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Jambalaya Protégé Conference 2006

Jambalaya Protégé Conference 2006. Chris Callendar Margaret-Anne Storey. Computer Human Interaction & Software Engineering Lab Department of Computer Science, University of Victoria. http://www.cs.uvic.ca/~chisel/projects/jambalaya/tutorial/. Introduction. Who am I?

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Jambalaya Protégé Conference 2006

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  1. JambalayaProtégé Conference 2006 Chris Callendar Margaret-Anne Storey Computer Human Interaction & Software Engineering Lab Department of Computer Science, University of Victoria http://www.cs.uvic.ca/~chisel/projects/jambalaya/tutorial/

  2. Introduction • Who am I? • Computer Science and Physics bachelor’s degree from University of Victoria, BC, Canada • 10 months of part time work on Shrimp and Jambalaya • Involved with the NCI project – migrating to Protégé-OWL • Part of the National Centre for Biomedical Ontology (NCBO) Introduction Visualizations Installation Features Quick Views Tools Options Advanced Features OWL New Features Future Work Questions Links The CHISEL Group, University of Victoria

  3. Visualizations and Jambalaya • Why are Visualizations important? • Ontologies can be extremely large and complex – too difficult to navigate using just trees and lists • Visualizations can help users understand ontologies by showing overviews and identifying hub concepts • Other visualization approaches: • OntoViz, OWLViz, TGViz, ezOWL • IsaViz: visual RDF editor • Many graph-like visualization tools! • What is Jambalaya? • Protégé Plug-in built on top of SHriMP • What is SHriMP? • Nested or flat graphs • Originally for software understanding – analyzing source code • Also comes as a plugin for Eclipse (Creole) • Smooth animated zooming & layouts • Embedded AWT/Swing widgets (e.g. Protégé forms) Introduction Visualizations Installation Features Quick Views Tools Options Advanced Features OWL New Features Future Work Questions Links The CHISEL Group, University of Victoria

  4. The CHISEL Group, University of Victoria

  5. Installation • Download latest version (v2.4.0) from http://www.cs.uvic.ca/~chisel/projects/jambalaya/tutorial/ • Close Protégé if it is open • Remove previous version from ../Protégé/plugins/ca.uvic.cs.chisel.jambalaya/ • Unzip into ../Protege/plugins • Restart Protégé and open a project (e.g. newspaper.pprj) • Open Jambalaya from the menu: Project > Configure > JambalayaTab Introduction Visualizations Installation Features Quick Views Tools Options Advanced Features OWL New Features Future Work Questions Links The CHISEL Group, University of Victoria

  6. Main Features • Zoomable User Interface (ZUI) – Piccolo library • Nested changeable hierarchy (including “no” hierarchy) • Merges graph visualization with regular swing widgets • “Hyper linking” between concepts • Classes and instances/individuals are represented by nodes in the graph • Slots or properties are represented by arcs between nodes Introduction Visualizations Installation Features Quick Views Tools Options Advanced Features OWL New Features Future Work Questions Links The CHISEL Group, University of Victoria

  7. Features Walkthrough • Open the newspaper.pprj example if you want to follow along • Then click on the Jambalaya Tab (if the tab isn’t visible, go under the “Project > Configure” menu) • The first time Jambalaya is opened the “Getting Started” dialog will be displayed • The Nested View is the default view which will be opened when you click on the Jambalaya Tab • By default the nested view will show the root classes and the direct subclasses Introduction Visualizations Installation Features Quick Views Tools Options Advanced Features OWL New Features Future Work Questions Links The CHISEL Group, University of Victoria

  8. Overview of Features • Node Labels • Above Node (fixed) • Above Node (level) • On Node • Arc Labels • Not shown by default • Navigation • Zoom, Magnify, and Fisheye • Cursors: select [ ], zoom in [ ], zoom out [ ] • Back [ ], Forward [ ], Home [ ], Refresh [ ] • Hyper linking • Searching [ ] Introduction Visualizations Installation Features Quick Views Tools Options Advanced Features OWL New Features Future Work Questions Links The CHISEL Group, University of Victoria

  9. Overview of Features • Layouts • Grid (default) [ ] • Radial [ ] • Spring [ ] • Tree – vertical and horizontal [ ] • TreeMap [ ] • Filtering nodes [ ] and arcs [ ] • Node Attribute Panel [ ] • node colour and tooltip by any attribute • filter by any attribute (e.g. number of children) • Changing root classes (“Jambalaya > Edit” menu) Introduction Visualizations Installation Features Quick Views Tools Options Advanced Features OWL New Features Future Work Questions Links The CHISEL Group, University of Victoria

