Margaret-Anne Storey University of Victoria

1. Interactive Views for Navigating Ontologies and Data at the National Center for Biomedical Ontology Margaret-Anne Storey University of Victoria

2. 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) the CHISEL group, University of Victoria

3. DIaMOND—Degree of Interest Modeling for Ontology Navigation and Development • http://www.thechiselgroup.org/diamond the CHISEL group, University of Victoria

4. 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 the CHISEL group, University of Victoria

5. 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 the CHISEL group, University of Victoria

6. 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 the CHISEL group, University of Victoria

7. Highlighting and Filtering in the Class Browser (integration with Protégé for now) Standard Highlighting Highlighting & Filtering the CHISEL group, University of Victoria

8. Diamond Demo: NCI Anatomy the CHISEL group, University of Victoria

9. 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? the CHISEL group, University of Victoria

10. 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? the CHISEL group, University of Victoria

11. 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 the CHISEL group, University of Victoria

12. Different Views • Nested View (Default) • Flat views • Class Tree • Class & Instance Tree • Domain & Range (OWL) • TreeMap View • Query View • Filmstrip • Customized views the CHISEL group, University of Victoria

13. BioPortalViz • Currently implemented as a Java Applet • Integration of key ideas from Jambalaya with BioPortal • Not sure which features are needed? Need input! BioPortalViz Java Demo BioPortalViz Flex Demo the CHISEL group, University of Victoria

14. CogZ • Cognitive Support and Visualization for Human-Guided Mapping Systems the CHISEL group, University of Victoria

15. Ontology alignment • Mapping terms from one ontology to another, preserving structural relationships • Research emphasis has been on the algorithm Select ontologies Alignment algorithm Candidate mappings Verified mappings the CHISEL group, University of Victoria

16. 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 the CHISEL group, University of Victoria

17. 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

18. the CHISEL group, University of Victoria

19. 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

20. 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 the CHISEL group, University of Victoria

21. Collaborative visualization CTExplorer Demo the CHISEL group, University of Victoria

22. 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? the CHISEL group, University of Victoria

23. 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

24. Web 1.0 description of results

25. Web 1.0 description of results

26. Web 1.0 description of results

27. 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

28. CiteULike

29. 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.

30. Tag Clouds for summarizing Web Search Results

31. 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). CTSearchDemo the CHISEL group, University of Victoria

32. Where next… • Evaluation of CTExplorer and CTSearch • Closer integration of CTExplorer and CTSearch? • Where to host CTExplorer and CTSearch? the CHISEL group, University of Victoria

33. Ontrez

34. Integration in BioPortal Ontrez+TagClouds approach (Option1) Condition Phase Study Design Eligibility Criteria Interventions Size Primary Outcomes Secondary Outcomes Overall Status

35. Integration in BioPortalTagClouds approach (Option2) Search Clinical Trials Select source Advanced Search Search Heart AttackANDSeniorsANDLos Angeles Preferences 34 Trials from Heart Attack AND Seniors AND Los Angeles Bank-a-Trial 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 OCRe 200 Publications from Heart Attack AND Seniors AND Los Angeles

36. Condition Phase Study Design Eligibility Criteria Interventions Size Interventions Primary Outcomes Secondary Outcomes 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 BioPortalTagClouds approach (Option2 continuation) Search Trials Select source Advanced Search Search Heart AttackANDSeniorsANDLos Angeles Preferences 34 Trials from Heart Attack AND Seniors AND Los Angeles Conditions

37. Integration in BioPortalOntrez+Ranking+Commenting (option3) 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 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: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 timesRelated 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 2009Active, not recruiting Viewed 1200 times

38. 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 the CHISEL group, University of Victoria

39. 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 the CHISEL group, University of Victoria

40. 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 the CHISEL group, University of Victoria

41. Input and suggestions would be greatly appreciated! mstorey@uvic.ca Computer Human Interaction & Software Engineering Lab Department of Computer Science, University of Victoria the CHISEL group, University of Victoria

42. 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) the CHISEL group, University of Victoria

43. Slides in lieu of demos… the CHISEL group, University of Victoria

44. Jambalaya… the CHISEL group, University of Victoria

45. the CHISEL group, University of Victoria

46. Composite Arcs • High level edges (lifted) the CHISEL group, University of Victoria

47. Inconsistencies “pop-out” in some views the CHISEL group, University of Victoria

48. the CHISEL group, University of Victoria

49. the CHISEL group, University of Victoria

50. the CHISEL group, University of Victoria