Pubmed Tools

Configuration File: pubmed_tools.json Tool Type: Local Tools Count: 5

This page contains all tools defined in the pubmed_tools.json configuration file.

Available Tools

PubMed_get_article (Type: PubMedRESTTool)

Get complete metadata for a specific PubMed article by its PMID (PubMed ID) using efetch. Returns…

PubMed_get_article tool specification

Tool Information:

  • Name: PubMed_get_article

  • Type: PubMedRESTTool

  • Description: Get complete metadata for a specific PubMed article by its PMID (PubMed ID) using efetch. Returns comprehensive article information including title, full abstract, complete author list with affiliations, journal details (name, volume, issue, pages), publication dates, DOI, MeSH terms, article type, grant information, and references. Essential for accessing full abstracts, detailed metadata, and citation information. Find PMIDs using PubMed_search_articles (format: integer like 12345678).

Parameters:

  • pmid (string) (required) PubMed ID (PMID) as string or integer (e.g., ‘12345678’, ‘33250470’). Find PMIDs using PubMed_search_articles. Can also accept comma-separated PMIDs for multiple articles.

Example Usage:

query = {
    "name": "PubMed_get_article",
    "arguments": {
        "pmid": "example_value"
    }
}
result = tu.run(query)

PubMed_get_cited_by (Type: PubMedRESTTool)

Get a list of PubMed articles that cite a specific PMID using elink. Returns PMIDs of articles th…

PubMed_get_cited_by tool specification

Tool Information:

  • Name: PubMed_get_cited_by

  • Type: PubMedRESTTool

  • Description: Get a list of PubMed articles that cite a specific PMID using elink. Returns PMIDs of articles that have cited the input article in their reference list. Use this to track citation impact, find more recent work building on a paper, or explore how research has been applied. Essential for literature reviews, impact analysis, and staying current with research developments. Find PMIDs using PubMed_search_articles.

Parameters:

  • pmid (string) (required) PubMed ID (PMID) for which to find citing articles (e.g., ‘12345678’). Find PMIDs using PubMed_search_articles.

  • limit (integer) (optional) Maximum number of citing articles to return (default: 20, max: 100).

Example Usage:

query = {
    "name": "PubMed_get_cited_by",
    "arguments": {
        "pmid": "example_value"
    }
}
result = tu.run(query)

PubMed_search_articles (Type: PubMedRESTTool)

Search PubMed biomedical literature database using NCBI E-utilities (esearch + esummary). Returns…

PubMed_search_articles tool specification

Tool Information:

  • Name: PubMed_search_articles

  • Type: PubMedRESTTool

  • Description: Search PubMed biomedical literature database using NCBI E-utilities (esearch + esummary). Returns articles with title, journal, authors, publication year, DOI, MeSH keywords, and PubMed URL. Use this to discover medical/life sciences literature, find articles by topic, or search for publications by author or journal. Find PMIDs (PubMed IDs) to use with other PubMed tools for detailed information, abstracts, citations, or related articles. Rate limiting is automatically handled (3 req/sec without API key, 10 req/sec with key set via NCBI_API_KEY environment variable).

Parameters:

  • query (string) (required) Search query for PubMed articles. Use keywords, author names, journal names, or MeSH terms. Examples: ‘cancer immunotherapy’, ‘Smith J[Author]’, ‘Nature[Journal]’, ‘diabetes[MeSH]’. Use AND/OR/NOT for complex queries.

  • limit (integer) (optional) Number of articles to return. This sets the maximum number of articles retrieved from PubMed (max: 200).

Example Usage:

query = {
    "name": "PubMed_search_articles",
    "arguments": {
        "query": "example_value"
    }
}
result = tu.run(query)