The RICORDO approach to semantic interoperability for biomedical data and models: strategy, standards and solutions.

BACKGROUND: The practice and research of medicine generates considerable quantities of data and model resources (DMRs). Although in principle biomedical resources are re-usable, in practice few can currently be shared. In particular, the clinical communities in physiology and pharmacology research, as well as medical education, (i.e. PPME communities) are facing considerable operational and technical obstacles in sharing data and models. FINDINGS: We outline the efforts of the PPME communities to achieve automated semantic interoperability for clinical resource documentation in collaboration with the RICORDO project. Current community practices in resource documentation and knowledge management are overviewed. Furthermore, requirements and improvements sought by the PPME communities to current documentation practices are discussed. The RICORDO plan and effort in creating a representational framework and associated open software toolkit for the automated management of PPME metadata resources is also described. CONCLUSIONS: RICORDO is providing the PPME community with tools to effect, share and reason over clinical resource annotations. This work is contributing to the semantic interoperability of DMRs through ontology-based annotation by (i) supporting more effective navigation and re-use of clinical DMRs, as well as (ii) sustaining interoperability operations based on the criterion of biological similarity. Operations facilitated by RICORDO will range from automated dataset matching to model merging and managing complex simulation workflows. In effect, RICORDO is contributing to community standards for resource sharing and interoperability.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

Systematizing FAIR research data management in biomedical research projects: a data life cycle approach

Biomedical researchers are facing data management challenges brought by a new generation of data driven by the advent of translational medicine research. These challenges are further complicated by the recent calls for data re-use and long-term stewardship spearheaded by the FAIR principles initiative. As a result, there is an increasingly wide-spread recognition that advancing biomedical science is becoming dependent on the application of data science to manage and utilize highly diverse and complex data in ways that give it context, meaning, and longevity beyond its initial purpose. However, current methods and practices in biomedical informatics remain to adopt a traditional linear view of the informatics process (collect, store and analyse); focusing primarily on the challenges in data integration and analysis, which are challenges only pertaining to a part of the overall life cycle of research data. The aim of this research is to facilitate the adoption and integration of data management practices into the research life cycle of biomedical projects, thus improving their capabilities into solving data management-related challenges that they face throughout the course of their research work. To achieve this aim, this thesis takes a data life cycle approach to define and develop a systematic methodology and framework towards the systematization of FAIR data management in biomedical research projects. The overarching contribution of this research is the provision of a data-state life cycle model for research data management in Biomedical Translational Research Projects. This model provides insight into the dynamics between 1) the purpose of a research-driven data use case, 2) the data requirements that renders data in a state fit for purpose, 3) the data management functions that prepare and act upon data and 4) the resulting state of data that is _t to serve the use case. This insight led to the development of a FAIR data management framework, which is another contribution of this thesis. This framework provides data managers the groundwork, including the data models, resources and capabilities, needed to build a FAIR data management environment to manage data during the operational stages of a biomedical research project. An exemplary implementation of this architecture (PlatformTM) was developed and validated by real-world research datasets produced by collaborative research programs funded by the Innovative Medicine Initiative (IMI) BioVacSafe 1 , eTRIKS 2 and FAIRplus 3.Open Acces

Front-Line Physicians' Satisfaction with Information Systems in Hospitals

Day-to-day operations management in hospital units is difficult due to continuously varying situations, several actors involved and a vast number of information systems in use. The aim of this study was to describe front-line physicians' satisfaction with existing information systems needed to support the day-to-day operations management in hospitals. A cross-sectional survey was used and data chosen with stratified random sampling were collected in nine hospitals. Data were analyzed with descriptive and inferential statistical methods. The response rate was 65 % (n = 111). The physicians reported that information systems support their decision making to some extent, but they do not improve access to information nor are they tailored for physicians. The respondents also reported that they need to use several information systems to support decision making and that they would prefer one information system to access important information. Improved information access would better support physicians' decision making and has the potential to improve the quality of decisions and speed up the decision making process.Peer reviewe

Interoperability middleware for IIoT gateways based on international standard ontologies and standardized digital representation

