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ovid medline imports

  • asm

    asm - 2009-05-15


    i've been trying for some time now to get ovid medline records imported into refbase using the file upload method. unfortunately, i've had no success... i've tried saving records from searches in the several different formats available, but not one of them works: i always get the error "Unrecognized data format!"

    does anyone have any suggestions? as alternatives, i figured for a while i would just use the pubmed ids to import data, and this worked fine. however, i really want to be able to share the installation with less technically-minded people at my institutionm and therefore make things as easy as possible for them.

    thanks for any suggestions/advice,


    • Richard Karnesky

      I have very intermittent access to ovid.  I'll try to check this the next time I do have access.  Do you have bibutils installed?  If so, the table below gives the import files that refbase accepts:

      Does ovid export any of those formats?  If so, please try to verify that they are valid.  If you think they are, send an example to me.  If Ovid doesn't support those formats, what formats does it export?


    • izahn

      izahn - 2009-05-15

      It just so happens that I'm having the same issue. Here are the formats OVID exports:
      Brief (Titles) Display

      Ovid looks like this:
      Title    <title>
      Year of Publication    <yeaf>
      Author    <authors> separated by ";"
      E-Mail Address    <contact email>
      Source    <journal, valume, year, pages>
      Abstract    <abstract>

      BRS/Tagged looks like this:
      TI <title>
      YR <year>
      AU <authors> separated by ";"
      MA <contact author>
      SO <Journal, volume, pages>
      AB <abstract>

      Reprint/Medlars looks like this:
      TI  - <title>
      YR  - <year>
      AU  - <first author>
      AU  - <second author>
      AU  - <etc. author>
      MA  - <contact author>
      SO  - <journal, volume, pages> sic
      AB  - <abstract>
      JN  - <journal> sic
      VO  - <volume> sic
      IP  - <?>
      MO  - <Month>
      PG  - <pages> sic

      Finally, Brief titles display looks like this:
      1. <title>
      <authors> separated by ";"
      <journal, volume, pages>

      Year of Publication
      E-Mail Address
      <contact author email>

      Jabref can import OVID format, so for now I download the results, import into jabref, export to bibtex, and import to refbase.


      • Richard Karnesky

        refbase cannot yet import any of those, but they seem to be straight forward & we could add support in the future.  Thanks for suggesting JabRef as an intermediary!  The Wikipedia page lists other programs that can import the ovid format.

    • Matthias Steffens

      Hi, thanks for posting the format specs for the Ovid format. To look into this further, we'd need someone with access to Ovid to send us a comprehensive & representative set of sample records. Please send these (as a zipped attachment) in an email to msteffens -at- refbase dot net.

      Thanks! Matthias

    • izahn

      izahn - 2009-05-18

      I'm happy to send a set of sample records. Do you want just OVID format, or the others as well (BRS/Tagged etc.)?


    • Matthias Steffens

      Hi Ista,

      I'd be mostly interested in the format that is most complete and granular. From your above format descriptions, it looks as if the "Reprint/Medlars" format is the most interesting.

      That said, I'd appreciate if you could also export the same set of sample records in the "Ovid" and "BRS/Tagged" formats.

      Thanks for your help!


    • asm

      asm - 2009-05-19

      hello everyone,

      sorry for the delay in coming back to check this - and i'm glad to hear it's not just me having this problem ;-)

      anyway, am very happy to send you a bunch of references if ista hasn't done so already - or, of course, in addition to ista.  i'm not quite sure what you mean by "comprehensive and representative" but it would be easy to do a search and send you a few 100 references etc.

      also, ista - many thanks for the tip about jabref: i will try doing that again (my recollection from my previous experience is that it didn't import all the fields correctly, but i will have another go).



      • Matthias Steffens

        Hi Andrei,

        > am very happy to send you a bunch of references

        Thanks, that would be appreciated.

        > i'm not quite sure what you mean by "comprehensive and
        > representative"

        By "comprehensive", I guess I meant "more than 3 records, please". :-)

        And by "representative" I meant that, if Ovid supports references of multiple ressource type (e.g. journal articles, books, book chapters, or articles from proceedings, newspapers, magazines, etc), then it would be good to have examples for all of these types. Similarly, the examples should ideally cover all possible fields and in-field formatting options.

        Lacking a formal format description, any attempt to write an Ovid importer will only be as good as the set of available examples, thus the request for a good set of examples.

        > but it would be easy to do a search and send you a few 100 references etc.

        That would be a good start, thanks!



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