Difference between revisions of "Chado Natural Diversity Module Working Group"
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| − | The [[Chado | + | 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 [[Talk:Chado Natural Diversity Module Working Group|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. | ||
| + | |||
| + | * See [http://www.ncbi.nlm.nih.gov/pubmed/22120662 the publication]. | ||
| + | |||
| + | |||
| + | = History = | ||
This section describes important events in the development of the module. Detailed discussion of functionality is a separate section below. | This section describes important events in the development of the module. Detailed discussion of functionality is a separate section below. | ||
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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 was 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]]. | 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 was 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]]. | ||
| + | |||
| + | === Links === | ||
| + | |||
| + | * The [http://sourceforge.net/projects/heliconiusdb/develop beta natural diversity module] is in [http://sourceforge.net/projects/heliconiusdb/develop Soureforge]. | ||
| + | ** [http://heliconiusdb.svn.sourceforge.net/viewvc/heliconiusdb/trunk/doc/ documentation] directory | ||
| + | ** [http://heliconiusdb.svn.sourceforge.net/viewvc/heliconiusdb/trunk/schema/ schema definitions]. | ||
| + | ** [http://heliconiusdb.svn.sourceforge.net/viewvc/heliconiusdb/trunk/schema/doc/diversity.html Table Documentation] | ||
| + | * 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]]. | ||
== 2009 == | == 2009 == | ||
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As of July 2010, the schema is undergoing final tweaks before it is moved into production [[Chado]]. | As of July 2010, the schema is undergoing final tweaks before it is moved into production [[Chado]]. | ||
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= Participation = | = Participation = | ||
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If you are interested, please add your name below. (Either update this page directly, or send your contact info to [mailto:clements@nescent.org Dave Clements].) | If you are interested, please add your name below. (Either update this page directly, or send your contact info to [mailto:clements@nescent.org Dave Clements].) | ||
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!|Name!!Email!!Affiliation!!Comments | !|Name!!Email!!Affiliation!!Comments | ||
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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. | + | 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 | + | 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] | [http://www.genome.clemson.edu/ CUGI] | ||
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[[User:Sficklin|Stephen Ficklin]] | [[User:Sficklin|Stephen Ficklin]] | ||
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[http://www.genome.clemson.edu/ CUGI] | [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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[[User:Scott|Scott Cain]] | [[User:Scott|Scott Cain]] | ||
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OICR / GMOD | OICR / GMOD | ||
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Genevieve DeClerk | Genevieve DeClerk | ||
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Cornell / Gramene | 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]] | [[User:NaamaMenda | Naama Menda]] | ||
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sol genomics network / [http://solgenomics.net SGN] | 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 | + | Medicago ecological genomics |
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Yuri Bendana | Yuri Bendana | ||
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University of southern California | University of southern California | ||
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| − | Medicago ecological genomics | + | Medicago ecological genomics |
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Pantelis Topalis | Pantelis Topalis | ||
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[http://vectorbase.org VectorBase] @IMBB | [http://vectorbase.org VectorBase] @IMBB | ||
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| − | Ontology developer | + | Ontology developer |
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Emmanuel Dialynas | 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 | + | Ontology/Insecticide Resistance database developer |
| + | |- | ||
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| + | Dan Bolser | ||
| + | | | ||
| + | dan.bolser@gmail.com | ||
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| + | 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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Latest 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.
Contents
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.
- See the publication.
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
- 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.
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 | Affiliation | Comments | |
|---|---|---|---|
|
Dave Clements (organizer) |
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 |
||
|
ficklin * clemson.edu |
|||
|
Dorrie Main |
dorrie * wsu.edu |
Washington State University, GDR |
|
|
OICR / GMOD |
|||
|
Genevieve DeClerk |
Cornell / Gramene |
||
|
Bob MacCallum |
r.maccallum#imperial.ac.uk |
mosquitoes, ticks and other nasties... | |
|
Seth Redmond |
seth.redmond * imperial.ac.uk |
Imperial / VectorBase |
|
|
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... |
| edit table |
