style close to that of "Current Opinion" journals

dmk

Hi,

I am writing an article for one of the Current Opinion journals and I would like to know if someone knows of a format that roughly fits theirs. If there is an identical format, great, if not, I will edit my own, but I would like to start with something relatively close.

The full description of the citation format is below.

Thanks,
David

References should be numbered consecutively in the order in which they are cited in the text, followed by those that are only cited in the figure legends or tables. Please ensure that each item in the reference list has its own number, avoiding joint references (for example, references [32a,32b] should be listed and cited as [32,33] and subsequent references numbered accordingly). Papers accepted as ‘in press’ can be included (but see below). It is possible that the review will be published in advance of the cover date. Please contact your CDM for exact dates if you are concerned about the timing of the publication.
Style
The format for Current Opinion journals is available in Endnote 4.0. Each reference should be typed EXACTLY as shown in the following examples:

JOURNAL
de Alba E, Antoro J, Rico MA, Jimenez MA: De novo design of a monomeric three-stranded anti-parallel -sheet. Protein Sci 1999, 8:854-865.
BOOK
Archer MD, Barber J (Eds): Molecular to Global Photosynthesis. Imperial College Press; 2004.
CHAPTER IN BOOK
Barber J, Kuhlbrandt W: Photosynthesis and photoconversion. In Molecular to Global Photosynthesis. Edited by Archer M, Barber J. Imperial College Press; 2004:3-89.

Number of authors
If more than eleven authors are credited for an article, please list only the first ten, then add et al. Please DO NOT shorten the list of authors before the cut-off of ten. Journal names should be abbreviated in accordance with Index Medicus.
Online journal references
When citing online journal references, please adhere to the convention described above, inserting the digital object identifier (DOI) after the year.
In-text citation
When citing references in the text, please use [square brackets] rather than (parentheses) or superscript1,2 to denote the citations. Please also ensure the citations are numbered and NOT Harvard referencing style (i.e. [Moore 1965; Myrdal 1957]).

adamsmith

nothing super similar I know of.
If you go to the styles repository
http://www.zotero.org/styles
unselect the "show dependent style" box and you can see previews of the styles by hovering over them.
In looking for a similar style, be mostly concerned with the order of things and the included information. Changing (e.g.) titles to bold is very easy.
I'd think that your best guess would be the medical journals as a starting point.

dmk

Hi,

I went ahead and made a format for the Current Opinion journals. It works perfect for me and seems to do everything that is specified in the guide to authors, but there are probably cases I have missed. For the moment, I have placed the style on the following web site:

http://www.ur097.ird.fr/team/dkaplan/personal/current-opinion.csl

but I would like to have it integrated in Zotero. I am not sure how best to do that. A long time ago, I had a zotero subversion account for editing styles, but I think styles have moved since then and I am not sure how to get it in there. Perhaps someone can give me a hand.

This style would need to be linked to by a bunch of dependent styles, one for each current opinion journal:

Current Opinion in Biotechnology
Current Opinion in Cell Biology
Current Opinion in Chemical Biology
Current Opinion in Genetics & Development
Current Opinion in Immunology
Current Opinion in Microbiology
Current Opinion in Neurobiology
Current Opinion in Pharmacology
Current Opinion in Plant Biology
Current Opinion in Structural Biology
Current Opinion in Environmental Sustainability

Thanks,
David

dmk

One other comment - the one thing that I didn't implement was abbreviated journal titles. Last I heard, that wasn't implemented in zotero yet, but if that has changed, please let me know either how to do it or of a style that appropriately implements it.

adamsmith

hey - abbreviated journal titles are somewhat implemented:
Zotero uses the "Journal Abbreviation" field if you use
<text variable="collection-title" form="short"/>

I can upload the style for you if you want to.
Alternatively, you can check out the styles from
https://www.zotero.org/svn/csl
using svn. I don't know if your old account would still be valid - I have never heard anything about changing that, but maybe it did.

dmk

Hi,

The following is already in the csl file:



I imagine that this will make the container-title short if a short version exists, but since that field is rarely filled out, it doesn't work. NOTE: I use container-title and you suggested collection-title. Is this important?

That would be fine by me if you could put it in the database. I will try my subversion account down the road, but I have a feeling it stopped working at some point.

Thanks,
David

dmk

Sorry, the XML was treated like HTML in my last message and became invisible. I meant to say:

<text variable="container-title" suffix=" " form="short"
font-style="italic" />

As for abbreviated journal names, I know there has been quite a bit of discussion on this, but I just want to add my 2 cents. Using the zotero field is at best a patch because some journals want the abbrevation with the periods (i.e., J. Geophys. Res.), while others want them without periods (J Geophys Res). I believe that the latex and endnotes solution is a lookup table. Ideally, one would have a system where zotero would first look in the table and then fall back to the zotero field if no matching journal name was found. The lookup table could be a bit like styles in that it could be broken down into separate files for each discipline and people could just grab the disciplines of interest to keep things manageable.

adamsmith

No, I was wrong on collection-title.
The next version of csl will allow you to toggle the periods on and off, so that part of the issue will be solved.
Some version of a lookup table will be what's eventually included in Zotero/csl, but the developers of csl seem inclined not to push that for the forthcoming csl 1.0
I think the one part that will almost certainly not look like what you say is the "people could just grab the disciplines" part - any solution should include as little as possible hassle on the user side. As Bruce has said on another occasion "things should just work".

Rintze

The next version of csl will allow you to toggle the periods on and off, so that part of the issue will be solved.

Just to clarify things: what will be included in CSL 1.0 is the ability to strip periods from journal abbreviations (adding periods is very tricky without a lookup table, e.g. "Nature Biotech" shouldn't become "Nature. Biotech.", but "Nature Biotech."). Until lookup tables are implemented, it is therefore recommended to store journal abbreviations with periods in your Zotero library. CSL 1.0 styles can then either leave the periods in, or take them out.

dmk

I agree with the "just working" thing. My suggestion was based on the fact that there are a lot of journals and breaking the table into separate files might facilitate multiple people compiling lists of journal abbreviations (much like individual CSL files do) and would make whatever SQL query is used to match journal names to abbreviations work faster if there are fewer journals to search. But these problems can probably be worked around. No matter what, there should be some way for the average user to add journals to the table as new journals appear every day and a centralized zotero-distributed repository could become impossible to keep up to date.

In any case, I am getting things a bit off topic. I tried my subversion account and it worked. I ADDED CURRENT-OPINION.CSL TO ZOTERO'S REPOSITORY. I also added some dependent csl files for all the current opinion journals. For some reason, the generic file appears on the Zotero style page, but the dependent files don't (yet) even though the box "show dependent styles" is checked. Please let me know if I did something wrong.

dmk

By the way, I have noticed that on the Zotero Style Repository, the Current Opinion csl is listed as "invalid". How would I find out why this is and debug the problem?

Thanks,
David

Rintze

You should validate your style:
http://www.zotero.org/support/dev/creating_citation_styles#xml_validation

In your case, the error is in the line:

<text term="no volume" prefix="[" suffix="]"/>

"no volume" isn't a valid term. If you just want to output the text string "no volume", use:

<text value="no volume" prefix="[" suffix="]"/>

dmk

thanks, fixed now.