Re: [Gusdev-gusdev] GUS 3.0 schema changes

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

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
>>
>>--
>>Jonathan Crabtree
>>Center for Bioinformatics, University of Pennsylvania
>>1406 Blockley Hall, 423 Guardian Drive Philadelphia, PA 19104-6021
>>215-573-3115
>>
>>  ------------------------------------------------------------------------
>>                              Name: gus.phenotype_draft.doc
>>   gus.phenotype_draft.doc    Type: Winword File (application/msword)
>>                          Encoding: base64
>>    
>>
>
>  
>