[Gmod-schema] strains, alleles ,genotypes and things that go bump in the night

[Charles H. <ch...@du...>]

Hi all,

I'm looking to try to populate chado with data pertaining to
Locus,allele,strains.

A locus for me is any mappable entity. 
While many loci are also genes, molecular markers such as RFLPs can also
qualify as loci. 
An allele is a genetic variant form of a locus. 
A strain (fly stock for you) is an organism carrying a set of alleles.

 
Contained in the gadfly_08 release is a table 'genotype' which can hold
allele data.

To denote a strain, is the plan then to create a table 'Stock/Strain'
with FKs to genotype and organism?

    Column     |  Type   |                               Modifiers                               
---------------+---------+-----------------------------------------------------------------------
 strain_id 	| integer | not null default nextval('public.strain_strain_id_seq'::text)
 genotype_id    | integer | not null
 organism_id    | integer | not null


Ideas,suggestions,plans?

regards,

Charles


example of allele class data:


<?xml version="1.0" standalone="yes"?>

<Allele class="Allele" value="arg7">
    <Locus class="Locus" value="ARG7" />
    <Phenotype class="#Text" value="Arginine-requiring" />
    <Mutagen class="Reagent" value="Nitrosoguanidine" />
    <Origin class="#Text" value="Isolated by Gillham in Levine's laboratory, after mutagenesis with 50 micrograms/ml nitrosoguanidine" />
    <Strain class="Strain" value="CC-50 arg7 mt+" />
    <Strain class="Strain" value="CC-127 arg2/arg7 mt-" />
    <Strain class="Strain" value="CC-1306 arg7 cw15 imp2" />
    <Strain class="Strain" value="CC-1308 arg7 cw15 imp7" />
    <Paper class="Paper" value="Gillham (1965a)" />
</Allele>