON:0000483", + "UBERON:0002384", + "UBERON:0000153", + "UBERON:0011676", + "UBERON:0013701", + "UBERON:0000063", + "UBERON:0013702", + "UBERON:0006003", + "UBERON:0013703", + "UBERON:0000033", + ], + "object_label": "Scarring alopecia of scalp (HPO)", "object_closure_label": [ "All (HPO)", - "Mode of inheritance (HPO)", - "Autosomal dominant inheritance (HPO)", - "Mendelian inheritance", - ], + "Phenotypic abnormality (HPO)", + "Abnormality of head or neck (HPO)", + "Abnormality of the head (HPO)", + "Abnormality of the skin (HPO)", + "Atypical scarring of skin (HPO)", + "Abnormality of the integument (HPO)", + "Abnormal hair morphology (HPO)", + "Alopecia (HPO)", + "Abnormal scalp morphology (HPO)", + "Alopecia of scalp (HPO)", + "Abnormality of connective tissue (HPO)", + "Scarring alopecia of scalp (HPO)", + "Abnormality of skin morphology (HPO)", + "Abnormality of skin adnexa morphology (HPO)", + "Localized skin lesion (HPO)", + "Abnormal hair quantity (HPO)", + "Abnormality of the musculoskeletal system (HPO)", + "Abnormality of the scalp hair (HPO)", + "Scarring (HPO)", + "cutaneous appendage", + "head", + "anatomical structure", + "organ", + "organ subunit", + "organ part", + "anterior region of body", + "scalp", + "material anatomical entity", + "anatomical system", + "multicellular organism", + "organism subdivision", + "tissue", + "epithelium", + "skin epidermis", + "strand of hair", + "anatomical entity", + "skin of body", + "integument", + "connective tissue", + "integumental system", + "surface structure", + "ectoderm-derived structure", + "anatomical projection", + "integumentary adnexa", + "outer epithelium", + "craniocervical region", + "multicellular anatomical structure", + "structure with developmental contribution from neural crest", + "ecto-epithelium", + "organ system subdivision", + "subdivision of organism along main body axis", + "pilosebaceous unit", + "main body axis", + "body proper", + "integumentary projection", + "hair of head", + "morphological feature", + "multi organ part structure", + "external integument structure", + ], + "object_taxon": None, + "object_taxon_label": None, "primary_knowledge_source": "infores:hpo-annotations", "aggregator_knowledge_source": ["infores:monarchinitiative"], - "category": "biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation", + "category": "biolink:DiseaseToPhenotypicFeatureAssociation", "negated": None, - "provided_by": "hpoa_disease_mode_of_inheritance_edges", - "publications": ["OMIM:609384"], + "provided_by": "hpoa_disease_phenotype_edges", + "publications": ["OMIM:226670"], "qualifiers": [], "frequency_qualifier": None, "has_evidence": ["ECO:0000501"], @@ -2145,94 +3651,208 @@ def associations(): "stage_qualifier_closure_label": [], }, { - "id": "uuid:c304ba49-212f-11ee-873a-cd90a19c4085", - "subject": "MONDO:0012277", - "original_subject": "OMIM:609452", + "id": "uuid:62c348df-212f-11ee-873a-cd90a19c4085", + "subject": "MONDO:0010680", + "original_subject": "OMIM:310300", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ + "MONDO:0004994", "MONDO:0000001", - "MONDO:0016186", - "MONDO:0000429", + "MONDO:0010680", "MONDO:0005071", + "MONDO:0005267", "MONDO:0020121", - "MONDO:0018943", - "MONDO:0700223", + "MONDO:0004995", + "MONDO:0016196", "BFO:0000002", - "MONDO:0019952", - "MONDO:0016190", "BFO:0000017", "BFO:0000020", + "MONDO:0016106", + "MONDO:0005217", "BFO:0000016", "MONDO:0020120", "MONDO:0019056", "MONDO:0016139", "MONDO:0700096", - "MONDO:0002921", + "MONDO:0000591", "MONDO:0005218", "MONDO:0005336", "MONDO:0002081", - "MONDO:0000426", + "MONDO:0016333", + "MONDO:0016830", "OGMS:0000031", + "MONDO:0000425", + "MONDO:0005021", + "MONDO:0021106", "MONDO:0003847", "MONDO:0003939", - "MONDO:0012277", "BFO:0000001", - "MONDO:0002320", - "MONDO:0016108", - "MONDO:0018949", + "MONDO:0020606", ], - "subject_label": "myofibrillar myopathy 4", + "subject_label": "X-linked Emery-Dreifuss muscular dystrophy", "subject_closure_label": [ "disease or disorder", - "autosomal dominant disease", - "autosomal genetic disease", + "X-linked disease", + "intrinsic cardiomyopathy", "musculoskeletal system disorder", - "congenital nervous system disorder", - "congenital structural myopathy", "hereditary disease", "muscle tissue disorder", + "cardiomyopathy", + "cardiovascular disorder", + "dilated cardiomyopathy", "nervous system disorder", + "familial cardiomyopathy", "obsolete muscular disorder", + "heart disorder", "myopathy", - "myofibrillar myopathy 4", - "autosomal dominant distal myopathy", + "X-linked Emery-Dreifuss muscular dystrophy", + "progressive muscular dystrophy", "qualitative or quantitative protein defects in neuromuscular diseases", - "qualitative or quantitative defects of myofibrillar proteins", - "qualitative or quantitative defects of protein ZASP", - "myofibrillar myopathy", - "distal myopathy", + "qualitative or quantitative defects of emerin", + "familial dilated cardiomyopathy", + "Emery-Dreifuss muscular dystrophy", "neuromuscular disease", - "congenital myopathy", "skeletal muscle disorder", "muscular dystrophy", + "sex-linked disease", + "laminopathy", "human disease or disorder", - "hereditary skeletal muscle disorder", ], - "predicate": "biolink:has_mode_of_inheritance", - "object": "HP:0000006", + "subject_taxon": None, + "subject_taxon_label": None, + "predicate": "biolink:has_phenotype", + "object": "HP:0004631", "original_object": None, "object_namespace": "HP", - "object_category": "biolink:GeneticInheritance", + "object_category": "biolink:PhenotypicQuality", "object_closure": [ "HP:0000001", - "HP:0000006", - "HP:0000005", - "HP:0034345", - ], - "object_label": "Autosomal dominant inheritance (HPO)", + "UPHENO:0082875", + "UPHENO:0046505", + "UPHENO:0075696", + "UPHENO:0068971", + "UPHENO:0001001", + "HP:0001371", + "HP:0003549", + "HP:0011729", + "UPHENO:0076703", + "HP:0100261", + "UPHENO:0001005", + "HP:0011842", + "HP:0011805", + "UPHENO:0001002", + "HP:0004631", + "HP:0034430", + "HP:0000924", + "HP:0000118", + "BFO:0000002", + "HP:0034392", + "UPHENO:0021425", + "BFO:0000020", + "UPHENO:0075195", + "HP:0003011", + "UPHENO:0002816", + "UPHENO:0002332", + "UPHENO:0015280", + "UPHENO:0002964", + "UPHENO:0081581", + "HP:0033127", + "UPHENO:0001003", + "UPHENO:0002536", + "UPHENO:0046759", + "UPHENO:0020584", + "UPHENO:0031839", + "UPHENO:0076692", + "UPHENO:0081440", + "UPHENO:0076710", + "UPHENO:0002712", + "BFO:0000001", + "PATO:0000001", + "UPHENO:0012541", + "HP:0011843", + "BFO:0000001", + "BFO:0000002", + "BFO:0000004", + "BFO:0000040", + "UBERON:0001062", + "CARO:0000000", + "UBERON:0000465", + "UBERON:0000383", + "UBERON:0001015", + "UBERON:0007845", + "UBERON:0002204", + "UBERON:0005090", + "UBERON:0000061", + "UBERON:0034925", + "UBERON:0007846", + "UBERON:0001630", + "UBERON:0010000", + "UBERON:0000467", + "UBERON:0004770", + "UBERON:0000043", + "UBERON:0000479", + "UBERON:0000468", + "UBERON:0000062", + "UBERON:0011216", + "UBERON:0034921", + "UBERON:0002384", + "UBERON:0004905", + "UBERON:0001434", + "UBERON:0011823", + "UBERON:0000982", + ], + "object_label": "Decreased cervical spine flexion due to contractures of posterior cervical muscles (HPO)", "object_closure_label": [ "All (HPO)", - "Mode of inheritance (HPO)", - "Autosomal dominant inheritance (HPO)", - "Mendelian inheritance", - ], + "Phenotypic abnormality (HPO)", + "Abnormality of the skeletal system (HPO)", + "Flexion contracture (HPO)", + "Abnormality of the musculature (HPO)", + "Abnormality of connective tissue (HPO)", + "Decreased cervical spine flexion due to contractures of posterior cervical muscles (HPO)", + "Abnormality of joint mobility (HPO)", + "Abnormal skeletal muscle morphology (HPO)", + "Abnormal skeletal morphology (HPO)", + "Abnormality of musculoskeletal physiology (HPO)", + "Abnormality of the musculoskeletal system (HPO)", + "Joint contracture", + "Abnormal joint physiology", + "Abnormal tendon morphology (HPO)", + "tendon", + "anatomical structure", + "organ", + "musculature of body", + "material anatomical entity", + "anatomical system", + "multicellular organism", + "tissue", + "skeletal joint", + "musculature", + "anatomical entity", + "skeletal system", + "muscle organ", + "musculoskeletal system", + "connective tissue", + "articular system", + "articulation", + "muscle structure", + "regular connective tissue", + "dense regular connective tissue", + "multicellular anatomical structure", + "organ system subdivision", + "dense connective tissue", + "multi organ part structure", + "anatomical collection", + ], + "object_taxon": None, + "object_taxon_label": None, "primary_knowledge_source": "infores:hpo-annotations", "aggregator_knowledge_source": ["infores:monarchinitiative"], - "category": "biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation", + "category": "biolink:DiseaseToPhenotypicFeatureAssociation", "negated": None, - "provided_by": "hpoa_disease_mode_of_inheritance_edges", - "publications": ["OMIM:609452"], + "provided_by": "hpoa_disease_phenotype_edges", + "publications": ["OMIM:310300"], "qualifiers": [], "frequency_qualifier": None, "has_evidence": ["ECO:0000501"], diff --git a/backend/tests/fixtures/histopheno.py b/backend/tests/fixtures/histopheno.py index 8fb186377..31819235a 100644 --- a/backend/tests/fixtures/histopheno.py +++ b/backend/tests/fixtures/histopheno.py @@ -6,25 +6,25 @@ def histopheno(): return { "id": "MONDO:0020121", "items": [ - {"label": "musculature", "count": 1747, "id": "HP:0003011"}, - {"label": "nervous_system", "count": 1118, "id": "HP:0000707"}, - {"label": "head_neck", "count": 573, "id": "HP:0000152"}, - {"label": "skeletal_system", "count": 504, "id": "HP:0000924"}, - {"label": "respiratory", "count": 318, "id": "HP:0002086"}, - {"label": "eye", "count": 276, "id": "HP:0000478"}, - {"label": "metabolism_homeostasis", "count": 219, "id": "HP:0001939"}, - {"label": "cardiovascular_system", "count": 192, "id": "HP:0001626"}, - {"label": "blood", "count": 185, "id": "HP:0001871"}, - {"label": "connective_tissue", "count": 165, "id": "HP:0003549"}, - {"label": "digestive_system", "count": 143, "id": "HP:0025031"}, - {"label": "integument", "count": 48, "id": "HP:0001574"}, - {"label": "genitourinary_system", "count": 43, "id": "HP:0000119"}, - {"label": "growth", "count": 33, "id": "HP:0001507"}, - {"label": "ear", "count": 27, "id": "HP:0000598"}, - {"label": "endocrine", "count": 25, "id": "HP:0000818"}, - {"label": "immune_system", "count": 21, "id": "HP:0002715"}, - {"label": "prenatal_or_birth", "count": 20, "id": "HP:0001197"}, - {"label": "neoplasm", "count": 7, "id": "HP:0002664"}, + {"label": "musculature", "count": 1787, "id": "HP:0003011"}, + {"label": "nervous_system", "count": 1144, "id": "HP:0000707"}, + {"label": "head_neck", "count": 658, "id": "HP:0000152"}, + {"label": "skeletal_system", "count": 627, "id": "HP:0000924"}, + {"label": "respiratory", "count": 333, "id": "HP:0002086"}, + {"label": "eye", "count": 298, "id": "HP:0000478"}, + {"label": "metabolism_homeostasis", "count": 228, "id": "HP:0001939"}, + {"label": "cardiovascular_system", "count": 196, "id": "HP:0001626"}, + {"label": "connective_tissue", "count": 192, "id": "HP:0003549"}, + {"label": "blood", "count": 189, "id": "HP:0001871"}, + {"label": "digestive_system", "count": 176, "id": "HP:0025031"}, + {"label": "integument", "count": 65, "id": "HP:0001574"}, + {"label": "genitourinary_system", "count": 49, "id": "HP:0000119"}, + {"label": "growth", "count": 40, "id": "HP:0001507"}, + {"label": "ear", "count": 32, "id": "HP:0000598"}, + {"label": "endocrine", "count": 27, "id": "HP:0000818"}, + {"label": "immune_system", "count": 24, "id": "HP:0002715"}, + {"label": "prenatal_or_birth", "count": 24, "id": "HP:0001197"}, + {"label": "neoplasm", "count": 8, "id": "HP:0002664"}, {"label": "breast", "count": 1, "id": "HP:0000769"}, ], } diff --git a/backend/tests/fixtures/histopheno_response.py b/backend/tests/fixtures/histopheno_response.py index 37f8ec838..0208f34ee 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": 2, + "QTime": 1, "params": { "facet.query": [ 'object_closure:"HP:0000924"', @@ -39,29 +39,29 @@ def histopheno_response(): "facet": "true", }, }, - "response": {"num_found": 4538, "start": 0, "docs": []}, + "response": {"num_found": 4852, "start": 0, "docs": []}, "facet_counts": { "facet_fields": {}, "facet_queries": { - 'object_closure:"HP:0000924"': 504, - 'object_closure:"HP:0000707"': 1118, - 'object_closure:"HP:0000152"': 573, - 'object_closure:"HP:0001574"': 48, - 'object_closure:"HP:0000478"': 276, - 'object_closure:"HP:0001626"': 192, - 'object_closure:"HP:0001939"': 219, - 'object_closure:"HP:0000119"': 43, - 'object_closure:"HP:0025031"': 143, - 'object_closure:"HP:0002664"': 7, - 'object_closure:"HP:0001871"': 185, - 'object_closure:"HP:0002715"': 21, - 'object_closure:"HP:0000818"': 25, - 'object_closure:"HP:0003011"': 1747, - 'object_closure:"HP:0002086"': 318, - 'object_closure:"HP:0000598"': 27, - 'object_closure:"HP:0003549"': 165, - 'object_closure:"HP:0001197"': 20, - 'object_closure:"HP:0001507"': 33, + 'object_closure:"HP:0000924"': 627, + 'object_closure:"HP:0000707"': 1144, + 'object_closure:"HP:0000152"': 658, + 'object_closure:"HP:0001574"': 65, + 'object_closure:"HP:0000478"': 298, + 'object_closure:"HP:0001626"': 196, + 'object_closure:"HP:0001939"': 228, + 'object_closure:"HP:0000119"': 49, + 'object_closure:"HP:0025031"': 176, + 'object_closure:"HP:0002664"': 8, + 'object_closure:"HP:0001871"': 189, + 'object_closure:"HP:0002715"': 24, + 'object_closure:"HP:0000818"': 27, + 'object_closure:"HP:0003011"': 1787, + 'object_closure:"HP:0002086"': 333, + 'object_closure:"HP:0000598"': 32, + 'object_closure:"HP:0003549"': 192, + 'object_closure:"HP:0001197"': 24, + 'object_closure:"HP:0001507"': 40, 'object_closure:"HP:0000769"': 1, }, }, diff --git a/backend/tests/fixtures/node.py b/backend/tests/fixtures/node.py index 4314d12a2..a95e3b361 100644 --- a/backend/tests/fixtures/node.py +++ b/backend/tests/fixtures/node.py @@ -30,26 +30,26 @@ def node(): "association_counts": [ { "label": "Phenotypes", - "count": 4011, + "count": 4312, "category": "biolink:DiseaseToPhenotypicFeatureAssociation", }, { "label": "Causal Genes", - "count": 121, + "count": 123, "category": "biolink:CausalGeneToDiseaseAssociation", }, { "label": "Correlated Genes", - "count": 147, + "count": 149, "category": "biolink:CorrelatedGeneToDiseaseAssociation", }, ], "node_hierarchy": { "super_classes": [ { - "id": "MONDO:0019056", + "id": "MONDO:0005336", "category": "biolink:Disease", - "name": "neuromuscular disease", + "name": "myopathy", "full_name": None, "description": None, "xref": [], @@ -60,9 +60,9 @@ def node(): "synonym": [], }, { - "id": "MONDO:0700223", + "id": "MONDO:0019056", "category": "biolink:Disease", - "name": "hereditary skeletal muscle disorder", + "name": "neuromuscular disease", "full_name": None, "description": None, "xref": [], @@ -73,9 +73,9 @@ def node(): "synonym": [], }, { - "id": "MONDO:0005336", + "id": "MONDO:0700223", "category": "biolink:Disease", - "name": "myopathy", + "name": "hereditary skeletal muscle disorder", "full_name": None, "description": None, "xref": [], diff --git a/backend/tests/fixtures/search_response.py b/backend/tests/fixtures/search_response.py index 1cc7ba67f..f29467560 100644 --- a/backend/tests/fixtures/search_response.py +++ b/backend/tests/fixtures/search_response.py @@ -5,7 +5,7 @@ def search_response(): return { "responseHeader": { - "QTime": 2, + "QTime": 1, "params": { "mm": "100%", "q": "fanconi", diff --git a/frontend/fixtures/association-counts.json b/frontend/fixtures/association-counts.json index 290d0882c..3b69cb1ea 100644 --- a/frontend/fixtures/association-counts.json +++ b/frontend/fixtures/association-counts.json @@ -2,17 +2,17 @@ "items": [ { "label": "Phenotypes", - "count": 4011, + "count": 4312, "category": "biolink:DiseaseToPhenotypicFeatureAssociation" }, { "label": "Causal Genes", - "count": 121, + "count": 123, "category": "biolink:CausalGeneToDiseaseAssociation" }, { "label": "Correlated Genes", - "count": 147, + "count": 149, "category": "biolink:CorrelatedGeneToDiseaseAssociation" } ] diff --git a/frontend/fixtures/association-table.json b/frontend/fixtures/association-table.json index e5fd56c8d..e405d5fac 100644 --- a/frontend/fixtures/association-table.json +++ b/frontend/fixtures/association-table.json @@ -1,7 +1,7 @@ { "limit": 5, "offset": 0, - "total": 4011, + "total": 4312, "items": [ { "id": "uuid:632c5b16-212f-11ee-873a-cd90a19c4085", @@ -15,7 +15,6 @@ "MONDO:0005071", "MONDO:0025193", "MONDO:0020121", - "MONDO:0700223", "BFO:0000002", "MONDO:0020793", "BFO:0000017", @@ -61,9 +60,10 @@ "oculopharyngodistal myopathy 1", "disorder of visual system", "oculopharyngodistal myopathy", - "human disease or disorder", - "hereditary skeletal muscle disorder" + "human disease or disorder" ], + "subject_taxon": null, + "subject_taxon_label": null, "predicate": "biolink:has_phenotype", "object": "HP:0002460", "original_object": null, @@ -93,18 +93,18 @@ "BFO:0000001", "HP:0011804", "PATO:0000001", - "CARO:0000000", "BFO:0000001", - "UBERON:0000383", - "UBERON:0001015", - "UBERON:0005090", "BFO:0000002", - "UBERON:0001630", "BFO:0000004", "BFO:0000040", "UBERON:0001062", + "CARO:0000000", "UBERON:0000465", + "UBERON:0000383", + "UBERON:0001015", + "UBERON:0005090", "UBERON:0000061", + "UBERON:0001630", "UBERON:0010000", "UBERON:0000467", "UBERON:0000468", @@ -133,6 +133,8 @@ "multicellular anatomical structure", "organ system subdivision" ], + "object_taxon": null, + "object_taxon_label": null, "primary_knowledge_source": "infores:hpo-annotations", "aggregator_knowledge_source": ["infores:monarchinitiative"], "category": "biolink:DiseaseToPhenotypicFeatureAssociation", @@ -185,7 +187,6 @@ "MONDO:0005071", "MONDO:0025193", "MONDO:0020121", - "MONDO:0700223", "BFO:0000002", "MONDO:0020793", "BFO:0000017", @@ -231,9 +232,10 @@ "oculopharyngodistal myopathy 1", "disorder of visual system", "oculopharyngodistal myopathy", - "human disease or disorder", - "hereditary skeletal muscle disorder" + "human disease or disorder" ], + "subject_taxon": null, + "subject_taxon_label": null, "predicate": "biolink:has_phenotype", "object": "HP:0002015", "original_object": null, @@ -269,42 +271,43 @@ "HP:0025031", "UPHENO:0002474", "HP:0012638", - "CARO:0000000", - "CARO:0000003", "BFO:0000001", - "UBERON:0004921", - "UBERON:0001555", - "UBERON:0001016", - "UBERON:0000915", "BFO:0000002", - "UBERON:0004908", - "UBERON:0001043", "BFO:0000004", "BFO:0000040", "UBERON:0001062", - "RO:0002577", + "CARO:0000000", "UBERON:0000465", + "RO:0002577", + "CARO:0000006", + "UBERON:0004921", + "UBERON:0001555", + "UBERON:0001016", "UBERON:0000061", + "CARO:0000003", + "UBERON:0004908", + "UBERON:0001043", "UBERON:0010000", "UBERON:0000467", + "UBERON:0000915", "UBERON:0000468", "UBERON:0000475", "UBERON:0000064", "UBERON:0000062", "UBERON:0004111", - "UBERON:0005409", "UBERON:0001007", + "UBERON:0005409", "UBERON:0011676", "UBERON:0013701", "UBERON:0009569", - "UBERON:0013702", "UBERON:0013522", + "UBERON:0013702", "UBERON:0013765", "UBERON:0005177", "UBERON:0000025", - "UBERON:0002100", "UBERON:0005181", "UBERON:0002075", + "UBERON:0002100", "UBERON:0005178" ], "object_label": "Dysphagia (HPO)", @@ -350,6 +353,8 @@ "body proper", "digestive system element" ], + "object_taxon": null, + "object_taxon_label": null, "primary_knowledge_source": "infores:hpo-annotations", "aggregator_knowledge_source": ["infores:monarchinitiative"], "category": "biolink:DiseaseToPhenotypicFeatureAssociation", @@ -405,7 +410,6 @@ "MONDO:0013049", "MONDO:0020121", "MONDO:0004995", - "MONDO:0700223", "MONDO:0024322", "BFO:0000002", "BFO:0000017", @@ -462,9 +466,10 @@ "skeletal muscle disorder", "muscular dystrophy", "disorder of glycosylation", - "human disease or disorder", - "hereditary skeletal muscle disorder" + "human disease or disorder" ], + "subject_taxon": null, + "subject_taxon_label": null, "predicate": "biolink:has_phenotype", "object": "HP:0003236", "original_object": null, @@ -515,41 +520,41 @@ "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", "GO:0008152", + "BFO:0000030", + "UBERON:0000465", "GO:0005575", - "PR:000050567", + "UBERON:0000178", + "UBERON:0004120", + "UBERON:0000061", + "UBERON:0000463", "CHEBI:24431", - "UBERON:0000465", "GO:0032991", + "UBERON:0002390", + "UBERON:0010000", + "UBERON:0000467", + "UBERON:0006314", "CHEBI:23367", - "UBERON:0000061", - "UBERON:0000463", "GO:1902494", + "UBERON:0000468", + "UBERON:0001004", + "UBERON:0002193", + "UBERON:0000179", "CHEBI:36357", "CHEBI:33579", - "UBERON:0010000", - "UBERON:0000467", - "UBERON:0006314", "GO:1990234", "CHEBI:33839", "CHEBI:33675", "CHEBI:138675", - "UBERON:0000468", - "UBERON:0001004", - "UBERON:0002193", - "UBERON:0000179", "GO:0061695", "CHEBI:16670", "CHEBI:33302", @@ -631,6 +636,8 @@ "bodily fluid", "multicellular anatomical structure" ], + "object_taxon": null, + "object_taxon_label": null, "primary_knowledge_source": "infores:hpo-annotations", "aggregator_knowledge_source": ["infores:monarchinitiative"], "category": "biolink:DiseaseToPhenotypicFeatureAssociation", @@ -672,157 +679,299 @@ "direction": "outgoing" }, { - "id": "uuid:64b6842f-212f-11ee-873a-cd90a19c4085", - "subject": "MONDO:0009681", - "original_subject": "OMIM:254090", + "id": "uuid:59b1387d-212f-11ee-873a-cd90a19c4085", + "subject": "MONDO:0100435", + "original_subject": "OMIM:255800", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ "MONDO:0000001", + "MONDO:0018230", + "MONDO:0016121", + "MONDO:0005381", + "MONDO:0000429", + "MONDO:0019689", "MONDO:0005071", "MONDO:0020121", - "MONDO:0700223", + "MONDO:0016151", "BFO:0000002", - "MONDO:0019952", "BFO:0000017", "BFO:0000020", - "MONDO:0100225", + "MONDO:0006025", + "MONDO:0016106", + "MONDO:0005172", "BFO:0000016", "MONDO:0020120", "MONDO:0019056", + "MONDO:0005497", "MONDO:0016139", "MONDO:0700096", "MONDO:0005218", "MONDO:0005336", + "MONDO:0016761", "MONDO:0002081", - "MONDO:0009681", + "MONDO:0002254", + "MONDO:0021147", + "MONDO:0009717", "OGMS:0000031", + "MONDO:0100435", "MONDO:0003847", "MONDO:0003939", + "MONDO:0016120", "BFO:0000001", "MONDO:0002320", - "MONDO:0000355", - "MONDO:0019950" + "MONDO:0005516" ], - "subject_label": "Ullrich congenital muscular dystrophy 1", + "subject_label": "Schwartz-Jampel syndrome type 1", "subject_closure_label": [ "disease or disorder", - "Ullrich congenital muscular dystrophy", + "autosomal genetic disease", "musculoskeletal system disorder", + "syndromic disease", "congenital nervous system disorder", "hereditary disease", "muscle tissue disorder", "nervous system disorder", + "skeletal system disorder", "obsolete muscular disorder", "myopathy", - "Ullrich congenital muscular dystrophy 1", + "bone disorder", + "bone development disease", + "osteochondrodysplasia", + "autosomal recessive disease", + "Schwartz-Jampel syndrome", + "progressive muscular dystrophy", + "myotonic syndrome", + "congenital myotonia", "qualitative or quantitative protein defects in neuromuscular diseases", + "qualitative or quantitative defects of perlecan", + "spondyloepiphyseal dysplasia", + "skeletal dysplasia", "neuromuscular disease", - "congenital muscular dystrophy", - "congenital myopathy", + "perlecan-related bone disorder", "skeletal muscle disorder", "muscular dystrophy", - "collagen 6-related myopathy", - "human disease or disorder", - "hereditary skeletal muscle disorder" + "disorder of development or morphogenesis", + "Schwartz-Jampel syndrome type 1", + "human disease or disorder" ], + "subject_taxon": null, + "subject_taxon_label": null, "predicate": "biolink:has_phenotype", - "object": "HP:0020152", + "object": "HP:0002979", "original_object": null, "object_namespace": "HP", "object_category": "biolink:PhenotypicQuality", "object_closure": [ "HP:0000001", - "HP:0020152", - "UPHENO:0082875", - "HP:0001388", + "UPHENO:0031310", + "UPHENO:0041226", + "UPHENO:0041610", + "UPHENO:0041098", "UPHENO:0075696", + "UPHENO:0076740", + "HP:0002981", + "HP:0002814", "UPHENO:0001001", - "HP:0011729", + "UPHENO:0080300", + "UPHENO:0041573", + "UPHENO:0076703", + "UPHENO:0075952", + "UPHENO:0019749", "UPHENO:0001005", + "HP:0011314", + "UPHENO:0082449", + "HP:0011842", "UPHENO:0001002", - "HP:0034430", "HP:0000924", "HP:0000118", "BFO:0000002", + "HP:0002813", "BFO:0000020", - "UPHENO:0002332", + "UPHENO:0041536", + "UPHENO:0077858", + "UPHENO:0082467", + "UPHENO:0002896", + "UPHENO:0015280", + "UPHENO:0031193", "UPHENO:0002964", + "UPHENO:0041258", + "UPHENO:0082129", + "HP:0006487", + "UPHENO:0081581", "HP:0033127", "UPHENO:0001003", "UPHENO:0002536", - "UPHENO:0081440", + "HP:0002979", + "HP:0011844", + "UPHENO:0020041", + "UPHENO:0076727", + "UPHENO:0020584", + "UPHENO:0076692", + "UPHENO:0003070", + "UPHENO:0041591", + "HP:0040064", "BFO:0000001", "PATO:0000001", - "HP:0011843", - "CARO:0000000", + "HP:0040068", + "UPHENO:0002830", + "HP:0000940", + "UPHENO:0079873", "BFO:0000001", - "UBERON:0002204", "BFO:0000002", "BFO:0000004", "BFO:0000040", "UBERON:0001062", + "CARO:0000000", "UBERON:0000465", + "RO:0002577", + "UBERON:0001474", + "UBERON:0002204", + "CARO:0000006", + "UBERON:0006058", + "UBERON:0010712", + "UBERON:0005913", + "UBERON:0010538", + "UBERON:0004120", "UBERON:0000061", "UBERON:0034925", + "UBERON:0010740", + "UBERON:0002495", + "UBERON:0002513", + "CARO:0000003", + "UBERON:0000978", + "UBERON:0004381", + "UBERON:0005055", + "UBERON:0002529", + "UBERON:0011582", + "UBERON:0015061", + "UBERON:0004375", "UBERON:0010000", "UBERON:0000467", - "UBERON:0004770", + "UBERON:0015212", + "UBERON:0004288", + "UBERON:0002428", + "UBERON:0004708", + "UBERON:0010709", + "UBERON:0004769", + "UBERON:0008784", + "UBERON:0002471", "UBERON:0000468", + "UBERON:0000475", + "UBERON:0000064", + "UBERON:0000062", "UBERON:0011216", - "UBERON:0034921", + "UBERON:0010707", + "UBERON:0002101", + "UBERON:0004709", + "UBERON:0003823", + "UBERON:0000154", + "UBERON:0000026", + "UBERON:0010758", + "UBERON:0034944", + "UBERON:0004765", + "UBERON:0000075", + "UBERON:0010912", "UBERON:0001434", - "UBERON:0004905", - "UBERON:0000982" + "UBERON:0002103", + "UBERON:0010363", + "UBERON:0011249", + "UBERON:0002091" ], - "object_label": "Distal joint laxity (HPO)", + "object_label": "Bowing of the legs (HPO)", "object_closure_label": [ "All (HPO)", "Phenotypic abnormality (HPO)", "Abnormality of the skeletal system (HPO)", - "Joint laxity (HPO)", - "Abnormality of joint mobility (HPO)", - "Abnormality of musculoskeletal physiology (HPO)", - "Distal joint laxity (HPO)", + "Abnormal diaphysis morphology (HPO)", + "Abnormality of limb bone morphology (HPO)", + "Abnormality of the lower limb (HPO)", + "Bowing of the legs (HPO)", + "Abnormality of the calf (HPO)", + "Bowing of the long bones (HPO)", + "Abnormality of long bone morphology (HPO)", + "Abnormal skeletal morphology (HPO)", + "Abnormal appendicular skeleton morphology (HPO)", "Abnormality of the musculoskeletal system (HPO)", - "Abnormal joint physiology", + "Abnormality of limbs (HPO)", + "Abnormality of limb bone (HPO)", + "appendage", "anatomical structure", + "organ", + "organ part", + "subdivision of skeletal system", + "posterior region of body", "material anatomical entity", "anatomical system", "multicellular organism", - "skeletal joint", + "organism subdivision", + "leg", "anatomical entity", "skeletal system", + "bone element", + "appendicular skeleton", + "limb", + "hindlimb", "musculoskeletal system", - "articular system", - "articulation", + "limb bone", + "zeugopod", + "long bone", + "endochondral bone", + "limb segment", + "hindlimb zeugopod", + "mesoderm-derived structure", + "skeleton", + "bone of free limb or fin", + "skeleton of limb", + "paired limb/fin", + "pelvic appendage", + "skeletal element", + "diaphysis", + "zone of long bone", + "zone of bone organ", + "multi-limb segment region", + "lower limb segment", "multicellular anatomical structure", + "endochondral element", + "paired limb/fin segment", + "appendage girdle complex", + "pelvic complex", + "limb skeleton subdivision", + "bone of appendage girdle complex", + "subdivision of organism along appendicular axis", + "subdivision of skeleton", "organ system subdivision", - "multi organ part structure", - "anatomical collection" + "appendicular skeletal system", + "paired limb/fin skeleton", + "limb endochondral element", + "lateral structure", + "anatomical collection", + "zone of organ" ], + "object_taxon": null, + "object_taxon_label": null, "primary_knowledge_source": "infores:hpo-annotations", "aggregator_knowledge_source": ["infores:monarchinitiative"], "category": "biolink:DiseaseToPhenotypicFeatureAssociation", "negated": null, "provided_by": "hpoa_disease_phenotype_edges", - "publications": ["PMID:16258657", "OMIM:254090"], + "publications": ["PMID:16927315", "PMID:11941538"], "qualifiers": [], - "frequency_qualifier": "HP:0040280", + "frequency_qualifier": "HP:0040283", "has_evidence": ["ECO:0000269"], "onset_qualifier": null, "sex_qualifier": null, "stage_qualifier": null, "evidence_count": 5, "pathway": null, - "frequency_qualifier_label": "Obligate (HPO)", + "frequency_qualifier_label": "Occasional (HPO)", "frequency_qualifier_namespace": "HP", "frequency_qualifier_category": "biolink:PhenotypicFeature", - "frequency_qualifier_closure": ["HP:0000001", "HP:0040279", "HP:0040280"], + "frequency_qualifier_closure": ["HP:0000001", "HP:0040283", "HP:0040279"], "frequency_qualifier_closure_label": [ "All (HPO)", "Frequency (HPO)", - "Obligate (HPO)" + "Occasional (HPO)" ], "onset_qualifier_label": null, "onset_qualifier_namespace": null, @@ -842,153 +991,199 @@ "direction": "outgoing" }, { - "id": "uuid:628f3d98-212f-11ee-873a-cd90a19c4085", - "subject": "MONDO:0009676", - "original_subject": "OMIM:253601", + "id": "uuid:59b13885-212f-11ee-873a-cd90a19c4085", + "subject": "MONDO:0100435", + "original_subject": "OMIM:255800", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ "MONDO:0000001", - "MONDO:0016971", + "MONDO:0018230", + "MONDO:0016121", + "MONDO:0005381", "MONDO:0000429", - "MONDO:0016145", + "MONDO:0019689", "MONDO:0005071", "MONDO:0020121", - "MONDO:0700223", + "MONDO:0016151", "BFO:0000002", "BFO:0000017", "BFO:0000020", "MONDO:0006025", "MONDO:0016106", + "MONDO:0005172", "BFO:0000016", "MONDO:0020120", "MONDO:0019056", + "MONDO:0005497", "MONDO:0016139", "MONDO:0700096", "MONDO:0005218", "MONDO:0005336", + "MONDO:0016761", "MONDO:0002081", - "MONDO:0009676", + "MONDO:0002254", + "MONDO:0021147", + "MONDO:0009717", "OGMS:0000031", + "MONDO:0100435", "MONDO:0003847", "MONDO:0003939", + "MONDO:0016120", "BFO:0000001", - "MONDO:0015152" + "MONDO:0002320", + "MONDO:0005516" ], - "subject_label": "autosomal recessive limb-girdle muscular dystrophy type 2B", + "subject_label": "Schwartz-Jampel syndrome type 1", "subject_closure_label": [ "disease or disorder", "autosomal genetic disease", "musculoskeletal system disorder", + "syndromic disease", + "congenital nervous system disorder", "hereditary disease", "muscle tissue disorder", "nervous system disorder", + "skeletal system disorder", "obsolete muscular disorder", "myopathy", + "bone disorder", + "bone development disease", + "osteochondrodysplasia", "autosomal recessive disease", - "autosomal recessive limb-girdle muscular dystrophy type 2B", - "autosomal recessive limb-girdle muscular dystrophy", + "Schwartz-Jampel syndrome", "progressive muscular dystrophy", + "myotonic syndrome", + "congenital myotonia", "qualitative or quantitative protein defects in neuromuscular diseases", - "qualitative or quantitative defects of dysferlin", - "limb-girdle muscular dystrophy", + "qualitative or quantitative defects of perlecan", + "spondyloepiphyseal dysplasia", + "skeletal dysplasia", "neuromuscular disease", + "perlecan-related bone disorder", "skeletal muscle disorder", "muscular dystrophy", - "human disease or disorder", - "hereditary skeletal muscle disorder" + "disorder of development or morphogenesis", + "Schwartz-Jampel syndrome type 1", + "human disease or disorder" ], + "subject_taxon": null, + "subject_taxon_label": null, "predicate": "biolink:has_phenotype", - "object": "HP:0003701", + "object": "HP:0002751", "original_object": null, "object_namespace": "HP", "object_category": "biolink:PhenotypicQuality", "object_closure": [ "HP:0000001", - "UPHENO:0082875", + "HP:0002808", "UPHENO:0075696", - "UPHENO:0002320", "UPHENO:0001001", + "UPHENO:0076703", "UPHENO:0001005", - "HP:0003701", + "HP:0011842", "UPHENO:0001002", - "HP:0001324", + "HP:0000924", "HP:0000118", "BFO:0000002", "BFO:0000020", - "UPHENO:0080555", - "HP:0003011", - "UPHENO:0002816", - "UPHENO:0002332", - "UPHENO:0080556", + "HP:0009121", + "HP:0010674", + "HP:0000925", + "UPHENO:0015280", + "UPHENO:0002964", + "UPHENO:0081581", "HP:0033127", "UPHENO:0001003", "UPHENO:0002536", + "UPHENO:0002813", + "UPHENO:0020584", + "UPHENO:0076692", + "HP:0002650", "BFO:0000001", - "HP:0011804", + "HP:0002751", "PATO:0000001", - "CARO:0000000", + "UPHENO:0022529", "BFO:0000001", - "UBERON:0000383", - "UBERON:0001015", - "UBERON:0005090", "BFO:0000002", - "UBERON:0001630", "BFO:0000004", "BFO:0000040", "UBERON:0001062", + "CARO:0000000", "UBERON:0000465", + "UBERON:0011137", + "UBERON:0002204", + "UBERON:0005944", + "UBERON:0002090", + "UBERON:0001130", + "UBERON:0011138", "UBERON:0000061", + "UBERON:0034925", "UBERON:0010000", "UBERON:0000467", + "UBERON:0004288", "UBERON:0000468", - "UBERON:0000062", - "UBERON:0011216" + "UBERON:0011216", + "UBERON:0000075", + "UBERON:0010912", + "UBERON:0001434" ], - "object_label": "Proximal muscle weakness (HPO)", + "object_label": "Kyphoscoliosis (HPO)", "object_closure_label": [ "All (HPO)", "Phenotypic abnormality (HPO)", - "Muscle weakness (HPO)", - "Abnormality of the musculature (HPO)", - "Proximal muscle weakness (HPO)", - "Abnormal muscle physiology (HPO)", + "Abnormality of the skeletal system (HPO)", + "Abnormality of the vertebral column (HPO)", + "Scoliosis (HPO)", + "Kyphoscoliosis (HPO)", + "Kyphosis (HPO)", + "Abnormal axial skeleton morphology (HPO)", + "Abnormality of the curvature of the vertebral column (HPO)", + "Abnormal skeletal morphology (HPO)", "Abnormality of the musculoskeletal system (HPO)", "anatomical structure", - "organ", - "musculature of body", + "subdivision of skeletal system", "material anatomical entity", "anatomical system", "multicellular organism", - "musculature", "anatomical entity", - "muscle