Ontology Based Data Access in Statoil

Ontology Based Data Access (OBDA) is a prominent approach to query databases which uses an ontology to expose data in a conceptually clear manner by abstracting away from the technical schema-level details of the underlying data. The ontology is ‘connected’ to the data via mappings that allow to automatically translate queries posed over the ontology into data-level queries that can be executed by the underlying database management system. Despite a lot of attention from the research community, there are still few instances of real world industrial use of OBDA systems. In this work we present data access challenges in the data-intensive petroleum company Statoil and our experience in addressing these challenges with OBDA technology. In particular, we have developed a deployment module to create ontologies and mappings from relational databases in a semi-automatic fashion; a query processing module to perform and optimise the process of translating ontological queries into data queries and their execution over either a single DB of federated DBs; and a query formulation module to support query construction for engineers with a limited IT background. Our modules have been integrated in one OBDA system, deployed at Statoil, integrated with Statoil’s infrastructure, and evaluated with Statoil’s engineers and data

Semantic Data Management in Data Lakes

In recent years, data lakes emerged as away to manage large amounts of heterogeneous data for modern data analytics. One way to prevent data lakes from turning into inoperable data swamps is semantic data management. Some approaches propose the linkage of metadata to knowledge graphs based on the Linked Data principles to provide more meaning and semantics to the data in the lake. Such a semantic layer may be utilized not only for data management but also to tackle the problem of data integration from heterogeneous sources, in order to make data access more expressive and interoperable. In this survey, we review recent approaches with a specific focus on the application within data lake systems and scalability to Big Data. We classify the approaches into (i) basic semantic data management, (ii) semantic modeling approaches for enriching metadata in data lakes, and (iii) methods for ontologybased data access. In each category, we cover the main techniques and their background, and compare latest research. Finally, we point out challenges for future work in this research area, which needs a closer integration of Big Data and Semantic Web technologies

Supporting Tools for Automated Generation and Visual Editing of Relational-to-Ontology Mappings

