diff variant_effect_predictor/Bio/Ontology/RelationshipI.pm @ 0:2bc9b66ada89 draft default tip

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/Ontology/RelationshipI.pm	Thu Apr 11 06:29:17 2013 -0400
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+# $Id: RelationshipI.pm,v 1.2.2.2 2003/03/27 10:07:56 lapp Exp $
+#
+# BioPerl module for RelationshipI
+#
+# Cared for by Peter Dimitrov <[e-mail]>
+#
+# (c) Peter Dimitrov
+# (c) GNF, Genomics Institute of the Novartis Research Foundation, 2002.
+#
+# You may distribute this module under the same terms as perl itself.
+# Refer to the Perl Artistic License (see the license accompanying this
+# software package, or see http://www.perl.com/language/misc/Artistic.html)
+# for the terms under which you may use, modify, and redistribute this module.
+#
+# THIS PACKAGE IS PROVIDED "AS IS" AND WITHOUT ANY EXPRESS OR IMPLIED
+# WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED WARRANTIES OF
+# MERCHANTIBILITY AND FITNESS FOR A PARTICULAR PURPOSE.
+#
+# You may distribute this module under the same terms as perl itself
+
+# POD documentation - main docs before the code
+
+=head1 NAME
+
+RelationshipI - Interface for a relationship between ontology terms
+
+=head1 SYNOPSIS
+
+    # see documentation of methods and an implementation, e.g.,
+    # Bio::Ontology::Relationship
+
+=head1 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.
+
+=head1 FEEDBACK
+
+=head2 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.
+
+  [e-mail]              - General discussion
+  http://bioperl.org/MailList.shtml  - About the mailing lists
+
+=head2 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
+email or the web:
+
+  [e-mail]
+  http://bugzilla.bioperl.org/
+
+=head1 AUTHOR - Peter Dimitrov
+
+Email [e-mail]
+
+=head1 CONTRIBUTORS
+
+ Hilmar Lapp, email: hlapp at gmx.net
+
+=head1 APPENDIX
+
+The rest of the documentation details each of the object methods.
+Internal methods are usually preceded with a _
+
+=cut
+
+
+# Let the code begin...
+
+
+package Bio::Ontology::RelationshipI;
+use vars qw(@ISA);
+use strict;
+use Bio::Root::RootI;
+
+@ISA = qw( Bio::Root::RootI );
+
+=head2 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    : 
+
+=cut
+
+sub identifier{
+    shift->throw_not_implemented();
+}
+
+=head2 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    : 
+
+=cut
+
+sub subject_term{
+    shift->throw_not_implemented();
+}
+
+=head2 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    : 
+
+=cut
+
+sub object_term{
+    shift->throw_not_implemented();
+}
+
+=head2 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    : 
+
+=cut
+
+sub predicate_term{
+    shift->throw_not_implemented();
+}
+
+=head2 ontology
+
+ Title   : ontology
+ Usage   : $ont = $obj->ontology()
+ Function: Get the ontology that defined (is the scope for) this
+           relationship.
+ Example : 
+ Returns : an object implementing L<Bio::Ontology::OntologyI>
+ Args    : 
+
+
+=cut
+
+sub ontology{
+    shift->throw_not_implemented();
+}
+
+1;