Ontology-based interactive visualization of patient-generated research questions
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1 Ontology-based interactive visualization of patient-generated research questions David Borland Laura Christopherson Charles Schmitt RENCI, UNC-Chapel Hill RENCI, UNC-Chapel Hill NIEHS
2 Overview Background Crohn s disease & colitis IBD Partners discussion forum Ontology creation CCFA Explorer Ontology visualization Research topic visualization Overview Details Example scenario Feedback and future work Ontology-based interactive visualization of patient-generated research questions: Overview 2
3 Crohn s Disease and Colitis Crohn s disease Inflammatory bowel disease (IBD) Chronic Diverse set of symptoms Diarrhea Inflammation (gut and other body parts) Fatigue Abdominal pain Weight loss Etc. Colitis Inflammation of the inner lining of the colon Commonly co-occurs with Crohn s disease Ontology-based interactive visualization of patient-generated research questions: Background 3
4 Crohn s Disease and Colitis Crohn s disease Inflammatory bowel disease (IBD) Chronic Diverse set of symptoms Diarrhea Inflammation (gut and other body parts) Fatigue Abdominal pain Weight loss Etc. Colitis Inflammation of the inner lining of the colon Commonly co-occurs with Crohn s disease No known cure Certain therapies can help treat symptoms Treatment largely consists of disease management Ontology-based interactive visualization of patient-generated research questions: Background 4
5 IBD Partners (formerly CCFA Partners) Patient-powered online research network Crohn s and Colitis Foundation UNC-Chapel Hill School of Medicine Discussion forum Patients propose and discuss research ideas Researchers engage in discussion Ontology-based interactive visualization of patient-generated research questions: Background 5
6 Discussion Forum Data Research topic Research question Description User ID, Votes, Category Comment User ID Comment User ID Ontology-based interactive visualization of patient-generated research questions: Background 6
7 Discussion Forum Data Research topic Research question Description User ID, Votes, Category Comment User ID Forum snapshot: 97 research topics 121 total comments 400 unique users 1246 total votes Comment User ID Ontology-based interactive visualization of patient-generated research questions: Background 7
8 Discussion Forum Data Research topic Research question Description User ID, Votes, Category Comment User ID Comment User ID Example topic post: Question: Nicotine has shown to be effective for UC [ulcerative colitis] in some individuals, both prior- and nonsmokers. What is the mechanism? Does nicotine affect the microbiome, the immune system or both? Description: Big Pharma will not take on the role of studying nicotine as there is no $$$ in it. Few studies with small sample sizes have been done but more research is needed. Ontology-based interactive visualization of patient-generated research questions: Background 8
9 Discussion Forum Data Research topic Research question Description User ID, Votes, Category Comment User ID Comment User ID One of 9 predefined categories: diet medications procedures and testing environment alternative therapies lifestyle genetics exercise other Ontology-based interactive visualization of patient-generated research questions: Background 9
10 Discussion Forum Data Research topic Research question Description User ID, Votes, Category Comment User ID Goals: Identify common themes Prioritize patient-generated research questions Comment User ID Ontology-based interactive visualization of patient-generated research questions: Background 10
11 Initial Approach Words Cou nts ulcerative colitis 20 in ammatory bowel 13 Phrases were extracted from forum controlled trial 10 text (i.e., from questions, descriptions, in ammatory bowel disease 10 and comments). Those phrases with >2 bowel disease 10 appearances were used to create the initial visualizations. top priority 10 periodontal disease 9 disease activity 8 vitamind 7 ibd management 5 other auto-immune 4 disease course 4 small bowelthis didn t turn out 4 to be as informative as we d hoped. combinationtherapy 4 The frequency of words and/or word phrases didn t successfully capture the aboutness of the conversation on the CCFA forum. Ontology-based interactive visualization of patient-generated research questions: Background 11
