diff --git a/backend/src/monarch_py/utils/association_type_mappings.yaml b/backend/src/monarch_py/utils/association_type_mappings.yaml index 1e4e70d94..6ca72982a 100644 --- a/backend/src/monarch_py/utils/association_type_mappings.yaml +++ b/backend/src/monarch_py/utils/association_type_mappings.yaml @@ -80,11 +80,11 @@ category: "biolink:GenotypeToDiseaseAssociation" subject_category: "biolink:Genotype" object_category: "biolink:Disease" -- subject_label: Medical Action - object_label: Medical Action +- subject_label: Indications + object_label: Treatments category: "biolink:ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation" - # Note: subject_category/object_category omitted - this association uses disease_context_qualifier - # and requires special 1-hop handling that isn't yet implemented in the entity grid + subject_category: "biolink:ChemicalEntity" + object_category: "biolink:Disease" - subject_label: Variant to Phenotype object_label: Variant to Phenotype category: "biolink:VariantToPhenotypicFeatureAssociation" diff --git a/backend/tests/fixtures/association_counts.py b/backend/tests/fixtures/association_counts.py index 30bff467a..233772e9d 100644 --- a/backend/tests/fixtures/association_counts.py +++ b/backend/tests/fixtures/association_counts.py @@ -3,4 +3,4 @@ @pytest.fixture def association_counts(): - return {'items': [{'label': 'Disease Model', 'count': 246, 'category': 'biolink:GenotypeToDiseaseAssociation', 'count_direct': 14, 'count_with_orthologs': None}, {'label': 'Disease to Phenotype', 'count': 4247, 'category': 'biolink:DiseaseToPhenotypicFeatureAssociation', 'count_direct': 0, 'count_with_orthologs': None}, {'label': 'Causal Gene', 'count': 133, 'category': 'biolink:CausalGeneToDiseaseAssociation', 'count_direct': 0, 'count_with_orthologs': None}, {'label': 'Correlated Gene', 'count': 156, 'category': 'biolink:CorrelatedGeneToDiseaseAssociation', 'count_direct': 0, 'count_with_orthologs': None}, {'label': 'Variant to Disease', 'count': 701, 'category': 'biolink:VariantToDiseaseAssociation', 'count_direct': 0, 'count_with_orthologs': None}, {'label': 'Medical Action', 'count': 6, 'category': 'biolink:ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation', 'count_direct': 0, 'count_with_orthologs': None}, {'label': 'Cases', 'count': 136, 'category': 'biolink:CaseToDiseaseAssociation', 'count_direct': 0, 'count_with_orthologs': None}]} + return {'items': [{'label': 'Disease Model', 'count': 246, 'category': 'biolink:GenotypeToDiseaseAssociation', 'count_direct': 14, 'count_with_orthologs': None}, {'label': 'Disease to Phenotype', 'count': 4247, 'category': 'biolink:DiseaseToPhenotypicFeatureAssociation', 'count_direct': 0, 'count_with_orthologs': None}, {'label': 'Causal Gene', 'count': 133, 'category': 'biolink:CausalGeneToDiseaseAssociation', 'count_direct': 0, 'count_with_orthologs': None}, {'label': 'Correlated Gene', 'count': 156, 'category': 'biolink:CorrelatedGeneToDiseaseAssociation', 'count_direct': 0, 'count_with_orthologs': None}, {'label': 'Variant to Disease', 'count': 701, 'category': 'biolink:VariantToDiseaseAssociation', 'count_direct': 0, 'count_with_orthologs': None}, {'label': 'Treatments', 'count': 6, 'category': 'biolink:ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation', 'count_direct': 0, 'count_with_orthologs': None}, {'label': 'Cases', 'count': 136, 'category': 'biolink:CaseToDiseaseAssociation', 'count_direct': 0, 'count_with_orthologs': None}]} diff --git a/backend/tests/fixtures/node.py b/backend/tests/fixtures/node.py index 98d6266f0..32d30b5c3 100644 --- a/backend/tests/fixtures/node.py +++ b/backend/tests/fixtures/node.py @@ -3,4 +3,4 @@ @pytest.fixture def node(): - return {'id': 'MONDO:0020121', 'category': 'biolink:Disease', 'name': 'muscular dystrophy', 'description': 'Muscular dystrophy (MD) refers to a group of more than 30 genetic diseases characterized by progressive weakness and degeneration of the skeletal muscles that control movement. Some forms of MD are seen in newborns, infants or children, while others have late-onset and may not appear until middle age or later. The disorders differ in terms of the distribution and extent of muscle weakness (some forms of MD also affect cardiac muscle), age of onset, rate of progression, and pattern of inheritance. The prognosis for people with MD varies according to the type and progression of the disorder. There is no specific treatment to stop or reverse any form of MD. Treatment is supportive and may include physical therapy, respiratory therapy, speech therapy, orthopedic appliances used for support, corrective orthopedic surgery, and medicationsincluding corticosteroids, anticonvulsants (seizure medications), immunosuppressants, and antibiotics. Some individuals may need assisted ventilation to treat respiratory muscle weaknessor a pacemaker for cardiac (heart)abnormalities.', 'xref': ['DOID:9884', 'GARD:0007922', 'ICD10CM:G71.0', 'ICD9:359.1', 'MEDGEN:44527', 'MESH:D009136', 'MedDRA:10028356', 'NANDO:1200486', 'NANDO:2100233', 'NCIT:C84910', 'Orphanet:98473', 'SCTID:73297009', 'UMLS:C0026850', 'icd11.foundation:1464662404'], 'synonym': None, 'exact_synonym': None, 'broad_synonym': None, 'narrow_synonym': None, 'related_synonym': None, 'deprecated': None, 'in_taxon': None, 'in_taxon_label': None, 'iri': None, 'same_as': None, 'subsets': ['disease_grouping', 'doid_rare', 'gard_rare', 'ncit_rare', 'ordo_group_of_disorders', 'otar', 'rare'], 'file_source': 'phenio_nodes', 'provided_by': 'phenio_nodes', 'full_name': None, 'symbol': None, 'has_gene': None, 'type': None, 'has_attribute': None, 'has_biological_sex': None, 'synonyms': None, 