local list of journal abbreviations

parrenin
It would be nice to have one or serveral local lists of journal abbreviations which the user could modify.
Currently, there is only the possibility to use the Medline list or to define the abbreviation for each reference.
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  • adamsmith
    Zotero currently just uses the list under resources/schema/abbreviations.json
    in the zotero.jar It would not be terribly hard, I believe, to allow that to be changeable, but that would really only make sense if there were any alternative lists out there. Are there any particular shortcomings you're running into?
  • Simon
    If you put an abbreviations.json file in your Zotero data directory, Zotero will use that instead of the bundled abbreviations list. As adamsmith says, we could allow more flexibility here, either by bundling multiple lists or allowing users to install new lists, but that only makes sense if there are other lists to be had.

    If you're interested in creating a list, you can take a look at the abbreviations.json file bundled with Zotero, or if that's not sufficient, I can create some better documentation.
  • parrenin
    I noticed that 'Climate of the Past' is abbreviated in 'Clim.', which is wrong (correct one is 'Clim. Past').
  • parrenin
    It is not clear how the abbreviations.json file is structured.
    One would expect a simple two columns text file with the complete journal name in the first column and the abbreviation in the second column.
  • fbennett
    A document will go online in the next few days that explains what each segment is intended for.
  • parrenin
    I tried to create a simple abbreviations.json file in my data directory, as:

    {"info":{"URI":"http://www.zotero.org/abbreviations/default.json","name":"MEDLINE + Title Word Abbreviations"},"default":{"container-title":{"Climate of the Past":"Clim. Past"}}}

    However, it does not seem to work: "Climate of the Past" is abbreviated as before ("Clim.").
  • Simon
    edited May 24, 2013
    You have to restart Zotero after creating or editing the file to get it to update the list of abbreviations. Also, you should use a different URI and name from the built-in list to prevent confusion, and the keys in the abbreviations.json file have to be normalized. The normalizeKey function does this, but roughly this means that you should remove "the", "and", and any punctuation and they should be all lowercase.
  • js615
    edited September 17, 2013
    Did you get this to work?

    I am having a similar problem and can't get this fix to work. Simon, I've tried your suggestions. It's just not picking up on the file.
  • aurimas
    Can you post your abbreviations.json file on http://gist.github.com ?

    Are you placing abbreviations.json in the correct location (i.e. directly in your Zotero data directory, next to zotero.sqlite and the translators directory)?

    Also, what specific problem are you trying to solve? I'm submitting a fix for the Climates of the Past issue. Are you trying to get some special abbreviations to work or are you fixing an issue with an incorrect MEDLINE abbreviation?
  • ssauerw
    edited December 23, 2013
    Dear All:

    I have looked into journal abbreviations recently. It took me quite some time to figure out how zotero deals with this, but I seem to have figured it out.

    Now, I am using oXygen as JSON editor. However, not all abbrevations seem to be pulled from the abbreviations.json file. Here an excerpt:


    "info": {
    "URI": "http://www.zotero.org/abbreviations/default.json",
    "name": "MEDLINE + Title Word Abbreviations"
    },
    "default": {
    "container-title": {
    "academy of management journal": "Acad. Management J.",
    "academy of management review": "Acad. Management Rev.",
    "journal of political economy": "J. Political Econom.",
    "management science": "Management Sci.",
    "strategic management journal": "Strategic Management J.",
    "journal of financial and quantitative analysis": "J. Financial Quant. Anal.",


    I just added the entries all in the beginning without any particular order. Now, Journal of Political Economy is abbreviated properly whereas Journal of Financial and Quantitative Analysis uses a different abbreviation than is listed above. Any idea why this happens?

    Thanks much!
    Steve
  • aurimas
    Where is this file located? Is this the original file that was present in Zotero, just with your additions?
  • ssauerw
    Yes, that's the original file with my additions. Is there another way to modify the abbreviations?
  • aurimas
    Did you restart Zotero/Firefox after modifying the file? You would also need to refresh existing citations in your Word document for changes to take effect, so try it in a new document for testing.

    Do you have the automatic abbreviation option enabled in Zotero Document Preferences (in Word)?

    How are the references that are incorrectly abbreviated entered in Zotero? Right-click -> export one of them as Zotero RDF and post the contents to http://gist.github.com then link to it here.
  • ssauerw
    Yes, I did restart zotero standalone + created a new document testing the reference entries. Also, automatic abbreviations are enabled in the Word document. The problem is that some of my additions work (J. Political Econom.) while other don't (J. Financial Quant. Anal.).

    Instead of "J. Financial Quant. Anal." zotero shows "J. Financ. Quant. Anal."

    Also, here the link to the zotero RDF: https://gist.github.com/anonymous/8104264

    Thanks again!
    Steve
  • aurimas
    Ah, I see. Sorry I missed this before, but the journal name is supposed to be entered in a normalized form (which you mostly got). That currently means lower case, strip most punctuation (notably, don't strip brackets and parentheses), and strip out "and", "et", "y", "und", "la", "le", "the", "l'", "d'".

    So if you enter "journal of financial quantitative analysis": "J. Financial Quant. Anal."(no "and"), it should work.

    I'm not sure if there is ever a case where such normalization would result in an ambiguous journal name. If you find a case, do let us know.

    Finally, in the longer run, Zotero will probably have a much better way to tweak abbreviations. But don't hold your breath.
  • ssauerw
    Thanks, aurimas! That was it!

