Visual exploration of semantic-web-based knowledge structures

Humans have a curious nature and seek a better understanding of the world. Data, in- formation, and knowledge became assets of our modern society through the information technology revolution in the form of the internet. However, with the growing size of accumulated data, new challenges emerge, such as searching and navigating in these large collections of data, information, and knowledge. The current developments in academic and industrial contexts target the corresponding challenges using Semantic Web techno- logies. The Semantic Web is an extension of the Web and provides machine-readable representations of knowledge for various domains. These machine-readable representations allow intelligent machine agents to understand the meaning of the data and information; and enable additional inference of new knowledge. Generally, the Semantic Web is designed for information exchange and its processing and does not focus on presenting such semantically enriched data to humans. Visualizations support exploration, navigation, and understanding of data by exploiting humans’ ability to comprehend complex data through visual representations. In the context of Semantic- Web-Based knowledge structures, various visualization methods and tools are available, and new ones are being developed every year. However, suitable visualizations are highly dependent on individual use cases and targeted user groups. In this thesis, we investigate visual exploration techniques for Semantic-Web-Based knowledge structures by addressing the following challenges: i) how to engage various user groups in modeling such semantic representations; ii) how to facilitate understanding using customizable visual representations; and iii) how to ease the creation of visualizations for various data sources and different use cases. The achieved results indicate that visual modeling techniques facilitate the engagement of various user groups in ontology modeling. Customizable visualizations enable users to adjust visualizations to the current needs and provide different views on the data. Additionally, customizable visualization pipelines enable rapid visualization generation for various use cases, data sources, and user group

An intelligent linked data quality dashboard

This paper describes a new intelligent, data-driven dashboard for linked data quality assessment. The development goal was to assist data quality engineers to interpret data quality problems found when evaluating a dataset us-ing a metrics-based data quality assessment. This required construction of a graph linking the problematic things identified in the data, the assessment metrics and the source data. This context and supporting user interfaces help the user to un-derstand data quality problems. An analysis widget also helped the user identify the root cause multiple problems. This supported the user in identification and prioritization of the problems that need to be fixed and to improve data quality. The dashboard was shown to be useful for users to clean data. A user evaluation was performed with both expert and novice data quality engineers

Enhancement of the usability of SOA services for novice users

Recently, the automation of service integration has provided a significant advantage in delivering services to novice users. This art of integrating various services is known as Service Composition and its main purpose is to simplify the development process for web applications and facilitates reuse of services. It is one of the paradigms that enables services to end-users (i.e.service provisioning) through the outsourcing of web contents and it requires users to share and reuse services in more collaborative ways. Most service composers are effective at enabling integration of web contents, but they do not enable universal access across different groups of users. This is because, the currently existing content aggregators require complex interactions in order to create web applications (e.g., Web Service Business Process Execution Language (WS-BPEL)) as a result not all users are able to use such web tools. This trend demands changes in the web tools that end-users use to gain and share information, hence this research uses Mashups as a service composition technique to allow novice users to integrate publicly available Service Oriented Architecture (SOA) services, where there is a minimal active web application development. Mashups being the platforms that integrate disparate web Application Programming Interfaces (APIs) to create user defined web applications; presents a great opportunity for service provisioning. However, their usability for novice users remains invalidated since Mashup tools are not easy to use they require basic programming skills which makes the process of designing and creating Mashups difficult. This is because Mashup tools access heterogeneous web contents using public web APIs and the process of integrating them become complex since web APIs are tailored by different vendors. Moreover, the design of Mashup editors is unnecessary complex; as a result, users do not know where to start when creating Mashups. This research address the gap between Mashup tools and usability by the designing and implementing a semantically enriched Mashup tool to discover, annotate and compose APIs to improve the utilization of SOA services by novice users. The researchers conducted an analysis of the already existing Mashup tools to identify challenges and weaknesses experienced by novice Mashup users. The findings from the requirement analysis formulated the system usability requirements that informed the design and implementation of the proposed Mashup tool. The proposed architecture addressed three layers: composition, annotation and discovery. The researchers developed a simple Mashup tool referred to as soa-Services Provisioner (SerPro) that allowed novice users to create web application flexibly. Its usability and effectiveness was validated. The proposed Mashup tool enhanced the usability of SOA services, since data analysis and results showed that it was usable to novice users by scoring a System Usability Scale (SUS) score of 72.08. Furthermore, this research discusses the research limitations and future work for further improvements

A Query Integrator and Manager for the Query Web

We introduce two concepts: the Query Web as a layer of interconnected queries over the document web and the semantic web, and a Query Web Integrator and Manager (QI) that enables the Query Web to evolve. QI permits users to write, save and reuse queries over any web accessible source, including other queries saved in other installations of QI. The saved queries may be in any language (e.g. SPARQL, XQuery); the only condition for interconnection is that the queries return their results in some form of XML. This condition allows queries to chain off each other, and to be written in whatever language is appropriate for the task. We illustrate the potential use of QI for several biomedical use cases, including ontology view generation using a combination of graph-based and logical approaches, value set generation for clinical data management, image annotation using terminology obtained from an ontology web service, ontology-driven brain imaging data integration, small-scale clinical data integration, and wider-scale clinical data integration. Such use cases illustrate the current range of applications of QI and lead us to speculate about the potential evolution from smaller groups of interconnected queries into a larger query network that layers over the document and semantic web. The resulting Query Web could greatly aid researchers and others who now have to manually navigate through multiple information sources in order to answer specific questions

