[Gmod-help] Re: Natural diversity module

[Naama Menda]

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>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://brie4.cshl.edu/pipermail/gmod-help/attachments/20100127/22c76af0/attachment.html>