Enhancing K-12 science education through a multi-device web tool to facilitate content integration and e-infrastructure access

An effective K-12 science education is essential to succeed in future phases of the curriculum and the e-Infrastructures for education provide new opportunities to enhance it. This paper presents ViSH Viewer, an innovative web tool to consume educational content which aims to facilitate e-Science infrastructures access through a next generation learning object called "Virtual Excursion". Virtual Excursions provide a new way to explore science in class by taking advantage of e-Infrastructure resources and their integration with other educational contents, resulting in the creation of a reusable, interoperable and granular learning object. In order to better understand how this tool can allow teachers and students a joyful exploration of e-Science, we also present three Virtual Excursion examples. Details about the design, development and the tool itself are explained in this paper as well as the concept, structure and metadata of the new learning object.

Competence Monitoring in Project Teams by using Web based portfolio management systems

This paper reports a learning experience related to the acquisition of project management competences. Students from three different universities and backgrounds, cooperate in a common project that drives the learning-teaching process. Previous related works on this initiative have already evaluated the goodness of this multidisciplinary, project-based learning approach in the context of a new educative paradigm. Yet the innovative experience has allowed the authors to define a rubric in order to measure specific competences in project management. The study shows the rubric’s main aspects as well as competence acquisition evaluation alternatives, based in the metrics defined. Key indicators and specific reports obtained from data base fields in the web tool will support this work. As a result, new competences can be assessed, such ones like teamwork, problem solving, communication and leadership. Final goal is to provide an overall competence map to the students at the same time they improve their skills.

Validation tool for smart screening of language disorders in pediatrics care

Primary-care pediatricians could play a key role in early detection of development disorders as quick as they might have enough time and knowledge for suitable screenings at clinical routine. This research paper focuses on the development and validation of a knowledge-based web tool whose aim is to support a smart detection of developmental disorders in early childhood. Thus, the use of the system can trigger the necessary preventive and therapeutic actions from birth until the age of six. The platform was designed on the basis of an analysis of significant 21 cases of children with language disorders that supported the creation of a specific knowledge base, its ontology and a set of description logic relations. The resulting system is being validated in a scalable approach with a team of seven experts from the fields of neonathology, pediatrics, neurology and language therapy.

Desarrollo de una aplicación web orientada a la asistencia en el diseño de protocolos de biología sintética

Se plantea desarrollar una herramienta que ofrezca un soporte eficiente para la creación y el diseño de protocolos biológicos a los investigadores en biología sintética. Partiendo de este objetivo, se definen dos cometidos principales: Realizar un estudio de las herramientas existentes que ofrezcan soporte al diseño y aquellas pensadas para diseñar protocolos biológicos, el fin de este estudio es descubrir las funcionalidades que implementan estas herramientas para mejorarlas. Además, se ha de desarrollar una herramienta web que, mediante un lenguaje visual, permita diseñar y crear protocolos de biología sintética, guardándolos en un formato de archivo independiente del lenguaje. En este documento se encuentra, en primer lugar, la definición de objetivos y la descripción del método de desarrollo seguido durante la implementación del proyecto; después, el marco teórico, donde se exponen las herramientas estudiadas y las similitudes y diferencias con la idea que se tiene de la aplicación, y también las herramientas de desarrollo web con las que se va a implementar el proyecto. A continuación, se muestran los resultados obtenidos, mediante la definición de requisitos, así como una exposición de la propia herramienta. Por último, se encuentra la estrategia de validación que se ha seguido en el desarrollo del proyecto y se exponen las conclusiones obtenidas de estas validaciones; también se incluyen al final las conclusiones del proyecto y las líneas futuras de desarrollo.---ABSTRACT---It is planned to develop a tool that provides efficient support for the creation and design of biological protocols researchers in synthetic biology. Based on this goal, two main tasks are defined: Conduct a study of existing tools that provide design support and those intended to design biological protocols, the purpose of this study is to discover the functionalities that implement these tools to improve them. Furthermore, it has to develop a web tool that, through a visual language, allowing design and create synthetic biology protocols, storing them in an independent language file format. In this document is located, first, the definition of objectives and description of the development method followed during project implementation; then the theoretical framework where tools and studied the similarities and differences with the idea we have of the application are discussed, and development tools with which they will implement the project. Then the results obtained, by defining requirements as well as an exhibition of the own tool. Finally, the validation strategy that has been followed in the development of the project and the conclusions drawn from these validations are exposed; also, it is included at the end of the project conclusions and future lines of development.

Herramienta Web para el modelado de consultas CEP (Complex Event Processing)

RESUMEN En los últimos años, debido al incremento en la demanda por parte de las empresas de tecnologías que posibiliten la monitorización y el análisis de un gran volumen de datos en tiempo real, la tecnología CEP (Complex Event Processing) ha surgido como una potencia en alza y su uso se ha incrementado notablemente en ciertos sectores como, por ejemplo, la gestión y automatización de procesos de negocios, finanzas, monitorización de redes y aplicaciones, así como redes de sensores inteligentes como el caso de estudio en el que nos centraremos. CEP se basa en un lenguaje de procesamiento de eventos (Event Processing Language,EPL) cuya utilización puede resultar bastante compleja para usuarios inexpertos. Esta complejidad supone un hándicap y, por lo tanto, un problema a la hora de que su uso se extienda. Este Proyecto Fin de Grado (PFG) pretende dar una solución a este problema, acercando al usuario la tecnología CEP mediante técnicas de abstracción y modelado. Para ello, este PFG ha definido un lenguaje de modelado específico dominio, sencillo e intuitivo para el usuario inexperto, al que se ha dado soporte mediante el desarrollo de una herramienta de modelado gráfico (CEP Modeler) en la que se pueden modelar consultas CEP de forma gráfica, sencilla y de manera más accesible para el usuario. ABSTRACT Over recent years, more and more companies demand technology for monitoring and analyzing a vast volume of data in real time. In this regard, the CEP technology (Complex Event Processing) has emerged as a novel approach to that end, and its use has increased dramatically in certain domains, such as, management and automation of business processes, finance, monitoring of networks and applications, as well as smart sensor networks as the case study in which we will focus. CEP is based on in the Event Processing Language (EPL). This language can be rather difficult to use for new users. This complexity can be a handicap, and therefore, a problem at the time of extending its use. This project aims to provide a solution to this problem, trying to approach the CEP technology to users through abstraction and modelling techniques. To that end, this project has defined an intuitive and simple domain-specific modelling language for new users through a web tool (CEP Modeler) for graphically modeling CEP queries, in an easier and more accessible way.

