Ontology-based interactive visualization of patient-generated - PowerPoint PPT Presentation

Ontology-based interactive visualization of patient-generated research questions David Borland RENCI, UNC-Chapel Hill Laura Christopherson RENCI, UNC-Chapel Hill Charles Schmitt NIEHS

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

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

Crohn’s Disease and Colitis • Crohn’s disease – Inflammatory bowel disease (IBD) No known cure – Chronic – Diverse set of symptoms Certain therapies can help • Diarrhea • Inflammation (gut and other body parts) treat symptoms • Fatigue • Abdominal pain Treatment largely consists • Weight loss of disease management • 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 4

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

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

Discussion Forum Data Research topic Forum snapshot: Research question Description 97 research topics User ID, Votes, Category 121 total comments 400 unique users Comment 1246 total votes User ID Comment User ID Ontology-based interactive visualization of patient-generated research questions: Background 7

Discussion Forum Data Example topic post: Research topic Question : Research question Nicotine has shown to be effective for UC Description [ulcerative colitis] in some individuals, both User ID, Votes, Category prior- and nonsmokers. What is the mechanism? Does nicotine affect the microbiome, the immune system or both? Comment User ID Description : Big Pharma will not take on the role of studying Comment nicotine as there is no $$$ in it. Few studies with User ID small sample sizes have been done but more research is needed. Ontology-based interactive visualization of patient-generated research questions: Background 8

Discussion Forum Data One of 9 predefined categories: Research topic diet Research question medications Description procedures and testing environment User ID, Votes, Category alternative therapies lifestyle Comment genetics User ID exercise other Comment User ID Ontology-based interactive visualization of patient-generated research questions: Background 9

Discussion Forum Data Research topic Goals: Research question Description Identify common themes User ID, Votes, Category Prioritize patient-generated Comment research questions User ID Comment User ID Ontology-based interactive visualization of patient-generated research questions: Background 10

Initial Approach Words Counts ulcerative colitis 20 in ammatory bowel 13 Phrases were extracted from forum text (i.e., from questions, descriptions, controlled trial 10 and comments). Those phrases with >2 in ammatory bowel disease 10 appearances were used to create the bowel disease 10 initial visualizations. top priority 10 periodontal disease 9 disease activity 8 vitamin d 7 ibd management 5 other auto-immune 4 disease course 4 This didn’t turn out to be as small bowel 4 informative as we’d hoped. combination therapy 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

Initial Approach Words Counts ulcerative colitis 20 in ammatory bowel 13 Phrases were extracted from forum text (i.e., from questions, descriptions, controlled trial 10 and comments). Those phrases with >2 in ammatory bowel disease 10 appearances were used to create the bowel disease 10 initial visualizations. top priority 10 periodontal disease 9 disease activity 8 vitamin d 7 ibd management 5 other auto-immune 4 disease course 4 This didn’t turn out to be as small bowel 4 informative as we’d hoped. combination therapy 4 The frequency of words and/or word phrases didn’t successfully ‘aboutness’ capture the ‘aboutness’ of the conversation on the CCFA forum. Ontology-based interactive visualization of patient-generated research questions: Background 12

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

Content Analysis Ontology-based interactive visualization of patient-generated research questions: Ontology creation 14

Content Analysis Manifest Content vs. Latent Content The appearance of a Conceptual and cannot be given word in a text directly observed Ontology-based interactive visualization of patient-generated research questions: Ontology creation 15

Content Analysis Manifest Content vs. Latent Content The appearance of a Conceptual and cannot be given word in a text 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; 2009. Ontology-based interactive visualization of patient-generated research questions: Ontology creation 16

Content Analysis Manifest Content vs. Latent Content The appearance of a Conceptual and cannot be given word in a text directly observed E.g., “…the level of research anxiety present in user narratives about their experiences at the library.” “My heart won’t “I am so anxious” stop beating” Wildemuth BM. Applications of Social Research Methods to Questions in Information and Library Science. Westport, Conn: “I wish I could relax” Libraries Unlimited; 2009. Ontology-based interactive visualization of patient-generated research questions: Ontology creation 17

Content Analysis Other 34 Diet 16 Medications 14 Procedures and testing 10 Category Alternative therapies 8 Environment 8 Lifestyle 4 Genetics 2 Exercise 1 0 5 10 15 20 25 30 35 40 Research Topic Count Ontology-based interactive visualization of patient-generated research questions: Ontology creation 18

Content Analysis Other 34 Diet 16 “Sometimes there is no existing theory Medications 14 or research on your message populations; you may not know what Procedures and testing 10 the important variables are. The only Category Alternative therapies way to discover them is to explore the 8 content.” Environment 8 Wildemuth BM. Applications of Social Research Methods to Lifestyle 4 Questions in Information and Library Science. Westport, Conn: Genetics Libraries Unlimited; 2009. 2 Exercise 1 0 5 10 15 20 25 30 35 40 Research Topic Count Ontology-based interactive visualization of patient-generated research questions: Ontology creation 19

REPRESENTATIVE CLASSES POSTS The Ontology comorbidity 11 diagnosis/monitoring method 7 IBD course 39 Protégé 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 holistic treatment 12 Borrows some terms from pre-existing ontologies: medication 28 Ontology of Adverse Events, Disease Ontology surgery 13 Ontology-based interactive visualization of patient-generated research questions: Ontology creation 20