Advice On Effective Transition From EndNote To Zotero

joelgross
1) I am switching to Zotero due to problems with EndNote and Mac Sierra. It hangs up and is unusable, unless I rename or move the PDF folder
I have > 1600 references in EndNote, many of which have attached PDFs.
In order to run EndNote to allow an export of my library, I have to change the name of the PDF library or move it to another location. This prevents EndNote from being able to “see” my PDFs
When I export my EndNote database, is there a way to export the PDFs along with their link/reference/address in each item, so they can stay associated in Zotero?

2) If I can import the PDFs, can I associate the PDFs to items as linked files? (This seems like it would work best for me as it would allow those files to be synced across my devices using normal DropBox features, and only the database of my items (references) would need to be synced by Zotero. )

3) When I export from EndNote, can/does it export other info such as Groups, etc.
  • adamsmith
    In reverse order: No on 3.) That information isn't included in EndNote export

    2.) No in the technical sense -- import with PDFs attaches the files in Zotero and there's no option to link them at this time, though there may be in the future -- but you can convert the attached files to linked files in batch afterwards using Zotfile, www.zotfile.com

    1.) I don't fully understand this question, but the extent I do: Zotero looks for the PDFs in the same folder from which you open the RIS or Endnote XML file so you can place it there after exporting and that should work. I'd try this with small samples so that you don't have to repeated import and delete the full 1600 items into Zotero.
  • joelgross
    Adam,

    Thank you so, so much for your response. I was able to import my EndNote library and attached PDFs, I will try to deal with #2 and #3 later.

    For others with similar questions running EndNote:
    I changed the "PDF" folder in Endnote to "xPDF" so that it would run despite its PDF issues.
    I then exported my EndNote library as an XML file type. *
    Then I deleted the empty "PDF" folder that Endnote created, and changed the folder name from "xPDF" to "PDF" in case the Zotero import requires the PDFs to be in a folder named "PDF".
    I then imported into Zotero.

    Most of the fields imported correctly, but there were a few which did not.

    * It was not clear to me what Output Style to use for the export step.
    I believe it was set to RefMan (RIS) Export.
    Does anyone know what impact this has?
    Does it just set the default style in Zotero or does it determine the data exported, which might be related to the fields which did not export/import correctly, which I will describe in a separate post.
  • joelgross
    There were some fields that did not import correctly from EndNote to Zotero. I have described the problem below, in the hope that someone can help guide those of us with this problem, to find a more optimal transfer of data.

    I list them under the article/reference for which it was a problem., in case you might want to try for yourself.

    The most important ones for me are:
    Accession-num (i.e. PubMed ID).
    Number (i.e. Issue)
    But some of the others may also turn out to be important in the future.

    ******Article: 64 MDCT in multiple trauma patients: imaging manifestations and clinical implications of active extravasation

    The following values have no corresponding Zotero field:

    number: 3
    Listed as Issue in EndNote, but not imported into Issue in Zotero.

    accession-num: 17483969
    This is PubMed ID (PMID), a very helpful field. It did not come over to Zotero.

    auth-address: Department of Radiology, Boston University Medical Center, 88 East Newton Street, 2nd Floor, Boston, MA 02215, USA. stephan.anderson@bmc.org
    Listed as Author Address in EndNote

    edition: 2007/05/08
    Listed as Epub Date in EN

    ******Article: 23-Hour observation solely for identification of missed injuries after trauma: is it justified?

    The following values have no corresponding Zotero field:
    alt-title: J Trauma

    ******Article: A new classification of thoracolumbar injuries: the importance of injury morphology, the integrity of the posterior ligamentous complex, and neurologic status

    The following values have no corresponding Zotero field:
    work-type: Research Support, Non-U.S. Gov't

    ******Book: Clinically oriented anatomy. 5th Ed
    This is a book by Keith L Moore et al.

    The following values have no corresponding Zotero field:
    remote-database-provider: http://worldcat.org

  • karnesky
    The preferred format for migrating from Endnote is Endnote XML. Based on field names & your description, it appears that this is what you've done. However, this should also be distinct/independent from any mention of RIS, which is a wholly different file format.

