Shiva: A Framework for Graph Based Ontology Matching

Since long, corporations are looking for knowledge sources which can provide structured description of data and can focus on meaning and shared understanding. Structures which can facilitate open world assumptions and can be flexible enough to incorporate and recognize more than one name for an entity. A source whose major purpose is to facilitate human communication and interoperability. Clearly, databases fail to provide these features and ontologies have emerged as an alternative choice, but corporations working on same domain tend to make different ontologies. The problem occurs when they want to share their data/knowledge. Thus we need tools to merge ontologies into one. This task is termed as ontology matching. This is an emerging area and still we have to go a long way in having an ideal matcher which can produce good results. In this paper we have shown a framework to matching ontologies using graphs

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 matching: state of the art and future challenges

shvaiko2013aInternational audienceAfter years of research on ontology matching, it is reasonable to consider several questions: is the field of ontology matching still making progress? Is this progress significant enough to pursue some further research? If so, what are the particularly promising directions? To answer these questions, we review the state of the art of ontology matching and analyze the results of recent ontology matching evaluations. These results show a measurable improvement in the field, the speed of which is albeit slowing down. We conjecture that significant improvements can be obtained only by addressing important challenges for ontology matching. We present such challenges with insights on how to approach them, thereby aiming to direct research into the most promising tracks and to facilitate the progress of the field

VOAR: A Visual and Integrated Ontology Alignment Environment

International audienceOntology alignment is a key process for enabling interoperability between ontology-based systems in the Linked Open Data age. From two input ontologies, this process generates an alignment (set of correspondences) between them. In this paper we present VOAR, a new web-based environment for ontology alignment visualization and manipulation. Within this graphical environment, users can manually create/edit correspondences and apply a set of operations on alignments (filtering, merge, difference, etc.). VOAR allows invoking external ontology matching systems that implement a specific alignment interface, so that the generated alignments can be manipulated within the environment. Evaluating multiple alignments together against a reference one can also be carried out, using classical evaluation metrics (precision, recall and f-measure). The status of each correspondence with respect to its presence or absence in reference alignment is visually represented. Overall, the main new aspect of VOAR is the visualization and manipulation of alignments at schema level, in an integrated, visual and web-based environment

Using MathML to Represent Units of Measurement for Improved Ontology Alignment

Ontologies provide a formal description of concepts and their relationships in a knowledge domain. The goal of ontology alignment is to identify semantically matching concepts and relationships across independently developed ontologies that purport to describe the same knowledge. In order to handle the widest possible class of ontologies, many alignment algorithms rely on terminological and structural meth- ods, but the often fuzzy nature of concepts complicates the matching process. However, one area that should provide clear matching solutions due to its mathematical nature, is units of measurement. Several on- tologies for units of measurement are available, but there has been no attempt to align them, notwithstanding the obvious importance for tech- nical interoperability. We propose a general strategy to map these (and similar) ontologies by introducing MathML to accurately capture the semantic description of concepts specified therein. We provide mapping results for three ontologies, and show that our approach improves on lexical comparisons.Comment: Conferences on Intelligent Computer Mathematics (CICM 2013), Bath, Englan

Automated extension of biomedical ontologies

Developing and extending a biomedical ontology is a very demanding process, particularly because biomedical knowledge is diverse, complex and continuously changing and growing. Existing automated and semi-automated techniques are not tailored to handling the issues in extending biomedical ontologies. This thesis advances the state of the art in semi-automated ontology extension by presenting a framework as well as methods and methodologies for automating ontology extension specifically designed to address the features of biomedical ontologies.The overall strategy is based on first predicting the areas of the ontology that are in need of extension and then applying ontology learning and ontology matching techniques to extend them. A novel machine learning approach for predicting these areas based on features of past ontology versions was developed and successfully applied to the Gene Ontology. Methods and techniques were also specifically designed for matching biomedical ontologies and retrieving relevant biomedical concepts from text, which were shown to be successful in several applications.O desenvolvimento e extensão de uma ontologia biomédica é um processo muito exigente, dada a diversidade, complexidade e crescimento contínuo do conhecimento biomédico. As técnicas existentes nesta área não estão preparadas para lidar com os desafios da extensão de uma ontologia biomédica. Esta tese avança o estado da arte na extensão semi-automática de ontologias, apresentando uma framework assim como métodos e metodologias para a automação da extensão de ontologias especificamente desenhados tendo em conta as características das ontologias biomédicas. A estratégia global é baseada em primeiro prever quais as áreas da ontologia que necessitam extensão, e depois usá-las como enfoque para técnicas de alinhamento e aprendizagem de ontologias, com o objectivo de as estender. Uma nova estratégia de aprendizagem automática para prever estas áreas baseada em atributos de antigas versões de ontologias foi desenvolvida e testada com sucesso na Gene Ontology. Foram também especificamente desenvolvidos métodos e técnicas para o alinhamento de ontologias biomédicas e extracção de conceitos relevantes de texto, cujo sucesso foi demonstrado em várias aplicações.Fundação para a Ciência e a Tecnologi

