Cheap electronic storage and Internet bandwidth has increased the amount of online data. Large quantities of metadata are created to manage this wealth of information. Methods to organize and structure metadata has led to the development of ontologies - data that is organized to describe the relation between elements. The creation of large ontologies has brought forth the need for ontology management strategies. Ontology alignment and merging techniques are standard operations for ontology management. Accurate ontology alignment methods are typically semi-automatic, meaning they require periodic user input. This becomes infeasible on large ontologies and the accuracy and efficiency drops significantly when these algorithms are forced to align without human interaction. Bioinformatics, for example, has seen the influx of large ontologies, such as signal pathway sets with thousands of elements or protein-protein interaction (PPI) databases with hundreds of thousands of elements. This drives the need for a reliable method of large-scale ontology alignment. Many bioinformatics ontologies contain references to domain ontologies - manually curated ontologies describing additional, general information about the terms in the ontologies. For example, more than 2/3 of proteins in PPI data sets contain at least one annotation to the domain ontology the Gene Ontology. We use the domain ontology references as features to compute similarity between elements. However, there are few efficient ways to compute similarity from structured features. We present a novel, automatic method for aligning ontologies based on such domain ontology features. Specifically, we use simulated annealing to reduce the complexity of the domain ontologys structure by finding approximate relevant clusters of elements. An intermediate step performs hierarchical clustering based on the similarity between elements of the ontology. Then the mapping between clusters across aligning ontologies is built. The final step builds an alignment between matched clusters. To evaluate our methods, we perform an alignment between Human (Homo Sapiens) and Yeast (Saccharomyces cerevisiae) signal pathways provided by the Reactome database. The results were compared against reliable homology studies of proteins. The final mapping produces alignments that are significantly more accurate than the traditional ontology alignment methods, without any human involvement.

Cheap electronic storage and Internet bandwidth has increased the amount of online data. Large quantities of metadata are created to manage this wealth of information. Methods to organize and structure metadata has led to the development of ontologies - data that is organized to describe the relation between elements. The creation of large ontologies has brought forth the need for ontology management strategies. Ontology alignment and merging techniques are standard operations for ontology management. Accurate ontology alignment methods are typically semi-automatic, meaning they require periodic user input. This becomes infeasible on large ontologies and the accuracy and efficiency drops significantly when these algorithms are forced to align without human interaction. Bioinformatics, for example, has seen the influx of large ontologies, such as signal pathway sets with thousands of elements or protein-protein interaction (PPI) databases with hundreds of thousands of elements. This drives the need for a reliable method of large-scale ontology alignment. Many bioinformatics ontologies contain references to domain ontologies - manually curated ontologies describing additional, general information about the terms in the ontologies. For example, more than 2/3 of proteins in PPI data sets contain at least one annotation to the domain ontology the Gene Ontology. We use the domain ontology references as features to compute similarity between elements. However, there are few efficient ways to compute similarity from structured features. We present a novel, automatic method for aligning ontologies based on such domain ontology features. Specifically, we use simulated annealing to reduce the complexity of the domain ontologys structure by finding approximate relevant clusters of elements. An intermediate step performs hierarchical clustering based on the similarity between elements of the ontology. Then the mapping between clusters across aligning ontologies is built. The final step builds an alignment between matched clusters. To evaluate our methods, we perform an alignment between Human (Homo Sapiens) and Yeast (Saccharomyces cerevisiae) signal pathways provided by the Reactome database. The results were compared against reliable homology studies of proteins. The final mapping produces alignments that are significantly more accurate than the traditional ontology alignment methods, without any human involvement.

Cheap electronic storage and Internet bandwidth has increased the amount of online data. Large quantities of metadata are created to manage this wealth of information. Methods to organize and structure metadata has led to the development of ontologies - data that is organized to describe the relation between elements. The creation of large ontologies has brought forth the need for ontology management strategies. Ontology alignment and merging techniques are standard operations for ontology management. Accurate ontology alignment methods are typically semi-automatic, meaning they require periodic user input. This becomes infeasible on large ontologies and the accuracy and efficiency drops significantly when these algorithms are forced to align without human interaction. Bioinformatics, for example, has seen the influx of large ontologies, such as signal pathway sets with thousands of elements or protein-protein interaction (PPI) databases with hundreds of thousands of elements. This drives the need for a reliable method of large-scale ontology alignment. Many bioinformatics ontologies contain references to domain ontologies - manually curated ontologies describing additional, general information about the terms in the ontologies. For example, more than 2/3 of proteins in PPI data sets contain at least one annotation to the domain ontology the Gene Ontology. We use the domain ontology references as features to compute similarity between elements. However, there are few efficient ways to compute similarity from structured features. We present a novel, automatic method for aligning ontologies based on such domain ontology features. Specifically, we use simulated annealing to reduce the complexity of the domain ontologys structure by finding approximate relevant clusters of elements. An intermediate step performs hierarchical clustering based on the similarity between elements of the ontology. Then the mapping between clusters across aligning ontologies is built. The final step builds an alignment between matched clusters. To evaluate our methods, we perform an alignment between Human (Homo Sapiens) and Yeast (Saccharomyces cerevisiae) signal pathways provided by the Reactome database. The results were compared against reliable homology studies of proteins. The final mapping produces alignments that are significantly more accurate than the traditional ontology alignment methods, without any human involvement. / Science, Faculty of / Computer Science, Department of / Graduate

Seamless computer-based knowledge sharing between departments of a manufacturing enterprise is useful in preventing unnecessary design revisions. A lack of interoperability between independently developed knowledge bases, however, is a major impediment in the development of a seamless knowledge sharing system. Interoperability, being an ability to overcome semantic and syntactic differences during computer-based knowledge sharing can be enhanced through the use of ontologies. Ontologies in computer science terms are hierarchical structures of knowledge stored in a computer-based knowledge base. Ontologies have been accepted by all as an interoperable medium to provide a non-subjective way of storing and sharing knowledge across diverse domains. Some semantic and syntactic differences, however, still crop up when these ontological knowledge bases are developed independently. A case study in an aerospace components manufacturing company suggests that shape features of a component are perceived differently by the designing and manufacturing departments. These differences cause further misunderstanding and misinterpretation when computer-based knowledge sharing systems are used across the two domains. Foundation or core ontologies can be used to overcome these differences and to ensure a seamless sharing of knowledge. This is because these ontologies provide a common grounding for domain ontologies to be used by individual domains or department. This common grounding can be used by the mediation and knowledge verification systems to authenticate the meaning of knowledge understood across different domains. For this reason, this research proposes a knowledge verification framework for developing a system capable of verifying knowledge between those domain ontologies which are developed out of a common core or foundation ontology. This framework makes use of ontology logic to standardize the way concepts from a foundation and core-concepts ontology are used in domain ontologies and then by using the same principles the knowledge being shared is verified. The Knowledge Frame Language which is based on Common Logic is used for formalizing example ontologies. The ontology editor used for browsing and querying ontologies is the Integrated Ontology Development Environment (IODE) by Highfleet Inc. An ontological product modelling technique is also developed in this research, to test the proposed framework in the scenario of manufacturability analysis. The proposed framework is then validated through a Java API specially developed for this purpose. Real industrial examples experienced during the case study are used for validation.

