Re: [Gmod-schema] defining organism groups

[Scott C. <cai...@gm...>]

Hi Naama,

To to be too much of a pain, but would this make more sense as a  
taxonomy/phylogeny module?

Scott


On Sep 23, 2009, at 12:21 PM, Naama Menda wrote:

> If nobody objects, I'm going to add these 2 tables to the Chado  
> schema.
> This means we'll have DBIC objects for the 2 tables in  
> Bio::Chado::Schema::Organism
>
>
> CREATE TABLE organismgroup (
>  organismgroup_id serial NOT NULL PRIMARY KEY,
>  name varchar (255),
>  type varchar (32)
> );
>
> CREATE TABLE organismgroup_member (
>  organismgroup_member_id serial NOT NULL PRIMARY KEY,
>  organismgroup_id integer REFERENCES organismgroup,
>  organism_id integer REFERENCES organism
> );
>
>
> thanks!
> -Naama
>
>
> On Sun, Sep 20, 2009 at 9:28 PM, Naama Menda <nm...@co...>  
> wrote:
>
> How can Chado handle defining several organisms as members of a group?
> For example creating a unigene build from several tobacco species,  
> or defining which Solanum species share the common name  
> 'potato' (this is not intuitive from the taxonomy tree) .
>
> I thought of adding an organismgroup table defining the group name  
> and type, and organismgroup_member linking table (organismgroup and  
> organism)
> Is this something other Chado users might be interested in?
>
> Any ideas?
>
> 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
> nm...@co...
>
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Scott Cain, Ph. D. scott at scottcain dot net
GMOD Coordinator (http://gmod.org/) 216-392-3087
Ontario Institute for Cancer Research