12 Initial Approach Words Cou nts ulcerative colitis 20 in ammatory bowel 13 Phrases were extracted from forum controlled trial 10 text (i.e., from questions, descriptions, in ammatory bowel disease 10 and comments). Those phrases with >2 bowel disease 10 appearances were used to create the initial visualizations. top priority 10 periodontal disease 9 disease activity 8 vitamind 7 ibd management 5 other auto-immune 4 disease course 4 small bowelthis didn t turn out 4 to be as informative as we d hoped. combinationtherapy 4 The frequency of words and/or word phrases didn t successfully capture the aboutness of the conversation on the CCFA forum. Ontology-based interactive visualization of patient-generated research questions: Background 12
13 Ontology Creation Ontology Controlled vocabulary Represent knowledge about a domain of interest Enable multiple types of relationships is a treats Etc. Ontology-based interactive visualization of patient-generated research questions: Ontology creation 13
14 Content Analysis Ontology-based interactive visualization of patient-generated research questions: Ontology creation 14
15 Content Analysis Manifest Content vs. Latent Content The appearance of a given word in a text Conceptual and cannot be directly observed Ontology-based interactive visualization of patient-generated research questions: Ontology creation 15
16 Content Analysis Manifest Content vs. Latent Content The appearance of a given word in a text Conceptual and cannot be directly observed E.g., the level of research anxiety present in user narratives about their experiences at the library. Wildemuth BM. Applications of Social Research Methods to Questions in Information and Library Science. Westport, Conn: Libraries Unlimited; Ontology-based interactive visualization of patient-generated research questions: Ontology creation 16
17 Content Analysis Manifest Content vs. Latent Content The appearance of a given word in a text Conceptual and cannot be directly observed E.g., the level of research anxiety present in user narratives about their experiences at the library. I am so anxious My heart won t stop beating I wish I could relax Wildemuth BM. Applications of Social Research Methods to Questions in Information and Library Science. Westport, Conn: Libraries Unlimited; Ontology-based interactive visualization of patient-generated research questions: Ontology creation 17
18 Content Analysis Other 34 Diet 16 Medications 14 Category Procedures and testing Alternative therapies Environment Lifestyle 4 Genetics 2 Exercise Research Topic Count Ontology-based interactive visualization of patient-generated research questions: Ontology creation 18
19 Content Analysis Other 34 Diet 16 Category Medications Procedures and testing Alternative therapies Environment Lifestyle Genetics Sometimes there is no existing theory or research on your message populations; you may not know what the important variables are. The only way to discover them is to explore the content. Wildemuth BM. Applications of Social Research Methods to Questions in Information and Library Science. Westport, Conn: Libraries Unlimited; Exercise Research Topic Count Ontology-based interactive visualization of patient-generated research questions: Ontology creation 19
20 The Ontology Protégé REPRESENTATIVE CLASSES POSTS comorbidity 11 diagnosis/monitoring method 7 IBD course 39 pre-diagnosis time period 1 diagnosis event 5 post-diagnosis time period 31 quality of life 8 risk factor 58 demographic factor 7 environmental factor 18 lifestyle factor 20 physiological factor 28 psychological factor 5 symptom 36 gastrointestional manifestation 12 extra-gastrointestinal manifestation 3 treatment method 50 alternative therapy 7 Borrows some terms from pre-existing ontologies: Ontology of Adverse Events, Disease Ontology holistic treatment 12 medication 28 surgery 13 Ontology-based interactive visualization of patient-generated research questions: Ontology creation 20
21 The Ontology Protégé 337 classes 7 top-level classes OWL ROBOT OBO Graph (JSON) REPRESENTATIVE CLASSES POSTS comorbidity 11 diagnosis/monitoring method 7 IBD course 39 pre-diagnosis time period 1 diagnosis event 5 post-diagnosis time period 31 quality of life 8 risk factor 58 demographic factor 7 environmental factor 18 lifestyle factor 20 physiological factor 28 psychological factor 5 symptom 36 gastrointestional manifestation 12 extra-gastrointestinal manifestation 3 treatment method 50 alternative therapy 7 Borrows some terms from pre-existing ontologies: Ontology of Adverse Events, Disease Ontology holistic treatment 12 medication 28 surgery 13 Ontology-based interactive visualization of patient-generated research questions: Ontology creation 21
