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

2. July 23, 2006The CHISEL Group, University of Victoria2 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)National Centre for Biomedical Ontology Introduction Visualizations Installation Features Quick Views Tools Options New Features Future Work Questions Advanced Features OWL Links

3. July 23, 2006The CHISEL Group, University of Victoria3 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 New Features Future Work Questions Advanced Features OWL Links

4. July 23, 2006The CHISEL Group, University of Victoria4

5. July 23, 2006The CHISEL Group, University of Victoria5 Installation 1.Download latest version (v2.4.0) from http://www.cs.uvic.ca/~chisel/projects/jambalaya/tutorial/ http://www.cs.uvic.ca/~chisel/projects/jambalaya/tutorial/ 2.Close Protégé if it is open 3.Remove previous version from../Protégé/plugins/ca.uvic.cs.chisel.jambalaya/ 4.Unzip into../Protege/plugins 5.Restart Protégé and open a project (e.g. newspaper.pprj) 6.Open Jambalaya from the menu: Project > Configure > JambalayaTab Introduction Visualizations Installation Features Quick Views Tools Options New Features Future Work Questions Advanced Features OWL Links

6. July 23, 2006The CHISEL Group, University of Victoria6 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 New Features Future Work Questions Advanced Features OWL Links

7. July 23, 2006The CHISEL Group, University of Victoria7 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 New Features Future Work Questions Advanced Features OWL Links

8. July 23, 2006The CHISEL Group, University of Victoria8 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 New Features Future Work Questions Advanced Features OWL Links

9. July 23, 2006The CHISEL Group, University of Victoria9 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 New Features Future Work Questions Advanced Features OWL Links

10. July 23, 2006The CHISEL Group, University of Victoria10 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 New Features Future Work Questions Advanced Features OWL Links

11. July 23, 2006The CHISEL Group, University of Victoria11 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 New Features Future Work Questions Advanced Features OWL Links

12. July 23, 2006The CHISEL Group, University of Victoria12 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 New Features Future Work Questions Advanced Features OWL Links

13. July 23, 2006The CHISEL Group, University of Victoria13 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 New Features Future Work Questions Advanced Features OWL Links

14. July 23, 2006The CHISEL Group, University of Victoria14 Composite Arcs High level edges (lifted) Introduction Visualizations Installation Features Quick Views Tools Options New Features Future Work Questions Advanced Features OWL Links

15. July 23, 2006The CHISEL Group, University of Victoria15 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 New Features Future Work Questions Advanced Features OWL Links

16. July 23, 2006The CHISEL Group, University of Victoria16 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 New Features Future Work Questions Advanced Features OWL Links

17. July 23, 2006The CHISEL Group, University of Victoria17 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 New Features Future Work Questions Advanced Features OWL Links

18. July 23, 2006The CHISEL Group, University of Victoria18 Orthogonal Layout (not released yet) Manhattan edges, control flow diagrams Introduction Visualizations Installation Features Quick Views Tools Options New Features Future Work Questions Advanced Features OWL Links

19. July 23, 2006The CHISEL Group, University of Victoria19 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 New Features Future Work Questions Advanced Features OWL Links

20. July 23, 2006The CHISEL Group, University of Victoria20 Integration with DIaMOND Degree of Interesting Modeling for Ontology Navigation and Development (Protégé Plug-In) Tuesday July 25 th, 3:30-3:50pm Introduction Visualizations Installation Features Quick Views Tools Options New Features Future Work Questions Advanced Features OWL Links

21. July 23, 2006The CHISEL Group, University of Victoria21 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 New Features Future Work Questions Advanced Features OWL Links

22. July 23, 2006The CHISEL Group, University of Victoria22 Questions? Take the survey! –http://www.surveymonkey.com/s.asp?u=833691872585http://www.surveymonkey.com/s.asp?u=833691872585 Introduction Visualizations Installation Features Quick Views Tools Options New Features Future Work Questions Advanced Features OWL Links

23. July 23, 2006The CHISEL Group, University of Victoria23 More Information & Links Chisel Group –http://www.thechiselgroup.orghttp://www.thechiselgroup.org DIaMOND –http://www.thechiselgroup.org/diamondhttp://www.thechiselgroup.org/diamond Piccolo –http://www.cs.umd.edu/hcil/jazz/index.shtmlhttp://www.cs.umd.edu/hcil/jazz/index.shtml National Center for Biomedical Ontology –http://bioontology.orghttp://bioontology.org National Cancer Institute (NCI) –http://www.cancer.gov/http://www.cancer.gov/ Introduction Visualizations Installation Features Quick Views Tools Options New Features Future Work Questions Advanced Features OWL Links