#
# BioPerl module for Bio::Ontology::Term
#
# Please direct questions and support issues to <bioperl-l@bioperl.org>
#
# Cared for by Christian M. Zmasek <czmasek-at-burnham.org> or <cmzmasek@yahoo.com>
#
# (c) Christian M. Zmasek, czmasek-at-burnham.org, 2002.
# (c) GNF, Genomics Institute of the Novartis Research Foundation, 2002.
#
# You may distribute this module under the same terms as perl itself.
# Refer to the Perl Artistic License (see the license accompanying this
# software package, or see http://www.perl.com/language/misc/Artistic.html)
# for the terms under which you may use, modify, and redistribute this module.
#
# THIS PACKAGE IS PROVIDED "AS IS" AND WITHOUT ANY EXPRESS OR IMPLIED
# WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED WARRANTIES OF
# MERCHANTIBILITY AND FITNESS FOR A PARTICULAR PURPOSE.
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=head1 NAME
Bio::Ontology::Term - implementation of the interface for ontology terms
=head1 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";
}
=head1 DESCRIPTION
This is a simple implementation for ontology terms providing basic
methods (it provides no functionality related to graphs). It
implements the L<Bio::Ontology::TermI> interface.
This class also implements L<Bio::IdentifiableI> and
L<Bio::DescribableI>.
=head1 FEEDBACK
=head2 Mailing Lists
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
=head2 Support
Please direct usage questions or support issues to the mailing list:
I<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.
=head2 Reporting Bugs
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://github.com/bioperl/bioperl-live/issues
=head1 AUTHOR
Christian M. Zmasek
Email: czmasek-at-burnham.org or cmzmasek@yahoo.com
WWW: http://monochrome-effect.net/
Address:
Genomics Institute of the Novartis Research Foundation
10675 John Jay Hopkins Drive
San Diego, CA 92121
=head1 APPENDIX
The rest of the documentation details each of the object
methods.
=cut
# Let the code begin...
package Bio::Ontology::Term;
use strict;
use Bio::Ontology::Ontology;
use Bio::Ontology::OntologyStore;
use Bio::Annotation::DBLink;
use Data::Dumper;
use constant TRUE => 1;
use constant FALSE => 0;
use base qw(Bio::Root::Root Bio::Ontology::TermI Bio::IdentifiableI Bio::DescribableI);
=head2 new
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 L<Bio::Ontology::OntologyI>, L<Bio::Annotation::Reference>,
L<Bio::Annotation::DBLink>.
=cut
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 => $dbxrefs);
# deprecated methods, allow to pass on to get the dep. notification
ref($dblinks) && $self->add_dblink(@$dblinks);
ref($references) && $self->add_reference(@$references);
return $self;
} # new
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();
} # init
=head2 identifier
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).
=cut
sub identifier {
my $self = shift;
return $self->{'identifier'} = shift if @_;
return $self->{'identifier'};
} # identifier
=head2 name
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).
=cut
sub name {
my $self = shift;
return $self->{'name'} = shift if @_;
return $self->{'name'};
} # name
=head2 definition
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).
=cut
sub definition {
my $self = shift;
return $self->{'definition'} = shift if @_;
return $self->{'definition'};
} # definition
=head2 ontology
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 L<Bio::Ontology::OntologyI>.
=cut
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"};
} # ontology
=head2 version
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).
=cut
sub version {
my $self = shift;
return $self->{'version'} = shift if @_;
return $self->{'version'};
} # version
=head2 is_obsolete
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).
=cut
sub is_obsolete{
my $self = shift;
return $self->{'is_obsolete'} = shift if @_;
return $self->{'is_obsolete'};
} # is_obsolete
=head2 comment
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).
=cut
sub comment{
my $self = shift;
return $self->{'comment'} = shift if @_;
return $self->{'comment'};
} # comment
=head2 get_synonyms
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 :
=cut
sub get_synonyms {
my $self = shift;
return @{ $self->{ "_synonyms" } } if exists($self->{ "_synonyms" });
return ();
} # get_synonyms
=head2 add_synonym
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]].
=cut
sub add_synonym {
my ( $self, @values ) = @_;
return unless( @values );
# avoid duplicates
foreach my $syn (@values) {
next if grep { $_ eq $syn; } @{$self->{ "_synonyms" }};
push( @{ $self->{ "_synonyms" } }, $syn );
}
} # add_synonym
=head2 remove_synonyms
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 :
=cut
sub remove_synonyms {
my ( $self ) = @_;
my @a = $self->get_synonyms();
$self->{ "_synonyms" } = [];
return @a;
} # remove_synonyms
=head2 get_dblinks
Title : get_dblinks()
Usage : @ds = $term->get_dblinks();
Function: Returns a list of each dblinks of this GO term.
Returns : A list of dblinks [array of [scalars]].
Args : A scalar indicating the context (optional).
If omitted, all dblinks will be returned.
Note : deprecated method due to past use of mixed data types; use
get_dbxrefs() instead, which handles both strings and DBLink
instances
=cut
sub get_dblinks {
my ($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);
} # get_dblinks
=head2 get_dbxrefs
Title : get_dbxrefs()
Usage : @ds = $term->get_dbxrefs();
Function: Returns a list of each link for this term.
If an implementor of this interface permits modification of
this array property, the class should define at least
methods add_dbxref() and remove_dbxrefs(), with obvious
functionality.