organ", - "muscle structure", + "vertebral column", + "skeletal system", + "postcranial axial skeleton", + "musculoskeletal system", + "skeleton", + "axial skeleton plus cranial skeleton", "multicellular anatomical structure", - "organ system subdivision" + "subdivision of skeleton", + "axial skeletal system", + "postcranial axial skeletal system", + "organ system subdivision", + "anatomical collection" ], + "object_taxon": null, + "object_taxon_label": null, "primary_knowledge_source": "infores:hpo-annotations", "aggregator_knowledge_source": ["infores:monarchinitiative"], "category": "biolink:DiseaseToPhenotypicFeatureAssociation", "negated": null, "provided_by": "hpoa_disease_phenotype_edges", - "publications": ["PMID:9731527", "PMID:9009996"], + "publications": ["PMID:16927315", "PMID:11941538"], "qualifiers": [], - "frequency_qualifier": "HP:0040280", + "frequency_qualifier": "HP:0040283", "has_evidence": ["ECO:0000269"], "onset_qualifier": null, "sex_qualifier": null, "stage_qualifier": null, "evidence_count": 5, "pathway": null, - "frequency_qualifier_label": "Obligate (HPO)", + "frequency_qualifier_label": "Occasional (HPO)", "frequency_qualifier_namespace": "HP", "frequency_qualifier_category": "biolink:PhenotypicFeature", - "frequency_qualifier_closure": ["HP:0000001", "HP:0040279", "HP:0040280"], + "frequency_qualifier_closure": ["HP:0000001", "HP:0040283", "HP:0040279"], "frequency_qualifier_closure_label": [ "All (HPO)", "Frequency (HPO)", - "Obligate (HPO)" + "Occasional (HPO)" ], "onset_qualifier_label": null, "onset_qualifier_namespace": null, diff --git a/frontend/fixtures/associations.json b/frontend/fixtures/associations.json index 2a0b320b3..e4682bf41 100644 --- a/frontend/fixtures/associations.json +++ b/frontend/fixtures/associations.json @@ -1,26 +1,28 @@ { "limit": 20, "offset": 0, - "total": 4806, + "total": 5124, "items": [ { - "id": "uuid:c2a45bf5-212f-11ee-873a-cd90a19c4085", - "subject": "MONDO:0008028", - "original_subject": "OMIM:158800", + "id": "uuid:628f39f7-212f-11ee-873a-cd90a19c4085", + "subject": "MONDO:0008050", + "original_subject": "OMIM:160500", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ "MONDO:0000001", "MONDO:0005071", "MONDO:0020121", - "MONDO:0008028", - "MONDO:0700223", "BFO:0000002", + "MONDO:0019952", "BFO:0000017", "BFO:0000020", + "MONDO:0008050", + "MONDO:0016195", "BFO:0000016", "MONDO:0020120", "MONDO:0019056", + "MONDO:0016139", "MONDO:0700096", "MONDO:0005218", "MONDO:0005336", @@ -28,48 +30,128 @@ "OGMS:0000031", "MONDO:0003847", "MONDO:0003939", - "BFO:0000001" + "BFO:0000001", + "MONDO:0002320", + "MONDO:0018949" ], - "subject_label": "muscular dystrophy, Barnes type", + "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, Barnes type", + "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", - "human disease or disorder", - "hereditary skeletal muscle disorder" + "human disease or disorder" ], - "predicate": "biolink:has_mode_of_inheritance", - "object": "HP:0000006", + "subject_taxon": null, + "subject_taxon_label": null, + "predicate": "biolink:has_phenotype", + "object": "HP:0003803", "original_object": null, "object_namespace": "HP", - "object_category": "biolink:GeneticInheritance", + "object_category": "biolink:PhenotypicQuality", "object_closure": [ "HP:0000001", - "HP:0000006", - "HP:0000005", - "HP:0034345" - ], - "object_label": "Autosomal dominant inheritance (HPO)", + "HP:0004303", + "UPHENO:0001001", + "HP:0003803", + "HP:0033684", + "UPHENO:0001005", + "HP:0011805", + "UPHENO:0001002", + "HP:0000118", + "BFO:0000002", + "HP:0025354", + "BFO:0000020", + "HP:0003011", + "UPHENO:0002816", + "UPHENO:0081581", + "HP:0033127", + "UPHENO:0001003", + "UPHENO:0002536", + "UPHENO:0076692", + "UPHENO:0076710", + "BFO:0000001", + "PATO:0000001", + "BFO:0000001", + "BFO:0000002", + "BFO:0000004", + "BFO:0000040", + "UBERON:0001062", + "CARO:0000000", + "CL:0000000", + "UBERON:0000465", + "UBERON:0000383", + "UBERON:0001015", + "UBERON:0018254", + "UBERON:0005090", + "UBERON:0004120", + "CL:0000003", + "UBERON:0000061", + "UBERON:0001630", + "UBERON:0002385", + "CL:0002371", + "UBERON:0010000", + "UBERON:0000467", + "UBERON:0014892", + "UBERON:0002036", + "CL:0000188", + "UBERON:0000479", + "UBERON:0000468", + "UBERON:0000062", + "UBERON:0011216", + "UBERON:0001134" + ], + "object_label": "Type 1 muscle fiber predominance (HPO)", "object_closure_label": [ "All (HPO)", - "Mode of inheritance (HPO)", - "Autosomal dominant inheritance (HPO)", - "Mendelian inheritance" - ], + "Phenotypic abnormality (HPO)", + "Abnormality of the musculature (HPO)", + "Type 1 muscle fiber predominance (HPO)", + "Abnormal muscle fiber morphology (HPO)", + "Abnormal skeletal muscle morphology (HPO)", + "Abnormal cellular phenotype (HPO)", + "Abnormality of the musculoskeletal system (HPO)", + "Abnormal muscle fiber-type distribution (HPO)", + "anatomical structure", + "organ", + "musculature of body", + "material anatomical entity", + "anatomical system", + "multicellular organism", + "tissue", + "musculature", + "anatomical entity", + "skeletal muscle tissue", + "muscle organ", + "striated muscle tissue", + "muscle tissue", + "mesoderm-derived structure", + "muscle structure", + "multicellular anatomical structure", + "organ system subdivision", + "skeletal muscle organ", + "skeletal musculature" + ], + "object_taxon": null, + "object_taxon_label": null, "primary_knowledge_source": "infores:hpo-annotations", "aggregator_knowledge_source": ["infores:monarchinitiative"], - "category": "biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation", + "category": "biolink:DiseaseToPhenotypicFeatureAssociation", "negated": null, - "provided_by": "hpoa_disease_mode_of_inheritance_edges", - "publications": ["OMIM:158800"], + "provided_by": "hpoa_disease_phenotype_edges", + "publications": ["OMIM:160500"], "qualifiers": [], "frequency_qualifier": null, "has_evidence": ["ECO:0000304"], @@ -100,82 +182,154 @@ "stage_qualifier_closure_label": [] }, { - "id": "uuid:c304bcf2-212f-11ee-873a-cd90a19c4085", - "subject": "MONDO:0008030", - "original_subject": "OMIM:158900", + "id": "uuid:64b68436-212f-11ee-873a-cd90a19c4085", + "subject": "MONDO:0009681", + "original_subject": "OMIM:254090", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ - "MONDO:0008030", "MONDO:0000001", - "MONDO:0019303", "MONDO:0005071", "MONDO:0020121", - "MONDO:0700223", - "MONDO:0001347", "BFO:0000002", "BFO:0000017", "BFO:0000020", - "MONDO:0016106", - "MONDO:0100137", + "MONDO:0100225", "BFO:0000016", "MONDO:0020120", "MONDO:0019056", + "MONDO:0016139", "MONDO:0700096", "MONDO:0005218", "MONDO:0005336", "MONDO:0002081", - "MONDO:0021147", + "MONDO:0009681", "OGMS:0000031", "MONDO:0003847", "MONDO:0003939", - "BFO:0000001" + "BFO:0000001", + "MONDO:0002320", + "MONDO:0000355", + "MONDO:0019950" ], - "subject_label": "facioscapulohumeral muscular dystrophy 1", + "subject_label": "Ullrich congenital muscular dystrophy 1", "subject_closure_label": [ "disease or disorder", - "facioscapulohumeral muscular dystrophy", + "Ullrich congenital muscular dystrophy", "musculoskeletal system disorder", + "congenital nervous system disorder", "hereditary disease", "muscle tissue disorder", "nervous system disorder", "obsolete muscular disorder", "myopathy", - "facioscapulohumeral muscular dystrophy 1", - "progressive muscular dystrophy", + "Ullrich congenital muscular dystrophy 1", + "qualitative or quantitative protein defects in neuromuscular diseases", "neuromuscular disease", - "premature aging syndrome", + "congenital muscular dystrophy", "skeletal muscle disorder", "muscular dystrophy", - "disorder of development or morphogenesis", - "telomere syndrome", - "human disease or disorder", - "hereditary skeletal muscle disorder" + "collagen 6-related myopathy", + "human disease or disorder" ], - "predicate": "biolink:has_mode_of_inheritance", - "object": "HP:0000006", + "subject_taxon": null, + "subject_taxon_label": null, + "predicate": "biolink:has_phenotype", + "object": "HP:0003803", "original_object": null, "object_namespace": "HP", - "object_category": "biolink:GeneticInheritance", + "object_category": "biolink:PhenotypicQuality", "object_closure": [ "HP:0000001", - "HP:0000006", - "HP:0000005", - "HP:0034345" - ], - "object_label": "Autosomal dominant inheritance (HPO)", + "HP:0004303", + "UPHENO:0001001", + "HP:0003803", + "HP:0033684", + "UPHENO:0001005", + "HP:0011805", + "UPHENO:0001002", + "HP:0000118", + "BFO:0000002", + "HP:0025354", + "BFO:0000020", + "HP:0003011", + "UPHENO:0002816", + "UPHENO:0081581", + "HP:0033127", + "UPHENO:0001003", + "UPHENO:0002536", + "UPHENO:0076692", + "UPHENO:0076710", + "BFO:0000001", + "PATO:0000001", + "BFO:0000001", + "BFO:0000002", + "BFO:0000004", + "BFO:0000040", + "UBERON:0001062", + "CARO:0000000", + "CL:0000000", + "UBERON:0000465", + "UBERON:0000383", + "UBERON:0001015", + "UBERON:0018254", + "UBERON:0005090", + "UBERON:0004120", + "CL:0000003", + "UBERON:0000061", + "UBERON:0001630", + "UBERON:0002385", + "CL:0002371", + "UBERON:0010000", + "UBERON:0000467", + "UBERON:0014892", + "UBERON:0002036", + "CL:0000188", + "UBERON:0000479", + "UBERON:0000468", + "UBERON:0000062", + "UBERON:0011216", + "UBERON:0001134" + ], + "object_label": "Type 1 muscle fiber predominance (HPO)", "object_closure_label": [ "All (HPO)", - "Mode of inheritance (HPO)", - "Autosomal dominant inheritance (HPO)", - "Mendelian inheritance" - ], + "Phenotypic abnormality (HPO)", + "Abnormality of the musculature (HPO)", + "Type 1 muscle fiber predominance (HPO)", + "Abnormal muscle fiber morphology (HPO)", + "Abnormal skeletal muscle morphology (HPO)", + "Abnormal cellular phenotype (HPO)", + "Abnormality of the musculoskeletal system (HPO)", + "Abnormal muscle fiber-type distribution (HPO)", + "anatomical structure", + "organ", + "musculature of body", + "material anatomical entity", + "anatomical system", + "multicellular organism", + "tissue", + "musculature", + "anatomical entity", + "skeletal muscle tissue", + "muscle organ", + "striated muscle tissue", + "muscle tissue", + "mesoderm-derived structure", + "muscle structure", + "multicellular anatomical structure", + "organ system subdivision", + "skeletal muscle organ", + "skeletal musculature" + ], + "object_taxon": null, + "object_taxon_label": null, "primary_knowledge_source": "infores:hpo-annotations", "aggregator_knowledge_source": ["infores:monarchinitiative"], - "category": "biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation", + "category": "biolink:DiseaseToPhenotypicFeatureAssociation", "negated": null, - "provided_by": "hpoa_disease_mode_of_inheritance_edges", - "publications": ["OMIM:158900"], + "provided_by": "hpoa_disease_phenotype_edges", + "publications": ["OMIM:254090"], "qualifiers": [], "frequency_qualifier": null, "has_evidence": ["ECO:0000501"], @@ -206,100 +360,152 @@ "stage_qualifier_closure_label": [] }, { - "id": "uuid:c3cdad58-212f-11ee-873a-cd90a19c4085", - "subject": "MONDO:0008034", - "original_subject": "OMIM:159050", + "id": "uuid:628f39f6-212f-11ee-873a-cd90a19c4085", + "subject": "MONDO:0008050", + "original_subject": "OMIM:160500", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ - "MONDO:0004994", "MONDO:0000001", - "MONDO:0008034", "MONDO:0005071", - "MONDO:0016147", - "MONDO:0005267", "MONDO:0020121", - "MONDO:0004995", - "MONDO:0700223", "BFO:0000002", + "MONDO:0019952", "BFO:0000017", "BFO:0000020", - "MONDO:0010542", - "MONDO:0016106", - "MONDO:0015470", - "MONDO:0005217", - "MONDO:0016899", + "MONDO:0008050", + "MONDO:0016195", "BFO:0000016", "MONDO:0020120", "MONDO:0019056", "MONDO:0016139", "MONDO:0700096", - "MONDO:0000591", "MONDO:0005218", "MONDO:0005336", "MONDO:0002081", - "MONDO:0016333", "OGMS:0000031", - "MONDO:0005021", "MONDO:0003847", "MONDO:0003939", "BFO:0000001", - "MONDO:0010311" + "MONDO:0002320", + "MONDO:0018949" ], - "subject_label": "muscular dystrophy, pseudohypertrophic, with Internalized capillaries", + "subject_label": "MYH7-related skeletal myopathy", "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", "nervous system disorder", - "familial cardiomyopathy", "obsolete muscular disorder", - "heart disorder", "myopathy", - "muscular dystrophy, pseudohypertrophic, with Internalized capillaries", - "Becker muscular dystrophy", - "dilated cardiomyopathy 3B", - "familial isolated dilated cardiomyopathy", - "progressive muscular dystrophy", + "MYH7-related skeletal myopathy", "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 beta-myosin heavy chain (MYH7)", + "distal myopathy", "neuromuscular disease", + "congenital myopathy", "skeletal muscle disorder", "muscular dystrophy", - "human disease or disorder", - "hereditary skeletal muscle disorder" + "human disease or disorder" ], - "predicate": "biolink:has_mode_of_inheritance", - "object": "HP:0000006", + "subject_taxon": null, + "subject_taxon_label": null, + "predicate": "biolink:has_phenotype", + "object": "HP:0003805", "original_object": null, "object_namespace": "HP", - "object_category": "biolink:GeneticInheritance", + "object_category": "biolink:PhenotypicQuality", "object_closure": [ "HP:0000001", - "HP:0000006", - "HP:0000005", - "HP:0034345" - ], - "object_label": "Autosomal dominant inheritance (HPO)", + "HP:0004303", + "UPHENO:0001001", + "UPHENO:0001005", + "HP:0011805", + "UPHENO:0001002", + "HP:0000118", + "BFO:0000002", + "HP:0025354", + "BFO:0000020", + "HP:0003011", + "UPHENO:0002816", + "UPHENO:0081581", + "HP:0033127", + "UPHENO:0001003", + "UPHENO:0002536", + "UPHENO:0076692", + "UPHENO:0076710", + "BFO:0000001", + "HP:0003805", + "PATO:0000001", + "BFO:0000001", + "BFO:0000002", + "BFO:0000004", + "BFO:0000040", + "UBERON:0001062", + "CARO:0000000", + "CL:0000000", + "UBERON:0000465", + "UBERON:0000383", + "UBERON:0001015", + "UBERON:0018254", + "UBERON:0005090", + "UBERON:0004120", + "CL:0000003", + "UBERON:0000061", + "UBERON:0001630", + "UBERON:0002385", + "CL:0002371", + "UBERON:0010000", + "UBERON:0000467", + "UBERON:0014892", + "UBERON:0002036", + "CL:0000188", + "UBERON:0000479", + "UBERON:0000468", + "UBERON:0000062", + "UBERON:0011216", + "UBERON:0001134" + ], + "object_label": "Rimmed vacuoles (HPO)", "object_closure_label": [ "All (HPO)", - "Mode of inheritance (HPO)", - "Autosomal dominant inheritance (HPO)", - "Mendelian inheritance" - ], + "Phenotypic abnormality (HPO)", + "Abnormality of the musculature (HPO)", + "Rimmed vacuoles (HPO)", + "Abnormal muscle fiber morphology (HPO)", + "Abnormal skeletal muscle morphology (HPO)", + "Abnormal cellular phenotype (HPO)", + "Abnormality of the musculoskeletal system (HPO)", + "anatomical structure", + "organ", + "musculature of body", + "material anatomical entity", + "anatomical system", + "multicellular organism", + "tissue", + "musculature", + "anatomical entity", + "skeletal muscle tissue", + "muscle organ", + "striated muscle tissue", + "muscle tissue", + "mesoderm-derived structure", + "muscle structure", + "multicellular anatomical structure", + "organ system subdivision", + "skeletal muscle organ", + "skeletal musculature" + ], + "object_taxon": null, + "object_taxon_label": null, "primary_knowledge_source": "infores:hpo-annotations", "aggregator_knowledge_source": ["infores:monarchinitiative"], - "category": "biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation", + "category": "biolink:DiseaseToPhenotypicFeatureAssociation", "negated": null, - "provided_by": "hpoa_disease_mode_of_inheritance_edges", - "publications": ["OMIM:159050"], + "provided_by": "hpoa_disease_phenotype_edges", + "publications": ["OMIM:160500"], "qualifiers": [], "frequency_qualifier": null, "has_evidence": ["ECO:0000501"], @@ -330,77 +536,163 @@ "stage_qualifier_closure_label": [] }, { - "id": "uuid:c3367408-212f-11ee-873a-cd90a19c4085", - "subject": "MONDO:0008049", - "original_subject": "OMIM:160300", + "id": "uuid:5ebb4d1e-212f-11ee-873a-cd90a19c4085", + "subject": "MONDO:0010401", + "original_subject": "OMIM:300696", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ + "MONDO:0004994", "MONDO:0000001", "MONDO:0005071", + "MONDO:0005267", "MONDO:0020121", - "MONDO:0700223", + "MONDO:0004995", "BFO:0000002", + "MONDO:0010401", "BFO:0000017", - "MONDO:0008049", "BFO:0000020", + "MONDO:0016106", + "MONDO:0005217", "BFO:0000016", "MONDO:0020120", "MONDO:0019056", "MONDO:0700096", + "MONDO:0000591", "MONDO:0005218", "MONDO:0005336", "MONDO:0002081", + "MONDO:0016333", + "MONDO:0016830", "OGMS:0000031", + "MONDO:0005021", "MONDO:0003847", "MONDO:0003939", - "BFO:0000001", - "MONDO:0018949" + "BFO:0000001" ], - "subject_label": "myopathy, distal, infantile-onset", + "subject_label": "X-linked myopathy with postural muscle atrophy", "subject_closure_label": [ "disease or disorder", + "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", - "myopathy, distal, infantile-onset", - "distal myopathy", + "X-linked myopathy with postural muscle atrophy", + "progressive muscular dystrophy", + "familial dilated cardiomyopathy", + "Emery-Dreifuss muscular dystrophy", "neuromuscular disease", "skeletal muscle disorder", "muscular dystrophy", - "human disease or disorder", - "hereditary skeletal muscle disorder" + "human disease or