Re: [Gusdev-gusdev] GUS 3.0 schema changes

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

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
>> >
>> > --
>> > 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
>> >