Clona Results for OAEI 2015

Abstract. This paper presents the results of Clona in the Ontology Alignment Evaluation Initiative campaign (OAEI) 2015. We only participated in Multifarm track, since Clona develops specic techniques for aligning multilingual ontologies. We rst give an overview of our alignment system; then we detail the techniques used in our contribution to deal with cross-lingual ontology alignment. Last, we present the results with a thorough analysis and discussion, then we conclude by listing some future work on Clona

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)

OACAS - Ontologies Alignment using Composition and Aggregation of Similarities

International audienc

Contributions à l'alignement d'ontologies OWL par agrégation de similarités

Dans le cadre de cette thèse, nous avons proposé plusieurs méthodes d'alignement à savoir: la méthode EDOLA, la méthode SODA et la méthode OACAS. Les trois méthodes procèdent dans une première phase à la transformation des deux ontologies à aligner sous la forme d'un graphe, O-Graph, pour chaque ontologie. Ces graphes permettent la représentation des ontologies sous une forme facile à l'exploitation. La méthode EDOLA est une approche se basant sur un modèle de calcul des similarités locale et globale. Ce modèle suit la structure du graphe pour calculer les mesures de similarité entre les noeuds des deux ontologies. Le module d'alignement associe pour chaque catégorie de noeuds une fonction d'agrégation. La fonction d'agrégation prend en considération toutes les mesures de similarités entre les couples de noeuds voisins au couple de noeud à apparier. La méthode SODA est une amélioration de la méthode EDOLA. En effet, la méthode SODA opère sur les ontologies OWL-DL, pour les aligner, à la place des ontologies décrites en OWL-Lite. La méthode SODA est une approche structurelle pour l'alignement d'ontologies OWL-DL. Elle opère en 3 étapes successives. La première étape permet de calculer la similarité linguistique à travers des mesures de similarité plus adaptées aux descripteurs des constituants des ontologies à apparier. La seconde étape détermine la similarité structurelle en exploitant la structure des deux graphes O-Graphs. La troisième étape déduit la similarité sémantique, en prenant en considération les deux types de similarités déjà calculées. La méthode d'alignement, OACAS, opère en 3 étapes successives pour produire l'alignement. La première étape permet de calculer la similarité linguistique composée. La similarité linguistique composée prend en considération tous les descripteurs des entités ontologiques à aligner. La seconde étape détermine la similarité de voisinage par niveau. La troisième étape agrège les composants de la similarité linguistique composée et la similarité de voisinage par niveau pour déterminer la similarité agrégée.In this thesis, we have proposed three ontology alignment methods: EDOLA (Extended Diameter OWL-Lite Alignment) method, SODA (Structural Ontology OWL-DL Alignment) method and OACAS (Ontologies Alignment using Composition and Aggregation of Similarities) method. These methods rely on aggregation and composition of similarities and check the spread structure of the ontologies to be aligned. EDOLA method allows to align OWL-Lite ontologies whereas SODA and OACAS consider OWL-DL ontologies. The three proposed methods operate in a first step by transforming both ontologies to aligned as a graph, named O-Graph, for each ontology. This graph reproduces OWL ontologies to be easily manipulated during the alignment process. The obtained graphs describe all the information contained in the ontologies: entities, relations between entities and instances. Besides, the EDOLA method is a new approach that computes local and global similarities using a propagation technique of similarities through the O-Graphs. This model explores the structure of the considered O-Graphs to compute the similarity values between the nodes of both ontologies. The alignment model associates for each category of nodes an aggregation function. This function takes in consideration all the similarity measures of the couple of nodes to match. This aggregation function explores all descriptive information of this couple. EDOLA operates in two succesive steps. The first step computes the local similarity, terminological one, whereas the second step computes the global one. The SODA method is an improved version of EDOLA. In fact, it uses OWL-DL ontologies. SODA method is a structures approach for OWL-DL ontologies. The method operates in three successive steps and explores the structure the ontologies using O-Graphs. The first step computes linguistic similarity using appropriate similarity measures corresponding to the descriptors of ontological entities. The second step allows to compute structural similarity using the two graphs O-Graphs. The third step deduces the semantic similarity, by combining both similarities already computed, in order to outperform the alignment task.ARRAS-Bib.electronique (620419901) / SudocSudocFranceF

