1 / 24

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

steffi
Télécharger la présentation

CHISEL Group Dept of Computer Science University of Victoria, Canada

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  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]

More Related