A side-by-side look at the Pubtator and Pubmed Search 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 Pubmed Search for biology, medicine and bioinformatics over a hosted endpoint. You can also run both side by side in one mcpServers block.
search_pubmed, get_abstract, summarize_findings.Rows where the two servers differ are marked.
| Spec | ||
|---|---|---|
| Category | Biology, Medicine and Bioinformatics | Biology, Medicine and Bioinformatics |
| Quality signal | 37/100 · Fair | 51/100 · Good |
| Install command | Confirmed | Confirmed |
| Transport | Local subprocess (stdio) | Remote HTTP/SSE |
| Auth | No auth required | API key required |
| Pricing | Free | Freemium |
| Required env vars | None listed | None listed |
| Verified owner | Community listing | Community listing |
| GitHub stars | 0 | 2 |
| Directory activity | 0 views 0 installs 0 upvotes | 2 views 0 installs 0 upvotes |
| Tools | Not listed | 5 |
| Full listing | View Pubtator | View Pubmed Search |
No tool names declared yet. Check the project README from the listing page.
search_pubmedkeyword, MeSH, author, date range searchget_abstractfull abstract retrieval by PMIDsummarize_findingsplain-language summary with PICO framingget_citationsAMA / APA / Vancouver formatted citationsfind_reviewssystematic reviews and meta-analyses onlyPaste 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": {
"pubspro-pubmed-search": {
"url": "https://mcpize.com/mcp/pubmed-search"
}
}
}