PubTator3 API compatible with the MCP agent protocol
Most database access work still happens through a UI a human drives. MCP MCP server moves it into the conversation instead. PubTator3 API compatible with the MCP agent protocol.
This project provides an async Python server for interacting with the PubTator3 API. It exposes multiple biomedical text-mining tools compatible with the MCP agent protocol, supporting tasks such as entity lookup, biomedical literature search, and text extraction from PubMed/PMC articles.
The server ships on PyPI as mcp-server-pubtator3, so your MCP client can launch it on demand — there is no separate build step. Add the server block to your client's configuration, restart it, and the tools register themselves.
This sits in the database access group, where several servers overlap in what they claim to do but differ sharply once you actually set them up. It is maintained by Qingyuan Zhang; worth a glance at recent repository activity before you build anything load-bearing on it.
We check each listing at SyncDev against the project's documentation before it goes live — if something here drifts out of date, it is a bug worth reporting.
{
"mcpServers": {
"server-pubtator3": {
"command": "uvx",
"args": ["mcp-server-pubtator3"]
}
}
}Add to claude_desktop_config.json, then restart Claude Desktop.
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