Estudio y desarrollo del plan de negocio de una empresa: Sistema Web que gestiona e informa sobre las cuentas digitales que el cliente ingresa

El presente documento tiene como objetivo general desarrollar un plan de negocio para analizar la viabilidad de la creación de una nueva empresa, “MyTested S.L.”. Pretende ofrecer una herramienta para que las personas puedan comunicar a sus familiares el acceso a sus cuentas digitales una vez fallecidos. En cuanto a cómo surge la idea, fue a través de una noticia que trataba sobre el derecho al olvido en las redes sociales y en internet. Investigando un poco y prestando atención a los movimientos de las grandes empresas de internet, mi compañero/socio y yo, nos dimos cuenta de que ofrecer este servicio podría valer como negocio, ya que no existe mucha competencia en el mercado. Gracias a eso, nos planteamos en más de una ocasión la posibilidad de montar nuestro propio negocio, de forma que pudiéramos utilizar los conocimientos adquiridos en la universidad como base para crear la herramienta web. Escogimos empezar el proyecto utilizándolo como materia para el trabajo de fin de grado porque nos aporta dos valores muy importantes, ayuda de la comunidad de profesores existentes en la UPM, siendo una persona de gran aporte nuestro tutor Oscar Corcho y también, porque como estamos dedicando todo el tiempo a este proyecto, tener una fecha límite para presentar tanto la parte de modelo de negocio como la parte de desarrollo en una fecha concreta, nos ayuda a planificar y mantener una presión constante sobre el proyecto y así forzar a no abandonarlo ni prolongarlo. Con ello, nos encontramos con dos grupos de dificultades, la escasa formación a nivel empresarial y creación de modelos de negocio y en el ámbito del desarrollo al desconocimiento de tecnologías y APIs de las redes sociales. Al tratarse de una herramienta Web, parte de unos costes muy bajos como el alojamiento del servidor o la contratación temporal de comerciales para publicitar la herramienta entre funerarias y hospitales. Estos factores positivos benefician tanto la realización del proyecto como su avance. Como ya se puede intuir de la lectura del párrafo anterior, el servicio que ofrece la herramienta “MyTested S.L.” está relacionado con el segmento testamental de una persona fallecida, podríamos definirlo como testamento digital. Actualmente, vivimos en un mundo que se centra cada vez más en la parte digital y es por ello, que en un futuro cercano, todas las cuentas que creamos en internet tendrán que ser cerradas o bloqueadas cuando caen en el desuso por el fallecimiento del propietario, es en ese hueco donde podemos situarnos, ofreciendo una herramienta para poder trasladar la información necesaria a las personas elegidas por el cliente para que puedan cerrar o bloquear sus cuentas digitales. Consideramos que existe una interesante oportunidad debido a la escasez de oferta de este tipo de servicios en España y a nivel mundial. En Abril de 2015 hay inscritos en el registro Nacional de últimas voluntades 185.6651 personas por lo que encontramos que un 0,397%1 de las personas en España ha registrado su testamento. El gasto medio al hacer un testamento vital ante notario de tus bienes tiene un coste de 40 a 80 euros2 , este es el principal motivo por el que la mayoría de españoles no realiza su testamento antes de morir. Con este dato obtenemos dos lecciones, lo que la herramienta ofrece no es el documento notarial de los bienes del cliente, sino la sistema, puedan bloquear o cerrar sus cuentas. La segunda lección que obtenemos es que el precio tiene que ser muy reducido para poder llegar a un gran número de personas, añadiendo también el criterio de que el cliente podrá actualizar su información, ya que la información digital es muy fácil de cambiar y frecuente. Como se podrá leer en al apartado dedicado a nuestra visión, misión y valores, aunque estamos convencidos que se puede extraer de la lectura de cualquier parte de este documento, todos nuestros objetivos los queremos conseguir no sólo buscando un enfoque empresarial a nuestro día a día, sino convirtiendo nuestra responsabilidad social sincera, en uno de los retos que más nos ilusionan, fomentando para ello, aspectos como el desarrollo web, estudios de mercado, conocimiento de las necesidades de la población, nuevas tecnologías y negocio. En general, los objetivos que se pretenden cumplir con este estudio son: - Conocer los pasos para crear una empresa - Desarrollar un documento de plan de negocio que contenga lo siguiente: - Análisis de mercado - Definición de productos y/o servicios - Plan de publicidad y expansión (marketing) - Plan financiero - Capacidad para definir los requisitos de una aplicación Web. - Capacidad de elegir la tecnología idónea y actual de un sistema Web. - Conocer el funcionamiento de una empresa y cómo comunicarse con las herramientas gubernamentales. - Comprobar si las posibilidades que nos ofrece el entorno son las adecuadas para nuestras actividades. - Estudio, análisis de la competencia - Definir los diferentes perfiles de cliente para nuestro negocio. - Analizar la viabilidad de nuestro modelo de negocio. Para ello, comenzamos realizando una definición de las características generales del proyecto, detallando cuáles son las motivaciones que han hecho a los emprendedores embarcarse en el mismo, qué servicios ofreceremos a nuestros clientes, el porqué de la elección del sector, así́ como nuestra misión, visión y valores.---ABSTRACT---The goal and aim of the present document is to develop a business plan in order to analyze the viability of build a new enterprise, that we will name MyTested S.L., it wants offer a tool for sharing and to facilitate to the relatives of a dead person the access to the digital accounts. Talking about how come up the idea, it was once a have read a news over the “right of forgotten” throughout social nets and inside internet, researching a little and paying attention to the different movements of the biggest internet companies, my peer ( and partner) and I were aware that to offer this service might be a good business, because does not exist many competitors on this kind of market service, mainly thanks of that, we have planned on several times the possibility to build our owner company, in the way to use the capabilities that we achieved in the University as based to develop and make a web tool. We choose begin this project as subject of our Final Project Degree after analyze the positive and negative point of views: The positive was because it has two main values, firstly the support of the current teachers UPM community, specially our fellow Oscar Corcho and also because we can´t dedicate all our time to this project, so to have a deadline to present either the business model as the develop on time, help us to plan and remain a constant pressure over the project and neither drop out it or extend it more that the necessary. As a web tool, neither the hosting of maintenance or for sort out a net of temporary commercials for visiting hospitals or undertaker´s or insurances, the cost don´t are expensive In the negative side, however, we found twice some main difficulties, the few training as entrepreneur level and how to build a business model and on the other hand the lack of awareness of the technologies and apps of the social net software as well. As summary, these positives facts enhance to work project out and also to develop it. As we could understand reading on the latest paragraph, the service that will do MyTested tool is relation with the testament issue of a dead person, we might call as a digital testament. Currently we are living in world which is focus further on the digital life, for that in a near future every internet accounts should be closed or locked whenever aren´t used by the dead of the owner, this is a market niche (never better said) where we can lead, offering a tool that might transfer the necessary information to the chosen persons by the client in order to allow either close or lock his digital accounts. We are considering that there are interesting opportunities due to the few offers of that kind of service in Spain and at global level. In April 2015 there were 185.6651 persons registered in the Official National last will and testament, this figure mean that the 0,397%1 of the Spaniards citizens have registered their testaments. The average cost of doing the testament of your assets with a Notary is since 40 up to 80€2, this is one of the principal motives because the majority of the Spaniards don´t do it before dead. With these data we might get two lessons, we are not talking about an official notary testament at all, it is only for close or lock the digital accounts by the chosen person by the dead client, and the latest lesson, but not least, the price of our service must be very cheaper in order to achieve touch an important amount of people, knowing also that he client will be able update the information filled, considering that this kind of information is very easy to change and update frequently. As we can read on the stage dedicated to our Vision, Mission and Values, although we are persuaded that can be read in everywhere of this document as well, our aim doesn´t be an business focus on day to day, is also to become our honest social responsibility in this challenge, that is our mainly eagerness, enhancing some aspects as the web development, market research and the knowledge of the population needs, new technologies and new market opportunities. In general the goals that we would like get within this project are: - Achieve the knowledge needs for be an entrepreneurial, and find out the steps for star a business - Achieve market research skills - Products and services definitions - Advertising plan and growth (marketing plan) - Financial plan knowledge - Capability of a web design requirements - Capability for choose the best and actual technology for web design - Knowledge over how work out inside a company and how communicate with official tools. - Check whether the possibilities of the environment are the adequate for our activities. - Research and competitiveness analysis - Define the different profiles of the target for our business. - Analyze the viability of the business model For all that, we began with a definition of the general features of the project, detailing which are the motivations those done to the entrepreneurial get on board, which kind of service we offered to the client, also why the selection of the market sector and our mission, vision and value as well.