Recent advances in the areas of microelectronics, information technology, and communication protocols have made the development of smaller devices with greater processing capacity and lower energy consumption. This context contributed to the growing number of physical devices in industrial environments which are interconnected and communicate via the internet, enabling concepts such as Industry 4.0 and the Industrial Internet of Things (IIoT). These nodes have different sensors and actuators that monitor and control environment data. Several companies develop these devices, including diverse communication protocols, data structures, and IoT platforms, which leads to interoperability issues. In IoT scenarios, interoperability is the ability of two systems to communicate and share services. Therefore, communication problems can make it unfeasible to use heterogeneous devices, increasing the project’s financial cost and development time. In an industry, interoperability is related to different aspects, such as physical communication, divergent device communication protocols, and syntactical problems, referring to the distinct data structure. Developing a new standard for solving these matters may bring interoperability-related drawbacks rather than effectively solving these issues. Therefore, to mitigate interoperability problems in industrial applications, this work proposes the development of an interoperability middleware for Edge-enabled IIoT gateways based on international standards. The middleware is responsible for translating communication protocols, updating data from simulations or physical nodes to the assets’ digital representations, and storing data locally or remotely. The middleware adopts the IEEE industrial standard ontologies combined with assets’ standardized digital models. As a case study, a simulation replicates the production of a nutrient solution for agriculture, controlled by IIoT nodes. The use case consists of three devices, each equipped with at least five sensors or actuators, communicating in different communication protocols and exchanging data using diverse structures. The performance of the proposed middleware and its proposed translations algorithms were evaluated, obtaining satisfactory results for mitigating interoperable in industrial applications.Devido a recentes avanços nas áreas de microeletrônica, tecnologia da informação, e protocolos de comunicação tornaram possível o desenvolvimento de dispositivos cada vez menores com maior capacidade de processamento e menor consumo energético. Esse contexto contribuiu para o crescente nú- mero desses dispositivos na industria que estão interligados via internet, viabilizando conceitos como Indústria 4.0 e Internet das Coisas Industrial (IIoT). Esses nós possuem diferentes sensores e atuadores que monitoram e controlam os dados do ambiente. Esses equipamentos são desenvolvidos por diferentes empresas, incluindo protocolos de comunicação, estruturas de dados e plataformas de IoT distintos, acarretando em problemas de interoperabilidade. Em cenários de IoT, interoperabilidade, é a capacidade de sistemas se comunicarem e compartilharem serviços. Portanto, esses problemas podem inviabilizar o uso de dispositivos heterogêneos, aumentando o custo financeiro do projeto e seu tempo de desenvolvimento. Na indústria, interoperabilidade se divide em diferentes aspectos, como comunicação e problemas sintáticos, referentes à estrutura de dados distinta. O desenvolvimento de um padrão industrial pode trazer mais desvantagens relacionadas à interoperabilidade, em vez de resolver esses problemas. Portanto, para mitigar problemas relacionados a intoperabilidade industrial, este trabalho propõe o desenvolvimento de um middleware de interoperável para gateways IIoT baseado em padrões internacionais e ontologias. O middleware é responsável por traduzir diferentes protocolos de comunicação, atualizar os dados dos ativos industriais por meio de suas representações digitais, esses armazenados localmente ou remotamente. O middleware adota os padrões ontológicos industriais da IEEE combinadas com modelos digitais padronizados de ativos industriais. Como estudo de caso, são realizadas simulações para a produção de uma solução nutritiva para agricultura, controlada por nós IIoT. O processo utiliza três dispositivos, cada um equipado com pelo menos cinco sensores ou atuadores, por meio de diferentes protocolos de comunicação e estruturas de dados. O desempenho do middleware proposto e seus algoritmos de tradução foram avaliados e apresentados no final do trabalho, os quais resultados foram satisfatórios para mitigar a interoperabilidade em aplicações industriais

Network-driven strategies to integrate and exploit biomedical data

[eng] In the quest for understanding complex biological systems, the scientific community has been delving into protein, chemical and disease biology, populating biomedical databases with a wealth of data and knowledge. Currently, the field of biomedicine has entered a Big Data era, in which computational-driven research can largely benefit from existing knowledge to better understand and characterize biological and chemical entities. And yet, the heterogeneity and complexity of biomedical data trigger the need for a proper integration and representation of this knowledge, so that it can be effectively and efficiently exploited. In this thesis, we aim at developing new strategies to leverage the current biomedical knowledge, so that meaningful information can be extracted and fused into downstream applications. To this goal, we have capitalized on network analysis algorithms to integrate and exploit biomedical data in a wide variety of scenarios, providing a better understanding of pharmacoomics experiments while helping accelerate the drug discovery process. More specifically, we have (i) devised an approach to identify functional gene sets associated with drug response mechanisms of action, (ii) created a resource of biomedical descriptors able to anticipate cellular drug response and identify new drug repurposing opportunities, (iii) designed a tool to annotate biomedical support for a given set of experimental observations, and (iv) reviewed different chemical and biological descriptors relevant for drug discovery, illustrating how they can be used to provide solutions to current challenges in biomedicine.[cat] En la cerca d’una millor comprensió dels sistemes biològics complexos, la comunitat científica ha estat aprofundint en la biologia de les proteïnes, fàrmacs i malalties, poblant les bases de dades biomèdiques amb un gran volum de dades i coneixement. En l’actualitat, el camp de la biomedicina es troba en una era de “dades massives” (Big Data), on la investigació duta a terme per ordinadors se’n pot beneficiar per entendre i caracteritzar millor les entitats químiques i biològiques. No obstant, la heterogeneïtat i complexitat de les dades biomèdiques requereix que aquestes s’integrin i es representin d’una manera idònia, permetent així explotar aquesta informació d’una manera efectiva i eficient. L’objectiu d’aquesta tesis doctoral és desenvolupar noves estratègies que permetin explotar el coneixement biomèdic actual i així extreure informació rellevant per aplicacions biomèdiques futures. Per aquesta finalitat, em fet servir algoritmes de xarxes per tal d’integrar i explotar el coneixement biomèdic en diferents tasques, proporcionant un millor enteniment dels experiments farmacoòmics per tal d’ajudar accelerar el procés de descobriment de nous fàrmacs. Com a resultat, en aquesta tesi hem (i) dissenyat una estratègia per identificar grups funcionals de gens associats a la resposta de línies cel·lulars als fàrmacs, (ii) creat una col·lecció de descriptors biomèdics capaços, entre altres coses, d’anticipar com les cèl·lules responen als fàrmacs o trobar nous usos per fàrmacs existents, (iii) desenvolupat una eina per descobrir quins contextos biològics corresponen a una associació biològica observada experimentalment i, finalment, (iv) hem explorat diferents descriptors químics i biològics rellevants pel procés de descobriment de nous fàrmacs, mostrant com aquests poden ser utilitzats per trobar solucions a reptes actuals dins el camp de la biomedicina

