bio-ortholog-inference

80 / 100 · Low risk

Fine to try.

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

Pull pre-computed ortholog calls from public databases (OrthoDB, Ensembl Compara, OMA browser, eggNOG, PANTHER, KEGG Orthology, HomoloGene) via their REST APIs. Use when orthologs are already curated upstream, when the question is "what is the X ortholog of Y" rather than "how to infer orthology de novo", when batch-mapping gene IDs across species, or when comparing the resources for consensus calls. Encodes confidence-level semantics, 1:1 vs 1:many vs many:many, HomoloGene deprecation, and whe…

Works with any agent that supports SKILL.md skills.

What this skill can do

Sends data to these websites: data.orthodb.org, omabrowser.org, rest.kegg.jp

The author does not mention this.

Found in 17 places.

skills/bio-ortholog-inference/SKILL.md, line 33- Python: `requests.get()` against REST endpoints; `pandas` for parsing
skills/bio-ortholog-inference/SKILL.md, line 77r = requests.get('https://data.orthodb.org/v12/search',
skills/bio-ortholog-inference/SKILL.md, line 100r = requests.get(url, params=params, headers={'Accept': 'application/json'})

Show 14 more

skills/bio-ortholog-inference/SKILL.md, line 124r = requests.get(f'https://omabrowser.org/api/protein/{uniprot_acc}/orthologs/')
skills/bio-ortholog-inference/SKILL.md, line 142r = requests.get(f'https://rest.kegg.jp/link/ko/{species_code}:{gene}')
skills/bio-ortholog-inference/SKILL.md, line 148r = requests.get(f'https://rest.kegg.jp/link/genes/{ko_id}')
skills/bio-ortholog-inference/SKILL.md, line 204r = requests.get(url, params={'type': 'orthologues', 'target_species': target},
skills/bio-ortholog-inference/SKILL.md, line 275r = requests.get(f'https://omabrowser.org/api/protein/{oma_or_uniprot_id}/')
skills/bio-ortholog-inference/SKILL.md, line 283r = requests.get(url, params=params)
skills/bio-ortholog-inference/examples/compara_orthologs.py, line 14r = requests.get(url, params=params, headers=HEADERS)
skills/bio-ortholog-inference/examples/cross_resource.py, line 13r = requests.get(f'{ENSEMBL}/homology/symbol/{source}/{symbol}',
skills/bio-ortholog-inference/examples/cross_resource.py, line 24r = requests.get(f'{OMA}/protein/{uniprot_acc}/orthologs/')
skills/bio-ortholog-inference/examples/cross_resource.py, line 32r = requests.get(f'{ORTHODB}/search', params={'query': symbol, 'species': species_taxid})
skills/bio-ortholog-inference/examples/cross_resource.py, line 39r = requests.get(f'{ORTHODB}/orthologs', params={'id': og_id, 'species': species_taxid})
skills/bio-ortholog-inference/examples/kegg_orthology.py, line 12r = requests.get(f'{BASE}/link/ko/{species}:{gene}')
skills/bio-ortholog-inference/examples/kegg_orthology.py, line 19r = requests.get(f'{BASE}/link/genes/{ko_id}')
skills/bio-ortholog-inference/examples/kegg_orthology.py, line 26r = requests.get(f'{BASE}/get/{ko_id}')

Downloads and installs other software

The author does not mention this.

Found in 1 place.

skills/bio-ortholog-inference/usage-guide.md, line 10pip install requests pandas

Install

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

if [ -e ~/.agents/skills/'bio-ortholog-inference' ] || [ -L ~/.agents/skills/'bio-ortholog-inference' ]; then echo 'A skill folder named bio-ortholog-inference 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 "$d" checkout --quiet '908229c955510a1841b216e8bf58f6b22818d4dc' -- 'skills/bio-ortholog-inference' && mkdir -p ~/.agents/skills && cp -R "$d"/'skills/bio-ortholog-inference' ~/.agents/skills/'bio-ortholog-inference' && 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/'bio-ortholog-inference' ~/.claude/skills/'bio-ortholog-inference' (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`	80