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:

  https://github.com/bioperl/bioperl-live/issues

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.