Virtual Excursions: a new way to explore science in class

The educational platform Virtual Science Hub (ViSH) has been developed as part of the GLOBAL excursion European project. ViSH (http://vishub.org/) is a portal where teachers and scientist interact to create virtual excursions to science infrastructures. The main motivation behind the project was to connect teachers - and in consequence their students - to scientific institutions and their wide amount of infrastructures and resources they are working with. Thus the idea of a hub was born that would allow the two worlds of scientists and teachers to connect and to innovate science teaching. The core of the ViSH?s concept design is based on virtual excursions, which allow for a number of pedagogical models to be applied. According to our internal definition a virtual excursion is a tour through some digital context by teachers and pupils on a given topic that is attractive and has an educational purpose. Inquiry-based learning, project-based and problem-based learning are the most prominent approaches that a virtual excursion may serve. The domain specific resources and scientific infrastructures currently available on the ViSH are focusing on life sciences, nano-technology, biotechnology, grid and volunteer computing. The virtual excursion approach allows an easy combination of these resources into interdisciplinary teaching scenarios. In addition, social networking features support the users in collaborating and communicating in relation to these excursions and thus create a community of interest for innovative science teaching. The design and development phases were performed following a participatory design approach. An important aspect in this process was to create design partnerships amongst all actors involved, researchers, developers, infrastructure providers, teachers, social scientists, and pedagogical experts early in the project. A joint sense of ownership was created and important changes during the conceptual phase were implemented in the ViSH due to early user feedback. Technology-wise the ViSH is based on the latest web technologies in order to make it cross-platform compatible so that it works on several operative systems such as Windows, Mac or Linux and multi-device accessible, such as desktop, tablet and mobile devices. The platform has been developed in HTML5, the latest standard for web development, assuring that it can run on any modern browser. In addition to social networking features a core element on the ViSH is the virtual excursions editor. It is a web tool that allows teachers and scientists to create rich mash-ups of learning resources provided by the e-Infrastructures (i.e. remote laboratories and live webcams). These rich mash-ups can be presented in either slides or flashcards format. Taking advantage of the web architecture supported, additional powerful components have been integrated like a recommendation engine to provide personalized suggestions about educational content or interesting users and a videoconference tool to enhance real-time collaboration like MashMeTV (http://www.mashme.tv/).

