OpenWetWare:Software/Extensions/Biblio

Description

The Biblio extension for MediaWiki written by Martin Jambon allows users to define and cite bibliographic entries by their key. It also downloads bibliographic references from PubMed and formats them using only the PubMed identifier (PMID). Similarly, books can be cited using their ISBN. See Biblio page for installation instructions and an example of use. OpenWetWare is currently using version 0.7.

For up to date install details, see http://www.mediawiki.org/wiki/Extension:Biblio

How to use

You can easily add citations by typing <cite>Goldbeter-PNAS-1981 Jacob-JMB-1961 Ptashne-Genetic-Switch Website</cite> which gives [1, 2, 3, 4].

To insert a list of references type

<biblio>
#Goldbeter-PNAS-1981 pmid=6947258
#Jacob-JMB-1961 pmid=13718526
// you can even leave a comment on a paper
#Ptashne-Genetic-Switch isbn=0879697164
#Website http://openwetware.org
</biblio>

which gives

1. Goldbeter A and Koshland DE Jr. An amplified sensitivity arising from covalent modification in biological systems. Proc Natl Acad Sci U S A. 1981 Nov;78(11):6840-4. DOI:10.1073/pnas.78.11.6840 |
2. JACOB F and MONOD J. Genetic regulatory mechanisms in the synthesis of proteins. J Mol Biol. 1961 Jun;3:318-56. DOI:10.1016/s0022-2836(61)80072-7 |

   you can even leave a comment on a paper

3. ISBN:0879697164

4. http://openwetware.org

Notes

1. Cite keys cannot contain either periods (.) or colons (:). They can contain dashes.
2. Some references, particularly old ones will yield references with odd formatting or absent information. (See the Jacob 1961 reference above for an example). This is due to the information in the relevant database (like Pubmed). If this bothers you, you can replace the call to the pubmed data with a correctly formatted citation. (e.g. replace " #Jacob-JMB-1961 pmid=13718526" with " #Jacob-JMB-1961 Jacob F and Monod J. Genetic regulatory mechanisms in the synthesis of proteins. J Mol Biol 1961 Jun; 3 318-56. ") This does "break" the all pubmed links, however. This feature can also be useful if your reference is not in the Pubmed or ISBN databases.