Help:References

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

The basics

In some sense, Biblio works a bit like the software program EndNote, in that it automatically numbers the bibliography based on the order that citations appear in the text. Also like EndNote, Biblio relies on two pieces of information to make this happen:

1. a bibliography section containing a list of the references you would like to cite in the text, and,
2. An in-text citation, which "calls" the reference from the bibliography.

The bibliography

This section is placed at the bottom of the page, between the <biblio>...</biblio> tags, under the heading Reference list. Each reference begins on a new line with a hash sign (#), followed by a citation tag, and finally the reference itself.

For example, a bibliography section might look like this in the wiki editor:

---

<biblio>
#Comfort2007 pmid=17323919
#He1999 pmid=9312086
#StickWillamsCarbohydrates isbn=978-0-240-52118-3
#Sinnott1990 Sinnott, M.L. (1990) Catalytic mechanisms of enzymic glycosyl transfer. Chem. Rev. 90, 1171-1202. [http://dx.doi.org/10.1021/cr00105a006 DOI: 10.1021/cr00105a006]
</biblio>

Note that:

• The citation tag can be whatever you want; e.g. Sinnott1990, StickWillamsCarbohydrates, or even a number.
• References can be in one of three different forms:
  1. PubMed IDs (pmid=number): If the reference has a PubMed ID, placing this after the citation tag will insert to complete reference, as well as DOI and PubMed links, with no addition typing whatsoever on your part. (See Comfort2007 and He1999 refs. above.)
  2. ISBN (isbn=number): For books, this will insert the full reference automatically, based only on the ISBN. (See StickWillamsCarbohydrates ref. above.)
  3. A full, typed reference: Here, whatever follows the reference code is placed verbatim into the reference list - you can put in any text, with any formatting you want. This should only be used when the reference does not have a PubMed ID or ISBN. (See Sinnott1990 ref. above.)

The in-text citation

To cite a specific reference from the bibliography in a page, the citation tag of that reference is placed between the two <cite> </cite> tags in the main text.

For example, citations in the main text might look like this in the wiki editor:

---

• Robert Stick and Spencer Williams wrote a book about carbohydrates and enzymes <cite>StickWillamsCarbohydrates</cite>.
• The catalytic mechanisms of enzymic glycosyl transfer have been reviewed <cite>Sinnott1990</cite>.
• If you want to include multiple references in one place, that is OK too (just separate them with spaces in one pair of <cite> tags) <cite>He1999 Comfort2007</cite>.

Note that:

• The citation tags will be automatically converted into reference numbers according to their first use in the text. You should not try to type/correct the reference numbers; errors in numbering are usually due to typos in the citation tags themselves (either in the text or in the bibliography).
• To make it easier keep track of your citation tags, using something like Harvard style (author-year) referencing can be helpful (e.g., Sinnott1990)
• Citation tags are case sensitive.

How it looks on the page

If the bibliography and in-text citations from above are combined, as they would be on a real CAZypedia page, the result looks like this:

Main text:

---

• Robert Stick and Spencer Williams wrote a book about carbohydrates and enzymes [1].
• The catalytic mechanisms of enzymic glycosyl transfer have been reviewed [2].
• If you want to include multiple references in one place, that is OK too (just separate them with spaces in one pair of <cite> tags) [3, 4].

Reference list:

---

2. Sinnott, M.L. (1990) Catalytic mechanisms of enzymic glycosyl transfer. Chem. Rev. 90, 1171-1202. DOI: 10.1021/cr00105a006

3. He S and Withers SG. (1997). Assignment of sweet almond beta-glucosidase as a family 1 glycosidase and identification of its active site nucleophile. J Biol Chem. 1997;272(40):24864-7. DOI:10.1074/jbc.272.40.24864 |
4. Comfort DA, Bobrov KS, Ivanen DR, Shabalin KA, Harris JM, Kulminskaya AA, Brumer H, and Kelly RM. (2007). Biochemical analysis of Thermotoga maritima GH36 alpha-galactosidase (TmGalA) confirms the mechanistic commonality of clan GH-D glycoside hydrolases. Biochemistry. 2007;46(11):3319-30. DOI:10.1021/bi061521n |

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 with MS Word in Windows to format text to cut and paste into CAZypedia.

Download the CAZypedia EndNote style, CAZypedia.ens, from this link (http://www.biotech.kth.se/cazypedia/CAZypedia.ens) and save the file in your EndNote styles folder (e.g. C:\Program Files\EndNote 9\Styles). Write your CAZypedia entry in MS Word, inserting references via EndNote as usual. Format your entry using the CAZypedia style (CAZypedia.ens) Note that all references in the bibliography will now start with "#N, where N is the reference number and that these numbers will be referenced in the text with <cite>N</cite>. Save your Word file with an informative field name such as CAZypediaText.doc Select all of your text + references by pressing Ctrl+A (Windows) With everything selected, press Ctrl+6 to remove all EndNote "field codes." Save this version as a Word new file, e.g. CAZypediaText_NoFields.doc Copy and paste your main text into a CAZypedia page edit window. Copy and paste your bibliography under a heading titled References. Add the tag <biblio> before the bibliography. Add the tag </biblio> after the bibliography. Preview and save your entry.

This procedure will work best when writing a page from scratch. Be very careful when adding text to a page that reference codes are not used more than once in the bibliography. (You can cite a reference as much as you like in the text.)

Using EndNote to format references with PubMed IDs and ISBNs

It should be possible to combine the above two methods for building a bibliography and referencing it in the text. This would require:

• PubMed IDs or ISBNs must be added in fields in your EndNote records.
• The CAZypedia EndNote style must be altered to output bibliographic records in the format "#refN pmid=nnnnnnn" and "#refN isbn=yyyyyyyyyy"

Since this depends on how CAZypedia editors add PubMed IDs and ISBNs to their EndNote libraries, no general solution can be given.