knowledgebase-mcp

Overview

BioContextAI Knowledgebase MCP is a specialized Model Context Protocol server that connects AI systems with biomedical resources. It offers a standardized access layer to numerous APIs including Ensembl, EuropePMC, KEGG, and STRING, enabling LLMs to retrieve verified biomedical information. The server is designed for both local deployment and cloud hosting, with comprehensive documentation and integration options for various environments including Claude Desktop and popular IDEs.

Try asking AI

After installing, here are 5 things you can ask your AI assistant:

• antibody_registry

  Gene id conversion through Antibody Registry

  Try:Convert gene symbol to Entrez ID using Antibody RegistryTry:Find antibodies for a specific gene
• biorxiv_medrxiv

  Search recent preprints and access metadata from bioRxiv/medRxiv

  Try:Find recent preprints about COVID-19 vaccinesTry:Search medRxiv for papers on machine learning in healthcare
• ensembl

  Gene ID conversion and information from Ensembl

  Try:Convert Ensembl gene ID to symbolTry:Get gene information for ENSG00000141510
• europmc

  Literature search and full-text access from EuropePMC

  Try:Find recent papers about CRISPR gene editingTry:Search for full-text articles on Alzheimer's disease treatment
• interpro

  Protein families, domains, and functional sites classification

  Try:Find protein domains for P53Try:Classify protein sequence families
• kegg

  Access pathways, gene and drug-drug interaction database from KEGG

  Try:Find the insulin signaling pathway in KEGGTry:Get drug-drug interactions for metformin
• opentargets

  Access target-disease associations from OpenTargets

  Try:Find disease associations for the BRCA1 geneTry:Get targets for Alzheimer's disease
• panglaodb

  Access single-cell RNA-seq cell type markers from PanglaoDB

  Try:Find cell markers for T cellsTry:Get markers for neurons in the human brain
• pride

  Access proteomics data repository from PRIDE

  Try:Find mass spectrometry datasets for breast cancerTry:Search for proteomics data related to protein folding
• protein_atlas

  Access protein expression data from Protein Atlas

  Try:Find expression levels of the BRCA1 proteinTry:Get tissue-specific expression for TP53
• reactome

  Access pathways database from Reactome

  Try:Find the apoptosis pathway in ReactomeTry:Get information about DNA repair mechanisms
• string

  Access protein-protein interaction networks from STRING

  Try:Find protein interactions for p53Try:Get interaction network for insulin receptor

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Installation

{
  "mcpServers": {
    "biocontext_kb": {
      "command": "uvx",
      "args": [
        "biocontext_kb@latest"
      ],
      "env": {
        "UV_PYTHON": "3.12"
      }
    }
  }
}

export MCP_ENVIRONMENT=PRODUCTION && export PORT=8000 && uvx biocontext_kb

export MCP_ENVIRONMENT=DEVELOPMENT && uvx biocontext_kb

{
  "mcpServers": {
    "biocontext_kb": {
      "command": "uvx",
      "args": [
        "biocontext_kb@latest"
      ]
    }
  }
}

FAQ

Can I use this MCP server commercially?

The project is licensed under Apache License 2.0, but individual APIs may have their own terms of service. Users must comply with both the Apache License and the terms of each integrated API provider.

What biomedical resources are available?

The server provides access to 15+ biomedical databases including Ensembl, EuropePMC, KEGG, STRING, AlphaFold DB, Reactome, and more. Full list available in the README documentation.

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