VOWL 2: User-Oriented Visualization of Ontologies

Abstract. Ontologies become increasingly important as a means to structure and organize information. This requires methods and tools that enable not only ontol-ogy experts but also other user groups to work with ontologies and related data. We have developed VOWL, a comprehensive and well-specified visual language for the user-oriented representation of ontologies, and conducted a comparative study on an initial version of VOWL. Based upon results from that study, as well as an extensive review of other ontology visualizations, we have reworked many parts of VOWL. In this paper, we present the new version VOWL 2 and describe how the initial definitions were used to systematically redefine the visual notation. Besides the novelties of the visual language, which is based on a well-defined set of graphical primitives and an abstract color scheme, we briefly describe two im-plementations of VOWL 2. To gather some insight into the user experience with the new version of VOWL, we have conducted a qualitative user study. We report on the study and its results, which confirmed that not only the general ideas of VOWL but also most of our enhancements for VOWL 2 can be well understood by casual ontology users

Specification and implementation of mapping rule visualization and editing : MapVOWL and the RMLEditor

Visual tools are implemented to help users in defining how to generate Linked Data from raw data. This is possible thanks to mapping languages which enable detaching mapping rules from the implementation that executes them. However, no thorough research has been conducted so far on how to visualize such mapping rules, especially if they become large and require considering multiple heterogeneous raw data sources and transformed data values. In the past, we proposed the RMLEditor, a visual graph-based user interface, which allows users to easily create mapping rules for generating Linked Data from raw data. In this paper, we build on top of our existing work: we (i) specify a visual notation for graph visualizations used to represent mapping rules, (ii) introduce an approach for manipulating rules when large visualizations emerge, and (iii) propose an approach to uniformly visualize data fraction of raw data sources combined with an interactive interface for uniform data fraction transformations. We perform two additional comparative user studies. The first one compares the use of the visual notation to present mapping rules to the use of a mapping language directly, which reveals that the visual notation is preferred. The second one compares the use of the graph-based RMLEditor for creating mapping rules to the form-based RMLx Visual Editor, which reveals that graph-based visualizations are preferred to create mapping rules through the use of our proposed visual notation and uniform representation of heterogeneous data sources and data values. (C) 2018 Elsevier B.V. All rights reserved

Helping scientists integrate and interact with biomedical data

Tese de mestrado, Bioinformática e Biologia Computacional , 2021, Universidade de Lisboa, Faculdade de CiênciasFor the past decades, the amount and complexity of biomedical data available have increased and far exceeded the human capacity to process it. To support this, knowledge graphs and ontologies have been increasingly used, allowing semantic integration of heterogeneous data within and across domains. However, the independent development of biomedical ontologies has created heterogeneity problems, with the design of ontologies with overlapping domains or significant differences. Automated ontology alignment techniques have been developed to tackle the semantic heterogeneity problem, by establishing meaningful correspondences between entities of two ontologies. However, their performance is limited, and the alignments they produce can contain erroneous, incoherent, or missing mappings. Therefore, manual validation of automated ontology alignments remains essential to ensure their quality. Given the complexity of the ontology matching process, is important to provide visualization and a user interface with the necessary features to support the exploration, validation, and edition of alignments. However, these aspects are often overlooked, as few alignment systems feature user interfaces enabling alignment visualization, fewer allow editing alignments, and fewer provide the functionalities needed to make the task seamless for users. This dissertation developed VOWLMap — an extension for the standalone web application, WebVOWL — for visualizing, editing, and validating biomedical ontology alignments. This work extended the Visual Notation for OWL Ontologies (VOWL), which defines a visual representation for most language constructs of OWL, to support graphical representations of alignments and restructured WebVOWL to load and visualize alignments. VOWLMap employs modularization techniques to facilitate the visualization of large alignments, while maintaining the context of each mapping, and offers a dynamic visualization that supports interaction mechanisms, including direct interaction with and editing of graph representations. A user study was conducted to evaluate the usability and performance of VOWLMap, having obtained positive feedback with an excellent score in a standard usability questionnaire

