A side-by-side look at the Europepmc and Pubmed MCP Server MCP servers: transport, auth, tools, quality signals, and the config to install either one in Claude, Cursor, Windsurf or VS Code.
Verdict: choose Europepmc for biology, medicine and bioinformatics work as a local process; choose Pubmed MCP Server for biology, medicine and bioinformatics as a local process. You can also run both side by side in one mcpServers block.
search, get_article, abstract.pubmed_search_articles, pubmed_fetch_articles, pubmed_fetch_fulltext.Rows where the two servers differ are marked.
| Spec | ||
|---|---|---|
| Category | Biology, Medicine and Bioinformatics | Biology, Medicine and Bioinformatics |
| Quality signal | 60/100 · Good | 63/100 · Good |
| Install command | Confirmed | Confirmed |
| Transport | Local subprocess (stdio) | Local subprocess (stdio) |
| Auth | Not declared | Not declared |
| Pricing | Not declared | Not declared |
| Required env vars | None listed | None listed |
| Verified owner | Community listing | Community listing |
| GitHub stars | 0 | 161 |
| Directory activity | 2 views 0 installs 0 upvotes | 1 views 0 installs 0 upvotes |
| Tools | 10 | 11 |
| Full listing | View Europepmc | View Pubmed MCP Server |
searchEurope PMC search for biomedical literature and preprints — the preprint server index for medicine and life sciences (bioRxiv, medRxiv, Research Square), for drug/clinical/disease preprint questions where arXiv (physics/CS) has nothing. Lucene-style query — use SRC:PPR to filter to preprints only (e.g. "lecanemab AND alzheimer AND SRC:PPR"), AUTH: for author, ABSTRACT: for abstract text. Returns metadata for matching articles.get_articleFull record for one article by (source, id). Source: MED (Medline), PMC, PPR (preprints), CTX (clinicaltrials).abstractJust the title + abstract for one article (faster than get_article).referencesEurope PMC literature database — the reference list of one biomedical article, identified by source (MED, PMC, PPR) plus its id. Returns each cited work's title, authors, journal, publication year and its own Europe PMC / PubMed identifiers, with the total count and a pageSize control. Answers what prior work a paper cites.citationsEurope PMC literature database — the citing side of the citation graph: the biomedical articles that cite one article, identified by source (MED, PMC, PPR) plus its id. Returns each citing work's title, authors, journal, publication year and Europe PMC / PubMed identifiers, with the total citation count and a pageSize control. Answers who has cited a paper and how many times it has been cited.europepmc_trial_evidence_mapMap publications that explicitly mention a ClinicalTrials.gov NCT identifier. Summarizes publication types, years, citation counts, preprints, and linked status notices. A mention can be background or secondary analysis—not necessarily the primary trial result.europepmc_evidence_landscapeSummarize a bounded Europe PMC literature sample for a biomedical topic by publication year/type, citations, open-access status, preprints, journals, and authors. This is bibliographic mapping—not evidence grading, replication analysis, or a clinical conclusion.europepmc_citation_velocityAggregate Europe PMC citing-publication records by year for one article and return a recent citation sample. Coverage is Europe PMC’s citation graph, so counts are a floor and citation volume is not evidence quality, replication, or endorsement.europepmc_publication_integrity_profileInspect one Europe PMC article for linked retractions, corrections, errata, expressions of concern, comments, versions, and preprint/published-version metadata. No linked notice means none was found in Europe PMC—not proof the article is free of concerns.europepmc_research_affiliation_profileSummarize publications whose author affiliations match an organization, optionally within a topic. Reports authors, journals, publication types, years, and citations from a bounded sample; affiliation text is not proof of sponsorship, ownership, or institutional endorsement.pubmed_search_articlesSearch PubMed with full query syntax, structured filters, date ranges, and optional summariespubmed_fetch_articlesFetch article metadata by PMID: abstract, authors, journal, MeSH terms, grants, a collective author's investigators on request, linked retraction and correction noticespubmed_fetch_fulltextFetch full text by PMID, PMCID, or DOI, falling back from PMC to Europe PMC to Unpaywallpubmed_europepmc_searchSearch Europe PMC for preprints, patents, Agricola, and open-access records PubMed doesn't carrypubmed_europepmc_fetchFetch complete Europe PMC records, including the untruncated abstract, as `records: [{ source, epmcId }]pubmed_format_citationsFormat citations in APA 7th, MLA 9th, BibTeX, RIS, or Vancouver (ICMJE/NLM), with linked retraction and correction noticespubmed_find_relatedFind similar articles, citing articles, or references for a PMIDpubmed_spell_checkCorrect a misspelled PubMed query via NCBI ESpellpubmed_lookup_meshLook up MeSH headings with tree numbers, scope notes, and entry termspubmed_lookup_citationResolve partial references, up to 25 at a time, to PMIDs via ECitMatchpubmed_convert_idsConvert between DOI, PMID, and PMCID via the PMC ID ConverterPaste 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": {
"europepmc": {
"command": "npx",
"args": [
"-y",
"@pipeworx/mcp-europepmc"
]
}
}
}
{
"mcpServers": {
"pubmed-mcp-server-2": {
"command": "bunx",
"args": [
"@cyanheads/pubmed-mcp-server@latest"
]
}
}
}