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unibio-intelligence

biomedmcp

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by unibio-intelligence
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Python
Hybrid

biomedmcp

Search biomedical literature, read accessible full-text papers, inspect variant evidence and explore genes, drugs and clinical trials through one MCP interface. The same tools are available through Python and a JSON CLI.

Get started

Connect an MCP client: use https://biomedmcp.unibiointelligence.com/mcp as a Streamable HTTP endpoint. Availability and sign-in depend on the hosted service. See the connection guide for local setup and troubleshooting.

Run locally: install Python 3.13+ and uv, then run from this repository:

uv sync --frozen
UBI_PROFILE=local uv run --frozen biomedmcp literature_search '{"query":"BRAF V600E melanoma","filters":{"source":"pubmed"}}'

The release also includes a single Python wheel with all adapters bundled. Install it in a Python 3.13+ environment with uv pip install ./biomedmcp-0.2.1-py3-none-any.whl; third-party dependencies are resolved automatically.

To start a local MCP server:

UBI_PROFILE=local uv run --frozen biomedmcp-server --transport http --host 127.0.0.1 --port 8000

Connect your client to http://127.0.0.1:8000/mcp.

Related MCP server: pubmed-search

What you can do

Goal

Tool

Find papers, with optional source, date and ranking controls

literature_search

Read accessible article text and tables in pages of up to 100 lines

get with entity: "article" and sections: ["fulltext"]

Look up ClinVar or CIViC assertions for a variant

variant_evidence

Search clinical trials

trial_search

Explore genes, proteins, drugs, diseases and pathways

search, get, resolve, relate

Build a focused research dossier

research

Analyze an installed public study

study_analysis

Try asking your agent to “find recent BRAF V600E melanoma papers,” “compare ClinVar evidence for BRAF V600E and V600K,” or “retrieve the tables from this PMC article.” Use the call examples for exact arguments and investigations for longer workflows.

UBI_PROFILE=local uv run biomedmcp get '{"entity":"gene","id":"ERBB2","species":9606,"sections":["expression"]}'
UBI_PROFILE=local uv run biomedmcp literature_search '{"query":"BRAF","filters":{"source":"pubmed","date_from":"2024-01-01"}}'
UBI_PROFILE=local uv run biomedmcp variant_evidence '{"id":"BRAF V600E"}'

Available data and results

Some sources require a key or an installed dataset. Check source access, or run uv run --frozen biomedmcp diagnose when setup is uncertain. Keep keys in environment variables or client secret storage.

Follow next_cursor and returned continuation links to read more. An unavailable source does not mean no evidence exists; results may be partial. Full-text access depends on the article. See result handling for details.

Integration code is licensed under Apache-2.0. Provider data has its own terms. See release notes and contributing.

This server cannot be deployed

One endpoint for every MCP toolRayrun runs every MCP server behind one URL and holds the credentials. Each call is decided per client, tool, and argument, then recorded.ray.runAd

Maintenance

ActivityMaintained
ResponsivenessNo issues

Resources

Related MCP Connectors

Related MCP Servers

  • PubMed MCP Server

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    Provides comprehensive access to NCBI's PubMed database of over 36 million biomedical citations, allowing users to search, retrieve, and analyze literature directly through MCP tools. It supports advanced queries, citation management, full-text retrieval from PubMed Central, and precise discovery using MeSH terms.
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  • pubmed-search

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    Enables searching PubMed using natural language questions by translating queries to PubMed syntax and returning semantically relevant results. It also supports related articles, citation chains, and bibliography export via MCP tools.
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