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Venkatesan bosc2010 onto-toolkit

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Venkatesan bosc2010 onto-toolkit

  1. 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. 2. Overview <ul><li>Galaxy </li></ul><ul><li>Ontology for Life Sciences </li></ul><ul><li>ONTO-Toolkit </li></ul><ul><li>Use Cases </li></ul><ul><li>Conclusion </li></ul><ul><li>Future Directions </li></ul><ul><li>Acknowledgment </li></ul><ul><li>References </li></ul>
  3. 3. <ul><li>Web application that allows flexible retrieval and analyses of the data. </li></ul><ul><li>Integrated with other resources such the UCSC Genome browsers, BioMart. </li></ul><ul><li>Galaxy environment aids biologists to manipulate, analyse and build workflows. </li></ul><ul><li>Is an open-source scalable framework for tool and data integration suitable for tool developers. </li></ul>
  4. 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. 5. Ontology for Life Sciences <ul><li>Ontologies aid in knowledge formalisation and machine interoperability </li></ul><ul><li>The success of ontologies in the Life Sciences is marked by the wide spread use of Gene Ontology 1 (GO) </li></ul><ul><li>Application ontologies such as the Cell Cycle Ontology 2 </li></ul><ul><li>The OBO flat file format 3 (OBOF) and the Web Ontology Language 4 (OWL) have gained wide acceptance as knowledge representation languages. </li></ul>
  6. 6. ONTO-Toolkit <ul><li>Is a collection of tools to manage ontologies represented in the OBO file format within Galaxy environment </li></ul><ul><li>The tools are wrappers for commonly used functions provided by ONTO-PERL 5 </li></ul><ul><li>ONTO-PERL was developed as part of the Semantic Systems Biology 6 (SSB) initiative </li></ul><ul><li>ONTO-PERL (OBOF-centered PERL API) comprises of extensible set of (Object-oriented) PERL modules </li></ul><ul><li>These have an organised set of subroutines to deal with ontologies and is fully compatible with the current OBO specifications (ver. 1.2) </li></ul><ul><li>The latest version (ver.1.22) of ONTO-PERL can be directly downloaded from CPAN, http://search.cpan.org/dist/ONTO-PERL/ </li></ul>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. 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. 8. ONTO-Toolkit - GALAXY Define arguments
  9. 9. ONTO-Toolkit - GALAXY
  10. 10. Use Cases <ul><li>To investigate similarities between given molecular functions </li></ul><ul><li>Collecting all the upstream terms (ancestors) of two given molecular function terms and to identify common ancestors terms. </li></ul><ul><li>Motivation: </li></ul><ul><li>To demonstrate the functionality of ONTO-Toolkit in GALAXY </li></ul><ul><li>To demonstrate the usefulness of ontology engineering in biological domain </li></ul>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. 11. Use Case I Uploading an obo ontology file – e.g.: cco_S_pombe
  12. 12. Conti… Molecular function Term ID: CCO:F0000004
  13. 13. <ul><li>This step is repeated for the second term - CCO:F0000820 </li></ul>List of ancestor terms for the given Molecular function Term 1 List of ancestor terms for Term 2
  14. 14. Common ancestor terms Gets the overlapping ancestor terms
  15. 15. Use Case II <ul><li>Identifying overlapping annotations for a given pair of distinct biological process terms </li></ul><ul><li>Chosen Ontology: Cell Cycle Ontology </li></ul><ul><li>Chosen Terms: </li></ul><ul><li>Term 1 : </li></ul><ul><li>id: CCO:P0000005 </li></ul><ul><li>name: cell cycle checkpoint </li></ul><ul><li>Term 2 : </li></ul><ul><li>id: CCO:P0000069 </li></ul><ul><li>name: mitosis </li></ul>Term ID 1 Term ID 2
  16. 16. Use Case II Gets the sub-ontology for the given terms
  17. 17. Generated sub-ontology of Term 1 : CCO:P0000005 Generated sub-ontology of Term 2 : CCO:P0000069
  18. 18. Gets the intersection of the two sub-ontologies
  19. 19. Conclusion <ul><li>Use Case I – the results provides evidence that the two molecular functions are unrelated as only the high level terms are shared by them. </li></ul><ul><li>Use Case II – the results suggests the possibility of an overlap between two distinct biological processes </li></ul><ul><li>ONTO-Toolkit functionalities provides rich-ontology driven solutions within the Galaxy framework </li></ul>Future Directions <ul><li>Provide interface to perform SPARQL queries within Galaxy </li></ul><ul><li>Provide visualisation module </li></ul>
  20. 20. Acknowledgment <ul><li>Dr. Erick Antezana, NTNU </li></ul><ul><li>Dr. Vladimir Mironov, NTNU </li></ul><ul><li>Dr. Martin Kuiper, NTNU </li></ul>References <ul><li>M. Ashburner, et al. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet, 25:25– 29, May 2000. </li></ul><ul><li>The Cell Cycle Ontology, http://www.semantic-systems-biology.org/cco </li></ul><ul><li>The OBO Flat File Format Specification (ver.1.2), http://www.geneontology.org/GO.format.obo-1_2.shtml </li></ul><ul><li>OWL Web Ontology Language, http://www.w3.org/TR/owl-semantics/ </li></ul><ul><li>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 </li></ul><ul><li>Semantic Systems Biology, </li></ul><ul><li>http://www.semantic-systems-biology.org/ </li></ul>

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