Bio::Annotation OntologyTerm
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Summary
Bio::Annotation::OntologyTerm - An ontology term adapted to AnnotationI
Package variables
Privates (from "my" definitions)
$DEFAULT_CB = sub { $_[0]->identifier || ''}
Included modules
Bio::Ontology::Term
Inherit
Bio::AnnotationI Bio::Ontology::TermI Bio::Root::Root
Synopsis
   use Bio::Annotation::OntologyTerm;
use Bio::Annotation::Collection;
use Bio::Ontology::Term;
my $coll = Bio::Annotation::Collection->new(); # this also implements a tag/value pair, where tag _and_ value are treated # as ontology terms my $annterm = Bio::Annotation::OntologyTerm->new(-label => 'ABC1', -tagname => 'Gene Name'); # ontology terms can be added directly - they implicitly have a tag $coll->add_Annotation($annterm); # implementation is by composition - you can get/set the term object # e.g. my $term = $annterm->term(); # term is-a Bio::Ontology::TermI print "ontology term ",$term->name()," (ID ",$term->identifier(), "), ontology ",$term->ontology()->name(),"\n"; $term = Bio::Ontology::Term->new(-name => 'ABC2', -ontology => 'Gene Name'); $annterm->term($term);
Description
Ontology term annotation object
Methods
newDescriptionCode
as_textDescriptionCode
display_textDescriptionCode
hash_treeDescriptionCode
tagnameDescriptionCode
termDescriptionCode
identifierDescriptionCode
nameDescriptionCode
definitionDescriptionCode
ontologyDescriptionCode
is_obsoleteDescriptionCode
commentDescriptionCode
get_synonymsDescriptionCode
add_synonymDescriptionCode
remove_synonymsDescriptionCode
get_dblinksDescriptionCode
get_dbxrefsDescriptionCode
add_dblinkDescriptionCode
add_dbxrefDescriptionCode
remove_dblinksDescriptionCode
remove_dbxrefsDescriptionCode
get_secondary_idsDescriptionCode
add_secondary_idDescriptionCode
remove_secondary_idsDescriptionCode
Methods description
newcode    nextTop
 Title   : new
Usage : my $sv = Bio::Annotation::OntologyTerm->new();
Function: Instantiate a new OntologyTerm object
Returns : Bio::Annotation::OntologyTerm object
Args : -term => $term to initialize the term data field [optional]
Most named arguments that Bio::Ontology::Term accepts will work
here too. -label is a synonym for -name, -tagname is a synonym for
-ontology.
as_textcodeprevnextTop
 Title   : as_text
Usage : my $text = $obj->as_text
Function: Returns a textual representation of the annotation that
this object holds. Presently, it is tag name, name of the
term, and the is_obsolete attribute concatenated togather
with a delimiter (|).
Returns : string Args : none
display_textcodeprevnextTop
 Title   : display_text
Usage : my $str = $ann->display_text();
Function: returns a string. Unlike as_text(), this method returns a string
formatted as would be expected for te specific implementation.
One can pass a callback as an argument which allows custom text generation; the callback is passed the current instance and any text returned Example : Returns : a string Args : [optional] callback
hash_treecodeprevnextTop
 Title   : hash_tree
Usage : my $hashtree = $value->hash_tree
Function: For supporting the AnnotationI interface just returns the value
as a hashref with the key 'value' pointing to the value
Returns : hashrf
Args : none
tagnamecodeprevnextTop
 Title   : tagname
Usage : $obj->tagname($newval)
Function: Get/set the tagname for this annotation value.
Setting this is optional. If set, it obviates the need to provide a tag to AnnotationCollection when adding this object. This is aliased to ontology() here. Example : Returns : value of tagname (a scalar) Args : new value (a scalar, optional)
termcodeprevnextTop
 Title   : term
Usage : $obj->term($newval)
Function: Get/set the Bio::Ontology::TermI implementing object.
