Completing and Debugging Ontologies: state of the art and challenges

As semantically-enabled applications require high-quality ontologies, developing and maintaining ontologies that are as correct and complete as possible is an important although difficult task in ontology engineering. A key step is ontology debugging and completion. In general, there are two steps: detecting defects and repairing defects. In this paper we discuss the state of the art regarding the repairing step. We do this by formalizing the repairing step as an abduction problem and situating the state of the art with respect to this framework. We show that there are still many open research problems and show opportunities for further work and advancing the field.Comment: 56 page

Detecting and Correcting Conservativity Principle Violations in Ontology-to-Ontology Mappings

In order to enable interoperability between ontology-based systems, ontology matching techniques have been proposed. However, when the generated mappings suffer from logical flaws, their usefulness may be diminished. In this paper we present an approximate method to detect and correct violations to the so-called conservativity principle where novel subsumption entailments between named concepts in one of the input ontologies are considered as unwanted. We show that this is indeed the case in our application domain based on the EU Optique project. Additionally, our extensive evaluation conducted with both the Optique use case and the data sets from the Ontology Alignment Evaluation Initiative (OAEI) suggests that our method is both useful and feasible in practice.Copyright 2014 Springer International Publishing Switzerland. The final publication is available at http://link.springer.com/chapter/10.1007%2F978-3-319-11915-1_

Alignment of multi-cultural knowledge repositories

The ability to interconnect multiple knowledge repositories within a single framework is a key asset for various use cases such as document retrieval and question answering. However, independently created repositories are inherently heterogeneous, reflecting their diverse origins. Thus, there is a need to align concepts and entities across knowledge repositories. A limitation of prior work is the assumption of high afinity between the repositories at hand, in terms of structure and terminology. The goal of this dissertation is to develop methods for constructing and curating alignments between multi-cultural knowledge repositories. The first contribution is a system, ACROSS, for reducing the terminological gap between repositories. The second contribution is two alignment methods, LILIANA and SESAME, that cope with structural diversity. The third contribution, LAIKA, is an approach to compute alignments between dynamic repositories. Experiments with a suite ofWeb-scale knowledge repositories show high quality alignments. In addition, the application benefits of LILIANA and SESAME are demonstrated by use cases in search and exploration.Die Fähigkeit mehrere Wissensquellen in einer Anwendung miteinander zu verbinden ist ein wichtiger Bestandteil für verschiedene Anwendungsszenarien wie z.B. dem Auffinden von Dokumenten und der Beantwortung von Fragen. Unabhängig erstellte Datenquellen sind allerdings von Natur aus heterogen, was ihre unterschiedlichen Herkünfte widerspiegelt. Somit besteht ein Bedarf darin, die Konzepte und Entitäten zwischen den Wissensquellen anzugleichen. Frühere Arbeiten sind jedoch auf Datenquellen limitiert, die eine hohe Ähnlichkeit im Sinne von Struktur und Terminologie aufweisen. Das Ziel dieser Dissertation ist, Methoden für Aufbau und Pflege zum Angleich zwischen multikulturellen Wissensquellen zu entwickeln. Der erste Beitrag ist ein System names ACROSS, das auf die Reduzierung der terminologischen Kluft zwischen den Datenquellen abzielt. Der zweite Beitrag sind die Systeme LILIANA und SESAME, welche zum Angleich eben dieser Datenquellen unter Berücksichtigung deren struktureller Unterschiede dienen. Der dritte Beitrag ist ein Verfahren names LAIKA, das den Angleich dynamischer Quellen unterstützt. Unsere Experimente mit einer Reihe von Wissensquellen in Größenordnung des Web zeigen eine hohe Qualität unserer Verfahren. Zudem werden die Vorteile in der Verwendung von LILIANA und SESAME in Anwendungsszenarien für Suche und Exploration dargelegt

