PubTator MCP Server

Example Use Cases

• 1

  Search biomedical literature and retrieve PubTator annotations programmatically (PMID-based exports in pubtator/biocxml/biocjson formats).

• 2

  Resolve biomedical entity names to standard identifiers (genes, diseases, chemicals, species, mutations) from free-text queries.

• 3

  Discover relationships between biomedical entities (e.g., treat/cause/interact queries) and perform batch exports from search results.

Description

A lightweight MCP server that exposes PubTator3 functionality (annotation export, entity identifier lookup, relationship queries, and literature search) to AI agents and tools. It supports multiple export formats, batch processing, and both stdio and TCP transports, with Docker support for easy deployment. The server is designed for programmatic access and integrates rate limiting and graceful shutdown handling for robust operation. It is distributed under the MIT License and intended for research-oriented use.