gh-k-dense-ai-claude-scientific-skills-scientific-skills/skills/clinpgx-database/references/api_reference.md

ClinPGx API Reference

Complete reference documentation for the ClinPGx REST API.

Base URL

https://api.clinpgx.org/v1/

Rate Limiting

• Maximum rate: 2 requests per second
• Enforcement: Requests exceeding the limit will receive HTTP 429 (Too Many Requests)
• Best practice: Implement 500ms delay between requests (0.5 seconds)
• Recommendation: For substantial API use, contact api@clinpgx.org

Authentication

No authentication is required for basic API access. All endpoints are publicly accessible.

Data License

All data accessed through the API is subject to:

• Creative Commons Attribution-ShareAlike 4.0 International License
• ClinPGx Data Usage Policy

Response Format

All successful responses return JSON with appropriate HTTP status codes:

• 200 OK: Successful request
• 404 Not Found: Resource does not exist
• 429 Too Many Requests: Rate limit exceeded
• 500 Internal Server Error: Server error

Core Endpoints

1. Gene Endpoint

Retrieve pharmacogene information including function, variants, and clinical significance.

Get Gene by Symbol

GET /v1/gene/{gene_symbol}

Parameters:

• gene_symbol (path, required): Gene symbol (e.g., CYP2D6, TPMT, DPYD)

Example Request:

curl "https://api.clinpgx.org/v1/gene/CYP2D6"

Example Response:

{
  "id": "PA126",
  "symbol": "CYP2D6",
  "name": "cytochrome P450 family 2 subfamily D member 6",
  "chromosome": "22",
  "chromosomeLocation": "22q13.2",
  "function": "Drug metabolism",
  "description": "Highly polymorphic gene encoding enzyme...",
  "clinicalAnnotations": [...],
  "relatedDrugs": [...]
}

Search Genes

GET /v1/gene?q={search_term}

Parameters:

• q (query, optional): Search term for gene name or symbol

Example:

curl "https://api.clinpgx.org/v1/gene?q=CYP"

2. Chemical/Drug Endpoint

Access drug and chemical compound information including pharmacogenomic annotations.

Get Drug by ID

GET /v1/chemical/{drug_id}

Parameters:

• drug_id (path, required): ClinPGx drug identifier (e.g., PA448515)

Example Request:

curl "https://api.clinpgx.org/v1/chemical/PA448515"

Search Drugs by Name

GET /v1/chemical?name={drug_name}

Parameters:

• name (query, optional): Drug name or synonym

Example:

curl "https://api.clinpgx.org/v1/chemical?name=warfarin"

Example Response:

[
  {
    "id": "PA448515",
    "name": "warfarin",
    "genericNames": ["warfarin sodium"],
    "tradeNames": ["Coumadin", "Jantoven"],
    "drugClasses": ["Anticoagulants"],
    "indication": "Prevention of thrombosis",
    "relatedGenes": ["CYP2C9", "VKORC1", "CYP4F2"]
  }
]

3. Gene-Drug Pair Endpoint

Query curated gene-drug interaction relationships with clinical annotations.

Get Gene-Drug Pairs

GET /v1/geneDrugPair?gene={gene}&drug={drug}

Parameters:

• gene (query, optional): Gene symbol
• drug (query, optional): Drug name
• cpicLevel (query, optional): Filter by CPIC recommendation level (A, B, C, D)

Example Requests:

# Get all pairs for a gene
curl "https://api.clinpgx.org/v1/geneDrugPair?gene=CYP2D6"

# Get specific gene-drug pair
curl "https://api.clinpgx.org/v1/geneDrugPair?gene=CYP2D6&drug=codeine"

# Get all CPIC Level A pairs
curl "https://api.clinpgx.org/v1/geneDrugPair?cpicLevel=A"

Example Response:

[
  {
    "gene": "CYP2D6",
    "drug": "codeine",
    "sources": ["CPIC", "FDA", "DPWG"],
    "cpicLevel": "A",
    "evidenceLevel": "1A",
    "clinicalAnnotationCount": 45,
    "hasGuideline": true,
    "guidelineUrl": "https://www.clinpgx.org/guideline/..."
  }
]

4. Guideline Endpoint

Access clinical practice guidelines from CPIC, DPWG, and other sources.

