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Articles CLI Documentation

The Articles CLI module provides commands for searching and retrieving biomedical research articles using the PubTator3 API.

API Documentation: For details about the underlying API, see the PubTator3 API Documentation.

Tip: Use the --help flag with any command (e.g., biomcp article search --help) to see the most up-to-date options directly from the tool.

Search for biomedical research articles based on various filters.

Usage

biomcp article search [OPTIONS]

Options

  • -g, --gene TEXT: Gene name to search for (e.g., BRAF). Can be specified multiple times.
  • -v, --variant TEXT: Genetic variant to search for (e.g., "BRAF V600E"). Can be specified multiple times.
  • -d, --disease TEXT: Disease name to search for (e.g., Melanoma). Can be specified multiple times.
  • -c, --chemical TEXT: Chemical or drug name to search for (e.g., Vemurafenib). Can be specified multiple times.
  • -k, --keyword TEXT: Additional keyword to search for. Can be specified multiple times.
  • -j, --json: Render output in JSON format instead of Markdown.
  • --help: Show help message and exit.

Examples

Search for articles about the BRAF gene:

biomcp article search --gene BRAF

Search for articles about the BRAF V600E mutation in melanoma:

biomcp article search --gene BRAF --variant "BRAF V600E" --disease Melanoma

Search with multiple gene filters:

biomcp article search --gene BRAF --gene KRAS --disease Melanoma

Get results as JSON:

biomcp article search --gene BRAF --json

Get Command (get)

Retrieve detailed information (abstract, metadata) for specific articles using their PubMed IDs (PMIDs).

Usage

biomcp article get [OPTIONS] PMIDS...

Arguments

  • PMIDS: One or more PubMed IDs (integers) of the articles to retrieve. [required]

Options

  • -f, --full: Attempt to retrieve full text if available via the API (Abstract is always retrieved). [default: False]
  • -j, --json: Render output in JSON format instead of Markdown.
  • --help: Show help message and exit.

Examples

Get article abstract by PMID:

biomcp article get 21717063

Get multiple articles:

biomcp article get 21717063 22301848

Get full text (if available):

biomcp article get 21717063 --full

Get results as JSON:

biomcp article get 21717063 --json