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bio::ontology::goterm(3pm) [debian man page]

Bio::Ontology::GOterm(3pm)				User Contributed Perl Documentation				Bio::Ontology::GOterm(3pm)

NAME
Bio::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, " "; } # 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: https://redmine.open-bio.org/projects/bioperl/ 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 v5.14.2 2012-03-02 Bio::Ontology::GOterm(3pm)
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