MCP server exposing 5 tools for pubtator.
This URL is a JSON-RPC 2.0 endpoint over HTTP. Issue POST requests with a JSON-RPC body. Browsers and search crawlers land here on GET.
POST https://gateway.pipeworx.io/pubtator/mcp
Content-Type: application/json
{"jsonrpc":"2.0","id":1,"method":"tools/list"}pubtator_find_entity — 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 PubTator 3 autocomplete index at NCBI/NLM, which normalizes to NCBI Gene, MeSH, LitVar/dbSNP and NCBI Taxonomy. Keyless.pubtator_search — 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 with AND/OR ("@GENE_BRCA1 AND @DISEASE_Breast_Neoplasms"), or by a relation ("relations:treat|@CHEMICAL_Doxorubicin|@DISEASE_Breast_Neoplasms"). 10 results per page; total count and page count returned. Sourced from the PubTator 3 search index at NCBI/NLM (~36M PubMed abstracts + PMC open-access full text). Keyless.pubtator_relations — 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 supporting passages (the actual sentences, with PMIDs). Filter by relation type (treat, cause, associate, interact, inhibit, stimulate, prevent, positive/negative_correlate, cotreat, drug_interact, compare) and/or by a second entity. Accepts a PubTator id (@GENE_BRCA1) or a plain name. Sourced from the PubTator 3 relation-extraction model at NCBI/NLM — predictions from text, not curated. Keyless.pubtator_relation_evidence — 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. Use after pubtator_relations to audit a predicted relation. Sourced from the PubTator 3 search index at NCBI/NLM; the relation itself is machine-extracted, not curated. Keyless.pubtator_annotations — 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 the article. Up to 20 PMIDs per call. Sourced from the PubTator 3 BioC JSON export at NCBI/NLM; all annotations are machine-extracted. Keyless.Code samples (curl / TypeScript / one-click client install), schemas, and the live playground are on the pack page:
https://pipeworx.io/packs/pubtator/
Pipeworx is an open MCP gateway connecting AI agents to live data. pipeworx.io