Diamond
Interactive Views for Navigating Ontologies and
Data at the National Center for Biomedical Ontology
Jambalaya
BioPortalViz
CogZ
Margaret-Anne Storey
CTExplorer
Summary/
Future
University of Victoria
Diamond
Jambalaya
Our goal: Provide cognitive support for
ontology developers and users through
visual and intelligent user interfaces
BioPortalViz
CogZ
CTExplorer
Summary/
Future
Subprojects:
• Diamond: Degree of interest browsing
• Jambalaya: visualization in Protégé
• BioPortalViz
• CogZ: Cognitive support for ontology
alignment
• Visualizing Clinical Trials:
– CTExplorer
– CTSearch (TagClouds)
the CHISEL group, University of Victoria
Diamond
Jambalaya
BioPortalViz
CogZ
CTExplorer
• DIaMOND—Degree of Interest Modeling
for Ontology Navigation and Development
• http://www.thechiselgroup.org/diamond
Summary/
Future
the CHISEL group, University of Victoria
Motivation
Diamond
Jambalaya
BioPortalViz
CogZ
CTExplorer
Summary/
Future
• Navigating ontologies can be tedious…
– Long scrolling lists, expanding/collapsing
nodes
– Large number of irrelevant elements
occlude relevant information
• Users often don’t know where to start when
navigating an unfamiliar ontology
– Might appreciate “worn paths”
• Visualizations of structure often very dense
and complex
– Hard to know which elements to display
the CHISEL group, University of Victoria
DIaMOND -- Approach
Diamond
Jambalaya
BioPortalViz
CogZ
CTExplorer
Summary/
Future
• Applies principles of attention-reactive
interfaces
– Mechanism to calculate user’s degree of
interest (DOI)
– Dynamic display of information using the DOI
• Goals
– Draw user’s attention to interesting elements
– Reduce navigation overhead
the CHISEL group, University of Victoria
DIaMOND (plug-in)
Diamond
Jambalaya
• Three levels of interest
– Landmark: Hub concept
• Manually specified by user
• DOI value exceeds a threshold value
BioPortalViz
CogZ
CTExplorer
Summary/
Future
– Interesting
• Has been interacted with such that the DOI
value exceeds a (lower) threshold value
– Uninteresting
• DOI value falls below the lower threshold value
• Lightweight, easily reversible focus
techniques
• Consistent with existing, familiar views
the CHISEL group, University of Victoria
Highlighting and Filtering in the Class
Browser (integration with Protégé for now)
Diamond
Jambalaya
BioPortalViz
CogZ
CTExplorer
Summary/
Future
Standard
Highlighting
the CHISEL group, University of Victoria
Highlighting
& Filtering
• Diamond Demo: NCI Anatomy
Diamond
Jambalaya
BioPortalViz
CogZ
CTExplorer
Summary/
Future
the CHISEL group, University of Victoria
Diamond’s Future Work
• Currently being evaluated in user studies
Diamond
Jambalaya
BioPortalViz
• Sharing DOI among users (many requests)
• Role and Task-based DOI calculations
• Use of instance data and annotated data to
supplement DOI calculations
CogZ
CTExplorer
• Integrate and evaluate Diamond approach in
BioPortal
Summary/
Future
• Ideas?
the CHISEL group, University of Victoria
Visualization and Jambalaya
• Why are visualizations important?
Diamond
Jambalaya
– Ontologies can be extremely large and complex,
difficult to navigate using just trees and lists
– Visualizations help users understand ontologies
by showing overviews and hub concepts
BioPortalViz
• Other visualization approaches:
CogZ
CTExplorer
Summary/
Future
– OntoViz, OWLViz, TGViz, ezOWL
– IsaViz: visual RDF editor
– Many graph-like visualization tools!
• What is Jambalaya?
