Medical Research Toolkit

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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.

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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.

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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

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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:

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

# 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.

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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

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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