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Bio::Ontology::Relationship.3pm

NAME

Bio::Ontology::Relationship - a relationship for an ontology

SYNOPSIS

   $rel = Bio::Ontology::Relationship->new( -identifier     => "16847",
                                            -subject_term   => $subj,
                                            -object_term    => $obj,
                                            -predicate_term => $pred );
 
 

DESCRIPTION

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

The terminology we use here is the one commonly used for ontologies, namely the triple of (subject, predicate, object), which in addition is scoped in a namespace (ontology). It is called triple because it is a tuple of three ontology terms.

There are other terminologies in use for expressing relationships. For those who it helps to better understand the concept, the triple of (child, relationship type, parent) would be equivalent to the terminology chosen here, disregarding the question whether the notion of parent and child is sensible in the context of the relationship type or not. Especially in the case of ontologies with a wide variety of predicates the parent/child terminology and similar ones can quickly become ambiguous (e.g., A synthesises B), meaningless (e.g., A binds B), or even conflicting (e.g., A is-parent-of B), and are therefore strongly discouraged.

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:

   http://bugzilla.open-bio.org/
 
 

AUTHOR

Christian M. Zmasek

Email: czmasek-at-burnham.org or cmzmasek@yahoo.com

WWW: http://monochrome-effect.net/

Address:

   Genomics Institute of the Novartis Research Foundation
   10675 John Jay Hopkins Drive
   San Diego, CA 92121
 
 

CONTRIBUTORS

  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   : $rel = Bio::Ontology::Relationship->new(-identifier   => "16847",
                                                    -subject_term => $subject,
                                                    -object_term  => $object,
                                                    -predicate_term => $type );
  Function: Creates a new Bio::Ontology::Relationship.
  Returns : A new Bio::Ontology::Relationship 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]
 
 

init

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

identifier

  Title   : identifier
  Usage   : $rel->identifier( "100050" );
            or
            print $rel->identifier();
  Function: Set/get for the identifier of this Relationship.
  Returns : The identifier [scalar].
  Args    : The identifier [scalar] (optional).
 
 

subject_term

  Title   : subject_term
  Usage   : $rel->subject_term( $subject );
            or
            $subject = $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    : The subject term [Bio::Ontology::TermI] (optional).
 
 

object_term

  Title   : object_term
  Usage   : $rel->object_term( $object );
            or
            $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    : The object term [Bio::Ontology::TermI] (optional).
 
 

predicate_term

  Title   : predicate_term
  Usage   : $rel->predicate_term( $type );
            or
            $type = $rel->predicate_term();
  Function: Set/get for the predicate (relationship type) of this
            relationship.
 
            The common convention for ontologies is to express
            relationships between terms as triples (subject, predicate,
            object).
 
  Returns : The predicate term [Bio::Ontology::TermI].
  Args    : The predicate term [Bio::Ontology::TermI] (optional).
 
 

ontology

  Title   : ontology
  Usage   : $ont = $obj->ontology()
  Function: Get/set the ontology that defined this relationship.
  Example : 
  Returns : an object implementing L<Bio::Ontology::OntologyI>
  Args    : on set, undef or an object implementing 
            Bio::Ontology::OntologyI (optional)
 
 

See Bio::Ontology::OntologyI.

to_string

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

Deprecated Methods

   These methods are deprecated and defined here solely to preserve
   backwards compatibility.