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

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

NAME

       Bio::Ontology::OBOterm - representation of OBO terms

SYNOPSIS

	 $term = Bio::Ontology::OBOterm->new
	   ( -identifier       => "GO:0005623",
	     -name	  => "Cell",
	     -definition  => "The basic structural and functional unit ...",
	     -is_obsolete => 0,
	     -comment	  => "" );

	 $term->add_reference( @refs );
	 $term->add_secondary_id( @ids );
	 $term->add_synonym( @synonym );

	 # etc.

DESCRIPTION

       This is data holder class for OBO terms. It is currently a dummy class since we anticipate that the OBO term will become more richer with
       more features being added to OBO flat-file format.

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 one
       of 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

       Sohel Merchant

       Email: s-merchant@northwestern.edu

       Address:

	 Northwestern University
	 Center for Genetic Medicine (CGM), dictyBase
	 Suite 1206,
	 676 St. Clair st
	 Chicago IL 60611

APPENDIX

       The rest of the documentation details each of the object methods.

   new
	Title	: new
	Usage	:   $term = Bio::Ontology::OBOterm->new
	    ( -identifier	=> "GO:0005623",
	     -name	  => "Cell",
	     -definition  => "The basic structural and functional unit ...",
	     -is_obsolete => 0,
	     -comment	  => "" );

	Function: Creates a new Bio::Ontology::OBOterm.
	Returns : A new Bio::Ontology::OBOterm object.
	Args	: -identifier	 => the id of this OBO term [GO:nnnnnnn]
				    integer of seven digits)
		  -name 	 => the name of this OBO term [scalar]
		  -definition	 => the definition of this OBO term [scalar]
		  -ontology	 => the ontology for this term (a
				    Bio::Ontology::OntologyI compliant object)
		  -version	 => version information [scalar]
		  -is_obsolete	 => the obsoleteness of this OBO term [0 or 1]
		  -comment	 => a comment [scalar]

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

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)