Issues with importing from Ovid

heddam
A few months ago I asked about using Zotero for systematic reviews. I've run into some issues with importing citations from the Ovid platform. When I import from the Ovid platform the data on volume, issue, page numbers, and year are often incorrect or missing. I've experienced various degrees of this with different databases. When on Medline, almost all of the information for each article is intact, with just a few entries here and there missing things. When importing from Embase almost all of the imported articles lack volume, issue, page, and date information. (I also tested this with Agricola since it is also on the Ovid platform, and I'm met with about the same results as with Medline).

Does any one have a work around for this issue? When just importing a few references at a time it's very little trouble to edit as you add, but in the case of a systematic review, when importing hundreds of records manually proof-reading becomes to much of a burden.
  • aurimas
    Can you provide some concrete examples of articles that are missing metadata? Either links or article IDs/titles are ok.
  • heddam
    This is an example of an article that does not import with all of the metadata:


    A cross-national comparative study of metabolic syndrome among non-diabetic Dutch and English ethnic groups.

    Agyemang C., Kunst A.E., Bhopal R., Zaninotto P., Nazroo J., Unwin N., van Valkengoed I., Redekop W.K., Stronks K.

    European journal of public health. 23 (3) (pp 447-452), 2013. Date of Publication: 01 Jun 2013.
    [Journal: Article]

    Here is a entry that does import with the correct metadata:



    An open-label extension study to evaluate safety and efficacy of pazopanib in patients with advanced renal cell carcinoma.

    Sternberg CN; Davis ID; Deen KC; Sigal E; Hawkins RE.

    Oncology. 87(6):342-50, 2014.
    [Clinical Trial, Phase III. Journal Article. Randomized Controlled Trial. Research Support, Non-U.S. Gov't]

    My hypothesis that Zotero does not know how to interpret the format of the journal information in the first entry.
  • aurimas
    Which Ovid database is this? Embase?
  • heddam
    The first was from Embase, the second from Medline because I couldn't find an example that had worked from Embase quick enough.
  • aurimas
    OK, thanks. Will take a look.
  • plabelle
    I believe that this issue is still there. Has it been resolved. My issue is that all references exported in RIS from EMBASE (Ovid) are imported in Zotero as Web pages rather than journal articles. I open the .ris file in Notepad and the TY field is set to ELEC. Is there a way to resolve this issue? Thanks.
  • adamsmith
    right we can't fix Ovid's bad RIS import in our standard RIS importer.
    Two options:
    1. Use Ovid's Tagged export format, Zotero can import that
    2. Use the Zotero icon in your browser to import.
  • plabelle
    I understand.

    Ovid's Tagged export format doesn't appear in the list of options when clicking on the Export option. I see the following:

    Microsoft Word
    PDF
    .txt
    Excel Sheet
    Citavi
    EndNote
    ProCite
    Reference Manager
    RefWorks
    BRS/Tagged
    Reprint/Medlars
    RIS
    XML

    I have tried all obvious options and the Tagged one gives me this error message in Zotero Standalone "The selected file is not in a supported format."
  • adamsmith
    Sorry, they call it "Endnote". I forgot about that.
  • plabelle
    edited April 22, 2016
    Choosing this format with EMBASE does not work well at all. For instance, first and last name are inverted, so initials are used for the last names. Volume, issue and page numbers are missing.

    Here is a sample reference exported using the EndNote format:

