A side-by-side look at the Pubtator and MCP Simple Pubmed MCP servers: transport, auth, tools, quality signals, and the config to install either one in Claude, Cursor, Windsurf or VS Code.
Verdict: choose Pubtator for biology, medicine and bioinformatics work as a local process; choose MCP Simple Pubmed for biology, medicine and bioinformatics as a local process. You can also run both side by side in one mcpServers block.
PUBMED_EMAIL, PUBMED_API_KEY.Rows where the two servers differ are marked.
| Spec | ||
|---|---|---|
| Category | Biology, Medicine and Bioinformatics | Biology, Medicine and Bioinformatics |
| Quality signal | 37/100 · Fair | 41/100 · Fair |
| Install command | Confirmed | Confirmed |
| Transport | Local subprocess (stdio) | Local subprocess (stdio) |
| Auth | No auth required | API key required |
| Pricing | Free | Free |
| Required env vars | None listed | PUBMED_EMAILPUBMED_API_KEY |
| Verified owner | Community listing | Community listing |
| GitHub stars | 0 | 172 |
| Directory activity | 0 views 0 installs 0 upvotes | 2 views 0 installs 0 upvotes |
| Tools | Not listed | Not listed |
| Full listing | View Pubtator | View MCP Simple Pubmed |
No tool names declared yet. Check the project README from the listing page.
No tool names declared yet. Check the project README from the listing page.
Paste either block (or both) into your client config, e.g. claude_desktop_config.json or ~/.cursor/mcp.json. We only show a config when the install command is confirmed.
{
"mcpServers": {
"pubtator": {
"command": "npx",
"args": [
"-y",
"@pipeworx/mcp-pubtator"
]
}
}
}
{
"mcpServers": {
"andybrandt-mcp-simple-pubmed": {
"command": "uvx",
"args": [
"mcp-simple-pubmed"
],
"env": {
"PUBMED_EMAIL": "YOUR_PUBMED_EMAIL_HERE",
"PUBMED_API_KEY": "YOUR_PUBMED_API_KEY_HERE"
}
}
}
}