Bio::GMOD 0.28

Bio::GMOD is a unified API for Model Organism Databases.

SYNOPSIS

Check the installed version of a MOD
use Bio::GMOD::Util::CheckVersions.pm
my $mod = Bio::GMOD::Util::CheckVersions->new(-mod=>WormBase);
my $version = $mod->live_version;
Update a MOD installation
use Bio::GMOD::Update;
my $mod = Bio::GMOD::Update->new(-mod=>WormBase);
$gmod->update();
Fetch a list of genes from a MOD
use Bio::GMOD::Query;
my $mod = Bio::GMOD::Query->new(-mod=>WormBase);
my @genes = $mod->fetch(-class=>Gene,-name=>unc-26);

Bio::GMOD is a unified API for accessing various Model Organism Databases. It is a part of the Generic Model Organism Database project, as well as distributed on CPAN.

MODs are highly curated resources of biological data. Although they typically incorporate sequence data housed at community repositories such as NCBI, they place this information within a framework of biological fuction gelaned from the published literature of experiments in model organisms.

Given the great proliferation of MODs, cross-site data mining strategies have been difficult to implement. Such strategies typically require a familiarity with both the underlying data model and the historical vocabulary of the model system.

Furthermore, the quickly-evolving nature of these projects have made installing a MOD locally and keeping it up-to-date a delicate and time-consuming experience.