[Answered] Zotero and Journals abbreviations

pedrom34
edited August 11, 2017
Hi,

I've read the different discussions on the forums about this topic, but I cannot find a clear answer.

I'm using Zotero to store my references, and I'm not using the word processor as I don't cite my ref in word. Basically, I use Zotero by right-clicking on a ref and "Create a bibliography". I'm in the medicine field, and journals abbreviations are quite a thing...

Is there a way to automatically fill in the "Journal Abbreviation" field in Zotero?
If no, is there a way, to use Abbreviation Filter without Word (or LibreOffice)?

Thanks!
  • adamsmith
    Sorry, the answer to both your questions is no. Automated abbreviations only work in the word processor add-ons. If the journal abbreviation field isn't filled on import (which it is on many databases), there's no way to automatically populate it later (though there may be in the future).
  • pedrom34
    :'(

    I was expecting this answer...

    When you say future... is it more 2 months or 10 years?
  • adamsmith
    Most likely neither. I'd be disappointed if it doesn't happen within the next 2 years, but I'd be very surprised if it happens within the next 3 months.
  • pedrom34
    At least it's sort of planned :D
  • Gurdas_Sandhu
    For my own learning, can the OP use a method to bulk update the journal abbreviation field, for a given journal? I would assume there are maybe 10-20 journals where the field is not imported, or that form the bulk of journal items. So, running the bulk code 10-20 times (or having a code that does it in one go), should bring the database up to speed?
  • adamsmith
    I think the easiest would be to do this via a python script through the web API. That could even match against a list. So if low-level python scripting is an option and the database is synced, then yes, this can be done.
  • pedrom34
    This cannot be done locally?
    Anyhow, I'm interested in any documentation that you may give to me!
  • bwiernik
    edited August 14, 2017
    @dstillman Is there any chance of adding/exposing a terminal to use the Javascript API with Zotero Standalone? With Zotero for Firefox, it was possible to install the Execute-JS plugin, but this plugin doesn't work with Zotero 5 (even if the install.rdf is changed to permit installation).
  • adamsmith
    The server API is documented here: https://www.zotero.org/support/dev/web_api/v3/start
    but I'd actually recommend doing this with pyzotero:
    https://github.com/urschrei/pyzotero
    which makes accessing the API super simple.

    (As bwiernik's question indicates, there _is_ a local API, but there's currently not a good way to access it).
  • bmaranville
    The journal abbreviation is provided for the Citeproc CSL (JSON) output format of the Crossref lookup (for DOIs), as "container-title-short" (when it is available). Is there any chance this information can be used for DOI imports through "Add item(s) by identifier"?
  • adamsmith
    we currrently are still using the XML (UnixRef) export from CrossRef and would be picking up the journal abbreviation from abbrev_title -- I've been wanting to switch to CSL JSON, but currently it's missing data for books and book chapters. Ticket here: https://github.com/CrossRef/rest-api-doc/issues/152
  • bmaranville
    The abbreviation is indeed there for many of the citations I'm looking at, e.g. for this DOI:
    10.1103/physrevb.94.060411

    The result returned from api.crossref.org has "abbrev_title" defined, but Zotero is still not including it in the "Journal Abbr" field on import from DOI. Is this a bug?
  • adamsmith
    Yes, looks like we're looking in the wrong section of the XML:
    https://github.com/zotero/translators/blob/master/CrossRef.js#L155
    would have to check if there's a reason for this (i.e. this is inconsistent in the metadata) or if we can just switch before fixing.
  • bmaranville
    I looked at the schema for unixref1.1 and the abbrev_title element can only show up in this spot in the hierarchy:
    <crossref>
    <journal>
    <journal_metadata>
    <abbrev_title>...</abbrev_title>
    </journal_metadata>
    </journal>
    </crossref>
    (see https://data.crossref.org/reports/help/schema_doc/unixref1.1/unixref1.1.html )
  • adamsmith
    Pull Requests welcome, but I'll also fix this myself when I get to it. Thanks.
  • balabi
    Automatically filling Journal Abbreviation will be very useful. Currently, there are many blanks in my library regarding " Journal Abbreviation" field. But if I use journal full name, the column will be too narrow to show. Hope this feature will come soon.
  • bwiernik
    @balabi The field is automatically populated when such data is provided by the site you are importing from.
  • balabi
    @bwiernik Yeah, I know, but not always. For example, look at this https://pasteboard.co/H3MHWeH.png These four paper are all "nature physics", but only two have abbreviation name. This is quite annoying
  • bwiernik
    It’s likely you imported those articles from different websites (e.g., the publisher versus google scholar). If the site provides the journal abbreviation, Zotero will import it, but it can’t if that information is missing. If there is a site you expect to provide the abbreviation that doesn’t get imported, please post a specific URL.

    Note that Journal Abbreviation is probably the most inconsistently provided and formatted field across publishers and sites. You will in many cases have to adjust the imported information anyway.
  • fredericky
    @adamsmith Is this function available right now?
  • adamsmith
    No, I'm afraid not
  • fredericky
    Two years later o(╥﹏╥)o
  • adamsmith
    If you're referring to journal abbreviations, I'd still take that PR.

    If you're referring to updating item metadata, that's 20 month, not 2 years, and a PR is under review.
  • fredericky
    I am referring to the updating journal abbreviations automatically, so you mean Z will have this function very soon? That's a piece of good news.
  • mjahmad
    has Zotero added this feature for Overleaf or latex?
  • adamsmith
    The BetterBibTeX add-on is able to include Zotero's automated abbreviations in bib(la)tex output. Its output can be used with Overleaf with a little set-up. Overleaf's out-of-the-box Zotero support doesn't get automated abbreviations.
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