Bio::OntologyIO::dagflat(3) 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/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" );
my $RELATED_TO = Bio::Ontology::RelationshipType->get_instance( "RELATED_TO" );


Needs from CPAN.


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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:


Christian M. Zmasek

Email: or [email protected]



  Genomics Institute of the Novartis Research Foundation
  10675 John Jay Hopkins Drive
  San Diego, CA 92121


 Hilmar Lapp, hlapp at


The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _


 Title   : new
 Usage   : $parser = Bio::OntologyIO->new(
                             -format => "go",
                             -defs_file => "/path/to/GO.defs",
                             -files => ["/path/to/component.ontology",
                                        "/path/to/process.ontology"] );
 Function: Creates a new dagflat parser.
 Returns : A new dagflat parser object, implementing Bio::OntologyIO.
 Args    : -defs_file  => the name of the file holding the term
           -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,
           -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

See Bio::OntologyIO.


 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)


 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
 Returns : [Bio::Ontology::OntologyEngineI]
 Args    :


 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    :


 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).


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


 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


 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)