We implement TermI by composition, and this method sets/gets the object we delegate to. Example : Returns : value of term (a Bio::Ontology::TermI compliant object) Args : new value (a Bio::Ontology::TermI compliant object, optional)
identifiercodeprevnextTop
 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).
namecodeprevnextTop
 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).
definitioncodeprevnextTop
 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).
ontologycodeprevnextTop
 Title   : ontology
Usage : $term->ontology( $top );
or
$top = $term->ontology();
Function: Set/get for a relationship between this Term and
another Term (e.g. the top level of the ontology).
Returns : The ontology of this Term [TermI].
Args : The ontology of this Term [TermI or scalar -- which
becomes the name of the catagory term] (optional).
is_obsoletecodeprevnextTop
 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).
commentcodeprevnextTop
 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).
get_synonymscodeprevnextTop
 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 :
add_synonymcodeprevnextTop
 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]].
remove_synonymscodeprevnextTop
 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 :
get_dblinkscodeprevnextTop
 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 :
Note : this is deprecated in favor of get_dbxrefs(), which works with strings
or Bio::Annotation::DBLink instances
get_dbxrefscodeprevnextTop
 Title   : get_dbxrefs()
Usage : @ds = $term->get_dbxrefs();
Function: Returns a list of each dblinks of this GO term.
Returns : A list of dblinks [array of [scalars] or Bio::Annotation::DBLink instances].
Args :
add_dblinkcodeprevnextTop
 Title   : add_dblink
Usage : $term->add_dblink( @dbls );
or
$term->add_dblink( $dbl );
Function: Pushes one or more dblinks
into the list of dblinks.
Returns :
Args : One dblink [scalar] or a list of
dblinks [array of [scalars]].
Note : this is deprecated in favor of add_dbxref(), which works with strings
or Bio::Annotation::DBLink instances
add_dbxrefcodeprevnextTop
 Title   : add_dbxref
Usage : $term->add_dbxref( @dbls );
or
$term->add_dbxref( $dbl );
Function: Pushes one or more dblinks
into the list of dblinks.
Returns :
Args :
remove_dblinkscodeprevnextTop
 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 :
Note : this is deprecated in favor of remove_dbxrefs(), which works with strings
or Bio::Annotation::DBLink instances
remove_dbxrefscodeprevnextTop
 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 :
get_secondary_idscodeprevnextTop
 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 :
add_secondary_idcodeprevnextTop
 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]
remove_secondary_idscodeprevnextTop
 Title   : remove_secondary_ids
Usage : $term->remove_secondary_ids();
Function: Deletes (and returns) the secondary identifiers of this Term.
Returns : The previous list of secondary identifiers [array of [scalars]]
Args :
Methods code
newdescriptionprevnextTop
sub new {
    my ($class,@args) = @_;

    my $self = $class->SUPER::new(@args);
    my ($term,$name,$label,$identifier,$definition,$ont,$tag) =
	$self->_rearrange([qw(TERM
                          NAME
                          LABEL
                          IDENTIFIER
                          DEFINITION
                          ONTOLOGY
                          TAGNAME)],
                      @args);
    if($term) {
        $self->term($term);
    } else {
        $self->name($name || $label) if $name || $label;
        $self->identifier($identifier) if $identifier;
        $self->definition($definition) if $definition;
    }
    $self->ontology($ont || $tag) if $ont || $tag;
    return $self;
}
as_textdescriptionprevnextTop
sub as_text {
