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

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(OK, I'm an idiot)
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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]].
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The '''[[Chado]] Natural Diversity Module]] Working Group''' was established with the aim of getting the Chado Natural Diversity Module into the production version of [[Chado]].
: As of x, it has been? when was this last updated?
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Linking phenotype with genotype is an important and challenging task in biological research. To meet this need, a database for efficiently storing, querying, and analyzing large studies of this kind is necessary. A new Chado module called '''Natural Diversity''' has been developed to store any type of experiment that either uses or generates specimens or stock organisms. ... and genotypes... presumably.
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: I tried to adapt the abstract from [http://www.ncbi.nlm.nih.gov/pubmed/22120662 here], but it doesn't really mention genotyping, which I thought was half the idea. Can you improve it? --[[User:DanBolser|DanBolser]] 21:54, 3 February 2012 (UTC)
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[[User:Clements|Dave Clements]] (organizer)
 
[[User:Clements|Dave Clements]] (organizer)
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[http://nescent.org NESCent], GMOD
 
[http://nescent.org NESCent], GMOD
 
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Please let me know if you are interested in participating in this group, or if you have any questions.  
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Please let me know if you are interested in participating in this group, or if you have any questions.
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Sook Jung
 
Sook Jung
 
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sook * bioinfo.wsu.edu
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sook * bioinfo.wsu.edu
 
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Washington State University, [http://www.bioinfo.wsu.edu/gdr/ GDR]
 
Washington State University, [http://www.bioinfo.wsu.edu/gdr/ GDR]
 
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Meg Staton
 
Meg Staton
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[http://www.genome.clemson.edu/ CUGI]
 
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[http://www.genome.clemson.edu/ CUGI]
 
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Dorrie Main
 
Dorrie Main
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Washington State University, [http://www.bioinfo.wsu.edu/gdr/ GDR]
 
Washington State University, [http://www.bioinfo.wsu.edu/gdr/ GDR]
 
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OICR / GMOD
 
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Cornell  / Gramene
 
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Bob MacCallum
 
Bob MacCallum
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mosquitoes, ticks and other nasties...
 
mosquitoes, ticks and other nasties...
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Seth Redmond
 
Seth Redmond
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Imperial / [http://vectorbase.org VectorBase]
 
Imperial / [http://vectorbase.org VectorBase]
 
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[[User:NaamaMenda | Naama Menda]]
 
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sol genomics network / [http://solgenomics.net SGN]
 
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Maren Friesen
 
Maren Friesen
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University of Southern California
 
University of Southern California
 
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Medicago ecological genomics  
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Medicago ecological genomics
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Yuri Bendana
 
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University of southern California
 
University of southern California
 
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Medicago ecological genomics
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Pantelis Topalis
 
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[http://vectorbase.org VectorBase] @IMBB
 
[http://vectorbase.org VectorBase] @IMBB
 
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Ontology developer
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Emmanuel Dialynas
 
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[http://vectorbase.org VectorBase] @IMBB
 
[http://vectorbase.org VectorBase] @IMBB
 
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Ontology/Insecticide Resistance database developer  
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Ontology/Insecticide Resistance database developer
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Dan Bolser
 
Dan Bolser
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Ensembl Genomes, Plants division
 
Ensembl Genomes, Plants division
 
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We need to store millions of SNPs from hundreds of thousands of varieties. An unknown volume of phenotyping data to follow...  
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We need to store millions of SNPs from hundreds of thousands of varieties. An unknown volume of phenotyping data to follow...
  
 
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Revision as of 15:04, 4 February 2012

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


Discussion

See the discussion page for notes on what we've talked about and where we are heading. Once the discussion settle, a summary of decisions will appear here.


History

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 was 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.

Links

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

Several working group participants met at a January 2010 GMOD Satellite Meeting during PAG 2010. Discussion has continued in teleconferences and on the Chado mailing list. The design has changed considerable during this time. It has become more Chadoesque: it is a very flexible and generic design.

As of July 2010, the schema is undergoing final tweaks before it is moved into production Chado.


Participation

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

Genevieve DeClerk

Cornell / Gramene

Bob MacCallum

r.maccallum#imperial.ac.uk

VectorBase

mosquitoes, ticks and other nasties...

Seth Redmond

seth.redmond * imperial.ac.uk

Imperial / VectorBase

Naama Menda

naama.menda * cornell.edu

sol genomics network / SGN

Maren Friesen

University of Southern California

Medicago ecological genomics

Yuri Bendana

University of southern California

Medicago ecological genomics

Pantelis Topalis

topalis*imbb.forth.gr

VectorBase @IMBB

Ontology developer

Emmanuel Dialynas

ed * imbb.forth.gr

VectorBase @IMBB

Ontology/Insecticide Resistance database developer

Dan Bolser

dan.bolser@gmail.com

Ensembl Genomes, Plants division

We need to store millions of SNPs from hundreds of thousands of varieties. An unknown volume of phenotyping data to follow...

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Stock Relationship Ontology

Stock Relationship Ontology