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Re: [Gusdev-gusdev] GUS 3.0 schema changes
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From: mazz <ma...@sn...> - 2003-01-20 20:51:18
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Chris, This is the designation for the table Object. package GUS::Model::DoTS::Gene; I thought this is what is needed for the table tag. Joan This is what it is for a RAD table package GUS::Model::RAD3::ElementAnnotation; Chris Stoeckert wrote: > Dear Joan and Arnaud, > The CVS structure should not come into the XML used by the plug-in. It > is my understanding that only the actual schema of the structure: > Database.Namespace.Table.Attribute should be used. > > Chris > > On Monday, January 20, 2003, at 10:23 AM, mazz wrote: > > > Dear Arnaud, > > > > Model is a directory of Steve's new CVS structure under which the DoTS > > table Objects (eg > > > > Gene) are found. > > I do not know why Steve named the directory Model. > > > > Joan > > > > Arnaud Kerhornou wrote: > > > >> Hi Joan > >> > >> Thanks. Just a quick question, what is Model for ? > >> > >> <GUS::Model::DoTS::Gene> > >> > >> Arnaud > >> > >> mazz wrote: > >> > >>> Hi Arnaud, > >>> > >>> > >>> Below is a sample of the XML for a table (e.g. Gene) the plugin > >>> will > >>> use. > >>> The controlled vocabulary table DoTS::EffectorActionType also needs > >>> to > >>> be populated. > >>> > >>> I will try to go though and make a list of the new controlled > >>> vocabulary > >>> tables. > >>> Tables such as geneCategory & rnaCategory are tables I created for my > >>> planned future annotation tasks. > >>> > >>> > >>> Joan > >>> > >>> <GUS::Model::DoTS::Gene> > >>> <gene_id>10288603</gene_id> > >>> <name>test</name> > >>> <review_status_id>1</review_status_id> > >>> <description>gene desc test</description> > >>> <reviewer_summary>test</reviewer_summary> > >>> </GUS::Model::DoTS::Gene> > >>> > >>> Arnaud Kerhornou wrote: > >>> > >>> Arnaud Kerhornou wrote: > >>> > >>> > >>> > >>>> Hi Joan > >>>> > >>>> I'll get the new controlled vocabularies ready for population. If > >>>> you're planning to use the UpdateFromXML.pm plugin for populating > >>>> GUS > >>>> I should have examples. > >>>> > >>>> Regarding ComplexType it should be covered by GO component. > >>>> Regarding InteractionType, we need to find a controlled vocabulary > >>>> which I'm not aware of yet ! > >>>> > >>>> cheers > >>>> Arnaud > >>>> > >>>> mazz wrote: > >>>> > >>>> > >>>> > >>>>> Hi Jonathan, > >>>>> > >>>>> Perhaps we can ask Matt to revisit his documentation plugin. There > >>>>> are probably > >>>>> additional changes he will have to make for its use with GUS30 now. > >>>>> Also, I can send Arnaud an example of the XML for a table. We can > >>>>> use the XML to > >>>>> populate the rows of the controlled vocabulary tables (ids, terms > >>>>> (names) and > >>>>> definitions (descriptions). > >>>>> > >>>>> > >>>>> Joan > >>>>> > >>>>> Jonathan Crabtree wrote: > >>>>> > >>>>> > >>>>> > >>>>> > >>>>>> Hi Joan- > >>>>>> > >>>>>> Arnaud did supply us with documentation (attached) for the new > >>>>>> Phenotype tables, > >>>>>> but I just haven't loaded it into the database yet (I've also been > >>>>>> quite busy :)) > >>>>>> I started working on updating the documentation a couple of days > >>>>>> ago, but in the > >>>>>> process discovered that there are some invalid rows in > >>>>>> core.DatabaseDocumentation > >>>>>> that should be corrected first. A query shows that there are 73 > >>>>>> rows in this > >>>>>> table that reference nonexistent columns in GUS 3.0. For the most > >>>>>> part I think > >>>>>> that these are relatively minor problems stemming from the fact > >>>>>> that the schema > >>>>>> has been updated more recently than the documentation. However, > >>>>>> there