Biological APIs MCP Server

MCP server that integrates multiple biological and medical databases for research purposes.

Quick Start

Connect to Production Server

The easiest way to use this MCP server is to connect to the production deployment. All APIs are available through a unified endpoint that gives you access to all tools in one place.

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

Configure in Cursor (or other MCP client)

Add this to your .cursor/mcp.json (or equivalent MCP client configuration):

{
    "mcpServers": {
        "medical-apis": {
            "url": "https://mcp.cloud.curiloo.com/tools/unified/mcp"
        }
    }
}

What You Get

Once connected, you’ll have access to 100+ tools across 14 biological and medical APIs:

• Pathways: Reactome, KEGG, Pathway Commons
• Genes & Proteins: UniProt, MyGene.info, Node Normalization
• Targets & Associations: OpenTargets Platform
• Variants: MyVariant.info, GWAS Catalog
• Diseases: OMIM, MyDisease.info
• Drugs: ChEMBL, MyChem.info, OpenFDA
• Literature: PubMed/PubTator3
• Trials: ClinicalTrials.gov, NCI Clinical Trials
• Knowledge Graphs: Every Cure Matrix Knowledge Graph

Example: Search for a Gene

{
    "jsonrpc": "2.0",
    "method": "tools/call",
    "params": {
        "name": "mygene_get_gene",
        "arguments": {
            "gene_id_or_symbol": "TP53"
        }
    }
}

Individual API Endpoints

If you prefer to use individual APIs separately, each API has its own endpoint:

• /tools/reactome/mcp - Reactome only
• /tools/pubmed/mcp - PubMed only
• /tools/chembl/mcp - ChEMBL only
• … (see Available Endpoints for full list)

Local Development

To run your own instance locally, you can either:

• Use Docker Compose (recommended for quick setup) - see Docker Compose Setup
• Run directly with Python/uv - see Running the Server below

APIs Integrated

✅ Implemented APIs

• Reactome API - Pathway information, gene/protein queries, disease associations
• KEGG API - Pathway maps, gene annotations, disease and drug information
• UniProt API - Protein sequences, functional annotations, disease associations
• OMIM API - Genetic disease information, gene-disease associations (requires API key)