Bio::Ontology::Relationship - a relationship for an ontology

BioPerl documentation Contained in the BioPerl distribution.

Index

Code Index:

NAME

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Bio::Ontology::Relationship - a relationship for an ontology

SYNOPSIS

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  $rel = Bio::Ontology::Relationship->new( -identifier     => "16847",
                                           -subject_term   => $subj,
                                           -object_term    => $obj,
                                           -predicate_term => $pred );

DESCRIPTION

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This is a basic implementation of Bio::Ontology::RelationshipI.

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

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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 lists 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 the bugs and their resolution. Bug reports can be submitted via the web:

  https://redmine.open-bio.org/projects/bioperl/

AUTHOR

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Christian M. Zmasek

Email: czmasek-at-burnham.org or cmzmasek@yahoo.com

WWW: http://monochrome-effect.net/

Address: 

  Genomics Institute of the Novartis Research Foundation
  10675 John Jay Hopkins Drive
  San Diego, CA 92121

CONTRIBUTORS

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 Hilmar Lapp, email: hlapp at gmx.net

APPENDIX

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The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

new

 Title   : new
 Usage   : $rel = Bio::Ontology::Relationship->new(-identifier   => "16847",
                                                   -subject_term => $subject,
                                                   -object_term  => $object,
                                                   -predicate_term => $type );
 Function: Creates a new Bio::Ontology::Relationship.
 Returns : A new Bio::Ontology::Relationship object.
 Args    : -identifier     => the identifier of this relationship [scalar]
           -subject_term   => the subject term [Bio::Ontology::TermI]
           -object_term    => the object term [Bio::Ontology::TermI]  
           -predicate_term => the predicate term [Bio::Ontology::TermI]

init

 Title   : init()
 Usage   : $rel->init();   
 Function: Initializes this Relationship to all undef.
 Returns : 
 Args    :

identifier

 Title   : identifier
 Usage   : $rel->identifier( "100050" );
           or
           print $rel->identifier();
 Function: Set/get for the identifier of this Relationship.
 Returns : The identifier [scalar].
 Args    : The identifier [scalar] (optional).

subject_term

 Title   : subject_term
 Usage   : $rel->subject_term( $subject );
           or
           $subject = $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    : The subject term [Bio::Ontology::TermI] (optional).

object_term

 Title   : object_term
 Usage   : $rel->object_term( $object );
           or
           $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    : The object term [Bio::Ontology::TermI] (optional).

predicate_term

 Title   : predicate_term
 Usage   : $rel->predicate_term( $type );
           or
           $type = $rel->predicate_term();
 Function: Set/get for the predicate (relationship type) of this
           relationship.

           The common convention for ontologies is to express
           relationships between terms as triples (subject, predicate,
           object).

 Returns : The predicate term [Bio::Ontology::TermI].
 Args    : The predicate term [Bio::Ontology::TermI] (optional).

ontology

 Title   : ontology
 Usage   : $ont = $obj->ontology()
 Function: Get/set the ontology that defined this relationship.
 Example : 
 Returns : an object implementing L<Bio::Ontology::OntologyI>
 Args    : on set, undef or an object implementing 
           Bio::Ontology::OntologyI (optional)

See Bio::Ontology::OntologyI.

to_string

 Title   : to_string()
 Usage   : print $rel->to_string();
 Function: to_string method for Relationship.
 Returns : A string representation of this Relationship.
 Args    :

Deprecated Methods

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  These methods are deprecated and defined here solely to preserve
  backwards compatibility.
BioPerl documentation Contained in the BioPerl distribution. 
#
# BioPerl module for Relationship
#
# Please direct questions and support issues to <bioperl-l@bioperl.org> 
#
# Cared for by Christian M. Zmasek <czmasek-at-burnham.org> or <cmzmasek@yahoo.com>
#
# (c) Christian M. Zmasek, czmasek-at-burnham.org, 2002.
# (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



