[GUSDEV] Fwd: SequenceGroup table

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

Hi All,
Have not gotten any response to the email so am taking this as an  
indication that it's OK to move ahead with this proposal.
Will set this up in our local instances but also put this on the GUS  
bug tracker for inclusion in the next release.

BTW, we really are planning to have another release. This month we  
hope to have someone start going through all the patch, bug fixes,  
and schema changes on the tracker to plan the release.

Cheers,
Chris

Begin forwarded message:

> From: Chris Stoeckert <sto...@pc...>
> Date: February 21, 2007 6:09:07 PM EST
> To: GUS-Dev gusdev-gusdev <gus...@li...>
> Subject: SequenceGroup table
>
> Hi,
> We are loading a new set of OrthoMCL generated ortholog groups into  
> an instance of GUS and found that the current  SequenceGroup parent  
> table has several specifically-named attributes (i.e., no generic  
> attributes) that we can use for our purposes without renaming. The  
> attributes we want to capture are quality metrics for an ortholog  
> group. For example we'd like to capture the ave e-value rather that  
> min and max as currently provided in SequenceGroup and all of its  
> views including OrthologGroup.
>
> I'd like to make the following proposal, get feedback, and put in  
> the GUS schema bug tracker.
> 1) Create a OrthoMCL view. This would be specific to our GUS  
> instances but could be used as a template for renaming attributes  
> in OrthologGroup. On the right I've indicated with <- the parent  
> attribute that might be used where the name differs.
>
> Column	nulls?	type
> SEQUENCE_GROUP_ID	NO	NUMBER
> SUBCLASS_VIEW	NO	STRING(100)
> NAME		STRING(500)
> DESCRIPTION		STRING(2000)
> NUMBER_OF_MEMBERS	NO	NUMBER
> NUMBER_OF_TAXA		NUMBER
> AVE_PERCENT_IDENTITY		FLOAT <-MIN_MATCH_IDENTITY
> AVE_PERCENT_COVERAGE		FLOAT  <- MIN_PERCENT_MATCH
> AVE_E_VALUE		FLOAT <- MIN_PVALUE_MANT
> AVE_DOMAIN_SHARING		FLOAT <- MAX_SCORE
> BLAST_MATCH_RATIO		FLOAT <- MIN_SCORE
> SEQ_GROUP_EXPERIMENT_ID		FOREIGN KEY
> plus the usual housekeeping columns
>
> In this proposal, the OrthoMCLGroup attributes would have the same  
> type but different semantics as implied by the names of attributes  
> in the parent class and queries can easily avoid this by use of  
> subclass view.
>
> 2) Rename the SequenceGroup attributes to be more generic.  
> Suggested changes are:
> MAX_MATCH_IDENTITY -> GROUP_IDENTITY_METRIC1
> MIN_MATCH_IDENTITY -> GROUP_IDENTITY_METRIC2
> MAX_PERCENT_MATCH -> GROUP_MATCH_METRIC1
> MIN_PERCENT_MATCH -> GROUP_MATCH_METRIC2
> MAX_PVALUE_MANT -> GROUP_PVALUE_MANT
> MAX_PVALUE_EXP -> GROUP_PVALUE_EXP
> MAX_PVALUE_MANT -> GROUP_EVALUE_MANT
> MAX_PVALUE_EXP -> GROUP_EVALUE_EXP
> MAX_SCORE -> GROUP_QUALITY_METRIC1
> MIN_SCORE -> GROUP_QUALITY_METRIC2
>
> Thoughts?
> Chris
>
> Chris Stoeckert, Ph.D.
> Research Professor, Dept. of Genetics
> 1415 Blockley Hall, Center for Bioinformatics
> 423 Guardian Dr., University of Pennsylvania
> Philadelphia, PA 19104
> Ph: 215-573-4409 FAX: 215-573-3111
> http://www.cbil.upenn.edu
>
>