Bio::Ontology::OBOtermUser Contributed Perl DocumentaBio::Ontology::OBOterm(3)NAMEBio::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
Support
Please direct usage questions or support issues to the mailing list:
bioperl-l@bioperl.org
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly address
it. Please include a thorough description of the problem with code and
data examples if at all possible.
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]
perl v5.14.1 2011-07-22 Bio::Ontology::OBOterm(3)