'namespace': 'MONDO', 'has_phenotype': None, 'has_phenotype_label': None, 'has_phenotype_count': 0, 'has_phenotype_closure': None, 'has_phenotype_closure_label': None, 'has_descendant': None, 'has_descendant_label': None, 'has_descendant_count': 201, 'uri': 'http://purl.obolibrary.org/obo/MONDO_0020121', 'inheritance': None, 'causal_gene': [], 'causes_disease': None, 'node_relationships': [], 'mappings': [{'id': 'Orphanet:98473', 'url': 'https://www.orpha.net/en/disease/detail/98473'}, {'id': 'NCIT:C84910', 'url': 'http://purl.obolibrary.org/obo/NCIT_C84910'}, {'id': 'icd11.foundation:1464662404', 'url': None}, {'id': 'MEDGEN:44527', 'url': 'http://identifiers.org/medgen/44527'}, {'id': 'UMLS:C0026850', 'url': 'http://identifiers.org/umls/C0026850'}, {'id': 'MESH:D009136', 'url': 'http://identifiers.org/mesh/D009136'}, {'id': 'DOID:9884', 'url': 'http://purl.obolibrary.org/obo/DOID_9884'}, {'id': 'ICD10CM:G71.0', 'url': 'https://www.icd10data.com/search?s=G71.0'}, {'id': 'SCTID:73297009', 'url': 'http://identifiers.org/snomedct/73297009'}], 'external_links': [{'id': 'DOID:9884', 'url': 'http://purl.obolibrary.org/obo/DOID_9884'}, {'id': 'GARD:0007922', 'url': 'https://rarediseases.info.nih.gov/diseases/0007922/index'}, {'id': 'ICD10CM:G71.0', 'url': 'https://www.icd10data.com/search?s=G71.0'}, {'id': 'ICD9:359.1', 'url': None}, {'id': 'MEDGEN:44527', 'url': 'http://identifiers.org/medgen/44527'}, {'id': 'MESH:D009136', 'url': 'http://identifiers.org/mesh/D009136'}, {'id': 'MedDRA:10028356', 'url': None}, {'id': 'NANDO:1200486', 'url': 'http://identifiers.org/NANDO:1200486'}, {'id': 'NANDO:2100233', 'url': 'http://identifiers.org/NANDO:2100233'}, {'id': 'NCIT:C84910', 'url': 'http://purl.obolibrary.org/obo/NCIT_C84910'}, {'id': 'Orphanet:98473', 'url': 'https://www.orpha.net/en/disease/detail/98473'}, {'id': 'SCTID:73297009', 'url': 'http://identifiers.org/snomedct/73297009'}, {'id': 'UMLS:C0026850', 'url': 'http://identifiers.org/umls/C0026850'}, {'id': 'icd11.foundation:1464662404', 'url': None}], 'provided_by_link': {'id': 'phenio', 'url': 'https://monarch-app.monarchinitiative.org/Sources/phenio/'}, 'association_counts': [{'label': 'Disease Model', 'count': 246, 'category': 'biolink:GenotypeToDiseaseAssociation', 'count_direct': 14, 'count_with_orthologs': None}, {'label': 'Disease to Phenotype', 'count': 4247, 'category': 'biolink:DiseaseToPhenotypicFeatureAssociation', 'count_direct': 0, 'count_with_orthologs': None}, {'label': 'Causal Gene', 'count': 133, 'category': 'biolink:CausalGeneToDiseaseAssociation', 'count_direct': 0, 'count_with_orthologs': None}, {'label': 'Correlated Gene', 'count': 156, 'category': 'biolink:CorrelatedGeneToDiseaseAssociation', 'count_direct': 0, 'count_with_orthologs': None}, {'label': 'Variant to Disease', 'count': 701, 'category': 'biolink:VariantToDiseaseAssociation', 'count_direct': 0, 'count_with_orthologs': None}, {'label': 'Medical Action', 'count': 6, 'category': 'biolink:ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation', 'count_direct': 0, 'count_with_orthologs': None}, {'label': 'Cases', 'count': 136, 'category': 'biolink:CaseToDiseaseAssociation', 'count_direct': 0, 'count_with_orthologs': None}], 'cross_species_term_clique': None, 'node_hierarchy': {'super_classes': [{'id': 'MONDO:0005336', 'category': 'biolink:Disease', 'name': 'myopathy', 'description': None, 'xref': None, 'synonym': None, 'exact_synonym': None, 'broad_synonym': None, 'narrow_synonym': None, 'related_synonym': None, 'deprecated': None, 'in_taxon': None, 'in_taxon_label': None, 'iri': None, 'same_as': None, 'subsets': None, 'file_source': None, 'provided_by': None, 'full_name': None, 'symbol': None, 'has_gene': None, 'type': None, 'has_attribute': None, 'has_biological_sex': None, 'synonyms': None, 'namespace': None, 'has_phenotype': None, 'has_phenotype_label': None, 'has_phenotype_count': None, 'has_phenotype_closure': None, 'has_phenotype_closure_label': None, 'has_descendant': None, 'has_descendant_label': None, 'has_descendant_count': None}, {'id': 'MONDO:0100546', 'category': 'biolink:Disease', 'name': 'hereditary neuromuscular disease', 'description': None, 'xref': None, 'synonym': None, 'exact_synonym': None, 'broad_synonym': None, 'narrow_synonym': None, 'related_synonym': None, 'deprecated': None, 'in_taxon': None, 'in_taxon_label': None, 'iri': None, 'same_as': None, 'subsets': None, 'file_source': None, 'provided_by': None, 'full_name': None, 'symbol': None, 'has_gene': None, 'type': None, 'has_attribute': None, 'has_biological_sex': None, 'synonyms': None, 'namespace': None, 'has_phenotype': None, 'has_phenotype_label': None, 'has_phenotype_count': None, 'has_phenotype_closure': None, 'has_phenotype_closure_label': None, 'has_descendant': None, 'has_descendant_label': None, 'has_descendant_count': None}, {'id': 'MONDO:0700223', 'category': 'biolink:Disease', 'name': 'hereditary skeletal muscle disorder', 'description': None, 'xref': None, 'synonym': None, 'exact_synonym': None, 'broad_synonym': None, 'narrow_synonym': None, 'related_synonym': None, 'deprecated': None, 'in_taxon': None, 'in_taxon_label': None, 'iri': None, 'same_as': None, 'subsets': None, 'file_source': None, 'provided_by': None, 'full_name': None, 'symbol': None, 'has_gene': None, 'type': None, 'has_attribute': None, 'has_biological_sex': None, 'synonyms': None, 'namespace': None, 'has_phenotype': None, 'has_phenotype_label': None, 'has_phenotype_count': None, 'has_phenotype_closure': None, 'has_phenotype_closure_label': None, 'has_descendant': None, 'has_descendant_label': None, 'has_descendant_count': None}], 'sub_classes': [{'id': 