    Happy holidays, and looking forward to the new journal abbreviation features yet to come!

    Steve
  • bwiernik
    I've found an error in the stock abbreviations.JSON and I'm not sure how to correctly fix it.

    There are two journals called Biochemistry. One is simply "Biochemistry". The other is "Biochemistry (Moscow)". What is the correct way to normalize these titles so that both are formatted correctly?

    At present, the list says:
    "biochemistry" : "Biochemistry (Mosc.)
  • aurimas
    What do you expect the Moscow version to be abbreviated as?
  • aurimas
    edited January 11, 2014
    Oh, sorry. I see what you mean. That's a known issue, unfortunately, with no good solution at the moment. You will have to edit it at the end of your final review process. For reference, the issue was discussed here https://forums.zotero.org/discussion/32232/journal-name-is-slightly-incorrect/
  • vfatemi
    Is there any way to extract the list of journals and abbreviations from this site? It appears to be much more comprehensive than what is built-in.

    http://woodward.library.ubc.ca/research-help/journal-abbreviations/
  • adamsmith
    what makes you say so? The built in list is much, much bigger than that (and also includes a word list and an algorithm) so if something isn't getting abbreviated, that's likely not an issue with the list, but something different.
  • vfatemi
    I looked at the abbreviations.json file linked earlier by Simon and didn't find some journals or words that I would need, such as Physical Review Letters (and related journals) or, as far as words, even just the word "physical". That comment is a bit old though. The link I noted has pretty much all the journals I would need.

    I guess I am also confused about when Zotero automatically fills in the Journal Abbr field for the citation info. It hasn't been consistent about adding that info, even when papers are from the same journal.
  • Simon
    The abbreviations file is not a simple mapping between journal names and abbreviations. It is primarily a list of abbreviations for individual words and word stems (including "physica-"), although it also contains some mappings for full journal titles where the MEDLINE abbreviation does not follow the rules. The best way to know how a publication title will be abbreviated is to try it. (Physical Review Letters is abbreviated as "Phys. Rev. Lett.")

    Zotero only populates the Journal Abbr field when the database provides it.
  • vfatemi
    Ah, I see. I missed that word apparently. I'll play with it and make sure everything comes out alright. Thanks!
  • pastorgad
    The local journal abbreviation list is not correct for the journals that are the official journals of the societies of the specialities. And then they are not coorectly cited in vancouver style. the programa inserts the full journal name because it is not in the list. For instance: Journal of clinical oncology: official journal of the American Society of Clinical Oncology. In the list this journal and others are only Journal of clinical oncology, so they are not recognized
  • adamsmith
    remove the subtite in your Zotero data - you'd never want that whole journal title cited.
  • adamsmith
    @aurimas - should we consider removing those subtitles on pubmed import?
  • pastorgad
    Remove the subtite en my Zotero data is time consuming, and that is the official full journal name that figure in the catalog oj journals in pubmed. http://www.ncbi.nlm.nih.gov/nlmcatalog?cmd=historysearch&querykey=9
    I think de local journals list in zotero should be updated, because this problem is with all the official journals of the societies
  • NMonteix
    Dear all,
    I wanted to prepare a huge list, but before that, I tried to create an abbreviations.json file.
    Following what Simon and aurimas wrote above, I prepared the list in lowercase, without punctuation and removing any of those:
    and, et, y, und, la, le, the, l', d'

    From there some questions:
    1/ What should be done with Italian (e, il, lo, dell')?

    2/ I ran a test with this, called abbreviations.json and saved in my Zotero data directory:
    {
    "info": {
    "URI": "http://www.zotero.org/abbreviations/american-journal-of-archaeology.json",
    "name": "Abbreviations American Journal of Archaeology"
    },
    "default": {
    "container-title": {
    "mélanges de école française de rome antiquité": "MéFRA",
    "atene e roma": "AeR",
    },
    }
    }

    For Atene e Roma, it worked perfectly
    For Mélanges de l'École française de Rome. Antiquité, it did not work so well:

    With "Mélanges de École française de Rome. Antiquité", I got this result: MéFRA
    With "Mélanges de l'École française de Rome. Antiquité" in Zotero, I got this result: Mélanges De LÉcole Française De Rome Antiquité

    a) Given it might be needed to cite the whole name, I cannot just remove l', etc. from all titles in my Zotero database.
    b) Why the capitalization to each word? If it doesn’t recognize the title to be abbreviated, shouldn’t it cite it as it was?
    c) I suppose that the problem lies with the apostrophe, how to deal with it given its high frequency in Italian and French?


    3/ The subtitle issue. I guess it can be solved by duplicating the name of the journal?
    "studi miscellanei seminario di archeologia e storia dell'arte greca e romana dell'università di roma": "StMisc", "studi miscellanei": "StMisc" [not such a good example, it has apostrophes...]
  • deszoeke
    The way journal titles should be abbreviated depends on the journal, so it is specific to a particular style.

    It follows that there are not universal rules for abbreviations. The Zotero procedure should substitute style-specific abbreviations for particular journal titles first, and only thereafter attempt to guess the abbreviation with more general rules.

    This approach prioritizes correctness in the context of style. After all, that is the job of a reference manager/formatter. It may come at the expense of quality of artificial intelligence that guesses journal name abbreviations, which is impossible to perfect.
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