Jonathan Bona


Jonathan P. Bona, Ph.D.
Assistant Professor
Department of Biomedical Informatics
University of Arkansas for Medical Sciences

jpbona@uams.edu
jonathanbona@gmail.com

curriculum vitae | researchgate | scholar | dblp | linkedin



About

My work as an informatics researcher focuses on developing and applying knowledge representation techniques to organize and use information about biology, medicine, and health. This work leverages my expertise in the development, evaluation, and use of biomedical ontologies, which provide machine-interpretable logical background knowledge about a domain. These form the basis for ontology-based semantic representations that can be stored, queried, and reasoned about, using description logic reasoners, triple store databases, and other semantic web tools.

An illustrative example is our recent work with clinical and neuroinformatics data in the Arkansas Enterprise Imaging Repository, which we presented at the National Cancer Institute (NCI) Informatics Technology for Cancer Research (ITCR) meeting in May 2019:

  • Jonathan P. Bona, Aaron S. Kemp, Tracy Nolan, Linda Larson-Prior, Aparna Das, Tuhin Virmani, Lakshmi Pillai, Mathias Brochhausen, and Fred Prior. Semantic Integration of Neuroinformatics Data in the Arkansas Image Enterprise System (ARIES). 2019 ITCR Annual Meeting, Deer Valley, UT, May 29 - 31, 2019.
    http://doi.org/10.13140/RG.2.2.31693.90087/1
  • Recent Work
      2019
    • Accepted Jonathan P. Bona, Joseph Utecht, and Mathias Brochhausen. Providing a User-oriented Interface to Enable Semantic Queries in PRISM . American Medical Informatics Association 2019 (AMIA) Annual Symposium, Poster session, Washington, DC, November 16 - 20, 2019.
    • Accepted Aaron S. Kemp, Jonathan P. Bona, Tracy S. Nola, Linda Larson-Prior, Tuhin Virmani, Lakshmi Pillai, Mathias Brochhausen, Lawrence Tarbox, and Fred Prior. Semantic Representations of Multi-Modal Data, NeuroInformatic Processing Pipelines, and Derived Neuroimaging Results in the Arkansas Image Enterprise System (ARIES). American Medical Informatics Association 2019 (AMIA) Annual Symposium, Poster session, Washington, DC, November 16 - 20, 2019.
    • Accepted Corey J. Hayes, Jonathan P. Bona, and Mathias Brochhausen. Using Semantic Representations for Urine Drug Tests in the Veterans Health Administration. American Medical Informatics Association 2019 (AMIA) Annual Symposium, Poster session, Washington, DC, November 16 - 20, 2019.
    • Accepted Jonathan P. Bona, Joseph Utecht, Sarah Bost, Corey Hayes, and Mathias Brochhausen. Building a Shared Ontology Use Patterns Repository. International Conference on Biomedical Ontology (ICBO) 2019, Buffalo, NY, July 30 - August 2, 2019.
    • Accepted Jonathan P. Bona, Aaron S. Kemp, Tracy Nolan, Linda Larson-Prior, Aparna Das,Tuhin Virmani, Lakshmi Pillai, Mathias Brochhausen, and Fred Prior. Semantic Integration of Neuroinformatics Data in the Arkansas Image Enterprise System with Open Biomedical Ontologies. International Conference on Biomedical Ontology (ICBO) 2019, Poster session, Buffalo, NY, July 30 - August 2, 2019.
    • Forthcoming Jonathan P. Bona, Fred W. Prior, Meredith N. Zozus, and Mathias Brochhausen. Enhancing Clinical and Clinical Research Data with Biomedical Ontologies - Insights from the Knowledge Representation Perspective. In Press at 2019 Yearbook of Medical Informatics.
      2018
    • Jonathan P. Bona, Tracy S. Nolan, Dillon Gibson, and Mathias Brochhausen. Ontologies Enabling Non-image Data Queries in The Cancer Imaging Archive. American Medical Informatics Association 2018 (AMIA) Annual Symposium, Poster session, San Francisco, CA, November 3 - 7, 2018.
    • Jonathan P. Bona, Tracy S. Nolan, and Mathias Brochhausen. Ontology-Enhanced Representations of Non-image Data in The Cancer Imaging Archive. International Conference on Biological Ontology 2018, Corvallis, OR, August 7 - 10, 2018. CEUR-WS.org, online http://ceur-ws.org/Vol-2285/ICBO_2018_paper_37.pdf
    • Corey J. Hayes, Jonathan P. Bona, and Mathias Brochhausen. Towards the Development of an Opioid Misuse Ontology. International Conference on Biological Ontology 2018 Poster Session, Corvallis, OR, August 7 - 10, 2018. CEUR-WS.org, online http://ceur-ws.org/Vol-2285/ICBO_2018_paper_56.pdf
    • Mathias Brochhausen, Jonathan Bona, and Bernd Blobel. The Role of Axiomatically-Rich Ontologies in Transforming Medical Data to Knowledge. Studies in Health Technology and Informatics 249 (2018): 38-49. PMID: 29866954
    • Jonathan P. Bona and Werner Ceusters. Mismatches between major subhierarchies and semantic tags in SNOMED CT. Journal of Biomedical Informatics 81 (2018): 1-15. PMID: 29462668
      2017
    • Jonathan Bona. Does Semantic Tag Usage in SNOMED CT Match its Concept Hierarchy? American Medical Informatics Association 2017 Annual Symposium Poster Session, Washington, DC, November 4 - 8, 2017; 1973.
