From 263bc33b7620ecefa91c4fe9a0357917fcbc6df0 Mon Sep 17 00:00:00 2001 From: Kevin Schaper Date: Thu, 17 Oct 2024 13:43:29 -0700 Subject: [PATCH] minor tweaks to association count label code/config, plus a mess of regenerated fixtures --- .../implementations/solr/solr_parsers.py | 4 +- .../utils/association_type_mappings.yaml | 22 +-- backend/tests/fixtures/association_counts.py | 2 +- .../fixtures/association_counts_response.py | 2 +- backend/tests/fixtures/node.py | 2 +- backend/tests/fixtures/object_formatted.py | 6 +- backend/tests/fixtures/search_response.py | 2 +- backend/tests/integration/test_solr_search.py | 2 +- frontend/fixtures/association-counts.json | 2 +- frontend/fixtures/node.json | 2 +- .../fixtures/phenotype-explorer-compare.json | 8 +- .../phenotype-explorer-multi-compare.json | 172 +++++++++--------- .../fixtures/phenotype-explorer-search.json | 82 ++++----- 13 files changed, 157 insertions(+), 151 deletions(-) diff --git a/backend/src/monarch_py/implementations/solr/solr_parsers.py b/backend/src/monarch_py/implementations/solr/solr_parsers.py index 2fb058816..cb18e878e 100644 --- a/backend/src/monarch_py/implementations/solr/solr_parsers.py +++ b/backend/src/monarch_py/implementations/solr/solr_parsers.py @@ -84,11 +84,11 @@ def parse_association_counts(query_result: SolrQueryResult, entity: str) -> Asso if k.endswith(subject_query): original_query = k.replace(f" {subject_query}", "").lstrip("(").rstrip(")") agm = get_association_type_mapping_by_query_string(original_query) - label = agm.object_label + label = agm.subject_label elif k.endswith(object_query): original_query = k.replace(f" {object_query}", "").lstrip("(").rstrip(")") agm = get_association_type_mapping_by_query_string(original_query) - label = agm.subject_label + label = agm.object_label # always use forward for symmetric association types else: raise ValueError(f"Unexpected facet query when building association counts: {k}") diff --git a/backend/src/monarch_py/utils/association_type_mappings.yaml b/backend/src/monarch_py/utils/association_type_mappings.yaml index 3697c422d..a72582d1c 100644 --- a/backend/src/monarch_py/utils/association_type_mappings.yaml +++ b/backend/src/monarch_py/utils/association_type_mappings.yaml @@ -1,15 +1,15 @@ - subject_label: Disease to Phenotype - object_label: Phenotype to Disease + object_label: Disease to Phenotype category: "biolink:DiseaseToPhenotypicFeatureAssociation" - subject_label: Gene to Phenotype - object_label: Phenotype to Gene + object_label: Gene to Phenotype category: "biolink:GeneToPhenotypicFeatureAssociation" - subject_label: Interactions object_label: Interactions symmetric: true category: "biolink:PairwiseGeneToGeneInteraction" - subject_label: Gene to Pathway - object_label: Pathway to Gene + object_label: Gene to Pathway category: "biolink:GeneToPathwayAssociation" - subject_label: Gene Expression object_label: Gene Expression @@ -19,22 +19,22 @@ symmetric: true category: "biolink:GeneToGeneHomologyAssociation" - subject_label: Chemical to Pathway - object_label: Pathway to Chemical + object_label: Chemical to Pathway category: "biolink:ChemicalToPathwayAssociation" - subject_label: Gene to Molecular Function - object_label: Molecular Function to Gene + object_label: Gene to Molecular Function category: "biolink:MacromolecularMachineToMolecularActivityAssociation" - subject_label: Gene to Cellular Component - object_label: Cellular Component to Gene + object_label: Gene to Cellular Component category: "biolink:MacromolecularMachineToCellularComponentAssociation" - subject_label: Gene to Biological Process - object_label: Biological Process to Gene + object_label: Gene to Biological Process category: "biolink:MacromolecularMachineToBiologicalProcessAssociation" -- subject_label: Causal Gene - object_label: Causal Disease +- subject_label: Causal Disease + object_label: Causal Gene category: "biolink:CausalGeneToDiseaseAssociation" -- subject_label: Correlated Gene - object_label: Correlated Disease +- subject_label: Correlated Disease + object_label: Correlated Gene category: "biolink:CorrelatedGeneToDiseaseAssociation" - subject_label: Variant to Gene object_label: Variant to Gene diff --git a/backend/tests/fixtures/association_counts.py b/backend/tests/fixtures/association_counts.py index 689aba5d0..a7cba13d9 100644 --- a/backend/tests/fixtures/association_counts.py +++ b/backend/tests/fixtures/association_counts.py @@ -6,7 +6,7 @@ def association_counts(): return { "items": [ { - "label": "Phenotype to Disease", + "label": "Disease to Phenotype", "count": 4115, "category": "biolink:DiseaseToPhenotypicFeatureAssociation", }, diff --git a/backend/tests/fixtures/association_counts_response.py b/backend/tests/fixtures/association_counts_response.py index d2b288345..a506c9e96 100644 --- a/backend/tests/fixtures/association_counts_response.py +++ b/backend/tests/fixtures/association_counts_response.py @@ -5,7 +5,7 @@ def association_counts_response(): return { "responseHeader": { - "QTime": 1, + "QTime": 0, "params": { "facet.query": [ '(category:"biolink:DiseaseToPhenotypicFeatureAssociation") AND (subject:"MONDO:0020121" OR subject_closure:"MONDO:0020121")', diff --git a/backend/tests/fixtures/node.py b/backend/tests/fixtures/node.py index bfcd8f87e..4e3d5a3b8 100644 --- a/backend/tests/fixtures/node.py +++ b/backend/tests/fixtures/node.py @@ -75,7 +75,7 @@ def node(): }, "association_counts": [ { - "label": "Phenotype to Disease", + "label": "Disease to Phenotype", "count": 4115, "category": "biolink:DiseaseToPhenotypicFeatureAssociation", }, diff --git a/backend/tests/fixtures/object_formatted.py