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PubMed

PubMed is the starting point for most biomedical literature work because it gives researchers a shared identifier system, durable abstracts, and the fastest path from a gene, disease, or drug question to the papers that matter. If you want an MCP-friendly literature workflow that still speaks the language of PMIDs, this is the page to start with.

In BioMCP, PubMed is both a direct article-search source and part of the default compatible article federation. search article --source pubmed uses BioMCP's PubMed ESearch/ESummary loop directly, while the default --source all route combines PubTator3, Europe PMC, and PubMed when the selected filters are PubMed-compatible. Full-text resolution still uses PMC OA plus the NCBI ID Converter. Semantic Scholar TLDR, citation, reference, and recommendation helpers belong on the Semantic Scholar page because they come from a different provider surface.

What BioMCP exposes

Command What BioMCP gets from this source Integration note
search article PMID-ranked literature search results with typed filters Direct --source pubmed route plus default compatible federation with PubTator3 and Europe PMC
get article <id> Article summary card with identifiers, journal, and abstract context Uses Europe PMC metadata with BioMCP normalization
get article <id> annotations PubTator entity annotations for a paper PubTator3-only section
get article <id> fulltext Open-access full-text handoff with saved Markdown path Uses PMC OA plus NCBI ID Converter
article entities <pmid> Entity-grouped follow-up view for a PMID Derived from PubTator3 annotation output

Example commands

biomcp search article -g BRAF --limit 3

Returns an article table with PMID and title columns for a fast literature scan.

biomcp search article -g BRAF --source pubmed --limit 3

Queries PubMed directly while preserving the standard article table contract.

biomcp get article 22663011

Returns an article card with PMID, journal, and summary metadata.

biomcp get article 22663011 annotations

Returns a PubTator annotation section with entity groups and counts.

biomcp article entities 22663011

Returns an entity-grouped follow-up view with separate genes, diseases, and drugs sections.

biomcp get article 27083046 fulltext

Returns a full-text section when PMC OA is available and prints a Saved to: cache path.

API access

Optional NCBI_API_KEY for higher NCBI throughput. Set it through the API Keys guide and create one in My NCBI.

Official source

PubMed is the official NLM literature search surface most researchers already anchor on.