Creating Citation Styles

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Leon

08 Mar, 2011 11:45 PM

Papers 2 does not include the citation format for certain Journals. Is there a way of creating citation styles or importing the citation styles?


Edit from Mekentosj with more details below:

All the styles available with Papers are listed in the style browser that you can access as follows:

  • Go into the Papers Preferences...Manuscripts
  • Click on the popup menu 'Favorite Styles' and select 'More Styles...'
  • This will open the Style Browser

Note that many journals actually point in their instructions to authors to some generic standard styles like 'Vancouver', 'APA' or 'Chicago' to be used for their publications. That's often a good way to get the style you want.

Now, if you find a style that's close to what you need, but not quite there, we'd be very happy to apply the necessary tweaks and make it work for you. In this case, please show us an example of the wrong format and what you would expect it to be (both the in-text cite and the bibliography entries). In such case, please be sure to also give us a link to the instruction to authors so I can add this link to the style as well for reference.

If you are curious, we made it possible to overwrite the styles present in Papers2, or to add more styles, by dragging CSL files into Papers, or adding them to the 'Styles' subfolder that you will find in your Papers2 library folder. This however requires you to edit the XML files that are used by CSL, and to read the CSL specifications. It's not for the feint of heart, but if you are comfortable with XML and have a good text editor like TextMate or similar, then it's not out of reach. The advantage of CSL is that it is used by other applications, it has been developed in the open by many others before Papers adopted it, and there is a lot of material online about it.

Here is more info on our Knowledge Base:
http://support.mekentosj.com/kb/pro-tips/pro-tip-adding-additional-...

Here is the CSL reference:
http://citationstyles.org/downloads/specification.html

And here are the main repositories for CSL stylesheets:
http://www.zotero.org/styles
https://github.com/citation-style-language/styles

Finally, if you create a new style and submit it to the CSL repository, you can claim a free Papers2 serial: http://support.mekentosj.com/kb/read-write-cite/a-serial-for-a-style

  1. 2 Posted by 153957 on 08 Mar, 2011 11:47 PM

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    I have not found the answer to this either, I hope it will be made possible.

  2. 3 Posted by Martin Brazeau on 09 Mar, 2011 12:53 PM

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    I crossposted this same question in the wrong forum.

  3. 4 Posted by Joshua Jendza on 09 Mar, 2011 10:07 PM

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    My guess would be that you could manually locate where papers stores the default styles and then simply add a style file created in another software package like Sente, Endnote, et al.

    Try: Applications/Papers2/Contents/Resources/Styles/Default
    (you'll need to right click on the Papers2 application and select "Show Package Contents") The file should have a .csl extension.

    I tried making my own style description in Sente, but never ended up getting the full software for various usability reasons. Hopefully I can find the style document and drop it into papers2.

  4. 5 Posted by Christophe Leterrier on 09 Mar, 2011 10:20 PM

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    I also created a discussion about that, asking if support of custom .csl style is possible.

  5. 6 Posted by Martin Brazeau on 10 Mar, 2011 07:50 AM

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    Thanks Joshua,
    I really should have thought of that.

    There is this online .csl editor: http://csleditor.quist.de/csleditor/show/1/example-citation-style

  6. 7 Posted by Martin Brazeau on 10 Mar, 2011 09:15 AM

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    Okay, I can successfully create a style for Biological Journal of the Linnean Society, but I can't get Papers 2 to load it. It won't show up on the menu. I wonder if there's a Papers-specific .csl header or something?

  7. 8 Posted by Christophe Leterrier on 10 Mar, 2011 09:57 AM

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    I opened the nature.csl file inside Papers 2. It is the exact nature.xml file found in Zotero's style repository (http://www.zotero.org/styles/nature). So I guess there is no special header, but maybe styles loading is not just done by scanning the folder. You can try to put your style in Styles/Additional/ and see if you can then add it in the Preferences. Are you sure you csl style is functional (did you test it in another software like Mendeley or Zotero) ?

  8. 9 Posted by Martin Brazeau on 10 Mar, 2011 10:07 AM

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    Yeah, I also noticed that they are all Zotero files.

    I discovered that that editor I linked to does not read Zotero files, so probably you're right: there might be a problem with my file.

    However, it also appears to be the case that styles aren't loaded simply by scanning the folder, as you say. I experimented with moving one of the styles to another directory. The style's name remains in the list when you navigate to it under Preferences, but an error appears in the style preview. So, it appears that simply adding styles to the folder won't work.

    However, as a workaround, for now, one might try altering one of the styles that you would never use. I have about 1400 of those . . .