A integração e a troca de informação na Web é uma necessidade reconhecida no mundo atual nos mais diversos domínios de aplicação. A Web constitui hoje o principal meio de acesso a informações, disponibilizando várias formas de acesso a esse conteúdo. No entanto, disponibilizar essa informação de forma integrada para o usuário ainda é um desafio. O Serviço Web Semântico é uma tecnologia de Inteligência Artificial promissora a qual pode contribuir significativamente com o processo de integração tanto de dados como de processos disponíveis em portais Web. O objetivo do presente trabalho é realizar a integração das diferentes funcionalidades oferecidas por portais disponibilizados na Web, fazendo uso de ontologias de domínio através de Serviços Web Semânticos. Para alcançar o objetivo proposto, um sistema de busca e integração, denominado W-KIS, foi projetado e desenvolvido, fornecendo uma visão unificada e transparente ao usuário de toda informação disponível em um determinado número de portais Web, contextualizados a um domínio de aplicação específico. Dois domínios de aplicação foram explorados neste trabalho através de dois estudos de caso: a Biomedicina e a Geologia, cada um fornecendo sua própria ontologia de domínio. Serviços Web Semânticos foram desenvolvidos para encapsular portais Web em ambos os domínios, permitindo ao sistema realizar a integração em cada domínio, separadamente. A aplicação proposta foi validada através da avaliação de sua atuação em ambos os domínios, além de testes com usuários finais e comparações com outras abordagens para integração na Web e motores de busca tradicionais. Através da utilização de Serviços Web Semânticos, W-KIS é capaz de localizar e executar os serviços de forma automática, além de lidar com a heterogeneidade semântica entre as fontes de informação por meio das ontologias de domínio. Desta forma, o sistema fornece apenas informação contextualizada ao interesse do usuário. / Integration and exchange of information across the Internet is a universally recognized need, in a wide variety of domains. Nowadays, the Web is the main source of information, providing many ways to access this content. However, making this information available to the user in an integrated way is still a challenge. New promising application fields such as Semantic Web Services can improve the integration process of data and processes available in Web portals. The goal of the present research is to accomplish the integration of the different functionalities offered by portals available in the Web, making use of domain ontologies through Semantic Web Services. In order to achieve the proposed goal, a search and integration system, named W-KIS, was designed and developed. The system provides the user with a unified and transparent view of the whole information available in a number of Web portals, related to a specific application domain. Two application domains were explored in this work through two case studies: the Biomedicine and the Geology, each one providing its own domain ontology. Semantic Web Services were designed to encapsulate Web portals in both domains, allowing the system to accomplish the integration in each domain, separately. The application proposed in this project was validated through the evaluation of its behavior in both domains, besides other tests with final users and comparisons with other approaches for integration in the Web, and traditional search engines. Making use of Semantic Web Services, W-KIS is able to find and execute the services in an automatic way, besides dealing with the semantic heterogeneity in the information sources by means of domain ontologies. This way, the system provides the user with information contextualized to its interest.

A integração e a troca de informação na Web é uma necessidade reconhecida no mundo atual nos mais diversos domínios de aplicação. A Web constitui hoje o principal meio de acesso a informações, disponibilizando várias formas de acesso a esse conteúdo. No entanto, disponibilizar essa informação de forma integrada para o usuário ainda é um desafio. O Serviço Web Semântico é uma tecnologia de Inteligência Artificial promissora a qual pode contribuir significativamente com o processo de integração tanto de dados como de processos disponíveis em portais Web. O objetivo do presente trabalho é realizar a integração das diferentes funcionalidades oferecidas por portais disponibilizados na Web, fazendo uso de ontologias de domínio através de Serviços Web Semânticos. Para alcançar o objetivo proposto, um sistema de busca e integração, denominado W-KIS, foi projetado e desenvolvido, fornecendo uma visão unificada e transparente ao usuário de toda informação disponível em um determinado número de portais Web, contextualizados a um domínio de aplicação específico. Dois domínios de aplicação foram explorados neste trabalho através de dois estudos de caso: a Biomedicina e a Geologia, cada um fornecendo sua própria ontologia de domínio. Serviços Web Semânticos foram desenvolvidos para encapsular portais Web em ambos os domínios, permitindo ao sistema realizar a integração em cada domínio, separadamente. A aplicação proposta foi validada através da avaliação de sua atuação em ambos os domínios, além de testes com usuários finais e comparações com outras abordagens para integração na Web e motores de busca tradicionais. Através da utilização de Serviços Web Semânticos, W-KIS é capaz de localizar e executar os serviços de forma automática, além de lidar com a heterogeneidade semântica entre as fontes de informação por meio das ontologias de domínio. Desta forma, o sistema fornece apenas informação contextualizada ao interesse do usuário. / Integration and exchange of information across the Internet is a universally recognized need, in a wide variety of domains. Nowadays, the Web is the main source of information, providing many ways to access this content. However, making this information available to the user in an integrated way is still a challenge. New promising application fields such as Semantic Web Services can improve the integration process of data and processes available in Web portals. The goal of the present research is to accomplish the integration of the different functionalities offered by portals available in the Web, making use of domain ontologies through Semantic Web Services. In order to achieve the proposed goal, a search and integration system, named W-KIS, was designed and developed. The system provides the user with a unified and transparent view of the whole information available in a number of Web portals, related to a specific application domain. Two application domains were explored in this work through two case studies: the Biomedicine and the Geology, each one providing its own domain ontology. Semantic Web Services were designed to encapsulate Web portals in both domains, allowing the system to accomplish the integration in each domain, separately. The application proposed in this project was validated through the evaluation of its behavior in both domains, besides other tests with final users and comparisons with other approaches for integration in the Web, and traditional search engines. Making use of Semantic Web Services, W-KIS is able to find and execute the services in an automatic way, besides dealing with the semantic heterogeneity in the information sources by means of domain ontologies. This way, the system provides the user with information contextualized to its interest.

