Agent skill

Clinpgx

Query the ClinPGx API for pharmacogenomic gene-drug data, clinical annotations, CPIC guidelines, and FDA drug labels

Install Clinpgx

skills CLI

$ npx skills add ClawBio/ClawBio --skill clinpgx -a claude-code

Project install by default; add -g for ~/.claude/skills/.

GitHub CLI

$ gh skill install ClawBio/ClawBio clinpgx --agent claude-code

Project scope by default; add --scope user for a personal install. Needs GitHub CLI 2.90.0 or later (public preview).

Manual copy

$ git clone --depth 1 https://github.com/ClawBio/ClawBio.git skills-src && mkdir -p .claude/skills && cp -r skills-src/skills/clinpgx .claude/skills/clinpgx && rm -rf skills-src

Use ~/.claude/skills/ instead of .claude/skills for a personal install. The folder must contain SKILL.md.

Claude Code skills documentation · loads skills from .claude/skills/

Paste into Claude Code

Install the "clinpgx" agent skill from https://github.com/ClawBio/ClawBio/tree/main/skills/clinpgx into .claude/skills/clinpgx/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "clinpgx", then confirm the skill loads.

Claude Code copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

$skill-installer

$skill-installer install https://github.com/ClawBio/ClawBio/tree/main/skills/clinpgx

Type this inside Codex. $skill-installer <name> installs a curated skill from openai/skills. The installer writes to $CODEX_HOME/skills (default ~/.codex/skills). Restart Codex if the skill does not show up.

skills CLI

$ npx skills add ClawBio/ClawBio --skill clinpgx -a codex

Project install goes to .agents/skills/; add -g for ~/.codex/skills/.

GitHub CLI

$ gh skill install ClawBio/ClawBio clinpgx --agent codex

Project scope by default (.agents/skills/); add --scope user for a personal install.

Manual copy

$ git clone --depth 1 https://github.com/ClawBio/ClawBio.git skills-src && mkdir -p .agents/skills && cp -r skills-src/skills/clinpgx .agents/skills/clinpgx && rm -rf skills-src

Use ~/.agents/skills/ instead of .agents/skills for a personal install.

Codex skills documentation · loads skills from .agents/skills/

Paste into Codex

Install the "clinpgx" agent skill from https://github.com/ClawBio/ClawBio/tree/main/skills/clinpgx into .agents/skills/clinpgx/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "clinpgx", then confirm the skill loads.

Codex copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

skills CLI

$ npx skills add ClawBio/ClawBio --skill clinpgx -a cursor

Project install goes to .agents/skills/; add -g for ~/.cursor/skills/.

GitHub CLI

$ gh skill install ClawBio/ClawBio clinpgx --agent cursor

Project scope by default (.agents/skills/); add --scope user for a personal install.

Manual copy

$ git clone --depth 1 https://github.com/ClawBio/ClawBio.git skills-src && mkdir -p .cursor/skills && cp -r skills-src/skills/clinpgx .cursor/skills/clinpgx && rm -rf skills-src

Use ~/.cursor/skills/ instead of .cursor/skills for a personal install.

Cursor skills documentation · loads skills from .cursor/skills/, .agents/skills/, .claude/skills/, .codex/skills/

Paste into Cursor

Install the "clinpgx" agent skill from https://github.com/ClawBio/ClawBio/tree/main/skills/clinpgx into .cursor/skills/clinpgx/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "clinpgx", then confirm the skill loads.

Cursor copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

gemini skills install

$ gemini skills install https://github.com/ClawBio/ClawBio.git --path skills/clinpgx

--scope user (default) or --scope workspace; --path is the subfolder of the repo that holds the skill; --consent skips the security confirmation prompt.

skills CLI

$ npx skills add ClawBio/ClawBio --skill clinpgx -a gemini-cli

Project install goes to .agents/skills/; add -g for ~/.gemini/skills/.

GitHub CLI

$ gh skill install ClawBio/ClawBio clinpgx --agent gemini-cli

Project scope by default (.agents/skills/); add --scope user for a personal install.

Manual copy

$ git clone --depth 1 https://github.com/ClawBio/ClawBio.git skills-src && mkdir -p .gemini/skills && cp -r skills-src/skills/clinpgx .gemini/skills/clinpgx && rm -rf skills-src

Use ~/.gemini/skills/ instead of .gemini/skills for a personal install, then run /skills reload.

Gemini CLI skills documentation · loads skills from .gemini/skills/, .agents/skills/

Paste into Gemini CLI

Install the "clinpgx" agent skill from https://github.com/ClawBio/ClawBio/tree/main/skills/clinpgx into .gemini/skills/clinpgx/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "clinpgx", then confirm the skill loads.

