I’m using Endnote X6 to manage the citations for my PhD thesis, which I’m writing in LaTeX. I want my citations to appear as footnotes with abbreviated journal name as well as in the bibliography with full journal name. For this I created a customized BibTex export. The formatting is done outside Endnote. I just need to tell BibTex the two journal names.
This is how the relevant lines of my customized BibTex export template looks like
In my Endnote Library the fields “Journal” and “Alternate Journal” are heterogeneous, containing either full or abbreviated journal names or one of them is empty. For other styles I’m using journal terms lists to make them appear uniform. In the case of my BibTex export this leads to the same string appearing in both positions.
How can I tell Endnote to automatically put the full name in the Journal field and the abbreviation in the Alternate Journal field of my Library (so I can disable the journal terms list afterwards)? Alternatively: how can I tell Endnote to put the full AND the abbreviated journal name in the appropriate positions of my BibTex export file?
Segregate your EndNote library into 2 groups: 1) one group of references where the EndNote Journal field contains an abbreviated journal title; and 2) the second group of references where the EndNote Journal field contains an unabbreviated journal title.
Export the EndNote references from one group (e.g., references having an abbreviated journal title) in a “tagged” text file format. This is achieved by creating an EndNote output style which adds a “tag” to each field name. For example, an “AU” tag corresponds to the Author field; a “JN” tag corresponds to the Journal Title – you can specify your own set of tags but each tag should correspond to the EndNote field you want to import into BibTex. (An example of a tagged file may be found in this thread.)
Since your exported “tagged” Endnote text file comprises references where the abbreviated title appears in the EndNote “Journal” field (and the non-abbreviated journal title appears in the Alternative Journal field), switch the EndNote fields in your BibTex template:
Finally, export the second group of references (references having non-abbreviated journal titles in the EndNote “Journal” field) in a “tagged” text file format. Switch the EndNote fields in your BibTex template:
If I understand the concept of tagged exports correctly the BibTex export itself is a type of tagged export with “author”, “title” etc. being the tags. Correct? These are used by BibTex to format the citation correctly.
So, for the export file to contain both Journal and Abbreviated Journal in the correct positions I have to clean up my references, segregate them into two lists as you proposed, and turn off the Journal terms list before exporting, otherwise the Journal and Alternate Journal will contain the same. Is there a way to turn off the journal terms list only for my BibTex export?
To speed up the uniforming process of my library:
Is there a way to…
automatically update all my references and limit this to the Journal/Alternate Journal fields? (eg if I update all references from PubMed the fields will be uniform and I could simply turn off the journal terms list.)
switch the contents of two fields?
use the Journal terms lists to update the Journal/Alternate Journal fields in the references (not only when exporting)?
There’s a thread concerning switching Journal and Alternative Journal fields by editing the Journal Terms list which may be less complicated so you might try and see if that resolves your problem first (see TMartin’s response).
In response to your other questions:
>If I understand the concept of tagged exports correctly the BibTex export itself is a type of tagged export with “author”, “title” etc. being the tags. Correct? These are used by BibTex to format the citation correctly.
*Yes, the BibTex appears to use a tagged format.
>So, for the export file to contain both Journal and Abbreviated Journal in the correct positions I have to clean up my references, segregate them into two lists as you proposed, and turn off the Journal terms list before exporting, otherwise the Journal and Alternate Journal will contain the same. Is there a way to turn off the journal terms list only for my BibTex export?
*If editing the terms list as described in TMartin’s post doesn’t resolve your issue, you could proceed as described (suggest you make a backup copy of your EndNote library). You can turn-off the journal terms list by going to the EndNote toolbar, selecting Edit > Preferences, then select the Term Lists panel. Click the check boxes for “Update lists when importing or pasting references” and “Update lists during data entry” to remove the check mark.
