How best to organize my PDF attachments?


I want to be able to store all my PDF files in the cloud (Dropbox) so that I have access to them at all times.  But how do I do this without getting into a chaotic situation with Endnote? I tried saving all my libraries, files, pdf’s etc in Dropbox but all my libraries got corrupted so I gave up on that idea.  Basically,  I want to:

  1. have access to my PDF files, and

  2. attach the PDFs to the Endnote reference,

Currently, I put all my PDFs in one folder called articles.  But Endnote seems to copy them into an Endnote folder/s so I now longer now what is the master copy and what folder to ensure I have a copy of in Dropbox. Between the corrupted endnot library files an folders I must have dozens of copies of my pdf’s.  I would just like one copy, in one place but backed up and available via the Cloud.  Has any one have this figured out?  I sure wish Thompson Reuters could make syncing work in a simple way.


This is an excellent idea and it seems you have most of the pieces together, but one. There is a setting in EndNote that allows you to use Absolute Links rather than Relative Links. The Absolute Links option will leave the original attached file where it is and just point to it there.

So, if you go to Edit / Preferences (EndNote / Preferences on Mac) and select the URLs and Links option you can change the setting. Unchecking the box labeled “Copy new file attachments…” will change the program to Absolute links.

Now any attached file will stay in the original location and not copy to the .data folder. You will need to make sure that you are using dropbox in the same location on each machine to ensure the links will work.

This will not, however, change your existing file attachments. You can re-attach the files after turning on the Relative Link option in the Edit / Preferences / URLs & Links section, which will copy the files to the data folder when attached.

You can also use the Edit / Find and Replace option in any text editor to change the old path to the new path.

To do this you will fist need to export your library to a text file. You can do this as follows:

1)    In EndNote with your library open, go to File / Export
2)    In the Window that comes up, choose your desktop.
3)    Give the text file any name.
4)    Make sure the Save As type is set to Text File (*.txt)
5)    Set the Output Style to RefMan (RIS) Export.
6)    Do not check the box labeled Export Selected References.

This will give you a text file with all your reference information. You will now need to change the file attachment field to point to the correct location. First make a backup of the text file you exported. Next, open the text file in Notepad or another plain text compliant editor. Then you just need to do a search and replace in the text file.

Example: the file location currently points to internal-pdf:// EndNote_X4_Class_Outlines -4023044902/EndNote_X4_Class_Outlines.pdf but you want the file to point to a new location in dropbox, in a folder named.

Search for:  internal-pdf:// EndNote_X4_Class_Outlines -4023044902/

Replace with: file://C:\Documents and Settings\YourUsername\Documents\DropBox\Attachments\

Now the field will point to C:\Documents and Settings\YourUsername\Documents\DropBox\Attachments\EndNote_X4_Class_Outlines.pdf which is the correct location for the pdf files.

This will only work for one reference at a time since each PDF is held in it’s own folder. If you wanted to take a copy of the entire PDF folder from the library’s .data folder and place it in DropBox, you could then just search for and replace with the following:

Search for:  internal-pdf://

Replace with: file://C:\Documents and Settings\YourUsername\Documents\DropBox\PDF\

Otherwise if you have a nice text editor that allows you to use variables or wildcards, you can get a bit more creative.

Once you’ve done this, you can then import the text file into a new library using the RefMan RIS import filter and choose to convert to relative links.

If you need further assistance with this, tech support should be able to help.