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
2. 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

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 E. Antezana; M. Egana; B. De Baets; M. Kuiper; V. Mironov Bioinformatics 2008; doi: 10.1093/bioinformatics/btn042

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