b/backend/tests/fixtures/object_formatted.py index 1958b21b1..826b0e593 100644 --- a/backend/tests/fixtures/object_formatted.py +++ b/backend/tests/fixtures/object_formatted.py @@ -145,7 +145,7 @@ def node_json(): }, "association_counts": [ { - "label": "Phenotype to Disease", + "label": "Disease to Phenotype", "count": 4115, "category": "biolink:DiseaseToPhenotypicFeatureAssociation" }, @@ -514,7 +514,7 @@ def node_json(): def node_tsv(): return """ id category name full_name deprecated description xref provided_by in_taxon in_taxon_label symbol synonym uri iri namespace has_phenotype has_phenotype_label has_phenotype_closure has_phenotype_closure_label has_phenotype_count inheritance causal_gene causes_disease mappings external_links provided_by_link association_counts node_hierarchy -MONDO:0020121 biolink:Disease muscular dystrophy None None 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. ['DOID:9884', 'GARD:7922', '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'] phenio_nodes None None None None http://purl.obolibrary.org/obo/MONDO_0020121 None MONDO None None None None 0 None [] None [{'id': 'DOID:9884', 'url': 'http://purl.obolibrary.org/obo/DOID_9884'}, {'id': 'ICD10CM:G71.0', 'url': 'https://icd.codes/icd10cm/G71.0'}, {'id': 'MEDGEN:44527', 'url': 'http://identifiers.org/medgen/44527'}, {'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}, {'id': 'MESH:D009136', 'url': 'http://identifiers.org/mesh/D009136'}] [{'id': 'DOID:9884', 'url': 'http://purl.obolibrary.org/obo/DOID_9884'}, {'id': 'GARD:7922', 'url': 'https://rarediseases.info.nih.gov/diseases/7922/index'}, {'id': 'ICD10CM:G71.0', 'url': 'https://icd.codes/icd10cm/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}] {'id': 'phenio', 'url': 'https://monarch-initiative.github.io/monarch-ingest/Sources/phenio/#'} [{'label': 'Phenotype to Disease', 'count': 4115, 'category': 'biolink:DiseaseToPhenotypicFeatureAssociation'}, {'label': 'Causal Gene', 'count': 126, 'category': 'biolink:CausalGeneToDiseaseAssociation'}, {'label': 'Correlated Gene', 'count': 151, 'category': 'biolink:CorrelatedGeneToDiseaseAssociation'}, {'label': 'Variant to Disease', 'count': 1, 'category': 'biolink:VariantToDiseaseAssociation'}, {'label': 'Disease Model', 'count': 237, 'category': 'biolink:GenotypeToDiseaseAssociation'}] {'super_classes': [{'id': 'MONDO:0005336', 'category': 'biolink:Disease', 'name': 'myopathy', 'full_name': None, 'deprecated': None, 'description': None, 'xref': None, 'provided_by': None, 'in_taxon': None, 'in_taxon_label': None, 'symbol': None, 'synonym': None, 'uri': None, 'iri': None, 'namespace': None, 'has_phenotype': None, 'has_phenotype_label': None, 'has_phenotype_closure': None, 'has_phenotype_closure_label': None, 'has_phenotype_count': None}, {'id': 'MONDO:0100546', 'category': 'biolink:Disease', 'name': 'hereditary neuromuscular disease', 'full_name': None, 'deprecated': None, 'description': None, 'xref': None, 'provided_by': None, 'in_taxon': None, 'in_taxon_label': None, 'symbol': None, 'synonym': None, 'uri': None, 'iri': None, 'namespace': None, 'has_phenotype': None, 'has_phenotype_label': None, 'has_phenotype_closure': None, 'has_phenotype_closure_label': None, 'has_phenotype_count': None}, {'id': 'MONDO:0700223', 'category': 'biolink:Disease', 'name': 'hereditary skeletal muscle disorder', 'full_name': None, 'deprecated': None, 'description': None, 'xref': None, 'provided_by': None, 'in_taxon': None, 'in_taxon_label': None, 'symbol': None, 'synonym': None, 'uri': None, 'iri': None, 'namespace': None, 'has_phenotype': None, 'has_phenotype_label': None, 'has_phenotype_closure': None, 'has_phenotype_closure_label': None, 'has_phenotype_count': None}], 'sub_classes': [{'id': 'MONDO:0008028', 'category': 'biolink:Disease', 'name': 'muscular dystrophy, Barnes type', 'full_name': None, 'deprecated': None, 'description': None, 'xref': None, 'provided_by': None, 'in_taxon': None, 'in_taxon_label': None, 'symbol': None, 'synonym': None, 'uri': None, 'iri': None, 'namespace': None, 'has_phenotype': None, 'has_phenotype_label': None, 'has_phenotype_closure': None, 'has_phenotype_closure_label': None, 'has_phenotype_count': None}, {'id': 'MONDO:0010311', 'category': 'biolink:Disease', 'name': 'Becker muscular dystrophy', 'full_name': None, 'deprecated': None, 'description': None, 'xref': None, 'provided_by': None, 'in_taxon': None, 'in_taxon_label': None, 'symbol': None, 'synonym': None, 'uri': None, 'iri': None, 'namespace': None, 'has_phenotype': None, 'has_phenotype_label': None, 'has_phenotype_closure': None, 'has_phenotype_closure_label': None, 'has_phenotype_count': None}, {'id': 'MONDO:0010675', 'category': 'biolink:Disease', 'name': 'muscular dystrophy, cardiac type', 'full_name': None, 'deprecated': None, 'description': None, 'xref': None, 'provided_by': None, 'in_taxon': None, 'in_taxon_label': None, 'symbol': None, 'synonym': None, 'uri': None, 'iri': None, 'namespace': None, 'has_phenotype': None, 'has_phenotype_label': None, 'has_phenotype_closure': None, 'has_phenotype_closure_label': None, 'has_phenotype_count': None}, {'id': 'MONDO:0010676', 'category': 'biolink:Disease', 'name': 'muscular dystrophy, Hemizygous lethal type', 'full_name': None, 'deprecated': None, 'description': None, 'xref': None, 'provided_by': None, 'in_taxon': None, 'in_taxon_label': None, 'symbol': None, 'synonym': None, 'uri': None, 'iri': None, 'namespace': None, 'has_phenotype': None, 'has_phenotype_label': None, 'has_phenotype_closure': None, 'has_phenotype_closure_label': None, 'has_phenotype_count': None}, {'id': 'MONDO:0010677', 'category': 'biolink:Disease', 'name': 'muscular dystrophy, Mabry