NAME

TermI - 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).

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 lists

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 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 92121

APPENDIX

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).

category

 Title   : category
 Usage   : $term->category( $top );
           or 
           $top = $term->category();
 Function: Set/get for a relationship between this Term and
           another Term (e.g. the top level of the ontology).
 Returns : The category of this Term [TermI].
 Args    : The category of this Term [TermI or scalar -- which
           becomes the name of the catagory term] (optional).

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).

each_synonym

 Title   : each_synonym()
 Usage   : @aliases = $term->each_synonym();                 
 Function: Returns a list of aliases of this Term.
 Returns : A list of aliases [array of [scalar]].
 Args    :

add_synonyms

 Title   : add_synonyms
 Usage   : $term->add_synonyms( @asynonyms );
           or
           $term->add_synonyms( $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    :

cpanm LocalConfig

perl -MCPAN -e shell
install LocalConfig