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Posts: 3
Registered: ‎10-17-2019

Re: Merging references

I stumbled accross this threat because I am transfering my library from Papers3 to EndNote and encountered exactly the same problem as many people here, in that I ended up with lots of references und lots of seperate entries with imported pdfs that failed to match to any metadata. Like everybody here I was looking for a merge function to merge the entry with the proper metadata with the entry with the pdf, but had to learn that this function does not exist. So here is what I did instead as a workaround:


I noticed that when I imported my library as a .ris or .xml file from Papers3 to EndNote, the references had a broken link to the pdf. The workaround described in the following shows you how to fix the broken links by placing the pdfs exactly in the location where EndNote is looking for them and then using the "converting to relative links" function to move the pdfs into the EndNote library folder. You might need to play around a little to get it to work, but I hope these instructions will save you some time to get it done.


  1. In Papers3 export your entire library as a .ris file (.xml should also work).
  2. Copy your Library.papers3 folder.
  3. Create a new library in EndNote if you don’t have one already.
  4. Make a backup copy of your Endnote Library (even if it’s empty still).
  5. Turn Sync with EndNote-web off while you perform the next steps to avoid duplicate copies of references if you have to play around a little to get it to work.
  6. In EndNote import the .ris file (Edit>Import>File). Make sure you select the file type correctly under “Import Option”.
  7. Cancel the EndNote Find Full Text feature, because you don’t want to add full text from the internet but rather use your PDFs.
  8. Now you should have all your references in your EndNote library but the paths to the PDFs are incorrect, so the PDFs won’t show.
  9. To fix this, check where EndNote is searching for the PDFs by right-clicking the tab with the missing PDF (of any imported reference) and selecting “Open with Adobe Acrobat DC”. An error message shows you where EndNote is looking for the file. For me that was for example C:\Program Files (x86)\EndNote X8\localhost\Volumes\Sandra_Data\Library.papers3\Files\... or \Articles\... or \Books\... or \Reports\.... depending on the type of reference.
  10. Create the folders exactly as in the above identified path and copy the folders (Files, Articles, Books, Reports, etc.) that contain all your pdfs from the Library.papers3 file to the newly created folder.
  11. Check whether the pdfs now show up in EndNote.
  12. Revert back to your original EndNote Library by deleting your library files and pasting the backup copy in the same spot. (I don't know if this step and the following two steps are necessary, but that's the way I ended up doing it.)
  13. Now import the .ris file again. You will notice that the step “Indexing PDFs” now takes quite a bit longer, because there actually are pdfs there for EndNote to find.
  14. Cancel the “EndNote Find Full Text” feature again, because you don’t want to add full text from the internet but rather use your own PDFs.
  15. Now all your PDFs should be visible in EndNote. Unfortunately there are no annotations visible that were made in Papers3, because Papers3 does not save the annotations directly in the PDFs.
  16. Now you will want to make sure that all the PDFs are saved in your EndNote Library folder and not in the folder that you created (inside Program Files (x86) in my case). For that select all your imported references, right click and select File Attachments>Convert to Relative Links.
  17. The pdfs should now be all saved in the EndNote .Data library file in the “PDF” folder. You should see folders with random numbers and each folder should contain a pdf file.
  18. Delete the folders you created in step 10 (with all the PDFs copied from the Papers3 Library).
  19. Reactivate sync option if you use it.




About the annotations in pdfs in Papers3:

  1. You can export the annotated pdfs from Papers3 by exporting “pdfs and media files” and choosing the option “with annotations”.
  2. I could not find a way to import the annotated pdfs other than manually replacing the pdfs in the EndNote library file with the annotated versions (keeping the name the same).
  3. I tried using the import pdf function of EndNote, but this will create a new entry in your library and there is no easy way to merge duplicated entries in EndNote (like it can easily be done in Papers3). Also the matching of metadata to the imported pdfs failed more often than not.