Ontology-driven conceptual modeling: A'systematic literature mapping and review

All rights reserved. Ontology-driven conceptual modeling (ODCM) is still a relatively new research domain in the field of information systems and there is still much discussion on how the research in ODCM should be performed and what the focus of this research should be. Therefore, this article aims to critically survey the existing literature in order to assess the kind of research that has been performed over the years, analyze the nature of the research contributions and establish its current state of the art by positioning, evaluating and interpreting relevant research to date that is related to ODCM. To understand and identify any gaps and research opportunities, our literature study is composed of both a systematic mapping study and a systematic review study. The mapping study aims at structuring and classifying the area that is being investigated in order to give a general overview of the research that has been performed in the field. A review study on the other hand is a more thorough and rigorous inquiry and provides recommendations based on the strength of the found evidence. Our results indicate that there are several research gaps that should be addressed and we further composed several research opportunities that are possible areas for future research

OntoEng: A design method for ontology engineering in information systems

This paper addresses the design problem relating to ontology engineering in the discipline of information systems. Ontology engineering is a realm that covers issues related to ontology development and use throughout its life span. Nowadays, ontology as a new innovation promises to improve the design, semantic integration, and utilization of information systems. Ontologies are the backbone of knowledge-based systems. In addition, they establish sharable and reusable common understanding of specific domains amongst people, information systems, and software agents. Notwithstanding, the ontology engineering literature does not provide adequate guidance on how to build, evaluate, and maintain ontologies. On the basis of the gathered experience during the development of V4 Telecoms Business Model Ontology as well as the conducted integration of the related literature from the design science paradigm, this paper introduces OntoEng and its application as a novel systematic design method for ontology engineering

A literature review of expert problem solving using analogy

We consider software project cost estimation from a problem solving perspective. Taking a cognitive psychological approach, we argue that the algorithmic basis for CBR tools is not representative of human problem solving and this mismatch could account for inconsistent results. We describe the fundamentals of problem solving, focusing on experts solving ill-defined problems. This is supplemented by a systematic literature review of empirical studies of expert problem solving of non-trivial problems. We identified twelve studies. These studies suggest that analogical reasoning plays an important role in problem solving, but that CBR tools do not model this in a biologically plausible way. For example, the ability to induce structure and therefore find deeper analogies is widely seen as the hallmark of an expert. However, CBR tools fail to provide support for this type of reasoning for prediction. We conclude this mismatch between experts’ cognitive processes and software tools contributes to the erratic performance of analogy-based prediction

Computerization of workflows, guidelines and care pathways: a review of implementation challenges for process-oriented health information systems

There is a need to integrate the various theoretical frameworks and formalisms for modeling clinical guidelines, workflows, and pathways, in order to move beyond providing support for individual clinical decisions and toward the provision of process-oriented, patient-centered, health information systems (HIS). In this review, we analyze the challenges in developing process-oriented HIS that formally model guidelines, workflows, and care pathways. A qualitative meta-synthesis was performed on studies published in English between 1995 and 2010 that addressed the modeling process and reported the exposition of a new methodology, model, system implementation, or system architecture. Thematic analysis, principal component analysis (PCA) and data visualisation techniques were used to identify and cluster the underlying implementation ‘challenge’ themes. One hundred and eight relevant studies were selected for review. Twenty-five underlying ‘challenge’ themes were identified. These were clustered into 10 distinct groups, from which a conceptual model of the implementation process was developed. We found that the development of systems supporting individual clinical decisions is evolving toward the implementation of adaptable care pathways on the semantic web, incorporating formal, clinical, and organizational ontologies, and the use of workflow management systems. These architectures now need to be implemented and evaluated on a wider scale within clinical settings

Using Machine Learning and Natural Language Processing to Review and Classify the Medical Literature on Cancer Susceptibility Genes

PURPOSE: The medical literature relevant to germline genetics is growing exponentially. Clinicians need tools monitoring and prioritizing the literature to understand the clinical implications of the pathogenic genetic variants. We developed and evaluated two machine learning models to classify abstracts as relevant to the penetrance (risk of cancer for germline mutation carriers) or prevalence of germline genetic mutations. METHODS: We conducted literature searches in PubMed and retrieved paper titles and abstracts to create an annotated dataset for training and evaluating the two machine learning classification models. Our first model is a support vector machine (SVM) which learns a linear decision rule based on the bag-of-ngrams representation of each title and abstract. Our second model is a convolutional neural network (CNN) which learns a complex nonlinear decision rule based on the raw title and abstract. We evaluated the performance of the two models on the classification of papers as relevant to penetrance or prevalence. RESULTS: For penetrance classification, we annotated 3740 paper titles and abstracts and used 60% for training the model, 20% for tuning the model, and 20% for evaluating the model. The SVM model achieves 89.53% accuracy (percentage of papers that were correctly classified) while the CNN model achieves 88.95 % accuracy. For prevalence classification, we annotated 3753 paper titles and abstracts. The SVM model achieves 89.14% accuracy while the CNN model achieves 89.13 % accuracy. CONCLUSION: Our models achieve high accuracy in classifying abstracts as relevant to penetrance or prevalence. By facilitating literature review, this tool could help clinicians and researchers keep abreast of the burgeoning knowledge of gene-cancer associations and keep the knowledge bases for clinical decision support tools up to date