Re: [Gmod-schema] defining organism groups

[Naama M. <nm...@co...>]

I think it should be in the organism module since it has FK to organism.

so OrganismgroupMember.pm will have

__PACKAGE__->belongs_to(
 "organism",
  "Bio::Chado::Schema::Organism::Organism",
  { organism_id => "organism_id" },
);

and in Organismgroup.pm

__PACKAGE__->has_many(
  "organismgroup_members",
  "Bio::Chado::Schema::Organism::OrganismgroupMember",
  { "foreign.organismgroup_id" => "self.organismgroup_id" },
);




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...


On Wed, Sep 23, 2009 at 12:33 PM, Scott Cain <cai...@gm...> wrote:

> 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...
>>
>>
>> ------------------------------------------------------------------------------
>> Come build with us! The BlackBerry&reg; Developer Conference in SF, CA
>> is the only developer event you need to attend this year. Jumpstart your
>> developing skills, take BlackBerry mobile applications to market and stay
>> ahead of the curve. Join us from November 9&#45;12, 2009. Register
>> now&#33;
>> http://p.sf.net/sfu/devconf_______________________________________________
>> Gmod-schema mailing list
>> Gmo...@li...
>> https://lists.sourceforge.net/lists/listinfo/gmod-schema
>>
>
> -----------------------------------------------------------------------
> Scott Cain, Ph. D. scott at scottcain dot net
> GMOD Coordinator (http://gmod.org/) 216-392-3087
> Ontario Institute for Cancer Research
>
>
>
>
>