ucsc-conservation

name	ucsc-conservation
description	Fetch evolutionary conservation scores (phyloP, phastCons) and transcription-factor binding sites (ENCODE, JASPAR, ReMap) from the UCSC Genome Browser. Use to assess whether variants/regions are conserved or TF-bound. Public API, no credential needed.
license	Apache-2.0

Ucsc Conservation (Codex-native)

Codex-native adaptation of Google DeepMind's ucsc-conservation-and-tfbs 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

• UCSC Genome Browser API https://api.genome.ucsc.edu (/getData/track, /list/tracks)

Workflow

1. List available tracks for the assembly (/list/tracks?genome=hg38), then fetch track data for a region (/getData/track).
2. Report conservation scores and any overlapping TFBS for the region.

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

Boundaries

• State the assembly (hg38/hg19); coordinates and tracks are assembly-specific.
• Cite the track and source; conservation is a signal, not proof of function.