The OWL Reasoner Evaluation (ORE) 2015 Competition Report

Ontology Learning Applications of Knowledge Base Construction for Microelectronic Systems Information

Knowledge base construction (KBC) using AI has been one of the key goals of this highly popular technology since its emergence, as it helps to comprehend everything, including relations, around us. The construction of knowledge bases can summarize a piece of text in a machine-processable and understandable way. This can prove to be valuable and assistive to knowledge engineers. In this paper, we present the application of natural language processing in the construction of knowledge bases. We demonstrate how a trained bidirectional long short-term memory or bi-LSTM neural network model can be used to construct knowledge bases in accordance with the exact ISO26262 definitions as defined in the GENIAL! Basic Ontology. We provide the system with an electronic text document from the microelectronics domain and the system attempts to create a knowledge base from the available information in textual format. This information is then expressed in the form of graphs when queried by the user. This method of information retrieval presents the user with a much more technical and comprehensive understanding of an expert piece of text. This is achieved by applying the process of named entity recognition (NER) for knowledge extraction. This paper provides a result report of the current status of our knowledge construction process and knowledge base content, as well as describes our challenges and experiences.

Ontologies Applied in Clinical Decision Support System Rules: Systematic Review

BACKGROUND

Clinical 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.

OBJECTIVE

Ontologies 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.

METHODS

The 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.

RESULTS

CDSSs 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.

CONCLUSIONS

Ontologies 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.

An Automatic Ontology-Based Approach to Support Logical Representation of Observable and Measurable Data for Healthy Lifestyle Management: Proof-of-Concept Study

Background

Lifestyle diseases, because of adverse health behavior, are the foremost cause of death worldwide. An eCoach system may encourage individuals to lead a healthy lifestyle with early health risk prediction, personalized recommendation generation, and goal evaluation. Such an eCoach system needs to collect and transform distributed heterogenous health and wellness data into meaningful information to train an artificially intelligent health risk prediction model. However, it may produce a data compatibility dilemma. Our proposed eHealth ontology can increase interoperability between different heterogeneous networks, provide situation awareness, help in data integration, and discover inferred knowledge. This “proof-of-concept” study will help sensor, questionnaire, and interview data to be more organized for health risk prediction and personalized recommendation generation targeting obesity as a study case.

Objective

The aim of this study is to develop an OWL-based ontology (UiA eHealth Ontology/UiAeHo) model to annotate personal, physiological, behavioral, and contextual data from heterogeneous sources (sensor, questionnaire, and interview), followed by structuring and standardizing of diverse descriptions to generate meaningful, practical, personalized, and contextual lifestyle recommendations based on the defined rules.

Methods

We have developed a simulator to collect dummy personal, physiological, behavioral, and contextual data related to artificial participants involved in health monitoring. We have integrated the concepts of “Semantic Sensor Network Ontology” and “Systematized Nomenclature of Medicine—Clinical Terms” to develop our proposed eHealth ontology. The ontology has been created using Protégé (version 5.x). We have used the Java-based “Jena Framework” (version 3.16) for building a semantic web application that includes resource description framework (RDF) application programming interface (API), OWL API, native tuple store (tuple database), and the SPARQL (Simple Protocol and RDF Query Language) query engine. The logical and structural consistency of the proposed ontology has been evaluated with the “HermiT 1.4.3.x” ontology reasoner available in Protégé 5.x.

Results

The proposed ontology has been implemented for the study case “obesity.” However, it can be extended further to other lifestyle diseases. “UiA eHealth Ontology” has been constructed using logical axioms, declaration axioms, classes, object properties, and data properties. The ontology can be visualized with “Owl Viz,” and the formal representation has been used to infer a participant’s health status using the “HermiT” reasoner. We have also developed a module for ontology verification that behaves like a rule-based decision support system to predict the probability for health risk, based on the evaluation of the results obtained from SPARQL queries. Furthermore, we discussed the potential lifestyle recommendation generation plan against adverse behavioral risks.

