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

CODEBLOCK0

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

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Quick Recipes

Find Drugs for a Disease

CODEBLOCK1

Returns: Approved + investigational drugs with max phase reached

Find Disease Targets

CODEBLOCK2

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

Search Literature

CODEBLOCK3

Returns: PubMed articles on myasthenia gravis immunotherapy

Find Active Clinical Trials

CODEBLOCK4

Returns: Actively recruiting trials for the disease

Check Drug Safety

CODEBLOCK5

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

📊 Literature Mining

Systematically search biomedical research:

1. 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):
CODEBLOCK6

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

CODEBLOCK8

ID Conversion

Need to convert IDs between databases?

CODEBLOCK9

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. 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