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

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

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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