   my ($self) = @_;

   return $self->tagname()."|".$self->name()."|".($self->is_obsolete()||'');
}
display_textdescriptionprevnextTop
sub display_text {
    my ($self, $cb) = @_;
    $cb ||= $DEFAULT_CB;
    $self->throw("Callback must be a code reference") if ref $cb ne 'CODE';
    return $cb->($self);
  }
}
hash_treedescriptionprevnextTop
sub hash_tree {
   my ($self) = @_;

   my $h = {};
   $h->{'name'} = $self->name();
   $h->{'identifier'} = $self->identifier();
   $h->{'definition'} = $self->definition();
   $h->{'synonyms'} = [$self->get_synonyms()];
}
tagnamedescriptionprevnextTop
sub tagname {
    my $self = shift;

    return $self->ontology(@_) if @_;
    # if in get mode we need to get the name from the ontology
my $ont = $self->ontology(); return ref($ont) ? $ont->name() : $ont;
}
termdescriptionprevnextTop
sub term {
    my ($self,$value) = @_;
    if( defined $value) {
        $self->{'term'} = $value;
    }
    if(! exists($self->{'term'})) {
        $self->{'term'} = Bio::Ontology::Term->new();
    }
    return $self->{'term'};
}
identifierdescriptionprevnextTop
sub identifier {
    return shift->term()->identifier(@_);
} # identifier
}
namedescriptionprevnextTop
sub name {
    return shift->term()->name(@_);
} # name
}
definitiondescriptionprevnextTop
sub definition {
    return shift->term()->definition(@_);
} # definition
}
ontologydescriptionprevnextTop
sub ontology {
    return shift->term()->ontology(@_);
}
is_obsoletedescriptionprevnextTop
sub is_obsolete {
    return shift->term()->is_obsolete(@_);
} # is_obsolete
}
commentdescriptionprevnextTop
sub comment {
    return shift->term()->comment(@_);
} # comment
}
get_synonymsdescriptionprevnextTop
sub get_synonyms {
    return shift->term()->get_synonyms(@_);
} # get_synonyms
}
add_synonymdescriptionprevnextTop
sub add_synonym {
    return shift->term()->add_synonym(@_);
} # add_synonym
}
remove_synonymsdescriptionprevnextTop
sub remove_synonyms {
    return shift->term()->remove_synonyms(@_);
} # remove_synonyms
}
get_dblinksdescriptionprevnextTop
sub get_dblinks {
    my $self = shift;
    $self->deprecated('get_dblinks() is deprecated; use get_dbxrefs()');
    return $self->term->get_dbxrefs(@_);
} # get_dblinks
}
get_dbxrefsdescriptionprevnextTop
sub get_dbxrefs {
    return shift->term->get_dbxrefs(@_);
} # get_dblinks
}
add_dblinkdescriptionprevnextTop
sub add_dblink {
    my $self = shift;
    $self->deprecated('add_dblink() is deprecated; use add_dbxref()');
    return $self->term->add_dbxref(@_);
} # add_dblink
}
add_dbxrefdescriptionprevnextTop
sub add_dbxref {
    return shift->term->add_dbxref(@_);
}
remove_dblinksdescriptionprevnextTop
sub remove_dblinks {
    my $self = shift;
    $self->deprecated('remove_dblinks() is deprecated; use remove_dbxrefs()');
    return $self->term->remove_dbxrefs(@_);
} # remove_dblinks
}
remove_dbxrefsdescriptionprevnextTop
sub remove_dbxrefs {
    return shift->term->remove_dbxrefs(@_);
}
get_secondary_idsdescriptionprevnextTop
sub get_secondary_ids {
    return shift->term->get_secondary_ids(@_);
} # get_secondary_ids
}
add_secondary_iddescriptionprevnextTop
sub add_secondary_id {
    return shift->term->add_secondary_id(@_);
} # add_secondary_id
}
remove_secondary_idsdescriptionprevnextTop
sub remove_secondary_ids {
    return shift->term->remove_secondary_ids(@_);
} # remove_secondary_ids
1;
}
General documentation
FEEDBACKTop
Mailing ListsTop
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
Support Top
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.
Reporting BugsTop
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/
AUTHOR - Hilmar LappTop
Email hlapp at gmx.net
APPENDIXTop
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
AnnotationI implementing functionsTop
Methods for Bio::Ontology::TermI complianceTop