A New Method to Retrieve, Cluster And Annotate Clinical Literature Related To Electronic Health Records

The access to medical literature collections such as PubMed, MedScape or Cochrane has been increased notably in the last years by the web-based tools that provide instant access to the information. However, more sophisticated methodologies are needed to exploit efficiently all that information. The lack of advanced search methods in clinical domain produce that even using well-defined questions for a particular disease, clinicians receive too many results. Since no information analysis is applied afterwards, some relevant results which are not presented in the top of the resultant collection could be ignored by the expert causing an important loose of information. In this work we present a new method to improve scientific article search using patient information for query generation. Using federated search strategy, it is able to simultaneously search in different resources and present a unique relevant literature collection. And applying NLP techniques it presents semantically similar publications together, facilitating the identification of relevant information to clinicians. This method aims to be the foundation of a collaborative environment for sharing clinical knowledge related to patients and scientific publications.

Simulating Data Journalism to Communicate Hydrological Information from Sensor Networks

Presenting relevant information via web-based user friendly interfac- es makes the information more accessible to the general public. This is especial- ly useful for sensor networks that monitor natural environments. Adequately communicating this type of information helps increase awareness about the limited availability of natural resources and promotes their better use with sus- tainable practices. In this paper, I suggest an approach to communicating this information to wide audiences based on simulating data journalism using artifi- cial intelligence techniques. I analyze this approach by describing a pioneer knowledge-based system called VSAIH, which looks for news in hydrological data from a national sensor network in Spain and creates news stories that gen- eral users can understand. VSAIH integrates artificial intelligence techniques, including a model-based data analyzer and a presentation planner. In the paper, I also describe characteristics of the hydrological national sensor network and the technical solutions applied by VSAIH to simulate data journalism.

Advanced Videoconferencing based on WebRTC

Lately, videoconference applications have experienced an evolution towards the World Wide Web. New technologies have given browsers real-time communications capabilities. In this context, WebRTC aims to provide this functionality by following and defining standards. Being a new effort, WebRTC still lacks advanced videoconferencing services such as session recording, media mixing and adjusting to varying network conditions. This paper analyzes these challenges and proposes an architecture based on a traditional communications entity, the Multipoint Control Unit or MCU as a solution.

Opportunities and Challenges of Implementing P2P Streaming Applications in the Web

P2P applications are increasingly present on the web. We have identified a gap in current proposals when it comes to the use of traditional P2P overlays for real-time multimedia streaming. We analyze the possibilities and challenges to extend WebRTC in order to implement JavaScript APIs for P2P streaming algorithms.

The dicode workbench: A flexible framework for the integration of information and web services

Aiming to address requirements concerning integration of services in the context of ?big data?, this paper presents an innovative approach that (i) ensures a flexible, adaptable and scalable information and computation infrastructure, and (ii) exploits the competences of stakeholders and information workers to meaningfully confront information management issues such as information characterization, classification and interpretation, thus incorporating the underlying collective intelligence. Our approach pays much attention to the issues of usability and ease-of-use, not requiring any particular programming expertise from the end users. We report on a series of technical issues concerning the desired flexibility of the proposed integration framework and we provide related recommendations to developers of such solutions. Evaluation results are also discussed.

On a meaningful integration of web services in data-intensive biomedical environments: The DICODE approach

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.

Modeling Commercial Knowledge to Develop Advanced Agent-based Marketplaces for E-commerce

This paper argues about the utility of advanced knowledge-based techniques to develop web-based applications that help consumers in finding products within marketplaces in e-commerce. In particular, we describe the idea of model-based approach to develop a shopping agent that dynamically configures a product according to the needs and preferences of customers. Finally, the paper summarizes the advantages provided by this approach.

