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    node-europmc

    0.0.3 • Public • Published

    node-europmc

    A nodejs wrapper for the europe PMC RESTful API. https://europepmc.org/RestfulWebService

    Code based in node-ncib (https://github.com/CAYdenberg/node-ncbi) and getpapers(https://github.com/ContentMine/getpapers)

    Getting started

    npm install --save node-europepmc `

    And on your node code:

    var pmc = require('node-europepmc');

    Basic use

    Performing a search

    The basic function queries the Europe PMC API using 4 parameters:

    query : The search string of choice n_papers : the number of papers which info will be returned sorting_type : How the papers will be sorted. Default is "relevance", but can be changed to "date" or "citation". metadata : Amount of metadata required. Defaults to "lite" (essential metadata). The other option is "full", which includes abstract, full text links, and MeSH terms.

    let query = "dendritic cell"
     
     
    pmc.search_papers(query, n_papers = 2, sorting_type = "citation").then((results) => {
     
        console.log(results)
     
     
    })

    This will log

    { count: 230059,
      papers: 
       [ { id: '9521319',
           source: 'MED',
           pmid: '9521319',
           doi: '10.1038/32588',
           title: 'Dendritic cells and the control of immunity.',
           authorString: 'Banchereau J, Steinman RM.',
           journalTitle: 'Nature',
           issue: '6673',
           journalVolume: '392',
           pubYear: '1998',
           journalIssn: '0028-0836; 1476-4687; ',
           pageInfo: '245-252',
           pubType: 'research support, u.s. gov\'t, p.h.s.; review; journal article',
           isOpenAccess: 'N',
           inEPMC: 'N',
           inPMC: 'N',
           hasPDF: 'N',
           hasBook: 'N',
           citedByCount: 7201,
           hasReferences: 'Y',
           hasTextMinedTerms: 'Y',
           hasDbCrossReferences: 'N',
           hasLabsLinks: 'Y',
           hasTMAccessionNumbers: 'N',
           firstIndexDate: '2008-01-29',
           firstPublicationDate: '1998-03-01' },
         { id: '12490959',
           source: 'MED',
           pmid: '12490959',
           pmcid: 'PMC2803035',
           doi: '10.1038/nature01322',
           title: 'Inflammation and cancer.',
           authorString: 'Coussens LM, Werb Z.',
           journalTitle: 'Nature',
           issue: '6917',
           journalVolume: '420',
           pubYear: '2002',
           journalIssn: '0028-0836; 1476-4687; ',
           pageInfo: '860-867',
           pubType: 'research support, u.s. gov\'t, p.h.s.; research support, non-u.s. gov\'t; research-article; review; journal article',
           isOpenAccess: 'N',
           inEPMC: 'Y',
           inPMC: 'N',
           hasPDF: 'Y',
           hasBook: 'N',
           hasSuppl: 'N',
           citedByCount: 6011,
           hasReferences: 'Y',
           hasTextMinedTerms: 'Y',
           hasDbCrossReferences: 'N',
           hasLabsLinks: 'Y',
           hasTMAccessionNumbers: 'N',
           firstIndexDate: '2010-09-15',
           firstPublicationDate: '2002-12-01' } ] }
    

    where count is the total number of papers.

    To change the number of results retrieved at a time, just change the n_papers parameter

    pmc.search_papers(query, n_papers = 1, sorting_type = "citation").then((results) => {
      console.log(results.papers[0].abstractText)
    })

    Getting abstracts

    To get the abstract from the first paper, for example, you could do:

    pmc.search_papers(query, n_papers = 1, sorting_type = "citation", metadata = "full").then((results) => {
     
      console.log(results.papers[0].abstractText)
     
     
    })

    It will log:

    B and T lymphocytes are the mediators of immunity, but their function is under 
    the control of dendritic cells. Dendritic cells in the periphery capture and
    process antigens, express lymphocyte co-stimulatory molecules, migrate to 
    lymphoid organs and secrete cytokines to initiate immune responses. They not 
    only activate lymphocytes, they also tolerize T cells to antigens that are 
    innate to the body (self-antigens), thereby minimizing autoimmune reactions. 
    Once a neglected cell type, dendritic cells can now be readily obtained in 
    sufficient quantities to allow molecular and cell biological analysis. With 
    knowledge comes the realization that these cells are a powerful tool for 
    manipulating the immune system.
    

    Install

    npm i node-europmc

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    Version

    0.0.3

    License

    MIT

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