README
======

ONTO-Toolkit is a collection of Galaxy tools for managing ontologies 
that are represented in the OBO flat file format (spec 1.2). 

Those tools are basically wrappers around the most commonly used tools 
provided by the ONTO-PERL suite.

See also:

  1. 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; doi: 10.1093/bioinformatics/btn042
     
  2. 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

  3. OPPL-Galaxy: Enhancing ontology exploitation in Galaxy with OPPL.
     Egana M, Fernandez-Breis JT, Antezana E.
     Semantic Web Applications and Tools for Life Sciences (SWAT4LS), London, UK (2011)
  
For installing this collection of tools:

	see the file INSTALL

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

ONTO-Toolkit requires:

1. Galaxy (latest version is recommended):

	http://main.g2.bx.psu.edu/

2. ONTO-PERL (version >= 1.37):

	http://search.cpan.org/dist/ONTO-PERL/

CITING ONTO-Toolkit
===================

If you use ONTO-Toolkit in your work, you are kindly requested to cite:

    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

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

Copyright (c) 2010-2012 Erick Antezana. All rights reserved.
OONTO-Toolkit is free software; you can redistribute it and/or
modify it under the same terms as Perl itself.

N.B. Galaxy is distributed as open source under the conditions of the 
Academic Free License (http://www.opensource.org/licenses/academic.php).