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1. #GMOD RESOURCE DISTRIBUTION 3 MOD#
2. #GMOD RESOURCE DISTRIBUTION 3 UPDATE#
3. #GMOD RESOURCE DISTRIBUTION 3 UPGRADE#
4. #GMOD RESOURCE DISTRIBUTION 3 MODS#
5. #GMOD RESOURCE DISTRIBUTION 3 SOFTWARE#

This library is free software you can redistribute it and/or modify it under the same terms as Perl itself. The author hopes that this will change in the future! BUGSīio::GMOD::Update, Bio::GMOD::Adaptor AUTHORĬopyright (c) 2003-2005 Cold Spring Harbor Laboratory.

#GMOD RESOURCE DISTRIBUTION 3 MOD#

For example, a developer may wish to override the default methods for Update.pm by building a Bio::GMOD::Update::FlyBase package that provides an update() method, as well as various supporting methods.Ĭurrently, the only participating MOD is WormBase. # $mod contains 'WormBase' NOTES FOR DEVELOPERSīio::GMOD.pm uses a generically subclass-able architecture that lets MOD developers support various features as needed or desired. My $mod = $self->_organism2mod('nematode') Like species2mod(), _organism2mod translates a general organism into the most appropriate hosting MOD. # $mod contains 'WormBase' $self->organism2mod($organism) Name : organism2mod($organism) My $mod = $self->_species2mod('elegans') species", "Genus species", or simple "species" for the lazy. Provided with a single species, return the most appropriate MOD name. $self->species2mod($species) Name : species2mod($species)

Specifying a single MOD has special behavior fo use in things like updates.

#GMOD RESOURCE DISTRIBUTION 3 MODS#

It does provide a convenient mechanism to iteract with all MODs without too much extra coding. Note that this probably does not make sense for classes like Update::*.

If "-mod" is not specified, adaptors to all available MODs will be instantiated. See Bio::GMOD::Adaptor for additional details. A corresponding accessor method (ie $adaptor->name) will be generated. These values will be parsed and loaded into the Bio::GMOD::Adaptor::"your_mod" object. class Force instantiation of a specific class (eg see Bio::GMOD::Monitor)Īny additional options, passed in the named parameter "-name => value" style will automatically be considered to be default values specific to the MOD adaptor of choice. mod The symbolic name of the MOD to use (WormBase, FlyBase, SGD, etc) new() will create an object of the appropriate class, including dynamic subclassing when necessary, as well as initializing an appropriate default Bio::GMOD::Adaptor::* object. Returns : Bio::GMOD::* object as appropriate, with embeddedīio::GMOD->new() is the generic factory new constructor for all of Bio::GMOD.pm (with the exception of Bio::GMOD::Adaptor, discussed elsewhere). Optional args : hash of system defaults to override Required args : mod || organism || species

#GMOD RESOURCE DISTRIBUTION 3 UPGRADE#

Making MODs easy to upgrade PUBLIC METHODS Name : new()

Insulating programmatic end users from model changesĤ. Enabling cross-MOD data mining through a unified APIĢ. Such strategies typically require a familiarity with both the underlying data model and the historical vocabulary of the model system.įurthermore, 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.īio::GMOD aims to solve these problems by: 1. Given the great proliferation of MODs, cross-site data mining strategies have been difficult to implement. 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. MODs are highly curated resources of biological data. It is a part of the Generic Model Organism Database project, as well as distributed on CPAN. My = $mod->fetch(-class=>'Gene',-name=>'unc-26') DESCRIPTIONīio::GMOD is a unified API for accessing various Model Organism Databases. My $mod = Bio::GMOD::Query->new(-mod=>'WormBase') My $mod = Bio::GMOD::Update->new(-mod=>'WormBase') įetch a list of genes from a MOD use Bio::GMOD::Query

#GMOD RESOURCE DISTRIBUTION 3 UPDATE#

Update a MOD installation use Bio::GMOD::Update My $mod = Bio::GMOD::Util::CheckVersions->new(-mod=>'WormBase') Bio::GMOD - Unified API for Model Organism Databases SYNOPSISĬheck the installed version of a MOD use Bio::GMOD::Util::CheckVersions.pm