/ 
bioperl-1.2
/ Bio::Ontology::RelationshipType

NAME

RelationshipType - a relationship type for an ontology

SYNOPSIS

#

DESCRIPTION

This class can be used to model various types of relationships (such as "IS_A", "PART_OF", "CONTAINS", "FOUND_IN").

This class extends Bio::Ontology::Term.

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 the Bioperl mailing lists Your participation is much appreciated.

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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://bio.perl.org/bioperl-bugs/

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. Internal methods are usually preceded with a _

get_instance

Title   : get_instance
Usage   : $IS_A     = Bio::Ontology::RelationshipType->get_instance( "IS_A" );
          $PART_OF  = Bio::Ontology::RelationshipType->get_instance( "PART_OF" );
          $CONTAINS = Bio::Ontology::RelationshipType->get_instance( "CONTAINS" );
          $FOUND_IN = Bio::Ontology::RelationshipType->get_instance( "FOUND_IN" );
Function: Factory method to create instances of RelationshipType
Returns : [Bio::Ontology::RelationshipType]
Args    : "IS_A" or "PART_OF" or "CONTAINS" or "FOUND_IN" [scalar]

init

Title   : init()
Usage   : $type->init();
Function: Initializes this to all undef and empty lists.
Returns :
Args    :

equals

Title   : equals
Usage   : if ( $type->equals( $other_type ) ) { ...
Function: Compares this type to another one, based on string "eq" of
          the "identifier" field
Returns : true or false
Args    : [Bio::Ontology::RelationshipType]

identifier

Title   : identifier
Usage   : $term->identifier( "IS_A" );
          or
          print $term->identifier();
Function: Set/get for the immutable identifier of this Type.
Returns : The identifier [scalar].
Args    : The identifier [scalar] (optional).

name

Title   : name
Usage   : $term->name( "is a type" );
          or
          print $term->name();
Function: Set/get for the immutable name of this Type.
Returns : The name [scalar].
Args    : The name [scalar] (optional).

definition

Title   : definition
Usage   : $term->definition( "" );
          or
          print $term->definition();
Function: Set/get for the immutable definition of this Type.
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 immutable  relationship between this Type and
          another Term (e.g. the top level of the ontology).
Returns : The category [TermI].
Args    : The category [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 immutable 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 immutable obsoleteness of this Type.
Returns : the obsoleteness [0 or 1].
Args    : the obsoleteness [0 or 1] (optional).

comment

Title   : comment
Usage   : $term->comment( "..." );
          or
          print $term->comment();
Function: Set/get for an arbitrary immutable comment about this Type.
Returns : A comment.
Args    : A comment (optional).