Medline format

abelmora
First of all, thank you for zotero! It seems a dream come true.

My point is I work a lot with references in PubMed/Medline format. By now I do some twists to put it into zotero using scripts before but this is sometimes a cumbersome task. I don't see I can do this straightforward in zotero. Any idea?

Thank you!
  • dancohen
    Sorry for the delayed response, abelmora. Could you explain in a little more detail what you're trying to do?
  • abelmora
    I'm trying to put bibliographic references in Medline/Pubmed format into Zotero but as far I see this isn't possible by now. I've tried some other tools to translate Medline to RIS format so I can import the RIS file -even I've written quite a simple awk script- but nothing of this is completely satisfactory for me at present. Maybe I'm working on my own scripts later to work it out.

    Anyway, do you know how to put Medline format into Zotero? A bit more ambitious question is, do you think it's worth Zotero can do this in the future?

    Thank you!

    --
    Abel
  • noksagt
    There are scrips to convert from medline to bibtex. You might see if they're better for your needs.

    If you have or can get the medline xml format, bibutils is an excellent set of programs that can convert to MODS XML (which Zotero can import) or, from that bibtex/ris (which Zotero can also import).
  • Matthias
    I second noksagt's recommendation of the Bibutils utilities for conversion of bibliographic formats.

    However, AFAIK the Bibutils 'med2xml' tool requires PubMed XML as input data. If you're dependent on the MEDLINE format (i.e. somehow can't refetch your data in PubMed XML format), then you could also use the refbase demo database for conversion of MEDLINE-formatted records into, say, RIS format, then import the RIS data into Zotero. To do so:

    1. Login at the refbase demo database
    2. Import your MEDLINE data via the import page
    3. Display all your imported data on a single page (using the display options at the top right of the screen)
    4. Select all records and click on the "Export" button at the bottom of the page (with "RIS" selected from the dropdown menu)
    5. Choose the downloaded file when importing into Zotero
  • abelmora
    Thank you all! In the meanwhile I've met HubMed at http://www.hubmed.org/ This site is an interface to PubMed which -among other nice features- exports selected articles to various bib formats. I'll also try your suggestions mainly for cases I use a database without this capability.

    Regards,
  • abelmora
    medl2bib.pl -- a Medline to BibTeX converter

    This Perl script --included in the References bibliographic tools (RBT)-- does a clean translation from PubMed/Medline to BibTex. You can get it from
    http://prdownloads.sourceforge.net/references/rbt03.zip?download

    BTW you'll find it in the References home page, it's worth seeing at http://prdownloads.sourceforge.net/
  • abelmora
    "References" can be reached at http://references.sourceforge.net/ really. I've mistaken the URL in a previous post. Sorry!
  • Martin Hafner
    When you do your PubMed/Medline search on BioMed Central (http://www.biomedcentral.com/) you can export your results into zotero by just clicking "send to". You can choose different formats. I've used "Endnote + abstracts" and it worked fine.
    Unfortunately, for snapshoting pdfs of these articles you have to create additional entries andd copy their URL into the URL field of the entry that contains the references. In addition, right clicking and and snapshoting links to pdfs doesn't work for all journals. In these cases one has to store the pdf locally first and open the pdf in firefox. One the has to make a snapshot and copy the URL to the entry with the reference.
  • ordinary
    Hello, and thank you for the very helpful discussion. I'm succeeding for the most part in all of the above tasks. However, I cannot seem to get abstracts showing up through my "print bibliography" function. They show up inside of Zotero just fine over in the right hand column, but I cannot get them to cut and paste with the Print Bibliography function. Does anyone know if that is possible? Thanks!
  • petterwr
    My first post here, and I really want to say thank you to the team behind this project.

    I mainly work with articles from Medline and been trying to import them to Zotero directly without success.

    I found this link http://www.zotero.org/translators/ where it says that Medline should be compatible through Ebsco and linking there, the link only goes to a "file not found (404)" page though.

    Anyone knows anything more about this?
  • fabre
    I've found easier way if your MEDLINE formatted reference file contains PubMed ID (PMID) for each reference. If not, please disregard.

    First you need to clean-up your MEDLINE file using Find/Replace command from a text editor or writing a script.

