/ 
bioperl-1.2
/ Bio::Ontology::Term

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).

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.

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]  
          -category              => a relationship between this Term and another Term [TermI or scalar]
          -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).

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    :