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

Medical data processing and analysis for remote health and activities monitoring

Recent developments in sensor technology, wearable computing, Internet of Things (IoT), and wireless communication have given rise to research in ubiquitous healthcare and remote monitoring of human\u2019s health and activities. Health monitoring systems involve processing and analysis of data retrieved from smartphones, smart watches, smart bracelets, as well as various sensors and wearable devices. Such systems enable continuous monitoring of patients psychological and health conditions by sensing and transmitting measurements such as heart rate, electrocardiogram, body temperature, respiratory rate, chest sounds, or blood pressure. Pervasive healthcare, as a relevant application domain in this context, aims at revolutionizing the delivery of medical services through a medical assistive environment and facilitates the independent living of patients. In this chapter, we discuss (1) data collection, fusion, ownership and privacy issues; (2) models, technologies and solutions for medical data processing and analysis; (3) big medical data analytics for remote health monitoring; (4) research challenges and opportunities in medical data analytics; (5) examples of case studies and practical solutions

Engineering simulations for cancer systems biology

Computer simulation can be used to inform in vivo and in vitro experimentation, enabling rapid, low-cost hypothesis generation and directing experimental design in order to test those hypotheses. In this way, in silico models become a scientific instrument for investigation, and so should be developed to high standards, be carefully calibrated and their findings presented in such that they may be reproduced. Here, we outline a framework that supports developing simulations as scientific instruments, and we select cancer systems biology as an exemplar domain, with a particular focus on cellular signalling models. We consider the challenges of lack of data, incomplete knowledge and modelling in the context of a rapidly changing knowledge base. Our framework comprises a process to clearly separate scientific and engineering concerns in model and simulation development, and an argumentation approach to documenting models for rigorous way of recording assumptions and knowledge gaps. We propose interactive, dynamic visualisation tools to enable the biological community to interact with cellular signalling models directly for experimental design. There is a mismatch in scale between these cellular models and tissue structures that are affected by tumours, and bridging this gap requires substantial computational resource. We present concurrent programming as a technology to link scales without losing important details through model simplification. We discuss the value of combining this technology, interactive visualisation, argumentation and model separation to support development of multi-scale models that represent biologically plausible cells arranged in biologically plausible structures that model cell behaviour, interactions and response to therapeutic interventions

Docker container-based big data processing system in multiple clouds for everyone

Big data processing is progressively becoming essential for everyone to extract the meaningful information from their large volume of data irrespective of types of users and their application areas. Big data processing is a broad term and includes several operations such as the storage, cleaning, organization, modelling, analysis and presentation of data at a scale and efficiency. For ordinary users, the significant challenges are the requirement of the powerful data processing system and its provisioning, installation of complex big data analytics and difficulty in their usage. Docker is a container-based virtualization technology and it has recently introduced Docker Swarm for the development of various types of multi-cloud distributed systems, which can be helpful in solving all above problems for ordinary users. However, Docker is predominantly used in the software development industry, and less focus is given to the data processing aspect of this container-based technology. Therefore, this paper proposes the Docker container-based big data processing system in multiple clouds for everyone, which explores another potential dimension of Docker for big data analysis. This Docker container-based system is an inexpensive and user-friendly framework for everyone who has the knowledge of basic IT skills. Additionally, it can be easily developed on a single machine, multiple machines or multiple clouds. This paper demonstrates the architectural design and simulated development of the proposed Docker container-based big data processing system in multiple clouds. Subsequently, it illustrates the automated provisioning of big data clusters using two popular big data analytics, Hadoop and Pachyderm (without Hadoop) including the Web-based GUI interface Hue for easy data processing in Hadoop

Process-oriented Enterprise Mashups

Mashups, a new Web 2.0 technology provide the ability for easy creation of Web-Based applications by end-users. The uses of the mashups are often consumer related. In this paper we explore how mashups can be used in the enterprise area and hat the criteria for enterprise mashups are. We provide categories for the classification of enterprise mashups, and based upon a motivating example we go further in depth on business process enterprise mashup

Challenging problems of geospatial visual analytics

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Middleware Technologies for Cloud of Things - a survey

The next wave of communication and applications rely on the new services provided by Internet of Things which is becoming an important aspect in human and machines future. The IoT services are a key solution for providing smart environments in homes, buildings and cities. In the era of a massive number of connected things and objects with a high grow rate, several challenges have been raised such as management, aggregation and storage for big produced data. In order to tackle some of these issues, cloud computing emerged to IoT as Cloud of Things (CoT) which provides virtually unlimited cloud services to enhance the large scale IoT platforms. There are several factors to be considered in design and implementation of a CoT platform. One of the most important and challenging problems is the heterogeneity of different objects. This problem can be addressed by deploying suitable "Middleware". Middleware sits between things and applications that make a reliable platform for communication among things with different interfaces, operating systems, and architectures. The main aim of this paper is to study the middleware technologies for CoT. Toward this end, we first present the main features and characteristics of middlewares. Next we study different architecture styles and service domains. Then we presents several middlewares that are suitable for CoT based platforms and lastly a list of current challenges and issues in design of CoT based middlewares is discussed.Comment: http://www.sciencedirect.com/science/article/pii/S2352864817301268, Digital Communications and Networks, Elsevier (2017

Middleware Technologies for Cloud of Things - a survey

The next wave of communication and applications rely on the new services provided by Internet of Things which is becoming an important aspect in human and machines future. The IoT services are a key solution for providing smart environments in homes, buildings and cities. In the era of a massive number of connected things and objects with a high grow rate, several challenges have been raised such as management, aggregation and storage for big produced data. In order to tackle some of these issues, cloud computing emerged to IoT as Cloud of Things (CoT) which provides virtually unlimited cloud services to enhance the large scale IoT platforms. There are several factors to be considered in design and implementation of a CoT platform. One of the most important and challenging problems is the heterogeneity of different objects. This problem can be addressed by deploying suitable "Middleware". Middleware sits between things and applications that make a reliable platform for communication among things with different interfaces, operating systems, and architectures. The main aim of this paper is to study the middleware technologies for CoT. Toward this end, we first present the main features and characteristics of middlewares. Next we study different architecture styles and service domains. Then we presents several middlewares that are suitable for CoT based platforms and lastly a list of current challenges and issues in design of CoT based middlewares is discussed.Comment: http://www.sciencedirect.com/science/article/pii/S2352864817301268, Digital Communications and Networks, Elsevier (2017

An Open System for Social Computation

Part of the power of social computation comes from using the collective intelligence of humans to tame the aggregate uncertainty of (otherwise) low veracity data obtained from human and automated sources. We have witnessed a surge in development of social computing systems but, ironically, there have been few attempts to generalise across this activity so that creation of the underlying mechanisms themselves can be made more social. We describe a method for achieving this by standardising patterns of social computation via lightweight formal specifications (we call these social artifacts) that can be connected to existing internet architectures via a single model of computation. Upon this framework we build a mechanism for extracting provenance meta-data across social computations