AccScience Publishing / JCI / Online First / DOI: 10.36922/jci.8599
Submit to JCI
Cite this article
12
Download
92
Views
Journal Browser
Volume | Year
Issue
Search
Forthcoming Issue
Current Issue
View All
News and Announcements
View All
ORIGINAL RESEARCH ARTICLE

An ontology-based method for formalizing and encoding patient colonoscopy preparation using BPMN and OWL2 for automated tool development

Muhammad Amith1,2* ,  Yue Yu3 ,  Yuheng Shi3 ,  Brooks Cash4 ,  Barani Mayilvaganan4 ,  Anriudh Babu1 ,  Yang Gong3*
Show Less
1 Department of Biostatistics and Data Science, School of Public and Population Health, University of Texas Medical Branch, Galveston, Texas, United States of America
2 Department of Internal Medicine, John Sealy School of Medicine, University of Texas Medical Branch, Galveston, Texas, United States of America
3 Department of Clinical and Health Informatics, McWilliams School of Biomedical Informatics, University of Texas Health Science Center at Houston, Houston, Texas, United States of America
4 Department of Internal Medicine, McGovern School of Medicine, University of Texas Health Science Center at Houston, Houston, Texas, United States of America
JCI, 8599 https://doi.org/10.36922/jci.8599
Submitted: 19 January 2025 | Revised: 10 April 2025 | Accepted: 11 April 2025 | Published: 23 April 2025
© 2025 by the Author(s). This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution -Noncommercial 4.0 International License (CC-by the license) ( https://creativecommons.org/licenses/by-nc/4.0/ )
Download PDF
Cite
XML
Abstract

Colonoscopy is a proven procedure for mitigating the incidence of colorectal cancers in late adulthood. Despite its effectiveness, colonoscopy preparation presents several challenges for patients, including issues with adherence and misunderstanding. Information and communication technology (ICT) tools may offer valuable support for modern patients. To enable such tools, computable knowledge bases are essential. In this paper, we describe the development of an ontology-based knowledge graph representing four laxative-based pre-colonoscopy procedures. We used the business process modeling and notation and OWL2 formalisms to manifest machine-readable artifacts that model processes of colonoscopy preparation. Future work will focus on integrating extended knowledge bases from biomedical ontologies and developing prototype ICT tools to support decision-making in colonoscopy preparation.

Keywords
Process modelling
Knowledge engineering
Ontology
Knowledge graph
Semantic web
Consumer health informatics
Funding
This research is supported by the National Institutes of Health under awards #R21DK134815, #U01AG088076, and #R01HS027846 and by the Cancer Prevention and Research Institute of Texas (CPRIT) under award #RP220244.
Conflict of interest
Yang Gong and Muhammad Amith are the Editor-in-Chief and Editorial Board Member of this journal, respectively, but were not in any way involved in the editorial and peer-review process conducted for this paper, directly or indirectly. Separately, other authors declared that they have no known competing financial interests or personal relationships that could have influenced the work reported in this paper.
References
  1. Alzahrani SM, Al Doghaither HA, Al-Ghafari AB. General insight into cancer: An overview of colorectal cancer. Mol Clin Oncol. 2021;15(6):271. doi: 10.3892/mco.2021.2433

 

  1. Adelstein BA, Macaskill P, Chan SF, Katelaris PH, Irwig L. Most bowel cancer symptoms do not indicate colorectal cancer and polyps: A systematic review. BMC Gastroenterol. 2011;11:65. doi: 10.1186/1471-230X-11-65

 

  1. Jasperson KW, Tuohy TM, Neklason DW, Burt RW. Hereditary and familial colon cancer. Gastroenterology. 2010;138(6):2044-2058. doi: 10.1053/j.gastro.2010.01.054

 

  1. Yu J, Feng Q, Kim JH, Zhu Y. Combined effect of healthy lifestyle factors and risks of colorectal adenoma, colorectal cancer, and colorectal cancer mortality: Systematic review and meta-analysis. Front Oncol. 2022;12:827019. doi: 10.3389/fonc.2022.827019

 

  1. Siegel RL, Giaquinto AN, Jemal A. Cancer statistics, 2024. CA Cancer J Clin. 2024;74(1):12-49. doi: 10.3322/caac.21820

 

  1. Baidoun F, Elshiwy K, Elkeraie Y, et al. Colorectal cancer epidemiology: Recent trends and impact on outcomes. Curr Drug Targets. 2021;22(9):998-1009. doi: 10.2174/1389450121999201117115717

 

  1. Rawla P, Sunkara T, Barsouk A. Epidemiology of colorectal cancer: Incidence, mortality, survival, and risk factors. Prz Gastroenterol. 2019;14(2):89-103. doi: 10.5114/pg.2018.81072

