BioSWR - Semantic Web services Registry for Bioinformatics

Article About the Authors Metrics Comments Related Content Abstract Introduction Functionality Implementation Discussion Acknowledgments Author Contributions References Reader Comments (0) Figures Abstract Despite of the variety of available Web services registries specially aimed at Life Sciences, their scope is usually restricted to a limited set of well-defined types of services. While dedicated registries are generally tied to a particular format, general-purpose ones are more adherent to standards and usually rely on Web Service Definition Language (WSDL). Although WSDL is quite flexible to support common Web services types, its lack of semantic expressiveness led to various initiatives to describe Web services via ontology languages. Nevertheless, WSDL 2.0 descriptions gained a standard representation based on Web Ontology Language (OWL). BioSWR is a novel Web services registry that provides standard Resource Description Framework (RDF) based Web services descriptions along with the traditional WSDL based ones. The registry provides Web-based interface for Web services registration, querying and annotation, and is also accessible programmatically via Representational State Transfer (REST) API or using a SPARQL Protocol and RDF Query Language. BioSWR server is located at http://inb.bsc.es/BioSWR/and its code is available at https://sourceforge.net/projects/bioswr/​under the LGPL license.

Search Interfaces on the Web: Querying and Characterizing

Current-day web search engines (e.g., Google) do not crawl and index a significant portion of theWeb and, hence, web users relying on search engines only are unable to discover and access a large amount of information from the non-indexable part of the Web. Specifically, dynamic pages generated based on parameters provided by a user via web search forms (or search interfaces) are not indexed by search engines and cannot be found in searchers’ results. Such search interfaces provide web users with an online access to myriads of databases on the Web. In order to obtain some information from a web database of interest, a user issues his/her query by specifying query terms in a search form and receives the query results, a set of dynamic pages that embed required information from a database. At the same time, issuing a query via an arbitrary search interface is an extremely complex task for any kind of automatic agents including web crawlers, which, at least up to the present day, do not even attempt to pass through web forms on a large scale. In this thesis, our primary and key object of study is a huge portion of the Web (hereafter referred as the deep Web) hidden behind web search interfaces. We concentrate on three classes of problems around the deep Web: characterization of deep Web, finding and classifying deep web resources, and querying web databases. Characterizing deep Web: Though the term deep Web was coined in 2000, which is sufficiently long ago for any web-related concept/technology, we still do not know many important characteristics of the deep Web. Another matter of concern is that surveys of the deep Web existing so far are predominantly based on study of deep web sites in English. One can then expect that findings from these surveys may be biased, especially owing to a steady increase in non-English web content. In this way, surveying of national segments of the deep Web is of interest not only to national communities but to the whole web community as well. In this thesis, we propose two new methods for estimating the main parameters of deep Web. We use the suggested methods to estimate the scale of one specific national segment of the Web and report our findings. We also build and make publicly available a dataset describing more than 200 web databases from the national segment of the Web. Finding deep web resources: The deep Web has been growing at a very fast pace. It has been estimated that there are hundred thousands of deep web sites. Due to the huge volume of information in the deep Web, there has been a significant interest to approaches that allow users and computer applications to leverage this information. Most approaches assumed that search interfaces to web databases of interest are already discovered and known to query systems. However, such assumptions do not hold true mostly because of the large scale of the deep Web – indeed, for any given domain of interest there are too many web databases with relevant content. Thus, the ability to locate search interfaces to web databases becomes a key requirement for any application accessing the deep Web. In this thesis, we describe the architecture of the I-Crawler, a system for finding and classifying search interfaces. Specifically, the I-Crawler is intentionally designed to be used in deepWeb characterization studies and for constructing directories of deep web resources. Unlike almost all other approaches to the deep Web existing so far, the I-Crawler is able to recognize and analyze JavaScript-rich and non-HTML searchable forms. Querying web databases: Retrieving information by filling out web search forms is a typical task for a web user. This is all the more so as interfaces of conventional search engines are also web forms. At present, a user needs to manually provide input values to search interfaces and then extract required data from the pages with results. The manual filling out forms is not feasible and cumbersome in cases of complex queries but such kind of queries are essential for many web searches especially in the area of e-commerce. In this way, the automation of querying and retrieving data behind search interfaces is desirable and essential for such tasks as building domain-independent deep web crawlers and automated web agents, searching for domain-specific information (vertical search engines), and for extraction and integration of information from various deep web resources. We present a data model for representing search interfaces and discuss techniques for extracting field labels, client-side scripts and structured data from HTML pages. We also describe a representation of result pages and discuss how to extract and store results of form queries. Besides, we present a user-friendly and expressive form query language that allows one to retrieve information behind search interfaces and extract useful data from the result pages based on specified conditions. We implement a prototype system for querying web databases and describe its architecture and components design.

