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Re: [Gusdev-gusdev] Inconsistency among Sequence tables
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From: Steve F. <sfi...@pc...> - 2005-01-26 17:14:21
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Josef- Thanks for bringing up all these points. An answer to how AASequence has gone so long without taxon id is that historically, we have used proteins mostly in relationship to or translated from NASequences. But, clearly, they should have a taxon_id. Another place to look for schema issues is: http://gusdb.org/wiki/index.php/GusFourPointOhIdeas That page describes proposals being generated by a work-in-progress internal committee that is reviewing the schema for gus 4.0. You'll notice there that for 4.0 the proposal is to lose the distinction between internal and external sequences, making all sequences potentially external. steve Chris Stoeckert wrote: > Hi Josef, > Your comments are very timely in light of our plans to release GUS 3.5 > shortly which is meant to address issues such as you raise. Mike sent > mail earlier today on this but please see > http://gusdb.org/wiki/index.php/Gus3.5RoadMap > > I think that you are right about the need for taxon_id. Note that it > should probably go in AASequenceImp (the table) and be inherited by > all views. Anyone have a problem with that for GUS 3.5? > > Note that both AASequence and ExternalAASequence are views with > AASequence as the "superclass" view. external_database_release_id is a > named attribute of the parent table and so is inherited by all views. > > Cheers, > Chris > > On Jan 25, 2005, at 3:15 PM, ju...@cs... wrote: > >> >> I recently began working with the DoTS.ExternalAASequence table for >> the first time, and I noticed several discrepancies with this >> table and the DoTS.ExternalNASequence and DoTS.NASequence tables, >> one of which I feel is serious. >> >> name taxon_id description external_database_release_id >> varchar2(255) number(12) varchar2(2000) number(10) >> >> ExternalNASequence yes yes yes yes >> NASequence no yes yes no >> ExternalAASequence yes no yes yes >> AASequence no no yes yes >> >> >> Looking at the above chart, we see that both AASequence >> and ExternalAASequence lack the taxon_id. This surely must >> be an oversight, I cannot imagine why such a thing >> could be intentional. >> >> A minor annoyance is that NASequence and AASequence lack a >> "name varchar2(255)" column and therefore must have all text >> regarding a sequence in the description column. For query >> and display purposes, it is very useful to be >> able to refer to a sequence by a shorter handle. >> >> And a final odd observation: why does AASequence have >> a external_database_release_id column? If an AA sequence belongs >> to an external database, then it should be in the ExternalAASequence >> table. >> >> First, I wonder how the lack of a taxon_id column in the >> ExternalAASequence/AASequence tables has existed for so long. >> Have these tables not been used much by the GUS community? >> >> Second, I wonder if the maintainers of GUS are interested >> in addressing this issue and possibly resolving these >> discrepancies in a future GUS release. >> >> I am using Version 3.0 of the schema. >> >> >> Thanks, Josef >> >> >> >> >> Josef Jurek, Ph.D. >> >> Daphne Preuss Laboratory >> Molecular Genetics and Cell Biology >> The University of Chicago >> ju...@cs... >> >> voice: (773) 834-3985 >> fax: (773) 702-6648 >> >> >> >> >> >> ------------------------------------------------------- >> This SF.Net email is sponsored by: IntelliVIEW -- Interactive Reporting >> Tool for open source databases. Create drag-&-drop reports. Save time >> by over 75%! Publish reports on the web. Export to DOC, XLS, RTF, etc. >> Download a FREE copy at http://www.intelliview.com/go/osdn_nl >> _______________________________________________ >> Gusdev-gusdev mailing list >> Gus...@li... >> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > > > > > ------------------------------------------------------- > This SF.Net email is sponsored by: IntelliVIEW -- Interactive Reporting > Tool for open source databases. Create drag-&-drop reports. Save time > by over 75%! Publish reports on the web. Export to DOC, XLS, RTF, etc. > Download a FREE copy at http://www.intelliview.com/go/osdn_nl > _______________________________________________ > Gusdev-gusdev mailing list > Gus...@li... > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev |
