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

ONTO-PERL a collection of PERL modules for dealing with any OBO-formatted
ontology (such as the Gene Ontology). This code distribution gathers 
object-oriented modules (for dealing with ontology elements such as 
Term, Relationship, Synonym and so forth), scripts (for typical tasks 
such as format conversions: obo2rdf, rdf2obo; ONTO-perl provides an 
extensive documentation as well as several examples that can be easily 
adapted for specific applications that involve ontology processing), 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
     Antezana E, Egana M, De Baets B, Kuiper M, Mironov V.
     Bioinformatics (2008) 24 (6): 885-887; 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 requires the following modules:

1. Date::Manip (> v6.42):

	http://search.cpan.org/dist/Date-Manip/ (MANDATORY)

2. XML::Parser (> v2.34) is used in format conversions (obo2owl and owl2obo)

	http://search.cpan.org/~msergeant/XML-Parser/ (OPTIONAL)
	
2. XML::XPath (> v1.13) is used by the IntAct related modules:

   http://search.cpan.org/~msergeant/XML-XPath/ (OPTIONAL)

4. SWISS Knife (> v1.67) is used by the 'UniProtParser':

	ftp://ftp.ebi.ac.uk/pub/software/swissprot/Swissknife (OPTIONAL)	

5. Text::CSV (> v1.32) is used by 'bioportal_csv2obo.pl':

   http://search.cpan.org/~makamaka/Text-CSV/ (OPTIONAL)

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

Copyright (c) 2006-2014 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.