Re: [Gusdev-gusdev] GUS 3.0 schema changes

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

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