MCP server

Pubtator

io.github.pipeworx-io/pubtator

Checked 26 Oct 2026, 08:29 UTC · Connected to it and listed its tools

PubTator 3 MCP — biomedical entity search, literature search with entity

Website Source

At a glance

Type

MCP server

Publisher

pipeworx.io (verified by the MCP Registry)

Status

Working at last check

Tools

47

Token cost

About 28,117 tokens per request

Sets up in

Claude Code, Claude Desktop, Codex, Gemini CLI, Cursor, VS Code, Antigravity, ChatGPT, OpenAI API, Grok

Last checked

26 Oct 2026, 08:29 UTC

Connect it to your agent

Add to CursorAdd to VS CodeVS Code Insiders

Opens the app, which shows the server and asks you to confirm. For other apps, copy the setup below.

Claude Code

claude mcp add --transport http pubtator https://gateway.pipeworx.io/pubtator/mcp

Claude Desktop

Settings → Connectors → Add custom connector, and paste the URL.

Codex (config.toml)

[mcp_servers.pubtator]
url = "https://gateway.pipeworx.io/pubtator/mcp"

Gemini CLI

{"mcpServers":{"pubtator":{"httpUrl":"https://gateway.pipeworx.io/pubtator/mcp"}}}

Cursor

{"mcpServers":{"pubtator":{"url":"https://gateway.pipeworx.io/pubtator/mcp"}}}

VS Code

{"servers":{"pubtator":{"type":"http","url":"https://gateway.pipeworx.io/pubtator/mcp"}}}

Antigravity

agy mcp add pubtator https://gateway.pipeworx.io/pubtator/mcp

ChatGPT

Settings → Apps & Connectors → Advanced settings: turn on Developer mode, then Create a connector and paste the URL. Which plans can do this varies.

OpenAI API (Responses tools)

{"type":"mcp","server_label":"pubtator","server_url":"https://gateway.pipeworx.io/pubtator/mcp","require_approval":"always"}

Grok (xAI API tools)

{"type":"mcp","server_label":"pubtator","server_url":"https://gateway.pipeworx.io/pubtator/mcp"}

Tools

• pubtator_annotations ~272 tokens
  Entity annotations for specific PubMed articles: every gene, disease, chemical, variant, species and cell-line mention in the title and abstract (or PMC full text), each normalized to NCBI Gene / MeSH / dbSNP / Taxonomy ids with its character offsets, plus any relations PubTator 3 extracted within t
• pubtator_find_entity ~307 tokens
  Resolve a gene, disease, chemical/drug, variant, species or cell-line name to its normalized PubTator 3 entity id (e.g. "BRCA1" -> @GENE_BRCA1, NCBI Gene 672; "breast cancer" -> @DISEASE_Breast_Neoplasms, MeSH D001943). Use the id with pubtator_search and pubtator_relations. Sourced from the PubTato
• pubtator_relation_evidence ~384 tokens
  The supporting passages behind one specific PubTator 3 relation — every paper whose text the model read the relation from, with the matched sentence, both entities' mentions, PMID, journal and date. Give the relation type and both entities (ids or plain names); page through the results 10 at a time.
• pubtator_relations ~521 tokens
  List the relations PubTator 3 has extracted for a gene, disease, chemical or variant — which drugs treat a disease, which genes a disease is associated with, which chemicals inhibit a gene — ranked by supporting-publication count, each labelled machine-extracted, and the top relations carrying their
• pubtator_search ~330 tokens
  Search PubMed/PMC literature by biomedical entity and get back, for each paper, the sentence that matched with its entity mentions decoded (gene, disease, chemical, variant, species, cell line — each normalized to an id). Query by plain text ("metformin alzheimer"), by PubTator entity ids combined w

Browse

• GitHub tools
• GitHub and code hosting
• Research papers
• Health and medicine

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