PubTator-MCP-Server
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PubTator MCP Server provides AI assistants with access to the PubTator3 biomedical literature annotation system through the Model Context Protocol (MCP).
The PubTator MCP Server is a powerful tool designed to facilitate access to the PubTator3 biomedical literature annotation system via the Model Context Protocol (MCP). It enables AI models to programmatically search scientific literature, obtain annotation information, and analyze entity relationships. This server is particularly useful for researchers and developers working in the biomedical field, as it provides a streamlined way to access and process large volumes of scientific data. The server supports various features such as literature annotation export, entity ID lookup, relationship mining, literature search, and batch processing. It is compatible with multiple platforms and can be easily integrated into existing workflows using the FastMCP library. The server also supports both stdio and TCP transports, offering flexibility in deployment and usage.
Features
- Literature Annotation Export: Support exporting PubTator annotation results in multiple formats.
- Entity ID Lookup: Query standard identifiers for biological concepts through free text.
- Relationship Mining: Discover biomedical relationships between entities.
- Literature Search: Support literature retrieval by keywords and entity IDs.
- Batch Processing: Support batch export of annotation information from search results.