Improving Schema Mapping by Exploiting Domain Knowledge

This dissertation addresses the problem of semi-automatically creating schema mappings. The need for developing schema mappings is a pervasive problem in many integration scenarios. Although the problem is well-known and a large body of work exists in the area, the development of schema mappings is today largely performed manually in industrial integration scenarios. In this thesis an approach for the semi-automatic creation of high quality schema mappings is developed

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)

Improving Ontology Matching Using Application Requirements for Segmenting Ontologies

Ontology matching is concerned with finding relations between elements of different ontologies. In large-scale settings, some significant challenges arise, such as how to achieve a reduction in the time it takes to perform matching and how to improve the quality of results. Current techniques involve the use of ontology segmentation to overcome having such a large number of elements to compare. However, current methods usually select the most relevant ontology elements based on the number of relationships, which may dismiss some elements should they have fewer or no relationships. Therefore, we propose an algorithm for ontology segmentation based on application requirements, in such a way that the users can specify the concepts that are the most relevant in their application context to generate the segments which will be used as an input for the matching. In the experiments, we found a general reduction in the execution time and some significant quality improvements, depending on what matcher is applied. In order to assess the proposed algorithm, we considered some well-known evaluation measures, such as precision, recall, and F-Measure

Ontological View-driven Semantic Integration in Open Environments

In an open computing environment, such as the World Wide Web or an enterprise Intranet, various information systems are expected to work together to support information exchange, processing, and integration. However, information systems are usually built by different people, at different times, to fulfil different requirements and goals. Consequently, in the absence of an architectural framework for information integration geared toward semantic integration, there are widely varying viewpoints and assumptions regarding what is essentially the same subject. Therefore, communication among the components supporting various applications is not possible without at least some translation. This problem, however, is much more than a simple agreement on tags or mappings between roughly equivalent sets of tags in related standards. Industry-wide initiatives and academic studies have shown that complex representation issues can arise. To deal with these issues, a deep understanding and appropriate treatment of semantic integration is needed. Ontology is an important and widely accepted approach for semantic integration. However, usually there are no explicit ontologies with information systems. Rather, the associated semantics are implied within the supporting information model. It reflects a specific view of the conceptualization that is implicitly defining an ontological view. This research proposes to adopt ontological views to facilitate semantic integration for information systems in open environments. It proposes a theoretical foundation of ontological views, practical assumptions, and related solutions for research issues. The proposed solutions mainly focus on three aspects: the architecture of a semantic integration enabled environment, ontological view modeling and representation, and semantic equivalence relationship discovery. The solutions are applied to the collaborative intelligence project for the collaborative promotion / advertisement domain. Various quality aspects of the solutions are evaluated and future directions of the research are discussed

OM-2017: Proceedings of the Twelfth International Workshop on Ontology Matching

shvaiko2017aInternational audienceOntology matching is a key interoperability enabler for the semantic web, as well as auseful tactic in some classical data integration tasks dealing with the semantic heterogeneityproblem. It takes ontologies as input and determines as output an alignment,that is, a set of correspondences between the semantically related entities of those ontologies.These correspondences can be used for various tasks, such as ontology merging,data translation, query answering or navigation on the web of data. Thus, matchingontologies enables the knowledge and data expressed with the matched ontologies tointeroperate

Proceedings of The Tenth International Workshop on Ontology Matching (OM-2015)