Towards automated specifications of scenarios in enhanced learning technology

Recent standardization efforts in e-learning technology have resulted in a number of specifications, however, the automation process that is considered essential in a learning management system (LMS) is a lessexplored one. As learning technology becomes more widespread and more heterogeneous, there is a growing need to specify processes that cross the boundaries of a single LMS or learning resource repository. This article proposes to obtain a specification orientated to automation that takes on board the heterogeneity of systems and formats and provides a language for specifying complex and generic interactions. Having this goal in mind, a technique based on three steps is suggested. The semantic conformance profiles, the business process management (BPM) diagram, and its translation into the business process execution language (BPEL) seem to be suitable for achieving it.

Trilling race : the political economy of racialised visual-aural encounters

This thesis investigates the matter of race in the context of Finnish language acquisition among adult migrants in Finland. Here matter denotes both the materiality of race and how race comes to matter. Drawing primarily on an auto/ethno/graphic account of learning the Finnish language as a participant in the Finnish for foreigners classes, this thesis problematises the ontology and epistemology of race, i.e., what race is, how it is known, and what an engagement with race entails. Taking cues from the bodily practices of learning the Finnish trill or the rolling r, this study proposes a notion of “trilling race” and argues for an onto-epistemological dis/continuity that marks race’s arrival. The notion of dis/continuity reworks the distinction between continuity and discontinuity, and asks about the how of the arrival of any identity, the where, and the when. In so doing, an analysis of “trilling race” engages with one of the major problematics that has exercised much critical attention, namely: how to read race differently. That is, to rethink the conundrum of the need to counter “representational weight” (Puar 2007, 191) of race on the one hand, and to account for the racialised lived realities on the other. The link between a study of the phenomenon of host country language acquisition and an examination of the question of race is not as obvious as it might seem. For example, what does the argument that the process of language learning is racialised actually imply? Does it mean that race, as a process of racialisation or an ongoing configuration of sets of power relations, exerts force from an outside on the otherwise neutral process of learning the host country language? Or does it mean that race, as an identity category, presents as among the analytical perspectives, along with gender and class for instance, of the phenomenon of host country language acquisition? With these questions in mind, and to foreground the examination of the question of race in the context of Finnish language acquisition among adult migrants, this thesis opens with a discussion of the art installation Finnexia by Lisa Erdman. Finnexia is a fictitious drug said to facilitate Finnish language learning through accelerating the cognitive learning process and reducing the anxiety of speaking the Finnish language. Not only does the Finnexia installation make visible the ways in which the lack of skill in Finnish is fgured as the threshold – a border that separates the inside from the outside – to integration, but also, and importantly, it raises questions about the nature of difference, and the process of differentiation that separates the individual from the social, fact from fiction, nature from culture. These puzzles animate much of the analysis in this dissertation. These concerns continue to be addressed in the rest of part one. Whereas chapter two offers a reconsideration of the ambiguities of ethnisme/ethnicity and race, chapter three dilates on the methodological implications of a conception of the dis/continuity of race. Part two focuses on the matter of race and examines the political economy of visual-aural encounters, whereas part three shifts the focus and rethinks the possibilities and limitations of transforming racialised and normative constraints. Taking up these particular problematics, this thesis as a whole argues that race trills itself: its identity/difference is simultaneously made possible and impossible.

Myths of Modern Education

My focus is on assessment criteria of language proficiency in community college education. To demand clear writing is an application of scientism; it seeks to keep separate the fact/value distinction of positivism. This dangerously undermines the democratizing possibilities of education, since clear writing, taken to its extreme, is ultimately anonymous and dehumanizing. The active student-as-citizen is, therefore, subsumed under the neoliberal dictate of the passive student-as-consumer. The process of language acquisition is reduced to a fictitious act of knowledge transmission and regurgitation, and, therefore, those subversive aspects of language learning, such as creativity and critical inquiry, are undermined. An initial overview of the tenets of modernity will provide a conceptual framework for this examination.

An Abstract Algebraic Theory of L-Fuzzy Relations for Relational Databases

Classical relational databases lack proper ways to manage certain real-world situations including imprecise or uncertain data. Fuzzy databases overcome this limitation by allowing each entry in the table to be a fuzzy set where each element of the corresponding domain is assigned a membership degree from the real interval [0…1]. But this fuzzy mechanism becomes inappropriate in modelling scenarios where data might be incomparable. Therefore, we become interested in further generalization of fuzzy database into L-fuzzy database. In such a database, the characteristic function for a fuzzy set maps to an arbitrary complete Brouwerian lattice L. From the query language perspectives, the language of fuzzy database, FSQL extends the regular Structured Query Language (SQL) by adding fuzzy specific constructions. In addition to that, L-fuzzy query language LFSQL introduces appropriate linguistic operations to define and manipulate inexact data in an L-fuzzy database. This research mainly focuses on defining the semantics of LFSQL. However, it requires an abstract algebraic theory which can be used to prove all the properties of, and operations on, L-fuzzy relations. In our study, we show that the theory of arrow categories forms a suitable framework for that. Therefore, we define the semantics of LFSQL in the abstract notion of an arrow category. In addition, we implement the operations of L-fuzzy relations in Haskell and develop a parser that translates algebraic expressions into our implementation.

