Ontologies Applied in Clinical Decision Support System Rules:Systematic Review

BackgroundClinical decision support systems (CDSSs) are important for the quality and safety of health care delivery. Although CDSS rules guide CDSS behavior, they are not routinely shared and reused. ObjectiveOntologies have the potential to promote the reuse of CDSS rules. Therefore, we systematically screened the literature to elaborate on the current status of ontologies applied in CDSS rules, such as rule management, which uses captured CDSS rule usage data and user feedback data to tailor CDSS services to be more accurate, and maintenance, which updates CDSS rules. Through this systematic literature review, we aim to identify the frontiers of ontologies used in CDSS rules. MethodsThe literature search was focused on the intersection of ontologies; clinical decision support; and rules in PubMed, the Association for Computing Machinery (ACM) Digital Library, and the Nursing & Allied Health Database. Grounded theory and PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analyses) 2020 guidelines were followed. One author initiated the screening and literature review, while 2 authors validated the processes and results independently. The inclusion and exclusion criteria were developed and refined iteratively. ResultsCDSSs were primarily used to manage chronic conditions, alerts for medication prescriptions, reminders for immunizations and preventive services, diagnoses, and treatment recommendations among 81 included publications. The CDSS rules were presented in Semantic Web Rule Language, Jess, or Jena formats. Despite the fact that ontologies have been used to provide medical knowledge, CDSS rules, and terminologies, they have not been used in CDSS rule management or to facilitate the reuse of CDSS rules. ConclusionsOntologies have been used to organize and represent medical knowledge, controlled vocabularies, and the content of CDSS rules. So far, there has been little reuse of CDSS rules. More work is needed to improve the reusability and interoperability of CDSS rules. This review identified and described the ontologies that, despite their limitations, enable Semantic Web technologies and their applications in CDSS rules

A framework for developing engineering design ontologies within the aerospace industry

This paper presents a framework for developing engineering design ontologies within the aerospace industry. The aim of this approach is to strengthen the modularity and reuse of engineering design ontologies to support knowledge management initiatives within the aerospace industry. Successful development and effective utilisation of engineering ontologies strongly depends on the method/framework used to develop them. Ensuring modularity in ontology design is essential for engineering design activities due to the complexity of knowledge that is required to be brought together to support the product design decision-making process. The proposed approach adopts best practices from previous ontology development methods, but focuses on encouraging modular architectural ontology design. The framework is comprised of three phases namely: (1) Ontology design and development; (2) Ontology validation and (3) Implementation of ontology structure. A qualitative research methodology is employed which is composed of four phases. The first phase defines the capture of knowledge required for the framework development, followed by the ontology framework development, iterative refinement of engineering ontologies and ontology validation through case studies and experts’ opinion. The ontology-based framework is applied in the combustor and casing aerospace engineering domain. The modular ontologies developed as a result of applying the framework and are used in a case study to restructure and improve the accessibility of information on a product design information-sharing platform. Additionally, domain experts within the aerospace industry validated the strengths, benefits and limitations of the framework. Due to the modular nature of the developed ontologies, they were also employed to support other project initiatives within the case study company such as role-based computing (RBC), IT modernisation activity and knowledge management implementation across the sponsoring organisation. The major benefit of this approach is in the reduction of man-hours required for maintaining engineering design ontologies. Furthermore, this approach strengthens reuse of ontology knowledge and encourages modularity in the design and development of engineering ontologies

