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Bio::OntologyIO::obo(3User Contributed Perl DocumentatiBio::OntologyIO::obo(3)

       Bio::OntologyIO::obo - parser for OBO flat-file format

	 use Bio::OntologyIO;

	 # do not use directly -- use via Bio::OntologyIO
	 my $parser = Bio::OntologyIO->new
	       ( -format => "obo",
		 -file	 =>  "gene_ontology.obo");

	 while(my $ont = $parser->next_ontology()) {
	 print "read ontology ",$ont->name()," with ",
		      scalar($ont->get_root_terms), " root terms, and ",
		      scalar($ont->get_all_terms),  " total terms, and ",
		      scalar($ont->get_leaf_terms), " leaf terms\n";

       Parser for OBO flat-file	format.	'obo' example:

	format-version:	1.2
	ontology: so/dev/externalDerived
	property_value:	owl:versionInfo	"$Revision: 80 $" xsd:string
	default-namespace: SO

	id: SO_0000343
	name: match
	def: "A	region of sequence, aligned to another sequence." []

	id: SO_0000039
	name: match_part
	def: "A	part of	a match." []
	is_a: SO_0000343

       Specification: <>.

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       Sohel Merchant



	 Northwestern University
	 Center	for Genetic Medicine (CGM), dictyBase
	 Suite 1206,
	 676 St. Clair st
	 Chicago IL 60611

	Hilmar Lapp, hlapp at
	Chris Mungall, cjm at
	Brian Osborne,

       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 => "obo",
				    -file => "gene_ontology.obo");
	Function: Creates a new	dagflat	parser.
	Returns	: A new	dagflat	parser object, implementing Bio::OntologyIO.
	Args	: -file	     =>	a single ontology flat file holding the
				terms, descriptions and	relationships
		  -ontology_name => the	name of	the ontology; if not specified the
				 parser	will assign the	name of	the ontology as	the
				 default-namespace header value	from the OBO file.
		  -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 nothing if
		  there	is no more ontology in the input.
	Args	:

	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

perl v5.32.0			  2019-12-07	       Bio::OntologyIO::obo(3)


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