PubMed and DOI numbers?

klager
How do I get Zotero to also import the DOI numbers from a PubMed entry? The DOI number are available in the PubMed XLM format, but I can't get Zotero to import DOI numbers? And without DOI numbers are all citations worthless, since there's no link to the full text article.
  • Tjowens
    DOIs should now be captured from Pub Med Central. Please report back here if you have additional issues.
  • klager
    Yes The DOI numbers might be captured from PubMed Central. But PubMed Central isn't really interesting, it doesn't hold many articles. I was referring to NCBI PubMed (Medline with 17 000 000 references), where Zotero (version 1.0.4) fails to import the DOI number from the XML format of the PubMed entry. Most other reference management software can import NCBI PubMed entries using the XML format, which contains a lot of extra information. Including the DOI number of the article and other extra information.
  • mdoube
    The DOI number that is imported to Zotero (version 1.5-sync2.2) from a PubMed result is actually the PMID, which is not helpful, because the PMID is not a DOI. Try entering a PMID into http://dx.doi.org/ .

    If it's possible, please improve the PubMed translator to record the DOI in Zotero's DOI field, and not the PMID.
  • mdoube
    This is an xml snippet from the xml view in PubMed:

    <ArticleIdList>
    <ArticleId IdType="pii">S8756-3282(07)00062-2</ArticleId>
    <ArticleId IdType="doi">10.1016/j.bone.2007.02.013</ArticleId>
    <ArticleId IdType="pubmed">17400044</ArticleId>
    </ArticleIdList>

    Sometimes the translator saves the PII, sometimes the PMID but never the DOI to Zotero's DOI field. I have installed Scaffold but it shows an empty list of translators, so I can't hack this one myself, unfortunately.
  • mdoube
    OK, so a new installation of Zotero 1.0.7 and Scaffold and I can see this in the NCBI PubMed translator

    newItem.DOI = xml.PubmedArticle[i].PubmedData.ArticleIdList.ArticleId[0].text().toString();

    Which looks to me as though it is picking up the zeroth item in the <ArticleIdList> which isn't reliably picking up the DOI. How do we change this line to pick up the ArticleId with IdType="doi" ?
  • mcburton
    This problem has been fixed. Please wait 24 hours or manually update your Zotero translators in the preferences.
  • mdoube
    This is working properly now, thanks. I see the change in this line:

    newItem.DOI = xml.PubmedArticle[i].PubmedData.ArticleIdList.ArticleId.(@IdType == "doi").text().toString();
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