Assessing the Need for Semantic Data Integration for Surgical Biobanks-A Knowledge Representation Perspective

Mathias Brochhausen; Justin M Whorton; Cilia E Zayas; Monica P Kimbrell; Sarah J Bost; Nitya Singh; Christoph Brochhausen; Kevin W Sexton; Bernd Blobel

doi:10.3390/jpm12050757

Assessing the Need for Semantic Data Integration for Surgical Biobanks-A Knowledge Representation Perspective

J Pers Med. 2022 May 7;12(5):757. doi: 10.3390/jpm12050757.

Authors

Mathias Brochhausen¹, Justin M Whorton¹, Cilia E Zayas¹, Monica P Kimbrell², Sarah J Bost³, Nitya Singh^{4

5}, Christoph Brochhausen⁶, Kevin W Sexton^{1

7

8

9}, Bernd Blobel^{10

11

12}

Affiliations

¹ Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA.
² Trauma Performance Improvement Coordinator, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA.
³ Department of Health Outcomes and Biomedical Informatics, University of Florida, Gainesville, FL 32611, USA.
⁴ Department of Animal Sciences, University of Florida, Gainesville, FL 32611, USA.
⁵ Emerging Pathogens Institute, University of Florida, Gainesville, FL 32611, USA.
⁶ Central Biobank, Institute of Pathology, University and University Clinic of Regensburg, 93053 Regensburg, Germany.
⁷ Department of Surgery, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA.
⁸ Institute for Digital Health & Innovation, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA.
⁹ BioVentures LLC, Little Rock, AR 72205, USA.
¹⁰ Medical Faculty, University of Regensburg, 93053 Regensburg, Germany.
¹¹ eHealth Competence Center Bavaria, Deggendorf Institute of Technology, 94469 Deggendorf, Germany.
¹² First Medical Faculty, Charles University, 11636 Prague 1, Czech Republic.

Abstract

To improve patient outcomes after trauma, the need to decrypt the post-traumatic immune response has been identified. One prerequisite to drive advancement in understanding that domain is the implementation of surgical biobanks. This paper focuses on the outcomes of patients with one of two diagnoses: post-traumatic arthritis and osteomyelitis. In creating surgical biobanks, currently, many obstacles must be overcome. Roadblocks exist around scoping of data that is to be collected, and the semantic integration of these data. In this paper, the generic component model and the Semantic Web technology stack are used to solve issues related to data integration. The results are twofold: (a) a scoping analysis of data and the ontologies required to harmonize and integrate it, and (b) resolution of common data integration issues in integrating data relevant to trauma surgery.

Keywords: biomedical ontologies; knowledge representation; osteomyelitis; post-traumatic arthritis; semantic data integration; surgical biobank; system theory.

Abstract

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