domains / research / clinpgx-api-query / clinpgx-database

clinpgx-database

Skill card

combined

The copies overlap heavily on the ClinPGx REST API endpoints and rate limits, but they disagree on the execution model and add different material steps. The Vibe-Skills and OpenClaw copies are near-identical, providing a detailed API reference with inline Python examples. The aipoch copy is a wrapper that mandates a specific packaged script (scripts/query_clinpgx.py), a different dependency version (requests>=2.31.0), and a specific retry/backoff implementation. Because the aipoch copy provides a distinct, more robust execution path (script-based with retries) while the others provide a direct API reference, crowning one would hide the alternative implementation strategy.

Repositories

Other copies

Combined skill

# ClinPGx Database Access

## Overview
ClinPGx is a comprehensive pharmacogenomics resource (successor to PharmGKB) providing gene-drug interactions, CPIC guidelines, and allele data.

## Setup
1. Install dependencies: `pip install "requests>=2.31.0"`
2. Set base URL: `https://api.clinpgx.org/v1/`
3. Respect rate limits: Max 2 requests/second.

## Execution Strategy
Choose one of the following approaches:

### Option A: Direct API Queries (Reference)
Use `requests` to query specific endpoints:
- **Genes**: `GET /gene/{symbol}` or `GET /gene?q={query}`
- **Drugs**: `GET /chemical/{id}` or `GET /chemical?name={name}`
- **Gene-Drug Pairs**: `GET /geneDrugPair?gene={gene}&drug={drug}`
- **Guidelines**: `GET /guideline/{id}` or `GET /guideline?source=CPIC`
- **Alleles**: `GET /allele/{allele}` or `GET /allele?gene={gene}`

### Option B: Packaged Script (Robust)
If using the `aipoch/medical-research-skills` package:
1. Navigate to the skill folder.
2. Run `python scripts/query_clinpgx.py`.
3. This script includes built-in exponential backoff for HTTP 429 errors and session management.

## Key Data Points
- **Pharmacogenes**: CYP450 (CYP2D6, CYP2C19), Transporters (SLCO1B1), HLA genes.
- **Guidelines**: CPIC, DPWG, FDA labels.
- **Allele Info**: Functional status, population frequencies, defining variants.

## Conflicts
- **Repository**: `aipoch/medical-research-skills` requires the use of a specific script and pinned dependencies, while `foryourhealth111-pixel/Vibe-Skills` and `FreedomIntelligence/OpenClaw-Medical-Skills` provide direct API usage examples without a script wrapper.