Proceedings of the Fifth Italian Conference on Computational Linguistics CLiC-it 2018 : 10-12 December 2018, Torino

On behalf of the Program Committee, a very warm welcome to the Fifth Italian Conference on Computational Linguistics (CLiC-­‐it 2018). This edition of the conference is held in Torino. The conference is locally organised by the University of Torino and hosted into its prestigious main lecture hall “Cavallerizza Reale”. The CLiC-­‐it conference series is an initiative of the Italian Association for Computational Linguistics (AILC) which, after five years of activity, has clearly established itself as the premier national forum for research and development in the fields of Computational Linguistics and Natural Language Processing, where leading researchers and practitioners from academia and industry meet to share their research results, experiences, and challenges

Historical GIS Research in Canada

Fundamentally concerned with place, and our ability to understand human relationships with environment over time, Historical Geographic Information Systems (HGIS) as a tool and a subject has direct bearing for the study of contemporary environmental issues and realities. To date, HGIS projects in Canada are few and publications that discuss these projects directly even fewer. This book brings together case studies of HGIS projects in historical geography, social and cultural history, and environmental history from Canada's diverse regions. Projects include religion and ethnicity, migration, indigenous land practices, rebuilding a nineteenth-century neighborhood, and working with Google Earth. With contributions by: Colleen Beard Stephen Bocking Jennifer Bonnell Jim Clifford Joanna Dean François Dufaux Patrick A. Dunae Marcel Fortin Jason Gilliland William M. Glen Megan Harvey Matthew G. Hatvany Sally Hermansen Andrew Hinson Don Lafreniere John S. Lutz Joshua D. MacFadyen Daniel Macfarlane Jennifer Marvin Cameron Metcalf Byron Moldofsky Sherry Olson Jon Pasher Daniel Rueck R. W. Sandwell Henry Yu Barbara Znamirowsk

Sustainable Agriculture and Advances of Remote Sensing (Volume 1)

Agriculture, as the main source of alimentation and the most important economic activity globally, is being affected by the impacts of climate change. To maintain and increase our global food system production, to reduce biodiversity loss and preserve our natural ecosystem, new practices and technologies are required. This book focuses on the latest advances in remote sensing technology and agricultural engineering leading to the sustainable agriculture practices. Earth observation data, in situ and proxy-remote sensing data are the main source of information for monitoring and analyzing agriculture activities. Particular attention is given to earth observation satellites and the Internet of Things for data collection, to multispectral and hyperspectral data analysis using machine learning and deep learning, to WebGIS and the Internet of Things for sharing and publishing the results, among others

Proceedings of the Fifth Italian Conference on Computational Linguistics CLiC-it 2018

On behalf of the Program Committee, a very warm welcome to the Fifth Italian Conference on Computational Linguistics (CLiC-­‐it 2018). This edition of the conference is held in Torino. The conference is locally organised by the University of Torino and hosted into its prestigious main lecture hall “Cavallerizza Reale”. The CLiC-­‐it conference series is an initiative of the Italian Association for Computational Linguistics (AILC) which, after five years of activity, has clearly established itself as the premier national forum for research and development in the fields of Computational Linguistics and Natural Language Processing, where leading researchers and practitioners from academia and industry meet to share their research results, experiences, and challenges