Re: data modeling genes and alleles... help!

On Mar 30, 2013, at 3:38, Modulok <modulok(at)gmail(dot)com> wrote:

> List,
>
> I have a data modeling problem. That much, I know. The question is how do I
> model this? (Below.)
>
> I'm making a database which will store pseudo-genetic data. It's a basic
> many-to-many setup::
>
> create table person(
> name varchar(32) primary key
> );
> create table gene(
> name varchar(32) primary key
> );
> create table person_gene(
> person varchar(32) references person(name),
> gene varchar(32) references gene(name)
> );

If my vague memories of high-school biology are right, then I think you might be on the wrong track here.

> Great. This is important as I need to be able to ask questions like "who
> carries gene 'x'?" as well as "what genes does person 'y' carry?" But then
> things get thorny...
>
> I also need to store the properties of the individual genes (the alleles). This
> is akin to an instance of one of the many gene classes in my application code.
> So I make more tables::
>
> create table hair(
> id serial primary key,
> density float,
> thickness float
> );
> create table eye(
> id serial primary key,
> pupil_type int
> );
>
> How do I store a reference to this data? I'd add a column to the person_gene
> table, but it points to what? I can't reference a column name because they're
> all stored in different tables. I also can't store them in the same table, as
> they all store different data. Do I store the *table name* itself in a column
> of the gene_table? (Smells like a klude.)

Aren't alleles related to genes? (Hence my previous remark)

If that's the case, you'd add a gene foreign key to each allele table and then store which alleles are related to a person instead of which genes are related to a person. The genes then follow from the alleles.

Is that closer to what you're after?

Alban Hertroys
--
If you can't see the forest for the trees,
cut the trees and you'll find there is no forest.