CAZypedia needs your help!
We have many unassigned pages in need of Authors and Responsible Curators. See a page that's out-of-date and just needs a touch-up? - You are also welcome to become a CAZypedian. Here's how.
Scientists at all career stages, including students, are welcome to contribute.
Learn more about CAZypedia's misson here and in this article.
 Totally new to the CAZy classification? Read this first.

Difference between revisions of "Help:References"

From CAZypedia
Jump to navigation Jump to search
(fixed broken ISBN)
 
(31 intermediate revisions by the same user not shown)
Line 1: Line 1:
−
CAZypedia uses the '''Bibilo''' extension for creating in-text citations and a reference list.  Full details about '''Biblio''' can be found at the [http://wikiomics.org/wiki/Biblio Biblio page at Wikiomics].  The following is a succinct set of instructions for using '''Biblio''' with [[CAZypedia]].
+
''CAZypedia'' uses the '''BiblioPlus''' extension for creating in-text citations and a reference list.  Full details about '''BiblioPlus''' can be found at the [http://www.mediawiki.org/wiki/Extension:BiblioPlus BiblioPlus homepage] and the homepage of its predecessor, [http://openwetware.org/wiki/Wikiomics:Biblio Biblio].  The following is a succinct set of instructions for using '''BiblioPlus''' with ''CAZypedia''.
  
 
== The basics ==
 
== The basics ==
−
'''Biblio''' uses two types of tags to format references.  The first is the <nowiki><cite>...</cite></nowiki> 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 <nowiki><bibilo>...</biblio></nowiki> tags.
+
In some sense, '''BiblioPlus''' 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'', '''BiblioPlus''' relies on two pieces of information to make this happen:
 +
# a ''bibliography'' section containing a list of the references you would like to cite in the text, and,
 +
# an in-text ''citation'', which "calls" the reference from the bibliography.
  
−
''Example CAZypedia code would look like this:''
 
  
−
<pre>
+
=== The bibliography ===
−
'''Main text'''
+
This section is placed at the bottom of the page, between the <tt><nowiki><biblio>...</biblio></nowiki></tt> tags, under the heading '''Reference list'''.  Each reference begins on a new line with a ''hash sign'' (<tt>#</tt>), followed by a ''citation tag'', and finally the ''reference'' itself.
−
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'''
+
<blockquote class="toccolours" style="float:none; padding: 10px 15px 10px 15px; display:table;">
−
<biblio>
+
'''For example, a bibliography section might look like this in the wiki editor:'''<br>
−
#REF1 Barrett T, et al. Structure 1995 Sep 15; 3(9) 951-60.
+
----
−
#stryertext Berg, Tymoczko, & Stryer. Biochemistry. New York: W.H. Freeman, 2002.
+
<nowiki><biblio></nowiki><br>
−
</biblio>
+
<nowiki>#Comfort2007 pmid=17323919</nowiki><br>
−
</pre>
+
<nowiki>#He1999 pmid=9312086</nowiki><br>
 +
<nowiki>#StickWillams2009 isbn=9780240521183</nowiki><br>
 +
<nowiki>#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]</nowiki><br>
 +
<nowiki></biblio></nowiki>
 +
</blockquote>
  
−
''Which would give this on the actual CAZypedia page:''
+
'''''Note that:'''''
 +
* The ''citation tag'' should be in [http://en.wikipedia.org/wiki/Harvard_reference#Author-date Harvard-style] '''Author-Year''' format; ''e.g.'' <tt>Sinnott1990</tt>, <tt>StickWillams2009</tt>, ''etc''.
 +
* References can be in one of three different forms:
 +
*# '''PubMed IDs (<tt>pmid=</tt>''number''):''' If the reference has a PubMed ID, placing this after the ''citation tag'' will insert the complete reference, as well as DOI and PubMed links, ''with no additional typing whatsoever on your part.'' (See <tt>Comfort2007</tt> and <tt>He1999</tt> refs. above.)
 +
*# '''ISBN (<tt>isbn=</tt>''number''):''' For books, this will insert the full reference automatically, based only on the ISBN.  (See <tt>StickWillams2009</tt> ref. above.)
 +
*# '''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 <tt>Sinnott1990</tt> ref. above.)
 +
* References in the ''bibliography'' can be in any order, ''i.e.'', the reference list does not have to be in the same order as the citations appear in the text.  The '''BiblioPlus''' software will automatically number the reference list correctly regardless.
  