– Protégé Plug-in for visualization
– Want to integrate some of these ideas in
BioPortal – which ones?
the CHISEL group, University of Victoria
Main Features in Jambalaya
Diamond
Jambalaya
• Classes and instances/individuals are
represented by nodes in the graph
• Slots or properties are represented by arcs
between nodes
BioPortalViz
CogZ
Jambalaya Demo
CTExplorer
Summary/
Future
the CHISEL group, University of Victoria
Different Views
Diamond
Jambalaya
BioPortalViz
CogZ
– Nested View (Default)
– Flat views
• Class Tree
• Class & Instance Tree
• Domain & Range (OWL)
– TreeMap View
CTExplorer
Summary/
Future
– Query View
– Filmstrip
– Customized views
the CHISEL group, University of Victoria
BioPortalViz
• Currently implemented as a Java Applet
Diamond
Jambalaya
BioPortalViz
• Integration of key ideas from Jambalaya
with BioPortal
– Not sure which features are needed? Need
input!
CogZ
CTExplorer
Summary/
Future
NCBO Council Call, Mar 4th 2008
BioPortalViz Java Demo
BioPortalViz Flex Demo
the CHISEL group, University of Victoria
Diamond
Jambalaya
BioPortalViz
CogZ
• Cognitive Support and Visualization
for Human-Guided Mapping Systems
CogZ
CTExplorer
Summary/
Future
the CHISEL group, University of Victoria
Ontology alignment
Diamond
Jambalaya
• Mapping terms from one ontology to another,
preserving structural relationships
• Research emphasis has been on the algorithm
BioPortalViz
CogZ
CTExplorer
Select
ontologies
Alignment
algorithm
Summary/
Future
Verified
mappings
the CHISEL group, University of Victoria
Candidate
mappings
Ontology alignment continued
Diamond
• Very difficult cognitive task
Jambalaya
BioPortalViz
CogZ
CTExplorer
Summary/
Future
• The user must:
– Make decisions about mapping candidates
– Supply custom mappings that were missed
– Understand the domains and structure of both
ontologies
– Remember decisions that were made
the CHISEL group, University of Victoria
Visualization plug-in for Prompt
Diamond
• Prompt: framework to support ontology
alignment
Jambalaya
BioPortalViz
CogZ
CTExplorer
Summary/
Future
• Sean’s research:
– Added a plug-in mechanism and
perspectives to Prompt to support other
algorithms and visualizations
– CogZ: Integrating various visualizations
and filters to support the user’s decision
making process
CogZ Demo
the CHISEL group, University of Victoria
Diamond
Jambalaya
BioPortalViz
CogZ
CTExplorer
Summary/
Future
the CHISEL group, University of Victoria
Future work in visualizing alignments
Diamond
Jambalaya
BioPortalViz
CogZ
CTExplorer
• Carry out user studies to investigate the
cognitive processes involved during ontology
mapping
• Develop a model of cognitive support for
mapping tasks
• Develop design principles based on this model
• Develop techniques to support these design
principles in mapping tools
Summary/
Future
the CHISEL group, University of Victoria
Visualizing Clinical Trials
Diamond
Jambalaya
• Developing new ways of visualizing clinical
trials data
• Many different classes of users:
– Clinicians, trialists, researchers
BioPortalViz
CogZ
CTExplorer
Summary/
Future
• Current approach for accessing trials is
through RCT Presenter (Trial Bank) or
ClinicalTrials.gov
• Currently striving for
standard reporting
procedures
(ontology based)
• Visualization prototypes
being developed for
detailed and specific
use cases
the CHISEL group, University of Victoria
Collaborative visualization
Diamond
Jambalaya
BioPortalViz
CogZ
CTExplorer
Summary/
Future
CTExplorer Demo
the CHISEL group, University of Victoria
Issues
Diamond
Jambalaya
BioPortalViz
CogZ
• Use cases are highly specialized – trialist,
researcher
• Requires a lot of information (which is
currently not readily available)
• So what can we do with data that already
preexists in ClinicalTrials.gov?
