claude-scientific-skills/scientific-databases/clinpgx-database/SKILL.md

name, description

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description

clinpgx-database

Toolkit for accessing ClinPGx, a clinical pharmacogenomics database providing information on how genetic variation affects drug response. Use this skill when working with pharmacogenomics data, querying gene-drug interactions, accessing CPIC clinical guidelines, retrieving allele function and frequency information, exploring PharmGKB annotations, or conducting research on personalized medicine and precision pharmacotherapy. ClinPGx consolidates PharmGKB, CPIC, and PharmCAT resources.

ClinPGx Database

Overview

Facilitate access to and querying of ClinPGx (Clinical Pharmacogenomics Database), a comprehensive resource for clinical pharmacogenomics information. ClinPGx is the successor to PharmGKB (launched officially in July 2025) and consolidates data from PharmGKB, CPIC (Clinical Pharmacogenetics Implementation Consortium), and PharmCAT (Pharmacogenomics Clinical Annotation Tool). The database provides curated information on how human genetic variation affects medication response, including gene-drug pairs, clinical guidelines, allele functions, and drug labels. Managed at Stanford University as a ClinGen (Clinical Genome Resource) affiliate grant.

When to Use This Skill

Use this skill when queries involve:

• 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:

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 assignment
• References to PharmVar and other nomenclature systems

Phenotype categories:

• Ultra-rapid metabolizer (UM): Increased enzyme activity
• Normal metabolizer (NM): Normal enzyme activity
• Intermediate metabolizer (IM): Reduced enzyme activity
• Poor metabolizer (PM): Little to no enzyme activity

6. Variant Annotations

Access clinical annotations for specific genetic variants:

# Get variant information
response = requests.get("https://api.clinpgx.org/v1/variant/rs4244285")
variant_data = response.json()

# Search variants by position (if supported)
response = requests.get("https://api.clinpgx.org/v1/variant",
                       params={"chromosome": "10", "position": "94781859"})
variants = response.json()

Variant data includes:

• rsID and genomic coordinates
• Gene and functional consequence
• Allele associations
• Clinical significance
• Population frequencies
• Literature references

7. Clinical Annotations

Retrieve curated literature annotations (formerly PharmGKB clinical annotations):

# Get clinical annotations
response = requests.get("https://api.clinpgx.org/v1/clinicalAnnotation",
                       params={"gene": "CYP2D6"})
annotations = response.json()

# Filter by evidence level
response = requests.get("https://api.clinpgx.org/v1/clinicalAnnotation",
                       params={"evidenceLevel": "1A"})
high_evidence = response.json()

Evidence levels (from highest to lowest):

• Level 1A: High-quality evidence, CPIC/FDA/DPWG guidelines
• Level 1B: High-quality evidence, not yet guideline
• Level 2A: Moderate evidence from well-designed studies
• Level 2B: Moderate evidence with some limitations
• Level 3: Limited or conflicting evidence
• Level 4: Case reports or weak evidence

8. Drug Labels

Access pharmacogenomic information from drug labels:

# Get drug labels with PGx information
response = requests.get("https://api.clinpgx.org/v1/drugLabel",
                       params={"drug": "warfarin"})
labels = response.json()

# Filter by regulatory source
response = requests.get("https://api.clinpgx.org/v1/drugLabel",
                       params={"source": "FDA"})
fda_labels = response.json()

Label information includes:

• Testing recommendations
• Dosing guidance by genotype
• Warnings and precautions
• Biomarker information
• Regulatory source (FDA, EMA, PMDA, etc.)

9. Pathways

Explore pharmacokinetic and pharmacodynamic pathways:

# Get pathway information
response = requests.get("https://api.clinpgx.org/v1/pathway/PA146123006")  # Warfarin pathway
pathway_data = response.json()

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

Pathway diagrams show:

• Drug metabolism steps
• Enzymes and transporters involved
• Gene variants affecting each step
• Downstream effects on efficacy/toxicity
• Interactions with other pathways

Query Workflow

Workflow 1: Clinical Decision Support for Drug Prescription

1. Identify patient genotype for relevant pharmacogenes:

   # Example: Patient is CYP2C19 *1/*2 (intermediate metabolizer)
   response = requests.get("https://api.clinpgx.org/v1/allele/CYP2C19*2")
   allele_function = response.json()
   

2. Query gene-drug pairs for medication of interest:

   response = requests.get("https://api.clinpgx.org/v1/geneDrugPair",
                          params={"gene": "CYP2C19", "drug": "clopidogrel"})
   pair_info = response.json()
   

3. Retrieve CPIC guideline for dosing recommendations:

   response = requests.get("https://api.clinpgx.org/v1/guideline",
                          params={"gene": "CYP2C19", "drug": "clopidogrel"})
   guideline = response.json()
   # Recommendation: Alternative antiplatelet therapy for IM/PM
   

4. Check drug label for regulatory guidance:

   response = requests.get("https://api.clinpgx.org/v1/drugLabel",
                          params={"drug": "clopidogrel"})
   label = response.json()
   