Returns : A list of L<Bio::Annotation::DBLink> instances
Args : [optional] string which specifies context (default : returns all dbxrefs)
=cut
sub get_dbxrefs {
my ($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;
} # get_dbxrefs
=head2 get_dblink_context
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
=cut
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(@_);
}
=head2 get_dbxref_context
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]
=cut
sub get_dbxref_context {
my $self=shift;
return keys %{$self->{_dblinks}};
}
=head2 add_dblink
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 L<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
=cut
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");
# here we're assuming the data is in a simple DB:ID format
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');
} # add_dblink
=head2 add_dbxref
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)
=cut
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_dbxref
# alias, for consistency
*add_dbxrefs = \&add_dbxref;
=head2 has_dblink
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
=cut
sub has_dblink {
my ( $self, $value ) = @_;
$self->deprecated("use of has_dblink() is deprecated; use has_dbxref() instead");
return $self->has_dbxref($value);
}
=head2 has_dbxref
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.
=cut
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;
}
}
=head2 add_dblink_context
Title : add_dblink_context
Usage : $term->add_dblink_context($db, $context);
Function: add a dblink with its context
Return : [none]
Args : [arg1] a Bio::Annotation::DBLink instance
[arg2] a string for context; if omitted, the
default/context-less one will be used.
Note : deprecated method due to past use of mixed data types; use
add_dbxref() instead
=cut
sub add_dblink_context {
my ($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);
}
=head2 remove_dblinks
Title : remove_dblinks()
Usage : $term->remove_dblinks();
Function: Deletes (and returns) the definition references of this GO term.
Returns : A list of definition references [array of [scalars]].
Args : Context. If omitted or equal to 'all', all dblinks
will be removed.
Note : deprecated method due to past use of mixed data types; use
remove_dblinks() instead, which handles both strings and
DBLink instances
=cut
sub remove_dblinks {
my ($self, $context) = @_;
$self->deprecated("use of remove_dblinks() is deprecated; use remove_dbxrefs() instead");
return $self->remove_dbxrefs(@_);
} # remove_dblinks
=head2 remove_dbxrefs
Title : remove_dbxrefs()
Usage : $term->remove_dbxrefs();
Function: Deletes (and returns) the definition references of this GO term.
Returns : A list of definition references [array of [scalars]].
Args : Context. If omitted or equal to 'all', all dblinks
will be removed.
=cut
sub remove_dbxrefs {
my ($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;
} # remove_dbxrefs
=head2 get_references
Title : get_references
Usage : @references = $self->get_references
Fuctnion: Returns a list of references
Return : A list of objects
Args : [none]
=cut
sub get_references {
my $self=shift;
return @{$self->{_references}} if exists $self->{_references};
return ();
}
=head2 add_reference
Title : add_reference
Usage : $self->add_reference($reference);
$self->add_reference($reference1, $reference2);
Fuctnion: Add one or more references
Returns : [none]
=cut
sub add_reference {
my ($self, @values) =@_;
return unless @values;
# avoid duplicates and undefs
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;
}
}
=head2 remove_references
Title : remove_references
Usage : $self->remove_references;
Function: Deletes (and returns) all references
Returns : A list of references
Args : [none]
=cut
sub remove_references {
my $self=shift;
my @references=$self->get_references;
$self->{_references}=[];
return @references;
}
=head2 get_secondary_ids
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 :
=cut
sub get_secondary_ids {
my $self = shift;
return @{$self->{"_secondary_ids"}} if exists($self->{"_secondary_ids"});
return ();
} # get_secondary_ids
=head2 add_secondary_id
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]
=cut
sub add_secondary_id {
my $self = shift;
return unless @_;
# avoid duplicates
foreach my $id (@_) {
next if grep { !$_ or $_ eq $id; } @{$self->{ "_secondary_ids" }};
push( @{ $self->{ "_secondary_ids" } }, $id );
}
} # add_secondary_id
=head2 remove_secondary_ids
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 :
=cut
sub remove_secondary_ids {
my $self = shift;
my @a = $self->get_secondary_ids();
$self->{ "_secondary_ids" } = [];
return @a;
} # remove_secondary_ids
# Title :_is_true_or_false
# Function: Checks whether the argument is TRUE or FALSE.
# Returns :
# Args : The value to be checked.
sub _is_true_or_false {
my ( $self, $value ) = @_;
unless ( $value !~ /\D/ && ( $value == TRUE || $value == FALSE ) ) {
$self->throw( "Found [" . $value
. "] where " . TRUE . " or " . FALSE . " expected" );
}
} # _is_true_or_false
=head1 Methods implementing L<Bio::IdentifiableI> and L<Bio::DescribableI>
=cut
=head2 object_id
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
=cut
sub object_id {
return shift->identifier(@_);
}
=head2 authority
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)
=cut
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;
}
=head2 namespace
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)
=cut
sub namespace {
my $self = shift;
$self->ontology(@_) if(@_);
my $ont = $self->ontology();
return defined($ont) ? $ont->name() : undef;
}
=head2 display_name
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)
=cut
sub display_name {
return shift->name(@_);
}
=head2 description
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)
=cut
sub description {
return shift->definition(@_);
}
#################################################################
# aliases or forwards to maintain backward compatibility
#################################################################
=head1 Deprecated methods
Used for looking up the methods that supercedes them.
=cut
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")}
*each_synonym = \&get_synonyms;
*add_synonyms = \&add_synonym;
1;