> ## Documentation Index
> Fetch the complete documentation index at: https://kalarislabs.com/llms.txt
> Use this file to discover all available pages before exploring further.

# ontology-term-resolution — AI agent skill for scientific databases

> Resolve free-text scientific labels to ontology term IDs and validate existing CURIEs against the EBI Ontology Lookup Service (OLS4).

# `ontology-term-resolution`

> Resolve free-text scientific labels to ontology term IDs and validate existing CURIEs against the EBI Ontology Lookup Service (OLS4). Also look up prefixes in Bioregistry, resolve compact identifiers via Identifiers.org, map lab shorthand with ZOOMA, and build 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ENA, BioSamples, CELLxGENE, HCA, or ISA-Tab submission; auditing a metadata table of term IDs; checking whether a term is obsolete and what replaced it; or deciding HPO vs HP.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.

**Category:** [scientific-databases](/skills#scientific-databases) · **License:** MIT · **Version:** 1.2

## Install

```bash theme={null}
npx research-agent-skills install ontology-term-resolution
npx skills add KalarisLabs/research-agent-skills --skill ontology-term-resolution
```

## When to use it

Resolve free-text scientific labels to ontology term IDs and validate existing CURIEs against the EBI Ontology Lookup Service (OLS4). Also look up prefixes in Bioregistry, resolve compact identifiers via Identifiers.org, map lab shorthand with ZOOMA, and build 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ENA, BioSamples, CELLxGENE, HCA, or ISA-Tab submission; auditing a metadata table of term IDs; checking whether a term is obsolete and what replaced it; or deciding HPO vs HP.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.

## Full playbook

Read [SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/main/skills/ontology-term-resolution/SKILL.md) for the complete workflow, references and any scripts. The agent installer copies the full skill folder.