bio-ensembl-rest
Query the Ensembl REST API for gene/transcript/protein lookup, sequence retrieval, comparative genomics (Compara), variant effect prediction (VEP), regulatory features, and cross-species ortholog/paralog calls. Use when pulling Ensembl-native data (Ensembl Gene IDs, version-pinned releases, archive endpoints for reproducibility), gene/transcript/exon structure with stable IDs, or VEP for variant annotation. Encodes the 15 req/sec rate limit, archive (e110.rest.ensembl.org) for reproducibility, Ensembl divisions (vertebrates / plants / fungi / metazoa / bacteria), and the symbol-vs-ID stability
npx skills add BioTender-max/awesome-bio-agent-skills --skill ensembl-rest --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+, Ensembl REST API (release 110+); Ensembl release schedule is roughly quarterly Before using code patterns, verify installed versions match. If versions differ: - Python: `pip show requests` - API surface: check release notes at https://rest.ensembl.org Each Ensembl release has an archive REST endpoint (e.g. `https://e110.rest.ensembl.org`) for reproducibility. # Ensembl REST **"Pull Ensembl-native gene / transcript / variant data programmatically"** -> Ensembl REST is distinct from NCBI Entrez and BioMart. It is the right answer for: stable Ensembl IDs, transcript / exon structure, VEP (Variant Effect Predictor) annotation, Compara orthologs at vertebrate scale, regulatory feature annotation, and any workflow rooted in Ensembl's coordinate system. Two facts dominate Ensembl REST work: (1) the **15 req/sec / 55,000 req/hour rate limit** — high enough for hundreds of queries, low enough that bulk work (>5,000) belongs in BioMart instead; (2) **versioned archive endpoints** — `https://e110.rest.ensembl.org` pins to release 110 for reproducibility, while `https://rest.ensembl.org` follows the current release. - Py
- Version Compatibility
- Required Setup
- Ensembl divisions
- Version pinning
- Major endpoint groups
- The symbol-vs-ID stability problem
- Rate-limit math
- VEP (Variant Effect Predictor)
- Compara homology
- Code patterns
- Symbol -> stable Ensembl Gene ID
- Sequence retrieval by Ensembl ID
- Overlap: what genes are in this region
- VEP for a single variant
What does the bio-ensembl-rest skill do?
Query the Ensembl REST API for gene/transcript/protein lookup, sequence retrieval, comparative genomics (Compara), variant effect prediction (VEP), regulatory features, and cross-species ortholog/paralog calls. Use when pulling Ensembl-native data (Ensembl Gene IDs, version-pinned releases, archive endpoints for reproducibility), gene/transcript/exon structure with stable IDs, or VEP for variant annotation. Encodes the 15 req/sec rate limit, archive (e110.rest.ensembl.org) for reproducibility, Ensembl divisions (vertebrates / plants / fungi / metazoa / bacteria), and the symbol-vs-ID stability
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill ensembl-rest --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.