ontology-term-resolution

92 / 100 · Low risk

Fine to try.

By lilinji/GeneTind-Life-Skills (GitHub) · other · 17 stars · scanned at commit 908229c

Resolve free-text scientific labels to ontology term IDs and validate existing CURIEs against the EBI Ontology Lookup Service (OLS4). 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ENA, BioSamples, CELLxGENE, HCA, or ISA-Tab submission; auditing a metadata table of term IDs; checking whether a term is obsolete and what replaced it; or ma…

Works with any agent that supports SKILL.md skills.

What this skill can do

Runs commands on your computer

The author does not mention this.

Found in 4 places.

skills/ontology-term-resolution/SKILL.md, line 44cd skills/ontology-term-resolution/scripts
skills/ontology-term-resolution/SKILL.md, line 57python3 resolve_terms.py --input tissues.txt --ontology uberon \
skills/ontology-term-resolution/SKILL.md, line 76python3 validate_terms.py UBERON:0002107 EFO:0001067 UBERON:9999999

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skills/ontology-term-resolution/SKILL.md, line 91python3 validate_terms.py --input metadata.tsv --strict

Connects to the internet

This is disclosed by the author in the skill's SKILL.md or README.

Found in 5 places.

skills/ontology-term-resolution/scripts/ols_client.py, line 29import urllib.request
skills/ontology-term-resolution/scripts/ols_client.py, line 67request = urllib.request.Request(url, headers={"User-Agent": USER_AGENT})
skills/ontology-term-resolution/scripts/ols_client.py, line 72with urllib.request.urlopen(request, timeout=TIMEOUT) as response:

Show 2 more

skills/ontology-term-resolution/scripts/ols_client.py, line 211request = urllib.request.Request(url, headers={"User-Agent": USER_AGENT})
skills/ontology-term-resolution/scripts/ols_client.py, line 213with urllib.request.urlopen(request, timeout=TIMEOUT) as response:

Install

Paste this into your terminal. It downloads exactly the version we scanned, not whatever is newest.

if [ -e ~/.agents/skills/'ontology-term-resolution' ] || [ -L ~/.agents/skills/'ontology-term-resolution' ]; then echo 'A skill folder named ontology-term-resolution already exists — not replacing it' >&2; false; else d=$(mktemp -d) && git clone --quiet --filter=blob:none --no-checkout 'https://github.com/lilinji/GeneTind-Life-Skills' "$d" && git -C "$d" checkout --quiet '908229c955510a1841b216e8bf58f6b22818d4dc' -- 'skills/ontology-term-resolution' && mkdir -p ~/.agents/skills && cp -R "$d"/'skills/ontology-term-resolution' ~/.agents/skills/'ontology-term-resolution' && rm -rf "$d"; fi

Codex reads ~/.agents/skills directly. For Claude Code, Cursor, Copilot, Gemini CLI, Antigravity or OpenCode, also link it. For Claude Code: ln -s ~/.agents/skills/'ontology-term-resolution' ~/.claude/skills/'ontology-term-resolution' (other agents: ~/.cursor/skills, ~/.copilot/skills, ~/.gemini/skills, ~/.gemini/config/skills, ~/.config/opencode/skills). Or install through the finder skill, which does both.

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Score history

Date	Version	Score
2026-11-11	`908229c`	92