GMOD

Gbol

This is a scratch page for thoughts on development of the GMOD Bio Object Layer (GBOL).

== Note: This project is no longer active. ==

Contents

Object Layer Design Goals

Diagrams

Primitive Architecture Diagram

Simple Object Layer

As stated above, the simple object layer is essentially the chado schema in java object form.

Bio Object Layer

These BioObjects will be extensions of the simple object class Feature. We’ve discussed the idea of having some sort of “configuration adaptor” assigned to each bio object instance that would essentially specify the object’s type, detail how other bio objects are related to it, and tell what sorts of features to save should the object be written to a data store. See Configuration Adaptor Thoughts for more details.

Central Dogma Model thoughts:

Extended Objects and methods:

Others….

Configuration Adaptor Thoughts

Hmmm….

Analyses

I’d like a bioperl set of objects that allow you to traverse sequence alignments, hits, & HSPs. Certainly, people are always asking how to get analyses in and out of Chado. I think this will involve an extension of the Feature class like the bio object layer. Err… It probably should be part of the bio object layer.

Annotation Properties

Is there a controlled vocabulary for annotation properties? We need to specify conventions for things like, storing feature comments and comment properties. How about annotation evidence structure and confidence codes from GO?

Categories:

Documentation

Community

Tools