Access ClinPGx pharmacogenomics data (successor to PharmGKB). Query gene-drug interactions, CPIC guidelines, allele functions, for precision medicine and genotype-guided dosing decisions.
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Access ClinPGx pharmacogenomics data (successor to PharmGKB). Query gene-drug interactions, CPIC guidelines, allele functions, for precision medicine and genotype-guided dosing decisions.
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
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()
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
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.
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
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
Download bundled/skills/clinpgx-database/SKILL.md from the publisher, or copy the path and open the repository. PlugMCP lists the skill and does not host the file.
Where does clinpgx-database live?
The publisher keeps it at https://github.com/foryourhealth111-pixel/Vibe-Skills.
Which agents can use clinpgx-database?
Claude, Cursor, and Codex can read a SKILL.md you add from the publisher's repository.