Visualization of ontology evolution using OntoDiffGraph

Dissertação de mestrado em Ciências da ComputaçãoOntologies evolve with the passing of time due to improvements, corrections or changes in requirements that need to be made. It is hard to keep track of these changes made in an ontology without a tool built specifically for that purpose. The goal of this master’s work is the creation of a visualization technique with the objective of allowing the viewer to easily identify changes made in an ontology by comparing two versions of it. The proposed approach adapts the already existing VOWL (Visual Notation for OWL On tologies) specification so that it can also display the differences between two versions of an ontology through the use of a graph. This was implemented in an application, called On toDiffGraph, however this feature is not all that this application has implemented. In fact, to be able to detect the changes that were made, an algorithm was developed that allows the application to find the axioms that were added or removed in an ontology and display them in a graph. OntoDiffGraph also contains several other features that help with the identification of the changes that were made, such as displaying all axioms of the ontology in a list or filtering nodes and edges of the graph that are not relevant to the visualization of changes made in the ontology. OntoDiffGraph was used in an experiment to obtain user feedback and discover how it performed when compared to a similar application (OWLDiff). The participants gave a lot of important constructive feedback and they also displayed a preference of OntoDiffGraph over the other alternative.As ontologias evoluem com o passar do tempo devido a melhoramentos, correções ou mu danças nos requisitos que necessitam de ser feitas. É difícil observar estas mudanças feitas numa ontologia sem utilizar ferramentas especializadas para este fim. O objetivo deste trabalho de mestrado é a criação de uma técnica de visualização com a intenção de oferecer ao observador a capacidade de fácil identificação das mudanças feitas numa ontologia ao comparar duas versões distintas. A abordagem tomada adapta a especificação VOWL (Visual Notation for OWL Ontologies) de forma a que também seja possível visualizar as diferenças entre duas versões de uma ontologia através do uso de um grafo. Esta abordagem foi implementada numa aplicação, com o nome de OntoDiffGraph, no entanto esta funcionalidade não é tudo o que foi im plementado. Para que seja possível detetar as mudanças que foram feitas, um algoritmo foi desenvolvido que permite que a aplicação, além de identificar os conceitos/relações e propriedades que sofreram mudanças, encontre os axiomas que foram adicionados ou re movidos da ontologia e os apresente num grafo. OntoDiffGraph também tem diversas outras funcionalidades que ajudam na identificação de mudanças, tal como a apresentação de todos os axiomas da ontologia numa lista ou a filtração de nodos e arestas que não são relevantes para a visualização das mudanças feitas na ontologia. OntoDiffGraph foi também utilizado num experimento com o objetivo de obter críticas e comparar o seu desempenho com uma aplicação similar (OWLDiff). Os participantes no experimento ofereceram bastantes críticas construtivas e demonstraram uma preferência por OntoDiffGraph em vez de OWLDiff

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

Drawing OWL 2 ontologies with Eddy the editor

In this paper we introduce Eddy, a new open-source tool for the graphical editing of OWL~2 ontologies. Eddy is specifically designed for creating ontologies in Graphol, a completely visual ontology language that is equivalent to OWL~2. Thus, in Eddy ontologies are easily drawn as diagrams, rather than written as sets of formulas, as commonly happens in popular ontology design and engineering environments. This makes Eddy particularly suited for usage by people who are more familiar with diagramatic languages for conceptual modeling rather than with typical ontology formalisms, as is often required in non-academic and industrial contexts. Eddy provides intuitive functionalities for specifying Graphol diagrams, guarantees their syntactic correctness, and allows for exporting them in standard OWL 2 syntax. A user evaluation study we conducted shows that Eddy is perceived as an easy and intuitive tool for ontology specification

A comparative study of state-of-the-art linked data visualization tools

Data visualization tools are of great importance for the exploration and the analysis of Linked Data (LD) datasets. Such tools allow users to get an overview, understand content, and discover interesting insights of a dataset. Visualization approaches vary according to the domain, the type of data, the task that the user is trying to perform, as well as the skills of the user. Thus, the study of the capabilities that each approach offers is crucial in supporting users to select the proper tool/technique based on their need. In this paper we present a comparative study of the state-of-the-art LD visualization tools over a list of fundamental use cases. First, we define 16 use cases that are representative in the setting of LD visual exploration, examining several tool's aspects; e.g., functionality capabilities, feature richness. Then, we evaluate these use cases over 10 LD visualization tools, examining: (1) if the tools have the required functionality for the tasks; and (2) if they allow the successful completion of the tasks over the DBpedia dataset. Finally, we discuss the insights derived from the evaluation, and we point out possible future directions