type', 'full_name': None, 'deprecated': None, 'description': None, 'xref': None, 'provided_by': None, 'in_taxon': None, 'in_taxon_label': None, 'symbol': None, 'synonym': None, 'uri': None, 'iri': None, 'namespace': None, 'has_phenotype': None, 'has_phenotype_label': None, 'has_phenotype_closure': None, 'has_phenotype_closure_label': None, 'has_phenotype_count': None}, {'id': 'MONDO:0010678', 'category': 'biolink:Disease', 'name': 'muscular dystrophy, progressive Pectorodorsal', 'full_name': None, 'deprecated': None, 'description': None, 'xref': None, 'provided_by': None, 'in_taxon': None, 'in_taxon_label': None, 'symbol': None, 'synonym': None, 'uri': None, 'iri': None, 'namespace': None, 'has_phenotype': None, 'has_phenotype_label': None, 'has_phenotype_closure': None, 'has_phenotype_closure_label': None, 'has_phenotype_count': None}, {'id': 'MONDO:0010679', 'category': 'biolink:Disease', 'name': 'Duchenne muscular dystrophy', 'full_name': None, 'deprecated': None, 'description': None, 'xref': None, 'provided_by': None, 'in_taxon': None, 'in_taxon_label': None, 'symbol': None, 'synonym': None, 'uri': None, 'iri': None, 'namespace': None, 'has_phenotype': None, 'has_phenotype_label': None, 'has_phenotype_closure': None, 'has_phenotype_closure_label': None, 'has_phenotype_count': None}, {'id': 'MONDO:0016106', 'category': 'biolink:Disease', 'name': 'progressive muscular dystrophy', 'full_name': None, 'deprecated': None, 'description': None, 'xref': None, 'provided_by': None, 'in_taxon': None, 'in_taxon_label': None, 'symbol': None, 'synonym': None, 'uri': None, 'iri': None, 'namespace': None, 'has_phenotype': None, 'has_phenotype_label': None, 'has_phenotype_closure': None, 'has_phenotype_closure_label': None, 'has_phenotype_count': None}, {'id': 'MONDO:0019950', 'category': 'biolink:Disease', 'name': 'congenital muscular dystrophy', 'full_name': None, 'deprecated': None, 'description': None, 'xref': None, 'provided_by': None, 'in_taxon': None, 'in_taxon_label': None, 'symbol': None, 'synonym': None, 'uri': None, 'iri': None, 'namespace': None, 'has_phenotype': None, 'has_phenotype_label': None, 'has_phenotype_closure': None, 'has_phenotype_closure_label': None, 'has_phenotype_count': None}, {'id': 'MONDO:0018949', 'category': 'biolink:Disease', 'name': 'distal myopathy', 'full_name': None, 'deprecated': None, 'description': None, 'xref': None, 'provided_by': None, 'in_taxon': None, 'in_taxon_label': None, 'symbol': None, 'synonym': None, 'uri': None, 'iri': None, 'namespace': None, 'has_phenotype': None, 'has_phenotype_label': None, 'has_phenotype_closure': None, 'has_phenotype_closure_label': None, 'has_phenotype_count': None}, {'id': 'MONDO:0023204', 'category': 'biolink:Disease', 'name': 'Fukuda-Miyanomae-Nakata syndrome', 'full_name': None, 'deprecated': None, 'description': None, 'xref': None, 'provided_by': None, 'in_taxon': None, 'in_taxon_label': None, 'symbol': None, 'synonym': None, 'uri': None, 'iri': None, 'namespace': None, 'has_phenotype': None, 'has_phenotype_label': None, 'has_phenotype_closure': None, 'has_phenotype_closure_label': None, 'has_phenotype_count': None}, {'id': 'MONDO:0100228', 'category': 'biolink:Disease', 'name': 'LAMA2-related muscular dystrophy', 'full_name': None, 'deprecated': None, 'description': None, 'xref': None, 'provided_by': None, 'in_taxon': None, 'in_taxon_label': None, 'symbol': None, 'synonym': None, 'uri': None, 'iri': None, 'namespace': None, 'has_phenotype': None, 'has_phenotype_label': None, 'has_phenotype_closure': None, 'has_phenotype_closure_label': None, 'has_phenotype_count': None}]} +MONDO:0020121 biolink:Disease muscular dystrophy None None 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. ['DOID:9884', 'GARD:7922', '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'] phenio_nodes None None None None http://purl.obolibrary.org/obo/MONDO_0020121 None MONDO None None None None 0 None [] None [{'id': 'DOID:9884', 'url': 'http://purl.obolibrary.org/obo/DOID_9884'}, {'id': 'ICD10CM:G71.0', 'url': 'https://icd.codes/icd10cm/G71.0'}, {'id': 'MEDGEN:44527', 'url': 'http://identifiers.org/medgen/44527'}, {'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}, {'id': 'MESH:D009136', 'url': 'http://identifiers.org/mesh/D009136'}] [{'id': 'DOID:9884', 'url': 'http://purl.obolibrary.org/obo/DOID_9884'}, {'id': 'GARD:7922', 'url': 'https://rarediseases.info.nih.gov/diseases/7922/index'}, {'id': 'ICD10CM:G71.0', 'url': 'https://icd.codes/icd10cm/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}] {'id': 'phenio', 'url': 'https://monarch-initiative.github.io/monarch-ingest/Sources/phenio/#'} [{'label': 'Disease to Phenotype', 'count': 4115, 'category': 'biolink:DiseaseToPhenotypicFeatureAssociation'}, {'label': 'Causal Gene', 'count': 126, 'category': 'biolink:CausalGeneToDiseaseAssociation'}, {'label': 'Correlated Gene', 'count': 151, 'category': 'biolink:CorrelatedGeneToDiseaseAssociation'}, {'label': 'Variant to Disease', 'count': 1, 'category': 'biolink:VariantToDiseaseAssociation'}, {'label': 'Disease Model', 'count': 237, 'category': 'biolink:GenotypeToDiseaseAssociation'}] {'super_classes': [{'id': 'MONDO:0005336', 'category': 'biolink:Disease', 'name': 'myopathy', 'full_name': None, 'deprecated': None, 'description': None, 'xref': None, 'provided_by': None, 'in_taxon': None, 'in_taxon_label': None, 'symbol': None, 'synonym': None, 'uri': None, 'iri': None, 'namespace': None, 'has_phenotype': None, 'has_phenotype_label': None, 'has_phenotype_closure': None, 'has_phenotype_closure_label': None, 'has_phenotype_count': None}, {'id': 'MONDO:0100546', 'category': 'biolink:Disease', 'name': 