From 79ff82bebec78ca6c34eb1299d01c50f72e8608d Mon Sep 17 00:00:00 2001 From: Kevin Schaper Date: Tue, 4 Jun 2024 10:44:55 -0700 Subject: [PATCH] Show association selection as association category (#733) Change up association table category count outputs to be based on the association category, rather than counterpart category. This can potentially be simplified by just generating labels from the association categories, but for now this PR is going to make a smaller change. Downstream, the UI needs a minor shift in the "sentence" structure of the association table heading/controls. --- .../implementations/solr/solr_query_utils.py | 14 +- .../utils/association_type_mappings.yaml | 40 ++--- backend/tests/fixtures/association_counts.py | 10 +- .../fixtures/association_counts_query.py | 2 +- .../fixtures/association_counts_response.py | 4 +- .../fixtures/association_query_direct.py | 2 +- .../fixtures/association_query_indirect.py | 2 +- .../tests/fixtures/association_response.py | 2 +- .../fixtures/association_table_response.py | 4 +- .../tests/fixtures/autocomplete_response.py | 2 +- backend/tests/fixtures/node.py | 10 +- backend/tests/fixtures/object_formatted.py | 14 +- backend/tests/fixtures/search_response.py | 2 +- backend/tests/integration/test_solr_search.py | 8 +- backend/tests/unit/test_solr_queries.py | 2 +- frontend/fixtures/association-counts.json | 6 +- frontend/fixtures/node.json | 6 +- .../phenotype-explorer-multi-compare.json | 148 +++++++++--------- .../fixtures/phenotype-explorer-search.json | 94 +++++------ .../src/pages/node/SectionAssociations.vue | 7 +- frontend/src/pages/node/SectionOverview.vue | 2 +- 21 files changed, 190 insertions(+), 191 deletions(-) diff --git a/backend/src/monarch_py/implementations/solr/solr_query_utils.py b/backend/src/monarch_py/implementations/solr/solr_query_utils.py index d48281d01..690a84ab6 100644 --- a/backend/src/monarch_py/implementations/solr/solr_query_utils.py +++ b/backend/src/monarch_py/implementations/solr/solr_query_utils.py @@ -52,14 +52,11 @@ def build_association_query( query.add_filter_query(" OR ".join([f'object:"{o}" OR object_closure:"{o}"' for o in object])) if entity: if direct: - query.add_filter_query(" OR ".join([f'subject:"{escape(e)}" OR object:"{escape(e)}"' for e in entity])) + query.add_filter_query(" OR ".join([f'subject:"{e}" OR object:"{e}"' for e in entity])) else: query.add_filter_query( " OR ".join( - [ - f'subject:"{escape(e)}" OR subject_closure:"{escape(e)}" OR object:"{escape(e)}" OR object_closure:"{escape(e)}"' - for e in entity - ] + [f'subject:"{e}" OR subject_closure:"{e}" OR object:"{e}" OR object_closure:"{e}"' for e in entity] ) ) if q: @@ -91,12 +88,7 @@ def build_association_table_query( ] query = build_association_query( - entity=entity, - category=[category], - q=q, - sort=sort, - offset=offset, - limit=limit, + entity=entity, category=[category], q=q, sort=sort, offset=offset, limit=limit, direct=False ) return query diff --git a/backend/src/monarch_py/utils/association_type_mappings.yaml b/backend/src/monarch_py/utils/association_type_mappings.yaml index 2382da8ae..65e445fc2 100644 --- a/backend/src/monarch_py/utils/association_type_mappings.yaml +++ b/backend/src/monarch_py/utils/association_type_mappings.yaml @@ -1,38 +1,38 @@ -- subject_label: Diseases - object_label: Phenotypes +- subject_label: Disease to Phenotype + object_label: Phenotype to Disease category: "biolink:DiseaseToPhenotypicFeatureAssociation" -- subject_label: Genes - object_label: Phenotypes +- subject_label: Gene to Phenotype + object_label: Phenotype to Gene category: "biolink:GeneToPhenotypicFeatureAssociation" - subject_label: Interactions object_label: Interactions symmetric: true category: "biolink:PairwiseGeneToGeneInteraction" -- subject_label: Genes - object_label: Pathways +- subject_label: Gene to Pathway + object_label: Pathway to Gene category: "biolink:GeneToPathwayAssociation" -- subject_label: Genes - object_label: Anatomy +- subject_label: Gene Expression + object_label: Gene Expression category: "biolink:GeneToExpressionSiteAssociation" - subject_label: Orthologs object_label: Orthologs symmetric: true category: "biolink:GeneToGeneHomologyAssociation" -- subject_label: Chemicals - object_label: Pathways +- subject_label: Chemical to Pathway + object_label: Pathway to Chemical category: "biolink:ChemicalToPathwayAssociation" -- subject_label: Genes - object_label: Molecular Functions +- subject_label: Gene to Molecular Function + object_label: Molecular Function to Gene category: "biolink:MacromolecularMachineToMolecularActivityAssociation" -- subject_label: Genes - object_label: Cellular Components +- subject_label: Gene to Cellular Component + object_label: Cellular Component to Gene category: "biolink:MacromolecularMachineToCellularComponentAssociation" -- subject_label: Genes - object_label: Biological Processes +- subject_label: Gene to Biological Process + object_label: Biological Process to Gene category: "biolink:MacromolecularMachineToBiologicalProcessAssociation" -- subject_label: Causal Genes - object_label: Causal Diseases +- subject_label: Causal Gene + object_label: Causal Disease category: "biolink:CausalGeneToDiseaseAssociation" -- subject_label: "Correlated Genes" - object_label: "Correlated Diseases" +- subject_label: Correlated Gene + object_label: Correlated Disease category: "biolink:CorrelatedGeneToDiseaseAssociation" diff --git a/backend/tests/fixtures/association_counts.py b/backend/tests/fixtures/association_counts.py index 1f95df1b2..2f72b0d00 100644 --- a/backend/tests/fixtures/association_counts.py +++ b/backend/tests/fixtures/association_counts.py @@ -5,8 +5,12 @@ def association_counts(): return { "items": [ - {"label": "Phenotypes", "count": 3932, "category": "biolink:DiseaseToPhenotypicFeatureAssociation"}, - {"label": "Causal Genes", "count": 126, "category": "biolink:CausalGeneToDiseaseAssociation"}, - {"label": "Correlated Genes", "count": 146, "category": "biolink:CorrelatedGeneToDiseaseAssociation"}, + { + "label": "Phenotype to Disease", + "count": 