814 resultados para Semantic Web, Cineca,data warehouse, Università italiane
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Background The RCSB Protein Data Bank (PDB) provides public access to experimentally determined 3D-structures of biological macromolecules (proteins, peptides and nucleic acids). While various tools are available to explore the PDB, options to access the global structural diversity of the entire PDB and to perceive relationships between PDB structures remain very limited. Methods A 136-dimensional atom pair 3D-fingerprint for proteins (3DP) counting categorized atom pairs at increasing through-space distances was designed to represent the molecular shape of PDB-entries. Nearest neighbor searches examples were reported exemplifying the ability of 3DP-similarity to identify closely related biomolecules from small peptides to enzyme and large multiprotein complexes such as virus particles. The principle component analysis was used to obtain the visualization of PDB in 3DP-space. Results The 3DP property space groups proteins and protein assemblies according to their 3D-shape similarity, yet shows exquisite ability to distinguish between closely related structures. An interactive website called PDB-Explorer is presented featuring a color-coded interactive map of PDB in 3DP-space. Each pixel of the map contains one or more PDB-entries which are directly visualized as ribbon diagrams when the pixel is selected. The PDB-Explorer website allows performing 3DP-nearest neighbor searches of any PDB-entry or of any structure uploaded as protein-type PDB file. All functionalities on the website are implemented in JavaScript in a platform-independent manner and draw data from a server that is updated daily with the latest PDB additions, ensuring complete and up-to-date coverage. The essentially instantaneous 3DP-similarity search with the PDB-Explorer provides results comparable to those of much slower 3D-alignment algorithms, and automatically clusters proteins from the same superfamilies in tight groups. Conclusion A chemical space classification of PDB based on molecular shape was obtained using a new atom-pair 3D-fingerprint for proteins and implemented in a web-based database exploration tool comprising an interactive color-coded map of the PDB chemical space and a nearest neighbor search tool. The PDB-Explorer website is freely available at www.cheminfo.org/pdbexplorer and represents an unprecedented opportunity to interactively visualize and explore the structural diversity of the PDB.
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After the extraordinary spread of the World Wide Web during the last fifteen years, engineers and developers are pushing now the Internet to its next border. A new conception in computer science and networks communication has been burgeoning during roughly the last decade: a world where most of the computers of the future will be extremely downsized, to the point that they will look like dust at its most advanced prototypes. In this vision, every single element of our “real” world has an intelligent tag that carries all their relevant data, effectively mapping the “real” world into a “virtual” one, where all the electronically augmented objects are present, can interact among them and influence with their behaviour that of the other objects, or even the behaviour of a final human user. This is the vision of the Internet of the Future, which also draws ideas of several novel tendencies in computer science and networking, as pervasive computing and the Internet of Things. As it has happened before, materializing a new paradigm that changes the way entities interrelate in this new environment has proved to be a goal full of challenges in the way. Right now the situation is exciting, with a plethora of new developments, proposals and models sprouting every time, often in an uncoordinated, decentralised manner away from any standardization, resembling somehow the status quo of the first developments of advanced computer networking, back in the 60s and the 70s. Usually, a system designed after the Internet of the Future will consist of one or several final user devices attached to these final users, a network –often a Wireless Sensor Network- charged with the task of collecting data for the final user devices, and sometimes a base station sending the data for its further processing to less hardware-constrained computers. When implementing a system designed with the Internet of the Future as a pattern, issues, and more specifically, limitations, that must be faced are numerous: lack of standards for platforms and protocols, processing bottlenecks, low battery lifetime, etc. One of the main objectives of this project is presenting a functional model of how a system based on the paradigms linked to the Internet of the Future works, overcoming some of the difficulties that can be expected and showing a model for a middleware architecture specifically designed for a pervasive, ubiquitous system. This Final Degree Dissertation is divided into several parts. Beginning with an Introduction to the main topics and concepts of this new model, a State of the Art is offered so as to provide a technological background. After that, an example of a semantic and service-oriented middleware is shown; later, a system built by means of this semantic and service-oriented middleware, and other components, is developed, justifying its placement in a particular scenario, describing it and analysing the data obtained from it. Finally, the conclusions inferred from this system and future works that would be good to be tackled are mentioned as well. RESUMEN Tras el extraordinario desarrollo de la Web durante los últimos quince años, ingenieros y desarrolladores empujan Internet hacia su siguiente frontera. Una nueva concepción en la computación y la comunicación a través de las redes ha estado floreciendo durante la última década; un mundo donde la mayoría de los ordenadores del futuro serán extremadamente reducidas de tamaño, hasta el punto que parecerán polvo en sus más avanzado prototipos. En esta visión, cada uno de los elementos de nuestro mundo “real” tiene una etiqueta inteligente que porta sus datos relevantes, mapeando de manera efectiva el mundo “real” en uno “virtual”, donde todos los objetos electrónicamente aumentados están presentes, pueden interactuar entre ellos e influenciar con su comportamiento el de los otros, o incluso el comportamiento del usuario final humano. Ésta es la visión del Internet del Futuro, que también toma ideas de varias tendencias nuevas en las ciencias de la computación y las redes de