Extension:BiblioPlus

BiblioPlus performs automated retrieval of citations from Pub Med and the ISBN database. It formats these citations for inclusion in a reference section at the bottom of a page, and autonumbers and formats in-text citations.

BiblioPlus was created to correct an error in some PubMed references containing special characters. The original Biblio extension used the National Center for Biotechnology Information (NCBI)'s SOAP service, which returns data in ISO 8859-1, but does not specify this encoding type in the XML header. Therefore, the SOAP parser reads the data as UTF-8 (the default), which results in incorrect output of some special characters. BiblioPlus uses the NCBI's eUtilities service instead, which returns XML data in UTF-8, solving the problem with special characters.

BiblioPlus uses the same tags as the Biblio extension, so if you are currently using Biblio, you can switch to using BiblioPlus without having to change the code in your pages. However, you must delete or comment out the include statement for Biblio, as you cannot run both simultaneously.

Acknowledgement
Coding of BiblioPlus was supported by faculty funding to the laboratory of Prof. Harry Brumer at the Michael Smith Laboratories and Department of Chemistry, University of British Columbia, Vancouver, Canada.

Installation
1) Place the BiblioPlus folder in the extensions subdirectory of your MediaWiki installation 2) Make sure you have the following variables set in LocalSettings.php. These variables are used to make the call to the PubMed database. $wgSitename = YourSiteName $wgEmergencyContact = YourEmailAddress 3) You are strongly encouraged to register your site name and email address with the NCBI. The reason for this is outlined here: NCBI (See Frequency, Timing and Registration of E-utility URL Requests). The values you register with them must be the values of variables $wgSitename and $wgEmergencyContact that you set in LocalSettings.php. To do this, simply send an e-mail to [mailto:eutilities@ncbi.nlm.nih.gov NCBI EUtilities] including these values, along with a contact name.

4) Get an access key for the ISBN database (isbndb.com). It is highly recommended since the daily quota of queries is by default limited to 500. Otherwise, you would share a key with everyone else. Follow this link, register and create a key: create ISBN account

Please contact [mailto:support@isbndb.com ISBN support] if you want to increase your quota. Tell them you are using the BiblioPlus extension for Mediawiki, and that it links each ISBN-referenced book to their site.

5) Update your LocalSettings.php file with these lines, in that order:        $isbndb_access_key = '12345678'; // your access key         require_once("extensions/BiblioPlus/BiblioPlus.php");

How To Use
This module provides tags and. tags create a citation within the text. You must create a unique key (can be any string with no spaces) for each citation. You can put 1 or more keys, separated by spaces, inside a tag. The keys do not have to be numbers; the citations are automatically numbered in order. You must also list these keys in the section, inside the tag. There is at most one section on the page and it must come after the last citation. Notes to be added after a reference should be separated from the biblio key listing by //, as in the example below.

In-text citation:
To cite a specific reference from the bibliography in a page, the citation tag of that reference is placed between the 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 StickWillams2009. The catalytic mechanisms of enzymic glycosyl transfer have been reviewed Sinnott1990. If you want to include multiple references in one place, that is OK, too. Just separate them with spaces in one pair of tags, like this: He1999 Comfort2007.

References:
This section is placed at the bottom of the page, between the ... tags. 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:


 * 1) Comfort2007 pmid=17323919
 * 2) He1999 pmid=9312086
 * 3) StickWillams2009 isbn=978-0-240-52118-3 // Figure 5, page 72 is particularly interesting
 * 4) Sinnott1990 Sinnott, M.L. (1990) Catalytic mechanisms of enzymic glycosyl transfer. Chem. Rev. 90, 1171-1202. DOI: 10.1021/cr00105a006

How it will look on the page:
If the bibliography and in-text citations from above are combined, 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 tags, like this: [3, 4].

References:

1. Robert V. Stick, Spencer J. Williams. Carbohydrates. Amsterdam; Elsevier, 2009. ISBN:978-0-240-52118-3 [StickWillams2009]
 * Figure 5, page 72 is particularly interesting

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. Assignment of sweet almond beta-glucosidase as a family 1 glycosidase and identification of its active site nucleophile. J Biol Chem. 1997 Oct 3;272(40):24864-7. PubMed ID:9312086 | HubMed [He1999] 4. Comfort DA, Bobrov KS, Ivanen DR, Shabalin KA, Harris JM, Kulminskaya AA, Brumer H, and Kelly RM. Biochemical analysis of Thermotoga maritima GH36 alpha-galactosidase (TmGalA) confirms the mechanistic commonality of clan GH-D glycoside hydrolases. Biochemistry. 2007 Mar 20;46(11):3319-30. DOI:10.1021/bi061521n | PubMed ID:17323919 | HubMed [Comfort2007] All Medline abstracts: PubMed | HubMed