22 The Ontology Protégé 337 classes 7 top-level classes OWL ROBOT OBO Graph (JSON) REPRESENTATIVE CLASSES POSTS comorbidity 11 diagnosis/monitoring method 7 IBD course 39 pre-diagnosis time period 1 diagnosis event 5 post-diagnosis time period 31 quality of life 8 risk factor 58 demographic factor 7 environmental factor 18 lifestyle factor 20 physiological factor 28 Research Topics Ontology Terms (Classes) psychological factor 5 symptom 36 gastrointestional manifestation 12 extra-gastrointestinal manifestation 3 treatment method 50 alternative therapy 7 Borrows some terms from pre-existing ontologies: Ontology of Adverse Events, Disease Ontology holistic treatment 12 medication 28 surgery 13 Ontology-based interactive visualization of patient-generated research questions: Ontology creation 22
23 CCFA Explorer Ontology Visualization Topic Overview Topic Details 3 linked views D3 React/Flux Bootstrap Ontology-based interactive visualization of patient-generated research questions: CCFA Explorer 23
24 Ontology Visualization Topic Overview Topic Details Ontology-based interactive visualization of patient-generated research questions: CCFA Explorer 24
25 Ontology Visualization Force-directed network Node size Number of topics labeled with term Labeled with child implies labeled with parent Links Class relationships Currently only is a Ontology-based interactive visualization of patient-generated research questions: CCFA Explorer 25
26 Topic Overview Ontology Visualization Topic Details Ontology-based interactive visualization of patient-generated research questions: CCFA Explorer 26
27 Topic Overview t-sne Layout Based on labeled ontology terms Clusters of topics with similar ontology terms Glyph Size Number of comments Border width Number of votes Color Category van der Maaten LJP, Hinton GE. Visualizing High-Dimensional Data Using t-sne. Journal of Machine Learning Research. 2008;9: exercise genetics lifestyle environment alternative therapies procedures and testing medications diet other Ontology-based interactive visualization of patient-generated research questions: CCFA Explorer 27
28 t-sne Modifications van der Maaten LJP, Hinton GE. Visualizing High-Dimensional Data Using t-sne. Journal of Machine Learning Research. 2008;9: Force-directed layout of overlapping glyphs Ontology-based interactive visualization of patient-generated research questions: CCFA Explorer 28
29 t-sne Modifications van der Maaten LJP, Hinton GE. Visualizing High-Dimensional Data Using t-sne. Journal of Machine Learning Research. 2008;9: Differential weighting of higher-level (left) vs. lower level (right) ontology terms Ontology-based interactive visualization of patient-generated research questions: CCFA Explorer 29
30 t-sne Modifications van der Maaten LJP, Hinton GE. Visualizing High-Dimensional Data Using t-sne. Journal of Machine Learning Research. 2008;9: Emphasizing selected ontology terms for layout Ontology-based interactive visualization of patient-generated research questions: CCFA Explorer 30
31 Topic Details Ontology Visualization Topic Overview Ontology-based interactive visualization of patient-generated research questions: CCFA Explorer 31
32 Topic Details Ontology-based interactive visualization of patient-generated research questions: CCFA Explorer 32
33 Topic Details Ontology-based interactive visualization of patient-generated research questions: CCFA Explorer 33
34 Topic Details Ontology-based interactive visualization of patient-generated research questions: CCFA Explorer 34
35 Topic Details List Sort Topic ID User ID Votes Comments Category Filter Selected topics Selected ontology terms Highlight Text from search box in red Ontology-based interactive visualization of patient-generated research questions: CCFA Explorer 35
36 Interactive Selection and Highlighting Selection Ontology terms Research topics Selection in any view updates all views Relationships Co-occurrence Between ontology terms Number of topics in common Union for multiple Association Between research topics Number of terms in common Union for multiple Connection Between terms and topics Topic labeled with term or not Sum for multiple Ontology-based interactive visualization of patient-generated research questions: CCFA Explorer 36
37 Interactive Selection and Highlighting Selection Ontology terms Research topics Selection in any view updates all views Relationships Co-occurrence Between ontology terms Number of topics in common Union for multiple Association Between research topics Number of terms in common Union for multiple Connection Between terms and topics Topic labeled with term or not Sum for multiple Ontology-based interactive visualization of patient-generated research questions: CCFA Explorer 37
38 Interactive Selection and Highlighting Selection Ontology terms Research topics Selection in any view updates all views Relationships Co-occurrence Between ontology terms Number of topics in common Union for multiple Association Between research topics Number of terms in common Union for multiple Connection Between terms and topics Topic labeled with term or not Sum for multiple Topic 1 Term 1, Term 2, Term 3 Topic 2 Term 1 Topic 3 Term 2, Term 3, Term 4 Ontology-based interactive visualization of patient-generated research questions: CCFA Explorer 38
39 Interactive Selection and Highlighting Selection Ontology terms Research topics Selection in any view updates all views Relationships Co-occurrence Between ontology terms Number of topics in common Union for multiple Association Between research topics Number of terms in common Union for multiple Connection Between terms and topics Topic labeled with term or not Sum for multiple Select Term 3 and Term 4 Topic 1 Term 1, Term 2, Term 3 Topic 2 Term 1 Topic 3 Term 2, Term 3, Term 4 Ontology-based interactive visualization of patient-generated research questions: CCFA Explorer 39
40 Interactive Selection and Highlighting Selection Ontology terms Research topics Selection in any view updates all views Relationships Co-occurrence Between ontology terms Number of topics in common Union for multiple Association Between research topics Number of terms in common Union for multiple Connection Between terms and topics Topic labeled with term or not Sum for multiple Select Term 3 and Term 4 Topic 1 Term 1, Term 2, Term 3 Topic 2 Term 1 Topic 3 Term 2, Term 3, Term 4 Co-occurrence: Term 1: 1 Term 2: 2 Term 3: 2 Term 4: 1 Ontology-based interactive visualization of patient-generated research questions: CCFA Explorer 40
41 Interactive Selection and Highlighting Selection Ontology terms Research topics Selection in any view updates all views Relationships Co-occurrence Between ontology terms Number of topics in common Union for multiple Association Between research topics Number of terms in common Union for multiple Connection Between terms and topics Topic labeled with term or not Sum for multiple Select Term 3 and Term 4 Topic 1 Term 1, Term 2, Term 3 Topic 2 Term 1 Topic 3 Term 2, Term 3, Term 4 Co-occurrence: Term 1: 1 Term 2: 2 Term 3: 2 Term 4: 1 Connection: Topic 1: 1 Topic 2: 0 Topic 3: 2 Ontology-based interactive visualization of patient-generated research questions: CCFA Explorer 41
42 Interactive Selection and Highlighting Selection Ontology terms Research topics Selection in any view updates all views Relationships Co-occurrence Between ontology terms Number of topics in common Union for multiple Association Between research topics Number of terms in common Union for multiple Connection Between terms and topics Topic labeled with term or not Sum for multiple Select Topic 2 and Topic 3 Topic 1 Term 1, Term 2, Term 3 Topic 2 Term 1 Topic 3 Term 2, Term 3, Term 4 Ontology-based interactive visualization of patient-generated research questions: CCFA Explorer 42
43 Interactive Selection and Highlighting Selection Ontology terms Research topics Selection in any view updates all views Relationships Co-occurrence Between ontology terms Number of topics in common Union for multiple Association Between research topics Number of terms in common Union for multiple Connection Between terms and topics Topic labeled with term or not Sum for multiple Select Topic 2 and Topic 3 Topic 1 Term 1, Term 2, Term 3 Topic 2 Term 1 Topic 3 Term 2, Term 3, Term 4 Association: Topic 1: 3 Topic 2: 1 Topic 3: 3 Ontology-based interactive visualization of patient-generated research questions: CCFA Explorer 43
