Endnote XML Import

jfhughes
Hello,

Hoping someone can help - and hoping it's an easy fix...

I am returning to an old reference database last I used with the now-defunct Sente, and before that Reference Manager, and before that doubtless something else.

Having had my fingers burned, I want to move to open source (Zotero) and have got the Sente data temporarily into Bookends and from that exported into an Endnote XML file.

For me personally, this has been the best way to retain as much of the data as I can, in as meaningful a way as possible (ie, retaining keywords properly, date details, and so on). I have spent a week trying different approaches including Bibtex and different export/import routes.

But, there are four data items I held in RefMan/Sente which I don't have appropriate homes for in Zotero (, , , ). So I am thinking of using some of the Zotero fields to hold this data, as follows:

- Endnote XML field to Zotero field "Archive"
- to "Extra"
- to "Call Number"
- to "Loc. in Archive"

My question is: is it easier to find/replace the field names in XML and then import? If so, what labels do I replace the XML names with to get them into the desired Zotero fields?

Or, is it easier to edit a Zotero translator to achieve the same thing?

Any help would be most gratefully appreciated.

Many thanks,

Jonathan
  • zuphilip
    I guess you used some brackets around the four specific Endnote fields, which where not allowed in this markup language. Can you please name them again by either adding spaces like < any field name > or put them inside a <code> block?
  • jfhughes
    Hello zuphilip,

    Many thanks for your response - for some reason, I see the query has been edited. and so probably doesn't make much sense. The key part should have read:

    ----

    I am thinking of using some of the Zotero fields to hold this data, as follows:

    - Endnote XML field *user16* to Zotero field "Archive"
    - *user15* to "Extra"
    - *user18* to "Call Number"
    - *notes* to "Loc. in Archive"

    ----

    All of the field names in the Endnote XML export file (including the four above) have enclosing angled brackets (I'm guessing these are being edited out in the post so I'm not using them again here). The bracketed field name is repeated before and after the field text, with an additional "/" when terminating it.

    I hope this makes it clearer! Any help much appreciated.

    Many thanks,

    Jonathan
  • zuphilip
    Okay, yes this makes it clearer now.

    I guess that it might be easier to adapt your EndNote XML translator file than to search and replace text in the XML file. It might be enough to change the mapping in fieldMap a little.

    However, note that the extra field is used in the translator for PMCID as well and your information there could be overwritten by that. Are you sure you don't have PMCID in your database? Or would maybe libraryCatalog be a better field to use for you? Moreover, the notes are already exported into a note but I think that a mapping from fieldMap would overrule that. Iust try it out to be sure.

    Anyways, there should always been a note created in Zotero with all the information from the fields which could not been maped, i.e. your information will already now (without any changes of your translator) been imported in Zotero.
  • jfhughes
    Many thanks for the swift reply.

    I don't use PubMed at all so I think I can repurpose that field safely.

    So I've tried adding lines for the four fields to the fieldMap section in the translator (Endnote XML.js), in the format:

    "Endnote Field Name": "Zotero Field Name",

    I'm taking the Endnote field name as the ones in the XML file (user16, user18, etc).

    However, the import fails wth the message "The selected file is not in a supported format."

    Any suggestions as to where I'm going wrong would be greatly appreciated.

    Thanks,

    Jonathan
  • zuphilip
    Either your EndNote XML file is strange or the changes to the translator did not go well. Try to import the test file https://pastebin.com/SASHPdfh . Does that work?
  • jfhughes
    Sadly not quite - a Journal Article entry is created, but it only has data in the title field (namely: "Plain Bold Italics Underline Superscript Subscript SymbolFont CourierNew SmallerSize Size12 TimesNewRoman-Bold-Italics-Underline-Superscript")

    The same (default) translator works fine for my Endnote XML file exported from Bookends, I just can't make the edit to work to import the four extra fields...
  • jfhughes
    The quoted type above is actually in code in the Zotero field...
  • zuphilip
    edited January 6, 2020
    A journal article with a title is fine for the example data, because there is not more information in that file.
    The same (default) translator works fine for my Endnote XML file exported from Bookends, I just can't make the edit to work to import the four extra fields...
    Do I understand that correctly, that the default translator works with your file, but not anymore when you change it?
  • jfhughes
    Ok - guess I was just surprised that all the formatting codes had come through raw, as it were.

    The translator works fine with my base export file; it's when I try and change the fieldMap section it stops working. I'm wondering if I need to amend other sections as well?

    Thanks.
  • zuphilip
    No, fieldMap should be enough to change. Moreover, you are experience an error. Thus, I expect that you did some typo or maybe wrote the Zotero fields not correctly. Try something like this
    var fieldMap = {
    //same for all itemTypes
    abstract: "abstractNote",
    //"call-num": "callNumber",
    "electronic-resource-num": "DOI",
    "remote-database-name": "libraryCatalog",
    "abbr-1": "journalAbbreviation",
    "short-title": "shortTitle",
    "full-title": "publicationTitle",
    language: "language",
    "access-date": "accessDate",
    //These two are in the RIS - not sure what they'd be in Endnote XML
    user15: "extra",
    user16: "archive",
    notes: "archiveLocation",
    user18: "callNumber",

    Don't forget to update the translators (or restart Zotero) after the changes. Moreover, it might help to look for some further error message (in the report error box, or when you activate loging and then have a look).
  • adamsmith
    (and if you continue to experience problems, please share your modified code so we can take a quick look -- either by pasting it to hastebin.com or by putting a small snippet between <code> tags as zuphilip suggests above)
  • jfhughes
    Hello zuphilip,

    That's worked perfectly - thank you so much! Not quite sure which bit solved the problem, but I hadn't realised about updating the translators, or the error logging, which is good to know.

    I'm delighted not to have lost anything!

    Best wishes,

    Jonathan
  • AllenFinley
    I have a 1200 reference database, almost all with attached PDFs, in Sente. This is still working in Mac Catalina but is no longer supported, and I am afraid it will die in Big Sur. Suggestions for exporting to Zotero? I did exports to BibTex and EndNote, but the files are only a couple of KB, so I am not even sure they exported properly. Even if those import to Zotero, how do I link the PDFs?
  • bwiernik
    When you export to those formats, generally the XML or BibTeX files refer to pdf files from that location. So, if you place the xml or bib file in the same folder as the PDFs, it should import correctly. See https://www.zotero.org/support/kb/endnote_import

    If importing the XML file doesn’t bring the PDF, can you post the xml file to Dropbox or similar and link here?
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