JabRef 3.7: Journal Abbreviations and other things

Help
#1

After the forced update to JabRef 3.7 (b/c of Medline), some things are behaving quite strangely for me.

  1. Journal abbreviations are not automatically used anymore when I import an article via Medline. This means that always the full journal name is used.

  2. Journal names have changed and are now missing in the standard JabRef abbreviation list. I guess this is a thing on Medline’s end, but just to give some examples:

  • Science is now “Science (New York, N.Y.)” instead of just “Science”

  • RNA is now “RNA (New York, N.Y.)” instead of just “RNA”

  • PLoS Genetics gets imported as “PLoS genetics”, which would be fine, but the toggling of the abbreviation changes it to “PLos Genet” instead of “PLoS Genet” like it did previously. It’s not in the standard JabRef abbreviation list, so I have no idea where this comes from

The only solution I’ve found so far is to add all those journals to a manual abbreviation list and then toggle the abbreviation, which is really cumbersome.

  1. JabRef now imports all special characters as special characters instead of LaTeX, e.g. ä instead of {"{a}}. I usually wouldn’t care since I’m using UTF-8, but sometimes I have to work with Word and bibtex4word has no UTF-8 support. Since all my entries are in the LaTeX style, however, the export as .xml for Word will of course result in “{”{a}}" in Word instead of “ä”. In this case, the new import style would be preferred but the mixture of the two is just not usable in either case.
    I haven’t yet checked what happens if the title or abstract contains a “%”.

  2. When importing Medline, it adds the DOI but not the URL for the DOI.

  3. When importing Medline, the “other fields” now contain “Chemicals” (which are some kind of keywords where I don’t know where they come from), “Citation-subset”, “Completed”, “Country”, “Created”, “ISSN”, “Issn-linking”, “Issue”.
    Before, it was “Institution” (which I really miss), “Language”, “Medline-pst”, “Pii”, “Pmc”, “PMID” (which I also miss).

  4. The issue number of an article is now stored as “issue”. This was “number” before. “Month” doesn’t get an entry.

I upgraded from 3.5 since 3.6 wasn’t properly working for me.

#2

Let me answer your points one by one.

  1. This change is intended. Some users prefer abbreviated and some full journal names. We thus opted for the option which contains the most information (= full name). However, we plan to implement that cleanup operations can be invoked directly after import and in this way it would be possible to automatically convert to abbreviated journal names.

  2. I couldn’t find any reference to “Science (New York, N.Y.)” or “RNA (New York, N.Y.)” in our code. Thus this should be a problem on your side (sorry can’t help you further since I’m not that familiar with the journal abbreviation code). The “PloS” problem will be resolved in the next version with the PR. Thanks for reporting this issue!

  3. As for 1., we keep the format we get from medline. You can use JabRef’s Quality -> Cleanup functionality to automatically convert unicode characters to LaTeX (field formatter: “Unicode to LaTeX”).

  4. Having the DOI in the doi field and not as a url is the desired format. If you want your DOI’s to be clickable in the Latex-PDF, you have to slightly change the BibTeX style.

  5. These fields are returned from the medline api and thus are kept in the imported bibtex. The help contains a list of all supported fields. The PMID field usually should be exported, for example for “pmid = 27670948” it works. Can you please open a new issue on github and include the search query so that we can reproduce the issue (same for the missing “institution”).

  6. See 5., please report at github with more details. For example “pmid = 27670445” has a month.

#3

Thanks for your reply.

  1. Ok, that’d be great.

  2. I think it’s that PubMed / Medline changed something. If you import 27120414 for example, it will have the new Science name. This new name can also be found here:
    ftp://ftp.ncbi.nih.gov/pubmed/J_Medline.txt
    So probably I have to go with the manual abbreviation for now.

  3. Thanks!

  4. Thanks!

5.+6. Ok, I’m gonna try it a little bit more and if it’s still like that, I’ll report it on GitHub.

#4

In my case, PMID was imported, but since many new info is now imported, it’s under “other fields” and you have to scroll down to see it. However the institution is empty (but was present previously).
If I could also add a problem : journal is imported instead of journaltitle. I know I can clean up entries, but it’s not so intuitive.
I’m on Biblatex mode, Jabref 3.7, win7
PMID : 24708236

#5

The incorrect journal abbreviation problem continues in JabRef 5.2. I upgraded probably from 5.1 to 5.2 and the journal abbreviations have been changed in a wrong way!

For example, “Nature Communications” should be “Nat. Commun.” but it now abbreviates to “Nat Commun” without the periods (see https://www.nature.com/ncomms/about/aims).

“Nature Nanotechnology” should be “Nat. Nanotechnol.” but it’s now “Nat. Nanotechnology” (see https://www.nature.com/nnano/about).

“Nature Photonics” should be “Nat. Photon.” but it’s now “Nat. Photonics”.

It seems my personal list does not override the JabRef built-in list. Even if I add those changes manually in my personal list, JabRef always finds the built-in list first and it abbreviates according to the built-in list, which is incorrect. Is there any way to fix this? I cannot fix the built-in list (double-click or right-click doesn’t allow me to change in the built-in list).

#6

@Yoseob_Yoon Hi, the best way is to directly change them here or to file an issue https://github.com/JabRef/abbrv.jabref.org

Due to the large number of Journals, for performance reasons the JabRef internal list is now compiled to a database file.