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

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

NAME

       Bio::Ontology::PathI - Interface for a path between ontology terms

SYNOPSIS

	   # see documentation of methods and an implementation, e.g.,
	   # Bio::Ontology::Path

DESCRIPTION

       This is the minimal interface for a path between two terms in an ontology. Ontology engines may use this.

       Essentially this is a very thin extension of the Bio::Ontology::RelationshipI interface. It basically adds an attribute distance(). For a
       RelationshipI, you can think of distance as equal to zero (subject == object) or 1 (subject != object).

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 _

   distance
	Title	: distance
	Usage	: $obj->distance($newval)
	Function: Get (and set if the implementation allows it) the distance
		  between the two terms connected by this path.

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

Bio::Ontology::RelationshipI Methods
   subject_term
	Title	: subject_term
	Usage	: $subj = $rel->subject_term();
	Function: Set/get for the subject term of this Relationship.

		  The common convention for ontologies is to express
		  relationships between terms as triples (subject, predicate,
		  object).

	Returns : The subject term [Bio::Ontology::TermI].
	Args	:

   object_term
	Title	: object_term
	Usage	: $object = $rel->object_term();
	Function: Set/get for the object term of this Relationship.

		  The common convention for ontologies is to express
		  relationships between terms as triples (subject, predicate,
		  object).

	Returns : The object term [Bio::Ontology::TermI].
	Args	:

   predicate_term
	Title	: predicate_term
	Usage	: $type = $rel->predicate_term();
	Function: Set/get for the predicate of this relationship.

		  For a path the predicate (relationship type) is defined as
		  the greatest common denominator of all predicates
		  (relationship types) encountered along the path. I.e., if
		  predicate A is-a predicate B, the greatest common
		  denominator for a path containing both predicates A and B is B

	Returns : The predicate term [Bio::Ontology::TermI].
	Args	:

   ontology
	Title	: ontology
	Usage	: $ont = $obj->ontology()
	Function: Get the ontology that defined this relationship.
	Example :
	Returns : an object implementing Bio::Ontology::OntologyI
	Args	:

       See Bio::Ontology::OntologyI.

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

Check Out this Related 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)
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