Contribution to the Federation of the asynchronous SmartSantander service layer within the European Fed4FIRE context

This thesis is a contribution to the federation of asynchronous SmartSantander service layer within the European Fed4FIRE context. The thesis was developed in a Smart City background, and its main aims were both to gain knowledge of how Smart Cities, Testbeds and Federations of Testbeds are structured by working on a real deployed system, i.e. SmartSantander framework and Fed4FIRE federation, and to contribute with some of the components required for the integratio

Resolving horizontal partitioning and schematic variances using metadatabase approach.

by Poon, Koon-hei.Thesis (M.Phil.)--Chinese University of Hong Kong, 2000.Includes bibliographical references (leaves 80-83).Abstracts in English and Chinese.Chapter CHAPTER 1 --- INTRODUCTION --- p.6Chapter CHAPTER 2 --- LITERATURE REVIEW --- p.13Chapter 2.1. --- BACKGROUND --- p.13Chapter 2.2. --- example systems --- p.20Chapter 2.2.1 --- Multibase --- p.20Chapter 2.2.2. --- Mermai d --- p.23Chapter 2.2.3. --- The Metadatabase Approach --- p.26Chapter 2.3. --- SUMMARY --- p.29Chapter CHAPTER 3 --- THE METADATABASE APPROACH --- p.31Chapter 3.1. --- Two-Stage Entity Relationship (TSER) model --- p.31Chapter 3.2. --- The GIRD --- p.34Chapter 3.3. --- The Metadatabase system in action --- p.36Chapter 3.3. --- global query formulations and processing in the metadatabase system --- p.37Chapter CHAPTER 4 --- PROBLEM OUTLINES FOR HORIZONTAL PARTITIONING AND ITS VARIANTS --- p.39Chapter 4.1. --- Horizontal partitioning --- p.39Chapter 4.2. --- Level of abstraction --- p.41Chapter 4.3. --- Schematic variances --- p.42Chapter 4.4. --- Summary --- p.43Chapter 4.5. --- The Scenario --- p.44Chapter 4.6. --- Populating the Metadatabase --- p.48Chapter CHAPTER 5 --- THE ENHANCEMENTS FOR GLOBAL QUERY WITH HORIZONTAL PARTITIONED DATA OBJECTS --- p.51Chapter 5.1. --- Identifying partitioned data objects --- p.51Chapter 5.2. --- Additional metadata for the horizontal partitioned data objects --- p.52Chapter 5.3. --- Complications of horizontal partitioning problem --- p.54Chapter 5.3.1. --- Level of abstraction --- p.55Chapter 5.3.2. --- Schematic variances --- p.57Chapter 5.4. --- Global query with horizontal partitioning data objects --- p.59Chapter 5.5. --- Housing the new metadata --- p.68Chapter 5.6. --- Example --- p.72Chapter CHAPTER 6 --- ANALYSIS --- p.75Chapter CHAPTER 7 --- CONCLUSION AND FUTURE WORKS --- p.78REFERENCES --- p.80APPENDICES --- p.84Chapter A. --- GIRD Definitions --- p.84Chapter A1. --- GIRD Model --- p.84Chapter A2. --- GIRD/SER Contents --- p.84Chapter A3. --- GIRD/OER Constructs --- p.87Chapter A4. --- Definition of Meta-attributes --- p.89Chapter B. --- Problems Representations in Relation Algebra --- p.96Chapter B1. --- Horizontal problem --- p.96Chapter B2. --- Level of abstraction --- p.96Chapter B3. --- Schematic Variance --- p.97Chapter C. --- Details of local systems --- p.9

Enabling Complex Semantic Queries to Bioinformatics Databases through Intuitive Search Over Data

