Support for CiTO (Citation Typing Ontology)

[RichardJActon]

I think support for CiTO would be a really interesting addition to the bibliographic features in Quarto. It lets you document the way in which you are citing a source so that you can see for example that an article has been cited many times because people disagree with it's conclusions instead rather than because people agree with it.

It'd be cool to be able to have autocomplete prompts for the citation ontology terms when you are adding a citation in the visual editor in RStudio and have the terms appear in front of the citations in the bibliography & hover-over tooltips

I'm not sure how you'd go about implementing it though.

• website: http://www.sparontologies.net/ontologies/cito
• Original reference: https://doi.org/10.1016/j.websem.2012.08.001
• Recent example of adoption:
  • https://doi.org/10.1186/s13321-020-00448-1
  • https://www.biomedcentral.com/collections/cito
• Docs: https://sparontologies.github.io/cito/current/cito.html

[cscheid]

We've talked about using shortcodes for this sort of stuff (I'd love to do it too. I'm a former academic from a field that does not have a rich citation culture like, for example, law does, and I agree that we need more of this)

With that said, a feature like this is at least 12-18 months away in terms of dependencies on other features that are on our plans. So, nothing concrete to report in the short-to-medium term.

[egonw]

To fully integrate CiTO in the citation ecosystem, I think it should be made part of CSL

Yes, agreed. But we have a bit of a chicken-and-egg situation here. It won't all happen in one step, and if no one makes a step, not one else will either. I will be excited about any current form of implementation. We have to start somewhere.

[nichtich]

Yes thanks for the initiative and for building a working prototype! Extending CSL is no easy task, so the approach to first show it should and can be done, then encourage adoption and discuss with community of interest (Pandoc, Quarto...) and finally get it implemented as standard feature seems promising!

[RichardJActon]

Thanks @nichtich that's very useful to know. So with the current pre/suffix features in pandoc we could adopt the convention of something like this [@foo [cito:citesAsAuthority] [cito:agreesWith]; @bar] based on the syntax adopted by Journal of Cheminformatics to represent the CiTO terms in their bibliographies (e.g. https://jcheminf.biomedcentral.com/articles/10.1186/s13321-020-00448-1#Bib1) in their trial with @egonw. But different from their syntax for adding a citation in the body of the text: https://jcheminform.github.io/jcheminform-author-guidelines/cito-guidelines/markdown.html and placing the CiTO terms in the .bib notes. Though as you say this syntax might want some further discussion.

One of the complications I can see arising from having the CiTO terms in the .bib file is I might want to cite the same source from a .bib file with different CiTO terms in different documents with the same set underlying bibliography managed by Zotero or similar. Putting them in the suffix in pandoc would at least not cause this problem... though I'm not sure what happens if you cite the same thing in more than one place in the same document with different pre/suffixes I'll have to check that.

A plugin/extension that does [@foo [cito:<tab auto-completion for cito terms>] in VScode &/or RStudio visual mode could help out with adoption of this approach if we wanted to adopt something like this as an semi-formal convention for CiTO in pandoc.

Though yes adoption in CSL would be better for the wider citation ecosystem beyond pandoc.

I think I'll try this approach out in the ebook I'm writing in Quarto atm and see how it turns out.

[RichardJActon]

Interesting I tried this out in my book and it is not doing quite what I thought it would. The suffix is in-line at the point of the citation and not in the bibliography. My interpretation of the pandoc docs was that this wouldn't be visible in-line and would be in the bibliography.

[egonw]

Egon writes Support in pandoc of CiTO annotations dates back to 2017 [@usesMethodIn:Krewinkel2017] but this is misleading.

@nichtich, I reworded this now to: Support of CiTO annotations in the pandoc platform via extensions dates back to 2017 [@usesMethodIn:Krewinkel2017].

[egonw]

A summary of the Journal of Cheminformatics CiTO Pilot has been published now:
https://jcheminf.biomedcentral.com/articles/10.1186/s13321-023-00683-2

The Pilot has ended and the matching Editorial is here: https://jcheminf.biomedcentral.com/articles/10.1186/s13321-023-00684-1

[RichardJActon]

Thanks for the update @egonw, shame it was discontinued though I can understand why from your editorial. Seems like improving the tooling so it's not a nightmare to actually use would be a major help towards cracking that chicken & egg problem.

[egonw]

Actually, the Pilot is over. The journal will continue to accept articles with CiTO annotation (and do their best). Btw, the decision was not mine (I am not an editor anymore).

[cderv]

As I don't think it was share here (or couldn't find it) but seems directly related to CiTo support with Pandoc, there is Lua filter available for that, that is organized in a way it can be used as a Quarto extension https://github.com/pandoc-ext/cito

Disclaimer: did not try it yet, and don't know much about it. I just wanted to share in this discussion that it exists