[Gmod-help] Re: Natural diversity module

[Dave Clements]

Hi Naama,

I am available Thursday at 11 Eastern until about 11:45, and then again
after 12).  I would love to participate in the call.  My Skype ID is
tnabtaf.

Also, I'm spending part of today typing up notes from the meetings that
happened at at PAG.  Once I have something typed up, I'll send the notes to
the GMOD schema list.

Thanks,

Dave C.

On Wed, Jan 27, 2010 at 10:11 AM, Naama Menda <nm249 at cornell.edu> wrote:

> hi Sook,
>
> we are currently thinking about different ways for implementing schema for
> QTL and mapping populations, and in the future pedigrees.
> Isaak is working on the QTL module, and we'll have a meeting over Skype
> tomorrow 11AM EST (Rob will call in too)
> Do you think you can join and contribute your input? My Skype user is
> NaamaMenda.
>
> It would be great if Dave could join as well.
>
> thanks!
> -Naama
>
>
> Naama Menda
> Boyce Thompson Institute for Plant Research
> Tower Rd
> Ithaca NY 14853
> USA
>
> (607) 254 3569
> Sol Genomics Network
> http://www.sgn.cornell.edu
> nm249 at cornell.edu
>
>
> On Tue, Jan 26, 2010 at 12:11 PM, Sook Jung <sookjc at gmail.com> wrote:
>
>> Hi Naama,
>> So the schema is not developed by Dave, but some other butterfly
>> people, based heavily on GDPDM. It's very nice and comprehensive, but
>> Dave felt it's not really 'chado-like'.
>>
>> So one of the big change we'll make is to get rid of biotype, stock
>> (we can't get rid of from the currently established chado), and
>> individual, but put everything in one table, for example
>> 'observation_unit'. We now store in OU anything - population,
>> cultivar, or individual tree. The OU_relationship table can record the
>> relationship between the population and cultivar or cultivar and
>> individual or whatever - just like the notorious 'feature' table.
>> Since with SNP, we know that the individual tree (plant) from the same
>> cultivar can have different snp genotypes, we will associate genotype
>> and phenotype with 'individual' - when the individual name is not
>> known, we'll just make an entry.
>> The pedigree data will be stored in a table like 'OU_relationship'
>> also.  We can use ontology to represent various relationship.
>> You might not like this new 'chado' like diversity module since you
>> already have germplasm tables such as individual, right? But the OU
>> with relationship table will solve the organismgroup concept and any
>> unforeseen grouping need.. For example we may even need to store
>> phenotype information for part of the tree or part of an apple (sunny
>> side/shady side) - that's what the apple breeders told me!!
>>
>>  Well if I don't hear from Dave in a couple of days, I'll try to
>> summarize what we discussed.
>>
>> Sook
>>
>> On Tue, Jan 26, 2010 at 11:51 AM, Naama Menda <nm249 at cornell.edu> wrote:
>> > thanks Sook! The schema looks nice and comprehensive.
>> >
>> > so basically
>> > 'biotype' is an accession
>> > and 'stock' is a germplasm ?
>> >
>> > Do you store info about populations?
>> > I guess Dave says it's an 'individualprop', which brings us back to a
>> > similar discussion we had a couple of months ago
>> > about organismgroups ..
>> >
>> > thanks,
>> > -Naama
>> >
>> >
>> >
>> > On Tue, Jan 26, 2010 at 11:32 AM, Sook Jung <sookjc at gmail.com> wrote:
>> >>
>> >> Hi Naama,
>> >> I'm attaching the current version of the diversity module. After we
>> >> met with Dave Clements at San Diego, however, we agreed to change it
>> >> quite a bit. He will send us summary to go over and then send it to
>> >> the general GMOD schema mailing list before finalizing it.Once we get
>> >> a summary from him I'll send it to you also.
>> >> Thanks
>> >> Sook
>> >>
>> >> On Tue, Jan 26, 2010 at 10:48 AM, Naama Menda <nm249 at cornell.edu>
>> wrote:
>> >> > hi Sook,
>> >> > we'd like to implement in SGN the natural diversity module.
>> >> > Do you have a current version for the schema?
>> >> > Are you using it for anything in GDR?
>> >> >
>> >> > The plan is to use it in the first stage for pedigrees of mapping and
>> >> > QLT
>> >> > populations
>> >> >
>> >> > Thanks!
>> >> > -Naama
>> >> >
>> >> >
>> >>
>> >> > Naama Menda
>> >> > Boyce Thompson Institute for Plant Research
>> >> > Tower Rd
>> >> > Ithaca NY 14853
>> >> > USA
>> >> >
>> >> > (607) 254 3569
>> >> > Sol Genomics Network
>> >> > http://www.sgn.cornell.edu
>> >> > nm249 at cornell.edu
>> >> >
>> >>
>> >>
>> >>
>> >> --
>> >> Sook Jung, PhD
>> >> Assistant Research Professor of Bioinformatics
>> >> Dept of Horticulture and Landscape Architecture
>> >> Washington State University
>> >> 45 Johnson Hall, Pullman, WA 99164-6414
>> >> Email:sook at bioinfo.wsu.edu <Email%3Asook at bioinfo.wsu.edu>
>> >
>> >
>>
>>
>>
>> --
>> Sook Jung, PhD
>> Assistant Research Professor of Bioinformatics
>> Dept of Horticulture and Landscape Architecture
>> Washington State University
>> 45 Johnson Hall, Pullman, WA 99164-6414
>> Email:sook at bioinfo.wsu.edu <Email%3Asook at bioinfo.wsu.edu>
>>
>
>


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