Re: [Gusdev-gusdev] GUS 3.0 schema changes

[Arnaud K. <ax...@sa...>]

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