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]