Re: [XMLPipeDB-developer] Multi-species GMBuilder testing info at link below

[Richard B. <rbr...@gm...>]

Hi Dondi,

Yes the idea was to compare the original row count values of the Combined
GDB to the sum of the original row count values of each Single Species GDB.

I updated the spreadsheet for clarity so I hope it makes more sense when
reviewed.

In regard to spreadsheet comments, the sharing of GO terms made sense to me
but the InterPro and Pfam results did not.

But my assumption of InterPro and Pfam being another full gene id system
was incorrect...

   - InterPro is a db of protein signatures which likely doesn't have
   1:1 correspondence to the Ordered Locus IDs
   - Pfam is a db of protein multiple sequence alignment and profile hidden
   Markov models which also doesn't likely have a 1:1 correspondence to the
   Ordered Locus IDs.

So I withdraw my questions and submit that the Ms-Mt combined GDB in fact
is OK. Of course Dr. D still has to weigh in on the matter =D

Richard

On Mon, Jan 2, 2012 at 2:06 AM, John David N. Dionisio <do...@lm...>wrote:

> Hi Rich,
>
> Thank you for the updates.  There's been quite a bit of information to
> absorb, but that last wiki page really helped to sum things up.  Things
> look OK to me; on the combined export, what precisely do the "combined
> rows" and "individs added" columns mean?  My guess is that "combined rows"
> is the actual number of rows found, while "individs added" is the sum of
> what you found for each individual species. It seems, then, that your
> questions on the InterPro and Pfam rows hint at strong overlap between IDs
> from the two species.  Am I understanding the numbers and your questions
> correctly?
>
> If so, then it seems that the course of investigation would be to identify
> the overlapping IDs (i.e., IDs that are in both individual species records)
> then count them up to see if they make up the difference.  You can probably
> hit either the PostgreSQL database or the original XML files; what would
> vary would be the tools you would use (SQL in the former, assorted text
> processing commands in the latter).
>
> The above course of action is based on whether I understand the issue, so
> please see first if what I've written lines up with your thoughts, or if
> further explanation is required.
>
> The other data look good though --- nice to see things line up well
> otherwise!
>
> John David N. Dionisio, PhD
> Associate Professor, Computer Science
> Associate Director, University Honors Program
> Loyola Marymount University
>
>
>
> On Jan 1, 2012, at 9:23 PM, Richard Brous wrote:
>
> > The GDB testing results have been updated (and corrected in some cases)
> and placed on wiki.
> >
> > Please review and provide feedback when able.
> >
> >
> https://sourceforge.net/apps/mediawiki/xmlpipedb/index.php?title=GDB_Verification_and_Testing
> >
> > Thank you!
> >
> > Richard
> >
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