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

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

NAME

       Bio::Ontology::Path - a path for an ontology term graph

SYNOPSIS

	 $path = Bio::Ontology::Path->new( -identifier	   => "16847",
					   -subject_term   => $subj,
					   -object_term    => $obj,
					   -predicate_term => $pred,
					   -distance	   => 3 );

DESCRIPTION

       This is a basic implementation of Bio::Ontology::PathI.

       Essiantially this is a very thin extension of Bio::Ontology::Relationship. It basically adds a method distance().

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 lists  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 the bugs and their resolution.  Bug reports can be submitted via the
       web:

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

AUTHOR

	Hilmar Lapp <hlapp@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	: $rel = Bio::Ontology::Path->new(-identifier	=> "16847",
						  -subject_term => $subject,
						  -object_term	=> $object,
						  -predicate_term => $type );
						  -distance	=> 3 );
	Function: Creates a new Bio::Ontology::Path.
	Returns : A new Bio::Ontology::Path object.
	Args	: -identifier	  => the identifier of this relationship [scalar]
		  -subject_term   => the subject term [Bio::Ontology::TermI]
		  -object_term	  => the object term [Bio::Ontology::TermI]
		  -predicate_term => the predicate term [Bio::Ontology::TermI]
		  -distance	  => the distance between subject and object

   init
	Title	: init()
	Usage	: $rel->init();
	Function: Initializes this Path to all undef.
	Returns :
	Args	:

   distance
	Title	: distance
	Usage	: $obj->distance($newval)
	Function: Get/set the distance between the two terms connected
		  by this path.

		  Note that modifying the distance may not be meaningful. The
		  implementation here is not connected to any graph engine,
		  so changing an existing value may simply render the
		  attribute's value wrong.

	Example :
	Returns : value of distance (a scalar)
	Args	: on set, new value (a scalar or undef, optional)

   to_string
	Title	: to_string()
	Usage	: print $rel->to_string();
	Function: to_string method for Path.
	Returns : A string representation of this Path.
	Args	:

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

Check Out this Related 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)
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