[GUSDEV] GUS schema questions

[Robert O. <ol...@mc...>]

I've been trolling thru the schema browser trying to map the concepts  
in SEED to those in the schema. (If you want an idea about the system  
I am discussing, our public SEED server is available at http:// 
theseed.uchicago.edu/FIG/index.cgi ).

I think I've mapped most of them, with the following exceptions.

I asked this in the workshop yesterday, thought I'd repeat it here  
for the larger group, with a motivating example.

In the SEED, we support having multiple genomes installed for any  
given taxon. For instance, we have a genome we tag as 630.1 which is  
Yersinia enterocolitica from NCBI Refseq, and 630.2 which is Sanger's  
version of that organism. It was discussed in the workshop to use the  
external database version to tag the difference between these in GUS,  
but that seems clumsy to me (since I may want that to tag overall  
SEED data versions). I'm curious what the rank attribute on  
DoTS.Taxon is intended to be used for; it seems possible I could  
subvert that to use as the organism version indicator.

The other one is mapping feature annotations. The SEED being a genome  
annotation system, we need to support the storage of multiple  
annotations for each feature. The presentation software uses a set of  
rules to decide which annotation to display as the "current"  
annotation for a feature (where the usual rule is "latest annotation  
from a trusted user"). Is DoTS.NAGene the right place to put this,  
where I'd create a NAFeatureNAGene entry that links the NAFeature for  
the feature in question to the set of NAGenes containing the  
annotations?

thanks,
--bob