Re: [Gmod-schema] defining organism groups

[Stephen F. <FI...@ex...>]

We have the same problem of how to map multiple organisms to a single unigene.  The way pull out this information, which is probably not ideal, but the only way we could think to do so in chado is by way of the analysisfeature table.  We correlate the features that are used in an analysis using the analysisfeature table.   An inner join between this table, the feature table and the organism table gives you the the list of organisms with features in your unigene builds.  It may not be fast enough for a quick query on a web page, but can give you the information you want.



-----Original Message-----
From: naama.menda [mailto:naa...@gm...]
Sent: Thu 9/24/2009 12:19 PM
To: fa...@mo...
Cc: Chris Mungall; gmo...@li...; Don Gilbert; sc...@sc...
Subject: Re: [Gmod-schema] defining organism groups
 
The issue we have is not only how to distinguish different organisms by
taxonomy, but rather how to link to these groups.
If you have a unigene build of 10 drosophilids, where would you make the
link between the unigene build and the member organisms?


-Naama




On Thu, Sep 24, 2009 at 11:46 AM, kathleen.flybase <
kat...@gm...> wrote:

> Hi,
> Just a quick note. Very timely discussion.
>  Flybase is considering adding to the organism module, organism_cvterm as
> well as an organism_cvtermprop. We've ruffed out some use cases but I'm out
> of the office until next week so they are not readily available.  Basically
> the organism_cvterm table would hold more detailed info on how to build the
> taxonomic name. We are considering using organismprop to distinguish
> drosophilids vs non-drosophilids.
>
> Cheers,
> Kathleen Falls
>
>
> On Wed, Sep 23, 2009 at 7:14 PM, Chris Mungall <cj...@be...>wrote:
>
>>
>> I agree the cv module makes most sense here.
>>
>> I think ideally a new organism_cvterm relationship would be preferable
>> to organismprop.
>>
>> On Sep 23, 2009, at 7:27 PM, Don Gilbert wrote:
>>
>> > What about using the organismprop table, and creating a CV term to
>> > handle this? Much of chado's biological logic has been pushed into
>> > CV terms for various reasons. It seems to me that adding organism
>> > grouping
>> > CV terms would let you classify and group the species you want, much
>> > like having CV terms for the other bits (feature types, etc.) do.
>> > - Don
>> >
>> >
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>
> --
> Kathleen Falls
> FlyBase
> Department of Molecular and Cellular Biology
> Harvard University
> BL 4053
> 16 Divinity Ave
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