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.

Knowledgeable Feedback via a Cast of Virtual Characters with Different Competences

DynaLearn (http://www.DynaLearn.eu) develops a cognitive artefact that engages learners in an active learning by modelling process to develop conceptual system knowledge. Learners create external representations using diagrams. The diagrams capture conceptual knowledge using the Garp3 Qualitative Reasoning (QR) formalism [2]. The expressions can be simulated, confronting learners with the logical consequences thereof. To further aid learners, DynaLearn employs a sequence of knowledge representations (Learning Spaces, LS), with increasing complexity in terms of the modelling ingredients a learner can use [1]. An online repository contains QR models created by experts/teachers and learners. The server runs semantic services [4] to generate feedback at the request of learners via the workbench. The feedback is communicated to the learner via a set of virtual characters, each having its own competence [3]. A specific feedback thus incorporates three aspects: content, character appearance, and a didactic setting (e.g. Quiz mode). In the interactive event we will demonstrate the latest achievements of the DynaLearn project. First, the 6 learning spaces for learners to work with. Second, the generation of feedback relevant to the individual needs of a learner using Semantic Web technology. Third, the verbalization of the feedback via different animated virtual characters, notably: Basic help, Critic, Recommender, Quizmaster & Teachable agen

datos.bne.es: A library linked dataset

We describe the datos.bne.es library dataset. The dataset makes available the authority and bibliography catalogue from the Biblioteca Nacional de España (BNE, National Library of Spain) as Linked Data. The catalogue contains around 7 million authority and bibliographic records. The records in MARC 21 format were transformed to RDF and modelled using IFLA (International Federation of Library Associations) ontologies and other well-established vocabularies such as RDA (Resource Description and Access) or the Dublin Core Metadata Element Set. A tool named MARiMbA automatized the RDF generation process and the data linkage to DBpedia and other library linked data resources such as VIAF (Virtual International Authority File) or GND (Gemeinsame Normdatei, the authority dataset from the German National Library).

Using Provenance for Quality Assessment and Repair in Linked Open Data

As the number of data sources publishing their data on the Web of Data is growing, we are experiencing an immense growth of the Linked Open Data cloud. The lack of control on the published sources, which could be untrustworthy or unreliable, along with their dynamic nature that often invalidates links and causes conflicts or other discrepancies, could lead to poor quality data. In order to judge data quality, a number of quality indicators have been proposed, coupled with quality metrics that quantify the “quality level” of a dataset. In addition to the above, some approaches address how to improve the quality of the datasets through a repair process that focuses on how to correct invalidities caused by constraint violations by either removing or adding triples. In this paper we argue that provenance is a critical factor that should be taken into account during repairs to ensure that the most reliable data is kept. Based on this idea, we propose quality metrics that take into account provenance and evaluate their applicability as repair guidelines in a particular data fusion setting.

Did you validate your ontology? OOPS!

The application of methodologies for building ontologies can im-prove ontology quality. However, such quality is not guaranteed because of the difficulties involved in ontology modelling. These difficulties are related to the inclusion of anomalies or bad practices within the ontology development. Sev-eral authors have provided lists of typical anomalies detected in ontologies dur-ing the last decade. In this context, our aim in this paper is to describe OOPS! (OntOlogy Pitfall Scanner!), a tool for detecting pitfalls in ontologies.

A Reuse-based Lightweight Method for Developing Linked Data Ontologies and Vocabularies

The uptake of Linked Data (LD) has promoted the proliferation of datasets and their associated ontologies for describing different domains. Par-ticular LD development characteristics such as agility and web-based architec-ture necessitate the revision, adaption, and lightening of existing methodologies for ontology development. This thesis proposes a lightweight method for ontol-ogy development in an LD context which will be based in data-driven agile de-velopments, existing resources to be reused, and the evaluation of the obtained products considering both classical ontological engineering principles and LD characteristics.

Translational research combining orthologous genes and human diseases with the OGOLOD dataset

OGOLOD is a Linked Open Data dataset derived from different biomedical resources by an automated pipeline, using a tailored ontology as a scaffold. The key contribution of OGOLOD is that it links, in new RDF triples, genetic human diseases and orthologous genes, paving the way for a more efficient translational biomedical research exploiting the Linked Open Data cloud.

