Application of Semantics to Solve Problems in Life Sciences

Fecha de lectura de Tesis: 10 de diciembre de 2018La cantidad de información que se genera en la Web se ha incrementado en los últimos años. La mayor parte de esta información se encuentra accesible en texto, siendo el ser humano el principal usuario de la Web. Sin embargo, a pesar de todos los avances producidos en el área del procesamiento del lenguaje natural, los ordenadores tienen problemas para procesar esta información textual. En este cotexto, existen dominios de aplicación en los que se están publicando grandes cantidades de información disponible como datos estructurados como en el área de las Ciencias de la Vida. El análisis de estos datos es de vital importancia no sólo para el avance de la ciencia, sino para producir avances en el ámbito de la salud. Sin embargo, estos datos están localizados en diferentes repositorios y almacenados en diferentes formatos que hacen difícil su integración. En este contexto, el paradigma de los Datos Vinculados como una tecnología que incluye la aplicación de algunos estándares propuestos por la comunidad W3C tales como HTTP URIs, los estándares RDF y OWL. Haciendo uso de esta tecnología, se ha desarrollado esta tesis doctoral basada en cubrir los siguientes objetivos principales: 1) promover el uso de los datos vinculados por parte de la comunidad de usuarios del ámbito de las Ciencias de la Vida 2) facilitar el diseño de consultas SPARQL mediante el descubrimiento del modelo subyacente en los repositorios RDF 3) crear un entorno colaborativo que facilite el consumo de Datos Vinculados por usuarios finales, 4) desarrollar un algoritmo que, de forma automática, permita descubrir el modelo semántico en OWL de un repositorio RDF, 5) desarrollar una representación en OWL de ICD-10-CM llamada Dione que ofrezca una metodología automática para la clasificación de enfermedades de pacientes y su posterior validación haciendo uso de un razonador OWL

Políticas de Copyright de Publicações Científicas em Repositórios Institucionais: O Caso do INESC TEC

A progressiva transformação das práticas científicas, impulsionada pelo desenvolvimento das novas Tecnologias de Informação e Comunicação (TIC), têm possibilitado aumentar o acesso à informação, caminhando gradualmente para uma abertura do ciclo de pesquisa. Isto permitirá resolver a longo prazo uma adversidade que se tem colocado aos investigadores, que passa pela existência de barreiras que limitam as condições de acesso, sejam estas geográficas ou financeiras. Apesar da produção científica ser dominada, maioritariamente, por grandes editoras comerciais, estando sujeita às regras por estas impostas, o Movimento do Acesso Aberto cuja primeira declaração pública, a Declaração de Budapeste (BOAI), é de 2002, vem propor alterações significativas que beneficiam os autores e os leitores. Este Movimento vem a ganhar importância em Portugal desde 2003, com a constituição do primeiro repositório institucional a nível nacional. Os repositórios institucionais surgiram como uma ferramenta de divulgação da produção científica de uma instituição, com o intuito de permitir abrir aos resultados da investigação, quer antes da publicação e do próprio processo de arbitragem (preprint), quer depois (postprint), e, consequentemente, aumentar a visibilidade do trabalho desenvolvido por um investigador e a respetiva instituição. O estudo apresentado, que passou por uma análise das políticas de copyright das publicações científicas mais relevantes do INESC TEC, permitiu não só perceber que as editoras adotam cada vez mais políticas que possibilitam o auto-arquivo das publicações em repositórios institucionais, como também que existe todo um trabalho de sensibilização a percorrer, não só para os investigadores, como para a instituição e toda a sociedade. A produção de um conjunto de recomendações, que passam pela implementação de uma política institucional que incentive o auto-arquivo das publicações desenvolvidas no âmbito institucional no repositório, serve como mote para uma maior valorização da produção científica do INESC TEC.The progressive transformation of scientific practices, driven by the development of new Information and Communication Technologies (ICT), which made it possible to increase access to information, gradually moving towards an opening of the research cycle. This opening makes it possible to resolve, in the long term, the adversity that has been placed on researchers, which involves the existence of barriers that limit access conditions, whether geographical or financial. Although large commercial publishers predominantly dominate scientific production and subject it to the rules imposed by them, the Open Access movement whose first public declaration, the Budapest Declaration (BOAI), was in 2002, proposes significant changes that benefit the authors and the readers. This Movement has gained importance in Portugal since 2003, with the constitution of the first institutional repository at the national level. Institutional repositories have emerged as a tool for disseminating the scientific production of an institution to open the results of the research, both before publication and the preprint process and postprint, increase the visibility of work done by an investigator and his or her institution. The present study, which underwent an analysis of the copyright policies of INESC TEC most relevant scientific publications, allowed not only to realize that publishers are increasingly adopting policies that make it possible to self-archive publications in institutional repositories, all the work of raising awareness, not only for researchers but also for the institution and the whole society. The production of a set of recommendations, which go through the implementation of an institutional policy that encourages the self-archiving of the publications developed in the institutional scope in the repository, serves as a motto for a greater appreciation of the scientific production of INESC TEC