Managing Quality Properties of Web Service Compositions

Web services from different partners can be combined to applications that realize a more complex business goal. Such applications built as Web service compositions define how interactions between Web services take place in order to implement the business logic. Web service compositions not only have to provide the desired functionality but also have to comply with certain Quality of Service (QoS) levels. Maximizing the users' satisfaction, also reflected as Quality of Experience (QoE), is a primary goal to be achieved in a Service-Oriented Architecture (SOA). Unfortunately, in a dynamic environment like SOA unforeseen situations might appear like services not being available or not responding in the desired time frame. In such situations, appropriate actions need to be triggered in order to avoid the violation of QoS and QoE constraints. In this thesis, proper solutions are developed to manage Web services and Web service compositions with regard to QoS and QoE requirements. The Business Process Rules Language (BPRules) was developed to manage Web service compositions when undesired QoS or QoE values are detected. BPRules provides a rich set of management actions that may be triggered for controlling the service composition and for improving its quality behavior. Regarding the quality properties, BPRules allows to distinguish between the QoS values as they are promised by the service providers, QoE values that were assigned by end-users, the monitored QoS as measured by our BPR framework, and the predicted QoS and QoE values. BPRules facilitates the specification of certain user groups characterized by different context properties and allows triggering a personalized, context-aware service selection tailored for the specified user groups. In a service market where a multitude of services with the same functionality and different quality values are available, the right services need to be selected for realizing the service composition. We developed new and efficient heuristic algorithms that are applied to choose high quality services for the composition. BPRules offers the possibility to integrate multiple service selection algorithms. The selection algorithms are applicable also for non-linear objective functions and constraints. The BPR framework includes new approaches for context-aware service selection and quality property predictions. We consider the location information of users and services as context dimension for the prediction of response time and throughput. The BPR framework combines all new features and contributions to a comprehensive management solution. Furthermore, it facilitates flexible monitoring of QoS properties without having to modify the description of the service composition. We show how the different modules of the BPR framework work together in order to execute the management rules. We evaluate how our selection algorithms outperform a genetic algorithm from related research. The evaluation reveals how context data can be used for a personalized prediction of response time and throughput.

Using eye movements to investigate word frequency effects in children’s sentence reading

While eye movements have been used widely to investigate how skilled adult readers process written language, relatively little research has used this methodology with children. This is unfortunate as, as we discuss here, eye-movement studies have significant potential to inform our understanding of children’s reading development. We consider some of the empirical and theoretical issues that arise when using this methodology with children, illustrating our points with data from an experiment examining word frequency effects in 8-year-old children’s sentence reading. Children showed significantly longer gaze durations to low than high-frequency words, demonstrating that linguistic characteristics of text drive children’s eye movements as they read. We discuss these findings within the broader context of how eye-movement studies can inform our understanding of children’s reading, and can assist with the development of appropriately targeted interventions to support children as they learn to read.

Seamlessly integrating similarity queries in SQL

Modern database applications are increasingly employing database management systems (DBMS) to store multimedia and other complex data. To adequately support the queries required to retrieve these kinds of data, the DBMS need to answer similarity queries. However, the standard structured query language (SQL) does not provide effective support for such queries. This paper proposes an extension to SQL that seamlessly integrates syntactical constructions to express similarity predicates to the existing SQL syntax and describes the implementation of a similarity retrieval engine that allows posing similarity queries using the language extension in a relational DBM. The engine allows the evaluation of every aspect of the proposed extension, including the data definition language and data manipulation language statements, and employs metric access methods to accelerate the queries. Copyright (c) 2008 John Wiley & Sons, Ltd.