Get Guidelines

GET /v1/guideline?source={source}&gene={gene}&drug={drug}

Parameters:

• source (query, optional): Guideline source (CPIC, DPWG, FDA)
• gene (query, optional): Gene symbol
• drug (query, optional): Drug name

Example Requests:

# Get all CPIC guidelines
curl "https://api.clinpgx.org/v1/guideline?source=CPIC"

# Get guideline for specific gene-drug
curl "https://api.clinpgx.org/v1/guideline?gene=CYP2C19&drug=clopidogrel"

Get Guideline by ID

GET /v1/guideline/{guideline_id}

Example:

curl "https://api.clinpgx.org/v1/guideline/PA166104939"

Example Response:

{
  "id": "PA166104939",
  "name": "CPIC Guideline for CYP2C19 and Clopidogrel",
  "source": "CPIC",
  "genes": ["CYP2C19"],
  "drugs": ["clopidogrel"],
  "recommendationLevel": "A",
  "lastUpdated": "2023-08-01",
  "summary": "Alternative antiplatelet therapy recommended for...",
  "recommendations": [...],
  "pdfUrl": "https://www.clinpgx.org/...",
  "pmid": "23400754"
}

5. Allele Endpoint

Query allele definitions, functions, and population frequencies.

Get All Alleles for a Gene

GET /v1/allele?gene={gene_symbol}

Parameters:

• gene (query, required): Gene symbol

Example Request:

curl "https://api.clinpgx.org/v1/allele?gene=CYP2D6"

Example Response:

[
  {
    "name": "CYP2D6*1",
    "gene": "CYP2D6",
    "function": "Normal function",
    "activityScore": 1.0,
    "frequencies": {
      "European": 0.42,
      "African": 0.37,
      "East Asian": 0.50,
      "Latino": 0.44
    },
    "definingVariants": ["Reference allele"],
    "pharmVarId": "PV00001"
  },
  {
    "name": "CYP2D6*4",
    "gene": "CYP2D6",
    "function": "No function",
    "activityScore": 0.0,
    "frequencies": {
      "European": 0.20,
      "African": 0.05,
      "East Asian": 0.01,
      "Latino": 0.10
    },
    "definingVariants": ["rs3892097"],
    "pharmVarId": "PV00004"
  }
]

Get Specific Allele

GET /v1/allele/{allele_name}

Parameters:

• allele_name (path, required): Allele name with star nomenclature (e.g., CYP2D6*4)

Example:

curl "https://api.clinpgx.org/v1/allele/CYP2D6*4"

6. Variant Endpoint

Search for genetic variants and their pharmacogenomic annotations.

Get Variant by rsID

GET /v1/variant/{rsid}

Parameters:

• rsid (path, required): dbSNP reference SNP ID

Example Request:

curl "https://api.clinpgx.org/v1/variant/rs4244285"

Example Response:

{
  "rsid": "rs4244285",
  "chromosome": "10",
  "position": 94781859,
  "gene": "CYP2C19",
  "alleles": ["CYP2C19*2"],
  "consequence": "Splice site variant",
  "clinicalSignificance": "Pathogenic - reduced enzyme activity",
  "frequencies": {
    "European": 0.15,
    "African": 0.18,
    "East Asian": 0.29,
    "Latino": 0.12
  },
  "references": [...]
}

Search Variants by Position

GET /v1/variant?chromosome={chr}&position={pos}

Parameters:

• chromosome (query, optional): Chromosome number (1-22, X, Y)
• position (query, optional): Genomic position (GRCh38)

Example:

curl "https://api.clinpgx.org/v1/variant?chromosome=10&position=94781859"

7. Clinical Annotation Endpoint

Access curated literature annotations for gene-drug-phenotype relationships.

