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.

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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

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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 | | |

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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

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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 ```

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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.

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Workflow Example

Complete Drug Repurposing Pipeline:

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

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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 |

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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)

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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.

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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

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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

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Resources

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

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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