Bio/Ontology/PathI.pm

   1 # $Id$
   2 #
   3 # BioPerl module for PathI
   4 #
   5 # Cared for by Hilmar Lapp <hlapp at gmx.net>
   6 #
   7 # (c) Hilmar Lapp, hlapp at gmx.net, 2003.
   8 # (c) GNF, Genomics Institute of the Novartis Research Foundation, 2003.
   9 #
  10 # You may distribute this module under the same terms as perl itself.
  11 # Refer to the Perl Artistic License (see the license accompanying this
  12 # software package, or see http://www.perl.com/language/misc/Artistic.html)
  13 # for the terms under which you may use, modify, and redistribute this module.
  14 #
  15 # THIS PACKAGE IS PROVIDED "AS IS" AND WITHOUT ANY EXPRESS OR IMPLIED
  16 # WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED WARRANTIES OF
  17 # MERCHANTIBILITY AND FITNESS FOR A PARTICULAR PURPOSE.
  18 #
  19 # You may distribute this module under the same terms as perl itself
  20
  21 # POD documentation - main docs before the code
  22
  23 =head1 NAME
  24
  25 Bio::Ontology::PathI - Interface for a path between ontology terms
  26
  27 =head1 SYNOPSIS
  28
  29     # see documentation of methods and an implementation, e.g.,
  30     # Bio::Ontology::Path
  31
  32 =head1 DESCRIPTION
  33
  34 This is the minimal interface for a path between two terms in
  35 an ontology. Ontology engines may use this.
  36
  37 Essentially this is a very thin extension of the
  38 L<Bio::Ontology::RelationshipI> interface. It basically adds an
  39 attribute distance(). For a RelationshipI, you can think of distance as
  40 equal to zero (subject == object) or 1 (subject != object).
  41
  42 =head1 FEEDBACK
  43
  44 =head2 Mailing Lists
  45
  46 User feedback is an integral part of the evolution of this and other
  47 Bioperl modules. Send your comments and suggestions preferably to
  48 the Bioperl mailing list.  Your participation is much appreciated.
  49
  50   bioperl-l@bioperl.org                  - General discussion
  51   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
  52
  53 =head2 Reporting Bugs
  54
  55 Report bugs to the Bioperl bug tracking system to help us keep track
  56 of the bugs and their resolution. Bug reports can be submitted via
  57 the web:
  58
  59   http://bugzilla.open-bio.org/
  60
  61 =head1 AUTHOR - Hilmar Lapp
  62
  63 Email hlapp at gmx.net
  64
  65 =head1 APPENDIX
  66
  67 The rest of the documentation details each of the object methods.
  68 Internal methods are usually preceded with a _
  69
  70 =cut
  71
  72
  73 # Let the code begin...
  74
  75
  76 package Bio::Ontology::PathI;
  77 use strict;
  78
  79 use base qw(Bio::Ontology::RelationshipI);
  80
  81
  82 =head2 distance
  83
  84  Title   : distance
  85  Usage   : $obj->distance($newval)
  86  Function: Get (and set if the implementation allows it) the distance
  87            between the two terms connected by this path.
  88
  89  Example :
  90  Returns : value of distance (a scalar)
  91  Args    : on set, new value (a scalar or undef, optional)
  92
  93 =cut
  94
  95 sub distance{
  96     return shift->throw_not_implemented();
  97 }
  98
  99 =head1 Bio::Ontology::RelationshipI Methods
 100
 101 =cut
 102
 103 =head2 subject_term
 104
 105  Title   : subject_term
 106  Usage   : $subj = $rel->subject_term();
 107  Function: Set/get for the subject term of this Relationship.
 108
 109            The common convention for ontologies is to express
 110            relationships between terms as triples (subject, predicate,
 111            object).
 112
 113  Returns : The subject term [Bio::Ontology::TermI].
 114  Args    :
 115
 116 =cut
 117
 118 =head2 object_term
 119
 120  Title   : object_term
 121  Usage   : $object = $rel->object_term();
 122  Function: Set/get for the object term of this Relationship.
 123
 124            The common convention for ontologies is to express
 125            relationships between terms as triples (subject, predicate,
 126            object).
 127
 128  Returns : The object term [Bio::Ontology::TermI].
 129  Args    :
 130
 131 =cut
 132
 133 =head2 predicate_term
 134
 135  Title   : predicate_term
 136  Usage   : $type = $rel->predicate_term();
 137  Function: Set/get for the predicate of this relationship.
 138
 139            For a path the predicate (relationship type) is defined as
 140            the greatest common denominator of all predicates
 141            (relationship types) encountered along the path. I.e., if
 142            predicate A is-a predicate B, the greatest common
 143            denominator for a path containing both predicates A and B is B
 144
 145  Returns : The predicate term [Bio::Ontology::TermI].
 146  Args    :
 147
 148 =cut
 149
 150 =head2 ontology
 151
 152  Title   : ontology
 153  Usage   : $ont = $obj->ontology()
 154  Function: Get the ontology that defined this relationship.
 155  Example :
 156  Returns : an object implementing Bio::Ontology::OntologyI
 157  Args    :
 158
 159 See L<Bio::Ontology::OntologyI>.
 160
 161 =cut
 162
 163 1;