Essentials in Ontology Engineering: Methodologies, Languages, and Tools

In the beginning of the 90s, ontology development was similar to an art: ontology developers did not have clear guidelines on how to build ontologies but only some design criteria to be followed. Work on principles, methods and methodologies, together with supporting technologies and languages, made ontology development become an engineering discipline, the so-called Ontology Engineering. Ontology Engineering refers to the set of activities that concern the ontology development process and the ontology life cycle, the methods and methodologies for building ontologies, and the tool suites and languages that support them. Thanks to the work done in the Ontology Engineering field, the development of ontologies within and between teams has increased and improved, as well as the possibility of reusing ontologies in other developments and in final applications. Currently, ontologies are widely used in (a) Knowledge Engineering, Artificial Intelligence and Computer Science, (b) applications related to knowledge management, natural language processing, e-commerce, intelligent information integration, information retrieval, database design and integration, bio-informatics, education, and (c) the Semantic Web, the Semantic Grid, and the Linked Data initiative. In this paper, we provide an overview of Ontology Engineering, mentioning the most outstanding and used methodologies, languages, and tools for building ontologies. In addition, we include some words on how all these elements can be used in the Linked Data initiative.

Sharing analysis of arrays, collections, and recursive structures

Precise modeling of the program heap is fundamental for understanding the behavior of a program, and is thus of signiflcant interest for many optimization applications. One of the fundamental properties of the heap that can be used in a range of optimization techniques is the sharing relationships between the elements in an array or collection. If an analysis can determine that the memory locations pointed to by different entries of an array (or collection) are disjoint, then in many cases loops that traverse the array can be vectorized or transformed into a thread-parallel versión. This paper introduces several novel sharing properties over the concrete heap and corresponding abstractions to represent them. In conjunction with an existing shape analysis technique, these abstractions allow us to precisely resolve the sharing relations in a wide range of heap structures (arrays, collections, recursive data structures, composite heap structures) in a computationally efflcient manner. The effectiveness of the approach is evaluated on a set of challenge problems from the JOlden and SPECjvm98 suites. Sharing information obtained from the analysis is used to achieve substantial thread-level parallel speedups.

Semantic technologies in idea management systems: a model for interoperability, linking and filtering

Abstract Idea Management Systems are web applications that implement the notion of open innovation though crowdsourcing. Typically, organizations use those kind of systems to connect to large communities in order to gather ideas for improvement of products or services. Originating from simple suggestion boxes, Idea Management Systems advanced beyond collecting ideas and aspire to be a knowledge management solution capable to select best ideas via collaborative as well as expert assessment methods. In practice, however, the contemporary systems still face a number of problems usually related to information overflow and recognizing questionable quality of submissions with reasonable time and effort allocation. This thesis focuses on idea assessment problem area and contributes a number of solutions that allow to filter, compare and evaluate ideas submitted into an Idea Management System. With respect to Idea Management System interoperability the thesis proposes theoretical model of Idea Life Cycle and formalizes it as the Gi2MO ontology which enables to go beyond the boundaries of a single system to compare and assess innovation in an organization wide or market wide context. Furthermore, based on the ontology, the thesis builds a number of solutions for improving idea assessment via: community opinion analysis (MARL), annotation of idea characteristics (Gi2MO Types) and study of idea relationships (Gi2MO Links). The main achievements of the thesis are: application of theoretical innovation models for practice of Idea Management to successfully recognize the differentiation between communities, opinion metrics and their recognition as a new tool for idea assessment, discovery of new relationship types between ideas and their impact on idea clustering. Finally, the thesis outcome is establishment of Gi2MO Project that serves as an incubator for Idea Management solutions and mature open-source software alternatives for the widely available commercial suites. From the academic point of view the project delivers resources to undertake experiments in the Idea Management Systems area and managed to become a forum that gathered a number of academic and industrial partners. Resumen Los Sistemas de Gestión de Ideas son aplicaciones Web que implementan el concepto de innovación abierta con técnicas de crowdsourcing. Típicamente, las organizaciones utilizan ese tipo de sistemas para conectar con comunidades grandes y así recoger ideas sobre cómo mejorar productos o servicios. Los Sistemas de Gestión de Ideas lian avanzado más allá de recoger simplemente ideas de buzones de sugerencias y ahora aspiran ser una solución de gestión de conocimiento capaz de seleccionar las mejores ideas por medio de técnicas colaborativas, así como métodos de evaluación llevados a cabo por expertos. Sin embargo, en la práctica, los sistemas contemporáneos todavía se enfrentan a una serie de problemas, que, por lo general, están relacionados con la sobrecarga de información y el reconocimiento de las ideas de dudosa calidad con la asignación de un tiempo y un esfuerzo razonables. Esta tesis se centra en el área de la evaluación de ideas y aporta una serie de soluciones que permiten filtrar, comparar y evaluar las ideas publicadas en un Sistema de Gestión de Ideas. Con respecto a la interoperabilidad de los Sistemas de Gestión de Ideas, la tesis propone un modelo teórico del Ciclo de Vida de la Idea y lo formaliza como la ontología Gi2MO que permite ir más allá de los límites de un sistema único para comparar y evaluar la innovación en un contexto amplio dentro de cualquier organización o mercado. Por otra parte, basado en la ontología, la tesis desarrolla una serie de soluciones para mejorar la evaluación de las ideas a través de: análisis de las opiniones de la comunidad (MARL), la anotación de las características de las ideas (Gi2MO Types) y el estudio de las relaciones de las ideas (Gi2MO Links). Los logros principales de la tesis son: la aplicación de los modelos teóricos de innovación para la práctica de Sistemas de Gestión de Ideas para reconocer las diferenciasentre comu¬nidades, métricas de opiniones de comunidad y su reconocimiento como una nueva herramienta para la evaluación de ideas, el descubrimiento de nuevos tipos de relaciones entre ideas y su impacto en la agrupación de estas. Por último, el resultado de tesis es el establecimiento de proyecto Gi2MO que sirve como incubadora de soluciones para Gestión de Ideas y herramientas de código abierto ya maduras como alternativas a otros sistemas comerciales. Desde el punto de vista académico, el proyecto ha provisto de recursos a ciertos experimentos en el área de Sistemas de Gestión de Ideas y logró convertirse en un foro que reunión para un número de socios tanto académicos como industriales.