Nanoinformatics approaches for information extraction and text mining in nanomedical research texts

La nanotecnología es un área de investigación de reciente creación que trata con la manipulación y el control de la materia con dimensiones comprendidas entre 1 y 100 nanómetros. A escala nanométrica, los materiales exhiben fenómenos físicos, químicos y biológicos singulares, muy distintos a los que manifiestan a escala convencional. En medicina, los compuestos miniaturizados a nanoescala y los materiales nanoestructurados ofrecen una mayor eficacia con respecto a las formulaciones químicas tradicionales, así como una mejora en la focalización del medicamento hacia la diana terapéutica, revelando así nuevas propiedades diagnósticas y terapéuticas. A su vez, la complejidad de la información a nivel nano es mucho mayor que en los niveles biológicos convencionales (desde el nivel de población hasta el nivel de célula) y, por tanto, cualquier flujo de trabajo en nanomedicina requiere, de forma inherente, estrategias de gestión de información avanzadas. Desafortunadamente, la informática biomédica todavía no ha proporcionado el marco de trabajo que permita lidiar con estos retos de la información a nivel nano, ni ha adaptado sus métodos y herramientas a este nuevo campo de investigación. En este contexto, la nueva área de la nanoinformática pretende detectar y establecer los vínculos existentes entre la medicina, la nanotecnología y la informática, fomentando así la aplicación de métodos computacionales para resolver las cuestiones y problemas que surgen con la información en la amplia intersección entre la biomedicina y la nanotecnología. Las observaciones expuestas previamente determinan el contexto de esta tesis doctoral, la cual se centra en analizar el dominio de la nanomedicina en profundidad, así como en el desarrollo de estrategias y herramientas para establecer correspondencias entre las distintas disciplinas, fuentes de datos, recursos computacionales y técnicas orientadas a la extracción de información y la minería de textos, con el objetivo final de hacer uso de los datos nanomédicos disponibles. El autor analiza, a través de casos reales, alguna de las tareas de investigación en nanomedicina que requieren o que pueden beneficiarse del uso de métodos y herramientas nanoinformáticas, ilustrando de esta forma los inconvenientes y limitaciones actuales de los enfoques de informática biomédica a la hora de tratar con datos pertenecientes al dominio nanomédico. Se discuten tres escenarios diferentes como ejemplos de actividades que los investigadores realizan mientras llevan a cabo su investigación, comparando los contextos biomédico y nanomédico: i) búsqueda en la Web de fuentes de datos y recursos computacionales que den soporte a su investigación; ii) búsqueda en la literatura científica de resultados experimentales y publicaciones relacionadas con su investigación; iii) búsqueda en registros de ensayos clínicos de resultados clínicos relacionados con su investigación. El desarrollo de estas actividades requiere el uso de herramientas y servicios informáticos, como exploradores Web, bases de datos de referencias bibliográficas indexando la literatura biomédica y registros online de ensayos clínicos, respectivamente. Para cada escenario, este documento proporciona un análisis detallado de los posibles obstáculos que pueden dificultar el desarrollo y el resultado de las diferentes tareas de investigación en cada uno de los dos campos citados (biomedicina y nanomedicina), poniendo especial énfasis en los retos existentes en la investigación nanomédica, campo en el que se han detectado las mayores dificultades. El autor ilustra cómo la aplicación de metodologías provenientes de la informática biomédica a estos escenarios resulta efectiva en el dominio biomédico, mientras que dichas metodologías presentan serias limitaciones cuando son aplicadas al contexto nanomédico. Para abordar dichas limitaciones, el autor propone un enfoque nanoinformático, original, diseñado específicamente para tratar con las características especiales que la información presenta a nivel nano. El enfoque consiste en un análisis en profundidad de la literatura científica y de los registros de ensayos clínicos disponibles para extraer información relevante sobre experimentos y resultados en nanomedicina —patrones textuales, vocabulario en común, descriptores de experimentos, parámetros de caracterización, etc.—, seguido del desarrollo de mecanismos para estructurar y analizar dicha información automáticamente. Este análisis concluye con la generación de un modelo de datos de referencia (gold standard) —un conjunto de datos de entrenamiento y de test anotados manualmente—, el cual ha sido aplicado a la clasificación de registros de ensayos clínicos, permitiendo distinguir automáticamente los estudios centrados en nanodrogas y nanodispositivos de aquellos enfocados a testear productos farmacéuticos tradicionales. El presente trabajo pretende proporcionar los métodos necesarios para organizar, depurar, filtrar y validar parte de los datos nanomédicos existentes en la actualidad a una escala adecuada para la toma de decisiones. Análisis similares para otras tareas de investigación en nanomedicina ayudarían a detectar qué recursos nanoinformáticos se requieren para cumplir los objetivos actuales en el área, así como a generar conjunto de datos de referencia, estructurados y densos en información, a partir de literatura y otros fuentes no estructuradas para poder aplicar nuevos algoritmos e inferir nueva información de valor para la investigación en nanomedicina. ABSTRACT Nanotechnology is a research area of recent development that deals with the manipulation and control of matter with dimensions ranging from 1 to 100 nanometers. At the nanoscale, materials exhibit singular physical, chemical and biological phenomena, very different from those manifested at the conventional scale. In medicine, nanosized compounds and nanostructured materials offer improved drug targeting and efficacy with respect to traditional formulations, and reveal novel diagnostic and therapeutic properties. Nevertheless, the complexity of information at the nano level is much higher than the complexity at the conventional biological levels (from populations to the cell). Thus, any nanomedical research workflow inherently demands advanced information management. Unfortunately, Biomedical Informatics (BMI) has not yet provided the necessary framework to deal with such information challenges, nor adapted its methods and tools to the new research field. In this context, the novel area of nanoinformatics aims to build new bridges between medicine, nanotechnology and informatics, allowing the application of computational methods to solve informational issues at the wide intersection between biomedicine and nanotechnology. The above observations determine the context of this doctoral dissertation, which is focused on analyzing the nanomedical domain in-depth, and developing nanoinformatics strategies and tools to map across disciplines, data sources, computational resources, and information extraction and text mining techniques, for leveraging available nanomedical data. The author analyzes, through real-life case studies, some research tasks in nanomedicine that would require or could benefit from the use of nanoinformatics methods and tools, illustrating present drawbacks and limitations of BMI approaches to deal with data belonging to the nanomedical domain. Three different scenarios, comparing both the biomedical and nanomedical contexts, are discussed as examples of activities that researchers would perform while conducting their research: i) searching over the Web for data sources and computational resources supporting their research; ii) searching the literature for experimental results and publications related to their research, and iii) searching clinical trial registries for clinical results related to their research. The development of these activities will depend on the use of informatics tools and services, such as web browsers, databases of citations and abstracts indexing the biomedical literature, and web-based clinical trial registries, respectively. For each scenario, this document provides a detailed analysis of the potential information barriers that could hamper the successful development of the different research tasks in both fields (biomedicine and nanomedicine), emphasizing the existing challenges for nanomedical research —where the major barriers have been found. The author illustrates how the application of BMI methodologies to these scenarios can be proven successful in the biomedical domain, whilst these methodologies present severe limitations when applied to the nanomedical context. To address such limitations, the author proposes an original nanoinformatics approach specifically designed to deal with the special characteristics of information at the nano level. This approach consists of an in-depth analysis of the scientific literature and available clinical trial registries to extract relevant information about experiments and results in nanomedicine —textual patterns, common vocabulary, experiment descriptors, characterization parameters, etc.—, followed by the development of mechanisms to automatically structure and analyze this information. This analysis resulted in the generation of a gold standard —a manually annotated training or reference set—, which was applied to the automatic classification of clinical trial summaries, distinguishing studies focused on nanodrugs and nanodevices from those aimed at testing traditional pharmaceuticals. The present work aims to provide the necessary methods for organizing, curating and validating existing nanomedical data on a scale suitable for decision-making. Similar analysis for different nanomedical research tasks would help to detect which nanoinformatics resources are required to meet current goals in the field, as well as to generate densely populated and machine-interpretable reference datasets from the literature and other unstructured sources for further testing novel algorithms and inferring new valuable information for nanomedicine.