Combining ontologies and rules with clinical archetypes

Al igual que otros campos que dependen en gran medida de las funcionalidades ofrecidas por las tecnologías de la información y las comunicaciones (IT), la biomedicina y la salud necesitan cada vez más la implantación de normas y mecanismos ampliamente aceptados para el intercambio de datos, información y conocimiento. Dicha necesidad de compatibilidad e interoperabilidad va más allá de las cuestiones sintácticas y estructurales, pues la interoperabilidad semántica es también requerida. La interoperabilidad a nivel semántico es esencial para el soporte computarizado de alertas, flujos de trabajo y de la medicina basada en evidencia cuando contamos con la presencia de sistemas heterogéneos de Historia Clínica Electrónica (EHR). El modelo de arquetipos clínicos respaldado por el estándar CEN/ISO EN13606 y la fundación openEHR ofrece un mecanismo para expresar las estructuras de datos clínicos de manera compartida e interoperable. El modelo ha ido ganando aceptación en los últimos años por su capacidad para definir conceptos clínicos basados en un Modelo de Referencia común. Dicha separación a dos capas permite conservar la heterogeneidad de las implementaciones de almacenamiento a bajo nivel, presentes en los diferentes sistemas de EHR. Sin embargo, los lenguajes de arquetipos no soportan la representación de reglas clínicas ni el mapeo a ontologías formales, ambos elementos fundamentales para alcanzar la interoperabilidad semántica completa pues permiten llevar a cabo el razonamiento y la inferencia a partir del conocimiento clínico existente. Paralelamente, es reconocido el hecho de que la World Wide Web presenta requisitos análogos a los descritos anteriormente, lo cual ha fomentado el desarrollo de la Web Semántica. El progreso alcanzado en este terreno, con respecto a la representación del conocimiento y al razonamiento sobre el mismo, es combinado en esta tesis con los modelos de EHR con el objetivo de mejorar el enfoque de los arquetipos clínicos y ofrecer funcionalidades que se corresponden con nivel más alto de interoperabilidad semántica. Concretamente, la investigación que se describe a continuación presenta y evalúa un enfoque para traducir automáticamente las definiciones expresadas en el lenguaje de definición de arquetipos de openEHR (ADL) a una representación formal basada en lenguajes de ontologías. El método se implementa en la plataforma ArchOnt, que también es descrita. A continuación se estudia la integración de dichas representaciones formales con reglas clínicas, ofreciéndose un enfoque para reutilizar el razonamiento con instancias concretas de datos clínicos. Es importante ver como el acto de compartir el conocimiento clínico expresado a través de reglas es coherente con la filosofía de intercambio abierto fomentada por los arquetipos, a la vez que se extiende la reutilización a proposiciones de conocimiento declarativo como las utilizadas en las guías de práctica clínica. De esta manera, la tesis describe una técnica de mapeo de arquetipos a ontologías, para luego asociar reglas clínicas a la representación resultante. La traducción automática también permite la conexión formal de los elementos especificados en los arquetipos con conceptos clínicos equivalentes provenientes de otras fuentes como son las terminologías clínicas. Dichos enlaces fomentan la reutilización del conocimiento clínico ya representado, así como el razonamiento y la navegación a través de distintas ontologías clínicas. Otra contribución significativa de la tesis es la aplicación del enfoque mencionado en dos proyectos de investigación y desarrollo clínico, llevados a cabo en combinación con hospitales universitarios de Madrid. En la explicación se incluyen ejemplos de las aplicaciones más representativas del enfoque como es el caso del desarrollo de sistemas de alertas orientados a mejorar la seguridad del paciente. No obstante, la traducción automática de arquetipos clínicos a lenguajes de ontologías constituye una base común para la implementación de una amplia gama de actividades semánticas, razonamiento y validación, evitándose así la necesidad de aplicar distintos enfoques ad-hoc directamente sobre los arquetipos para poder satisfacer las condiciones de cada contexto

SNOMED CT standard ontology based on the ontology for general medical science

Background: Systematized Nomenclature of Medicine—Clinical Terms (SNOMED CT, hereafter abbreviated SCT) is acomprehensive medical terminology used for standardizing the storage, retrieval, and exchange of electronic healthdata. Some efforts have been made to capture the contents of SCT as Web Ontology Language (OWL), but theseefforts have been hampered by the size and complexity of SCT. Method: Our proposal here is to develop an upper-level ontology and to use it as the basis for defining the termsin SCT in a way that will support quality assurance of SCT, for example, by allowing consistency checks ofdefinitions and the identification and elimination of redundancies in the SCT vocabulary. Our proposed upper-levelSCT ontology (SCTO) is based on the Ontology for General Medical Science (OGMS). Results: The SCTO is implemented in OWL 2, to support automatic inference and consistency checking. Theapproach will allow integration of SCT data with data annotated using Open Biomedical Ontologies (OBO) Foundryontologies, since the use of OGMS will ensure consistency with the Basic Formal Ontology, which is the top-levelontology of the OBO Foundry. Currently, the SCTO contains 304 classes, 28 properties, 2400 axioms, and 1555annotations. It is publicly available through the bioportal athttp://bioportal.bioontology.org/ontologies/SCTO/. Conclusion: The resulting ontology can enhance the semantics of clinical decision support systems and semanticinteroperability among distributed electronic health records. In addition, the populated ontology can be used forthe automation of mobile health applications

