Chado Natural Diversity Module Working Group

This page or section is under construction.

The Chado Natural Diversity Working Group has been established with the aim of getting the Chado Natural Diversity Module into the production version of Chado.

Background and Timeline

This section describes important events in the development of the module. Detailed discussion of functionality is a separate section below.

2007

The initial version of the Natural Diversity Module was developed by several people associated with NESCent. The initial application was heliconius research. This first version (and subsequent versions) are directly inspired by the Genomic Diversity and Phenotype Data Model (GDPDM), which comes out of Cornell. The GDPDM has great documentation and is also described in this presentation.

2009

In the fall of 2009, Sook Jung of Washington State downloaded the initial version (becoming the first known user outside heliconius) and started looking at it with the goal of using for GDR, a plant genome database. Sook found that a number of things weren't clear, and her input led to a rethinking of the design, and to the formation of this working group.

2010

January 2010 GMOD Satellite Meeting

Several working group participants met twice during PAG 2010, immediately before the January 2010 GMOD Meeting.

Discussion

At this time (January 2010), most of this discussion is about making changes relative to the version that was created in 2007, referred to below as V2007.

Observational Unit

V2007 has several different levels of biological unit, all represented with a different set of tables

• Organism - This already exists and comes from the Chado Organism Module. It defines a species.
• Biotype -
• Stock -
• Individual -

Links

• The beta natural diversity module is in Soureforge.
  • documentation directory
  • schema definitions.
  • Table Documentation
• The module is based heavily on the Genomic Diversity and Phenotype Data Model (GDPDM), which comes out of Cornell, and also has nice documentation. The GDPDM is also described in this presentation.

Membership

If you are interested, please add your name below. (Either update this page directly, or send your contact info to Dave Clements.)

Name	Email	Affiliation	Comments
Dave Clements (organizer)	clements@nescent.org	NESCent, GMOD	Please let me know if you are interested in participating in this group, or if you have any questions.
Sook Jung	sook * bioinfo.wsu.edu	Washington State University, GDR
Meg Staton	mestato * yahoo.com	CUGI
Stephen Ficklin	ficklin * clemson.edu	CUGI
Dorrie Main	dorrie * wsu.edu	Washington State University, GDR
Scott Cain		OICR / GMOD
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