bio-ortholog-inference SKILL.md skillA
bio-ortholog-inference from pku-yuangroup/openai4s is an agent skill: a SKILL.md folder an AI agent loads when a task calls for it.
mdr add pku-yuangroup/openai4s/bio-ortholog-inference@git:20260821.2d1b678Pins git:20260821.2d1b678 in mdr.lock. Pin the fingerprint instead.
- Audit grade
- A, 17 of 17 checks passed
- Kind
- SKILL.md skill
- Repository
- pku-yuangroup/openai4s
- Path
skills/bioskills/bio-database-access-ortholog-inference/SKILL.md- Versions recorded
- 1
- Latest version
- git:20260821.2d1b678, committed Aug 21, 2026
- Size
- 18,868 bytes
- Repository stars
- 662
- License
- MIT
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…
Collected from public GitHub. Every version is saved exactly as it was and never changes. Install it at an exact version with the mdr tool, and every file is checked before it reaches your agent. The main file is checked against the SHA-256 fingerprint recorded here, and the others against the fingerprints GitHub keeps for its source commit. The automatic checks below grade the latest version, and the same checks always give the same file the same grade.
What the file says
## 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. …
Read the whole file at its exact version.
How to install
mdr add pku-yuangroup/openai4s/bio-ortholog-inference@sha256:e7d96fa8a3a16f36The line at the top of this page pins the label git:20260821.2d1b678, which is what most people want. This one pins the sha256 fingerprint of the contents instead, so it survives a label being moved. Either way the exact version is written to mdr.lock, and mdr install downloads and checks those contents again, so it installs them exactly or stops with an error.
[](https://markdownregistry.com/a/art_n4b47pdlpfbek4rt)
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Versions
The registry has recorded 1 version of this file, committed on Aug 21, 2026.
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Source
pku-yuangroup/openai4s · 662 stars · license MIT · pushed 2026-11-03 · branch main
API
GET https://markdownregistry.com/api/v1/artifacts/art_n4b47pdlpfbek4rt GET https://markdownregistry.com/api/v1/resolve?ref=pku-yuangroup/openai4s/bio-ortholog-inference GET https://markdownregistry.com/api/v1/blob/e7d96fa8a3a16f369065448c08dfc42bf8e91ded5c22fd8c65407bf3fa85b8bc
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Guides: the SKILL.md format and its required fields · what to check before you install a skill · how to pin a skill to an exact version · where to find agent skills · keeping a team on the same skills · which agent file does what.