dbsnp-search

name	dbsnp-search
description	Look up and map short human variants (SNPs, indels) in NCBI dbSNP: resolve between rsIDs, GRCh38 coordinates, and HGVS, and get variant type, gene, clinical significance, and allele frequencies. Public NCBI API, no credential needed.
license	Apache-2.0

Dbsnp Search (Codex-native)

Codex-native adaptation of Google DeepMind's dbsnp-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

• NCBI Variation Services https://api.ncbi.nlm.nih.gov/variation/v0/
• NCBI E-utilities https://eutils.ncbi.nlm.nih.gov/entrez/eutils/ (db=snp)

Workflow

1. Given an rsID, fetch the refsnp record for type, gene, clinical significance, allele frequencies, and GRCh38 coordinates.
2. Map between rsID / VCF coordinates / HGVS with the Variation Services endpoints.

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

Boundaries

• Report the assembly (GRCh38) explicitly; coordinates differ across builds.
• Cite only rsIDs actually returned; never invent frequencies.