Workflow 2: Gene Panel Analysis

1. Get list of pharmacogenes in clinical panel:

   pgx_panel = ["CYP2C19", "CYP2D6", "CYP2C9", "TPMT", "DPYD", "SLCO1B1"]
   

2. For each gene, retrieve all drug interactions:

   all_interactions = {}
   for gene in pgx_panel:
       response = requests.get("https://api.clinpgx.org/v1/geneDrugPair",
                              params={"gene": gene})
       all_interactions[gene] = response.json()
   

3. Filter for CPIC guideline-level evidence:

   for gene, pairs in all_interactions.items():
       for pair in pairs:
           if pair.get('cpicLevel'):  # Has CPIC guideline
               print(f"{gene} - {pair['drug']}: {pair['cpicLevel']}")
   

4. Generate patient report with actionable pharmacogenomic findings.

Workflow 3: Drug Safety Assessment

1. Query drug for PGx associations:

   response = requests.get("https://api.clinpgx.org/v1/chemical",
                          params={"name": "abacavir"})
   drug_id = response.json()[0]['id']
   

2. Get clinical annotations:

   response = requests.get("https://api.clinpgx.org/v1/clinicalAnnotation",
                          params={"drug": drug_id})
   annotations = response.json()
   

3. Check for HLA associations and toxicity risk:

   for annotation in annotations:
       if 'HLA' in annotation.get('genes', []):
           print(f"Toxicity risk: {annotation['phenotype']}")
           print(f"Evidence level: {annotation['evidenceLevel']}")
   

4. Retrieve screening recommendations from guidelines and labels.

Workflow 4: Research Analysis - Population Pharmacogenomics

1. Get allele frequencies for population comparison:

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

2. Extract population-specific frequencies:

   populations = ['European', 'African', 'East Asian', 'Latino']
   frequency_data = {}
   for allele in alleles:
       allele_name = allele['name']
       frequency_data[allele_name] = {
           pop: allele.get(f'{pop}_frequency', 'N/A')
           for pop in populations
       }
   

3. Calculate phenotype distributions by population:

   # Combine allele frequencies with function to predict phenotypes
   phenotype_dist = calculate_phenotype_frequencies(frequency_data)
   

4. Analyze implications for drug dosing in diverse populations.

Workflow 5: Literature Evidence Review

1. Search for gene-drug pair:

   response = requests.get("https://api.clinpgx.org/v1/geneDrugPair",
                          params={"gene": "TPMT", "drug": "azathioprine"})
   pair = response.json()
   

2. Retrieve all clinical annotations:

   response = requests.get("https://api.clinpgx.org/v1/clinicalAnnotation",
                          params={"gene": "TPMT", "drug": "azathioprine"})
   annotations = response.json()
   

3. Filter by evidence level and publication date:

   high_quality = [a for a in annotations
                   if a['evidenceLevel'] in ['1A', '1B', '2A']]
   

4. Extract PMIDs and retrieve full references:

   pmids = [a['pmid'] for a in high_quality if 'pmid' in a]
   # Use PubMed skill to retrieve full citations
   

Rate Limiting and Best Practices

Rate Limit Compliance

import time

def rate_limited_request(url, params=None, delay=0.5):
    """Make API request with rate limiting (2 req/sec max)"""
    response = requests.get(url, params=params)
    time.sleep(delay)  # Wait 0.5 seconds between requests
    return response

# Use in loops
genes = ["CYP2D6", "CYP2C19", "CYP2C9"]
for gene in genes:
    response = rate_limited_request(
        "https://api.clinpgx.org/v1/gene/" + gene
    )
    data = response.json()

Error Handling

def safe_api_call(url, params=None, max_retries=3):
    """API call with error handling and retries"""
    for attempt in range(max_retries):
        try:
            response = requests.get(url, params=params, timeout=10)

            if response.status_code == 200:
                return response.json()
            elif response.status_code == 429:
                # Rate limit exceeded
                wait_time = 2 ** attempt  # Exponential backoff
                print(f"Rate limit hit. Waiting {wait_time}s...")
                time.sleep(wait_time)
            else:
                response.raise_for_status()

        except requests.exceptions.RequestException as e:
            print(f"Attempt {attempt + 1} failed: {e}")
            if attempt == max_retries - 1:
                raise
            time.sleep(1)

Caching Results

import json
from pathlib import Path

def cached_query(cache_file, api_func, *args, **kwargs):
    """Cache API results to avoid repeated queries"""
    cache_path = Path(cache_file)

    if cache_path.exists():
        with open(cache_path) as f:
            return json.load(f)

    result = api_func(*args, **kwargs)

    with open(cache_path, 'w') as f:
        json.dump(result, f, indent=2)

    return result

# Usage
gene_data = cached_query(
    'cyp2d6_cache.json',
    rate_limited_request,
    "https://api.clinpgx.org/v1/gene/CYP2D6"
)

