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

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

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 ...).

e.g. Transposable Elements annotations:

The different types of transposable elements would be given by specific 
SO terms. Bear in mind the procaryotes transposable elements are not 
covered by SO, but we are working on addings SO procaryotes specific terms.

Here the current SO tree for transposable elements:

Transposable Element
   ---> Non Retrotransposon
           ---> TIR Element
                   ----> Terminal Inverted Repeat
           ---> Foldback Element
  ---> Retrotransposon
           ---> LTR Retrotransposon
                  ----> Long Terminal Repeat
           ---> non LTR Retrotransposon
                 ----> LINE Element
                 ----> SINE Element

LTRs, as well as genes, part of a transposable element would be features 
attached to a TransposableElement Feature. These genes would have the 
following SO term : transposable element gene, SO0000111.
Regarding LTRs, they will be considered as Repeat Feature, annotated 
with the right Sequence Ontology terms.

Let me know if you have any comments.

cheers
Arnaud

PS: Sequence Ontology URL

=> http://www.geneontology.org/gobo/sequence.ontology/sequence.ontology