Ontology Pattern-Based Data Integration

Data integration is concerned with providing a unified access to data residing at multiple sources. Such a unified access is realized by having a global schema and a set of mappings between the global schema and the local schemas of each data source, which specify how user queries at the global schema can be translated into queries at the local schemas. Data sources are typically developed and maintained independently, and thus, highly heterogeneous. This causes difficulties in integration because of the lack of interoperability in the aspect of architecture, data format, as well as syntax and semantics of the data. This dissertation represents a study on how small, self-contained ontologies, called ontology design patterns, can be employed to provide semantic interoperability in a cross-repository data integration system. The idea of this so-called ontology pattern- based data integration is that a collection of ontology design patterns can act as the global schema that still contains sufficient semantics, but is also flexible and simple enough to be used by linked data providers. On the one side, this differs from existing ontology-based solutions, which are based on large, monolithic ontologies that provide very rich semantics, but enforce too restrictive ontological choices, hence are shunned by many data providers. On the other side, this also differs from the purely linked data based solutions, which do offer simplicity and flexibility in data publishing, but too little in terms of semantic interoperability. We demonstrate the feasibility of this idea through the actual development of a large scale data integration project involving seven ocean science data repositories from five institutions in the U.S. In addition, we make two contributions as part of this dissertation work, which also play crucial roles in the aforementioned data integration project. First, we develop a collection of more than a dozen ontology design patterns that capture the key notions in the ocean science occurring in the participating data repositories. These patterns contain axiomatization of the key notions and were developed with an intensive involvement from the domain experts. Modeling of the patterns was done in a systematic workflow to ensure modularity, reusability, and flexibility of the whole pattern collection. Second, we propose the so-called pattern views that allow data providers to publish their data in very simple intermediate schema and show that they can greatly assist data providers to publish their data without requiring a thorough understanding of the axiomatization of the patterns

Linked Data Entity Summarization

On the Web, the amount of structured and Linked Data about entities is constantly growing. Descriptions of single entities often include thousands of statements and it becomes difficult to comprehend the data, unless a selection of the most relevant facts is provided. This doctoral thesis addresses the problem of Linked Data entity summarization. The contributions involve two entity summarization approaches, a common API for entity summarization, and an approach for entity data fusion

Heterogeneous data to knowledge graphs matching

Many applications rely on the existence of reusable data. The FAIR (Findability, Accessibility, Interoperability, and Reusability) principles identify detailed descriptions of data and metadata as the core ingredients for achieving reusability. However, creating descriptive data requires massive manual effort. One way to ensure that data is reusable is by integrating it into Knowledge Graphs (KGs). The semantic foundation of these graphs provides the necessary description for reuse. In the Open Research KG, they propose to model artifacts of scientific endeavors, including publications and their key messages. Datasets supporting these publications are essential carriers of scientific knowledge and should be included in KGs. We focus on biodiversity research as an example domain to develop and evaluate our approach. Biodiversity is the assortment of life on earth covering evolutionary, ecological, biological, and social forms. Understanding such a domain and its mechanisms is essential to preserving this vital foundation of human well-being. It is imperative to monitor the current state of biodiversity and its change over time and to understand its forces driving and preserving life in all its variety and richness. This need has resulted in numerous works being published in this field. For example, a large amount of tabular data (datasets), textual data (publications), and metadata (e.g., dataset description) have been generated. So, it is a data-rich domain with an exceptionally high need for data reuse. Managing and integrating these heterogeneous data of biodiversity research remains a big challenge. Our core research problem is how to enable the reusability of tabular data, which is one aspect of the FAIR data principles. In this thesis, we provide answer for this research problem

