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CHISEL Group Dept of Computer Science University of Victoria, Canada

Visualization of ontologies and data annotations. CHISEL Group Dept of Computer Science University of Victoria, Canada. Team Members. Margaret-Anne Storey (PI) Chris Callendar (Programmer) Visualization framework for Bioportal Degree of Interest model implementation

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CHISEL Group Dept of Computer Science University of Victoria, Canada

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  1. Visualization of ontologies and data annotations CHISEL Group Dept of Computer Science University of Victoria, Canada

  2. Team Members • Margaret-Anne Storey (PI) • Chris Callendar (Programmer) • Visualization framework for Bioportal • Degree of Interest model implementation • Tricia d’Entremont (PhD student) • Pictorial based ontology navigation (assisting Nigam) • Degree of interest models and ontologies • Sean Falconer (PhD student) • Ontology search • Algorithms and visualizations of ontology alignments • Maria-Elena Hernandez (Phd student) • Visualizing data annotations – clinical trial visualization

  3. Our research goals Core 1: • Develop visualization services for Bioportal • A visualization toolkit • A visualization ontology • A mapping mechanism to specify how to integrate and customize the available services for particular ontologies and tasks • Evaluate through • instrumentation and integration case studies Core 2: • Visualization of data annotations and meta-data analysis • HIV clinical trials • Phenotype annotations

  4. Approach • Determine requirements for visualization in an iterative manner: • Identify different user groups and user tasks (driven by the Core 3 projects) • Draw from research on: • Human computer interaction • Visualization • Adaptive interfaces • Computer supported collaborative work

  5. Previous work and expertise • Jambalaya – visualization support for Protégé • Developed and evaluated visualization tools to support comprehension, navigation and collaboration in software engineering

  6. History of Jambalaya • What is Jambalaya? • Jambalaya = SHriMP + Protégé & Protégé-OWL glue • What is SHriMP? • Nested (or un-nested) graph • Smooth animated zooming & graph layouts • Embedding of AWT/Swing widgets (e.g. Protégé forms) within visualization

  7. Jambalaya: Protégé + SHriMP

  8. Express views

  9. Query View • Bottom up approach instead of top down (like others) • invoked from Class’ right-click menu, on any tab

  10. PromptViz: visualizing two versions of an ontology

  11. Determining requirements • Unanswered questions… • Where should a visualization be used? • When would the user want to see it? • How is the data best represented in the visualization? • Fundamental Visualization Question • How can we provide a useful visualization at the moment a user needs it? • Need better support for task-driven “visualization-on-demand” • Visualizations should be readily available from familiar tools • A visualization should immediately answer a specific question or support a particular task • They should not take too much effort to generate and they should be efficient

  12. Views currently proposed for the toolkit • Overviews • Hub concepts • Query views • Navigational views • Difference views

  13. Engineering goals and Evaluation Services provided by the toolkit will have well-defined and clearly documented APIs to support the BioPortal tools • Software engineering principles: • Interoperability • Customizability • Extensibility • Evaluation: • Instrumentation • Integration case studies

  14. Demonstrations of Current Work • Degree of Interest Model (Chris) • Jambalaya Lite Applets (Chris) • Ontology Search (Sean) • Pictorial based ontology navigation (Nigam/Tricia)

  15. Degree of Interest Model • To address the problem of information overload with large ontologies and to identify relevant information • A degree of interest model is developed by monitoring the user’s activities (e.g. navigation actions, editing and annotations) • The model is used to highlight or filter more “interesting” elements in the ontology • Extending the work of Stuart Card (Degree of Interest Trees) and Mik Kersten (Mylar)

  16. Jambalaya Lite with Mylar activated

  17. Ontology Alignment • Current approaches • rely heavily on syntactic comparison • problems with synonymous concepts • Need semantic comparison • skull -> cranium • DNA -> deoxyribonucleic acid

  18. Ontology Alignment • Developed semantic comparison algorithm • Can match synonyms, abbreviations, phrases, etc. • Tested against synonym datasets • Plan to develop a new alignment algorithm and incorporate this technique

  19. Pictorial guided ontology navigation

  20. Short term goals (next year) • Jambalaya Lite applets – deploy and integrate with Bioportal (May 2006) • Initial prototype of Jambalaya thin client for Bioportal (Dec 2006) • Degree of interest model – evaluate through integrations with Protégé and OBOEdit (Dec 2006) • Ontology search (September 2006) • Support for visualizing clinical trial data (Dec 2006)

  21. Longer term goals • Visualization framework: [Chris] • Toolkit of visualization views and widgets • Visualization ontology • Mappings (graph transformations) • Visualization thin client for Bioportal: proposed technology SVG and Ajax • Ontology alignment visualizations and algorithms [Sean] • Degree of interest model integrated and evaluated with Bioportal [Tricia] • Visualizing data annotations across the DBPs [Maleh]

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