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.