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bio::ontology::documentregistry(3pm) [debian man page]

Bio::Ontology::DocumentRegistry(3pm)			User Contributed Perl Documentation		      Bio::Ontology::DocumentRegistry(3pm)

NAME

       Bio::Ontology::DocumentRegistry - Keep track of where to find ontologies.  Allows lookups by name.

SYNOPSIS

	 my $registry = Bio::Ontology::DocumentRegistry->get_instance();
	 my($ont,$def,$fmt) = $registry->documents('Sequence Ontology');

	 my $io = Bio::OntologyIO->new(-url => $ont,
				       -defs_url => $def,
				       -format => $fmt);
	 my $so = $io->next_ontology();
	 #...

DESCRIPTION

       Do not use this directly, use Bio::Ontology::OntologyStore instead.  Bio::Ontology::OntologyStore uses Bio::Ontology::DocumentRegistry to
       load and cache ontologies as object graphs, you can just ask it for what you want by name.  See Bio::Ontology::OntologyStore for details.

FEEDBACK

   Mailing Lists
       User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the
       Bioperl mailing list.  Your participation is much appreciated.

	 bioperl-l@bioperl.org			- General discussion
	 http://bioperl.org/wiki/Mailing_lists	- About the mailing lists

   Support
       Please direct usage questions or support issues to the mailing list:

       bioperl-l@bioperl.org

       rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address
       it. Please include a thorough description of the problem with code and data examples if at all possible.

   Reporting Bugs
       Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the
       web:

	 https://redmine.open-bio.org/projects/bioperl/

AUTHOR - Allen Day
       Email allenday@ucla.edu

APPENDIX

       The rest of the documentation details each of the object methods.  Internal methods are usually preceded with a _

   get_instance
	Title	: get_instance
	Usage	: my $singleton = Bio::Ontology::DocumentRegistry->get_instance();
	Function: constructor
	Returns : The Bio::Ontology::DocumentRegistry singleton.
	Args	: None
	Usage

   documents
	Title	: documents
	Usage	: my($ontology_url, $definitions_url, $format) = $obj->documents('Sequence Ontology');
	Function: Maps an ontology name to a list of (local or) remote URIs where the
		  files can be located.
	Returns : A 3-item list:(1) URI for the ontology file(2) URI for the ontology definitions file(3) format of the files (dagedit, obo, etc)
	Args	: Name of an ontology, e.g. 'Sequence Ontology', or 'Cellular Component
		  (Gene Ontology)'

perl v5.14.2							    2012-03-02				      Bio::Ontology::DocumentRegistry(3pm)

Check Out this Related Man Page

Bio::Ontology::RelationshipFactory(3pm) 		User Contributed Perl Documentation		   Bio::Ontology::RelationshipFactory(3pm)

NAME

       Bio::Ontology::RelationshipFactory - Instantiates a new Bio::Ontology::RelationshipI (or derived class) through a factory

SYNOPSIS

	   use Bio::Ontology::RelationshipFactory;

	   # the default type is Bio::Ontology::Relationship
	   my $factory = Bio::Ontology::RelationshipFactory->new(
					-type => 'Bio::Ontology::GOterm');
	   my $clu = $factory->create_object(-name => 'peroxisome',
					     -ontology => 'Gene Ontology',
					     -identifier => 'GO:0005777');

DESCRIPTION

       This object will build Bio::Ontology::RelationshipI objects generically.

FEEDBACK

   Mailing Lists
       User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the
       Bioperl mailing list.  Your participation is much appreciated.

	 bioperl-l@bioperl.org			- General discussion
	 http://bioperl.org/wiki/Mailing_lists	- About the mailing lists

   Support
       Please direct usage questions or support issues to the mailing list:

       bioperl-l@bioperl.org

       rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address
       it. Please include a thorough description of the problem with code and data examples if at all possible.

   Reporting Bugs
       Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the
       web:

	 https://redmine.open-bio.org/projects/bioperl/

AUTHOR - Hilmar Lapp
       Email hlapp at gmx.net

APPENDIX

       The rest of the documentation details each of the object methods.  Internal methods are usually preceded with a _

   new
	Title	: new
	Usage	: my $obj = Bio::Ontology::RelationshipFactory->new();
	Function: Builds a new Bio::Ontology::RelationshipFactory object
	Returns : Bio::Ontology::RelationshipFactory
	Args	: -type => string, name of a Bio::Ontology::RelationshipI
			   derived class.
			   The default is Bio::Ontology::Relationship.

       See Bio::Ontology::Relationship, Bio::Ontology::RelationshipI.

perl v5.14.2							    2012-03-02				   Bio::Ontology::RelationshipFactory(3pm)
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