Re: [Gusdev-gusdev] GUS 3.0 schema changes

[mazz <ma...@sn...>]

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
> >>>>
> >>>>
> >>>>
>
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