Reference

Bio::OntologyIO::obo(3pm)

parser for OBO flat-file format

NAME

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

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.

  [email protected]                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Support

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

[email protected]

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: [email protected]

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, [email protected]

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

History