Marco de diseño de la interacción para aplicaciones móviles

El desarrollo de aplicaciones móviles multiplataforma se ha convertido en una tarea compleja debido al alto crecimiento de dispositivos móviles y a la diversidad de plataformas que existen en el mercado. Tras identificar que las principales plataformas utilizadas por los usuarios a nivel mundial son iOS y Android y observar la evolución que han sufrido dichas plataformas desde un punto de vista de diseño de la interacción en los últimos años se establecen las bases para la realización del marco de diseño de la interacción en aplicaciones móviles. El marco de diseño pretende identificar la estructura de las aplicaciones en ambas plataformas y observar las similitudes y diferencias que existen entre las mismas. Por otra parte, se analizan, como parte del mismo, los elementos presentes en el diseño de la interacción de aplicaciones en las plataformas estudiadas con el fin de establecer similitudes y equivalencias entre los mismos. Para evaluar la viabilidad del marco propuesto, se ha llevado a cabo un caso de estudio en el que se aplica el marco sobre una aplicación real. Por último, se realiza una herramienta web con la que se permite a los usuarios poder acceder a la información propuesta en el marco de una forma más sencilla.---ABSTRACT---The mobile app development field has become a very complex task due to the increase of mobile devices and the diversity of the market existing platforms. After identifying that the most used platforms by the users are iOS and Android, and observing the evolution of both from the point of view of the interaction design, the basis for an interaction design frame are established. The design presents the basic structure of a mobile application in both platforms, identifying the existing similarities and differences among them. Moreover, the elements present in the design of the interaction are analysed, in order to establish similarities and equivalences among those elements. In addition, a case study was carried out in which the design frame was applied in a real application. Finally, a web tool which allow users to access the proposed information was developed, in order to have an easier access to the information.

Study on heuristic usability evaluation for mobile applications

Usability guidelines are a useful tool for the developers to improve interaction with systems. It includes knowledge of different disciplines related to usability and provides solutions and best practices to achieve the objectives of usability. Heuristic evaluation is one of the methods most widely used to evaluate and user interfaces. The objective of this study is to enrich the process of heuristic evaluation with the design guidelines focusing it on the evaluation of applications for mobile devices. As well as generate a homogeneous classification of guidelines content, in order to help that from design and development process, be included solutions and good practices provided by the guidelines. In order to achieve the objectives of this work, it is provides a method for generating heuristics for mobile applications, with which four applications were evaluated, and a web tool has also been developed that allows access to the content of the guidelines using the homogeneous classification of guidelines content. The results showed the ease and utility of performing heuristic evaluations using a set of heuristics focused on mobile applications.

Weblog sobre tecnología e Internet utilizando la metodología December

Este proyecto trata el desarrollo de un weblog sobre tecnología e internet siguiendo la Metodología de December, abordando todas sus etapas e incorporando otros aspectos a la metodología que han enriquecido el proyecto hasta su resultado final. Se pretende realizar una aplicación web con la funcionalidad de un weblog centrándose tanto en la parte del usuario final como del administrador de la web. Que este weblog sirva para compartir conocimientos de forma dinámica actualizándose con frecuencia y para usuarios con inquietudes tecnologías y con mayor o menor nivel de conocimientos. Se pone especial interés en la usabilidad de la herramienta y es tenida en cuenta a lo largo de todo el ciclo de vida de la metodología. Como punto de partida para estructurar la aplicación se toma como metodología de desarrollo la metodología December enfocada al desarrollo web y como a partir de ella se da forma a lo que hoy es el proyecto completo. Se tienen en cuenta cada una de sus etapas en las cuales se va avanzando para ir completando cada pieza del desarrollo final. Se intenta también en esta memoria abordar datos más técnicos de la herramienta, desde la elección de los lenguajes utilizados hasta el diseño de la estructura de base de datos, los procesos que intervienen en la aplicación y las decisiones más subjetivas de diseño de la interface web. En todo momento se ha intentado estructurar la memoria de tal forma que resultará clara y concisa, fácil de leer. Plasmando en ella todo el proceso de realización del proyecto. ABSTRACT This project involves the development of a technology and internet weblog following the December’s Methodology, covering all stages and adding other aspects to this methodology that have enriched the project to its final result. I plan to develop a web application with the functionality of a weblog focusing on both, the end user and the webmaster. A weblog to share knowledge in a dynamic and updated way, for users concerned with technologies and different levels of expertise. Special emphasis has been made on the usability of the web tool, taking this aspect into account through the entire methodology’s life cycle. To begin the development, the application structure is based on December’s methodology focused on web development. The whole project is built from this methodology. All the stages have been taken into account to complete each part of the final development. This project deals with technical data of the web tool, from the choice of the programming languages used to the design of the database structure, the processes involved in the application and the subjective decisions of interface design. At all times I have tried to structure the report in a clear, concise and easy to read way, reflecting it in the whole process of the project.

Enhancing web-based learning resources with quizzes through an Authoring Tool and an Audience Response System

Quizzes are among the most widely used resources in web-based education due to their many benefits. However, educators need suitable authoring tools that can be used to create reusable quizzes and to enhance existing materials with them. On the other hand, if teachers use Audience Response Systems (ARSs) they can get instant feedback from their students and thereby enhance their instruction. This paper presents an online authoring tool for creating reusable quizzes and enhancing existing learning resources with them, and a web-based ARS that enables teachers to launch the created quizzes and get instant feedback from the class. Both the authoring tool and the ARS were evaluated. The evaluation of the authoring tool showed that educators can effectively enhance existing learning resources in an easy way by creating and adding quizzes using that tool. Besides, the different factors that assure the reusability of the created quizzes are also exposed. Finally, the evaluation of the developed ARS showed an excellent acceptance of the system by teachers and students, and also it indicated that teachers found the system easy to set up and use in their classrooms.