disorder" ], - "predicate": "biolink:has_mode_of_inheritance", - "object": "HP:0000006", + "subject_taxon": null, + "subject_taxon_label": null, + "predicate": "biolink:has_phenotype", + "object": "HP:0003805", "original_object": null, "object_namespace": "HP", - "object_category": "biolink:GeneticInheritance", + "object_category": "biolink:PhenotypicQuality", "object_closure": [ "HP:0000001", - "HP:0000006", - "HP:0000005", - "HP:0034345" - ], - "object_label": "Autosomal dominant inheritance (HPO)", + "HP:0004303", + "UPHENO:0001001", + "UPHENO:0001005", + "HP:0011805", + "UPHENO:0001002", + "HP:0000118", + "BFO:0000002", + "HP:0025354", + "BFO:0000020", + "HP:0003011", + "UPHENO:0002816", + "UPHENO:0081581", + "HP:0033127", + "UPHENO:0001003", + "UPHENO:0002536", + "UPHENO:0076692", + "UPHENO:0076710", + "BFO:0000001", + "HP:0003805", + "PATO:0000001", + "BFO:0000001", + "BFO:0000002", + "BFO:0000004", + "BFO:0000040", + "UBERON:0001062", + "CARO:0000000", + "CL:0000000", + "UBERON:0000465", + "UBERON:0000383", + "UBERON:0001015", + "UBERON:0018254", + "UBERON:0005090", + "UBERON:0004120", + "CL:0000003", + "UBERON:0000061", + "UBERON:0001630", + "UBERON:0002385", + "CL:0002371", + "UBERON:0010000", + "UBERON:0000467", + "UBERON:0014892", + "UBERON:0002036", + "CL:0000188", + "UBERON:0000479", + "UBERON:0000468", + "UBERON:0000062", + "UBERON:0011216", + "UBERON:0001134" + ], + "object_label": "Rimmed vacuoles (HPO)", "object_closure_label": [ "All (HPO)", - "Mode of inheritance (HPO)", - "Autosomal dominant inheritance (HPO)", - "Mendelian inheritance" - ], + "Phenotypic abnormality (HPO)", + "Abnormality of the musculature (HPO)", + "Rimmed vacuoles (HPO)", + "Abnormal muscle fiber morphology (HPO)", + "Abnormal skeletal muscle morphology (HPO)", + "Abnormal cellular phenotype (HPO)", + "Abnormality of the musculoskeletal system (HPO)", + "anatomical structure", + "organ", + "musculature of body", + "material anatomical entity", + "anatomical system", + "multicellular organism", + "tissue", + "musculature", + "anatomical entity", + "skeletal muscle tissue", + "muscle organ", + "striated muscle tissue", + "muscle tissue", + "mesoderm-derived structure", + "muscle structure", + "multicellular anatomical structure", + "organ system subdivision", + "skeletal muscle organ", + "skeletal musculature" + ], + "object_taxon": null, + "object_taxon_label": null, "primary_knowledge_source": "infores:hpo-annotations", "aggregator_knowledge_source": ["infores:monarchinitiative"], - "category": "biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation", + "category": "biolink:DiseaseToPhenotypicFeatureAssociation", "negated": null, - "provided_by": "hpoa_disease_mode_of_inheritance_edges", - "publications": ["OMIM:160300"], + "provided_by": "hpoa_disease_phenotype_edges", + "publications": ["OMIM:300696"], "qualifiers": [], "frequency_qualifier": null, - "has_evidence": ["ECO:0000304"], + "has_evidence": ["ECO:0000501"], "onset_qualifier": null, "sex_qualifier": null, "stage_qualifier": null, @@ -428,40 +720,46 @@ "stage_qualifier_closure_label": [] }, { - "id": "uuid:c39b4534-212f-11ee-873a-cd90a19c4085", - "subject": "MONDO:0008050", - "original_subject": "OMIM:160500", + "id": "uuid:607e98ad-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:0000429", "MONDO:0005071", "MONDO:0020121", - "MONDO:0700223", + "MONDO:0100175", "BFO:0000002", "MONDO:0019952", "BFO:0000017", "BFO:0000020", - "MONDO:0008050", - "MONDO:0016195", + "MONDO:0016191", "BFO:0000016", "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:0002320", + "MONDO:0016108", "MONDO:0018949" ], - "subject_label": "MYH7-related skeletal myopathy", + "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", @@ -469,44 +767,118 @@ "nervous system disorder", "obsolete muscular disorder", "myopathy", - "MYH7-related skeletal myopathy", + "tibial muscular dystrophy", + "autosomal dominant distal myopathy", "qualitative or quantitative protein defects in neuromuscular diseases", - "qualitative or quantitative defects of beta-myosin heavy chain (MYH7)", + "qualitative or quantitative defects of titin", "distal myopathy", "neuromuscular disease", "congenital myopathy", "skeletal muscle disorder", "muscular dystrophy", - "human disease or disorder", - "hereditary skeletal muscle disorder" + "TTN-related myopathy", + "autosomal dominant titinopathy", + "human disease or disorder" ], - "predicate": "biolink:has_mode_of_inheritance", - "object": "HP:0000006", + "subject_taxon": null, + "subject_taxon_label": null, + "predicate": "biolink:has_phenotype", + "object": "HP:0003805", "original_object": null, "object_namespace": "HP", - "object_category": "biolink:GeneticInheritance", + "object_category": "biolink:PhenotypicQuality", "object_closure": [ "HP:0000001", - "HP:0000006", - "HP:0000005", - "HP:0034345" - ], - "object_label": "Autosomal dominant inheritance (HPO)", + "HP:0004303", + "UPHENO:0001001", + "UPHENO:0001005", + "HP:0011805", + "UPHENO:0001002", + "HP:0000118", + "BFO:0000002", + "HP:0025354", + "BFO:0000020", + "HP:0003011", + "UPHENO:0002816", + "UPHENO:0081581", + "HP:0033127", + "UPHENO:0001003", + "UPHENO:0002536", + "UPHENO:0076692", + "UPHENO:0076710", + "BFO:0000001", + "HP:0003805", + "PATO:0000001", + "BFO:0000001", + "BFO:0000002", + "BFO:0000004", + "BFO:0000040", + "UBERON:0001062", + "CARO:0000000", + "CL:0000000", + "UBERON:0000465", + "UBERON:0000383", + "UBERON:0001015", + "UBERON:0018254", + "UBERON:0005090", + "UBERON:0004120", + "CL:0000003", + "UBERON:0000061", + "UBERON:0001630", + "UBERON:0002385", + "CL:0002371", + "UBERON:0010000", + "UBERON:0000467", + "UBERON:0014892", + "UBERON:0002036", + "CL:0000188", + "UBERON:0000479", + "UBERON:0000468", + "UBERON:0000062", + "UBERON:0011216", + "UBERON:0001134" + ], + "object_label": "Rimmed vacuoles (HPO)", "object_closure_label": [ "All (HPO)", - "Mode of inheritance (HPO)", - "Autosomal dominant inheritance (HPO)", - "Mendelian inheritance" - ], + "Phenotypic abnormality (HPO)", + "Abnormality of the musculature (HPO)", + "Rimmed vacuoles (HPO)", + "Abnormal muscle fiber morphology (HPO)", + "Abnormal skeletal muscle morphology (HPO)", + "Abnormal cellular phenotype (HPO)", + "Abnormality of the musculoskeletal system (HPO)", + "anatomical structure", + "organ", + "musculature of body", + "material anatomical entity", + "anatomical system", + "multicellular organism", + "tissue", + "musculature", + "anatomical entity", + "skeletal muscle tissue", + "muscle organ", + "striated muscle tissue", + "muscle tissue", + "mesoderm-derived structure", + "muscle structure", + "multicellular anatomical structure", + "organ system subdivision", + "skeletal muscle organ", + "skeletal musculature" + ], + "object_taxon": null, + "object_taxon_label": null, "primary_knowledge_source": "infores:hpo-annotations", "aggregator_knowledge_source": ["infores:monarchinitiative"], - "category": "biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation", + "category": "biolink:DiseaseToPhenotypicFeatureAssociation", "negated": null, - "provided_by": "hpoa_disease_mode_of_inheritance_edges", - "publications": ["PMID:15322983"], + "provided_by": "hpoa_disease_phenotype_edges", + "publications": ["OMIM:600334"], "qualifiers": [], "frequency_qualifier": null, - "has_evidence": ["ECO:0000269"], + "has_evidence": ["ECO:0000304"], "onset_qualifier": null, "sex_qualifier": null, "stage_qualifier": null, @@ -534,106 +906,156 @@ "stage_qualifier_closure_label": [] }, { - "id": "uuid:c2d3e237-212f-11ee-873a-cd90a19c4085", - "subject": "MONDO:0008056", - "original_subject": "OMIM:160900", + "id": "uuid:5f90dae3-212f-11ee-873a-cd90a19c4085", + "subject": "MONDO:0011170", + "original_subject": "OMIM:601954", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ - "MONDO:0004994", - "MONDO:0020158", "MONDO:0000001", - "MONDO:0016107", + "MONDO:0016971", + "MONDO:0000429", "MONDO:0005071", - "MONDO:0005267", "MONDO:0020121", - "MONDO:0005045", - "MONDO:0004995", - "MONDO:0700223", "BFO:0000002", "BFO:0000017", "BFO:0000020", + "MONDO:0006025", "MONDO:0016106", - "MONDO:0005217", - "MONDO:0024573", - "MONDO:0003382", "BFO:0000016", "MONDO:0020120", "MONDO:0019056", - "MONDO:0008056", + "MONDO:0016139", "MONDO:0700096", - "MONDO:0000591", - "MONDO:0024458", + "MONDO:0011170", "MONDO:0005218", "MONDO:0005336", "MONDO:0002081", - "MONDO:0002254", "OGMS:0000031", + "MONDO:0016192", "MONDO:0003847", "MONDO:0003939", - "MONDO:0002022", - "MONDO:0016120", "BFO:0000001", - "MONDO:0000462", - "MONDO:0005328" + "MONDO:0015152" ], - "subject_label": "myotonic dystrophy type 1", + "subject_label": "autosomal recessive limb-girdle muscular dystrophy type 2G", "subject_closure_label": [ "disease or disorder", - "eye adnexa disorder", - "intrinsic cardiomyopathy", - "disorder of orbital region", + "autosomal genetic disease", "musculoskeletal 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", - "myotonic dystrophy type 1", + "autosomal recessive disease", + "autosomal recessive limb-girdle muscular dystrophy type 2G", + "autosomal recessive limb-girdle muscular dystrophy", "progressive muscular dystrophy", - "myotonic dystrophy", - "myotonic syndrome", + "qualitative or quantitative protein defects in neuromuscular diseases", + "qualitative or quantitative defects of telethonin", + "limb-girdle muscular dystrophy", "neuromuscular disease", "skeletal muscle disorder", "muscular dystrophy", - "eyelids malposition disorder", - "disorder of visual system", - "familial hypertrophic cardiomyopathy", - "human disease or disorder", - "hereditary skeletal muscle disorder" + "human disease or disorder" ], - "predicate": "biolink:has_mode_of_inheritance", - "object": "HP:0000006", + "subject_taxon": null, + "subject_taxon_label": null, + "predicate": "biolink:has_phenotype", + "object": "HP:0003805", "original_object": null, "object_namespace": "HP", - "object_category": "biolink:GeneticInheritance", + "object_category": "biolink:PhenotypicQuality", "object_closure": [ "HP:0000001", - "HP:0000006", - "HP:0000005", - "HP:0034345" - ], - "object_label": "Autosomal dominant inheritance (HPO)", + "HP:0004303", + "UPHENO:0001001", + "UPHENO:0001005", + "HP:0011805", + "UPHENO:0001002", + "HP:0000118", + "BFO:0000002", + "HP:0025354", + "BFO:0000020", + "HP:0003011", + "UPHENO:0002816", + "UPHENO:0081581", + "HP:0033127", + "UPHENO:0001003", + "UPHENO:0002536", + "UPHENO:0076692", + "UPHENO:0076710", + "BFO:0000001", + "HP:0003805", + "PATO:0000001", + "BFO:0000001", + "BFO:0000002", + "BFO:0000004", + "BFO:0000040", + "UBERON:0001062", + "CARO:0000000", + "CL:0000000", + "UBERON:0000465", + "UBERON:0000383", + "UBERON:0001015", + "UBERON:0018254", + "UBERON:0005090", + "UBERON:0004120", + "CL:0000003", + "UBERON:0000061", + "UBERON:0001630", + "UBERON:0002385", + "CL:0002371", + "UBERON:0010000", + "UBERON:0000467", + "UBERON:0014892", + "UBERON:0002036", + "CL:0000188", + "UBERON:0000479", + "UBERON:0000468", + "UBERON:0000062", + "UBERON:0011216", + "UBERON:0001134" + ], + "object_label": "Rimmed vacuoles (HPO)", "object_closure_label": [ "All (HPO)", - 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"category": "biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation", + "category": "biolink:DiseaseToPhenotypicFeatureAssociation", "negated": null, - "provided_by": "hpoa_disease_mode_of_inheritance_edges", - "publications": ["OMIM:160900"], + "provided_by": "hpoa_disease_phenotype_edges", + "publications": ["OMIM:601954"], "qualifiers": [], "frequency_qualifier": null, "has_evidence": ["ECO:0000501"], @@ -664,88 +1086,166 @@ "stage_qualifier_closure_label": [] }, { - "id": "uuid:c400607b-212f-11ee-873a-cd90a19c4085", - "subject": "MONDO:0008116", - "original_subject": "OMIM:164300", + "id": "uuid:63fd8f8b-212f-11ee-873a-cd90a19c4085", + "subject": "MONDO:0011362", + "original_subject": "OMIM:603689", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ - "MONDO:0020158", "MONDO:0000001", + "MONDO:0016112", + "MONDO:0000429", "MONDO:0005071", "MONDO:0020121", - "MONDO:0700223", - "MONDO:0004746", + "MONDO:0100175", "BFO:0000002", + "MONDO:0019952", "BFO:0000017", "BFO:0000020", "MONDO:0016106", - "MONDO:0003382", + "MONDO:0016191", "BFO:0000016", "MONDO:0020120", "MONDO:0019056", + "MONDO:0100494", + "MONDO:0016139", "MONDO:0700096", - "MONDO:0024458", "MONDO:0005218", "MONDO:0005336", "MONDO:0002081", - "MONDO:0008116", + "MONDO:0000426", + "MONDO:0011362", "OGMS:0000031", "MONDO:0003847", "MONDO:0003939", - "MONDO:0002022", "BFO:0000001", - "MONDO:0000462", - "MONDO:0005328" + "MONDO:0002320", + "MONDO:0016108", + "MONDO:0018949" ], - "subject_label": "oculopharyngeal muscular dystrophy", + "subject_label": "myopathy, myofibrillar, 9, with early respiratory failure", "subject_closure_label": [ "disease or disorder", - "eye adnexa disorder", - "disorder of orbital region", + "autosomal dominant disease", + "autosomal genetic disease", "musculoskeletal system disorder", - "eyelid disorder", + "congenital nervous system disorder", "hereditary disease", "muscle tissue disorder", - "myopathy of extraocular muscle", "nervous system disorder", "obsolete muscular disorder", - "eye disorder", "myopathy", - "oculopharyngeal muscular dystrophy", + "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", - "eyelids malposition disorder", - "disorder of visual system", - "human disease or disorder", - "hereditary skeletal muscle disorder" + "TTN-related myopathy", + "autosomal dominant titinopathy", + "human disease or disorder" ], - "predicate": "biolink:has_mode_of_inheritance", - "object": "HP:0000006", + "subject_taxon": null, + "subject_taxon_label": null, + "predicate": "biolink:has_phenotype", + "object": "HP:0003805", "original_object": null, "object_namespace": "HP", - "object_category": "biolink:GeneticInheritance", + "object_category": "biolink:PhenotypicQuality", "object_closure": [ "HP:0000001", - "HP:0000006", - "HP:0000005", - "HP:0034345" - ], - "object_label": "Autosomal dominant inheritance (HPO)", + "HP:0004303", + "UPHENO:0001001", + "UPHENO:0001005", + "HP:0011805", + "UPHENO:0001002", + "HP:0000118", + "BFO:0000002", + "HP:0025354", + "BFO:0000020", + "HP:0003011", + "UPHENO:0002816", + "UPHENO:0081581", + "HP:0033127", + "UPHENO:0001003", + "UPHENO:0002536", + "UPHENO:0076692", + "UPHENO:0076710", + "BFO:0000001", + "HP:0003805", + "PATO:0000001", + "BFO:0000001", + "BFO:0000002", + "BFO:0000004", + "BFO:0000040", + "UBERON:0001062", + "CARO:0000000", + "CL:0000000", + "UBERON:0000465", + "UBERON:0000383", + "UBERON:0001015", + "UBERON:0018254", + "UBERON:0005090", + "UBERON:0004120", + "CL:0000003", + "UBERON:0000061", + "UBERON:0001630", + "UBERON:0002385", + "CL:0002371", + "UBERON:0010000", + "UBERON:0000467", + "UBERON:0014892", + "UBERON:0002036", + "CL:0000188", + "UBERON:0000479", + "UBERON:0000468", + "UBERON:0000062", + "UBERON:0011216", + "UBERON:0001134" + ], + "object_label": "Rimmed vacuoles (HPO)", "object_closure_label": [ "All (HPO)", - 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"category": "biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation", + "category": "biolink:DiseaseToPhenotypicFeatureAssociation", "negated": null, - "provided_by": "hpoa_disease_mode_of_inheritance_edges", - "publications": ["PMID:9462747"], + "provided_by": "hpoa_disease_phenotype_edges", + "publications": ["PMID:22577215"], "qualifiers": [], "frequency_qualifier": null, "has_evidence": ["ECO:0000269"], @@ -776,87 +1276,153 @@ "stage_qualifier_closure_label": [] }, { - "id": "uuid:c3cdaddf-212f-11ee-873a-cd90a19c4085", - "subject": "MONDO:0009681", - "original_subject": "OMIM:254090", + "id": "uuid:649c482d-212f-11ee-873a-cd90a19c4085", + "subject": "MONDO:0011466", + "original_subject": "OMIM:604454", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ "MONDO:0000001", + "MONDO:0011466", + "MONDO:0000429", "MONDO:0005071", "MONDO:0020121", - "MONDO:0700223", "BFO:0000002", - "MONDO:0019952", "BFO:0000017", "BFO:0000020", - "MONDO:0100225", "BFO:0000016", "MONDO:0020120", "MONDO:0019056", - "MONDO:0016139", "MONDO:0700096", "MONDO:0005218", "MONDO:0005336", "MONDO:0002081", - "MONDO:0009681", + "MONDO:0000426", "OGMS:0000031", "MONDO:0003847", "MONDO:0003939", "BFO:0000001", - "MONDO:0002320", - "MONDO:0000355", - "MONDO:0019950" + "MONDO:0016108", + "MONDO:0018949" ], - "subject_label": "Ullrich congenital muscular dystrophy 1", + "subject_label": "distal myopathy, Welander type", "subject_closure_label": [ "disease or disorder", - "Ullrich congenital muscular dystrophy", + "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", - "Ullrich congenital muscular dystrophy 1", - "qualitative or quantitative protein defects in neuromuscular diseases", + "distal myopathy, Welander type", + "autosomal dominant distal myopathy", + "distal myopathy", "neuromuscular disease", - "congenital muscular dystrophy", - "congenital myopathy", "skeletal muscle disorder", "muscular dystrophy", - "collagen 6-related myopathy", - "human disease or disorder", - "hereditary skeletal muscle disorder" + "human disease or disorder" ], - "predicate": "biolink:has_mode_of_inheritance", - "object": "HP:0000006", + "subject_taxon": null, + "subject_taxon_label": null, + "predicate": "biolink:has_phenotype", + "object": "HP:0003805", "original_object": null, "object_namespace": "HP", - "object_category": "biolink:GeneticInheritance", + "object_category": "biolink:PhenotypicQuality", "object_closure": [ "HP:0000001", - "HP:0000006", - "HP:0000005", - "HP:0034345" - ], - "object_label": "Autosomal dominant inheritance (HPO)", + "HP:0004303", + "UPHENO:0001001", + "UPHENO:0001005", + "HP:0011805", + "UPHENO:0001002", + "HP:0000118", + "BFO:0000002", + "HP:0025354", + "BFO:0000020", + "HP:0003011", + "UPHENO:0002816", + "UPHENO:0081581", + "HP:0033127", + "UPHENO:0001003", + "UPHENO:0002536", + "UPHENO:0076692", + "UPHENO:0076710", + "BFO:0000001", + "HP:0003805", + "PATO:0000001", + "BFO:0000001", + "BFO:0000002", + "BFO:0000004", + "BFO:0000040", + "UBERON:0001062", + "CARO:0000000", + "CL:0000000", + "UBERON:0000465", + "UBERON:0000383", + "UBERON:0001015", + "UBERON:0018254", + "UBERON:0005090", + "UBERON:0004120", + "CL:0000003", + "UBERON:0000061", + "UBERON:0001630", + "UBERON:0002385", + "CL:0002371", + "UBERON:0010000", + "UBERON:0000467", + "UBERON:0014892", + "UBERON:0002036", + "CL:0000188", + "UBERON:0000479", + "UBERON:0000468", + "UBERON:0000062", + "UBERON:0011216", + "UBERON:0001134" + ], + "object_label": "Rimmed vacuoles (HPO)", "object_closure_label": [ "All (HPO)", - 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"category": "biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation", + "category": "biolink:DiseaseToPhenotypicFeatureAssociation", "negated": null, - "provided_by": "hpoa_disease_mode_of_inheritance_edges", - "publications": ["OMIM:254090"], + "provided_by": "hpoa_disease_phenotype_edges", + "publications": ["PMID:23348830"], "qualifiers": [], "frequency_qualifier": null, - "has_evidence": ["ECO:0000501"], + "has_evidence": ["ECO:0000269"], "onset_qualifier": null, "sex_qualifier": null, "stage_qualifier": null, @@ -884,75 +1450,189 @@ "stage_qualifier_closure_label": [] }, { - "id": "uuid:c275a020-212f-11ee-873a-cd90a19c4085", - "subject": "MONDO:0010676", - "original_subject": "OMIM:309950", + "id": "uuid:65070139-212f-11ee-873a-cd90a19c4085", + "subject": "MONDO:0011603", + "original_subject": "OMIM:605820", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ "MONDO:0000001", + "MONDO:0002245", + "MONDO:0016112", + "MONDO:0000429", + "MONDO:0005570", "MONDO:0005071", "MONDO:0020121", - "MONDO:0700223", + "MONDO:0021166", + "MONDO:0024322", "BFO:0000002", + "MONDO:0016200", "BFO:0000017", "BFO:0000020", + "MONDO:0100241", + "MONDO:0006025", + "MONDO:0007827", + "MONDO:0011603", "BFO:0000016", "MONDO:0020120", "MONDO:0019056", + "MONDO:0016139", "MONDO:0700096", "MONDO:0005218", "MONDO:0005336", + "MONDO:0009332", "MONDO:0002081", + "MONDO:0021167", + "MONDO:0016109", + "MONDO:0018795", + "MONDO:0017749", + "MONDO:0002049", "OGMS:0000031", "MONDO:0003847", "MONDO:0003939", + "MONDO:0015286", "BFO:0000001", - "MONDO:0010676" + "MONDO:0002320", + "MONDO:0019052", + "MONDO:0005066", + "MONDO:0018949" ], - "subject_label": "muscular dystrophy, Hemizygous lethal type", + "subject_label": "GNE myopathy", "subject_closure_label": [ "disease or disorder", + "autosomal genetic disease", + "thrombocytopenia", "musculoskeletal system disorder", + "blood platelet disease", + "congenital nervous system disorder", "hereditary disease", "muscle tissue disorder", + "metabolic disease", "nervous system disorder", "obsolete muscular disorder", "myopathy", - "muscular dystrophy, Hemizygous lethal type", + "hematologic disorder", + "autosomal recessive disease", + "inclusion body myositis", + "congenital hematological disorder", + "GNE myopathy", + "congenital disorder of glycosylation", + "autosomal recessive distal myopathy", + "hereditary inclusion-body myopathy", + "qualitative or quantitative protein defects in neuromuscular diseases", + "qualitative or quantitative defects of glucosamine (UDP-N-acetyl)-2-epimerase/N-acetylmannosamine kinase", + "disorder of multiple glycosylation", + "syndromic constitutional thrombocytopenia", + "distal myopathy", + "inborn errors of metabolism", "neuromuscular disease", "skeletal muscle disorder", "muscular dystrophy", - "human disease or disorder", - "hereditary skeletal muscle disorder" - ], - "predicate": "biolink:has_mode_of_inheritance", - "object": "HP:0000006", + "inflammatory disease", + "myositis disease", + "disorder of glycosylation", + "inherited thrombocytopenia", + "human disease or disorder" + ], + "subject_taxon": null, + "subject_taxon_label": null, + "predicate": "biolink:has_phenotype", + "object": "HP:0003805", "original_object": null, "object_namespace": "HP", - "object_category": "biolink:GeneticInheritance", + "object_category": "biolink:PhenotypicQuality", "object_closure": [ "HP:0000001", - "HP:0000006", - "HP:0000005", - "HP:0034345" - ], - "object_label": "Autosomal dominant inheritance (HPO)", + "HP:0004303", + "UPHENO:0001001", + "UPHENO:0001005", + "HP:0011805", + "UPHENO:0001002", + "HP:0000118", + "BFO:0000002", + "HP:0025354", + "BFO:0000020", + "HP:0003011", + "UPHENO:0002816", + "UPHENO:0081581", + "HP:0033127", + "UPHENO:0001003", + "UPHENO:0002536", + "UPHENO:0076692", + "UPHENO:0076710", + "BFO:0000001", + "HP:0003805", + "PATO:0000001", + "BFO:0000001", + "BFO:0000002", + "BFO:0000004", + "BFO:0000040", + "UBERON:0001062", + "CARO:0000000", + "CL:0000000", + "UBERON:0000465", + "UBERON:0000383", + "UBERON:0001015", + "UBERON:0018254", + "UBERON:0005090", + "UBERON:0004120", + "CL:0000003", + "UBERON:0000061", + "UBERON:0001630", + "UBERON:0002385", + "CL:0002371", + "UBERON:0010000", + "UBERON:0000467", + "UBERON:0014892", + "UBERON:0002036", + "CL:0000188", + "UBERON:0000479", + "UBERON:0000468", + "UBERON:0000062", + "UBERON:0011216", + "UBERON:0001134" + ], + "object_label": "Rimmed vacuoles (HPO)", "object_closure_label": [ "All (HPO)", - 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"category": "biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation", + "category": "biolink:DiseaseToPhenotypicFeatureAssociation", "negated": null, - "provided_by": "hpoa_disease_mode_of_inheritance_edges", - "publications": ["OMIM:309950"], + "provided_by": "hpoa_disease_phenotype_edges", + "publications": ["PMID:12177386"], "qualifiers": [], "frequency_qualifier": null, - "has_evidence": ["ECO:0000304"], + "has_evidence": ["ECO:0000269"], "onset_qualifier": null, "sex_qualifier": null, "stage_qualifier": null, @@ -980,29 +1660,26 @@ "stage_qualifier_closure_label": [] }, { - "id": "uuid:c336741f-212f-11ee-873a-cd90a19c4085", - "subject": "MONDO:0010870", - "original_subject": "OMIM:600334", + "id": "uuid:60cdba46-212f-11ee-873a-cd90a19c4085", + "subject": "MONDO:0012034", + "original_subject": "OMIM:608423", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ - "MONDO:0010870", "MONDO:0000001", + "MONDO:0016971", "MONDO:0000429", "MONDO:0005071", "MONDO:0020121", - "MONDO:0100175", - "MONDO:0700223", + "MONDO:0012034", "BFO:0000002", - "MONDO:0019952", "BFO:0000017", "BFO:0000020", - "MONDO:0016191", + "MONDO:0016106", "BFO:0000016", "MONDO:0020120", "MONDO:0019056", - "MONDO:0100494", - "MONDO:0016139", + "MONDO:0015151", "MONDO:0700096", "MONDO:0005218", "MONDO:0005336", @@ -1011,64 +1688,127 @@ "OGMS:0000031", "MONDO:0003847", "MONDO:0003939", - "BFO:0000001", - "MONDO:0002320", - "MONDO:0016108", - "MONDO:0018949" + "BFO:0000001" ], - "subject_label": "tibial muscular dystrophy", + "subject_label": "autosomal dominant limb-girdle muscular dystrophy type 1F", "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", - "tibial muscular dystrophy", - "autosomal dominant distal myopathy", - "qualitative or quantitative protein defects in neuromuscular diseases", - "qualitative or quantitative defects of titin", - "distal myopathy", + "autosomal dominant limb-girdle muscular dystrophy type 1F", + "muscular dystrophy, limb-girdle, autosomal dominant", + "progressive muscular dystrophy", + "limb-girdle muscular dystrophy", "neuromuscular disease", - "congenital myopathy", "skeletal muscle disorder", "muscular dystrophy", - "TTN-related myopathy", - "autosomal dominant titinopathy", - "human disease or disorder", - "hereditary skeletal muscle disorder" + "human disease or disorder" ], - "predicate": "biolink:has_mode_of_inheritance", - "object": "HP:0000006", + "subject_taxon": null, + "subject_taxon_label": null, + "predicate": "biolink:has_phenotype", + "object": "HP:0003805", "original_object": null, "object_namespace": "HP", - "object_category": "biolink:GeneticInheritance", + "object_category": "biolink:PhenotypicQuality", "object_closure": [ "HP:0000001", - "HP:0000006", - "HP:0000005", - "HP:0034345" - ], - "object_label": "Autosomal dominant inheritance (HPO)", + "HP:0004303", + "UPHENO:0001001", + "UPHENO:0001005", + "HP:0011805", + "UPHENO:0001002", + "HP:0000118", + "BFO:0000002", + "HP:0025354", + "BFO:0000020", + "HP:0003011", + "UPHENO:0002816", + "UPHENO:0081581", + "HP:0033127", + "UPHENO:0001003", + "UPHENO:0002536", + "UPHENO:0076692", + "UPHENO:0076710", + "BFO:0000001", + "HP:0003805", + "PATO:0000001", + "BFO:0000001", + "BFO:0000002", + "BFO:0000004", + "BFO:0000040", + "UBERON:0001062", + "CARO:0000000", + "CL:0000000", + "UBERON:0000465", + "UBERON:0000383", + "UBERON:0001015", + "UBERON:0018254", + "UBERON:0005090", + "UBERON:0004120", + "CL:0000003", + "UBERON:0000061", + "UBERON:0001630", + "UBERON:0002385", + "CL:0002371", + "UBERON:0010000", + "UBERON:0000467", + "UBERON:0014892", + "UBERON:0002036", + "CL:0000188", + "UBERON:0000479", + "UBERON:0000468", + "UBERON:0000062", + "UBERON:0011216", + "UBERON:0001134" + ], + "object_label": "Rimmed vacuoles (HPO)", "object_closure_label": [ "All (HPO)", - 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"category": "biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation", + "category": "biolink:DiseaseToPhenotypicFeatureAssociation", "negated": null, - "provided_by": "hpoa_disease_mode_of_inheritance_edges", - "publications": ["OMIM:600334"], + "provided_by": "hpoa_disease_phenotype_edges", + "publications": ["PMID:23543484"], "qualifiers": [], "frequency_qualifier": null, - "has_evidence": ["ECO:0000501"], + "has_evidence": ["ECO:0000269"], "onset_qualifier": null, "sex_qualifier": null, "stage_qualifier": null, @@ -1096,105 +1836,155 @@ "stage_qualifier_closure_label": [] }, { - "id": "uuid:c275a16e-212f-11ee-873a-cd90a19c4085", - "subject": "MONDO:0010912", - "original_subject": "OMIM:600638", + "id": "uuid:62f7ecd4-212f-11ee-873a-cd90a19c4085", + "subject": "MONDO:0012193", + "original_subject": "OMIM:609115", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ - "MONDO:0020158", "MONDO:0000001", - "MONDO:0007614", + "MONDO:0016971", + "MONDO:0000429", "MONDO:0005071", "MONDO:0020121", - "MONDO:0700223", - "MONDO:0004746", "BFO:0000002", - "MONDO:0957003", "BFO:0000017", "BFO:0000020", "MONDO:0016106", - "MONDO:0003382", "BFO:0000016", "MONDO:0020120", "MONDO:0019056", - "MONDO:0003569", + "MONDO:0015151", "MONDO:0700096", - "MONDO:0001584", - "MONDO:0024458", "MONDO:0005218", "MONDO:0005336", "MONDO:0002081", - "MONDO:0100153", + "MONDO:0012193", + "MONDO:0000426", "OGMS:0000031", "MONDO:0003847", - "MONDO:0100154", "MONDO:0003939", - "MONDO:0002022", - "MONDO:0015368", - "BFO:0000001", - "MONDO:0000462", - "MONDO:0005328", - "MONDO:0010912" + "BFO:0000001" ], - "subject_label": "fibrosis of extraocular muscles, congenital, 3A, with or without extraocular involvement", + "subject_label": "autosomal dominant limb-girdle muscular dystrophy type 1G", "subject_closure_label": [ "disease or disorder", - "eye adnexa disorder", - "ocular motility disease", - "disorder of orbital region", + "autosomal dominant disease", + "autosomal genetic disease", "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", - "congenital fibrosis of extraocular muscles", - "fibrosis of extraocular muscles, congenital, 3A, with or without extraocular involvement", - "neuro-ophthalmological disease", + "autosomal dominant limb-girdle muscular dystrophy type 1G", + "muscular dystrophy, limb-girdle, autosomal dominant", "progressive muscular dystrophy", + "limb-girdle muscular dystrophy", "neuromuscular disease", "skeletal muscle disorder", "muscular dystrophy", - "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_mode_of_inheritance", - "object": "HP:0000006", + "human disease or disorder" + ], + "subject_taxon": null, + "subject_taxon_label": null, + "predicate": "biolink:has_phenotype", + "object": "HP:0003805", "original_object": null, "object_namespace": "HP", - "object_category": "biolink:GeneticInheritance", + "object_category": "biolink:PhenotypicQuality", "object_closure": [ "HP:0000001", - "HP:0000006", - "HP:0000005", - "HP:0034345" - ], - "object_label": "Autosomal dominant inheritance (HPO)", + "HP:0004303", + "UPHENO:0001001", + "UPHENO:0001005", + "HP:0011805", + "UPHENO:0001002", + "HP:0000118", + "BFO:0000002", + "HP:0025354", + "BFO:0000020", + "HP:0003011", + "UPHENO:0002816", + "UPHENO:0081581", + "HP:0033127", + "UPHENO:0001003", + "UPHENO:0002536", + "UPHENO:0076692", + "UPHENO:0076710", + "BFO:0000001", + "HP:0003805", + "PATO:0000001", + "BFO:0000001", + "BFO:0000002", + "BFO:0000004", + "BFO:0000040", + "UBERON:0001062", + "CARO:0000000", + "CL:0000000", + "UBERON:0000465", + "UBERON:0000383", + "UBERON:0001015", + "UBERON:0018254", + "UBERON:0005090", + "UBERON:0004120", + "CL:0000003", + "UBERON:0000061", + "UBERON:0001630", + "UBERON:0002385", + "CL:0002371", + "UBERON:0010000", + "UBERON:0000467", + "UBERON:0014892", + "UBERON:0002036", + "CL:0000188", + "UBERON:0000479", + "UBERON:0000468", + "UBERON:0000062", + "UBERON:0011216", + "UBERON:0001134" + ], + "object_label": "Rimmed vacuoles (HPO)", "object_closure_label": [ "All (HPO)", - 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"category": "biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation", + "category": "biolink:DiseaseToPhenotypicFeatureAssociation", "negated": null, - "provided_by": "hpoa_disease_mode_of_inheritance_edges", - "publications": ["PMID:20074521"], + "provided_by": "hpoa_disease_phenotype_edges", + "publications": ["OMIM:609115"], "qualifiers": [], "frequency_qualifier": null, - "has_evidence": ["ECO:0000269"], + "has_evidence": ["ECO:0000304"], "onset_qualifier": null, "sex_qualifier": null, "stage_qualifier": null, @@ -1222,95 +2012,153 @@ "stage_qualifier_closure_label": [] }, { - "id": "uuid:c367df60-212f-11ee-873a-cd90a19c4085", - "subject": "MONDO:0011266", - "original_subject": "OMIM:602668", + "id": "uuid:5d3057d5-212f-11ee-873a-cd90a19c4085", + "subject": "MONDO:0012410", + "original_subject": "OMIM:610099", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ - "MONDO:0020158", "MONDO:0000001", - "MONDO:0016107", + "MONDO:0000429", "MONDO:0005071", "MONDO:0020121", - "MONDO:0700223", "BFO:0000002", "BFO:0000017", "BFO:0000020", - "MONDO:0016106", - "MONDO:0003382", "BFO:0000016", "MONDO:0020120", "MONDO:0019056", "MONDO:0700096", - "MONDO:0024458", "MONDO:0005218", "MONDO:0005336", "MONDO:0002081", - "MONDO:0002254", - "MONDO:0011266", + "MONDO:0012410", + "MONDO:0000426", "OGMS:0000031", "MONDO:0003847", "MONDO:0003939", - "MONDO:0002022", - "MONDO:0016120", "BFO:0000001", - "MONDO:0000462", - "MONDO:0005328" + "MONDO:0016108", + "MONDO:0018949" ], - "subject_label": "myotonic dystrophy type 2", + "subject_label": "Finnish upper limb-onset distal myopathy", "subject_closure_label": [ "disease or disorder", - "eye adnexa disorder", - "disorder of orbital region", + "autosomal dominant disease", + "autosomal genetic disease", "musculoskeletal system disorder", - "syndromic disease", - "eyelid disorder", "hereditary disease", "muscle tissue disorder", "nervous system disorder", "obsolete muscular disorder", - "eye disorder", "myopathy", - "myotonic dystrophy type 2", - "progressive muscular dystrophy", - "myotonic dystrophy", - "myotonic syndrome", + "Finnish upper limb-onset distal myopathy", + "autosomal dominant distal myopathy", + "distal myopathy", "neuromuscular disease", "skeletal muscle disorder", "muscular dystrophy", - "eyelids malposition disorder", - "disorder of visual system", - "human disease or disorder", - "hereditary skeletal muscle disorder" + "human disease or disorder" ], - "predicate": "biolink:has_mode_of_inheritance", - "object": "HP:0000006", + "subject_taxon": null, + "subject_taxon_label": null, + "predicate": "biolink:has_phenotype", + "object": "HP:0003805", "original_object": null, "object_namespace": "HP", - "object_category": "biolink:GeneticInheritance", + "object_category": "biolink:PhenotypicQuality", "object_closure": [ "HP:0000001", - "HP:0000006", - "HP:0000005", - "HP:0034345" - ], - "object_label": "Autosomal dominant inheritance (HPO)", + "HP:0004303", + "UPHENO:0001001", + "UPHENO:0001005", + "HP:0011805", + "UPHENO:0001002", + "HP:0000118", + "BFO:0000002", + "HP:0025354", + "BFO:0000020", + "HP:0003011", + "UPHENO:0002816", + "UPHENO:0081581", + "HP:0033127", + "UPHENO:0001003", + "UPHENO:0002536", + "UPHENO:0076692", + "UPHENO:0076710", + "BFO:0000001", + "HP:0003805", + "PATO:0000001", + "BFO:0000001", + "BFO:0000002", + "BFO:0000004", + "BFO:0000040", + "UBERON:0001062", + "CARO:0000000", + "CL:0000000", + "UBERON:0000465", + "UBERON:0000383", + "UBERON:0001015", + "UBERON:0018254", + "UBERON:0005090", + "UBERON:0004120", + "CL:0000003", + "UBERON:0000061", + "UBERON:0001630", + "UBERON:0002385", + "CL:0002371", + "UBERON:0010000", + "UBERON:0000467", + "UBERON:0014892", + "UBERON:0002036", + "CL:0000188", + "UBERON:0000479", + "UBERON:0000468", + "UBERON:0000062", + "UBERON:0011216", + "UBERON:0001134" + ], + "object_label": "Rimmed