Data integration promises to be one of the main catalysts in enabling new insights to be drawn from the wealth of biological data already available publicly. However, the heterogene- ity of the existing data sources still poses significant challenges for achieving interoperability among biological databases. Furthermore, merely solving the technical challenges of data in- tegration, for example through the use of common data representation formats, leaves open the larger problem. Namely, the steep learning curve required for understanding the data models of each public source, as well as the technical language through which the sources can be queried and joined. As a consequence, most of the available biological data remain practically unexplored today. In this thesis, we address these problems jointly, by first introducing an ontology-based data integration solution in order to mitigate the data source heterogeneity problem. We illustrate through the concrete example of Bgee, a gene expression data source, how relational databases can be exposed as virtual Resource Description Framework (RDF) graphs, through relational-to-RDF mappings. This has the important advantage that the original data source can remain unmodified, while still becoming interoperable with external RDF sources. We complement our methods with applied case studies designed to guide domain experts in formulating expressive federated queries targeting the integrated data across the domains of evolutionary relationships and gene expression. More precisely, we introduce two com- parative analyses, first within the same domain (using orthology data from multiple, inter- operable, data sources) and second across domains, in order to study the relation between expression change and evolution rate following a duplication event. Finally, in order to bridge the semantic gap between users and data, we design and im- plement Bio-SODA, a question answering system over domain knowledge graphs, that does not require training data for translating user questions to SPARQL. Bio-SODA uses a novel ranking approach that combines syntactic and semantic similarity, while also incorporating node centrality metrics to rank candidate matches for a given user question. Our results in testing Bio-SODA across several real-world databases that span multiple domains (both within and outside bioinformatics) show that it can answer complex, multi-fact queries, be- yond the current state-of-the-art in the more well-studied open-domain question answering. -- L’intégration des données promet d’être l’un des principaux catalyseurs permettant d’extraire des nouveaux aperçus de la richesse des données biologiques déjà disponibles publiquement. Cependant, l’hétérogénéité des sources de données existantes pose encore des défis importants pour parvenir à l’interopérabilité des bases de données biologiques. De plus, en surmontant seulement les défis techniques de l’intégration des données, par exemple grâce à l’utilisation de formats standard de représentation de données, on laisse ouvert un problème encore plus grand. À savoir, la courbe d’apprentissage abrupte nécessaire pour comprendre la modéli- sation des données choisie par chaque source publique, ainsi que le langage technique par lequel les sources peuvent être interrogés et jointes. Par conséquent, la plupart des données biologiques publiquement disponibles restent pratiquement inexplorés aujourd’hui. Dans cette thèse, nous abordons l’ensemble des deux problèmes, en introduisant d’abord une solution d’intégration de données basée sur ontologies, afin d’atténuer le problème d’hété- rogénéité des sources de données. Nous montrons, à travers l’exemple de Bgee, une base de données d’expression de gènes, une approche permettant les bases de données relationnelles d’être publiés sous forme de graphes RDF (Resource Description Framework) virtuels, via des correspondances relationnel-vers-RDF (« relational-to-RDF mappings »). Cela présente l’important avantage que la source de données d’origine peut rester inchangé, tout en de- venant interopérable avec les sources RDF externes. Nous complétons nos méthodes avec des études de cas appliquées, conçues pour guider les experts du domaine dans la formulation de requêtes fédérées expressives, ciblant les don- nées intégrées dans les domaines des relations évolutionnaires et de l’expression des gènes. Plus précisément, nous introduisons deux analyses comparatives, d’abord dans le même do- maine (en utilisant des données d’orthologie provenant de plusieurs sources de données in- teropérables) et ensuite à travers des domaines interconnectés, afin d’étudier la relation entre le changement d’expression et le taux d’évolution suite à une duplication de gène. Enfin, afin de mitiger le décalage sémantique entre les utilisateurs et les données, nous concevons et implémentons Bio-SODA, un système de réponse aux questions sur des graphes de connaissances domaine-spécifique, qui ne nécessite pas de données de formation pour traduire les questions des utilisateurs vers SPARQL. Bio-SODA utilise une nouvelle ap- proche de classement qui combine la similarité syntactique et sémantique, tout en incorporant des métriques de centralité des nœuds, pour classer les possibles candidats en réponse à une question utilisateur donnée. Nos résultats suite aux tests effectués en utilisant Bio-SODA sur plusieurs bases de données à travers plusieurs domaines (tantôt liés à la bioinformatique qu’extérieurs) montrent que Bio-SODA réussit à répondre à des questions complexes, en- gendrant multiples entités, au-delà de l’état actuel de la technique en matière de systèmes de réponses aux questions sur les données structures, en particulier graphes de connaissances

