Foundational Ontologies meet Ontology Matching: A Survey

Ontology matching is a research area aimed at finding ways to make different ontologies interoperable. Solutions to the problem have been proposed from different disciplines, including databases, natural language processing, and machine learning. The role of foundational ontologies for ontology matching is an important one. It is multifaceted and with room for development. This paper presents an overview of the different tasks involved in ontology matching that consider foundational ontologies. We discuss the strengths and weaknesses of existing proposals and highlight the challenges to be addressed in the future

An automatic method for reporting the quality of thesauri

Thesauri are knowledge models commonly used for information classification and retrieval whose structure is defined by standards such as the ISO 25964. However, when creators do not correctly follow the specifications, they construct models with inadequate concepts or relations that provide a limited usability. This paper describes a process that automatically analyzes the thesaurus properties and relations with respect to ISO 25964 specification, and suggests the correction of potential problems. It performs a lexical and syntactic analysis of the concept labels, and a structural and semantic analyses of the relations. The process has been tested with Urbamet and Gemet thesauri and the results have been analyzed to determine how well the proposed process works

A multi-strategy methodology for ontology integration and reuse. Integrating large and heterogeneous knowledge bases in the rise of Big Data

The new revolutionary web today, i.e., the Semantic Web, has augmented the previous one by promoting common data formats and exchange protocols in order to provide a framework that allows data to be shared and reused across application, enterprise, and community boundaries. This revolution, along with the increasing digitization of the world, has led to a high availability of knowledge models, viz., formal representations of concepts and relations between concepts underlying a certain universe of discourse or knowledge domain, which span throughout a wide range of topics, fields of study and applications, from biomedical to advanced manufacturing, mostly heterogeneous from each other at a different levels. As more and more outbreaks of this new revolution light up, a major challenge came soon into sight: addressing the main objectives of the semantic web, the sharing and reuse of data, demands effective and efficient methodologies to mediate between models characterized by such a heterogeneity. Since ontologies are the de facto standard in representing and sharing knowledge models over the web, this doctoral thesis presents a comprehensive methodology to ontology integration and reuse based on various matching techniques. The proposed approach is supported by an ad hoc software framework whose scope is easing the creation of new ontologies by promoting the reuse of existing ones and automatizing, as much as possible, the whole ontology construction procedure