OOPS! (OntOlogy Pitfall Scanner!): a web-based tool for ontology evaluation

Presentación en Workshop EUON 2014

End-User Development Success Factors and their Application to Composite Web Development Environments

The Future Internet is expected to be composed of a mesh of interoperable Web services accessed from all over the Web. This approach has not yet caught on since global user-service interaction is still an open issue. Successful composite applications rely on heavyweight service orchestration technologies that raise the bar far above end-user skills. The weakness lies in the abstraction of the underlying service front-end architecture rather than the infrastructure technologies themselves. In our opinion, the best approach is to offer end-to-end composition from user interface to service invocation, as well as an understandable abstraction of both building blocks and a visual composition technique. In this paper we formalize our vision with regard to the next-generation front-end Web technology that will enable integrated access to services, contents and things in the Future Internet. We present a novel reference architecture designed to empower non-technical end users to create and share their own self-service composite applications. A tool implementing this architecture has been developed as part of the European FP7 FAST Project and EzWeb Project, allowing us to validate the rationale behind our approach.

OntoTag - A Linguistic and Ontological Annotation Model Suitable for the Semantic Web

OntoTag - A Linguistic and Ontological Annotation Model Suitable for the Semantic Web 1. INTRODUCTION. LINGUISTIC TOOLS AND ANNOTATIONS: THEIR LIGHTS AND SHADOWS Computational Linguistics is already a consolidated research area. It builds upon the results of other two major ones, namely Linguistics and Computer Science and Engineering, and it aims at developing computational models of human language (or natural language, as it is termed in this area). Possibly, its most well-known applications are the different tools developed so far for processing human language, such as machine translation systems and speech recognizers or dictation programs. These tools for processing human language are commonly referred to as linguistic tools. Apart from the examples mentioned above, there are also other types of linguistic tools that perhaps are not so well-known, but on which most of the other applications of Computational Linguistics are built. These other types of linguistic tools comprise POS taggers, natural language parsers and semantic taggers, amongst others. All of them can be termed linguistic annotation tools. Linguistic annotation tools are important assets. In fact, POS and semantic taggers (and, to a lesser extent, also natural language parsers) have become critical resources for the computer applications that process natural language. Hence, any computer application that has to analyse a text automatically and ‘intelligently’ will include at least a module for POS tagging. The more an application needs to ‘understand’ the meaning of the text it processes, the more linguistic tools and/or modules it will incorporate and integrate. However, linguistic annotation tools have still some limitations, which can be summarised as follows: 1. Normally, they perform annotations only at a certain linguistic level (that is, Morphology, Syntax, Semantics, etc.). 2. They usually introduce a certain rate of errors and ambiguities when tagging. This error rate ranges from 10 percent up to 50 percent of the units annotated for unrestricted, general texts. 3. Their annotations are most frequently formulated in terms of an annotation schema designed and implemented ad hoc. A priori, it seems that the interoperation and the integration of several linguistic tools into an appropriate software architecture could most likely solve the limitations stated in (1). Besides, integrating several linguistic annotation tools and making them interoperate could also minimise the limitation stated in (2). Nevertheless, in the latter case, all these tools should produce annotations for a common level, which would have to be combined in order to correct their corresponding errors and inaccuracies. Yet, the limitation stated in (3) prevents both types of integration and interoperation from being easily achieved. In addition, most high-level annotation tools rely on other lower-level annotation tools and their outputs to generate their own ones. For example, sense-tagging tools (operating at the semantic level) often use POS taggers (operating at a lower level, i.e., the morphosyntactic) to identify the grammatical category of the word or lexical unit they are annotating. Accordingly, if a faulty or inaccurate low-level annotation tool is to be used by other higher-level one in its process, the errors and inaccuracies of the former should be minimised in advance. Otherwise, these errors and inaccuracies would be transferred to (and even magnified in) the annotations of the high-level annotation tool. Therefore, it would be quite useful to find a way to (i) correct or, at least, reduce the errors and the inaccuracies of lower-level linguistic tools; (ii) unify the annotation schemas of different linguistic annotation tools or, more generally speaking, make these tools (as well as their annotations) interoperate. Clearly, solving (i) and (ii) should ease the automatic annotation of web pages by means of linguistic tools, and their transformation into Semantic Web pages (Berners-Lee, Hendler and Lassila, 2001). Yet, as stated above, (ii) is a type of interoperability problem. There again, ontologies (Gruber, 1993; Borst, 1997) have been successfully applied thus far to solve several interoperability problems. Hence, ontologies should help solve also the problems and limitations of linguistic annotation tools aforementioned. Thus, to summarise, the main aim of the present work was to combine somehow these separated approaches, mechanisms and tools for annotation from Linguistics and Ontological Engineering (and the Semantic Web) in a sort of hybrid (linguistic and ontological) annotation model, suitable for both areas. This hybrid (semantic) annotation model should (a) benefit from the advances, models, techniques, mechanisms and tools of these two areas; (b) minimise (and even solve, when possible) some of the problems found in each of them; and (c) be suitable for the Semantic Web. The concrete goals that helped attain this aim are presented in the following section. 