Bio/Ontology/PathI.pm

   1 #
   2 # BioPerl module for PathI
   3 #
   4 # Please direct questions and support issues to <bioperl-l@bioperl.org>
   5 #
   6 # Cared for by Hilmar Lapp <hlapp at gmx.net>
   7 #
   8 # (c) Hilmar Lapp, hlapp at gmx.net, 2003.
   9 # (c) GNF, Genomics Institute of the Novartis Research Foundation, 2003.
  10 #
  11 # You may distribute this module under the same terms as perl itself.
  12 # Refer to the Perl Artistic License (see the license accompanying this
  13 # software package, or see http://www.perl.com/language/misc/Artistic.html)
  14 # for the terms under which you may use, modify, and redistribute this module.
  15 #
  16 # THIS PACKAGE IS PROVIDED "AS IS" AND WITHOUT ANY EXPRESS OR IMPLIED
  17 # WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED WARRANTIES OF
  18 # MERCHANTIBILITY AND FITNESS FOR A PARTICULAR PURPOSE.
  19 #
  20 # You may distribute this module under the same terms as perl itself
  21
  22 # POD documentation - main docs before the code
  23
  24 =head1 NAME
  25
  26 Bio::Ontology::PathI - Interface for a path between ontology terms
  27
  28 =head1 SYNOPSIS
  29
  30     # see documentation of methods and an implementation, e.g.,
  31     # Bio::Ontology::Path
  32
  33 =head1 DESCRIPTION
  34
  35 This is the minimal interface for a path between two terms in
  36 an ontology. Ontology engines may use this.
  37
  38 Essentially this is a very thin extension of the
  39 L<Bio::Ontology::RelationshipI> interface. It basically adds an
  40 attribute distance(). For a RelationshipI, you can think of distance as
  41 equal to zero (subject == object) or 1 (subject != object).
  42
  43 =head1 FEEDBACK
  44
  45 =head2 Mailing Lists
  46
  47 User feedback is an integral part of the evolution of this and other
  48 Bioperl modules. Send your comments and suggestions preferably to
  49 the Bioperl mailing list.  Your participation is much appreciated.
  50
  51   bioperl-l@bioperl.org                  - General discussion
  52   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
  53
  54 =head2 Support
  55
  56 Please direct usage questions or support issues to the mailing list:
  57
  58 I<bioperl-l@bioperl.org>
  59
  60 rather than to the module maintainer directly. Many experienced and
  61 reponsive experts will be able look at the problem and quickly
  62 address it. Please include a thorough description of the problem
  63 with code and data examples if at all possible.
  64
  65 =head2 Reporting Bugs
  66
  67 Report bugs to the Bioperl bug tracking system to help us keep track
  68 of the bugs and their resolution. Bug reports can be submitted via
  69 the web:
  70
  71   https://github.com/bioperl/bioperl-live/issues
  72
  73 =head1 AUTHOR - Hilmar Lapp
  74
  75 Email hlapp at gmx.net
  76
  77 =head1 APPENDIX
  78
  79 The rest of the documentation details each of the object methods.
  80 Internal methods are usually preceded with a _
  81
  82 =cut
  83
  84
  85 # Let the code begin...
  86
  87
  88 package Bio::Ontology::PathI;
  89 use strict;
  90
  91 use base qw(Bio::Ontology::RelationshipI);
  92
  93
  94 =head2 distance
  95
  96  Title   : distance
  97  Usage   : $obj->distance($newval)
  98  Function: Get (and set if the implementation allows it) the distance
  99            between the two terms connected by this path.
 100
 101  Example :
 102  Returns : value of distance (a scalar)
 103  Args    : on set, new value (a scalar or undef, optional)
 104
 105 =cut
 106
 107 sub distance{
 108     return shift->throw_not_implemented();
 109 }
 110
 111 =head1 Bio::Ontology::RelationshipI Methods
 112
 113 =cut
 114
 115 =head2 subject_term
 116
 117  Title   : subject_term
 118  Usage   : $subj = $rel->subject_term();
 119  Function: Set/get for the subject term of this Relationship.
 120
 121            The common convention for ontologies is to express
 122            relationships between terms as triples (subject, predicate,
 123            object).
 124
 125  Returns : The subject term [Bio::Ontology::TermI].
 126  Args    :
 127
 128 =cut
 129
 130 =head2 object_term
 131
 132  Title   : object_term
 133  Usage   : $object = $rel->object_term();
 134  Function: Set/get for the object term of this Relationship.
 135
 136            The common convention for ontologies is to express
 137            relationships between terms as triples (subject, predicate,
 138            object).
 139
 140  Returns : The object term [Bio::Ontology::TermI].
 141  Args    :
 142
 143 =cut
 144
 145 =head2 predicate_term
 146
 147  Title   : predicate_term
 148  Usage   : $type = $rel->predicate_term();
 149  Function: Set/get for the predicate of this relationship.
 150
 151            For a path the predicate (relationship type) is defined as
 152            the greatest common denominator of all predicates
 153            (relationship types) encountered along the path. I.e., if
 154            predicate A is-a predicate B, the greatest common
 155            denominator for a path containing both predicates A and B is B
 156
 157  Returns : The predicate term [Bio::Ontology::TermI].
 158  Args    :
 159
 160 =cut
 161
 162 =head2 ontology
 163
 164  Title   : ontology
 165  Usage   : $ont = $obj->ontology()
 166  Function: Get the ontology that defined this relationship.
 167  Example :
 168  Returns : an object implementing Bio::Ontology::OntologyI
 169  Args    :
 170
 171 See L<Bio::Ontology::OntologyI>.
 172
 173 =cut
 174
 175 1;