Investigating semantic similarity for biomedical ontology alignment

Tese de mestrado, Bioinformática e Biologia Computacional (Bioinformática) Universidade de Lisboa, Faculdade de Ciências, 2017A heterogeneidade dos dados biomédicos e o crescimento exponencial da informação dentro desse domínio tem levado à utilização de ontologias, que codificam o conhecimento de forma computacionalmente tratável. O desenvolvimento de uma ontologia decorre, em geral, com base nos requisitos da equipa que a desenvolve, podendo levar à criação de ontologias diferentes e potencialmente incompatíveis por várias equipas de investigação. Isto implica que as várias ontologias existentes para codificar conhecimento biomédico possam, entre elas, sofrer de heterogeneidade: mesmo quando o domínio por elas codificado é idêntico, os conceitos podem ser representados de formas diferentes, com diferente especificidade e/ou granularidade. Para minimizar estas diferenças e criar representações mais standard e aceites pela comunidade, foram desenvolvidos algoritmos (matchers) que encontrassem pontes de conhecimento (mappings) entre as ontologias de forma a alinharem-nas. O tipo de algoritmos mais utilizados no Alinhamento de Ontologias (AO) são os que utilizam a informação léxica (isto é, os nomes, sinónimos e descrições dos conceitos) para calcular as semelhanças entre os conceitos a serem mapeados. Uma abordagem complementar a esses algoritmos é a utilização de Background Knowledge (BK) como forma de aumentar o número de sinónimos usados e assim aumentar a cobertura do alinhamento produzido. Uma alternativa aos algoritmos léxicos são os algoritmos estruturais que partem do pressuposto que as ontologias foram desenvolvidas com pontos de vista semelhantes – realidade pouco comum. Surge então o tema desta dissertação onde toma-se partido da Semelhança Semântica (SS) para o desenvolvimento de novos algoritmos de AO. É de salientar que até ao momento a utilização de SS no Alinhamento de Ontologias é cingida à verificação de mappings e não à sua procura. Esta dissertação apresenta o desenvolvimento, implementação e avaliação de dois algoritmos que utilizam SS, ambos usados como forma de estender alinhamentos produzidos previamente, um para encontrar mappings de equivalências e o outro de subsunção (onde um conceito de uma ontologia é mapeado como sendo descendente do conceito proveniente de outra ontologia). Os algoritmos propostos foram implementados no AML que é um sistema topo de gama em Alinhamento de Ontologias. O algoritmo de equivalência demonstrou uma melhoria de até 0.2% em termos de F-measure em comparação com o alinhamento âncora utilizado; e um aumento de até 11.3% quando comparado a outro sistema topo de gama (LogMapLt) que não utiliza BK. É importante referir que, dentro do espaço de procura do algoritmo o Recall variou entre 66.7% e 100%. Já o algoritmo de subsunção apresentou precisão entre 75.9% e 95% (avaliado manualmente).The heterogeneity of biomedical data and the exponential growth of the information within this domain has led to the usage of ontologies, which encode knowledge in a computationally tractable way. Usually, the ontology’s development is based on the requirements of the research team, which means that ontologies of the same domain can be different and potentially incompatible among several research teams. This fact implies that the various existing ontologies encoding biomedical knowledge can, among them, suffer from heterogeneity: even when the encoded domain is identical, the concepts may be represented in different ways, with different specificity and/or granularity. To minimize these differences and to create representations that are more standard and accepted by the community, algorithms (known as matchers) were developed to search for bridges of knowledge (known as mappings) between the ontologies, in order to align them. The most commonly used type of matchers in Ontology Matching (OM) are the ones taking advantage of the lexical information (names, synonyms and textual description of the concepts) to calculate the similarities between the concepts to be mapped. A complementary approach to those algorithms is the usage of Background Knowledge (BK) as a way to increase the number of synonyms used, and further increase of the coverage of the produced alignment. An alternative to lexical algorithms are the structural ones which assume that the ontologies were developed with similar points of view - an unusual reality. The theme of this dissertation is to take advantage of Semantic Similarity (SS) for the development of new OM algorithms. It is important to emphasize that the use of SS in Ontology Alignment has, until now, been limited to the verification of mappings and not to its search. This dissertation presents the development, implementation, and evaluation of two algorithms that use SS. Both algorithms were used to extend previously produced alignments, one to search for equivalence and the other for subsumption mappings (where a concept of an ontology is mapped as descendant from a concept from another ontology). The proposed algorithms were implemented in AML, which is a top performing system in Ontology Matching. The equivalence algorithm showed an improvement in F-measure up to 0.2% when compared to the anchor alignment; and an increase of up to 11.3% when compared to another high-end system (LogMapLt) which lacks the usage of BK. It is important to note that, within the search space of the algorithm, the Recall ranged from 66.7% to 100%. On the other hand, the subsumption algorithm presented an accuracy between 75.9% and 95% (manually evaluated)

Uncertainty in Automated Ontology Matching: Lessons Learned from an Empirical Experimentation

Data integration is considered a classic research field and a pressing need within the information science community. Ontologies play a critical role in such a process by providing well-consolidated support to link and semantically integrate datasets via interoperability. This paper approaches data integration from an application perspective, looking at techniques based on ontology matching. An ontology-based process may only be considered adequate by assuming manual matching of different sources of information. However, since the approach becomes unrealistic once the system scales up, automation of the matching process becomes a compelling need. Therefore, we have conducted experiments on actual data with the support of existing tools for automatic ontology matching from the scientific community. Even considering a relatively simple case study (i.e., the spatio-temporal alignment of global indicators), outcomes clearly show significant uncertainty resulting from errors and inaccuracies along the automated matching process. More concretely, this paper aims to test on real-world data a bottom-up knowledge-building approach, discuss the lessons learned from the experimental results of the case study, and draw conclusions about uncertainty and uncertainty management in an automated ontology matching process. While the most common evaluation metrics clearly demonstrate the unreliability of fully automated matching solutions, properly designed semi-supervised approaches seem to be mature for a more generalized application

Using the semantic web as background knowledge for ontology mapping

While current approaches to ontology mapping produce good results by mainly relying on label and structure based similarity measures, there are several cases in which they fail to discover important mappings. In this paper we describe a novel approach to ontology mapping, which is able to avoid this limitation by using background knowledge. Existing approaches relying on background knowledge typically have one or both of two key limitations: 1) they rely on a manually selected reference ontology; 2) they suffer from the noise introduced by the use of semi-structured sources, such as text corpora. Our technique circumvents these limitations by exploiting the increasing amount of semantic resources available online. As a result, there is no need either for a manually selected reference ontology (the relevant ontologies are dynamically selected from an online ontology repository), or for transforming background knowledge in an ontological form. The promising results from experiments on two real life thesauri indicate both that our approach has a high precision and also that it can find mappings, which are typically missed by existing approaches