are also > >>>>>> a few rows that suggest we need to improve the plugin and/or > >>>>>> procedure used to > >>>>>> populate this table. For example, the following rows have spaces > >>>>>> in the column > >>>>>> name (attribute_name), probably because the input files were > >>>>>> invalid and the plugin > >>>>>> has no restrictions on the format of the attribute_name: > >>>>>> > >>>>>> DATABASE_DOCUMENTATION_ID > >>>>>> ------------------------- > >>>>>> ATTRIBUTE_NAME > >>>>>> ------------------------------------------------------------------ > >>>>>> -------------- > >>>>>> 1419 > >>>>>> bio_material_id fk to LabelledExtract view of BioMaterial > >>>>>> > >>>>>> 1103 > >>>>>> bio_source_characteristic_id primary key > >>>>>> > >>>>>> 1120 > >>>>>> treatment_id fk to Treatment > >>>>>> > >>>>>> DATABASE_DOCUMENTATION_ID > >>>>>> ------------------------- > >>>>>> ATTRIBUTE_NAME > >>>>>> ------------------------------------------------------------------ > >>>>>> -------------- > >>>>>> 1374 > >>>>>> review_status_id The identifer of the review status > >>>>>> > >>>>>> 1418 > >>>>>> assay_id fk to Assay > >>>>>> > >>>>>> 1373 > >>>>>> synonym_name The gene symbol > >>>>>> > >>>>>> 6 rows selected. > >>>>>> > >>>>>> Also, as an aside (and not a comment to you in particular), it > >>>>>> strikes me that > >>>>>> column "documentation" of the form "fk to Table X" and "Primary > >>>>>> key" could be > >>>>>> generated automatically from the schema. However, comments on > >>>>>> foreign keys > >>>>>> are useful if they identify the specific subclass (i.e. view) to > >>>>>> which the > >>>>>> reference is expected to link, or if they explain what the > >>>>>> referenced value is > >>>>>> used for (if not obvious). Anyway, since there are still some > >>>>>> minor schema > >>>>>> changes taking place, I think that next week might be a good time > >>>>>> to worry > >>>>>> about updating all the documentation, since the database will be > >>>>>> locked down > >>>>>> for the migration at that point anyway. As for the controlled > >>>>>> vocabularies, > >>>>>> I think you're right, and we should try to populate these as soon > >>>>>> as we can, > >>>>>> even if it will be an iterative process in some cases. > >>>>>> > >>>>>> Jonathan > >>>>>> > >>>>>> > >>>>>> > >> > >> ------------------------------------------------------- > >> This SF.NET email is sponsored by: FREE SSL Guide from Thawte > >> are you planning your Web Server Security? Click here to get a FREE > >> Thawte SSL guide and find the answers to all your SSL security > >> issues. > >> http://ads.sourceforge.net/cgi-bin/redirect.pl?thaw0026en > >> _______________________________________________ > >> Gusdev-gusdev mailing list > >> Gus...@li... > >> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > > > > > > > > ------------------------------------------------------- > > This SF.NET email is sponsored by: FREE SSL Guide from Thawte > > are you planning your Web Server Security? Click here to get a FREE > > Thawte SSL guide and find the answers to all your SSL security issues. > > http://ads.sourceforge.net/cgi-bin/redirect.pl?thaw0026en > > _______________________________________________ > > Gusdev-gusdev mailing list > > Gus...@li... > > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > > > > ------------------------------------------------------- > This SF.NET email is sponsored by: FREE SSL Guide from Thawte > are you planning your Web Server Security? Click here to get a FREE > Thawte SSL guide and find the answers to all your SSL security issues. > http://ads.sourceforge.net/cgi-bin/redirect.pl?thaw0026en > _______________________________________________ > Gusdev-gusdev mailing list > Gus...@li... > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev |
