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bio-ortholog-inference
80 / 100 · Low risk
Fine to try.
By BioTender-max/awesome-bio-agent-skills (GitHub) · design · 219 stars · scanned at commit 8cbdd18
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.
Show 14 more
- skills/bioskills/bioskills__database-access__ortholog-inference/SKILL.md, line 125
r = requests.get(f'https://omabrowser.org/api/protein/{uniprot_acc}/orthologs/') - skills/bioskills/bioskills__database-access__ortholog-inference/SKILL.md, line 144
r = requests.get(f'https://rest.kegg.jp/link/ko/{species_code}:{gene}') - skills/bioskills/bioskills__database-access__ortholog-inference/SKILL.md, line 150
r = requests.get(f'https://rest.kegg.jp/link/genes/{ko_id}') - skills/bioskills/bioskills__database-access__ortholog-inference/SKILL.md, line 207
r = requests.get(url, params={'type': 'orthologues', 'target_species': target}, - skills/bioskills/bioskills__database-access__ortholog-inference/SKILL.md, line 278
r = requests.get(f'https://omabrowser.org/api/protein/{oma_or_uniprot_id}/') - skills/bioskills/bioskills__database-access__ortholog-inference/SKILL.md, line 286
r = requests.get(url, params=params) - skills/bioskills/bioskills__database-access__ortholog-inference/examples/compara_orthologs.py, line 14
r = requests.get(url, params=params, headers=HEADERS) - skills/bioskills/bioskills__database-access__ortholog-inference/examples/cross_resource.py, line 13
r = requests.get(f'{ENSEMBL}/homology/symbol/{source}/{symbol}', - skills/bioskills/bioskills__database-access__ortholog-inference/examples/cross_resource.py, line 24
r = requests.get(f'{OMA}/protein/{uniprot_acc}/orthologs/') - skills/bioskills/bioskills__database-access__ortholog-inference/examples/cross_resource.py, line 32
r = requests.get(f'{ORTHODB}/search', params={'query': symbol, 'species': species_taxid}) - skills/bioskills/bioskills__database-access__ortholog-inference/examples/cross_resource.py, line 39
r = requests.get(f'{ORTHODB}/orthologs', params={'id': og_id, 'species': species_taxid}) - skills/bioskills/bioskills__database-access__ortholog-inference/examples/kegg_orthology.py, line 12
r = requests.get(f'{BASE}/link/ko/{species}:{gene}') - skills/bioskills/bioskills__database-access__ortholog-inference/examples/kegg_orthology.py, line 19
r = requests.get(f'{BASE}/link/genes/{ko_id}') - skills/bioskills/bioskills__database-access__ortholog-inference/examples/kegg_orthology.py, line 26
r = requests.get(f'{BASE}/get/{ko_id}')
Downloads and installs other software
The author does not mention this.
Found in 1 place.
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=$(mktemp -d) && git clone --quiet --filter=blob:none --no-checkout 'https://github.com/BioTender-max/awesome-bio-agent-skills' "$d" && git -C "$d" checkout --quiet '8cbdd18837aa6296c4e77616a03b323bd69b57b1' -- 'skills/bioskills/bioskills__database-access__ortholog-inference' && mkdir -p ~/.agents/skills && cp -R "$d"/'skills/bioskills/bioskills__database-access__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.
Badge for your README
The badge for BioTender-max/awesome-bio-agent-skills shows the score of its lowest-scoring skill.
[](https://zalavijaysinh.github.io/skilltrust/repos/BioTender-max/awesome-bio-agent-skills/)
Score history
| Date | Version | Score |
|---|
| 2026-11-07 | 8cbdd18 | 80 |
Also found in
Identical copies of this skill exist at:
- BioTender-max/awesome-bio-agent-skills/skills/bioskills/database-access__ortholog-inference