🔍 A biomedical literature annotation and relationship mining server based on PubTator3, providing convenient access through the MCP interface.
PubTator MCP server exists for a simple reason — assistants are far more useful when they can act on PubTator directly instead of describing what you should do. 🔍 A biomedical literature annotation and relationship mining server based on PubTator3, providing convenient access through the MCP interface.
Once PubTator is connected, these are the calls the assistant has available:
Requirements — The Requirements tool exposed by this serverInstallation — The Installation tool exposed by this serverTroubleshooting — 1. Check the console output for error messages. 2. Ensure all required dependencies are installed (see Requirements section). 3. Verify that theConfiguration — The Configuration tool exposed by this server@smithery/cli on npm is all you need. Most clients run it directly, so configuration is a few lines and a restart.
You will need 3 environment variables: MCP_TRANSPORT, MCP_HOST, MCP_PORT. Keep credentials in your client's env block or a secrets manager rather than in a file you might commit.
Plenty of developer tooling servers cover similar ground. The differences that matter in practice are scope of access and how much setup stands between you and a working tool call. PubTator's toolset — Requirements, Installation, Troubleshooting and 1 more — is a fair guide to whether it matches your workflow. It is maintained by JackKuo666; 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We check each listing at SyncDev against the project's documentation before it goes live — if something here drifts out of date, it is a bug worth reporting.
| Tool | What it does |
|---|---|
| Requirements | The Requirements tool exposed by this server. |
| Installation | The Installation tool exposed by this server. |
| Troubleshooting | 1. Check the console output for error messages. 2. Ensure all required dependencies are installed (see Requirements section). 3. Verify that the environment variables are set correctly. 4. If the server fails to start, t |
| Configuration | The Configuration tool exposed by this server. |
(Windows)
```json
{
"mcpServers": {
"pubtator": {
"command": "C:\\Users\\YOUR\\PATH\\miniconda3\\envs\\mcp_server\\python.exe",
"args": [
"D:\\code\\YOUR\\PATH\\PubTator-MCP-Server\\pubtator_server.py"
],
"env": {},
"disabled": false,
"autoApprove": []
}
}
}Configuration as documented by the project. Restart the client after saving.
| Variable | Description | Required |
|---|---|---|
| MCP_TRANSPORT | Configuration value read at startup. | Optional |
| MCP_HOST | Endpoint or connection string the server talks to. | Optional |
| MCP_PORT | Configuration value read at startup. | Optional |
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