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clinpgx-database

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Updated 10-15 22:40

About this skill

ClinPGx (PharmGKB) Pharmacogenomics Database

Overview

PharmGKB rebranded as ClinPGx in 2024 and the API moved from api.pharmgkb.org to api.clinpgx.org. The old host now returns 404/405; every example here uses the new endpoints. Two complementary APIs are used together:

  • ClinPGx Data API (api.clinpgx.org/v1) — record-style access to genes, drugs, variants, clinical annotations, guideline annotations, drug labels, and pathways. Responses wrap data as {"data": [...], "status": "success"}. Filters use dotted property paths (e.g. relatedChemicals.name=clopidogrel, levelOfEvidence.term=1A).
  • CPIC PostgREST API (api.cpicpgx.org/v1) — relational lookup of genotype → drug recommendation rows. PostgREST filter syntax (column=eq.value, JSON cs.{...} for jsonb containment). Returns flat JSON arrays.

Use ClinPGx for what is known about a gene/drug/variant; use CPIC for how to prescribe given a phenotype. The pattern is ClinPGx for annotations, CPIC for recommendations.

When to Use

  • Retrieving CPIC genotype-specific dosing recommendations for a gene-drug pair (e.g., CYP2C19 + clopidogrel) — use CPIC
  • Looking up all pharmacogenomic clinical annotations for a drug or evidence level — use ClinPGx data/clinicalAnnotation
  • Finding all CPIC/DPWG guideline annotations for a pharmacogene — use ClinPGx data/guidelineAnnotation
  • Resolving a gene symbol, drug name, or rsID to ClinPGx PA identifiers — use data/{gene,drug,variant}
  • Free-text search across all ClinPGx record types (genes, drugs, variants, annotations) — use POST /site/search
  • Retrieving FDA/EMA pharmacogenomic drug label annotations — use ClinPGx data/label
  • Building precision-medicine prescribing workflows that combine annotation evidence with phenotype-specific recommendations
  • For germline disease pathogenicity (not PGx) use clinvar-database
  • For somatic cancer pharmacogenomics use cosmic-database or opentargets-database

Prerequisites

  • Python packages: requests, pandas — both already in standard environments
  • Data requirements: HGNC gene symbols, drug names (lowercase generic), dbSNP rsIDs, or PA identifiers
  • Environment: internet connection; no authentication required for either host
  • Rate limits: the ClinPGx host occasionally returns HTTP 429; insert time.sleep(0.3–0.5) between sequential calls. CPIC is more permissive.

If you are inside a pixi/conda environment that already provides requests and pandas, skip the install — invoke scripts with pixi run python ....

pip install requests pandas

Quick Start

import requests

CLINPGX = "https://api.clinpgx.org/v1"
CPIC    = "https://api.cpicpgx.org/v1"

# CPIC genotype → recommendation: clopidogrel + CYP2C19 Poor Metabolizer
drug = requests.get(f"{CPIC}/drug", params={"name": "eq.clopidogrel"}).json()[0]
recs = requests.get(f"{CPIC}/recommendation",
                    params={"drugid": f"eq.{drug['drugid']}",
                            "phenotypes": 'cs.{"CYP2C19":"Poor Metabolizer"}'}).json()
print(f"clopidogrel CYP2C19=PM: {len(recs)} recommendation(s)")
for rec in recs[:2]:
    print(f"  [{rec['classification']}] {rec['drugrecommendation'][:80]}…")

# ClinPGx side: how many CPIC guideline annotations cover CYP2C19?
glines = requests.get(f"{CLINPGX}/data/guidelineAnnotation",
                      params={"relatedGenes.symbol": "CYP2C19",
                              "source": "CPIC", "view": "base"}).json()["data"]
print(f"CYP2C19 CPIC guidelines: {len(glines)}")

Core API

Module 1: Free-text site search

POST /site/search with a JSON body {"query": "<term>"} is the canonical entry point when you don't know the PA ID. It searches across drugs, genes, variants, clinical annotations, guideline annotations, and labels in one shot.

