Re: [GUSDEV] Preliminary 3.5 Schema

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Hi Mike,

Here are what I found from different documents which show difference.

  	Gus 3.5 Road Map 	schemaBrowser35 (online) 	gus_35 (distributed 
schema file)
table name 	  	DoTS::AASequenceImp 	DoTS.AASequence 
  	  	DoTS::AAFeatureImp 	DoTS.AAFeature
  	  	DoTS::NASequenceImp 	DoTS.NASequence 
  	  	DoTS::NAFeatureImp 	DoTS.NAFeature

column 	SRes.ExternalDatabase remove lowercase_name column 
lowercase_name column exists 	lowercase_name column is gone

Also, for DoTS::AASequenceImp and DoTS::NASequenceImp, the online 
schemaBrowser35 doesn't display for details of columns.

Thanks,

Jian

Michael Saffitz wrote:

>
> All,
>
> The latest proposed GUS 3.5 schema is attached.  This draft has 
> numerous changes since the previous release, including the addition of 
> a few dozen missing views, the changes outlined below, and other cleanup.
>
> This draft has a small error in which the first subclass for a 
> particular superclass appears twice.  I'm trying to track down and 
> resolve that, but it appears to only affect this simple text reports, 
> not the actual DDL. Schemas and tables are in alphabetical order, but 
> capitalization is wreaking a little bit of havok on that.  I hope to 
> fix that in a future draft as well.
>
> There are some additional PROT changes that this draft does not 
> include.  I will send another draft Wednesday with those changes.
>
> Please submit comments/changes/etc. as soon as possible.  The 3.5 
> schema is scheduled to be frozen at the end of this week and all 
> resources will turn at that time to preparing the application level 
> code for release.
>
> Thanks,
>
> Mike
>
> DoTS:
>
> * Drop DoTS.PlasmoAPFeature view
>
> * Drop DoTS.MassSpecSummary
>
> * DoTS.GeneFeatureSeqOverlap.SIMILARITY_ID will have a foreign key 
> constraint to DoTS.SIMILARITY
>
> * DoTS.NASequenceImp.SOURCE_NA_SEQUENCE_ID will have a foreign key 
> constraint to DoTS.NASequenceImp
>
> * DoTS.SecondaryStructure.AA_SEQUENCE_ID will have a foreign key 
> constraint to DoTS.AASequenceImp.  
> DoTS.SecondaryStructure.PRED_ALG_INVOCATION_ID will have a foreign key 
> constraint to Core.AlgorithmInvocation.
>
> * DoTS.SecondaryStructureCall.Secondary_Structure_ID will have a 
> foreign key constraint to DoTS.SecondaryStructure
>
> * DoTS.AASequenceEnzymeClass.AA_Sequence_ID will have a foreign key 
> constraint to DoTS.AASequenceImp, and 
> DoTS.AASequenceEnzymeClass.EC_ASSIGNMENT_CONTACT_ID will have a 
> foreign key constraint to SRES.CONTACT
>
> * DoTS.ConsistentAlignment.SIMILARITY_ID will have a foreign key 
> constraint to DoTS.Similarity
>
> * DoTS.RejectedMotif.External_Database_Id will have a foreign key 
> constraint to SRes.ExternalDatabase. 
> DoTS.RejectedMotif.External_Database_release_id will have a foreign 
> key constraint to SRes.ExternalDatabaseRelease
>
> * DoTS.Similarity.Subject_Table_ID and DoTS.Similarity.Query_Table_id 
> will have foreign key constraints to core.tableinfo
>
> * DoTS.PlasmoMap has been renamed to DoTS.MicroSatelliteMap
>
> Prot:
>
> * Prot.OntologyEntry has been removed
>
> * Prot.StudyAssay has been added.
>
> * Prot.StudyDesignAssay has been added
>
> * Prot.StudyBioMaterial has been added
>
> * Prot.AcquisitionChannel has been added
>
> SRes:
>
> * SRes.ExternalDatabaseKeyword has been moved to DoTS
>
> RAD:
>
> * RAD.ScanAlyzeElementResult.top,left,bot,right have had _coordinate 
> appended to them
>
> * The RAD.DataTransformationResult has been added as a view on 
> RAD.AnalysisResultImp
>
> * RAD.ReporterArray has been renamed to RAD.ArrayDesign.  This impacts 
> the following changes:
>  - RAD.ArrayAnnotation -> RAD.ArrayDesignAnnotation
>  - RAD.ArrayGroup -> RAD.ArrayDesignGroup
>  - RAD.ArrayGroupLink -> RAD.ArrayDesignGroupLink
>  - and associated column changes
>
> * RAD.CompositeElementGus has been dropped
>
> * RAD.MageDocumentation and RAD.Mage_ML have been dropped.
>
> * RAD.Channel has been removed
>
> Study:
>
> * Study.Ontology* tables have been dropped.  This includes ontology, 
> ontologyannotation, ontologyrelationship, ontologyterm, ontologytype.  
> This DOES NOT include study.ontologyentry.
>
> * Study.BioSample, Study.BioSource, and Study.LabeledExtract have been 
> added as views on Study.BioMaterial
>
> * Moved Study.BioMaterialMeasurement to Prot and a copy to RAD.
>
> * Study.Parameter* tables have been moved to prot.  This includes 
