Computer Human Interaction & Software Engineering LabDepartment of Computer Science, University of Victoria

JambalayaJambalayaProtégé Conference 2006Protégé Conference 2006

Chris CallendarChris Callendar

Margaret-Anne StoreyMargaret-Anne Storey

http://www.cs.uvic.ca/~chisel/projects/jambalaya/tutorial/

July 23, 2006 The CHISEL Group, University of Victoria 2

IntroductionIntroduction

• 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

New Features

Future Work

Questions

Advanced Features

OWL

Links

July 23, 2006 The CHISEL Group, University of Victoria 3

Visualizations and JambalayaVisualizations 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

July 23, 2006 The CHISEL Group, University of Victoria 4

July 23, 2006 The CHISEL Group, University of Victoria 5

InstallationInstallation

1. Download latest version (v2.4.0) from http://www.cs.uvic.ca/~chisel/projects/jambalaya/tutorial/

2. Close Protégé if it is open3. 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

July 23, 2006 The CHISEL Group, University of Victoria 6

Main FeaturesMain 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

July 23, 2006 The CHISEL Group, University of Victoria 7

Features WalkthroughFeatures 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

July 23, 2006 The CHISEL Group, University of Victoria 8

Overview of FeaturesOverview 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

July 23, 2006 The CHISEL Group, University of Victoria 9

Overview of FeaturesOverview 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

July 23, 2006 The CHISEL Group, University of Victoria 10

Context Menu (right click)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

July 23, 2006 The CHISEL Group, University of Victoria 11

Quick ViewsQuick 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

July 23, 2006 The CHISEL Group, University of Victoria 12

Overview of Jambalaya ToolsOverview 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

July 23, 2006 The CHISEL Group, University of Victoria 13

OptionsOptions

• 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

July 23, 2006 The CHISEL Group, University of Victoria 14

Composite ArcsComposite Arcs

• High level edges (lifted)

Introduction

Visualizations

Installation

Features

Quick Views

Tools

Options

New Features

Future Work

Questions

Advanced Features

OWL

Links

July 23, 2006 The CHISEL Group, University of Victoria 15

Reified RelationshipsReified 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

July 23, 2006 The CHISEL Group, University of Victoria 16

OWLOWL

• 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

July 23, 2006 The CHISEL Group, University of Victoria 17

New Features and Future WorkNew 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

July 23, 2006 The CHISEL Group, University of Victoria 18

Orthogonal Layout (not released yet)Orthogonal Layout (not released yet)

• Manhattan edges, control flow diagramsIntroduction

Visualizations

Installation

Features

Quick Views

Tools

Options

New Features

Future Work

Questions

Advanced Features

OWL

Links

July 23, 2006 The CHISEL Group, University of Victoria 19

Integration with Prompt (not released Integration with Prompt (not released yet)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

July 23, 2006 The CHISEL Group, University of Victoria 20

Integration with DIaMONDIntegration 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

New Features

Future Work

Questions

Advanced Features

OWL

Links

July 23, 2006 The CHISEL Group, University of Victoria 21

Visualizing Clinical TrialsVisualizing 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

July 23, 2006 The CHISEL Group, University of Victoria 22

Questions?Questions?

• Take the survey!– http://www.surveymonkey.com/s.asp?

u=833691872585

Introduction

Visualizations

Installation

Features

Quick Views

Tools

Options

New Features

Future Work

Questions

Advanced Features

OWL

Links

July 23, 2006 The CHISEL Group, University of Victoria 23

More Information & LinksMore 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

New Features

Future Work

Questions

Advanced Features

OWL

Links