vacuoles (HPO)", "object_closure_label": [ "All (HPO)", - "Mode of inheritance (HPO)", - "Autosomal dominant inheritance (HPO)", - "Mendelian inheritance" - ], + "Phenotypic abnormality (HPO)", + "Abnormality of the musculature (HPO)", + "Rimmed vacuoles (HPO)", + "Abnormal muscle fiber morphology (HPO)", + "Abnormal skeletal muscle morphology (HPO)", + "Abnormal cellular phenotype (HPO)", + "Abnormality of the musculoskeletal system (HPO)", + "anatomical structure", + "organ", + "musculature of body", + "material anatomical entity", + "anatomical system", + "multicellular organism", + "tissue", + "musculature", + "anatomical entity", + "skeletal muscle tissue", + "muscle organ", + "striated muscle tissue", + "muscle tissue", + "mesoderm-derived structure", + "muscle structure", + "multicellular anatomical structure", + "organ system subdivision", + "skeletal muscle organ", + "skeletal musculature" + ], + "object_taxon": null, + "object_taxon_label": null, "primary_knowledge_source": "infores:hpo-annotations", "aggregator_knowledge_source": ["infores:monarchinitiative"], - "category": "biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation", + "category": "biolink:DiseaseToPhenotypicFeatureAssociation", "negated": null, - "provided_by": "hpoa_disease_mode_of_inheritance_edges", - "publications": ["PMID:11486088"], + "provided_by": "hpoa_disease_phenotype_edges", + "publications": ["OMIM:610099"], "qualifiers": [], "frequency_qualifier": null, - "has_evidence": ["ECO:0000269"], + "has_evidence": ["ECO:0000501"], "onset_qualifier": null, "sex_qualifier": null, "stage_qualifier": null, @@ -1338,96 +2186,144 @@ "stage_qualifier_closure_label": [] }, { - "id": "uuid:c3cdac2c-212f-11ee-873a-cd90a19c4085", - "subject": "MONDO:0011362", - "original_subject": "OMIM:603689", + "id": "uuid:64816953-212f-11ee-873a-cd90a19c4085", + "subject": "MONDO:0014945", + "original_subject": "OMIM:617158", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ "MONDO:0000001", - "MONDO:0016112", - "MONDO:0000429", "MONDO:0005071", "MONDO:0020121", - "MONDO:0100175", - "MONDO:0700223", "BFO:0000002", - "MONDO:0019952", "BFO:0000017", "BFO:0000020", - "MONDO:0016106", - "MONDO:0016191", "BFO:0000016", "MONDO:0020120", + "MONDO:0014945", "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": "myopathy, myofibrillar, 9, with early respiratory failure", + "subject_label": "myopathy, distal, with rimmed vacuoles", "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", - "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", + "myopathy, distal, with rimmed vacuoles", "distal myopathy", "neuromuscular disease", - "congenital myopathy", "skeletal muscle disorder", "muscular dystrophy", - "TTN-related myopathy", - "autosomal dominant titinopathy", - "human disease or disorder", - "hereditary skeletal muscle disorder" + "human disease or disorder" ], - "predicate": "biolink:has_mode_of_inheritance", - "object": "HP:0000006", + "subject_taxon": null, + "subject_taxon_label": null, + "predicate": "biolink:has_phenotype", + "object": "HP:0003805", "original_object": null, "object_namespace": "HP", - "object_category": "biolink:GeneticInheritance", + "object_category": "biolink:PhenotypicQuality", "object_closure": [ "HP:0000001", - "HP:0000006", - "HP:0000005", - "HP:0034345" - ], - "object_label": "Autosomal dominant inheritance (HPO)", + "HP:0004303", + "UPHENO:0001001", + "UPHENO:0001005", + "HP:0011805", + "UPHENO:0001002", + "HP:0000118", + "BFO:0000002", + "HP:0025354", + "BFO:0000020", + "HP:0003011", + "UPHENO:0002816", + "UPHENO:0081581", + "HP:0033127", + "UPHENO:0001003", + "UPHENO:0002536", + "UPHENO:0076692", + "UPHENO:0076710", + "BFO:0000001", + "HP:0003805", + "PATO:0000001", + "BFO:0000001", + "BFO:0000002", + "BFO:0000004", + "BFO:0000040", + "UBERON:0001062", + "CARO:0000000", + "CL:0000000", + "UBERON:0000465", + "UBERON:0000383", + "UBERON:0001015", + "UBERON:0018254", + "UBERON:0005090", + "UBERON:0004120", + "CL:0000003", + "UBERON:0000061", + "UBERON:0001630", + "UBERON:0002385", + "CL:0002371", + "UBERON:0010000", + "UBERON:0000467", + "UBERON:0014892", + "UBERON:0002036", + "CL:0000188", + "UBERON:0000479", + "UBERON:0000468", + "UBERON:0000062", + "UBERON:0011216", + "UBERON:0001134" + ], + "object_label": "Rimmed vacuoles (HPO)", "object_closure_label": [ "All (HPO)", - "Mode of inheritance (HPO)", - "Autosomal dominant inheritance (HPO)", - "Mendelian inheritance" - ], + "Phenotypic abnormality (HPO)", + "Abnormality of the musculature (HPO)", + "Rimmed vacuoles (HPO)", + "Abnormal muscle fiber morphology (HPO)", + "Abnormal skeletal muscle morphology (HPO)", + "Abnormal cellular phenotype (HPO)", + "Abnormality of the musculoskeletal system (HPO)", + "anatomical structure", + "organ", + "musculature of body", + "material anatomical entity", + "anatomical system", + "multicellular organism", + "tissue", + "musculature", + "anatomical entity", + "skeletal muscle tissue", + "muscle organ", + "striated muscle tissue", + "muscle tissue", + "mesoderm-derived structure", + "muscle structure", + "multicellular anatomical structure", + "organ system subdivision", + "skeletal muscle organ", + "skeletal musculature" + ], + "object_taxon": null, + "object_taxon_label": null, "primary_knowledge_source": "infores:hpo-annotations", "aggregator_knowledge_source": ["infores:monarchinitiative"], - "category": "biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation", + "category": "biolink:DiseaseToPhenotypicFeatureAssociation", "negated": null, - "provided_by": "hpoa_disease_mode_of_inheritance_edges", - "publications": ["PMID:22577215"], + "provided_by": "hpoa_disease_phenotype_edges", + "publications": ["PMID:26208961"], "qualifiers": [], "frequency_qualifier": null, "has_evidence": ["ECO:0000269"], @@ -1458,83 +2354,338 @@ "stage_qualifier_closure_label": [] }, { - "id": "uuid:c3cdadba-212f-11ee-873a-cd90a19c4085", - "subject": "MONDO:0011466", - "original_subject": "OMIM:604454", + "id": "uuid:6481675d-212f-11ee-873a-cd90a19c4085", + "subject": "MONDO:0012270", + "original_subject": "OMIM:609428", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ + "MONDO:0020158", "MONDO:0000001", - "MONDO:0011466", - "MONDO:0000429", + "MONDO:0007614", "MONDO:0005071", "MONDO:0020121", - "MONDO:0700223", + "MONDO:0004746", "BFO:0000002", "BFO:0000017", "BFO:0000020", + "MONDO:0016106", + "MONDO:0003382", "BFO:0000016", "MONDO:0020120", "MONDO:0019056", + "MONDO:0003569", "MONDO:0700096", + "MONDO:0001584", + "MONDO:0024458", "MONDO:0005218", "MONDO:0005336", "MONDO:0002081", - "MONDO:0000426", + "MONDO:0012270", "OGMS:0000031", "MONDO:0003847", "MONDO:0003939", + "MONDO:0002022", + "MONDO:0015368", "BFO:0000001", - "MONDO:0016108", - "MONDO:0018949" + "MONDO:0000462", + "MONDO:0005328" ], - "subject_label": "distal myopathy, Welander type", + "subject_label": "Tukel syndrome", "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", - "distal myopathy, Welander type", - "autosomal dominant distal myopathy", - "distal myopathy", + "congenital fibrosis of extraocular muscles", + "Tukel syndrome", + "neuro-ophthalmological disease", + "progressive muscular dystrophy", "neuromuscular disease", "skeletal muscle disorder", "muscular dystrophy", - "human disease or disorder", - "hereditary skeletal muscle disorder" + "eyelids malposition disorder", + "disorder of visual system", + "human disease or disorder" ], - "predicate": "biolink:has_mode_of_inheritance", - "object": "HP:0000006", + "subject_taxon": null, + "subject_taxon_label": null, + "predicate": "biolink:has_phenotype", + "object": "HP:0004231", "original_object": null, "object_namespace": "HP", - "object_category": "biolink:GeneticInheritance", + "object_category": "biolink:PhenotypicQuality", "object_closure": [ "HP:0000001", - "HP:0000006", - "HP:0000005", - "HP:0034345" - ], - "object_label": "Autosomal dominant inheritance (HPO)", + "HP:0006502", + "UPHENO:0079870", + "UPHENO:0075696", + "UPHENO:0076740", + "UPHENO:0080325", + "UPHENO:0001001", + "UPHENO:0080079", + "UPHENO:0080126", + "UPHENO:0026183", + "UPHENO:0026181", + "UPHENO:0020968", + "UPHENO:0026023", + "HP:0009823", + "UPHENO:0076703", + "UPHENO:0081524", + "HP:0045060", + "UPHENO:0001005", + "HP:0009825", + "HP:0005922", + "UPHENO:0076718", + "HP:0009815", + "HP:0001155", + "HP:0011842", + "UPHENO:0002696", + "UPHENO:0001002", + "UPHENO:0076723", + "HP:0000924", + "UPHENO:0016527", + "HP:0000118", + "BFO:0000002", + "HP:0002813", + "UPHENO:0011498", + "HP:0003019", + "UPHENO:0026028", + "HP:0002817", + "HP:0005927", + "BFO:0000020", + "UPHENO:0002708", + "HP:0001367", + "UPHENO:0080173", + "UPHENO:0026001", + "UPHENO:0002896", + "HP:0001191", + "UPHENO:0026144", + "UPHENO:0015280", + "UPHENO:0002964", + "UPHENO:0002961", + "UPHENO:0081451", + "UPHENO:0006910", + "UPHENO:0008523", + "UPHENO:0081581", + "HP:0033127", + "UPHENO:0001003", + "UPHENO:0002536", + "HP:0006496", + "HP:0009115", + "HP:0011844", + "UPHENO:0026506", + "UPHENO:0076727", + "UPHENO:0020584", + "UPHENO:0076692", + "HP:0009810", + "HP:0004231", + "HP:0040064", + "BFO:0000001", + "HP:0040070", + "PATO:0000001", + "HP:0040068", + "UPHENO:0076767", + "UPHENO:0002880", + "UPHENO:0002830", + "UPHENO:0079876", + "BFO:0000001", + "BFO:0000002", + "BFO:0000004", + "BFO:0000040", + "UBERON:0001062", + "CARO:0000000", + "UBERON:0000465", + "RO:0002577", + "UBERON:0001474", + "UBERON:0002204", + "CARO:0000006", + "UBERON:0006058", + "UBERON:0010712", + "UBERON:0010538", + "UBERON:0004120", + "UBERON:0000061", + "UBERON:0034925", + "UBERON:0010740", + "UBERON:0013630", + "UBERON:0002513", + "CARO:0000003", + "UBERON:0001460", + "UBERON:0004381", + "UBERON:0009878", + "UBERON:0006717", + "UBERON:0002529", + "UBERON:0011582", + "UBERON:0015061", + "UBERON:0004375", + "UBERON:0010000", + "UBERON:0000467", + "UBERON:0015212", + "UBERON:0004288", + "UBERON:0004770", + "UBERON:0010741", + "UBERON:0003656", + "UBERON:0002428", + "UBERON:0004708", + "UBERON:0002470", + "UBERON:0010708", + "UBERON:0012475", + "UBERON:0006716", + "UBERON:0001440", + "UBERON:0009880", + "UBERON:0001442", + "UBERON:0008785", + "UBERON:0007272", + "UBERON:0015021", + "UBERON:0015063", + "UBERON:0000468", + "UBERON:0000475", + "UBERON:0000062", + "UBERON:0011216", + "UBERON:0034921", + "UBERON:0010707", + "UBERON:0008962", + "UBERON:0001435", + "UBERON:0011250", + "UBERON:0002101", + "UBERON:0004710", + "UBERON:0002398", + "UBERON:0004452", + "UBERON:0015049", + "UBERON:0000153", + "UBERON:0000026", + "UBERON:0010758", + "UBERON:0004765", + "UBERON:0000075", + "UBERON:0010912", + "UBERON:0004905", + "UBERON:0001434", + "UBERON:0005897", + "UBERON:0002102", + "UBERON:0010363", + "UBERON:0011249", + "UBERON:0000982", + "UBERON:0002091" + ], + "object_label": "Carpal bone aplasia (HPO)", "object_closure_label": [ "All (HPO)", - "Mode of inheritance (HPO)", - "Autosomal dominant inheritance (HPO)", - "Mendelian inheritance" - ], + "Phenotypic abnormality (HPO)", + "Abnormality of the skeletal system (HPO)", + "Abnormality of the hand (HPO)", + "Abnormal carpal morphology (HPO)", + "Abnormal joint morphology (HPO)", + "Abnormality of limb bone morphology (HPO)", + "Abnormality of the upper limb (HPO)", + "Abnormality of the wrist (HPO)", + "Carpal bone aplasia (HPO)", + "Abnormal hand morphology (HPO)", + "Aplasia/hypoplasia involving bones of the hand (HPO)", + "Aplasia/hypoplasia involving bones of the upper limbs (HPO)", + "Aplasia/Hypoplasia involving the carpal bones (HPO)", + "Aplasia/hypoplasia involving the skeleton (HPO)", + "Abnormality of upper limb joint (HPO)", + "Aplasia/hypoplasia of the extremities (HPO)", + "Aplasia involving bones of the upper limbs (HPO)", + "Aplasia involving bones of the extremities (HPO)", + "Abnormal skeletal morphology (HPO)", + "Abnormal appendicular skeleton morphology (HPO)", + "Abnormality of the musculoskeletal system (HPO)", + "Abnormality of limbs (HPO)", + "Abnormality of limb bone (HPO)", + "Abnormal upper limb bone morphology (HPO)", + "Aplasia/hypoplasia involving bones of the extremities (HPO)", + "appendage", + "anatomical structure", + "organ", + "subdivision of skeletal system", + "anterior region of body", + "material anatomical entity", + "anatomical system", + "multicellular organism", + "organism subdivision", + "skeletal joint", + "anatomical entity", + "skeletal system", + "carpal bone", + "forelimb skeleton", + "skeleton of manus", + "arm", + "bone element", + "appendicular skeleton", + "limb", + "forelimb", + "musculoskeletal system", + "manus", + "limb bone", + "autopod region", + "endochondral bone", + "limb segment", + "mesopodium bone", + "mesoderm-derived structure", + "skeleton", + "bone of free limb or fin", + "skeleton of limb", + "carpal region", + "paired limb/fin", + "pectoral appendage", + "skeletal element", + "articular system", + "articulation", + "manus bone", + "multi-limb segment region", + "mesopodium region", + "autopodial skeleton", + "pectoral appendage skeleton", + "upper limb segment", + "forelimb bone", + "mesopodial skeleton", + "carpal skeleton", + "multicellular anatomical structure", + "endochondral element", + "paired limb/fin segment", + "appendage girdle complex", + "pectoral complex", + "limb skeleton subdivision", + "bone of appendage girdle complex", + "bone of pectoral complex", + "subdivision of organism along appendicular axis", + "subdivision of skeleton", + "organ system subdivision", + "appendicular skeletal system", + "autopod bone", + "paired limb/fin skeleton", + "skeleton of pectoral complex", + "short bone", + "forelimb endochondral element", + "carpus endochondral element", + "limb endochondral element", + "autopod endochondral element", + "lateral structure", + "multi organ part structure", + "anatomical collection" + ], + "object_taxon": null, + "object_taxon_label": null, "primary_knowledge_source": "infores:hpo-annotations", "aggregator_knowledge_source": ["infores:monarchinitiative"], - "category": "biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation", + "category": "biolink:DiseaseToPhenotypicFeatureAssociation", "negated": null, - "provided_by": "hpoa_disease_mode_of_inheritance_edges", - "publications": ["PMID:23348830"], + "provided_by": "hpoa_disease_phenotype_edges", + "publications": ["OMIM:609428"], "qualifiers": [], "frequency_qualifier": null, - "has_evidence": ["ECO:0000269"], + "has_evidence": ["ECO:0000501"], "onset_qualifier": null, "sex_qualifier": null, "stage_qualifier": null, @@ -1562,85 +2713,156 @@ "stage_qualifier_closure_label": [] }, { - "id": "uuid:c367df64-212f-11ee-873a-cd90a19c4085", - "subject": "MONDO:0012034", - "original_subject": "OMIM:608423", + "id": "uuid:624032ae-212f-11ee-873a-cd90a19c4085", + "subject": "MONDO:0009181", + "original_subject": "OMIM:226670", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ "MONDO:0000001", + "MONDO:0016198", "MONDO:0016971", "MONDO:0000429", "MONDO:0005071", "MONDO:0020121", - "MONDO:0700223", - "MONDO:0012034", "BFO:0000002", + "MONDO:0006617", "BFO:0000017", "BFO:0000020", + "MONDO:0017610", + "MONDO:0006025", "MONDO:0016106", + "MONDO:0002051", "BFO:0000016", "MONDO:0020120", "MONDO:0019056", - "MONDO:0015151", + "MONDO:0016139", "MONDO:0700096", "MONDO:0005218", "MONDO:0005336", "MONDO:0002081", - "MONDO:0000426", + "MONDO:0002254", + "MONDO:0009181", + "MONDO:0019276", + "MONDO:0005093", "OGMS:0000031", + "MONDO:0019268", "MONDO:0003847", "MONDO:0003939", - "BFO:0000001" + "MONDO:0006541", + "BFO:0000001", + "MONDO:0015152" ], - "subject_label": "autosomal dominant limb-girdle muscular dystrophy type 1F", + "subject_label": "epidermolysis bullosa simplex 5B, with muscular dystrophy", "subject_closure_label": [ "disease or disorder", - "autosomal dominant disease", "autosomal genetic disease", + "integumentary system disorder", "musculoskeletal system disorder", + "syndromic disease", "hereditary disease", "muscle tissue disorder", "nervous system disorder", + "skin disorder", "obsolete muscular disorder", "myopathy", - "autosomal dominant limb-girdle muscular dystrophy type 1F", - "muscular dystrophy, limb-girdle, autosomal dominant", + "autosomal recessive disease", + "epidermolysis bullosa", + "vesiculobullous skin disease", + "epidermolysis bullosa simplex 5B, with muscular dystrophy", + "autosomal recessive limb-girdle muscular dystrophy", "progressive muscular dystrophy", + "qualitative or quantitative protein defects in neuromuscular diseases", + "qualitative or quantitative defects of plectin", "limb-girdle muscular dystrophy", + "epidermolysis bullosa simplex", "neuromuscular disease", + "epidermal disease", + "inherited epidermolysis bullosa", "skeletal muscle disorder", "muscular dystrophy", - "human disease or disorder", - "hereditary skeletal muscle disorder" + "human disease or