'hereditary neuromuscular disease', 'full_name': None, 'deprecated': None, 'description': None, 'xref': None, 'provided_by': None, 'in_taxon': None, 'in_taxon_label': None, 'symbol': None, 'synonym': None, 'uri': None, 'iri': None, 'namespace': None, 'has_phenotype': None, 'has_phenotype_label': None, 'has_phenotype_closure': None, 'has_phenotype_closure_label': None, 'has_phenotype_count': None}, {'id': 'MONDO:0700223', 'category': 'biolink:Disease', 'name': 'hereditary skeletal muscle disorder', 'full_name': None, 'deprecated': None, 'description': None, 'xref': None, 'provided_by': None, 'in_taxon': None, 'in_taxon_label': None, 'symbol': None, 'synonym': None, 'uri': None, 'iri': None, 'namespace': None, 'has_phenotype': None, 'has_phenotype_label': None, 'has_phenotype_closure': None, 'has_phenotype_closure_label': None, 'has_phenotype_count': None}], 'sub_classes': [{'id': 'MONDO:0008028', 'category': 'biolink:Disease', 'name': 'muscular dystrophy, Barnes type', 'full_name': None, 'deprecated': None, 'description': None, 'xref': None, 'provided_by': None, 'in_taxon': None, 'in_taxon_label': None, 'symbol': None, 'synonym': None, 'uri': None, 'iri': None, 'namespace': None, 'has_phenotype': None, 'has_phenotype_label': None, 'has_phenotype_closure': None, 'has_phenotype_closure_label': None, 'has_phenotype_count': None}, {'id': 'MONDO:0010311', 'category': 'biolink:Disease', 'name': 'Becker muscular dystrophy', 'full_name': None, 'deprecated': None, 'description': None, 'xref': None, 'provided_by': None, 'in_taxon': None, 'in_taxon_label': None, 'symbol': None, 'synonym': None, 'uri': None, 'iri': None, 'namespace': None, 'has_phenotype': None, 'has_phenotype_label': None, 'has_phenotype_closure': None, 'has_phenotype_closure_label': None, 'has_phenotype_count': None}, {'id': 'MONDO:0010675', 'category': 'biolink:Disease', 'name': 'muscular dystrophy, cardiac type', 'full_name': None, 'deprecated': None, 'description': None, 'xref': None, 'provided_by': None, 'in_taxon': None, 'in_taxon_label': None, 'symbol': None, 'synonym': None, 'uri': None, 'iri': None, 'namespace': None, 'has_phenotype': None, 'has_phenotype_label': None, 'has_phenotype_closure': None, 'has_phenotype_closure_label': None, 'has_phenotype_count': None}, {'id': 'MONDO:0010676', 'category': 'biolink:Disease', 'name': 'muscular dystrophy, Hemizygous lethal type', 'full_name': None, 'deprecated': None, 'description': None, 'xref': None, 'provided_by': None, 'in_taxon': None, 'in_taxon_label': None, 'symbol': None, 'synonym': None, 'uri': None, 'iri': None, 'namespace': None, 'has_phenotype': None, 'has_phenotype_label': None, 'has_phenotype_closure': None, 'has_phenotype_closure_label': None, 'has_phenotype_count': None}, {'id': 'MONDO:0010677', 'category': 'biolink:Disease', 'name': 'muscular dystrophy, Mabry type', 'full_name': None, 'deprecated': None, 'description': None, 'xref': None, 'provided_by': None, 'in_taxon': None, 'in_taxon_label': None, 'symbol': None, 'synonym': None, 'uri': None, 'iri': None, 'namespace': None, 'has_phenotype': None, 'has_phenotype_label': None, 'has_phenotype_closure': None, 'has_phenotype_closure_label': None, 'has_phenotype_count': None}, {'id': 'MONDO:0010678', 'category': 'biolink:Disease', 'name': 'muscular dystrophy, progressive Pectorodorsal', 'full_name': None, 'deprecated': None, 'description': None, 'xref': None, 'provided_by': None, 'in_taxon': None, 'in_taxon_label': None, 'symbol': None, 'synonym': None, 'uri': None, 'iri': None, 'namespace': None, 'has_phenotype': None, 'has_phenotype_label': None, 'has_phenotype_closure': None, 'has_phenotype_closure_label': None, 'has_phenotype_count': None}, {'id': 'MONDO:0010679', 'category': 'biolink:Disease', 'name': 'Duchenne muscular dystrophy', 'full_name': None, 'deprecated': None, 'description': None, 'xref': None, 'provided_by': None, 'in_taxon': None, 'in_taxon_label': None, 'symbol': None, 'synonym': None, 'uri': None, 'iri': None, 'namespace': None, 'has_phenotype': None, 'has_phenotype_label': None, 'has_phenotype_closure': None, 'has_phenotype_closure_label': None, 'has_phenotype_count': None}, {'id': 'MONDO:0016106', 'category': 'biolink:Disease', 'name': 'progressive muscular dystrophy', 'full_name': None, 'deprecated': None, 'description': None, 'xref': None, 'provided_by': None, 'in_taxon': None, 'in_taxon_label': None, 'symbol': None, 'synonym': None, 'uri': None, 'iri': None, 'namespace': None, 'has_phenotype': None, 'has_phenotype_label': None, 'has_phenotype_closure': None, 'has_phenotype_closure_label': None, 'has_phenotype_count': None}, {'id': 'MONDO:0019950', 'category': 'biolink:Disease', 'name': 'congenital muscular dystrophy', 'full_name': None, 'deprecated': None, 'description': None, 'xref': None, 'provided_by': None, 'in_taxon': None, 'in_taxon_label': None, 'symbol': None, 'synonym': None, 'uri': None, 'iri': None, 'namespace': None, 'has_phenotype': None, 'has_phenotype_label': None, 'has_phenotype_closure': None, 'has_phenotype_closure_label': None, 'has_phenotype_count': None}, {'id': 'MONDO:0018949', 'category': 'biolink:Disease', 'name': 'distal myopathy', 'full_name': None, 'deprecated': None, 'description': None, 'xref': None, 'provided_by': None, 'in_taxon': None, 'in_taxon_label': None, 'symbol': None, 'synonym': None, 'uri': None, 'iri': None, 'namespace': None, 'has_phenotype': None, 'has_phenotype_label': None, 'has_phenotype_closure': None, 'has_phenotype_closure_label': None, 'has_phenotype_count': None}, {'id': 'MONDO:0023204', 'category': 'biolink:Disease', 'name': 'Fukuda-Miyanomae-Nakata syndrome', 'full_name': None, 'deprecated': None, 