Una arquitectura de referencia para ambientes web de ingeniería ontológica

Ontology authoring, maintenance and use are never easy tasks, mostly due to the complexity of real domains and how they dynamically change as well as different background possessed by modellers about methodologies and formal languages. However, although the needs for ontologies are well-understood, not less important is to provide editing tools to manipulate and understand them. In this context, this work proposes and documents a reference architecture for such tools running in web environments. Moreover, it provides the rationale for boosting the collaborative development of a novel tool based on this architecture, named crowd. Previous surveys reveal that few Webbased ontology engineering environments have been developed and in addition, almost all of them are mere visualisers, with limited graphical features and lacking inference services.La definición, mantenimiento y use de ontologías son tareas difíciles debido, en mayor medida, a la complejidad inherente al mundo real y a como éste cambia dinámicamente. Asimismo, también se debe a las diferencias en conocimiento sobre metodologías y lenguajes formales por parte de los modeladores. Sin embargo, aunque la necesidad de crear y obtener ontologías es clave, es también importante contar con herramientas para manipularlas y entenderlas. Este trabajo propone y documenta una arquitectura de referencia para ambientes Web y ofrece los fundamentos para impulsar el desarrollo colaborativo de la herramienta crowd, la cual esta basada sobre dicha architectura. Revisiones previas de la literatura indican la existencia de un numero reducido ambientes para la Ingeniería Ontológica basados en tecnologías Web, sin embargo, casi en su totalidad son solo visualizadores de modelos con soporte gráfico limitado y ausencia de razonamiento lógico integrado.Facultad de Informátic

Time-Sensitive Ontology Evolution Visualization

With the integration of IoT in the industry, interest has risen regarding predictive approaches to maintenance, in hopes of predicting equipment or system anomalies before they take place. Ontologies, a crucial part of the semantic web, have found a use in these industries, as a way to semantically describe the data related to these equipments and systems. The ontology maintenance process, however, relies heavily on understanding the evolution of knowledge of the domain, over time. Visual representations of these ontologies and their evolution are very useful to ontology engineers (particularly in time-sensitive scenarios), even if tools that offer a service of this kind are fairly limited. Considering this, this dissertation presents a state of the art review of the existing ontology evolution visualization methods and tools, in the context of in time-sensitive scenarios, ending up by choosing to develop the solution using the WebVOWL viewer, React and Fuseki. It then describes the analysis of the requirements for the project, as well as a design proposal for a solution, taking into consideration the need to integrate with an already existing Java back-end application, and that the application must allow for the creation, loading and visualization of an ontology’s evolution. The solution is described in detail, before concluding that it fulfills the requirements proposed at the beginning of the project, and successfully allows for the visualization of the evolutionary process of ontologies.Com a integração da IoT na indústria, o interesse relacionado com manutenção preditiva subiu, com a intenção de prever anomalias em equipamentos ou sistemas antes que estas ocorram. Ontologias, um componente crucial da web semântica, encontraram um uso nestas indústrias, como uma forma de representar semanticamente os dados relacionados com estes equipamentos ou sistemas. Contudo, o processo de manutenção de ontologias depende muito do entendimento da evolução do conhecimento do domínio, ao longo do tempo. A representação visual destas ontologias e da sua evolução são muito úteis para engenheiros de ontologias (especialmente em cenários sensíveis ao tempo), embora ferramentas que ofereçam serviços deste género sejam um pouco limitadas. Considerando isso, esta dissertação apresenta uma análise do estado da arte dos métodos e ferramentas existentes para a visualização da evolução de ontologias, no contexto de cenários sensíveis ao tempo, acabando por selecionar para o desenvolvimento da solução o visualizador WebVOWL, React e Fuseki. Depois, descreve a análise dos requisitos do projeto, bem como a proposta de arquitetura para uma solução, considerando a necessidade de integrar uma aplicação back-end Java já existente, e que a aplicação tem que permitir a criação, carrega mento e visualização da evolução de uma ontologia. A solução é descrita em detalhe, antes de concluir que a mesma cumpre os requisitos propostos na definição do projeto, e é bem sucedido em permitir a visualização do processo evolutivo de ontologias