Genquire under the hood: live database-driven graphical objects

David Block
National Research Council Plant Biotechnology Institute
Saskatoon, Saskatchewan

In order to allow real-time annotation of biological sequences, it was
necessary to create an object framework with all the functionality of
BioPerl SeqFeatures, but stored in a relational database.  Starting from
example code from 'Object Oriented Perl' by Damian Conway(1), such a
framework was implemented, first without persistence, then with a MySQL
backend.  The GFF framework is the basis for the storage of features, with
a flexible tag-value scheme added to provide extensibility.

The actual text of source sequences is stored in the database, with
optimized loading and caching for better client performance.  The presence
of a Tiling_Path table allows the loading of any arbitrary length of
sequence, in the reference frame of any of the contigs that make up the
tiling path.  This functionality is used in the genome browser window of
Genquire.

Hand annotation requires mutable sequence features, but it was thought
important to preserve original data from annotation pipelines.
Feature::mod was developed to allow such modification.  Annotation was
conceived of as a process of defining gene structure, so a Gene class,
with associated Feature::Annotation exon objects, was defined.  These
classes have built-in logging of every change, which theoretically allows
for Undo functionality.

Gene Ontology annotation is seen as the future of biological integration,
and GO annotations are stored simply and completely by these Feature
Objects.

Extension of these classes back away from database integration was
trivially implemented as Feature::inMemory, which will be demonstrated.

Current work on adding transaction support, Corba client/server
integration, and DAS will be presented.  The trend in this work is to
separate the biological logic from the database implementation, and a
strategy to this end will be presented.

1. Conway, Damian.  Object-Oriented Perl. Manning, 1999.

--
David Block
dblock@gene.pbi.nrc.ca
http://bioinfo.pbi.nrc.ca/dblock/wiki
NRC Plant Biotechnology Institute
Saskatoon, SK, Canada