−
{| {{Prettytable}}
+
=== 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 <tt><nowiki><cite> </cite></nowiki></tt> tags in the main text.
−
'''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'''
+
<blockquote class="toccolours" style="float:none; padding: 10px 15px 10px 15px; display:table;">
−
<biblio>
+
'''For example, citations in the main text might look like this in the wiki editor:'''
−
#REF1 Barrett T, et al. Structure 1995 Sep 15; 3(9) 951-60.
+
----
−
#stryertext Berg, Tymoczko, & Stryer. Biochemistry. New York: W.H. Freeman, 2002.
+
* Robert Stick and Spencer Williams wrote a book about carbohydrates and enzymes <nowiki><cite>StickWillams2009</cite></nowiki>.
−
</biblio>
+
* The catalytic mechanisms of enzymic glycosyl transfer have been reviewed <nowiki><cite>Sinnott1990</cite></nowiki>.
−
|}
+
* If you want to include multiple references in one place, that is OK, too. Just separate them with spaces in one pair of <tt><nowiki><cite></nowiki></tt> tags, like this: <nowiki><cite>He1999 Comfort2007</cite></nowiki>.
 +
</blockquote>
  
 
'''''Note that:'''''
 
'''''Note that:'''''
−
* The reference code can be whatever you want (e.g.: REF1, stryertext)
+
* The ''citation tags'' will be automatically converted into reference numbers according to their first use in the text.  '''You should not try to (and you won't be able 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).'''
−
* Whatever follows the reference code is placed verbatim into the reference list - you can put any text here, with any formatting you want.
+
* As mentioned above, ''citation tags'', should be in [http://en.wikipedia.org/wiki/Harvard_reference#Author-date Harvard-style] '''Author-Year''' format (e.g., <tt>Sinnott1990</tt>)
 +
* ''Citation tags'' are case sensitive.
  
  
−
== Citing works using PubMed IDs and ISBNs ==
+
=== How it looks on the page ===
−
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.
+
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:
  
−
''The code for our previous example would then look like this:''
+
<blockquote class="toccolours" style="float:none; padding: 10px 15px 10px 15px; display:table;">
−
 
 
−
<pre>
 
 
'''Main text:'''
 
'''Main text:'''
 +
----
 +
* Robert Stick and Spencer Williams wrote a book about carbohydrates and enzymes <cite>StickWillams2009</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 <tt><nowiki><cite></nowiki></tt> tags, like this:  <cite>He1999 Comfort2007</cite>.
  
−
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>
 
−
</pre>
 
−
 
−
''Which would give this on the CAZypedia page:''
 
  
−
{| {{Prettytable}}
 
−
|'''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:'''
 
'''Reference list:'''
 +
----
 
<biblio>
 
<biblio>
−
#REF1 pmid=8535788
+
#Comfort2007 pmid=17323919
−
#stryertext isbn=0-7167-4954-8
+
#He1999 pmid=9312086
 +
#StickWillams2009 isbn=9780240521183
 +
#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>
 
</biblio>
−
|}
+
</blockquote>
−
 
 
−
'''''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 [http://en.wikipedia.org/wiki/EndNote EndNote].  '''EndNote''' can be used to both insert the in-text citations (e.g. ''<nowiki><cite>REF1</cite></nowiki>'' and format content to go in the <nowiki><biblio>...</bibilo></nowiki> tags.
 
−
 
 
−
''The following is a step-by-step guide to using '''EndNote''' to format text to cut and paste into CAZypedia.''
 
−
 
 
−
{| {{Prettytable}}
 
−
|
 
−
# 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).
 
−
# 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 "#ref'''N''', where '''N''' is the reference number and that these numbers will be referenced in the text with <nowiki><cite>refN</cite></nowiki>.''
 
−
# 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 <nowiki><biblio</nowiki>> before the bibliography.
 
−
# Add the tag <nowiki></biblio</nowiki>> 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 that 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.
+
=== More referencing examples ===
 +
This page demonstrates how the above would be used in a real ''CAZypedia'' page, and also includes some extra examples: [[Help:References/More examples]]

Latest revision as of 07:38, 4 June 2013

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

The basics

In some sense, BiblioPlus 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, BiblioPlus 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
#StickWillams2009 isbn=9780240521183
#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 should be in Harvard-style Author-Year format; e.g. Sinnott1990, StickWillams2009, etc.
  • 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 the complete reference, as well as DOI and PubMed links, with no additional 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 StickWillams2009 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.)
  • References in the bibliography can be in any order, i.e., the reference list does not have to be in the same order as the citations appear in the text. The BiblioPlus software will automatically number the reference list correctly regardless.

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>StickWillams2009</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, like this: <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 (and you won't be able 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).
  • As mentioned above, citation tags, should be in Harvard-style Author-Year format (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, like this: [3, 4].


Reference list:

  1. [StickWillams2009]

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

    [Sinnott1990]
  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 | PubMed ID:9312086 [He1999]
  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 | PubMed ID:17323919 [Comfort2007]

All Medline abstracts: PubMed

More referencing examples

This page demonstrates how the above would be used in a real CAZypedia page, and also includes some extra examples: Help:References/More examples

Retrieved from "http://www.cazypedia.org/index.php?title=Help:References&oldid=8792"