'description': None, 'xref': None, 'provided_by': None, 'in_taxon': None, 'in_taxon_label': None, 'symbol': None, 'synonym': None, 'uri': None, 'iri': None, 'namespace': None, 'has_phenotype': None, 'has_phenotype_label': None, 'has_phenotype_closure': None, 'has_phenotype_closure_label': None, 'has_phenotype_count': None}, {'id': 'MONDO:0100228', 'category': 'biolink:Disease', 'name': 'LAMA2-related muscular dystrophy', 'full_name': None, 'deprecated': None, 'description': None, 'xref': None, 'provided_by': None, 'in_taxon': None, 'in_taxon_label': None, 'symbol': None, 'synonym': None, 'uri': None, 'iri': None, 'namespace': None, 'has_phenotype': None, 'has_phenotype_label': None, 'has_phenotype_closure': None, 'has_phenotype_closure_label': None, 'has_phenotype_count': None}]} """ @@ -524,7 +524,7 @@ def node_yaml(): association_counts: - category: biolink:DiseaseToPhenotypicFeatureAssociation count: 4115 - label: Phenotype to Disease + label: Disease to Phenotype - category: biolink:CausalGeneToDiseaseAssociation count: 126 label: Causal Gene diff --git a/backend/tests/fixtures/search_response.py b/backend/tests/fixtures/search_response.py index 6703604fa..285dcfa8f 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": 0, "params": { "mm": "100%", "q": "fanconi", diff --git a/backend/tests/integration/test_solr_search.py b/backend/tests/integration/test_solr_search.py index 2b5003d4e..3a8435c56 100644 --- a/backend/tests/integration/test_solr_search.py +++ b/backend/tests/integration/test_solr_search.py @@ -114,7 +114,7 @@ def test_association_counts_for_disease(): disease_phenotype = [ ac for ac in association_counts.items if ac.category == "biolink:DiseaseToPhenotypicFeatureAssociation" ][0] - assert disease_phenotype.label == "Phenotype to Disease" + assert disease_phenotype.label == "Disease to Phenotype" def test_association_counts_for_eds(): diff --git a/frontend/fixtures/association-counts.json b/frontend/fixtures/association-counts.json index 3428f6a85..4afc85909 100644 --- a/frontend/fixtures/association-counts.json +++ b/frontend/fixtures/association-counts.json @@ -1,7 +1,7 @@ { "items": [ { - "label": "Phenotype to Disease", + "label": "Disease to Phenotype", "count": 4115, "category": "biolink:DiseaseToPhenotypicFeatureAssociation" }, diff --git a/frontend/fixtures/node.json b/frontend/fixtures/node.json index 1199f4322..6651cddd1 100644 --- a/frontend/fixtures/node.json +++ b/frontend/fixtures/node.json @@ -139,7 +139,7 @@ }, "association_counts": [ { - "label": "Phenotype to Disease", + "label": "Disease to Phenotype", "count": 4115, "category": "biolink:DiseaseToPhenotypicFeatureAssociation" }, diff --git a/frontend/fixtures/phenotype-explorer-compare.json b/frontend/fixtures/phenotype-explorer-compare.json index 2e550f8db..1b8f5d773 100644 --- a/frontend/fixtures/phenotype-explorer-compare.json +++ b/frontend/fixtures/phenotype-explorer-compare.json @@ -1,12 +1,12 @@ { "subject_termset": { - "MP:0010771": { - "id": "MP:0010771", - "label": "integument phenotype" - }, "MP:0002169": { "id": "MP:0002169", "label": "no abnormal phenotype detected" + }, + "MP:0010771": { + "id": "MP:0010771", + "label": "integument phenotype" } }, "object_termset": { diff --git a/frontend/fixtures/phenotype-explorer-multi-compare.json b/frontend/fixtures/phenotype-explorer-multi-compare.json index 14ef49949..5b315f4d4 100644 --- a/frontend/fixtures/phenotype-explorer-multi-compare.json +++ b/frontend/fixtures/phenotype-explorer-multi-compare.json @@ -25,51 +25,54 @@ "score": 8.60883472685004, "similarity": { "subject_termset": { - "HP:0012450": { "id": "HP:0012450", "label": "Chronic constipation" }, - "HP:0002616": { "id": "HP:0002616", "label": "Aortic root aneurysm" }, + "HP:0002020": { + "id": "HP:0002020", + "label": "Gastroesophageal reflux" + }, "HP:0001533": { "id": "HP:0001533", "label": "Slender build" }, + "HP:0010749": { "id": "HP:0010749", "label": "Blepharochalasis" }, "HP:0004944": { "id": "HP:0004944", "label": "Dilatation of the cerebral artery" }, "HP:0001763": { "id": "HP:0001763", "label": "Pes planus" }, - "HP:0010749": { "id": "HP:0010749", "label": "Blepharochalasis" }, - "HP:0002020": { "id": "HP:0002020", "label": "Gastroesophageal reflux" } + "HP:0002616": { "id": "HP:0002616", "label": "Aortic root aneurysm" }, + "HP:0012450": { "id": "HP:0012450", "label": "Chronic constipation" } }, "object_termset": { "MP:0001262": { "id": "MP:0001262", "label": "decreased body weight" }, + "MP:0011960": { + "id": "MP:0011960", + "label": "abnormal eye anterior chamber depth" + }, + "MP:0011965": { + "id": "MP:0011965", + "label": "decreased total retina thickness" + }, "MP:0002834": { "id": "MP:0002834", "label": "decreased heart weight" }, "MP:0008489": { "id": "MP:0008489", "label": "slow postnatal weight gain" }, + "MP:0003731": { + "id": "MP:0003731", + "label": "abnormal retina outer nuclear layer morphology" + }, "MP:0003291": { "id": "MP:0003291", "label": "interstinal hyperperistalsis" }, - "MP:0011960": { - "id": "MP:0011960", - "label": "abnormal eye anterior chamber depth" - }, "MP:0011962": { "id": "MP:0011962", "label": "increased cornea thickness" - }, - "MP:0011965": { - "id": "MP:0011965", - "label": "decreased total retina thickness" - }, - "MP:0003731": { - "id": "MP:0003731", - "label": "abnormal retina outer nuclear layer morphology" } }, "subject_best_matches": { "HP:0001533": { "match_source": "HP:0001533", "match_source_label": "Slender build", - "match_target": "MP:0001262", - "match_target_label": "decreased body weight", + "match_target": "MP:0008489", + "match_target_label": "slow postnatal weight gain", "score": 