ONTO-PERL suite

'ONTO-PERL' a collection of PERL modules for dealing with OBO-formatted ontologies (like the Gene Ontology). This code distribution gathers object-oriented modules (for dealing with ontology elements such as Term, Relationship and so forth), scripts (for typical tasks such as format conversions: obo2owl, owl2obo; besides, there are also many examples that can be easily adapted for specific applications), 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
  3. Antezana; M. Egana; B. De Baets; M. Kuiper; V. Mironov Bioinformatics 2008; doi: 10.1093/bioinformatics/btn042
  4. ONTO-Toolkit: A set of Galaxy tools to deal with OBO-formatted ontologies, http://bitbucket.org/easr/onto-toolkit

Visit the following URLs:

For installing this collection of modules:

see the file INSTALL

or follow the standard CPAN procedure:

type the following: 

        perl Makefile.PL
        make
        make test
        make install

DEPENDENCIES

ONTO-PERL might require the following 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/

COPYRIGHT AND LICENCE

Copyright (c) 2006-2011 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.