>To speed up the uniforming process of my library…
I’m already using the journal terms list and it works fine with output styles other than BibTex. If I understand the purpose of the terms lists correctly they don’t actually change the data in the references, but only influence the appearance of the output. Which is why the “journal” and “shortjournal” fileds of my BibTex export contain exactly the same: Either the full journal or one of the abbreviations from the terms list, depending on what I choose when editing the output style.
Thus far my idea is to deactivate the terms lists to allow for different outputs for “journal” and “shortjournal”, which should be taken from 2 fields of my references (preferably Journal and Alternate Journal). This is where my questions concerning unifying my references in my last post arise.
Just to make sure I understood your first suggestion correctly: does that involve exporting the whole library in a tagged format and reimporting them afterwards to switch fields?
I just tried this and it appeared to work for the RefMan (RIS) output style.
You can create two different Journal tems list with the opposite info in Column 1 (full title in Journal Terms list A and abbrev in terms list B) and Column 2 (abbreviation in Journal Terms list A and full title in terms list B) and then link them to the to each of the Journal and the Alt Journal fields in the tools>link terms. You first need to manipulate the corresponding terms lists so that one has the Full title in the first column and the other has the abbreviation in the 1st column. You should be able to easily swap the two columns in one terms list to create the other, and import them and link to the corresponding fields.
Then just set the output style to use the 1st column “full title” and it should export correctly.
You are correct: 1) journal term lists affect how EndNote generates/displays the bibliography list in an MS Word document; 2) journal term lists do not change the data within the EndNote reference type fields themselves (i.e., exchanging the data in the Journal and Alternative Journal fields).
Using the Refman (RIS) Export output style (raised by Leanne; file is located in the EndNote Styles folder) enables exporting EndNote references while maintaining the Journal and Alternative Journal fields and without having to link the terms lists. A test export using the Refman (RIS) Export generated a text file with unique tag identifiers for the Journal and Alternative Journal fields (further discussion below). However, you should also adjust the journal terms list so as you write, the bibliography list generated by EndNote displays journal titles in their non-abbreviated form.
To answer your question about exporting the library in a tagged text file then reimporting the file back into EndNote, there’s no need to do so providing you adjust the journal terms list. Reimporting the file back into the same EndNote library is problematic as 1) it will create a duplicate entry (if “discard duplicates” isn’t selected) with different record numbers; or 2) won’t be imported (if “discard duplicates” is selected. Another issue occurs when reimporting the file into new EndNote library as the record numbers will change from the original library, affecting locating the “correct” record.
So the procedure entails the following:
EXPORT ENDNOTE REFERENCES
Export the EndNote references from one group (e.g., references having an abbreviated journal title) using the Refman (RIS) Export simplifies the process. No prior group sorting is needed.
Looking at the exported text file it looks like the “J2” tag corresponds to the full title; the “T2” tag corresponds to the abbreviated title. So adjust your BibTex template:
| journal = {J2},
| shortjournal = {T2},
Now import the text file into Bibtex.
EDIT THE JOURNAL TERMS LIST (Make backups of both your EndNote library and term list files before proceeding)
*Note: do not edit the term list in the way TMartin described as that procedure would delete the Alternative Journal field; moreover importing terms from prepared files may not include journals in your references.
You can maintain one list by exporting the journal terms list file and using MS Excel to “switch” the Journal and Alternative Journal columns. [Go to the toolbar, select Tools > Open Tools List > Journal Terms List; click the “ Lists” tab then the “Export List” button.]
Launch MS Excel and open the journal terms file. In the Text Import Wizard, use the default settings and click the “Finish” button.
3.The exported journal terms list file displays the Alternative Journal column in the first position (Column A), and the Journal column in the second column (Column B). Just “drag” (or copy and paste” to reverse the columns.
Save the file as a tabbed delimited text file then import the file into the term list (make sure you delete the existing list before importing).
The workaround with two Journal terms lists worked well. The only downside is that each reference needs an entry in both the Journal and Alternate Journal field. But I can very well live with that.