import requests

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

r = requests.post(f"{CLINPGX}/site/search",
                  json={"query": "rs4149056"}, timeout=15)
r.raise_for_status()
hits = r.json()["data"]["hits"]
print(f"Total hits: {r.json()['data']['total']}")
for h in hits[:5]:
    print(f"  id={h.get('id')}  name={h.get('name')[:80]}")

# Broader concept search
r = requests.post(f"{CLINPGX}/site/search",
                  json={"query": "TPMT azathioprine"}, timeout=15)
hits = r.json()["data"]["hits"]
print(f"TPMT+azathioprine hits: {len(hits)}")
for h in hits[:5]:
    print(f"  {h.get('id'):>15}  {h.get('name','')[:80]}")

Module 2: Gene, drug, and variant record lookup

The /data/{type} endpoints accept simple property filters. All return {"data": [...], "status": "success"} — use view=base for summary, view=max for full nested objects.

import requests

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

# Gene by HGNC symbol
gene = requests.get(f"{CLINPGX}/data/gene",
                    params={"symbol": "CYP2D6", "view": "base"}).json()["data"][0]
print(f"{gene['symbol']}  id={gene['id']}  {gene['name']}")

# Drug by name (lowercase generic preferred)
drug = requests.get(f"{CLINPGX}/data/drug",
                    params={"name": "warfarin", "view": "base"}).json()["data"][0]
print(f"{drug['name']}  id={drug['id']}")

# Variant by rsID
var = requests.get(f"{CLINPGX}/data/variant",
                   params={"name": "rs4149056", "view": "base"}).json()["data"][0]
print(f"{var['name']}  id={var['id']}  significance={var.get('clinicalSignificance')}")

# Direct record fetch when you already have a PA ID
r = requests.get(f"{CLINPGX}/data/drug/PA449088", params={"view": "max"}).json()
d = r["data"]
print(f"PA449088 → {d['name']}  (objCls={d['objCls']})")

Module 3: Clinical annotations

data/clinicalAnnotation records associate a variant (location) with one or more drugs (relatedChemicals) and an evidence level (levelOfEvidence.term). The two supported filters are relatedChemicals.name= and levelOfEvidence.term=. There is no working gene= filter on this endpoint — see Module 4 for gene-driven access.

import requests, pandas as pd

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

# All clinical annotations for clopidogrel
data = requests.get(f"{CLINPGX}/data/clinicalAnnotation",
                    params={"relatedChemicals.name": "clopidogrel",
                            "view": "base"}).json()["data"]
print(f"clopidogrel annotations: {len(data)}")

rows = []
for ann in data[:10]:
    loc = ann.get("location") or {}
    drugs = ", ".join(c.get("name", "") for c in ann.get("relatedChemicals", []))
    rows.append({
        "id": ann["id"],
        "variant": loc.get("displayName"),
        "gene": (loc.get("genes") or [{}])[0].get("symbol"),
        "drug": drugs,
        "level": (ann.get("levelOfEvidence") or {}).get("term"),
        "score": ann.get("score"),
    })
print(pd.DataFrame(rows).to_string(index=False))

# All Level 1A clinical annotations (highest evidence)
data = requests.get(f"{CLINPGX}/data/clinicalAnnotation",
                    params={"levelOfEvidence.term": "1A",
                            "view": "base"}).json()["data"]
print(f"Level 1A annotations: {len(data)}")

drug_to_count = {}
for ann in data:
    for c in ann.get("relatedChemicals") or []:
        drug_to_count[c["name"]] = drug_to_count.get(c["name"], 0) + 1
top = sorted(drug_to_count.items(), key=lambda x: -x[1])[:10]
for d, n in top:
    print(f"  {n:3}  {d}")

Module 4: Guideline annotations (gene-driven access)

data/guidelineAnnotation supports both relatedGenes.symbol= and relatedChemicals.name=, plus source= (CPIC, DPWG, CPNDS, RNPGx). This is the canonical way to get gene→guideline coverage.

import requests

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

# All CPIC guidelines mentioning CYP2C19
data = requests.get(f"{CLINPGX}/data/guidelineAnnotation",
                    params={"relatedGenes.symbol": "CYP2C19",
                            "source": "CPIC",
                            "view": "base"}).json()["data"]
print(f"CYP2C19 CPIC guidelines: {len(data)}")
for g in data[:5]:
    print(f"  PA{g['id']}: {g['name'][:80]}")

