Schema: per-taxon abundances + reusable CommonTaxon gene records#161
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Two schema-first additions (datamodel regenerated via `just gen-python`):
1. Separate, optional abundance fields on TaxonomicComposition:
- absolute_abundance (float) + absolute_abundance_unit
- relative_abundance (float, >=0) + relative_abundance_unit
Both independent and optional; the legacy free-text abundance_value is kept
for back-compat and marked deprecated.
2. Reusable per-taxon gene records (new classes CommonTaxon / GenomeRecord /
GeneAnnotation), stored as standalone YAML under kb/taxa/ and referenced from
taxonomy[].common_taxon, so a curated genome + gene set for an organism can be
shared across community records instead of duplicated.
- taxa: NCBITaxon (TaxonDescriptor, id-label gated)
- genome: NCBI Assembly accession (GCF_/GCA_, pattern-validated)
- gene: standardized gene_id CURIE (NCBIGene / UniProtKB / KEGG) + optional
locus_tag, kegg_ortholog (KO), GO function terms, supported roles, and
evidence. Records link to communities via a dedicated id
(CommunityMech:taxon:NNNNNN).
Wiring + examples:
- `just validate-taxa` validates kb/taxa/ against CommonTaxon (--target-class).
- conf/id_label_targets.yaml: new `taxa_yaml` target so NCBITaxon/GO terms in
kb/taxa/ are canonical-checked by the blocking validate-products gate.
- kb/taxa/: two example records (Shewanella oneidensis MR-1 Mtr pathway;
Geobacter sulfurreducens conductive-pili/cytochromes) — OAK-verified terms,
real assemblies/locus tags; gene EvidenceItems omitted rather than fabricated.
- Demonstrated common_taxon links in the Shewanella-Geobacter exoelectrogenic
community.
- tests/test_taxon_records.py (5 tests): records validate, schema slots/classes
present, community linkage, separate-abundance smoke test.
Verified: `just validate-taxa`, validate-strict, `just validate-products`
(5505 OK_CANONICAL, 0 errors), `just lint`, and full pytest (193 passed) all pass.
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
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Schema-first expansion (two requested capabilities).
1. Separate community-member abundances
TaxonomicCompositiongains four optional, independent fields:absolute_abundance(float) +absolute_abundance_unit(e.g. cells/mL, reads)relative_abundance(float ≥ 0) +relative_abundance_unit(default: fraction 0–1)The legacy free-text
abundance_valueis kept for back-compat and marked deprecated (it was being misused for role text).2. Reusable per-taxon gene records (
kb/taxa/)New classes CommonTaxon / GenomeRecord / GeneAnnotation. Each
kb/taxa/record holds an NCBITaxon-grounded organism + reference genome(s) + the genes that support its community role/interactions, and is referenced fromtaxonomy[].common_taxonso the curated gene set is shared across communities instead of duplicated.Standardized IDs (per your choices):
GCF_/GCA_(pattern-validated)gene_idCURIE accepting NCBIGene / UniProtKB / KEGG, plus optionallocus_tag,kegg_ortholog(KO), GO functiongo_terms,supports_roles,supports_interaction, evidenceCommunityMech:taxon:NNNNNNWiring + examples
just validate-taxa(linkml-validate--target-class CommonTaxon)conf/id_label_targets.yaml: newtaxa_yamltarget → NCBITaxon/GO terms inkb/taxa/are canonical-checked by the blockingvalidate-productsgateEvidenceItems omitted rather than fabricatedcommon_taxonlinks demonstrated in the Shewanella–Geobacter exoelectrogenic communitytests/test_taxon_records.py(5 tests)Verification
just gen-python(datamodel regenerated)just validate-taxa,just validate-all/strict,just validate-products(5505 OK_CANONICAL, 0 errors)just lint(black/ruff/mypy) clean; 193 pytest passed🤖 Generated with Claude Code