Style Request: The Journal of Physiology & Experimental Physiology

I am not aware of these journals sharing a style with another journal already in the repository. However Experimental Physiology can be a dependent of The Journal of Physiology as they share styles.

A similar style I know of that could be used as a starting point is: The Journal of Neuroscience (Author-Date)

The style guide for The Journal of Physiology is here:
http://jp.physoc.org/site/misc/author.xhtml#refs

The style guide for Experimental Physiology is here:
http://ep.physoc.org/site/misc/author.xhtml#references

However, they lack sufficient detail. The following modifications needed to convert JN to JP style are also based on inspecting recent JP articles.

In the main text:

1. et al. should be ilalicised. Note that the full stop after et al. should be retained.

2. & should be used instead of and, e.g. (Bloggs & Bloggs, 2011) instead of (Bloggs and Bloggs, 2011)

3. Within a group of references, the primary order scheme should be chronological (as is currently the behaviour in JN style). But when a group of references includes citations from the same year, these should be ordered alphabetically, e.g. (Smith, 2010; Bloggs, 2011; Doe, 2011) instead of (Smith, 2010; Doe, 2011; Bloggs, 2011)

4. Letters used to disambiguate same author, same year papers are correctly placed, but they should be italicased.

In the bibliography:

5. Letters used to disambiguate same author, same year citations should be moved inside the year brackets and should be italicised e.g. Bloggs(2011a). instead of Bloggs(2011)(a)

6. For all entries, there should be a full stop after the year of publication, e.g. Bloggs (2011). instead of Bloggs (2011)

7. For all entries, there should be no comma between the penultimate and final author. Instead there should be an &. e.g. Bloggs J, Doe J & Smith J (2011). instead of Bloggs J, Doe J, Smith J (2011).

8. The order of entries should be made strictly alphabetical regardless of chronology, e.g. Bloggs J, Doe J (2011). should come before Bloggs J, Smith J (2010).

9. The title of journal articles and the title of books (in both book & book section entries) should be italicised.

10. The volume of a journal should be in bold font.

11. The journal volume should be followed by a comma, there should be a space before the page numbers, and there should be a full stop after the page numbers, e.g. J Physiol 500, 100-108. instead of J Physiol 500:100-108

12. If there is no volume/page number info for a journal article (e.g. an in press article), the DOI should be provided with a semicolon and space after the journal name, e.g. J Physiol; DOI: 12.1113/jphysiol.2001.013382.

13. For books, the publisher should be before the city and there should be a comma instead of colon between them, e.g. Humphrey Milford, London. instead of London: Humphrey Milford.

14. For book sections,
a) the edition of the book should be provided,
b) the formatting of the editor names should follow the formatting for the main authors of all entries, rather than have initials before surname.
c) eds. should be replaced with ed.
d) page numbers should be preceded by pp. instead of p.
e) Publisher should be provided before City, with a comma in between instead of colon.
e) the order of presentation of the book details needs re-arranging. Thus, the order should be: In [Book Name (italicised)], [edition], ed. [editors], pp. [page numbers]. [Publisher], [City].

e.g., In Gut Hormones, 2nd edn, ed. Bloom SR & Polak JM, pp. 119–124. Churchill Livingstone, Edinburgh.
instead of, In S. R. Bloom & J. M. Polak, eds. Gut Hormones Edinburgh: Churchill Livingstone, p. 119–124.

If possible:

15. When page numbers in zotero entries use short forms (e.g. 156-60), the bibliography should be forced to use the long form (156-160).

16. When titles of citations do not contain full stops in Zotero, they should be forced to end with a full stop in the bibliography,
e.g. Adrian ED (1932). The Mechanism of Nervous Action. Humphrey Milford, London.
instead of Adrian ED (1932). The Mechanism of Nervous Action Humphrey Milford, London.
  • OK, it'll take some time but I'll get to this eventually.
    As for 15 and 16 - you should save all of your page ranges in long form - Zotero can shorten them when required by a style but cannot do the reverse.
    You should never save a title with a period at the end - this will lead wrong formatting in most styles.
  • @adamsmith: are you sure that Zotero/citeproc-js cannot parse shortened page ranges, and reformat them to an expanded range?