Exploring Data Hierarchies to Discover Knowledge in Different Domains

L'abstract è presente nell'allegato / the abstract is in the attachmen

Strategies for Managing Linked Enterprise Data

Data, information and knowledge become key assets of our 21st century economy. As a result, data and knowledge management become key tasks with regard to sustainable development and business success. Often, knowledge is not explicitly represented residing in the minds of people or scattered among a variety of data sources. Knowledge is inherently associated with semantics that conveys its meaning to a human or machine agent. The Linked Data concept facilitates the semantic integration of heterogeneous data sources. However, we still lack an effective knowledge integration strategy applicable to enterprise scenarios, which balances between large amounts of data stored in legacy information systems and data lakes as well as tailored domain specific ontologies that formally describe real-world concepts. In this thesis we investigate strategies for managing linked enterprise data analyzing how actionable knowledge can be derived from enterprise data leveraging knowledge graphs. Actionable knowledge provides valuable insights, supports decision makers with clear interpretable arguments, and keeps its inference processes explainable. The benefits of employing actionable knowledge and its coherent management strategy span from a holistic semantic representation layer of enterprise data, i.e., representing numerous data sources as one, consistent, and integrated knowledge source, to unified interaction mechanisms with other systems that are able to effectively and efficiently leverage such an actionable knowledge. Several challenges have to be addressed on different conceptual levels pursuing this goal, i.e., means for representing knowledge, semantic data integration of raw data sources and subsequent knowledge extraction, communication interfaces, and implementation. In order to tackle those challenges we present the concept of Enterprise Knowledge Graphs (EKGs), describe their characteristics and advantages compared to existing approaches. We study each challenge with regard to using EKGs and demonstrate their efficiency. In particular, EKGs are able to reduce the semantic data integration effort when processing large-scale heterogeneous datasets. Then, having built a consistent logical integration layer with heterogeneity behind the scenes, EKGs unify query processing and enable effective communication interfaces for other enterprise systems. The achieved results allow us to conclude that strategies for managing linked enterprise data based on EKGs exhibit reasonable performance, comply with enterprise requirements, and ensure integrated data and knowledge management throughout its life cycle

Federated Query Processing over Heterogeneous Data Sources in a Semantic Data Lake

Data provides the basis for emerging scientific and interdisciplinary data-centric applications with the potential of improving the quality of life for citizens. Big Data plays an important role in promoting both manufacturing and scientific development through industrial digitization and emerging interdisciplinary research. Open data initiatives have encouraged the publication of Big Data by exploiting the decentralized nature of the Web, allowing for the availability of heterogeneous data generated and maintained by autonomous data providers. Consequently, the growing volume of data consumed by different applications raise the need for effective data integration approaches able to process a large volume of data that is represented in different format, schema and model, which may also include sensitive data, e.g., financial transactions, medical procedures, or personal data. Data Lakes are composed of heterogeneous data sources in their original format, that reduce the overhead of materialized data integration. Query processing over Data Lakes require the semantic description of data collected from heterogeneous data sources. A Data Lake with such semantic annotations is referred to as a Semantic Data Lake. Transforming Big Data into actionable knowledge demands novel and scalable techniques for enabling not only Big Data ingestion and curation to the Semantic Data Lake, but also for efficient large-scale semantic data integration, exploration, and discovery. Federated query processing techniques utilize source descriptions to find relevant data sources and find efficient execution plan that minimize the total execution time and maximize the completeness of answers. Existing federated query processing engines employ a coarse-grained description model where the semantics encoded in data sources are ignored. Such descriptions may lead to the erroneous selection of data sources for a query and unnecessary retrieval of data, affecting thus the performance of query processing engine. In this thesis, we address the problem of federated query processing against heterogeneous data sources in a Semantic Data Lake. First, we tackle the challenge of knowledge representation and propose a novel source description model, RDF Molecule Templates, that describe knowledge available in a Semantic Data Lake. RDF Molecule Templates (RDF-MTs) describes data sources in terms of an abstract description of entities belonging to the same semantic concept. Then, we propose a technique for data source selection and query decomposition, the MULDER approach, and query planning and optimization techniques, Ontario, that exploit the characteristics of heterogeneous data sources described using RDF-MTs and provide a uniform access to heterogeneous data sources. We then address the challenge of enforcing privacy and access control requirements imposed by data providers. We introduce a privacy-aware federated query technique, BOUNCER, able to enforce privacy and access control regulations during query processing over data sources in a Semantic Data Lake. In particular, BOUNCER exploits RDF-MTs based source descriptions in order to express privacy and access control policies as well as their automatic enforcement during source selection, query decomposition, and planning. Furthermore, BOUNCER implements query decomposition and optimization techniques able to identify query plans over data sources that not only contain the relevant entities to answer a query, but also are regulated by policies that allow for accessing these relevant entities. Finally, we tackle the problem of interest based update propagation and co-evolution of data sources. We present a novel approach for interest-based RDF update propagation that consistently maintains a full or partial replication of large datasets and deal with co-evolution