13.667892510789482, "match_subsumer": null, "match_subsumer_label": null, @@ -77,27 +80,27 @@ "subject_id": "HP:0001533", "subject_label": null, "subject_source": null, - "object_id": "MP:0001262", + "object_id": "MP:0008489", "object_label": null, "object_source": null, - "ancestor_id": "UPHENO:0082794", - "ancestor_label": "Decreased multicellular organism mass", + "ancestor_id": "UPHENO:0054299", + "ancestor_label": "decreased multicellular organism mass", "ancestor_source": null, "object_information_content": null, "subject_information_content": null, "ancestor_information_content": 13.667892510789482, - "jaccard_similarity": 0.40384615384615385, + "jaccard_similarity": 0.38333333333333336, "cosine_similarity": null, "dice_similarity": null, - "phenodigm_score": 2.34940967514501 + "phenodigm_score": 2.2889645684900053 }, "score_metric": "ancestor_information_content" }, "HP:0001763": { "match_source": "HP:0001763", "match_source_label": "Pes planus", - "match_target": "MP:0011962", - "match_target_label": "increased cornea thickness", + "match_target": "MP:0002834", + "match_target_label": "decreased heart weight", "score": 3.066606173373863, "match_subsumer": null, "match_subsumer_label": null, @@ -105,7 +108,7 @@ "subject_id": "HP:0001763", "subject_label": null, "subject_source": null, - "object_id": "MP:0011962", + "object_id": "MP:0002834", "object_label": null, "object_source": null, "ancestor_id": "UPHENO:0015280", @@ -114,10 +117,10 @@ "object_information_content": null, "subject_information_content": null, "ancestor_information_content": 3.066606173373863, - "jaccard_similarity": 0.16049382716049382, + "jaccard_similarity": 0.203125, "cosine_similarity": null, "dice_similarity": null, - "phenodigm_score": 0.7015492578278222 + "phenodigm_score": 0.7892429150563 }, "score_metric": "ancestor_information_content" }, @@ -208,8 +211,8 @@ "HP:0010749": { "match_source": "HP:0010749", "match_source_label": "Blepharochalasis", - "match_target": "MP:0011960", - "match_target_label": "abnormal eye anterior chamber depth", + "match_target": "MP:0003731", + "match_target_label": "abnormal retina outer nuclear layer morphology", "score": 6.6792078240173165, "match_subsumer": null, "match_subsumer_label": null, @@ -217,7 +220,7 @@ "subject_id": "HP:0010749", "subject_label": null, "subject_source": null, - "object_id": "MP:0011960", + "object_id": "MP:0003731", "object_label": null, "object_source": null, "ancestor_id": "UPHENO:0087924", @@ -226,10 +229,10 @@ "object_information_content": null, "subject_information_content": null, "ancestor_information_content": 6.6792078240173165, - "jaccard_similarity": 0.26865671641791045, + "jaccard_similarity": 0.23076923076923078, "cosine_similarity": null, "dice_similarity": null, - "phenodigm_score": 1.3395574053669028 + "phenodigm_score": 1.2415134520802842 }, "score_metric": "ancestor_information_content" }, @@ -322,8 +325,8 @@ "MP:0003291": { "match_source": "MP:0003291", "match_source_label": "interstinal hyperperistalsis", - "match_target": "HP:0002020", - "match_target_label": "Gastroesophageal reflux", + "match_target": "HP:0012450", + "match_target_label": "Chronic constipation", "score": 9.97713534604573, "match_subsumer": null, "match_subsumer_label": null, @@ -331,7 +334,7 @@ "subject_id": "MP:0003291", "subject_label": null, "subject_source": null, - "object_id": "HP:0002020", + "object_id": "HP:0012450", "object_label": null, "object_source": null, "ancestor_id": "UPHENO:0002443", @@ -340,10 +343,10 @@ "object_information_content": null, "subject_information_content": null, "ancestor_information_content": 9.97713534604573, - "jaccard_similarity": 0.3684210526315789, + "jaccard_similarity": 0.4117647058823529, "cosine_similarity": null, "dice_similarity": null, - "phenodigm_score": 1.9172341292700534 + "phenodigm_score": 2.026877450985369 }, "score_metric": "ancestor_information_content" }, @@ -390,8 +393,8 @@ "object_id": "HP:0001533", "object_label": null, "object_source": null, - "ancestor_id": "UPHENO:0082794", - "ancestor_label": "Decreased multicellular organism mass", + "ancestor_id": "UPHENO:0054299", + "ancestor_label": "decreased multicellular organism mass", "ancestor_source": null, "object_information_content": null, "subject_information_content": null, @@ -519,54 +522,57 @@ "score": 7.343905449061465, "similarity": { "subject_termset": { + "HP:0002020": { + "id": "HP:0002020", + "label": "Gastroesophageal reflux" + }, "HP:0010749": { "id": "HP:0010749", "label": "Blepharochalasis" }, - "HP:0002616": { "id": "HP:0002616", "label": "Aortic root aneurysm" }, + "HP:0001533": { "id": "HP:0001533", "label": "Slender build" }, "HP:0012450": { "id": "HP:0012450", "label": "Chronic constipation" }, - "HP:0001763": { "id": "HP:0001763", "label": "Pes planus" }, "HP:0004944": { "id": "HP:0004944", "label": "Dilatation of the cerebral artery" }, - "HP:0001533": { "id": "HP:0001533", "label": "Slender build" }, - "HP:0002020": { "id": "HP:0002020", "label": "Gastroesophageal reflux" } + "HP:0001763": { "id": "HP:0001763", "label": "Pes planus" }, + "HP:0002616": { "id": "HP:0002616", "label": "Aortic root aneurysm" } }, "object_termset": { + "MP:0006264": { + "id": "MP:0006264", + "label": "decreased systemic arterial systolic blood pressure" + }, + "MP:0000230": { + "id": "MP:0000230", + "label": "abnormal systemic arterial blood pressure" + }, "MP:0004022": { "id": "MP:0004022", "label": "abnormal cone electrophysiology" }, - "MP:0000233": { - "id": "MP:0000233", - "label": "abnormal blood flow velocity" - }, - "MP:0000272": { - "id": "MP:0000272", - "label": "abnormal aorta