ONTO-PERL suite
===============
ONTO-PERL a collection of PERL modules for dealing with any OBO-formatted
ontology (such as the Gene Ontology). This code distribution gathers
object-oriented modules (for dealing with ontology elements such as
Term, Relationship, Synonym and so forth), scripts (for typical tasks
such as format conversions: obo2rdf, rdf2obo; ONTO-perl provides an
extensive documentation as well as several examples that can be easily
adapted for specific applications that involve ontology processing), 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
Antezana E, Egana M, De Baets B, Kuiper M, Mironov V.
Bioinformatics (2008) 24 (6): 885-887; doi: 10.1093/bioinformatics/btn042
3. 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
Visit the following URLs:
- http://search.cpan.org/~easr/ONTO-PERL/
For installing this collection of modules:
see the file INSTALL
or follow the standard CPAN procedure:
type the following mantra:
perl -w Makefile.PL
make
make test
make install
Other useful commands:
make clean
make distcheck
DEPENDENCIES
============
ONTO-PERL requires the following modules:
1. Date::Manip (> v6.42):
http://search.cpan.org/dist/Date-Manip/ (MANDATORY)
2. XML::Parser (> v2.34) is used in format conversions (obo2owl and owl2obo)
http://search.cpan.org/~msergeant/XML-Parser/ (OPTIONAL)
2. XML::XPath (> v1.13) is used by the IntAct related modules:
http://search.cpan.org/~msergeant/XML-XPath/ (OPTIONAL)
4. SWISS Knife (> v1.67) is used by the 'UniProtParser':
ftp://ftp.ebi.ac.uk/pub/software/swissprot/Swissknife (OPTIONAL)
5. Text::CSV (> v1.32) is used by 'bioportal_csv2obo.pl':
http://search.cpan.org/~makamaka/Text-CSV/ (OPTIONAL)
COPYRIGHT AND LICENCE
=====================
Copyright (c) 2006-2014 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.