Graph Data-Models and Semantic Web Technologies in Scholarly Digital Editing

This volume is based on the selected papers presented at the Workshop on Scholarly Digital Editions, Graph Data-Models and Semantic Web Technologies, held at the Uni- versity of Lausanne in June 2019. The Workshop was organized by Elena Spadini (University of Lausanne) and Francesca Tomasi (University of Bologna), and spon- sored by the Swiss National Science Foundation through a Scientific Exchange grant, and by the Centre de recherche sur les lettres romandes of the University of Lausanne. The Workshop comprised two full days of vibrant discussions among the invited speakers, the authors of the selected papers, and other participants.1 The acceptance rate following the open call for papers was around 60%. All authors – both selected and invited speakers – were asked to provide a short paper two months before the Workshop. The authors were then paired up, and each pair exchanged papers. Paired authors prepared questions for one another, which were to be addressed during the talks at the Workshop; in this way, conversations started well before the Workshop itself. After the Workshop, the papers underwent a second round of peer-review before inclusion in this volume. This time, the relevance of the papers was not under discus- sion, but reviewers were asked to appraise specific aspects of each contribution, such as its originality or level of innovation, its methodological accuracy and knowledge of the literature, as well as more formal parameters such as completeness, clarity, and coherence. The bibliography of all of the papers is collected in the public Zotero group library GraphSDE20192, which has been used to generate the reference list for each contribution in this volume. The invited speakers came from a wide range of backgrounds (academic, commer- cial, and research institutions) and represented the different actors involved in the remediation of our cultural heritage in the form of graphs and/or in a semantic web en- vironment. Georg Vogeler (University of Graz) and Ronald Haentjens Dekker (Royal Dutch Academy of Sciences, Humanities Cluster) brought the Digital Humanities research perspective; the work of Hans Cools and Roberta Laura Padlina (University of Basel, National Infrastructure for Editions), as well as of Tobias Schweizer and Sepi- deh Alassi (University of Basel, Digital Humanities Lab), focused on infrastructural challenges and the development of conceptual and software frameworks to support re- searchers’ needs; Michele Pasin’s contribution (Digital Science, Springer Nature) was informed by his experiences in both academic research, and in commercial technology companies that provide services for the scientific community. The Workshop featured not only the papers of the selected authors and of the invited speakers, but also moments of discussion between interested participants. In addition to the common Q&A time, during the second day one entire session was allocated to working groups delving into topics that had emerged during the Workshop. Four working groups were created, with four to seven participants each, and each group presented a short report at the end of the session. Four themes were discussed: enhancing TEI from documents to data; ontologies for the Humanities; tools and infrastructures; and textual criticism. All of these themes are represented in this volume. The Workshop would not have been of such high quality without the support of the members of its scientific committee: Gioele Barabucci, Fabio Ciotti, Claire Clivaz, Marion Rivoal, Greta Franzini, Simon Gabay, Daniel Maggetti, Frederike Neuber, Elena Pierazzo, Davide Picca, Michael Piotrowski, Matteo Romanello, Maïeul Rouquette, Elena Spadini, Francesca Tomasi, Aris Xanthos – and, of course, the support of all the colleagues and administrative staff in Lausanne, who helped the Workshop to become a reality. The final versions of these papers underwent a single-blind peer review process. We want to thank the reviewers: Helena Bermudez Sabel, Arianna Ciula, Marilena Daquino, Richard Hadden, Daniel Jeller, Tiziana Mancinelli, Davide Picca, Michael Piotrowski, Patrick Sahle, Raffaele Viglianti, Joris van Zundert, and others who preferred not to be named personally. Your input enhanced the quality of the volume significantly! It is sad news that Hans Cools passed away during the production of the volume. We are proud to document a recent state of his work and will miss him and his ability to implement the vision of a digital scholarly edition based on graph data-models and semantic web technologies. The production of the volume would not have been possible without the thorough copy-editing and proof reading by Lucy Emmerson and the support of the IDE team, in particular Bernhard Assmann, the TeX-master himself. This volume is sponsored by the University of Bologna and by the University of Lausanne. Bologna, Lausanne, Graz, July 2021 Francesca Tomasi, Elena Spadini, Georg Vogele

