| ONTO-Toolkit is a collection of Galaxy tools which support the manipulation of OBO-formatted bio-ontologies (such as the Gene Ontology (GO).
ONTO-Toolkit provides tools to perform various operations on OBO-formatted ontologies (spec 1.2): * Get all the ancestors of a given term * Get the child terms of a given term * Get all the descendents of a given term * Get the parent terms of a given term * Get the relationship types of a given ontology * Get all the term names and their IDs of a given ontology * Get all the terms and theirs definitions of a given ontology * Transform an OBO-formatted ontology to: o RDF o RDF + transitive closure o OWL ONTO-Toolkit requires: * Galaxy (latest version is recommended): - http://www.bx.psu.edu/hg/galaxy galaxy_dist * ONTO-PERL (version >= 1.37): - http://search.cpan.org/dist/ONTO-PERL/ Citing ONTO-Toolkit: ONTO-ToolKit: enabling bio-ontology engineering via Galaxy. Antezana E, Venkatesan A, Mungall C, Mironov V, Kuiper M. BMC Bioinformatics 11(Suppl 12):S8 Copyright (c) 2010-2012 Erick Antezana. All rights reserved. ONTO-Toolkit is free software you can redistribute it and/or modify it under the same terms as Perl itself. N.B. Galaxy is distributed as open source under the conditions of the Academic Free License (http://www.opensource.org/licenses/academic.php). |
hg clone https://toolshed.g2.bx.psu.edu/repos/erick-antezana/onto-toolkit
| Name | Description | Version | Minimum Galaxy Version |
|---|---|---|---|
| Collects the terms that are related by a concrete relationship type | 1.22 | any | |
| Converts an OBO formatted ontology to RDF/XML format | 1.22 | any | |
| Extracts a subontology (in OBO format) of a given ontology having as root node the provided term ID | 1.22 | any | |
| Get all the term IDs and term definitions of a given OBO ontology | 1.22 | any | |
| Collects the ancestor terms from a given term in the given OBO ontology | 1.22 | any | |
| Provides an intersection of the given ontologies (in OBO format) | 1.22 | any | |
| Collects the parent terms from a given term in the given OBO ontology | 1.22 | any | |
| Get all the term IDs and term names of a given OBO ontology | 1.22 | any | |
| Converts an OBO formatted ontology to RDF/XML format with transitive closure | 1.22 | any | |
| Collects the relationship types in the given OBO ontology | 1.22 | any | |
| Collects the terms from a given term in the given OBO ontology, filtered by a relationship type | 1.22 | any | |
| Converts an OBO formatted ontology to OWL format | 1.22 | any | |
| Collects the descendent terms from a given term in the given OBO ontology | 1.22 | any | |
| Collects common OBO terms from a given set of list containing OBO terms | 1.22 | any | |
| Collects the child terms from a given term in the given OBO ontology | 1.22 | any | |