Bio::OntologyIO(3pm) User Contributed Perl Documentation Bio::OntologyIO(3pm)
NAME
Bio::OntologyIO - Parser factory for Ontology formats
SYNOPSIS
use Bio::OntologyIO;
my $parser = Bio::OntologyIO->new(-format => "go",
-file=> $file);
while(my $ont = $parser->next_ontology()) {
print "read ontology ",$ont->name()," with ",
scalar($ont->get_root_terms)," root terms, and ",
scalar($ont->get_leaf_terms)," leaf terms
";
}
DESCRIPTION
This is the parser factory for different ontology sources and formats. Conceptually, it is very similar to Bio::SeqIO, but the difference
is that the chunk of data returned as an object is an entire ontology.
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 list. 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 of the bugs and their resolution. Bug reports can be submitted via the
web:
https://redmine.open-bio.org/projects/bioperl/
AUTHOR - Hilmar Lapp
Email hlapp at gmx.net
APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
new
Title : new
Usage : my $parser = Bio::OntologyIO->new(-format => 'go', @args);
Function: Returns a stream of ontologies opened on the specified input
for the specified format.
Returns : An ontology parser (an instance of Bio::OntologyIO) initialized
for the specified format.
Args : Named parameters. Common parameters are
-format - the format of the input; the following are
presently supported:
goflat: DAG-Edit Gene Ontology flat files
go : synonymous to goflat
soflat: DAG-Edit Sequence Ontology flat files
so : synonymous to soflat
simplehierarchy: text format with one term per line
and indentation giving the hierarchy
evoc : synonymous to simplehierarchy
interpro: InterPro XML
interprosax: InterPro XML - this is actually not a
Bio::OntologyIO compliant parser; instead it
persists terms as they are encountered.
L<Bio::OntologyIO::Handlers::InterPro_BioSQL_Handler>
obo : OBO format style from Gene Ontology Consortium
-file - the file holding the data
-fh - the stream providing the data (-file and -fh are
mutually exclusive)
-ontology_name - the name of the ontology
-engine - the L<Bio::Ontology::OntologyEngineI> object
to be reused (will be created otherwise); note
that every L<Bio::Ontology::OntologyI> will
qualify as well since that one inherits from the
former.
-term_factory - the ontology term factory to use. Provide a
value only if you know what you are doing.
DAG-Edit flat file parsers will usually also accept the
following parameters.
-defs_file - the name of the file holding the term
definitions
-files - an array ref holding the file names (for GO,
there will usually be 3 files: component.ontology,
function.ontology, process.ontology)
Other parameters are specific to the parsers.
next_ontology
Title : next_ontology
Usage : $ont = $stream->next_ontology()
Function: Reads the next ontology object from the stream and returns it.
Returns : a L<Bio::Ontology::OntologyI> compliant object, or undef at the
end of the stream
Args : none
term_factory
Title : term_factory
Usage : $obj->term_factory($newval)
Function: Get/set the ontology term factory to use.
As a user of this module it is not necessary to call this
method as there will be default. In order to change the
default, the easiest way is to instantiate
L<Bio::Ontology::TermFactory> with the proper -type
argument. Most if not all parsers will actually use this
very implementation, so even easier than the aforementioned
way is to simply call
$ontio->term_factory->type("Bio::Ontology::MyTerm").
Example :
Returns : value of term_factory (a Bio::Factory::ObjectFactoryI object)
Args : on set, new value (a Bio::Factory::ObjectFactoryI object, optional)
Private Methods
Some of these are actually 'protected' in OO speak, which means you
may or will want to utilize them in a derived ontology parser, but
you should not call them from outside.
_load_format_module
Title : _load_format_module
Usage : *INTERNAL OntologyIO stuff*
Function: Loads up (like use) a module at run time on demand
Example :
Returns :
Args :
perl v5.14.2 2012-03-02 Bio::OntologyIO(3pm)