| name | nmdc-ontology-mapping |
| description | Use this skill to decide whether a source vocabulary warrants a reusable mapping artifact and, when it does, author a validated SSSOM mapping set (subject/predicate/object with provenance) from a source controlled vocabulary (land-cover classes, habitat ontologies, GOLD ecosystem paths, EMPO, sample-type codes) to NMDC ENVO/NCBITaxon slot values. Trigger when many biosamples share a source vocabulary you want to resolve once instead of record-by-record, or when building or extending an ontology mapping. Not for a handful of one-off term lookups; use nmdc-env-triad or nmdc-taxon-resolution for those. |
Ontology mapping (SSSOM)
Build a reusable, validated mapping from a source controlled vocabulary to NMDC slot
values (ENVO for the env triad, NCBITaxon for taxa, …), so that many records sharing the
same source term are resolved by one curated decision instead of one at a time.
Read nmdc-curation-rules first — no CURIE from memory, evidence for every commit, omit
rather than guess. Those rules govern every row you write here.
Step 0 — Reuse before build
Before deciding anything, check whether an authoritative mapping already exists for this
source vocabulary — a committed crosswalk under examples/<project>/, a data/ lookup, or a
published mapping set. If one does, apply it, do not author a new one. Re-deriving a
mapping (e.g. from the coarse NCBI isolation_source) when a richer curated crosswalk exists
just yields a worse duplicate that drifts from the validated original. For the env-triad
specifically, an existing per-biosample crosswalk is applied by the ingest via
--env-triad-crosswalk, not by this skill. Only proceed to Step 1 for vocabularies with no
existing mapping.
Step 1 — Decide the regime (do this before writing any rows)
A mapping table is only worth building when the source terms form a closed, recurring
set. Pick the regime; record the choice in the run notes.