  10. Context Menu (right click) • Labels • Arrange • layout children • layout selected items • Select • inverse, all children… • Show • closed, children, form, attributes • Expand – show children • Collapse – hide children • Filter – hide selected nodes • Unfilter All – show all nodes Introduction Visualizations Installation Features Quick Views Tools Options Advanced Features OWL New Features Future Work Questions Links The CHISEL Group, University of Victoria

  11. Quick Views • Nested View (Default) • Flat views • Class Tree • Class & Instance Tree • Domain & Range (OWL) • TreeMap View • Query View Introduction Visualizations Installation Features Quick Views Tools Options Advanced Features OWL New Features Future Work Questions Links The CHISEL Group, University of Victoria

  12. Overview of Jambalaya Tools • Thumbnail View • quick overview • Filmstrip • take snapshots, save & load a current state • Scripting • interact with Jambalaya using JavaScript • Hierarchical View • Query View • show neighbourhoods etc. Introduction Visualizations Installation Features Quick Views Tools Options Advanced Features OWL New Features Future Work Questions Links The CHISEL Group, University of Victoria

  13. Options • General • animation preferences • motion highlighting options • Labels • default label mode • how many levels to show • Layouts • choose the default layout • User controls • shortcut keys • Data filters • for increasing performance • Rendering • render quality and zoom/magnify speeds Introduction Visualizations Installation Features Quick Views Tools Options Advanced Features OWL New Features Future Work Questions Links The CHISEL Group, University of Victoria

  14. Composite Arcs • High level edges (lifted) Introduction Visualizations Installation Features Quick Views Tools Options Advanced Features OWL New Features Future Work Questions Links The CHISEL Group, University of Victoria

  15. Reified Relationships • E.g. Newspaper • :DIRECTED-BINARY-RELATION • Look at Employee – Manager/Director, Editor • Make this customizable? Introduction Visualizations Installation Features Quick Views Tools Options Advanced Features OWL New Features Future Work Questions Links The CHISEL Group, University of Victoria

  16. OWL • Almost all the features demonstrated so far work with OWL projects • One extra quick view: • Domain/Range • Resource Actions • Open in Query View Introduction Visualizations Installation Features Quick Views Tools Options Advanced Features OWL New Features Future Work Questions Links The CHISEL Group, University of Victoria

  17. New Features and Future Work • Motion highlighting (“Dancing Shrimp”) • ALT-click on a node with connected arcs • more research is being done on this to determine the ideal motion and duration • Filter all descendents • hides the selected node and its descendents • Synchronized selections and expansions between Jambalaya and the Class and Instance browsers • Show instance count in the Class Browser • Improved Query View • Many fixes! Introduction Visualizations Installation Features Quick Views Tools Options Advanced Features OWL New Features Future Work Questions Links The CHISEL Group, University of Victoria

  18. Orthogonal Layout (not released yet) • Manhattan edges, control flow diagrams Introduction Visualizations Installation Features Quick Views Tools Options Advanced Features OWL New Features Future Work Questions Links The CHISEL Group, University of Victoria

  19. Integration with Prompt (not released yet) • Provide a structural context for the operations being performed • Provide filters to help the user focus on the most important operations Introduction Visualizations Installation Features Quick Views Tools Options Advanced Features OWL New Features Future Work Questions Links The CHISEL Group, University of Victoria

  20. Integration with DIaMOND • Degree of Interesting Modeling for Ontology Navigation and Development (Protégé Plug-In) • Tuesday July 25th, 3:30-3:50pm Introduction Visualizations Installation Features Quick Views Tools Options Advanced Features OWL New Features Future Work Questions Links The CHISEL Group, University of Victoria

  21. Visualizing Clinical Trials • Adding new layouts and views to Jambalaya to support visualizing clinical trials data – parallel coordinates? Introduction Visualizations Installation Features Quick Views Tools Options Advanced Features OWL New Features Future Work Questions Links The CHISEL Group, University of Victoria

  22. Questions? • Take the survey! • http://www.surveymonkey.com/s.asp?u=833691872585 Introduction Visualizations Installation Features Quick Views Tools Options Advanced Features OWL New Features Future Work Questions Links The CHISEL Group, University of Victoria

  23. More Information & Links • Chisel Group • http://www.thechiselgroup.org • DIaMOND • http://www.thechiselgroup.org/diamond • Piccolo • http://www.cs.umd.edu/hcil/jazz/index.shtml • National Center for Biomedical Ontology • http://bioontology.org • National Cancer Institute (NCI) • http://www.cancer.gov/ Introduction Visualizations Installation Features Quick Views Tools Options Advanced Features OWL New Features Future Work Questions Links The CHISEL Group, University of Victoria

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