Combining ontologies and rules with clinical archetypes

Al igual que otros campos que dependen en gran medida de las funcionalidades ofrecidas por las tecnologías de la información y las comunicaciones (IT), la biomedicina y la salud necesitan cada vez más la implantación de normas y mecanismos ampliamente aceptados para el intercambio de datos, información y conocimiento. Dicha necesidad de compatibilidad e interoperabilidad va más allá de las cuestiones sintácticas y estructurales, pues la interoperabilidad semántica es también requerida. La interoperabilidad a nivel semántico es esencial para el soporte computarizado de alertas, flujos de trabajo y de la medicina basada en evidencia cuando contamos con la presencia de sistemas heterogéneos de Historia Clínica Electrónica (EHR). El modelo de arquetipos clínicos respaldado por el estándar CEN/ISO EN13606 y la fundación openEHR ofrece un mecanismo para expresar las estructuras de datos clínicos de manera compartida e interoperable. El modelo ha ido ganando aceptación en los últimos años por su capacidad para definir conceptos clínicos basados en un Modelo de Referencia común. Dicha separación a dos capas permite conservar la heterogeneidad de las implementaciones de almacenamiento a bajo nivel, presentes en los diferentes sistemas de EHR. Sin embargo, los lenguajes de arquetipos no soportan la representación de reglas clínicas ni el mapeo a ontologías formales, ambos elementos fundamentales para alcanzar la interoperabilidad semántica completa pues permiten llevar a cabo el razonamiento y la inferencia a partir del conocimiento clínico existente. Paralelamente, es reconocido el hecho de que la World Wide Web presenta requisitos análogos a los descritos anteriormente, lo cual ha fomentado el desarrollo de la Web Semántica. El progreso alcanzado en este terreno, con respecto a la representación del conocimiento y al razonamiento sobre el mismo, es combinado en esta tesis con los modelos de EHR con el objetivo de mejorar el enfoque de los arquetipos clínicos y ofrecer funcionalidades que se corresponden con nivel más alto de interoperabilidad semántica. Concretamente, la investigación que se describe a continuación presenta y evalúa un enfoque para traducir automáticamente las definiciones expresadas en el lenguaje de definición de arquetipos de openEHR (ADL) a una representación formal basada en lenguajes de ontologías. El método se implementa en la plataforma ArchOnt, que también es descrita. A continuación se estudia la integración de dichas representaciones formales con reglas clínicas, ofreciéndose un enfoque para reutilizar el razonamiento con instancias concretas de datos clínicos. Es importante ver como el acto de compartir el conocimiento clínico expresado a través de reglas es coherente con la filosofía de intercambio abierto fomentada por los arquetipos, a la vez que se extiende la reutilización a proposiciones de conocimiento declarativo como las utilizadas en las guías de práctica clínica. De esta manera, la tesis describe una técnica de mapeo de arquetipos a ontologías, para luego asociar reglas clínicas a la representación resultante. La traducción automática también permite la conexión formal de los elementos especificados en los arquetipos con conceptos clínicos equivalentes provenientes de otras fuentes como son las terminologías clínicas. Dichos enlaces fomentan la reutilización del conocimiento clínico ya representado, así como el razonamiento y la navegación a través de distintas ontologías clínicas. Otra contribución significativa de la tesis es la aplicación del enfoque mencionado en dos proyectos de investigación y desarrollo clínico, llevados a cabo en combinación con hospitales universitarios de Madrid. En la explicación se incluyen ejemplos de las aplicaciones más representativas del enfoque como es el caso del desarrollo de sistemas de alertas orientados a mejorar la seguridad del paciente. No obstante, la traducción automática de arquetipos clínicos a lenguajes de ontologías constituye una base común para la implementación de una amplia gama de actividades semánticas, razonamiento y validación, evitándose así la necesidad de aplicar distintos enfoques ad-hoc directamente sobre los arquetipos para poder satisfacer las condiciones de cada contexto

