EndNote X2 - First Impressions and suggestions

I have to say that despite the many enhancements in X2 (especially the trash folder), I may soon find myself back to using X1.

I certainly preferred the opening dialog allowing me to choose which database to open, if any at all.  I also liked being able to perform a PubMed database search without opening any library/local database file.  I now find myself forced to create a new local library first before being allowed to perform any online searches. 

I  also miss the Groups icon on the toolbar.   A keyboard shortcut for opening/closing the Groups panel would be welcome.  Customization of the toolbar is another feature that users nowadays routinely expect.

Some minor bugs are still there:

When saving local  database searches, the “Number” field of journals is replaced by “Number of Volumes” which probably only needs a very simple program fix.

Starting with X1, a confirmation box before saving changes to the record would appear.  There is also a checkbox to prevent the dialog from happening again.  If this was checked, there were no program options to restore the confirmation dialog and the user would have to edit registry values to restore the funcitonality.  X2 seems to be the same, although I have not yet checked the confirmation dialog off permanently to test it.

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Hi nmadani,

thanks a lot for your annotations. I miss exactley the same features you were writing about.

  • Opening dialog

  • Goups icon on the toolbar

  • Shortcut for opening / closing the Groups panel

  • Customization of the toolbar

but also

  • When you perform an online search in X2 all the hits get automaticly  imported to your existing library. You really should be able to deactivate this feature. 

Yes I agree. If I was fully aware of the deleterious workflow implications of automatic import of online searches into the library, I would not have upgraded.  It is such a nuisance. EndNote should really release a patch to address this.  Without it, I would not recommend to anyone to upgrade from X1 unless they would not need to perform any online searches.

Along this same thread - with EndNote X2 I was instantly set back by this new “feature” of automatically downloading and then saving of retrieved online records to the currently open library.

With this new feature you have to go through all of the retrieved references and manually delete any that you don’t want.  

And if you don’t delete the downloaded references they end up in your EndNote library, causing your library to quickly grow by the number of results from each online search.  Moreover, it is very easy to accumulate duplicates (triplicates, quadruplicates, etc…) since the same or similar search terms will retrieve the same references.  OK, granted, you can set up the search to not download anything already in your library, but for me that simply defeats the purpose of doing a quick online search.

In all - this new feature results in (1) more mouse clicks, (2) having to be vigilant in making sure that I sort through and delete any unwanted records and (3) a very unpleasant EndNote experience each time I use it.  Please EndNote – give us the option of turning this huge annoyance off!

Message Edited by jblack5 on 06-24-2008 06:43 AM

The changes to the Online Search behavior in EndNote X2 were driven by several things:

-  First, the old, Temporary library model caused much confusion for new/novice users of EndNote. One of our most common Technical Support calls involves users downloading records (into a temp library) and then inserting these into a Word document. Once the temp library is deleted, these references become orphaned.  We needed to do something to minimize this on-going confusion.

  • Second, last year we spend a lot of time and money on a large-scale usability study leveraging industry-standrad methodologies and involving many users. The Onlines Search worflow - multiple windows, copying between databases, etc. was looked at closely and earned miserable test scores - again, we needed to do something to try to improve this.  As part of this study, we asked users to point to other software that they use in their daily work. We did this and tried to based EndNote work flows on this.

A few questions for the group that might help us improve this workflow further:

  • Is the reaction to this change simply that it is different than it has been?

  • Is there a search model or other software that has a similar work flow that we should look to as a model for EndNote? 

With EndNote X2, it is still very easy to create temporary library to use for remote searching and then copy records into your main library. This is exactly how EndNote used to work - this is just no longer the default behavior.

In X2, the opening dialog is still there and available from the Help menu (Show Getting Started dialog). For upgrade users, we do not show this dialog automatically but for new users we do.


As you are probably aware (grin) I too am not happy with the importing into my main library by default.   When I search online, I don’t want everything that matches. I want to chose which items will end up with the privilege of meriting inclusion in my library! This means that  I have to perform an extra step to avoid this happening. I have to manually create a new library before performing the search.

Therefore, I would prefer a warning prior to running the search (I know, there is a little note that comes up, but I mean a real WARNING, that perhaps users could chose to “not show again”), or even better! the option to change the default to automatically opening a “temporary library”. 

