clinpgx-database

仓库: davila7/claude-code-templates
安装量: 139
排名: #6192

安装

npx skills add https://github.com/davila7/claude-code-templates --skill clinpgx-database

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 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

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()

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()

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

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

Get list of pharmacogenes in clinical panel:

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

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()

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']}")

Generate patient report with actionable pharmacogenomic findings.

Workflow 3: Drug Safety Assessment

Query drug for PGx associations:

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

Get clinical annotations:

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

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']}")

Retrieve screening recommendations from guidelines and labels.

Workflow 4: Research Analysis - Population Pharmacogenomics

Get allele frequencies for population comparison:

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

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 }

Calculate phenotype distributions by population:

Combine allele frequencies with function to predict phenotypes

phenotype_dist = calculate_phenotype_frequencies(frequency_data)

Analyze implications for drug dosing in diverse populations.

Workflow 5: Literature Evidence Review

Search for gene-drug pair:

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

Retrieve all clinical annotations:

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

Filter by evidence level and publication date:

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

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)

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