Integration of an OWL-DL Knowledge Base with an EHR Prototype and Providing Customized Information

Jing, Xia; Kay, Stephen; Marley, Thomas; Hardiker, Nicholas R.

doi:10.1007/s10916-014-0075-4

Cited by 10 publications

(9 citation statements)

References 15 publications

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“…A couple of studies focused on the logistics process with EHR using Web Ontology Language-Description Logic (OWL-DL) [13,16]. Jing et al [13] intended to establish a standardized prototype to manage customized information from the information exchanges using manual and automatic methods. Their project developed the integration of customized information based on existing patient record and individual patient characteristics.…”

Section: Barriers In Implementing Hermentioning

confidence: 99%

A Workaround of EHR - A Logistics/Reporting System Development

Hsu

Dick

2018

Proceedings of the 51st Hawaii International Conference on System Sciences

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This project presents a use case-The Lab (TL) services multiple hospitals, medical centers, and physicians' offices in the southern area of the United States. Applying systematic methods of business process management, the project manager and development team clarify requirements, analyze the processes, develop logistics and create a reporting system for TL. The system must be designed to retrieve data with limited time and costs for an inundated EHR system. In this project, the authors try to define the logistic requirements of TL and the needs an electronic form for an information management system. For example, automate processes and eliminate waste. Besides the EHR software, the goal of this project is to improve web-based logistics and reporting system while maintaining HIPAA compliant controls. The project achieves the goals, but the workaround system is still cumbersome yet workable.

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Section: Barriers In Implementing Hermentioning

confidence: 99%

A Workaround of EHR - A Logistics/Reporting System Development

Hsu

Dick

2018

Proceedings of the 51st Hawaii International Conference on System Sciences

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“…Notably, semantic web (SW) is an extension of world wide web, and it qualifies as a Web of Data. Some of the semantic web technologies commonly used in data include but not limited to Resource Description Framework (RDF), Web Ontology Language (OWL), Simple Knowledge Organization System (SKOS), and SPARQL (Anonymous, 2014;Jing, Kay, Marley, & Hardiker, 2014;Scharffe, Zamazal, & Fensel, 2014). Despite the difference between SW and XML data format, applications and services must coexist within the web framework, and as such their interoperation is critical to the existence of applications with unfettered access to legacy systems (Zemmouchi-Ghomari, 2018).…”

Section: Introductionmentioning

confidence: 99%

The XML and Semantic Web: A Systematic Review on Technologies

Alloghani¹,

Al‐Jumeily²,

Hussain³

et al. 2019

Proceedings of the International Conferences Big Data Analytics, Data Mining and Computational Intelligence 2019; And Theory An

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The web and associated data have been around before the advent of big data and its related concepts. The semantic web refers to a Web of Data consisting of all sorts of data types and forms. In the context of Web of Data, many organizations prefer Linked Data formats for data publication, sharing and usage based on semantic web (SW) technologies. Conversely, the Extensible Markup Language (XML) is the commonly used data exchange format that the world wide web (WWW) uses today. Furthermore, innumerable international data exchange formats including Moving Picture Experts Group-7 (MPEG-7) and Institute of Electrical and Electronics Engineers Learning Object Metadata (IEEE LOM) rely on XML schema, and consequently, the web has a massive volume of XML format-based datasets. Of interest is the difference between SW and XML data models, frameworks as well as the language for implementing data queries. Hence, it is necessary to pursue interoperability and integration technologies for bridging the gap between SW and XML frameworks to ensure seamless data handling and retrieval in the web. The systematic survey used Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) methodology alongside DistillerSR to review articles addressing the interoperability and integration of XML and SW. The advanced search query focused on the article title, abstract, full text, and keywords that are related to the XML and SW technologies.

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“…We use a knowledge base prototype instead of a knowledge base because we include different levels of facts in OntoKBCF, for example, nucleotide changes, amino acid changes, and clinical phenotypes. The facts are not exhaustive at any horizontal level within OntoKBCF; however, the facts are sufficient to organize the relationships at cross-horizontal levels [8,9] and to demonstrate how to generate a knowledge resource including molecular genetics information and health information via an EHR prototype [14,15].…”

Section: Introductionmentioning

confidence: 99%

“…An overview of the project, showing how OntoKBCF supplies computable and formally represented molecular and health information to an EHR in a dynamic manner has been published previously [14], as has the technical integration of OntoKBCF and the EHR prototype [15]. A further related source [8], published at an early stage of the project, mainly describes the domain coverage of OntoKBCF.…”

Section: Introductionmentioning

confidence: 99%

Identifying Principles for the Construction of an Ontology-Based Knowledge Base: A Case Study Approach

Jing

Hardiker

Kay³

et al. 2018

JMIR Med Inform

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BackgroundOntologies are key enabling technologies for the Semantic Web. The Web Ontology Language (OWL) is a semantic markup language for publishing and sharing ontologies.ObjectiveThe supply of customizable, computable, and formally represented molecular genetics information and health information, via electronic health record (EHR) interfaces, can play a critical role in achieving precision medicine. In this study, we used cystic fibrosis as an example to build an Ontology-based Knowledge Base prototype on Cystic Fibrobis (OntoKBCF) to supply such information via an EHR prototype. In addition, we elaborate on the construction and representation principles, approaches, applications, and representation challenges that we faced in the construction of OntoKBCF. The principles and approaches can be referenced and applied in constructing other ontology-based domain knowledge bases.MethodsFirst, we defined the scope of OntoKBCF according to possible clinical information needs about cystic fibrosis on both a molecular level and a clinical phenotype level. We then selected the knowledge sources to be represented in OntoKBCF. We utilized top-to-bottom content analysis and bottom-up construction to build OntoKBCF. Protégé-OWL was used to construct OntoKBCF. The construction principles included (1) to use existing basic terms as much as possible; (2) to use intersection and combination in representations; (3) to represent as many different types of facts as possible; and (4) to provide 2-5 examples for each type. HermiT 1.3.8.413 within Protégé-5.1.0 was used to check the consistency of OntoKBCF.ResultsOntoKBCF was constructed successfully, with the inclusion of 408 classes, 35 properties, and 113 equivalent classes. OntoKBCF includes both atomic concepts (such as amino acid) and complex concepts (such as “adolescent female cystic fibrosis patient”) and their descriptions. We demonstrated that OntoKBCF could make customizable molecular and health information available automatically and usable via an EHR prototype. The main challenges include the provision of a more comprehensive account of different patient groups as well as the representation of uncertain knowledge, ambiguous concepts, and negative statements and more complicated and detailed molecular mechanisms or pathway information about cystic fibrosis.ConclusionsAlthough cystic fibrosis is just one example, based on the current structure of OntoKBCF, it should be relatively straightforward to extend the prototype to cover different topics. Moreover, the principles underpinning its development could be reused for building alternative human monogenetic diseases knowledge bases.

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Integration of an OWL-DL Knowledge Base with an EHR Prototype and Providing Customized Information

Cited by 10 publications

References 15 publications

A Workaround of EHR - A Logistics/Reporting System Development

A Workaround of EHR - A Logistics/Reporting System Development

The XML and Semantic Web: A Systematic Review on Technologies

Identifying Principles for the Construction of an Ontology-Based Knowledge Base: A Case Study Approach

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