Visualization for biomedical ontologies alignment

Tese de mestrado, Bioinformática e Biologia Computacional (Bioinformática), Universidade de Lisboa, Faculdade de Ciências, 2016Desde o início do século, a investigação biomédica e a prática clínica levaram a uma acumulação de grandes quantidades de informação, por exemplo, os dados resultantes da sequenciação genómica ou os registos médicos. As ontologias fornecem um modelo estruturado com o intuito de representar o conhecimento e têm sido bem sucedidas no domínio biomédico na melhoria da interoperabilidade e partilha. O desenvolvimento desconectado das ontologias biomédicas levou à criação de modelos que apresentam domínios idênticos ou sobrepostos. As técnicas de emparelhamento de ontologias foram desenvolvidas afim de estabelecer ligações significativas entre as classes das ontologias, por outras palavras, para criar alinhamentos. Para alcançar um alinhamento ótimo é, não só importante melhorar as técnicas de emparelhamentos mas também criar as ferramentas necessárias para que possa existir intervenção humana, particularmente na visualização. Apesar da importância da intervenção de utilizadores e da visualização no emparelhamento de ontologias, poucos sistemas o suportam, sobretudo para grandes e complexas ontologias como as do domínio biomédico, concretamente no contexto da revisão de alinhamentos e interpretação de incoerências lógicas. O objetivo central desta tese consistiu na investigação dos principais paradigmas de visualização de ontologias, no contexto do alinhamento de ontologias biomédicas, e desenvolver abordagens de visualização e interação que vão de encontro a estes desafios. O trabalho desenvolvido levou, então, à criação de um novo módulo de visualização para um sistema de emparelhamento do state of the art que suporta a revisão de alinhamentos, e à construção de uma ferramenta online que visa ajudar o utilizador a compreender os conflitos encontrados nos alinhamentos, ambos baseados numa abordagem de visualização de subgrafos. Ambas as contribuições foram avaliadas em pequena escala, por testes a utilizadores que revelaram a relevância da visualização de subgrafos contra a visualização em árvore, mais comum no domínio biomédico.Since the begin of the century, biomedical research and clinical practice have resulted in the accumulation of very large amounts of information, e.g. data from genomic sequencing or medical records. Ontologies provide a structured model to represent knowledge and have been quite successful in the biomedical domain at improving interoperability and sharing. The disconnected development of biomedical ontologies has led to the creation of models that have overlapping or even equal domains. Ontology matching techniques were developed to establish meaningful connections between classes of the ontologies, in other words to create alignments. In order to achieve an optimal alignment, it is not only important to improve the matching techniques but also to create the necessary tools for human intervention, namely in visualization. Despite the importance of user intervention and visualization in ontology matching, few systems support these, especially for large and complex ontologies such as those in the biomedical domain, specifically in the context of the alignment revision and logical incoherence explanation. The central objective of this thesis was to investigate the main ontology visualization paradigms, in the context of biomedical ontology matching, and to develop visualization and interaction approaches addressing those challenges. The work developed lead to the creation of a new visualization module for a state of the art ontology matching system, that supports the alignment review, and to the construction of an online tool that aims to help the user understand the conflicts found in the alignments both based on a subgraph visualization approach. Both contributions were evaluated, in a small-scale, by user tests that revealed the relevance of subgraph visualization versus the more common tree visualization for the biomedical domain

A framework for analyzing changes in health care lexicons and nomenclatures

Ontologies play a crucial role in current web-based biomedical applications for capturing contextual knowledge in the domain of life sciences. Many of the so-called bio-ontologies and controlled vocabularies are known to be seriously defective from both terminological and ontological perspectives, and do not sufficiently comply with the standards to be considered formai ontologies. Therefore, they are continuously evolving in order to fix the problems and provide valid knowledge. Moreover, many problems in ontology evolution often originate from incomplete knowledge about the given domain. As our knowledge improves, the related definitions in the ontologies will be altered. This problem is inadequately addressed by available tools and algorithms, mostly due to the lack of suitable knowledge representation formalisms to deal with temporal abstract notations, and the overreliance on human factors. Also most of the current approaches have been focused on changes within the internal structure of ontologies, and interactions with other existing ontologies have been widely neglected. In this research, alter revealing and classifying some of the common alterations in a number of popular biomedical ontologies, we present a novel agent-based framework, RLR (Represent, Legitimate, and Reproduce), to semi-automatically manage the evolution of bio-ontologies, with emphasis on the FungalWeb Ontology, with minimal human intervention. RLR assists and guides ontology engineers through the change management process in general, and aids in tracking and representing the changes, particularly through the use of category theory. Category theory has been used as a mathematical vehicle for modeling changes in ontologies and representing agents' interactions, independent of any specific choice of ontology language or particular implementation. We have also employed rule-based hierarchical graph transformation techniques to propose a more specific semantics for analyzing ontological changes and transformations between different versions of an ontology, as well as tracking the effects of a change in different levels of abstractions. Thus, the RLR framework enables one to manage changes in ontologies, not as standalone artifacts in isolation, but in contact with other ontologies in an openly distributed semantic web environment. The emphasis upon the generality and abstractness makes RLR more feasible in the multi-disciplinary domain of biomedical Ontology change management