bio-ortholog-inference
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 when to defect to de novo computation.
npx skills add BioTender-max/awesome-bio-agent-skills --skill bioskills__database-access__ortholog-inference --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
## Version Compatibility Reference examples tested with: requests 2.31+, pandas 2.2+; OrthoDB v12 API, Ensembl REST (Ensembl release 112+), OMA REST API, eggNOG 6.0+, PANTHER v18+ Before using code patterns, verify installed versions match. If versions differ: - Python: `pip show requests pandas` - API surface: confirm endpoint URLs and JSON schema match the current API docs If endpoints return 404 or unexpected JSON, check release notes for the resource; schema migrations happen with each major version (Ensembl release is the biggest moving target). # Ortholog Inference (Database Access) **"What is the X ortholog of gene Y?"** -> Many ortholog resources have already done the inference at scale. Pulling their answers is faster and often more reliable than re-computing. This skill is the **database-access** view: how to query the major orthology resources programmatically, what their confidence semantics mean, and when their disagreements matter. For **de novo orthology inference** (running OrthoFinder, SonicParanoid, OMA standalone on local proteomes), see `comparative-genomics/ortholog-inference` — that's a much deeper treatment of the computational side. This skill is about pulli
- Version Compatibility
- Required Setup
- Decision matrix: which resource for which question?
- Per-resource API reference
- OrthoDB v12
- Ensembl Compara (via Ensembl REST)
- OMA REST API
- eggNOG (5/6)
- KEGG Orthology (KO)
- PANTHER
- HomoloGene (deprecated)
- Confidence-level semantics
- The orthology conjecture (and why resources disagree)
- Code patterns
What does the bio-ortholog-inference skill do?
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 when to defect to de novo computation.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill bioskills__database-access__ortholog-inference --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From BioTender-max/awesome-bio-agent-skills, a repository with 135 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.