query-biomedical-databases-drug-discovery

Imported from rondoflow/rondoflow (packages/catalog/content/skills/query-biomedical-databases-drug-discovery/SKILL.md). Install upstream with npx skills add rondoflow/rondoflow --skill query-biomedical-databases-drug-discovery. Copyright stays with the author.

Medical Research Toolkit

Query 14+ biomedical databases for drug repurposing, target discovery, clinical evidence, and literature research — all via a unified MCP endpoint.

⚡ 30-Second Start

# Find drugs for myasthenia gravis
curl -X POST https://mcp.cloud.curiloo.com/tools/unified/mcp \
  -H "Content-Type: application/json" -H "Accept: application/json" \
  -d '{"jsonrpc":"2.0","method":"tools/call","params":{"name":"chembl_find_drugs_by_indication","arguments":{"indication":"myasthenia gravis","max_results":10}},"id":1}'

That's it! You now have approved and investigational drugs for the disease.

Quick Recipes

Find Drugs for a Disease

curl -X POST https://mcp.cloud.curiloo.com/tools/unified/mcp \
  -H "Content-Type: application/json" -H "Accept: application/json" \
  -d '{"jsonrpc":"2.0","method":"tools/call","params":{"name":"chembl_find_drugs_by_indication","arguments":{"indication":"myasthenia gravis","max_results":20}},"id":1}'

Returns: Approved + investigational drugs with max phase reached

Find Disease Targets

# First: Find disease ID
curl -X POST https://mcp.cloud.curiloo.com/tools/unified/mcp \
  -H "Content-Type: application/json" -H "Accept: application/json" \
  -d '{"jsonrpc":"2.0","method":"tools/call","params":{"name":"opentargets_search","arguments":{"query":"myasthenia gravis","entity_type":"disease"}},"id":1}'

# Returns: disease ID (e.g., EFO_0004991)
# Then: Get targets
curl -X POST https://mcp.cloud.curiloo.com/tools/unified/mcp \
  -H "Content-Type: application/json" -H "Accept: application/json" \
  -d '{"jsonrpc":"2.0","method":"tools/call","params":{"name":"opentargets_get_associations","arguments":{"disease_id":"EFO_0004991","size":20}},"id":2}'

Returns: Top disease targets ranked by evidence strength (0-1 score)

Search Literature

curl -X POST https://mcp.cloud.curiloo.com/tools/unified/mcp \
  -H "Content-Type: application/json" -H "Accept: application/json" \
  -d '{"jsonrpc":"2.0","method":"tools/call","params":{"name":"pubmed_search_articles","arguments":{"diseases":["myasthenia gravis"],"keywords":["immunotherapy"],"max_results":20}},"id":1}'

Returns: PubMed articles on myasthenia gravis immunotherapy

Find Active Clinical Trials

curl -X POST https://mcp.cloud.curiloo.com/tools/unified/mcp \
  -H "Content-Type: application/json" -H "Accept: application/json" \
  -d '{"jsonrpc":"2.0","method":"tools/call","params":{"name":"ctg_search_studies","arguments":{"condition":"myasthenia gravis","recruitment_status":"RECRUITING","max_results":20}},"id":1}'

Returns: Actively recruiting trials for the disease

Check Drug Safety

curl -X POST https://mcp.cloud.curiloo.com/tools/unified/mcp \
  -H "Content-Type: application/json" -H "Accept: application/json" \
  -d '{"jsonrpc":"2.0","method":"tools/call","params":{"name":"openfda_search_adverse_events","arguments":{"drug_name":"eculizumab","limit":50}},"id":1}'

Returns: FDA adverse event reports—check for serious outcomes, death, hospitalization

What You Get

14+ Integrated Databases

Use Cases

🧬 Drug Repurposing

Find non-standard-care drugs for rare/complex diseases:

1. Find disease targets (OpenTargets)
2. Search for drugs targeting those genes (ChEMBL)
3. Check ongoing trials (ClinicalTrials)
4. Verify safety (OpenFDA, PubMed)

🔬 Target Discovery

Identify novel therapeutic targets:

