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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 - PowerPoint PPT Presentation
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cBio Meeting, March 2-3, 2006
CHISEL GroupDept of Computer ScienceUniversity 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
“Express View” buttons
“Root Classes”
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
cBio Meeting, March 2-3, 2006
cBio Meeting, March 2-3, 2006
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]