jaspar-search

name	jaspar-search
description	Retrieve transcription-factor binding profiles (PFMs/PWMs) from JASPAR, resolve gene symbols to JASPAR matrix IDs, and get TF metadata in multiple formats (MEME, TRANSFAC, PFM, JASPAR). Public API, no credential needed.
license	Apache-2.0

Jaspar Search (Codex-native)

Codex-native adaptation of Google DeepMind's jaspar-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

• JASPAR API https://jaspar.elixir.no/api/v1/

Workflow

1. Resolve a TF symbol to a matrix id via /matrix/?search=<TF>, then fetch /matrix/<MA_ID>/ in the desired format.
2. Report the matrix id, TF name, collection, and version.

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

Boundaries

• Report the JASPAR release/collection (e.g. CORE) and matrix version.
• Cite only matrix IDs actually returned.