Preprint formatting for Molecular Biology & Evolution

whenriques
edited January 12, 2024
Hi there,

I'm trying to troubleshoot a bibliography in the Molecular Biology & Evolution style in Zotero. The journal's guidelines currently state for preprints that preprints should be referred to as unpublished data, but I have recently received feedback that my preprint citations should be formatted other than the official submission guidelines on the website.

Current formatting requested by MBE (https://academic.oup.com/mbe/pages/General_Author_Guidelines):
Pre-prints: Campodonico W, Black HH, Lau CI, Whiteley AM, unpublished data, https://www.biorxiv.org/content/10.1101/2023.02.03.527044v1, last accessed May 5, 2023

Current formatting from Zotero's MBE style:
Campodonico W, Black HH, Lau CI, Whiteley AM. 2023. The gag-like gene RTL8 antagonizes PEG10-mediated virus like particles in humans. :2023.02.03.527044. Available from: https://www.biorxiv.org/content/10.1101/2023.02.03.527044v1

Requested formatting from reviewer:
Campodonico W, Black HH, Lau CI, Whiteley AM. 2023. The gag-like gene RTL8 antagonizes PEG10-mediated virus like particles in humans. bioRxiv (italics) :2023.02.03.527044. Available from: https://www.biorxiv.org/content/10.1101/2023.02.03.527044v1

What fields would you recommend editing in the MBE .csl file so that bioRxiv appears in Italics after the title and year of the paper? Currently, there is no reference to either repository or library catalog macros in the MBE .csl file. I tried copying the journal macro:

<macro name="journal">
<text variable="container-title" form="short" font-style="italic"/>
<choose>
<if variable="URL">
<text term="internet" prefix=" [" suffix="]" text-case="capitalize-first"/>
</if>
</choose>
</macro>


And replacing with:

<macro name="repository">
<text variable="container-title" form="short" font-style="italic"/>
<choose>
<if variable="URL">
<text term="internet" prefix=" [" suffix="]" text-case="capitalize-first"/>
</if>
</choose>
</macro>

But this did not seem to work.

Any suggestions would be welcome!
  • adamsmith
    I can't see your code exceprts (use HTML <code> tags for that) but FWIW, the relevant item type for preprint is article
  • whenriques
    Wow, thanks for the quick response.
    I was trying to replace

    <macro name="journal">
    <text variable="container-title" form="short" font-style="italic"/>
    <choose>
    <if variable="URL">
    <text term="internet" prefix=" [" suffix="]" text-case="capitalize-first"/>
    </if>
    </choose>
    </macro>

    with:

    <macro name="repository">
    <text variable="container-title" form="short" font-style="italic"/>
    <choose>
    <if variable="URL">
    <text term="internet" prefix=" [" suffix="]" text-case="capitalize-first"/>
    </if>
    </choose>
    </macro>

    but I didn't see any changes in the Style editor.
  • whenriques
    I don't see an article item type in the MB&E .csl file - am I looking in the wrong place? What would I change in the .csl to get bioRxiv to show up in italics after the title?

    Thanks!
  • whenriques
    As a preprint item in my Zotero library, bioRxiv shows up in the "Repository" and "Library Catalog" fields.

    I tried editing the bibliography portion of the .csl to include either one of those:

    <bibliography hanging-indent="true" et-al-min="11" et-al-use-first="10">
    <sort>
    <key macro="author"/>
    <key macro="year-date"/>
    </sort>
    <layout>
    <group suffix="." delimiter=". ">
    <text macro="author"/>
    <text macro="year-date"/>
    <text macro="title"/>
    <text macro="repository"/> ### Added this line, no change in bibliography
    <text macro="library-catalog"/> ### Also tried adding this line, no change
  • adamsmith
    You need to define the macros that you call... just changing their name or adding undefined macros won't do anything (other than potentially break the style). The reason you're not seeing article in the CSL style is that it just doesn't account for preprints -- you'd have to edit it to do so.
  • whenriques
    I updated the MB&E .csl file to include preprints.
    This item types table was useful: https://aurimasv.github.io/z2csl/typeMap.xml

    I'm not super familiar with editing .csl files, but I think this is what's going on: The preprint location can be accessed through the Zotero field "Repository", which is mapped to the CSL item type "publisher"

    I defined a new macro

    <macro name="preprint">
    <group delimiter=" " prefix=" " suffix=".">
    <text variable="publisher" font-style="italic"/>
    </group>

    In the "bibliography" section of the .csl file, I added the following else-if statement before the final else:

    <else-if type="article" match="any">
    <text macro="preprint"/>
    </else-if>



    Old preprint format: Campodonico W, Black HH, Lau CI, Whiteley AM. 2023. The gag-like gene RTL8 antagonizes PEG10-mediated virus like particles in humans. :2023.02.03.527044. Available from: https://www.biorxiv.org/content/10.1101/2023.02.03.527044v1

    New format: Campodonico W, Black HH, Lau CI, Whiteley AM. 2023. The gag-like gene RTL8 antagonizes PEG10-mediated virus like particles in humans. bioRxiv. Available from: https://www.biorxiv.org/content/10.1101/2023.02.03.527044v1

    I saved this as a new style (so as not to break the current MB&E style), called molecular-biology-and-evolution-biorxiv-modified.csl, and validated it here: https://validator.citationstyles.org/

    @adamsmith - thanks for being so responsive!
  • whenriques
    Full CSL file here: https://github.com/ricosuavee/MBE-modified-csl
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