Bio::Ontology
Term
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Summary
Bio::Ontology::Term - implementation of the 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
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]
-ontology => the ontology this term lives in
(a Bio::Ontology::OntologyI object)
-version => version information [scalar]
-is_obsolete => the obsoleteness of this term [0 or 1]
-comment => a comment [scalar]
-dblinks => Bio::Annotation::DBLink objects
[reference to array]
-references => Bio::Annotation::Reference objects
[reference to array]
See Bio::Ontology::OntologyI, Bio::Annotation::Reference,
Bio::Annotation::DBLink. |
Title : identifier
Usage : $term->identifier( "GO: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 : ontology
Usage : $ont = $term->ontology();
or
$term->ontology( $ont );
Function: Get the ontology this term is in.
Note that with the ontology in hand you can query for all
related terms etc.
Returns : The ontology of this Term as a Bio::Ontology::OntologyI
implementing object.
Args : On set, the ontology of this Term as a Bio::Ontology::OntologyI
implementing object or a string representing its name.
See Bio::Ontology::OntologyI. |
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 : get_synonyms
Usage : @aliases = $term->get_synonyms;
Function: Returns a list of aliases of this Term.
Returns : A list of aliases [array of [scalar]].
Args : |
Title : add_synonym
Usage : $term->add_synonym( @asynonyms );
or
$term->add_synonym( $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 : |
Title : get_dblinks()
Usage : @ds = $term->get_dblinks();
Function: Returns a list of each dblinks of this GO term.
Returns : A list of dblinks [array of [scalars]].
Args : A scalar indicating the context (optional).
If omitted, all dblinks will be returned.
Note : deprecated method due to past use of mixed data types; use
get_dbxrefs() instead, which handles both strings and DBLink
instances |
Title : get_dbxrefs()
Usage : @ds = $term->get_dbxrefs();
Function: Returns a list of each link for this term.
If an implementor of this interface permits modification of
this array property, the class should define at least
methods add_dbxref() and remove_dbxrefs(), with obvious
functionality.
Returns : A list of Bio::Annotation::DBLink instances
Args : [optional] string which specifies context (default : returns all dbxrefs) |
Title : get_dblink_context
Usage : @context = $term->get_dblink_context;
Function: Return all context existing in Term
Returns : a list of scalar
Args : [none]
Note : deprecated method due to past use of mixed data types; use
get_dbxref_context() instead |
Title : get_dbxref_context
Usage : @context = $term->get_dbxref_context;
Function: Return all context strings existing in Term
Returns : a list of scalars
Args : [none] |
Title : add_dblink
Usage : $term->add_dblink( @dbls );
or
$term->add_dblink( $dbl );
Function: Pushes one or more dblinks onto the list of dblinks.
Returns :
Args : One or more Bio::Annotation::DBLink instances
Note : deprecated method due to past use of mixed data types; use
add_dbxref() instead, which handles both strings and
DBLink instances |
Title : add_dbxref
Usage : $term->add_dbxref( @dbls );
or
$term->add_dbxref( $dbl );
Function: Pushes one or more dblinks onto the list of dblinks.
Returns :
Args : -dbxrefs : array ref of Bio::Annotation::DBLink instances
-context : string designating the context for the DBLink
(default : '_default' - contextless) |
Title : has_dblink
Usage : $term->has_dblink($dblink);
Function: Checks if a DBXref is already existing in the OBOterm object
Return : TRUE/FALSE
Args : [arg1] A DBxref identifier
Note : deprecated method due to past use of mixed data types; use
has_dbxref() instead, which handles both strings and
DBLink instances |
Title : has_dbxref
Usage : $term->has_dbxref($dbxref);
Function: Checks if a dbxref string is already existing in the OBOterm object
Return : TRUE/FALSE
Args : [arg1] A DBxref identifier (string).
Bio::Annotation::DBLink::display_text() is used for comparison
against the string. |
Title : add_dblink_context
Usage : $term->add_dblink_context($db, $context);
Function: add a dblink with its context
Return : [none]
Args : [arg1] a Bio::Annotation::DBLink instance
[arg2] a string for context; if omitted, the
default/context-less one will be used.
