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This is "dumb" interface for ontology terms providing basic methods
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(it provides no functionality related to graphs). It implements the
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L<Bio::Ontology::TermI> interface.
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This is a simple implementation for ontology terms providing basic
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methods (it provides no functionality related to graphs). It
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implements the L<Bio::Ontology::TermI> interface.
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This class also implements L<Bio::IdentifiableI> and
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L<Bio::DescribableI>.
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Bioperl modules. Send your comments and suggestions preferably to one
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of the Bioperl mailing lists. Your participation is much appreciated.
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bioperl-l@bioperl.org - General discussion
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http://bio.perl.org/MailList.html - About the mailing lists
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bioperl-l@bioperl.org - General discussion
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http://bioperl.org/wiki/Mailing_lists - About the mailing lists
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=head2 Reporting Bugs
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Report bugs to the Bioperl bug tracking system to help us keep track
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the bugs and their resolution. Bug reports can be submitted via email
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the bugs and their resolution. Bug reports can be submitted via the web:
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bioperl-bugs@bio.perl.org
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http://bugzilla.bioperl.org/
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http://bugzilla.open-bio.org/
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# Let the code begin...
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package Bio::Ontology::Term;
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use Bio::Root::Object;
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use Bio::Ontology::TermI;
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use Bio::Ontology::Ontology;
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use Bio::Ontology::OntologyStore;
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use Bio::IdentifiableI;
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use Bio::DescribableI;
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use constant TRUE => 1;
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use constant FALSE => 0;
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@ISA = qw( Bio::Root::Root
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use base qw(Bio::Root::Root Bio::Ontology::TermI Bio::IdentifiableI Bio::DescribableI);
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Usage : $term = Bio::Ontology::Term->new(
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Usage : $term = Bio::Ontology::Term->new(
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-identifier => "16847",
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-name => "1-aminocyclopropane-1-carboxylate synthase",
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-definition => "Catalysis of ...",
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-name => the name of this term [scalar]
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-definition => the definition of this term [scalar]
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-ontology => the ontology this term lives in
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(a L<Bio::Ontology::OntologyI> object)
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(a Bio::Ontology::OntologyI object)
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-version => version information [scalar]
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-is_obsolete => the obsoleteness of this term [0 or 1]
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-comment => a comment [scalar]
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-dblinks => L<Bio::Annotation::DBLink> objects
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-references => L<Bio::Annotation::Reference> objects
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-dblinks => Bio::Annotation::DBLink objects
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-references => Bio::Annotation::Reference objects
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See L<Bio::Ontology::OntologyI>, L<Bio::Annotation::Reference>,
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L<Bio::Annotation::DBLink>.
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my( $class,@args ) = @_;
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my $self = $class->SUPER::new( @args );
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# my ($self, @args) =@_;
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my ( $identifier,
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$dblinks, $references)
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= $self->_rearrange( [ qw( IDENTIFIER
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= $self->_rearrange( [ qw( IDENTIFIER
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defined($identifier) && $self->identifier( $identifier );
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defined($name) && $self->name( $name );
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defined($definition) && $self->definition( $definition );
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Function: Get the ontology this term is in.
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Note that with the ontology in hand you can query for all
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related terms etc. See L<Bio::Ontology::OntologyI>.
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Returns : The ontology of this Term as a L<Bio::Ontology::OntologyI>
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Returns : The ontology of this Term as a Bio::Ontology::OntologyI
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implementing object.
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Args : On set, the ontology of this Term as a L<Bio::Ontology::OntologyI>
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Args : On set, the ontology of this Term as a Bio::Ontology::OntologyI
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implementing object or a string representing its name.
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See L<Bio::Ontology::OntologyI>.
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$ont = Bio::Ontology::Ontology->new(-name => $ont) if ! ref($ont);
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if(! $ont->isa("Bio::Ontology::OntologyI")) {
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$self->throw(ref($ont)." does not implement ".
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"Bio::Ontology::OntologyI. Bummer.");
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return $self->{"_ontology"} = $ont;
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$ont = Bio::Ontology::Ontology->new(-name => $ont) if ! ref($ont);
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if(! $ont->isa("Bio::Ontology::OntologyI")) {
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$self->throw(ref($ont)." does not implement ".
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"Bio::Ontology::OntologyI. Bummer.");
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return $self->{"_ontology"} = $ont;
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return $self->{"_ontology"};
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# avoid duplicates
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foreach my $syn (@values) {
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next if grep { $_ eq $syn; } @{$self->{ "_synonyms" }};
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push( @{ $self->{ "_synonyms" } }, $syn );
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next if grep { $_ eq $syn; } @{$self->{ "_synonyms" }};
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push( @{ $self->{ "_synonyms" } }, $syn );
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Usage : @ds = $term->get_dblinks();
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Function: Returns a list of each dblinks of this GO term.
