medical-research-toolkit

name medical-research-toolkit description Query 14+ biomedical databases for drug repurposing, target discovery, clinical trials, and literature research. Access ChEMBL, PubMed, ClinicalTrials.gov, OpenTargets, OpenFDA, OMIM, Reactome, KEGG, UniProt, and more through a unified MCP endpoint. Use when researching disease targets, finding approved/investigational drugs, searching clinical evidence, discovering genetic associations, or analyzing compound bioactivity data. 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 Database What's Inside Use For ChEMBL 2M drugs, bioactivity data Finding approved/investigational drugs OpenTargets Disease-target links + evidence Identifying therapeutic targets PubMed 35M+ articles + preprints Literature review & validation ClinicalTrials.gov 400K+ active trials Finding ongoing studies OpenFDA Adverse events, drug labels Safety assessment OMIM Genetic diseases, genes → phenotypes Understanding disease genetics Reactome Pathways, protein interactions Mechanism understanding UniProt Protein sequences, annotations Protein properties KEGG Metabolic & disease pathways Systems-level view GWAS Catalog Genetic associations Variant discovery Pathway Commons Integrated pathway data Network analysis MyGene.info Gene annotations ID mapping MyVariant.info Variant effects Variant interpretation + more Use Cases 🧬 Drug Repurposing Find non-standard-care drugs for rare/complex diseases: Find disease targets (OpenTargets) Search for drugs targeting those genes (ChEMBL) Check ongoing trials (ClinicalTrials) Verify safety (OpenFDA, PubMed) 🔬 Target Discovery Identify novel therapeutic targets: Find disease associations (OpenTargets, GWAS) Get pathway context (Reactome, KEGG) Review literature (PubMed) Check protein properties (UniProt) 📋 Clinical Evidence Review Compile evidence for a hypothesis: Search trials (ClinicalTrials.gov) Find literature (PubMed) Check FDA data (OpenFDA) 📊 Literature Mining Systematically search biomedical research: PubMed: 35M+ articles searchable by gene, disease, drug, chemical Preprints: bioRxiv, medRxiv 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: Database Key? Why Get Key ChEMBL No Public data (not needed) OpenTargets No Public data (not needed) PubMed No Public data (not needed) ClinicalTrials No Public data (not needed) OMIM Yes Proprietary data https://omim.org/api OpenFDA Optional Higher rate limits https://open.fda.gov NCI Clinical Trials Optional Higher rate limits https://clinicaltrialsapi.cancer.gov 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 Pick a use case (drug repurposing, target discovery, etc.) Read the relevant database guide from References section Copy a quick recipe from above Customize parameters for your disease/gene/drug 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