CTExplorer
Summary/
Future
NCBO Council Call, Mar 4th 2008
the CHISEL group, University of Victoria
CTSearch
Diamond
Jambalaya
BioPortalViz
CogZ
CTExplorer
Summary/
Future
• Objective
– To improve the experience of seeking and comparing
clinical trials
• Research questions
– How can we visualize and filter query results for large
and sometimes incomplete collections of clinical trials?
– How can we improve existing tags/annotations in
controlled data collections to obtain better query
results? (e.g. different terms used to describe the same
underlying concept)
• Hypothesis
– Seeking and comparing clinical trials can be improved
by using tag clouds that afford dynamic filtering of the
query results
– Searching clinical trials can be improved by extending
their existing annotations/tags using controlled
vocabularies (e.g. UMLS) to provide better query
results
Diamond
Jambalaya
BioPortalViz
CogZ
CTExplorer
Summary/
Future
Web 1.0
description
of results
Diamond
Jambalaya
BioPortalViz
CogZ
CTExplorer
Summary/
Future
Web 1.0
description
of results
Diamond
Jambalaya
BioPortalViz
CogZ
CTExplorer
Summary/
Future
Web 1.0
description
of results
Searching ClinicalTrials.gov
Diamond
Jambalaya
BioPortalViz
CogZ
CTExplorer
Summary/
Future
• How many trials are there related
to the concept “liver cancer”??
•Cancer liver, 670
• Carcinoma of Liver Cells, 344
• Carcinoma, hepatocellular, 257
• HCC, 411
• Hepatocellular Carcinoma, 400
• Hepatoma, 396
•Liver cancer, 683
• Liver Cell Carcinoma, 432
• Liver metastases, 333
• Metastases liver, 329
• Primary Carcinoma of Liver Cells, 320
CiteULike
Diamond
Jambalaya
BioPortalViz
CogZ
CTExplorer
Summary/
Future
CiteUlike
• Features:
Diamond
Jambalaya
BioPortalViz
CogZ
CTExplorer
Summary/
Future
– The user queries one or more tags and
receives a list of users and groups that
are interested in those tags
– Result: list of hyperlinks to articles, books
or other sources of information.
– A tag cloud shows related tags for the
user to use in further queries
– Results are based on the ‘union’ rather
than the ‘intersection’ of tags.
• Querying for ‘Hepatocelluar carcinoma’ will
bring all the resources tagged as
‘Hepatocelluar ’, ‘carcinoma’, or
‘Hepatocelluar carcinoma’. As a
consequence, ‘breast-carcinoma’ will be
part of the results.
– The tag cloud can be filtered. For
example, filtering on ‘ca’ displays:
‘cancer’, ‘classification’, ‘communication’,
and ‘education’. This only filters the
cloud and not the list of results.
Diamond
Jambalaya
BioPortalViz
CogZ
CTExplorer
Summary/
Future
Tag Clouds for summarizing
Web Search Results
Tag Cloud visualization: CTSearch
Diamond
Jambalaya
BioPortalViz
CogZ
• Browsing a larger set of trials through
ClinicalTrials.gov
• Scenario
• A trial designer wants to see all the
conditions and interventions for “liver
cancer”. She wants to select one condition
and see all the associated interventions (or
vice versa).
CTExplorer
Summary/
Future
CTSearchDemo
the CHISEL group, University of Victoria
Where next…
• Evaluation of CTExplorer and CTSearch
Diamond
Jambalaya
• Closer integration of CTExplorer and
CTSearch?
• Where to host CTExplorer and CTSearch?