Multi-attribute decision making with weighted description logics

We introduce a decision-theoretic framework based on Description Logics (DLs), which can be used to encode and solve single stage multi-attribute decision problems. In particular, we consider the background knowledge as a DL knowledge base where each attribute is represented by a concept, weighted by a utility value which is asserted by the user. This yields a compact representation of preferences over attributes. Moreover, we represent choices as knowledge base individuals, and induce a ranking via the aggregation of attributes that they satisfy. We discuss the benefits of the approach from a decision theory point of view. Furthermore, we introduce an implementation of the framework as a Protégé plugin called uDecide. The plugin takes as input an ontology as background knowledge, and returns the choices consistent with the user’s (the knowledge base) preferences. We describe a use case with data from DBpedia. We also provide empirical results for its performance in the size of the ontology using the reasoner Konclude

Semantic Search Engine as tool for clinical decision support in Register for Acute Coronary Syndrome

This paper presents the implementation and use of Semantic Search Engine (SSE) as part of knowledge management system functionalities in Register for Acute Coronary Syndrome (REACS). REACS SSE is part of a clinical decision support system and is used as an aid in decision making in clinical processes related to the care and treatment of patients with Acute Coronary Syndrome (ACS)

An Ontology-Based Approach for Closed-Loop Product Lifecycle Management

The main goal of the Product Lifecycle Management (PLM) is the management of all the data associated to a product during its lifecycle. Lifecycle data is being generated by events and actions (of various lifecycle agents which are humans and/or software systems) and it is distributed along the product's lifecycle phases: Beginning of Life (BOL) including design and manufacturing, Middle of Life (MOL) including usage and maintenance and End of Life (EOL) including recycling, disposal or other options. Closed-Loop PLM extends the meaning of PLM in order to close the loop of the information among the different lifecycle phases. The idea is that information of MOL could be used at the EOL stage to support deciding the most appropriate EOL option (especially to make decision for re-manufacturing and re-use) and combined with the EOL information it could be used as feedback in the BOL for improving the new generations of the product. Several PLM models have been developed utilising various technologies and methods towards providing aspects of the Closed-Loop PLM concept. Ontologies are rapidly becoming popular in various research fields. There is a tendency both in converting existing models into ontology-based models, and in creating new ontology-based models from scratch. The aim of this dissertation is to include the advantages and features provided by the ontologies into PLM models towards achieving Closed-Loop PLM. Hence, an ontology model of a Product Data and Knowledge Management Semantic Object Model for PLM has been developed. The transformation process of the model into an ontology-based one, using Web Ontology Language-Description Logic (OWL-DL), is described in detail. The background and the motives for converting existing PLM models to ontologies are also provided. The new model facilitates several of the OWL-DL capabilities, while maintaining previously achieved characteristics. Furthermore, case studies based on various application scenarios, are presented. These case studies deal with data integration and interoperability problems, in which a significant number of reasoning capabilities is implemented, and highlight the utilisation of the developed model. Moreover, in this work, a generic concept has been developed, tackling the time treatment in PLM models. Time is the only fundamental dimension which exists along the entire life of an artefact and it affects all artefacts and their qualities. Most commonly in PLM models, time is an attribute in parts such as "activities" and "events" or is a separate part of the model ("four dimensional models"). In this work the concept is that time should not be one part of the model, but it should be the basis of the model, and all other elements should be parts of it. Thus, we introduce the "Duration of Time concept". According to this concept all aspects and elements of a model are parts of time. Case studies demonstrate the applicability and the advantages of the concept in comparison to existing methodologies

Ontology-based solutions for interoperability among product lifecycle management systems: A systematic literature review

