Learning Ontology Relations by Combining Corpus-Based Techniques and Reasoning on Data from Semantic Web Sources

The manual construction of formal domain conceptualizations (ontologies) is labor-intensive. Ontology learning, by contrast, provides (semi-)automatic ontology generation from input data such as domain text. This thesis proposes a novel approach for learning labels of non-taxonomic ontology relations. It combines corpus-based techniques with reasoning on Semantic Web data. Corpus-based methods apply vector space similarity of verbs co-occurring with labeled and unlabeled relations to calculate relation label suggestions from a set of candidates. A meta ontology in combination with Semantic Web sources such as DBpedia and OpenCyc allows reasoning to improve the suggested labels. An extensive formal evaluation demonstrates the superior accuracy of the presented hybrid approach

Ontology Learning and Knowledge Discovery Using the Web: Challenges and Recent Advances

By providing interoperability and shared meaning across actors and domains, lightweight domain ontologies are a cornerstone technology of the Semantic Web. This chapter investigates evidence sources for ontology learning and describes a generic and extensible approach to ontology learning that combines such evidence sources to extract domain concepts, identify relations between the ontology’s concepts, and detect relation labels automatically. An implementation illustrates the presented ontology learning and relation labeling framework and serves as the basis for dis- cussing possible pitfalls in ontology learning. Afterwards, three use cases demonstrate the usefulness of the presented framework and its application to real-world problems

Enabling Complex Semantic Queries to Bioinformatics Databases through Intuitive Search Over Data

Data integration promises to be one of the main catalysts in enabling new insights to be drawn from the wealth of biological data already available publicly. However, the heterogene- ity of the existing data sources still poses significant challenges for achieving interoperability among biological databases. Furthermore, merely solving the technical challenges of data in- tegration, for example through the use of common data representation formats, leaves open the larger problem. Namely, the steep learning curve required for understanding the data models of each public source, as well as the technical language through which the sources can be queried and joined. As a consequence, most of the available biological data remain practically unexplored today. In this thesis, we address these problems jointly, by first introducing an ontology-based data integration solution in order to mitigate the data source heterogeneity problem. We illustrate through the concrete example of Bgee, a gene expression data source, how relational databases can be exposed as virtual Resource Description Framework (RDF) graphs, through relational-to-RDF mappings. This has the important advantage that the original data source can remain unmodified, while still becoming interoperable with external RDF sources. We complement our methods with applied case studies designed to guide domain experts in formulating expressive federated queries targeting the integrated data across the domains of evolutionary relationships and gene expression. More precisely, we introduce two com- parative analyses, first within the same domain (using orthology data from multiple, inter- operable, data sources) and second across domains, in order to study the relation between expression change and evolution rate following a duplication event. Finally, in order to bridge the semantic gap between users and data, we design and im- plement Bio-SODA, a question answering system over domain knowledge graphs, that does not require training data for translating user questions to SPARQL. Bio-SODA uses a novel ranking approach that combines syntactic and semantic similarity, while also incorporating node centrality metrics to rank candidate matches for a given user question. Our results in testing Bio-SODA across several real-world databases that span multiple domains (both within and outside bioinformatics) show that it can answer complex, multi-fact queries, be- yond the current state-of-the-art in the more well-studied open-domain question answering. -- L’intégration des données promet d’être l’un des principaux catalyseurs permettant d’extraire des nouveaux aperçus de la richesse des données biologiques déjà disponibles publiquement. Cependant, l’hétérogénéité des sources de données existantes pose encore des défis importants pour parvenir à l’interopérabilité des bases de données biologiques. De plus, en surmontant seulement les défis techniques de l’intégration des données, par exemple grâce à l’utilisation de formats standard de représentation de données, on laisse ouvert un problème encore plus grand. À savoir, la courbe d’apprentissage abrupte nécessaire pour comprendre la modéli- sation des données choisie par chaque source publique, ainsi que le langage technique par lequel les sources peuvent être interrogés et jointes. Par conséquent, la plupart des données biologiques publiquement disponibles restent pratiquement inexplorés aujourd’hui. Dans cette thèse, nous abordons l’ensemble des deux problèmes, en introduisant d’abord une solution d’intégration de données basée sur ontologies, afin d’atténuer le problème d’hété- rogénéité des sources de données. Nous montrons, à travers l’exemple de Bgee, une base de données d’expression de gènes, une approche permettant les bases de données relationnelles d’être publiés sous forme de graphes RDF (Resource Description Framework) virtuels, via des correspondances relationnel-vers-RDF (« relational-to-RDF mappings »). Cela présente l’important avantage que la source de données d’origine peut rester inchangé, tout en de- venant interopérable avec les sources RDF externes. Nous complétons nos méthodes avec des études de cas appliquées, conçues pour guider les experts du domaine dans la formulation de requêtes fédérées expressives, ciblant les don- nées intégrées dans les domaines des relations évolutionnaires et de l’expression des gènes. Plus précisément, nous introduisons deux analyses comparatives, d’abord dans le même do- maine (en utilisant des données d’orthologie provenant de plusieurs sources de données in- teropérables) et ensuite à travers des domaines interconnectés, afin d’étudier la relation entre le changement d’expression et le taux d’évolution suite à une duplication de gène. Enfin, afin de mitiger le décalage sémantique entre les utilisateurs et les données, nous concevons et implémentons Bio-SODA, un système de réponse aux questions sur des graphes de connaissances domaine-spécifique, qui ne nécessite pas de données de formation pour traduire les questions des utilisateurs vers SPARQL. Bio-SODA utilise une nouvelle ap- proche de classement qui combine la similarité syntactique et sémantique, tout en incorporant des métriques de centralité des nœuds, pour classer les possibles candidats en réponse à une question utilisateur donnée. Nos résultats suite aux tests effectués en utilisant Bio-SODA sur plusieurs bases de données à travers plusieurs domaines (tantôt liés à la bioinformatique qu’extérieurs) montrent que Bio-SODA réussit à répondre à des questions complexes, en- gendrant multiples entités, au-delà de l’état actuel de la technique en matière de systèmes de réponses aux questions sur les données structures, en particulier graphes de connaissances