Gemini CLI copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

GitHub CLI

$ gh skill install ClawBio/ClawBio clinpgx

Installs for Copilot at project scope by default; add --scope user for a personal install. Preview a skill first with gh skill preview. Needs GitHub CLI 2.90.0 or later (public preview).

skills CLI

$ npx skills add ClawBio/ClawBio --skill clinpgx -a github-copilot

Project install goes to .agents/skills/; add -g for ~/.copilot/skills/.

Manual copy

$ git clone --depth 1 https://github.com/ClawBio/ClawBio.git skills-src && mkdir -p .github/skills && cp -r skills-src/skills/clinpgx .github/skills/clinpgx && rm -rf skills-src

Use ~/.copilot/skills/ instead of .github/skills for a personal install. Commit .github/skills so cloud agent and code review can use it.

GitHub Copilot skills documentation · loads skills from .github/skills/, .claude/skills/, .agents/skills/

Paste into GitHub Copilot

Install the "clinpgx" agent skill from https://github.com/ClawBio/ClawBio/tree/main/skills/clinpgx into .github/skills/clinpgx/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "clinpgx", then confirm the skill loads.

GitHub Copilot copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

skills CLI

$ npx skills add ClawBio/ClawBio --skill clinpgx -a opencode

OpenCode documents no install command of its own. Project install goes to .agents/skills/; add -g for ~/.config/opencode/skills/.

GitHub CLI

$ gh skill install ClawBio/ClawBio clinpgx --agent opencode

Project scope by default (.agents/skills/); add --scope user for a personal install.

Manual copy

$ git clone --depth 1 https://github.com/ClawBio/ClawBio.git skills-src && mkdir -p .opencode/skills && cp -r skills-src/skills/clinpgx .opencode/skills/clinpgx && rm -rf skills-src

Use ~/.config/opencode/skills/ instead of .opencode/skills for a personal install.

OpenCode skills documentation · loads skills from .opencode/skills/, .claude/skills/, .agents/skills/

Paste into OpenCode

Install the "clinpgx" agent skill from https://github.com/ClawBio/ClawBio/tree/main/skills/clinpgx into .opencode/skills/clinpgx/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "clinpgx", then confirm the skill loads.

OpenCode copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

Facts

Skill name: clinpgx
GitHub stars: 1.2k
Used in: 3 other repos
Token cost: ~963 tokens
SKILL.md length: 416 words
Files: 6
Skills in repo: 104
Repo updated: Oct 7, 2026
First seen: Oct 7, 2026
Licence: MIT

At a glance

Query the ClinPGx API for pharmacogenomic gene-drug data, clinical annotations, CPIC guidelines, and FDA drug labels

Works in 6 steps: Gene lookup: Retrieve gene info, known… → Drug lookup: Search drugs by name and… → Gene-drug pair analysis: Query specific… → …
Backend & APIs work in your project
SKILL.md covers Core Capabilities, Input Formats, Workflow and Example Queries, plus 4 more sections
Runs Python scripts from its folder

What it does

Clinpgx is an agent skill from ClawBio/ClawBio. Query the ClinPGx API for pharmacogenomic gene-drug data, clinical annotations, CPIC guidelines, and FDA drug labels

Its SKILL.md is about 960 tokens, which your agent loads only when the skill is triggered. The skill folder holds 6 other files (for example `INTENTS.json`, `api.py` and `clinpgx.py`).

It sits in Backend & APIs. The repository describes itself as: 🦖 ClawBio - The first bioinformatics-native AI agent skill library. Local-first. Reproducible. Open. Free. The licence is MIT.

When your agent uses it

Backend & APIs work in your project

Example prompts

“/clinpgx”

Requirements

Python 3

Workflow steps

6 steps, taken from the first numbered list in SKILL.md.

Gene lookup: Retrieve gene info, known alleles, and function annotations for any pharmacogene (e.g., CYP2D6, CYP2C19)
Drug lookup: Search drugs by name and retrieve associated PGx data
Gene-drug pair analysis: Query specific gene-drug interactions with CPIC evidence levels
Clinical annotation retrieval: Get curated variant-drug-phenotype annotations with evidence levels
CPIC guideline retrieval: Fetch clinical practice guidelines for gene-drug pairs
FDA drug label lookup: Find pharmacogenomic information from FDA-approved drug labels

What it can do on your machine

Read from SKILL.md and the folder at commit 5e045e3. It shows what the files ask for, not the result of running them.

Tool permissions
Pre-approves nothing: there is no allowed-tools line, so your agent's usual permission prompts apply.
From allowed-tools in the SKILL.md frontmatter.
Runs code
Ships script files (Python), which the agent can run.
From the folder's file list and the shell code blocks in SKILL.md.
Network
Links to these hosts (documentation or services it may open):
- api.clinpgx.org
From URLs in SKILL.md, links to its own repository left out.
Credentials
Names no API keys, tokens, secrets or passwords.
From names ending in _API_KEY, _TOKEN, _SECRET, _KEY or _PASSWORD in SKILL.md.

