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Jambalaya
Diamond
CogZ
CTExplorer
Summary/Future
BioPortalViz
Interactive Views for Navigating Ontologies and Data at the National
Center for Biomedical Ontology
Margaret-Anne StoreyMargaret-Anne Storey
University of VictoriaUniversity of Victoria
Jambalaya
Diamond
CogZ
CTExplorer
Summary/Future
BioPortalViz
the CHISEL group, University of Victoria
Our goal: Provide cognitive support for ontology developers and users through visual and intelligent user interfaces
Subprojects:
• Diamond: Degree of interest browsing
• Jambalaya: visualization in Protégé
• BioPortalViz
• CogZ: Cognitive support for ontology alignment
• Visualizing Clinical Trials:
– CTExplorer
– CTSearch (TagClouds)
Jambalaya
Diamond
CogZ
CTExplorer
Summary/Future
BioPortalViz
the CHISEL group, University of Victoria
• DIaMOND—Degree of Interest Modeling for Ontology Navigation and Development
• http://www.thechiselgroup.org/diamond
Jambalaya
Diamond
CogZ
CTExplorer
Summary/Future
BioPortalViz
the CHISEL group, University of Victoria
Motivation
• 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
Jambalaya
Diamond
CogZ
CTExplorer
Summary/Future
BioPortalViz
the CHISEL group, University of Victoria
DIaMOND -- Approach
• 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
Jambalaya
Diamond
CogZ
CTExplorer
Summary/Future
BioPortalViz
the CHISEL group, University of Victoria
DIaMOND (plug-in)
• Three levels of interest
– Landmark: Hub concept• Manually specified by user
• DOI value exceeds a threshold value
– 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
Jambalaya
Diamond
CogZ
CTExplorer
Summary/Future
BioPortalViz
the CHISEL group, University of Victoria
Highlighting and Filtering in the Class Browser (integration with Protégé for now)
Standard Highlighting Highlighting & Filtering
Jambalaya
Diamond
CogZ
CTExplorer
Summary/Future
BioPortalViz
• Diamond Demo: NCI Anatomy
the CHISEL group, University of Victoria
Jambalaya
Diamond
CogZ
CTExplorer
Summary/Future
BioPortalViz
the CHISEL group, University of Victoria
Diamond’s Future Work• Currently being evaluated in user studies
• Sharing DOI among users (many requests)
• Role and Task-based DOI calculations
• Use of instance data and annotated data to supplement DOI calculations
• Integrate and evaluate Diamond approach in BioPortal
• Ideas?
Jambalaya
Diamond
CogZ
CTExplorer
Summary/Future
BioPortalViz
the CHISEL group, University of Victoria
Visualization and Jambalaya• Why are visualizations important?
– 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
• Other visualization approaches:– 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?
Jambalaya
Diamond
CogZ
CTExplorer
Summary/Future
BioPortalViz
the CHISEL group, University of Victoria
Main Features in Jambalaya• Classes and instances/individuals are
represented by nodes in the graph
• Slots or properties are represented by arcs between nodes
Jambalaya Demo
Jambalaya
Diamond
CogZ
CTExplorer
Summary/Future
BioPortalViz
the CHISEL group, University of Victoria
Different Views
– Nested View (Default)– Flat views
• Class Tree• Class & Instance Tree• Domain & Range (OWL)
– TreeMap View
– Query View
– Filmstrip
– Customized views
Jambalaya
Diamond
CogZ
CTExplorer
Summary/Future
BioPortalViz
BioPortalViz• Currently implemented as a Java Applet
• Integration of key ideas from Jambalaya with BioPortal
– Not sure which features are needed? Need input!