'MONDO:0008028', 'category': 'biolink:Disease', 'name': 'muscular dystrophy, Barnes type', 'description': None, 'xref': None, 'synonym': None, 'exact_synonym': None, 'broad_synonym': None, 'narrow_synonym': None, 'related_synonym': None, 'deprecated': None, 'in_taxon': None, 'in_taxon_label': None, 'iri': None, 'same_as': None, 'subsets': None, 'file_source': None, 'provided_by': None, 'full_name': None, 'symbol': None, 'has_gene': None, 'type': None, 'has_attribute': None, 'has_biological_sex': None, 'synonyms': None, 'namespace': None, 'has_phenotype': None, 'has_phenotype_label': None, 'has_phenotype_count': None, 'has_phenotype_closure': None, 'has_phenotype_closure_label': None, 'has_descendant': None, 'has_descendant_label': None, 'has_descendant_count': None}, {'id': 'MONDO:0010675', 'category': 'biolink:Disease', 'name': 'muscular dystrophy, cardiac type', 'description': None, 'xref': None, 'synonym': None, 'exact_synonym': None, 'broad_synonym': None, 'narrow_synonym': None, 'related_synonym': None, 'deprecated': None, 'in_taxon': None, 'in_taxon_label': None, 'iri': None, 'same_as': None, 'subsets': None, 'file_source': None, 'provided_by': None, 'full_name': None, 'symbol': None, 'has_gene': None, 'type': None, 'has_attribute': None, 'has_biological_sex': None, 'synonyms': None, 'namespace': None, 'has_phenotype': None, 'has_phenotype_label': None, 'has_phenotype_count': None, 'has_phenotype_closure': None, 'has_phenotype_closure_label': None, 'has_descendant': None, 'has_descendant_label': None, 'has_descendant_count': None}, {'id': 'MONDO:0018949', 'category': 'biolink:Disease', 'name': 'distal myopathy', 'description': None, 'xref': None, 'synonym': None, 'exact_synonym': None, 'broad_synonym': None, 'narrow_synonym': None, 'related_synonym': None, 'deprecated': None, 'in_taxon': None, 'in_taxon_label': None, 'iri': None, 'same_as': None, 'subsets': None, 'file_source': None, 'provided_by': None, 'full_name': None, 'symbol': None, 'has_gene': None, 'type': None, 'has_attribute': None, 'has_biological_sex': None, 'synonyms': None, 'namespace': None, 'has_phenotype': None, 'has_phenotype_label': None, 'has_phenotype_count': None, 'has_phenotype_closure': None, 'has_phenotype_closure_label': None, 'has_descendant': None, 'has_descendant_label': None, 'has_descendant_count': None}, {'id': 'MONDO:0016106', 'category': 'biolink:Disease', 'name': 'progressive muscular dystrophy', 'description': None, 'xref': None, 'synonym': None, 'exact_synonym': None, 'broad_synonym': None, 'narrow_synonym': None, 'related_synonym': None, 'deprecated': None, 'in_taxon': None, 'in_taxon_label': None, 'iri': None, 'same_as': None, 'subsets': None, 'file_source': None, 'provided_by': None, 'full_name': None, 'symbol': None, 'has_gene': None, 'type': None, 'has_attribute': None, 'has_biological_sex': None, 'synonyms': None, 'namespace': None, 'has_phenotype': None, 'has_phenotype_label': None, 'has_phenotype_count': None, 'has_phenotype_closure': None, 'has_phenotype_closure_label': None, 'has_descendant': None, 'has_descendant_label': None, 'has_descendant_count': None}, {'id': 'MONDO:0023204', 'category': 'biolink:Disease', 'name': 'Fukuda-Miyanomae-Nakata syndrome', 'description': None, 'xref': None, 'synonym': None, 'exact_synonym': None, 'broad_synonym': None, 'narrow_synonym': None, 'related_synonym': None, 'deprecated': None, 'in_taxon': None, 'in_taxon_label': None, 'iri': None, 'same_as': None, 'subsets': None, 'file_source': None, 'provided_by': None, 'full_name': None, 'symbol': None, 'has_gene': None, 'type': None, 'has_attribute': None, 'has_biological_sex': None, 'synonyms': None, 'namespace': None, 'has_phenotype': None, 'has_phenotype_label': None, 'has_phenotype_count': None, 'has_phenotype_closure': None, 'has_phenotype_closure_label': None, 'has_descendant': None, 'has_descendant_label': None, 'has_descendant_count': None}, {'id': 'MONDO:0019950', 'category': 'biolink:Disease', 'name': 'congenital muscular dystrophy', 'description': None, 'xref': None, 'synonym': None, 'exact_synonym': None, 'broad_synonym': None, 'narrow_synonym': None, 'related_synonym': None, 'deprecated': None, 'in_taxon': None, 'in_taxon_label': None, 'iri': None, 'same_as': None, 'subsets': None, 'file_source': None, 'provided_by': None, 'full_name': None, 'symbol': None, 'has_gene': None, 'type': None, 'has_attribute': None, 'has_biological_sex': None, 'synonyms': None, 'namespace': None, 'has_phenotype': None, 'has_phenotype_label': None, 'has_phenotype_count': None, 'has_phenotype_closure': None, 'has_phenotype_closure_label': None, 'has_descendant': None, 'has_descendant_label': None, 'has_descendant_count': None}, {'id': 'MONDO:0700285', 'category': 'biolink:Disease', 'name': 'DMD-related muscular dystrophy', 'description': None, 'xref': None, 'synonym': None, 'exact_synonym': None, 'broad_synonym': None, 'narrow_synonym': None, 'related_synonym': None, 'deprecated': None, 'in_taxon': None, 'in_taxon_label': None, 'iri': None, 'same_as': None, 'subsets': None, 'file_source': None, 'provided_by': None, 'full_name': None, 'symbol': None, 'has_gene': None, 'type': None, 'has_attribute': None, 'has_biological_sex': None, 'synonyms': None, 'namespace': None, 'has_phenotype': None, 'has_phenotype_label': None, 'has_phenotype_count': None, 'has_phenotype_closure': None, 'has_phenotype_closure_label': None, 'has_descendant': None, 'has_descendant_label': None, 'has_descendant_count': None}, {'id': 'MONDO:0010676', 'category': 'biolink:Disease', 'name': 'muscular dystrophy, Hemizygous lethal type', 'description': None, 'xref': None, 'synonym': None, 'exact_synonym': None, 