The Infectious Disease Ontology in the Age of COVID-19

The Infectious Disease Ontology (IDO) is a suite of interoperable ontology modules that aims to provide coverage of all aspects of the infectious disease domain, including biomedical research, clinical care, and public health. IDO Core is designed to be a disease and pathogen neutral ontology, covering just those types of entities and relations that are relevant to infectious diseases generally. IDO Core is then extended by a collection of ontology modules focusing on specific diseases and pathogens. In this paper we present applications of IDO Core within various areas of infectious disease research, together with an overview of all IDO extension ontologies and the methodology on the basis of which they are built. We also survey recent developments involving IDO, including the creation of IDO Virus; the Coronaviruses Infectious Disease Ontology (CIDO); and an extension of CIDO focused on COVID-19 (IDO-CovID-19).We also discuss how these ontologies might assist in information-driven efforts to deal with the ongoing COVID-19 pandemic, to accelerate data discovery in the early stages of future pandemics, and to promote reproducibility of infectious disease research

Comprehensive Security Framework for Global Threats Analysis

Cyber criminality activities are changing and becoming more and more professional. With the growth of financial flows through the Internet and the Information System (IS), new kinds of thread arise involving complex scenarios spread within multiple IS components. The IS information modeling and Behavioral Analysis are becoming new solutions to normalize the IS information and counter these new threads. This paper presents a framework which details the principal and necessary steps for monitoring an IS. We present the architecture of the framework, i.e. an ontology of activities carried out within an IS to model security information and User Behavioral analysis. The results of the performed experiments on real data show that the modeling is effective to reduce the amount of events by 91%. The User Behavioral Analysis on uniform modeled data is also effective, detecting more than 80% of legitimate actions of attack scenarios

Automated data integration for developmental biological research

In an era exploding with genome-scale data, a major challenge for developmental biologists is how to extract significant clues from these publicly available data to benefit our studies of individual genes, and how to use them to improve our understanding of development at a systems level. Several studies have successfully demonstrated new approaches to classic developmental questions by computationally integrating various genome-wide data sets. Such computational approaches have shown great potential for facilitating research: instead of testing 20,000 genes, researchers might test 200 to the same effect. We discuss the nature and state of this art as it applies to developmental research

Use of COTS functional analysis software as an IVHM design tool for detection and isolation of UAV fuel system faults

This paper presents a new approach to the development of health management solutions which can be applied to both new and legacy platforms during the conceptual design phase. The approach involves the qualitative functional modelling of a system in order to perform an Integrated Vehicle Health Management (IVHM) design – the placement of sensors and the diagnostic rules to be used in interrogating their output. The qualitative functional analysis was chosen as a route for early assessment of failures in complex systems. Functional models of system components are required for capturing the available system knowledge used during various stages of system and IVHM design. MADe™ (Maintenance Aware Design environment), a COTS software tool developed by PHM Technology, was used for the health management design. A model has been built incorporating the failure diagrams of five failure modes for five different components of a UAV fuel system. Thus an inherent health management solution for the system and the optimised sensor set solution have been defined. The automatically generated sensor set solution also contains a diagnostic rule set, which was validated on the fuel rig for different operation modes taking into account the predicted fault detection/isolation and ambiguity group coefficients. It was concluded that when using functional modelling, the IVHM design and the actual system design cannot be done in isolation. The functional approach requires permanent input from the system designer and reliability engineers in order to construct a functional model that will qualitatively represent the real system. In other words, the physical insight should not be isolated from the failure phenomena and the diagnostic analysis tools should be able to adequately capture the experience bases. This approach has been verified on a laboratory bench top test rig which can simulate a range of possible fuel system faults. The rig is fully instrumented in order to allow benchmarking of various sensing solution for fault detection/isolation that were identified using functional analysis

Autonomic care platform for optimizing query performance

Background: As the amount of information in electronic health care systems increases, data operations get more complicated and time-consuming. Intensive Care platforms require a timely processing of data retrievals to guarantee the continuous display of recent data of patients. Physicians and nurses rely on this data for their decision making. Manual optimization of query executions has become difficult to handle due to the increased amount of queries across multiple sources. Hence, a more automated management is necessary to increase the performance of database queries. The autonomic computing paradigm promises an approach in which the system adapts itself and acts as self-managing entity, thereby limiting human interventions and taking actions. Despite the usage of autonomic control loops in network and software systems, this approach has not been applied so far for health information systems. Methods: We extend the COSARA architecture, an infection surveillance and antibiotic management service platform for the Intensive Care Unit (ICU), with self-managed components to increase the performance of data retrievals. We used real-life ICU COSARA queries to analyse slow performance and measure the impact of optimizations. Each day more than 2 million COSARA queries are executed. Three control loops, which monitor the executions and take action, have been proposed: reactive, deliberative and reflective control loops. We focus on improvements of the execution time of microbiology queries directly related to the visual displays of patients' data on the bedside screens. Results: The results show that autonomic control loops are beneficial for the optimizations in the data executions in the ICU. The application of reactive control loop results in a reduction of 8.61% of the average execution time of microbiology results. The combined application of the reactive and deliberative control loop results in an average query time reduction of 10.92% and the combination of reactive, deliberative and reflective control loops provides a reduction of 13.04%. Conclusions: We found that by controlled reduction of queries' executions the performance for the end-user can be improved. The implementation of autonomic control loops in an existing health platform, COSARA, has a positive effect on the timely data visualization for the physician and nurse