Information retrieval and text mining technologies for chemistry

Efficient access to chemical information contained in scientific literature, patents, technical reports, or the web is a pressing need shared by researchers and patent attorneys from different chemical disciplines. Retrieval of important chemical information in most cases starts with finding relevant documents for a particular chemical compound or family. Targeted retrieval of chemical documents is closely connected to the automatic recognition of chemical entities in the text, which commonly involves the extraction of the entire list of chemicals mentioned in a document, including any associated information. In this Review, we provide a comprehensive and in-depth description of fundamental concepts, technical implementations, and current technologies for meeting these information demands. A strong focus is placed on community challenges addressing systems performance, more particularly CHEMDNER and CHEMDNER patents tasks of BioCreative IV and V, respectively. Considering the growing interest in the construction of automatically annotated chemical knowledge bases that integrate chemical information and biological data, cheminformatics approaches for mapping the extracted chemical names into chemical structures and their subsequent annotation together with text mining applications for linking chemistry with biological information are also presented. Finally, future trends and current challenges are highlighted as a roadmap proposal for research in this emerging field.A.V. and M.K. acknowledge funding from the European Community’s Horizon 2020 Program (project reference: 654021 - OpenMinted). M.K. additionally acknowledges the Encomienda MINETAD-CNIO as part of the Plan for the Advancement of Language Technology. O.R. and J.O. thank the Foundation for Applied Medical Research (FIMA), University of Navarra (Pamplona, Spain). This work was partially funded by Consellería de Cultura, Educación e Ordenación Universitaria (Xunta de Galicia), and FEDER (European Union), and the Portuguese Foundation for Science and Technology (FCT) under the scope of the strategic funding of UID/BIO/04469/2013 unit and COMPETE 2020 (POCI-01-0145-FEDER-006684). We thank Iñigo Garciá -Yoldi for useful feedback and discussions during the preparation of the manuscript.info:eu-repo/semantics/publishedVersio

Realizing interoperability of e-learning repositories

Tesis doctoral inédita. Universidad Autónoma de Madrid, Escuela Politécnica Superior, marzo 200

The Nexus Between Security Sector Governance/Reform and Sustainable Development Goal-16

This Security Sector Reform (SSR) Paper offers a universal and analytical perspective on the linkages between Security Sector Governance (SSG)/SSR (SSG/R) and Sustainable Development Goal-16 (SDG-16), focusing on conflict and post-conflict settings as well as transitional and consolidated democracies. Against the background of development and security literatures traditionally maintaining separate and compartmentalized presence in both academic and policymaking circles, it maintains that the contemporary security- and development-related challenges are inextricably linked, requiring effective measures with an accurate understanding of the nature of these challenges. In that sense, SDG-16 is surely a good step in the right direction. After comparing and contrasting SSG/R and SDG-16, this SSR Paper argues that human security lies at the heart of the nexus between the 2030 Agenda of the United Nations (UN) and SSG/R. To do so, it first provides a brief overview of the scholarly and policymaking literature on the development-security nexus to set the background for the adoption of The Agenda 2030. Next, it reviews the literature on SSG/R and SDGs, and how each concept evolved over time. It then identifies the puzzle this study seeks to address by comparing and contrasting SSG/R with SDG-16. After making a case that human security lies at the heart of the nexus between the UN’s 2030 Agenda and SSG/R, this book analyses the strengths and weaknesses of human security as a bridge between SSG/R and SDG-16 and makes policy recommendations on how SSG/R, bolstered by human security, may help achieve better results on the SDG-16 targets. It specifically emphasizes the importance of transparency, oversight, and accountability on the one hand, and participative approach and local ownership on the other. It concludes by arguing that a simultaneous emphasis on security and development is sorely needed for addressing the issues under the purview of SDG-16

Big Data in Bioeconomy

This edited open access book presents the comprehensive outcome of The European DataBio Project, which examined new data-driven methods to shape a bioeconomy. These methods are used to develop new and sustainable ways to use forest, farm and fishery resources. As a European initiative, the goal is to use these new findings to support decision-makers and producers – meaning farmers, land and forest owners and fishermen. With their 27 pilot projects from 17 countries, the authors examine important sectors and highlight examples where modern data-driven methods were used to increase sustainability. How can farmers, foresters or fishermen use these insights in their daily lives? The authors answer this and other questions for our readers. The first four parts of this book give an overview of the big data technologies relevant for optimal raw material gathering. The next three parts put these technologies into perspective, by showing useable applications from farming, forestry and fishery. The final part of this book gives a summary and a view on the future. With its broad outlook and variety of topics, this book is an enrichment for students and scientists in bioeconomy, biodiversity and renewable resources