44 Interactive Selection and Highlighting Selection Ontology terms Research topics Selection in any view updates all views Relationships Co-occurrence Between ontology terms Number of topics in common Union for multiple Association Between research topics Number of terms in common Union for multiple Connection Between terms and topics Topic labeled with term or not Sum for multiple Select Topic 2 and Topic 3 Topic 1 Term 1, Term 2, Term 3 Topic 2 Term 1 Topic 3 Term 2, Term 3, Term 4 Association: Topic 1: 3 Topic 2: 1 Topic 3: 3 Connection: Term 1: 1 Term 2: 1 Term 3: 1 Term 4: 1 Ontology-based interactive visualization of patient-generated research questions: CCFA Explorer 44
45 Ontology Highlighting Node interior size and color proportional to co-occurrence/connection Labels shown if > 25% Ontology-based interactive visualization of patient-generated research questions: CCFA Explorer 45
46 Topic Overview Highlighting Glyph saturation proportional to association/connection drug Ontology-based interactive visualization of patient-generated research questions: CCFA Explorer 46
47 Topic Overview Highlighting Glyph saturation proportional to association/connection drug drug + remission Ontology-based interactive visualization of patient-generated research questions: CCFA Explorer 47
48 Topic Overview Highlighting Glyph saturation proportional to association/connection drug drug + remission drug + remission weighted t-sne Ontology-based interactive visualization of patient-generated research questions: CCFA Explorer 48
49 Topic Details Highlighting Filtered by selected topics Ontology terms colored as in ontology network visualization Ontology-based interactive visualization of patient-generated research questions: CCFA Explorer 49
50 Example Scenario User searches for genetic makeup Highlighted in red User selects genetic makeup Notices medication co-occurs with genetic makeup User select medication also Ontology-based interactive visualization of patient-generated research questions: Example scenario 50
51 Example Scenario User re-runs t-sne Notices cluster of three topics, including one very large glyph User selects these three topics Ontology-based interactive visualization of patient-generated research questions: Example scenario 51
52 Example Scenario User filters topic details to show only these topics for indepth inspection/comparison Ontology-based interactive visualization of patient-generated research questions: Example scenario 52
53 Feedback and Future Work Demonstration to IBD Partners Generally positive feedback Useful way to explore the forum data Quickly identify major themes and popular research topics Some features may be too complex for more naïve users Two particular themes identified Patient-facing interface Find similar patients More easily identify research topics relevant to them Researcher-facing interface Quickly identify relevant information in their research area Quickly generate summaries of relevant information Easily presented to stakeholders Ontology-based interactive visualization of patient-generated research questions: Feedback and future work 53
54 Feedback and Future Work Interface Redesign ontology visualization Improve navigation Explore automatic text summarization Include in summary panel for selected terms/topics Data processing Explore ways to automate/semiautomate topic classification Enable ontology editing/expansion User evaluations Ontology-based interactive visualization of patient-generated research questions: Feedback and future work 54
55 Feedback and Future Work Interface Redesign ontology visualization Improve navigation Explore automatic text summarization Include in summary panel for selected terms/topics Data processing Explore ways to automate/semiautomate topic classification Enable ontology editing/expansion 15,680 > 400 User evaluations Ontology-based interactive visualization of patient-generated research questions: Feedback and future work 55
56 Feedback and Future Work Interface Redesign ontology visualization Improve navigation Explore automatic text summarization Include in summary panel for selected terms/topics Data processing Explore ways to automate/semiautomate topic classification Enable ontology editing/expansion 15,680 > 400 User evaluations Ontology-based interactive visualization of patient-generated research questions: Feedback and future work 56
57 Questions? Thanks to IBD Partners for their help with this work! Ontology-based interactive visualization of patient-generated research questions: Feedback and future work 57
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