medical-research-toolkit

# 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 ```bash # 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 ```bash 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 ```bash # 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 ```bash 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 ```bash 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 ```bash 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: 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:** ```bash pip install medical-mcps medical-mcps # Available at: http://localhost:8000/tools/unified/mcp ``` --- ## Complete References See detailed guides for each database: - **[PubMed Guide](./references/pubmed.md)** — Literature search (genes, diseases, keywords) - **[ClinicalTrials Guide](./references/clinical-trials.md)** — Find active trials - **[ChEMBL Guide](./references/chembl.md)** — Drug-target data & bioactivity - **[OpenTargets Guide](./references/opentargets.md)** — Disease-target associations - **[OpenFDA Guide](./references/openfda.md)** — Drug safety & adverse events - **[OMIM Guide](./references/omim.md)** — Genetic diseases (requires API key) - **[Other APIs](./references/other-apis.md)** — Reactome, UniProt, KEGG, GWAS, etc. --- ## Workflow Example **Complete Drug Repurposing Pipeline:** See [drug-repurposing-workflow.md](./scripts/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**: $0 (all databases public or researcher-accessible) --- ## Common Patterns ### Batch Query Loop ```bash # Search multiple targets for gene in CHRNE RAPSN LRP4; do curl -X POST https://mcp.cloud.curiloo.com/tools/unified/mcp \ -H "Content-Type: application/json" -H "Accept: application/json" \ -d "{\"jsonrpc\":\"2.0\",\"method\":\"tools/call\",\"params\":{\"name\":\"chembl_find_drugs_by_target\",\"arguments\":{\"target_name\":\"$gene\",\"max_results\":10}},\"id\":1}" sleep 1 # Be nice to the API done ``` ### ID Conversion Need to convert IDs between databases? ```bash 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](#troubleshooting) - Want detailed guide? → See [Complete References](#complete-references) - Need a workflow example? → See [drug-repurposing-workflow.md](./scripts/drug-repurposing-workflow.md) - Question about OpenClaw? → See [OPENCLAW-USAGE.md](./OPENCLAW-USAGE.md)