Get Clinical Annotations

GET /v1/clinicalAnnotation?gene={gene}&drug={drug}&evidenceLevel={level}

Parameters:

• gene (query, optional): Gene symbol
• drug (query, optional): Drug name
• evidenceLevel (query, optional): Evidence level (1A, 1B, 2A, 2B, 3, 4)
• phenotype (query, optional): Phenotype or outcome

Example Requests:

# Get all annotations for a gene
curl "https://api.clinpgx.org/v1/clinicalAnnotation?gene=CYP2D6"

# Get high-quality evidence only
curl "https://api.clinpgx.org/v1/clinicalAnnotation?evidenceLevel=1A"

# Get annotations for specific gene-drug pair
curl "https://api.clinpgx.org/v1/clinicalAnnotation?gene=TPMT&drug=azathioprine"

Example Response:

[
  {
    "id": "PA166153683",
    "gene": "CYP2D6",
    "drug": "codeine",
    "phenotype": "Reduced analgesic effect",
    "evidenceLevel": "1A",
    "annotation": "Poor metabolizers have reduced conversion...",
    "pmid": "24618998",
    "studyType": "Clinical trial",
    "population": "European",
    "sources": ["CPIC"]
  }
]

Evidence Levels:

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

8. Drug Label Endpoint

Retrieve regulatory drug label information with pharmacogenomic content.

Get Drug Labels

GET /v1/drugLabel?drug={drug_name}&source={source}

Parameters:

• drug (query, required): Drug name
• source (query, optional): Regulatory source (FDA, EMA, PMDA, Health Canada)

Example Requests:

# Get all labels for warfarin
curl "https://api.clinpgx.org/v1/drugLabel?drug=warfarin"

# Get only FDA labels
curl "https://api.clinpgx.org/v1/drugLabel?drug=warfarin&source=FDA"

Example Response:

[
  {
    "id": "DL001234",
    "drug": "warfarin",
    "source": "FDA",
    "sections": {
      "testing": "Consider CYP2C9 and VKORC1 genotyping...",
      "dosing": "Dose adjustment based on genotype...",
      "warnings": "Risk of bleeding in certain genotypes"
    },
    "biomarkers": ["CYP2C9", "VKORC1"],
    "testingRecommended": true,
    "labelUrl": "https://dailymed.nlm.nih.gov/...",
    "lastUpdated": "2024-01-15"
  }
]

9. Pathway Endpoint

Access pharmacokinetic and pharmacodynamic pathway diagrams and information.

Get Pathway by ID

GET /v1/pathway/{pathway_id}

Parameters:

• pathway_id (path, required): ClinPGx pathway identifier

Example:

curl "https://api.clinpgx.org/v1/pathway/PA146123006"

Search Pathways

GET /v1/pathway?drug={drug_name}&gene={gene}

Parameters:

• drug (query, optional): Drug name
• gene (query, optional): Gene symbol

Example:

curl "https://api.clinpgx.org/v1/pathway?drug=warfarin"

Example Response:

{
  "id": "PA146123006",
  "name": "Warfarin Pharmacokinetics and Pharmacodynamics",
  "drugs": ["warfarin"],
  "genes": ["CYP2C9", "VKORC1", "CYP4F2", "GGCX"],
  "description": "Warfarin is metabolized primarily by CYP2C9...",
  "diagramUrl": "https://www.clinpgx.org/pathway/...",
  "steps": [
    {
      "step": 1,
      "process": "Absorption",
      "genes": []
    },
    {
      "step": 2,
      "process": "Metabolism",
      "genes": ["CYP2C9", "CYP2C19"]
    },
    {
      "step": 3,
      "process": "Target interaction",
      "genes": ["VKORC1"]
    }
  ]
}

Query Patterns and Examples

Common Query Patterns

1. Patient Medication Review

Query all gene-drug pairs for a patient's medications:

import requests

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

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

2. Actionable Gene Panel

Find all genes with CPIC Level A recommendations:

response = requests.get(
    "https://api.clinpgx.org/v1/geneDrugPair",
    params={"cpicLevel": "A"}
)
actionable_pairs = response.json()

genes = set(pair['gene'] for pair in actionable_pairs)
print(f"Panel should include: {sorted(genes)}")

3. Population Frequency Analysis

Compare allele frequencies across populations:

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

# Calculate phenotype frequencies
pm_freq = {}  # Poor metabolizer frequencies
for allele in alleles:
    if allele['function'] == 'No function':
        for pop, freq in allele['frequencies'].items():
            pm_freq[pop] = pm_freq.get(pop, 0) + freq

4. Drug Safety Screen

Check for high-risk gene-drug associations:

# Screen for HLA-B*57:01 before abacavir
response = requests.get(
    "https://api.clinpgx.org/v1/geneDrugPair",
    params={"gene": "HLA-B", "drug": "abacavir"}
)
pair = response.json()[0]

if pair['cpicLevel'] == 'A':
    print("CRITICAL: Do not use if HLA-B*57:01 positive")