 

  1. Leszczynski AM, MacArthur KL, Nelson KP, Schueler SA, Quatromoni PA, Jacobson BC. The association among diet, dietary fiber, and bowel preparation at colonoscopy. Gastrointest Endosc. 2018;88(4):685-694. doi: 10.1016/j.gie.2018.06.034

 

  1. Bizri ME, Sheikh ME, Lee GE, Sewitch MJ. Mobile health technologies supporting colonoscopy preparation: A systematic review and meta-analysis of randomized controlled trials. PLoS One. 2021;16(3):e0248679. doi: 10.1371/journal.pone.0248679

 

  1. Zapata MC, Ha JB, Hernandez-Barco YG, Richter JM. Using a customized SMS program to promote colonoscopy adherence and support bowel cleanliness for Spanish-speaking patients. J Health Care Poor Underserved. 2022;33(2):1069-1082. doi: 10.1353/hpu.2022.0081

 

  1. Ho LH, Montealegre JR, Al-Arabi S, Jibaja-Weiss ML, Suarez MG. Impact of colonoscopy preparation video on Boston bowel preparation scale score. Gastroenterol Nurs. 2019;42(3):251-258. doi: 10.1097/SGA.0000000000000391

 

  1. Dankner L, Quiros JA, Volpert D, Atreja A. Evaluating the use of a customized digital navigation program to optimize bowel preparation in pediatric colonsocopy. Front Pediatr. 2023;11:1271222. doi: 10.3389/fped.2023.1271222

 

  1. Smith JK, Ashcraft A. Moving the needle on patient cancellations through mobile integration: A hospital-based quality improvement project. Gastroenterol Nurs. 2022;45(6):419-427. doi: 10.1097/SGA.0000000000000682

 

  1. Garde S, Knaup P. Requirements engineering in health care: The example of chemotherapy planning in paediatric oncology. Requir Eng. 2006;11(4):265-278. doi: 10.1007/s00766-006-0029-6

 

  1. Pufahl L, Zerbato F, Weber B, Weber I. BPMN in healthcare: Challenges and best practices. Inf Syst. 2022;107:102013. doi: 10.1016/j.is.2022.102013

 

  1. Chiao CM, Kunzle V, Reichert M. Integrated Modeling of Process- and Data-centric Software Systems with PHILharmonicFlows. In: 2013 IEEE 1st International Workshop on Communicating Business Process and Software Models Quality, Understandability, and Maintainability (CPSM). Eindhoven, Netherlands: IEEE; 2013. p. 1-10. doi: 10.1109/CPSM.2013.6703085

 

  1. Malhotra S, Jordan D, Shortliffe E, Patel VL. Workflow modeling in critical care: Piecing together your own puzzle. J Biomed Inform. 2007;40(2):81-92. doi: 10.1016/j.jbi.2006.06.002

 

  1. Schweitzer M, Lasierra N, Oberbichler S, Toma I, Fensel A, Hoerbst A. Structuring clinical workflows for diabetes care: An overview of the OntoHealth approach. Appl Clin Inform. 2014;5(2):512-526. doi: 10.4338/ACI-2014-04-RA-0039

 

  1. Barbarito F, Pinciroli F, Mason J, Marceglia S, Mazzola L, Bonacina S. Implementing standards for the interoperability among healthcare providers in the public regionalized Healthcare Information System of the Lombardy Region. J Biomed Inform. 2012;45(4):736-745. doi: 10.1016/j.jbi.2012.01.006

 

  1. Steadman A, McGregor C, Percival J, James A. Using PaJMa to Enable Comparative Assessment of Health Care Processes within Canadian Neonatal Intensive Care Units. In: Proceedings of the Advances in Health Informatics Conference, AHIC. 2012.

 

  1. Trebble TM, Hansi N, Hydes T, Smith MA, Baker M. Process mapping the patient journey: An introduction. BMJ. 2010;341:c4078. doi: 10.1136/bmj.c4078

 

  1. Golbreich C, Wallace EK, Patel-Schneider PF. OWL 2 Web Ontology Language New Features and Rationale. W3C Working Draft. W3C; 2009. Available from: https://wwww3 org/tr/2009/wd-owl2-new-features-20090611 [Last accessed on 2025 Jan 22].

 

  1. W3C Owl Working Group. OWL 2 Web Ontology Language Document Overview. 2nd ed. 2012. Available from: https://www.w3.org/tr/owl2-overview [Last accessed on 2014 Jul 09].

 

  1. Object Management Group. Business Process Modeling and Notation. 2014. Available from: https://www.bpmn.org [Last accessed on 2025 Jan 22].

 

  1. Object Management Group. Unified Modeling Language, v2.5.1. 2017. Available from: https://www.omg.org/spec/ UML/2.5.1/PDF [Last accessed on 2025 Jan 22].