1. Find disease associations (OpenTargets, GWAS)
2. Get pathway context (Reactome, KEGG)
3. Review literature (PubMed)
4. Check protein properties (UniProt)

📋 Clinical Evidence Review

Compile evidence for a hypothesis:

1. Search trials (ClinicalTrials.gov)
2. Find literature (PubMed)
3. Check FDA data (OpenFDA)

📊 Literature Mining

Systematically search biomedical research:

1. PubMed: 35M+ articles searchable by gene, disease, drug, chemical
2. Preprints: bioRxiv, medRxiv
3. Filter by keywords, date, study type

API Endpoint

Production (No setup needed):

https://mcp.cloud.curiloo.com/tools/unified/mcp

All 14+ databases unified into one endpoint.

Running Locally:

pip install medical-mcps
medical-mcps
# Available at: http://localhost:8000/tools/unified/mcp

Complete References

See detailed guides for each database:

• PubMed Guide — Literature search (genes, diseases, keywords)
• ClinicalTrials Guide — Find active trials
• ChEMBL Guide — Drug-target data & bioactivity
• OpenTargets Guide — Disease-target associations
• OpenFDA Guide — Drug safety & adverse events
• OMIM Guide — Genetic diseases (requires API key)
• Other APIs — Reactome, UniProt, KEGG, GWAS, etc.

Workflow Example

Complete Drug Repurposing Pipeline:

See drug-repurposing-workflow.md for step-by-step example with all 8 steps + curl commands.

API Keys

Most APIs are free, no key required. Optional keys for higher rate limits:

Rate Limits & Caching

• No authentication for production endpoint (public)
• Rate limits: Generous (~1000+ requests/day per database)
• Caching: Automatic 30-day HTTP caching (RFC 9111)
• Cost: $0 (all databases public or researcher-accessible)

Common Patterns

Batch Query Loop

# Search multiple targets
for gene in CHRNE RAPSN LRP4; do
  curl -X POST https://mcp.cloud.curiloo.com/tools/unified/mcp \
    -H "Content-Type: application/json" -H "Accept: application/json" \
    -d "{\"jsonrpc\":\"2.0\",\"method\":\"tools/call\",\"params\":{\"name\":\"chembl_find_drugs_by_target\",\"arguments\":{\"target_name\":\"$gene\",\"max_results\":10}},\"id\":1}"
  sleep 1  # Be nice to the API
done

ID Conversion

Need to convert IDs between databases?

curl -X POST https://mcp.cloud.curiloo.com/tools/unified/mcp \
  -H "Content-Type: application/json" -H "Accept: application/json" \
  -d '{"jsonrpc":"2.0","method":"tools/call","params":{"name":"nodenorm_get_normalized_nodes","arguments":{"curie":"HGNC:11998"}},"id":1}'

Returns: Equivalent IDs in NCBI Gene, Uniprot, Ensembl, MyGene, etc.

Troubleshooting

No results?

• Try alternative terms (gene symbol vs protein name)
• Check spelling
• Use standardized IDs (gene symbols, disease names)
• Some APIs use specific ID formats (EFO vs MONDO, etc.)

Too many results?

• Add filters (max_results, phase, recruitment status)
• Use limit or size parameters
• Combine with other databases to narrow focus

API key errors?

• OMIM requires API key — get from https://omim.org/api
• Other databases optional — request key if hitting rate limits

Next Steps

1. Pick a use case (drug repurposing, target discovery, etc.)
2. Read the relevant database guide from References section
3. Copy a quick recipe from above
4. Customize parameters for your disease/gene/drug
5. Scale up — build your full research workflow

Resources

• Source Code: https://github.com/pascalwhoop/medical-mcps
• Author: Pascal Brockmeyer (@pascalwhoop)
• Organization: Every Cure (https://www.everycure.org)
• License: MIT

Getting Help

• Database not working? → Check Troubleshooting
• Want detailed guide? → See Complete References
• Need a workflow example? → See drug-repurposing-workflow.md
• Question about OpenClaw? → See OPENCLAW-USAGE.md