2. GOALS OF THE PRESENT WORK As mentioned above, the main goal of this work was to specify a hybrid (that is, linguistically-motivated and ontology-based) model of annotation suitable for the Semantic Web (i.e. it had to produce a semantic annotation of web page contents). This entailed that the tags included in the annotations of the model had to (1) represent linguistic concepts (or linguistic categories, as they are termed in ISO/DCR (2008)), in order for this model to be linguistically-motivated; (2) be ontological terms (i.e., use an ontological vocabulary), in order for the model to be ontology-based; and (3) be structured (linked) as a collection of ontology-based triples, as in the usual Semantic Web languages (namely RDF(S) and OWL), in order for the model to be considered suitable for the Semantic Web. Besides, to be useful for the Semantic Web, this model should provide a way to automate the annotation of web pages. As for the present work, this requirement involved reusing the linguistic annotation tools purchased by the OEG research group (http://www.oeg-upm.net), but solving beforehand (or, at least, minimising) some of their limitations. Therefore, this model had to minimise these limitations by means of the integration of several linguistic annotation tools into a common architecture. Since this integration required the interoperation of tools and their annotations, ontologies were proposed as the main technological component to make them effectively interoperate. From the very beginning, it seemed that the formalisation of the elements and the knowledge underlying linguistic annotations within an appropriate set of ontologies would be a great step forward towards the formulation of such a model (henceforth referred to as OntoTag). Obviously, first, to combine the results of the linguistic annotation tools that operated at the same level, their annotation schemas had to be unified (or, preferably, standardised) in advance. This entailed the unification (id. standardisation) of their tags (both their representation and their meaning), and their format or syntax. Second, to merge the results of the linguistic annotation tools operating at different levels, their respective annotation schemas had to be (a) made interoperable and (b) integrated. And third, in order for the resulting annotations to suit the Semantic Web, they had to be specified by means of an ontology-based vocabulary, and structured by means of ontology-based triples, as hinted above. Therefore, a new annotation scheme had to be devised, based both on ontologies and on this type of triples, which allowed for the combination and the integration of the annotations of any set of linguistic annotation tools. This annotation scheme was considered a fundamental part of the model proposed here, and its development was, accordingly, another major objective of the present work. All these goals, aims and objectives could be re-stated more clearly as follows: Goal 1: Development of a set of ontologies for the formalisation of the linguistic knowledge relating linguistic annotation. Sub-goal 1.1: Ontological formalisation of the EAGLES (1996a; 1996b) de facto standards for morphosyntactic and syntactic annotation, in a way that helps respect the triple structure recommended for annotations in these works (which is isomorphic to the triple structures used in the context of the Semantic Web). Sub-goal 1.2: Incorporation into this preliminary ontological formalisation of other existing standards and standard proposals relating the levels mentioned above, such as those currently under development within ISO/TC 37 (the ISO Technical Committee dealing with Terminology, which deals also with linguistic resources and annotations). Sub-goal 1.3: Generalisation and extension of the recommendations in EAGLES (1996a; 1996b) and ISO/TC 37 to the semantic level, for which no ISO/TC 37 standards have been developed yet. Sub-goal 1.4: Ontological formalisation of the generalisations and/or extensions obtained in the previous sub-goal as generalisations and/or extensions of the corresponding ontology (or ontologies). Sub-goal 1.5: Ontological formalisation of the knowledge required to link, combine and unite the knowledge represented in the previously developed ontology (or ontologies). Goal 2: Development of OntoTag’s annotation scheme, a standard-based abstract scheme for the hybrid (linguistically-motivated and ontological-based) annotation of texts. Sub-goal 2.1: Development of the standard-based morphosyntactic annotation level of OntoTag’s scheme. This level should include, and possibly extend, the recommendations of EAGLES (1996a) and also the recommendations included in the ISO/MAF (2008) standard draft. Sub-goal 2.2: Development of the standard-based syntactic annotation level of the hybrid abstract scheme. This level should include, and possibly extend, the recommendations of EAGLES (1996b) and the ISO/SynAF (2010) standard draft. Sub-goal 2.3: Development of the standard-based semantic annotation level of OntoTag’s (abstract) scheme. Sub-goal 2.4: Development of the mechanisms for a convenient integration of the three annotation levels already mentioned. These mechanisms should take into account the recommendations included in the ISO/LAF (2009) standard draft. Goal 3: Design of OntoTag’s (abstract) annotation architecture, an abstract architecture for the hybrid (semantic) annotation of texts (i) that facilitates the integration and interoperation of different linguistic annotation tools, and (ii) whose results comply with OntoTag’s annotation scheme. Sub-goal 3.1: Specification of the decanting processes that allow for the classification and separation, according to their corresponding levels, of the results of the linguistic tools annotating at several different levels. Sub-goal 3.2: Specification of the standardisation processes that allow (a) complying with the standardisation requirements of OntoTag’s annotation scheme, as well as (b) combining the results of those linguistic tools that share some level of annotation. Sub-goal 3.3: Specification of the merging processes that allow for the combination of the output annotations and the interoperation of those linguistic tools that share some level of annotation. Sub-goal 3.4: Specification of the merge processes that allow for the integration of the results and the interoperation of those tools performing their annotations at different levels. Goal 4: Generation of OntoTagger’s schema, a concrete instance of OntoTag’s abstract scheme for a concrete set of linguistic annotations. These linguistic annotations result from the tools and the resources available in the research group, namely • Bitext’s DataLexica (http://www.bitext.com/EN/datalexica.asp), • LACELL’s (POS) tagger (http://www.um.es/grupos/grupo-lacell/quees.php), • Connexor’s FDG (http://www.connexor.eu/technology/machinese/glossary/fdg/), and • EuroWordNet (Vossen et al., 1998). This schema should help evaluate OntoTag’s underlying hypotheses, stated below. Consequently, it should implement, at least, those levels of the abstract scheme dealing with the annotations of the set of tools considered in this implementation. This includes the morphosyntactic, the syntactic and the semantic levels. Goal 5: Implementation of OntoTagger’s configuration, a concrete instance of OntoTag’s abstract architecture for this set of linguistic tools and annotations. This configuration (1) had to use the schema generated in the previous goal; and (2) should help support or refute the hypotheses of this work as well (see the next section). Sub-goal 5.1: Implementation of the decanting processes that facilitate the classification and separation of the results of those linguistic resources that provide annotations at several different levels (on the one hand, LACELL’s tagger operates at the morphosyntactic level and, minimally, also at the semantic level; on the other hand, FDG operates at the morphosyntactic and the syntactic levels and, minimally, at the semantic level as well). Sub-goal 5.2: Implementation of the standardisation processes that allow (i) specifying the results of those linguistic tools that share some level of annotation according to the requirements of OntoTagger’s schema, as well as (ii) combining these shared level results. In particular, all the tools selected perform morphosyntactic annotations and they had to be conveniently combined by means of these processes. Sub-goal 5.3: Implementation of the merging processes that allow for the combination (and possibly the improvement) of the annotations and the interoperation of the tools that share some level of annotation (in particular, those relating the morphosyntactic level, as in the previous sub-goal). Sub-goal 5.4: Implementation of the merging processes that allow for the integration of the different standardised and combined annotations aforementioned, relating all the levels considered. Sub-goal 5.5: Improvement of the semantic level of this configuration by adding a named entity recognition, (sub-)classification and annotation subsystem, which also uses the named entities annotated to populate a domain ontology, in order to provide a concrete application of the present work in the two areas involved (the Semantic Web and Corpus Linguistics). 3. MAIN RESULTS: ASSESSMENT OF ONTOTAG’S UNDERLYING HYPOTHESES The model developed in the present thesis tries to shed some light on (i) whether linguistic annotation tools can effectively interoperate; (ii) whether their results can be combined and integrated; and, if they can, (iii) how they can, respectively, interoperate and be combined and integrated. Accordingly, several hypotheses had to be supported (or rejected) by the development of the OntoTag model and OntoTagger (its implementation). The hypotheses underlying OntoTag are surveyed below. Only one of the hypotheses (H.6) was rejected; the other five could be confirmed. H.1 The annotations of different levels (or layers) can be integrated into a sort of overall, comprehensive, multilayer and multilevel annotation, so that their elements can complement and refer to each other. • CONFIRMED by the development of: o OntoTag’s annotation scheme, o OntoTag’s annotation architecture, o OntoTagger’s (XML, RDF, OWL) annotation schemas, o OntoTagger’s configuration. H.2 Tool-dependent annotations can be mapped onto a sort of tool-independent annotations and, thus, can be standardised. • CONFIRMED by means of the standardisation phase incorporated into OntoTag and OntoTagger for the annotations yielded by the tools. H.3 Standardisation should ease: H.3.1: The interoperation of linguistic tools. H.3.2: The comparison, combination (at the same level and layer) and integration (at different levels or layers) of annotations. • H.3 was CONFIRMED by means of the development of OntoTagger’s ontology-based configuration: o Interoperation, comparison, combination and integration of the annotations of three different linguistic tools (Connexor’s FDG, Bitext’s DataLexica and LACELL’s tagger); o Integration of EuroWordNet-based, domain-ontology-based and named entity annotations at the semantic level. o Integration of morphosyntactic, syntactic and semantic annotations. H.4 Ontologies and Semantic Web technologies (can) play a crucial role in the standardisation of linguistic annotations, by providing consensual vocabularies and standardised formats for annotation (e.g., RDF triples). • CONFIRMED by means of the development of OntoTagger’s RDF-triple-based annotation schemas. H.5 The rate of errors introduced by a linguistic tool at a given level, when annotating, can be reduced automatically by contrasting and combining its results with the ones coming from other tools, operating at the same level. However, these other tools might be built following a different technological (stochastic vs. rule-based, for example) or theoretical (dependency vs. HPS-grammar-based, for instance) approach. • CONFIRMED by the results yielded by the evaluation of OntoTagger. H.6 Each linguistic level can be managed and annotated independently. • REJECTED: OntoTagger’s experiments and the dependencies observed among the morphosyntactic annotations, and between them and the syntactic annotations. In fact, Hypothesis H.6 was already rejected when OntoTag’s ontologies were developed. We observed then that several linguistic units stand on an interface between levels, belonging thereby to both of them (such as morphosyntactic units, which belong to both the morphological level and the syntactic level). Therefore, the annotations of these levels overlap and cannot be handled independently when merged into a unique multileveled annotation. 4. OTHER MAIN RESULTS AND CONTRIBUTIONS First, interoperability is a hot topic for both the linguistic annotation community and the whole Computer Science field. The specification (and implementation) of OntoTag’s architecture for the combination and integration of linguistic (annotation) tools and annotations by means of ontologies shows a way to make these different linguistic annotation tools and annotations interoperate in practice. Second, as mentioned above, the elements involved in linguistic annotation were formalised in a set (or network) of ontologies (OntoTag’s linguistic ontologies). • On the one hand, OntoTag’s network of ontologies consists of − The Linguistic Unit Ontology (LUO), which includes a mostly hierarchical formalisation of the different types of linguistic elements (i.e., units) identifiable in a written text; − The Linguistic Attribute Ontology (LAO), which includes also a mostly hierarchical formalisation of the different types of features that characterise the linguistic units included in the LUO; − The Linguistic Value Ontology (LVO), which includes the corresponding formalisation of the different values that the attributes in the LAO can take; − The OIO (OntoTag’s Integration Ontology), which  Includes the knowledge required to link, combine and unite the knowledge represented in the LUO, the LAO and the LVO;  Can be viewed as a knowledge representation ontology that describes the most elementary vocabulary used in the area of annotation. • On the other hand, OntoTag’s ontologies incorporate the knowledge included in the different standards and recommendations for linguistic annotation released so far, such as those developed within the EAGLES and the SIMPLE European projects or by the ISO/TC 37 committee: − As far as morphosyntactic annotations are concerned, OntoTag’s ontologies formalise the terms in the EAGLES (1996a) recommendations and their corresponding terms within the ISO Morphosyntactic Annotation Framework (ISO/MAF, 