PubMed MCP Server

fetch_pubmed_content

Fetches detailed information from PubMed using NCBI EFetch. Can be used with a direct list of PMIDs or with queryKey/webEnv from an ESearch history entry. Supports pagination (retstart, retmax) when using history. Available 'detailLevel' options: 'abstract_plus' (parsed title, abstract, authors, journal, keywords, DOI, optional MeSH/grant info), 'full_xml' (JSON representation of the PubMedArticle XML structure), 'medline_text' (MEDLINE format), or 'citation_data' (minimal data for citations). Returns a JSON object containing results, any PMIDs not found (if applicable), and EFetch details.

generate_pubmed_chart

Generates a customizable chart (PNG) from structured data. Supports 'bar', 'line', 'scatter', 'pie', 'doughnut', 'bubble', 'radar', and 'polarArea' plots. Requires data values and field mappings for axes. Optional parameters allow for titles and dimensions. Internally uses Chart.js and chartjs-node-canvas to produce a Base64-encoded PNG image.

get_pubmed_article_connections

Finds articles related to a source PubMed ID (PMID) or retrieves formatted citations for it. Supports finding similar articles, articles that cite the source, articles referenced by the source (via NCBI ELink), or fetching data to generate citations in various styles (RIS, BibTeX, APA, MLA via NCBI EFetch and server-side formatting). Returns a JSON object detailing the connections or formatted citations.

pubmed_research_agent

Generates a standardized JSON research plan outline from component details you provide. It accepts granular inputs for all research phases (conception, data collection, analysis, dissemination, cross-cutting concerns). If `include_detailed_prompts_for_agent` is true, the output plan will embed instructive prompts and detailed guidance notes to aid the research agent. The tool's primary function is to organize and structure your rough ideas into a formal, machine-readable plan. This plan is intended for further processing; as the research agent, you should then utilize your full suite of tools (e.g., file manipulation, `get_pubmed_article_connections` for literature/data search via PMID) to execute the outlined research, tailored to the user's request.

search_pubmed_articles

Searches PubMed for articles using a query term and optional filters (max results, sort, date range, publication types). Uses NCBI ESearch to find PMIDs and ESummary (optional) for brief summaries. Returns a JSON object with search parameters, ESearch term, result counts, PMIDs, optional summaries (PMID, title, authors, source, dates), and E-utility URLs.