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

[Arnaud K. <ax...@sa...>]

Chris

please find attached the documentation file. Let me know if the syntax 
is not correct.

This doc file gives information about the proposal I sent. It also 
includes some comments, following the feed-back you sent.

The proposal needs now to incorporate your feed-back, in particular 
regarding the controlled vocabulary tables.

cheers
Arnaud

Chris Stoeckert wrote:

> 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 ...).
>
>
>