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?
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.