A integração e a troca de informação na Web é uma necessidade reconhecida no mundo atual nos mais diversos domínios de aplicação. A Web constitui hoje o principal meio de acesso a informações, disponibilizando várias formas de acesso a esse conteúdo. No entanto, disponibilizar essa informação de forma integrada para o usuário ainda é um desafio. O Serviço Web Semântico é uma tecnologia de Inteligência Artificial promissora a qual pode contribuir significativamente com o processo de integração tanto de dados como de processos disponíveis em portais Web. O objetivo do presente trabalho é realizar a integração das diferentes funcionalidades oferecidas por portais disponibilizados na Web, fazendo uso de ontologias de domínio através de Serviços Web Semânticos. Para alcançar o objetivo proposto, um sistema de busca e integração, denominado W-KIS, foi projetado e desenvolvido, fornecendo uma visão unificada e transparente ao usuário de toda informação disponível em um determinado número de portais Web, contextualizados a um domínio de aplicação específico. Dois domínios de aplicação foram explorados neste trabalho através de dois estudos de caso: a Biomedicina e a Geologia, cada um fornecendo sua própria ontologia de domínio. Serviços Web Semânticos foram desenvolvidos para encapsular portais Web em ambos os domínios, permitindo ao sistema realizar a integração em cada domínio, separadamente. A aplicação proposta foi validada através da avaliação de sua atuação em ambos os domínios, além de testes com usuários finais e comparações com outras abordagens para integração na Web e motores de busca tradicionais. Através da utilização de Serviços Web Semânticos, W-KIS é capaz de localizar e executar os serviços de forma automática, além de lidar com a heterogeneidade semântica entre as fontes de informação por meio das ontologias de domínio. Desta forma, o sistema fornece apenas informação contextualizada ao interesse do usuário. / Integration and exchange of information across the Internet is a universally recognized need, in a wide variety of domains. Nowadays, the Web is the main source of information, providing many ways to access this content. However, making this information available to the user in an integrated way is still a challenge. New promising application fields such as Semantic Web Services can improve the integration process of data and processes available in Web portals. The goal of the present research is to accomplish the integration of the different functionalities offered by portals available in the Web, making use of domain ontologies through Semantic Web Services. In order to achieve the proposed goal, a search and integration system, named W-KIS, was designed and developed. The system provides the user with a unified and transparent view of the whole information available in a number of Web portals, related to a specific application domain. Two application domains were explored in this work through two case studies: the Biomedicine and the Geology, each one providing its own domain ontology. Semantic Web Services were designed to encapsulate Web portals in both domains, allowing the system to accomplish the integration in each domain, separately. The application proposed in this project was validated through the evaluation of its behavior in both domains, besides other tests with final users and comparisons with other approaches for integration in the Web, and traditional search engines. Making use of Semantic Web Services, W-KIS is able to find and execute the services in an automatic way, besides dealing with the semantic heterogeneity in the information sources by means of domain ontologies. This way, the system provides the user with information contextualized to its interest.