Global research alliance modelling platform (GRAMP): an open web platform for modelling greenhouse gas emissions from agro-ecosystems

Carbon (C) and nitrogen (N) process-based models are important tools for estimating and reporting greenhouse gas emissions and changes in soil C stocks. There is a need for continuous evaluation, development and adaptation of these models to improve scientific understanding, national inventories and assessment of mitigation options across the world. To date, much of the information needed to describe different processes like transpiration, photosynthesis, plant growth and maintenance, above and below ground carbon dynamics, decomposition and nitrogen mineralization. In ecosystem models remains inaccessible to the wider community, being stored within model computer source code, or held internally by modelling teams. Here we describe the Global Research Alliance Modelling Platform (GRAMP), a web-based modelling platform to link researchers with appropriate datasets, models and training material. It will provide access to model source code and an interactive platform for researchers to form a consensus on existing methods, and to synthesize new ideas, which will help to advance progress in this area. The platform will eventually support a variety of models, but to trial the platform and test the architecture and functionality, it was piloted with variants of the DNDC model. The intention is to form a worldwide collaborative network (a virtual laboratory) via an interactive website with access to models and best practice guidelines; appropriate datasets for testing, calibrating and evaluating models; on-line tutorials and links to modelling and data provider research groups, and their associated publications. A graphical user interface has been designed to view the model development tree and access all of the above functions.

