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What Is BioMCP?

BioMCP is a biomedical command-line interface and MCP server designed for practical research and clinical-informatics workflows.

It combines two ideas:

  1. A stable command grammar for entity retrieval and search.
  2. A protocol surface for agent runtimes through MCP tools and resources.

Core goal

The project goal is not to mirror every field from every API. The goal is to deliver dependable, compact answers that can be expanded on demand.

The command grammar

BioMCP uses one consistent grammar:

  • search <entity> [filters]
  • get <entity> <id> [section...]

This grammar is intentionally shared across entities so users and agents do not need a different mental model per endpoint.

Entities

BioMCP covers entities across clinical, research, and regulatory domains:

Core clinical entities: gene, variant, trial, article, drug, disease

Extended entities: pathway, protein, adverse-event, PGx (pharmacogenomics)

Discovery entities: GWAS, phenotype search, biomarker, organization, intervention

Why this matters for agents

Agent runtimes often fail on data tooling for three reasons:

  • command discovery is inconsistent,
  • output is too verbose or unstable,
  • source provenance is unclear.

BioMCP addresses these with:

  • predictable commands,
  • compact markdown-first defaults,
  • explicit source mapping in docs.

What BioMCP is not

BioMCP is not a local biomedical warehouse. It is also not a replacement for formal clinical interpretation systems.

It is a workflow interface that normalizes retrieval from trusted public APIs.

Progressive detail

BioMCP starts concise, then expands by section.

Examples:

biomcp get gene BRAF
biomcp get gene BRAF pathways
biomcp get article 22663011
biomcp get article 22663011 fulltext

The first command gives orientation. The second command gives focused depth.

MCP mode

biomcp serve runs a stdio MCP server.

The server advertises:

  • tools: one execution tool (shell)
  • resources: curated markdown help and pattern documents

This keeps client integration simple while preserving discoverability.

Where BioMCP fits

BioMCP works well for:

  • trial searching triage,
  • variant-to-literature pivots,
  • disease normalization and downstream lookups,
  • adverse-event and recall quick checks.

Design priorities

The design priorities are:

  • deterministic command behavior,
  • explicit error messages,
  • low context overhead,
  • documented API provenance,
  • CI-backed contract checks.

Next reading

  • Concept: Progressive disclosure
  • User guides: docs/user-guide/
  • Data provenance: docs/reference/data-sources.md
  • MCP behavior: docs/reference/mcp-server.md