3932, + "category": "biolink:DiseaseToPhenotypicFeatureAssociation", + }, + {"label": "Causal Gene", "count": 126, "category": "biolink:CausalGeneToDiseaseAssociation"}, + {"label": "Correlated Gene", "count": 146, "category": "biolink:CorrelatedGeneToDiseaseAssociation"}, ] } diff --git a/backend/tests/fixtures/association_counts_query.py b/backend/tests/fixtures/association_counts_query.py index 95cf33cb8..39ceb7dc9 100644 --- a/backend/tests/fixtures/association_counts_query.py +++ b/backend/tests/fixtures/association_counts_query.py @@ -37,7 +37,7 @@ def association_counts_query(): '(category:"biolink:CorrelatedGeneToDiseaseAssociation") AND (object:"MONDO:0020121" OR object_closure:"MONDO:0020121")', ], "filter_queries": [ - 'subject:"MONDO\\:0020121" OR subject_closure:"MONDO\\:0020121" OR object:"MONDO\\:0020121" OR object_closure:"MONDO\\:0020121"' + 'subject:"MONDO:0020121" OR subject_closure:"MONDO:0020121" OR object:"MONDO:0020121" OR object_closure:"MONDO:0020121"' ], "query_fields": None, "def_type": "edismax", diff --git a/backend/tests/fixtures/association_counts_response.py b/backend/tests/fixtures/association_counts_response.py index 6b73281c7..33331f445 100644 --- a/backend/tests/fixtures/association_counts_response.py +++ b/backend/tests/fixtures/association_counts_response.py @@ -5,7 +5,7 @@ def association_counts_response(): return { "responseHeader": { - "QTime": 2, + "QTime": 1, "params": { "facet.query": [ '(category:"biolink:DiseaseToPhenotypicFeatureAssociation") AND (subject:"MONDO:0020121" OR subject_closure:"MONDO:0020121")', @@ -39,7 +39,7 @@ def association_counts_response(): "facet_min_count": "1", "start": "0", "q.op": "AND", - "fq": 'subject:"MONDO\\:0020121" OR subject_closure:"MONDO\\:0020121" OR object:"MONDO\\:0020121" OR object_closure:"MONDO\\:0020121"', + "fq": 'subject:"MONDO:0020121" OR subject_closure:"MONDO:0020121" OR object:"MONDO:0020121" OR object_closure:"MONDO:0020121"', "rows": "20", "facet": "true", }, diff --git a/backend/tests/fixtures/association_query_direct.py b/backend/tests/fixtures/association_query_direct.py index b63e0a81d..d02137c71 100644 --- a/backend/tests/fixtures/association_query_direct.py +++ b/backend/tests/fixtures/association_query_direct.py @@ -24,7 +24,7 @@ def association_query_direct(): "object_taxon:NCBITaxon\\:2222", "subject:TEST\\:0000001", "object:TEST\\:0000002", - 'subject:"TEST\\:0000005" OR object:"TEST\\:0000005"', + 'subject:"TEST:0000005" OR object:"TEST:0000005"', ], "query_fields": "subject subject_label^2 subject_label_t subject_closure subject_closure_label subject_closure_label_t predicate predicate_t object object_label^2 object_label_t object_closure object_closure_label object_closure_label_t publications has_evidence primary_knowledge_source aggregator_knowledge_source provided_by ", "def_type": "edismax", diff --git a/backend/tests/fixtures/association_query_indirect.py b/backend/tests/fixtures/association_query_indirect.py index 3577f4c31..faaf6ab28 100644 --- a/backend/tests/fixtures/association_query_indirect.py +++ b/backend/tests/fixtures/association_query_indirect.py @@ -24,7 +24,7 @@ def association_query_indirect(): "object_taxon:NCBITaxon\\:2222", 'subject:"TEST:0000001" OR subject_closure:"TEST:0000001"', 'object:"TEST:0000002" OR object_closure:"TEST:0000002"', - 'subject:"TEST\\:0000005" OR subject_closure:"TEST\\:0000005" OR object:"TEST\\:0000005" OR object_closure:"TEST\\:0000005"', + 'subject:"TEST:0000005" OR subject_closure:"TEST:0000005" OR object:"TEST:0000005" OR object_closure:"TEST:0000005"', ], "query_fields": "subject subject_label^2 subject_label_t subject_closure subject_closure_label subject_closure_label_t predicate predicate_t object object_label^2 object_label_t object_closure object_closure_label object_closure_label_t publications has_evidence primary_knowledge_source aggregator_knowledge_source provided_by ", "def_type": "edismax", diff --git a/backend/tests/fixtures/association_response.py b/backend/tests/fixtures/association_response.py index dc03be25a..0915b7e13 100644 --- a/backend/tests/fixtures/association_response.py +++ b/backend/tests/fixtures/association_response.py @@ -13,7 +13,7 @@ def association_response(): "facet_min_count": "1", "start": "0", "q.op": "AND", - "fq": 'subject:"MONDO\\:0020121" OR subject_closure:"MONDO\\:0020121" OR object:"MONDO\\:0020121" OR object_closure:"MONDO\\:0020121"', + "fq": 'subject:"MONDO:0020121" OR subject_closure:"MONDO:0020121" OR object:"MONDO:0020121" OR object_closure:"MONDO:0020121"', "rows": "20", "facet": "true", }, diff --git a/backend/tests/fixtures/association_table_response.py b/backend/tests/fixtures/association_table_response.py index 0c099f35c..ba38a9185 100644 --- a/backend/tests/fixtures/association_table_response.py +++ b/backend/tests/fixtures/association_table_response.py @@ -5,7 +5,7 @@ def association_table_response(): return { "responseHeader": { - "QTime": 1, + "QTime": 0, "params": { "mm": "100%", "q": "*:*", @@ -15,7 +15,7 @@ def association_table_response(): "q.op": "AND", "fq": [ "category:biolink\\:DiseaseToPhenotypicFeatureAssociation", - 'subject:"MONDO\\:0020121" OR subject_closure:"MONDO\\:0020121" OR object:"MONDO\\:0020121" OR object_closure:"MONDO\\:0020121"', + 'subject:"MONDO:0020121" OR subject_closure:"MONDO:0020121" OR object:"MONDO:0020121" OR object_closure:"MONDO:0020121"', ], "sort": "frequency_computed_sortable_float desc, evidence_count desc, subject_label asc, predicate asc, object_label asc, primary_knowledge_source asc", "rows": "5", diff --git a/backend/tests/fixtures/autocomplete_response.py b/backend/tests/fixtures/autocomplete_response.py index 45291b1ff..4ccadfb15 100644 --- a/backend/tests/fixtures/autocomplete_response.py +++ b/backend/tests/fixtures/autocomplete_response.py @@ -5,7 +5,7 @@ def autocomplete_response(): return { "responseHeader": { - "QTime": 1, + "QTime": 0, "params": { "mm": "100%", "q": "fanc", diff --git a/backend/tests/fixtures/node.py b/backend/tests/fixtures/node.py index 13a2a55f7..9ea75319b 100644 --- a/backend/tests/fixtures/node.py +++ b/backend/tests/fixtures/node.py @@ -66,9 +66,13 @@ def node(): "url": "https://monarch-initiative.github.io/monarch-ingest/Sources/phenio/#", }, "association_counts": [ - {"label": "Phenotypes", "count": 3932, "category": "biolink:DiseaseToPhenotypicFeatureAssociation"}, - {"label": "Causal Genes", "count": 126, "category": "biolink:CausalGeneToDiseaseAssociation"}, - {"label": "Correlated Genes", "count": 146, "category": "biolink:CorrelatedGeneToDiseaseAssociation"}, + { + "label": "Phenotype to Disease", + "count": 3932, + "category": "biolink:DiseaseToPhenotypicFeatureAssociation", + }, + {"label": "Causal Gene", "count": 126, "category": "biolink:CausalGeneToDiseaseAssociation"}, + {"label": "Correlated Gene", "count": 146, "category": "biolink:CorrelatedGeneToDiseaseAssociation"}, ], "node_hierarchy": { "super_classes": [ diff --git a/backend/tests/fixtures/object_formatted.py b/backend/tests/fixtures/object_formatted.py index 9b17b4665..b598aa5ee 100644 --- a/backend/tests/fixtures/object_formatted.py +++ b/backend/tests/fixtures/object_formatted.py @@ -122,17 +122,17 @@ def node_json(): }, "association_counts": [ { - "label": "Phenotypes", + "label": "Phenotype to Disease", "count": 3932, "category": "biolink:DiseaseToPhenotypicFeatureAssociation" }, { - "label": "Causal Genes", + "label": "Causal Gene", "count": 126, "category": "biolink:CausalGeneToDiseaseAssociation" }, { - "label": "Correlated Genes", + "label": "Correlated Gene", "count": 146, "category": "biolink:CorrelatedGeneToDiseaseAssociation" } @@ -481,7 +481,7 @@ 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', 'MESH:D009136', 'MedDRA:10028356', 'NCIT:C84910', 'Orphanet:98473', 'SCTID:73297009', 'UMLS:C0026850', 'icd11.foundation:1464662404'] phenio_nodes None None None [] http://purl.obolibrary.org/obo/MONDO_0020121 None MONDO [] [] [] [] 0 None [] [] [{'id': 'DOID:9884', 'url': 'http://purl.obolibrary.org/obo/DOID_9884'}, {'id': 'ICD10CM:G71.0', 'url': 'https://icd.codes/icd10cm/G71.0'}, {'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': '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': 'MESH:D009136', 'url': 'http://identifiers.org/mesh/D009136'}, {'id': 'MedDRA:10028356', 'url': None}, {'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': 'Phenotypes', 'count': 3932, 'category': 'biolink:DiseaseToPhenotypicFeatureAssociation'}, {'label': 'Causal Genes', 'count': 126, 'category': 'biolink:CausalGeneToDiseaseAssociation'}, {'label': 'Correlated Genes', 'count': 146, 'category': 'biolink:CorrelatedGeneToDiseaseAssociation'}] {'super_classes': [{'id': 'MONDO:0100546', 'category': 'biolink:Disease', 'name': 'hereditary neuromuscular disease', 'full_name': None, 'deprecated': None, 'description': None, 'xref': [], 'provided_by': None, 'in_taxon': None, 'in_taxon_label': None, 'symbol': None, 'synonym': [], 'uri': None, 'iri': None, 'namespace': None, 'has_phenotype': [], 'has_phenotype_label': [], 'has_phenotype_closure': [], 'has_phenotype_closure_label': [], 'has_phenotype_count': None}, {'id': 'MONDO:0700223', 'category': 'biolink:Disease', 'name': 'hereditary skeletal muscle disorder', 'full_name': None, 'deprecated': None, 'description': None, 'xref': [], 'provided_by': None, 'in_taxon': None, 'in_taxon_label': None, 'symbol': None, 'synonym': [], 'uri': None, 'iri': None, 'namespace': None, 'has_phenotype': [], 'has_phenotype_label': [], 'has_phenotype_closure': [], 'has_phenotype_closure_label': [], 'has_phenotype_count': None}, {'id': 'MONDO:0005336', 'category': 'biolink:Disease', 'name': 'myopathy', 'full_name': None, 'deprecated': None, 'description': None, 'xref': [], 'provided_by': None, 'in_taxon': None, 'in_taxon_label': None, 'symbol': None, 'synonym': [], 'uri': None, 'iri': None, 'namespace': None, 'has_phenotype': [], 'has_phenotype_label': [], 'has_phenotype_closure': [], 'has_phenotype_closure_label': [], 'has_phenotype_count': None}], 'sub_classes': [{'id': 'MONDO:0010311', 'category': 'biolink:Disease', 'name': 'Becker muscular dystrophy', 'full_name': None, 'deprecated': None, 'description': None, 'xref': [], 'provided_by': None, 'in_taxon': None, 'in_taxon_label': None, 'symbol': None, 'synonym': [], 'uri': None, 'iri': None, 'namespace': None, 'has_phenotype': [], 'has_phenotype_label': [], 'has_phenotype_closure': [], 'has_phenotype_closure_label': [], 'has_phenotype_count': None}, {'id': 'MONDO:0010675', 'category': 'biolink:Disease', 'name': 'muscular dystrophy, cardiac type', 'full_name': None, 'deprecated': None, 'description': None, 'xref': [], 'provided_by': None, 'in_taxon': None, 'in_taxon_label': None, 'symbol': None, 'synonym': [], 'uri': None, 'iri': None, 'namespace': None, 'has_phenotype': [], 'has_phenotype_label': [], 'has_phenotype_closure': [], 'has_phenotype_closure_label': [], 'has_phenotype_count': None}, {'id': 'MONDO:0010676', 'category': 'biolink:Disease', 'name': 'muscular dystrophy, Hemizygous lethal type', 'full_name': None, 'deprecated': None, 'description': None, 'xref': [], 'provided_by': None, 'in_taxon': None, 'in_taxon_label': None, 'symbol': None, 'synonym': [], 'uri': None, 'iri': None, 'namespace': None, 'has_phenotype': [], 'has_phenotype_label': [], 'has_phenotype_closure': [], 'has_phenotype_closure_label': [], 'has_phenotype_count': None}, {'id': 'MONDO:0010677', 'category': 'biolink:Disease', 'name': 'muscular dystrophy, Mabry type', 'full_name': None, 'deprecated': None, 'description': None, 'xref': [], 'provided_by': None, 'in_taxon': None, 'in_taxon_label': None, 'symbol': None, 'synonym': [], 'uri': None, 'iri': None, 'namespace': None, 'has_phenotype': [], 'has_phenotype_label': [], 'has_phenotype_closure': [], 'has_phenotype_closure_label': [], 'has_phenotype_count': None}, {'id': 'MONDO:0010678', 'category': 'biolink:Disease', 'name': 'muscular dystrophy, progressive Pectorodorsal', 'full_name': None, 'deprecated': None, 'description': None, 'xref': [], 'provided_by': None, 'in_taxon': None, 'in_taxon_label': None, 'symbol': None, 'synonym': [], 'uri': None, 'iri': None, 'namespace': None, 'has_phenotype': [], 'has_phenotype_label': [], 'has_phenotype_closure': [], 