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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+ | As of x, it has been ... | ||
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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. | ||
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+ | 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. | ||
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+ | Experiments may be grouped or structured hierarchically, whereas any kind of biological entity can be stored as the observed unit, from a specimen to be used in genotyping or phenotyping experiments, to a group of species collected in the field that will undergo further lab analysis. | ||
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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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Revision as of 21:54, 3 February 2012
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.
As of x, it has been ...
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.
Experiments may be grouped or structured hierarchically, whereas any kind of biological entity can be stored as the observed unit, from a specimen to be used in genotyping or phenotyping experiments, to a group of species collected in the field that will undergo further lab analysis.
- I tried to adapt the abstract from here, but it doesn't really mention genotyping, which I thought was half the idea. Can you improve it? --DanBolser 21:54, 3 February 2012 (UTC)
Contents
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 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.
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.
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 | |
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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 |
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Meg Staton |
mestato * yahoo.com |
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ficklin * clemson.edu |
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Dorrie Main |
dorrie * wsu.edu |
Washington State University, GDR |
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OICR / GMOD |
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Genevieve DeClerk |
Cornell / Gramene |
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Bob MacCallum |
r.maccallum#imperial.ac.uk |
mosquitoes, ticks and other nasties... | |
Seth Redmond |
seth.redmond * imperial.ac.uk |
Imperial / VectorBase |
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naama.menda * cornell.edu |
sol genomics network / SGN |
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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 |
edit table |