CiTO annotation with Markdown

Author: Egon Willighagen, https://orcid.org/0000-0001-7542-0286
License: CC-BY 4.0 International

This JCheminform Markdown template ready for use as option to submit articles to the journal. The setup is similar to that of LaTeX and you need a local processor (Pandoc) to convert PDF (for preprint servers) or a Word .docx document for submission to the journal [0].

One important different, is that this template annotates the citation at citation level, and not in the bibliography. Therefore, the CiTO annotation must not be included as notes in the .bib bibliography file. And entry has the normal form, and looks like:

  author  = {Koonin, E V and Altschul, S F and P Bork}, 
  title   = {BRCA1 protein products: functional motifs}, 
  journal = {Nat Genet}, 
  year    = {1996},
  volume  = {13}, 
  pages   = {266-267}

In the Markdown, a citation is made by adding an \@someBibTeXKey. To add the CiTO intention annotation, you would replace this with for example \@uses_method_in:someBibTeXKey. The template has examples.

Initial results indicate that it works too in RStudio.


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