'has_phenotype_closure_label': [], 'has_phenotype_count': None}, {'id': 'MONDO:0010679', 'category': 'biolink:Disease', 'name': 'Duchenne muscular dystrophy', 'full_name': None, 'deprecated': None, 'description': None, 'xref': [], 'provided_by': None, 'in_taxon': None, 'in_taxon_label': None, 'symbol': None, 'synonym': [], 'uri': None, 'iri': None, 'namespace': None, 'has_phenotype': [], 'has_phenotype_label': [], 'has_phenotype_closure': [], 'has_phenotype_closure_label': [], 'has_phenotype_count': None}, {'id': 'MONDO:0016106', 'category': 'biolink:Disease', 'name': 'progressive muscular dystrophy', 'full_name': None, 'deprecated': None, 'description': None, 'xref': [], 'provided_by': None, 'in_taxon': None, 'in_taxon_label': None, 'symbol': None, 'synonym': [], 'uri': None, 'iri': None, 'namespace': None, 'has_phenotype': [], 'has_phenotype_label': [], 'has_phenotype_closure': [], 'has_phenotype_closure_label': [], 'has_phenotype_count': None}, {'id': 'MONDO:0018949', 'category': 'biolink:Disease', 'name': 'distal myopathy', 'full_name': None, 'deprecated': None, 'description': None, 'xref': [], 'provided_by': None, 'in_taxon': None, 'in_taxon_label': None, 'symbol': None, 'synonym': [], 'uri': None, 'iri': None, 'namespace': None, 'has_phenotype': [], 'has_phenotype_label': [], 'has_phenotype_closure': [], 'has_phenotype_closure_label': [], 'has_phenotype_count': None}, {'id': 'MONDO:0019950', 'category': 'biolink:Disease', 'name': 'congenital muscular dystrophy', 'full_name': None, 'deprecated': None, 'description': None, 'xref': [], 'provided_by': None, 'in_taxon': None, 'in_taxon_label': None, 'symbol': None, 'synonym': [], 'uri': None, 'iri': None, 'namespace': None, 'has_phenotype': [], 'has_phenotype_label': [], 'has_phenotype_closure': [], 'has_phenotype_closure_label': [], 'has_phenotype_count': None}, {'id': 'MONDO:0023204', 'category': 'biolink:Disease', 'name': 'Fukuda-Miyanomae-Nakata syndrome', 'full_name': None, 'deprecated': None, 'description': None, 'xref': [], 'provided_by': None, 'in_taxon': None, 'in_taxon_label': None, 'symbol': None, 'synonym': [], 'uri': None, 'iri': None, 'namespace': None, 'has_phenotype': [], 'has_phenotype_label': [], 'has_phenotype_closure': [], 'has_phenotype_closure_label': [], 'has_phenotype_count': None}, {'id': 'MONDO:0100228', 'category': 'biolink:Disease', 'name': 'LAMA2-related muscular dystrophy', 'full_name': None, 'deprecated': None, 'description': None, 'xref': [], 'provided_by': None, 'in_taxon': None, 'in_taxon_label': None, 'symbol': None, 'synonym': [], 'uri': None, 'iri': None, 'namespace': None, 'has_phenotype': [], 'has_phenotype_label': [], 'has_phenotype_closure': [], 'has_phenotype_closure_label': [], 'has_phenotype_count': None}, {'id': 'MONDO:0008028', 'category': 'biolink:Disease', 'name': 'muscular dystrophy, Barnes type', 'full_name': None, 'deprecated': None, 'description': None, 'xref': [], 'provided_by': None, 'in_taxon': None, 'in_taxon_label': None, 'symbol': None, 'synonym': [], 'uri': None, 'iri': None, 'namespace': None, 'has_phenotype': [], 'has_phenotype_label': [], 'has_phenotype_closure': [], 'has_phenotype_closure_label': [], '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', 'MESH:D009136', 'MedDRA:10028356', 'NCIT:C84910', 'Orphanet:98473', 'SCTID:73297009', 'UMLS:C0026850', 'icd11.foundation:1464662404'] phenio_nodes None None None [] http://purl.obolibrary.org/obo/MONDO_0020121 None MONDO [] [] [] [] 0 None [] [] [{'id': 'DOID:9884', 'url': 'http://purl.obolibrary.org/obo/DOID_9884'}, {'id': 'ICD10CM:G71.0', 'url': 'https://icd.codes/icd10cm/G71.0'}, {'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': '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': 'MESH:D009136', 'url': 'http://identifiers.org/mesh/D009136'}, {'id': 'MedDRA:10028356', 'url': None}, {'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': 3932, 'category': 'biolink:DiseaseToPhenotypicFeatureAssociation'}, {'label': 'Causal Gene', 'count': 126, 'category': 'biolink:CausalGeneToDiseaseAssociation'}, {'label': 'Correlated Gene', 'count': 146, 'category': 'biolink:CorrelatedGeneToDiseaseAssociation'}] {'super_classes': [{'id': 'MONDO:0100546', 'category': 'biolink:Disease', 'name': 'hereditary neuromuscular disease', 'full_name': None, 'deprecated': None, 'description': None, 'xref': [], 'provided_by': None, 'in_taxon': None, 'in_taxon_label': None, 'symbol': None, 'synonym': [], 'uri': None, 'iri': None, 'namespace': None, 'has_phenotype': [], 'has_phenotype_label': [], 'has_phenotype_closure': [], 'has_phenotype_closure_label': [], 'has_phenotype_count': None}, {'id': 'MONDO:0700223', 'category': 'biolink:Disease', 'name': 'hereditary skeletal muscle disorder', 'full_name': None, 'deprecated': None, 'description': None, 'xref': [], 'provided_by': None, 'in_taxon': None, 'in_taxon_label': None, 'symbol': None, 'synonym': [], 'uri': None, 'iri': None, 'namespace': None, 'has_phenotype': [], 'has_phenotype_label': [], 'has_phenotype_closure': [], 'has_phenotype_closure_label': [], 'has_phenotype_count': None}, {'id': 'MONDO:0005336', 'category': 'biolink:Disease', 'name': 'myopathy', 'full_name': None, 'deprecated': None, 'description': None, 'xref': [], 'provided_by': None, 'in_taxon': None, 'in_taxon_label': None, 'symbol': None, 'synonym': [], 'uri': None, 'iri': None, 'namespace': None, 'has_phenotype': [], 'has_phenotype_label': [], 'has_phenotype_closure': [], 'has_phenotype_closure_label': [], 'has_phenotype_count': None}], 'sub_classes': [{'id': 'MONDO:0010311', 'category': 'biolink:Disease', 'name': 'Becker muscular dystrophy', 'full_name': None, 'deprecated': None, 'description': None, 'xref': [], 'provided_by': None, 'in_taxon': None, 'in_taxon_label': None, 'symbol': None, 'synonym': [], 'uri': None, 'iri': None, 'namespace': None, 'has_phenotype': [], 'has_phenotype_label': [], 'has_phenotype_closure': [], 'has_phenotype_closure_label': [], 'has_phenotype_count': None}, {'id': 'MONDO:0010675', 'category': 'biolink:Disease', 'name': 'muscular dystrophy, cardiac type', 'full_name': None, 'deprecated': None, 