Bio::Ontology
TermI
Summary
TermI - 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 : 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 identifier
{ my ( $self ) = @_;
$self->throw_not_implemented();
}
} | sub name
{ my ( $self ) = @_;
$self->throw_not_implemented();
}
} | sub definition
{ my ( $self ) = @_;
$self->throw_not_implemented();
}
} | sub category
{ my ( $self ) = @_;
$self->throw_not_implemented();
}
} | sub version
{ my ( $self ) = @_;
$self->throw_not_implemented();
}
} | sub is_obsolete
{ my ( $self ) = @_;
$self->throw_not_implemented();
}
} | sub comment
{ my ( $self ) = @_;
$self->throw_not_implemented();
}
} | sub each_synonym
{ my ( $self ) = @_;
$self->throw_not_implemented();
}
} | sub add_synonyms
{ my ( $self ) = @_;
$self->throw_not_implemented();
}
} | sub remove_synonyms
{ my ( $self ) = @_;
$self->throw_not_implemented();
}
} | General documentation
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to one
of the Bioperl mailing lists. Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://bio.perl.org/MailList.html - About the mailing lists
Report bugs to the Bioperl bug tracking system to help us keep track
the bugs and their resolution. Bug reports can be submitted via email
or the web:
bioperl-bugs@bio.perl.org
http://bugzilla.bioperl.org/
The rest of the documentation details each of the object
methods.