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Follow biolink 4.4.5 category changes for correlated genes and disease models - #1439
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Biolink 4.4+ closes CorrelatedGeneToDiseaseAssociation to the correlated_with predicate family, so Monarch's non-causal gene-to-disease sources (OMIM, HPOA) now emit the parent biolink:GeneToDiseaseAssociation with contributes_to or associated_with. The "Correlated Genes" section becomes a keyed section (correlated_gene_to_disease) matched on that category plus those predicates, using the same full-criteria mechanism the LOINC sections use. Causal edges keep their own category. Frontend lookups that are keyed by section id move to the new key; the entity-grid lookups, which are keyed by category, move to the parent category. Fixtures follow the new Solr fragment and key. Claude-Session: https://claude.ai/code/session_01V4T7NDQUNm5nXB7jtTEorT
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Biolink 4.4+ closes GenotypeToDiseaseAssociation to the related_condition predicate, so alliance-ingest now emits its is_model_of rows as GenotypeAsAModelOfDiseaseAssociation with the model_of predicate unchanged. The "Disease Models" section, its frontend lookups, the API category enum and the fixtures follow the new category. Claude-Session: https://claude.ai/code/session_01V4T7NDQUNm5nXB7jtTEorT
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Summary
Companion to the biolink-model 4.4.5 upgrade in the ingest repos (part of #1424). Two sections follow category changes forced by biolink 4.4+'s predicate enforcement; predicates are unchanged in both cases.
Correlated genes. Biolink closes
CorrelatedGeneToDiseaseAssociationto thecorrelated_withpredicate family, so OMIM and HPOA now emit non-causal gene-to-disease edges on the parentbiolink:GeneToDiseaseAssociationwithcontributes_toorassociated_with(monarch-initiative/omim-ingest#13, monarch-initiative/monarch-phenotype-profile-ingest#20). The "Correlated Genes" section becomes a keyed section,correlated_gene_to_disease, matched on that category plus those predicates viamatch_criteria: full, the mechanism the LOINC sections already use. Causal edges are unchanged.Disease models. Biolink closes
GenotypeToDiseaseAssociationtorelated_condition, so alliance-ingest now emits itsis_model_ofrows asGenotypeAsAModelOfDiseaseAssociation(monarch-initiative/alliance-ingest#13). The "Disease Models" section moves to that category.Details:
AssociationCategorygainsGENE_TO_DISEASE_ASSOCIATIONandGENOTYPE_AS_A_MODEL_OF_DISEASE_ASSOCIATION; the enum is normally regenerated from Solr and will pick these up on the next build.Notes
categoryfilter being an exact match, which is how every section works today. It would need revisiting if counts ever moved tocategory_closure.tests/integration/test_solr_association.pystill asserts the old correlated category against live Solr; it passes again once a KG built from the upgraded ingests is loaded.https://claude.ai/code/session_01V4T7NDQUNm5nXB7jtTEorT