μGIM - Microgrid intelligent management system based on a multi-agent approach and the active participation of end-users

[ES] Los sistemas de potencia y energía están cambiando su paradigma tradicional, de sistemas centralizados a sistemas descentralizados. La aparición de redes inteligentes permite la integración de recursos energéticos descentralizados y promueve la gestión inclusiva que involucra a los usuarios finales, impulsada por la gestión del lado de la demanda, la energía transactiva y la respuesta a la demanda. Garantizar la escalabilidad y la estabilidad del servicio proporcionado por la red, en este nuevo paradigma de redes inteligentes, es más difícil porque no hay una única sala de operaciones centralizada donde se tomen todas las decisiones. Para implementar con éxito redes inteligentes, es necesario combinar esfuerzos entre la ingeniería eléctrica y la ingeniería informática. La ingeniería eléctrica debe garantizar el correcto funcionamiento físico de las redes inteligentes y de sus componentes, estableciendo las bases para un adecuado monitoreo, control, gestión, y métodos de operación. La ingeniería informática desempeña un papel importante al proporcionar los modelos y herramientas computacionales adecuados para administrar y operar la red inteligente y sus partes constituyentes, representando adecuadamente a todos los diferentes actores involucrados. Estos modelos deben considerar los objetivos individuales y comunes de los actores que proporcionan las bases para garantizar interacciones competitivas y cooperativas capaces de satisfacer a los actores individuales, así como cumplir con los requisitos comunes con respecto a la sostenibilidad técnica, ambiental y económica del Sistema. La naturaleza distribuida de las redes inteligentes permite, incentiva y beneficia enormemente la participación activa de los usuarios finales, desde actores grandes hasta actores más pequeños, como los consumidores residenciales. Uno de los principales problemas en la planificación y operación de redes eléctricas es la variación de la demanda de energía, que a menudo se duplica más que durante las horas pico en comparación con la demanda fuera de pico. Tradicionalmente, esta variación dio como resultado la construcción de plantas de generación de energía y grandes inversiones en líneas de red y subestaciones. El uso masivo de fuentes de energía renovables implica mayor volatilidad en lo relativo a la generación, lo que hace que sea más difícil equilibrar el consumo y la generación. La participación de los actores de la red inteligente, habilitada por la energía transactiva y la respuesta a la demanda, puede proporcionar flexibilidad en desde el punto de vista de la demanda, facilitando la operación del sistema y haciendo frente a la creciente participación de las energías renovables. En el ámbito de las redes inteligentes, es posible construir y operar redes más pequeñas, llamadas microrredes. Esas son redes geográficamente limitadas con gestión y operación local. Pueden verse como áreas geográficas restringidas para las cuales la red eléctrica generalmente opera físicamente conectada a la red principal, pero también puede operar en modo isla, lo que proporciona independencia de la red principal. Esta investigación de doctorado, realizada bajo el Programa de Doctorado en Ingeniería Informática de la Universidad de Salamanca, aborda el estudio y el análisis de la gestión de microrredes, considerando la participación activa de los usuarios finales y la gestión energética de lascarga eléctrica y los recursos energéticos de los usuarios finales. En este trabajo de investigación se ha analizado el uso de conceptos de ingeniería informática, particularmente del campo de la inteligencia artificial, para apoyar la gestión de las microrredes, proponiendo un sistema de gestión inteligente de microrredes (μGIM) basado en un enfoque de múltiples agentes y en la participación activa de usuarios. Esta solución se compone de tres sistemas que combinan hardware y software: el emulador de virtual a realidad (V2R), el enchufe inteligente de conciencia ambiental de Internet de las cosas (EnAPlug), y la computadora de placa única para energía basada en el agente (S4E) para permitir la gestión del lado de la demanda y la energía transactiva. Estos sistemas fueron concebidos, desarrollados y probados para permitir la validación de metodologías de gestión de microrredes, es decir, para la participación de los usuarios finales y para la optimización inteligente de los recursos. Este documento presenta todos los principales modelos y resultados obtenidos durante esta investigación de doctorado, con respecto a análisis de vanguardia, concepción de sistemas, desarrollo de sistemas, resultados de experimentación y descubrimientos principales. Los sistemas se han evaluado en escenarios reales, desde laboratorios hasta sitios piloto. En total, se han publicado veinte artículos científicos, de los cuales nueve se han hecho en revistas especializadas. Esta investigación de doctorado realizó contribuciones a dos proyectos H2020 (DOMINOES y DREAM-GO), dos proyectos ITEA (M2MGrids y SPEAR), tres proyectos portugueses (SIMOCE, NetEffiCity y AVIGAE) y un proyecto con financiación en cascada H2020 (Eco-Rural -IoT)