Ce mémoire porte sur l'utilisation des ontologies dans les systèmes de recherche d'information SRI dédiés à des domaines particuliers. Il se base sur une approche à deux niveaux, à savoir la formulation et la recommandation des requêtes. La formulation consiste à assister l'utilisateur dans l'expression de sa requête en se basant sur des concepts et des propriétés de l'ontologie de domaine utilisée. La recommandation consiste à proposer des résultats de recherche en utilisant la méthode du raisonnement à partir de cas. Dans cette méthode, une nouvelle requête est considérée comme un nouveau cas.La résolution de ce nouveau cas consiste à réutiliser les anciens cas similaires qui ne sont que des requêtes traitées auparavant. Afin de valider l'approche proposée, un système OntoCBRIR a été développé et un ensemble d'expérimentations a été élaboré. Enfin, les perspectives de recherche concluent le présent rapport. / This thesis study the using of ontologies in information retrieval systemdedicated to a specific domain. For that we propose a two-level approach to deal with i) the query formulation that assists the user in selecting concepts and properties of the used ontology ; ii) the query recommendation that uses the case-based reasoning method, where a new query is considered as a new case. Solving a new case consists of reusing similar cases from the history of the previous similar cases already processed. For the validation of the proposed approaches, a system was developed and a set of computational experimentations was made. Finally, research perspectives conclude that this present report.

Made available in DSpace on 2016-12-23T14:33:47Z (GMT). No. of bitstreams: 1 Alex Pinheiro das Gracas.pdf: 2761846 bytes, checksum: a904945394b1c705b72df3268f5bdab8 (MD5) Previous issue date: 2010-08-27 / The adoption of ontologically well founded languages for building ontologies has acquiring more adopters, however its widespread use stumble on using difficulties by inexperienced modelers. This dissertation proposes a methodological guide to support the building of domain ontologies using the ontologically well founded language OntoUML. This guide through the analysis of language structure, restrictions and design patterns helps the designer on the modeling process. Beyond, the building support interactions are used to generate a design rationale. At last, it is presented a Web application implementing the ideas proposed in this work / A adoção de linguagens ontologicamente bem fundamentadas para construção de ontologias, apesar de vir ganhando mais adeptos, esbarra nas dificuldades da utilização desta linguagem por modeladores inexperientes. Este trabalho propõe um guia metodológico para apoiar as construções de ontologias utilizando a linguagem OntoUML Este guia auxilia o projetista no processo de modelagem através do estudo da estrutura da linguagem, suas restrições sintáticas e padrões de projetos. Além disso, as interações com o modelador na utilização deste guia são utilizadas para gerar um design rationale do processo de modelagem. Por final é apresentada uma implementação Web de uma ferramenta que demonstra as propostas apresentadas neste trabalho

Submitted by Patrícia Valim Labres de Freitas (patricial) on 2016-03-18T14:03:10Z No. of bitstreams: 1 Luciana Monteiro Krebs_.pdf: 1391795 bytes, checksum: 587648c97bd0ea733d4c41cbe74697be (MD5) / Made available in DSpace on 2016-03-18T14:03:10Z (GMT). No. of bitstreams: 1 Luciana Monteiro Krebs_.pdf: 1391795 bytes, checksum: 587648c97bd0ea733d4c41cbe74697be (MD5) Previous issue date: 2016-01-25 / CAPES - Coordenação de Aperfeiçoamento de Pessoal de Nível Superior / O trabalho tem por objetivo analisar a variação conceitual de termos do domínio jurídico, compreendendo como um procedimento que contribui para implementação de uma ontologia do domínio jurídico. Caracteriza-se como um estudo exploratório e interdisciplinar, baseado na Teoria Comunicativa da Terminologia (Cabré), trabalhando com o conceito de variação terminológica. Metodologicamente, utiliza-se a Lexicologia da Verticalidade (Wichter) que possibilita a análise da variação através de categorias conceituais. No estudo examinam-se os termos feminicídio, lenocínio e descaminho, três crimes previstos no Código Penal brasileiro. Para a análise, utilizou-se para cada termo três gêneros textuais com níveis de especialidade diferentes: a legislação, o artigo especializado e uma notícia de imprensa. No desenvolvimento do trabalho foram utilizadas categorias conceituais que emergiram dos textos analisados e balizaram o trabalho comparativo. Propuseram-se as seguintes categorias conceituais: Legislação, Classificação, Tipo, Sujeito do delito, Motivação, Características, Agravantes, Pena e Crimes relacionados. Algumas delas apresentaram facetas internas às quais chamou-se de subcategorias: Legislação (lei), Legislação (artigo do CPB), Legislação (nome popular), Sujeito do delito (ativo), Sujeito do delito (passivo), Motivação (individual), Motivação (coletiva), Pena (tempo), Pena (regime), Pena (com agravantes), Pena (se culposo) e