Re: Advice for using integer arrays?

[Michael Heaney <mheaney@xxxxxxxx>]

On 1/6/2015 2:19 PM, Jeff Janes wrote:

On Tue, Jan 6, 2015 at 9:09 AM, Michael Heaney <mheaney@xxxxxxxx> wrote:

I'm fairly new to Postgres, and have a design issue for which an array of integers might be a good solution.  But I'd like to hear from the experts before proceeding down this path.

Essentially, I'm trying to model the relationship between a group of biological samples and their genes. Each sample (there are ~10K of them now, with more coming) will have about 30,000 genes. Conversely, a particular gene may be present in almost all samples.

So I've created the following table to handle the many-to-many relationship:

 create table sample_gene (id serial, sample_id int, gene_id int);

What is the value of having this table at all?  It doesn't seem to contain anything informative, like an allele identifier, a resequence, or a copy number variation.  If you are just trying to record the fact that a gene was present in that sample, perhaps it would be better to instead record the genes have been deleted, rather than the ones that have not been deleted?  That would probably be a much smaller list.

I suppose there could be a gene table which would contain data about each gene_id.
But I'm an IT guy, not a biologist, and my sample_gene table doesn't actually
exist.  I'm more concerned with how to deal with many-to-many relationships
when each parent could have tens of thousands of children.  Collapsing all
the children into an array for each parent looked intriguing - but maybe it's
not a good idea.  I just don't know, so I thought I'd ask you guys.

 

 create table sample_gene_array (id serial, sample_id int, gene_id int [] );

So now the table data looks like this:

sample_id    |    gene_id []
---------------------------------------
1                 |      [1:30475]
2                 |      [1:29973]
etc.

I'm not familiar with the square bracket and colon as a syntax for expressing int arrays.  Are you taking liberties with the psql output, or using a different client program?  Does that represent the range from 1 to 30475, or the two values 1 and 30475?

Yes, it's shorthand for the full range of values from 1 to 30475.  Wasn't sure how
to represent it, and almost went with (1,2,3...30475).  Apologies...


Michael Heaney
JCVI