Ontology-Based Interactive Visualization of Patient-Generated Research Questions
12 December 2018
17 April 2019
05 June 2019 (online)
Background Crohn's disease and colitis are chronic conditions that affect every facet of patients' lives (e.g., social interaction, family, work, diet, and sleep). Thus, treatment consists largely of disease management. The University of North Carolina at Chapel Hill chapter of the Crohn's and Colitis Foundation—IBD Partners—has created an interactive website that, in addition to providing helpful information and disease management tools, provides a discussion forum for patients to talk about their experiences and suggest new lines of research into Crohn's disease and colitis.
Objectives The primary objective of this work is to enable researchers to more effectively browse the forum content. Researchers wish to identify important/popular patient-suggested research topics, appreciate the full breadth of the research topics, and see connections between them, in order to more effectively prioritize research agendas.
Methods To help structure the forum content we have developed an ontology describing the major themes in the discussion forum. We have also created a prototype interactive visualization tool that leverages the ontology to help researchers identify common themes and related patient-generated research topics via linked views of (1) the ontology, (2) a research topic overview clustered by relevant ontology terms, and (3) a detailed view of the discussion forum content.
Results We discuss visualizations and interactions enabled by the visualization tool, provide an example scenario using the tool, and discuss limitations and future work based on feedback from potential users.
Conclusion The integration of a user-community specific ontology with an interactive visualization tool is a promising approach for enabling researchers to more effectively study user-generated research questions.
Protection of Human and Animal Subjects
This research was conducted with de-identified data from the CCFA Partners (now IBD Partners) Internet Cohort, made available via a Data Use Agreement with the University of North Carolina at Chapel Hill for a research project approved by the CCFA Partners Research Team.
- 1 Chung AE, Sandler RS, Long MD. , et al. Harnessing person-generated health data to accelerate patient-centered outcomes research: the Crohn's and Colitis Foundation of America PCORnet Patient Powered Research Network (CCFA Partners). J Am Med Inform Assoc 2016; 23 (03) 485-490
- 2 Gotz D, Borland D. Data-driven healthcare: Challenges and opportunities for interactive visualization. IEEE Comput Graph Appl 2016; 36 (03) 90-96
- 3 Shneiderman B, Plaisant C, Hesse BW. Improving healthcare with interactive visualization. Computer 2013; 46 (05) 58-66
- 4 Simpao AF, Ahumada LM, Larru Martinez B. , et al. Design and Implementation of a visual analytics electronic antibiogram within an electronic health record system at a tertiary pediatric hospital. Appl Clin Inform 2018; 9 (01) 37-45
- 5 Radhakrishnan K, Monsen KA, Bae SH, Zhang W. ; Clinical Relevance for Quality Improvement. Visual analytics for pattern discovery in home care. Appl Clin Inform 2016; 7 (03) 711-730
- 6 Wanderer JP, Gruss CL, Ehrenfeld JM. Using visual analytics to determine the utilization of preoperative anesthesia assessments. Appl Clin Inform 2015; 6 (04) 629-637
- 7 Karami M, Safdari R. From information management to information visualization: development of radiology dashboards. Appl Clin Inform 2016; 7 (02) 308-329
- 8 Rao G, Kirley K, Epner P. , et al. Identifying, analyzing, and visualizing diagnostic paths for patients with nonspecific abdominal pain. Appl Clin Inform 2018; 9 (04) 905-913
- 9 Sorbello A, Ripple A, Tonning J. , et al. Harnessing scientific literature reports for pharmacovigilance. Prototype software analytical tool development and usability testing. Appl Clin Inform 2017; 8 (01) 291-305
- 10 Stasko J, Gorg C, Liu Z, Singhal K. Jigsaw: Supporting Investigative Analysis through Interactive Visualization. In: 2007 IEEE Symposium on Visual Analytics Science and Technology; 2007: 131-138
- 11 Sampathkumar H, Chen XW, Luo B. Ontology-based visualization of healthcare data mined from online healthcare forums. Paper presented at: 2015 International Conference on Healthcare Informatics; Dallas, TX; IEEE, 2015: 325-334
- 12 Harpring P. Introduction to Controlled Vocabularies: Terminology for Art, Architecture, and Other Cultural Works. Los Angeles, CA: Getty Publications; 2010
- 13 Ashburner M, Ball CA, Blake JA. , et al; The Gene Ontology Consortium. Gene ontology: tool for the unification of biology. Nat Genet 2000; 25 (01) 25-29
- 14 The Gene Ontology Consortium. Expansion of the gene ontology knowledgebase and resources. Nucleic Acids Res 2017; 45 (D1): D331-D338
- 15 Köhler S, Vasilevsky NA, Engelstad M. , et al. The human phenotype ontology in 2017. Nucleic Acids Res 2017; 45 (D1): D865-D876
- 16 Rubin DL, Shah NH, Noy NF. Biomedical ontologies: a functional perspective. Brief Bioinform 2008; 9 (01) 75-90
- 17 Bodenreider O. Biomedical ontologies in action: role in knowledge management, data integration and decision support. Yearb Med Inform 2008; (Suppl. 01) 67-79
- 18 Wildemuth BM. Applications of Social Research Methods to Questions in Information and Library Science. Westport, CT: Libraries Unlimited; 2009
- 19 Musen MA. ; Protégé Team. The Protégé Project: a look back and a look forward. AI Matters 2015; 1 (04) 4-12
- 20 Bostock M, Ogievetsky V, Heer J. D3: data-driven documents. IEEE Trans Vis Comput Graph 2011; 17 (12) 2301-2309
- 21 Shneiderman B. The eyes have it: a task by data type taxonomy for information visualizations. Paper presented at: Proceedings 1996 IEEE Symposium on Visual Languages; 1996: 336-343
- 22 Shneiderman B. Tree visualization with tree-maps: 2-d space-filling approach. ACM Trans Graph 1992; 11 (01) 92-99
- 23 Kruskal JB, Landwehr JM. Icicle plots: better displays for hierarchical clustering. Am Stat 1983; 37 (02) 162-168
- 24 Reingold EM, Tilford JS. Tidier drawings of trees. IEEE Trans Softw Eng 1981; 7 (02) 223-228
- 25 Kamdar MR, Walk S, Tudorache T, Musen MA. Analyzing user interactions with biomedical ontologies: a visual perspective. J Web Semant 2018; 49: 16-30
- 26 van der Maaten LJP, Hinton GE. Visualizing high-dimensional data using t-SNE. J Mach Learn Res 2008; 9: 2579-2605
- 27 Nelson SD, Del Fiol G, Hanseler H, Crouch BI, Cummins MR. Software prototyping: a case report of refining user requirements for a health information exchange dashboard. Appl Clin Inform 2016; 7 (01) 22-32
- 28 Dowding D, Merrill JA. The development of heuristics for evaluation of dashboard visualizations. Appl Clin Inform 2018; 9 (03) 511-518
- 29 Burckhardt P, Padman R. Analyzing self-help forums with ontology-based text mining: an exploration in kidney space. AMIA Annu Symp Proc 2015; 2015: 1821-1830