[BioSQL-l] Microarrays and BioSQL

[Jansen E Lim]

Marc,

If you're interested in storing Affy data you might want to look at their GATC
schema.  We've
implemented this schema back in 1999. We've added many other tables to the
schema to
capture other types of info.  The BioSQL schema is really meant as sequence
repository; e.g.
GenBank sequence, SwissProt, etc.

Marc Colosimo wrote:

> Like William, I am interested in building a database to sort our Affy
> Microarray data. I came to the conclusion that I cannot use much of BioSQL
> to store our data. It came as a surprise to me that I cannot easily
> incorporate the simplest sequence data. Here is my problem:
>
> Each gene has at least 11 oligos for it. They have the same name, like
> 171720_x_at. I have files for the target sequence (500bp), the sequence of
> each oligo and their positions, and a file that has descriptions of the
> probes. At a minimum I have 13 items, each with the same name.
>
> For the descriptions, I have references to various databases and in many
> cases the chromosome the gene is on and the what protein it codes. From
> what I can tell, there is no simple way to incorporate this data about a
> gene. Features really do not cover this. I could make several externalDB
> refs for the other stuff. But, I would like it all to be in one place.
>
> Maybe I completely missed the boat. Do people know of any other opensource
> db for this that also has MIAME tables? I really do not want to reinvent
> the wheel here.
>
> Thanks,
> Marc
>
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