[Gusdev-gusdev] Protein properties and protein features in GUS

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

  Hi everyone

I would like to report a new table, ProteinProperty and new views on the 
top of AAFeatureImp table for protein features such as domains.

* Protein properties :

There are 4 protein properties :
   * Isoelectric point (1),
   * Molecular mass (2),
   * Charge (3),
   * Average residue mass (4).

The 3 first ones may have several values as they can be characterized 
experimentally.

 From a design point of view, we can have a unique ProteinProperty table 
or a view foreach proterty (a ProteinPropertyImp table and three views: 
IsoElectricPointProperty, MolecularMassProperty and ChargeProperty).
The number of properties may not changed in the future so I may be 
simpler to create a unique ProteinProperty table.

Specification => A property would behave like a feature, ie :
   * it is attached to a sequence modulo the fact it doesn't have a 
location within it,
   * it can be supported by evidences such as an experiment, published 
or from a personal communication.
   * have external db refs.

ProteinProperty table:
   * protein_property_id : number
   * property_name : varchar2(50)
   * property_value : number (5)
   * & stuff common to any GUS table: modification_date ...

The 4th property, average residue mass, could be an extra attribute in 
the proteinSequence or TranslatedAASequence view.

******************
* Protein Features :

Features attached to a protein sequence.

The new features objects are:
    (1) Signal Peptide Feature :
It's already a view in GUS, but we will store curated data, such as 
targetting information.

    (2) Domains:
It can be:
    * a Leucine Zipper domain,
    * a coiled-coil domain,
    * a Pfam, Smart or Prosite domain.

DomainFeature view:
    * aa_feature_id : number (10),
    * aa_sequence_id : number (10),
    * name : varchar2 (50),
    * description : varchar2 (100),
    * score : number (4)
    * e_value : number (10),
+ external database link entries and a location object.

    (3) Transmenbrane domain feature:
Question : PlasmoDB web site shows hydrophobicity graphics, where is it 
stored in GUS ?

    (4) Post-translational modification feature:
    * type : varchar2 (50) (e.g. glycosylation, phosphorylation ...)
    * modified_by : use of the Interaction table ?
    * Coordinates of the phosphorylation site in a AALocation object.
 
    (5) Repeat Features, should be the same design that at the DNA level :
        * RepeatRegionFeature as a set of RepeatUnitFeatures,
        * RepeatUnitFeature, with the consensus sequence, name and size
        * RepeatType table

Another question : What about 2D structures (beta-sheet and 
alpha-helice) in GUS ?

Let me know if you have any comments. I'll send another email for extra 
features at the DNA/RNA level.

Cheers
Arnaud