NCBO Council Call, Mar 4th 2008
the CHISEL group, University of Victoria
BioPortalViz Java Demo
BioPortalViz Flex Demo
Jambalaya
Diamond
CogZ
CTExplorer
Summary/Future
BioPortalViz
the CHISEL group, University of Victoria
CogZ• Cognitive Support and Visualization
for Human-Guided Mapping Systems
Jambalaya
Diamond
CogZ
CTExplorer
Summary/Future
BioPortalViz
the CHISEL group, University of Victoria
Ontology alignment
• Mapping terms from one ontology to another, preserving structural relationships
• Research emphasis has been on the algorithm
Selectontologies
Alignment algorithm
Candidatemappings
Verified mappings
Jambalaya
Diamond
CogZ
CTExplorer
Summary/Future
BioPortalViz
the CHISEL group, University of Victoria
Ontology alignment continued
• Very difficult cognitive task
• 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
Jambalaya
Diamond
CogZ
CTExplorer
Summary/Future
BioPortalViz
Visualization plug-in for Prompt
• Prompt: framework to support ontology alignment
• 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
Jambalaya
Diamond
CogZ
CTExplorer
Summary/Future
BioPortalViz
the CHISEL group, University of Victoria
Jambalaya
Diamond
CogZ
CTExplorer
Summary/Future
BioPortalViz
Future work in visualizing alignments
• 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
the CHISEL group, University of Victoria
Jambalaya
Diamond
CogZ
CTExplorer
Summary/Future
BioPortalViz
the CHISEL group, University of Victoria
Visualizing Clinical Trials• Developing new ways of visualizing clinical
trials data
• Many different classes of users:
– Clinicians, trialists, researchers
• 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
Jambalaya
Diamond
CogZ
CTExplorer
Summary/Future
BioPortalViz
Collaborative visualization
the CHISEL group, University of Victoria
CTExplorer Demo
Jambalaya
Diamond
CogZ
CTExplorer
Summary/Future
BioPortalViz
Issues• 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?
NCBO Council Call, Mar 4th 2008
the CHISEL group, University of Victoria
Jambalaya
Diamond
CogZ
CTExplorer
Summary/Future
BioPortalViz
CTSearch
• 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
Jambalaya
Diamond
CogZ
CTExplorer
Summary/Future
BioPortalViz Web 1.0 description of results
Jambalaya
Diamond
CogZ
CTExplorer
Summary/Future
BioPortalViz
Web 1.0 description of results
Jambalaya
Diamond
CogZ
CTExplorer
Summary/Future
BioPortalViz Web 1.0 description of results
Jambalaya
Diamond
CogZ
CTExplorer
Summary/Future
BioPortalViz
Searching ClinicalTrials.gov
• 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
Jambalaya
Diamond
CogZ
CTExplorer
Summary/Future
BioPortalViz
CiteULike
Jambalaya
Diamond
CogZ
CTExplorer
Summary/Future
BioPortalViz
CiteUlike• Features:
– 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.
Jambalaya
Diamond
CogZ
CTExplorer
Summary/Future
BioPortalViz
Tag Clouds for summarizing Web Search Results
Jambalaya
Diamond
CogZ
CTExplorer
Summary/Future
BioPortalViz
Tag Cloud visualization: CTSearch• 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).
the CHISEL group, University of Victoria
CTSearchDemo
Jambalaya
Diamond
CogZ
CTExplorer
Summary/Future
BioPortalViz
Where next… • Evaluation of CTExplorer and CTSearch
• Closer integration of CTExplorer and CTSearch?
• Where to host CTExplorer and CTSearch?
