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

A middleware for creating physical mashups of things

Indexación: Scopus.Nowadays, “things” deployed in cities are crucial to gather data to support decision making systems. Unfortunately, there is a low level of reuse of “things” between smart city applications of different organizations because “things” were unknown to developers or because it was harder to reuse them than use new ones due to technical details. In this ongoing work, we propose to convert “things” into active entities capable of discovering and organizing themselves driven by the applications goals’ satisfaction. Moreover, “things” are capable of collaborating between them in order to satisfy or maintain satisfied the published goals of applications. To validate the feasibility of our proposal, we are building mashThings, an Internet of Things (IoT) platform to build smart city applications as physical mashups, where the middleware layer is augmented by a multiagent layer of broker agents representing the available “things” in the city.http://ceur-ws.org/Vol-1950/paper11.pd

Agent-based modeling: a systematic assessment of use cases and requirements for enhancing pharmaceutical research and development productivity.

A crisis continues to brew within the pharmaceutical research and development (R&D) enterprise: productivity continues declining as costs rise, despite ongoing, often dramatic scientific and technical advances. To reverse this trend, we offer various suggestions for both the expansion and broader adoption of modeling and simulation (M&S) methods. We suggest strategies and scenarios intended to enable new M&S use cases that directly engage R&D knowledge generation and build actionable mechanistic insight, thereby opening the door to enhanced productivity. What M&S requirements must be satisfied to access and open the door, and begin reversing the productivity decline? Can current methods and tools fulfill the requirements, or are new methods necessary? We draw on the relevant, recent literature to provide and explore answers. In so doing, we identify essential, key roles for agent-based and other methods. We assemble a list of requirements necessary for M&S to meet the diverse needs distilled from a collection of research, review, and opinion articles. We argue that to realize its full potential, M&S should be actualized within a larger information technology framework--a dynamic knowledge repository--wherein models of various types execute, evolve, and increase in accuracy over time. We offer some details of the issues that must be addressed for such a repository to accrue the capabilities needed to reverse the productivity decline

Thirty years of artificial intelligence in medicine (AIME) conferences: A review of research themes

Over the past 30 years, the international conference on Artificial Intelligence in MEdicine (AIME) has been organized at different venues across Europe every 2 years, establishing a forum for scientific exchange and creating an active research community. The Artificial Intelligence in Medicine journal has published theme issues with extended versions of selected AIME papers since 1998

Modeling and Analyzing Systemic Risk in Complex Sociotechnical Systems The Role of Teleology, Feedback, and Emergence

Recent systemic failures such as the BP Deepwater Horizon Oil Spill, Global Financial Crisis, and Northeast Blackout have reminded us, once again, of the fragility of complex sociotechnical systems. Although the failures occurred in very different domains and were triggered by different events, there are, however, certain common underlying mechanisms of abnormalities driving these systemic failures. Understanding these mechanisms is essential to avoid such disasters in the future. Moreover, these disasters happened in sociotechnical systems, where both social and technical elements can interact with each other and with the environment. The nonlinear interactions among these components can lead to an “emergent” behavior – i.e., the behavior of the whole is more than the sum of its parts – that can be difficult to anticipate and control. Abnormalities can propagate through the systems to cause systemic failures. To ensure the safe operation and production of such complex systems, we need to understand and model the associated systemic risk. Traditional emphasis of chemical engineering risk modeling is on the technical components of a chemical plant, such as equipment and processes. However, a chemical plant is more than a set of equipment and processes, with the human elements playing a critical role in decision-making. Industrial statistics show that about 70% of the accidents are caused by human errors. So, new modeling techniques that go beyond the classical equipment/process-oriented approaches to include the human elements (i.e., the “socio” part of the sociotechnical systems) are needed for analyzing systemic risk of complex sociotechnical systems. This thesis presents such an approach. This thesis presents a new knowledge modeling paradigm for systemic risk analysis that goes beyond chemical plants by unifying different perspectives. First, we develop a unifying teleological, control theoretic framework to model decision-making knowledge in a complex system. The framework allows us to identify systematically the common failure mechanisms behind systemic failures in different domains. We show how cause-and-effect knowledge can be incorporated into this framework by using signed directed graphs. We also develop an ontology-driven knowledge modeling component and show how this can support decision-making by using a case study in public health emergency. This is the first such attempt to develop an ontology for public health documents. Lastly, from a control-theoretic perspective, we address the question, “how do simple individual components of a system interact to produce a system behavior that cannot be explained by the behavior of just the individual components alone?” Through this effort, we attempt to bridge the knowledge gap between control theory and complexity science