 

  1. Centers for Disease Control and Prevention. Stay safe from COVID-19: How I Wash My Hands. 2021. Available from: https://www.cdc.gov/ncbddd/humandevelopment/ documents/covid-easy-read/CDC-RTI-Handwashing-activity-p.pdf [Last accessed on 2024 May 02].

 

  1. Arp R, Smith B, Spear AD. Building Ontologies with Basic Formal Ontology. United States: MIT Press; 2015.

 

  1. Noy NF, McGuinness DL. Ontology Development 101: A Guide to Creating Your First Ontology. Knowledge Systems Laboratory Stanford Univeristy; 2001. p. 25. Available from: https://www.ksl.stanford.edu/people/dlm/papers/ontology-tutorial-noy-mcguinness-abstract.html [Last accessed on 2022 Apr 01].

 

  1. Annane A. BPMN Based Ontology (BBO). 2019. Available from: https://github.com/aminaannane/bbo_ bpmnbasedontology [Last accessed on 2024 Mar 10].

 

  1. Annane A, Aussenac-Gilles N, Kamel M. BBO: BPMN 2.0 Based Ontology for Business Process Representation. In: 20th European Conference on Knowledge Management (ECKM 2019). Vol. 1. Lisbonne, Portugal; 2019. p. 49-59.

 

  1. WebMD. Golytely Oral: Uses, Side Effects, Interactions. WebMD; 2024. Available from: https://www.webmd.com/ drugs/2/drug-3728/golytely-oral/details [Last accessed on 2024 May 02].

 

  1. WebMD. Miralax Oral: Uses, Side Effects, Interactions. WebMD; 2024. Available from: https://www.webmd.com/ drugs/2/drug-17116/miralax-oral/details [Last accessed on 2024 May 02].

 

  1. Braintree Laboratories I. SUTAB® (Sodium Sulfate, Magnesium Sulfate, Potassium Chloride). 2024. Available from: https://sutab.com [Last accessed on 2024 May 02].

 

  1. Salix Pharmaceuticals. A Formula Designed With You In Mind. 2023. Available from: https://www.myplenvu.com [Last accessed on 2024 May 02].

 

  1. Diagrams.net. draw.io. 2020. Available from: https://www. diagrams.net [Last accessed on 2020 Aug 01].

 

  1. Apache Software Foundation. Apache POI - the Java API for Microsoft Documents. 2024. Available from: https://poi. apache.org [Last accessed on 2024 May 27].

 

  1. Google. Guava: Google Core Libraries for Java. 2024. Available from: https://github.com/google/guava [Last accessed on 2025 Jan 22].

 

  1. Apache Software Foundation. Apache Commons. 2024. Available from: https://commons.apache.org [Last accessed on 2025 Jan 22].

 

  1. Grau BC, Horrocks I, Motik B, Parsia B, Patel-Schneider P, Sattler U. OWL 2: The next step for OWL. J Web Semant. 2008;6(4):309-322.

 

  1. Krötzsch M, Simancik F, Horrocks I. A Description Logic Primer. [arXiv Preprint arXiv:12014089]. 2012. Available from: https://arxiv.org/abs/1201.4089 [Last accessed on 2016 May 15].

 

  1. Tsarkov D, Horrocks I. FaCT++ Description Logic Reasoner: System Description. In: Automated Reasoning: Third International Joint Conference, IJCAR 2006. Proceedings. Vol. 4130. Seattle, WA, USA: Springer; 2006. p. 292-297.

 

  1. Amith T. JFact Reasoning Check for Colonoscopy Knowledge Graphs. 2025. Available from: https://github.com/proftuan/bpmn-knowledge-graph-rendering-engine/tree/main/ examples/colonoscopy%20preparation%20process/evaluation%20jfact/jfactreasoncheck [Last accessed on 2025 Jan 22].

 

  1. Musen MA. The protégé project: A look back and a look forward. AI Matters. 2015;1(4):4-12. doi: 10.1145/2757001.2757003

 

  1. Open Biomedical Ontology Technical Working Group. OBO Foundry Identifier Policy. OBO Foundry. 2024. Available from: https://obofoundry.org/id-policy [Last accessed on 2024 May 27].

