Help:References

CAZypedia uses the Bibilo extension for creating in-text citations and a reference list. Full details about Biblio can be found at the Biblio page at Wikiomics. The following is a succinct set of instructions for using Biblio with CAZypedia.

The basics

Biblio uses two types of tags to format references. The first is the <cite>...</cite> pair of tags, which specify where a reference should be placed in the text. Within these tags, one places a reference code that points to an entry in the bibliography, specified within the <bibilo>...</biblio> tags.

Example CAZypedia code would look like this:

'''Main text'''
The first structure of a GH1 enzyme was solved in 1995 <cite>REF1</cite>.
Stryer wrote a book about biochemistry <cite>stryertext</cite>.

'''Reference list'''
<biblio>
#REF1 Barrett T, et al. Structure 1995 Sep 15; 3(9) 951-60.
#stryertext Berg, Tymoczko, & Stryer. Biochemistry. New York: W.H. Freeman, 2002.
</biblio>

Which would give this on the actual CAZypedia page:

Main text The first structure of a GH1 enzyme was solved in 1995 [1]. Stryer wrote a book about biochemistry [2]. Reference list Barrett T, et al. Structure 1995 Sep 15; 3(9) 951-60. Berg, Tymoczko, & Stryer. Biochemistry. New York: W.H. Freeman, 2002.

Note that:

• The reference code can be whatever you want (e.g.: REF1, stryertext)
• Whatever follows the reference code is placed verbatim into the reference list - you can put any text here, with any formatting you want.

Citing works using PubMed ID's and ISBN codes

One very slick feature of Biblio is that it can retrive entire references directly from PubMed or a ISBN server. That means you can just enter the PubMed ID (pmid) or ISBN directly after the reference code, and CAZypedia will do the rest for you.

The code for our previous example would then look like this:

'''Main text:'''

The first structure of a GH1 enzyme was solved in 1995 <cite>REF1</cite>.
Stryer wrote a book about biochemistry <cite>stryertext</cite>.

'''Reference list:'''
<biblio>
#REF1 pmid=8535788
#stryertext isbn=0-7167-4954-8
</biblio>

Which would give this on the CAZypedia page:

Main text: The first structure of a GH1 enzyme was solved in 1995 [1]. Stryer wrote a book about biochemistry [2]. Reference list: Barrett T, Suresh CG, Tolley SP, Dodson EJ, and Hughes MA. (1995). The crystal structure of a cyanogenic beta-glucosidase from white clover, a family 1 glycosyl hydrolase. Structure. 1995;3(9):951-60. DOI:10.1016/s0969-2126(01)00229-5 |

Note here that all the references are automatically linked to various external web sources.

Using EndNote for formatting references in CAZypedia

It is anticipated that many CAZypedia editors will be regular users of the reference management software EndNote. EndNote can be used to both insert the in-text citations (e.g. <cite>REF1</cite> and format content to go in the <biblio>...</bibilo> tags.

The following is a step-by-step guide to using EndNote to format text to cut and paste into CAZypedia.

1. Download the CAZypedia EndNote style, CAZypedia.ens, from this link (http://www.biotech.kth.se/cazypedia/CAZypedia.ens) and save the file in your EndNotes styles folder (e.g. C:\Program Files\EndNote 9\Styles).
2. Write your CAZypedia entry in MS Word, inserting references via EndNote as usual.
3. Format your entry using the CAZypedia style (CAZypedia.ens)
   • Note that all references in the bibliography will now start with "#refN, where N is the reference number and that these numbers will be referenced in the text with <cite>refN</cite>.
4. Copy and paste your main text into a CAZypedia page edit window.
5. Copy and paste your bibliography under a heading titled "References".
6. Add the tag <biblio> before the bibliography.
7. Add the tag </biblio> after the bibliography.
8. Preview and save your entry.