Read HPO's 2023 phenotype_to_genes.txt and backfill HPO to gene relations #1862 - #1864
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Read HPO's 2023 phenotype_to_genes.txt and backfill HPO to gene relations #1862#1864davmlaw wants to merge 1 commit into
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…o gene relations #1862 load_phenotype_to_genes only knew the old seven column file, so the 2023 format imported as zero relations and every HPO term on a phenotype node warned it had no associated genes. The loader now detects the format from the first line, keeps OMIM rows for either, and raises if nothing is left. backfill_phenotype_to_genes (registered as a manual migration step when the latest OntologyVersion's phenotype_to_genes import owns no relations) downloads the current file and loads it into that existing import via OntologyBuilder(existing_import=...), so deployments gain the relations without a new OntologyVersion, annotation sub-version or gene annotation build. create_test_ontology_version now records imports that already exist, which was masked by the seeded test database.
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Addresses #1862 - every HPO term on a phenotype node warned "have no associated genes".
Cause
HPO changed phenotype_to_genes.txt in 2023 from seven columns behind a
#Format:comment to five columns with a header row.load_phenotype_to_genesread it with the old column names, thesource == mim2genefilter emptied the frame, and the import completed with zero relations.Changes
load_phenotype_to_genesdetects the format from the first line, keeps OMIM rows for either format, and raises if the frame is empty.processor_versionbumped to 2.OntologyBuilder(existing_import=...)writes into an existing import's partition instead of creating a new import.backfill_phenotype_to_genescommand: downloads the current file (or takes--phenotype_to_genes) and loads it into the import the latestOntologyVersionalready points at, so no new OntologyVersion / annotation sub-version / gene annotation build follows. Registered as a manual migration step (ontology/migrations/0028) whose test fires only when that import owns no relations.create_test_ontology_versionnow records imports that already exist (was masked by the seeded test database).claude/research/ontology.md.Verification
--keepdbdatabase.HP:0004808resolves to CEBPA, BRCA2, GATA2 and others. A second run is a no-op.After deploy
Gene annotation
hpo_terms/omim_termsfor the existing ontology version were built without these relations; the command printsgene_annotation --latest-releases --forcefor rebuilding them. Phenotype nodes cache empty term lookups for a day, so a term viewed before the backfill may keep its warning until then.🤖 Generated with Claude Code
https://claude.ai/code/session_01BtmQtLeDUcDJz5kMdEfhhe