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Bio::Ontology::RelationshipI.3pm

NAME

Bio::Ontology::RelationshipI - Interface for a relationship between ontology terms

SYNOPSIS

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

DESCRIPTION

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

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 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:

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

AUTHOR - Peter Dimitrov

Email dimitrov@gnf.org

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 _

identifier

  Title   : identifier
  Usage   : print $rel->identifier();
  Function: Set/get for the identifier of this Relationship.
 
            Note that this may not necessarily be used by a particular
            ontology.
 
  Returns : The identifier [scalar].
  Args    :
 
 

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 relationship type of this relationship.
 
            The common convention for ontologies is to express
            relationships between terms as triples (subject, predicate,
            object).
 
  Returns : The relationship type [Bio::Ontology::TermI].
  Args    :
 
 

ontology

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

See Bio::Ontology::OntologyI.