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.\" ========================================================================
.\"
.IX Title "Bio::Ontology::RelationshipI 3pm"
.TH Bio::Ontology::RelationshipI 3pm "2020-10-28" "perl v5.30.3" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
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.SH "NAME"
Bio::Ontology::RelationshipI \- Interface for a relationship between ontology terms
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
.Vb 2
\&    # see documentation of methods and an implementation, e.g.,
\&    # Bio::Ontology::Relationship
.Ve
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
This is the minimal interface for a relationship between two terms in
an ontology. Ontology engines will use this.
.PP
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.
.PP
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.
.SH "FEEDBACK"
.IX Header "FEEDBACK"
.SS "Mailing Lists"
.IX Subsection "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.
.PP
.Vb 2
\&  bioperl\-l@bioperl.org                  \- General discussion
\&  http://bioperl.org/wiki/Mailing_lists  \- About the mailing lists
.Ve
.SS "Support"
.IX Subsection "Support"
Please direct usage questions or support issues to the mailing list:
.PP
\&\fIbioperl\-l@bioperl.org\fR
.PP
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.
.SS "Reporting Bugs"
.IX Subsection "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:
.PP
.Vb 1
\&  https://github.com/bioperl/bioperl\-live/issues
.Ve
.SH "AUTHOR \- Peter Dimitrov"
.IX Header "AUTHOR - Peter Dimitrov"
Email dimitrov@gnf.org
.SH "CONTRIBUTORS"
.IX Header "CONTRIBUTORS"
.Vb 1
\& Hilmar Lapp, email: hlapp at gmx.net
.Ve
.SH "APPENDIX"
.IX Header "APPENDIX"
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
.SS "identifier"
.IX Subsection "identifier"
.Vb 3
\& 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    :
.Ve
.SS "subject_term"
.IX Subsection "subject_term"
.Vb 3
\& 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    :
.Ve
.SS "object_term"
.IX Subsection "object_term"
.Vb 3
\& 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    :
.Ve
.SS "predicate_term"
.IX Subsection "predicate_term"
.Vb 3
\& 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    :
.Ve
.SS "ontology"
.IX Subsection "ontology"
.Vb 7
\& 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    :
.Ve
.PP
See Bio::Ontology::OntologyI.