# Guidelines for a specific drug across all bodies (CPIC, DPWG, …)
data = requests.get(f"{CLINPGX}/data/guidelineAnnotation",
                    params={"relatedChemicals.name": "clopidogrel",
                            "view": "base"}).json()["data"]
by_source = {}
for g in data:
    for s in (g.get("crossReferences") or []):
        by_source.setdefault(s.get("resource", "?"), 0)
        by_source[s["resource"]] = by_source.get(s["resource"], 0) + 1
print(f"clopidogrel guidelines: {len(data)} ({list({g.get('source') for g in data})})")

Module 5: Regulatory drug labels (FDA / EMA)

data/label records are PharmGKB-curated annotations of FDA/EMA pharmacogenomic labeling. Filter by relatedChemicals.name= and source= (FDA, EMA, HCSC, PMDA, Swissmedic).

import requests, pandas as pd

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

data = requests.get(f"{CLINPGX}/data/label",
                    params={"relatedChemicals.name": "warfarin",
                            "source": "FDA",
                            "view": "base"}).json()["data"]
print(f"warfarin FDA labels: {len(data)}")

rows = [{
    "name": d["name"][:60],
    "biomarker_status": d.get("biomarkerStatus"),
    "testing_required": d.get("testingRequired"),
    "alternate_drug": d.get("alternateDrugAvailable"),
} for d in data]
print(pd.DataFrame(rows).to_string(index=False))

Module 6: CPIC genotype → recommendation chain

CPIC's PostgREST API uses column=eq.value for equality and column=cs.{...} for JSONB containment. The standard lookup chain is drug → drugid → recommendation, optionally filtered by phenotype.

import requests

CPIC = "https://api.cpicpgx.org/v1"

# Resolve drug name to drugid (RxNorm-prefixed)
drug = requests.get(f"{CPIC}/drug",
                    params={"name": "eq.clopidogrel"}).json()[0]
print(f"clopidogrel drugid: {drug['drugid']}")

# All phenotype-specific recommendations for clopidogrel
recs = requests.get(f"{CPIC}/recommendation",
                    params={"drugid": f"eq.{drug['drugid']}"}).json()
print(f"Total recommendations: {len(recs)}")
for rec in recs[:3]:
    print(f"  {rec['phenotypes']}  [{rec['classification']}]")
    print(f"    {rec['drugrecommendation'][:90]}…")

# Phenotype filter via jsonb containment (cs.{...})
# The phenotypes column is a jsonb dict; cs. checks that the query is a subset.
recs = requests.get(f"{CPIC}/recommendation",
                    params={"drugid": f"eq.{drug['drugid']}",
                            "phenotypes": 'cs.{"CYP2C19":"Poor Metabolizer"}'}
                    ).json()
for rec in recs:
    print(f"  [{rec['classification']}] {rec['drugrecommendation'][:90]}…")

# Gene-driven: list every drug with a CPIC pair for CYP2C19
pairs = requests.get(f"{CPIC}/pair",
                     params={"genesymbol": "eq.CYP2C19"}).json()
print(f"\nCYP2C19 CPIC pairs: {len(pairs)}")
drug_ids = sorted({p["drugid"] for p in pairs})
print(f"Sample drug IDs: {drug_ids[:5]}")

Key Concepts

Two-host architecture

Question Use Why
What clinical annotations exist for this drug? ClinPGx data/clinicalAnnotation Annotation-level evidence with curated levelOfEvidence.term
What CPIC guidelines cover this gene? ClinPGx data/guidelineAnnotation Filter by relatedGenes.symbol; no working gene= filter on clinicalAnnotation
Given phenotype X, what should I prescribe? CPIC recommendation + phenotypes Structured genotype→action rows; CPIC is the prescribing-rule oracle
What FDA labels mention this drug + gene? ClinPGx data/label?source=FDA Curated regulatory PGx labeling
Free-text "anything about X" ClinPGx POST /site/search Cross-record-type fan-out

PharmGKB / ClinPGx evidence levels

Levels 1A → 4 in decreasing evidence quality:

  • 1A — Annotation of a variant–drug pair in a clinical guideline or FDA label (strongest)
  • 1B — Significant association replicated in multiple studies
  • 2A — Variant in a known PGx gene, significant association
  • 2B — Moderate evidence, often single study
  • 3 — Limited evidence (single study or unreplicated)
  • 4 — Case reports / biological plausibility only

Filter via levelOfEvidence.term on data/clinicalAnnotation. The term is a string, not an enum ("1A" not 1A).

