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 mantra:

	perl Makefile.PL
	make
	make test
	sudo make install

Other useful commands:

	make clean	
	make distcheck
	
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
     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
     
Citing ONTO-PERL
================

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

    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

Third part modules
==================

Required module:

1. Date::Manip (> v6.24) is used by the OBOParser (to check dates):

   http://search.cpan.org/~sbeck/Date-Manip/

Optional modules:

1. XML::Parser (> v2.41) is used in format conversions (obo2owl and owl2obo):

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

2. XML::XPath (> v1.13) is used by the IntAct related modules:

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

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

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

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

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