1. Jambalaya Diamond CogZ CTExplorer Summary/ Future BioPortalViz Interactive Views for Navigating Ontologies and Data at the National Center for Biomedical Ontology Margaret-Anne Storey University of Victoria

2. 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)

3. 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

4. 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

5. 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

6. 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

7. 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) StandardHighlightingHighlighting & Filtering

8. Jambalaya Diamond CogZ CTExplorer Summary/ Future BioPortalViz Diamond Demo: NCI Anatomy the CHISEL group, University of Victoria

9. 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?

10. 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?

11. 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

12. 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

13. Jambalaya Diamond CogZ CTExplorer Summary/ Future 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 4 th 2008the CHISEL group, University of Victoria BioPortalViz Java Demo BioPortalViz Flex Demo

14. Jambalaya Diamond CogZ CTExplorer Summary/ Future BioPortalViz the CHISEL group, University of Victoria CogZ Cognitive Support and Visualization for Human-Guided Mapping Systems

15. 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 Select ontologies Alignment algorithm Candidate mappings Verified mappings

16. 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

17. 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

18. Jambalaya Diamond CogZ CTExplorer Summary/ Future BioPortalViz the CHISEL group, University of Victoria

19. 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

20. 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

21. Jambalaya Diamond CogZ CTExplorer Summary/ Future BioPortalViz Collaborative visualization the CHISEL group, University of Victoria CTExplorer Demo

22. 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 4 th 2008the CHISEL group, University of Victoria

23. 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

24. Jambalaya Diamond CogZ CTExplorer Summary/ Future BioPortalViz Web 1.0 description of results

25. Jambalaya Diamond CogZ CTExplorer Summary/ Future BioPortalViz Web 1.0 description of results

26. Jambalaya Diamond CogZ CTExplorer Summary/ Future BioPortalViz Web 1.0 description of results

27. 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

28. Jambalaya Diamond CogZ CTExplorer Summary/ Future BioPortalViz CiteULike

29. 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.

30. Jambalaya Diamond CogZ CTExplorer Summary/ Future BioPortalViz Tag Clouds for summarizing Web Search Results

31. 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

32. 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 4 th 2008the CHISEL group, University of Victoria

33. Jambalaya Diamond CogZ CTExplorer Summary/ Future BioPortalViz Ontrez

34. 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

35. Jambalaya Diamond CogZ CTExplorer Summary/ Future BioPortalViz Select source OCRe Search Clinical Trials Search Advanced Search Preferences Heart 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 BioPortal TagClouds approach (Option2)

36. 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 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 Conditions Select source Search Trials Search Advanced Search Preferences Heart Attack AND Seniors AND Los Angeles 34 Trials from Heart Attack AND Seniors AND Los Angeles Integration in BioPortal TagClouds approach (Option2 continuation)

37. 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: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 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 recruitingViewed 1200 times Integration in BioPortal Ontrez+Ranking+Commenting (option3)

38. 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

39. 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

40. Jambalaya Diamond CogZ CTExplorer Summary/ Future BioPortalViz CSER Meeting October 2006the 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

41. Jambalaya Diamond CogZ CTExplorer Summary/ Future BioPortalViz CSER Meeting October 2006the CHISEL group, University of Victoria Input and suggestions would be greatly appreciated! mstorey@uvic.ca Computer Human Interaction & Software Engineering Lab Department of Computer Science, University of Victoria

42. Jambalaya Diamond CogZ CTExplorer Summary/ Future BioPortalViz the CHISEL group, University of Victoria References and websites Diamond: –http://thechiselgroup.org/diamondhttp://thechiselgroup.org/diamond Jambalaya and BioPortalViz: –Jambalaya: http://www.thechiselgroup.org/jambalayahttp://www.thechiselgroup.org/jambalaya –BioPortalViz: http://webhome.cs.uvic.ca/~chisel/projects/jambalaya/ncboa pplet/demo_applet.html 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 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) http://dufflite.cs.uvic.ca:8080/CTPrototypeWeb.html

43. Jambalaya Diamond CogZ CTExplorer Summary/ Future BioPortalViz the CHISEL group, University of Victoria Slides in lieu of demos…

44. Jambalaya Diamond CogZ CTExplorer Summary/ Future BioPortalViz Jambalaya… NCBO Council Call, Mar 4 th 2008the CHISEL group, University of Victoria

45. Jambalaya Diamond CogZ CTExplorer Summary/ Future BioPortalViz the CHISEL group, University of Victoria

46. Jambalaya Diamond CogZ CTExplorer Summary/ Future BioPortalViz the CHISEL group, University of Victoria Composite Arcs High level edges (lifted)

47. Jambalaya Diamond CogZ CTExplorer Summary/ Future BioPortalViz the CHISEL group, University of Victoria Inconsistencies “pop-out” in some views

48. Jambalaya Diamond CogZ CTExplorer Summary/ Future BioPortalViz the CHISEL group, University of Victoria

49. Jambalaya Diamond CogZ CTExplorer Summary/ Future BioPortalViz the CHISEL group, University of Victoria

50. Jambalaya Diamond CogZ CTExplorer Summary/ Future BioPortalViz the CHISEL group, University of Victoria

51. Jambalaya Diamond CogZ CTExplorer Summary/ Future BioPortalViz CogZ… NCBO Council Call, Mar 4 th 2008the CHISEL group, University of Victoria

52. Jambalaya Diamond CogZ CTExplorer Summary/ Future BioPortalViz CSER Meeting October 2006the CHISEL group, University of Victoria