Error Handling

Common Error Responses

404 Not Found

{
  "error": "Resource not found",
  "message": "Gene 'INVALID' does not exist"
}

429 Too Many Requests

{
  "error": "Rate limit exceeded",
  "message": "Maximum 2 requests per second allowed"
}

Recommended Error Handling Pattern

import requests
import time

def safe_query(url, params=None, max_retries=3):
    for attempt in range(max_retries):
        try:
            response = requests.get(url, params=params, timeout=10)

            if response.status_code == 200:
                time.sleep(0.5)  # Rate limiting
                return response.json()
            elif response.status_code == 429:
                wait = 2 ** attempt
                print(f"Rate limited. Waiting {wait}s...")
                time.sleep(wait)
            elif response.status_code == 404:
                print("Resource not found")
                return None
            else:
                response.raise_for_status()

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

    return None

Best Practices

Rate Limiting

• Implement 500ms delay between requests (2 requests/second maximum)
• Use exponential backoff for rate limit errors
• Consider caching results for frequently accessed data
• For bulk operations, contact api@clinpgx.org

Caching Strategy

import json
from pathlib import Path

def cached_query(cache_file, query_func, *args, **kwargs):
    cache_path = Path(cache_file)

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

    result = query_func(*args, **kwargs)

    if result:
        with open(cache_path, 'w') as f:
            json.dump(result, f)

    return result

Batch Processing

import time

def batch_gene_query(genes, delay=0.5):
    results = {}
    for gene in genes:
        response = requests.get(f"https://api.clinpgx.org/v1/gene/{gene}")
        if response.status_code == 200:
            results[gene] = response.json()
        time.sleep(delay)
    return results

Data Schema Definitions

Gene Object

{
  id: string;              // ClinPGx gene ID
  symbol: string;          // HGNC gene symbol
  name: string;            // Full gene name
  chromosome: string;      // Chromosome location
  function: string;        // Pharmacogenomic function
  clinicalAnnotations: number;  // Count of annotations
  relatedDrugs: string[];  // Associated drugs
}

Drug Object

{
  id: string;              // ClinPGx drug ID
  name: string;            // Generic name
  tradeNames: string[];    // Brand names
  drugClasses: string[];   // Therapeutic classes
  indication: string;      // Primary indication
  relatedGenes: string[];  // Pharmacogenes
}

Gene-Drug Pair Object

{
  gene: string;            // Gene symbol
  drug: string;            // Drug name
  sources: string[];       // CPIC, FDA, DPWG, etc.
  cpicLevel: string;       // A, B, C, D
  evidenceLevel: string;   // 1A, 1B, 2A, 2B, 3, 4
  hasGuideline: boolean;   // Has clinical guideline
}

Allele Object

{
  name: string;            // Allele name (e.g., CYP2D6*4)
  gene: string;            // Gene symbol
  function: string;        // Normal/decreased/no/increased/uncertain
  activityScore: number;   // 0.0 to 2.0+
  frequencies: {           // Population frequencies
    [population: string]: number;
  };
  definingVariants: string[];  // rsIDs or descriptions
}

API Stability and Versioning

Current Status

• API version: v1
• Stability: Beta - endpoints stable, parameters may change
• Monitor: https://blog.clinpgx.org/ for updates

Migration from PharmGKB

As of July 2025, PharmGKB URLs redirect to ClinPGx. Update references:

• Old: https://api.pharmgkb.org/
• New: https://api.clinpgx.org/

Future Changes

• Watch for API v2 announcements
• Breaking changes will be announced on ClinPGx Blog
• Consider version pinning for production applications

Support and Contact

• API Issues: api@clinpgx.org
• Documentation: https://api.clinpgx.org/
• General Questions: https://www.clinpgx.org/page/faqs
• Blog: https://blog.clinpgx.org/
• CPIC Guidelines: https://cpicpgx.org/

Related Resources

• PharmCAT: Pharmacogenomic variant calling and annotation tool
• PharmVar: Pharmacogene allele nomenclature database
• CPIC: Clinical Pharmacogenetics Implementation Consortium
• DPWG: Dutch Pharmacogenetics Working Group
• ClinGen: Clinical Genome Resource