mcp-server-pubtator3
3
The Pubtator MCP Server is an asynchronous Python server that interfaces with the PubTator3 API to facilitate biomedical text-mining through MCP protocol. It offers tools for entity lookup, literature search, and extraction of biomedical knowledge from PubMed and PMC articles.
Pubtator MCP Server
This project provides an async Python server for interacting with the PubTator3 API. It offers biomedical text-mining tools for tasks like entity lookup, literature search, and text extraction from PubMed/PMC articles.
Features
- Entity Autocomplete: Find biomedical entities using free-text queries.
- Literature Search: Search using keywords, entity IDs, or relations.
- Article Retrieval: Download and extract text from articles.
- Find Related Entities: Query related entities with filters.
- Async and Fast: Uses aiohttp for integration into MCP environments.
Available Tools
- find_entity: Identifies bioconcepts using text queries.
- search_pubtator: Searches for relevant articles.
- get_paper_text: Extracts text from articles.
- find_related_entities: Finds related entities based on criteria.