PubTator-MCP-Server
Biomedical literature annotation server via MCP. PubTator-MCP-Server is a Model Context Protocol (MCP) server maintained by JackKuo666. It connects to MCP-compatible clients such as Claude Desktop, Cursor, Cline, and other agents that speak the protocol. It exposes 5 tools, including export_publications, find_entity_id, find_related_entities, search_pubtator and batch_export_from_search, that an agent can call directly. It is categorized under AI/Research and Data/PubMed.
What is this MCP
This MCP provides programmatic access to PubTator3's biomedical literature annotation system, enabling AI models to search scientific literature, extract annotations, and analyze entity relationships.
How to use this MCP
The server can be installed via Smithery or manually, and supports both stdio and TCP transports. It offers API endpoints for literature export, entity lookup, relationship mining, and batch processing.
What this MCP can be used for
This MCP enables biomedical research automation, including literature mining, entity relationship analysis, and knowledge graph construction for AI assistants in healthcare/life sciences.
AIMCP authority
DR and traffic signal for the AIMCP public domain.
Frequently asked questions
What is the PubTator-MCP-Server MCP server?
PubTator-MCP-Server is a Model Context Protocol server from JackKuo666. It lets MCP-compatible AI clients call its tools over a standard interface, so agents like Claude, Cursor, and Cline can use it without custom integration.
How do I connect PubTator-MCP-Server to my AI client?
Add PubTator-MCP-Server to your client's MCP configuration using the stdio or SSE connection shown in the usage examples on this page, then restart the client to load the server.
What tools does PubTator-MCP-Server provide?
PubTator-MCP-Server provides 5 tools: export_publications, find_entity_id, find_related_entities, search_pubtator and batch_export_from_search.
Is PubTator-MCP-Server free to use?
PubTator-MCP-Server is listed on AIMCP for free. Any API keys or accounts required by the underlying service are set by its provider.
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