This would be useful to convert manuscripts written with a word processor with embedded citations in the format (Author1 YEAR1, Author2 YEAR2). You can copy&paste the text to an editor save the file and convert citations to [@Author1YEAR1; @Author2YEAR2]

For use with my own tools, I have created a number of markup elements which are very useful for scientific publishing -- mostly notable, author which is obvious and cite which we use to generate in text citations. This very thin piece of semantics is very useful and can be made to percolate through to the HTML layer, so it's easy to extract.

In one sense, it doesn't matter what the syntax is, but if it is shared, then it can minimize the need for tooling support, as well as increasing familiarity for authors.

For my usage, I simply make use of shortcodes like so: [author]Phillip Lord[/author]. A shared syntax, or failing that a shared vocabulary for this sort of markup would be a good thing.

The group is probably fully aware of this one, but I'll point it out just in case:

http://zotero-odf-scan.github.io/zotero-odf-scan/

What the tool does is to implement drag-and-drop markers that provide (a) minimal human-readable cite details; (b) slots for adding prefix, suffix and pinpoint details; and (c) a machine-readable identifier for the full underlying metadata of the cited item.

The markers can be added to any text document, including Markdown documents. If the text is later converted to ODF format, the markers can be converted into fully linked, dynamic Zotero citations for final formatting.

There are compromises, of course: the tool is specific to Zotero; the markers link to a specific (set of) Zotero database(s); and conversion to ODF is a necessary precondition to producing final, formatted citations. In addition, the syntax used (with fields separated by pipe characters, for ease of parsing) may be awkward for some text processors to handle (specifically reStructuredText, where pipe characters are used in unrelated markup).

On the other hand, in terms of workflow it is hard to beat drag-and-drop for ease of use, and the tool is agnostic to the authoring environment -- if you can paste text into it, you can use it with Zotero.

Happy to answer questions or collab if there is interest.

When using the command:

$git clone [email protected]:karthik/markdown_science.git

The terminal answer:

Cloning into 'markdown_science'...
Permission denied (publickey).
fatal: Could not read from remote repository.

Please make sure you have the correct access rights
and the repository exists.

I suggest to rather use:

$git clone https://github.com/karthik/markdown_science.git

In this case, it seems to work.

Cheers!

Guillaume

This link is dead http://sourceforge.net/p/retext/home/ReText/

eLife articles are provides as markdown when using the "text/plain" content header:
curl -H "Accept: text/plain" http://elife.elifesciences.org/content/1/e00047