Skills clinpgx-database
D

clinpgx-database

Safe ⚙️ External commands🌐 Network access📁 Filesystem access

Query ClinPGx pharmacogenomics database

Also available from: davila7

Access ClinPGx to retrieve pharmacogenomics data including gene-drug interactions, CPIC guidelines, and allele function information. This skill supports precision medicine by providing clinical decision support for genotype-guided medication dosing.

Supports: Claude Codex Code(CC)
🥉 73 Bronze
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Test it

Using "clinpgx-database". Get information about the CYP2C19 gene and its relationship with clopidogrel

Expected outcome:

  • CYP2C19 is a cytochrome P450 enzyme involved in drug metabolism
  • CYP2C19-clopidogrel pair has CPIC Level A recommendation
  • Poor metabolizers should receive alternative antiplatelet therapy
  • Associated alleles: *2 (no function), *3 (no function), *17 (increased function)

Using "clinpgx-database". What are the CPIC guidelines for warfarin dosing based on CYP2C9 genotype?

Expected outcome:

  • CPIC provides genotype-guided warfarin dosing recommendations
  • CYP2C9*2 and *3 alleles are associated with reduced enzyme activity
  • Patients with reduced function alleles require lower warfarin doses
  • VKORC1 genotype also influences dosing requirements

Using "clinpgx-database". Find all clinically actionable pharmacogenes with CPIC Level A recommendations

Expected outcome:

  • CYP2D6-codeine (avoid in ultra-rapid metabolizers)
  • CYP2C19-clopidogrel (alternative therapy for poor metabolizers)
  • TPMT-azathioprine (dose reduction for intermediate/poor metabolizers)
  • DPYD-fluoropyrimidines (dose adjustment based on activity score)

Security Audit

Safe
v4 • 1/17/2026

All 376 static findings are FALSE POSITIVES. The skill is a legitimate pharmacogenomics database API client accessing the public ClinPGx API (api.clinpgx.org). The static analyzer misidentified Markdown code fences (using backticks) as shell command execution, gene function descriptions as cryptographic algorithms, and clinical decision support tool references as system reconnaissance. Network calls are to a known public API, file writes are for caching API results, and there is no malicious code present.

4
Files scanned
3,859
Lines analyzed
3
findings
4
Total audits

Risk Factors

⚙️ External commands (3)
references/api_reference.md:7-10 SKILL.md:36-38 SKILL.md:522-530
🌐 Network access (3)
references/api_reference.md:521-527 scripts/query_clinpgx.py:24-36 SKILL.md:66-72
📁 Filesystem access (2)
scripts/query_clinpgx.py:105-106 SKILL.md:484-485
Audited by: claude View Audit History →

Quality Score

64
Architecture
90
Maintainability
87
Content
20
Community
100
Security
78
Spec Compliance

What You Can Build

Review Patient Medications

Check patient genotypes against prescribed medications to identify drug-gene interactions requiring dose adjustment.

Analyze Gene-Drug Evidence

Query clinical annotations and CPIC guidelines to support pharmacogenomics research studies.

Build PGx Applications

Integrate ClinPGx API into electronic health records or clinical decision support systems.

Try These Prompts

Gene Lookup 
Use the ClinPGx skill to find information about the CYP2D6 gene including its function and related drugs.
Drug Interactions 
Query ClinPGx for all gene-drug pairs involving clopidogrel and CYP2C19 with CPIC guideline information.
Clinical Guidelines 
Get the CPIC guideline recommendations for codeine prescribing based on CYP2D6 metabolizer status.
Allele Frequencies 
Find allele frequency data for CYP2D6 across European, African, and East Asian populations.

Best Practices

  • Always implement rate limiting (0.5 second delay) when making API calls to respect the 2 req/sec limit
  • Cache frequently accessed data locally to reduce API calls and improve performance
  • Verify clinical decisions against primary sources like CPIC guidelines and FDA drug labels

Avoid

  • Do not make clinical decisions based solely on API results without verifying against primary sources
  • Do not exceed the API rate limit as this will result in HTTP 429 errors
  • Do not hardcode sensitive credentials in client code when substantial API use requires authentication

Frequently Asked Questions

What is ClinPGx?
ClinPGx is a comprehensive pharmacogenomics database that consolidates data from PharmGKB, CPIC, and PharmCAT for clinical use.
Is authentication required?
No authentication is required for basic API access. Contact api@clinpgx.org for substantial use.
What rate limits apply?
The API allows a maximum of 2 requests per second. Implement 500ms delay between requests.
What genes are covered?
Key pharmacogenes include CYP450 enzymes (CYP2D6, CYP2C19, CYP2C9), transporters (SLCO1B1), and others like TPMT and DPYD.
What evidence levels are available?
Evidence levels range from 1A (CPIC/FDA guideline) to Level 4 (case reports), with 1A being highest quality.
Can this be used for clinical decisions?
The skill provides data for research and decision support. Always verify clinical decisions against primary sources.

Developer Details

Author

K-Dense-AI

License

CC-BY-SA-4.0

Repository

https://github.com/K-Dense-AI/claude-scientific-skills/tree/main/scientific-skills/clinpgx-database

Ref

main

File structure

📁 references/

📄 api_reference.md

📁 scripts/

📄 query_clinpgx.py

📄 SKILL.md