/clinpgx-database

name: clinpgx-database
description: Access ClinPGx pharmacogenomics data (successor to PharmGKB). Query gene-drug interactions, CPIC guidelines, allele functions, for precision medicine and genotype-guided dosing decisions.
license: Unknown
metadata:
    skill-author: K-Dense Inc.

ClinPGx Database

Overview

ClinPGx (Clinical Pharmacogenomics Database) is a comprehensive resource for clinical pharmacogenomics information, successor to PharmGKB. It consolidates data from PharmGKB, CPIC, and PharmCAT, providing curated information on how genetic variation affects medication response. Access gene-drug pairs, clinical guidelines, allele functions, and drug labels for precision medicine applications.

When to Use This Skill

This skill should be used when:

• **Gene-drug interactions**: Querying how genetic variants affect drug metabolism, efficacy, or toxicity
• **CPIC guidelines**: Accessing evidence-based clinical practice guidelines for pharmacogenetics
• **Allele information**: Retrieving allele function, frequency, and phenotype data
• **Drug labels**: Exploring FDA and other regulatory pharmacogenomic drug labeling
• **Pharmacogenomic annotations**: Accessing curated literature on gene-drug-disease relationships
• **Clinical decision support**: Using PharmDOG tool for phenoconversion and custom genotype interpretation
• **Precision medicine**: Implementing pharmacogenomic testing in clinical practice
• **Drug metabolism**: Understanding CYP450 and other pharmacogene functions
• **Personalized dosing**: Finding genotype-guided dosing recommendations
• **Adverse drug reactions**: Identifying genetic risk factors for drug toxicity

Installation and Setup

Python API Access

The ClinPGx REST API provides programmatic access to all database resources. Basic setup:

uv pip install requests

API Endpoint

BASE_URL = "https://api.clinpgx.org/v1/"

**Rate Limits**:

• 2 requests per second maximum
• Excessive requests will result in HTTP 429 (Too Many Requests) response

**Authentication**: Not required for basic access

**Data License**: Creative Commons Attribution-ShareAlike 4.0 International License

For substantial API use, notify the ClinPGx team at api@clinpgx.org

Core Capabilities

1. Gene Queries

**Retrieve gene information** including function, clinical annotations, and pharmacogenomic significance:

import requests

# Get gene details
response = requests.get("https://api.clinpgx.org/v1/gene/CYP2D6")
gene_data = response.json()

# Search for genes by name
response = requests.get("https://api.clinpgx.org/v1/gene",
                       params={"q": "CYP"})
genes = response.json()

**Key pharmacogenes**:

• **CYP450 enzymes**: CYP2D6, CYP2C19, CYP2C9, CYP3A4, CYP3A5
• **Transporters**: SLCO1B1, ABCB1, ABCG2
• **Other metabolizers**: TPMT, DPYD, NUDT15, UGT1A1
• **Receptors**: OPRM1, HTR2A, ADRB1
• **HLA genes**: HLA-B, HLA-A

2. Drug and Chemical Queries

**Retrieve drug information** including pharmacogenomic annotations and mechanisms:

# Get drug details
response = requests.get("https://api.clinpgx.org/v1/chemical/PA448515")  # Warfarin
drug_data = response.json()

# Search drugs by name
response = requests.get("https://api.clinpgx.org/v1/chemical",
                       params={"name": "warfarin"})
drugs = response.json()

**Drug categories with pharmacogenomic significance**:

• Anticoagulants (warfarin, clopidogrel)
• Antidepressants (SSRIs, TCAs)
• Immunosuppressants (tacrolimus, azathioprine)
• Oncology drugs (5-fluorouracil, irinotecan, tamoxifen)
• Cardiovascular drugs (statins, beta-blockers)
• Pain medications (codeine, tramadol)
• Antivirals (abacavir)

3. Gene-Drug Pair Queries

**Access curated gene-drug relationships** with clinical annotations:

# Get gene-drug pair information
response = requests.get("https://api.clinpgx.org/v1/geneDrugPair",
                       params={"gene": "CYP2D6", "drug": "codeine"})
pair_data = response.json()

# Get all pairs for a gene
response = requests.get("https://api.clinpgx.org/v1/geneDrugPair",
                       params={"gene": "CYP2C19"})
all_pairs = response.json()

**Clinical annotation sources**:

• CPIC (Clinical Pharmacogenetics Implementation Consortium)
• DPWG (Dutch Pharmacogenetics Working Group)
• FDA (Food and Drug Administration) labels
• Peer-reviewed literature summary annotations

4. CPIC Guidelines

**Access evidence-based clinical practice guidelines**:

# Get CPIC guideline
response = requests.get("https://api.clinpgx.org/v1/guideline/PA166104939")
guideline = response.json()

# List all CPIC guidelines
response = requests.get("https://api.clinpgx.org/v1/guideline",
                       params={"source": "CPIC"})
guidelines = response.json()

**CPIC guideline components**:

• Gene-drug pairs covered
• Clinical recommendations by phenotype
• Evidence levels and strength ratings
• Supporting literature
• Downloadable PDFs and supplementary materials
• Implementation considerations

**Example guidelines**:

• 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)
• HLA-B*57:01-abacavir (avoid if positive)

5. Allele and Variant Information

**Query allele function and frequency data**:

# Get allele information
response = requests.get("https://api.clinpgx.org/v1/allele/CYP2D6*4")
allele_data = response.json()

# Get all alleles for a gene
response = requests.get("https://api.clinpgx.org/v1/allele",
                       params={"gene": "CYP2D6"})
alleles = response.json()

**Allele information includes**:

• Functional status (normal, decreased, no function, increased, uncertain)
• Population frequencies across ethnic groups
• Defining variants (SNPs, indels, CNVs)
• Phenotype