As to work flows - searching databases routinely give you the option of importing everything that matches, or allowing you to check a box for each item to select which should be saved/copied/whatever.  

The other fix, is to make impossible to insert a search window reference.  Older versions of endnote did not assign a record number to these, until they were copied into the user library.  I am not sure when that changed.   I got bit by that once… but only once!

Message Edited by Leanne on 06-23-2008 01:52 PM


When you say:

“…As to work flows - searching databases routinely give you the option of importing everything that matches, or allowing you to check a box for each item to select which should be saved/copied/whatever…” 

You are referring to Web-based content databases - that then offer an option to export to bibliographic software?

I was hoping for some suggestions from other desktop software. One thing we looked at as a model is Microsoft Outlook (the most widely-used non-web browser software in the world). With Outlook (and other email packages) messages come in, users organize them (using Rules [Smart Groups]) and then delete the items that are not wanted. Based on our usability testing, this was a mental model that resonanted for many people.

Yes, I was thinking about PubMed’s Web-based content interface in that example. 

Ahhh but the comparison to Outlook,  I have NO control over what gets sent to me in Outlook, but I do have over 90 rules to hide stuff in folders that I am not immediately interested in and can go check in my “unread folder” when I have time (and so it doesn’t ever get sent to my Blackberry for example) and then there is the stuff that my Institution’s spam filter throws away before it ever gets to me.  Unless I know and put in enough specifics in my Endnote search to get the ONE paper I want - and that is way to much more work than getting the 5 papers an author published this year and picking the relevent one  to keep. 

I will be interested in seeing what other upgrade users as compared to new users think, – those that aren’t Old Dogs having to learn New Tricks…

I understand the academics behind the Online Search behavior in EndNote X2, I just don’t like it.  As Leanne puts it (above), I want to make that critical decision as to which of the search results end up in mylibrary.

JasonR, as to your questions –

I don’t think my reaction is simply a matter of it being a different workflow. Here’s a real world example. Yesterday I did a search and retrieved ~150 records.  Of those retrieved records I wanted to add 2 of them to my library.   This meant fishing through the records, selecting them one-by-one and then moving the unwanted records to the trash (or Apple-D).   After all of that I finally had the 2 desired new records.  In EndNote X1, the same workflow was: search > pop-down window > move to my library.  There was something more elegant with the X1 workflow.

As far as other search models go, Sente may have something that’s worth consideration.  Retrieved records are stored within your library in what are called Search Collections, but not in your main working library.  It’s a simple drag-and-drop if you decide that a retrieved reference should be in your main working library.  The main thing that I dislike about the Sente workflow is that your entire library becomes quite large quickly since all the Search Collections are being saved.   To get around this issue you can trash the Search Collections.

A reasonable solution could be that EndNote X2 Online Search stores the results in its own folder and then allows drag-and-drop of individual references into the user’s main library.  Perhaps this behavior could be made as a Preference choice. 

Hi Jason:

My answer to your first question:

The reaction is not because there is a difference. Users have generally been very perceptive of the positive changes.  I have used every version since 3 with the exception of either 7 or 8.  You will not hear anyone complain about the trash folder or the ability to drag and drop PDF files onto references.  However, the new online workflow is really terrible (and that is euphemism right there). 

Your second question is really not applicable here.  Why should anyone care about other software workflow?  This is not something that you never got right!  The fact is, EndNote really hit the mark on this issue, and it is now missing it.  The change in the workflow is a step in the wrong direction. If you don’t believe us, use it yourself and maintain real libraries that are used like we do. 

EndNote should also listen to its existing customers for suggestions, and not just to the new users with less experience.  That you get support calls about this from new users is because of inadequate documentation and not due to a flawed workflow. You could for example make the user interface more intuitive instead (not that it was not intuitive in the first place).  Trust that the folks who used EndNote will be able to figure out!

Hi JasonR,

you asked if there is other software that has a similar work flow that you should look to as a model for EndNote.

Well just have a look at JabRef. I´ve tried to attach a screenshot from the online search there - but your maximun file size for attachments is very low (32 kb!). Anyway they handle online searches quite well.


