Re: [GUSDEV] GUS schema questions

[Chris S. <sto...@pc...>]

Hi Bob,
Will try to elaborate on the answer given yesterday. Taxon is NOT to  
be used for designating version. It is the controlled vocabulary for  
organism whose genome has been sequenced (e.g., Yersinia) and is used  
to annotate any genome sequence (or transcript or protein) that  
originated from that organism. ExternalDatabase is used to tag  
datasets that have been loaded into GUS. It can be a genome sequence,  
or microarray data, or a set of ESTs. Project is used to tag datasets  
that belong together. In PlasmoDB we use this to tag the current  
genome and associated automated analyses that we may have run. In RAD  
we use this to relate microarray datasets from the same group.

In terms of the annotations, what you describe I believe is intended  
to assign a possible gene name to the feature. This is different from  
assigning the gene name (or any other annotation) to the gene itself.  
That's done at the central dogma table (DoTS.Gene). To identify the  
gene feature that is reference for a give Gene, you use  
GeneInstance.is_reference.

Hope this helps.
Chris

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

> 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
>
>
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