Switched computers; how to re-activate links to PDF?

Hi.  Lab recently changed computers.  Old computer had End Note 9.  New computer has End Note 10.  None of the links to PDF can be opened.  Thought it was because of the change in End Note versions, but when link to PDF was deleted and a new link was created, the same problem occurred.  Anyone know how to fix this?

Dear experts,

I am currently using Endnote X.0.2. (installed on my machine), with the “pdf” documents residing at a network location. At present, absolute path (relative link option - unchecked) is used for accessing the pdfs that reside outside the “Endnote” folder. My colleagues and I frequently experience broken links (especially the “Link to pdf”). Moreover, sometimes, the links are not uniformly accessible to all.

Is there a way to:

a) Prevent / minimize the breaking of links?

 b Monitor and fix links?

My apologies if I posted to a wrong group. Would highly appreciate your leads in this regard… 


It is for this reason, that I always use the relative link option, as it works, even if the drive name changes or the location of the library (with associated files) is changed. 

You can, with X2 and later anyway and maybe some earlier versions, convert absolute to relative, and it will go out and copy the papers from the “absolute” location to the relative .DATA folder folders. Obviously whoever runs this, needs to have access and the correct network configuration, so they are accessible for the copy procedures. 

Thanks for your quick response. The reason for not using relative links is the creation of subfolders under “Data/PDF”. Is it possible to avoid that? I would rather have all files under “DATA/PDF”, navigating through the pdf files, otherwise, is a hassle.

I am not sure if library with relative links is an efficient way to store pdf references. Would you not end up with mulitple copies of pdfs if different libraries have common references? If there are multiple copies of pdfs on a fileserver, would it not violate copyright and distribution rights (in cases where only 1 copy is allowed)?

To overcome the above problems, is it not possible to use relative links to folders outside the “LibraryName.data” folder so that different libraries “relatively” point only to one location of non-duplicated references (thus pointing to only 1 copy per article)?

Message Edited by santosh on 09-15-2009 12:41 PM

Message Edited by santosh on 09-15-2009 12:42 PM

It may not be the most efficient, but any other mechanism is an absolute link, and absolute links, if the structure of the server is changed or the way individuals access the drives are different, are subject to breaking, as described in the original post. Electronic access issues affect who can access a paper and not just how many electronic copies there are.  Review the complicated “Fair Use” of Copyright materials discussions which are out there, everywhere-just do a google search. 

If numbers of copies were at issue, than we couldn’t backup our drives, that would create multiple copies. If you have one copy of a copyright protected document and publish it to the internet so anyone can read it, you would probably be violating the copyright, even if they couldn’t copy it. The argument for efficiency of disk drive space in these days of cheap memory should not be an issue. 

Endnote has had this facility (as do several other Bibliography packages and information organizing programs) and I haven’t heard of a publisher protesting the storage of these PDF files. 

Thanks for your quick response, again. I notice that the relative links create subfolders under “Data\PDF” for each pdf file. Is it possible to to have the pdf files reside under one folder of “Data\PDF” instead of residing under different subfolders? Is there any reason specific reason why the subfolders need to be created?

Endnote creates these subfolders by naming (name of the attachment) -(some kind of ID number of the folder). If you remove the ID number part, Endnote fails to open the attachment. The problem is the folder name gets easily very long, if you name the PDF file with author+title+journal+year etc. Often, the file name exceeds 256 character limit by OS, so you should be careful about naming the attachment, and the location of the library. If it is too deep, 256 character includes path name as well.

Due to these reasons, I don’t use File attachment field. I use URL filed to attach PDF file, which can open file path.

As to the multiple copies of PDF files, most of the file downloaded through institutional subscription, they are okay. However, many eBooks, and purchased chapters don’t allow duplicates, and if the file is moved Acrobat’s security feature kicks in and you can’t open it anymore. So, if you have those eBooks and alike, and want to link Endnote, it’s better to use absolute link.

Message Edited by myoshigi on 09-15-2009 11:25 AM

Remember that would still be susceptible to the absolute path redirection problem, but you can edit those links more easily in Endnote. 

Yes, as Leanne points out, the URL link is an absolute link and may be prone to link breaks. Another prospect of headache with relative links is… management of different libraries (especially those having common references)… I am forced to add the reference in each applicable library!! I am yet to come to terms with optimal handling of endnote libraries!:cry:

Well, not to put my oar in again, bu why do you have different libraries.  I have one big library with multiple topics, as there is the overlap.  In fact my lab library is my library … As then when we co-author papers we have the same references, the same library.  (we use a read only (RO) for most access and a read-write (RW) when we want to be able to manipulate the library, but I am pretty heavy handed about who can mess with my library to minimize errors, duplicates, etc.  Each evening the RW folders are  copied over RO version. 

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Thanks for your suggestions! I would consider those options. …

"…Each evening the RW folders are  copied over RO version. "

Are there any programs/scripts to implement the above and for creating RO subsets?

My IT guys run a script they wrote.  I am not sure if it is easy or hard, but I suspect easy and I could ask them.  Private message me and I will see what I can get. 

Another newbie question…

Is it possible to change the links to pdf globally instead of opening references one by one? Links are absolute.

If the filepath of data and library change, is it possible to update the absolute links to pdf globally?


With URL filed, yes (that’s one of the major reasons I use URL field), but No for the Attachment field.

I included “Ability to batch edit Attachment path” in the “X4 wish list”. This feature was requested by several others. See this thread .

Of course, if you still have electronic access to the publishers PDFs you can use the “find full text” feature to reacquire the PDFs (recommend in batches not all at once) which places them in the relative folder location, and then reattach only those that fail. 

Hi folks,

I have more than one version of Acrobat Reader running in my PC. I installed EndNote X4, and added a few references. When I click on a PDF link, it opens the file using Acrobat Reader 3D. I want it to open files using Acrobat Reader 9. I can´t find any way to do this. Can anybody help?

If you want only the EndNote pdf attachments to be viewed by Acrobat 9 Reader have you tried changing the “Open with” setting for each pdf?  Right-click on the pdf, click “Open with” then locate/select Acrobat Reader 9, close and save the file. Then add the pdf into the EndNote reference type template (e.g, File Attachment field).

An easier method is to do a global file association so pdf files (.pdf) are associated with Acrobat Reader 9.  If you’re running Windows, this feature may be accessed via the Control Panel> Programs > Make a file type always open in a specific program.