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

[Kam D. <kda...@lm...>]

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

At 10:33 AM 2/3/2010, Kam Dahlquist wrote:
>Hi,
>
>In my past experience, it does not matter which name is chosen in the GUI
>wizard, the program does what it does anyway (that's one of the issues with
>the GUI, that drop down menu for species doesn't seem to matter).
>
>I can confirm this, but since the export takes so long, I don't want to
>start it this morning while my students need the computer.  I can start it
>later, but we won't know the answer until tomorrow.
>
>At some point in the near future, I hope we can dump the OrderedLocusNames
>set of tables since we don't need them and creating them is probably adding
>a lot of time to the export.
>
>Kam
>
>At 10:16 AM 2/3/2010, John David N. Dionisio wrote:
> >Greetings,
> >
> >I believe the first two items may be related --- the species profile may
> >not have been triggered correctly if "Baker's yeast" is the chosen species
> >name.  Would it be possible to re-run an export with "Saccharomyces..."
> >chosen as the name?
> >
> >Good suggestion about embedding the version information...I'll include
> >that in some future build.
> >
> >John David N. Dionisio, PhD
> >Assistant Professor, Computer Science
> >Loyola Marymount University
> >
> >
> >On Feb 3, 2010, at 8:24 AM, Kam Dahlquist wrote:
> >
> > > Hi,
> > >
> > > I checked the yeast gdb export that Bernadette started yesterday 
> using the
> > > gmbuilder-2.0b39.  There are a couple issues I can see right away:
> > >
> > > 1.  The SGD table is being created, but all it has are the fields ID,
> > Date,
> > > Remarks.  The ID is the "S" form of the ID.  I went back and looked 
> at the
> > > export run last week with gmbuilder-2.ob38 and the SGD table is there,
> > > exactly like this (I just must've missed it last time).  So anyway, this
> > > build did not have any of the customizations you made for the SGD table.
> > >
> > > 2.  For some reason, these two versions of gmbuilder (38 and 39) are 
> using
> > > "Baker's yeast" instead of "Saccharomyces cerevisiae" as the species
> > > name.  This means that they are automatically naming the database with a
> > > "By_" prefix and also inserting "Baker's yeast" into the species fields
> > > throughout the database.  This is odd because I don't think it was doing
> > > this before.
> > >
> > > 3.  One last random thought.  Would it be possible to display the version
> > > of GenMAPP Builder somewhere in the GUI interface, either in an About 
> drop
> > > down menu, or just as text at the bottom the active window like
> > > "gmbuilder-2.0b39".  I realized that I could not easily check the version
> > > number of the program while it was open.  Also, it would be nice to embed
> > > the version of GenMAPP Builder into the gdb itself.  Perhaps by inserting
> > > it into the Notes field of the Info table.  Language like "Created with
> > > gmbuilder-2.0b39 available from
> > > http://sourceforge.net/projects/xmlpipedb".  I know this is an extra
> > > feature request, but it would be helpful.
> > >
> > > Thanks,
> > > Kam
> >
> >
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