How do I install the Pharmgkb Clinpgx skill?

Run npx skillmds@latest add gabrielmoreira/pharmgkb-clinpgx in your terminal (requires Node.js), paste this page's agent-chat prompt into Claude, Cursor, or any MCP-connected agent, or download the SKILL.md file and copy it into your agent's skills directory.

Is Pharmgkb Clinpgx safe to use?

This skill has not completed SkillMD's automated safety review yet. Independent scanners report: SkillSpector: PASS, Skill Scanner: PASS. Capability flags: executes scripts, makes network calls. SkillMD never runs a skill's scripts for you; review the SKILL.md before installing.

Which AI agents work with Pharmgkb Clinpgx?

This skill is tagged as working with Claude Code, Claude.ai, OpenAI Codex. SKILL.md is an open format, so most agents that read a skills directory can load it too.

Is Pharmgkb Clinpgx free to use?

Yes. Installing skills from SkillMD is free, and the skill stays under its author's original license.

Who published Pharmgkb Clinpgx?

gabrielmoreira (@gabrielmoreira) published this skill. Their other Agent Skills are listed on their SkillMD profile.

Pharmgkb Clinpgx by gabrielmoreira — Agent Skill

Name: Pharmgkb Clinpgx
Rating: 4.2 (5 reviews)
Author: gabrielmoreira

Pharmgkb Clinpgx

Query ClinPGx (PharmGKB) and CPIC for pharmacogenomics data. Use whenever the user asks about gene-drug interactions, pharmacogenomics clinical annotations, drug-metabolizing enzymes, CPIC guidelines, or variant-level PGx evidence for any gene symbol, drug name, rsID, or ClinPGx accession.

gabrielmoreira Updated Sep 9, 2026 17 repo stars

File contents

PharmGKB / ClinPGx Query Skill

Queries two complementary APIs:

ClinPGx API (api.clinpgx.org/v1) — gene, chemical, variant detail
CPIC API (api.cpicpgx.org/v1) — gene-drug pairs, CPIC guideline levels (PostgREST)

Auto-detects input entity type by pattern:

Input Pattern	Detected As	Data Sources
`PA128`	ClinPGx accession	gene or chemical detail + CPIC pairs
`rs4244285`	dbSNP rsID	variant lookup
`CYP2D6`	gene symbol (uppercase, 2-15 chars)	gene detail + CPIC pairs
anything else	drug / free text	chemical detail + CPIC pairs

API

Function	Input	Returns
`search(entity)`	single entity string	dict with `genes`, `chemicals`, `variants`, `cpic_pairs`, `related`
`search_batch(entities)`	list of entity strings	dict[str → search result]
`summarize(result, entity)`	search result + label	compact text (one line per hit)
`to_json(result)`	search result	indented JSON string
`search_gene(symbol)`	gene symbol	list of gene dicts (ClinPGx)
`search_drug(name)`	drug name	list of chemical dicts (ClinPGx)
`search_variant(rsid)`	rsID string	list of variant dicts (ClinPGx)
`get_cpic_pairs_by_gene(symbol)`	gene symbol	list of pair dicts (CPIC `pair_view`)
`get_cpic_pairs_by_drug(name)`	drug name	list of pair dicts (CPIC `pair_view`)

Usage

See if __name__ == "__main__" block in 49_PHARMGKB_CLINPGX.py for runnable examples covering: gene symbol, drug name, rsID, ClinPGx accession, batch search, and JSON output.

Key Fields

Gene (ClinPGx): id, symbol, name, hasCpicGuideline

Chemical (ClinPGx): id, name, types

Variant (ClinPGx): id, symbol, genes, location

CPIC Pair (pair_view): genesymbol, drugname, cpiclevel (A/B/C/D), clinpgxlevel (evidence), pgxtesting, guidelinename

Data Sources

ClinPGx (Stanford / NIH) — https://www.clinpgx.org/ — REST JSON, no key, ≤2 req/s, CC BY-SA 4.0
CPIC API — https://api.cpicpgx.org/ — PostgREST, no key — gene-drug guideline pairs
Note: PharmGKB was subsumed by ClinPGx (July 2025). CPIC API remains at api.cpicpgx.org.

---name: pharmgkb-clinpgxdescription: Query ClinPGx (PharmGKB) and CPIC for pharmacogenomics data. Use whenever the user asks about gene-drug interactions, pharmacogenomics clinical annotations, drug-metabolizing enzymes, CPIC guidelines, or variant-level PGx evidence for any gene symbol, drug name, rsID, or ClinPGx accession.--- # PharmGKB / ClinPGx Query Skill Queries two complementary APIs: - **ClinPGx API** (`api.clinpgx.org/v1`) — gene, chemical, variant detail - **CPIC API** (`api.cpicpgx.org/v1`) — gene-drug pairs, CPIC guideline levels (PostgREST) Auto-detects input entity type by pattern: | Input Pattern | Detected As | Data Sources | |---|---|---| | `PA128` | ClinPGx accession | gene or chemical detail + CPIC pairs | | `rs4244285` | dbSNP rsID | variant lookup | | `CYP2D6` | gene symbol (uppercase, 2-15 chars) | gene detail + CPIC pairs | | anything else | drug / free text | chemical detail + CPIC pairs | ## API | Function | Input | Returns | |---|---|---| | `search(entity)` | single entity string | dict with `genes`, `chemicals`, `variants`, `cpic_pairs`, `related` | | `search_batch(entities)` | list of entity strings | dict[str → search result] | | `summarize(result, entity)` | search result + label | compact text (one line per hit) | | `to_json(result)` | search result | indented JSON string | | `search_gene(symbol)` | gene symbol | list of gene dicts (ClinPGx) | | `search_drug(name)` | drug name | list of chemical dicts (ClinPGx) | | `search_variant(rsid)` | rsID string | list of variant dicts (ClinPGx) | | `get_cpic_pairs_by_gene(symbol)` | gene symbol | list of pair dicts (CPIC `pair_view`) | | `get_cpic_pairs_by_drug(name)` | drug name | list of pair dicts (CPIC `pair_view`) | ## Usage See `if __name__ == "__main__"` block in `49_PHARMGKB_CLINPGX.py` for runnable examples covering: gene symbol, drug name, rsID, ClinPGx accession, batch search, and JSON output. ## Key Fields **Gene** (ClinPGx): `id`, `symbol`, `name`, `hasCpicGuideline` **Chemical** (ClinPGx): `id`, `name`, `types` **Variant** (ClinPGx): `id`, `symbol`, `genes`, `location` **CPIC Pair** (`pair_view`): `genesymbol`, `drugname`, `cpiclevel` (A/B/C/D), `clinpgxlevel` (evidence), `pgxtesting`, `guidelinename` ## Data Sources - **ClinPGx** (Stanford / NIH) — https://www.clinpgx.org/ — REST JSON, no key, ≤2 req/s, CC BY-SA 4.0 - **CPIC API** — https://api.cpicpgx.org/ — PostgREST, no key — gene-drug guideline pairs - **Note**: PharmGKB was subsumed by ClinPGx (July 2025). CPIC API remains at `api.cpicpgx.org`.

Frequently asked questions