Difference between revisions of "Chado Natural Diversity Module Working Group"

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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]].
 
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]].
 +
 +
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= 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 [http://sourceforge.net/projects/heliconiusdb/develop initial version] of the Natural Diversity Module was developed by several people associated with [http://nescent.org NESCent].  The initial application was ''heliconius'' research.  This first version (and subsequent versions) are directly inspired by the [http://www.maizegenetics.net/gdpdm/ Genomic Diversity and Phenotype Data Model (GDPDM)], which comes out of Cornell.  The GDPDM has great documentation and is also described in [[:Image:GDPDM_GMOD_presentation20060630.ppt|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 [http://www.rosaceae.org/ 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 Meeting#Satellite Meetings|January 2010 GMOD Satellite Meeting]] ===
 +
 +
Several working group participants met twice during [[PAG 2010]], immediately before the [[January 2010 GMOD Meeting]].
 +
 +
 +
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= Discussion =
 +
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At this time (January 2010), most of this discussion is about making changes 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.
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* Biotype -
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* Stock -
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* Individual -
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= Links =
 +
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* The [http://sourceforge.net/projects/heliconiusdb/develop beta natural diversity module] is in [http://sourceforge.net/projects/heliconiusdb/develop Soureforge].  This includes some [http://heliconiusdb.svn.sourceforge.net/viewvc/heliconiusdb/trunk/doc/ documentation], and the [http://heliconiusdb.svn.sourceforge.net/viewvc/heliconiusdb/trunk/schema/ schema definitions].
 +
* The module is based heavily on the [http://www.maizegenetics.net/gdpdm/ Genomic Diversity and Phenotype Data Model (GDPDM)], which comes out of Cornell, and also has nice documentation.  The GDPDM is also described in [[:Image:GDPDM_GMOD_presentation20060630.ppt|this presentation]].
  
 
== Members ==
 
== Members ==
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{{ThisIsATET}}
 
{{ThisIsATET}}
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= 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 [http://sourceforge.net/projects/heliconiusdb/develop initial version] of the Natural Diversity Module was developed by several people associated with [http://nescent.org NESCent].  The initial application was ''heliconius'' research.  This first version (and subsequent versions) are directly inspired by the [http://www.maizegenetics.net/gdpdm/ Genomic Diversity and Phenotype Data Model (GDPDM)], which comes out of Cornell.  The GDPDM has great documentation and is also described in [[:Image:GDPDM_GMOD_presentation20060630.ppt|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 [http://www.rosaceae.org/ 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 Meeting#Satellite Meetings|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 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 [http://sourceforge.net/projects/heliconiusdb/develop beta natural diversity module] is in [http://sourceforge.net/projects/heliconiusdb/develop Soureforge].  This includes some [http://heliconiusdb.svn.sourceforge.net/viewvc/heliconiusdb/trunk/doc/ documentation], and the [http://heliconiusdb.svn.sourceforge.net/viewvc/heliconiusdb/trunk/schema/ schema definitions].
 
−
* The module is based heavily on the [http://www.maizegenetics.net/gdpdm/ Genomic Diversity and Phenotype Data Model (GDPDM)], which comes out of Cornell, and also has nice documentation.  The GDPDM is also described in [[:Image:GDPDM_GMOD_presentation20060630.ppt|this presentation]].
 
  
 
[[Category:Meetings]]
 
[[Category:Meetings]]
 
[[Category:Chado Modules]]
 
[[Category:Chado Modules]]

Revision as of 21:17, 27 January 2010

Under Construction

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 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

Members

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


edit table

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