BioPortalViz
CogZ
CTExplorer
Summary/
Future
NCBO Council Call, Mar 4th 2008
the CHISEL group, University of Victoria
Ontrez
Diamond
Jambalaya
BioPortalViz
CogZ
CTExplorer
Summary/
Future
Integration in BioPortal
Ontrez+TagClouds approach (Option1)
Diamond
Jambalaya
BioPortalViz
CogZ
Condition
Phase
CTExplorer
Study Design
Eligibility Criteria
Summary/
Future
Interventions
Size
Primary Outcomes
Secondary Outcomes
Overall Status
Integration in BioPortal
TagClouds approach (Option2)
Diamond
Search Clinical Trials
Select source
Heart Attack AND Seniors AND Los Angeles
Jambalaya
BioPortalViz
Bank-a-Trial
CogZ
CTExplorer
Summary/
OCRe
Future
Search
Advanced Search
Preferences
34 Trials from Heart Attack AND Seniors AND Los Angeles
14 Trials from Heart Attack AND Seniors AND Los Angeles
10 Trials from Heart Attack AND Seniors AND Los Angeles
9 Trials from Heart Attack AND Seniors AND Los Angeles
200 Publications from Heart Attack AND Seniors AND Los Angeles
Integration in BioPortal
TagClouds approach (Option2 continuation)
Diamond
Search Trials
Select source
Heart Attack AND Seniors AND Los Angeles
Jambalaya
BioPortalViz
Condition
Search
Advanced Search
Preferences
34 Trials from Heart Attack AND Seniors AND Los Angeles
Conditions
Phase
CogZ
Study Design
Eligibility Criteria
CTExplorer
Interventions
Size
Primary Outcomes
Summary/
Future
Secondary
Outcomes
Interventions
Overall Status
1 A Study of the Safety and Efficacy of Nitric Oxide Reduction in Patients With Cardiogenic Shock After a Heart Attack
By Judith S. Hochman, M.D Funded By:INDUSTRY
A Phase III International, Multi-Center, Prospective, Randomized, Double-Blind, Placebo-Controlled Study to Assess the Safety and Efficacy of Nitric
Oxide Synthase Inhibition With Tilarginine Acetate Injection in Patients With Cardiogenic Shock Complicating Acute Myocardial Infarction, or the
TRIUMPH Trial
May 2005-January 2007 Terminated
Integration in BioPortal
Ontrez+Ranking+Commenting (option3)
Diamond
Jambalaya
BioPortalViz
CogZ
1 A Study of the Safety and Efficacy of Nitric Oxide Reduction in Patients With Cardiogenic Shock After a
Heart Attack
By Judith S. Hochman, M.D Funded By:INDUSTRY
CTExplorer
A Phase III International, Multi-Center, Prospective, Randomized, Double-Blind, Placebo-Controlled Study to Assess the Safety and
Efficacy of Nitric Oxide Synthase Inhibition With Tilarginine Acetate Injection in Patients With Cardiogenic Shock Complicating Acute
Myocardial Infarction, or the TRIUMPH Trial
May 2005-January 2007 Terminated
Viewed 790 times
Summary/
Future
2 Effectiveness of Combining Beta-Blocker Therapy and a Pacemaker Following a Heart Attack (The PACEMI Trial)
By Jeffrey Goldberger, MD, MBA Funded By:NIH
Beta-blockers are recommended to individuals who have recently had a heart attack. They are contraindicated for individuals with
abnormally slow heart rates or significant conduction system disease; however, the addition of a pacemaker may make beta-blocker
therapy safe for these individuals. This study will evaluate the effectiveness of a pacemaker combined with beta-blocker therapy at
improving survival rates and preventing subsequent heart attacks in individuals with abnormally slow heart rates who have recently
experienced a heart attack.
April 2007-April 2010 *Recruiting
Viewed 90 times
Related Links
3 IMPROVE HF: Registry to Improve the Use of Evidence-Based Heart Failure Therapies in the Outpatient
Setting
By Gregg Fonarow, MD and Clyde Yancy, MD Funded By:INDUSTRY
The purpose of this study is to characterize current management of patients with either heart failure or prior myocardial infarction
and left ventricular dysfunction and to assess the effect of education, specific clinical guidelines, reminder systems, comprehensive
disease state management tools, benchmarked quality reports, and academic detailing on the use of evidence-based heart failure
therapies in cardiology practices. This study is a quality improvement initiative that is being conducted through review of patient
records.
May 2005-July 2009 Active, not recruiting
Viewed 1200 times
Summary
Diamond
Jambalaya
BioPortalViz
CogZ
CTExplorer
• Dealing with information overload and
providing views that are useful (Diamond)
• Exploring visualization approaches in
Jambalaya for integration in BioPortal
• CogZ: Cognitive support for ontology
alignment (useful on BioPortal?)