Neural Networks forBuilding Semantic Models and Knowledge Graphs

1noL'abstract è presente nell'allegato / the abstract is in the attachmentopen677. INGEGNERIA INFORMATInoopenFutia, Giusepp

Legal knowledge extraction in the data protection domain based on Ontology Design Patterns

In the European Union, the entry into force of the General Data Protection Regulation (GDPR) has brought the domain of data protection to the fore-front, encouraging the research in knowledge representation and natural language processing (NLP). On the one hand, several ontologies adopted Semantic Web standards to provide a formal representation of the data protection framework set by the GDPR. On the other hand, different NLP techniques have been utilised to implement services addressed to individuals, for helping them in understanding privacy policies, which are notoriously difficult to read. Few efforts have been devoted to the mapping of the information extracted from privacy policies to the conceptual representations provided by the existing ontologies modelling the data protection framework. In the first part of the thesis, I propose and put in the context of the Semantic Web a comparative analysis of existing ontologies that have been developed to model different legal fields. In the second part of the thesis, I focus on the data protection domain and I present a methodology that aims to fill the gap between the multitude of ontologies released to model the data protection framework and the disparate approaches proposed to automatically process the text of privacy policies. The methodology relies on the notion of Ontology Design Pattern (ODP), i.e. a modelling solution to solve a recurrent ontology design problem. Implementing a pipeline that exploits existing vocabularies and different NLP techniques, I show how the information disclosed in privacy policies could be extracted and modelled through some existing ODPs. The benefit of such an approach is the provision of a methodology for processing privacy policies texts that overlooks the different ontological models. Instead, it uses ODPs as a semantic middle-layer of processing that different ontological models could refine and extend according to their own ontological commitments

Domain ontology learning from the web

El Aprendizaje de Ontologías se define como el conjunto de métodos utilizados para construir, enriquecer o adaptar una ontología existente de forma semiautomática, utilizando fuentes de información heterogéneas. En este proceso se emplea texto, diccionarios electrónicos, ontologías lingüísticas e información estructurada y semiestructurada para extraer conocimiento. Recientemente, gracias al enorme crecimiento de la Sociedad de la Información, la Web se ha convertido en una valiosa fuente de información para casi cualquier dominio. Esto ha provocado que los investigadores empiecen a considerar a la Web como un repositorio válido para Recuperar Información y Adquirir Conocimiento. No obstante, la Web presenta algunos problemas que no se observan en repositorios de información clásicos: presentación orientada al usuario, ruido, fuentes no confiables, alta dinamicidad y tamaño abrumador. Pese a ello, también presenta algunas características que pueden ser interesantes para la adquisición de conocimiento: debido a su enorme tamaño y heterogeneidad, se asume que la Web aproxima la distribución real de la información a nivel global. Este trabajo describe una aproximación novedosa para el aprendizaje de ontologías, presentando nuevos métodos para adquirir conocimiento de la Web. La propuesta se distingue de otros trabajos previos principalmente en la particular adaptación de algunas técnicas clásicas de aprendizaje al corpus Web y en la explotación de las características interesantes del entorno Web para componer una aproximación automática, no supervisada e independiente del dominio. Con respecto al proceso de construcción de la ontologías, se han desarrollado los siguientes métodos: i) extracción y selección de términos relacionados con el dominio, organizándolos de forma taxonómica; ii) descubrimiento y etiquetado de relaciones no taxonómicas entre los conceptos; iii) métodos adicionales para mejorar la estructura final, incluyendo la detección de entidades con nombre, atributos, herencia múltiple e incluso un cierto grado de desambiguación semántica. La metodología de aprendizaje al completo se ha implementado mediante un sistema distribuido basado en agentes, proporcionando una solución escalable. También se ha evaluado para varios dominios de conocimiento bien diferenciados, obteniendo resultados de buena calidad. Finalmente, se han desarrollado varias aplicaciones referentes a la estructuración automática de librerías digitales y recursos Web, y la recuperación de información basada en ontologías.Ontology Learning is defined as the set of methods used for building from scratch, enriching or adapting an existing ontology in a semi-automatic fashion using heterogeneous information sources. This data-driven procedure uses text, electronic dictionaries, linguistic ontologies and structured and semi-structured information to acquire knowledge. Recently, with the enormous growth of the Information Society, the Web has become a valuable source of information for almost every possible domain of knowledge. This has motivated researchers to start considering the Web as a valid repository for Information Retrieval and Knowledge Acquisition. However, the Web suffers from problems that are not typically observed in classical information repositories: human oriented presentation, noise, untrusted sources, high dynamicity and overwhelming size. Even though, it also presents characteristics that can be interesting for knowledge acquisition: due to its huge size and heterogeneity it has been assumed that the Web approximates the real distribution of the information in humankind. The present work introduces a novel approach for ontology learning, introducing new methods for knowledge acquisition from the Web. The adaptation of several well known learning techniques to the web corpus and the exploitation of particular characteristics of the Web environment composing an automatic, unsupervised and domain independent approach distinguishes the present proposal from previous works.With respect to the ontology building process, the following methods have been developed: i) extraction and selection of domain related terms, organising them in a taxonomical way; ii) discovery and label of non-taxonomical relationships between concepts; iii) additional methods for improving the final structure, including the detection of named entities, class features, multiple inheritance and also a certain degree of semantic disambiguation. The full learning methodology has been implemented in a distributed agent-based fashion, providing a scalable solution. It has been evaluated for several well distinguished domains of knowledge, obtaining good quality results. Finally, several direct applications have been developed, including automatic structuring of digital libraries and web resources, and ontology-based Web Information Retrieval