PharmDOG Tool

PharmDOG (formerly DDRx) is ClinPGx's clinical decision support tool for interpreting pharmacogenomic test results:

Key features:

• Phenoconversion calculator: Adjusts phenotype predictions for drug-drug interactions affecting CYP2D6
• Custom genotypes: Input patient genotypes to get phenotype predictions
• QR code sharing: Generate shareable patient reports
• Flexible guidance sources: Select which guidelines to apply (CPIC, DPWG, FDA)
• Multi-drug analysis: Assess multiple medications simultaneously

Access: Available at https://www.clinpgx.org/pharmacogenomic-decision-support

Use cases:

• Clinical interpretation of PGx panel results
• Medication review for patients with known genotypes
• Patient education materials
• Point-of-care decision support

Resources

scripts/query_clinpgx.py

Python script with ready-to-use functions for common ClinPGx queries:

• get_gene_info(gene_symbol) - Retrieve gene details
• get_drug_info(drug_name) - Get drug information
• get_gene_drug_pairs(gene, drug) - Query gene-drug interactions
• get_cpic_guidelines(gene, drug) - Retrieve CPIC guidelines
• get_alleles(gene) - Get all alleles for a gene
• get_clinical_annotations(gene, drug, evidence_level) - Query literature annotations
• get_drug_labels(drug) - Retrieve pharmacogenomic drug labels
• search_variants(rsid) - Search by variant rsID
• export_to_dataframe(data) - Convert results to pandas DataFrame

Consult this script for implementation examples with proper rate limiting and error handling.

references/api_reference.md

Comprehensive API documentation including:

• Complete endpoint listing with parameters
• Request/response format specifications
• Example queries for each endpoint
• Filter operators and search patterns
• Data schema definitions
• Rate limiting details
• Authentication requirements (if any)
• Troubleshooting common errors

Refer to this document when detailed API information is needed or when constructing complex queries.

Important Notes

Data Sources and Integration

ClinPGx consolidates multiple authoritative sources:

• PharmGKB: Curated pharmacogenomics knowledge base (now part of ClinPGx)
• CPIC: Evidence-based clinical implementation guidelines
• PharmCAT: Allele calling and phenotype interpretation tool
• DPWG: Dutch pharmacogenetics guidelines
• FDA/EMA labels: Regulatory pharmacogenomic information

As of July 2025, all PharmGKB URLs redirect to corresponding ClinPGx pages.

Clinical Implementation Considerations

• Evidence levels: Always check evidence strength before clinical application
• Population differences: Allele frequencies vary significantly across populations
• Phenoconversion: Consider drug-drug interactions that affect enzyme activity
• Multi-gene effects: Some drugs affected by multiple pharmacogenes
• Non-genetic factors: Age, organ function, drug interactions also affect response
• Testing limitations: Not all clinically relevant alleles detected by all assays

Data Updates

• ClinPGx continuously updates with new evidence and guidelines
• Check publication dates for clinical annotations
• Monitor ClinPGx Blog (https://blog.clinpgx.org/) for announcements
• CPIC guidelines updated as new evidence emerges
• PharmVar provides nomenclature updates for allele definitions

API Stability

• API endpoints are relatively stable but may change during development
• Parameters and response formats subject to modification
• Monitor API changelog and ClinPGx blog for updates
• Consider version pinning for production applications
• Test API changes in development before production deployment

Common Use Cases

Pre-emptive Pharmacogenomic Testing

Query all clinically actionable gene-drug pairs to guide panel selection:

# Get all CPIC guideline pairs
response = requests.get("https://api.clinpgx.org/v1/geneDrugPair",
                       params={"cpicLevel": "A"})  # Level A recommendations
actionable_pairs = response.json()

Medication Therapy Management

Review patient medications against known genotypes:

patient_genes = {"CYP2C19": "*1/*2", "CYP2D6": "*1/*1", "SLCO1B1": "*1/*5"}
medications = ["clopidogrel", "simvastatin", "escitalopram"]

for med in medications:
    for gene in patient_genes:
        response = requests.get("https://api.clinpgx.org/v1/geneDrugPair",
                               params={"gene": gene, "drug": med})
        # Check for interactions and dosing guidance

Clinical Trial Eligibility

Screen for pharmacogenomic contraindications:

# Check for HLA-B*57:01 before abacavir trial
response = requests.get("https://api.clinpgx.org/v1/geneDrugPair",
                       params={"gene": "HLA-B", "drug": "abacavir"})
pair_info = response.json()
# CPIC: Do not use if HLA-B*57:01 positive

Additional Resources

• ClinPGx website: https://www.clinpgx.org/
• ClinPGx Blog: https://blog.clinpgx.org/
• API documentation: https://api.clinpgx.org/
• CPIC website: https://cpicpgx.org/
• PharmCAT: https://pharmcat.clinpgx.org/
• ClinGen: https://clinicalgenome.org/
• Contact: api@clinpgx.org (for substantial API use)