Is a collection of tools to manage ontologies represented in the OBO file format within Galaxy environment
The tools are wrappers for commonly used functions provided by ONTO-PERL 5
ONTO-PERL was developed as part of the Semantic Systems Biology 6 (SSB) initiative
ONTO-PERL (OBOF-centered PERL API) comprises of extensible set of (Object-oriented) PERL modules
These have an organised set of subroutines to deal with ontologies and is fully compatible with the current OBO specifications (ver. 1.2)
The latest version (ver.1.22) of ONTO-PERL can be directly downloaded from CPAN, http://search.cpan.org/dist/ONTO-PERL/
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; doi: 10.1093/bioinformatics/btn042
Examples of ONTO-PERL functionalities Scripts Functionality get_ancestor_terms.pl Collects the ancestor terms (list of IDs) from a given term (existing ID) in the given OBO ontology. get_child_terms.pl Collects the child terms (list of term IDs and their names) from a given term (existing ID) in the given OBO ontology. get_descendent_terms.pl Collects the descendent terms (list of IDs) from a given term (existing ID) in the given OBO ontology. get_subontology_from.pl Extracts a subontology (in OBO format) of a given ontology having the given term ID as the root. get_intersection_ontology.pl Provides an intersection of the given ontologies (in OBO format) obo2owl.pl OBO to OWL translator. obo2rdf.pl OBO to RDF translator. obo_trimming.pl This script trims a given branch of an OBO ontology.
To investigate similarities between given molecular functions
Collecting all the upstream terms (ancestors) of two given molecular function terms and to identify common ancestors terms.
To demonstrate the functionality of ONTO-Toolkit in GALAXY
To demonstrate the usefulness of ontology engineering in biological domain
Use Case I : Chosen Ontology: Cell Cycle Ontology Chosen Terms: Term 1: id: CCO:F0000004 name: trans-hexaprenyltranstransferase activity Term 2: id: CCO:F0000820 name: homogentisate 1,2-dioxygenase activity Term ID 1 Term ID 2
Use Case I Uploading an obo ontology file – e.g.: cco_S_pombe
Conti… Molecular function Term ID: CCO:F0000004