Re: [Gusdev-gusdev] DNA, RNA and Protein GUS Features + PeptidePropertyType Table

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

Hi Arnaud,
I finally went through your list. These will certainly enrich GUS! Some 
questions/issues though.
First a general request for documentation of the tables and attributes 
to explain what they are to be used for. We have a plug-in that takes a 
file in the format:

TableName\t\tdescription
TableName\tAttributeName\tDescription

In particular, I am curious as to what InflectionPointFeature and 
ReplicationFeature are.

For the NAFeature views you propose, are you using "source_id" to point 
to SRes:SequenceOntology? If so, why not call the attribute "so_id"?
Similarly, for GenomeSequence as a view of NASequence, is this what 
"source_id" is for?

The AAFeature views have "name" attributes and I wonder whether we 
should have a table in SRes for controlled vocabulary terms for protein 
features that we can point to (as with sequence ontology). This would 
avoid the uncontrolled use of "name." I notice that PeptideProperty has 
been given a controlled vocabulary table PeptidePropertyType in this 
regard. Rather than have a table for each, we could centralize them. 
Any choices for the resource to use for these names? SWISS-PROT?

Cheers,
Chris

On Tuesday, October 8, 2002, at 09:00 AM, Arnaud Kerhornou wrote:

> From: Arnaud Kerhornou <ax...@sa...>
> Date: Tue Oct 8, 2002  9:00:32 AM US/Eastern
> To: gusdev-gusdev <gus...@li...>, 
> gen...@li...
> Subject: [Gusdev-gusdev] DNA, RNA and Protein GUS Features + 
> PeptidePropertyType Table
>
> Hi
>
> I've attached the SQL statements for new views/tables in GUS3, as well 
> as updates of existing views/tables. It covers a new sequence object 
> and new DNA, RNA and protein features that we would like to use. Some 
> of them have been designed to go along Sequence Ontology 
> classification (see below).
>
> Here a summary of the list of new views or tables:
>
> Updated views/tables:
>   * NAFeatureImp - modified:
>      * name from varchar2(30) to varchar2(50)
>   * RestrictionFragmentFeature - added:
>      * type_of_cut (sticky or blunt)
>   * SignalPeptideFeature - added:
>      * targetting
>   * GeneSynonym - added:
>      * is_obsolete
>
> New views/tables:
>
> A new sequence object on the top of NASequenceImp:
>   * GenomicSequence
>
> New views on the top of NAFeatureImp:
>   * ChromosomeElement
> NB : (centromere, telomere => SO)
>   * InflectionPointFeature
>   * RepeatFeature
> NB : repeat type => SO
>   * RepeatRegionFeature
>   * ReplicationFeature
>   * TransposableElementFeature
> NB: SO would give the type
>   * RNARegulatory
>   * RNASecondaryStructure
>   * SpliceSiteFeature
>
> New views on the top of AAFeatureImp:
>   * AASecondaryStructure
>   * AATertiaryStructure
>   * DomainFeature
>   * PeptideProperty
>   * PostTranslationModification
>   * TransmembraneDomainFeature
>
> A new table:
>   * PeptidePropertyType
>
>
> Note that the design takes into account the use of the Sequence 
> Ontology (SO) to refine the types of some the features, eg to 
> differentiate the different types of transposable elements, of repeats 
> or of chromosome elements (centromere, telomere ...).