How to escape a ":" in a bibliographic reference with pandoc?

Question

Basically, a have a bibtex file that gets automatically generated by Zotero 4.0.17 and I am using it to generate the bibliography in a markdown file. The tools used are pandoc-1.12.1 and pandoc-citeproc-0.2 .

This is the markdown file named notes.md

# State of the art

 - Wikipathways [@pico_wikipathways\:_2008]

# Bibliography

<!-- TODO is this usefull?
bibliography::research.bib -->
<!-- \bibliography{research} So that RefTeX knows about the bibliography -->

This is the bibtex file named research.bib

@ARTICLE{pico_wikipathways:_2008,
 author = {Pico, Alexander R and Kelder, Thomas and van Iersel, Martijn P and Hanspers, Kristina and Conklin, Bruce R and Evelo, Chris},
 title = {{WikiPathways:} Pathway Editing for the People},
 journal = {{PLoS} Biol},
 year = {2008},
 volume = {6},
 pages = {e184},
 number = {7},
 month = jul,
 abstract = {{WikiPathways} provides a collaborative platform for creating, updating, and sharing pathway diagrams and serves as an example of content  curation by the biology community.},
 doi = {10.1371/journal.pbio.0060184},
 keywords = {\_tablet},
 shorttitle = {{WikiPathways}},
 url = {http://dx.doi.org/10.1371/journal.pbio.0060184},
 urldate = {2013-11-20}
}

And this is the command I run

pandoc --bibliography=research.bib notes.md -o notes.md.pdf

I was expecting everything to go fine but the presence of a : character makes the generation of a PDF succeed with the following error

pandoc-citeproc: reference pico_wikipathways not found

The PDF will have an incorrect bibliography.

Any idea how to escape the : in notes.md so that the bibliographic reference gets recognized?

Answer 1

You'll have to change your key. Pandoc's citation key parser doesn't currently allow more than one non-alphanumeric symbol in a row, so the key with :_ fails. Also, don't use a backslash before the : in a citation key.

Answer 2

It looks like this issue has been fixed as of version 1.12.3. Uninstall your current version using

sudo rm -f /usr/local/bin/pandoc /usr/local/doc/pandoc-1.9.4.2 /usr/local/share/man/man1/pandoc.1.gz /usr/local/share/man/man5/pandoc_markdown.5.gz /usr/local/share/pandoc-1.9.4.2

then reinstall pandoc and you should be good to go.