Date: 18 February 2005
New CPAN namespace proposal: Bio::GMOD
Author: Todd Harris (harris@cshl.edu)

Description in module list: 
Unified Generic Model Organism Database API

Rationale:

Background:
Bio::GMOD::* is a unified Perl interface to participating Model
Organism Databases (MOD).  MODs serve as a clearing house of
biological data, housing a vast variety of data relating to
widely-used experimental systems.  This data includes genomic
sequence, gene model predictions, experimental reagents, curated
literature, and functional annotations.

To promote software reuse, MODs have organized into the Generic Model
Organism Database (GMOD) project which has given rise to a number of
projects including a generic graphical genome browser, a generic
schema for storing biological data, and a template-driven website
system.

Although each MOD may use distinct DBMSs, data models, and data mining
protocols, they all confront similar issues - namely, how to store and
present biological information of experiment model organism systems.
The evolutionary relationships between model organisms -- and between
the data housed in MODs -- is a central cornerstone of modern biology.

Approach:
Bio::GMOD::* seeks to further the GMOD project by providing a unified
API across participating MODs.  Bio::GMOD::* uses a strongly
object-oriented adaptor based architecture that serves to insulate end
users from differences in naming schemes, data mining protocols, and
adjustments to data models.  Core modules are generically subclassable
in order to create custom solutions for different MODs.  Among current
features are facilities for updates/maintainence of remote
installations and remote version checking.  Features currently under
development include cross-MOD querying and data fetching.

Namespace rationale:
Bio::GMOD is most appropriately associated with other
biologically-related modules and hence does not require a new
root-level namespace.  Although many features of Bio::GMOD will be
used by a small core group of MOD developers, the data mining
facilities will be of general use to all biologists using
computational approaches. For this reason, Bio::GMOD should be listed
in the main module list.