Re: [Gmod-schema] [Heliconiusdb-devel] stock module

[<wom...@nc...>]

I agree.  We have a sample table that seems exactly the same thing as
biomaterial and designed for the same reasons.  Owen



> For biodiversity or population diversity studies a stock is a
> collection of animals which share common properties, for example
> ancestry (cross) or field collection. While I suppose you can call a
> collection of animals 'biomaterial' if you wanted to I am a bit
> concerned that we might be conflating things that are possibly
> conceptually different enough to have less in common that they do share.
>
> A 'biomaterial' used for an experiment may reference a stock; I guess
> you could express this as a relationship between biomaterials if you
> want.
>
> This is the comment in the DDL:
>
> a biomaterial represents the MAGE concept of BioSource, BioSample,
> and LabeledExtract.  it is essentially some biological material
> (tissue, cells, serum) that may have been processed.  processed
> biomaterials should be traceable back to raw biomaterials via the
> biomaterialrelationship table.
>
> This definition makes a lot of sense in the context of expression
> profiling, but makes no sense if used for stocks in the context of
> diversity studies.
>
> This is the comment in the stock DDL:
>
> A stock is the physical entities, either living or preserved, held by
> collect
> ions. Stocks belong to a collection; they have IDs, type, organism,
> description
> and may have a genotype.
>
> What is the definition that people at FlyBase is using for the stock
> table?
>
> 	-hilmar
>
> On Jan 24, 2007, at 3:41 PM, Kathleen Falls wrote:
>
>> Dear all,
>>
>> When Flybase needed to implement stocks in chado I actually had a look
>> at rad in the expression module. The entities needed for the stock
>> table
>> were very close to what was in the biomaterial table. I didn't use
>> it as
>> the comments were very microarray oriented.
>> Could biomaterial and biomaterial_relationship be extracted out, as
>> proposed below? Would there be a biomaterials module to replace the
>> stock module? The relationship and prop tables now in stock could be
>> biomaterial relationships and prop.
>>
>> Cheers,
>>
>> Kathleen
>>
>>> One option that occurs to me is to extract out the tables in the
>>> expression module that could be used as a stock module and make the
>>> expression module depend on those tables (thus not really changing
>>> the
>>> expression module) to make the (new-expression derived) stock module
>>> more logically stand alone.  How's that for an option?
>>>
>>> Thanks,
>>> Scott
>>>
>>>
>>> On Thu, 2007-01-18 at 16:37 -0500, Hilmar Lapp wrote:
>>>> I see that there's a new module called 'stock'. This is very
>>>> interesting to our work on the diversity extension, but I don't
>>>> recall that this has been discussed on the list before.
>>>>
>>>> What I can find on the list is the recent phenotype thread in which
>>>> it is mentioned that ParameciumDB (and FlyBase?) had added this to
>>>> their installation. Is there more where I can read up on the
>>>> rationale or use case or context?
>>>>
>>>> If anyone is interested, the extension module we are developing is
>>>> right now in the heliconiusdb project on sf.net. The schema is at
>>>>
>>>> http://heliconiusdb.svn.sourceforge.net/viewvc/heliconiusdb/trunk/
>>>> schema/diversity.sql?view=markup
>>>>
>>>> (or http://tinyurl.com/yvq9b2 if your email reader breaks up the
>>>> long
>>>> url)
>>>>
>>>> You will see that we also have a table "stock". At this point it is
>>>> incompatible with the table in the stock module, which I find
>>>> undesirable (I'd rather reuse the one from the stock module).
>>>> Specifically, some of the things we need to be able to do but can't
>>>> with the stock.stock table:
>>>>
>>>> 	- there is no single organism, instead there are multiple due to
>>>> hybridization (the collection of which we call biotype right now)
>>>> 	- need references to the parental biotypes
>>>> 	- need to reference a geolocation
>>>> 	- need to reference the experimenter
>>>>
>>>> Except for the mandatory organism foreign key in the stock module, I
>>>> think the differences are reconcilable though through association
>>>> tables and attribute/value tags. I was wondering who is best to
>>>> be in
>>>> touch with, and I'm also happy to thrash this out on the list.
>>>>
>>>> Finally, it seemed that there needed to be a vetting period or
>>>> general consensus before a module would be added. Is this a
>>>> misconception of mine, and should I maybe just go ahead and commit
>>>> the diversity module to the chado/modules directory and continue to
>>>> develop it there? This may help with reconciling differences and
>>>> avoiding duplication.
>>>>
>>>> Any feedback/suggestions appreciated ...
>>>>
>>>> 	-hilmar
>>> --
>>> ---------------------------------------------------------------------
>>> ---
>>> Scott Cain, Ph. D.
>>> ca...@cs...
>>> GMOD Coordinator (http://www.gmod.org/)
>>> 216-392-3087
>>> Cold Spring Harbor Laboratory
>>>
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> --
> ===========================================================
> : Hilmar Lapp  -:-  Durham, NC  -:- hlapp at duke dot edu :
> ===========================================================
>
>
>
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