Clinical & Translational API Skills
Query clinical databases directly via curl. These endpoints complement the Life Sciences MCPs.
Quick Reference
| Task | API | Endpoint |
|---|---|---|
| Target-disease associations | Open Targets | GraphQL /graphql |
| Target tractability | Open Targets | GraphQL tractability |
| Known drugs for target | Open Targets | GraphQL knownDrugs |
| Search clinical trials | ClinicalTrials.gov | /studies |
| Get trial details | ClinicalTrials.gov | /studies/{NCT} |
Open Targets GraphQL
Open Targets uses GraphQL - construct queries to get exactly what you need in one call.
Basic Target-Disease Associations
bash
# 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
bash
# 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
bash
# 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
bash
# 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
bash
# 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
bash
# 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
bash
# 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
bash
# 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
bash
# 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
bash
# 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
bash
# 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
| API | Limit | Notes |
|---|---|---|
| Open Targets | 100 req/s | No auth required |
| ClinicalTrials.gov | Varies | May block automated clients |
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