Bio::Ontology
Term
Summary
Term - interface for ontology terms
Package variables
No package variables defined.
Included modules
Inherit
Synopsis
#get Bio::Ontology::TermI somehow.
print $term->identifier(), "\n";
print $term->name(), "\n";
print $term->definition(), "\n";
print $term->is_obsolete(), "\n";
print $term->comment(), "\n";
foreach my $synonym ( $term->each_synonym() ) {
print $synonym, "\n";
}
Description
This is "dumb" interface for ontology terms providing basic methods
(it provides no functionality related to graphs).
Methods
Methods description
Title : new
Usage : $term = Bio::Ontology::Term->new( -identifier => "16847",
-name => "1-aminocyclopropane-1-carboxylate synthase",
-definition => "Catalysis of ...",
-is_obsolete => 0,
-comment => "" );
Function: Creates a new Bio::Ontology::Term.
Returns : A new Bio::Ontology::Term object.
Args : -identifier => the identifier of this term [scalar]
-name => the name of this term [scalar]
-definition => the definition of this term [scalar]
-category => a relationship between this Term and another Term [TermI or scalar]
-version => version information [scalar]
-is_obsolete => the obsoleteness of this term [0 or 1]
-comment => a comment [scalar] |
Title : identifier
Usage : $term->identifier( "0003947" );
or
print $term->identifier();
Function: Set/get for the identifier of this Term.
Returns : The identifier [scalar].
Args : The identifier [scalar] (optional). |
Title : name
Usage : $term->name( "N-acetylgalactosaminyltransferase" );
or
print $term->name();
Function: Set/get for the name of this Term.
Returns : The name [scalar].
Args : The name [scalar] (optional). |
Title : definition
Usage : $term->definition( "Catalysis of ..." );
or
print $term->definition();
Function: Set/get for the definition of this Term.
Returns : The definition [scalar].
Args : The definition [scalar] (optional). |
Title : category
Usage : $term->category( $top );
or
$top = $term->category();
Function: Set/get for a relationship between this Term and
another Term (e.g. the top level of the ontology).
Returns : The category of this Term [TermI].
Args : The category of this Term [TermI or scalar -- which
becomes the name of the catagory term] (optional). |
Title : version
Usage : $term->version( "1.00" );
or
print $term->version();
Function: Set/get for version information.
Returns : The version [scalar].
Args : The version [scalar] (optional). |
Title : is_obsolete
Usage : $term->is_obsolete( 1 );
or
if ( $term->is_obsolete() )
Function: Set/get for the obsoleteness of this Term.
Returns : the obsoleteness [0 or 1].
Args : the obsoleteness [0 or 1] (optional). |
Title : comment
Usage : $term->comment( "Consider the term ..." );
or
print $term->comment();
Function: Set/get for an arbitrary comment about this Term.
Returns : A comment.
Args : A comment (optional). |
Title : each_synonym()
Usage : @aliases = $term->each_synonym();
Function: Returns a list of aliases of this Term.
Returns : A list of aliases [array of [scalar]].
Args : |
Title : add_synonyms
Usage : $term->add_synonyms( @asynonyms );
or
$term->add_synonyms( $synonym );
Function: Pushes one or more synonyms into the list of synonyms.
Returns :
Args : One synonym [scalar] or a list of synonyms [array of [scalar]]. |
Title : remove_synonyms()
Usage : $term->remove_synonyms();
Function: Deletes (and returns) the synonyms of this Term.
Returns : A list of synonyms [array of [scalar]].
Args : |
Methods code
sub new
{
my( $class,@args ) = @_;
my $self = $class->SUPER::new( @args );
my ( $identifier,
$name,
$definition,
$category,
$version,
$is_obsolete,
$comment )
= $self->_rearrange( [ qw( IDENTIFIER
NAME
DEFINITION
CATEGORY
VERSION
IS_OBSOLETE
COMMENT ) ], @args );
$self->init();
$identifier && $self->identifier( $identifier );
$name && $self->name( $name );
$definition && $self->definition( $definition );
$category && $self->category( $category );
$version && $self->version( $version );
$is_obsolete && $self->is_obsolete( $is_obsolete );
$comment && $self->comment( $comment );
return $self;
}
} | sub init
{
my( $self ) = @_;
$self->identifier( "" );
$self->name( "" );
$self->definition( "" );
$self->version( "" );
$self->is_obsolete( FALSE );
$self->comment( "" );
$self->remove_synonyms();
}
} | sub identifier
{ my ( $self, $value ) = @_;
if ( defined $value ) {
$self->{ "_identifier" } = $value ? $value : undef;
}
return $self->{ "_identifier" };
}
} | sub name
{ my ( $self, $value ) = @_;
if ( defined $value ) {
$self->{ "_name" } = $value ? $value : undef;
}
return $self->{ "_name" };
}
} | sub definition
{ my ( $self, $value ) = @_;
if ( defined $value ) {
$self->{ "_definition" } = $value ? $value : undef;
}
return $self->{ "_definition" };
}
} | sub category
{ my ( $self, $value ) = @_;
if ( defined $value ) {
if(! $value) {
$self->{"_category"} = undef;
}
elsif ( ! ref( $value ) ) {
my $term = $self->new();
$term->name( $value );
$self->{ "_category" } = $term;
}
elsif ( $value->isa( "Bio::Ontology::TermI" ) ) {
$self->{ "_category" } = $value;
}
else {
$self->throw( "Found [". ref( $value )
. "] where [Bio::Ontology::TermI] or [scalar] expected" );
}
}
return $self->{ "_category" };
}
} | sub version
{ my ( $self, $value ) = @_;
if ( defined $value ) {
$self->{ "_version" } = $value ? $value : undef;
}
return $self->{ "_version" };
}
} | sub is_obsolete
{ my ( $self, $value ) = @_;
if ( defined $value ) {
$self->_is_true_or_false( $value );
$self->{ "_is_obsolete" } = $value;
}
return $self->{ "_is_obsolete" };
}
} | sub comment
{ my ( $self, $value ) = @_;
if ( defined $value ) {
$self->{ "_comment" } = $value ? $value : undef;
}
return $self->{ "_comment" };
}
} | sub each_synonym
{ my ( $self ) = @_;
if ( $self->{ "_synonyms" } ) {
return @{ $self->{ "_synonyms" } };
}
else {
return my @a = ();
}
}
} | sub add_synonyms
{ my ( $self, @values ) = @_;
return unless( @values );
push( @{ $self->{ "_synonyms" } }, @values );
}
} | sub remove_synonyms
{ my ( $self ) = @_;
my @a = $self->each_synonym();
$self->{ "_synonyms" } = [];
return @a;
}
} | | _is_true_or_false | description | prev | next | Top |
sub _is_true_or_false
{ my ( $self, $value ) = @_;
unless ( $value !~ /\D/ && ( $value == TRUE || $value == FALSE ) ) {
$self->throw( "Found [" . $value
. "] where " . TRUE . " or " . FALSE . " expected" );
}
}
} | General documentation
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The rest of the documentation details each of the object
methods.