INSTALL
=======

There are two typical ways:

Using CPAN.  
==========

You'll want to use CPAN to install the modules by performing the 
following steps:

From the root prompt on your server, invoke the CPAN shell:

# perl -MCPAN -e shell

Once the PERL interpreter has loaded (and been configured), you can 
install modules by issuing the command install MODULENAME.

The first thing you should do is upgrade your CPAN:

cpan> install Bundle::CPAN

Once it's done, type:

cpan> reload cpan

Now, enter the following command to retrieve all of the required modules:

cpan> install OBO::Core::Ontology

Manually
========

By typing the following:

	perl Makefile.PL
	make
	make test
	sudo make install
	
Documentation
=============

For more information about these modules, check:

 - http://search.cpan.org/~easr/ONTO-PERL/
 - http://www.cellcycleontology.org
 - http://www.semantic-systems-biology.org
 
See also:
 
  1. 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

  2. ONTO-Toolkit: A set of Galaxy tools to deal with OBO-formatted ontologies,
     http://bitbucket.org/easr/onto-toolkit

Third part 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/

Bugs/comments/questions/etc
===========================

We are regularly improving this API, please report any bugs 
or send your comments to erick.antezana -@- gmail.com