Bio::OntologyIO::soflat(3) a parser for the Sequence Ontology flat-file format


use Bio::OntologyIO;
# do not use directly -- use via Bio::OntologyIO
my $parser = Bio::OntologyIO->new
( -format => "so", # or soflat
-defs_file => "/home/czmasek/SO/SO.defs",
-file => "/home/czmasek/SO/sofa.ontology" );
my $sofa_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 from CPAN.

This is essentially a very thin derivation of the dagflat base-parser.


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Reporting Bugs

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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 => "soflat",
                             -files => ["/path/to/sofa.ontology"] );
 Function: Creates a new soflat parser.
 Returns : A new soflat 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
           -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::Ontology::OntologyI.