Bio::OntologyIO::soflat - a parser for the Sequence Ontology flat-file format
# 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 Graph.pm from CPAN.
This is essentially a very thin derivation of the dagflat base-parser.
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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: czmasek-at-burnham.org or email@example.com
Genomics Institute of the Novartis Research Foundation
10675 John Jay Hopkins Drive
San Diego, CA 92121
Hilmar Lapp, hlapp at gmx.net
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
-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
To install BioPerl, copy and paste the appropriate command in to your terminal.
perl -MCPAN -e shell
For more information on module installation, please visit the detailed CPAN module installation guide.