    • Joseph R. Utecht, Jonathan P. Bona, and Mathias Brochhausen. Creating RDF Data on Trauma Care Organizations from Questionnaires. American Medical Informatics Association 2017 Annual Symposium Poster Session, Washington, DC, November 4 - 8, 2017; 2228.
    • Jonathan Bona and Werner Ceusters. Scrutinizing the relationships between SNOMED CT concepts and semantic tags. Proceedings of the 8th International Conference on Biomedical Ontology (ICBO 2017), Newcastle-upon-Tyne, United Kingdom, September 13th - 15th, 2017, CEUR-WS.org, online http://ceur-ws.org/Vol-2137/paper_34.pdf.
    • Jonathan Bona, John Grohol, Meredith Zozus, Robert Zozus, and Mathias Brochhausen. Toward using ontologies to improve results in searches for mental health information. Proceedings of the 8th International Conference on Biomedical Ontology (ICBO 2017), Newcastle-upon-Tyne, United Kingdom, September 13th - 15th, 2017, CEUR-WS.org, online http://ceur-ws.org/Vol-2137/paper_37.pdf. Awarded best poster.
      2016
    • Werner Ceusters and Jonathan Bona. Pain in SNOMED CT: is there an anesthetic? In Zaibert, Leo (ed.) The Theory and Practice of Ontology. Palgrave MacMillan, 2016:157-185. DOI: 10.1057/978-1-137-55278-5_9.
    • Darren A. Natale, Cecilia N. Arighi, Judith A. Blake, Jonathan Bona, Chuming Chen, Sheng-Chih Chen, Karen R. Christie, Julie Cowart, Peter D'Eustachio, Alexander D. Diehl, Harold J. Drabkin, William D. Duncan, Hongzhan Huang, Jia Ren, Karen Ross, Alan Ruttenberg, Veronica Shamovsky, Barry Smith, Qinghua Wang, Jian Zhang, Abdelrahman El-Sayed, Cathy H. Wu. Protein Ontology (PRO): enhancing and scaling up the representation of protein entities. Nucleic Acids Research 2016; 45 (D1): D339-D346. PMID: 27899649
    • Werner Ceusters and Jonathan Bona. Analyzing SNOMED CT's Historical Data: Pitfalls and Possibilities. American Medical Informatics Association 2016 Annual Symposium Proceedings, Chicago IL, November 12-16, 2016;361-370. PMID: 28269831
    • Jonathan Bona and Werner Ceusters. Identifying Missing Finding Site Relations in SNOMED CT. American Medical Informatics Association 2016 Annual Symposium Proceedings, Chicago IL, November 12-16, 2016;1347.
    • Jonathan Bona, Selja Seppälä, and Werner Ceusters. Analysis of SNOMED 'Bleeding' Concepts & Terms. Proceedings of the Joint International Conference on Biological Ontology and BioCreative (ICBO-BioCreative 2016), Corvallis, Oregon, United States, August 1-4, 2016, CEUR-WS.org, online http://ceur-ws.org/Vol-1747/IP10_ICBO2016.pdf.
    • William Duncan, Travis Allen, Jonathan Bona, Olivia Helfer, Barry Smith, Alan Ruttenberg, Alexander D. Diehl. The ImmPort Antibody Ontology. Proceedings of the Joint International Conference on Biological Ontology and BioCreative (ICBO-BioCreative 2016), Corvallis, Oregon, United States, August 1-4, 2016, CEUR-WS.org, online http://ceur-ws.org/Vol-1747/IP18_ICBO2016.pdf.
    • Werner Ceusters and Jonathan Bona. Representing SNOMED CT Concept Evolutions using Process Profiles. International Workshop on Ontology Modularity, Contextuality, and Evolution (WOMoCoE 2016), Annecy, France, July 6, 2016
    • Thomas Bittner, Jonathan Bona, and Werner Ceusters. Ontologies of Dynamical Systems and Verifiable Ontology-based Computation: Towards a Haskell-based Implementation of Referent Tracking. Ninth International Conference on Formal Ontology in Information Systems (FOIS 2016), Annecy, France, July 6th-9th, 2016. DOI: 10.3233/978-1-61499-660-6-313.
    • Werner Ceusters and Jonathan Bona. Ontological Foundations for Tracking Data Quality through the Internet of Things. Special Topic Conference Transforming Healthcare with the Internet of Things (EFMI-STC2016), Paris, France, April 17-19, 2016. PMID: 27071880
      2013
    • Jonathan P. Bona and Stuart C. Shapiro. Specifying Modalities in the MGLAIR Architecture. In Ahmed M. H. Abdel-Fattah and Kai-Uwe Kühnberger, Eds., Proceedings of the Workshop on Formalizing Mechanisms for Artificial General Intelligence and Cognition (Formal MAGIC), PICS: Publication Series of the Institute of Cognitive Science (ISSN 1610-5389), Institute of Cognitive Science, University of Osnabrück, Germany, 2013.
    • Albert Goldfain, Min Xu, Jonathan Bona, and Barry Smith. Ontology Based Annotation of Contextualized Vital Signs. Proceedings of the International Conference on Biomedical Ontology 2013 (ICBO 2013), Montreal, Canada, July 7-12, 2013, CEUR-WS.org, online http://ceur-ws.org/Vol-1060/icbo2013_submission_18.pdf.
    • Jonathan P. Bona and Stuart C. Shapiro. Modality in the MGLAIR Architecture. In: Chella A., Pirrone R., Sorbello R., Jóhannsdóttir K. (eds) Biologically Inspired Cognitive Architectures 2012. Advances in Intelligent Systems and Computing, vol 196. Springer, Berlin, Heidelberg, 2013. DOI: 10.1007/978-3-642-34274-5_18.