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Re: [Gmod-schema] defining organism groups
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From: David E. <em...@mo...> - 2009-09-24 14:40:37
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Hi Naama,
>> I can think now of groups of organisms or accessions (stocks).
>> This means a more generic 'groups' table will be more suitable.
I'm not sure I understand what you mean. Maybe it would help if you gave a few
examples of these groups. That is, if we go back to your suggestion for an
organismgroup table, what would the types be?
Re-reading this thread, I see two "grouping" use-cases at hand, namely,
creating a unigene set and setting the common name "potato" to a set of
Solanum species. It seems to me like both of these things can be done within
existing chado structures: using library module to define a unigene set, and
using organism.common_name for "potato". So what are specific use-cases which
make organismgroup and organismgroup_member necessary?
Best,
-Dave
>From gmo...@li... Thu Sep 24 10:06:51 2009
>> To: David Emmert <em...@mo...>
>> Cc: gmo...@li...
>> Subject: Re: [Gmod-schema] defining organism groups
>>
>> yes, if you have a library from multiple organisms or multiple accessions
>> you would need wither a linking table
>> (library_organism, library_stock)
>> or a group_id.
>>
>> I can think now of groups of organisms or accessions (stocks).
>> This means a more generic 'groups' table will be more suitable.
>>
>> Storing the grouping info in organismprop or stockprop will give the same
>> data about the group members, but wouldn't it be difficult to link other
>> objects (libraries, unigenes,) to the group?
>>
>> -Naama
>>
>>
>>
>>
>>
>> On Thu, Sep 24, 2009 at 9:47 AM, David Emmert <em...@mo...>wrote:
>>
>> >
>> > Hi,
>> >
>> > >> Good point. A group can include accessions stored in the stock table.
>> > >> If I have a library constructed from several strains, where would this
>> > >> grouping info go?
>> >
>> >
>> > I hate to muddy the waters (yet more!?), but if what we're talking about
>> > is libraries and collections, maybe it would make more sense to use the
>> > library module?
>> >
>> > FlyBase currently is using the library module to manage the following
>> > collections of features:
>> >
>> > fb_2009_08_reporting_test=> select distinct(cvt.name)
>> > from cvterm cvt, library l
>> > where l.type_id = cvt.cvterm_id;
>> > name
>> > -----------------------------
>> > dsRNA construct collection
>> > cDNA collection
>> > dsRNA amplicon platform
>> > expression microarray
>> > RNA-Seq junction collection
>> > cDNA library
>> > (6 rows)
>> >
>> > Everything but the RNA-Seq junctions are public in FlyBase now. This link
>> > will give you a list of library/collection reports in FlyBase:
>> >
>> >
>> > http://flybase.org/cgi-bin/quicksearch.cgi?species=all&field=ALLTEXT&db=fblc&addata=all&context=FBlc*&authors=&year=&alltext=&caller=quicksearch
>> >
>> > If I'm understanding your requirements, we'd probably need to move
>> > library.organism_id into a linking table (library_organism or whatever)
>> > to support libraries from multiple organisms, but if it makes the library
>> > module more generally useable, we should do it.
>> >
>> > Anyway, just a suggestion...
>> >
>> > -D
>> >
>> >
>> > From gmo...@li... Thu Sep 24 00:20:18 2009
>> > >> To: Isabelle Phan <isa...@sb...>
>> > >> Cc: "sc...@sc..." <sc...@sc...>,
>> > >> gmod schema <gmo...@li...>
>> > >> Subject: Re: [Gmod-schema] defining organism groups
>> > >>
>> > >> Good point. A group can include accessions stored in the stock table.
>> > >> If I have a library constructed from several strains, where would this
>> > >> grouping info go?
>> > >>
>> > >> -Naama
>> > >>
>> > >>
>> > >>
>> > >> On Wed, Sep 23, 2009 at 8:36 PM, Isabelle Phan <isa...@sb...
>> > >wrote:
>> > >>
>> > >> > Agreed. I think the correct module would be 'taxonomy', but organism
>> > is
>> > >> > fine.
>> > >> > Note that the current table structure (genus, species, strain) breaks
>> > down
>> > >> > for some bacteria (and also viruses, though I guess these are not
>> > included
>> > >> > in Model Organisms).
>> > >> >
>> > >> > Isabelle
>> > >> >
>> > >> > --
>> > >> > Isabelle Phan, DPhil
>> > >> > Seattle Biomedical Research Institute
>> > >> > +1(206)256 7113
>> > >> >
>> > >> >
>> > >> >
>> > >> > > -----Original Message-----
>> > >> > > From: Hilmar Lapp [mailto:hl...@du...]
>> > >> > > Sent: Wednesday, September 23, 2009 2:07 PM
>> > >> > > To: Robert Buels
>> > >> > > Cc: sc...@sc...; gmod schema
>> > >> > > Subject: Re: [Gmod-schema] defining organism groups
>> > >> > >
>> > >> > >
>> > >> > > On Sep 23, 2009, at 2:12 PM, Robert Buels wrote:
>> > >> > >
>> > >> > > > Question is, should they go into
>> > >> > > >
>> > >> > > > A.) the organism module
>> > >> > > > B.) the phylogeny module
>> > >> > >
>> > >> > >
>> > >> > > As stated so far the rationale behind it doesn't strike me as
>> > >> > > having much or anything to do with phylogeny, so I vote for A.
>> > >> > >
>> > >> > > Organismprop could be used too. If you wanted to attach
>> > >> > > semantics to the grouping, it'd probably be the better way of
>> > >> > > doing this. Or the group table should have a link to cvterm.
>> > >> > >
>> > >> > > -hilmar
>> > >> > > --
>> > >> > > ===========================================================
>> > >> > > : Hilmar Lapp -:- Durham, NC -:- hlapp at duke dot edu :
>> > >> > > ===========================================================
>> > >> > >
>> > >> > >
>> > >> > >
>> > >> > >
>> > >> > >
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