Modelado de sistemas multimedia para personalización y recomendación híbrida a partir del consumo audiovisual de los usuarios

This doctoral thesis focuses on the modeling of multimedia systems to create personalized recommendation services based on the analysis of users’ audiovisual consumption. Research is focused on the characterization of both users’ audiovisual consumption and content, specifically images and video. This double characterization converges into a hybrid recommendation algorithm, adapted to different application scenarios covering different specificities and constraints. Hybrid recommendation systems use both content and user information as input data, applying the knowledge from the analysis of these data as the initial step to feed the algorithms in order to generate personalized recommendations. Regarding the user information, this doctoral thesis focuses on the analysis of audiovisual consumption to infer implicitly acquired preferences. The inference process is based on a new probabilistic model proposed in the text. This model takes into account qualitative and quantitative consumption factors on the one hand, and external factors such as zapping factor or company factor on the other. As for content information, this research focuses on the modeling of descriptors and aesthetic characteristics, which influence the user and are thus useful for the recommendation system. Similarly, the automatic extraction of these descriptors from the audiovisual piece without excessive computational cost has been considered a priority, in order to ensure applicability to different real scenarios. Finally, a new content-based recommendation algorithm has been created from the previously acquired information, i.e. user preferences and content descriptors. This algorithm has been hybridized with a collaborative filtering algorithm obtained from the current state of the art, so as to compare the efficiency of this hybrid recommender with the individual techniques of recommendation (different hybridization techniques of the state of the art have been studied for suitability). The content-based recommendation focuses on the influence of the aesthetic characteristics on the users. The heterogeneity of the possible users of these kinds of systems calls for the use of different criteria and attributes to create effective recommendations. Therefore, the proposed algorithm is adaptable to different perceptions producing a dynamic representation of preferences to obtain personalized recommendations for each user of the system. The hypotheses of this doctoral thesis have been validated by conducting a set of tests with real users, or by querying a database containing user preferences - available to the scientific community. This thesis is structured based on the different research and validation methodologies of the techniques involved. In the three central chapters the state of the art is studied and the developed algorithms and models are validated via self-designed tests. It should be noted that some of these tests are incremental and confirm the validation of previously discussed techniques. Resumen Esta tesis doctoral se centra en el modelado de sistemas multimedia para la creación de servicios personalizados de recomendación a partir del análisis de la actividad de consumo audiovisual de los usuarios. La investigación se focaliza en la caracterización tanto del consumo audiovisual del usuario como de la naturaleza de los contenidos, concretamente imágenes y vídeos. Esta doble caracterización de usuarios y contenidos confluye en un algoritmo de recomendación híbrido que se adapta a distintos escenarios de aplicación, cada uno de ellos con distintas peculiaridades y restricciones. Todo sistema de recomendación híbrido toma como datos de partida tanto información del usuario como del contenido, y utiliza este conocimiento como entrada para algoritmos que permiten generar recomendaciones personalizadas. Por la parte de la información del usuario, la tesis se centra en el análisis del consumo audiovisual para inferir preferencias que, por lo tanto, se adquieren de manera implícita. Para ello, se ha propuesto un nuevo modelo probabilístico que tiene en cuenta factores de consumo tanto cuantitativos como cualitativos, así como otros factores de contorno, como el factor de zapping o el factor de compañía, que condicionan la incertidumbre de la inferencia. En cuanto a la información del contenido, la investigación se ha centrado en la definición de descriptores de carácter estético y morfológico que resultan influyentes en el usuario y que, por lo tanto, son útiles para la recomendación. Del mismo modo, se ha considerado una prioridad que estos descriptores se puedan extraer automáticamente de un contenido sin exigir grandes requisitos computacionales y, de tal forma que se garantice la posibilidad de aplicación a escenarios reales de diverso tipo. Por último, explotando la información de preferencias del usuario y de descripción de los contenidos ya obtenida, se ha creado un nuevo algoritmo de recomendación basado en contenido. Este algoritmo se cruza con un algoritmo de filtrado colaborativo de referencia en el estado del arte, de tal manera que se compara la eficiencia de este recomendador híbrido (donde se ha investigado la idoneidad de las diferentes técnicas de hibridación del estado del arte) con cada una de las técnicas individuales de recomendación. El algoritmo de recomendación basado en contenido que se ha creado se centra en las posibilidades de la influencia de factores estéticos en los usuarios, teniendo en cuenta que la heterogeneidad del conjunto de usuarios provoca que los criterios y atributos que condicionan las preferencias de cada individuo sean diferentes. Por lo tanto, el algoritmo se adapta a las diferentes percepciones y articula una metodología dinámica de representación de las preferencias que permite obtener recomendaciones personalizadas, únicas para cada usuario del sistema. Todas las hipótesis de la tesis han sido debidamente validadas mediante la realización de pruebas con usuarios reales o con bases de datos de preferencias de usuarios que están a disposición de la comunidad científica. La diferente metodología de investigación y validación de cada una de las técnicas abordadas condiciona la estructura de la tesis, de tal manera que los tres capítulos centrales se estructuran sobre su propio estudio del estado del arte y los algoritmos y modelos desarrollados se validan mediante pruebas autónomas, sin impedir que, en algún caso, las pruebas sean incrementales y ratifiquen la validación de técnicas expuestas anteriormente.