shvaiko2016aInternational audienceno abstrac

Web-scale web table to knowledge base matching

Millions of relational HTML tables are found on the World Wide Web. In contrast to unstructured text, relational web tables provide a compact representation of entities described by attributes. The data within these tables covers a broad topical range. Web table data is used for question answering, augmentation of search results, and knowledge base completion. Until a few years ago, only search engines companies like Google and Microsoft owned large web crawls from which web tables are extracted. Thus, researches outside the companies have not been able to work with web tables. In this thesis, the first publicly available web table corpus containing millions of web tables is introduced. The corpus enables interested researchers to experiment with web tables. A profile of the corpus is created to give insights to the characteristics and topics. Further, the potential of web tables for augmenting cross-domain knowledge bases is investigated. For the use case of knowledge base augmentation, it is necessary to understand the web table content. For this reason, web tables are matched to a knowledge base. The matching comprises three matching tasks: instance, property, and class matching. Existing web table to knowledge base matching systems either focus on a subset of these matching tasks or are evaluated using gold standards which also only cover a subset of the challenges that arise when matching web tables to knowledge bases. This thesis systematically evaluates the utility of a wide range of different features for the web table to knowledge base matching task using a single gold standard. The results of the evaluation are used afterwards to design a holistic matching method which covers all matching tasks and outperforms state-of-the-art web table to knowledge base matching systems. In order to achieve these goals, we first propose the T2K Match algorithm which addresses all three matching tasks in an integrated fashion. In addition, we introduce the T2D gold standard which covers a wide variety of challenges. By evaluating T2K Match against the T2D gold standard, we identify that only considering the table content is insufficient. Hence, we include features of three categories: features found in the table, in the table context like the page title, and features that base on external resources like a synonym dictionary. We analyze the utility of the features for each matching task. The analysis shows that certain problems cannot be overcome by matching each table in isolation to the knowledge base. In addition, relying on the features is not enough for the property matching task. Based on these findings, we extend T2K Match into T2K Match++ which exploits indirect matches to web tables about the same topic and uses knowledge derived from the knowledge base. We show that T2K Match++ outperforms all state-of-the-art web table to knowledge base matching approaches on the T2D and Limaye gold standard. Most systems show good results on one matching task but T2K Match++ is the only system that achieves F-measure scores above 0:8 for all tasks. Compared to results of the best performing system TableMiner+, the F-measure for the difficult property matching task is increased by 0.08, for the class and instance matching task by 0.05 and 0.03, respectively

Extensible metadata management framework for personal data lake

Common Internet users today are inundated with a deluge of diverse data being generated and siloed in a variety of digital services, applications, and a growing body of personal computing devices as we enter the era of the Internet of Things. Alongside potential privacy compromises, users are facing increasing difficulties in managing their data and are losing control over it. There appears to be a de facto agreement in business and scientific fields that there is critical new value and interesting insight that can be attained by users from analysing their own data, if only it can be freed from its silos and combined with other data in meaningful ways. This thesis takes the point of view that users should have an easy-to-use modern personal data management solution that enables them to centralise and efficiently manage their data by themselves, under their full control, for their best interests, with minimum time and efforts. In that direction, we describe the basic architecture of a management solution that is designed based on solid theoretical foundations and state of the art big data technologies. This solution (called Personal Data Lake - PDL) collects the data of a user from a plurality of heterogeneous personal data sources and stores it into a highly-scalable schema-less storage repository. To simplify the user-experience of PDL, we propose a novel extensible metadata management framework (MMF) that: (i) annotates heterogeneous data with rich lineage and semantic metadata, (ii) exploits the garnered metadata for automating data management workflows in PDL – with extensive focus on data integration, and (iii) facilitates the use and reuse of the stored data for various purposes by querying it on the metadata level either directly by the user or through third party personal analytics services. We first show how the proposed MMF is positioned in PDL architecture, and then describe its principal components. Specifically, we introduce a simple yet effective lineage manager for tracking the provenance of personal data in PDL. We then introduce an ontology-based data integration component called SemLinker which comprises two new algorithms; the first concerns generating graph-based representations to express the native schemas of (semi) structured personal data, and the second algorithm metamodels the extracted representations to a common extensible ontology. SemLinker outputs are utilised by MMF to generate user-tailored unified views that are optimised for querying heterogeneous personal data through low-level SPARQL or high-level SQL-like queries. Next, we introduce an unsupervised automatic keyphrase extraction algorithm called SemCluster that specialises in extracting thematically important keyphrases from unstructured data, and associating each keyphrase with ontological information drawn from an extensible WordNet-based ontology. SemCluster outputs serve as semantic metadata and are utilised by MMF to annotate unstructured contents in PDL, thus enabling various management functionalities such as relationship discovery and semantic search. Finally, we describe how MMF can be utilised to perform holistic integration of personal data and jointly querying it in native representations