A model-driven approach for facilitating user-friendly design of complex event patterns

Complex Event Processing (CEP) is an emerging technology which allows us to efficiently process and correlate huge amounts of data in order to discover relevant or critical situations of interest (complex events) for a specific domain. This technology requires domain experts to define complex event patterns, where the conditions to be detected are specified by means of event processing languages. However, these experts face the handicap of defining such patterns with editors which are not user-friendly enough. To solve this problem, a model-driven approach for facilitating user-friendly design of complex event patterns is proposed and developed in this paper. Besides, the proposal has been applied to different domains and several event processing languages have been compared. As a result, we can affirm that the presented approach is independent both of the domain where CEP technology has to be applied to and of the concrete event processing language required for defining event patterns

Developing a distributed electronic health-record store for India

The DIGHT project is addressing the problem of building a scalable and highly available information store for the Electronic Health Records (EHRs) of the over one billion citizens of India

A Middleware framework for self-adaptive large scale distributed services

Modern service-oriented applications demand the ability to adapt to changing conditions and unexpected situations while maintaining a required QoS. Existing self-adaptation approaches seem inadequate to address this challenge because many of their assumptions are not met on the large-scale, highly dynamic infrastructures where these applications are generally deployed on. The main motivation of our research is to devise principles that guide the construction of large scale self-adaptive distributed services. We aim to provide sound modeling abstractions based on a clear conceptual background, and their realization as a middleware framework that supports the development of such services. Taking the inspiration from the concepts of decentralized markets in economics, we propose a solution based on three principles: emergent self-organization, utility driven behavior and model-less adaptation. Based on these principles, we designed Collectives, a middleware framework which provides a comprehensive solution for the diverse adaptation concerns that rise in the development of distributed systems. We tested the soundness and comprehensiveness of the Collectives framework by implementing eUDON, a middleware for self-adaptive web services, which we then evaluated extensively by means of a simulation model to analyze its adaptation capabilities in diverse settings. We found that eUDON exhibits the intended properties: it adapts to diverse conditions like peaks in the workload and massive failures, maintaining its QoS and using efficiently the available resources; it is highly scalable and robust; can be implemented on existing services in a non-intrusive way; and do not require any performance model of the services, their workload or the resources they use. We can conclude that our work proposes a solution for the requirements of self-adaptation in demanding usage scenarios without introducing additional complexity. In that sense, we believe we make a significant contribution towards the development of future generation service-oriented applications.Las Aplicaciones Orientadas a Servicios modernas demandan la capacidad de adaptarse a condiciones variables y situaciones inesperadas mientras mantienen un cierto nivel de servio esperado (QoS). Los enfoques de auto-adaptación existentes parecen no ser adacuados debido a sus supuestos no se cumplen en infrastructuras compartidas de gran escala. La principal motivación de nuestra investigación es inerir un conjunto de principios para guiar el desarrollo de servicios auto-adaptativos de gran escala. Nuesto objetivo es proveer abstraciones de modelaje apropiadas, basadas en un marco conceptual claro, y su implemetnacion en un middleware que soporte el desarrollo de estos servicios. Tomando como inspiración conceptos económicos de mercados decentralizados, hemos propuesto una solución basada en tres principios: auto-organización emergente, comportamiento guiado por la utilidad y adaptación sin modelos. Basados en estos principios diseñamos Collectives, un middleware que proveer una solución exhaustiva para los diversos aspectos de adaptación que surgen en el desarrollo de sistemas distribuidos. La adecuación y completitud de Collectives ha sido provada por medio de la implementación de eUDON, un middleware para servicios auto-adaptativos, el ha sido evaluado de manera exhaustiva por medio de un modelo de simulación, analizando sus propiedades de adaptación en diversos escenarios de uso. Hemos encontrado que eUDON exhibe las propiedades esperadas: se adapta a diversas condiciones como picos en la carga de trabajo o fallos masivos, mateniendo su calidad de servicio y haciendo un uso eficiente de los recusos disponibles. Es altamente escalable y robusto; puedeoo ser implementado en servicios existentes de manera no intrusiva; y no requiere la obtención de un modelo de desempeño para los servicios. Podemos concluir que nuestro trabajo nos ha permitido desarrollar una solucion que aborda los requerimientos de auto-adaptacion en escenarios de uso exigentes sin introducir complejidad adicional. En este sentido, consideramos que nuestra propuesta hace una contribución significativa hacia el desarrollo de la futura generación de aplicaciones orientadas a servicios.Postprint (published version