  9. 10 Posted by Christophe Leterrier on 10 Mar, 2011 10:11 AM

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    I too could'nt get a new style to show up in the Preferences styles list, using a custom .csl file (that works in Zotero) in Papers2.app/Contents/Resources/Styles/Additional/

  10. 11 Posted by Christophe Leterrier on 10 Mar, 2011 10:13 AM

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    All we need really in Papers 2.1 is a way to manually add .csl files from the preferences. In the meantime, modifying existing ones will do I guess.

  11. 12 Posted by oscarbrouwer on 10 Mar, 2011 10:15 AM

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    "However, as a workaround, for now, one might try altering one of the styles that you would never use. I have about 1400 of those . . "

    @ Martin; And how would you do that; altering a style?

  12. 13 Posted by Christophe Leterrier on 10 Mar, 2011 10:21 AM

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    styles are csl files that are in fact xml files. You can open them with a text or xml editor and modify them. You'll have to look at the CSL syntax explained here :
    http://citationstyles.org/downloads/specification.html

  13. 14 Posted by Carleov on 10 Mar, 2011 10:23 AM

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    I back the point that papers2 should support citation formats that are compatible with other programs like Zotero.

  14. 15 Posted by charles on 10 Mar, 2011 10:25 AM

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    Hi all,

    I am sorry we are still struggling with support, so I can't expand too much on that. We'll have some more info on that in the coming weeks. Here is a boilerplate answer I can give you for now.

    We made it possible indeed to overwrite the styles present in Papers2, or to add more styles (the exact way to do this will be documented after the release). This however requires you to edit the XML files that are used by CSL, and to read the CSL specifications. It's not for the feint of heart, but if you are comfortable with XML and have a good text editor like TextMate or similar, then it's not out of reach. The advantage of CSL is that it is used by other applications, it has been developed in the open by many others before Papers adopted it, and there is a lot of material online about it.

    Here is the CSL reference:
    http://citationstyles.org/downloads/specification.html

    And here is the official repository for CSL stylesheets:
    https://github.com/citation-style-language/styles

    For reference, the styles currently shipping with Zotero are similar to the above, but they are still at version 0.8.1, so you should not use these with Papers, but that gives you an idea of the scope of the styles:
    http://www.zotero.org/styles

  15. 16 Posted by oscarbrouwer on 10 Mar, 2011 02:29 PM

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    'but if you are comfortable with xml' -> you got me there. (have my hands full with my medical research as it is haha)

    If anyone happens to know how to do this, and edits one of the styles to include abbreviated journal names and post it here, that would be highly appreciated ;-)

  16. 17 Posted by charles on 10 Mar, 2011 02:33 PM

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    and edits one of the styles to include abbreviated journal names

    I have come to the conclusion that this is in fact a bug in Papers2, we don't respect journal abbreviations. I am sorry about that, we'll have to address this limitation in a future update.

  17. 18 Posted by oscarbrouwer on 10 Mar, 2011 03:50 PM

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    Well, that at least prevents me from spending more time to find a solution ;-).
    All we can do, I guess, is be patient! Untill then, we still have endnote!

    Judging all the comments on the forum, I really hope the first update will atleast include these citation bug fixes and maybe include some custom editing of citation styles. It would be a pity if the use of such a genius function as the magic manuscript/citations function would be hampered by such a 'trivial' detail.

    So for now; papers 1 and endnote will do for me. I'll be regularly checking if there's an update the coming weeks!

  18. 19 Posted by charles on 10 Mar, 2011 04:02 PM

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    maybe include some custom editing of citation styles

    This one will not be coming soon, I am afraid. But we will be pushing fixes to the CSL styles as much as possible based on the feedback (in addition to our own Papers2 bugs).

  19. 20 Posted by Tom Flint on 10 Mar, 2011 04:38 PM

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    Thing is,

    I was all up for buying Papers 2 to get the ability to cite but we use a of APA where a single author is cited in text as Author (date). Is there a style that already does this? I am just about to construct a 50 page report and if I can't use Papers 2, I'll have to use EndNote (yuk)

  20. 21 Posted by charles on 10 Mar, 2011 05:18 PM

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    Tom: not sure, did you check the style browser in Preferences...manuscripts...Favorite styles...Edit List?

  21. 22 Posted by tom flint on 10 Mar, 2011 05:23 PM

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    I went through some on the list but without trying each one there's no way of telling. I've found some CSL styles created by other British unis and they're usually in the format i need, I'm now trying to see where Papers2 stores these so I can add one or two to try them out.

  22. 23 Posted by charles on 10 Mar, 2011 05:39 PM

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    I'm now trying to see where Papers2 stores these so I can add one or two to try them out.