    - Remove all fields except for PMID.
    - Append "[uid]" after the PMID, e.g. 1234567[uid]. (This is required for multiple search)
    - Connect each PMID using (space)OR(space). (Remove line breaks)

    You should have a file reads like this:
    PMID_1[uid] OR PMID_2[uid] OR ... OR PMID_n[uid]

    Then copy and paste this string into PubMed search field.

    Now you can import all references into Zotero by clicking a folder icon in the location bar. Be aware that you can export only you see on a single page (20 by default). If necessary, increase the number in "show" tab. Your Firefox may hung up (or take infinite time to be done) if you try to import too many references at once.
  • DWL-SDCA
    Is there a way to export from Zotero into PubMed/MEDLINE XML format?

    If not, is there a way for me to create an export script to do so? Although I'm very new to Zotero I am familiar with converting bib formats. I can currently create the XML file by 1) exporting from Zotero into RIS format, 2) importing the file into Reference Manager 3) using a self-created script to export into a text file that is almost the right format, and finally 4) using PowerGrep to automatically manipulate the text file into the exact XML format. This is not only tedious and time-consuming but, because Reference Manager isn't UTF-8 friendly, I have character problems.

    Thanks
  • Tjowens
    In this case your best bet would be to build a export translator for the MEDLINE XML format. To get a sense of what those look like take a peak at the RIS translator you can make sense of it through some of this somewhat outdated technical documentation about translators.
  • DWL-SDCA
    This is EXACTLY what I need.
    Thank you.
  • petterwr
    Fabre's way of doing it is excellent if you only want a few articles.
    Thanks a lot Fabre!

    Here's the way i use it:

    Once i found the article(s) I want i choose show as Medline.
    Search the page for pmid and cut and paste the number just after that into a new window, end with [uid] just like Fabre described it and put OR between each entry if you're looking up more than one article. Voilá! just add as references the usual way andabstract author etc is instantly registered in zotero :)

    If im going to convert an entire collection though, I find using the perlscrip as described above more convenient.
  • hoogland
    edited February 16, 2009
    The easiest way for me has been to use the Hubmed firefox search plugin in combination with Zotero. The reference can be automatically added to the Zotero library by clicking the Notes icon in the address bar when the search item has been selected in Hubmed.
  • ajadad
    I exported some references from OVID's MEDLINE to a text file and now need to get them into Zotero. Any suggestions?
  • Tjowens
    As the posts in this thread indicate have two options. One is to forget about MEDLINE XML and search for you items online and import them into Zotero through the icon in the location bar. The second is to build an import translator for MEDLINE XML.
  • hostos
    Could hoogland please explain his method?

    Do you mean the Notes icon in the Zotero toolbar?
    I selected (i.e checked the box or highligthed) a reference found in Hubmed and clicked the notes icon but that didn't work.
    Please advise.
    Thanks
  • noksagt
    Do you mean the Notes icon in the Zotero toolbar?
    No. Automatic capture works with HubMed:
    http://www.zotero.org/support/getting_stuff_into_your_library#automatically_capture_bibliographic_information_from_the_web
  • hostos
    Thanks noksagt.
    Work fine with PubMed as well.
  • walentas
    This is a side comment, but has anyone used zotero with python/biopython?

    I'm utterly new to all of this so I could definitely use some informed guidance...

    Cheers in advance,
    chris
  • papio100
    It is very easy to transfer PubMed-listed references to Zotero by following these few steps:

    1. Place your search term in the box on www.ncbi.nlm.nih/pubmed/
    2. When you have the listing of references tick at left those titles you need in your Zotero library
    3. Click on Send To (top, right), choose File, and in the Format drop-down menu click on XML. Create the file and save it to your hard disk.
    4. Open Zotero and click on the cogwheel
    5. Choose Import, find your .xml file on the disk and let it roll
    6. You should find your references listed under a collection bearing the name of the file saved on your hard disk
  • petterwr
    In case anyone missed it, PMID can now be entered directly into the magic wand function. Just get the PMID as described above and click the magic wand in the zotero window, paste the PMID and you got it :)
  • 8caratteri
    Reply to the very first question by user abelmora:

    "My point is I work a lot with references in PubMed/Medline format. By now I do some twists to put it into zotero using scripts before but this is sometimes a cumbersome task. I don't see I can do this straightforward in zotero. Any idea?"

    Search in the Zotero Styles Repository the "National Library of Medicine" style (
    https://www.zotero.org/styles/national-library-of-medicine-grant-proposals)
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