# Let the code begin...


package Bio::Ontology::Relationship;
use strict;
use Bio::Ontology::TermI;

use base qw(Bio::Root::Root Bio::Ontology::RelationshipI);





sub new {

    my( $class, @args ) = @_;
    
    my $self = $class->SUPER::new( @args );
   
    my ( $identifier,
         $subject_term,
			$child,        # for backwards compatibility
         $object_term,
			$parent,       # for backwards compatibility
         $predicate_term,
			$reltype,      # for backwards compatibility
			$ont)
	= $self->_rearrange( [qw( IDENTIFIER
				  SUBJECT_TERM
				  CHILD_TERM
				  OBJECT_TERM
				  PARENT_TERM
				  PREDICATE_TERM
				  RELATIONSHIP_TYPE
				  ONTOLOGY)
			      ], @args );
   
    $self->init(); 
    
    $self->identifier( $identifier );
    $subject_term = $child unless $subject_term;
    $object_term = $parent unless $object_term;
    $predicate_term = $reltype unless $predicate_term;
    $self->subject_term( $subject_term) if $subject_term;
    $self->object_term( $object_term) if $object_term;
    $self->predicate_term( $predicate_term ) if $predicate_term;
    $self->ontology($ont) if $ont;
                                                    
    return $self;
    
} # new




sub init {
    my( $self ) = @_;
    
    $self->{ "_identifier" }     = undef;
    $self->{ "_subject_term" }   = undef;
    $self->{ "_object_term" }    = undef;
    $self->{ "_predicate_term" } = undef;
    $self->ontology(undef);
   
} # init




sub identifier {
    my ( $self, $value ) = @_;

    if ( defined $value ) {
        $self->{ "_identifier" } = $value;
    }

    return $self->{ "_identifier" };
} # identifier





sub subject_term {
    my ( $self, $term ) = @_;
  
    if ( defined $term ) {
        $self->_check_class( $term, "Bio::Ontology::TermI" );
        $self->{ "_subject_term" } = $term;
    }

    return $self->{ "_subject_term" };
    
} # subject_term




sub object_term {
    my ( $self, $term ) = @_;
  
    if ( defined $term ) {
        $self->_check_class( $term, "Bio::Ontology::TermI" );
        $self->{ "_object_term" } = $term;
    }

    return $self->{ "_object_term" };
}




sub predicate_term {
    my ( $self, $term ) = @_;
  
    if ( defined $term ) {
        $self->_check_class( $term, "Bio::Ontology::TermI" );
        $self->{ "_predicate_term" } = $term;
    }

    return $self->{ "_predicate_term" };
}



sub ontology{
    my $self = shift;
    my $ont;

    if(@_) {
	$ont = shift;
	if($ont) {
	    $ont = Bio::Ontology::Ontology->new(-name => $ont) if ! ref($ont);
	    if(! $ont->isa("Bio::Ontology::OntologyI")) {
		$self->throw(ref($ont)." does not implement ".
			     "Bio::Ontology::OntologyI. Bummer.");
	    }
	} 
	return $self->{"_ontology"} = $ont;
    } 
    return $self->{"_ontology"};
}


sub to_string {
    my( $self ) = @_;
    
    local $^W = 0;

    my $s = "";

    $s .= "-- Identifier:\n";
    $s .= $self->identifier()."\n";
    $s .= "-- Subject Term Identifier:\n";
    $s .= $self->subject_term()->identifier()."\n";
    $s .= "-- Object Term Identifier:\n";
    $s .= $self->object_term()->identifier()."\n";
    $s .= "-- Relationship Type Identifier:\n";
    $s .= $self->predicate_term()->identifier();
    
    return $s;
    
} # to_string



sub _check_class {
    my ( $self, $value, $expected_class ) = @_;
    
    if ( ! defined( $value ) ) {
        $self->throw( "Found [undef] where [$expected_class] expected" );
    }
    elsif ( ! ref( $value ) ) {
        $self->throw( "Found [scalar] where [$expected_class] expected" );
    } 
    elsif ( ! $value->isa( $expected_class ) ) {
        $self->throw( "Found [" . ref( $value ) . "] where [$expected_class] expected" );
    }    

} # _check_type

#################################################################
# aliases for backwards compatibility
#################################################################


*child_term        = \&subject_term;
*parent_term       = \&object_term;
*relationship_type = \&predicate_term;

1;