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Bio::Ontology::Term(3)User Contributed Perl DocumentatioBio::Ontology::Term(3)

NAME
       Bio::Ontology::Term - implementation of the 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 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
   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

   Support
       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 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:

	 http://bugzilla.open-bio.org/

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

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.

perl v5.14.1			  2011-07-22		Bio::Ontology::Term(3)
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