How can I import Pubmed Field Designations OT (other term) and MH (MeSH terms)

When importing an nbib file from Pubmed into Zotero, I cannot see the data from the OT or MH fields to be imported. These data are actually tags, which I would have to enter manually to make the entries retrievable by these tags. Is there any way to have Zotero import the OT and MH fields?
  • I'd have to check nbib, but you can export to pubmed XML from pubmed (it's under Display on the left instead of under Export), Zotero will get MeSH tags (and I assume but am not sure OT) on that format.
  • Thanks for the reply! Just tried it out, Your are right, MH terms are imported as tags from XML files, but OT terms not. Earlier Pubmed did not have OT terms at all and now the database contains probably more OT terms than MeSH terms. I will see whether there is a feature suggestion entry somewhere here around.
  • No need. I've created a ticket:
    (those tickets are for dev use and you will be able to track when this is implemented, though I'll also try to remember to post here; the forum is exactly the right place for feature requests&questions)
  • Please note that the NLM has several literature databases. The two of interest here are PubMed and Medline. Essentially everything that is in Medline is available in PubMed but the opposite is not true. There are now many, many journals that, while included in PubMed, are not indexed for Medline. That means there are no MeSH terms to be had. Some PubMed items that do not have MeSH index terms do have OT keywords. These OTs are generally terms added by the author(s) of the articles -- sometimes these are modified or expanded by the journal editors or publishers.

    For some PubMed articles -- particularly those that are not in Medline AND are presented in more than one language -- the screen will display author keywords below the abstract but these are not included in the PubMed XML or in the tagged export presentation. There is another issue with these articles. Instead of an abstract the text similar to the words "Abstract available from the publisher" is within the XML abstract tags. For these articles, the English language abstract is presented on screen view and the screen view has, immediately above the abstract, links that will display the abstract in other languages.
  • not sure I understand where you're going with this. Is this a warning to be cautious in importing OT terms because they're less systematic?
  • "Not sure..."

    I posted not as a warning but to reinforce that

    many PubMed articles will never have MeSH
    some PubMed articles will never have MeSH nor will the metadata have OT

    I believe that it would be a good thing for Zotero to capture OTs but some PubMed records will not include either of these terms. A growing number of PubMed items are included with only minimum curation by NLM staff and contractors. That means that, for some of these articles, metadata will be less complete. For these, there will be no terms for Zotero to import. Even with a sophisticated scraper to add the abstract and keywords that are only on the screen version of the record, it is unlikely that the screen keywords will always be found. We, because we manually get all language versions of the abstracts, also get the keywords. I have noted that the format, labeling, punctuation, and position or placement of the terms on the screen can vary article to article. We tried to use a combination of metadata in both the XML and tagged formats in hope that we could get the abstract language versions and the keywords. Neither of the formats had all of what we need to get comprehensive metadata. That can only be achieved by the efforts of our volunteers who do the work by hand.

    Yes, the OTs, when available are less systematic. While that may be a small problem for some, for my shop (SafetyLit) this is easily handled by the synonym-ring function of our thesaurus. For others, this merely will require searching Zotero with a few more terms in the query.
  • ok, OTs are now in both nbib and Pubmed XML import
  • Thanks, great! Better OTs and MeSHs imported than nothing. Still I can add my own Tags or delete OTs, in case I don't like them.
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