Add it to Claude Code
claude mcp add --transport http biobtree https://sugi.bio/biobtree/mcpMake your agent remember this setup
biobtree's config, env vars, and the gotchas you hit — recalled in every future Claude Code, Cursor, and Codex session.
npx conare@latestFree · one command · indexes the sessions already on disk. Set up in the browser instead →
What it does
- Integrates 50+ primary biomedical data sources including genes, proteins, and compounds
- Provides billions of cross-reference edges for complex biomedical queries
- Supports natural language querying for structured biomedical data
- Enables cross-database mapping (e.g., Ensembl to UniProt to PDB)
Tools 1
query_biobtreeQuery the BioBTree graph database using natural language or specific identifiers to retrieve cross-referenced biomedical data.Try it
Original README from tamerh/biobtree
🧬 BioBTree v2
A unified biomedical graph database that integrates 50+ primary data sources — genes, proteins, compounds, diseases, pathways, and clinical data — into a single queryable graph with billions of cross-reference edges. Its native MCP server gives LLMs direct access to structured, authoritative biomedical data, complementing their reasoning with reliable identifiers and up-to-date database content.
BRCA1 >> ensembl >> uniprot >> pdb[resolution<2.0]
This finds BRCA1 in Ensembl, maps to UniProt proteins, and returns high-resolution PDB structures — crossing three databases in a single line.
🔗 Try It
The fastest way to experience BioBTree v2 is through MCP. We recommend Claude CLI (tested extensively), though Codex CLI and Gemini CLI also work:
{
"mcpServers": {
"biobtree": {
"type": "http",
"url": "https://sugi.bio/biobtree/mcp"
}
}
}
Once connected, just ask questions in natural language — the AI will query BioBTree automatically:
💊 "What tissues express SCN9A most highly? Are there safety concerns for a Nav1.7 inhibitor?"
🧪 "How many ClinVar variants does BRCA1 have? How many are pathogenic?"
🎯 "What are all the protein targets of Alectinib with IC50 values?"
A REST API is also available for direct programmatic access:
https://sugi.bio/biobtree/api/ws/?i=BRCA1
https://sugi.bio/biobtree/api/ws/map/?i=BRCA1&m=>>ensembl>>uniprot>>chembl_target
https://sugi.bio/biobtree/api/ws/entry/?i=P38398&s=uniprot
📖 Documentation
Query syntax, integrated databases, development, and other details check the : docs/ or refer to latest preprint.
For any questions, issues, or collaboration ideas, feel free to create an issue or reach out at [email protected].
📄 Publication
BioBTree v2: Grounding LLM Responses with Large-Scale Structured Biomedical Data
The full preprint manuscript, detailing the graph architecture and comparative LLM use cases is available on Zenodo: https://zenodo.org/records/18962899
BioBTree v1: F1000Research
⚖️ License
AGPL-v3
The public MCP server hosted at sugi.bio is for academic and personal use only due to upstream non-commercial data licenses.