Lifesciences Clinical

Clinical & Translational API Skills

Query clinical databases directly via curl. These endpoints complement the Life Sciences MCPs.

Quick Reference

Open Targets GraphQL

Open Targets uses GraphQL - construct queries to get exactly what you need in one call.

Basic Target-Disease Associations

# Get diseases associated with target (TP53)
curl -s -X POST "https://api.platform.opentargets.org/api/v4/graphql" \
  -H "Content-Type: application/json" \
  -d '{"query": "{ target(ensemblId: \"ENSG00000141510\") { approvedSymbol associatedDiseases(page: {index: 0, size: 5}) { rows { disease { id name } score } } } }"}' \
  | jq '.data.target.associatedDiseases.rows[] | {disease: .disease.name, score}'

Target Details with Tractability

# Get target with druggability assessment
curl -s -X POST "https://api.platform.opentargets.org/api/v4/graphql" \
  -H "Content-Type: application/json" \
  -d '{"query": "{ target(ensemblId: \"ENSG00000141510\") { approvedSymbol biotype tractability { label modality value } } }"}' \
  | jq '.data.target | {symbol: .approvedSymbol, tractability}'

Known Drugs for Target

# Get approved drugs targeting a protein
curl -s -X POST "https://api.platform.opentargets.org/api/v4/graphql" \
  -H "Content-Type: application/json" \
  -d '{"query": "{ target(ensemblId: \"ENSG00000171791\") { approvedSymbol knownDrugs(page: {size: 5}) { rows { drug { name } phase mechanismOfAction } } } }"}' \
  | jq '.data.target.knownDrugs.rows[] | {drug: .drug.name, phase, mechanism: .mechanismOfAction}'

Nested Query: All-in-One

# Get target + diseases + drugs + tractability in single call
curl -s -X POST "https://api.platform.opentargets.org/api/v4/graphql" \
  -H "Content-Type: application/json" \
  -d '{
    "query": "{
      target(ensemblId: \"ENSG00000141510\") {
        approvedSymbol
        biotype
        tractability { label value }
        knownDrugs(page: {size: 3}) {
          rows { drug { name } phase }
        }
        associatedDiseases(page: {size: 3}) {
          rows { disease { name } score }
        }
      }
    }"
  }' | jq '.data.target'

Disease-Centric Queries

# Get targets associated with disease (breast cancer = EFO_0000305)
curl -s -X POST "https://api.platform.opentargets.org/api/v4/graphql" \
  -H "Content-Type: application/json" \
  -d '{"query": "{ disease(efoId: \"EFO_0000305\") { name associatedTargets(page: {size: 5}) { rows { target { approvedSymbol } score } } } }"}' \
  | jq '.data.disease.associatedTargets.rows[] | {target: .target.approvedSymbol, score}'

# Search for disease by name
curl -s -X POST "https://api.platform.opentargets.org/api/v4/graphql" \
  -H "Content-Type: application/json" \
  -d '{"query": "{ search(queryString: \"breast cancer\", entityNames: [\"disease\"]) { hits { id name } } }"}' \
  | jq '.data.search.hits[:3]'

Evidence Breakdown

# Get association with evidence type scores
curl -s -X POST "https://api.platform.opentargets.org/api/v4/graphql" \
  -H "Content-Type: application/json" \
  -d '{"query": "{ disease(efoId: \"MONDO_0018875\") { name associatedTargets(page: {size: 3}) { rows { target { approvedSymbol } score datatypeScores { id score } } } } }"}' \
  | jq '.data.disease.associatedTargets.rows[] | {target: .target.approvedSymbol, overall: .score, evidence: .datatypeScores}'

ClinicalTrials.gov API v2

Search Clinical Trials

# Search by condition
curl -s "https://clinicaltrials.gov/api/v2/studies?query.cond=breast+cancer&pageSize=3&format=json" \
  | jq '.studies[] | {nct: .protocolSection.identificationModule.nctId, title: .protocolSection.identificationModule.briefTitle, status: .protocolSection.statusModule.overallStatus}'

# Search by intervention (drug)
curl -s "https://clinicaltrials.gov/api/v2/studies?query.intr=venetoclax&pageSize=3&format=json" \
  | jq '.studies[] | {nct: .protocolSection.identificationModule.nctId, phase: .protocolSection.designModule.phases, status: .protocolSection.statusModule.overallStatus}'

# Filter by status
curl -s "https://clinicaltrials.gov/api/v2/studies?filter.overallStatus=RECRUITING&query.cond=leukemia&pageSize=3&format=json" \
  | jq '.studies[] | {nct: .protocolSection.identificationModule.nctId, title: .protocolSection.identificationModule.briefTitle}'

