Provided by: libbio-perl-perl_1.6.901-2_all bug

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:

         https://redmine.open-bio.org/projects/bioperl/

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.