The development of non-coding RNA ontology

Identification of non-coding RNAs (ncRNAs) has been significantly improved over the past decade. On the other hand, semantic annotation of ncRNA data is facing critical challenges due to the lack of a comprehensive ontology to serve as common data elements and data exchange standards in the field. We developed the Non-Coding RNA Ontology (NCRO) to handle this situation. By providing a formally defined ncRNA controlled vocabulary, the NCRO aims to fill a specific and highly needed niche in semantic annotation of large amounts of ncRNA biological and clinical data

An Ontology-Based Interpretable Fuzzy Decision Support System for Diabetes Diagnosis

Diabetes is a serious chronic disease. The importance of clinical decision support systems (CDSSs) to diagnose diabetes has led to extensive research efforts to improve the accuracy, applicability, interpretability, and interoperability of these systems. However, this problem continues to require optimization. Fuzzy rule-based systems are suitable for the medical domain, where interpretability is a main concern. The medical domain is data-intensive, and using electronic health record data to build the FRBS knowledge base and fuzzy sets is critical. Multiple variables are frequently required to determine a correct and personalized diagnosis, which usually makes it difficult to arrive at accurate and timely decisions. In this paper, we propose and implement a new semantically interpretable FRBS framework for diabetes diagnosis. The framework uses multiple aspects of knowledge-fuzzy inference, ontology reasoning, and a fuzzy analytical hierarchy process (FAHP) to provide a more intuitive and accurate design. First, we build a two-layered hierarchical and interpretable FRBS; then, we improve this by integrating an ontology reasoning process based on SNOMED CT standard ontology. We incorporate FAHP to determine the relative medical importance of each sub-FRBS. The proposed system offers numerous unique and critical improvements regarding the implementation of an accurate, dynamic, semantically intelligent, and interpretable CDSS. The designed system considers the ontology semantic similarity of diabetes complications and symptoms concepts in the fuzzy rules' evaluation process. The framework was tested using a real data set, and the results indicate how the proposed system helps physicians and patients to accurately diagnose diabetes mellitusThis work was supported by National Research Foundation of Korea-Grant funded by the Korean Government (Ministry of Science, ICT and Future Planning)-NRF-2017R1A2B2012337)S

Automatic Generation of Personalized Recommendations in eCoaching

Denne avhandlingen omhandler eCoaching for personlig livsstilsstøtte i sanntid ved bruk av informasjons- og kommunikasjonsteknologi. Utfordringen er å designe, utvikle og teknisk evaluere en prototyp av en intelligent eCoach som automatisk genererer personlige og evidensbaserte anbefalinger til en bedre livsstil. Den utviklede løsningen er fokusert på forbedring av fysisk aktivitet. Prototypen bruker bærbare medisinske aktivitetssensorer. De innsamlede data blir semantisk representert og kunstig intelligente algoritmer genererer automatisk meningsfulle, personlige og kontekstbaserte anbefalinger for mindre stillesittende tid. Oppgaven bruker den veletablerte designvitenskapelige forskningsmetodikken for å utvikle teoretiske grunnlag og praktiske implementeringer. Samlet sett fokuserer denne forskningen på teknologisk verifisering snarere enn klinisk evaluering.publishedVersio

A Novel Ontology and Machine Learning Driven Hybrid Clinical Decision Support Framework for Cardiovascular Preventative Care