Otimização de Portfólio de Participação em Mercados de Energia Elétrica

Na atualidade são visíveis as mudanças ocorridas nos mercados de energia elétrica, em consequência da introdução maciça de energia proveniente de fontes renováveis. Pelo facto de serem renováveis são de grande interesse para a população, pois o custo de produção e as emissões de gases, que contribuem para o efeito de estufa durante o seu funcionamento, são nulas. Estas características são essenciais para as mais altas chefias das instituições europeias, que impuseram políticas para promover a utilização e instalação de tecnologia para o aproveitamento das fontes que facultam as energias renováveis. Os estados membros europeus mostraram-se recetíveis a estas políticas e incentivaram o investimento nestas tecnologias. Deste modo, houve uma enorme introdução de energias de arater intermitente e instável que condicionaram o normal funcionamento dos sistemas de energia elétrica, o que, por sua vez, conduziu a inúmeras mudanças no setor. Esta reestruturação teve impacto em todo o setor, como é o caso dos mercados de energia elétrica, onde surgiram novas formas de negociação e foram criadas novas entidades de mercado. Com estas alterações, a complexidade dos mercados de energia elétrica aumentou, assim como a imprevisibilidade dos mesmos. Por isso, tornou-se essencial a existência de formas de apoio que auxilie a tomada de decisão por parte das entidades de mercado. Com a emergência de todas estas exigências, tornou-se fundamental o desenvolvimento de ferramentas para auxílio na tomada de decisão. Estas ferramentas ajudam as diversas entidades a perceber o funcionamento dos mercados e prever as interações que ocorrerão entre as diferentes entidades existentes no mercado. A inteligência artificial teve um papel crucial no desenvolvimento destas ferramentas, nomeadamente os sistemas multiagente, que têm sido uma solução muito explorada pelos interessados no setor. Estes, utilizam várias técnicas da inteligência artificial, o que lhes permite serem adaptativos a diferentes situações, simular os diferentes agentes existentes no mercado, permitir diversos tipos de negociação, e ainda aprender ao longo da sua utilização. No entanto, apesar de estas ferramentas atualmente estarem voltadas para o estudo do funcionamento do sistema elétrico, deixam de lado o contexto de negociação e descartam o apoio às decisões do vendedor/comprador de eletricidade. O largo âmbito de aplicação da inteligência artificial fornece diversas experiências, nomeadamente ferramentas de otimização meta-heurísticas, que permitem a resolução de problemas num curto espaço de tempo, e com uma qualidade de resultados muito próxima daquela alcançada por técnicas determinísticas à custa de um elevado tempo de execução. O trabalho desenvolvido nesta dissertação tem como objeto de estudo a falha supra referenciada. Sugere uma metodologia de negociação da energia elétrica que permite vender e comprar a mesma em diferentes mercados com regras específicas, e indica um portfólio de participação nos vários mercados em que cada interveniente pode negociar. A metodologia apresentada permite gerar cenários realistas a partir do resultado da otimização do portfólio, que podem ser tomados em consideração na decisão dos intervenientes de mercado, e assim conseguirem retirar o máximo proveito das suas negociações. Os resultados apresentados foram obtidos através da utilização de dados reais provenientes dos diferentes operadores de mercados. Estes dados são válidos para a formulação de diferentes cenários que possam ser considerados no ato da negociação.Nowadays, there are several relevant changes in electricity markets, which are a consequence of the massive introduction of renewable energies. The fact that they are renewable is of great interest for all of us, because the cost of production of this energy is null and emissions of greenhouse gases are also zero during operation. This feature aroused great interest in the high European institutions that have imposed policies to promote the use and installation of technology for the use of sources that provide renewable energy. European member states have shown receptiveness to these policies, potentiating the investment in these technologies and thus hearing a great introduction of intermittent and unstable energy that conditioned the normal operation of power systems and led to further inevitable changes in an already under-restructuring power and energy sector. This restructuring had an impact throughout the industry, as is the case of the electricity markets, where new forms of trading emerged and new market entities were created. With these changes the complexity of electricity markets increased as well as the associated unpredictability. This made is essential to have support tools to aid decision making by the arket entities. With the emergence of all these requirements it is fundamental to develop tools in order to assist the decision-making process, and to help understanding the functioning of markets and predict the interactions that occur between the existing market entities. Artificial intelligence has an important role in the development of these tools. Multi-agent systems, in particular, have been much explored by stakeholders in the sector as a valid solution. They use various techniques of artificial intelligence that allows them to be adaptive to any situation, to simulate the different existing players in the market, allowing any type of trading and enabling them to learn the logo of its use. However, these tools are directed to study of the proper functioning of the electrical system, leaving aside the negotiation context and the decision support for the seller / buyer of electricity. The applicability of artificial intelligence is not limited to electricity markets. It is also applied in many other areas due to its optimization tools that enable solving problems in a short time and with very similar results to those achieved by deterministic techniques, at the cost of a high execution time. The work in this dissertation addresses the above-mentioned gaps, and suggests an electricity trading decision support methodology to buy and sell electricity in different markets with specific rules. This is done by suggesting a portfolio of market participation that each party can perform. The presented methodology generates realistic scenarios from the portfolio optimization of the results that may be taken into account in the decision of market participants; and allow these players to take full advantage of it. The results were obtained through the use of real data stemmed from different market operators, which are valid for the generation of different scenarios that can be taken into account in the negotiation act

