One master library or different libraries for each group of references?

Hi all,

I am wondering which would be more efficient way to work with Endnote libraries:

Is it to have one master library in which we have all references in different groups, one group per topic, or to have an independent library per topic?


If I have to deal with references about stem cell, cancer, and mouse mutants…, which is better in this case: to have one Endnote library for all these items, in different groups:

  • Endnote Master Library=>
  •                                              group1: references about stem cell
  •                                              group2: references about cancer
  •                                              group3: references about mouse 

or, to have one library per topic:

  • Endnote libray1: references about stem cell
  • Endnote library2: references  cancer references
  • Endnote library3: references mouse references
  • …etc.

What are the advantage/disadvantages for each option?

Combining all references in one library could be handy, but it may slow down the program, especially when there is a lot of references.

Is there any people who tried these different options?

What are your recommendations?

Thank you


  1. duplicates in several libraries, because many papers may cross over, (in one library these can be kept in multiple groups).
  2. or you need to remember which library or have them all open
  3. searching across multiple libraries is not as simple as searching one library
  4. if duplicated in multiple libraries you need to update them all if you want to add make an addition or correction, add a keyword or an attachment for example. 
  5. multiple copies of the PDFs and other attachments if duplicated between multiple libraries (or need to be very careful if using absolute links if you plan to move the library from one machine to another).  
  6. You can always download/export parts of your library for sharing or to create independent subject specific libraries later, for example, export a group, with or without attachments - if you should decide that performance is an issue.  
  7. you can only use the new “Sync” ability with one library.  

I have been using the same single library for - um, a really long time. and never have run into a performance problem.  

Advantages… can’t think of any.  

Thank you very much, Leanne.

Just to get things clearer: the disadvantages you are talking about are for multiples libraries or multiple groups in the same library?

Do you recommen to use different groups in one single master library? 

If we have 500 references with a PDF each (~ 1MO size), this will make 500 Mo! 

  • Then, how to export or backup only one group for example (ex. to send to a coauthor)?

As far as I know, the groups are relatively recent in Endnote. So, maybe be they are not largely used to decipher the problem associated with!

  •  If I have one library with 1000 references but I need to call, say 5 references only, would this be practical to open 1000 reference to use only 5 ? Endnote will not be slow for such simple task? 

  • If you recommend to use one master library, in this case how to merge different libraries into one library but in different group, each library in a new group? Is this possible?

Edit: if I need to check for duplicated references in different groups, will the same references duplicated in different groups be considered as duplicated or the duplication is searched only within the current or active group?

Thank you

Yes, sorry.  I recommend One library, and using the groups to categorize the records.

(added in edit answers to other questions:)

Today, we talk in Gb.  - the sync I think only goes to 5 Gb.  I am no where close.  

File, compress library gives you the choices with and without attachments and all the references, selected references, or All refs in a Group /Group set, as a single file (ext .enlx) and then when opened at the other end, unpacks as a sublibrary.  

No a library of 1000 records should not be a problem.  Mine is >5000 - many other users have libraries much bigger.  The program and modern computes  can easily handle this.  

Not sure - would have to play with importing features.  I suggest before merging, to edit the Keywords or another field adding the group name you would like them filed in (or multiple group names).  Then you can use a smart group to auto add those records to a group with the right search for the term.  You usually merge though with discard duplicates.  Then the discarded ones - you would need to go back to the the original in the library and add that key word I guess. I guess you could not discard duplicates and then do the duplicate resolution and add the key word to the one you were keeping.  I think that is possible.  (this section edited with more info AGAIN)  – To add a key word to a selected group - Select the records (or the whole library) – show selected, and then Tools>Change/move/copy, and add the new keyword to the end of the keyword field or to another field of your choice.  – Then create a smart group that searches for that word (in all fields or just in the keyword field, or whatever works for you).  New records added to the library with this keyword will automatically be added to that group too.  

and your edit question:  you only have one record in the master library which is assigned to multiple groups.  not duplicate records.  

  • I added a bunch to my previous post.  

PS  – I see you and I have had this discussion before!  

Thank you again, Leanne! 

I simply copied the references from different libraries and pasted them in new groups! It worked but I still have few references, not as much as you! So, I do not know how things will evolve later!

PS: I do not remember if we have had such a discussion before (about this issue)!

Anyway, my excuse if this is a duplication. 


Not a duplication of the “resolution” just the discussion that one library is preferred.

Ah, I see! 

It was for the deletion of non-cited references.

I indeed asked whether one library was better than multiple ones! but it was not the main question, so I did not remember of it! 

Again sorry, and thank you for your answer.