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 a simple implementation for ontology terms providing basic methods (it provides no functionality related to graphs). It implements the Bio::Ontology::TermI interface.This class also implements Bio::IdentifiableI and Bio::DescribableI.
FEEDBACK
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Reporting Bugs
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AUTHOR
Christian M. ZmasekEmail: czmasek-at-burnham.org or [email protected]
WWW: http://monochrome-effect.net/
Address:
Genomics Institute of the Novartis Research Foundation 10675 John Jay Hopkins Drive San Diego, CA 92121
APPENDIX
The rest of the documentation details each of the object methods.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 Bio::Ontology::OntologyI, Bio::Annotation::Reference, Bio::Annotation::DBLink.
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).
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).
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).
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 Bio::Ontology::OntologyI.
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).
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).
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).
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 :
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]].
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 :
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
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)
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
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]
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
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)
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
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.
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
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
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.
get_references
Title : get_references Usage : @references = $self->get_references Fuctnion: Returns a list of references Return : A list of objects Args : [none]
add_reference
Title : add_reference
Usage : $self->add_reference($reference);
$self->add_reference($reference1, $reference2);
Fuctnion: Add one or more references
Returns : [none]
remove_references
Title : remove_references Usage : $self->remove_references; Function: Deletes (and returns) all references Returns : A list of references Args : [none]
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 :
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]
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 :
Methods implementing Bio::IdentifiableI and Bio::DescribableI
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
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)
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)
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)
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)
Deprecated methods
Used for looking up the methods that supercedes them.