    (see http://citationstyles.org/downloads/specification.html#page-ranges )
  • oh good call - I'd always overlooked the "expanded" attribute - I'll test this but yeah, looks like it's possible.
  • Being nitpicky, "expanded" is the attribute value, and "page-range-format" is the attribute.
  • edited June 1, 2011
    Thanks a lot. Much appreciated.

    Regarding the issue about putting a period at the end of the title in the zotero entry. I've just imported some items from Pubmed, SpringerLink, and Amazon. In all cases the titles do not have a period at the end (does this mean I should be entering them manually?).

    In any case, I have just had a closer inspection of the consequence of this on the bibliography formatting done by my suggested base style (JN). The title of journal articles have a single period at the end in the bibliography regardless of whether or not there is a period at the end of the title in the zotero entry (which seems to suggest separation between the zotero entry and the bibliography formatting is being implemented for this item type). However, this is not the case for titles of books or book sections, or for the book title field of a book section (for these, the period must be present in the zotero entry to show up in the bibliography).

    EDIT: Sorry completely misread your advice. I thought you had written "you should never save a title WITHOUT a period at the end".
  • edited June 1, 2011
    EDIT: Message deleted and added as an edit to previous post
  • exactly - don't put periods at the end (which also means you can leave the titles as they are for 99% of translators - in most cases you'll be fine because Zotero prevents double periods, but there are, e.g., styles that require commas or no period and those would come out wrong with a period in the title.
  • I've started working on this style myself. Will post here when I'm done.
  • great, any questions feel free to ask (here).
  • edited June 4, 2011
    Here is my attempt:
    https://gist.github.com/1008092

    I managed to get most things done, but 3 issues remain:

    a. The style does not validate on http://validator.nu/ (even though it seems to work ok in Zotero) and I don't know why.

    b. For in text citations, the delimiter between author and year should be ", " except when et al. is used, then comma should be ommitted. e.g.
    (Bloggs, 2011; Bloggs & Doe, 2011; Bloggs et al. 2011)
    I don't know how to implement this.

    c. I can't seem to implement point 8 in from original post (desired order of bibliography).
  • Also, why do a number of styles have (dev) added to the end of the title? Should this be added?
  • There are three validation errors:
    http://validator.nu/?doc=https://gist.github.com/raw/1008092/7ccd653189004135b0b48735e8e08f71a699c9a5/journal-of-physiology&schema=http://bitbucket.org/bdarcus/csl-schema/raw/855dcc00cba7/csl.rnc&laxtype=yes&showsource=yes
    1. Attribute strip-periods not allowed on element name
    means what it says: take out strip-periods="true" in line 29
    Element text from namespace http://purl.org/net/xbiblio/csl not allowed as child of element date
    This comes up twice - l. 149 and 162: you can't use "text variable=...." when you're inside a date - put the line after </date>
    Attribute disambiguate-add-year-suffix not allowed on element bibliography
    that attribute needs to go up to cs:citation - it will automatically be reproduced in the bibliography.

    b) I don't think is possible

    c) should work with the style - doesn't it? example?
  • b) this will be possible in the next version of CSL: https://github.com/citation-style-language/schema/issues/12
  • I don't see how - this one concerns the delimiter _after_ et al, not preceding it, but I might be overlooking something.
  • You're right. That's not supported then.
  • edited June 4, 2011
    Thanks, I've updated the style at the original link.

    I didn't actually get those errors when I tried to validate. I just get an IO error (IO Error: Non-XML Content-Type: text/plain.) when I try to validate by precisely following the instructions here: http://www.zotero.org/support/dev/citation_styles#validation

    After making the amendments advised above and then setting the validator to "Be lax about HTTP Content-Type" the style validates, but with these warnings:

    Warning: Being lax about non-RNC Content-Type: text/plain
    https://github.com/citation-style-language/schema/raw/v1.0/csl.rnc
    Warning: Being lax about non-RNC Content-Type: text/plain
    https://github.com/citation-style-language/schema/raw/v1.0/csl-terms.rnc
    Warning: Being lax about non-RNC Content-Type: text/plain
    https://github.com/citation-style-language/schema/raw/v1.0/csl-types.rnc
    Warning: Being lax about non-RNC Content-Type: text/plain
    https://github.com/citation-style-language/schema/raw/v1.0/csl-variables.rnc
    Warning: Being lax about non-RNC Content-Type: text/plain
    https://github.com/citation-style-language/schema/raw/v1.0/csl-categories.rnc

    Anyway,

    I've left the comma as the author-year delimiter in the citations. They can be stripped away from et al., using find+replace in the word processor.

