[new csl] Trends In Parasitology

Zephyris
Hi all,

I am looking for some help in creating a csl for Trends in Parasitology (Cell Press)... I have got a basic level of understanding in csl hacking (minor changes only) but I need some significant help to build a new csl (or get someone to build a csl for me ;) ) for this journal.
Particular problems I am having are:
* Italicised "et al."
* Periods following journal title contractions
* General organisation for a full csl (ie. support for all media types)

I would have thought this would be a simple hack from existing Cell press journals, though sadly it is looking less and less like that! Any help would be much appreciated.

Some (possibly) useful links:
http://www.cell.com/trends/parasitology/home
http://www.cell.com/trends/parasitology/authors
  • fbennett
    edited December 30, 2009
    * Italicised "et al."
    This isn't possible currently. An upgrade to the Zotero CSL processor, to be introduced after version 2.0 is completed, will support it.
    * Periods following journal title contractions
    I don't know the behavior of the current CSL processor well enough to say whether there is a way to avoid extraneous periods following this field. Not much help, but the new processor should suppress all extraneous punctuation.
    * General organisation for a full csl (ie. support for all media types
    I'm not a style designer, but you'll probably get some useful responses if you can give a specific description of the problems you're seeing.
  • adamsmith
    what Franks says and on the last point:
    the best way to learn about style organization is from good existing styles - APA is pretty good for example and covers many different item types. Chicago Manual of Style covers even more, but might be too complicated.
  • Zephyris
    I guess my biggest question is how complex does the bibliography formatting really need to be? I notice the Nature style contains a far simpler bibliography.

    References in this journal are (as a modern biological review journal) almost exclusively previous papers so as far as I am concerned I only need to consider the formatting of references to papers... Is it "bad form" to simply ignore other types of reference if I submitted this style to the repository?

    Specific problems:
    I want to make sure all journal title contractions use periods to indicate the contraction; ie:
    Int. J. Parasit.
    Curr. Opin. Microbiol.
    Not:
    Int J Parasit
    Curr Opin Microbiol
    In short, how!?

    Secondly; what is the default text used as a prefix and suffix? I was having problems with formatting the volume number correctly until explicitly stating a prefix and suffix of "" (which I don't like as I feel it may mess up a reference with multiple volumes).

    My WIP csl can be downloaded here:
    http://dl.dropbox.com/u/1994002/cell_TrendsInParasitology.csl
  • adamsmith
    Yes, styles for 'hard-science' journals can often be quite a bit simpler.
    What you should do is to resolve one type of item through an <else> loop rather than by specifying the item type in an <else-if> of <if>. That way all the types that aren't specifically defined will default to something rather than not creating any visible entry. If that "something" isn't necessarily right for item types that are never going to be used in a style, i.e. if your parasitology journal doesn't deal with legal cases "correctly" no one will ever complain.
    Nevertheless, it would seem like any style should be able to do books, book sections, and journal articles and I have never seen authors instructions that didn't cover at least those three.

    As Frank notes above, no solution to the journal abbr. issue - Zotero will print exactly whatever is in the journal abbr. field.
  • Zephyris
    I have pulled together a style, unfortunately it does not work! When I try to use it with any bibliography-containing document with the Word plugin (Word 2007) it gives the error "Zotero experienced an error updating your document". This is a 100% repeatable error on any document containing a bibliography.

    The only potentially relavent error log message is:
    [JavaScript Error: "[Exception... "'CSL: style references undefined macro issuance' when calling method: [nsITimerCallback::notify]" nsresult: "0x8057001e (NS_ERROR_XPC_JS_THREW_STRING)" location: "<unknown>" data: no]"]

    What is likely to be the cause of this? You can download the WIP style here:
    http://dl.dropbox.com/u/1994002/TrendsInParasitology2.csl

    A second problem (when working without a bibliography) is it doesn't renumber the numerical citations correctly. Ie. if you add a new citation at the end of the document (further on than existing citations) it is given the number [1]. Refreshing the document doesn't help but if you reformat to an alternative (fully functional) numerical reference style then switch back to this style it fixes the problem...

    I'm guessing this is a problem with a sort tag somewhere, though I have no idea how to fix it!
  • adamsmith
    this looks like you looked at some wrong csl documentation.
    Neither "et. al. term" nor "include-period="true" "
    exist in the current csl, but I believe they are included in 1.0, which is forthcoming
    If you take these two out things may look better, at least then the style validates.
  • Zephyris
    Ok, that makes sense, thanks for the help. Is there a validator for zotero-specific features of csl? I guess that could save me some troubles!
  • adamsmith
    you're just validating against the wrong scheme.
    validating against
    http://xbiblio.svn.sourceforge.net/viewvc/xbiblio/csl/schema/tags/0.8/csl.rnc
    would have caught these errors.
    Any valid csl style will generally work with zotero, although there are some errors - especially referring to non existing macros - that the validator doesn't catch.
  • Zephyris
    I have sorted the "Zotero experienced an error updating your document", no just the citation sorting problem remains. Are ideas what is going wrong here?

    Latest version available here:
    http://dl.dropbox.com/u/1994002/TrendsInParasitology3.csl
  • adamsmith
    I don't have time to play around with this (might have later) but have you tried removing the sort tag from the bibliography section? There is no need as the default for numbered styles is to sort by citation number (see nature and IEEE styles) so it won't do any harm for sure.
  • Zephyris
    Yup, that worked! Thanks for your help!
  • suckale
    It looks like the Trends series journals use the same style. I just looked at TIP and TEM and found no differences. The reference examples are the same in the two guideline PDFs[1]. It also seems to be the same for review/opinion/etc.

    If this is true, we could use your style for all Trends Journals.

    Zephyris, where can the latest version of your CSL be found?

    1: http://download.cell.com/images/edimages/Trends/parasitology/TREPAR_Letter_Author_Guidelines_Feb_2009.pdf
    http://download.cell.com/images/edimages/Trends/Endometabolism/TEM_Review_Guidelines2010.pdf
  • Zephyris
    In the end I didn't publish it anywhere, I wasn't particularly happy putting a style out there which has several known issues (et al italic and periods following journal abbreviations)... Do you think it is worth "publishing" this style?
  • suckale
    I, for one, would like to see it. And somebody with the time to improve it could get it easily. So, I think it would be worth it.
  • adamsmith
    yes - use comments in
    <!-- -->
    to point out limitations in the current version
  • Zephyris
    Fair enough! The link below is for my latest version which, as far as I could see, works with no technical problems. It has styles for journal articles, books and book chapters, though the book chapter is 100% untested and the book had a bug of some sort (TBH I can't rember what it was). It also has no commented out unsupported features as I am not sure which problems are unsupported features and which were just my ignorance...

    Sorry it's not in a better state, but here you go:
    http://dl.dropbox.com/u/1994002/TrendsInParasitology4.csl
  • suckale
    Well done. Thanks.
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