clinpgx-database SKILL.md skillA
clinpgx-database from jaechang-hits/sciagent-skills is an agent skill: a SKILL.md folder an AI agent loads when a task calls for it.
mdr add jaechang-hits/sciagent-skills/clinpgx-database@git:20260528.3e3f998Pins git:20260528.3e3f998 in mdr.lock. Pin the fingerprint instead.
- Audit grade
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- Kind
- SKILL.md skill
- Repository
- jaechang-hits/sciagent-skills
- Path
skills/genomics-bioinformatics/databases/clinpgx-database/SKILL.md- Versions recorded
- 1
- Latest version
- git:20260528.3e3f998, committed May 28, 2026
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- 381
- License
- a license file GitHub does not identify
Query the ClinPGx (formerly PharmGKB) REST API plus the CPIC PostgREST companion API for pharmacogenomic clinical annotations, CPIC/DPWG dosing guidelines, gene-drug pairs, variant-drug associations, FDA/EMA drug labels, and PGx pathways. Two-host architecture: api.clinpgx.org for annotation records, api.cpicpgx.org for genotype→recommendation lookups. No auth. For germline pathogenicity use clinvar-database; for somatic cancer PGx use cosmic-database or opentargets-database; for drug…
Collected from public GitHub. Every version is saved exactly as it was and never changes. Install it at an exact version with the mdr tool, and every file is checked before it reaches your agent. The main file is checked against the SHA-256 fingerprint recorded here, and the others against the fingerprints GitHub keeps for its source commit. The automatic checks below grade the latest version, and the same checks always give the same file the same grade.
What the file says
# ClinPGx (PharmGKB) Pharmacogenomics Database
## Overview
PharmGKB rebranded as **ClinPGx** in 2024 and the API moved from `api.pharmgkb.org` to `api.clinpgx.org`. The old host now returns 404/405; every example here uses the new endpoints. Two complementary APIs are used together:
- **ClinPGx Data API** (`api.clinpgx.org/v1`) — record-style access to genes, drugs, variants, clinical annotations, guideline annotations, drug labels, and pathways. Responses wrap data as `{"data": [...], "status": "success"}`. Filters use dotted property paths (e.g. `relatedChemicals.name=clopidogrel`, `levelOfEvidence.term=1A`).
- **CPIC PostgREST API** (`api.cpicpgx.org/v1`) — relational lookup of genotype → drug recommendation rows. PostgREST filter syntax (`column=eq.value`, JSON `cs.{...}` for jsonb containment). Returns flat JSON arrays.
Use ClinPGx for *what is known* about a gene/drug/variant; use CPIC for *how to prescribe* given a phenotype. The pattern is `ClinPGx for annotations, CPIC for recommendations`.
## When to Use
- Retrieving CPIC genotype-specific dosing recommendations for a gene-drug pair (e.g., CYP2C19 + clopidogrel) — use CPIC
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How to install
mdr add jaechang-hits/sciagent-skills/clinpgx-database@sha256:c1da2938dbcd31dfThe line at the top of this page pins the label git:20260528.3e3f998, which is what most people want. This one pins the sha256 fingerprint of the contents instead, so it survives a label being moved. Either way the exact version is written to mdr.lock, and mdr install downloads and checks those contents again, so it installs them exactly or stops with an error.
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Versions
The registry has recorded 1 version of this file, committed on May 28, 2026.
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Source
jaechang-hits/sciagent-skills · 381 stars · license a license file GitHub does not identify · pushed 2026-10-16 · branch main
API
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