QB4OLAP : Enabling business intelligence over semantic web data

Premio Primer puesto otorgado por la Academia Nacional de Ingeniería.The World-Wide Web was initially conceived as a repository of information tailored for human consumption. In the last decade, the idea of transforming the web into a machine-understandable web of data, has gained momentum. To this end, the World Wide Web Consortium (W3C) maintains a set of standards, referred to as the Semantic Web (SW), which allow to openly share data and metadata. Among these is the Resource Description Framework (RDF), which represents data as graphs, RDF-S and OWL to describe the data structure via ontologies or vocabularies, and SPARQL, the RDF query language. On top of the RDF data model, standards and recommendations can be built to represent data that adheres to other models. The multidimensional (MD) model views data in an n-dimensional space, usually called a data cube, composed of dimensions and facts. The former reflect the perspectives from which data are viewed, and the latter correspond to points in this space, associated with (usually) quantitative data (also known as measures). Facts can be aggregated, disaggregated, and filtered using the dimensions. This process is called Online Analytical Processing (OLAP). Despite the RDF Data Cube Vocabulary (QB) is the W3C standard to represent statistical data, which resembles MD data, it does not include key features needed for OLAP analysis, like dimension hierarchies, dimension level attributes, and aggregate functions. To enable this kind of analysis over SW data cubes, in this thesis we propose the QB4 OLAP vocabulary, an extension of QB. A problem remains, however: writing efficient analytical queries over SW data cubes requires a deep knowledge of RDF and SPARQL, unlikely to be found in typical OLAP users. We address this problem in this thesis. Our approach is based on allowing analytical users to write queries using what they know best: OLAP operations over data cubes, without dealing with SW technicalities. For this, we devised CQL, a simple, high-level query language over data cubes. Then we make use of the structural metadata provided by QB4 OLAP to translate CQL queries into SPARQL ones. We adapt general-purpose SPARQL query optimization techniques, and propose query improvement strategies to produce efficient SPARQL queries. We evaluate our implementation tailoring the well known Star-Schema benchmark, which allows us to compare our proposal against existing ones in a fair way. We show that our approach outperforms other ones. Finally, as another result, our experiments allow us to study which combinations of improvement strategies fits better to an analytical scenario.La World-Wide Web fue concebida como un repositorio de informa- ción a ser procesada y consumida por humanos. Pero en la última década ha ganado impulso la idea de transformar a la Web en una gran base de datos procesables por máquinas. Con este fin, el World Wide Web Consortium (W3C) ha establecido una serie de estándares también conocidos como estándares para la Web Semántica (WS), los cuales permiten compartir datos y metadatos en formatos abiertos. Entre estos estándares se destacan: el Resource Description Framework (RDF), un modelo de datos basado en grafos para representar datos y relaciones entre ellos, RDF-S y OWL que permiten describir la estructura y el significado de los datos por medio de ontologías o vocabu- larios, y el lenguaje de consultas SPARQL. Estos estándares pueden ser utilizados para construir representaciones de otros modelos de datos, por ejemplo datos tabulares o datos relacionales. El modelo de datos multidimensional (MD) representa a los datos dentro de un espacio n-dimensional, usualmente denominado cubo de datos, que se compone de dimensiones y hechos. Las primeras reflejan las perspectivas desde las cuales interesa analizar los datos, mientras que las segundas corresponden a puntos en este espacio n- dimensional, a los cuales se asocian valores usualmente numéricos, conocidos como medidas. Los hechos pueden ser agregados y resumidos, desagregados, y filtrados utilizando las dimensiones. Este pro- ceso es conocido como Online Analytical Processing (OLAP). Pese a que la W3C ha establecido un estándar que puede ser utilizado para publicación de datos multidimensionales, conocido como el RDF Data Cube Vocabulary (QB), éste no incluye algunos aspectos del modelo MD que son imprescindibles para realizar análisis tipo OLAP como son las jerarquías de dimensión, los atributos en los niveles de dimensión, y las funciones de agregaciónpara resumir valores de medidas. Para permitir este tipo de análisis sobre cubos en la SW, en esta tesis se propone un vocabulario que extiende el vocabulario QB denominado QB4OLAP. Sin embargo, para realizar análisis tipo OLAP en forma eficiente sobre cubos QB4OLAP es necesario un conocimiento profundo de RDF y SPARQL, los cuales distan de ser populares entre los usuarios OLAP típicos. Esta tesis también aborda este problema. Nuestro enfoque consiste en brindar un conjunto de operaciones clásicas para los usuarios OLAP, y luego realizar la traducción en forma automática de estas operaciones en consultas SPARQL. Comenzamos definiendo un lenguaje de consultas para cubos en alto nivel: Cube Query Language (CQL), y luego explotamos la metadata representada mediante QB4OLAP para realizar la traducción a SPARQL. Asimismo, mejoramos el rendimiento de las consultas obtenidas, adaptando y aplicando técnicas existentes de optimización de consultas SPARQL. Para evaluar nuestra propuesta adaptamos a los estándares de la SW el Star Schema benchmark, el cual es el estándar para la evaluación de sistemas tipo OLAP. Esto permite comparar nuestro enfoque con otras propuestas existentes, asi como evaluar el impacto de nuestras estrategias de mejoras de consultas SPARQL. De esta comparación podemos concluir que nuestro enfoque supera a otras propuestas existentes, y que nuestras técnicas de mejoras logran incrementar en 10 veces el rendimiento del sistema