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

Matching Biomedical Knowledge Graphs with Neural Embeddings

Tese de mestrado, Ciência de Dados, Universidade de Lisboa, Faculdade de Ciências, 2020Os grafos de conhecimento são estruturas que se tornaram fundamentais para a organização dos dados biomédicos que têm sido produzidos a um ritmo exponencial nos últimos anos. A abrangente adoção desta forma de estruturar e descrever dados levou ao desenvolvimento de abordagens de prospeção de dados que tirassem partido desta informação com o intuito de auxiliar o progresso do conhecimento científico. Porém, devido à impossibilidade de isolamento de domínios de conhecimento e à idiossincrasia humana, grafos de conhecimento construídos por diferentes indivíduos contêm muitas vezes conceitos equivalentes descritos de forma diferente, dificultando uma análise integrada de dados de diferentes grafos de conhecimento. Vários sistemas de alinhamento de grafos de conhecimento têm focado a resolução deste desafio. Contudo, o desempenho destes sistemas no alinhamento de grafos de conhecimento biomédicos estagnou nos últimos quatro anos com algoritmos e recursos externos bastante trabalhados para aprimorar os resultados. Nesta dissertação, apresentamos duas novas abordagens de alinhamento de grafos de conhecimento empregando Neural Embeddings: uma utilizando semelhança simples entre embeddings à base de palavras e de entidades de grafos; outra treinando um modelo mais complexo que refinasse a informação proveniente de embeddings baseados em palavras. A metodologia proposta visa integrar estas abordagens no processo regular de alinhamento, utilizando como infraestrutura o sistema AgreementMakerLight. Estas novas componentes permitem extender os algoritmos de alinhamento do sistema, descobrindo novos mapeamentos, e criar uma abordagem de alinhamento mais generalizável e menos dependente de ontologias biomédicas externas. Esta nova metodologia foi avaliada em três casos de teste de alinhamento de ontologias biomédicas, provenientes da Ontology Alignment Evaluation Initiative. Os resultados demonstraram que apesar de ambas as abordagens não excederem o estado da arte, estas obtiveram um desempenho benéfico nas tarefas de alinhamento, superando a performance de todos os sistemas que não usam ontologias externas e inclusive alguns que tiram proveito das mesmas, o que demonstra o valor das técnicas de Neural Embeddings na tarefa de alinhamento de grafos do conhecimento biomédicos.Knowledge graphs are data structures which became essential to organize biomedical data produced at an exponential rate in the last few years. The broad adoption of this method of structuring and describing data resulted in the increased interest to develop data mining approaches which took advantage of these information structures in order to improve scientific knowledge. However, due to human idiosyncrasy and also the impossibility to isolate knowledge domains in separate pieces, knowledge graphs constructed by different individuals often contain equivalent concepts described differently. This obstructs the path to an integrated analysis of data described by multiple knowledge graphs. Multiple knowledge graph matching systems have been developed to address this challenge. Nevertheless, the performance of these systems has stagnated in the last four years, despite the fact that they were provided with highly tailored algorithms and external resources to tackle this task. In this dissertation, we present two novel knowledge graph matching approaches employing neural embeddings: one using plain embedding similarity based on word and graph models; the other one using a more complex word-based model which requires training data to refine embeddings. The proposed methodology aims to integrate these approaches in the regular matching process, using the AgreementMakerLight system as a foundation. These new components enable the extension of the system’s current matching algorithms, discovering new mappings, and developing a more generalizable and less dependent on external biomedical ontologies matching procedure. This new methodology was evaluated on three biomedical ontology matching test cases provided by the Ontology Alignment Evaluation Initiative. The results showed that despite both embedding approaches don’t exceed state of the art results, they still produce better results than any other matching systems which do not make use of external ontologies and also surpass some that do benefit from them. This shows that Neural Embeddings are a valuable technique to tackle the challenge of biomedical knowledge graph matching