During recent years, globalization has had an impact on the competitive capacity of industries, forcing them to integrate their productive processes with other, geographically distributed, facilities. This requires the information systems that support such processes to interoperate. Significant attention has been paid to the development of ontology-based solutions, which are meant to tackle issues from inconsistency to semantic interoperability and knowledge reusability. This paper looks into how the available technology, models and ontology-based solutions might interact within the manufacturing industry environment to achieve semantic interoperability among industrial information systems. Through a systematic literature review, this paper has aimed to identify the most relevant elements to consider in the development of an ontology-based solution and how these solutions are being deployed in industry. The research analyzed 54 studies in alignment with the specific requirements of our research questions. The most relevant results show that ontology-based solutions can be set up using OWL as the ontology language, Protégé as the ontology modeling tool, Jena as the application programming interface to interact with the built ontology, and different standards from the International Organization for Standardization Technical Committee 184, Subcommittee 4 or 5, to get the foundational concepts, axioms, and relationships to develop the knowledge base. We believe that the findings of this study make an important contribution to practitioners and researchers as they provide useful information about different projects and choices involved in undertaking projects in the field of industrial ontology application.Fil: Fraga, Alvaro Luis. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Santa Fe. Instituto de Desarrollo y Diseño. Universidad Tecnológica Nacional. Facultad Regional Santa Fe. Instituto de Desarrollo y Diseño; ArgentinaFil: Vegetti, Maria Marcela. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Santa Fe. Instituto de Desarrollo y Diseño. Universidad Tecnológica Nacional. Facultad Regional Santa Fe. Instituto de Desarrollo y Diseño; ArgentinaFil: Leone, Horacio Pascual. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Santa Fe. Instituto de Desarrollo y Diseño. Universidad Tecnológica Nacional. Facultad Regional Santa Fe. Instituto de Desarrollo y Diseño; Argentin

An Ontology Centric Architecture For Mediating Interactions In Semantic Web-Based E-Commerce Environments

Information freely generated, widely distributed and openly interpreted is a rich source of creative energy in the digital age that we live in. As we move further into this irrevocable relationship with self-growing and actively proliferating information spaces, we are also finding ourselves overwhelmed, disheartened and powerless in the presence of so much information. We are at a point where, without domain familiarity or expert guidance, sifting through the copious volumes of information to find relevance quickly turns into a mundane task often requiring enormous patience. The realization of accomplishment soon turns into a matter of extensive cognitive load, serendipity or just plain luck. This dissertation describes a theoretical framework to analyze user interactions based on mental representations in a medium where the nature of the problem-solving task emphasizes the interaction between internal task representation and the external problem domain. The framework is established by relating to work in behavioral science, sociology, cognitive science and knowledge engineering, particularly Herbert Simon’s (1957; 1989) notion of satisficing on bounded rationality and Schön’s (1983) reflective model. Mental representations mediate situated actions in our constrained digital environment and provide the opportunity for completing a task. Since assistive aids to guide situated actions reduce complexity in the task environment (Vessey 1991; Pirolli et al. 1999), the framework is used as the foundation for developing mediating structures to express the internal, external and mental representations. Interaction aids superimposed on mediating structures that model thought and action will help to guide the “perpetual novice” (Borgman 1996) through the vast digital information spaces by orchestrating better cognitive fit between the task environment and the task solution. This dissertation presents an ontology centric architecture for mediating interactions is presented in a semantic web based e-commerce environment. The Design Science approach is applied for this purpose. The potential of the framework is illustrated as a functional model by using it to model the hierarchy of tasks in a consumer decision-making process as it applies in an e-commerce setting. Ontologies are used to express the perceptual operations on the external task environment, the intuitive operations on the internal task representation, and the constraint satisfaction and situated actions conforming to reasoning from the cognitive fit. It is maintained that actions themselves cannot be enforced, but when the meaning from mental imagery and the task environment are brought into coordination, it leads to situated actions that change the present situation into one closer to what is desired. To test the usability of the ontologies we use the Web Ontology Language (OWL) to express the semantics of the three representations. We also use OWL to validate the knowledge representations and to make rule-based logical inferences on the ontological semantics. An e-commerce application was also developed to show how effective guidance can be provided by constructing semantically rich target pages from the knowledge manifested in the ontologies