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.

Transforming meteorological data into linked data

This paper describes the process followed in order to make some of the public meterological data from the Agencia Estatal de Meteorología (AEMET, Spanish Meteorological Office) available as Linked Data. The method followed has been already used to publish geographical, statistical, and leisure data. The data selected for publication are generated every ten minutes by the 250 automatic stations that belong to AEMET and that are deployed across Spain. These data are available as spreadsheets in the AEMET data catalog, and contain more than twenty types of measurements per station. Spreadsheets are retrieved from the website, processed with Python scripts, transformed to RDF according to an ontology network about meteorology that reuses the W3C SSN Ontology, published in a triple store and visualized in maps with Map4rdf.

A Keyword-driven approach for generating OWL DL conformance test data

The conformance of semantic technologies has to be systematically evaluated to measure and verify the real adherence of these technologies to the Semantic Web standards. Currente valuations of semantic technology conformance are not exhaustive enough and do not directly cover user requirements and use scenarios, which raises the need for a simple, extensible and parameterizable method to generate test data for such evaluations. To address this need, this paper presents a keyword-driven approach for generating ontology language conformance test data that can be used to evaluate semantic technologies, details the definition of a test suite for evaluating OWL DL conformance using this approach,and describes the use and extension of this test suite during the evaluation of some tools.

Combining data mining and ontology engineering to enrich ontologies and linked data

In this position paper, we claim that the need for time consuming data preparation and result interpretation tasks in knowledge discovery, as well as for costly expert consultation and consensus building activities required for ontology building can be reduced through exploiting the interplay of data mining and ontology engineering. The aim is to obtain in a semi-automatic way new knowledge from distributed data sources that can be used for inference and reasoning, as well as to guide the extraction of further knowledge from these data sources. The proposed approach is based on the creation of a novel knowledge discovery method relying on the combination, through an iterative ?feedbackloop?, of (a) data mining techniques to make emerge implicit models from data and (b) pattern-based ontology engineering to capture these models in reusable, conceptual and inferable artefacts.

SRBench: A streaming RDF/SPARQL benchmark

We introduce SRBench, a general-purpose benchmark primarily designed for streaming RDF/SPARQL engines, completely based on real-world data sets from the Linked Open Data cloud. With the increasing problem of too much streaming data but not enough tools to gain knowledge from them, researchers have set out for solutions in which Semantic Web technologies are adapted and extended for publishing, sharing, analysing and understanding streaming data. To help researchers and users comparing streaming RDF/SPARQL (strRS) engines in a standardised application scenario, we have designed SRBench, with which one can assess the abilities of a strRS engine to cope with a broad range of use cases typically encountered in real-world scenarios. The data sets used in the benchmark have been carefully chosen, such that they represent a realistic and relevant usage of streaming data. The benchmark defines a concise, yet omprehensive set of queries that cover the major aspects of strRS processing. Finally, our work is complemented with a functional evaluation on three representative strRS engines: SPARQLStream, C-SPARQL and CQELS. The presented results are meant to give a first baseline and illustrate the state-of-the-art.