Pena (anterior). A análise dividiu-se em duas partes, sendo a primeira organizada por termo e a segunda por gênero textual. Na primeira etapa (por termo) identificou-se que realização linguística privilegia o público alvo do gênero textual em questão. Também se destacaram diferentes níveis de profundidade conceitual na classificação dos crimes. Na segunda etapa (análise contrastiva entre os gêneros textuais), o texto menos especializado apresentou mais vazios conceituais e o mais especializado, menos. Também identificou-se três casos de esvaziamento conceitual, onde a densidade conceitual diminui do texto mais especializado para o menos especializado. Viu-se ainda que o artigo especializado apresentou mais repetidamente novos conteúdos conceituais no texto. Por fim, apresentou-se os componentes estruturais prototípicos de cada gênero textual para a variação conceitual dos crimes. As descobertas contribuem na implementação de uma ontologia do domínio jurídico em diversos aspectos: percebeu-se que através da análise de diferentes gêneros textuais é possível identificar a relação de causa e efeito de um crime, suas características, definir o que um crime não é, que diferentes leis influenciam a penalidade, que a classificação de um crime influencia diretamente o tempo de pena e a forma como ela será cumprida, e assim por diante. Em síntese, os textos permitiram recuperar atributos do conceito que podem ser aplicados tanto na criação da entidade quanto no posicionamento adequado da entidade em uma estrutura conceitual, atribuindo-lhe propriedades e estabelecendo diferentes tipos de relações. Concluímos que os termos apresentam diferentes densidades conceituais, variando conforme a situação discursiva imbricada no gênero textual e nível de especialidade do público a quem o texto se dirige. / This paper aims to analyze the conceptual variation of legal domain terms, seen here as a procedure that contributes to the implementation of a legal domain ontology. This procedure is an exploratory and interdisciplinary study based on the Communicative Theory of Terminology (Cabré), dealing with the concept of terminological variation. As a methodology, the Lexicology of Verticality (Wichter) is used to allow for the variation analysis through conceptual categories. Femicide, procuring, and embezzlement were the terms examined in the study, three crimes set forth in the Penal Code of Brazil. For this analysis, we used three text genres for each term with different levels of specialty: one legislation, one specialized article, and one press report. As the work unfolded, conceptual categories that emerged from the analyzed texts and that marked off the comparative work were used. The following conceptual categories were proposed: Legislation, Classification, Type, Subject of Crime, Motivation, Characteristics, Aggravating Circumstances, Penalty, and related Crimes. Some of them presented internal features, which were called subcategories: Legislation (law), Legislation (article of the Penal Code of Brazil), Legislation (popular name), Subject of Crime (active), Subject of Crime (passive), Motivation (individual), Motivation (collective), Penalty (time), Penalty (regime), Penalty (with aggravating circumstances), Penalty (if wrongful act) and Penalty (previous). The analysis was divided into two parts, being the first organized per term and the second per text genre. In the first stage (per term) we identified which linguistic realization favors the target-audience of the text genre at hand. We also highlighted different levels of conceptual depth in the classification of crimes. In the second stage (contrastive analysis among the text genres), the least specialized text presented more conceptual voids, and the most specialized one presented less conceptual voids. Three cases of conceptual emptying were also identified, where the conceptual density decreases from the most specialized to the least specialized texts. We further observed that the specialized article more repeatedly presented new conceptual contents in the text. Finally, we presented the structural components that are prototypical of each text genre for the conceptual variation of crimes. These findings contribute to the implementation of a legal domain ontology in several aspects: we realized that through the analysis of different text genres it is possible to identify the cause and effect relation of crime, its characteristics. It is also possible to define what crime is not, which different laws influence penalty, that crime classification directly influences the length of penalty and how it is to be served, and so forth. In sum, these texts allowed us to recover concept attributes that can be applied both to entity creation and to the entity proper positioning in a conceptual structure, assigning them with properties and setting different types of relations. We reached the conclusion that the terms present different conceptual densities, varying according to the discursive situation engendered in the text genre and to the level of specialty held by the audience the text is aimed at.