Serviços de integração de dados para aplicações biomédicas

Doutoramento em Informática (MAP-i)In the last decades, the field of biomedical science has fostered unprecedented scientific advances. Research is stimulated by the constant evolution of information technology, delivering novel and diverse bioinformatics tools. Nevertheless, the proliferation of new and disconnected solutions has resulted in massive amounts of resources spread over heterogeneous and distributed platforms. Distinct data types and formats are generated and stored in miscellaneous repositories posing data interoperability challenges and delays in discoveries. Data sharing and integrated access to these resources are key features for successful knowledge extraction. In this context, this thesis makes contributions towards accelerating the semantic integration, linkage and reuse of biomedical resources. The first contribution addresses the connection of distributed and heterogeneous registries. The proposed methodology creates a holistic view over the different registries, supporting semantic data representation, integrated access and querying. The second contribution addresses the integration of heterogeneous information across scientific research, aiming to enable adequate data-sharing services. The third contribution presents a modular architecture to support the extraction and integration of textual information, enabling the full exploitation of curated data. The last contribution lies in providing a platform to accelerate the deployment of enhanced semantic information systems. All the proposed solutions were deployed and validated in the scope of rare diseases.Nas últimas décadas, o campo das ciências biomédicas proporcionou grandes avanços científicos estimulados pela constante evolução das tecnologias de informação. A criação de diversas ferramentas na área da bioinformática e a falta de integração entre novas soluções resultou em enormes quantidades de dados distribuídos por diferentes plataformas. Dados de diferentes tipos e formatos são gerados e armazenados em vários repositórios, o que origina problemas de interoperabilidade e atrasa a investigação. A partilha de informação e o acesso integrado a esses recursos são características fundamentais para a extração bem sucedida do conhecimento científico. Nesta medida, esta tese fornece contribuições para acelerar a integração, ligação e reutilização semântica de dados biomédicos. A primeira contribuição aborda a interconexão de registos distribuídos e heterogéneos. A metodologia proposta cria uma visão holística sobre os diferentes registos, suportando a representação semântica de dados e o acesso integrado. A segunda contribuição aborda a integração de diversos dados para investigações científicas, com o objetivo de suportar serviços interoperáveis para a partilha de informação. O terceiro contributo apresenta uma arquitetura modular que apoia a extração e integração de informações textuais, permitindo a exploração destes dados. A última contribuição consiste numa plataforma web para acelerar a criação de sistemas de informação semânticos. Todas as soluções propostas foram validadas no âmbito das doenças raras

Design tools for ontology-based network communication protocols

Internet of Things has evolved quickly and reached to every aspect of our lives over the years. The number of new heterogeneous, distributed devices and applications connecting to the Internet is growing exponentially every day. As a result, data interoperability has become a prerequisite for IoT networks. However, the current infrastructures and communication protocols do not provide a convenient way for applications from different domains to interpret and process each other’s data, which is stored in vastly diversified, non-standardized formats. Due to this lack of common ground, in many cases, the integration overhead hinders organisations from exchanging their data to generate business values. Semantic technologies would be a promising solution for these issues, thanks to its ability to capture the high-level meaning of data. Asema is developing SmartAPI, a semantics-based API framework for sharing data between IoT systems. This thesis work is a part of SmartAPI project, focuses on designing and developing a data designer application. I build a single page web application with a modern graphical user interface, allowing users to create, organise and share data models

Methods and Tools for Management of Distributed Event Processing Applications

Die Erfassung und Verarbeitung von Ereignissen aus cyber-physischen Systemen bietet Anwendern die Möglichkeit, kontinuierlich über Leistungsdaten und aufkommende Probleme unterrichtet zu werden (Situational Awareness) oder Wartungsprozesse zustandsabhängig zu optimieren (Condition-based Maintenance). Derartige Szenarien verlangen aufgrund der Vielzahl und Frequenz der Daten sowie der Anforderung einer echtzeitnahen Auswertung den Einsatz geeigneter Technologien. Unter dem Namen Event Processing haben sich dabei Technologien etabliert, die in der Lage sind, Datenströme in Echtzeit zu verarbeiten und komplexe Ereignismuster auf Basis räumlicher, zeitlicher oder kausaler Zusammenhänge zu erkennen. Gleichzeitig sind heute in diesem Bereich verfügbare Systeme jedoch noch durch eine hohe technische Komplexität der zugrunde liegenden deklarativen Sprachen gekennzeichnet, die bei der Entwicklung echtzeitfähiger Anwendungen zu langsamen Entwicklungszyklen aufgrund notwendiger technischer Expertise führt. Gerade diese Anwendungen weisen allerdings häufig eine hohe Dynamik in Bezug auf Veränderungen von Anforderungen der zu erkennenden Situationen, aber auch der zugrunde liegenden Sensordaten hinsichtlich ihrer Syntax und Semantik auf. Der primäre Beitrag dieser Arbeit ermöglicht Fachanwendern durch die Abstraktion von technischen Details, selbständig verteilte echtzeitfähige Anwendungen in Form von sogenannten Echtzeit-Verarbeitungspipelines zu erstellen, zu bearbeiten und auszuführen. Die Beiträge der Arbeit lassen sich wie folgt zusammenfassen: 1. Eine Methodik zur Entwicklung echtzeitfähiger Anwendungen unter Berücksichtigung von Erweiterbarkeit sowie der Zugänglichkeit für Fachanwender. 2. Modelle zur semantischen Beschreibung der Charakteristika von Ereignisproduzenten, Ereignisverarbeitungseinheiten und Ereigniskonsumenten. 3. Ein System zur Ausführung von Verarbeitungspipelines bestehend aus geographisch verteilten Ereignisverarbeitungseinheiten. 4. Ein Software-Artefakt zur graphischen Modellierung von Verarbeitungspipelines sowie deren automatisierter Ausführung. Die Beiträge werden in verschiedenen Szenarien aus den Bereichen Produktion und Logistik vorgestellt, angewendet und evaluiert

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