Ten days ago Information Standards Quarterly (ISQ) published a special issue on altmetrics.

According to the description on the Citation Style Language (CSL) website, CSL is an open XML-based language to describe the formatting of citations and bibliographies . We use reference managers such as Zotero , Mendeley , or Papers to format our references in manuscripts we submit for publication, and underneath a CSL processor such as Citeproc-js -

Now that I can automatically import my publications from my ORCID profile and display them in this blog, I also want to visualize them. I have started with d3.js code that displays the number of publications per year - using the list of my publications in Citeproc JSON format.

The standard local file formats for bibliographic data are probably bibtex and RIS. They have been around for a long time, and are supported by all reference managers and many other tools and services.

Open Researcher & Contributor ID (ORCID) provides a persistent identifier for researchers and lets them claim their research outputs in the ORCID Registry. I have been involved with ORCID since early 2010 and I am happy to see that nine months after launch 200,000 researchers have signed up for the service, and the organization has more than 70 member organizations.

A few weeks ago Kafkas et al. (2013) published a paper looking at current patterns of how datasets o biological databases are cited in research articles, based on an analysis of the full text Open Access articles available from Europe PMC. They identified data citations by: Accession numbers available in articles as publisher-supplied, structured content; Accession numbers identified in articles by text mining;

Scholarly documents often need metadata that describe them: typically author(s), title and location (DOI or URL), but possibly many other things. For some metadata it makes sense to store them in the document text, e.g. as is typically done for citations. The problem is that this can make it hard to make the metadata machine-readable.

This paper in markdown format was written by Ethan White et al. The markdown file and the associated bibliogaphy and figure files are available from the Github repository of the paper. I used this version, an earlier version was published as PeerJ Preprint. Special thanks to Ethan White for allowing me to reuse this paper.

After the post last week and the crazy discussion that followed I would understand that you feel you have heard enough about citations in markdown. But I had the feeling last week that something was still missing, and I have done some more thinking.

In the comments on Monday’s blog post about the Markdown for Science workshop, Carl Boettiger had some good arguments against the proposal for how to do citations that we came up with during the workshop. As this is a complex topic, I decided to write this blog post. Citations of the scholarly literature are an essential part of scholarly texts and therefore have to be supported by scholarly markdown.