Style link for 'Biochemistry' not working

anoop
It seems like install link for 'Biochemistry' style is broken. Also, I have noted that the bibliography format which pops up upon mouse-over on Biochemistry link does not show the correct format. Could I get any help in this regard?
  • RintzeRintze
    edited October 27, 2008
    The Biochemistry style is a so called dependent style, and has the same bibliography format as it's parent, the American Chemical Society style (Biochemistry is an ACS publication). Only Zotero 1.5 Sync Preview 2.2 or later support the installation of these dependent styles (see the note at the top the "Additional Styles" listing in the style repository).

    In what way is the style shown in the mouse-over popup incorrect?
  • anoop
    Thanks Rintze for your reply.
    I am using Zotero 1.5 Sync Preview 2.2 in Firfox 3.0.1 on an Ubuntu 8.04 system.
    The American Chemical Society publishes several journals including Biochemistry. While the ACS style may be valid for other ACS publications like 'Journal of the American Chemical Society' (JACS) or 'Langmuir', it is not valid for 'Biochemistry'. Here is an example I have taken from the bibliography pop-up after mousing over the 'Biochemistry' link in 'additional styles' page which reads as:

    (4) Kotter, P; Ciriacy, M. App. Microbiol. Biotechnol. 1993, 38, 776-783.

    It is correct if it is published in 'JACS', but for 'Biochemistry' is should be:

    4. Kotter, P; Ciriacy, M. (1993) Xylose fermentation by Saccharomyces cerevisiae, App. Microbiol. Biotechnol, 38, 776-783.

    The journal name and the volume number being italicized in both cases and organism name italicized in later case.
    Similarly there are discrepancies with other exampes in bibliography pop-up as far as 'Biochemistry' is concerned.

    Also as mentioned in my earlier post, the install link for the same is broken.
  • RintzeRintze
    edited October 27, 2008
    I think it was supposed that all ACS publications shared the same citation format, but clearly that is not the case. Italic formatting of organism names is not yet supported.

    I tested the link under sync preview 2.2, and it did give an error on the first try. Then I tried to install the Inorganic Chemistry style (which also links to the ACS style), which went fine. I then tried to install Biochemistry again, and this time it installed without failure. The style itself looks fine, so I'm not sure what causes the problem.

    For future reference, the style guide for Biochemistry can be found at:

    http://pubs.acs.org/paragonplus/submission/bichaw/bichaw_references.html
  • anoop
    Many thanks Rintze for your valuable inputs.
    I retried installing biochemistry and inorganic chemistry without success. As pointed out in your first reply, these are dependent sytles, American Chemical Society being the mother style for all publications by the ACS. So I first installed ACS style and then biochemistry style installation went through successfully. However, it does not solve the core issue of the correct bibliographic formating for biochemistry.

    I think the matter should be filed as a bug with the developers as I do not know how to edit .csl files.
  • RintzeRintze
    Some additional information on the style installation error:

    After resetting the translators and styles, I tried the Biochemistry install link again under Firefox 3.0.3 under Windows XP and Zotero 1.5 Sync Preview 2.2. This gave the error: "http://www.zotero.org/styles/biochemistry/dev?install=1 references an invalid or non-existent CSL file at http://www.zotero.org/styles/american-chemical-society as its source."
    Even though the ACS style does exist. The error report generated for these steps is 937715152.

    You don't have to file a bug report. I you would like to have a correct style for Biochemistry, please put forward a style request in this thread (include the link to the style guide): http://forums.zotero.org/discussion/536/1/what-other-citation-formats-would-you-like-zotero-to-generate/
  • dstillman
    Unlike most of the other primary styles on which the dependent styles depend, the ACS style isn't a default style, so it's currently available at /dev rather than its main URI, and Zotero therefore can't find it. The styles code should probably be changed to serve the available dev style at the main URI if no stable style is available. I'll make this change later today.
  • anoop
    Thanks Rintze, thanks Dan.
    I installed American Chemical Society style from here (Just to restate, I am using Zotero 1.5 Sync Preview 2.2 under Firefox 3.0.1 in Ubuntu 8.04):
    http://www.zotero.org/styles/american-chemical-society/dev?install=1
    which worked perfectly for me. After this I installed Biochemistry style from here:
    http://www.zotero.org/styles/biochemistry/dev?install=1
    which again worked perfectly. So now the problem is not with the installation but with the format of bibliography which this style generate for the Biochemistry papers. It generates the default format for ACS which may be valid for JACS, Langmuir and others but not for Biochemistry.

    Right now I am not filing a bug report but trying to fix the .csl file for Biochemistry with the help of one of my friends. At the same time I am going to put a request for correct style for Biochemistry in the thread suggested by Rintze.
  • sean
    Sounds great, anoop. Many thanks for your helpful contributions to the Zotero project.
  • dstillman
    Installation problem should be fixed. Let us know if you find any further problems.
  • anoop
    Thanks Dan
    Installation problem is really fixed now.
    But as I have mentioned in my earlier posts, the problem is with the format of bibliographic citations which this style generates. This style generates default ACS format while the format for "Biochemistry" is different from the default ACS format, the details of which can be found here:
    http://pubs.acs.org/paragonplus/submission/bichaw/bichaw_references.html
    It will be of great help if this issue could be fixed.
  • RintzeRintze
    Your request for a correct Biochemistry has been noted. If I find the time I will take a look at it myself (probably somewhere this week).
  • RintzeRintze
    edited October 30, 2008
    Your style is finished (see the file repository). As the style guide wasn't very extensive, it currently only correctly supports journal articles, chapters and books.
  • anoop
    Thanks a lot Rintze
    It looks just fine at the first glance. This style is going to prove very useful for the researchers working in the areas of chemistry, biochemistry and biophysics. I will try it extensively and let you know how it works. Cheers!
  • zidarko
    Hi there.
    I am prepapring a manuscript for J. Chem. Phys B that uses the default ACS style, but I find that the style (or Zotero?) fails to generate a proper bibliography.

    The list of references is generated but the formatting is not OK (bold/italic characters at wrong positions).

    Any tips?

    Thanks in advance.
  • RintzeRintze
    Unfortunately the official ACS Style Guide isn't online available, although I did find this:

    http://www.libraries.psu.edu/temp/pams/Quick Guide ACS.pdf

    Could you describe the specific problems you encounter with the Zotero CSL style for ACS, and indicate how the output you get differs from the official ACS style?
  • zidarko
    edited December 1, 2008
    Hi.
    I made a PDF of the bibliography, part of which is available at the address: http://www.sicmm.org/~zidar/zotero-err.pdf

    Please note the missing bold/italic characters. It is also worth mentioning that the article title is missing (missing in the CSL altogether). The title field in the Zotero database is filled-in.

    I am using Zotero 1.5-sync3.3 with Firefox 3.0.4 with Office 2003 SP3 and Office plugin Zotero-Word-Plugin-Installer-1.0b3.

    zidarko
  • RintzeRintze
    edited December 1, 2008
    Please note the missing bold/italic characters. It is also worth mentioning that the article title is missing (missing in the CSL altogether).
    Could you be more specific with regard to the bold/italic characters you're missing? What are the affected fields? With regard to the missing article titles, the guide I linked to previously mentions that: "Article titles from print journals are usually not included in the citation.". So the CSL style seems to follow ACS guidelines there.

    Also, if you're running the Sync Preview, you should probably upgrade your Word Plugin to 1.0b4.
    http://www.zotero.org/support/sync_preview#word_processor_plugins
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