Re: [XMLPipeDB-developer] yeast export with gmbuilder-2.0b39

[John D. N. D. <do...@lm...>]

OK, thanks, I will investigate then report.

John David N. Dionisio, PhD
Assistant Professor, Computer Science
Loyola Marymount University


On Feb 4, 2010, at 8:18 AM, Kam Dahlquist wrote:

> Hi,
>
> I have results from a new export with gmb2b39 that I ran overnight.
>
> 1.  So, choosing "Saccharomyces cerevisiae" from the drop down menu  
> in the
> wizard does invoke a different species profile with different  
> modifications
> to the tables.  My recollection is that Arabidopsis and E. coli do  
> not work
> this way.  We need to think about how to deal with this issue.   
> Ideally,
> "Baker's yeast" would not be an option since it is the common name  
> for the
> species and we don't want people to use that.  However, at a  
> minimum, both
> should invoke the right species profile.
>
> 2.  However, the SGD table and the OrderedLocusNames tables are  
> completely
> missing from the exported gdb.  The TallyEngine is counting the IDs,  
> the
> relationship tables between SGD and the other ID systems are there,  
> but the
> SGD table itself is not there, nor is the OrderedLocusNames table.   
> The
> OrderedLocusNames relationship tables to other IDs are empty.  This is
> different than the "By" species profile where the SGD table got  
> made, but
> just had the "S000000000" IDs, and where the OrderedLocusNames table  
> had a
> mixture of ID types.
>
> Kam