ensembl-search

name	ensembl-search
description	Resolve gene/transcript/protein IDs, fetch genomic or protein sequences, retrieve gene structure (exons), and predict variant consequences (VEP) via the Ensembl REST API. Use as an ID translator, sequence source, and variant-effect tool. Public API, no credential needed.
license	Apache-2.0

Ensembl Search (Codex-native)

Codex-native adaptation of Google DeepMind's ensembl-database skill (science-skills, Apache-2.0). Uses the public API directly through Codex's own tools.

Gates (ask before proceeding)

• Terms notice: on first use in a workspace, tell the user to review the source's terms of use and record the notice in provenance.
• Network / install: read-only public access; be polite about rate limits. Write large responses to a file and parse them; if you write helper code, run it via uv run, never bare python3. Ask before installs or large downloads.

Endpoints

• Ensembl REST https://rest.ensembl.org (GRCh37 at https://grch37.rest.ensembl.org)

Workflow

1. Resolve IDs with /lookup/id/<id> or /xrefs/symbol/<species>/<symbol>; fetch sequence with /sequence/id/<id>.
2. Predict variant consequences with /vep/<species>/hgvs/<hgvs> or /vep/<species>/region.

• Provenance & review: record queries, endpoints, and cited identifiers with $science-provenance; check claims with $science-review before presenting.

Boundaries

• State the species and assembly (GRCh38 vs GRCh37) explicitly.
• Cite only Ensembl IDs actually returned; VEP predictions are computational.