Investigating business process elements: a journey from the field of Business Process Management to ontological analysis, and back

Business process modelling languages (BPMLs) typically enable the representation of business processes via the creation of process models, which are constructed using the elements and graphical symbols of the BPML itself. Despite the wide literature on business process modelling languages, on the comparison between graphical components of different languages, on the development and enrichment of new and existing notations, and the numerous definitions of what a business process is, the BPM community still lacks a robust (ontological) characterisation of the elements involved in business process models and, even more importantly, of the very notion of business process. While some efforts have been done towards this direction, the majority of works in this area focuses on the analysis of the behavioural (control flow) aspects of process models only, thus neglecting other central modelling elements, such as those denoting process participants (e.g., data objects, actors), relationships among activities, goals, values, and so on. The overall purpose of this PhD thesis is to provide a systematic study of the elements that constitute a business process, based on ontological analysis, and to apply these results back to the Business Process Management field. The major contributions that were achieved in pursuing our overall purpose are: (i) a first comprehensive and systematic investigation of what constitutes a business process meta-model in literature, and a definition of what we call a literature-based business process meta-model starting from the different business process meta-models proposed in the literature; (ii) the ontological analysis of four business process elements (event, participant, relationship among activities, and goal), which were identified as missing or problematic in the literature and in the literature-based meta-model; (iii) the revision of the literature-based business process meta-model that incorporates the analysis of the four investigated business process elements - event, participant, relationship among activities and goal; and (iv) the definition and evaluation of a notation that enriches the relationships between activities by including the notions of occurrence dependences and rationales

Privacy in trajectory micro-data publishing : a survey

We survey the literature on the privacy of trajectory micro-data, i.e., spatiotemporal information about the mobility of individuals, whose collection is becoming increasingly simple and frequent thanks to emerging information and communication technologies. The focus of our review is on privacy-preserving data publishing (PPDP), i.e., the publication of databases of trajectory micro-data that preserve the privacy of the monitored individuals. We classify and present the literature of attacks against trajectory micro-data, as well as solutions proposed to date for protecting databases from such attacks. This paper serves as an introductory reading on a critical subject in an era of growing awareness about privacy risks connected to digital services, and provides insights into open problems and future directions for research.Comment: Accepted for publication at Transactions for Data Privac