Hi Naama,<br><br>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.<br><br>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.<br>
<br>Thanks,<br><br>Dave C.<br><br><div class="gmail_quote">On Wed, Jan 27, 2010 at 10:11 AM, Naama Menda <span dir="ltr"><<a href="mailto:nm249@cornell.edu">nm249@cornell.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
hi Sook,<br><br>we are currently thinking about different ways for implementing schema for QTL and mapping populations, and in the future pedigrees.<br>Isaak is working on the QTL module, and we'll have a meeting over Skype tomorrow 11AM EST (Rob will call in too) <br>
Do you think you can join and contribute your input? My Skype user is NaamaMenda.<br><br>It would be great if Dave could join as well.<br><br>thanks!<br>-Naama<br> <br><br clear="all">Naama Menda<br>Boyce Thompson Institute for Plant Research<br>
Tower Rd<br>Ithaca NY 14853<br>USA<br><br>(607) 254 3569<br>Sol Genomics Network<br><a href="http://www.sgn.cornell.edu" target="_blank">http://www.sgn.cornell.edu</a><br><a href="mailto:nm249@cornell.edu" target="_blank">nm249@cornell.edu</a><br>
<br><br><div class="gmail_quote">On Tue, Jan 26, 2010 at 12:11 PM, Sook Jung <span dir="ltr"><<a href="mailto:sookjc@gmail.com" target="_blank">sookjc@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Hi Naama,<br>
So the schema is not developed by Dave, but some other butterfly<br>
people, based heavily on GDPDM. It's very nice and comprehensive, but<br>
Dave felt it's not really 'chado-like'.<br>
<br>
So one of the big change we'll make is to get rid of biotype, stock<br>
(we can't get rid of from the currently established chado), and<br>
individual, but put everything in one table, for example<br>
'observation_unit'. We now store in OU anything - population,<br>
cultivar, or individual tree. The OU_relationship table can record the<br>
relationship between the population and cultivar or cultivar and<br>
individual or whatever - just like the notorious 'feature' table.<br>
Since with SNP, we know that the individual tree (plant) from the same<br>
cultivar can have different snp genotypes, we will associate genotype<br>
and phenotype with 'individual' - when the individual name is not<br>
known, we'll just make an entry.<br>
The pedigree data will be stored in a table like 'OU_relationship'<br>
also. We can use ontology to represent various relationship.<br>
You might not like this new 'chado' like diversity module since you<br>
already have germplasm tables such as individual, right? But the OU<br>
with relationship table will solve the organismgroup concept and any<br>
unforeseen grouping need.. For example we may even need to store<br>
phenotype information for part of the tree or part of an apple (sunny<br>
side/shady side) - that's what the apple breeders told me!!<br>
<br>
Well if I don't hear from Dave in a couple of days, I'll try to<br>
summarize what we discussed.<br>
<font color="#888888"><br>
Sook<br>
</font><div><div></div><div><br>
On Tue, Jan 26, 2010 at 11:51 AM, Naama Menda <<a href="mailto:nm249@cornell.edu" target="_blank">nm249@cornell.edu</a>> wrote:<br>
> thanks Sook! The schema looks nice and comprehensive.<br>
><br>
> so basically<br>
> 'biotype' is an accession<br>
> and 'stock' is a germplasm ?<br>
><br>
> Do you store info about populations?<br>
> I guess Dave says it's an 'individualprop', which brings us back to a<br>
> similar discussion we had a couple of months ago<br>
> about organismgroups ..<br>
><br>
> thanks,<br>
> -Naama<br>
><br>
><br>
><br>
> On Tue, Jan 26, 2010 at 11:32 AM, Sook Jung <<a href="mailto:sookjc@gmail.com" target="_blank">sookjc@gmail.com</a>> wrote:<br>
>><br>
>> Hi Naama,<br>
>> I'm attaching the current version of the diversity module. After we<br>
>> met with Dave Clements at San Diego, however, we agreed to change it<br>
>> quite a bit. He will send us summary to go over and then send it to<br>
>> the general GMOD schema mailing list before finalizing it.Once we get<br>
>> a summary from him I'll send it to you also.<br>
>> Thanks<br>
>> Sook<br>
>><br>
>> On Tue, Jan 26, 2010 at 10:48 AM, Naama Menda <<a href="mailto:nm249@cornell.edu" target="_blank">nm249@cornell.edu</a>> wrote:<br>
>> > hi Sook,<br>
>> > we'd like to implement in SGN the natural diversity module.<br>
>> > Do you have a current version for the schema?<br>
>> > Are you using it for anything in GDR?<br>
>> ><br>
>> > The plan is to use it in the first stage for pedigrees of mapping and<br>
>> > QLT<br>
>> > populations<br>
>> ><br>
>> > Thanks!<br>
>> > -Naama<br>
>> ><br>
>> ><br>
>><br>
>> > Naama Menda<br>
>> > Boyce Thompson Institute for Plant Research<br>
>> > Tower Rd<br>
>> > Ithaca NY 14853<br>
>> > USA<br>
>> ><br>
>> > (607) 254 3569<br>
>> > Sol Genomics Network<br>
>> > <a href="http://www.sgn.cornell.edu" target="_blank">http://www.sgn.cornell.edu</a><br>
>> > <a href="mailto:nm249@cornell.edu" target="_blank">nm249@cornell.edu</a><br>
>> ><br>
>><br>
>><br>
>><br>
>> --<br>
>> Sook Jung, PhD<br>
>> Assistant Research Professor of Bioinformatics<br>
>> Dept of Horticulture and Landscape Architecture<br>
>> Washington State University<br>
>> 45 Johnson Hall, Pullman, WA 99164-6414<br>
>> <a href="mailto:Email%3Asook@bioinfo.wsu.edu" target="_blank">Email:sook@bioinfo.wsu.edu</a><br>
><br>
><br>
<br>
<br>
<br>
</div></div>--<br>
<div><div></div><div>Sook Jung, PhD<br>
Assistant Research Professor of Bioinformatics<br>
Dept of Horticulture and Landscape Architecture<br>
Washington State University<br>
45 Johnson Hall, Pullman, WA 99164-6414<br>
<a href="mailto:Email%3Asook@bioinfo.wsu.edu" target="_blank">Email:sook@bioinfo.wsu.edu</a><br>
</div></div></blockquote></div><br>
</blockquote></div><br><br clear="all"><br>-- <br><a href="http://gmod.org/wiki/GMOD_News">http://gmod.org/wiki/GMOD_News</a><br><br>