io.github.cyanheads/pubmed-mcp-server
MCP server for the NCBI E-utilities API. Search PubMed, fetch article metadata and full text, generate citations, explore MeSH terms, and discover related research.
Versions
2.10.2latest2.10.12.10.02.9.102.9.9+ show 92 moreshow less
2.9.82.9.72.9.62.9.52.9.42.9.32.9.22.9.12.9.02.8.02.7.112.7.102.7.92.7.82.7.72.7.62.7.52.7.42.7.32.7.22.7.12.7.02.6.122.6.112.6.102.6.92.6.82.6.72.6.62.6.52.6.42.6.32.6.22.6.12.6.02.5.62.5.52.5.42.5.32.5.22.5.12.5.02.4.12.4.02.3.112.3.102.3.92.3.82.3.72.3.62.3.52.3.42.3.32.3.22.3.12.3.02.2.62.2.52.2.42.2.32.2.22.2.12.2.02.1.62.1.52.1.42.1.32.1.22.1.12.1.02.0.11.4.51.4.41.4.31.4.11.3.51.3.41.3.31.3.21.3.11.3.01.2.41.2.31.2.21.2.11.1.41.1.21.1.11.0.161.0.141.0.131.0.12Tools 11
pubmed_europepmc_fetch Fetch complete Europe PMC records — including the full, untruncated abstract — for records addressed by `source` plus `epmcId`. Pairs with `pubmed_europepmc_search`, which returns bounded `abstractSnippet` values and flags cut ones with `abstractTruncated: true`; pass those hits' `source` and `epmcId` here to read the whole abstract. This is the retrieval path for preprint (`PPR`), patent (`PAT`), and Agricola (`AGR`) records, which frequently carry no PMID and no DOI, so `pubmed_fetch_articles` and `pubmed_fetch_fulltext` cannot address them. Up to 25 records per call.
pubmed_format_citations Get formatted citations for PubMed articles in one or more formats (apa, mla, bibtex, ris, vancouver). Pass a single format as a string or multiple as an array.
pubmed_lookup_citation Look up PubMed IDs from partial bibliographic citations. Useful when you have a reference (journal, year, volume, page, author) and need the PMID — deterministic citation matching, more reliable than free-text search for structured references. Each citation must include at least journal or year (ECitMatch primary-keys on journal+volume+page; author-only or volume-only inputs guarantee no match); more fields = better match accuracy.
pubmed_fetch_articles Fetch full article metadata by PubMed IDs. Returns detailed article information including abstract, authors, journal, MeSH terms. Set `maxResponseCharacters` to bound the whole response: articles past the ceiling are deferred whole and listed in `deferred.ids` for a follow-up call.
pubmed_lookup_mesh Search and explore the MeSH (Medical Subject Headings) controlled vocabulary. Returns descriptor records with tree numbers, scope notes, and entry terms, plus pagination via offset for paging past the maxResults cap.
pubmed_search_articles Search PubMed with full query syntax, filters, and date ranges. Returns PMIDs and optional brief summaries. Supports field-specific filters (author, journal, MeSH terms), common filters (language, species, free full text), and pagination via offset for paging through large result sets.
pubmed_convert_ids Convert between article identifiers (DOI, PMID, PMCID). Accepts up to 50 IDs of a single type per request. Only resolves articles indexed in PubMed Central — for articles not in PMC, use pubmed_search_articles instead.
pubmed_find_related Find articles related to a source article — similar content (similar), articles citing this one (cited_by), or articles this one cites (references). Uses NCBI ELink as the primary source; falls back to Europe PMC then OpenAlex when NCBI is unavailable.
pubmed_spell_check Spell-check a query and get NCBI's suggested correction. Useful for refining search queries.
pubmed_europepmc_search Search Europe PMC, a broad open-access biomedical corpus. Surfaces preprints (`source: PPR`), patents (`source: PAT`), Agricola (`source: AGR`), plus everything in PubMed (`MED`) and PMC. Use when additional coverage is needed — preprints and EPMC-only OA records are the typical recovery. Paginate via `cursorMark`. Defaults to `MED`, `PMC`, and `PPR`; pass `sources` to include `PAT` / `AGR`. Abstracts arrive as a bounded `abstractSnippet` with `abstractTruncated` marking the cut ones — pass a hit’s `source` and `epmcId` to `pubmed_europepmc_fetch` for the complete abstract.
pubmed_fetch_fulltext Permissions 3
network medium shell high env_vars low