A RDF Editor for Media wiki (draft)

(This page was copied from the article I started on mediawiki.org)
I've created an applet that can be used as a RDF editor for mediawiki, the wiki engine for Wikipedia. (This is mainly a proof-of-concept, I don't know if I'm going to use this system myself) The XML/RDF syntax of the document is checked and it is validated against a ~RDFS schema. This method was inspired from the one described in the article "Add Java extensions to your wiki".

On opening, the java applet is opened, and the user write a XML/RDF document in an input area.

The syntax of XML/RDF is checked. The document is also validated vs a schema localized in ${MW}/mwrdf/schema.rdf. If there is an error, a message is displayed and the 'Save Button' is disabled.

Once the document is saved, it is displayed as a <PRE> section.
Categories are bound to "mwrdf/shema.rdf and are automatically added.


and the RDF document can then be retrieved with the Mediawiki API.


Installation

• Install the java JRE (version > 1.6)
• The MediaWiki API must be enabled for action=query
• append the following code at the end of ${MW}/LocalSettings.php
  

  require_once("mwrdf/RDFEdit.php");

• download mwrdf.zip' from http://code.google.com/p/lindenb/downloads/list
• unzip the file mwrdf.zip in ${MW}
• edit the schema mwrdf/schema.rdf (TODO, describe the Schema for ... the schema... :-) )

That's it.
Pierre

IBD Status applet

I've just released an applet called IBDStatus. This applet (java 6 is required) is freely available at:

http://lindenb.integragen.org/breakpoint/

This applet takes as input the breakpoint analysis data (Nature. Dib et al.(1996); 380:152-154) from the 'Fondation Jean-Dausset' (CEPH) and display the Identical By Descent (IBD) regions between a pair of related individuals. Two people share an allele identical by descent if the two copies of the allele were inherited from a common ancestor. A pair of siblings can share 0, 1, or 2 alleles:

• 0: not the same alleles


• 1: only one allele in common


• 2: both same alleles

Picture from Abel & Dessein

As an example, this IBD status can be used to design the controls of a CGH assay.

• Top left pane: a linkage table with genotype=f(individual,marker)


• Middle left pane: the list of individual: using the Ctrl-key select
  two related
  individuals an press the Add sib button. Your new pair is added in
  the bottom left table.


• Bottom left pane: the list of sib-pairs: for each pair, the IBD status
  is displayed in the right table



• Right table:
  
  
  
  • Marker index
  
  
  • chromosome
  
  
  • STS D-Number
  
  
  • Start-position (build 36)
  
  
  • End-position (build 36)
  
  
  • IBD status of each sib-pair(if any)
  
  
  • Count IBD with unknown status
  
  
  • Count IBD. 0
  
  
  
  • Count IBD. 1
  
  
  • Count IBD. 2
  
  
  
  

I wrote this software a few monthes ago but it was not much used, so I
was given the permission to release this version to the community.
Enjoy.

Pierre