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Article

Use article commands for literature retrieval by disease, gene, drug, and identifier.

Typical article workflow

  1. search a topic,
  2. choose an identifier,
  3. retrieve default summary,
  4. request full text or annotations only when needed.

Search articles

By gene and disease:

biomcp search article -g BRAF -d melanoma --limit 5

By keyword:

biomcp search article -k "immunotherapy resistance" --limit 5

By date:

biomcp search article -g BRAF --since 2024-01-01 --limit 5

Exclude preprints when supported by source metadata:

biomcp search article -g BRAF --since 2024-01-01 --no-preprints --limit 5

Multi-source federation

Article search fans out to PubTator3 and Europe PMC in parallel by default. Results are deduplicated by PMID when both backends return the same paper. Output is grouped by source; PubTator rows include a score column.

Use --source <all|pubtator|europepmc> to select one backend or keep the default federated search.

To search a single backend:

biomcp search article -g BRAF --source pubtator --limit 5
biomcp search article -g BRAF --source europepmc --limit 5

Get an article

Supported IDs are PMID (digits only), PMCID (e.g., PMC9984800), and DOI (e.g., 10.1056/NEJMoa1203421). Publisher PIIs (e.g., S1535610826000103) are not indexed by PubMed or Europe PMC and cannot be resolved.

biomcp get article 22663011

Request specific sections

Full text section:

biomcp get article 22663011 fulltext

Annotation section:

biomcp get article 22663011 annotations

Helper commands

biomcp article entities 22663011   # extract annotated entities via PubTator

Caching behavior

Downloaded content is stored in the BioMCP cache directory. This avoids repeated large payload downloads during iterative workflows.

JSON mode

biomcp --json get article 22663011

Practical tips

  • Start with narrow --limit values.
  • Add a disease term when gene-only search is too broad.
  • Use section requests to avoid oversized responses.