'description': None, 'xref': [], 'provided_by': None, 'in_taxon': None, 'in_taxon_label': None, 'symbol': None, 'synonym': [], 'uri': None, 'iri': None, 'namespace': None, 'has_phenotype': [], 'has_phenotype_label': [], 'has_phenotype_closure': [], 'has_phenotype_closure_label': [], 'has_phenotype_count': None}, {'id': 'MONDO:0010676', 'category': 'biolink:Disease', 'name': 'muscular dystrophy, Hemizygous lethal type', 'full_name': None, 'deprecated': None, 'description': None, 'xref': [], 'provided_by': None, 'in_taxon': None, 'in_taxon_label': None, 'symbol': None, 'synonym': [], 'uri': None, 'iri': None, 'namespace': None, 'has_phenotype': [], 'has_phenotype_label': [], 'has_phenotype_closure': [], 'has_phenotype_closure_label': [], 'has_phenotype_count': None}, {'id': 'MONDO:0010677', 'category': 'biolink:Disease', 'name': 'muscular dystrophy, Mabry type', 'full_name': None, 'deprecated': None, 'description': None, 'xref': [], 'provided_by': None, 'in_taxon': None, 'in_taxon_label': None, 'symbol': None, 'synonym': [], 'uri': None, 'iri': None, 'namespace': None, 'has_phenotype': [], 'has_phenotype_label': [], 'has_phenotype_closure': [], 'has_phenotype_closure_label': [], 'has_phenotype_count': None}, {'id': 'MONDO:0010678', 'category': 'biolink:Disease', 'name': 'muscular dystrophy, progressive Pectorodorsal', 'full_name': None, 'deprecated': None, 'description': None, 'xref': [], 'provided_by': None, 'in_taxon': None, 'in_taxon_label': None, 'symbol': None, 'synonym': [], 'uri': None, 'iri': None, 'namespace': None, 'has_phenotype': [], 'has_phenotype_label': [], 'has_phenotype_closure': [], 'has_phenotype_closure_label': [], 'has_phenotype_count': None}, {'id': 'MONDO:0010679', 'category': 'biolink:Disease', 'name': 'Duchenne muscular dystrophy', 'full_name': None, 'deprecated': None, 'description': None, 'xref': [], 'provided_by': None, 'in_taxon': None, 'in_taxon_label': None, 'symbol': None, 'synonym': [], 'uri': None, 'iri': None, 'namespace': None, 'has_phenotype': [], 'has_phenotype_label': [], 'has_phenotype_closure': [], 'has_phenotype_closure_label': [], 'has_phenotype_count': None}, {'id': 'MONDO:0016106', 'category': 'biolink:Disease', 'name': 'progressive muscular dystrophy', 'full_name': None, 'deprecated': None, 'description': None, 'xref': [], 'provided_by': None, 'in_taxon': None, 'in_taxon_label': None, 'symbol': None, 'synonym': [], 'uri': None, 'iri': None, 'namespace': None, 'has_phenotype': [], 'has_phenotype_label': [], 'has_phenotype_closure': [], 'has_phenotype_closure_label': [], 'has_phenotype_count': None}, {'id': 'MONDO:0018949', 'category': 'biolink:Disease', 'name': 'distal myopathy', 'full_name': None, 'deprecated': None, 'description': None, 'xref': [], 'provided_by': None, 'in_taxon': None, 'in_taxon_label': None, 'symbol': None, 'synonym': [], 'uri': None, 'iri': None, 'namespace': None, 'has_phenotype': [], 'has_phenotype_label': [], 'has_phenotype_closure': [], 'has_phenotype_closure_label': [], 'has_phenotype_count': None}, {'id': 'MONDO:0019950', 'category': 'biolink:Disease', 'name': 'congenital muscular dystrophy', 'full_name': None, 'deprecated': None, 'description': None, 'xref': [], 'provided_by': None, 'in_taxon': None, 'in_taxon_label': None, 'symbol': None, 'synonym': [], 'uri': None, 'iri': None, 'namespace': None, 'has_phenotype': [], 'has_phenotype_label': [], 'has_phenotype_closure': [], 'has_phenotype_closure_label': [], 'has_phenotype_count': None}, {'id': 'MONDO:0023204', 'category': 'biolink:Disease', 'name': 'Fukuda-Miyanomae-Nakata syndrome', 'full_name': None, 'deprecated': None, 'description': None, 'xref': [], 'provided_by': None, 'in_taxon': None, 'in_taxon_label': None, 'symbol': None, 'synonym': [], 'uri': None, 'iri': None, 'namespace': None, 'has_phenotype': [], 'has_phenotype_label': [], 'has_phenotype_closure': [], 'has_phenotype_closure_label': [], 'has_phenotype_count': None}, {'id': 'MONDO:0100228', 'category': 'biolink:Disease', 'name': 'LAMA2-related muscular dystrophy', 'full_name': None, 'deprecated': None, 'description': None, 'xref': [], 'provided_by': None, 'in_taxon': None, 'in_taxon_label': None, 'symbol': None, 'synonym': [], 'uri': None, 'iri': None, 'namespace': None, 'has_phenotype': [], 'has_phenotype_label': [], 'has_phenotype_closure': [], 'has_phenotype_closure_label': [], 'has_phenotype_count': None}, {'id': 'MONDO:0008028', 'category': 'biolink:Disease', 'name': 'muscular dystrophy, Barnes type', 'full_name': None, 'deprecated': None, 'description': None, 'xref': [], 'provided_by': None, 'in_taxon': None, 'in_taxon_label': None, 'symbol': None, 'synonym': [], 'uri': None, 'iri': None, 'namespace': None, 'has_phenotype': [], 'has_phenotype_label': [], 'has_phenotype_closure': [], 'has_phenotype_closure_label': [], 'has_phenotype_count': None}]} """ @@ -491,13 +491,13 @@ def node_yaml(): association_counts: - category: biolink:DiseaseToPhenotypicFeatureAssociation count: 3932 - label: Phenotypes + label: Phenotype to Disease - category: biolink:CausalGeneToDiseaseAssociation count: 126 - label: Causal Genes + label: Causal Gene - category: biolink:CorrelatedGeneToDiseaseAssociation count: 146 - label: Correlated Genes + label: Correlated Gene category: biolink:Disease causal_gene: [] causes_disease: [] diff --git a/backend/tests/fixtures/search_response.py b/backend/tests/fixtures/search_response.py index cfa37159c..14563bf09 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": 1, + "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 59fd84cc7..2b5003d4e 100644 --- a/backend/tests/integration/test_solr_search.py +++ b/backend/tests/integration/test_solr_search.py @@ -109,12 +109,12 @@ def test_association_counts_for_disease(): assert len(association_counts.items) > 0 causal_genes = [ac for ac in association_counts.items if ac.category == "biolink:CausalGeneToDiseaseAssociation"][0] - assert causal_genes.label == "Causal Genes" + assert causal_genes.label == "Causal Gene" disease_phenotype = [ ac for ac in association_counts.items if ac.category == "biolink:DiseaseToPhenotypicFeatureAssociation" ][0] - assert