Note : deprecated method due to past use of mixed data types; use
add_dbxref() instead |
Title : remove_dblinks()
Usage : $term->remove_dblinks();
Function: Deletes (and returns) the definition references of this GO term.
Returns : A list of definition references [array of [scalars]].
Args : Context. If omitted or equal to 'all', all dblinks
will be removed.
Note : deprecated method due to past use of mixed data types; use
remove_dblinks() instead, which handles both strings and
DBLink instances |
Title : remove_dbxrefs()
Usage : $term->remove_dbxrefs();
Function: Deletes (and returns) the definition references of this GO term.
Returns : A list of definition references [array of [scalars]].
Args : Context. If omitted or equal to 'all', all dblinks
will be removed. |
Title : get_references
Usage : @references = $self->get_references
Fuctnion: Returns a list of references
Return : A list of objects
Args : [none] |
Title : add_reference
Usage : $self->add_reference($reference);
$self->add_reference($reference1, $reference2);
Fuctnion: Add one or more references
Returns : [none] |
Title : remove_references
Usage : $self->remove_references;
Function: Deletes (and returns) all references
Returns : A list of references
Args : [none] |
Title : get_secondary_ids
Usage : @ids = $term->get_secondary_ids();
Function: Returns a list of secondary identifiers of this Term.
Secondary identifiers mostly originate from merging terms,
or possibly also from splitting terms.
Returns : A list of secondary identifiers [array of [scalar]]
Args : |
Title : add_secondary_id
Usage : $term->add_secondary_id( @ids );
or
$term->add_secondary_id( $id );
Function: Adds one or more secondary identifiers to this term.
Returns :
Args : One or more secondary identifiers [scalars] |
Title : remove_secondary_ids
Usage : $term->remove_secondary_ids();
Function: Deletes (and returns) the secondary identifiers of this Term.
Returns : The previous list of secondary identifiers [array of [scalars]]
Args : |
Title : object_id
Usage : $string = $obj->object_id()
Function: a string which represents the stable primary identifier
in this namespace of this object.
This is a synonym for identifier().
Returns : A scalar |
Title : authority
Usage : $authority = $obj->authority()
Function: a string which represents the organisation which
granted the namespace, written as the DNS name for
organisation (eg, wormbase.org)
This forwards to ontology()->authority(). Note that you
cannot set the authority before having set the ontology or
the namespace (which will set the ontology).
Returns : A scalar
Args : on set, the new value (a scalar) |
Title : namespace
Usage : $string = $obj->namespace()
Function: A string representing the name space this identifier
is valid in, often the database name or the name
describing the collection.
This forwards to ontology() (set mode) and
ontology()->name() (get mode). I.e., setting the namespace
will set the ontology to one matching that name in the
ontology store, or to one newly created.
Returns : A scalar
Args : on set, the new value (a scalar) |
Title : display_name
Usage : $string = $obj->display_name()
Function: A string which is what should be displayed to the user.
The definition in Bio::DescribableI states that the
string should not contain spaces. As this is not very
sensible for ontology terms, we relax this here. The
implementation just forwards to name().
Returns : A scalar
Args : on set, the new value (a scalar) |
Title : description
Usage : $string = $obj->description()
Function: A text string suitable for displaying to the user a
description. This string is likely to have spaces, but
should not have any newlines or formatting - just plain
text.
This forwards to definition(). The caveat is that the text
will often be longer for ontology term definitions than the
255 characters stated in the definition in
Bio::DescribableI.
