[BioSQL-l] Microarrays and BioSQL

[Marc Colosimo]

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