# Filter by phase
curl -s "https://clinicaltrials.gov/api/v2/studies?filter.advanced=AREA[Phase]PHASE3&query.cond=cancer&pageSize=3&format=json" \
  | jq '.studies[] | {nct: .protocolSection.identificationModule.nctId, phases: .protocolSection.designModule.phases}'

Get Trial Details

# Get full trial by NCT ID
curl -s "https://clinicaltrials.gov/api/v2/studies/NCT00461032?format=json" \
  | jq '{
    nct: .protocolSection.identificationModule.nctId,
    title: .protocolSection.identificationModule.briefTitle,
    status: .protocolSection.statusModule.overallStatus,
    phase: .protocolSection.designModule.phases,
    conditions: .protocolSection.conditionsModule.conditions,
    interventions: [.protocolSection.armsInterventionsModule.interventions[]?.name]
  }'

# Get eligibility criteria
curl -s "https://clinicaltrials.gov/api/v2/studies/NCT00461032?format=json" \
  | jq '.protocolSection.eligibilityModule | {criteria: .eligibilityCriteria, minAge, maxAge, sex}'

Pagination

# Get page token for next page
RESPONSE=$(curl -s "https://clinicaltrials.gov/api/v2/studies?query.cond=cancer&pageSize=10&format=json")
NEXT_TOKEN=$(echo $RESPONSE | jq -r '.nextPageToken')

# Get next page
curl -s "https://clinicaltrials.gov/api/v2/studies?query.cond=cancer&pageSize=10&pageToken=$NEXT_TOKEN&format=json"

Common Workflows

Drug Target Validation Pipeline

# 1. Get target-disease association score
curl -s -X POST "https://api.platform.opentargets.org/api/v4/graphql" \
  -H "Content-Type: application/json" \
  -d '{"query": "{ target(ensemblId: \"ENSG00000171791\") { approvedSymbol associatedDiseases(page: {size: 1}) { rows { disease { id name } score } } } }"}' \
  | jq '.data.target'

# 2. Check tractability
curl -s -X POST "https://api.platform.opentargets.org/api/v4/graphql" \
  -H "Content-Type: application/json" \
  -d '{"query": "{ target(ensemblId: \"ENSG00000171791\") { tractability { label modality value } } }"}' \
  | jq '.data.target.tractability'

# 3. Find clinical trials for the target
curl -s "https://clinicaltrials.gov/api/v2/studies?query.intr=BCL2&filter.overallStatus=RECRUITING&pageSize=5&format=json" \
  | jq '.studies[] | {nct: .protocolSection.identificationModule.nctId, title: .protocolSection.identificationModule.briefTitle}'

Disease → Targets → Drugs → Trials

# 1. Find top targets for disease
curl -s -X POST "https://api.platform.opentargets.org/api/v4/graphql" \
  -H "Content-Type: application/json" \
  -d '{"query": "{ disease(efoId: \"EFO_0000574\") { name associatedTargets(page: {size: 3}) { rows { target { approvedSymbol } score } } } }"}' \
  | jq '.data.disease'

# 2. Get drugs for top target
curl -s -X POST "https://api.platform.opentargets.org/api/v4/graphql" \
  -H "Content-Type: application/json" \
  -d '{"query": "{ target(ensemblId: \"ENSG00000171791\") { knownDrugs(page: {size: 5}) { rows { drug { name id } phase } } } }"}' \
  | jq '.data.target.knownDrugs.rows'

# 3. Find trials for drug
curl -s "https://clinicaltrials.gov/api/v2/studies?query.intr=venetoclax&filter.overallStatus=RECRUITING&pageSize=3&format=json" \
  | jq '.studies[] | {nct: .protocolSection.identificationModule.nctId, condition: .protocolSection.conditionsModule.conditions[0]}'

Rate Limits

Notes

• ClinicalTrials.gov uses Cloudflare protection that may block Python httpx clients. Use curl for reliable access.
• Open Targets requires Ensembl Gene IDs (ENSG*) for target queries; use EFO IDs for disease queries.

Query Best Practices

Clinical Trials

• Default status=RECRUITING for active research landscape
• Use phase filter only for specific analysis:
  • PHASE3+: Commercialization/late-stage pipeline analysis
  • PHASE1/2: Early pipeline, first-in-human studies
  • No filter: Full landscape view (all phases)
• Don't assume phase filter is always needed

Open Targets

• Requires Ensembl Gene IDs (ENSG*) for target queries
• Use EFO IDs for disease queries (search first to resolve)
• Use nested GraphQL queries to minimize API calls

Common Pitfalls

• Don't filter by PHASE3+ for general drug discovery
• Recruiting trials are most relevant for collaboration opportunities
• Completed trials provide outcome data but may be outdated

See Also

• references/opentargets-schema.md - GraphQL schema reference
• references/clinicaltrials-fields.md - Study field reference

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