disease_phenotype.label == "Phenotypes" + assert disease_phenotype.label == "Phenotype to Disease" def test_association_counts_for_eds(): @@ -133,12 +133,12 @@ def test_association_counts_for_phenotype(): disease_phenotype = [ ac for ac in association_counts.items if ac.category == "biolink:DiseaseToPhenotypicFeatureAssociation" ][0] - assert disease_phenotype.label == "Diseases" + assert disease_phenotype.label == "Disease to Phenotype" gene_phenotype = [ ac for ac in association_counts.items if ac.category == "biolink:GeneToPhenotypicFeatureAssociation" ][0] - assert gene_phenotype.label == "Genes" + assert gene_phenotype.label == "Gene to Phenotype" def test_association_table(): diff --git a/backend/tests/unit/test_solr_queries.py b/backend/tests/unit/test_solr_queries.py index 3e10ce785..da9c18291 100644 --- a/backend/tests/unit/test_solr_queries.py +++ b/backend/tests/unit/test_solr_queries.py @@ -83,7 +83,7 @@ def test_build_association_multiple_entites(): entity_filter = [fq for fq in query.filter_queries if fq.startswith("subject:")][0] assert ( entity_filter - == 'subject:"MONDO\\:0020121" OR subject_closure:"MONDO\\:0020121" OR object:"MONDO\\:0020121" OR object_closure:"MONDO\\:0020121" OR subject:"HP\\:0000006" OR subject_closure:"HP\\:0000006" OR object:"HP\\:0000006" OR object_closure:"HP\\:0000006"' + == 'subject:"MONDO:0020121" OR subject_closure:"MONDO:0020121" OR object:"MONDO:0020121" OR object_closure:"MONDO:0020121" OR subject:"HP:0000006" OR subject_closure:"HP:0000006" OR object:"HP:0000006" OR object_closure:"HP:0000006"' ) diff --git a/frontend/fixtures/association-counts.json b/frontend/fixtures/association-counts.json index 39d36e58e..80aee6e11 100644 --- a/frontend/fixtures/association-counts.json +++ b/frontend/fixtures/association-counts.json @@ -1,17 +1,17 @@ { "items": [ { - "label": "Phenotypes", + "label": "Phenotype to Disease", "count": 3932, "category": "biolink:DiseaseToPhenotypicFeatureAssociation" }, { - "label": "Causal Genes", + "label": "Causal Gene", "count": 126, "category": "biolink:CausalGeneToDiseaseAssociation" }, { - "label": "Correlated Genes", + "label": "Correlated Gene", "count": 146, "category": "biolink:CorrelatedGeneToDiseaseAssociation" } diff --git a/frontend/fixtures/node.json b/frontend/fixtures/node.json index 52fc9016d..bc2caebe2 100644 --- a/frontend/fixtures/node.json +++ b/frontend/fixtures/node.json @@ -116,17 +116,17 @@ }, "association_counts": [ { - "label": "Phenotypes", + "label": "Phenotype to Disease", "count": 3932, "category": "biolink:DiseaseToPhenotypicFeatureAssociation" }, { - "label": "Causal Genes", + "label": "Causal Gene", "count": 126, "category": "biolink:CausalGeneToDiseaseAssociation" }, { - "label": "Correlated Genes", + "label": "Correlated Gene", "count": 146, "category": "biolink:CorrelatedGeneToDiseaseAssociation" } diff --git a/frontend/fixtures/phenotype-explorer-multi-compare.json b/frontend/fixtures/phenotype-explorer-multi-compare.json index b2491dd09..115173a85 100644 --- a/frontend/fixtures/phenotype-explorer-multi-compare.json +++ b/frontend/fixtures/phenotype-explorer-multi-compare.json @@ -22,29 +22,25 @@ "has_phenotype_closure_label": [], "has_phenotype_count": null }, - "score": 8.608834726850041, + "score": 8.60883472685004, "similarity": { "subject_termset": { - "HP:0010749": { "id": "HP:0010749", "label": "Blepharochalasis" }, - "HP:0001763": { "id": "HP:0001763", "label": "Pes planus" }, - "HP:0001533": { "id": "HP:0001533", "label": "Slender build" }, - "HP:0002616": { "id": "HP:0002616", "label": "Aortic root aneurysm" }, "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:0012450": { "id": "HP:0012450", "label": "Chronic constipation" }, + "HP:0001533": { "id": "HP:0001533", "label": "Slender build" }, "HP:0002020": { "id": "HP:0002020", "label": "Gastroesophageal reflux" }, - "HP:0012450": { "id": "HP:0012450", "label": "Chronic constipation" } + "HP:0002616": { "id": "HP:0002616", "label": "Aortic root aneurysm" } }, "object_termset": { "MP:0002834": { "id": "MP:0002834", "label": "decreased heart weight" }, - "MP:0003291": { - "id": "MP:0003291", - "label": "interstinal hyperperistalsis" - }, "MP:0011960": { "id": "MP:0011960", "label": "abnormal eye anterior chamber depth" @@ -53,18 +49,22 @@ "id": "MP:0011962", "label": "increased cornea thickness" }, - "MP:0011965": { - "id": "MP:0011965", - "label": "decreased total retina thickness" + "MP:0008489": { + "id": "MP:0008489", + "label": "slow postnatal weight gain" + }, + "MP:0003291": { + "id": "MP:0003291", + "label": "interstinal hyperperistalsis" }, - "MP:0001262": { "id": "MP:0001262", "label": "decreased body weight" }, "MP:0003731": { "id": "MP:0003731", "label": "abnormal retina outer nuclear layer morphology" }, - "MP:0008489": { - "id": "MP:0008489", - "label": "slow postnatal weight gain" + "MP:0001262": { "id": "MP:0001262", "label": "decreased body weight" }, + "MP:0011965": { + "id": "MP:0011965", + "label": "decreased total retina thickness" } }, "subject_best_matches": { @@ -99,8 +99,8 @@ "HP:0001763": { "match_source": "HP:0001763", "match_source_label": "Pes planus", - "match_target": "MP:0002834", - "match_target_label": "decreased heart weight", + "match_target": "MP:0011962", + "match_target_label": "increased cornea thickness", "score": 3.066606173373863, "match_subsumer": null, "match_subsumer_label": null, @@ -108,7 +108,7 @@ "subject_id": "HP:0001763", "subject_label": null, "subject_source": null, - "object_id": "MP:0002834", + "object_id": "MP:0011962", "object_label": null, "object_source": null, "ancestor_id": "UPHENO:0015280", @@ -117,10 +117,10 @@ "object_information_content": null, "subject_information_content": null, "ancestor_information_content": 3.066606173373863, - "jaccard_similarity": 0.203125, + "jaccard_similarity": 0.16049382716049382, "cosine_similarity": null, "dice_similarity": null, - "phenodigm_score": 0.7892429150563 + "phenodigm_score": 0.7015492578278222 }, "score_metric": "ancestor_information_content" }, @@ -211,8 +211,8 @@ "HP:0010749": { "match_source": "HP:0010749", "match_source_label": "Blepharochalasis", - "match_target": "MP:0011962", - "match_target_label": "increased cornea thickness", + "match_target": "MP:0011960", + "match_target_label": "abnormal eye anterior chamber depth", "score": 6.6792078240173165, "match_subsumer": null, "match_subsumer_label": null, @@ -220,7 +220,7 @@ "subject_id": "HP:0010749", "subject_label": null, "subject_source": null, - "object_id": "MP:0011962", + "object_id": "MP:0011960", "object_label": null, "object_source": null, "ancestor_id": "UPHENO:0087924", @@ -229,10 +229,10 @@ "object_information_content": null, "subject_information_content": null, "ancestor_information_content": 6.6792078240173165, - "jaccard_similarity": 0.25301204819277107, + "jaccard_similarity": 0.26865671641791045, "cosine_similarity": null, "dice_similarity": null, - "phenodigm_score": 1.2999692503516391 + "phenodigm_score": 1.3395574053669028 }, "score_metric": "ancestor_information_content" }, @@ -309,8 +309,8 @@ "object_id": "HP:0001533", "object_label": null, "object_source": null, - "ancestor_id": "UPHENO:0054261", - "ancestor_label": "decreased anatomical entity mass", + "ancestor_id": "UPHENO:0082761", + "ancestor_label": "Decreased anatomical entity mass", "ancestor_source": null, "object_information_content": null, "subject_information_content": null, @@ -491,7 +491,7 @@ "score_metric": "ancestor_information_content" } }, - "average_score": 8.608834726850041, + "average_score": 8.60883472685004, "best_score": 13.667892510789482, "metric": "AncestorInformationContent" } @@ -522,14 +522,14 @@ "score": 7.343905449061466, "similarity": { "subject_termset": { - "HP:0001763": { "id": "HP:0001763", "label": "Pes planus" }, - "HP:0001533": { "id": "HP:0001533", "label": "Slender build" }, "HP:0004944": { "id": "HP:0004944", "label": "Dilatation of the cerebral artery" }, - "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:0002616": { "id": "HP:0002616", "label": "Aortic root aneurysm" }, + "HP:0001763": { "id": "HP:0001763", "label": "Pes planus" }, "HP:0002020": { "id": "HP:0002020", "label": "Gastroesophageal reflux" @@ -537,42 +537,42 @@ "HP:0010749": { "id": "HP:0010749", "label": "Blepharochalasis" } }, "object_termset": { - "MP:0000272": { - "id": "MP:0000272", - "label": "abnormal aorta morphology" + "MP:0006264": { + "id": "MP:0006264", + "label": "decreased systemic arterial systolic blood pressure" }, - "MP:0009862": { - "id": "MP:0009862", - "label": "abnormal aorta elastic tissue morphology" + "MP:0002834": { "id": "MP:0002834", "label": "decreased heart weight" }, + "MP:0003070": { + "id": "MP:0003070", + "label": "increased vascular permeability" + }, + "MP:0004021": { + "id": "MP:0004021", + "label": "abnormal rod electrophysiology" }, "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:0000230": { "id": "MP:0000230", "label": "abnormal systemic arterial blood pressure" }, - "MP:0003070": { - "id": "MP:0003070", - "label": "increased vascular permeability" + "MP:0000233": { + "id": "MP:0000233", + "label": "abnormal blood flow velocity" + }, + "MP:0009862": { + "id": "MP:0009862", + "label": "abnormal aorta elastic tissue morphology" }, "MP:0003026": { "id": "MP:0003026", "label": "decreased vasoconstriction" - }, - "MP:0006264": { - "id": "MP:0006264", - "label": "decreased systemic arterial systolic blood pressure" - }, - "MP:0002834": { "id": "MP:0002834", "label": "decreased heart weight" }, - "MP:0004021": { - "id": "MP:0004021", - "label": "abnormal rod electrophysiology" } }, "subject_best_matches": { @@ -663,8 +663,8 @@ "HP:0002616": { "match_source": "HP:0002616", "match_source_label": "Aortic root aneurysm", - "match_target": "MP:0000272", - "match_target_label": "abnormal aorta morphology", + "match_target": "MP:0009862", + "match_target_label": "abnormal aorta elastic tissue morphology", "score": 9.580429669539143, "match_subsumer": null, "match_subsumer_label": null, @@ -672,7 +672,7 @@ "subject_id": "HP:0002616", "subject_label": null, "subject_source": null, - "object_id": "MP:0000272", + "object_id": "MP:0009862", "object_label": null, "object_source": null, "ancestor_id": "UPHENO:0076809", @@ -681,10 +681,10 @@ "object_information_content": null, "subject_information_content": null, "ancestor_information_content": 9.580429669539143, - "jaccard_similarity": 0.36363636363636365, + "jaccard_similarity": 0.32075471698113206, "cosine_similarity": null, "dice_similarity": null, - "phenodigm_score": 1.8664920592129888 + "phenodigm_score": 1.7529883077792243 }, "score_metric": "ancestor_information_content" }, @@ -889,8 +889,8 @@ "MP:0003026": { "match_source": "MP:0003026", "match_source_label": "decreased vasoconstriction", - "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, @@ -898,7 +898,7 @@ "subject_id": "MP:0003026", "subject_label": null, "subject_source": null, - "object_id": "HP:0004944", + "object_id": "HP:0002616", "object_label": null, "object_source": null, "ancestor_id": "UPHENO:0080362", @@ -907,18 +907,18 @@ "object_information_content": null, "subject_information_content": null, "ancestor_information_content": 7.3467487024345575, - "jaccard_similarity": 0.17391304347826086, + "jaccard_similarity": 0.21428571428571427, "cosine_similarity": null, "dice_similarity": null, - "phenodigm_score": 1.1303519038380736 + "phenodigm_score": 1.2547124345358316 }, "score_metric": "ancestor_information_content" }, "MP:0003070": { "match_source": "MP:0003070", "match_source_label": "increased vascular permeability", - "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, @@ -926,7 +926,7 @@ "subject_id": "MP:0003070", "subject_label": null, "subject_source": null, - "object_id": "HP:0004944", + "object_id": "HP:0002616", "object_label": null, "object_source": null, "ancestor_id": "UPHENO:0080362", @@ -935,10 +935,10 @@ "object_information_content": null, "subject_information_content": null, "ancestor_information_content": 7.3467487024345575, - "jaccard_similarity": 0.25806451612903225, + "jaccard_similarity": 0.32653061224489793, "cosine_similarity": null, "dice_similarity": null, - "phenodigm_score": 1.3769296093175458 + "phenodigm_score": 1.5488506551037662 }, "score_metric": "ancestor_information_content" }, @@ -1001,8 +1001,8 @@ "MP:0006264": { "match_source": "MP:0006264", "match_source_label": "decreased systemic arterial systolic blood pressure", - "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, @@ -1010,7 +1010,7 @@ "subject_id": "MP:0006264", "subject_label": null, "subject_source": null, - "object_id": "HP:0004944", + "object_id": "HP:0002616", "object_label": null, "object_source": null, "ancestor_id": "UPHENO:0080362", @@ -1019,10 +1019,10 @@ "object_information_content": null, "subject_information_content": null, "ancestor_information_content": 7.3467487024345575, - "jaccard_similarity": 0.1896551724137931, + "jaccard_similarity": 0.24444444444444444, "cosine_similarity": null, "dice_similarity": null, - "phenodigm_score": 1.1804020043362502 + "phenodigm_score": 1.340101453263729 }, "score_metric": "ancestor_information_content" }, diff --git a/frontend/fixtures/phenotype-explorer-search.json b/frontend/fixtures/phenotype-explorer-search.json index 82b428f7e..bfc473556 100644 --- a/frontend/fixtures/phenotype-explorer-search.json +++ b/frontend/fixtures/phenotype-explorer-search.json @@ -97,8 +97,8 @@ } }, "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:0018569": { @@ -376,8 +376,8 @@ "HP:0002104": { "match_source": "HP:0002104", "match_source_label": "Apnea", - "match_target": "ZP:0018569", - "match_target_label": "myeloid cell development absent, abnormal", + "match_target": "ZP:0018568", + "match_target_label": "primitive hemopoiesis absent, abnormal", "score": 8.79057503056431, "match_subsumer": null, "match_subsumer_label": null, @@ -385,7 +385,7 @@ "subject_id": "HP:0002104", "subject_label": null, "subject_source": null, - "object_id": "ZP:0018569", + "object_id": "ZP:0018568", "object_label": null, "object_source": null, "ancestor_id": "UPHENO:0034024", @@ -404,8 +404,8 @@ "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, @@ -413,7 +413,7 @@ "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", @@ -552,8 +552,8 @@ } }, "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": { @@ -617,8 +617,8 @@ "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, @@ -626,7 +626,7 @@ "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", @@ -799,8 +799,8 @@ } }, "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": { @@ -864,8 +864,8 @@ "HP:0002104": { "match_source": "HP:0002104", "match_source_label": "Apnea", - "match_target": "ZP:0018569", - "match_target_label": "myeloid cell development absent, abnormal", + "match_target": "ZP:0018568", + "match_target_label": "primitive hemopoiesis absent, abnormal", "score": 8.79057503056431, "match_subsumer": null, "match_subsumer_label": null, @@ -873,7 +873,7 @@ "subject_id": "HP:0002104", "subject_label": null, "subject_source": null, - "object_id": "ZP:0018569", + "object_id": "ZP:0018568", "object_label": null, "object_source": null, "ancestor_id": "UPHENO:0034024", @@ -892,8 +892,8 @@ "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, @@ -901,7 +901,7 @@ "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", @@ -1037,18 +1037,18 @@ "score": 7.011754466426716, "similarity": { "subject_termset": { - "ZP:0018569": { - "id": "ZP:0018569", - "label": "myeloid cell development absent, abnormal" - }, "ZP:0018568": { "id": "ZP:0018568", "label": "primitive hemopoiesis absent, abnormal" + }, + "ZP:0018569": { + "id": "ZP:0018569", + "label": "myeloid cell development absent, abnormal" } }, "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": { @@ -1112,8 +1112,8 @@ "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, @@ -1121,7 +1121,7 @@ "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", @@ -1347,13 +1347,13 @@ "score": 5.262083911717577, "similarity": { "subject_termset": { - "ZP:0100294": { - "id": "ZP:0100294", - "label": "visual perception absent, abnormal" - }, "ZP:0000945": { "id": "ZP:0000945", "label": "pigment cell quality, abnormal" + }, + "ZP:0100294": { + "id": "ZP:0100294", + "label": "visual perception absent, abnormal" } }, "object_termset": { @@ -1566,25 +1566,25 @@ "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": { - "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:0001841": { "match_source": "ZP:0001841", "match_source_label": "visual behavior quality, abnormal", - "match_target": "HP:0012378", - "match_target_label": "Fatigue", + "match_target": "HP:0002104", + "match_target_label": "Apnea", "score": 1.6752927740139332, "match_subsumer": null, "match_subsumer_label": null, @@ -1592,7 +1592,7 @@ "subject_id": "ZP:0001841", "subject_label": null, "subject_source": null, - "object_id": "HP:0012378", + "object_id": "HP:0002104", "object_label": null, "object_source": null, "ancestor_id": "UPHENO:0001005", @@ -1601,10 +1601,10 @@ "object_information_content": null, "subject_information_content": null, "ancestor_information_content": 1.6752927740139332, - "jaccard_similarity": 0.47058823529411764, + "jaccard_similarity": 0.2962962962962963, "cosine_similarity": null, "dice_similarity": null, - "phenodigm_score": 0.8879037504843663 + "phenodigm_score": 0.7045445650576523 }, "score_metric": "ancestor_information_content" }, @@ -1929,8 +1929,8 @@ } }, "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:0005756": { diff --git a/frontend/src/pages/node/SectionAssociations.vue b/frontend/src/pages/node/SectionAssociations.vue index e656df3e3..07a32ea61 100644 --- a/frontend/src/pages/node/SectionAssociations.vue +++ b/frontend/src/pages/node/SectionAssociations.vue @@ -12,15 +12,14 @@ - Associations between    - and + associations involving    + diff --git a/frontend/src/pages/node/SectionOverview.vue b/frontend/src/pages/node/SectionOverview.vue index 6624a2a83..f9df09455 100644 --- a/frontend/src/pages/node/SectionOverview.vue +++ b/frontend/src/pages/node/SectionOverview.vue @@ -142,7 +142,7 @@ :to="{ query: { associations: count.category || '' } }" @click="scrollToAssociations" > - {{ count.label }} {{ count.count?.toLocaleString() || 0 }} + {{ count.label }} ({{ count.count?.toLocaleString() || 0 }})