medical-research-toolkit

Medical Research Toolkit

Query 14+ biomedical databases for drug repurposing, target discovery, clinical evidence, and literature research.

Everything you need to build evidence-based research workflows using modern biomedical data.

What's Included

• Complete SKILL.md — Getting started guide with quick examples
• 6 Database Guides — PubMed, ClinicalTrials, ChEMBL, OpenTargets, OpenFDA, OMIM
• 2 API References — 8 additional databases + ID mapping
• 1 Complete Workflow — Drug repurposing example with all curl commands

Quick Start

1. Read SKILL.md — 5 minute overview
2. Pick a use case — Drug repurposing, target discovery, clinical evidence review, or literature mining
3. Read the relevant database guide — E.g., ChEMBL Guide
4. Copy/adapt the example queries — Use the curl commands provided
5. Scale up — Build your full research workflow

Structure

medical-research-toolkit/
├── SKILL.md                          # Main guide (START HERE)
├── references/
│   ├── pubmed.md                     # Literature search
│   ├── clinical-trials.md            # Clinical trial search
│   ├── chembl.md                     # Drug-target data
│   ├── opentargets.md                # Disease-target links
│   ├── openfda.md                    # Drug safety & FDA data
│   ├── omim.md                       # Genetic diseases
│   └── other-apis.md                 # Reactome, UniProt, KEGG, GWAS, etc.
└── scripts/
    └── drug-repurposing-workflow.md  # Step-by-step example

Key Features

✅ 14+ Databases — ChEMBL, PubMed, ClinicalTrials, OpenTargets, OpenFDA, OMIM, Reactome, UniProt, KEGG, GWAS, and more

✅ No Setup — Use the production endpoint immediately (https://mcp.cloud.curiloo.com)

✅ Real Examples — Every database has actual curl commands you can run

✅ Complete Workflows — Full drug repurposing pipeline with all steps

✅ Clear Documentation — Written for researchers (medical jargon included but explained)

✅ Multiple Use Cases — Drug repurposing, target discovery, clinical evidence, literature mining

Common Use Cases

Find Unapproved Drugs for a Disease

1. OpenTargets Guide — Find disease targets
2. ChEMBL Guide — Find drugs targeting those genes
3. ClinicalTrials Guide — Check for ongoing trials
4. OpenFDA Guide — Verify safety profile

Build Literature Review

1. PubMed Guide — Search relevant papers
2. Filter by gene, disease, chemical, or keyword
3. Get full text for key papers

Discover Novel Targets

1. OpenTargets Guide — Find disease targets
2. GWAS Guide — Check genetic associations
3. Reactome Guide — Understand biological mechanisms
4. UniProt Guide — Get protein details

Assess Candidate Drug Safety

1. OpenFDA Guide — Search adverse events
2. PubMed Guide — Search case reports/literature
3. ClinicalTrials Guide — Check trial data

API Endpoint

Production (Recommended):

https://mcp.cloud.curiloo.com/tools/unified/mcp

Includes all 14+ databases unified into one endpoint.

Individual endpoints also available — See SKILL.md for URLs

Example Query

curl -X POST https://mcp.cloud.curiloo.com/tools/unified/mcp \
  -H "Content-Type: application/json" \
  -d '{
    "jsonrpc": "2.0",
    "method": "tools/call",
    "params": {
      "name": "pubmed_search_articles",
      "arguments": {
        "query": "myasthenia gravis treatment",
        "max_results": 10
      }
    },
    "id": 1
  }'

Returns: Top 10 PubMed articles on MG treatment

Documentation Organization

• SKILL.md — High-level overview, workflows, and quick reference
• references/*.md — Deep dives into each database (read as needed)
• scripts/*.md — Complete worked examples

Start with SKILL.md. Refer to specific database guides as needed.

API Keys

Most APIs are free and don't require keys. Optional keys for higher rate limits:

Database	Key Required?	Why?	Get Key
OMIM	Yes	Proprietary medical 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
All others	No	Public endpoints	(not needed)

Questions?

Refer to the relevant database guide. All tools have examples and explanations of what they return.

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Source: https://github.com/pascalwhoop/medical-mcps

Author: Pascal Brockmeyer (@pascalwhoop)

Organization: Every Cure (https://www.everycure.org) — Reimagining drug development through computational drug repurposing