[Mged-mage] Proposed modifications to MAGE-OM for caRPLA project

[Gerald F. <gv...@me...>]

Hi,

We would like to get any feedback from members on the list on proposed 
modifications to the MAGE-OM v1.1 model for our caRPLA project. Thanks 
in advance.
---

The goal of the caRPLA project is to make the caArray system compatible 
with protein lysate array (PLA) data. We believe modest changes are 
required to the MAGE-OM:

*A new class, PLAFeature, inheriting from Feature, is introduced. 
PLAFeature requires composition with Measurement in order to record the 
dilution of the array feature.*
*A new class, PLAReporter, inheriting from Reporter, is introduced. 
PLAReporter requires a 1:n assocation with FactorValue in order to 
record biologically-significant experimental factor values.*

An EA project and modified DTD are available at:

http://sneezy.lbl.gov/caRPLA/EA/caRPLA.EAP
http://sneezy.lbl.gov/caRPLA/XML/


In the EA ( v. 6.0.781 ) project are modified versions of the MAGE-OM 
and database schema from caArray 1.4. MAGE-OM was imported into the 
project via the MAGE_OM v1.1 MAGE.xmi file available from 
http://mged.sourceforge.net/software/docs.php
*All object model modifications required for this project can be seen in 
the "Logical View.Data Model.MAGE-OM.DesignElement Overview" diagram. 
They are colored pink/red.*

The database schema was imported into the project using Oracle ODBC on 
our local caArray 1.4 instance.
*Proposed database schema changes can be seen in the "Logical 
View.caRPLA-relevant tables" diagram. They are also colored pink/red.*

In the XML directory is the modified MAGE-ML DTD. Changes were made to 
the existing DTD model rather than using automatic DTD generation from 
the object model. This was done in order to preserve any changes made to 
the DTD post-generation.

We would appreciate any feedback, comments, suggestions, etc.

Thanks again,
Gerald Fontenay
gvf...@lb...