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

'ONTO-PERL' a collection of Perl modules for dealing with the Cell
Cycle Ontology (CCO) and in general with OBO 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,
     http://bitbucket.org/easr/onto-toolkit

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:

	perl Makefile.PL
	make
	make test
	make install

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, 2007, 2008, 2009, 2010 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.