disorder" ], - "predicate": "biolink:has_mode_of_inheritance", - "object": "HP:0000006", + "subject_taxon": null, + "subject_taxon_label": null, + "predicate": "biolink:has_phenotype", + "object": "HP:0004322", "original_object": null, "object_namespace": "HP", - "object_category": "biolink:GeneticInheritance", + "object_category": "biolink:PhenotypicQuality", "object_closure": [ "HP:0000001", - "HP:0000006", - "HP:0000005", - "HP:0034345" - ], - "object_label": "Autosomal dominant inheritance (HPO)", + "UPHENO:0000543", + "UPHENO:0075696", + "HP:0001507", + "UPHENO:0081423", + "UPHENO:0068971", + "UPHENO:0001001", + "UPHENO:0069254", + "UPHENO:0075159", + "UPHENO:0001005", + "HP:0000002", + "UPHENO:0001002", + "UPHENO:0080351", + "HP:0000118", + "BFO:0000002", + "HP:0001510", + "BFO:0000020", + "UPHENO:0075195", + "UPHENO:0015280", + "UPHENO:0081581", + "UPHENO:0001003", + "UPHENO:0002536", + "UPHENO:0049874", + "UPHENO:0020584", + "UPHENO:0076692", + "UPHENO:0081424", + "UPHENO:0080352", + "UPHENO:0049587", + "BFO:0000001", + "HP:0004322", + "UPHENO:0000541", + "PATO:0000001", + "UPHENO:0012541", + "BFO:0000001", + "BFO:0000003", + "BFO:0000002", + "BFO:0000015", + "BFO:0000004", + "GO:0008150", + "BFO:0000040", + "UBERON:0001062", + "GO:0040007", + "UBERON:0000465", + "UBERON:0000061", + "UBERON:0010000", + "UBERON:0000468" + ], + "object_label": "Short stature (HPO)", "object_closure_label": [ "All (HPO)", - "Mode of inheritance (HPO)", - "Autosomal dominant inheritance (HPO)", - "Mendelian inheritance" - ], + "Abnormality of body height (HPO)", + "Phenotypic abnormality (HPO)", + "Growth abnormality (HPO)", + "Growth delay (HPO)", + "Short stature (HPO)", + "anatomical structure", + "material anatomical entity", + "multicellular organism", + "anatomical entity", + "multicellular anatomical structure" + ], + "object_taxon": null, + "object_taxon_label": null, "primary_knowledge_source": "infores:hpo-annotations", "aggregator_knowledge_source": ["infores:monarchinitiative"], - "category": "biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation", + "category": "biolink:DiseaseToPhenotypicFeatureAssociation", "negated": null, - "provided_by": "hpoa_disease_mode_of_inheritance_edges", - "publications": ["PMID:23543484"], + "provided_by": "hpoa_disease_phenotype_edges", + "publications": ["OMIM:226670"], "qualifiers": [], "frequency_qualifier": null, - "has_evidence": ["ECO:0000269"], + "has_evidence": ["ECO:0000501"], "onset_qualifier": null, "sex_qualifier": null, "stage_qualifier": null, @@ -1668,99 +2890,134 @@ "stage_qualifier_closure_label": [] }, { - "id": "uuid:c3367251-212f-11ee-873a-cd90a19c4085", - "subject": "MONDO:0012130", - "original_subject": "OMIM:608810", + "id": "uuid:5ad388d6-212f-11ee-873a-cd90a19c4085", + "subject": "MONDO:0012138", + "original_subject": "OMIM:608840", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ "MONDO:0000001", - "MONDO:0016186", - "MONDO:0000429", + "MONDO:0012138", + "MONDO:0018276", "MONDO:0005071", "MONDO:0020121", - "MONDO:0018943", - "MONDO:0700223", + "MONDO:0000172", "BFO:0000002", - "MONDO:0019952", "BFO:0000017", "BFO:0000020", - "MONDO:0020343", "BFO:0000016", "MONDO:0020120", "MONDO:0019056", - "MONDO:0016139", "MONDO:0700096", - "MONDO:0002921", "MONDO:0005218", "MONDO:0005336", "MONDO:0002081", - "MONDO:0012130", - "MONDO:0000426", "OGMS:0000031", "MONDO:0003847", "MONDO:0003939", "BFO:0000001", "MONDO:0002320", - "MONDO:0016188", - "MONDO:0016108", - "MONDO:0018949" + "MONDO:0019950" ], - "subject_label": "myofibrillar myopathy 2", + "subject_label": "muscular dystrophy-dystroglycanopathy type B6", "subject_closure_label": [ "disease or disorder", - "autosomal dominant disease", - "autosomal genetic disease", + "muscular dystrophy-dystroglycanopathy, type B", "musculoskeletal system disorder", "congenital nervous system disorder", - "congenital structural myopathy", "hereditary disease", "muscle tissue disorder", "nervous system disorder", "obsolete muscular disorder", "myopathy", - "myofibrillar myopathy 2", - "autosomal dominant distal myopathy", - "qualitative or quantitative protein defects in neuromuscular diseases", - "qualitative or quantitative defects of myofibrillar proteins", - "qualitative or quantitative defects of alphaB-cristallin", - "myofibrillar myopathy", - "distal myopathy", + "muscular dystrophy-dystroglycanopathy type B6", + "muscular dystrophy-dystroglycanopathy", "neuromuscular disease", - "congenital myopathy", + "congenital muscular dystrophy", "skeletal muscle disorder", "muscular dystrophy", - "alpha-crystallinopathy", - "human disease or disorder", - "hereditary skeletal muscle disorder" + "human disease or disorder" ], - "predicate": "biolink:has_mode_of_inheritance", - "object": "HP:0000006", + "subject_taxon": null, + "subject_taxon_label": null, + "predicate": "biolink:has_phenotype", + "object": "HP:0004322", "original_object": null, "object_namespace": "HP", - "object_category": "biolink:GeneticInheritance", + "object_category": "biolink:PhenotypicQuality", "object_closure": [ "HP:0000001", - "HP:0000006", - "HP:0000005", - "HP:0034345" - ], - "object_label": "Autosomal dominant inheritance (HPO)", + "UPHENO:0000543", + "UPHENO:0075696", + "HP:0001507", + "UPHENO:0081423", + "UPHENO:0068971", + "UPHENO:0001001", + "UPHENO:0069254", + "UPHENO:0075159", + "UPHENO:0001005", + "HP:0000002", + "UPHENO:0001002", + "UPHENO:0080351", + "HP:0000118", + "BFO:0000002", + "HP:0001510", + "BFO:0000020", + "UPHENO:0075195", + "UPHENO:0015280", + "UPHENO:0081581", + "UPHENO:0001003", + "UPHENO:0002536", + "UPHENO:0049874", + "UPHENO:0020584", + "UPHENO:0076692", + "UPHENO:0081424", + "UPHENO:0080352", + "UPHENO:0049587", + "BFO:0000001", + "HP:0004322", + "UPHENO:0000541", + "PATO:0000001", + "UPHENO:0012541", + "BFO:0000001", + "BFO:0000003", + "BFO:0000002", + "BFO:0000015", + "BFO:0000004", + "GO:0008150", + "BFO:0000040", + "UBERON:0001062", + "GO:0040007", + "UBERON:0000465", + "UBERON:0000061", + "UBERON:0010000", + "UBERON:0000468" + ], + "object_label": "Short stature (HPO)", "object_closure_label": [ "All (HPO)", - "Mode of inheritance (HPO)", - "Autosomal dominant inheritance (HPO)", - "Mendelian inheritance" - ], + "Abnormality of body height (HPO)", + "Phenotypic abnormality (HPO)", + "Growth abnormality (HPO)", + "Growth delay (HPO)", + "Short stature (HPO)", + "anatomical structure", + "material anatomical entity", + "multicellular organism", + "anatomical entity", + "multicellular anatomical structure" + ], + "object_taxon": null, + "object_taxon_label": null, "primary_knowledge_source": "infores:hpo-annotations", "aggregator_knowledge_source": ["infores:monarchinitiative"], - "category": "biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation", + "category": "biolink:DiseaseToPhenotypicFeatureAssociation", "negated": null, - "provided_by": "hpoa_disease_mode_of_inheritance_edges", - "publications": ["PMID:14681890"], + "provided_by": "hpoa_disease_phenotype_edges", + "publications": ["OMIM:608840"], "qualifiers": [], "frequency_qualifier": null, - "has_evidence": ["ECO:0000269"], + "has_evidence": ["ECO:0000501"], "onset_qualifier": null, "sex_qualifier": null, "stage_qualifier": null, @@ -1788,85 +3045,156 @@ "stage_qualifier_closure_label": [] }, { - "id": "uuid:c39b463c-212f-11ee-873a-cd90a19c4085", - "subject": "MONDO:0012193", - "original_subject": "OMIM:609115", + "id": "uuid:5a352272-212f-11ee-873a-cd90a19c4085", + "subject": "MONDO:0014144", + "original_subject": "OMIM:615356", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ "MONDO:0000001", + "MONDO:0000508", "MONDO:0016971", + "MONDO:0005503", + "MONDO:0002025", "MONDO:0000429", + "MONDO:0014144", "MONDO:0005071", "MONDO:0020121", - "MONDO:0700223", + "MONDO:0001071", "BFO:0000002", + "MONDO:0005395", "BFO:0000017", "BFO:0000020", + "MONDO:0006025", + "MONDO:0002602", "MONDO:0016106", "BFO:0000016", "MONDO:0020120", "MONDO:0019056", - "MONDO:0015151", "MONDO:0700096", "MONDO:0005218", "MONDO:0005336", "MONDO:0002081", - "MONDO:0012193", - "MONDO:0000426", + "MONDO:0002254", + "MONDO:0018243", + "MONDO:0005084", "OGMS:0000031", "MONDO:0003847", "MONDO:0003939", - "BFO:0000001" + "BFO:0000001", + "MONDO:0015152", + "MONDO:0005560" ], - "subject_label": "autosomal dominant limb-girdle muscular dystrophy type 1G", + "subject_label": "autosomal recessive limb-girdle muscular dystrophy type R18", "subject_closure_label": [ "disease or disorder", - "autosomal dominant disease", "autosomal genetic disease", + "syndromic intellectual disability", + "intellectual disability", + "psychiatric disorder", "musculoskeletal system disorder", + "syndromic disease", + "central nervous system disorder", "hereditary disease", "muscle tissue disorder", "nervous system disorder", + "mental disorder", "obsolete muscular disorder", "myopathy", - "autosomal dominant limb-girdle muscular dystrophy type 1G", - "muscular dystrophy, limb-girdle, autosomal dominant", + "movement disorder", + "developmental disorder of mental health", + "brain disorder", + "autosomal recessive disease", + "autosomal recessive limb-girdle muscular dystrophy type R18", + "autosomal recessive limb-girdle muscular dystrophy", "progressive muscular dystrophy", "limb-girdle muscular dystrophy", + "intellectual disability-hyperkinetic movement-truncal ataxia syndrome", "neuromuscular disease", "skeletal muscle disorder", "muscular dystrophy", - "human disease or disorder", - "hereditary skeletal muscle disorder" + "human disease or disorder" ], - "predicate": "biolink:has_mode_of_inheritance", - "object": "HP:0000006", + "subject_taxon": null, + "subject_taxon_label": null, + "predicate": "biolink:has_phenotype", + "object": "HP:0004322", "original_object": null, "object_namespace": "HP", - "object_category": "biolink:GeneticInheritance", + "object_category": "biolink:PhenotypicQuality", "object_closure": [ "HP:0000001", - "HP:0000006", - "HP:0000005", - "HP:0034345" - ], - "object_label": "Autosomal dominant inheritance (HPO)", + "UPHENO:0000543", + "UPHENO:0075696", + "HP:0001507", + "UPHENO:0081423", + "UPHENO:0068971", + "UPHENO:0001001", + "UPHENO:0069254", + "UPHENO:0075159", + "UPHENO:0001005", + "HP:0000002", + "UPHENO:0001002", + "UPHENO:0080351", + "HP:0000118", + "BFO:0000002", + "HP:0001510", + "BFO:0000020", + "UPHENO:0075195", + "UPHENO:0015280", + "UPHENO:0081581", + "UPHENO:0001003", + "UPHENO:0002536", + "UPHENO:0049874", + "UPHENO:0020584", + "UPHENO:0076692", + "UPHENO:0081424", + "UPHENO:0080352", + "UPHENO:0049587", + "BFO:0000001", + "HP:0004322", + "UPHENO:0000541", + "PATO:0000001", + "UPHENO:0012541", + "BFO:0000001", + "BFO:0000003", + "BFO:0000002", + "BFO:0000015", + "BFO:0000004", + "GO:0008150", + "BFO:0000040", + "UBERON:0001062", + "GO:0040007", + "UBERON:0000465", + "UBERON:0000061", + "UBERON:0010000", + "UBERON:0000468" + ], + "object_label": "Short stature (HPO)", "object_closure_label": [ "All (HPO)", - "Mode of inheritance (HPO)", - "Autosomal dominant inheritance (HPO)", - "Mendelian inheritance" - ], + "Abnormality of body height (HPO)", + "Phenotypic abnormality (HPO)", + "Growth abnormality (HPO)", + "Growth delay (HPO)", + "Short stature (HPO)", + "anatomical structure", + "material anatomical entity", + "multicellular organism", + "anatomical entity", + "multicellular anatomical structure" + ], + "object_taxon": null, + "object_taxon_label": null, "primary_knowledge_source": "infores:hpo-annotations", "aggregator_knowledge_source": ["infores:monarchinitiative"], - "category": "biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation", + "category": "biolink:DiseaseToPhenotypicFeatureAssociation", "negated": null, - "provided_by": "hpoa_disease_mode_of_inheritance_edges", - "publications": ["PMID:24647604"], + "provided_by": "hpoa_disease_phenotype_edges", + "publications": ["OMIM:615356"], "qualifiers": [], "frequency_qualifier": null, - "has_evidence": ["ECO:0000269"], + "has_evidence": ["ECO:0000304"], "onset_qualifier": null, "sex_qualifier": null, "stage_qualifier": null, @@ -1894,101 +3222,128 @@ "stage_qualifier_closure_label": [] }, { - "id": "uuid:c4006058-212f-11ee-873a-cd90a19c4085", - "subject": "MONDO:0012215", - "original_subject": "OMIM:609200", + "id": "uuid:64b682db-212f-11ee-873a-cd90a19c4085", + "subject": "MONDO:0024607", + "original_subject": "OMIM:617404", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ - "MONDO:0012215", "MONDO:0000001", - "MONDO:0016971", - "MONDO:0000429", + "MONDO:0024607", "MONDO:0005071", "MONDO:0020121", - "MONDO:0018943", - "MONDO:0700223", - "MONDO:0016201", "BFO:0000002", - "MONDO:0019952", "BFO:0000017", "BFO:0000020", - "MONDO:0016106", "BFO:0000016", "MONDO:0020120", "MONDO:0019056", - "MONDO:0016139", - "MONDO:0015151", "MONDO:0700096", - "MONDO:0002921", "MONDO:0005218", "MONDO:0005336", "MONDO:0002081", - "MONDO:0000426", "OGMS:0000031", - "MONDO:0003847", "MONDO:0003939", "BFO:0000001", "MONDO:0002320", - "MONDO:0016108", - "MONDO:0018949" + "MONDO:0019950" ], - "subject_label": "myofibrillar myopathy 3", + "subject_label": "congenital muscular dystrophy with cataracts and intellectual disability", "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", - "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", + "congenital muscular dystrophy", "skeletal muscle disorder", "muscular dystrophy", - "human disease or disorder", - "hereditary skeletal muscle disorder" + "congenital muscular dystrophy with cataracts and intellectual disability", + "human disease or disorder" ], - "predicate": "biolink:has_mode_of_inheritance", - "object": "HP:0000006", + "subject_taxon": null, + "subject_taxon_label": null, + "predicate": "biolink:has_phenotype", + "object": "HP:0004322", "original_object": null, "object_namespace": "HP", - "object_category": "biolink:GeneticInheritance", + "object_category": "biolink:PhenotypicQuality", "object_closure": [ "HP:0000001", - "HP:0000006", - "HP:0000005", - "HP:0034345" - ], - "object_label": "Autosomal dominant inheritance (HPO)", + "UPHENO:0000543", + "UPHENO:0075696", + "HP:0001507", + "UPHENO:0081423", + "UPHENO:0068971", + "UPHENO:0001001", + "UPHENO:0069254", + "UPHENO:0075159", + "UPHENO:0001005", + "HP:0000002", + "UPHENO:0001002", + "UPHENO:0080351", + "HP:0000118", + "BFO:0000002", + "HP:0001510", + "BFO:0000020", + "UPHENO:0075195", + "UPHENO:0015280", + "UPHENO:0081581", + "UPHENO:0001003", + "UPHENO:0002536", + "UPHENO:0049874", + "UPHENO:0020584", + "UPHENO:0076692", + "UPHENO:0081424", + "UPHENO:0080352", + "UPHENO:0049587", + "BFO:0000001", + "HP:0004322", + "UPHENO:0000541", + "PATO:0000001", + "UPHENO:0012541", + "BFO:0000001", + "BFO:0000003", + "BFO:0000002", + "BFO:0000015", + "BFO:0000004", + "GO:0008150", + "BFO:0000040", + "UBERON:0001062", + "GO:0040007", + "UBERON:0000465", + "UBERON:0000061", + "UBERON:0010000", + "UBERON:0000468" + ], + "object_label": "Short stature (HPO)", "object_closure_label": [ "All (HPO)", - "Mode of inheritance (HPO)", - "Autosomal dominant inheritance (HPO)", - "Mendelian inheritance" - ], + "Abnormality of body height (HPO)", + "Phenotypic abnormality (HPO)", + "Growth abnormality (HPO)", + "Growth delay (HPO)", + "Short stature (HPO)", + "anatomical structure", + "material anatomical entity", + "multicellular organism", + "anatomical entity", + "multicellular anatomical structure" + ], + "object_taxon": null, + "object_taxon_label": null, "primary_knowledge_source": "infores:hpo-annotations", "aggregator_knowledge_source": ["infores:monarchinitiative"], - "category": "biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation", + "category": "biolink:DiseaseToPhenotypicFeatureAssociation", "negated": null, - "provided_by": "hpoa_disease_mode_of_inheritance_edges", - "publications": ["OMIM:609200"], + "provided_by": "hpoa_disease_phenotype_edges", + "publications": ["OMIM:617404"], "qualifiers": [], "frequency_qualifier": null, - "has_evidence": ["ECO:0000501"], + "has_evidence": ["ECO:0000304"], "onset_qualifier": null, "sex_qualifier": null, "stage_qualifier": null, @@ -2016,100 +3371,251 @@ "stage_qualifier_closure_label": [] }, { - "id": "uuid:c275a325-212f-11ee-873a-cd90a19c4085", - "subject": "MONDO:0012262", - "original_subject": "OMIM:609384", + "id": "uuid:624032b1-212f-11ee-873a-cd90a19c4085", + "subject": "MONDO:0009181", + "original_subject": "OMIM:226670", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ - "MONDO:0020158", "MONDO:0000001", - "MONDO:0007614", + "MONDO:0016198", + "MONDO:0016971", + "MONDO:0000429", "MONDO:0005071", "MONDO:0020121", - "MONDO:0700223", - "MONDO:0004746", "BFO:0000002", - "MONDO:0012262", - "MONDO:0957003", + "MONDO:0006617", "BFO:0000017", "BFO:0000020", + "MONDO:0017610", + "MONDO:0006025", "MONDO:0016106", - "MONDO:0003382", + "MONDO:0002051", "BFO:0000016", "MONDO:0020120", "MONDO:0019056", - "MONDO:0003569", + "MONDO:0016139", "MONDO:0700096", - "MONDO:0001584", - "MONDO:0024458", "MONDO:0005218", "MONDO:0005336", "MONDO:0002081", + "MONDO:0002254", + "MONDO:0009181", + "MONDO:0019276", + "MONDO:0005093", "OGMS:0000031", + "MONDO:0019268", "MONDO:0003847", "MONDO:0003939", - "MONDO:0002022", - "MONDO:0015368", + "MONDO:0006541", "BFO:0000001", - "MONDO:0002320", - "MONDO:0000462", - "MONDO:0005328" + "MONDO:0015152" ], - "subject_label": "fibrosis of extraocular muscles, congenital, 