cBio Meeting, March 2-3, 2006 CHISEL Group Dept of Computer Science University of Victoria, Canada Visualization of ontologies and data annotations

cBio Meeting, March 2-3, 2006 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

cBio Meeting, March 2-3, 2006 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

cBio Meeting, March 2-3, 2006 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

cBio Meeting, March 2-3, 2006 Previous work and expertise Jambalaya – visualization support for Protégé Developed and evaluated visualization tools to support comprehension, navigation and collaboration in software engineering

cBio Meeting, March 2-3, 2006 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

cBio Meeting, March 2-3, 2006 Jambalaya: Protégé + SHriMP

cBio Meeting, March 2-3, 2006 Express views

cBio Meeting, March 2-3, 2006 Query View Bottom up approach instead of top down (like others) invoked from Class’ right-click menu, on any tab

cBio Meeting, March 2-3, 2006 PromptViz: visualizing two versions of an ontology

cBio Meeting, March 2-3, 2006 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

cBio Meeting, March 2-3, 2006 Views currently proposed for the toolkit Overviews Hub concepts Query views Navigational views Difference views

cBio Meeting, March 2-3, 2006 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

cBio Meeting, March 2-3, 2006 Demonstrations of Current Work Degree of Interest Model (Chris) Jambalaya Lite Applets (Chris) Ontology Search (Sean) Pictorial based ontology navigation (Nigam/Tricia)

cBio Meeting, March 2-3, 2006 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)

cBio Meeting, March 2-3, 2006 Jambalaya Lite with Mylar activated

cBio Meeting, March 2-3, 2006

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

cBio Meeting, March 2-3, 2006 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

cBio Meeting, March 2-3, 2006 Pictorial guided ontology navigation

cBio Meeting, March 2-3, 2006 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)

cBio Meeting, March 2-3, 2006 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]