'broad_synonym': None, 'narrow_synonym': None, 'related_synonym': None, 'deprecated': None, 'in_taxon': None, 'in_taxon_label': None, 'iri': None, 'same_as': None, 'subsets': None, 'file_source': None, 'provided_by': None, 'full_name': None, 'symbol': None, 'has_gene': None, 'type': None, 'has_attribute': None, 'has_biological_sex': None, 'synonyms': None, 'namespace': None, 'has_phenotype': None, 'has_phenotype_label': None, 'has_phenotype_count': None, 'has_phenotype_closure': None, 'has_phenotype_closure_label': None, 'has_descendant': None, 'has_descendant_label': None, 'has_descendant_count': None}, {'id': 'MONDO:0010677', 'category': 'biolink:Disease', 'name': 'muscular dystrophy, Mabry type', 'description': None, 'xref': None, 'synonym': None, 'exact_synonym': None, 'broad_synonym': None, 'narrow_synonym': None, 'related_synonym': None, 'deprecated': None, 'in_taxon': None, 'in_taxon_label': None, 'iri': None, 'same_as': None, 'subsets': None, 'file_source': None, 'provided_by': None, 'full_name': None, 'symbol': None, 'has_gene': None, 'type': None, 'has_attribute': None, 'has_biological_sex': None, 'synonyms': None, 'namespace': None, 'has_phenotype': None, 'has_phenotype_label': None, 'has_phenotype_count': None, 'has_phenotype_closure': None, 'has_phenotype_closure_label': None, 'has_descendant': None, 'has_descendant_label': None, 'has_descendant_count': None}, {'id': 'MONDO:0010678', 'category': 'biolink:Disease', 'name': 'muscular dystrophy, progressive Pectorodorsal', 'description': None, 'xref': None, 'synonym': None, 'exact_synonym': None, 'broad_synonym': None, 'narrow_synonym': None, 'related_synonym': None, 'deprecated': None, 'in_taxon': None, 'in_taxon_label': None, 'iri': None, 'same_as': None, 'subsets': None, 'file_source': None, 'provided_by': None, 'full_name': None, 'symbol': None, 'has_gene': None, 'type': None, 'has_attribute': None, 'has_biological_sex': None, 'synonyms': None, 'namespace': None, 'has_phenotype': None, 'has_phenotype_label': None, 'has_phenotype_count': None, 'has_phenotype_closure': None, 'has_phenotype_closure_label': None, 'has_descendant': None, 'has_descendant_label': None, 'has_descendant_count': None}, {'id': 'MONDO:0100228', 'category': 'biolink:Disease', 'name': 'LAMA2-related muscular dystrophy', 'description': None, 'xref': None, 'synonym': None, 'exact_synonym': None, 'broad_synonym': None, 'narrow_synonym': None, 'related_synonym': None, 'deprecated': None, 'in_taxon': None, 'in_taxon_label': None, 'iri': None, 'same_as': None, 'subsets': None, 'file_source': None, 'provided_by': None, 'full_name': None, 'symbol': None, 'has_gene': None, 'type': None, 'has_attribute': None, 'has_biological_sex': None, 'synonyms': None, 'namespace': None, 'has_phenotype': None, 'has_phenotype_label': None, 'has_phenotype_count': None, 'has_phenotype_closure': None, 'has_phenotype_closure_label': None, 'has_descendant': None, 'has_descendant_label': None, 'has_descendant_count': None}]}} + return {'id': 'MONDO:0020121', 'category': 'biolink:Disease', 'name': 'muscular dystrophy', 'description': 'Muscular dystrophy (MD) refers to a group of more than 30 genetic diseases characterized by progressive weakness and degeneration of the skeletal muscles that control movement. Some forms of MD are seen in newborns, infants or children, while others have late-onset and may not appear until middle age or later. The disorders differ in terms of the distribution and extent of muscle weakness (some forms of MD also affect cardiac muscle), age of onset, rate of progression, and pattern of inheritance. The prognosis for people with MD varies according to the type and progression of the disorder. There is no specific treatment to stop or reverse any form of MD. Treatment is supportive and may include physical therapy, respiratory therapy, speech therapy, orthopedic appliances used for support, corrective orthopedic surgery, and medicationsincluding corticosteroids, anticonvulsants (seizure medications), immunosuppressants, and antibiotics. Some individuals may need assisted ventilation to treat respiratory muscle weaknessor a pacemaker for cardiac (heart)abnormalities.', 'xref': ['DOID:9884', 'GARD:0007922', 'ICD10CM:G71.0', 'ICD9:359.1', 'MEDGEN:44527', 'MESH:D009136', 'MedDRA:10028356', 'NANDO:1200486', 'NANDO:2100233', 'NCIT:C84910', 'Orphanet:98473', 'SCTID:73297009', 'UMLS:C0026850', 'icd11.foundation:1464662404'], 'synonym': None, 'exact_synonym': None, 'broad_synonym': None, 'narrow_synonym': None, 'related_synonym': None, 'deprecated': None, 'in_taxon': None, 'in_taxon_label': None, 'iri': None, 'same_as': None, 'subsets': ['disease_grouping', 'doid_rare', 'gard_rare', 'ncit_rare', 'ordo_group_of_disorders', 'otar', 'rare'], 'file_source': 'phenio_nodes', 'provided_by': 'phenio_nodes', 'full_name': None, 'symbol': None, 'has_gene': None, 'type': None, 'has_attribute': None, 'has_biological_sex': None, 'synonyms': None, 'namespace': 'MONDO', 'has_phenotype': None, 'has_phenotype_label': None, 'has_phenotype_count': 0, 'has_phenotype_closure': None, 'has_phenotype_closure_label': None, 'has_descendant': None, 'has_descendant_label': None, 'has_descendant_count': 201, 'uri': 'http://purl.obolibrary.org/obo/MONDO_0020121', 'inheritance': None, 'causal_gene': [], 'causes_disease': None, 'node_relationships': [], 'mappings': [{'id': 'Orphanet:98473', 'url': 'https://www.orpha.net/en/disease/detail/98473'}, {'id': 'NCIT:C84910', 'url': 'http://purl.obolibrary.org/obo/NCIT_C84910'}, {'id': 'icd11.foundation:1464662404', 'url': None}, {'id': 'MEDGEN:44527', 'url': 'http://identifiers.org/medgen/44527'}, {'id': 'UMLS:C0026850', 'url': 