3c", + "subject_label": "epidermolysis bullosa simplex 5B, with muscular dystrophy", "subject_closure_label": [ "disease or disorder", - "eye adnexa disorder", - "ocular motility disease", - "disorder of orbital region", + "autosomal genetic disease", + "integumentary system disorder", "musculoskeletal system disorder", - "congenital nervous system disorder", - "eyelid disorder", - "cranial nerve neuropathy", + "syndromic disease", "hereditary disease", "muscle tissue disorder", - "myopathy of extraocular muscle", "nervous system disorder", + "skin disorder", "obsolete muscular disorder", - "eye disorder", "myopathy", - "congenital fibrosis of extraocular muscles", - "fibrosis of extraocular muscles, congenital, 3c", - "neuro-ophthalmological disease", + "autosomal recessive disease", + "epidermolysis bullosa", + "vesiculobullous skin disease", + "epidermolysis bullosa simplex 5B, with muscular dystrophy", + "autosomal recessive limb-girdle muscular dystrophy", "progressive muscular dystrophy", + "qualitative or quantitative protein defects in neuromuscular diseases", + "qualitative or quantitative defects of plectin", + "limb-girdle muscular dystrophy", + "epidermolysis bullosa simplex", "neuromuscular disease", + "epidermal disease", + "inherited epidermolysis bullosa", "skeletal muscle disorder", "muscular dystrophy", - "eyelids malposition disorder", - "disorder of visual system", - "human disease or disorder", - "hereditary skeletal muscle disorder", - "hereditary neuro-ophthalmological disease" + "human disease or disorder" ], - "predicate": "biolink:has_mode_of_inheritance", - "object": "HP:0000006", + "subject_taxon": null, + "subject_taxon_label": null, + "predicate": "biolink:has_phenotype", + "object": "HP:0004552", "original_object": null, "object_namespace": "HP", - "object_category": "biolink:GeneticInheritance", + "object_category": "biolink:PhenotypicQuality", "object_closure": [ "HP:0000001", - "HP:0000006", - "HP:0000005", - "HP:0034345" - ], - "object_label": "Autosomal dominant inheritance (HPO)", + "HP:0001965", + "UPHENO:0011535", + "UPHENO:0075696", + "UPHENO:0001001", + "HP:0003549", + "HP:0000152", + "UPHENO:0003811", + "UPHENO:0002768", + "UPHENO:0002844", + "UPHENO:0001005", + "HP:0000987", + "UPHENO:0002764", + "UPHENO:0001002", + "HP:0000118", + "BFO:0000002", + "HP:0011355", + "UPHENO:0011498", + "HP:0011121", + "HP:0002293", + "UPHENO:0076739", + "BFO:0000020", + "HP:0100699", + "UPHENO:0003035", + "HP:0000234", + "HP:0001595", + "UPHENO:0075677", + "UPHENO:0002635", + "UPHENO:0015280", + "HP:0011362", + "UPHENO:0006910", + "UPHENO:0081581", + "HP:0033127", + "UPHENO:0001003", + "UPHENO:0002536", + "UPHENO:0020584", + "HP:0100037", + "UPHENO:0019853", + "UPHENO:0076692", + "HP:0004552", + "UPHENO:0002712", + "HP:0001596", + "BFO:0000001", + "HP:0000951", + "HP:0011138", + "PATO:0000001", + "HP:0001574", + "BFO:0000001", + "BFO:0000002", + "BFO:0000004", + "BFO:0000040", + "UBERON:0001062", + "CARO:0000000", + "UBERON:0000465", + "RO:0002577", + "UBERON:0004121", + "CARO:0000006", + "UBERON:0002416", + "UBERON:0007811", + "UBERON:0002199", + "UBERON:0000403", + "UBERON:0010314", + "UBERON:0000061", + "UBERON:0001037", + "UBERON:0002097", + "UBERON:0010371", + "CARO:0000003", + "UBERON:0011932", + "UBERON:0010000", + "UBERON:0000467", + "UBERON:0034768", + "UBERON:0003102", + "UBERON:0016446", + "UBERON:0007376", + "UBERON:0000021", + "UBERON:0000479", + "UBERON:0000468", + "UBERON:0000475", + "UBERON:0000064", + "UBERON:0000062", + "UBERON:0011216", + "UBERON:0034921", + "UBERON:0004529", + "UBERON:3000961", + "UBERON:0001003", + "UBERON:0000483", + "UBERON:0002384", + "UBERON:0000153", + "UBERON:0011676", + "UBERON:0013701", + "UBERON:0000063", + "UBERON:0013702", + "UBERON:0006003", + "UBERON:0013703", + "UBERON:0000033" + ], + "object_label": "Scarring alopecia of scalp (HPO)", "object_closure_label": [ "All (HPO)", - "Mode of inheritance (HPO)", - "Autosomal dominant inheritance (HPO)", - "Mendelian inheritance" - ], + "Phenotypic abnormality (HPO)", + "Abnormality of head or neck (HPO)", + "Abnormality of the head (HPO)", + "Abnormality of the skin (HPO)", + "Atypical scarring of skin (HPO)", + "Abnormality of the integument (HPO)", + "Abnormal hair morphology (HPO)", + "Alopecia (HPO)", + "Abnormal scalp morphology (HPO)", + "Alopecia of scalp (HPO)", + "Abnormality of connective tissue (HPO)", + "Scarring alopecia of scalp (HPO)", + "Abnormality of skin morphology (HPO)", + "Abnormality of skin adnexa morphology (HPO)", + "Localized skin lesion (HPO)", + "Abnormal hair quantity (HPO)", + "Abnormality of the musculoskeletal system (HPO)", + "Abnormality of the scalp hair (HPO)", + "Scarring (HPO)", + "cutaneous appendage", + "head", + "anatomical structure", + "organ", + "organ subunit", + "organ part", + "anterior region of body", + "scalp", + "material anatomical entity", + "anatomical system", + "multicellular organism", + "organism subdivision", + "tissue", + "epithelium", + "skin epidermis", + "strand of hair", + "anatomical entity", + "skin of body", + "integument", + "connective tissue", + "integumental system", + "surface structure", + "ectoderm-derived structure", + "anatomical projection", + "integumentary adnexa", + "outer epithelium", + "craniocervical region", + "multicellular anatomical structure", + "structure with developmental contribution from neural crest", + "ecto-epithelium", + "organ system subdivision", + "subdivision of organism along main body axis", + "pilosebaceous unit", + "main body axis", + "body proper", + "integumentary projection", + "hair of head", + "morphological feature", + "multi organ part structure", + "external integument structure" + ], + "object_taxon": null, + "object_taxon_label": null, "primary_knowledge_source": "infores:hpo-annotations", "aggregator_knowledge_source": ["infores:monarchinitiative"], - "category": "biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation", + "category": "biolink:DiseaseToPhenotypicFeatureAssociation", "negated": null, - "provided_by": "hpoa_disease_mode_of_inheritance_edges", - "publications": ["OMIM:609384"], + "provided_by": "hpoa_disease_phenotype_edges", + "publications": ["OMIM:226670"], "qualifiers": [], "frequency_qualifier": null, "has_evidence": ["ECO:0000501"], @@ -2140,94 +3646,208 @@ "stage_qualifier_closure_label": [] }, { - "id": "uuid:c304ba49-212f-11ee-873a-cd90a19c4085", - "subject": "MONDO:0012277", - "original_subject": "OMIM:609452", + "id": "uuid:62c348df-212f-11ee-873a-cd90a19c4085", + "subject": "MONDO:0010680", + "original_subject": "OMIM:310300", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ + "MONDO:0004994", "MONDO:0000001", - "MONDO:0016186", - "MONDO:0000429", + "MONDO:0010680", "MONDO:0005071", + "MONDO:0005267", "MONDO:0020121", - "MONDO:0018943", - "MONDO:0700223", + "MONDO:0004995", + "MONDO:0016196", "BFO:0000002", - "MONDO:0019952", - "MONDO:0016190", "BFO:0000017", "BFO:0000020", + "MONDO:0016106", + "MONDO:0005217", "BFO:0000016", "MONDO:0020120", "MONDO:0019056", "MONDO:0016139", "MONDO:0700096", - "MONDO:0002921", + "MONDO:0000591", "MONDO:0005218", "MONDO:0005336", "MONDO:0002081", - "MONDO:0000426", + "MONDO:0016333", + "MONDO:0016830", "OGMS:0000031", + "MONDO:0000425", + "MONDO:0005021", + "MONDO:0021106", "MONDO:0003847", "MONDO:0003939", - "MONDO:0012277", "BFO:0000001", - "MONDO:0002320", - "MONDO:0016108", - "MONDO:0018949" + "MONDO:0020606" ], - "subject_label": "myofibrillar myopathy 4", + "subject_label": "X-linked Emery-Dreifuss muscular dystrophy", "subject_closure_label": [ "disease or disorder", - "autosomal dominant disease", - "autosomal genetic disease", + "X-linked disease", + "intrinsic cardiomyopathy", "musculoskeletal system disorder", - "congenital nervous system disorder", - "congenital structural myopathy", "hereditary disease", "muscle tissue disorder", + "cardiomyopathy", + "cardiovascular disorder", + "dilated cardiomyopathy", "nervous system disorder", + "familial cardiomyopathy", "obsolete muscular disorder", + "heart disorder", "myopathy", - "myofibrillar myopathy 4", - "autosomal dominant distal myopathy", + "X-linked Emery-Dreifuss muscular dystrophy", + "progressive muscular dystrophy", "qualitative or quantitative protein defects in neuromuscular diseases", - "qualitative or quantitative defects of myofibrillar proteins", - "qualitative or quantitative defects of protein ZASP", - "myofibrillar myopathy", - "distal myopathy", + "qualitative or quantitative defects of emerin", + "familial dilated cardiomyopathy", + "Emery-Dreifuss muscular dystrophy", "neuromuscular disease", - "congenital myopathy", "skeletal muscle disorder", "muscular dystrophy", - "human disease or disorder", - "hereditary skeletal muscle disorder" - ], - "predicate": "biolink:has_mode_of_inheritance", - "object": "HP:0000006", + "sex-linked disease", + "laminopathy", + "human disease or disorder" + ], + "subject_taxon": null, + "subject_taxon_label": null, + "predicate": "biolink:has_phenotype", + "object": "HP:0004631", "original_object": null, "object_namespace": "HP", - "object_category": "biolink:GeneticInheritance", + "object_category": "biolink:PhenotypicQuality", "object_closure": [ "HP:0000001", - "HP:0000006", - "HP:0000005", - "HP:0034345" - ], - "object_label": "Autosomal dominant inheritance (HPO)", + "UPHENO:0082875", + "UPHENO:0046505", + "UPHENO:0075696", + "UPHENO:0068971", + "UPHENO:0001001", + "HP:0001371", + "HP:0003549", + "HP:0011729", + "UPHENO:0076703", + "HP:0100261", + "UPHENO:0001005", + "HP:0011842", + "HP:0011805", + "UPHENO:0001002", + "HP:0004631", + "HP:0034430", + "HP:0000924", + "HP:0000118", + "BFO:0000002", + "HP:0034392", + "UPHENO:0021425", + "BFO:0000020", + "UPHENO:0075195", + "HP:0003011", + "UPHENO:0002816", + "UPHENO:0002332", + "UPHENO:0015280", + "UPHENO:0002964", + "UPHENO:0081581", + "HP:0033127", + "UPHENO:0001003", + "UPHENO:0002536", + "UPHENO:0046759", + "UPHENO:0020584", + "UPHENO:0031839", + "UPHENO:0076692", + "UPHENO:0081440", + "UPHENO:0076710", + "UPHENO:0002712", + "BFO:0000001", + "PATO:0000001", + "UPHENO:0012541", + "HP:0011843", + "BFO:0000001", + "BFO:0000002", + "BFO:0000004", + "BFO:0000040", + "UBERON:0001062", + "CARO:0000000", + "UBERON:0000465", + "UBERON:0000383", + "UBERON:0001015", + "UBERON:0007845", + "UBERON:0002204", + "UBERON:0005090", + "UBERON:0000061", + "UBERON:0034925", + "UBERON:0007846", + "UBERON:0001630", + "UBERON:0010000", + "UBERON:0000467", + "UBERON:0004770", + "UBERON:0000043", + "UBERON:0000479", + "UBERON:0000468", + "UBERON:0000062", + "UBERON:0011216", + "UBERON:0034921", + "UBERON:0002384", + "UBERON:0004905", + "UBERON:0001434", + "UBERON:0011823", + "UBERON:0000982" + ], + "object_label": "Decreased cervical spine flexion due to contractures of posterior cervical muscles (HPO)", "object_closure_label": [ "All (HPO)", - "Mode of inheritance (HPO)", - "Autosomal dominant inheritance (HPO)", - "Mendelian inheritance" - ], + "Phenotypic abnormality (HPO)", + "Abnormality of the skeletal system (HPO)", + "Flexion contracture (HPO)", + "Abnormality of the musculature (HPO)", + "Abnormality of connective tissue (HPO)", + "Decreased cervical spine flexion due to contractures of posterior cervical muscles (HPO)", + "Abnormality of joint mobility (HPO)", + "Abnormal skeletal muscle morphology (HPO)", + "Abnormal skeletal morphology (HPO)", + "Abnormality of musculoskeletal physiology (HPO)", + "Abnormality of the musculoskeletal system (HPO)", + "Joint contracture", + "Abnormal joint physiology", + "Abnormal tendon morphology (HPO)", + "tendon", + "anatomical structure", + "organ", + "musculature of body", + "material anatomical entity", + "anatomical system", + "multicellular organism", + "tissue", + "skeletal joint", + "musculature", + "anatomical entity", + "skeletal system", + "muscle organ", + "musculoskeletal system", + "connective tissue", + "articular system", + "articulation", + "muscle structure", + "regular connective tissue", + "dense regular connective tissue", + "multicellular anatomical structure", + "organ system subdivision", + "dense connective tissue", + "multi organ part structure", + "anatomical collection" + ], + "object_taxon": null, + "object_taxon_label": null, "primary_knowledge_source": "infores:hpo-annotations", "aggregator_knowledge_source": ["infores:monarchinitiative"], - "category": "biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation", + "category": "biolink:DiseaseToPhenotypicFeatureAssociation", "negated": null, - "provided_by": "hpoa_disease_mode_of_inheritance_edges", - "publications": ["OMIM:609452"], + "provided_by": "hpoa_disease_phenotype_edges", + "publications": ["OMIM:310300"], "qualifiers": [], "frequency_qualifier": null, "has_evidence": ["ECO:0000501"], diff --git a/frontend/fixtures/histopheno.json b/frontend/fixtures/histopheno.json index 841be77fb..6651cbdd2 100644 --- a/frontend/fixtures/histopheno.json +++ b/frontend/fixtures/histopheno.json @@ -3,97 +3,97 @@ "items": [ { "label": "musculature", - "count": 1747, + "count": 1787, "id": "HP:0003011" }, { "label": "nervous_system", - "count": 1118, + "count": 1144, "id": "HP:0000707" }, { "label": "head_neck", - "count": 573, + "count": 658, "id": "HP:0000152" }, { "label": "skeletal_system", - "count": 504, + "count": 627, "id": "HP:0000924" }, { "label": "respiratory", - "count": 318, + "count": 333, "id": "HP:0002086" }, { "label": "eye", - "count": 276, + "count": 298, "id": "HP:0000478" }, { "label": "metabolism_homeostasis", - "count": 219, + "count": 228, "id": "HP:0001939" }, { "label": "cardiovascular_system", - "count": 192, + "count": 196, "id": "HP:0001626" }, - { - "label": "blood", - "count": 185, - "id": "HP:0001871" - }, { "label": "connective_tissue", - "count": 165, + "count": 192, "id": "HP:0003549" }, + { + "label": "blood", + "count": 189, + "id": "HP:0001871" + }, { "label": "digestive_system", - "count": 143, + "count": 176, "id": "HP:0025031" }, { "label": "integument", - "count": 48, + "count": 65, "id": "HP:0001574" }, { "label": "genitourinary_system", - "count": 43, + "count": 49, "id": "HP:0000119" }, { "label": "growth", - "count": 33, + "count": 40, "id": "HP:0001507" }, { "label": "ear", - "count": 27, + "count": 32, "id": "HP:0000598" }, { "label": "endocrine", - "count": 25, + "count": 27, "id": "HP:0000818" }, { "label": "immune_system", - "count": 21, + "count": 24, "id": "HP:0002715" }, { "label": "prenatal_or_birth", - "count": 20, + "count": 24, "id": "HP:0001197" }, { "label": "neoplasm", - "count": 7, + "count": 8, "id": "HP:0002664" }, { diff --git a/frontend/fixtures/node.json b/frontend/fixtures/node.json index 2275f533c..8ea82f74f 100644 --- a/frontend/fixtures/node.json +++ b/frontend/fixtures/node.json @@ -25,26 +25,26 @@ "association_counts": [ { "label": "Phenotypes", - "count": 4011, + "count": 4312, "category": "biolink:DiseaseToPhenotypicFeatureAssociation" }, { "label": "Causal Genes", - "count": 121, + "count": 123, "category": "biolink:CausalGeneToDiseaseAssociation" }, { "label": "Correlated Genes", - "count": 147, + "count": 149, "category": "biolink:CorrelatedGeneToDiseaseAssociation" } ], "node_hierarchy": { "super_classes": [ { - "id": "MONDO:0019056", + "id": "MONDO:0005336", "category": "biolink:Disease", - "name": "neuromuscular disease", + "name": "myopathy", "full_name": null, "description": null, "xref": [], @@ -55,9 +55,9 @@ "synonym": [] }, { - "id": "MONDO:0700223", + "id": "MONDO:0019056", "category": "biolink:Disease", - "name": "hereditary skeletal muscle disorder", + "name": "neuromuscular disease", "full_name": null, "description": null, "xref": [], @@ -68,9 +68,9 @@ "synonym": [] }, { - "id": "MONDO:0005336", + "id": "MONDO:0700223", "category": "biolink:Disease", - "name": "myopathy", + "name": "hereditary skeletal muscle disorder", "full_name": null, "description": null, "xref": [], diff --git a/frontend/src/api/model.ts b/frontend/src/api/model.ts index 709d5ee0b..4e20a0f5c 100644 --- a/frontend/src/api/model.ts +++ b/frontend/src/api/model.ts @@ -32,6 +32,8 @@ export interface Association { subject_label?: string, /** Field containing subject name and the names of all of it's ancestors */ subject_closure_label?: string[], + subject_taxon?: string, + subject_taxon_label?: string, predicate: string, object: string, original_object?: string, @@ -45,6 +47,8 @@ export interface Association { object_label?: string, /** Field containing object name and the names of all of it's ancestors */ object_closure_label?: string[], + object_taxon?: string, + object_taxon_label?: string, primary_knowledge_source?: string, aggregator_knowledge_source?: string[], category?: string, @@ -169,6 +173,8 @@ export interface DirectionalAssociation extends Association { subject_label?: string, /** Field containing subject name and the names of all of it's ancestors */ subject_closure_label?: string[], + subject_taxon?: string, + subject_taxon_label?: string, predicate: string, object: string, original_object?: string, @@ -182,6 +188,8 @@ 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[], + object_taxon?: string, + object_taxon_label?: string, primary_knowledge_source?: string, aggregator_knowledge_source?: string[], category?: string,