biochemistry: incorrectly referred to as biochemistry (Mosc.)

shoulist
Firstly, thank you to the developers/participants of Zotero. I think the software is great.

This has come up in other discussion threads - i.e. that when referencing a article from the journal 'Biochemistry' (ACS), it gets shown as 'Biochemistry (Mosc.)' in the bibliography.

My question is whether there's a file on my computer where I can manually change this incorrect abbreviation so that it will provide the correct information moving forward? (I reference a lot of papers from this journal).

Thank you.
  • LiborA
    What style you use? Can you export and share Zotero record for some article from Biochemistry (ASC)?
  • DWL-SDCA
    Somehow, when questioning abbreviations in Zotero one comes close to touching a third rail. I am biased. Zotero's treatment of abbreviations is the _only_ aspect of the program that I dislike, but the level of my dislike is far beyond loathing. This is the only Zotero issue that by design makes me do extra work. I know that several well-meaning developers and volunteers spent many hours of work on this but this system causes me great frustration. Other than this I love everything else about Zotero. All this complaining aside, I don't know of any _current_ competitors that have a better system.

    There are at least 3 journals named "Biochemistry"

    Biochemistry (New York) published by Wiley 1980-1985
    Biochemistry (Wash) published by the ACS. (issn 0006-2960)
    Biochemistry (Mosc) published by MAIK Nauka/Interperiodica (issn 0006-2979)

    I don't know how Zotero guesses the abbreviation to use. It doesn't seem to use the ISSN. Items imported from PubMed should have the proper abbreviation placed into the Zotero field but that doesn't always seem to be used as a clue to help when there are multiple journals with the same name. As it stands now when one imports metadata from a publisher's site there is seldom an indication that one Biochemistry is different from another. Most publishers include the issn with their metadata but many do not.

    The ISO abbreviation for each of these differs a bit from the Medline abbreviations, above. The ISO abbreviations don't use parens and there are periods after the place-name abbreviation.

    More importantly, there are abbreviation conventions that differ from Medline / LTWA.

    My personal distaste is based on the often incorrect application of the Medline / psudo LTWA system. The Zotero application gets that right _most_ but not all of the time. The number of times it is wrong is few but still too often. Thus, I must check each abbreviation to verify correctness anyway. Not a work saver. I know that one can enter an abbreviation in Zotero's abbreviation field and get Zotero to use that instead of the automatic system but the automatic system cannot be turned off or on journal-by-journal. Further, I cannot turn off the importing of journal abbreviations. Most of the time, publishers either place the journal's full name in that metadata field or the included abbreviation is something that fits no recognizable standard. Often this is merely an arbitrarily truncated version of the title. Yes, I recognize that I can delete the incorrect abbreviation imported from the publisher but that is extra work.

    Other than it did a satisfactory job at bibliography maintenance and citations; one of the few things I liked about Reference Manager was that it allowed at least 3 different journal abbreviations for each title. I was allowed to set a preferred abbreviation for each citation style. Even back in the pre-DOS early c/pm days there was a journal table in the RM database that allowed an alternate title (maybe even two alternates) and the 3 abbreviations. The journal fields included the issn and other standard numbers. In the DOS version I could find duplicate journal entries and selectively merge data into one journal record. ISSNs and other standard numbers were included as fields in the journal table.

    I'd be happy if I could set the import translators to _never_ import journal abbreviations because those that are imported from publishers are usually incorrect. I'd rather edit an empty abbreviation field than a field with a useless string.
  • LiborA
    edited May 2, 2017
    only notes: I've imported articles from Biochemistry (ACS) and from Biochemistry (Moscow) web pages. In the first case, the imported journal abbreviation is "Biochemistry". In the second case, the Journal abbreviation field is empty.
  • DWL-SDCA
    Further complicating imports from publisher sites is choice of translator for the site.
  • bwiernik
    The issue with Biochemistry is that the list that Zotero pulls for automatic abbreviations incorrectly Identifies Biochemistry (and a few other journals with multiple publications with the same name) as the more obscure source. Fixing this is planned, but it's a somewhat complicated problem to avoid it breaking frequently.

    In the mean time, there is a (not very user friendly) way to add your own list of abbreviations. See Simon's comment here;
    https://forums.zotero.org/discussion/29501/local-list-of-journal-abbreviations/
  • adamsmith
    edited May 2, 2017
    (the actual file, btw. is part of the software in /resources/schema/abbrevations.json so it'd be a bit involved to change.)
    I think you may be able to override abbreviations with the abbreviation filter add-on? https://juris-m.github.io/downloads/ @bwiernik is that not the case?

  • bwiernik
    You can copy the abbreviations.json file out of /resources/schema/ and place a modified copy in your Zotero data directory to override the default list.

    The Abbreviations Filter plugin can handle this on a document-by-document basis. I'm not sure if you can set an always-on set of abbreviations with that that apply to all documents (I haven't used it that heavily).
  • dtwrublewski
    Hello! just putting a comment here as to when/if this issue will be fixed re: pulling incorrect citations from Medline? I literally just had a patron with this exact problem. We solved the problem by unchecking the "use MEDLINE abbreviations" box with the citation style. It would be nice if this was fixed - I'm not sure why the more obscure title is pulled if an ISSN is included in the citation? Shouldn't it just pull the abbreviation based on that? Thanks much!
  • dtwrublewski
    Ah, also just saw this thread: https://forums.zotero.org/discussion/32232/journal-name-is-slightly-incorrect/
    Still an open issue I take it.
  • adamsmith
    I'm afraid so, yes. @dstillman -- we can, I believe, fix this in the abbreviation list. One of the reasons to not do that so far is that we don't exactly understand how that list was compiled by Simon. Do you happen to know?
    Either way, would you take a PR with just this change?
  • dtwrublewski
    @adamsmith - thanks kindly!!
  • dstillman
    @adamsmith: I do not, but we can try to find out. PRs for any interim changes would be fine.
  • DWL-SDCA
    Please do not allow this problem to be dismissed with a fix to this single journal. While that is the immedite problem discussed here and needs immediate attention. This is a serious problem universally.

    Please allow us to universally turn off importing of journal abbreviations.

    Please refer to my agony post above for other suggestions. Different publishers and professional disciplines have different abbreviation requirements. Medline and LTWA abbreviations are not universal.
  • adamsmith
    Allowing users to select between and fine-tune abbreviation lists is definitely on my long-term wish list. (You're the only person who has every complained about journal abbreviation import, so I think that's probably a no, but also becomes less of a problem once we have batch editing).

    But I'm against letting the perfect be the enemy of the good and the specific issue that's been bugging multiple people here I can fix in 5mins.
  • adamsmith
    @dtwrublewski The fix for biochemistry is in the next version of Zotero.
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