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Returns : A list of dblinks [array of [scalars]].
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Args : A scalar indicating the context (optional).
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If omitted, all dblinks will be returned.
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sub get_dblinks {
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my $self = shift;
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return @{$self->{ "_dblinks" }} if exists($self->{ "_dblinks" });
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if (defined($context)) {
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return @{$self->{_dblinks}->{$context}}
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if exists($self->{_dblinks}->{$context});
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return map { @$_ } values %{$self->{_dblinks}};
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=head2 get_dblink_context
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Title : get_dblink_context
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Usage : @context = $term->get_dblink_context;
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Function: Return all context existing in Term
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Returns : a list of scalar
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sub get_dblink_context {
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return keys %{$self->{_dblinks}};
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=head2 add_dblink
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Title : add_dblink
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my ( $self, @values ) = @_;
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return unless( @values );
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foreach my $dbl (@values) {
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next if grep { $_ eq $dbl; } @{$self->{ "_dblinks" }};
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push( @{ $self->{ "_dblinks" } }, $dbl );
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$self->add_dblink_context($_,'_default') foreach @_;
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Usage : $term->has_dblink($dblink);
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Function: Checks if a DBXref is already existing in the OBOterm object
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Args : [arg1] A DBxref identifier
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my ( $self, $value ) = @_;
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return unless defined $value;
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my $context = "_default";
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$self->throw("'all' is a reserved word for context.") if $context eq 'all';
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$context ||= '_default';
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if ( ( $self->{_dblinks}->{$context} ) && grep { $_ eq $value }
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@{ $self->{_dblinks}->{$context} } )
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=head2 add_dblink_context
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Title : add_dblink_context
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Usage : $term->add_dblink_context($db, $context);
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Function: add a dblink with its context
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Args : [arg1] an object of Bio::Annotation::DBLink
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[arg2] a string for context; if omitted, the
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default/context-less one will be used.
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sub add_dblink_context {
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my ($self, $value, $context)=@_;
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return unless defined $value;
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$self->throw("'all' is a reserved word for context.") if $context eq 'all';
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$context ||= '_default';
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if (! exists($self->{_dblinks}->{$context})) {
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$self->{_dblinks}->{$context} = [];
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if (grep {$_ eq $value} @{$self->{_dblinks}->{$context}}) {
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$self->warn("$value exists in the dblink of $context");
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push @{$self->{_dblinks}->{$context}}, $value;
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=head2 remove_dblinks
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Title : remove_dblinks()
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Usage : $term->remove_dblinks();
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Function: Deletes (and returns) the definition references of this GO term.
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Returns : A list of definition references [array of [scalars]].
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Args : Context. If omitted or equal to 'all', all dblinks
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sub remove_dblinks {
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my @a = $self->get_dblinks();
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$self->{ "_dblinks" } = [];
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my ($self, $context) = @_;
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$context = undef if $context && ($context eq "all");
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my @old = $self->get_dblinks($context);
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if (defined($context)) {
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$self->{_dblinks}->{$context}=[];
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$self->{_dblinks} = {};
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} # remove_dblinks
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Usage : $string = $obj->display_name()
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Function: A string which is what should be displayed to the user.
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The definition in L<Bio::DescribableI> states that the
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string should not contain spaces. As this isn't very
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The definition in Bio::DescribableI states that the
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string should not contain spaces. As this is not very
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sensible for ontology terms, we relax this here. The
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implementation just forwards to name().
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Function: This method is deprecated. Use ontology() instead.
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$self->warn("TermI::category is deprecated and being phased out. ".
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"Use TermI::ontology instead.");
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# called in set mode?
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# yes; what is incompatible with ontology() is if we were given
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$arg = $arg->name() if ref($arg) && $arg->isa("Bio::Ontology::TermI");
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return $self->ontology($arg,@_);
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# No, called in get mode. This is always incompatible with ontology()
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# since category is supposed to return a TermI.
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my $ont = $self->ontology();
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$term = Bio::Ontology::Term->new(-name => $ont->name(),
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-identifier =>$ont->identifier());
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*each_synonym = \&get_synonyms;
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*add_synonyms = \&add_synonym;
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*each_dblink = \&get_dblinks;
added
removed
Bio/Ontology/Term.pm