    In any case: there is some confusion between various Endnote XML sources re. when to use 'issue' vs when to use 'number'. It should be possible to make the Zotero translator more robust here, but for now: you can prboably edit the XML file you have to use 'issue' & it will likely import just fine.

    "Accession number" is not guaranteed to be a PMID and notes within the sourcecode claim that we can't test for whether it is reliably enough (though I wonder if we can't use whatever magic the wand tool is using).
  • adamsmith
    though I wonder if we can't use whatever magic the wand tool is using
    The magic wand tool is actually also terrible at this. We frequently have it recognize pieces of ISBNs and DOIs import as if they were PMIDs, much to the consternation of users. PMIDs are just numbers between 1 and ~30 million, so no way to actually check whether something is a pubmed ID.

    I'm pretty sure the RIS setting does absolutely nothing when exporting to XML.
  • bwiernik
    Yes, the RIS setting doesn't apply to Endnote XML import. @dstilman, is there enough demand to add an analogous Endnote XML pref considering that XML import is higher quality and easier for users than RIS?
  • adamsmith
    is there enough demand to add an analogous Endnote XML pref considering that XML import is higher quality and easier for users than RIS?
    I don't understand that question -- I thought we're talking about an Endnote export setting. What Zotero setting are you referring to?
  • bwiernik
    Sorry, I was referring to the hidden pref to keep the Endnote ID numbers on RIS import. I got two recent Endnote threads mixed up.
  • joelgross
    Thank you to everyone for your comments and suggestions.

    This is in response to Karnesky's comment of 2 days ago "The preferred format for migrating ..."
    In "Save file as type", I selected XML, the preferred format.
    But below this in the Export File Name window on Mac is another selection, labelled "Output Style".
    I believe this was set to RefMan (RIS) Export when I did my export.
    I wasn't sure what should have been selected for Output Style, and this is not specified in the online documentation "Importing into Zotero"

    How do we submit a feature request to fix the issue problem described in the import?
    In the meantime, I'm not sure how to edit the XML file. Is this described somewhere in the documentation?
    Or, even better, is there a way to specify to Zotero to map "Number" in PubMed to "Issue" in Zotero.

    Regarding "Accession number" and PMID.
    Zotero seems to know the PMID, or at least it is listed as the last text in the PubMed link for my items. (This might be data from EndNote, so perhaps it wouldn't work in records created in Zotero).

    Is there a way to request that PMID be added as field to Zotero records, and to allow us to specify if we wish a field such as "accession-num" in EndNote to map to PMID in Zotero.
    I believe that would be extremely helpful for many users.

    Thanks again
  • bwiernik
    These are the general recommendations in the documentation for importing from Endnote:
    https://www.zotero.org/support/kb/importing_records_from_endnote

    PMID is currently stored in the Extra field. It will be added as a regular Zotero field in Zotero 5.1. The reason that Endnote Accession Number is not imported as a PMID is because this field is not universally used for PMID in Endnote (e.g., it is also sometimes used for PMCID and other identifiers). Because PMID has no fixed format (just a simple number), there isn't a reliable way to determine whether an accession number is a PMID or not. By default, Zotero will import Accession Numbers to the "Loc. in Archive" field.

    If Accession Number is consistently used to store PMID in your EndNote library, you can quickly modify either the exported file from EndNote or the Zotero import translator to add the values from Accession Number to the Zotero Extra field with the PMID label.

    The RefMan program sometimes stores PMIDs in the URL field with a "PM:" prefix; Zotero will import PMID from there. You could export from Endnote as a RIS file (follow the instructions at the bottom of the page linked above), then open the exported file in a text editor and use find-and-replace to replace "AN - " with "UR - PM:".

    You could also replace Zotero's RIS import translator with a modified one to import AN to the PMID field in Extra. Open the "translators" folder in the Zotero data directory Then, replace the "RIS.js" file with this version (right-click on the link and choose Save Linked File As…):
    https://gist.githubusercontent.com/bwiernik/8f3e5f0b3ea01a2859b7ea0dafd0df60/raw/34c997355a898aacd1154a5e444d439f6de58c77/RIS.js
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