'http://identifiers.org/umls/C0026850'}, {'id': 'MESH:D009136', 'url': 'http://identifiers.org/mesh/D009136'}, {'id': 'DOID:9884', 'url': 'http://purl.obolibrary.org/obo/DOID_9884'}, {'id': 'ICD10CM:G71.0', 'url': 'https://www.icd10data.com/search?s=G71.0'}, {'id': 'SCTID:73297009', 'url': 'http://identifiers.org/snomedct/73297009'}], 'external_links': 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'deprecated': None, 'in_taxon': None, 'in_taxon_label': None, 'iri': None, 'same_as': None, 'subsets': None, 'file_source': None, 'provided_by': None, 'full_name': None, 'symbol': None, 'has_gene': None, 'type': None, 'has_attribute': None, 'has_biological_sex': None, 'synonyms': None, 'namespace': None, 'has_phenotype': None, 'has_phenotype_label': None, 'has_phenotype_count': None, 'has_phenotype_closure': None, 'has_phenotype_closure_label': None, 'has_descendant': None, 'has_descendant_label': None, 'has_descendant_count': None}, {'id': 'MONDO:0019950', 'category': 'biolink:Disease', 'name': 'congenital muscular dystrophy', 'description': None, 'xref': None, 'synonym': None, 'exact_synonym': None, 'broad_synonym': None, 'narrow_synonym': None, 'related_synonym': None, 'deprecated': None, 'in_taxon': None, 'in_taxon_label': None, 'iri': None, 'same_as': None, 'subsets': None, 'file_source': None, 'provided_by': None, 'full_name': None, 'symbol': None, 'has_gene': None, 'type': None, 'has_attribute': None, 'has_biological_sex': None, 'synonyms': None, 'namespace': None, 'has_phenotype': None, 'has_phenotype_label': None, 'has_phenotype_count': None, 'has_phenotype_closure': None, 'has_phenotype_closure_label': None, 'has_descendant': None, 'has_descendant_label': None, 'has_descendant_count': None}, {'id': 'MONDO:0700285', 'category': 'biolink:Disease', 'name': 'DMD-related muscular dystrophy', 'description': None, 'xref': None, 'synonym': None, 'exact_synonym': None, 'broad_synonym': None, 'narrow_synonym': None, 'related_synonym': None, 'deprecated': None, 'in_taxon': None, 'in_taxon_label': None, 'iri': None, 'same_as': None, 'subsets': None, 'file_source': None, 'provided_by': None, 'full_name': None, 'symbol': None, 'has_gene': None, 'type': None, 'has_attribute': None, 'has_biological_sex': None, 'synonyms': None, 'namespace': None, 'has_phenotype': None, 'has_phenotype_label': None, 'has_phenotype_count': None, 'has_phenotype_closure': None, 'has_phenotype_closure_label': None, 'has_descendant': None, 'has_descendant_label': None, 'has_descendant_count': None}, {'id': 'MONDO:0010676', 'category': 'biolink:Disease', 'name': 'muscular dystrophy, Hemizygous lethal type', 'description': None, 'xref': None, 'synonym': None, 'exact_synonym': None, 'broad_synonym': None, 'narrow_synonym': None, 'related_synonym': None, 'deprecated': None, 'in_taxon': None, 'in_taxon_label': None, 'iri': None, 'same_as': None, 'subsets': None, 'file_source': None, 'provided_by': None, 'full_name': None, 'symbol': None, 'has_gene': None, 'type': None, 'has_attribute': None, 'has_biological_sex': None, 'synonyms': None, 'namespace': None, 'has_phenotype': None, 'has_phenotype_label': None, 'has_phenotype_count': None, 'has_phenotype_closure': None, 'has_phenotype_closure_label': None, 'has_descendant': None, 'has_descendant_label': None, 'has_descendant_count': None}, {'id': 'MONDO:0010677', 'category': 'biolink:Disease', 'name': 'muscular dystrophy, Mabry type', 'description': None, 'xref': None, 'synonym': None, 'exact_synonym': None, 'broad_synonym': None, 'narrow_synonym': None, 'related_synonym': None, 'deprecated': None, 'in_taxon': None, 'in_taxon_label': None, 'iri': None, 'same_as': None, 'subsets': None, 'file_source': None, 'provided_by': None, 'full_name': None, 'symbol': None, 'has_gene': None, 'type': None, 'has_attribute': None, 'has_biological_sex': None, 'synonyms': None, 'namespace': None, 'has_phenotype': None, 'has_phenotype_label': None, 'has_phenotype_count': None, 'has_phenotype_closure': None, 'has_phenotype_closure_label': None, 'has_descendant': None, 'has_descendant_label': None, 'has_descendant_count': None}, {'id': 'MONDO:0010678', 'category': 'biolink:Disease', 'name': 'muscular dystrophy, progressive Pectorodorsal', 'description': None, 'xref': None, 'synonym': None, 'exact_synonym': None, 'broad_synonym': None, 'narrow_synonym': None, 'related_synonym': None, 'deprecated': None, 'in_taxon': None, 'in_taxon_label': None, 'iri': None, 'same_as': None, 'subsets': None, 'file_source': None, 'provided_by': None, 'full_name': None, 'symbol': None, 'has_gene': None, 'type': None, 'has_attribute': None, 'has_biological_sex': None, 'synonyms': None, 'namespace': None, 'has_phenotype': None, 'has_phenotype_label': None, 'has_phenotype_count': None, 'has_phenotype_closure': None, 'has_phenotype_closure_label': None, 'has_descendant': None, 'has_descendant_label': None, 'has_descendant_count': None}, {'id': 'MONDO:0100228', 'category': 'biolink:Disease', 'name': 'LAMA2-related muscular dystrophy', 'description': None, 'xref': None, 'synonym': None, 'exact_synonym': None, 'broad_synonym': None, 'narrow_synonym': None, 'related_synonym': None, 'deprecated': None, 'in_taxon': None, 'in_taxon_label': None, 'iri': None, 'same_as': None, 'subsets': None, 'file_source': None, 'provided_by': None, 'full_name': None, 'symbol': None, 'has_gene': None, 'type': None, 'has_attribute': None, 'has_biological_sex': None, 'synonyms': None, 'namespace': None, 'has_phenotype': None, 'has_phenotype_label': None, 'has_phenotype_count': None, 'has_phenotype_closure': None, 'has_phenotype_closure_label': None, 'has_descendant': None, 'has_descendant_label': None, 