ClinPGx response envelope and view modes

Every ClinPGx /data/... response is {"data": [...] | {...}, "status": "success" | "fail"}. On failure the body is {"status": "fail", "data": {"errors": [{"message": "..."}]}} — always read both keys.

  • view=base (default) — flat summary record; recommended for bulk filters
  • view=max — full nested objects (relatedDiseases, allelePhenotypes, scoreDetails, …). Larger payload, slower; use only for single-record details.

Common Workflows

Workflow 1: Pharmacogene panel CPIC coverage

Goal: Given a patient's pharmacogene panel, count how many CPIC guideline annotations cover each gene.

import requests, pandas as pd, time

CLINPGX = "https://api.clinpgx.org/v1"
pharmacogenes = ["CYP2D6", "CYP2C19", "CYP2C9", "DPYD", "TPMT", "SLCO1B1"]

rows = []
for g in pharmacogenes:
    data = requests.get(f"{CLINPGX}/data/guidelineAnnotation",
                        params={"relatedGenes.symbol": g,
                                "source": "CPIC", "view": "base"},
                        timeout=20).json()["data"]
    drugs = sorted({c["name"] for guideline in data
                                for c in (guideline.get("relatedChemicals") or [])})
    rows.append({"gene": g, "cpic_guidelines": len(data),
                 "n_drugs": len(drugs), "sample": ", ".join(drugs[:3])})
    time.sleep(0.3)

df = pd.DataFrame(rows).sort_values("cpic_guidelines", ascending=False)
print(df.to_string(index=False))
df.to_csv("pharmacogene_cpic_coverage.csv", index=False)

Workflow 2: Drug panel — CPIC prescribing rule lookup

Goal: Given a prescribed drug list, identify which have CPIC genotype-specific recommendations and surface the rule rows.

import requests, pandas as pd, time

CPIC = "https://api.cpicpgx.org/v1"
drugs = ["warfarin", "clopidogrel", "codeine", "simvastatin",
         "metoprolol", "omeprazole", "azathioprine", "tacrolimus"]

rows = []
for name in drugs:
    drug = requests.get(f"{CPIC}/drug", params={"name": f"eq.{name}"}, timeout=15).json()
    if not drug:
        rows.append({"drug": name, "in_cpic": False, "n_recs": 0, "phenotypes": ""}); continue
    did = drug[0]["drugid"]
    recs = requests.get(f"{CPIC}/recommendation",
                        params={"drugid": f"eq.{did}"}, timeout=15).json()
    phens = sorted({f"{k}={v}" for rec in recs
                                  for k, v in (rec.get("phenotypes") or {}).items()})
    rows.append({"drug": name, "in_cpic": True, "n_recs": len(recs),
                 "phenotypes": "; ".join(phens[:3])})
    time.sleep(0.3)

df = pd.DataFrame(rows).sort_values(["in_cpic", "n_recs"], ascending=[False, False])
print(df.to_string(index=False))

Workflow 3: Variant → drug interactions (rsID-driven)

Goal: Starting from a single rsID (e.g., SLCO1B1 *5 = rs4149056), find every clinical annotation that involves it.

The Data API does not accept rsID as a filter property. Use POST /site/search to discover related annotation IDs, then fetch each by ID.

import requests

CLINPGX = "https://api.clinpgx.org/v1"
rsid = "rs4149056"

hits = requests.post(f"{CLINPGX}/site/search",
                     json={"query": rsid}, timeout=15).json()["data"]["hits"]
print(f"{rsid}: {len(hits)} hits")

# Filter hits that look like clinical annotations
ann_hits = [h for h in hits if h.get("name", "").lower().startswith("clinical annotation")]
print(f"Clinical-annotation hits: {len(ann_hits)}")
for h in ann_hits[:5]:
    print(f"  id={h['id']}  {h['name'][:90]}")

