NAME

Bio::Ontology::OBOterm - representation of OBO terms

SYNOPSIS

$term = Bio::Ontology::OBOterm->new
  ( -identifier       => "GO:0005623",
    -name        => "Cell",
    -definition  => "The basic structural and functional unit ...",
    -is_obsolete => 0,
    -comment     => "" );

$term->add_reference( @refs );
$term->add_secondary_id( @ids );
$term->add_synonym( @synonym );

# etc.

DESCRIPTION

This is data holder class for OBO terms. It is currently a dummy class since we anticipate that the OBO term will become more richer with more features being added to OBO flat-file format.

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://bioperl.org/wiki/Mailing_lists  - 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 the web:

http://bugzilla.open-bio.org/

AUTHOR

Sohel Merchant

Email: s-merchant@northwestern.edu

Address:

Northwestern University
Center for Genetic Medicine (CGM), dictyBase
Suite 1206,
676 St. Clair st
Chicago IL 60611

APPENDIX

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

new

Title   : new
Usage   :   $term = Bio::Ontology::OBOterm->new
    ( -identifier       => "GO:0005623",
     -name        => "Cell",
     -definition  => "The basic structural and functional unit ...",
     -is_obsolete => 0,
     -comment     => "" );

Function: Creates a new Bio::Ontology::OBOterm.
Returns : A new Bio::Ontology::OBOterm object.
Args    : -identifier    => the id of this OBO term [GO:nnnnnnn]
                            integer of seven digits)
          -name          => the name of this OBO term [scalar]
          -definition    => the definition of this OBO term [scalar]
          -ontology      => the ontology for this term (a
                            Bio::Ontology::OntologyI compliant object)
          -version       => version information [scalar]
          -is_obsolete   => the obsoleteness of this OBO term [0 or 1]
          -comment       => a comment [scalar]