Returns : A scalar
Args : on set, the new value (a scalar) |
Methods code
sub new
{
my( $class,@args ) = @_;
my $self = $class->SUPER::new( @args );
my ( $identifier, $name, $definition, $category, $ont, $version,
$is_obsolete, $comment, $dblinks, $dbxrefs, $references)
= $self->_rearrange( [
qw(IDENTIFIER NAME DEFINITION CATEGORY ONTOLOGY VERSION IS_OBSOLETE
COMMENT DBLINKS DBXREFS REFERENCES) ], @args );
$self->init();
defined($identifier) && $self->identifier( $identifier );
defined($name) && $self->name( $name );
defined($definition) && $self->definition( $definition );
defined($category) && $self->category( $category );
defined($ont) && $self->ontology( $ont );
defined($version) && $self->version( $version );
defined($is_obsolete) && $self->is_obsolete( $is_obsolete );
defined($comment) && $self->comment( $comment );
defined($dbxrefs) && $self->add_dbxref(-dbxrefs => $dbxrefs);
ref($dblinks) && $self->add_dblink(@$dblinks);
ref($references) && $self->add_reference(@$references);
return $self;
}
} | sub init
{
my $self = shift;
$self->identifier(undef);
$self->name(undef);
$self->comment(undef);
$self->definition(undef);
$self->ontology(undef);
$self->is_obsolete(0);
$self->remove_synonyms();
$self->remove_dbxrefs();
$self->remove_references;
$self->remove_secondary_ids();
}
} | sub identifier
{ my $self = shift;
return $self->{'identifier'} = shift if @_;
return $self->{'identifier'};
}
} | sub name
{ my $self = shift;
return $self->{'name'} = shift if @_;
return $self->{'name'};
}
} | sub definition
{ my $self = shift;
return $self->{'definition'} = shift if @_;
return $self->{'definition'};
}
} | 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 version
{ my $self = shift;
return $self->{'version'} = shift if @_;
return $self->{'version'};
}
} | sub is_obsolete
{ my $self = shift;
return $self->{'is_obsolete'} = shift if @_;
return $self->{'is_obsolete'};
}
} | sub comment
{ my $self = shift;
return $self->{'comment'} = shift if @_;
return $self->{'comment'};
}
} | sub get_synonyms
{ my $self = shift;
return @{ $self->{ "_synonyms" } } if exists($self->{ "_synonyms" });
return ();
}
} | sub add_synonym
{ my ( $self, @values ) = @_;
return unless( @values );
foreach my $syn (@values) {
next if grep { $_ eq $syn; } @{$self->{ "_synonyms" }};
push( @{ $self->{ "_synonyms" } }, $syn );
}
}
} | sub remove_synonyms
{ my ( $self ) = @_;
my @a = $self->get_synonyms();
$self->{ "_synonyms" } = [];
return @a;
}
} | sub get_dblinks
{ my ($self, $context) = @_;
$self->deprecated("Use of get_dblinks is deprecated. Note that prior use\n".
"of this method could return either simple scalar values\n".
"or Bio::Annotation::DBLink instances; only\n ".
"Bio::Annotation::DBLink is now supported.\n ".
"Use get_dbxrefs() instead");
$self->get_dbxrefs($context);
}
} | sub get_dbxrefs
{ my ($self, $context) = shift;
my @dbxrefs;
if (defined($context)) {
if (exists($self->{_dblinks}->{$context})) {
@dbxrefs = @{$self->{_dblinks}->{$context}};
}
} else {
@dbxrefs = map { @$_ } values %{$self->{_dblinks}} ;
}
return @dbxrefs;
}
} | sub get_dblink_context
{ my $self=shift;
$self->deprecated("Use of get_dblink_context() is deprecated; use get_dbxref_context() instead");
return $self->get_dbxref_context(@_);} | sub get_dbxref_context
{ my $self=shift;
return keys %{$self->{_dblinks}};} | sub add_dblink
{ my $self = shift;
$self->deprecated("Use of simple strings and add_dblink() is deprecated; use\n".
