Duplicate check between databases, for references of a search result or group, for single references

I switched from old Reference Manager 12 to Endnote X9 approx 8 months ago. My main library holds 35000 references accumulated over >20 years. Finding, avoiding and eliminating duplicates is therefore essential.

The suggestion made by someone on this community to merge found duplicates would be a tremendous help.

Most important is to avoid new duplicates e.g. while importing new Pubmed searches. Unfortunately it is of no help to simply not import the new duplicates, because usually i am searching and selecting through Pubmed each time for a slightly different reason. I usually add my own certain keywords for each Pubmed search during the import , so that i can find those references under those keywords later as a list. If i would dicard the duplicates, i would also fail to assign the new keywords and thus loose those references from my search.

In the old RefMan 12 duplicates could be searched between data bases. So i could import the new Pubmed search first into a new data base, then find the duplicates by comparing this new data base with my main base. Mark all duplicates with a keyword (e.g. “#Dup”), search for that keyword, then search for duplicates to that list of references and then copy my new keywords to all the duplicates already in my main data base. Then search for all references without the keyword #Dup and finally copy those into the main data base. If i then search for the new keywords assigned to that Pubmed search in my main data base, i get a complete list of my Pubmed search, but without duplicates. But this requires searching duplicates from one data base to another and for only a selection of references. This was obviously possible in Reference Manager 12.

I would therefore like to suggest to implement SEARCHING DUPLICATES BETWEEN (open) DATABASRES into EndNote, if that is possible in the Endnote structure. That would be fantastic.

Also for cleaning up duplicates already in the data base, it would be great being able to SEARCH, show, and further work on ONLY DUPLICATES FOR A SUBSET (e.g. a search result, a group, or marked references in a list) OF REFERENCES.

And sometimes just checking whether there is a DUPLICATE FOR A SINGLE highlighted/active REFERENCE would be great.

Many thanks for your consideration,


This feature was requested in 2016 by a user. Unfortunately, EndNote still has not had it. I also used “Reference Manager 12” for many years and switched to EndNote because RM12 has been stopped for updates. EndNote has problems to deal with my old library:

1) EndNote thinks “Smith, H.K.” and “Smith, H. K.” (a space between H. and K.) are different when determining if two references are possible duplicates.

2) EndNote does not retrieve duplicates from an online search if you have turned on “automatically discard duplicates”. So you will not have a chance to see what the duplicates are.