    I am confused about whether I am meant to put (dev) at the end of the title but I have now done so because it seems most of the styles I download have this. I can't find advice about this anywhere.

    Regarding the bibliography sort order. I want the primary sort to be done alphabetically on surnames [surname 1, surname2,…].
    But I suspect the sort order is actually [surname 1,forenames 1, surname 2……..] because when I change the author initials (or even reduce full given names to initials in the zotero entry) I affect the bibliography sort order. How do I achieve the first type of sort order?
  • In addition to the question at the end of my last post - how do I achieve the following sort order: [surname 1,Initials 1, surname 2......]
    i.e. initials of author 1 has precedence over surname of author 2 but the full forenames of author 1 are ignored - only the initials of the forenames are used in the sort.
  • edited June 4, 2011
    Great - yes, "be lax..." should be checked, that used to be in the instructions, not sure why it's not anymore - Rintze?

    For the sorting, try sorting by the author-cit instead of the author-bib macro, that might do it.

    And no, don't add (dev) - the repository does that by itself. That should be added to the instructions, too.

    edit: and the warnings about content type are normal, disregard them.
  • edited June 4, 2011
    @adamsmith: fixed in the wiki.

    @Dan Stillman: wouldn't it be better to just drop the addition of " (dev)" to style names? I think it only causes confusion.
  • edited June 5, 2011
    @adamsmith: sorting by author-cit does not seem to change things. My questions on sorting are getting a bit more general so I have created a different thread about sorting:
    http://forums.zotero.org/discussion/18246/sort-bibliography-by-name-priorty-of-surnames-given-names-and-initials/

    I'll post back here when style is done.
  • @Dan Stillman: wouldn't it be better to just drop the addition of " (dev)" to style names? I think it only causes confusion.
    That dated to when we differentiated between default styles and other styles. Since we no longer make that distinction, I've removed the "(dev)" labels.
  • edited June 5, 2011
    @Dan
    That dated to when we differentiated between default styles and other styles. Since we no longer make that distinction...
    does that mean that all styles auto-update?
  • edited June 5, 2011
    No styles auto-update right now. We're hoping to change that soon.
  • Thanks for removing the labels.
  • Ah, I had created a JPhysiol style during the last week and just wanted to post it when I saw your thread. Interestingly, I also chose the JNeurosci style as a template. However, you seem to have done a much more thorough job than I did. Thanks a lot, this is greatly appreciated!
  • edited June 7, 2011
    @jneef: That's unfortunate....perhaps styles here are a bit like buses!
    The latest version is here: https://gist.github.com/1008092
    It has not really changed from a few days ago apart from a bit of commenting and modification of the info section. It works for me. Would you like to check it works for you, and make any necessary amendments before asking for it to be put in the repository?

    To summarise from earlier in thread, there is one known limitation: It is not currently possible for in-text citations to have different prefixes for year based on presence of et al.

    Also, name sorting will not work properly at the moment, but should work properly (based on intialized names) as soon as Zotero receives a future update (see thread on sorting linked to earlier).
  • This looks pretty good to me. i made one small change, which is including a

    sort-separator=" "

    in the editor macro, line 34, to get rid of the comma between last name and initials of editors. I uploaded it to https://gist.github.com/1012212
    Thanks again!
  • Thanks.

    @adamsmith (or anyone else who can do so): please add the file in jneef's post to the repository and the dependent style - Experimental Physiology - https://gist.github.com/1012354
  • done - thanks again for contributing! (will show up on the repository soon).
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