• CTExplorer and CTSearch: browsing and
comparison of clinical trials
Summary/
Future
the CHISEL group, University of Victoria
Future research directions and themes
Diamond
Jambalaya
• Web based visualizations for a diverse
and evolving user base and task set
– Customizable and flexible views
• Cognitive support rather than visualization
BioPortalViz
CogZ
CTExplorer
Summary/
Future
– Ontologies, annotations and mappings
– Search
– Concept comparison (local, global and
historical information)
– Meta-analyses
• Collaborative support
– Humans and software agents
the CHISEL group, University of Victoria
Diamond
Acknowledgements:
Chris Callendar, Tricia d’Entremont,
Sean
Falconer
and
Maleh
Hernandez
–
BioPortalViz
The Chisel Group, UVic
Jambalaya
Ida Sim, Driving Biological Project Lead,
CTExplorer
and Simona Carini San Francisco
University
CogZ
Summary/
Future
CSER Meeting October 2006
the CHISEL group, University of Victoria
Diamond
Jambalaya
BioPortalViz
CogZ
Input and suggestions would
be greatly appreciated!
CTExplorer
Summary/
Future
mstorey@uvic.ca
Computer Human Interaction & Software Engineering Lab
Department of Computer Science, University of Victoria
CSER Meeting October 2006
the CHISEL group, University of Victoria
References and websites
•
Diamond:
–
Diamond
•
Jambalaya
Jambalaya and BioPortalViz:
–
Jambalaya: http://www.thechiselgroup.org/jambalaya
–
BioPortalViz:
BioPortalViz
CogZ
CTExplorer
Summary/
Future
•
http://thechiselgroup.org/diamond
http://webhome.cs.uvic.ca/~chisel/projects/jambalaya/ncboa
pplet/demo_applet.html
Visualization and Alignments:
–
CogZ website:
• CTeXplorer:
– http://webhome.cs.uvic.ca/~chisel/projects/ctexplorer/flex/
main.html
– Tag clouds and ClinicalTrials.gov:
http://dufflite.cs.uvic.ca:8080/CTPrototypeWeb.html
(temporary)
the CHISEL group, University of Victoria
• Slides in lieu of demos…
Diamond
Jambalaya
BioPortalViz
CogZ
CTExplorer
Summary/
Future
the CHISEL group, University of Victoria
• Jambalaya…
Diamond
Jambalaya
BioPortalViz
CogZ
CTExplorer
Summary/
Future
NCBO Council Call, Mar 4th 2008
the CHISEL group, University of Victoria
Diamond
Jambalaya
BioPortalViz
CogZ
CTExplorer
Summary/
Future
the CHISEL group, University of Victoria
Composite Arcs
Diamond
• High level edges (lifted)
Jambalaya
BioPortalViz
CogZ
CTExplorer
Summary/
Future
the CHISEL group, University of Victoria
• Inconsistencies “pop-out” in some views
Diamond
Jambalaya
BioPortalViz
CogZ
CTExplorer
Summary/
Future
the CHISEL group, University of Victoria
Diamond
Jambalaya
BioPortalViz
CogZ
CTExplorer
Summary/
Future
the CHISEL group, University of Victoria
Diamond
Jambalaya
BioPortalViz
CogZ
CTExplorer
Summary/
Future
the CHISEL group, University of Victoria
Diamond
Jambalaya
BioPortalViz
CogZ
CTExplorer
Summary/
Future
the CHISEL group, University of Victoria
• CogZ…
Diamond
Jambalaya
BioPortalViz
CogZ
CTExplorer
Summary/
Future
NCBO Council Call, Mar 4th 2008
the CHISEL group, University of Victoria
Diamond
Jambalaya
BioPortalViz
CogZ
CTExplorer
Summary/
Future
CSER Meeting October 2006
the CHISEL group, University of Victoria