'has_descendant_count': None}]}} diff --git a/backend/tests/fixtures/object_formatted.py b/backend/tests/fixtures/object_formatted.py index 6d9c76a2e..cec252f2f 100644 --- a/backend/tests/fixtures/object_formatted.py +++ b/backend/tests/fixtures/object_formatted.py @@ -736,7 +736,7 @@ def node_json(): def node_tsv(): return """ id category name description xref synonym exact_synonym broad_synonym narrow_synonym related_synonym deprecated in_taxon in_taxon_label iri same_as subsets file_source provided_by full_name symbol has_gene type has_attribute has_biological_sex synonyms namespace has_phenotype has_phenotype_label has_phenotype_count has_phenotype_closure has_phenotype_closure_label has_descendant has_descendant_label has_descendant_count uri inheritance causal_gene causes_disease node_relationships mappings external_links provided_by_link association_counts cross_species_term_clique node_hierarchy -MONDO:0020121 biolink:Disease muscular dystrophy Muscular dystrophy (MD) refers to a group of more than 30 genetic diseases characterized by progressive weakness and degeneration of the skeletal muscles that control movement. Some forms of MD are seen in newborns, infants or children, while others have late-onset and may not appear until middle age or later. The disorders differ in terms of the distribution and extent of muscle weakness (some forms of MD also affect cardiac muscle), age of onset, rate of progression, and pattern of inheritance. The prognosis for people with MD varies according to the type and progression of the disorder. There is no specific treatment to stop or reverse any form of MD. Treatment is supportive and may include physical therapy, respiratory therapy, speech therapy, orthopedic appliances used for support, corrective orthopedic surgery, and medicationsincluding corticosteroids, anticonvulsants (seizure medications), immunosuppressants, and antibiotics. Some individuals may need assisted ventilation to treat respiratory muscle weaknessor a pacemaker for cardiac (heart)abnormalities. 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None}, {'label': 'Medical Action', 'count': 6, 'category': 'biolink:ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation', 'count_direct': 0, 'count_with_orthologs': None}, {'label': 'Cases', 'count': 136, 'category': 'biolink:CaseToDiseaseAssociation', 'count_direct': 0, 'count_with_orthologs': None}] None {'super_classes': [{'id': 'MONDO:0005336', 'category': 'biolink:Disease', 'name': 'myopathy', 'description': None, 'xref': None, 'synonym': None, 'exact_synonym': None, 'broad_synonym': None, 'narrow_synonym': None, 'related_synonym': None, 'deprecated': None, 'in_taxon': None, 'in_taxon_label': None, 'iri': None, 'same_as': None, 'subsets': None, 'file_source': None, 'provided_by': None, 'full_name': None, 'symbol': None, 'has_gene': None, 'type': None, 'has_attribute': None, 'has_biological_sex': None, 'synonyms': None, 'namespace': None, 'has_phenotype': None, 'has_phenotype_label': None, 'has_phenotype_count': None, 'has_phenotype_closure': None, 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None, 'broad_synonym': None, 'narrow_synonym': None, 'related_synonym': None, 'deprecated': None, 'in_taxon': None, 'in_taxon_label': None, 'iri': None, 'same_as': None, 'subsets': None, 'file_source': None, 'provided_by': None, 'full_name': None, 'symbol': None, 'has_gene': None, 'type': None, 'has_attribute': None, 'has_biological_sex': None, 'synonyms': None, 'namespace': None, 'has_phenotype': None, 'has_phenotype_label': None, 'has_phenotype_count': None, 'has_phenotype_closure': None, 'has_phenotype_closure_label': None, 'has_descendant': None, 'has_descendant_label': None, 'has_descendant_count': None}, {'id': 'MONDO:0100228', 'category': 'biolink:Disease', 'name': 'LAMA2-related muscular dystrophy', 'description': None, 'xref': None, 'synonym': None, 'exact_synonym': None, 'broad_synonym': None, 'narrow_synonym': None, 'related_synonym': None, 'deprecated': None, 'in_taxon': None, 'in_taxon_label': None, 'iri': None, 'same_as': None, 'subsets': None, 'file_source': None, 'provided_by': None, 'full_name': None, 'symbol': None, 'has_gene': None, 'type': None, 'has_attribute': None, 'has_biological_sex': None, 'synonyms': None, 'namespace': None, 'has_phenotype': None, 'has_phenotype_label': None, 'has_phenotype_count': None, 'has_phenotype_closure': None, 'has_phenotype_closure_label': None, 'has_descendant': None, 'has_descendant_label': None, 'has_descendant_count': None}]} +MONDO:0020121 biolink:Disease muscular dystrophy Muscular dystrophy (MD) refers to a group of more than 30 genetic diseases characterized by progressive weakness and degeneration of the skeletal muscles that control movement. Some forms of MD are seen in newborns, infants or children, while others have late-onset and may not appear until middle age or later. The disorders differ in terms of the distribution and extent of muscle weakness (some forms of MD also affect cardiac muscle), age of onset, rate of progression, and pattern of inheritance. The prognosis for people with MD varies according to the type and progression of the disorder. There is no specific treatment to stop or reverse any form of MD. Treatment is supportive and may include physical therapy, respiratory therapy, speech therapy, orthopedic appliances used for support, corrective orthopedic surgery, and medicationsincluding corticosteroids, anticonvulsants (seizure medications), immunosuppressants, and antibiotics. Some individuals may need assisted ventilation to treat respiratory muscle weaknessor a pacemaker for cardiac (heart)abnormalities. 