A flexible open source web platform to facilitate Learning Object evaluation

Systematic evaluation of Learning Objects is essential to make high quality Web-based education possible. For this reason, several educational repositories and e-Learning systems have developed their own evaluation models and tools. However, the differences of the context in which Learning Objects are produced and consumed suggest that no single evaluation model is sufficient for all scenarios. Besides, no much effort has been put in developing open tools to facilitate Learning Object evaluation and use the quality information for the benefit of end users. This paper presents LOEP, an open source web platform that aims to facilitate Learning Object evaluation in different scenarios and educational settings by supporting and integrating several evaluation models and quality metrics. The work exposed in this paper shows that LOEP is capable of providing Learning Object evaluation to e-Learning systems in an open, low cost, reliable and effective way. Possible scenarios where LOEP could be used to implement quality control policies and to enhance search engines are also described. Finally, we report the results of a survey conducted among reviewers that used LOEP, showing that they perceived LOEP as a powerful and easy to use tool for evaluating Learning Objects.

GESTÃO DO CONHECIMENTO EM ARRANJOS PRODUTIVOS LOCAIS ESTUDO DE CASO DO PÓLO BRASILEIRO DE COSMÉTICO EM DIADEMA

Esta pesquisa apresenta um estudo de caso cujo objetivo é analisar se arranjos produtivos locais realizam a prática da gestão do conhecimento. A pesquisa foi realizada junto ao Pólo Brasileiro de Cosmético em Diadema, organização sem fins lucrativos, que articula as ações de micro, pequenas e médias empresas organizadas em fabricantes de cosméticos, produtores de bens e serviços, fornecedores de matéria-prima, prestadores de consultoria, comercializadores, clientes e parceiros. Para atender ao objetivo proposto recorreu-se a recursos quantitativo e qualitativo, com a utilização de formulários eletrônicos estruturados, disponibilizados na internet e técnicas da observação participante, envolvendo visitas previamente agendadas ao Pólo de Cosmético. O material de análise utilizou a pesquisa bibliográfica sobre arranjo produtivo local e gestão do conhecimento, caracterização da região do grande ABC e da cidade de Diadema, dados oficiais, políticas governamentais e entrevistas com o corpo diretivo do Pólo. Foi aplicado o instrumento de Terra (2005) que a partir de sete dimensões (estratégia e alta administração, sistemas de informação e comunicação, cultura organizacional, organização e processos de trabalho, políticas e práticas para a administração de recursos humanos e mensuração de resultados), avaliou se as organizações do arranjo produtivo realizam a prática da gestão do conhecimento. Os resultados obtidos apontaram a existência de práticas de gestão do conhecimento, com índices acima da média, convergindo para o entendimento de que se trata de um processo de gestão empresarial, além de confirmar, a partir de um sistema de intercâmbio social a origem do Pólo e seu desenvolvimento.(AU)

