ONTO-PERL suite
===============

ONTO-PERL a collection of PERL modules for dealing with OBO-formatted
ontologies (like the Gene Ontology). This code distribution gathers 
object-oriented modules (for dealing with ontology elements such as 
Term, Relationship and so forth), scripts (for typical tasks such as 
format conversions: obo2owl, owl2obo; besides, there are also many 
examples that can be easily adapted for specific applications), and a 
set of test files to ensure the suite's implementation quality.

See also:

  1. perldoc ONTO-PERL.pod
  
  2. ONTO-PERL: An API supporting the development and analysis of bio-ontologies
     E. Antezana; M. Egana; B. De Baets; M. Kuiper; V. Mironov
     Bioinformatics 2008; doi: 10.1093/bioinformatics/btn042

  3. ONTO-Toolkit: A set of Galaxy tools to deal with OBO-formatted ontologies,
     Antezana E, Venkatesan A, Mungall C, Mironov V, Kuiper M.
     BMC Bioinformatics 2010, 11(Suppl 12):S8 doi:10.1186/1471-2105-11-S12-S8

Visit the following URLs:

 - http://search.cpan.org/~easr/ONTO-PERL/

For installing this collection of modules:

	see the file INSTALL

or follow the standard CPAN procedure:

type the following mantra:

	perl -w Makefile.PL
	make
	make test
	make install

Other useful commands:

	make clean	
	make distcheck

DEPENDENCIES
============

ONTO-PERL might require the following modules:

1. SWISS Knife (> v1.65) is used by the 'UniProtParser':

	ftp://ftp.ebi.ac.uk/pub/software/swissprot/Swissknife

2. XML::Simple (> v2.16) is used by the IntAct related modules:

	http://search.cpan.org/~grantm/XML-Simple-2.16/
	
3. XML::Parser (> v2.34) is used in format conversions (obo2owl and owl2obo)

	http://search.cpan.org/~msergeant/XML-Parser-2.34/

COPYRIGHT AND LICENCE
=====================

Copyright (c) 2006-2012 by Erick Antezana. All rights reserved.
This program is free software; you can redistribute it and/or
modify it under the same terms as Perl itself.