A Semantic Transformation Methodology for the Secondary Use of Observational Healthcare Data in Postmarketing Safety Studies

2018-4-30
Pacaci, Anil
Gonul, Suat
Sinaci, A. Anil
Yuksel, Mustafa
Laleci Erturkmen, Gokce B.
Background: Utilization of the available observational healthcare datasets is key to complement and strengthen the postmarketing safety studies. Use of common data models (CDM) is the predominant approach in order to enable large scale systematic analyses on disparate data models and vocabularies. Current CDM transformation practices depend on proprietarily developed Extract-Transform-Load (ETL) procedures, which require knowledge both on the semantics and technical characteristics of the source datasets and target CDM. Purpose: In this study, our aim is to develop a modular but coordinated transformation approach in order to separate semantic and technical steps of transformation processes, which do not have a strict separation in traditional ETL approaches. Such an approach would discretize the operations to extract data from source electronic health record systems, alignment of the source, and target models on the semantic level and the operations to populate target common data repositories. Approach: In order to separate the activities that are required to transform heterogeneous data sources to a target CDM, we introduce a semantic transformation approach composed of three steps: (1) transformation of source datasets to Resource Description Framework (RDF) format, (2) application of semantic conversion rules to get the data as instances of ontological model of the target CDM, and (3) population of repositories, which comply with the specifications of the CDM, by processing the RDF instances from step 2. The proposed approach has been implemented on real healthcare settings where Observational Medical Outcomes Partnership (OMOP) CDM has been chosen as the common data model and a comprehensive comparative analysis between the native and transformed data has been conducted. Results: Health records of similar to 1 million patients have been successfully transformed to an OMOP CDM based database from the source database. Descriptive statistics obtained from the source and target databases present analogous and consistent results. Discussion and Conclusion: Our method goes beyond the traditional ETL approaches by being more declarative and rigorous. Declarative because the use of RDF based mapping rules makes each mapping more transparent and understandable to humans while retaining logic-based computability. Rigorous because the mappings would be based on computer readable semantics which are amenable to validation through logic-based inference methods.
Frontiers in Pharmacology

Suggestions

A Secure Semantic Interoperability Infrastructure for Inter-Enterprise Sharing of Electronic Healthcare Records
Boniface, Mike; Watkins, E. Rowland; Saleh, Ahmed; Doğaç, Asuman; Eichelberg, Marco (2006-06-09)
Healthcare professionals need access to accurate and complete healthcare records for effective assessment, diagnosis and treatment of patients. The non-interoperability of healthcare information systems means that inter-enterprise access to a patient's history over many distributed encounters is difficult to achieve. The ARTEMIS project has developed a secure semantic web service infrastructure for the interoperability of healthcare information systems. Healthcare professionals share services and medical in...
A medical image processing and analysis framework
Çevik, Alper; Eyüboğlu, Behçet Murat; Oğuz, Kader Karlı; Department of Biomedical Engineering (2011)
Medical image analysis is one of the most critical studies in field of medicine, since results gained by the analysis guide radiologists for diagnosis, treatment planning, and verification of administered treatment. Therefore, accuracy in analysis of medical images is at least as important as accuracy in data acquisition processes. Medical images require sequential application of several image post-processing techniques in order to be used for quantification and analysis of intended features. Main objective...
An Information theoretic representation of brain connectivity for cognitive state classification using functional magnetic resonance imaging
Önal, Itır; Yarman Vural, Fatoş Tunay; Department of Computer Engineering (2013)
In this study, a new method for analyzing and representing the discriminative information, distributed in functional Magnetic Resonance Imaging (fMRI) data, is proposed. For this purpose, a local mesh with varying size is formed around each voxel, called the seed voxel. The relationships among each seed voxel and its neighbors are estimated using a linear regression equation by minimizing the expectation of the squared error. This squared error coming from linear regression is used to calculate various info...
A novel approach to optimize workflow in grid-based teleradiology applications
Yilmaz, Ayhan Ozan; Baykal, Nazife (2016-01-01)
Background and objective: This study proposes an infrastructure with a reporting workflow optimization algorithm (RWOA) in order to interconnect facilities, reporting units and radiologists on a single access interface, to increase the efficiency of the reporting process by decreasing the medical report turnaround time and to increase the quality of medical reports by determining the optimum match between the inspection and radiologist in terms of subspecialty, workload and response time.
A robust optimization approach for the breast cancer targeted design of PEtOx-b-PLA polymersomes
Oz, Umut Can; Bolat, Zeynep Busra; Ozkose, Umut Ugur; Gulyuz, Sevgi; Kucukturkmen, Berrin; Khalily, Melek Parlak; Özçubukçu, Salih; Yilmaz, Ozgur; Telci, Dilek; ESENDAĞLI, GÜNEŞ; Sahin, Fikrettin; Bozkir, Asuman (2021-04-01)
© 2021 Elsevier B.V.The equipping of nanoparticles with the peptide moiety recognizing a particular receptor, enables cell or tissue-specific targeting, therefore the optimization of the targeted nanoparticles is a key factor in the formulation design process. In this paper, we report the optimization concept of Doxorubicin encapsulating PEtOx-b-PLA polymersome formulation equipped with Peptide18, which is a breast cancer recognizing tumor homing peptide, and the unveiling of the cell-specific delivery pote...
Citation Formats
A. Pacaci, S. Gonul, A. A. Sinaci, M. Yuksel, and G. B. Laleci Erturkmen, “A Semantic Transformation Methodology for the Secondary Use of Observational Healthcare Data in Postmarketing Safety Studies,” Frontiers in Pharmacology, 2018, Accessed: 00, 2020. [Online]. Available: https://hdl.handle.net/11511/51675.