Pubmed Utils Tools#

Configuration File: pubmed_utils_tools.json Tool Type: Local Tools Count: 2

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

Available Tools#

PubMed_convert_article_ids (Type: PubMedConvertIDsTool)#

Convert between PubMed IDs (PMIDs), PubMed Central IDs (PMCIDs), DOIs and NIH manuscript IDs with…

PubMed_convert_article_ids tool specification

Tool Information:

  • Name: PubMed_convert_article_ids

  • Type: PubMedConvertIDsTool

  • Description: Convert between PubMed IDs (PMIDs), PubMed Central IDs (PMCIDs), DOIs and NIH manuscript IDs with the NCBI PMC ID Converter. Give any mix of up to 200 identifiers; the type of each is detected (digits = PMID, PMC123 = PMCID, 10.xxxx/… = DOI, NIHMS123 = manuscript ID) or forced with id_type. Returns one row per identifier with pmid, pmcid and doi. Only articles indexed in PubMed Central can be converted: a PubMed-only article comes back found=false with the converter’s message, never a guessed mapping. Use the PMCID to fetch open full text (EuropePMC_get_full_text) or the PMID for PubMed_get_article.

Parameters:

  • ids (array) (required) Identifiers to convert (PMIDs, PMCIDs, DOIs, NIHMS IDs), e.g. [‘23193287’, ‘PMC3531190’, ‘10.1093/nar/gks1195’]. A comma-separated string is also accepted. Maximum 200.

  • id_type ([‘string’, ‘null’]) (optional) Force the identifier type for every id instead of auto-detecting it.

Example Usage:

query = {
    "name": "PubMed_convert_article_ids",
    "arguments": {
        "ids": ["item1", "item2"]
    }
}
result = tu.run(query)

PubMed_lookup_article_by_citation (Type: PubMedCitationLookupTool)#

Find the PMID of an article from its citation details with NCBI ECitMatch: journal, year, volume,…

PubMed_lookup_article_by_citation tool specification

Tool Information:

  • Name: PubMed_lookup_article_by_citation

  • Type: PubMedCitationLookupTool

  • Description: Find the PMID of an article from its citation details with NCBI ECitMatch: journal, year, volume, first page and first-author surname (with initials). Use it to resolve a reference-list entry or a partial citation to a PubMed record. Pass one citation through the individual fields or up to 100 through citations (each an object with journal, year, volume, first_page, author and an optional key). Each row is status found (with pmid), ambiguous (with candidate PMIDs) or not_found; the match is exact on the fields given, so a wrong page or a misspelt journal abbreviation gives not_found. For free-text searching use PubMed_search_articles.

Parameters:

  • journal ([‘string’, ‘null’]) (optional) Journal title or abbreviation, e.g. ‘Nature’ or ‘proc natl acad sci u s a’

  • year ([‘string’, ‘integer’, ‘null’]) (optional) Publication year, e.g. 2015

  • volume ([‘string’, ‘integer’, ‘null’]) (optional) Volume number

  • first_page ([‘string’, ‘integer’, ‘null’]) (optional) First page (or article number)

  • author ([‘string’, ‘null’]) (optional) First author surname and initials, e.g. ‘lecun y’

  • citations ([‘array’, ‘null’]) (optional) Several citations to resolve at once (maximum 100)

Example Usage:

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