Re: [GUSDEV] GUS schema questions

[Aaron J. M. <am...@pc...>]

On Jul 8, 2005, at 9:43 AM, Robert Olson wrote:

> 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.
>

You have multiple genomes for one organism.  That one organism is in  
DoTS.Taxon, and it's rank is what the NCBI taxonomy database  
specifies as "genus", "phylum", "subspecies", etc.

You want each version of the genome (i.e. the nasequence entries)  
"tagged" by the different database release versions.  You don't have  
to further "tag" the associated data, as they are already tied to the  
nasequence entries, so it's not as clumsy as it may seem at first.

-Aaron

--
Aaron J. Mackey, Ph.D.
Project Manager, ApiDB Bioinformatics Resource Center
Penn Genomics Institute, University of Pennsylvania
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