Transcriptional changes and oxidative stress associated with the synergistic interaction between potato virus X and potato virus Y and their relationship with symptom expression.

Many virus diseases of economic importance to agriculture result from mixtures of different pathogens invading the host at a given time. This contrasts with the relatively scarce studies available on the molecular events associated with virus---host interactions in mixed infections. Compared with single infections, co-infection of Nicotiana benthamiana with Potato virus X (PVX) and Potato virus Y (PVY) resulted in increased systemic symptoms (synergism) that led to necrosis of the newly emerging leaves and death of the plant. A comparative transcriptional analysis was undertaken to identify quantitative and qualitative differences in gene expression during this synergistic infection and correlate these changes with the severe symptoms it caused. Global transcription profiles of doubly infected leaves were compared with those from singly infected leaves using gene ontology enrichment analysis and metabolic pathway annotator software. Functional gene categories altered by the double infection comprise suites of genes regulated coordinately, which are associated with chloroplast functions (downregulated), protein synthesis and degradation (upregulated), carbohydrate metabolism (upregulated), and response to biotic stimulus and stress (upregulated). The expressions of reactive oxygen species?generating enzymes as well as several mitogen-activated protein kinases were also significantly induced. Accordingly, synergistic infection induced a severe oxidative stress in N. benthamiana leaves, as judged by increases in lipid peroxidation and by the generation of superoxide radicals in chloroplasts, which correlated with the misregulation of antioxidative genes in microarray data. Interestingly, expression of genes encoding oxylipin biosynthesis was uniquely upregulated by the synergistic infection. Virus-induced gene silencing of ?-dioxygenase1 delayed cell death during PVX?PVY infection.

Implantación de técnicas de QA en un proyecto de desarrollo software

Hoy en día existe una preocupación creciente por la calidad del software entregado en los proyectos que se realizan a lo largo del mundo. El trabajo de fin de grado que va a ser desarrollado en estas páginas pretende demostrar la importancia de la realización de tests funcionales durante el proceso de desarrollo de software para que el proyecto alcance la calidad requerida tan demandada en estos días. Para ello, después de una pequeña introducción a la historia del software, se presentarán y compararán diversos tipos de metodologías de desarrollo de software, tanto pesadas (cascada, espiral, etc.) como ágiles (Extreme Programming y Scrum), se enfatizará en dichas metodologías ágiles y cómo el proceso de testing y control de calidad encaja perfectamente con la filosofía de las citadas metodologías ágiles. Se desarrollará una explicación del papel de QA en el desarrollo de software, asi como una explicación de los tipos de test existentes, y las herramientas, tecnologías y patrones que existen a disposición de aquellos que quieran desempeñar el papel de QA. Para complementar el punto de vista teórico de este trabajo se presentará un caso práctico real realizado en la empresa bq bajo una metodología Scrum. Dicho caso práctico muestra el uso de ciertas herramientas y su aporte para el control de calidad del proyecto bajo desarrollo, demostrando su importancia. Se realizará énfasis en el proceso de automatización de ciertas baterías de test (llamadas test suites), mostrando desde el planteamiento inicial de las diferentes historias de usuario y la batería de test, pasando por la elección de las tecnologías más adecuadas para la elaboración de los test hasta llegar al lanzamiento de dicha batería de pruebas y la comprobación de éstas. El punto de vista práctico quedará complementado por una explicación del framework nightwatch.js, framework utilizado en el desarrollo del proyecto en bq para la automatización de test funcionales. Esta explicación comprenderá tanto la configuración y uso del framework como el uso de patrones y la estructura de las pruebas. ABSTRACT Nowadays there is a growing concern about the Quality of the software delivered in the projects that are made all around the world. This final project will try to prove the importance of performing functional tests during the Software Development Process in order to be able to reach the demanded Quality. To fulfill this objective, different types of Software Development methodologies will be presented and compared. Heavy methodologies (waterfall, spiral methodologies, etc.) as well as agile methodologies (Extreme Programming and Scrum). There will be an emphasis in the second kind (agile methodologies) and how the testing and quality assurance process fits perfectly in their philosophy. A deep explanation of the role that Quality Assurance holds on software development will be presented, as well as an explanation on the current types of testing and an explanation of the different tools; technologies and patrons that exist to help anyone who wants to perform the role of QA. To complement the theoretical perspective of this work a real case study, performed at the company bq under a Scrum methodology, will be presented. The mentioned study covers the use of certain tools and their input for the quality assurance of the project under development, proving its relevance. Emphasis will be made in the process of conducting a set of tests (called test suite), showing from the initial approach of the different users stories and the set of tests, going through the choosing of the most suitable technologies for the tests development, and ending with the performance of this battery of tests and their checkout. The practical point of view will be complemented by a deep explanation of the creation process using the nightwatch.js automated test framework, used in the project in bq. This explanation will cover both the configuration and use of the framework as the use of patterns and structure of the tests.