NCBO Council Call, Mar 4th 2008
the CHISEL group, University of Victoria
Jambalaya
Diamond
CogZ
CTExplorer
Summary/Future
BioPortalViz
Ontrez
Jambalaya
Diamond
CogZ
CTExplorer
Summary/Future
BioPortalViz
Integration in BioPortal Ontrez+TagClouds approach (Option1)
Condition
Phase
Study Design
Eligibility Criteria
Interventions
Size
Primary Outcomes
Secondary Outcomes
Overall Status
Jambalaya
Diamond
CogZ
CTExplorer
Summary/Future
BioPortalViz
Select source
OCRe
Search Clinical Trials
SearchAdvanced Search
PreferencesHeart Attack AND Seniors AND Los Angeles
Bank-a-Trial
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 BioPortalTagClouds approach (Option2)
Jambalaya
Diamond
CogZ
CTExplorer
Summary/Future
BioPortalViz
Condition
Phase
Study Design
Eligibility Criteria
Interventions
Size
Primary Outcomes
Secondary Outcomes
Overall Status
Interventions
1 A Study of the Safety and Efficacy of Nitric Oxide Reduction in Patients With Cardiogenic Shock After a Heart AttackBy Judith S. Hochman, M.D Funded By:INDUSTRYA 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
Conditions
Select source
Search Trials
SearchAdvanced Search
PreferencesHeart Attack AND Seniors AND Los Angeles
34 Trials from Heart Attack AND Seniors AND Los Angeles
Integration in BioPortalTagClouds approach (Option2 continuation)
Jambalaya
Diamond
CogZ
CTExplorer
Summary/Future
BioPortalViz
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:INDUSTRYA 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
2 Effectiveness of Combining Beta-Blocker Therapy and a Pacemaker Following a Heart Attack (The PACE-MI Trial)
By Jeffrey Goldberger, MD, MBA Funded By:NIHBeta-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:INDUSTRYThe 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
Integration in BioPortal Ontrez+Ranking+Commenting (option3)
Jambalaya
Diamond
CogZ
CTExplorer
Summary/Future
BioPortalViz
the CHISEL group, University of Victoria
Summary• 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
Jambalaya
Diamond
CogZ
CTExplorer
Summary/Future
BioPortalViz
the CHISEL group, University of Victoria
Future research directions and themes• Web based visualizations for a diverse
and evolving user base and task set
– Customizable and flexible views
• Cognitive support rather than visualization
– Ontologies, annotations and mappings
– Search
– Concept comparison (local, global and historical information)
– Meta-analyses
• Collaborative support
– Humans and software agents
Jambalaya
Diamond
CogZ
CTExplorer
Summary/Future
BioPortalViz
CSER Meeting October 2006 the CHISEL group, University of Victoria
Acknowledgements:
Chris Callendar, Tricia d’Entremont, Sean Falconer and Maleh Hernandez – The Chisel Group, UVic
Ida Sim, Driving Biological Project Lead, and Simona Carini San Francisco University
Jambalaya
Diamond
CogZ
CTExplorer
Summary/Future
BioPortalViz
CSER Meeting October 2006 the CHISEL group, University of Victoria
Input and suggestions would Input and suggestions would be greatly appreciated!be greatly appreciated!
[email protected]@uvic.ca
Computer Human Interaction & Software Engineering LabDepartment of Computer Science, University of Victoria
Jambalaya
Diamond
CogZ
CTExplorer
Summary/Future
BioPortalViz
the CHISEL group, University of Victoria
References and websites• Diamond:
– http://thechiselgroup.org/diamond
• Jambalaya and BioPortalViz: – Jambalaya: http://www.thechiselgroup.org/jambalaya
– BioPortalViz: http://webhome.cs.uvic.ca/~chisel/projects/jambalaya/ncboapplet/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)
Jambalaya
Diamond
CogZ
CTExplorer
Summary/Future
BioPortalViz
the CHISEL group, University of Victoria
• Slides in lieu of demos…
Jambalaya
Diamond
CogZ
CTExplorer
Summary/Future
BioPortalViz
• Jambalaya…
NCBO Council Call, Mar 4th 2008
the CHISEL group, University of Victoria
Jambalaya
Diamond
CogZ
CTExplorer
Summary/Future
BioPortalViz
the CHISEL group, University of Victoria
Jambalaya
Diamond
CogZ
CTExplorer
Summary/Future
BioPortalViz
the CHISEL group, University of Victoria
Composite Arcs
• High level edges (lifted)
Jambalaya
Diamond
CogZ
CTExplorer
Summary/Future
BioPortalViz
the CHISEL group, University of Victoria
• Inconsistencies “pop-out” in some views
Jambalaya
Diamond
CogZ
CTExplorer
Summary/Future
BioPortalViz
the CHISEL group, University of Victoria
Jambalaya
Diamond
CogZ
CTExplorer
Summary/Future
BioPortalViz
the CHISEL group, University of Victoria
Jambalaya
Diamond
CogZ
CTExplorer
Summary/Future
BioPortalViz
the CHISEL group, University of Victoria
Jambalaya
Diamond
CogZ
CTExplorer
Summary/Future
BioPortalViz
• CogZ…
NCBO Council Call, Mar 4th 2008
the CHISEL group, University of Victoria
Jambalaya
Diamond
CogZ
CTExplorer
Summary/Future
BioPortalViz
CSER Meeting October 2006 the CHISEL group, University of Victoria
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