NAME
Term - interface for ontology terms
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 "dumb" interface 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
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://bio.perl.org/MailList.html - About the mailing listsReporting 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 email or the web:
bioperl-bugs@bio.perl.org
http://bugzilla.bioperl.org/AUTHOR
Christian M. Zmasek
Email: czmasek@gnf.org or cmzmasek@yahoo.com
WWW: http://www.genetics.wustl.edu/eddy/people/zmasek/
Address:
Genomics Institute of the Novartis Research Foundation
10675 John Jay Hopkins Drive
San Diego, CA 92121APPENDIX
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 L<Bio::Ontology::OntologyI> object)
-version => version information [scalar]
-is_obsolete => the obsoleteness of this term [0 or 1]
-comment => a comment [scalar]identifier
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).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. See L<Bio::Ontology::OntologyI>.
Returns : The ontology of this Term as a L<Bio::Ontology::OntologyI>
implementing object.
Args : On set, the ontology of this Term as a L<Bio::Ontology::OntologyI>
implementing object or a string representing its name.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 :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 dblink [scalar] or a list of
dblinks [array of [scalars]].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 :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 scalarauthority
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 L<Bio::DescribableI> states that the
string should not contain spaces. As this isn't 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
L<Bio::DescribableI>.
Returns : A scalar
Args : on set, the new value (a scalar)Deprecated methods
Used for looking up the methods that supercedes them.
category
Title : category
Usage :
Function: This method is deprecated. Use ontology() instead.
Example :
Returns :
Args :