    <2. >
    VN - Ovid Technologies
    DB - Embase
    UI - 20160053627
    AU - Foumany G.H.E.
    AU - Salehi J.
    IN - (Foumany) Department of Psychology, Islamic Azad University, Zanjan branch, Zanjan, Iran, Islamic Republic of
    (Salehi) Department of Psychology, University of Zanjan, Zanjan, Iran, Islamic Republic of
    TI - The relationship between emotional intelligence and life satisfaction and the mediatory role of resiliency and emotional balance among the students of Zanjan University.
    SO - Acta Medica Mediterranea. 31 (7) (pp 1351-1357), 2015. Date of Publication: 2015.
    PB - A. CARBONE Editore
    MH - *emotional intelligence
    MH - human
    MH - *life satisfaction
    MH - major clinical study
    MH - path analysis
    MH - Positive and Negative Affect Schedule
    MH - Satisfaction with Life Scale
    MH - stratified sample
    MH - *student
    MH - university student
    AB - The present study aimed to investigate the relationship between emotional intelligence and life satisfaction and the mediating role of resiliency and emotional balance. In so doing, stratified sampling was employed to select 250 university students who were subsequently required to complete the study instruments. The required data were collected through Shearing's Emotional Intelligence Scale, Satisfaction with Life Scale by Diener et al (1999), PANAS Emotional Balance Scale and Conner and Davidson Resiliency Scale. The collected data were analyzed by path analysis method. The results of the study indicated that there is a direct significant relationship between emotional intelligence and satisfaction with life and between emotional balance and resiliency. Moreover, resiliency had a positive significant relationship with emotional balance and satisfaction with life. Therefore, emotional intelligence and resiliency can be improved through educational interventions, which leads to adjustment and increased satisfaction with life.
    XL - http://ovidsp.ovid.com/ovidweb.cgi?T=JS&CSC=Y&NEWS=N&PAGE=fulltext&D=emed13&AN=20160053627
    XL - http://sfx.scholarsportal.info/ottawa?sid=OVID:embase&amp;id=pmid:&amp;id=doi:&amp;issn=0393-6384&amp;isbn=&amp;volume=31&amp;issue=7&amp;spage=1351&amp;pages=1351-1357&amp;date=2015&amp;title=Acta+Medica+Mediterranea&amp;atitle=The+relationship+between+emotional+intelligence+and+life+satisfaction+and+the+mediatory+role+of+resiliency+and+emotional+balance+among+the+students+of+Zanjan+University&amp;aulast=Foumany&amp;pid=<author>Foumany+G.H.E.;Salehi+J.</author><AN>20160053627</AN><DT>Journal:+Article</DT>
  • adamsmith
    that's the problem with Ovid. I don't think this is much better in the RIS, either. If they provide crappy data, there's not much we can do.
  • plabelle
    Ok, thanks for the info.
  • plabelle
    The EndNote file does import properly in EndNote, which means that EndNote has set up its import filter to work with the poor data. Given this, is there anyway that Zotero might be able to tweak its translator to get references from EMBASE to import properly. The Zotero Chrome plug-in does the same poor job when creating references in Zotero.
  • noksagt
    If EndNote is addressing any of the issues re. missing metadata that caused you to raise this issue better, it'd be nice to understand how it did so.

    But what do you mean this "import[s] properly in EndNote"?

    The sample reference you provided lacks volume/issue/page number. Presumably, EndNote won't supply this missing data. The authors also likely import to EndNote as-is. I'm not sure I understand how this is different than what Zotero is able to do.
  • adamsmith
    You've tested this in Endnote? I do remember when we wrote the Ovid Tagged imported, we compared it to Endnote import and Zotero did at least as well as Endnote, but certainly possible something would have changed. I don't really see how we can do better given the data above, though.
  • plabelle
    Yes, I did test with EndNote using the same record as above and using the EndNote export option. This creates a .cgi file that I then imported in Zotero (very limited success) and then again imported the same file in EndNote.

    In EndNote, the authors are displayed appropriately and the volume and issue numbers appear in the right field. The page numbers appear together in the "Pages" field as 1351-1357.

    Producing a bibliography using EndNote is much more accurate than with Zotero in this case.
  • adamsmith
    hmmm -- we can take another look, but I'm really not sure how much is possible here, given how messy the data is (and it's not consistent across Ovid, so we can't rely on, e.g., the citation in SO looking the same way across the board). I wonder if Endnote uses the Ovid ID and queries some other API that we're not aware of?
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