Context cost

Clinpgx loads about 963 tokens when it runs. Until then it costs about 31 tokens; SKILL.md has 416 words of instructions outside code blocks.

Always · name and description, kept in context so the agent knows when to use it: ~31
When it runs · the whole SKILL.md, loaded when a task matches: ~963

Estimates: characters ÷ 4, the usual rule of thumb; real counts depend on the model's tokenizer. Scripts and assets cost tokens only if the agent reads them.

Safety

Auto-check passed

The automated check found no risky patterns in SKILL.md.

Automated static check — not a guarantee. Review scripts before installing. It scans the text of SKILL.md for risky patterns (piping downloads into a shell, reading credential files, hidden Unicode, destructive commands); files beside SKILL.md are not scanned.

SKILL.md

The full file from ClawBio/ClawBio at commit 5e045e3, republished under its MIT licence (© ClawBio). 416 words, ~963 tokens.

Download SKILL.mdSave it as .claude/skills/clinpgx/SKILL.md (or your agent's skills folder). This skill also uses 5 other files; get the full folder from GitHub.

name: clinpgx
description: Query the ClinPGx API for pharmacogenomic gene-drug data, clinical annotations, CPIC guidelines, and FDA drug labels
license: MIT
metadata.version: 0.1.0

🧬 ClinPGx

You are ClinPGx, a specialised ClawBio agent for querying the ClinPGx pharmacogenomics database. Your role is to look up gene-drug interactions, clinical annotations, CPIC guidelines, FDA drug labels, and allele definitions from the ClinPGx REST API (https://api.clinpgx.org/).

Core Capabilities

Gene lookup: Retrieve gene info, known alleles, and function annotations for any pharmacogene (e.g., CYP2D6, CYP2C19)
Drug lookup: Search drugs by name and retrieve associated PGx data
Gene-drug pair analysis: Query specific gene-drug interactions with CPIC evidence levels
Clinical annotation retrieval: Get curated variant-drug-phenotype annotations with evidence levels
CPIC guideline retrieval: Fetch clinical practice guidelines for gene-drug pairs
FDA drug label lookup: Find pharmacogenomic information from FDA-approved drug labels

Input Formats

Gene symbol (text): Standard HGNC gene symbols, e.g., CYP2D6, CYP2C19, VKORC1
Drug name (text): Generic drug names, e.g., warfarin, clopidogrel, codeine
Comma-separated lists: CYP2D6,CYP2C19 or warfarin,codeine for batch queries

Workflow

When the user asks about a gene or drug in the ClinPGx database:

Parse query: Extract gene symbols and/or drug names from the user's request
Query API: Hit the ClinPGx REST API with rate limiting (2 req/sec) and local caching
Assemble data: Collect gene info, gene-drug pairs, clinical annotations, guidelines, drug labels, and alleles
Generate report: Produce a markdown report with CSV tables for structured data
Attribute source: Always cite ClinPGx/PharmGKB with CC BY-SA 4.0 license

Example Queries

"Look up CYP2D6 on ClinPGx"
"What drugs interact with CYP2C19?"
"Show me CPIC guidelines for warfarin"
"Get ClinPGx data for codeine and tramadol"
"What FDA drug labels mention DPYD?"

Show full SKILL.md (157 more words)Show less

Output Structure

output_directory/
├── report.md                    # Full markdown report
└── tables/
    ├── gene_drug_pairs.csv      # Gene-drug interactions with evidence levels
    ├── clinical_annotations.csv # Curated variant-drug-phenotype annotations
    ├── guidelines.csv           # CPIC/DPWG clinical guidelines
    └── alleles.csv              # Known allele definitions

Dependencies

Required:

requests >= 2.28.0 (HTTP client for API access)

Optional: None

Safety

No patient data is uploaded — all queries are gene/drug name lookups
API responses are cached locally for 24 hours to minimise redundant calls
Rate limit of 2 requests/second is enforced to comply with ClinPGx API policy
Data is licensed under CC BY-SA 4.0 — attribution is included in every report
ClawBio is a research and educational tool. It is not a medical device and does not provide clinical diagnoses. Consult a healthcare professional before making any medical decisions.

Integration with Bio Orchestrator

This skill is invoked by the Bio Orchestrator when:

User mentions "ClinPGx", "PharmGKB", "gene-drug pair", "CPIC guideline", "drug label"
User asks to look up a specific pharmacogene or drug in the database

It can be chained with:

pharmgx-reporter: After generating a patient PGx report, query ClinPGx for deeper annotation on flagged gene-drug pairs
vcf-annotator: Use ClinPGx allele definitions to annotate VCF variants

Files

SKILL.md and 5 other files in skills/clinpgx of ClawBio/ClawBio.

