Bio::Ontology::GOterm(User Contributed Perl DocumentatBio::Ontology::GOterm(3)NAMEBio::Ontology::GOterm - representation of GO terms
SYNOPSIS
$term = Bio::Ontology::GOterm->new
( -go_id => "GO:0016847",
-name => "1-aminocyclopropane-1-carboxylate synthase",
-definition => "Catalysis of ...",
-is_obsolete => 0,
-comment => "" );
$term->add_definition_references( @refs );
$term->add_secondary_GO_ids( @ids );
$term->add_aliases( @aliases );
foreach my $dr ( $term->each_definition_reference() ) {
print $dr, "\n";
}
# etc.
DESCRIPTION
This is "dumb" class for GO terms (it provides no functionality related
to graphs). Implements Bio::Ontology::TermI.
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
Christian M. Zmasek
Email: czmasek-at-burnham.org or cmzmasek@yahoo.com
WWW: http://monochrome-effect.net/
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::GOterm->new(
-go_id => "GO:0016847",
-name => "1-aminocyclopropane-1-carboxylate synthase",
-definition => "Catalysis of ...",
-is_obsolete => 0,
-comment => "" );
Function: Creates a new Bio::Ontology::GOterm.
Returns : A new Bio::Ontology::GOterm object.
Args : -go_id => the goid of this GO term [GO:nnnnnnn]
or [nnnnnnn] (nnnnnnn is a zero-padded
integer of seven digits)
-name => the name of this GO term [scalar]
-definition => the definition of this GO term [scalar]
-ontology => the ontology for this term (a
Bio::Ontology::OntologyI compliant object)
-version => version information [scalar]
-is_obsolete => the obsoleteness of this GO term [0 or 1]
-comment => a comment [scalar]
init
Title : init()
Usage : $term->init();
Function: Initializes this GOterm to all "" and empty lists.
Returns :
Args :
GO_id
Title : GO_id
Usage : $term->GO_id( "GO:0003947" );
or
print $term->GO_id();
Function: Set/get for the goid of this GO term.
This is essentially an alias to identifier(), with added
format checking.
Returns : The goid [GO:nnnnnnn].
Args : The goid [GO:nnnnnnn] or [nnnnnnn] (nnnnnnn is a
zero-padded integer of seven digits) (optional).
get_secondary_GO_ids
Title : get_secondary_GO_ids
Usage : @ids = $term->get_secondary_GO_ids();
Function: Returns a list of secondary goids of this Term.
This is aliased to remove_secondary_ids().
Returns : A list of secondary goids [array of [GO:nnnnnnn]]
(nnnnnnn is a zero-padded integer of seven digits).
Args :
add_secondary_GO_id
Title : add_secondary_GO_id
Usage : $term->add_secondary_GO_id( @ids );
or
$term->add_secondary_GO_id( $id );
Function: Pushes one or more secondary goids into
the list of secondary goids.
This is aliased to remove_secondary_ids().
Returns :
Args : One secondary goid [GO:nnnnnnn or nnnnnnn] or a list
of secondary goids [array of [GO:nnnnnnn or nnnnnnn]]
(nnnnnnn is a zero-padded integer of seven digits).
remove_secondary_GO_ids
Title : remove_secondary_GO_ids()
Usage : $term->remove_secondary_GO_ids();
Function: Deletes (and returns) the secondary goids of this Term.
This is aliased to remove_secondary_ids().
Returns : A list of secondary goids [array of [GO:nnnnnnn]]
(nnnnnnn is a zero-padded integer of seven digits).
Args :
to_string
Title : to_string()
Usage : print $term->to_string();
Function: to_string method for GO terms.
Returns : A string representation of this GOterm.
Args :
perl v5.14.1 2011-07-22 Bio::Ontology::GOterm(3)
