Controlled vocabularies and semantics in systems biology

The use of computational modeling to describe and analyze biological systems is at the heart of systems biology. Model structures, simulation descriptions and numerical results can be encoded in structured formats, but there is an increasing need to provide an additional semantic layer. Semantic information adds meaning to components of structured descriptions to help identify and interpret them unambiguously. Ontologies are one of the tools frequently used for this purpose. We describe here three ontologies created specifically to address the needs of the systems biology community. The Systems Biology Ontology (SBO) provides semantic information about the model components. The Kinetic Simulation Algorithm Ontology (KiSAO) supplies information about existing algorithms available for the simulation of systems biology models, their characterization and interrelationships. The Terminology for the Description of Dynamics (TEDDY) categorizes dynamical features of the simulation results and general systems behavior. The provision of semantic information extends a model's longevity and facilitates its reuse. It provides useful insight into the biology of modeled processes, and may be used to make informed decisions on subsequent simulation experiments

Context Aware Computing for The Internet of Things: A Survey

As we are moving towards the Internet of Things (IoT), the number of sensors deployed around the world is growing at a rapid pace. Market research has shown a significant growth of sensor deployments over the past decade and has predicted a significant increment of the growth rate in the future. These sensors continuously generate enormous amounts of data. However, in order to add value to raw sensor data we need to understand it. Collection, modelling, reasoning, and distribution of context in relation to sensor data plays critical role in this challenge. Context-aware computing has proven to be successful in understanding sensor data. In this paper, we survey context awareness from an IoT perspective. We present the necessary background by introducing the IoT paradigm and context-aware fundamentals at the beginning. Then we provide an in-depth analysis of context life cycle. We evaluate a subset of projects (50) which represent the majority of research and commercial solutions proposed in the field of context-aware computing conducted over the last decade (2001-2011) based on our own taxonomy. Finally, based on our evaluation, we highlight the lessons to be learnt from the past and some possible directions for future research. The survey addresses a broad range of techniques, methods, models, functionalities, systems, applications, and middleware solutions related to context awareness and IoT. Our goal is not only to analyse, compare and consolidate past research work but also to appreciate their findings and discuss their applicability towards the IoT.Comment: IEEE Communications Surveys & Tutorials Journal, 201

Architecture-Driven Semantic Analysis of Embedded Systems (Eds) Dagstuhl Seminar 12272

Architectural modeling of complex embedded systems is gaining prominence in recent years, both in academia and in industry. An architectural model represents components in a distributed system as boxes with well-defined interfaces, connections between ports on component interfaces, and specifies component properties that can be used in analytical reasoning about the model. Models are hierarchically organized, so that each box can contain another system inside, with its own set of boxes and connections between them. The goal of Dagstuhl Seminar 12272 “Architecture-Driven Semantic Analysis of Embedded Systems” is to bring together researchers who are interested in defining precise semantics of an architecture description language and using it for building tools that generate analytical models from architectural ones, as well as generate code and configuration scripts for the system. This report documents the program and the outcomes of the presentations and working groups held during the seminar

UK utility data integration: overcoming schematic heterogeneity

In this paper we discuss syntactic, semantic and schematic issues which inhibit the integration of utility data in the UK. We then focus on the techniques employed within the VISTA project to overcome schematic heterogeneity. A Global Schema based architecture is employed. Although automated approaches to Global Schema definition were attempted the heterogeneities of the sector were too great. A manual approach to Global Schema definition was employed. The techniques used to define and subsequently map source utility data models to this schema are discussed in detail. In order to ensure a coherent integrated model, sub and cross domain validation issues are then highlighted. Finally the proposed framework and data flow for schematic integration is introduced

ERIGrid Holistic Test Description for Validating Cyber-Physical Energy Systems

Smart energy solutions aim to modify and optimise the operation of existing energy infrastructure. Such cyber-physical technology must be mature before deployment to the actual infrastructure, and competitive solutions will have to be compliant to standards still under development. Achieving this technology readiness and harmonisation requires reproducible experiments and appropriately realistic testing environments. Such testbeds for multi-domain cyber-physical experiments are complex in and of themselves. This work addresses a method for the scoping and design of experiments where both testbed and solution each require detailed expertise. This empirical work first revisited present test description approaches, developed a newdescription method for cyber-physical energy systems testing, and matured it by means of user involvement. The new Holistic Test Description (HTD) method facilitates the conception, deconstruction and reproduction of complex experimental designs in the domains of cyber-physical energy systems. This work develops the background and motivation, offers a guideline and examples to the proposed approach, and summarises experience from three years of its application.This work received funding in the European Community’s Horizon 2020 Program (H2020/2014–2020) under project “ERIGrid” (Grant Agreement No. 654113)

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

Machine Learning in Falls Prediction; A cognition-based predictor of falls for the acute neurological in-patient population

Background Information: Falls are associated with high direct and indirect costs, and significant morbidity and mortality for patients. Pathological falls are usually a result of a compromised motor system, and/or cognition. Very little research has been conducted on predicting falls based on this premise. Aims: To demonstrate that cognitive and motor tests can be used to create a robust predictive tool for falls. Methods: Three tests of attention and executive function (Stroop, Trail Making, and Semantic Fluency), a measure of physical function (Walk-12), a series of questions (concerning recent falls, surgery and physical function) and demographic information were collected from a cohort of 323 patients at a tertiary neurological center. The principal outcome was a fall during the in-patient stay (n = 54). Data-driven, predictive modelling was employed to identify the statistical modelling strategies which are most accurate in predicting falls, and which yield the most parsimonious models of clinical relevance. Results: The Trail test was identified as the best predictor of falls. Moreover, addition of any others variables, to the results of the Trail test did not improve the prediction (Wilcoxon signed-rank p < .001). The best statistical strategy for predicting falls was the random forest (Wilcoxon signed-rank p < .001), based solely on results of the Trail test. Tuning of the model results in the following optimized values: 68% (+- 7.7) sensitivity, 90% (+- 2.3) specificity, with a positive predictive value of 60%, when the relevant data is available. Conclusion: Predictive modelling has identified a simple yet powerful machine learning prediction strategy based on a single clinical test, the Trail test. Predictive evaluation shows this strategy to be robust, suggesting predictive modelling and machine learning as the standard for future predictive tools