# Dereference one annotation by ID for full detail
if ann_hits:
    ann = requests.get(f"{CLINPGX}/data/clinicalAnnotation/{ann_hits[0]['id']}",
                       params={"view": "max"}, timeout=15).json()["data"]
    drugs = ", ".join(c["name"] for c in (ann.get("relatedChemicals") or []))
    print(f"\nFirst annotation:")
    print(f"  drugs: {drugs}")
    print(f"  level: {(ann.get('levelOfEvidence') or {}).get('term')}")

Key Parameters

Parameter Module / Endpoint Default Range / Options Effect
view all /data/... base base, min, max Field detail level; max includes all nested arrays (slow but complete)
relatedChemicals.name clinicalAnnotation, variantAnnotation, guidelineAnnotation, label, pathway — lowercase generic drug name Filter records related to a drug
relatedGenes.symbol guidelineAnnotation, pathway — HGNC gene symbol Filter records related to a gene (not available on clinicalAnnotation)
levelOfEvidence.term clinicalAnnotation — "1A", "1B", "2A", "2B", "3", "4" Minimum evidence level
source guidelineAnnotation, label — CPIC, DPWG, FDA, EMA, HCSC, PMDA, Swissmedic Issuing body
symbol data/gene — HGNC gene symbol Gene record lookup
name data/drug, data/variant — drug name or rsID Record lookup by canonical name
CPIC column=eq.value all api.cpicpgx.org/v1/... — PostgREST equality Filter by exact match
CPIC phenotypes=cs.{json} recommendation — JSON-encoded jsonb subset Filter by phenotype containment (must URL-encode if special chars)

Best Practices

  1. Resolve PA identifiers once. Never hand-construct ClinPGx PA IDs. Call data/{type}?{symbol|name}=... (or site/search) once and cache the returned id for reuse — gene/PA128 for CYP2D6, drug/PA449088 for clopidogrel, variant/PA166154579 for rs4149056.

  2. Pick the right host for the question. Use ClinPGx for what is annotated and CPIC for what to prescribe. Trying to derive genotype-specific recommendations from ClinPGx alone misses the structured recommendation.phenotypes rows.

  3. Filter by evidence level upfront when building clinical workflows. levelOfEvidence.term=1A returns 312 actionable annotations across all of ClinPGx; Level 3/4 records are exploratory and shouldn't drive prescribing.

  4. Don't filter clinicalAnnotation by gene — filter by guidelineAnnotation with relatedGenes.symbol. The clinicalAnnotation endpoint has no working gene property and returns HTTP 400 for any attempt.

  5. Use view=base for bulk filters, view=max for single-record drill-downs. A list query with view=max can time out or hit 429; the difference is roughly 5–10× payload size.

  6. Throttle the ClinPGx host. Insert time.sleep(0.3) between sequential queries in loops; the API returns occasional HTTP 429s on tight loops. CPIC tolerates faster iteration.

  7. URL-encode cs.{...} jsonb filters when phenotype values contain spaces or special characters. requests.get(..., params={"phenotypes": 'cs.{"CYP2C19":"Poor Metabolizer"}'}) works because requests does the encoding; a manual URL string needs urllib.parse.quote.

Common Recipes

Recipe 1 — Free-text discovery via site/search

When to use: you have an arbitrary string (rsID, drug name, gene, allele) and want to find related ClinPGx records without knowing which endpoint to hit.

import requests
r = requests.post("https://api.clinpgx.org/v1/site/search",
                  json={"query": "VKORC1 warfarin"}, timeout=15)
hits = r.json()["data"]["hits"]
for h in hits[:10]:
    print(f"  {h.get('id'):>15}  {h.get('name','')[:80]}")

Recipe 2 — Top drugs by Level 1A annotation count

When to use: build a leaderboard of the most actionable PGx drugs.

import requests, pandas as pd
data = requests.get("https://api.clinpgx.org/v1/data/clinicalAnnotation",
                    params={"levelOfEvidence.term": "1A", "view": "base"},
                    timeout=30).json()["data"]
counts = {}
for ann in data:
    for c in ann.get("relatedChemicals") or []:
        counts[c["name"]] = counts.get(c["name"], 0) + 1
df = pd.DataFrame(sorted(counts.items(), key=lambda x: -x[1]),
                  columns=["drug", "n_1A_annotations"]).head(15)
print(df.to_string(index=False))