morphology" + "MP:0002834": { "id": "MP:0002834", "label": "decreased heart weight" }, + "MP:0003070": { + "id": "MP:0003070", + "label": "increased vascular permeability" }, "MP:0003026": { "id": "MP:0003026", "label": "decreased vasoconstriction" }, - "MP:0006264": { - "id": "MP:0006264", - "label": "decreased systemic arterial systolic blood pressure" + "MP:0009862": { + "id": "MP:0009862", + "label": "abnormal aorta elastic tissue morphology" }, "MP:0004021": { "id": "MP:0004021", "label": "abnormal rod electrophysiology" }, - "MP:0003070": { - "id": "MP:0003070", - "label": "increased vascular permeability" - }, - "MP:0002834": { "id": "MP:0002834", "label": "decreased heart weight" }, - "MP:0000230": { - "id": "MP:0000230", - "label": "abnormal systemic arterial blood pressure" + "MP:0000272": { + "id": "MP:0000272", + "label": "abnormal aorta morphology" }, - "MP:0009862": { - "id": "MP:0009862", - "label": "abnormal aorta elastic tissue morphology" + "MP:0000233": { + "id": "MP:0000233", + "label": "abnormal blood flow velocity" } }, "subject_best_matches": { @@ -629,8 +635,8 @@ "HP:0002020": { "match_source": "HP:0002020", "match_source_label": "Gastroesophageal reflux", - "match_target": "MP:0004022", - "match_target_label": "abnormal cone electrophysiology", + "match_target": "MP:0000230", + "match_target_label": "abnormal systemic arterial blood pressure", "score": 5.132448071645384, "match_subsumer": null, "match_subsumer_label": null, @@ -638,7 +644,7 @@ "subject_id": "HP:0002020", "subject_label": null, "subject_source": null, - "object_id": "MP:0004022", + "object_id": "MP:0000230", "object_label": null, "object_source": null, "ancestor_id": "UPHENO:0002332", @@ -647,10 +653,10 @@ "object_information_content": null, "subject_information_content": null, "ancestor_information_content": 5.132448071645384, - "jaccard_similarity": 0.32432432432432434, + "jaccard_similarity": 0.35294117647058826, "cosine_similarity": null, "dice_similarity": null, - "phenodigm_score": 1.2901851622794578 + "phenodigm_score": 1.3459020248817237 }, "score_metric": "ancestor_information_content" }, @@ -741,8 +747,8 @@ "HP:0012450": { "match_source": "HP:0012450", "match_source_label": "Chronic constipation", - "match_target": "MP:0004022", - "match_target_label": "abnormal cone electrophysiology", + "match_target": "MP:0004021", + "match_target_label": "abnormal rod electrophysiology", "score": 5.132448071645384, "match_subsumer": null, "match_subsumer_label": null, @@ -750,7 +756,7 @@ "subject_id": "HP:0012450", "subject_label": null, "subject_source": null, - "object_id": "MP:0004022", + "object_id": "MP:0004021", "object_label": null, "object_source": null, "ancestor_id": "UPHENO:0002332", @@ -771,8 +777,8 @@ "MP:0000230": { "match_source": "MP:0000230", "match_source_label": "abnormal systemic arterial blood pressure", - "match_target": "HP:0002616", - "match_target_label": "Aortic root aneurysm", + "match_target": "HP:0004944", + "match_target_label": "Dilatation of the cerebral artery", "score": 7.3467487024345575, "match_subsumer": null, "match_subsumer_label": null, @@ -780,7 +786,7 @@ "subject_id": "MP:0000230", "subject_label": null, "subject_source": null, - "object_id": "HP:0002616", + "object_id": "HP:0004944", "object_label": null, "object_source": null, "ancestor_id": "UPHENO:0080362", @@ -789,18 +795,18 @@ "object_information_content": null, "subject_information_content": null, "ancestor_information_content": 7.3467487024345575, - "jaccard_similarity": 0.2558139534883721, + "jaccard_similarity": 0.19642857142857142, "cosine_similarity": null, "dice_similarity": null, - "phenodigm_score": 1.3709124081630277 + "phenodigm_score": 1.2012956972635551 }, "score_metric": "ancestor_information_content" }, "MP:0000233": { "match_source": "MP:0000233", "match_source_label": "abnormal blood flow velocity", - "match_target": "HP:0004944", - "match_target_label": "Dilatation of the cerebral artery", + "match_target": "HP:0002616", + "match_target_label": "Aortic root aneurysm", "score": 7.3467487024345575, "match_subsumer": null, "match_subsumer_label": null, @@ -808,7 +814,7 @@ "subject_id": "MP:0000233", "subject_label": null, "subject_source": null, - "object_id": "HP:0004944", + "object_id": "HP:0002616", "object_label": null, "object_source": null, "ancestor_id": "UPHENO:0080362", @@ -817,10 +823,10 @@ "object_information_content": null, "subject_information_content": null, "ancestor_information_content": 7.3467487024345575, - "jaccard_similarity": 0.18333333333333332, + "jaccard_similarity": 0.23404255319148937, "cosine_similarity": null, "dice_similarity": null, - "phenodigm_score": 1.160561902174834 + "phenodigm_score": 1.311278698055469 }, "score_metric": "ancestor_information_content" }, diff --git a/frontend/fixtures/phenotype-explorer-search.json b/frontend/fixtures/phenotype-explorer-search.json index 391b75f5a..de8b0faff 100644 --- a/frontend/fixtures/phenotype-explorer-search.json +++ b/frontend/fixtures/phenotype-explorer-search.json @@ -100,8 +100,8 @@ } }, "object_termset": { - "HP:0012378": { "id": "HP:0012378", "label": "Fatigue" }, - "HP:0002104": { "id": "HP:0002104", "label": "Apnea" } + "HP:0002104": { "id": "HP:0002104", "label": "Apnea" }, + "HP:0012378": { "id": "HP:0012378", "label": "Fatigue" } }, "subject_best_matches": { "ZP:0018569": { @@ -318,8 +318,8 @@ } }, "object_termset": { - "HP:0002104": { "id": "HP:0002104", "label": "Apnea" }, - "HP:0012378": { "id": "HP:0012378", "label": "Fatigue" } + "HP:0012378": { "id": "HP:0012378", "label": "Fatigue" }, + "HP:0002104": { "id": "HP:0002104", "label": "Apnea" } }, "subject_best_matches": { "ZP:0018568": { @@ -383,8 +383,8 @@ "HP:0002104": { "match_source": "HP:0002104", "match_source_label": "Apnea", - "match_target": "ZP:0018568", - "match_target_label": "primitive hemopoiesis absent, abnormal", + "match_target": "ZP:0018569", + "match_target_label": "myeloid cell development absent, abnormal", "score": 8.79057503056431, "match_subsumer": null, "match_subsumer_label": null, @@ -392,7 +392,7 @@ "subject_id": "HP:0002104", "subject_label": null, "subject_source": null, - "object_id": "ZP:0018568", + "object_id": "ZP:0018569", "object_label": null, "object_source": null, "ancestor_id": "UPHENO:0034024", @@ -552,13 +552,13 @@ "score": 7.011754466426716, "similarity": { "subject_termset": { - "ZP:0018568": { - "id": "ZP:0018568", - "label": "primitive hemopoiesis absent, abnormal" - }, "ZP:0018569": { "id": "ZP:0018569", "label": "myeloid cell development absent, abnormal" + }, + "ZP:0018568": { + "id": "ZP:0018568", + "label": "primitive hemopoiesis absent, abnormal" } }, "object_termset": { @@ -627,8 +627,8 @@ "HP:0002104": { "match_source": "HP:0002104", "match_source_label": "Apnea", - "match_target": "ZP:0018568", - "match_target_label": "primitive hemopoiesis absent, abnormal", + "match_target": "ZP:0018569", + "match_target_label": "myeloid cell development absent, abnormal", "score": 8.79057503056431, "match_subsumer": null, "match_subsumer_label": null, @@ -636,7 +636,7 @@ "subject_id": "HP:0002104", "subject_label": null, "subject_source": null, - "object_id": "ZP:0018568", + "object_id": "ZP:0018569", "object_label": null, "object_source": null, "ancestor_id": "UPHENO:0034024", @@ -655,8 +655,8 @@ "HP:0012378": { "match_source": "HP:0012378", "match_source_label": "Fatigue", - "match_target": "ZP:0018568", - "match_target_label": "primitive hemopoiesis absent, abnormal", + "match_target": "ZP:0018569", + "match_target_label": "myeloid cell development absent, abnormal", "score": 1.6752927740139332, "match_subsumer": null, "match_subsumer_label": null, @@ -664,7 +664,7 @@ "subject_id": "HP:0012378", "subject_label": null, "subject_source": null, - "object_id": "ZP:0018568", + "object_id": "ZP:0018569", "object_label": null, "object_source": null, "ancestor_id": "UPHENO:0001005", @@ -813,8 +813,8 @@ } }, "object_termset": { - "HP:0012378": { "id": "HP:0012378", "label": "Fatigue" }, - "HP:0002104": { "id": "HP:0002104", "label": "Apnea" } + "HP:0002104": { "id": "HP:0002104", "label": "Apnea" }, + "HP:0012378": { "id": "HP:0012378", "label": "Fatigue" } }, "subject_best_matches": { "ZP:0018568": { @@ -1054,13 +1054,13 @@ "score": 7.011754466426716, "similarity": { "subject_termset": { - "ZP:0018568": { - "id": "ZP:0018568", - "label": "primitive hemopoiesis absent, abnormal" - }, "ZP:0018569": { "id": "ZP:0018569", "label": "myeloid cell development absent, abnormal" + }, + "ZP:0018568": { + "id": "ZP:0018568", + "label": "primitive hemopoiesis absent, abnormal" } }, "object_termset": { @@ -1157,8 +1157,8 @@ "HP:0012378": { "match_source": "HP:0012378", "match_source_label": "Fatigue", - "match_target": "ZP:0018568", - "match_target_label": "primitive hemopoiesis absent, abnormal", + "match_target": "ZP:0018569", + "match_target_label": "myeloid cell development absent, abnormal", "score": 1.6752927740139332, "match_subsumer": null, "match_subsumer_label": null, @@ -1166,7 +1166,7 @@ "subject_id": "HP:0012378", "subject_label": null, "subject_source": null, - "object_id": "ZP:0018568", + "object_id": "ZP:0018569", "object_label": null, "object_source": null, "ancestor_id": "UPHENO:0001005", @@ -1296,13 +1296,13 @@ "score": 5.262083911717577, "similarity": { "subject_termset": { - "ZP:0000945": { - "id": "ZP:0000945", - "label": "pigment cell quality, abnormal" - }, "ZP:0100294": { "id": "ZP:0100294", "label": "visual perception absent, abnormal" + }, + "ZP:0000945": { + "id": "ZP:0000945", + "label": "pigment cell quality, abnormal" } }, "object_termset": { @@ -1518,13 +1518,13 @@ "score": 5.232933902289122, "similarity": { "subject_termset": { - "ZP:0015039": { - "id": "ZP:0015039", - "label": "visual behavior absent, abnormal" - }, "ZP:0001841": { "id": "ZP:0001841", "label": "visual behavior quality, abnormal" + }, + "ZP:0015039": { + "id": "ZP:0015039", + "label": "visual behavior absent, abnormal" } }, "object_termset": { @@ -1621,8 +1621,8 @@ "HP:0012378": { "match_source": "HP:0012378", "match_source_label": "Fatigue", - "match_target": "ZP:0001841", - "match_target_label": "visual behavior quality, abnormal", + "match_target": "ZP:0015039", + "match_target_label": "visual behavior absent, abnormal", "score": 1.6752927740139332, "match_subsumer": null, "match_subsumer_label": null, @@ -1630,7 +1630,7 @@ "subject_id": "HP:0012378", "subject_label": null, "subject_source": null, - "object_id": "ZP:0001841", + "object_id": "ZP:0015039", "object_label": null, "object_source": null, "ancestor_id": "UPHENO:0001005", @@ -1639,10 +1639,10 @@ "object_information_content": null, "subject_information_content": null, "ancestor_information_content": 1.6752927740139332, - "jaccard_similarity": 0.47058823529411764, + "jaccard_similarity": 0.38095238095238093, "cosine_similarity": null, "dice_similarity": null, - "phenodigm_score": 0.8879037504843663 + "phenodigm_score": 0.7988784457305923 }, "score_metric": "ancestor_information_content" } @@ -2013,8 +2013,8 @@ } }, "object_termset": { - "HP:0012378": { "id": "HP:0012378", "label": "Fatigue" }, - "HP:0002104": { "id": "HP:0002104", "label": "Apnea" } + "HP:0002104": { "id": "HP:0002104", "label": "Apnea" }, + "HP:0012378": { "id": "HP:0012378", "label": "Fatigue" } }, "subject_best_matches": { "ZP:0001432": {