Clinical risk assessment of chronic illnesses is a challenging and complex task which requires the utilisation of standardised clinical practice guidelines and documentation procedures in order to ensure consistent and efficient patient care. Conventional cardiovascular decision support systems have significant limitations, which include the inflexibility to deal with complex clinical processes, hard-wired rigid architectures based on branching logic and the inability to deal with legacy patient data without significant software engineering work. In light of these challenges, we are proposing a novel ontology and machine learning-driven hybrid clinical decision support framework for cardiovascular preventative care. An ontology-inspired approach provides a foundation for information collection, knowledge acquisition and decision support capabilities and aims to develop context sensitive decision support solutions based on ontology engineering principles. The proposed framework incorporates an ontology-driven clinical risk assessment and recommendation system (ODCRARS) and a Machine Learning Driven Prognostic System (MLDPS), integrated as a complete system to provide a cardiovascular preventative care solution. The proposed clinical decision support framework has been developed under the close supervision of clinical domain experts from both UK and US hospitals and is capable of handling multiple cardiovascular diseases. The proposed framework comprises of two novel key components: (1) ODCRARS (2) MLDPS. The ODCRARS is developed under the close supervision of consultant cardiologists Professor Calum MacRae from Harvard Medical School and Professor Stephen Leslie from Raigmore Hospital in Inverness, UK. The ODCRARS comprises of various components, which include: (a) Ontology-driven intelligent context-aware information collection for conducting patient interviews which are driven through a novel clinical questionnaire ontology. (b) A patient semantic profile, is generated using patient medical records which are collated during patient interviews (conducted through an ontology-driven context aware adaptive information collection component). The semantic transformation of patients’ medical data is carried out through a novel patient semantic profile ontology in order to give patient data an intrinsic meaning and alleviate interoperability issues with third party healthcare systems. (c) Ontology driven clinical decision support comprises of a recommendation ontology and a NICE/Expert driven clinical rules engine. The recommendation ontology is developed using clinical rules provided by the consultant cardiologist from the US hospital. The recommendation ontology utilises the patient semantic profile for lab tests and medication recommendation. A clinical rules engine is developed to implement a cardiac risk assessment mechanism for various cardiovascular conditions. The clinical rules engine is also utilised to control the patient flow within the integrated cardiovascular preventative care solution. The machine learning-driven prognostic system is developed in an iterative manner using state of the art feature selection and machine learning techniques. A prognostic model development process is exploited for the development of MLDPS based on clinical case studies in the cardiovascular domain. An additional clinical case study in the breast cancer domain is also carried out for the development and validation purposes. The prognostic model development process is general enough to handle a variety of healthcare datasets which will enable researchers to develop cost effective and evidence based clinical decision support systems. The proposed clinical decision support framework also provides a learning mechanism based on machine learning techniques. Learning mechanism is provided through exchange of patient data amongst the MLDPS and the ODCRARS. The machine learning-driven prognostic system is validated using Raigmore Hospital's RACPC, heart disease and breast cancer clinical case studies

Mobile Health in Remote Patient Monitoring for Chronic Diseases: Principles, Trends, and Challenges

Chronic diseases are becoming more widespread. Treatment and monitoring of these diseases require going to hospitals frequently, which increases the burdens of hospitals and patients. Presently, advancements in wearable sensors and communication protocol contribute to enriching the healthcare system in a way that will reshape healthcare services shortly. Remote patient monitoring (RPM) is the foremost of these advancements. RPM systems are based on the collection of patient vital signs extracted using invasive and noninvasive techniques, then sending them in real-time to physicians. These data may help physicians in taking the right decision at the right time. The main objective of this paper is to outline research directions on remote patient monitoring, explain the role of AI in building RPM systems, make an overview of the state of the art of RPM, its advantages, its challenges, and its probable future directions. For studying the literature, five databases have been chosen (i.e., science direct, IEEE-Explore, Springer, PubMed, and science.gov). We followed the (Preferred Reporting Items for Systematic Reviews and Meta-Analyses) PRISMA, which is a standard methodology for systematic reviews and meta-analyses. A total of 56 articles are reviewed based on the combination of a set of selected search terms including RPM, data mining, clinical decision support system, electronic health record, cloud computing, internet of things, and wireless body area network. The result of this study approved the effectiveness of RPM in improving healthcare delivery, increase diagnosis speed, and reduce costs. To this end, we also present the chronic disease monitoring system as a case study to provide enhanced solutions for RPMsThis research work was partially supported by the Sejong University Research Faculty Program (20212023)S

The 3rd DBCLS BioHackathon: improving life science data integration with Semantic Web technologies.

BACKGROUND: BioHackathon 2010 was the third in a series of meetings hosted by the Database Center for Life Sciences (DBCLS) in Tokyo, Japan. The overall goal of the BioHackathon series is to improve the quality and accessibility of life science research data on the Web by bringing together representatives from public databases, analytical tool providers, and cyber-infrastructure researchers to jointly tackle important challenges in the area of in silico biological research. RESULTS: The theme of BioHackathon 2010 was the 'Semantic Web', and all attendees gathered with the shared goal of producing Semantic Web data from their respective resources, and/or consuming or interacting those data using their tools and interfaces. We discussed on topics including guidelines for designing semantic data and interoperability of resources. We consequently developed tools and clients for analysis and visualization. CONCLUSION: We provide a meeting report from BioHackathon 2010, in which we describe the discussions, decisions, and breakthroughs made as we moved towards compliance with Semantic Web technologies - from source provider, through middleware, to the end-consumer.RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are