PubMed¶
"PubMed" is an umbrella label for BioMCP's PMID-centric literature workflow, so it is the starting point for most biomedical literature work: researchers get 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. Direct PubMed search and the compatible
federated PubMed leg clean question-format unfielded article terms before
ESearch; BioMCP keeps the raw gene, disease, drug, or keyword wording in
markdown and JSON query echoes, and other article sources keep their existing
query behavior. Full-text resolution uses Europe PMC, NCBI E-utilities, PMC OA, NCBI ID Converter, PMC HTML, and opt-in Semantic Scholar PDF metadata; full text and PDFs remain governed by article-level licenses.
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 and rendered references when available | Uses Europe PMC, NCBI E-utilities, PMC OA, PMC HTML, and opt-in Semantic Scholar PDF fallbacks; NCBI ID Converter bridges PMID/DOI identifiers to PMCID before the PMCID-dependent source attempts |
article entities <pmid> |
Entity-grouped follow-up view for a PMID | Derived from PubTator3 annotation output |
Example commands¶
Returns an article table with PMID and title columns for a fast literature scan.
Returns an article card with PMID, journal, and summary metadata.
Returns a PubTator annotation section with entity groups and counts.
Returns an entity-grouped follow-up view with separate genes, diseases, and drugs sections.
Returns a full-text section with a Saved to: cache path.
XML, PMC HTML, or explicitly opted-in PDF sources can resolve, and JATS
bibliography data can render references. Semantic Scholar PDF is attempted only when the caller passes --pdf.
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.