 

  1. Ferrante S, Bonacina S, Pozzi G, Pinciroli F, Marceglia S. A design methodology for medical processes. Appl Clin Inform. 2016;7(1):191-210. doi: 10.4338/ACI-2015-08-RA-0111

 

  1. Reichert M. What BPM technology can do for healthcare process support. In: Peleg M, Lavrač N, Combi C, editors. Artificial Intelligence in Medicine. Lecture Notes in Computer Science. Vol. 6747. Berlin, Heidelberg: Springer; 2011. p. 2-13. doi: 10.1007/978-3-642-22218-4_2

 

  1. Rojas E, Munoz-Gama J, Sepúlveda M, Capurro D. Process mining in healthcare: A literature review. J Biomed Inform. 2016;61:224-236. doi: 10.1016/j.jbi.2016.04.007

 

  1. Scheuerlein H, Rauchfuss F, Dittmar Y, et al. New methods for clinical pathways-Business Process Modeling Notation (BPMN) and Tangible Business Process Modeling (t.BPM). Langenbecks Arch Surg. 2012;397(5):755-761. doi: 10.1007/s00423-012-0914-z

 

  1. Fellmann M, Koschmider A, Laue R, Schoknecht A, Vetter A. Business process model patterns: State-of-the-art, research classification and taxonomy. Bus Process Manag J. 2019;25(5):972-994. doi: 10.1108/BPMJ-01-2018-0021

 

  1. Rospocher M, Ghidini C, Serafini L. An ontology for the business process modelling notation. In: Formal Ontology in Information Systems. Amsterdam: IOS Press; 2014. p. 133-146. doi: 10.3233/978-1-61499-438-1-133

 

  1. Laurenza E, Quintano M, Schiavone F, Vrontis D. The effect of digital technologies adoption in healthcare industry: A case based analysis. Bus Process Manag J. 2018;24(5):1124-1144. doi: 10.1108/BPMJ-04-2017-0084

 

  1. Barrison PD, Flynn A, Richesson R, et al. Knowledge infrastructure: A priority to accelerate workflow automation in health care. J Am Med Inform Assoc. 2023;30(6):1222-1223. doi: 10.1093/jamia/ocad026

 

  1. Meyer P, Biston MC, Khamphan C, et al. Automation in radiotherapy treatment planning: Examples of use in clinical practice and future trends for a complete automated workflow. Cancer Radiothér. 2021;25(6-7):617-622. doi: 10.1016/j.canrad.2021.06.006

 

  1. Zayas-Cabán T, Okubo TH, Posnack S. Priorities to accelerate workflow automation in health care. J Am Med Inform Assoc. 2023;30(1):195-201. doi: 10.1093/jamia/ocac197

 

  1. Zayas-Cabán T, Haque SN, Kemper N. Identifying opportunities for workflow automation in health care: Lessons learned from other industries. Appl Clin Inform. 2021;12(3):686-697. doi: 10.1055/s-0041-1731744

 

  1. Smith B, Ashburner M, Rosse C, et al. The OBO foundry: Coordinated evolution of ontologies to support biomedical data integration. Nat Biotechnol. 2007;25(11):1251-1255. doi: 10.1038/nbt1346

 

  1. Noy NF, Shah NH, Whetzel PL, et al. BioPortal: Ontologies and integrated data resources at the click of a mouse. Nucleic Acids Res. 2009;37(suppl_2):W170-W173. doi: 10.1093/nar/gkp440

 

  1. Bordea G, Nikiema J, Griffier R, Hamon T, Mougin F. FIDEO: Food Interactions with Drugs Evidence Ontology. In: 11th International Conference on Biomedical Ontologies. 2020.

 

  1. Köhler S, Gargano M, Matentzoglu N, et al. The human phenotype ontology in 2021. Nucleic Acids Res. 2021;49(D1):D1207-D1217. doi: 10.1093/nar/gkaa1043

 

  1. Amith M, Roberts K, Tao C. Conceiving an application ontology to model patient human papillomavirus vaccine counseling for dialogue management. BMC Bioinformatics. 2019;20(21):706. doi: 10.1186/s12859-019-3193-7

 

  1. Amith M, Lin RZ, Cui L, et al. Conversational ontology operator: Patient-centric vaccine dialogue management engine for spoken conversational agents. BMC Med Inform Decis Mak. 2020;20(S4):259. doi: 10.1186/s12911-020-01267-y

 

  1. Moore N, Amith M, Neumann A, et al. Translating motivational interviewing for the HPV vaccine into a computable ontology model for automated AI conversational interaction. Ext Abstr Hum Factors Computing Syst. 2024;2024:341. doi: 10.1145/3613905.3651051

 

  1. Brooke J. SUS-A quick and dirty usability scale. Usability Eval Ind. 1996;189(194):4-7. doi: 10.1201/9781498710411-35

 

  1. Brooke J. SUS: A retrospective. J Usability Stud. 2013;8(2):29-40. doi: 10.5555/2817912.2817913

 

Previous article in this issue
Next article in this issue
Share
Back to top
Journal of Clinical Informatics, Published by AccScience Publishing
We use cookies on our website to ensure you get the best experience.
Read more about our cookies here
Accept