GESTÃO DO CONHECIMENTO EM ARRANJOS PRODUTIVOS LOCAIS ESTUDO DE CASO DO PÓLO BRASILEIRO DE COSMÉTICO EM DIADEMA

Esta pesquisa apresenta um estudo de caso cujo objetivo é analisar se arranjos produtivos locais realizam a prática da gestão do conhecimento. A pesquisa foi realizada junto ao Pólo Brasileiro de Cosmético em Diadema, organização sem fins lucrativos, que articula as ações de micro, pequenas e médias empresas organizadas em fabricantes de cosméticos, produtores de bens e serviços, fornecedores de matéria-prima, prestadores de consultoria, comercializadores, clientes e parceiros. Para atender ao objetivo proposto recorreu-se a recursos quantitativo e qualitativo, com a utilização de formulários eletrônicos estruturados, disponibilizados na internet e técnicas da observação participante, envolvendo visitas previamente agendadas ao Pólo de Cosmético. O material de análise utilizou a pesquisa bibliográfica sobre arranjo produtivo local e gestão do conhecimento, caracterização da região do grande ABC e da cidade de Diadema, dados oficiais, políticas governamentais e entrevistas com o corpo diretivo do Pólo. Foi aplicado o instrumento de Terra (2005) que a partir de sete dimensões (estratégia e alta administração, sistemas de informação e comunicação, cultura organizacional, organização e processos de trabalho, políticas e práticas para a administração de recursos humanos e mensuração de resultados), avaliou se as organizações do arranjo produtivo realizam a prática da gestão do conhecimento. Os resultados obtidos apontaram a existência de práticas de gestão do conhecimento, com índices acima da média, convergindo para o entendimento de que se trata de um processo de gestão empresarial, além de confirmar, a partir de um sistema de intercâmbio social a origem do Pólo e seu desenvolvimento.(AU)

trEST, trGEN and Hits: access to databases of predicted protein sequences

High throughput genome (HTG) and expressed sequence tag (EST) sequences are currently the most abundant nucleotide sequence classes in the public database. The large volume, high degree of fragmentation and lack of gene structure annotations prevent efficient and effective searches of HTG and EST data for protein sequence homologies by standard search methods. Here, we briefly describe three newly developed resources that should make discovery of interesting genes in these sequence classes easier in the future, especially to biologists not having access to a powerful local bioinformatics environment. trEST and trGEN are regularly regenerated databases of hypothetical protein sequences predicted from EST and HTG sequences, respectively. Hits is a web-based data retrieval and analysis system providing access to precomputed matches between protein sequences (including sequences from trEST and trGEN) and patterns and profiles from Prosite and Pfam. The three resources can be accessed via the Hits home page (http://hits.isb-sib.ch).

The Patient Informatics Consult Service (PICS): an approach for a patient-centered service

The Patient Informatics Consult Service (PICS) at the Eskind Biomedical Library at Vanderbilt University Medical Center (VUMC) provides patients with consumer-friendly information by using an information prescription mechanism. Clinicians refer patients to the PICS by completing the prescription and noting the patient's condition and any relevant factors. In response, PICS librarians critically appraise and summarize consumer-friendly materials into a targeted information report. Copies of the report are given to both patient and clinician, thus facilitating doctor-patient communication and closing the clinician-librarian feedback loop. Moreover, the prescription form also circumvents many of the usual barriers for patients in locating information, namely, patients' unfamiliarity with medical terminology and lack of knowledge of authoritative sources. PICS librarians capture the time and expertise put into these reports by creating Web-based pathfinders on prescription topics. Pathfinders contain librarian-created disease overviews and links to authoritative resources and seek to minimize the consumer's exposure to unreliable information. Pathfinders also adhere to strict guidelines that act as a model for locating, appraising, and summarizing information for consumers. These mechanisms—the information prescription, research reports, and pathfinders—serve as steps toward the long-term goal of full integration of consumer health information into patient care at VUMC.

Assessment of Web Content Accessibility Levels in Spanish Official Online Education Environments

Diversity-based designing, or the goal of ensuring that web-based information is accessible to as many diverse users as possible, has received growing international acceptance in recent years, with many countries introducing legislation to enforce it. This paper analyses web content accessibility levels in Spanish education portals according to the international guidelines established by the World Wide Web Consortium (W3C) and the Web Accessibility Initiative (WAI). Additionally, it suggests the calculation of an inaccessibility rate as a tool for measuring the degree of non-compliance with WAI Guidelines 2.0 as well as illustrating the significant gap that separates people with disabilities from digital education environments (with a 7.77% average). A total of twenty-one educational web portals with two different web depth levels (42 sampling units) were assessed for this purpose using the automated analysis tool Web Accessibility Test 2.0 (TAW, for its initials in Spanish). The present study reveals a general trend towards non-compliance with the technical accessibility recommendations issued by the W3C-WAI group (97.62% of the websites examined present mistakes in Level A conformance). Furthermore, despite the increasingly high number of legal and regulatory measures about accessibility, their practical application still remains unsatisfactory. A greater level of involvement must be assumed in order to raise awareness and enhance training efforts towards accessibility in the context of collective Information and Communication Technologies (ICTs), since this represents not only a necessity but also an ethical, social, political and legal commitment to be assumed by society.