Bio::Ontology
Relationship
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Summary
Bio::Ontology::Relationship - a relationship for an ontology
Package variables
No package variables defined.
Included modules
Inherit
Synopsis
$rel = Bio::Ontology::Relationship->new( -identifier => "16847",
-subject_term => $subj,
-object_term => $obj,
-predicate_term => $pred );
Description
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.
Methods
Methods description
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] |
Title : init()
Usage : $rel->init();
Function: Initializes this Relationship to all undef.
Returns :
Args : |
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). |
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). |
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). |
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). |
Title : ontology
Usage : $ont = $obj->ontology()
Function: Get/set the ontology that defined this relationship.
Example :
Returns : an object implementing Bio::Ontology::OntologyI
Args : on set, undef or an object implementing
Bio::Ontology::OntologyI (optional)
See Bio::Ontology::OntologyI. |
Title : to_string()
Usage : print $rel->to_string();
Function: to_string method for Relationship.
Returns : A string representation of this Relationship.
Args : |
Methods code
sub new
{
my( $class, @args ) = @_;
my $self = $class->SUPER::new( @args );
my ( $identifier,
$subject_term,
$child,
$object_term,
$parent,
$predicate_term,
$reltype,
$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;
}
} | sub init
{ my( $self ) = @_;
$self->{ "_identifier" } = undef;
$self->{ "_subject_term" } = undef;
$self->{ "_object_term" } = undef;
$self->{ "_predicate_term" } = undef;
$self->ontology(undef);
}
} | sub identifier
{ my ( $self, $value ) = @_;
if ( defined $value ) {
$self->{ "_identifier" } = $value;
}
return $self->{ "_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" };
}
} | 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;
}
} | 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" );
}
}
} | General documentation
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https://redmine.open-bio.org/projects/bioperl/
Hilmar Lapp, email: hlapp at gmx.net
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _
These methods are deprecated and defined here solely to preserve
backwards compatibility.