Markdown

• JupyText: Jupyter notebooks as Markdown documents
• Generate Google Slides from Markdown
• CriticMarkup - plaintext editing markup for humans

R Markdown

• https://github.com/rstudio/rmarkdown
• R Markdown: The Definitive Guide by Yihui Xie, J. J. Allaire and Garrett Grolemund (2020)
• Authoring books and technical documents with R Markdown by Yihui Xie (2021)
• Create blogs and websites with R Markdown
• Writing reproducible geoscience papers using R Markdown, Docker, and Gitlab by Daniel Nüst, Vicky Steeves, Rémi Rampin, Markus Konkol, Edzer Pebesma (2018)

pandoc

• https://pandoc.org/extras.html
• https://github.com/LaurentRDC/pandoc-plot
• A pandoc-based layout workflow for scholarly journals by Piero (2018)

Quarto

Quarto, by RStudio, sorry, Posit, a new scientific and technical publishing system.

Something to consider, especially if you are new to the field and aren't already invested in the earlier systems.

Adopted by the Journal of Cheminformatics (Aug 2020)

• First adoption by a scientific journal announced in editorial by Egon Willighagen
• Blog post by Willighagen on the same subject
• CiTO updates (another blog post by WIllighagen)
• Citation Typing: progress but we need more uptake
• CiTO updates #4: annotations in datasets
• FAIR blog-to-blog citations
• CiTO for blog citations

BioMedCentral on the CiTO Pilot (seems to only include Journal of Cheminformatics, for now).

Usage of CiTO is spreading. This page keeps track of CiTO annotation in Wikidata.

What about adoption by tools?

Willighagen offers rudimental instructions for BibTeX (but probably only suitable for Journal of Cheminformatics at the moment) as well as for Google Docs + Zotero (not really working) in this github repo.

Markdown template with CiTO for the Journal of Cheminformatics.

The best tool with support for CiTO: pandoc scholar

Pandoc Scholar appears to be our best bet at the moment if we want to use CiTO in our manuscripts.

Krewinkel A, Winkler R. 2017. Formatting Open Science: agilely creating multiple document formats for academic manuscripts with Pandoc Scholar. PeerJ Computer Science 3:e112 https://doi.org/10.7717/peerj-cs.112

Other notes

It looks like support for CiTO should happen at the document processing tool stage, and not in our reference managers (Zotero, etc.).
I wonder if something like Biber/BibLaTeX should add support for CiTO, or if that's the wrong abstraction level.

Martin Fenner has a blog post from 2011 (Google Cache) where he shows how to use CiTO with a Wordpress plugin, unfortunately both the post and the plugin appear to have gone offline.

Recently, ORCID promoted Scite_ on their blog. But Scite describes itself as a Brooklyn-based startup (I assume that's code for venture capital-backed), although it also acknowledges funding from public institutions such as NSF and NIH. Scite uses "a deep learning model" to identify "citations that display the context of the citation and describe whether the article provides supporting or contrasting evidence" (so they really only classify the citation as supporting or contrasting). In contrast to Scite, CiTO is an open standard that anyone can build on. Although Scite is currently much glitzier and fancier than anything CiTO can provide, we should encourage everyone to use CiTO (if they care about citation classification).