> parameter, parameterinstance, parameterizable, 
> parameterizableinstance, and paramterizablelink
>
> --On April 21, 2005 3:20:15 PM -0400 Michael Saffitz 
> <msa...@pc...> wrote:
>
>>
>> Since releasing the preliminary 3.5 schema, the following changes have
>> been proposed.  The list below only covers App, SRes, and Core-- other
>> schema changes will come early next week.
>>
>> The scheduled freeze date for the 3.5 schema is 4/29.  If there are no
>> objections to the items below, Core and App will be frozen for 3.5 on
>> 4/25 (more SRes changes may be coming early next week).
>>
>> Consult the road map for full changes.  The list below are just new
>> changes since sending this previous email.  They'll be added to the road
>> map after feedback from the list is received.
>>
>> App:
>>
>> * The App schema has been deprecated.  The remaining few tables that 
>> were
>> in app will be moved to non-GUS project specific schema (i.e. a Study
>> Annotator schema).
>>
>> Core:
>>
>> * The workflow tables have been deprecated as they were never actually
>> used.  This includes core.workflowstatus, core.workflowedge,
>> core.workflowinit, core.workflowedgesql, core.workflow,
>> core.workflowblackboard, and core.workflowstatus
>>
>> * core.generaldocumentation is tentatively deprecated, pending the lack
>> of objections from this list.
>>
>> * core.userdatabase is tenetively deprecated, pending the lack of
>> objections from this list.
>>
>> SRes (tentative, pending more review)
>>
>> * SRes.SequenceOntology.SO_ID will be a VARCHAR(12), not a NUMBER(10)
>>
>> * SRes.MGEDOntologyRelationship will be named SRes.OntologyRelationship
>>
>> * SRes.MGEDOntologyTerm will be named SRes.OntologyTerm
>>
>> * SRes.BibliographicReference.authors will be nullable, to support the
>> alternative BibRefAuthor linking table.
>> SRes.BibliographicReference.External_Database_Release_ID will gain 
>> the FK
>> the ExternalDatabaseRelease table
>>
>> * SRes.BibRefAnnotation is tentatively deprecated, pending the lack of
>> objections from this list.
>>
>> Thanks,
>>
>> Mike
>>
>>
>> --On April 7, 2005 1:53:44 PM -0400 Michael Saffitz
>> <msa...@pc...> wrote:
>>
>>>
>>> All,
>>>
>>> Development work on the GUS 3.5 Schema is nearing completion, and we'd
>>> like to take this opportunity to solicit community feedback and provide
>>> the 3.5 schema for review.
>>>
>>> With the 3.5 Schema nearly finalized, we're now turning our 
>>> attention to
>>> ensuring compatibility in the object layer and with plugins for 3.5. 
>>> Once
>>> done, GUS 3.5 will be ready for release.  It's my hope that that 
>>> will be
>>> as soon as possible, but I'm hesitant to give a firm date.
>>>
>>> The attached file contains the 3.5 schema, in a simple text summary
>>> format.  When reviewing the file, please keep the following in mind:
>>>
>>> * I've done a very preliminary analysis of the file--- there may be
>>> glaring mistakes/omissions.
>>>
>>> * All tables and views in GUS 3.5 are versioned, and the version
>>> tables/views are not displayed.
>>>
>>> * All tables and views in GUS 3.5 contain the standard housekeeping
>>> columns, which are also not displayed.
>>>
>>> * Subclass tables (marked by "extends superclass" where superclass 
>>> is the
>>> name of the parent table) only have the columns added by the subclass
>>> displayed.  For example, if the superclass has columns a, b, c, and d,
>>> then the subclass will display the column e but have all five 
>>> columns in
>>> the database.
>>>
>>> * This is an object-centric display-- the method of subclassing 
>>> (i.e. use
>>> of imp tables) is not changing.  As a result, Imp tables are not
>>> displayed, nor are super/sub classes flagged as views.
>>>
>>> * The Type of a column with a foreign key is the name of the foreign 
>>> key
>>> table.  For example, a table with a column NA_FEATURE_ID with a foreign
>>> key to DoTS.NAFEATURE will have a type of DoTSS.NAFEATURE.  This is the
>>> only way foreign keys are displayed in this view.
>>>
>>> * All tables first column serves as the Primary key.  There is no
>>> denotation for the primary key (although it will also appear as an 
>>> index
>>> against the first column).  Some tables are missing primary keys in 
>>> this
>>> document-- it will be fixed soon.
>>>
>>> * All indexes for a table are displayed.
>>>
>>> Please let me know if you have any questions/concerns.
>>>
>>> Thanks,
>>>
>>> Mike
>>
>>
>>
>>
>>
>>
>>
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>
>
>
>