Conclusions

This study has led to the creation of a meaningful, context-specific ontology to model massive, unintuitive, raw, unstructured observations for health and wellness data (eg, sensors, interviews, questionnaires) and to annotate them with semantic metadata to create a compact, intelligible abstraction for health risk predictions for individualized recommendation generation.

Developing an ontology for representing the domain knowledge specific to non-pharmacological treatment for agitation in dementia

INTRODUCTION

A large volume of clinical care data has been generated for managing agitation in dementia. However, the valuable information in these data has not been used effectively to generate insights for improving the quality of care. Application of artificial intelligence technologies offers us enormous opportunities to reuse these data. For health data science to achieve this, this study focuses on using ontology to coding clinical knowledge for non-pharmacological treatment of agitation in a machine-readable format.

METHODS

The resultant ontology-Dementia-Related Agitation Non-Pharmacological Treatment Ontology (DRANPTO)-was developed using a method adopted from the NeOn methodology.

RESULTS

DRANPTO consisted of 569 concepts and 48 object properties. It meets the standards for biomedical ontology.

DISCUSSION

DRANPTO is the first comprehensive semantic representation of non-pharmacological management for agitation in dementia in the long-term care setting. As a knowledge base, it will play a vital role to facilitate the development of intelligent systems for managing agitation in dementia.

LETHE: Forgetting and Uniform Interpolation for Expressive Description Logics

Uniform interpolation and forgetting describe the task of projecting a given ontology into a user-specified vocabulary, that is, of computing a new ontology that only uses names from a specified set of names, while preserving all logical entailments that can be expressed with those names. This is useful for ontology analysis, ontology reuse and privacy. Lethe is a tool for performing uniform interpolation on ontologies in expressive description logics, and it can be used from the command line, using a graphical interface, and as a Java library. It furthermore implements methods for computing logical difference and performing abduction using uniform interpolation. We present the tool together with an evaluation on a varied corpus of realistic ontologies.

Ontology-Based Model to Support Ubiquitous Healthcare Systems for COPD Patients

Over the past 30 years, information technology has gradually transformed the way health care is provisioned for patients. Chronic Obstructive Pulmonary Disease (COPD) is an incurable malady that threatens the lives of millions around the world. The huge amount of medical information in terms of complex interdependence between progression of health problems and various other factors makes the representation of data more challenging. This study investigated how formal semantic standards could be used for building an ontology knowledge repository to provide ubiquitous healthcare and medical recommendations for COPD patient to reduce preventable harm. The novel contribution of the suggested framework resides in the patient-centered monitoring approach, as we work to create dynamic adaptive protection services according to the current context of patient. This work executes a sequential modular approach consisting of patient, disease, location, devices, activities, environment and services to deliver personalized real-time medical care for COPD patients. The main benefits of this project are: (1) adhering to dynamic safe boundaries for the vital signs, which may vary depending on multiple factors; (2) assessing environmental risk factors; and (3) evaluating the patient’s daily activities through scheduled events to avoid potentially dangerous situations. This solution implements an interrelated set of ontologies with a logical base of Semantic Web Rule Language (SWRL) rules derived from the medical guidelines and expert pneumologists to handle all contextual situations.

Extending XNAT Platform with an Incremental Semantic Framework

Informatics increases the yield from neuroscience due to improved data. Data sharing and accessibility enable joint efforts between different research groups, as well as replication studies, pivotal for progress in the field. Research data archiving solutions are evolving rapidly to address these necessities, however, distributed data integration is still difficult because of the need of explicit agreements for disparate data models. To address these problems, ontologies are widely used in biomedical research to obtain common vocabularies and logical descriptions, but its application may suffer from scalability issues, domain bias, and loss of low-level data access. With the aim of improving the application of semantic models in biobanking systems, an incremental semantic framework that takes advantage of the latest advances in biomedical ontologies and the XNAT platform is designed and implemented. We follow a layered architecture that allows the alignment of multi-domain biomedical ontologies to manage data at different levels of abstraction. To illustrate this approach, the development is integrated in the JPND (EU Joint Program for Neurodegenerative Disease) APGeM project, focused on finding early biomarkers for Alzheimer's and other dementia related diseases.