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'file_source': None, 'provided_by': None, 'full_name': None, 'symbol': None, 'has_gene': None, 'type': None, 'has_attribute': None, 'has_biological_sex': None, 'synonyms': None, 'namespace': None, 'has_phenotype': None, 'has_phenotype_label': None, 'has_phenotype_count': None, 'has_phenotype_closure': None, 'has_phenotype_closure_label': None, 'has_descendant': None, 'has_descendant_label': None, 'has_descendant_count': None}, {'id': 'MONDO:0700285', 'category': 'biolink:Disease', 'name': 'DMD-related muscular dystrophy', 'description': None, 'xref': None, 'synonym': None, 'exact_synonym': None, 'broad_synonym': None, 'narrow_synonym': None, 'related_synonym': None, 'deprecated': None, 'in_taxon': None, 'in_taxon_label': None, 'iri': None, 'same_as': None, 'subsets': None, 'file_source': None, 'provided_by': None, 'full_name': None, 'symbol': None, 'has_gene': None, 'type': None, 'has_attribute': None, 'has_biological_sex': None, 'synonyms': None, 'namespace': None, 'has_phenotype': None, 'has_phenotype_label': None, 'has_phenotype_count': None, 'has_phenotype_closure': None, 'has_phenotype_closure_label': None, 'has_descendant': None, 'has_descendant_label': None, 'has_descendant_count': None}, {'id': 'MONDO:0010676', 'category': 'biolink:Disease', 'name': 'muscular dystrophy, Hemizygous lethal type', 'description': None, 'xref': None, 'synonym': None, 'exact_synonym': None, 'broad_synonym': None, 'narrow_synonym': None, 'related_synonym': None, 'deprecated': None, 'in_taxon': None, 'in_taxon_label': None, 'iri': None, 'same_as': None, 'subsets': None, 'file_source': None, 'provided_by': None, 'full_name': None, 'symbol': None, 'has_gene': None, 'type': None, 'has_attribute': None, 'has_biological_sex': None, 'synonyms': None, 'namespace': None, 'has_phenotype': None, 'has_phenotype_label': None, 'has_phenotype_count': None, 'has_phenotype_closure': None, 'has_phenotype_closure_label': None, 'has_descendant': None, 'has_descendant_label': None, 'has_descendant_count': None}, {'id': 'MONDO:0010677', 'category': 'biolink:Disease', 'name': 'muscular dystrophy, Mabry type', 'description': None, 'xref': None, 'synonym': None, 'exact_synonym': None, 'broad_synonym': None, 'narrow_synonym': None, 'related_synonym': None, 'deprecated': None, 'in_taxon': None, 'in_taxon_label': None, 'iri': None, 'same_as': None, 'subsets': None, 'file_source': None, 'provided_by': None, 'full_name': None, 'symbol': None, 'has_gene': None, 'type': None, 'has_attribute': None, 'has_biological_sex': None, 'synonyms': None, 'namespace': None, 'has_phenotype': None, 'has_phenotype_label': None, 'has_phenotype_count': None, 'has_phenotype_closure': None, 'has_phenotype_closure_label': None, 'has_descendant': None, 'has_descendant_label': None, 'has_descendant_count': None}, {'id': 'MONDO:0010678', 'category': 'biolink:Disease', 'name': 'muscular dystrophy, progressive Pectorodorsal', 'description': None, 'xref': None, 'synonym': None, 'exact_synonym': None, 'broad_synonym': None, 'narrow_synonym': None, 'related_synonym': None, 'deprecated': None, 'in_taxon': None, 'in_taxon_label': None, 'iri': None, 'same_as': None, 'subsets': None, 'file_source': None, 'provided_by': None, 'full_name': None, 'symbol': None, 'has_gene': None, 'type': None, 'has_attribute': None, 'has_biological_sex': None, 'synonyms': None, 'namespace': None, 'has_phenotype': None, 'has_phenotype_label': None, 'has_phenotype_count': None, 'has_phenotype_closure': None, 'has_phenotype_closure_label': None, 'has_descendant': None, 'has_descendant_label': None, 'has_descendant_count': None}, {'id': 'MONDO:0100228', 'category': 'biolink:Disease', 'name': 'LAMA2-related muscular dystrophy', 'description': None, 'xref': None, 'synonym': None, 'exact_synonym': None, 'broad_synonym': None, 'narrow_synonym': None, 'related_synonym': None, 'deprecated': None, 'in_taxon': None, 'in_taxon_label': None, 'iri': None, 'same_as': None, 'subsets': None, 'file_source': None, 'provided_by': None, 'full_name': None, 'symbol': None, 'has_gene': None, 'type': None, 'has_attribute': None, 'has_biological_sex': None, 'synonyms': None, 'namespace': None, 'has_phenotype': None, 'has_phenotype_label': None, 'has_phenotype_count': None, 'has_phenotype_closure': None, 'has_phenotype_closure_label': None, 'has_descendant': None, 'has_descendant_label': None, 'has_descendant_count': None}]} """ @pytest.fixture diff --git a/frontend/src/composables/use-association-categories.ts b/frontend/src/composables/use-association-categories.ts index 755f39cb1..c2fb65fc8 100644 --- a/frontend/src/composables/use-association-categories.ts +++ b/frontend/src/composables/use-association-categories.ts @@ -3,9 +3,7 @@ import { startCase } from "lodash"; import { TRAVERSE_ORTHOLOG_CATEGORIES } from "@/api/associations"; import type { Node } from "@/api/model"; -const HIDDEN_CATEGORIES = new Set([ - "biolink:ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation", -]); +const HIDDEN_CATEGORIES = new Set([]); export function useAssociationCategories(node: Node) { const options = computed(() => { diff --git a/frontend/src/pages/node/SectionAssociationDetails.vue b/frontend/src/pages/node/SectionAssociationDetails.vue index bc0c193ac..23822313e 100644 --- a/frontend/src/pages/node/SectionAssociationDetails.vue +++ b/frontend/src/pages/node/SectionAssociationDetails.vue @@ -48,6 +48,14 @@ + + {{ startCase(association.knowledge_level) }} + + {{ association.primary_knowledge_source }} @@ -79,6 +87,42 @@ + + +
+ {{ formatRole(source.resource_role) }}: + {{ source.resource_id }} + + ← {{ source.upstream_resource_ids.join(", ") }} + +