ordenadores, como la computación omnipresente y el Internet de las Cosas. Como ha sucedido antes, materializar un nuevo paradigma que cambia la manera en que las entidades se interrelacionan en este nuevo entorno ha demostrado ser una meta llena de retos en el camino. Ahora mismo la situación es emocionante, con una plétora de nuevos desarrollos, propuestas y modelos brotando todo el rato, a menudo de una manera descoordinada y descentralizada lejos de cualquier estandarización, recordando de alguna manera el estado de cosas de los primeros desarrollos de redes de ordenadores avanzadas, allá por los años 60 y 70. Normalmente, un sistema diseñado con el Internet del futuro como modelo consistirá en uno o varios dispositivos para usuario final sujetos a estos usuarios finales, una red –a menudo, una red de sensores inalámbricos- encargada de recolectar datos para los dispositivos de usuario final, y a veces una estación base enviando los datos para su consiguiente procesado en ordenadores menos limitados en hardware. Al implementar un sistema diseñado con el Internet del futuro como patrón, los problemas, y más específicamente, las limitaciones que deben enfrentarse son numerosas: falta de estándares para plataformas y protocolos, cuellos de botella en el procesado, bajo tiempo de vida de las baterías, etc. Uno de los principales objetivos de este Proyecto Fin de Carrera es presentar un modelo funcional de cómo trabaja un sistema basado en los paradigmas relacionados al Internet del futuro, superando algunas de las dificultades que pueden esperarse y mostrando un modelo de una arquitectura middleware específicamente diseñado para un sistema omnipresente y ubicuo. Este Proyecto Fin de Carrera está dividido en varias partes. Empezando por una introducción a los principales temas y conceptos de este modelo, un estado del arte es ofrecido para proveer un trasfondo tecnológico. Después de eso, se muestra un ejemplo de middleware semántico orientado a servicios; después, se desarrolla un sistema construido por medio de este middleware semántico orientado a servicios, justificando su localización en un escenario particular, describiéndolo y analizando los datos obtenidos de él. Finalmente, las conclusiones extraídas de este sistema y las futuras tareas que sería bueno tratar también son mencionadas.
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Sensor networks are increasingly becoming one of the main sources of Big Data on the Web. However, the observations that they produce are made available with heterogeneous schemas, vocabularies and data formats, making it difficult to share and reuse these data for other purposes than those for which they were originally set up. In this thesis we address these challenges, considering how we can transform streaming raw data to rich ontology-based information that is accessible through continuous queries for streaming data. Our main contribution is an ontology-based approach for providing data access and query capabilities to streaming data sources, allowing users to express their needs at a conceptual level, independent of implementation and language-specific details. We introduce novel query rewriting and data translation techniques that rely on mapping definitions relating streaming data models to ontological concepts. Specific contributions include: • The syntax and semantics of the SPARQLStream query language for ontologybased data access, and a query rewriting approach for transforming SPARQLStream queries into streaming algebra expressions. • The design of an ontology-based streaming data access engine that can internally reuse an existing data stream engine, complex event processor or sensor middleware, using R2RML mappings for defining relationships between streaming data models and ontology concepts. Concerning the sensor metadata of such streaming data sources, we have investigated how we can use raw measurements to characterize streaming data, producing enriched data descriptions in terms of ontological models. Our specific contributions are: • A representation of sensor data time series that captures gradient information that is useful to characterize types of sensor data. • A method for classifying sensor data time series and determining the type of data, using data mining techniques, and a method for extracting semantic sensor metadata features from the time series.
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The goal of the W3C's Media Annotation Working Group (MAWG) is to promote interoperability between multimedia metadata formats on the Web. As experienced by everybody, audiovisual data is omnipresent on today's Web. However, different interaction interfaces and especially diverse metadata formats prevent unified search, access, and navigation. MAWG has addressed this issue by developing an interlingua ontology and an associated API. This article discusses the rationale and core concepts of the ontology and API for media resources. The specifications developed by MAWG enable interoperable contextualized and semantic annotation and search, independent of the source metadata format, and connecting multimedia data to the Linked Data cloud. Some demonstrators of such applications are also presented in this article.
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This paper reports on an innovative approach that aims to reduce information management costs in data-intensive and cognitively-complex biomedical environments. Recognizing the importance of prominent high-performance computing paradigms and large data processing technologies as well as collaboration support systems to remedy data-intensive issues, it adopts a hybrid approach by building on the synergy of these technologies. The proposed approach provides innovative Web-based workbenches that integrate and orchestrate a set of interoperable services that reduce the data-intensiveness and complexity overload at critical decision points to a manageable level, thus permitting stakeholders to be more productive and concentrate on creative activities.
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Current methods and tools that support Linked Data publication have mainly focused so far on static data, without considering the growing amount of streaming data available on the Web. In this paper we describe a case study that involves the publication of static and streaming Linked Data for bike sharing systems and related entities. We describe some of the challenges that we have faced, the solutions that we have explored, the lessons that we have learned, and the opportunities that lie in the future for exploiting Linked Stream Data.