    Adding them to your Papers2 libray Styles subfolder should work, but be sure to quit/start the app for it to be taken into account.

    If that does not work, check the console log, that might give us a clue. Note that this is not yet officially supported, as this has not been fully tested by us. This is definitely something we thought about and want to fully support, but it needs more testing.

  23. 24 Posted by oscarbrouwer on 10 Mar, 2011 05:56 PM

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    @ charles; thats too bad!

    However; if the bugs in the citation styles as they are set up now are fixed, and if it will be possible to use/import citation style files provided on the journals websites that will be fine too!

    for instance, if you check any article in the journal of nuclear medicine; citing works like this;

    in text: (27)

    reference:
    27. Vermeeren L,Valds Olmos RA, Meinhardt W, et al. Value of SPECT/CT for detection and anatomical localization of sentinel lymph nodes before laparoscopic sentinel node lymphadenectomy in prostate carcinoma. J Nucl Med. 2009;50:865–870.

    If I use the new magic manuscript tool and select the journal of surgical oncology style; paste the same citation and format bibliography in a Word 2011 docx i get:

    In text: (27) (not italic, i know, that you know of this bug ;-))

    reference:
    1. Vermeeren L, Olmos RAV, Meinhardt W, Bex A, van der Poel HG, Vogel WV, e.a. Value of SPECT/CT for detection and anatomic localization of sentinel lymph nodes before laparoscopic sentinel node lymphadenectomy in prostate carcinoma. Journal of nuclear medicine : official publication, Society of Nuclear Medicine. 2009 jun. 1;50(6):865-870.

    Which is almost perfect, except for the abbreviation of the journal lacking, the not being in italic, and the appearance of publication type, society, and month of publication (the last three things should not be cited).

    First conclusion; the citation style for the JNM is obviously incorrect (as are many styles in papers 2).

    Secondly: i can't find a style that would exclude the ': official publication, Society of Nuclear Medicine' part.

    Furthermore, the italic part, well lets not talk about that anymore ;-).

    So, enough said! hope this helps.

  24. 25 Posted by oscarbrouwer on 10 Mar, 2011 05:58 PM

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    i know, i am kinda repeating myself, sorry for that; it just seems strange to me that journal citation styles don't match with the journal citation styles in the journals themselves!

  25. 26 Posted by charles on 10 Mar, 2011 06:07 PM

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    Oscar: regarding the journal name, can you check what is the name in the Periodicals section of Papers2 in your case?

  26. 27 Posted by oscarbrouwer on 11 Mar, 2011 12:41 PM

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    @ charles!

    You are right! the journal name in this case in my periodicals tab is:
    "Journal of nuclear medicine : official publication, Society of Nuclear Medicine."

    So seems like I was using a bad example haha, so that explains that part, sorry!

    Only thing thats left is the publication month being included in too many styles, the lack of italic format, and the abbrevated journal names!

    Thanks again, im impressed by how quickly and adequately and patiently you guys are responding to all the, sometimes too negative, comments posted here. Good luck with the working day and night part! Take some time to relax too ;-)

  27. 28 Posted by tom flint on 11 Mar, 2011 12:47 PM

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    Resolution!

    I can't get the style I want in Papers but after discussion with a colleague, we both agreed that using any in text citation tool was asking to be annoyed. What I love in Papers2 is that I can put the papers I'm citing into a collection and then export that selection as a formatted bibliography in Word. That's how I'm rolling and now have my card ready to purchase.

    The whole in text citation thing is a nightmare for every software on the market, I wish you luck with being the people who resolve it.

  28. 29 Posted by oscarbrouwer on 11 Mar, 2011 01:30 PM

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    @ tom flint:

    "export that selection as a formatted bibliography in Word".

    what do you mean, how?

  29. 30 Posted by Tom Flint on 11 Mar, 2011 02:16 PM

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    Ok so you have your collection selected, then go to
    File>Export>ReferenceList
    Choose
    Export: Selected Collection
    Style: (your style)
    File Format: Word

    Choose destination and name

    Then choose Export

    job's a good 'un

  30. 31 Posted by Pete on 19 Mar, 2011 06:49 PM

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    I would just like to chime in to Charles and the other mekentosj guys that as a papers 1 user who is looking to upgrade in order to get the citation capabilities of 2, the bug about not respecting journal name abbreviations is really a killer and I hope that it's at the top of your list for things to fix.

    Thanks. We all really appreciate the speed with which you guys released 2.0.1 and hope that you continue doing these minor releases to get the little bugs worked out while working on the hard stuff.

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