Problems with Journal name abbreviations

Dear memebers of the forum:

I am new to this forum, in fact, I statrted using EndNote couple weeks ago. As much as I like the software, I have encountered few problems. I will start with the most urgent one, so here is the question:

Some references seem to recognize the abbreviation, while other entries do not use the abbreviation for the same journal. For example: A journal called “Journal of Physical Chemistry” should be abbreviated as “J. Phys. Chem.”. And it does abbreviate acordingly for few references, but couple others are using the entire title of the journal in the list of references at the end of my document.

I tried to look for answers hoping if someone had already brought up this issue, but could not find any hint that would lead to a success. I tried to update my Term List according to this thread posted earlier, but did not succeed either. Can anyone please suggest what to do in order to have ALL MY REFERNCES PROPERLY ABBREVIATED THEIR JOURNAL TITLES???

Thaks so much in advance!


Message Edited by fatkhulla on 11-25-2008 11:56 PM

Message Edited by fatkhulla on 11-25-2008 11:57 PM

Message Edited by fatkhulla on 11-25-2008 11:59 PM

Message Edited by fatkhulla on 11-26-2008 12:25 AM

so you have updated your journal terms list according the instructions John East provided?  You also need to be sure that your selected style is set to change to the appropriate Journal abbreviation.  What style are you using?  To check, edit>output styles>edit “yourstyle”.  Go to the Journal Names and make sure the setting isn’t “don’t replace” but is Abbreviation 1.  Close the style and it will ask if you want to save it, say yes and either give it a new name and make sure that you switch to that new name by reformating the bibliography and changing the style to the altered style name (which you might have to “open style manager” or “browse” to see), or try saving it to the same name, since it is the correct setting. 

How journal abbreviation works or not is really dependent on what you have in your database in Endnote.

Say, you imported references from online sources such as Pubmed, using MEDLINE filter, articles like Journal of Biological Chemisty. are imported as " J Biol Chem". Journal title is imported from the data under “SO” tag which is already abbreviated. Pubmed also has “JT” tag data which full name of the journal, but typical MEDLINE filter does not import “JT” tag data. How your journal name entry look like? Abbreviated or full?

When Endnote finds definitions of Abbreviation 1 and 2 in the term list, it works as designed. When Endnote does not find the definitions for the Abbreviation 1 or Abbreviation 2, it just uses the data in journal fied. That means, “Don’t replace” option override the “Abbreviation 1” option, if the Abbreviation 1 is not defined in the Term list.

By the way, did you type the full journal title by yourself, or imported through filter? If you typed manually, check spell error or some extra spaces you might have missed. To be able to abbreviate journal tiltes automatically, you need to have full title in the Endnote entry and Term list that exactly defines the abbreviation type for the given full name.

Best regards,

Dear Leanne and Myoshigi,

Thanks for your time to respond to my question. I checked the points that both of you have raised and everything was OK, except the problem still was there. Eventually, I had to call the customer support in USA to solve this problem. Yes, John East did suggest correctly to replace the term list, but I their website failed to provide instructions how to do so. Anyway, after I solved this problem I made a quick note for myself how to do this and I am attaching it to this thread so whoever encounters the similar difficulty I hope will benefit from this.

Here is the complete procedure in text format:


How to update the Journals Terms List of EndNote version X2

Fatkhulla Tadjimukhamedov, NMSU 2008

The Journals Term List is a necessary component of EndNote program that enables to automatically update the journal names as well as abbreviation features that are predefined in Term List files (usually saved in the directory C:\Program Files\EndNote X2\Terms Lists). In order to successfully update the journal terms list the following steps must be taken, so that the program will recognize the updated list: If you are updating the journal list terms of an already built library, make sure you back up the original file. When building a new library or editing the existing library you may realize that some citations are being abbreviated accordingly, while the others are not after importing references.   The reason for such inconsistency is that the Term List does not have proper Journals Term Lists set up. To fix this: 

1. Go to Tools menu > Open Term Lists > Journal Term List. This will open Term Lists message dialog.


 2. On the Lists tab select journals and press Delete List… button. This will delete the Journals entry. Press Create List button and type Journals in the text field. Do not forget to check the Journal List under the text field otherwise it will result in error and the new list will not be recognized.

 3. Press OK button. Then press Import List button and navigate to C:\Program Files\EndNote X2\Terms Lists directory and select the desired term list. Press Open button to confirm the selection and press OK button in a message dialog prompted afterwards. Press Close button of Term Lists window. Now when you click on the references that did not use the journal title abbreviations previously, they will now show up in abbreviated format.

 4. One last important step that must to be done: Go to Edit menu > Preferences and select Term Lists  and uncheck the Update lists when importing or pasting references entry.

Dear Fatkhulla,

thank you for your very good instructions! It was very helpful for me.

Best regards,


glad you found it useful, Sabine.

Good luck in writing!

Dear fatkhulla

Thank you very much for you “amazing”  answer, I spent long hours trying to solve it till I found this forum and your answer!. 

Only, I would like to add that if this procedure  is applied on an already created library, is necessary click in “update list” in the “Term list” box in order to link the previous references with the term list, otherwise, you will find references without assigned abbreviation and so on. 

Handy dandy video instructions here:


You are welcome. Glad it helped you.



Thank you! 

Very helpful answer!

It soleves the problem fundenmentally. 

Make sure you follow fatkhulla’s response below, and you can also look at the video instructions here:  but don’t skip Fatkhulla’s last step.  

Remember that you also need to make sure the output style you are using is selected to use the correct column of the terms list.  Edit> edit output style, edit “your output style”  – as in the image attached.  Then Save as and give new name (or save if it is an option).  Then in the document make sure you are using the newly named output style on the Endnote X7 ribbon or toolbar.  (not necessary, if you were able to “save” – but never give it the same name if you have to choose “save as”!)  

Dear Fatkhulla,

many thanks for sharing this useful information.

All best


No problem, All! It is great to see that these notes can still be found usefull after all these years…


Hi there,

Good evening.

I am using Endnote X7.4 version on desktop. I have around 240 reference in my endnote library.

But recently I have problems in exporting the references from sites. The endnote gets hanged during the import and it shows “updating term list” icon and never recovers.

I have tried CWYW turn off in endnote and hyperlink turn off in word 2013. But both options are not working for me…

Please suggest me another option or whta I should do to get the Endnote working…

Thanks in advance

I always have the terms list update options firmly off in the preferences settings.  I don’t want endnote to assume I want things in my terms list.  – have you tried turning them off?  see this preference option in the attached image (for endnote for windows, these are accessed via Edit, Preferences in Endnote)

Thanks very much. You illustrated the solution clearly. It worked with me very well.

for me the problem was I imported from medline not nlm.

I fixed it by logging on to nlm (deleted medline) and updating all references

for me the problem was import thru medline and not NLM like outlined above (and thank you)

so I deleted medline, logged on to NLM and updated all references-and it worked


Thank you very much for the detailed stepwise instructions. But I still have the problem with some journals as non-abbreviated. Do you have any idea about that?

Does your output style have the Journal settings to use the correct abbreviation settings (see image attached)?  

If not, then it will use what is in the Journal field.  

Are they in your journal terms list?  If not, then it will use what is in the Journal field.  

Are they in your journal terms list correctly? If not then it will take the wrong item from the right column. 

The Clarivate Analytics Knowledgebase link is now: