NAME

Bio::OntologyIO::obo

SYNOPSIS

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";
}

DESCRIPTION

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

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

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

Specification: http://www.geneontology.org/GO.format.obo-1_2.shtml.

FEEDBACK

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://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Support

Please direct usage questions or support issues to the mailing list:

bioperl-l@bioperl.org

rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible.

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:

https://github.com/bioperl/bioperl-live/issues

AUTHOR

Sohel Merchant

Email: s-merchant@northwestern.edu

Address:

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

CONTRIBUTOR

Hilmar Lapp, hlapp at gmx.net
Chris Mungall, cjm at fruitfly.org
Brian Osborne, briano@bioteam.net

APPENDIX

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 => "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
                         former.

See Bio::OntologyIO.

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 nothing if
          there is no more ontology in the input.
Args    :

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

cpanm Bio::Seq

perl -MCPAN -e shell
install Bio::Seq