Evaluating Ontology Matching Systems on Large, Multilingual and Real-world Test Cases

In the field of ontology matching, the most systematic evaluation of matching systems is established by the Ontology Alignment Evaluation Initiative (OAEI), which is an annual campaign for evaluating ontology matching systems organized by different groups of researchers. In this paper, we report on the results of an intermediary OAEI campaign called OAEI 2011.5. The evaluations of this campaign are divided in five tracks. Three of these tracks are new or have been improved compared to previous OAEI campaigns. Overall, we evaluated 18 matching systems. We discuss lessons learned, in terms of scalability, multilingual issues and the ability do deal with real world cases from different domains

Final results of the Ontology Alignment Evaluation Initiative 2011

euzenat2011dInternational audienceOntology matching consists of finding correspondences between entities of two ontologies. OAEI campaigns aim at comparing ontology matching systems on precisely defined test cases. Test cases can use ontologies of different nature (from simple directories to expressive OWL ontologies) and use different modalities, e.g., blind evaluation, open evaluation, consensus. OAEI-2011 builds over previous campaigns by having 4 tracks with 6 test cases followed by 18 participants. Since 2010, the campaign introduces a new evaluation modality in association with the SEALS project. A subset of OAEI test cases is included in this new modality which provides more automation to the evaluation and more direct feedback to the participants. This paper is an overall presentation of the OAEI 2011 campaign

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

The Role of String Similarity Metrics in Ontology Alignment

Tim Berners-Lee originally envisioned a much different world wide web than the one we have today - one that computers as well as humans could search for the information they need [3]. There are currently a wide variety of research efforts towards achieving this goal, one of which is ontology alignment

Ontology Alignment using Biologically-inspired Optimisation Algorithms

It is investigated how biologically-inspired optimisation methods can be used to compute alignments between ontologies. Independent of particular similarity metrics, the developed techniques demonstrate anytime behaviour and high scalability. Due to the inherent parallelisability of these population-based algorithms it is possible to exploit dynamically scalable cloud infrastructures - a step towards the provisioning of Alignment-as-a-Service solutions for future semantic applications

Light-Weight Ontology Alignment using Best-Match Clone Detection

Abstract-Ontologies are a key component of the Semantic Web, providing a common basis for representing and exchanging domain meaning in web documents and resources. Ontology alignment is the problem of relating the elements of two formal ontologies for a semantic domain, in order to identify common concepts and relationships represented using different terminology or language, and thus allow meaningful communication and exchange of documents and resources represented using different ontologies for the same domain. Many algorithms have been proposed for ontology alignment, each with their own strengths and weaknesses. The problem is in many ways similar to nearmiss clone detection: while much of the description of concepts in two ontologies may be similar, there can be differences in structure or vocabulary that make similarity detection challenging. Based on our previous work extending clone detection to modelling languages such as WSDL using contextualization, in this work we apply near-miss clone detection to the problem of ontology alignment, and use the new notion of "best-match" clone detection to achieve results similar to many existing ontology alignment algorithms when applied to standard benchmarks

Memetic algorithms for ontology alignment

2011 - 2012Semantic interoperability represents the capability of two or more systems to meaningfully and accurately interpret the exchanged data so as to produce useful results. It is an essential feature of all distributed and open knowledge based systems designed for both e-government and private businesses, since it enables machine interpretation, inferencing and computable logic. Unfortunately, the task of achieving semantic interoperability is very difficult because it requires that the meanings of any data must be specified in an appropriate detail in order to resolve any potential ambiguity. Currently, the best technology recognized for achieving such level of precision in specification of meaning is represented by ontologies. According to the most frequently referenced definition [1], an ontology is an explicit specification of a conceptualization, i.e., the formal specification of the objects, concepts, and other entities that are presumed to exist in some area of interest and the relationships that hold them [2]. However, different tasks or different points of view lead ontology designers to produce different conceptualizations of the same domain of interest. This means that the subjectivity of the ontology modeling results in the creation of heterogeneous ontologies characterized by terminological and conceptual discrepancies. Examples of these discrepancies are the use of different words to name the same concept, the use of the same word to name different concepts, the creation of hierarchies for a specific domain region with different levels of detail and so on. The arising so-called semantic heterogeneity problem represents, in turn, an obstacle for achieving semantic interoperability... [edited by author]XI n.s

Analysing top-level and domain ontology alignments from matching systems

Top-level ontologies play an important role in the construction and integration of domain ontologies, providing a well-founded reference model that can be shared across knowledge domains. While most efforts in ontology matching have been particularly dedicated to domain ontologies, the problem of matching domain and top-level ontologies has been addressed to a lesser extent. This is a challenging task, specially due to the different levels of abstraction of these ontologies. In this paper, we present a comprehensive analysis of the alignments between one domain ontology from the OAEI Conference track and three well known top-level ontologies (DOLCE, GFO and SUMO), as generated by a set of matching tools. A discussion of the problem is presented on the basis of the alignments generated by the tools, compared to the analysis of three evaluators. This study provides insights for improving matching tools to better deal with this particular task