Confused new user


I am new to Endnote, in the past I have only had a brief encounter with Endnote Web but never used it seriously.

Having just started a PhD, I have already started a literature review and have folders with several pdf’s in from searching Web of Science and then manually downloading directly from the various journals.

I decided I needed to be more organised, so I have purchased and installed X4. I went back to the original Web of Science search and exported the results (27 references) to Endnote. So far so good, I have the references listed. Of these 27 I had already manually downloaded 14  full text pdfs (the others are not relevant) so I went through linking these downloaded papers to the entries in Endnote.

Now I have new folders in my Endnote folder, one for each paper, and some of these folders have copies of the papers, some don’t. The ones that don’t have copies won’t open from the file link in Endnote.

Two questions; why have only some of the papers copied over, and can I not just link to the papers in their original location instead of duplicating everything?

I guess that the answer is going to be simple, but I can’t find a full description in the documentation of how Endnote handles files.



EndNote supports both “absolute” (the exact location of the file on your hard drive for example) and “relative” (copies the file to the associated .data folder) links for file attachments. There are pros and cons to each of these choices. There is a Preference setting to control this on the URLS & Links Preference panel.

Using the relative link setting (with copies of the files added to the EndNote .data folder) allows for the indexing and searching of the full text of PDF files and makes the whole EndNote library more portable. This is the preferred method that we encourage customers to use but this is really a choice - so whichever method works best for your particular needs.

I hope this helps.

Jason Rollins, the EndNote team


Thanks for the reply, that makes things much clearer.

However, why haven’t all of the files been copied? I have had a look at the FAQs and checked that the pdfs are text and not scans, but although they appear to have been scans originally (they are quite old journal articles), it seems that they have been run through OCR as it is possible to highlight and copy text, even as individual words or letters.

Hmm. Without more details I am not sure why all of the files would not copy over. EndNote can support nearly any file type as an attachment (so long as it is supported by the Windows or Macintosh operating system). The distinction between a scanned or native PDF file would only matter when it comes to the indexing/searchability of the text in the PDF - this only works for real, native PDF files - not scans.

If you think something is truly not working properly with EndNote, please contact our Technical Support team - they are very knowledgeable and best positioned to help get things working for you.

Jason Rollins, the EndNote team