/ 
bioperl-1.4
/ Bio::Ontology::TermI

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->get_synonyms() ) {
    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).

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 L<Bio::Ontology::OntologyI>
          implementing object.
Args    : On set, the  ontology of this Term as a L<Bio::Ontology::OntologyI>
          implementing object or a string representing its name.

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    :
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    :

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    :