Steps towards interoperability in healthcare environment

Tese doutoramento - Programa Doutoral em Engenharia Biomédica, Informática MédicaHealthcare units have complex Information Systems (IS) made up from heterogeneous data sources, which speak di erent languages and with di erent objectives. Nevertheless, all these sources have indeed important information that can contribute in an active way to provide a healthcare system of excellence. The evolution that has been noticed in Health IS has promoted the development of new methodologies and tools that are intended to solve this complicated problem. In this manner, one of the main paradigms that arises is the interoperability among systems and its capability to allow a general and simpli ed access to relevant information. Another aspect that should be kept in mind, given the constrains of the global economic situation, is the reduction in the investment in national healthcare systems. This thesis is based on a set of studies performed at the Centro Hospitalar do T^amega e Sousa (CHTS) in which the main goals are promoting an improvement in the relation patient-hospital, having in consideration the reduction of implementation costs, but preserving the quality of information. The last one should be accessible everywhere and at anytime to help with clinical decision and, in the future, be available for clinical studies through data computationally interpretable. To do so, an Electronic Semantic Health Record was formalized and implemented, with the help of the clinical sta , which collects all the information considered important and relevant. This Health Record was delivered through a platform for the distribution and archive of clinical information, named Agency for the Integration, Di usion and Archive (AIDA), which is supported by intelligent agents that treat data in an ex-haustive and structured way. To test the proposed model and system and in order to strengthen the relation between the patient and the hospital, an appointment alert system based on SMS and electronic mail was developed, which allowed the reduction of non-programmed misses and that provided a decrease of costs by better re-distributed appointment schedules, and allocate human resources and physical spaces in a more e ective manner. Finally, to reduce stopping periods of systems and to promote the user's con dence on Information Systems, an open-source tool was developed that enables the scheduling of preventive actions according to a mathematical model. These tools allowed for a continuous improvement of systems and are currently well accepted by clinicians and Information Technologies (IT) specialists inside the healthcare unit, proving in real clinical situation the e ectiveness and usability of the model.As unidades de saúde possuem Sistemas de Informação (SI) complexos, compostos por fontes de dados heterogéneas com objectivos distintos. Por em, toda a informação e importante e pode contribuir de forma ativa para a prestação de cuidados de saúde de excelência. Com a evolução dos SI na Saúde novas metodologias têm sido desenvolvidas com o intuito de solucionar este problema complicado. Nesta perspectiva, um dos principais paradigmas que se coloca e a interoperabilidade entre sistemas e a sua capacidade para permitir um acesso simples a informação relevante. Outro factor relevante relaciona-se com os constrangimentos financeiros que toda a economia global atravessa e que se reflete numa diminuição no investimento nos servi cos nacionais de saúde. Esta tese tem como base um conjunto de estudos realizados no Centro Hospitalar do Tâmega e Sousa cujos principais objetivos se prendem com um esforço orientado para a melhoria da relação paciente-hospital, tendo em conta a redução de custos de implementação, mas garantindo sobretudo a qualidade de informação. Esta dever a estar disponível em qualquer lugar e a qualquer altura para o auxílio a decisão clinica e, em última instancia, disponível para estudos cl nicos através de dados interpretáveis computacionalmente. Para tal, recorreu-se a ajuda de pessoal clinico para a implementação de um Processo Clínico Eletrónico Semântico que recolhe toda a informação considerada relevante. Este Processo Clínico foi potenciado através de uma plataforma para a distribuição e arquivo de informação clinica, denominada de Agencia para a Interoperação, Difusão e Arquivo (AIDA), baseada em agentes inteligentes que tratam os dados de forma estruturada. Para testar o modelo e de forma a fortalecer a relação paciente-hospital foi desenvolvido um sistema de alertas para consulta via mensagens escritas e e-mail, que diminuiu o numero de faltas não programadas, proporcionando uma redução de custos através de uma redistribuição dos tempos de consulta alocando recursos humanos e físicos de forma mais eficaz. Por fim, com vista a redução dos tempos de paragem de sistemas, e potenciar a confiança dos utilizadores nos mesmos, foi desenvolvida uma ferramenta baseada em tecnologia open-source que permite o agendamento de intervenções preventivas de acordo com um modelo matemático. Esta ferramenta proporcionou uma melhoria contínua dos sistemas e está globalmente aceite por cl nicos e especialistas de Tecnologias de Informação (TI), provando em situações clínicas reais a usabilidade e eficácia do modelo