# BioContext Knowledgebase

> Use this tool when you need to access unified biomedical databases and research tools through a single interface, solving problems of custom integrations and fragmented data queries. It provides inputs such as protein sequences, gene IDs, and literature search terms, and outputs standardized data from over 20 specialized tools, including protein databases, genomics resources, and clinical data. Ideal for researchers, bioinformatics teams, and AI applications requiring verified biomedical information, this tool streamlines access to reliable data without managing multiple API integrations.

Canonical page: https://skillsregistry.net/skills/biocontext-ai-knowledgebase  
JSON: https://api.skillsregistry.net/v1/skills/biocontext-ai-knowledgebase

## Description

This MCP server provides AI assistants with unified access to biomedical databases and research tools through a single interface, built by the BioContextAI team using Python with FastMCP and designed to eliminate the need for custom integrations with each biomedical resource. The implementation offers over 20 specialized tools covering protein databases (UniProt, AlphaFold, Human Protein Atlas), genomics resources (Ensembl, KEGG), literature search (Europe PMC, Google Scholar), clinical data (ClinicalTrials.gov, OpenFDA), and ontologies (Gene Ontology, EFO, ChEBI), with both self-hosted deployment options and a hosted service at mcp.biocontext.ai. Built with comprehensive test coverage, Docker support, and integration with the BioContextAI Registry for community tool discovery, it serves researchers needing programmatic access to biomedical data, bioinformatics teams requiring standardized database queries, and AI applications that need verified biomedical information without managing multiple API integrations.

## Trust

- **Trust score (0–1):** 0.99
- **Verification tier:** verified
- **Last scanned:** 2026-09-19

## Facts

- **Version:** 1.0.0
- **Skill type:** atomic
- **Execution layer:** mcp-remote
- **Runtime environment:** api
- **Category:** database
- **Updated:** 2026-09-19

## Source

- **Source listing:** [PulseMCP](https://www.pulsemcp.com/servers/biocontext-ai-knowledgebase)
- **Repository:** <https://github.com/biocontext-ai/knowledgebase-mcp>

## Use it

Resolve this record through the SkillsRegistry MCP server (no auth, read-only):

```
claude mcp add --transport http --scope user skillsregistry https://api.skillsregistry.net/mcp
```

```json
{
  "jsonrpc": "2.0",
  "id": 1,
  "method": "tools/call",
  "params": {
    "name": "get_skill",
    "arguments": {
      "slug": "biocontext-ai-knowledgebase"
    }
  }
}
```

REST: `GET https://api.skillsregistry.net/v1/skills/biocontext-ai-knowledgebase` · pull for local use: `GET https://api.skillsregistry.net/v1/skills/biocontext-ai-knowledgebase/pull`

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SkillsRegistry indexes agent skills from public registries and GitHub. Skills we have analysed are scanned with Circle-IR and scored on six dimensions; each listing states its scan coverage. More: https://skillsregistry.net/llms.txt