dagflat - a base class parser for GO flat-file type formats use Bio::OntologyIO; # do not use directly -- use via Bio::OntologyIO # e.g., the GO parser is a simple extension of this class my $parser = Bio::OntologyIO->new ( -format => "go", -defs_file => "/home/czmasek/GO/GO.defs", -files => ["/home/czmasek/GO/component.ontology", "/home/czmasek/GO/function.ontology", "/home/czmasek/GO/process.ontology"] ); my $go_ontology = $parser->next_ontology(); my $IS_A = Bio::Ontology::RelationshipType->get_instance( "IS_A" ); my $PART_OF = Bio::Ontology::RelationshipType->get_instance( "PART_OF" ); Needs Graph.pm from CPAN.

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. bioperl-l@bioperl.org - General discussion http://bio.perl.org/MailList.html - 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 email or the web: bioperl-bugs@bio.perl.org http://bugzilla.bioperl.org/ 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

CONTRIBUTOR
Hilmar Lapp, hlapp at gmx.net The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

new
Title : new Usage : $parser = Bio::OntologyIO->new( -format => "go", -defs_file => "/path/to/GO.defs", -files => ["/path/to/component.ontology", "/path/to/function.ontology", "/path/to/process.ontology"] ); Function: Creates a new dagflat parser. Returns : A new dagflat parser object, implementing L<Bio::OntologyIO>. Args : -defs_file => the name of the file holding the term definitions -files => a single ontology flat file holding the term relationships, or an array ref holding the file names (for GO, there will usually be 3 files: component.ontology, function.ontology, process.ontology) -file => if there is only a single flat file, it may also be specified via the -file parameter -ontology_name => the name of the ontology; if not specified the parser will auto-discover it by using the term that starts with a '$', and converting underscores to spaces -engine => the Bio::Ontology::OntologyEngineI object to be reused (will be created otherwise); note that every Bio::Ontology::OntologyI will qualify as well since that one inherits from the former.

ontology_name
Title : ontology_name Usage : $obj->ontology_name($newval) Function: Get/set the name of the ontology parsed by this module. Example : Returns : value of ontology_name (a scalar) Args : on set, new value (a scalar or undef, optional)

parse
Title : parse() Usage : $parser->parse(); Function: Parses the files set with "new" or with methods defs_file and _flat_files. Normally you should not need to call this method as it will be called automatically upon the first call to next_ontology(). Returns : [Bio::Ontology::OntologyEngineI] Args :

next_ontology
Title : next_ontology Usage : Function: Get the next available ontology from the parser. This is the method prescribed by Bio::OntologyIO. Example : Returns : An object implementing Bio::Ontology::OntologyI, and undef if there is no more ontology in the input. Args :

defs_file
Title : defs_file Usage : $parser->defs_file( "GO.defs" ); Function: Set/get for the term definitions filename. Returns : The term definitions file name [string]. Args : On set, the term definitions file name [string] (optional).

close
Title : close Usage : Function: Closes this ontology stream and associated file handles. Clients should call this method especially when they write ontologies. We need to override this here in order to close the file handle for the term definitions file. Example : Returns : none Args : none

_flat_files
Title : _flat_files Usage : $files_to_parse = $parser->_flat_files(); Function: Get the array of ontology flat files that need to be parsed. Note that this array will decrease in elements over the parsing process. Therefore, it\'s value outside of this module will be limited. Also, be careful not to alter the array unless you know what you are doing. Returns : a reference to an array of zero or more strings Args : none

_defs_io
Title : _defs_io Usage : $obj->_defs_io($newval) Function: Get/set the Bio::Root::IO instance representing the definition file, if provided (see defs_file()). Example : Returns : value of _defs_io (a Bio::Root::IO object) Args : on set, new value (a Bio::Root::IO object or undef, optional)