Bio::Ontology::TermI - interface for ontology terms

       The rest of the documentation details each of the object methods.

   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.

                  An implementation may not permit the value of this
                  attribute to be changed once it is set, since that may have
                  serious consequences (note that with the ontology in hand
                  you can query for all related terms etc).

                  Note for implementors: you will almost certainly have to
                  take special precaution in order not to create cyclical
                  references in memory.

        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.

                  If an implementor of this interface permits modification of
                  this array property, the class should define at least
                  methods add_synonym() and remove_synonyms(), with obvious
                  functionality.

        Returns : A list of aliases [array of [scalar]].
        Args    :

   get_dblinks
        Title   : get_dblinks()
        Usage   : @ds = $term->get_dblinks();
        Function: Returns a list of each dblink of this term.

                  If an implementor of this interface permits modification of
                  this array property, the class should define at least
                  methods add_dblink() and remove_dblinks(), with obvious
                  functionality.

        Returns : A list of dblinks [array of [scalars]].
        Args    :
        Note    : This has been deprecated in favor of get_dbxrefs()

   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 dblinks.  This can return a mixed 'bag' of scalars and
                  L<Bio::Annotation::DBLink> instances, or specific subgroups
                  can be returned based on passed arguments
        Args    : implementation-specific

   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.

                  If an implementor of this interface permits modification of
                  this array property, the class should define at least
                  methods add_secondary_id() and remove_secondary_ids(), with
                  obvious functionality.

        Returns : A list of secondary identifiers [array of [scalar]]
        Args    :

       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

       Used for looking up the methods that supersedes them.

   category
        Title   : category
        Usage   :
        Function: This method is deprecated. Use ontology() instead. We provide
                  an implementation here that preserves backwards compatibility,
                  but if you do not have legacy code using it you should not be
                  calling this method.
        Example :
        Returns :
        Args    :

perl v5.32.1                                       2021-08-15                          Bio::Ontology::TermI(3pm)

       This is "dumb" interface for ontology terms providing basic methods (it provides no functionality related
       to graphs).

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       and suggestions preferably to one of the Bioperl mailing lists.  Your participation is much appreciated.

         bioperl-l@bioperl.org                  - General discussion
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   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.

   ReportingBugs
       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://github.com/bioperl/bioperl-live/issues

       Bio::Ontology::TermI - interface for ontology terms

         #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->get_synonyms() ) {
             print $synonym, "\n";
         }