JackKuo666_PubTator-MCP-Server
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The PubTator MCP Server is a biomedical literature annotation and relationship mining server that provides access to the PubTator3 system through the Model Context Protocol (MCP).
The PubTator MCP Server is designed to facilitate AI models in accessing and analyzing biomedical literature. By leveraging the PubTator3 annotation system, it allows for efficient literature searches, entity relationship mining, and annotation exports. The server supports both stdio and TCP transports, making it versatile for different deployment environments. It is particularly useful for researchers and developers working in the biomedical field, providing tools to query standard identifiers for biological concepts, discover relationships between entities, and retrieve literature based on keywords and entity IDs. The server is built with Python and requires the FastMCP library, ensuring a robust and scalable solution for handling large volumes of data. Additionally, it offers batch processing capabilities, allowing users to export annotation information from search results in bulk. The server is available for installation via Smithery or manual setup, and it can also be deployed using Docker for ease of use.
Features
- Literature Annotation Export: Supports exporting PubTator annotation results in multiple formats.
- Entity ID Lookup: Allows querying of standard identifiers for biological concepts through free text.
- Relationship Mining: Enables discovery of biomedical relationships between entities.
- Literature Search: Supports retrieval of literature by keywords and entity IDs.
- Batch Processing: Facilitates batch export of annotation information from search results.