Individual skill
ontology-term-resolution
Resolves free-text scientific labels to ontology term IDs and validates existing CURIEs against the EBI Ontology Lookup Service (OLS4). Also looks up prefixes in Bioregistry, resolves compact identifiers via Identifiers.org, maps lab shorthand with ZOOMA, and builds Ontobee term pages. Use whenever an ontology identifier must be produced or checked - annotating tissue, cell type, disease, phenotype, assay, chemical, organism, sex, or developmental stage fields; preparing metadata for GEO, ENA, BioSamples, CELLxGENE, HCA, or ISA-Tab submission; auditing a metadata table of term IDs; checking whether a term is obsolete and what replaced it; or deciding HPO vs HP. Triggers include "ontology term", "ontology ID", "CURIE", "controlled vocabulary", "UBERON", "CL:", "MONDO", "HPO", "EFO", "ChEBI", "NCBITaxon", "GO term", "PATO", "Zooma", "Bioregistry", "Identifiers.org", "Ontobee", "annotate this tissue/cell type/disease", and any request to emit or verify an identifier shaped like PREFIX:0001234.
skills/ontology-term-resolution/SKILL.md
Source commit 2d2065fb4520fa3f3f2bcf61cff26ec8b7eba4b5
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- Observed behavior
- Network or broad shell
- Last checked
- Nov 10, 2026
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- Repository stars (not skill ratings)
- 56,837
- Repository last updated
- Nov 9, 2026
- License
- MIT
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- ai-scientist Repository topic
- bioinformatics Repository topic
- chemoinformatics Repository topic
- claude Repository topic
- claude-skills Repository topic
- claudecode Repository topic
- clinical-research Repository topic
- computational-biology Repository topic
- data-analysis Repository topic
- drug-discovery Repository topic
- research Derived category
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Read excerpt
# Ontology Term Resolution
## When to use
Any time an ontology identifier is about to be written down or trusted: annotating a metadata
column, filling a submission template, auditing a table someone else produced, or checking whether
an ID in an old file is still current.
## The rule
**Never write an ontology ID from memory, and never accept one without checking it.**
Ontology IDs are memorable in form and arbitrary in detail. A plausible-looking `UBERON:0002108`
is a real term (small intestine) that is not the liver, and nothing downstream will catch the