LA ANSIEDAD Y SU RELACIÓN CON LA EXPRESIÓN ORAL EN EL APRENDIZAJE DE LENGUAS EXTRANJERAS : Una elaboración de revisión sistemática de la literatura

La importancia de la dimensión afectiva que acompaña el proceso de adquisición de lenguas extranjeras es indiscutible. Sin embargo, a pesar de esta realidad, y de la evolución de los enfoques comunicativos como métodos de enseñanza de idiomas, la literatura continúa asegurando la existencia de aprensión lingüística en el aula y su efecto debilitador en el proceso de aprendizaje de una nueva lengua. Este estudio tiene como objetivo examinar cómo el aprendiz experimenta la variable de la ansiedad al expresarse oralmente y en qué medida el profesorado de lenguas extranjeras puede lograr crear condiciones en la clase que reduzcan los niveles de ansiedad. En este trabajo utilizamos la revisión sistemática de literatura como estrategia de investigación, un método que constituye una buena herramienta, permitiéndonos sintetizar coherentemente, de forma rigurosa, los resultados de los estudios empíricos sobre el fenómeno de la ansiedad. Los análisis revelan, en primer lugar, que los síntomas experimentados por aprendices de una nueva lengua suelen manifestarse en cada uno de los niveles que integran al individuo, en un nivel emocional, psicológico, fisiológico, de comportamiento y psicopedagógico; en segundo lugar, los investigadores plantean diversas estrategias a nivel psicológico, pedagógico y socio ambiental con el objetivo principal de incrementar en el aprendiz una serie de recursos personales para hacer frente a la ansiedad. Comentamos las implicancias pedagógicas de estos resultados para una mejor comprensión de la ansiedad y del aprendizaje de una lengua extranjera.

Personalised Grid Service Discovery

The authors take a broad view that ultimately Grid- or Web-services must be located via personalised, semantic-rich discovery processes. They argue that such processes must rely on the storage of arbitrary metadata about services that originates from both service providers and service users. Examples of such metadata are reliability metrics, quality of service data, or semantic service description markup. This paper presents UDDI-MT, an extension to the standard UDDI service directory approach that supports the storage of such metadata via a tunnelling technique that ties the metadata store to the original UDDI directory. They also discuss the use of a rich, graph-based RDF query language for syntactic queries on this data. Finally, they analyse the performance of each of these contributions in our implementation.

Personalised Grid Service Discovery

We take a broad view that ultimately Grid- or Web-services must be located via personalised, semantic-rich discovery processes. We argue that such processes must rely on the storage of arbitrary metadata about services that originates from both service providers and service users. Examples of such metadata are reliability metrics, quality of service data, or semantic service description markup. This paper presents UDDI-MT, an extension to the standard UDDI service directory approach that supports the storage of such metadata via a tunnelling technique that ties the metadata store to the original UDDI directory. We also discuss the use of a rich, graph-based RDF query language for syntactic queries on this data. Finally, we analyse the performance of each of these contributions in our implementation.

Suporte a consultas no ambiente temporal de versões

O Modelo Temporal de Versões (TVM Vesions Model) foi proposto com base na união de um modelo de versões com informações temporais. Esse modelo permite o armazenamento de alternativas de projeto, o armazenamento da história dos dados em evolução, bem cmoo a reconstrução do estado da base em qualquer data passada, sem o uso de operações complexas de backup e recovery. Para realizar consultas nesse modelo foi definida uma linguagem de consulta, a TVQL (Temporal Versioned Query Language). Além das consultas básicas realizadas pela linguagem padrão AQL, a TVQL permite novas consultas que retornam valores específicos das características de tempo e versões, estabelecendo um comportamento o mais homogêneo possível para elementos normais e temporais vesionados. O objetivo principal deste trabalho e possibilitar a realização de consultas TVQL em um banco de dados convencional. Nesse contexto, o mapeamento da TVQL é implementando através da tradução de todas as propriedades e funções definidas na TVQL para SQL. Para que isso seja possível é necessário queos dados também estejam nesse banco de dados. Então, faz-se necessário o mapeamento das classes da hierarquia do TVM, bem como das classes da aplciação, para o banco de dados. Adicionalmente, é implementado um protótipo de uma interface de consultas realizadas em TVQL, para testar o funcionamento tanto da TVL como do seu mapeamento.

Extensão do padrão ODMG para suportar tempo e versões

Este trabalho apresenta uma extensão do padrão ODMG para o suporte ao versionamento de objetos e características temporais. Essa extensão, denominada TV_ODMG, é baseada no Modelo Temporal de Versões (TVM), que é um modelo de dados orientado a objetos desenvolvido para armazenar as versões do objeto e, para cada versão, o histórico dos valores dos atributos e dos relacionamentos dinâmicos. O TVM difere de outros modelos de dados temporais por apresentar duas diferentes ordens de tempo, ramificado para o objeto e linear para cada versão. O usuário pode também especificar, durante a modelagem, classes normais (sem tempo e versões), o que permite a integração desse modelo com outras modelagens existentes. Neste trabalho, os seguintes componentes da arquitetura do padrão ODMG foram estendidos: o Modelo de Objetos, a ODL (Object Definition Language) e a OQL (Object Query Language). Adicionalmente, foi desenvolvido um conjunto de regras para o mapeamento do TV_ODMG para o ODMG a fim de permitir o uso de qualquer ODBMS para suportar a extensão proposta.