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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/