Recipe 3 — Patient genotype → drug recommendations

When to use: given a phenotype call from a PGx test, surface every CPIC recommendation row.

import requests
CPIC = "https://api.cpicpgx.org/v1"

genotype = {"CYP2C19": "Poor Metabolizer"}
drug = "clopidogrel"

did = requests.get(f"{CPIC}/drug", params={"name": f"eq.{drug}"}).json()[0]["drugid"]
import json
recs = requests.get(f"{CPIC}/recommendation",
                    params={"drugid": f"eq.{did}",
                            "phenotypes": f"cs.{json.dumps(genotype)}"}).json()
for rec in recs:
    print(f"[{rec['classification']}] {rec['drugrecommendation']}")
    print(f"  implications: {rec['implications']}")

Recipe 4 — Robust session with retry

When to use: long-running loops over many genes / drugs / variants.

import requests
from requests.adapters import HTTPAdapter
from urllib3.util.retry import Retry

s = requests.Session()
s.headers.update({"Accept": "application/json"})
s.mount("https://", HTTPAdapter(max_retries=Retry(
    total=4, backoff_factor=1.0,
    status_forcelist=[429, 500, 502, 503, 504],
    allowed_methods=["GET", "POST"])))

r = s.get("https://api.clinpgx.org/v1/data/gene",
          params={"symbol": "CYP2D6", "view": "base"}, timeout=20)
r.raise_for_status()
print(r.json()["data"][0]["name"])

Troubleshooting

Problem Cause Solution
HTTP 404/405 on https://api.pharmgkb.org/v1/... Old PharmGKB host is dead; the service rebranded to ClinPGx in 2024 Migrate to https://api.clinpgx.org/v1/.... Old /clinicalAnnotation?gene=X is now data/clinicalAnnotation with different filters.
{"status":"fail","data":{"errors":[{"message":"No such property: 'gene'"}]}} data/clinicalAnnotation does not accept gene= or relatedGenes.symbol= Use data/guidelineAnnotation?relatedGenes.symbol=X for gene-driven access, or ?relatedChemicals.name=Y for drug-driven.
{"status":"fail","data":{"errors":[{"message":"Missing criteria."}]}} A data/{type} list query has no filter and no ID Add at least one filter (name=, symbol=, relatedChemicals.name=, …) or fetch by ID via data/{type}/{paId}.
HTTP 405 on GET /site/search?query=... site/search only accepts POST with a JSON body Use requests.post(url, json={"query": "..."}).
HTTP 429 mid-loop Hit ClinPGx rate limit Insert time.sleep(0.3–0.5) between calls; use the Retry session in Recipe 4.
HTTP 400 on https://api.cpicpgx.org/v1/recommendation?phenotypes=cs.{...} The cs. JSON wasn't URL-encoded Pass via requests params={"phenotypes": 'cs.{"CYP2C19":"Poor Metabolizer"}'} (auto-encoded) or urllib.parse.quote manually.
Empty data list for an obviously-real drug Drug name mismatch (brand vs. generic; capitalization) Try lowercase generic name; fall back to POST /site/search to fan out and find the canonical PA ID.
data/variant?name=rs... returns 1 record but data/clinicalAnnotation?location.name=rs... returns 404 rsID is stored under location.displayName/location.rsid, not exposed as a filterable property Use site/search to discover annotation IDs by rsID, then dereference each with data/clinicalAnnotation/{id}. (Workflow 3.)

Related Skills

  • clinvar-database — germline pathogenicity / clinical significance for variants found in PharmGKB (complementary; ClinVar is disease-focused, ClinPGx is drug-response-focused)
  • opentargets-database — drug-target associations and safety signals overlapping ClinPGx pharmacogene targets
  • chembl-database-bioactivity — bioactivity and binding data for the drugs annotated in ClinPGx
  • cosmic-database — somatic cancer mutations and tumor-specific PGx (orthogonal to germline PGx covered here)

References