No Journal Glossary update for BibTex files

[Nhaps]

My Sync Linked Bibtex File does not seem to update changes made in my Journal Glossary file. I removed some white spaces and Sync does not seem to register the changes. The other fields are updating fine so far.

[iandol]

How are you using the glossary to be able to make these changes exactly? I probably don't understand exactly the ins and outs, but i thought the glossary files only worked when editing a reference to add to the database or generating a finished bibliography? Then again bibtex is exported using a format so maybe my intuition that bibtex export doesn't use the glossary is wrong. Or maybe it only works when you first create the synced bibtex file (did you try to regenerate the bibtex file?), but the logic to work out which references a glossary change would impact to then apply it the bibtex file on every sync isn't in scope?

[Jon]

If you edit an entry in the journal glossary but not in the reference itself, Bookends may see them as matching anymore.

The glossary can be used when entering journal names manually (an abbreviation defined by you is expanded to the short or full journal name). But it's main use is for formatting. (1) it allow Bookends to convert between short and full names as specified by the format, and (2) makes it possible to have short journal names output with or without periods, again as specified by the format. To do this, Bookends has to search the glossary for the name (long or short) entered in the reference's Journal field. If you edit the glossary so that it no longer matches what's in the reference, Bookends can't find the match and outputs what is entered in the library.

Example: if the reference has the journal entry "J Biol Chem" and you edit the short name in the glossary to "J Biological Chem", there is no longer a match. The output will ge "J Biol Chem", because that is what is in the Journal field.

To fix this, you can use the Journal Term List merge feature to update all references that cite that journal so that they use the same form (in this case, the one you modified in the glossary). Please see the User Guide for how to merge (and otherwise use) items in Term Lists.

Jon
Sonny Software

[Nhaps]

How are you using the glossary to be able to make these changes exactly? I probably don't understand exactly the ins and outs, but i thought the glossary files only worked when editing a reference to add to the database or generating a finished bibliography? Then again bibtex is exported using a format so maybe my intuition that bibtex export doesn't use the glossary is wrong. Or maybe it only works when you first create the synced bibtex file (did you try to regenerate the bibtex file?), but the logic to work out which references a glossary change would impact to then apply it the bibtex file on every sync isn't in scope?

I am using glossary to control some fields in the references, like abbreviation for journals. I access the glossary file of my choosing under Window - Journal Glossary, where I can input three fields. Abbreviations, Short Name, and Full Name for journals or book in a series. These fields are integrated into the bib file and show up in the Format Reference Window. All changes made in the journal glossary list of your choosing should then be synced when you run File - Sync Linked BibTeX file. The empty spaces can be seen in these illustrations. [img]file:///Users/carlos/Desktop/White%20space.png[/img]

[Jon]

In addition to what I told you, only references that were modified since the last "sync" are updated. Changing the glossary doesn't modify any references. You'd have to remove the old .bib file and recreate it.

Jon
Sonny Software

[Nhaps]

If you edit an entry in the journal glossary but not in the reference itself, Bookends may see them as matching anymore.

The glossary can be used when entering journal names manually (an abbreviation defined by you is expanded to the short or full journal name). But it's main use is for formatting. (1) it allow Bookends to convert between short and full names as specified by the format, and (2) makes it possible to have short journal names output with or without periods, again as specified by the format. To do this, Bookends has to search the glossary for the name (long or short) entered in the reference's Journal field. If you edit the glossary so that it no longer matches what's in the reference, Bookends can't find the match and outputs what is entered in the library.

Example: if the reference has the journal entry "J Biol Chem" and you edit the short name in the glossary to "J Biological Chem", there is no longer a match. The output will ge "J Biol Chem", because that is what is in the Journal field.

To fix this, you can use the Journal Term List merge feature to update all references that cite that journal so that they use the same form (in this case, the one you modified in the glossary). Please see the User Guide for how to merge (and otherwise use) items in Term Lists.

Jon
Sonny Software

I use the Term List merge feature, but some things like empty spaces are not detectable there, as far as I know. It is interesting that the Format Reference Window updates the results whenever I delete empty spaces in the Glossary, so I assumed that Sync Linked BibTeX would catch that as well but no. I just wanted to inform you of this limitation. Right now I'm having to Create Synced BibTex File to update the changes, which is not a big deal because I have a fast laptop.

[Nhaps]

In addition to what I told you, only references that were modified since the last "sync" are updated. Changing the glossary doesn't modify any references. You'd have to remove the old .bib file and recreate it.

Jon
Sonny Software

Ok I did not know that. Thank you.