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Venkatesan bosc2010 onto-toolkit

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  • Explains the motivation of Galaxy – services it provides
  • Explains the basic features of Galaxy
  • The step is repeated for the second OBO term

Transcript

  • 1. ONTO-ToolKit: enabling bio-ontology engineering via Galaxy Aravind Venkatesan, ONTO-ToolKit: enabling bio-ontology engineering via Galaxy Aravind Venkatesan Systems Biology group, Department of Biology NTNU, Trondheim [email_address]
  • 2. Overview
    • Galaxy
    • Ontology for Life Sciences
    • ONTO-Toolkit
    • Use Cases
    • Conclusion
    • Future Directions
    • Acknowledgment
    • References
  • 3.
    • Web application that allows flexible retrieval and analyses of the data.
    • Integrated with other resources such the UCSC Genome browsers, BioMart.
    • Galaxy environment aids biologists to manipulate, analyse and build workflows.
    • Is an open-source scalable framework for tool and data integration suitable for tool developers.
  • 4. Tool pane – provides various functionality to handle data Data display area History pane –manipulate uploaded data and build workflow Visit Galaxy!! http:// galaxy.psu.edu /
  • 5. Ontology for Life Sciences
    • Ontologies aid in knowledge formalisation and machine interoperability
    • The success of ontologies in the Life Sciences is marked by the wide spread use of Gene Ontology 1 (GO)
    • Application ontologies such as the Cell Cycle Ontology 2
    • The OBO flat file format 3 (OBOF) and the Web Ontology Language 4 (OWL) have gained wide acceptance as knowledge representation languages.
  • 6. ONTO-Toolkit
    • 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
  • 7. 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.
  • 8. ONTO-Toolkit - GALAXY Define arguments
  • 9. ONTO-Toolkit - GALAXY
  • 10. Use Cases
    • 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.
    • Motivation:
    • 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
  • 11. Use Case I Uploading an obo ontology file – e.g.: cco_S_pombe
  • 12. Conti… Molecular function Term ID: CCO:F0000004
  • 13.
    • This step is repeated for the second term - CCO:F0000820
    List of ancestor terms for the given Molecular function Term 1 List of ancestor terms for Term 2
  • 14. Common ancestor terms Gets the overlapping ancestor terms
  • 15. Use Case II
    • Identifying overlapping annotations for a given pair of distinct biological process terms
    • Chosen Ontology: Cell Cycle Ontology
    • Chosen Terms:
    • Term 1 :
    • id: CCO:P0000005
    • name: cell cycle checkpoint
    • Term 2 :
    • id: CCO:P0000069
    • name: mitosis
    Term ID 1 Term ID 2
  • 16. Use Case II Gets the sub-ontology for the given terms
  • 17. Generated sub-ontology of Term 1 : CCO:P0000005 Generated sub-ontology of Term 2 : CCO:P0000069
  • 18. Gets the intersection of the two sub-ontologies
  • 19. Conclusion
    • Use Case I – the results provides evidence that the two molecular functions are unrelated as only the high level terms are shared by them.
    • Use Case II – the results suggests the possibility of an overlap between two distinct biological processes
    • ONTO-Toolkit functionalities provides rich-ontology driven solutions within the Galaxy framework
    Future Directions
    • Provide interface to perform SPARQL queries within Galaxy
    • Provide visualisation module
  • 20. Acknowledgment
    • Dr. Erick Antezana, NTNU
    • Dr. Vladimir Mironov, NTNU
    • Dr. Martin Kuiper, NTNU
    References
    • M. Ashburner, et al. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet, 25:25– 29, May 2000.
    • The Cell Cycle Ontology, http://www.semantic-systems-biology.org/cco
    • The OBO Flat File Format Specification (ver.1.2), http://www.geneontology.org/GO.format.obo-1_2.shtml
    • OWL Web Ontology Language, http://www.w3.org/TR/owl-semantics/
    • 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
    • Semantic Systems Biology,
    • http://www.semantic-systems-biology.org/