2008) standard; − As for syntactic annotations, OntoTag’s ontologies incorporate the terms in the EAGLES (1996b) recommendations and their corresponding terms within the ISO Syntactic Annotation Framework (ISO/SynAF, 2010) standard draft; − Regarding semantic annotations, OntoTag’s ontologies generalise and extend the recommendations in EAGLES (1996a; 1996b) and, since no stable standards or standard drafts have been released for semantic annotation by ISO/TC 37 yet, they incorporate the terms in SIMPLE (2000) instead; − The terms coming from all these recommendations and standards were supplemented by those within the ISO Data Category Registry (ISO/DCR, 2008) and also of the ISO Linguistic Annotation Framework (ISO/LAF, 2009) standard draft when developing OntoTag’s ontologies. Third, we showed that the combination of the results of tools annotating at the same level can yield better results (both in precision and in recall) than each tool separately. In particular, 1. OntoTagger clearly outperformed two of the tools integrated into its configuration, namely DataLexica and FDG in all the combination sub-phases in which they overlapped (i.e. POS tagging, lemma annotation and morphological feature annotation). As far as the remaining tool is concerned, i.e. LACELL’s tagger, it was also outperformed by OntoTagger in POS tagging and lemma annotation, and it did not behave better than OntoTagger in the morphological feature annotation layer. 2. As an immediate result, this implies that a) This type of combination architecture configurations can be applied in order to improve significantly the accuracy of linguistic annotations; and b) Concerning the morphosyntactic level, this could be regarded as a way of constructing more robust and more accurate POS tagging systems. Fourth, Semantic Web annotations are usually performed by humans or else by machine learning systems. Both of them leave much to be desired: the former, with respect to their annotation rate; the latter, with respect to their (average) precision and recall. In this work, we showed how linguistic tools can be wrapped in order to annotate automatically Semantic Web pages using ontologies. This entails their fast, robust and accurate semantic annotation. As a way of example, as mentioned in Sub-goal 5.5, we developed a particular OntoTagger module for the recognition, classification and labelling of named entities, according to the MUC and ACE tagsets (Chinchor, 1997; Doddington et al., 2004). These tagsets were further specified by means of a domain ontology, namely the Cinema Named Entities Ontology (CNEO). This module was applied to the automatic annotation of ten different web pages containing cinema reviews (that is, around 5000 words). In addition, the named entities annotated with this module were also labelled as instances (or individuals) of the classes included in the CNEO and, then, were used to populate this domain ontology. • The statistical results obtained from the evaluation of this particular module of OntoTagger can be summarised as follows. On the one hand, as far as recall (R) is concerned, (R.1) the lowest value was 76,40% (for file 7); (R.2) the highest value was 97, 50% (for file 3); and (R.3) the average value was 88,73%. On the other hand, as far as the precision rate (P) is concerned, (P.1) its minimum was 93,75% (for file 4); (R.2) its maximum was 100% (for files 1, 5, 7, 8, 9, and 10); and (R.3) its average value was 98,99%. • These results, which apply to the tasks of named entity annotation and ontology population, are extraordinary good for both of them. They can be explained on the basis of the high accuracy of the annotations provided by OntoTagger at the lower levels (mainly at the morphosyntactic level). However, they should be conveniently qualified, since they might be too domain- and/or language-dependent. It should be further experimented how our approach works in a different domain or a different language, such as French, English, or German. • In any case, the results of this application of Human Language Technologies to Ontology Population (and, accordingly, to Ontological Engineering) seem very promising and encouraging in order for these two areas to collaborate and complement each other in the area of semantic annotation. Fifth, as shown in the State of the Art of this work, there are different approaches and models for the semantic annotation of texts, but all of them focus on a particular view of the semantic level. Clearly, all these approaches and models should be integrated in order to bear a coherent and joint semantic annotation level. OntoTag shows how (i) these semantic annotation layers could be integrated together; and (ii) they could be integrated with the annotations associated to other annotation levels. Sixth, we identified some recommendations, best practices and lessons learned for annotation standardisation, interoperation and merge. They show how standardisation (via ontologies, in this case) enables the combination, integration and interoperation of different linguistic tools and their annotations into a multilayered (or multileveled) linguistic annotation, which is one of the hot topics in the area of Linguistic Annotation. And last but not least, OntoTag’s annotation scheme and OntoTagger’s annotation schemas show a way to formalise and annotate coherently and uniformly the different units and features associated to the different levels and layers of linguistic annotation. This is a great scientific step ahead towards the global standardisation of this area, which is the aim of ISO/TC 37 (in particular, Subcommittee 4, dealing with the standardisation of linguistic annotations and resources).

OPPL-Galaxy, a Galaxy tool for enhancing ontology exploitation as part of bioinformatics workflows

Biomedical ontologies are key elements for building up the Life Sciences Semantic Web. Reusing and building biomedical ontologies requires flexible and versatile tools to manipulate them efficiently, in particular for enriching their axiomatic content. The Ontology Pre Processor Language (OPPL) is an OWL-based language for automating the changes to be performed in an ontology. OPPL augments the ontologists’ toolbox by providing a more efficient, and less error-prone, mechanism for enriching a biomedical ontology than that obtained by a manual treatment. Results We present OPPL-Galaxy, a wrapper for using OPPL within Galaxy. The functionality delivered by OPPL (i.e. automated ontology manipulation) can be combined with the tools and workflows devised within the Galaxy framework, resulting in an enhancement of OPPL. Use cases are provided in order to demonstrate OPPL-Galaxy’s capability for enriching, modifying and querying biomedical ontologies. Conclusions Coupling OPPL-Galaxy with other bioinformatics tools of the Galaxy framework results in a system that is more than the sum of its parts. OPPL-Galaxy opens a new dimension of analyses and exploitation of biomedical ontologies, including automated reasoning, paving the way towards advanced biological data analyses.