"Bio::Annotation::DBLink instances and add_dbxref() instead");
my @dbxrefs;
for my $string (@_) {
my ($db, $id) = split(':',$string);
push @dbxrefs, Bio::Annotation::DBLink->new(-database => $db, -primary_id => $id);
}
return $self->add_dbxref(-dbxrefs =>\@ dbxrefs, -context => '_default');
}
} | sub add_dbxref
{ my $self = shift;
my ($links, $context) = $self->_rearrange([qw(DBXREFS CONTEXT)],@_);
return unless defined $links;
$context ||= '_default';
$self->throw("DBLinks must be passed as an array reference") if ref $links ne 'ARRAY';
foreach my $dbxref (@{$links}) {
$self->throw("$dbxref is not a DBLink") unless ref $dbxref &&
$dbxref->isa('Bio::Annotation::DBLink');
$self->throw("'all' is a reserved word for context.") if $context eq 'all';
if (! exists($self->{_dblinks}->{$context})) {
$self->{_dblinks}->{$context} = [];
}
my $linktext = ref $dbxref ? $dbxref->display_text : $dbxref;
if (grep {$_->display_text eq $linktext}
@{$self->{_dblinks}->{$context}})
{
$self->warn("DBLink exists in the dblink of $context");
}
push @{$self->{_dblinks}->{$context}}, $dbxref;
}
}
*add_dbxrefs =\& add_dbxref;} | sub has_dblink
{ my ( $self, $value ) = @_;
$self->deprecated("use of has_dblink() is deprecated; use has_dbxref() instead");
return $self->has_dbxref($value);} | sub has_dbxref
{ my ( $self, $value ) = @_;
return unless defined $value;
my $context = "_default";
$self->throw("'all' is a reserved word for context.") if $context eq 'all';
$context ||= '_default';
if ( ( $self->{_dblinks}->{$context} ) &&
grep { $_->display_text eq $value }
@{ $self->{_dblinks}->{$context} } )
{
return TRUE;
}
else {
return FALSE;
}} | sub add_dblink_context
{ my ($self, $value, $context) = @_;
$self->deprecated("Use of simple strings and add_dblink_context() is deprecated; use\n
Bio::Annotation::DBLink instances and add_dbxref() instead");
return $self->add_dbxref([$value],$context);} | sub remove_dblinks
{ my ($self, $context) = @_;
$self->deprecated("use of remove_dblinks() is deprecated; use remove_dbxrefs() instead");
return $self->remove_dbxrefs(@_);
}
} | sub remove_dbxrefs
{ my ($self, $context) = @_;
$context = undef if $context && ($context eq "all");
my @old = $self->get_dbxrefs($context);
if (defined($context)) {
$self->{_dblinks}->{$context}=[];
} else {
$self->{_dblinks} = {};
}
return @old;
}
} | sub get_references
{ my $self=shift;
return @{$self->{_references}} if exists $self->{_references};
return ();} | sub add_reference
{ my ($self, @values) =@_;
return unless @values;
foreach my $reference (@values){
$self->throw("Passed data not an Bio::Annotation::Reference") unless ref $reference &&
$reference->isa('Bio::AnnotationI');
next unless defined $reference;
next if grep{$_ eq $reference} @{$self->{_references}};
push @{$self->{_references}}, $reference;
}} | sub remove_references
{ my $self=shift;
my @references=$self->get_references;
$self->{_references}=[];
return @references;} | sub get_secondary_ids
{ my $self = shift;
return @{$self->{"_secondary_ids"}} if exists($self->{"_secondary_ids"});
return ();
}
} | sub add_secondary_id
{ my $self = shift;
return unless @_;
foreach my $id (@_) {
next if grep { !$_ or $_ eq $id; } @{$self->{ "_secondary_ids" }};
push( @{ $self->{ "_secondary_ids" } }, $id );
}
}
} | sub remove_secondary_ids
{ my $self = shift;
my @a = $self->get_secondary_ids();
$self->{ "_secondary_ids" } = [];
return @a;
}
} | sub _is_true_or_false
{ my ( $self, $value ) = @_;
unless ( $value !~ /\D/ && ( $value == TRUE || $value == FALSE ) ) {
$self->throw( "Found [" . $value
. "] where " . TRUE . " or " . FALSE . " expected" );
}
}
} | sub object_id
{ return shift->identifier(@_); } | sub authority
{ my $self = shift;
my $ont = $self->ontology();
return $ont->authority(@_) if $ont;
$self->throw("cannot manipulate authority prior to ".
"setting the namespace or ontology") if @_;
return;} | sub namespace
{ my $self = shift;
$self->ontology(@_) if(@_);
my $ont = $self->ontology();
return defined($ont) ? $ont->name() : undef;} | sub display_name
{ return shift->name(@_); } | sub description
{ return shift->definition(@_);
}
} | sub each_dblink
{shift->throw("use of each_dblink() is deprecated; use get_dbxrefs() instead")} | sub add_dblinks
{shift->throw("use of add_dblinks() is deprecated; use add_dbxref() instead")} | 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://bioperl.org/wiki/Mailing_lists - About the mailing lists
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.
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/
The rest of the documentation details each of the object
methods.
Used for looking up the methods that supercedes them.