Spatial ontologies for detecting abnormal maritime behaviour

International audienceThe upsurge in piracy and the impact of recent environmental disasters have highlighted the need to improve maritime surveillance. Governmental and private initiatives have developed monitoring systems with improved acquisition and analysis capabilities. These systems rely on one major component, namely the detection of abnormal ship behaviour. This implies a detailed formalisation of expert knowledge. However, the quantity of data, the complexity of situations, the failure to take into account their spatial characteristics and the potential for the same scenario to be interpreted in different ways have proved to be significant problems. We therefore propose a new prototype for the analysis of abnormal ship behaviour. The system is based on a spatial ontology associated with a geographical inference engine. It automatically identifies suspicious vessels and associates them with probable behaviours defined by operational staff

Ontology-based data semantic management and application in IoT- and cloud-enabled smart homes

The application of emerging technologies of Internet of Things (IoT) and cloud computing have increasing the popularity of smart homes, along with which, large volumes of heterogeneous data have been generating by home entities. The representation, management and application of the continuously increasing amounts of heterogeneous data in the smart home data space have been critical challenges to the further development of smart home industry. To this end, a scheme for ontology-based data semantic management and application is proposed in this paper. Based on a smart home system model abstracted from the perspective of implementing users’ household operations, a general domain ontology model is designed by defining the correlative concepts, and a logical data semantic fusion model is designed accordingly. Subsequently, to achieve high-efficiency ontology data query and update in the implementation of the data semantic fusion model, a relational-database-based ontology data decomposition storage method is developed by thoroughly investigating existing storage modes, and the performance is demonstrated using a group of elaborated ontology data query and update operations. Comprehensively utilizing the stated achievements, ontology-based semantic reasoning with a specially designed semantic matching rule is studied as well in this work in an attempt to provide accurate and personalized home services, and the efficiency is demonstrated through experiments conducted on the developed testing system for user behavior reasoning

Exploring The Responsibilities Of Single-Inhabitant Smart Homes With Use Cases

DOI: 10.3233/AIS-2010-0076This paper makes a number of contributions to the field of requirements analysis for Smart Homes. It introduces Use Cases as a tool for exploring the responsibilities of Smart Homes and it proposes a modification of the conventional Use Case structure to suit the particular requirements of Smart Homes. It presents a taxonomy of Smart-Home-related Use Cases with seven categories. It draws on those Use Cases as raw material for developing questions and conclusions about the design of Smart Homes for single elderly inhabitants, and it introduces the SHMUC repository, a web-based repository of Use Cases related to Smart Homes that anyone can exploit and to which anyone may contribute

An Enhanced Spatial Reasoning Ontology for Maritime Anomaly Detection

International audienceAlthough originally conceived as a conceptual object for modelling knowledge, current ontologies do not make it possible to manipulate spatial knowledge. However, spatial knowledge is an essential component of any modelling specification. This problem provided the motivation for the creation of an expert system driven by an ontology. The system enables experts in the maritime domain to characterise abnormal ship behaviour based on formal semantic properties. Users are able to specify and execute spatial rules that are directly integrated into the ontology and a map interface linked to the ontology displays the results of the inferences obtained

Multi-agent-based DDoS detection on big data systems

The Hadoop framework has become the most deployed platform for processing Big Data. Despite its advantages, Hadoop s infrastructure is still deployed within the secured network perimeter because the framework lacks adequate inherent security mechanisms against various security threats. However, this approach is not sufficient for providing adequate security layer against attacks such as Distributed Denial of Service. Furthermore, current work to secure Hadoop s infrastructure against DDoS attacks is unable to provide a distributed node-level detection mechanism. This thesis presents a software agent-based framework that allows distributed, real-time intelligent monitoring and detection of DDoS attack at Hadoop s node-level. The agent s cognitive system is ingrained with cumulative sum statistical technique to analyse network utilisation and average server load and detect attacks from these measurements. The framework is a multi-agent architecture with transducer agents that interface with each Hadoop node to provide real-time detection mechanism. Moreover, the agents contextualise their beliefs by training themselves with the contextual information of each node and monitor the activities of the node to differentiate between normal and anomalous behaviours. In the experiments, the framework was exposed to TCP SYN and UDP flooding attacks during a legitimate MapReduce job on the Hadoop testbed. The experimental results were evaluated regarding performance metrics such as false-positive ratio, false-negative ratio and response time to attack. The results show that UDP and TCP SYN flooding attacks can be detected and confirmed on multiple nodes in nineteen seconds with 5.56% false-positive ration, 7.70% false-negative ratio and 91.5% success rate of detection. The results represent an improvement compare to the state-of the-ar