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The creation of language resources is a time-consuming process requiring the efforts of many people. The use of resources collaboratively created by non-linguists can potentially ameliorate this situation. However, such resources often contain more errors compared to resources created by experts. For the particular case of lexica, we analyse the case of Wiktionary, a resource created along wiki principles and argue that through the use of a principled lexicon model, namely lemon, the resulting data could be better understandable to machines. We then present a platform called lemon source that supports the creation of linked lexical data along the lemon model. This tool builds on the concept of a semantic wiki to enable collaborative editing of the resources by many users concurrently. In this paper, we describe the model, the tool and present an evaluation of its usability based on a small group of users.
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In this paper we present a revisited classification of term variation in the light of the Linked Data initiative. Linked Data refers to a set of best practices for publishing and connecting structured data on the Web with the idea of transforming it into a global graph. One of the crucial steps of this initiative is the linking step, in which datasets in one or more languages need to be linked or connected with one another. We claim that the linking process would be facilitated if datasets are enriched with lexical and terminological information. Being that the final aim, we propose a classification of lexical, terminological and semantic variants that will become part of a model of linguistic descriptions that is currently being proposed within the framework of the W3C Ontology-Lexica Community Group to enrich ontologies and Linked Data vocabularies. Examples of modeling solutions of the different types of variants are also provided.
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In this paper we present a revisited classification of term variation in the light of the Linked Data initiative. Linked Data refers to a set of best practices for publishing and connecting structured data on the Web with the idea of transforming it into a global graph. One of the crucial steps of this initiative is the linking step, in which datasets in one or more languages need to be linked or connected with one another. We claim that the linking process would be facilitated if datasets are enriched with lexical and terminological information. Being that the final aim, we propose a classification of lexical, terminological and semantic variants that will become part of a model of linguistic descriptions that is currently being proposed within the framework of the W3C Ontology- Lexica Community Group to enrich ontologies and Linked Data vocabularies. Examples of modeling solutions of the different types of variants are also provided.
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There is an increasing tendency of turning the current power grid, essentially unaware of variations in electricity demand and scattered energy sources, into something capable of bringing a degree of intelligence by using tools strongly related to information and communication technologies, thus turning into the so-called Smart Grid. In fact, it could be considered that the Smart Grid is an extensive smart system that spreads throughout any area where power is required, providing a significant optimization in energy generation, storage and consumption. However, the information that must be treated to accomplish these tasks is challenging both in terms of complexity (semantic features, distributed systems, suitable hardware) and quantity (consumption data, generation data, forecasting functionalities, service reporting), since the different energy beneficiaries are prone to be heterogeneous, as the nature of their own activities is. This paper presents a proposal on how to deal with these issues by using a semantic middleware architecture that integrates different components focused on specific tasks, and how it is used to handle information at every level and satisfy end user requests.
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We present a methodology for legacy language resource adaptation that generates domain-specific sentiment lexicons organized around domain entities described with lexical information and sentiment words described in the context of these entities. We explain the steps of the methodology and we give a working example of our initial results. The resulting lexicons are modelled as Linked Data resources by use of established formats for Linguistic Linked Data (lemon, NIF) and for linked sentiment expressions (Marl), thereby contributing and linking to existing Language Resources in the Linguistic Linked Open Data cloud.
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Conferencia por invitación, impartida el 31 d mayo de 2014 en el Workshop on Language Technology Service Platforms: Synergies, Standards, Sharing at LREC2014
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The robotics is one of the most active areas. We also need to join a large number of disciplines to create robots. With these premises, one problem is the management of information from multiple heterogeneous sources. Each component, hardware or software, produces data with different nature: temporal frequencies, processing needs, size, type, etc. Nowadays, technologies and software engineering paradigms such as service-oriented architectures are applied to solve this problem in other areas. This paper proposes the use of these technologies to implement a robotic control system based on services. This type of system will allow integration and collaborative work of different elements that make up a robotic system.
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This paper introduces the Sm4RIA Extension for OIDE, which implements the Sm4RIA approach in OIDE (OOH4RIA Integrated Development Environment). The application, based on the Eclipse framework, supports the design of the Sm4RIA models as well as the model-to-model and model-to-text transformation processes that facilitate the generation of Semantic Rich Internet Applications, i.e., RIA applications capable of sharing data as Linked data and consuming external data from other sources in the same manner. Moreover, the application implements mechanisms for the creation of RIA interfaces from ontologies and the automatic generation of administration interfaces for a previously design application.
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In this work we present a semantic framework suitable of being used as support tool for recommender systems. Our purpose is to use the semantic information provided by a set of integrated resources to enrich texts by conducting different NLP tasks: WSD, domain classification, semantic similarities and sentiment analysis. After obtaining the textual semantic enrichment we would be able to recommend similar content or even to rate texts according to different dimensions. First of all, we describe the main characteristics of the semantic integrated resources with an exhaustive evaluation. Next, we demonstrate the usefulness of our resource in different NLP tasks and campaigns. Moreover, we present a combination of different NLP approaches that provide enough knowledge for being used as support tool for recommender systems. Finally, we illustrate a case of study with information related to movies and TV series to demonstrate that our framework works properly.