Re: [Gusdev-gusdev] GUS 3.0 schema changes

[Chris S. <sto...@pc...>]

Dear Joan and Arnaud,
The CVS structure should not come into the XML used by the plug-in. It  
is my understanding that only the actual schema of the structure:  
Database.Namespace.Table.Attribute should be used.

Chris

On Monday, January 20, 2003, at 10:23  AM, mazz wrote:

> 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
>>>>>>
>>>>>>
>>>>>>
>>
>> -------------------------------------------------------
>> This SF.NET email is sponsored by: FREE  SSL Guide from Thawte
>> are you planning your Web Server Security? Click here to get a FREE
>> Thawte SSL guide and find the answers to all your  SSL security  
>> issues.
>> http://ads.sourceforge.net/cgi-bin/redirect.pl?thaw0026en
>> _______________________________________________
>> Gusdev-gusdev mailing list
>> Gus...@li...
>> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>
>
>
> -------------------------------------------------------
> This SF.NET email is sponsored by: FREE  SSL Guide from Thawte
> are you planning your Web Server Security? Click here to get a FREE
> Thawte SSL guide and find the answers to all your  SSL security issues.
> http://ads.sourceforge.net/cgi-bin/redirect.pl?thaw0026en
> _______________________________________________
> Gusdev-gusdev mailing list
> Gus...@li...
> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>