La integració de dades amb formats heterogenis i de diversos dominis mitjançant tecnologies de la web semàntica permet solucionar la seva disparitat estructural i semàntica. L'accés a dades basat en ontologies (OBDA, en anglès) és una solució integral que es basa en l'ús d'ontologies com esquemes mediadors i el mapatge entre les dades i les ontologies per facilitar la consulta de les fonts de dades. No obstant això, una de les principals barreres que pot dificultar més l'adopció de OBDA és la manca d'eines per donar suport a la creació de mapatges entre dades i ontologies. L'objectiu d'aquesta investigació ha estat desenvolupar noves eines que permetin als experts sense coneixements d'ontologies la creació de mapatges entre dades i ontologies. Amb aquesta finalitat, s'han dut a terme dues línies de treball: la generació automàtica de mapatges entre dades relacionals i ontologies i l'edició dels mapatges a través de la seva representació visual. Les eines actualment disponibles per automatitzar la generació de mapatges estan lluny de proporcionar una solució completa, ja que es basen en els esquemes relacionals i amb prou feines tenen en compte els continguts de la font de dades relacional i les característiques de l'ontologia. No obstant això, les dades poden contenir relacions ocultes que poden ajudar a la generació de mapatges. Per superar aquesta limitació, hem desenvolupat AutoMap4OBDA, un sistema que genera automàticament mapatges R2RML a partir de l'anàlisi dels continguts de la font relacional i tenint en compte les característiques de l'ontologia. El sistema fa servir una tècnica d'aprenentatge d'ontologies per inferir jerarquies de classes, selecciona les mètriques de similitud de cadenes en base a les etiquetes de les ontologies i analitza les estructures de grafs per generar els mapatges a partir de l'estructura de l'ontologia. La representació visual per mitjà d'interfícies intuïtives pot ajudar els usuaris sense coneixements tècnics a establir mapatges entre una font relacional i una ontologia. No obstant això, les eines existents per a l'edició visual de mapatges mostren algunes limitacions. En particular, la representació visual de mapatges no contempla les estructures de la font relacional i de l'ontologia de forma conjunta. Per superar aquest inconvenient, hem desenvolupat Map-On, un entorn visual web per a l'edició manual de mapatges. AutoMap4OBDA ha demostrat que supera les prestacions de les solucions existents per a la generació de mapatges. Map-On s'ha aplicat en projectes d'investigació per verificar la seva eficàcia en la gestió de mapatges.La integración de datos con formatos heterogéneos y de diversos dominios mediante tecnologías de la Web Semántica permite solventar su disparidad estructural y semántica. El acceso a datos basado en ontologías (OBDA, en inglés) es una solución integral que se basa en el uso de ontologías como esquemas mediadores y mapeos entre los datos y las ontologías para facilitar la consulta de las fuentes de datos. Sin embargo, una de las principales barreras que puede dificultar más la adopción de OBDA es la falta de herramientas para apoyar la creación de mapeos entre datos y ontologías. El objetivo de esta investigación ha sido desarrollar nuevas herramientas que permitan a expertos sin conocimientos de ontologías la creación de mapeos entre datos y ontologías. Con este fin, se han llevado a cabo dos líneas de trabajo: la generación automática de mapeos entre datos relacionales y ontologías y la edición de los mapeos a través de su representación visual. Las herramientas actualmente disponibles para automatizar la generación de mapeos están lejos de proporcionar una solución completa, ya que se basan en los esquemas relacionales y apenas tienen en cuenta los contenidos de la fuente de datos relacional y las características de la ontología. Sin embargo, los datos pueden contener relaciones ocultas que pueden ayudar a la generación de mapeos. Para superar esta limitación, hemos desarrollado AutoMap4OBDA, un sistema que genera automáticamente mapeos R2RML a partir del análisis de los contenidos de la fuente relacional y teniendo en cuenta las características de la ontología. El sistema emplea una técnica de aprendizaje de ontologías para inferir jerarquías de clases, selecciona las métricas de similitud de cadenas en base a las etiquetas de las ontologías y analiza las estructuras de grafos para generar los mapeos a partir de la estructura de la ontología. La representación visual por medio de interfaces intuitivas puede ayudar a los usuarios sin conocimientos técnicos a establecer mapeos entre una fuente relacional y una ontología. Sin embargo, las herramientas existentes para la edición visual de mapeos muestran algunas limitaciones. En particular, la representación de mapeos no contempla las estructuras de la fuente relacional y de la ontología de forma conjunta. Para superar este inconveniente, hemos desarrollado Map-On, un entorno visual web para la edición manual de mapeos. AutoMap4OBDA ha demostrado que supera las prestaciones de las soluciones existentes para la generación de mapeos. Map-On se ha aplicado en proyectos de investigación para verificar su eficacia en la gestión de mapeos.Integration of data from heterogeneous formats and domains based on Semantic Web technologies enables us to solve their structural and semantic heterogeneity. Ontology-based data access (OBDA) is a comprehensive solution which relies on the use of ontologies as mediator schemas and relational-to-ontology mappings to facilitate data source querying. However, one of the greatest obstacles in the adoption of OBDA is the lack of tools to support the creation of mappings between physically stored data and ontologies. The objective of this research has been to develop new tools that allow non-ontology experts to create relational-to-ontology mappings. For this purpose, two lines of work have been carried out: the automated generation of relational-to-ontology mappings, and visual support for mapping editing. The tools currently available to automate the generation of mappings are far from providing a complete solution, since they rely on relational schemas and barely take into account the contents of the relational data source and features of the ontology. However, the data may contain hidden relationships that can help in the process of mapping generation. To overcome this limitation, we have developed AutoMap4OBDA, a system that automatically generates R2RML mappings from the analysis of the contents of the relational source and takes into account the characteristics of ontology. The system employs an ontology learning technique to infer class hierarchies, selects the string similarity metric based on the labels of ontologies, and analyses the graph structures to generate the mappings from the structure of the ontology. The visual representation through intuitive interfaces can help non-technical users to establish mappings between a relational source and an ontology. However, existing tools for visual editing of mappings show somewhat limitations. In particular, the visual representation of mapping does not embrace the structure of the relational source and the ontology at the same time. To overcome this problem, we have developed Map-On, a visual web environment for the manual editing of mappings. AutoMap4OBDA has been shown to outperform existing solutions in the generation of mappings. Map-On has been applied in research projects to verify its effectiveness in managing mappings