Contributions to OWL ontologies alignment using similarity aggregation

Dans le cadre de cette thèse, nous avons proposé plusieurs méthodes d'alignement à savoir: la méthode EDOLA, la méthode SODA et la méthode OACAS. Les trois méthodes procèdent dans une première phase à la transformation des deux ontologies à aligner sous la forme d'un graphe, O-Graph, pour chaque ontologie. Ces graphes permettent la représentation des ontologies sous une forme facile à l'exploitation. La méthode EDOLA est une approche se basant sur un modèle de calcul des similarités locale et globale. Ce modèle suit la structure du graphe pour calculer les mesures de similarité entre les noeuds des deux ontologies. Le module d'alignement associe pour chaque catégorie de noeuds une fonction d'agrégation. La fonction d'agrégation prend en considération toutes les mesures de similarités entre les couples de noeuds voisins au couple de noeud à apparier. La méthode SODA est une amélioration de la méthode EDOLA. En effet, la méthode SODA opère sur les ontologies OWL-DL, pour les aligner, à la place des ontologies décrites en OWL-Lite. La méthode SODA est une approche structurelle pour l'alignement d'ontologies OWL-DL. Elle opère en 3 étapes successives. La première étape permet de calculer la similarité linguistique à travers des mesures de similarité plus adaptées aux descripteurs des constituants des ontologies à apparier. La seconde étape détermine la similarité structurelle en exploitant la structure des deux graphes O-Graphs. La troisième étape déduit la similarité sémantique, en prenant en considération les deux types de similarités déjà calculées. La méthode d'alignement, OACAS, opère en 3 étapes successives pour produire l'alignement. La première étape permet de calculer la similarité linguistique composée. La similarité linguistique composée prend en considération tous les descripteurs des entités ontologiques à aligner. La seconde étape détermine la similarité de voisinage par niveau. La troisième étape agrège les composants de la similarité linguistique composée et la similarité de voisinage par niveau pour déterminer la similarité agrégée.In this thesis, we have proposed three ontology alignment methods: EDOLA (Extended Diameter OWL-Lite Alignment) method, SODA (Structural Ontology OWL-DL Alignment) method and OACAS (Ontologies Alignment using Composition and Aggregation of Similarities) method. These methods rely on aggregation and composition of similarities and check the spread structure of the ontologies to be aligned. EDOLA method allows to align OWL-Lite ontologies whereas SODA and OACAS consider OWL-DL ontologies. The three proposed methods operate in a first step by transforming both ontologies to aligned as a graph, named O-Graph, for each ontology. This graph reproduces OWL ontologies to be easily manipulated during the alignment process. The obtained graphs describe all the information contained in the ontologies: entities, relations between entities and instances. Besides, the EDOLA method is a new approach that computes local and global similarities using a propagation technique of similarities through the O-Graphs. This model explores the structure of the considered O-Graphs to compute the similarity values between the nodes of both ontologies. The alignment model associates for each category of nodes an aggregation function. This function takes in consideration all the similarity measures of the couple of nodes to match. This aggregation function explores all descriptive information of this couple. EDOLA operates in two succesive steps. The first step computes the local similarity, terminological one, whereas the second step computes the global one. The SODA method is an improved version of EDOLA. In fact, it uses OWL-DL ontologies. SODA method is a structures approach for OWL-DL ontologies. The method operates in three successive steps and explores the structure the ontologies using O-Graphs. The first step computes linguistic similarity using appropriate similarity measures corresponding to the descriptors of ontological entities. The second step allows to compute structural similarity using the two graphs O-Graphs. The third step deduces the semantic similarity, by combining both similarities already computed, in order to outperform the alignment task