SKILL.md
INTENTS.json
api.py
clinpgx.py
tests/__init__.py
tests/test_clinpgx.py

Open the folder on GitHubat commit 5e045e3

Used in 3 other repositories

We found 3 copies of this SKILL.md (exact, near-identical or edited) in other folders, from 3 other GitHub owners. This page covers the copy in ClawBio/ClawBio, which our catalogue first saw on October 7, 2026.

Compare with similar skills

Clinpgx next to the 5 skills that share the most tags, products or categories with it. Stars are the repository's; “used in” counts other GitHub owners with a copy.

Clinpgx compared with similar skills
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Octo SummaryMininglamp-OSS/octo-cli	918	—	~1k	Automated safety check: Pass	Apache-2.0	10 days ago
Goosetown Researcher GitHubaaif-goose/goosetown	154	—	~1.6k	Automated safety check: Pass	Apache-2.0	3 mo ago
Spatial S3 Domains SVGQING1105/ezST	101	—	~476	Automated safety check: Pass	MIT	1 mo ago
Tech Decisionteam-attention/hoyeon	173	—	~1.4k	Automated safety check: Pass	MIT	4 mo ago

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Questions about Clinpgx

What does Clinpgx do?

Query the ClinPGx API for pharmacogenomic gene-drug data, clinical annotations, CPIC guidelines, and FDA drug labels. Clinpgx is an agent skill from ClawBio/ClawBio.

When should I use Clinpgx?

Clinpgx fits situations like: backend & APIs work in your project.

How do I install Clinpgx in Claude Code?

Run `npx skills add ClawBio/ClawBio --skill clinpgx -a claude-code`. Or copy the skill folder (skills/clinpgx in ClawBio/ClawBio) into .claude/skills/clinpgx in your project. Claude Code loads it when a task matches its description.

How do I install Clinpgx in Codex?

Run `npx skills add ClawBio/ClawBio --skill clinpgx -a codex`. Or copy the skill folder (skills/clinpgx in ClawBio/ClawBio) into .agents/skills/clinpgx in your project. Codex loads it when a task matches its description.

Can I use Clinpgx in Cursor, Gemini CLI or GitHub Copilot?

Cursor, Gemini CLI, GitHub Copilot and OpenCode also load SKILL.md folders. With the skills CLI, run `npx skills add ClawBio/ClawBio --skill clinpgx -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/clinpgx, .gemini/skills/clinpgx, .github/skills/clinpgx and .opencode/skills/clinpgx in your project.

What does Clinpgx need to run?

Going by SKILL.md and its folder, Clinpgx needs Python for the scripts in its folder. Our summary lists: Python 3.

Does Clinpgx access the network?

SKILL.md names 1 domain. As links in the text: api.clinpgx.org. This is read from the text; nothing was executed.

Is Clinpgx safe to install?

Our automated static check of SKILL.md found no risky patterns, such as piping downloads into a shell, reading credential files or hidden Unicode. It is not a guarantee. Review the folder before installing.

What licence does Clinpgx use?

Clinpgx is published under the MIT licence (declared in SKILL.md). It allows redistribution, so the full SKILL.md is shown on this page.

How many tokens does Clinpgx use?

About 963 tokens (SKILL.md is roughly 3.9k characters). Agents keep only the skill's name and description in context until a task matches; then they load SKILL.md in full.

What are the alternatives to Clinpgx?

Skills that share tags, products or a category with Clinpgx: Tech Decision (team-attention/plugins-for-claude-natives, 827 stars), Octo Summary (Mininglamp-OSS/octo-cli, 918 stars), Goosetown Researcher GitHub (aaif-goose/goosetown, 154 stars) and Spatial S3 Domains SVG (QING1105/ezST, 101 stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.

Who maintains Clinpgx?

ClawBio (a GitHub organization) maintains it in ClawBio/ClawBio, which has 1,154 GitHub stars. The repository holds 104 skills in this directory. The repository was last updated on October 7, 2026.

Source: ClawBio/ClawBio on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.

Install Clinpgx

Facts

At a glance

What it does

When your agent uses it

Example prompts

Requirements

Workflow steps

What it can do on your machine

Tool permissions

Runs code

Network

Credentials

Context cost

Safety

SKILL.md

🧬 ClinPGx

Core Capabilities

Input Formats

Workflow

Example Queries

Output Structure

Dependencies

Safety

Integration with Bio Orchestrator

Files

Used in 3 other repositories

Compare with similar skills

Similar skills

More from ClawBio/ClawBio

Related

Questions about Clinpgx