PubTator MCP Server
by BioMCP-Hub
PubTator MCP Server provides AI assistants with access to the PubTator3 biomedical literature annotation system through the Model Context Protocol (MCP). It allows AI models to programmatically search scientific literature, obtain annotation information, and analyze entity relationships.
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What is PubTator MCP Server?
PubTator MCP Server is a server that provides AI assistants with access to the PubTator3 biomedical literature annotation system through the Model Context Protocol (MCP). It enables programmatic searching of scientific literature, annotation retrieval, and entity relationship analysis.
How to use PubTator MCP Server?
The server can be installed via Smithery or manually by cloning the repository and installing dependencies. It can be run directly using Python or deployed using Docker. Configuration examples are provided for Claude Desktop and CLine. The server exposes API features for exporting publications, entity ID lookup, relationship queries, literature search, and batch export.
Key features of PubTator MCP Server
Literature Annotation Export
Entity ID Lookup
Relationship Mining
Literature Search
Batch Processing
Use cases of PubTator MCP Server
Automated literature review for drug discovery
Identifying gene-disease associations
Analyzing protein-protein interactions
Extracting chemical-disease relationships
FAQ from PubTator MCP Server
What is the API request rate limit?
What is the API request rate limit?
The API request rate limit is a maximum of 3 requests per second.
What should I consider when batch exporting?
What should I consider when batch exporting?
When batch exporting, use a reasonable batch_size to avoid request timeout.
How should entity IDs be formatted for relationship queries?
How should entity IDs be formatted for relationship queries?
For relationship queries, entity IDs must start with "@", e.g., "@DISEASE_COVID-19".
What is the purpose of this tool?
What is the purpose of this tool?
This tool is for research purposes only.
What license is this project under?
What license is this project under?
This project is licensed under the MIT License.