+ + + + + + {{ agg }} + + + {{ association.provided_by_link?.id || association.provided_by }} @@ -97,6 +141,61 @@ + + {{ association.original_predicate }} + + + + +
+ {{ qualifier.label }}: {{ qualifier.value }} +
+ + + + + +
+ Count: {{ association.has_count }} +
+
+ Total: {{ association.has_total }} +
+
+ Percentage: {{ association.has_percentage }} +
+
+ Quotient: {{ association.has_quotient }} +
+ + + + + {{ association.FDA_adverse_event_level }} + + + + Yes + + import { computed, onMounted, watch } from "vue"; +import { startCase } from "lodash"; import type { DirectionalAssociation, Node } from "@/api/model"; import AppDetail from "@/components/AppDetail.vue"; import AppDetails from "@/components/AppDetails.vue"; @@ -127,6 +227,7 @@ import AppPredicateBadge from "@/components/AppPredicateBadge.vue"; import { useSourceVersions } from "@/composables/use-source-versions"; import { scrollTo } from "@/router"; import { getAgentTypeMeta } from "@/util/agentType"; +import { parseRetrievalSources } from "@/util/retrievalSources"; type Props = { /** current node */ @@ -148,6 +249,47 @@ const sourceVersion = computed(() => props.association ? versionForEdge(props.association) : null, ); +/** parse the nested retrieval-source provenance chain (JSON-encoded) */ +const retrievalSources = computed(() => + parseRetrievalSources(props.association?.sources), +); + +/** humanize a retrieval-source role, e.g. "primary_knowledge_source" */ +const formatRole = (role?: string) => (role ? startCase(role) : "Source"); + +/** present qualifier values, preferring labels over raw ids */ +const qualifierRows = computed(() => { + const a = props.association; + const rows: { label: string; value: string }[] = []; + if (!a) return rows; + const add = (label: string, value?: string | null) => { + if (value) rows.push({ label, value }); + }; + add("Frequency", a.frequency_qualifier_label || a.frequency_qualifier); + add("Onset", a.onset_qualifier_label || a.onset_qualifier); + add("Sex", a.sex_qualifier_label || a.sex_qualifier); + add("Stage", a.stage_qualifier_label || a.stage_qualifier); + add( + "Disease context", + a.disease_context_qualifier_label || a.disease_context_qualifier, + ); + add("Object specialization", a.object_specialization_qualifier); + (a.qualifiers ?? []).forEach((qualifier) => add("Qualifier", qualifier)); + return rows; +}); + +/** whether any frequency/count representation is present */ +const hasFrequencyData = computed(() => { + const a = props.association; + return ( + a != null && + (a.has_count != null || + a.has_total != null || + a.has_percentage != null || + a.has_quotient != null) + ); +}); + /** scroll details section into view */ async function scrollIntoView() { scrollTo("#association-details"); @@ -186,4 +328,19 @@ onMounted(scrollIntoView); color: $gray; font-size: 0.9em; } + +.retrieval-source { + display: flex; + flex-wrap: wrap; + align-items: baseline; + gap: 0 0.5em; +} + +.retrieval-source .role { + color: $gray; +} + +.retrieval-source .upstream { + color: $gray; +} diff --git a/frontend/src/util/retrievalSources.ts b/frontend/src/util/retrievalSources.ts new file mode 100644 index 000000000..2d49423cc --- /dev/null +++ b/frontend/src/util/retrievalSources.ts @@ -0,0 +1,26 @@ +export type RetrievalSource = { + resource_id?: string; + resource_role?: string; + upstream_resource_ids?: string[]; +}; + +/** + * Parse the `sources` field of an association into a flat list of + * retrieval-source records. Each entry may be a JSON-encoded string holding an + * array of records (as the API serializes it); malformed entries are skipped. + */ +export const parseRetrievalSources = ( + sources?: string[] | null, +): RetrievalSource[] => { + const out: RetrievalSource[] = []; + for (const entry of sources ?? []) { + try { + const parsed = typeof entry === "string" ? JSON.parse(entry) : entry; + if (Array.isArray(parsed)) out.push(...parsed); + else if (parsed) out.push(parsed); + } catch { + /* skip unparseable source entries */ + } + } + return out; +}; diff --git a/frontend/unit/retrievalSources.test.ts b/frontend/unit/retrievalSources.test.ts new file mode 100644 index 000000000..83e9b67ab --- /dev/null +++ b/frontend/unit/retrievalSources.test.ts @@ -0,0 +1,41 @@ +import { expect, test } from "vitest"; +import { parseRetrievalSources } from "@/util/retrievalSources"; + +test("parses a MEDIC-style nested retrieval-source chain", () => { + /** the API serializes `sources` as a list holding one JSON-encoded array */ + const sources = [ + JSON.stringify([ + { + resource_id: "infores:medic", + resource_role: "primary_knowledge_source", + upstream_resource_ids: ["infores:dailymed"], + }, + { + resource_id: "infores:dailymed", + resource_role: "supporting_data_source", + upstream_resource_ids: null, + }, + ]), + ]; + const parsed = parseRetrievalSources(sources); + expect(parsed).toHaveLength(2); + expect(parsed[0].resource_id).toBe("infores:medic"); + expect(parsed[0].resource_role).toBe("primary_knowledge_source"); + expect(parsed[0].upstream_resource_ids).toEqual(["infores:dailymed"]); + expect(parsed[1].resource_role).toBe("supporting_data_source"); +}); + +test("returns empty for missing or empty sources", () => { + expect(parseRetrievalSources(undefined)).toEqual([]); + expect(parseRetrievalSources(null)).toEqual([]); + expect(parseRetrievalSources([])).toEqual([]); +}); + +test("skips unparseable entries without throwing", () => { + const parsed = parseRetrievalSources([ + "not json", + JSON.stringify([{ resource_id: "infores:ctd" }]), + ]); + expect(parsed).toHaveLength(1); + expect(parsed[0].resource_id).toBe("infores:ctd"); +});