Trying to import PDFs from Endnote X4

andrechappel
Thank you for your help. I'm finding it difficult to transfer the PDFs in my Endnote library into Zotero. I tried using the script provided on the following webpage (http://www.zotero.org/support/kb/exporting_from_endnote_with_pdfs), but it's not working for me, because each of my Endnote PDFs is stored in its own subfolder.

For instance, I have a PDF named "00000658-200308000-00003.pdf", which is stored as follows "Endnote PDF Folder/8B4CB5E3d01-1663912065/8B4CB5E3d01.pdf"

When I run the above script, the following:

"internal-pdf://8B4CB5E3d01-1663912065/00000658-200308000-00003.pdf"

is replaced with:

"file://C:\Documents and Settings\...\parent PDF storage folder\00000658-200308000-00003.pdf"

In other words, I lose the unique subfolder associated with the PDF. Hence, Zotero can't find the PDF. Would someone please send some script that addresses this issue if you have it available?

Thanks!
  • romanov-umich
    You could try open your RIS file in any text editor and make a simple find/replace:

    FIND:
    internal-pdf://

    REPLACE with:
    file://C:/{...}/PDF/

    Where {...} is the the link to your Endnote PDF folder beginning with the letter of your drive and usually ending with /PDF/ - with SLASHes instead of BACK SLASHes.

    More primitive, but worked perfectly fine for me.
  • andrechappel
    Thanks! At first when I tried to do this manually, I used backward slashes, since this is what the script used. However, this left me with one forward slash between the subfolder name and the file name, which I figured would cause me problems. However, I can see your method will work, since the direction of the slashes will all be consistent.
  • andrechappel
    edited October 29, 2011
    For some reason a lot of my PDFs are not exporting from Endnote and are thus not being imported into Zotero. When I look at the RIS export file, no PDF file path is shown for these references. However, when I go back into Endnote to verify that the PDFs exist, they are shown in the references and they open fine. I tried re-exporting with the same result.

    Is this a common occurrence? Is there something I can do to get these PDFs to export that is not manually intensive. If not, than I guess I'm stuck with Endnote, since I have tons of PDFs and most of them are not transferring. I really hoping this is not the case!

    I should add that ALL of my PDFs are saved as "File Attachments" in Endnote.
  • romanov-umich
    edited October 29, 2011
    There is one thing I can think about...
    Where are all your PDFs stored? Are they stored in the PDF folder of your Endnote Library or scattered all over your HDD? Depending how they are stored, the links to the files will be recorded differently. They will be relative in the first case (internal-pdf://Almotkan-BP-3174516992/Almotkan-BP.pdf), and absolute in the second (these look like "file://D:\Downloads\Almotkan-BP.pdf"). Maybe you have a combination of both, and that is the reason why some get exported into Zotero, and some do not. Perhaps, you should try to convert all links into relative ones (Endnote will copy all the PDFs into its PDF folder) and then try to export your entire library again.

    Back up your Endnote library before trying anything of this!
  • andrechappel
    Thank you for your suggestion, but unfortunately all of my PDFs are already stored using relative links.
  • andrechappel
    I've figured out that Endnote's export file lists the reference's URL (for the PDF) in the L1 field instead of the link to the downloaded PDF if a URL is available. However, if one is not available, then it exports the link to the downloaded PDF. I would much prefer to have my downloaded PDFs carried over (since I highlight them) then the URL links. Does anyone know if there is a way to change this?
  • adamsmith
    I think Endnote's support forums are actually quite good - I'd try there. Most people here don't have EN (anymore).
  • andrechappel
    Ok, will do. Thanks for your assistance.
  • andrechappel
    In case anyone else runs into this problem...

    I figured out that I had to edit the style in Endnote. For some reason, the L1 export field for journal articles was pulling data from the URL field in the references, instead of the file attachments field. All of the other reference types had the file attachments field associated with L1. Not sure why this was the case, but changing this solved the problem.
  • romanov-umich
    @andrechappel: I am glad you have figured it out!
  • cadudesun
    Hi Andrechappel!

    I have the same problem you had to L1 export field for journal articles. But I couldn't understand your solution. What was the kind of changing you made?

    Thanks in advance,
    Cadu
  • andrechappel
    Hopefully, these instructions will make sense to you. If not, let me know where you are confused.

    Open Endnote > Edit > Output Styles > Edit "RefMan (RIS) Export"

    In the left hand box, look under "Bibliography" and click on "Templates".

    In the right hand box, change L1 to the following: L1 - `File Attachments|`

    File > Save

    Now try exporting again.
  • cadudesun
    Your tip worked perfectly! Thanks!

    Just to clarify to other people:

    ------------------------------------
    In the right hand box (reference type “Journal Article”) change:

    FROM:
    L1 - `URL|`

    TO:
    L1 - `File Attachments|`

    File > Save
    -------------------------------------

    I created the "RefMan (RIS)” style with this adaptation. So, it is just to download the style at http://www.4shared.com/file/v2xCFsiA/RefMan__RIS__Export__To_Zotero.html and the Endnote to Zotero (including PDF) exportation will work good!
  • andrechappel
    Glad it worked. Thanks for improving my instructions!
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