Enabling semantic queries across federated bioinformatics databases

MOTIVATION: Data integration promises to be one of the main catalysts in enabling new insights to be drawn from the wealth of biological data available publicly. However, the heterogeneity of the different data sources, both at the syntactic and the semantic level, still poses significant challenges for achieving interoperability among biological databases. RESULTS: We introduce an ontology-based federated approach for data integration. We applied this approach to three heterogeneous data stores that span different areas of biological knowledge: (i) Bgee, a gene expression relational database; (ii) Orthologous Matrix (OMA), a Hierarchical Data Format 5 orthology DS; and (iii) UniProtKB, a Resource Description Framework (RDF) store containing protein sequence and functional information. To enable federated queries across these sources, we first defined a new semantic model for gene expression called GenEx. We then show how the relational data in Bgee can be expressed as a virtual RDF graph, instantiating GenEx, through dedicated relational-to-RDF mappings. By applying these mappings, Bgee data are now accessible through a public SPARQL endpoint. Similarly, the materialized RDF data of OMA, expressed in terms of the Orthology ontology, is made available in a public SPARQL endpoint. We identified and formally described intersection points (i.e. virtual links) among the three data sources. These allow performing joint queries across the data stores. Finally, we lay the groundwork to enable nontechnical users to benefit from the integrated data, by providing a natural language template-based search interface

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

Semantic-guided predictive modeling and relational learning within industrial knowledge graphs

The ubiquitous availability of data in today’s manufacturing environments, mainly driven by the extended usage of software and built-in sensing capabilities in automation systems, enables companies to embrace more advanced predictive modeling and analysis in order to optimize processes and usage of equipment. While the potential insight gained from such analysis is high, it often remains untapped, since integration and analysis of data silos from different production domains requires high manual effort and is therefore not economic. Addressing these challenges, digital representations of production equipment, so-called digital twins, have emerged leading the way to semantic interoperability across systems in different domains. From a data modeling point of view, digital twins can be seen as industrial knowledge graphs, which are used as semantic backbone of manufacturing software systems and data analytics. Due to the prevalent historically grown and scattered manufacturing software system landscape that is comprising of numerous proprietary information models, data sources are highly heterogeneous. Therefore, there is an increasing need for semi-automatic support in data modeling, enabling end-user engineers to model their domain and maintain a unified semantic knowledge graph across the company. Once the data modeling and integration is done, further challenges arise, since there has been little research on how knowledge graphs can contribute to the simplification and abstraction of statistical analysis and predictive modeling, especially in manufacturing. In this thesis, new approaches for modeling and maintaining industrial knowledge graphs with focus on the application of statistical models are presented. First, concerning data modeling, we discuss requirements from several existing standard information models and analytic use cases in the manufacturing and automation system domains and derive a fragment of the OWL 2 language that is expressive enough to cover the required semantics for a broad range of use cases. The prototypical implementation enables domain end-users, i.e. engineers, to extend the basis ontology model with intuitive semantics. Furthermore it supports efficient reasoning and constraint checking via translation to rule-based representations. Based on these models, we propose an architecture for the end-user facilitated application of statistical models using ontological concepts and ontology-based data access paradigms. In addition to that we present an approach for domain knowledge-driven preparation of predictive models in terms of feature selection and show how schema-level reasoning in the OWL 2 language can be employed for this task within knowledge graphs of industrial automation systems. A production cycle time prediction model in an example application scenario serves as a proof of concept and demonstrates that axiomatized domain knowledge about features can give competitive performance compared to purely data-driven ones. In the case of high-dimensional data with small sample size, we show that graph kernels of domain ontologies can provide additional information on the degree of variable dependence. Furthermore, a special application of feature selection in graph-structured data is presented and we develop a method that allows to incorporate domain constraints derived from meta-paths in knowledge graphs in a branch-and-bound pattern enumeration algorithm. Lastly, we discuss maintenance of facts in large-scale industrial knowledge graphs focused on latent variable models for the automated population and completion of missing facts. State-of-the art approaches can not deal with time-series data in form of events that naturally occur in industrial applications. Therefore we present an extension of learning knowledge graph embeddings in conjunction with data in form of event logs. Finally, we design several use case scenarios of missing information and evaluate our embedding approach on data coming from a real-world factory environment. We draw the conclusion that industrial knowledge graphs are a powerful tool that can be used by end-users in the manufacturing domain for data modeling and model validation. They are especially suitable in terms of the facilitated application of statistical models in conjunction with background domain knowledge by providing information about features upfront. Furthermore, relational learning approaches showed great potential to semi-automatically infer missing facts and provide recommendations to production operators on how to keep stored facts in synch with the real world