[BioSQL-l] RE: [Bioperl-l] BioSQL and Bioperl-db inching towards release

[Hilmar Lapp]

> -----Original Message-----
> From: Allen Day [mailto:allenday at ucla.edu] 
> Sent: Friday, May 23, 2003 11:12 AM
> To: Hilmar Lapp
> Cc: Biosql; Bioperl
> Subject: Re: [Bioperl-l] BioSQL and Bioperl-db inching towards release
> 
> 
> > The next feature I'm going to add to biosql is a table for 
> expression
> > data that basically resembles the data cube with various dimensions 
> > (roughly, bioentry, term [quantitation type], term [sample 
> > annotation]). No LIMS info (yet) other than sample 
> annotation as far as 
> 
> Is the plan to add LIMS, etc info at some point?  Fully 
> represent the MAGE-OM?

No, not really. At least as far as I'm concerned. I'm happy though to
have somebody else drive this piece to be fully MAGE-OM compatible. I
just think that there are enough decent open-source expression schemas
out there already who try to do the full monty.

There may be more LIMS at some point as far as it is needed for sample
annotation, and where that can't be expressed very well using the term
table. Our use case here is tissue expression profiles, so the sample
annotation will be relatively simple and flat, at least initially.

	-hilmar

> 
> > it fits the term table. In my view, this would be a 
> post-1.0 thing. Do 
> > people agree?
> 
> Yes, if you intend to release next week :).
> 
> -Allen
> 
>