Integrating and querying linked datasets through ontological rules

The Web of Linked Open Data has developed from a few datasets in 2007 into a large data space containing billions of RDF triples published and stored in hundreds of independent datasets, so as to form the so called Linked Open Data Cloud. This information cloud, ranging over a wide set of data domains, poses a challenge when it comes to reconciling heterogeneous schemas or vocabularies adopted by data publishers. Motivated by this challenge, in this thesis was address the problem of integrating and querying multiple heterogeneous Linked Data sets through ontological rules. Firstly, we propose a formalisation of the notion of a peer-to-peer Linked Data integration system, where the mappings between peers comprise schema-level mappings and equality constraints between different IRIs; we call this formalism an RDF Peer System(RPS). We show that the semantics of the mappings preserve tractability of answering Basic Graph Pattern (BGP) SPARQL queries against the data stored in the RDF sources and the set of constraints given by the RPS mappings. Then, we address the problem of SPARQL query rewriting under RPSs and we show that it is not possible to rewrite an input BGP SPARQL query into a SPARQL 1.0 query under general RPSs, as the RPS peer mappings are not first-order-rewritable rules; this is a major drawback of general RPSs since data materialisation is required to exploit their full semantics. With the adoption of the more recent standard SPARQL 1.1 and its property paths we are able to extend the expressivity of the target language beyond first-order by including regular expressions in the body of the target SPARQL queries, that is, by expressing conjunctive two-way regular path queries (C2RPQs). Following this idea, in the second part of the thesis we step away from the language of RPSs to conduct a study on C2RPQ-rewritability under a broader ontology language. We define [ELHI`inh] (harmless linear ELHI), an ontology language that generalises both the DL-Lite[R] and linear ELH description logics. We prove the rewritability of instance queries (queries with a single atom in their body) under [ELHI`inh] knowledge bases with C2RPQs as the target language, presenting a query rewriting algorithm that makes use of non-deterministic finite-state automata. Following from that, we propose a query rewriting algorithm for answering conjunctive queries under [ELHI`inh] knowledge bases, with C2RPQs as the target language. Since C2RPQs can be straightforwardly expressed in SPARQL 1.1 by means of property paths, we believe that our approach is directly applicable to real-world querying settings. Lastly, we undertake a complexity analysis for query answering under [ELHI`inh]. We analyse the computational cost of query answering in terms of both data complexity (where the ontology and the query are fixed and the data alone is a variable input)and combined complexity (where query, ontology and data all constitute the variable input). We show that answering instance queries under [ELHI`inh] is NLogSpace-complete for data complexity and in PTime for combined complexity; we also show that answering CQs under [ELHI`inh] is NLogSpace-complete for data complexity and NP-complete for combined complexity