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

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(The history isn't that interesting, moved the discussion section up)
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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.
 
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.  
+
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 [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)
 
: 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)
  
  
 +
= 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.
  
= Background and Timeline =
 
  
 +
= 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.
  
 
== 2007 ==
 
== 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 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 ===
 
=== Links ===
 
 
* The [http://sourceforge.net/projects/heliconiusdb/develop beta natural diversity module] is in [http://sourceforge.net/projects/heliconiusdb/develop Soureforge].
 
* 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/doc/ documentation] directory
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== 2009 ==
 
== 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.
 
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 ==
 
== 2010 ==
 
 
Several working group participants met at a [[January 2010 GMOD Meeting#Satellite Meetings|January 2010 GMOD Satellite Meeting]] during [[PAG 2010]].  Discussion has continued in teleconferences and on the {{MailingListLink|Chado|Chado mailing list}}.  The design has changed considerable during this time.  It has become more ''Chadoesque'':  it is a very flexible and generic design.
 
Several working group participants met at a [[January 2010 GMOD Meeting#Satellite Meetings|January 2010 GMOD Satellite Meeting]] during [[PAG 2010]].  Discussion has continued in teleconferences and on the {{MailingListLink|Chado|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]].
 
As of July 2010, the schema is undergoing final tweaks before it is moved into production [[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.
 
  
 
= Participation =
 
= Participation =
 
 
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].)
  

Revision as of 22:10, 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)


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

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Stock Relationship Ontology

Stock Relationship Ontology