why endnote x3 retrieve full journal name?

With previous version, I always retrieve references with abbreviated journal name from PUBMED with default. Why endnote x3 full journal name?

I show it in attached picture, Can anyone give me the answer?

Message Edited by howtosearch on 10-18-2009 10:44 AM

Don’t know, but the Connect file from John in the thread below, returns the abbreviated title.  


 It doesn’t really matter as long as you have your Journal Terms list set up correctly and make sure the styles are set up to use it?   Here is the John East walk thru on how to implement those:


Thank you for your discussion.

most journals ask authors should abbreviate names of journals according to Index Medicus.  and I notice that many of  abbreviate journal names from original term list of ENDNOTE( web of science )are different from those from PUBMED. So I have already download the file you mentioned above.  with version earlier to x3, I retrieve reference directly from PUBMED, it  is always abbreviated journal name in “Jounal” of ENDNOTE and there is no neccesary to substitute journal names. it is only with x3 that problem above occurs. I wonder if others have the same problem and how to fix it.

Yes- download the Connect file  in the first link I provided  below from John East- and use that instead of the pubmed connect you are using.  this one fixes the double DOI too.  Alternatively download the pubmed connect (generic) from Endnote’s website. I don’t know why yours is different, as my X3 original pubmed connect file returns the abbreviated journal on a installation which includes only the original set. Maybe the JT is also being redirected to the Journal field in your connect file? 

with John East connection files, I solved the double DOI problem. but full journal name is still retrieved into “Journal”. and in my PUBMED connection files, the JT retrevied into Notes. when I modify “Notes” to “Alternate Journal” or “{IGNORE}”, both can be effective, with full journal name retrieved into “Alternate Journal” or disappear. when i reinstall endnote x3, the problem still occurs. maybe there is something wrong with my x3. Thank you anyway!

My X3 also does the same thing. I mean, It imports full journal names instead of abbreviated ones recently. But occasionally, some mionr journals are imported as abbreviated names.

I don’t use connection files, or online mode. I’m still using 9 year old “Medilne modified” import filter, which hasn’t been changed for years. In the Templates section of my custom import filter, TA is the tag for journal name. I checked my MEDLINE text export files from Pubmed, and MEDLINE text shows TA as abbreviated name, and JT as full journal name.

Soooo, it looks like EN X3 import journal name from TA tagged line, look it up in the Journal Term List, and import as full name if there is a definition in the term list. If it doesn’t find the name in the term list, it imports as it appears in the TA tagged line.

It is a bit frustrating because the journal name field has sometimes very long, sometimes short field data. But, as Leanne suggeted, it doesn’t matter when it comes to the formatting. Only thing I need to check, is when journal request full name of the journal (which is rare), I scan through the bibliography and replace by full name, which can be found by Google or something. Most of the journal styles request abbreviated name, so I’m not really worried about it except for the cosmetic aspect of my own library.

Well, it is a puzzle, cause when I pull that ref with X3, and the PubMed Connect –  I get    Arterioscler Thromb Vasc Biol   in the Journal field, so there must be some other setting that we differ on…

to myoshigi :

Soooo, it looks like EN X3 import journal name from TA tagged line, look it up in the Journal Term List, and import as full name if there is a definition in the term list. If it doesn’t find the name in the term list, it imports as it appears in the TA tagged line.

ti seems that you are right. what you said above give the answer to several of my questions.

 before i download the journal list from http://www.library.uq.edu.au/endnote/journal_terms.html, the same with you, mostly i retrieved abbreviated journal name from PUBMED. and full journal name only occured occasionnally. But after i delete the term list supplied with the EndNote and import the the new list from UQ, what i retrieved from PUBMED is always full journal name.

and when i see what you said, i deleted the imported UQ term list from ENDNOTE. then what i retrieved is abbreviated journal name.

so i think your answer is right.

Thank you very much!

Message Edited by howtosearch on 10-19-2009 12:38 AM

Message Edited by howtosearch on 10-19-2009 12:48 AM

to Leanne :

i don’t know what the problem is. but when i deleted the imported UQ term list and there is no term list available, I always retrieved the abbreviated journal name. so it seems that what myoshigi said is right. i hope you and others can figure this out.

Message Edited by howtosearch on 10-19-2009 07:39 AM

Well, I’m not sure my “analysis” was the solution for you, but I did some experiments (just out of curiosity).

I made a new library, switched to online mode, and imported some 50 references from Pubmed using standard connection file came with Endnote. All the journal names were imported as abbreviated, which is different from the recent behavior of my main library. Then, I looked at the Journal term list (in the local mode), and all the abbreviated journal names were placed in the full journal field. For example, “Circ Res” was in the full journal field (ATVB is too long to type, so let me use Circ Res). For each journal name, nothing was in the “Abbreviation 1” or “Abbreviation 2” field.

From this new local library, I imported a reference from Pubmed export text which has TA - Circ Res and JT -Ciurculation Research. I used my custom filter I’ve been using. Then, imported reference appeared as “Circ Res”.

The next thing I did was, I manually typed one term by defining “Circulation Research” in Full journal, and “Circ Res” as Abbriviated 1 field. Imported the same text from Pubmed, then it came out as “Circ Res” again.

Then, I deleted the one that has only “Circ Res” in Full journal name, leaving the manual definition of “Circulation Research”, then the imported reference appeared as “Circulation Research”.

From this experiment, it appears that EN searches “Circ Res”, which comes from the TA line, in the Journal term list from top to bottom order, and then hit “Circ Res” first. This term defines “Circ Res” as full name, so it understands “Circ Res” is full journal name of this reference. But when this term is deleted, it hits “Circulation Research” in the next term, and finds “Circ Res” is matched in the Abbreviation 1 field. Then, use full journal name “Circulation Research” to make this reference. Are you with me??

I’m afraid anybody understood what I’m talking about…Anyway, this explains why Leanne’s library and my library behaves differently. I probably deleted my Journal term list, before I imported from the UQ library’s term list. I guess Leanne “appended” the UQ library’s term list by updating term list. This probably left the “Circ Res” in Leanne’s term list, which makes the most of the import as abbreviated. If this is true, would you look up your term list for Arterioscler Thromb Vasc Biol, Leanne? Is it registered as full name in the term list?

I suppose this has become a bit of a detective story and may not be of interest to the general readers!  but: 

I am not exactly sure, but I did delete the original terms list, — a LONG time ago.  I haven’t rebuilt it lately, but attached is the image of the 3 variants of Arteriosclerosis Thrombosis and Vascular Biology I have in my terms list, so it is a bit redundant, but none are the abbeviation (in the first column), and the first appears to be the Arterioscler Thromb Vasc Biol match to TA in Abbr 1. 


I suspect duplicates are created since the “update terms lists” option is still ticked in my preferences. 

I think used to get something in the Alternate Journal field, which is where the update terms info I think comes from, but that doesn’t seem to happen anymore.  Perhaps I should turn off that preference.   


In your term list, the first two for ATVB may conflict each other, because Abbr 1 for the first one doesn’t have period, and Abbr 1 for the second one has period? What happens if you delete either one, and import again?

But, I still don’t know why you don’t have “Arterioscler Thromb Vasc Biol” in the full name, and your imported reference still appears abbreviated.

This is something only programers who developed parsing algorithms can answer.