I’ve started playing with the demo version of X2, and I’m not happy with the autodownload from search to library. I too would prefer that the items stayed in a temporary group for assessment before transferring them to custom groups or the main library. Many users will need to tinker with their search terms before finding specific enough search terms - meanwhile their library will blow out dramatically with non-relevant items. Will we have to go back to a custom group called “keep these” while sorting the results?

This assessment and deletion process will also play hob with record numbers - many of our researchers like to print out and make notes on articles, then store them by the Endnote record number. There are going to be some huge gaps in the running number sequence.  

I’m probably an “old dog” - have been using and teaching Endnote since version 6 (excepting version 8) and Procite.

Melinda Goodin, Swinburne University of Technology, Australia 

Find Duplicates

There is another change in Endnote X.2 which seems not quite lucky to me. When I try to find duplicates within the database Endnote now displays a temporary Duplicate References group - and shows only the potential duplicates. The group does not include the original reference for each set of duplicates anymore. 

The Endnote Manual says: We strongly suggest that you check the duplicate references before deleting them. You can peruse the references shown in the Duplicate References group to verify that you would like to elete them all.

But how to do that? I have to go back to “All References” find the reference I am not quite sure if it is a duplicate go back to the temporary Duplicate References group … Otherwise I fully have to trust Endnote, which is not always a good idea. Duplicate Check is a delicate job and you really want to make sure not to delete a reference just because there aren´t enough bibliografic details.

Thanx for posting this. I don’t understand how the writers of Endnote could possible think that it would be useful to dump all search items in the open library! Scientific usability studies aside (I could just image the opaque jargon in those documents) common sense should be enough to conclude that this is most inconvenient. Do you folks actually use this software? The change suggests you probably don’t. Surely there is a better way to address new users without messing up your already existing users. Wouldn’t it be simple to just have searches open in a special online search group? Groups are already in use for search results in general. If new users can’t figure that one out then you will have to have a canned email with the ABCs for those that contact you; such is life. Perhaps instead of usability studies Endnote should 1) trust in common sense, 2) consult existing users, 3) when in doubt, make the change one that is optional and can be controlled through the options pane. Please reverse this change or make it optional. Thanx

Well, I for one have now come full circle.  X2 is unusable.  I finally requested a refund for my upgrade.  Existing users should also think twice before upgrading.  I would recommend new users to look for X1 bargains, unless the developers make it a priority to fix the broken work flow.

I couldn’t agree with you more. How Thomson could think that an Outlook model would be analogous to the scholarly research process is beyond me.  Unless this radical change in workflow model is changed back ASAP, I think I might be bidding Endnote adieu.  To all good things…

One work around for the downloading of everything after an online search is, a) highlight the citations you want, b) choose “Hide Selected References,” c) hit control-a to select the remaining citations, then d) hit the delete key. The unwanted citations are deleted, and then the citations you “hid” will then pop-up, safe and sound.

No more clicking on the citations you don’t want.

This suggestion was given to me by EndNote tech support.

I’ll add my vote as well that the new online search mode is AWFUL. I love the smart groups and saved searches, but hate the add to library by default “feature.”  I found out the hard way by accidentally closing endnote before deleting my search results and now I have 500 extra references in my library that I’ll have to sort through and delete.

Jason, another good mac based model is Papers.  They also have built-in online searches, and previous searches are saved in the sidebar, but you have to drag and drop them into your library.  You can still  search in the same window, but please don’t add results by default to the main library.  It would be nice if the pdfs were attached to a reference were more easily accesible as well.

Hi Jason, 

I only am posting to voice my keen displeasure at the complete lack of thought that obviously went into the Online Search function/workflow. 

I am distinctly reminded of the story behind the unholy birth of the Pontiac Aztek.  They created a great concept vehicle that got rave reviews, but, apparently, no one at GM really knew what they wanted as an end product.  So they formed a committee to mold the concept into production.  They worked with focus groups and marketing people and came up with various parameters to which they tried to meet with the final product.  It was classic committee compromise and the result was a vehicle that is a perennial favorite on most folk’s “Most Hated” list of cars.  

Please make this “feature” go away or at least optional, or I will be quickly trading in my lemon.