| name | nmdc-taxon-resolution |
| description | Use this skill to resolve organism names to NCBITaxon CURIEs via runoak for samp_taxon, host_taxid, and host_name, applying NMDC's unambiguous-intent rule for host assignment. Trigger when a host or taxon slot is unset or holds free-text needing lifting to a CURIE. Do not infer a host from rhizosphere or host-associated context alone; leave it unset and flag for PI follow-up. |
NCBITaxon resolution for NMDC
Resolve organism names to NCBITaxon CURIEs for samp_taxon, host_taxid, and related slots. Source skills hand off here when the deterministic pipeline has either left a host slot unset or recorded a free-text organism string that needs lifting to a CURIE.
Before committing any value, read nmdc-curation-rules — its evidence-first / no-tautology / omit-rather-than-guess rules govern every commit you make in this skill. The host-disambiguation rule below is a slot-specific application of those general rules.
Runoak setup
See Runoak setup in nmdc-env-triad — the same uv sync --extra ontology install and the same runoak invocation pattern apply here. Use the sqlite:obo:ncbitaxon adapter (or ols:ncbitaxon for the live API).
Lookup pattern
uv run --extra ontology runoak -i sqlite:obo:ncbitaxon search "Phallus rugulosus"
uv run --extra ontology runoak -i sqlite:obo:ncbitaxon info NCBITaxon:5260
For each organism string to resolve:
- Search by scientific name. Prefer exact matches over fuzzy hits.
- Verify the hit with
info — check the label and rank match the source's intent.
- Record the
NCBITaxon:<id> CURIE and the official label.
Host disambiguation rule
Only set host_name / host_taxid when the submitter's intent is unambiguous. A BioProject title that names a host species, a BioSample with an explicit host attribute, or a study description that calls out a single host taxon all qualify.
Do not infer a host from rhizosphere or host-associated context alone (e.g. "tree-associated soil samples" does not justify guessing the tree species). When intent is ambiguous, leave the host slots unset and flag for PI follow-up in the source skill's run report — this is the omit-rather-than-guess rule (nmdc-curation-rules Rule 4) applied to host fields.
Slot value shape
Taxon slots typically range over ControlledIdentifiedTermValue, which wraps an OntologyClass (id: NCBITaxon CURIE, name: official label). When the submitter only supplied free text and no taxid resolves cleanly, use ControlledTermValue with has_raw_value. See nmdc-schema-reference for the full trap-and-shape reference.
