Submitted by Rosivalda Pereira (mrs.pereira@ufma.br) on 2017-08-14T18:09:29Z No. of bitstreams: 1 LucianaFarias.pdf: 24712291 bytes, checksum: d8760f57e945d0cde298c31a44b38539 (MD5) / Made available in DSpace on 2017-08-14T18:09:29Z (GMT). No. of bitstreams: 1 LucianaFarias.pdf: 24712291 bytes, checksum: d8760f57e945d0cde298c31a44b38539 (MD5) Previous issue date: 2009-11-04 / This work is discussed the conceptual model of a multi-agent system for environmental monitoring with the use of biomarkers of aquatic organisms present in the port complex of São Luís-Maranhão-Brasil, second most important in the country in cargo handling. Located in the São Marcos Bay, this complex have an estuarine ecosystems which have suffered attacks in the current process of economic development, caused by intense port handling, dumping of ballast water and washing the vessels, overfishing, introduction of exotic species in the middle pollution in urban and industrial effluents, subject to severe environmental impacts that should be monitored. Methodologically, the modeling of the monitoring solution, we used the existing environmental conditions and aquatic life caught in two different sites of the port complex, the first in a potentially contaminated area and the second in a contamination-free (control), proposing the creation of a network of sensors in these locations. Invest conceded data by Carvalho-Neta (2007) whose research includes to catch fish in these perimeters, then submitting them for laboratory analysis to measure the enzyme activity of glutathione S-transferase (GST) and Catalase (CAT), the result was processed and recorded in bio-ontology . The core of the solution of Multi-agent system is based on the results derived from the biochemical analysis of GST, inspiring the modeling software agent that simulates the behavior of this enzyme. The solution also includes an application running on mobile devices that makes the collection of environmental variables in the selected points, validates them and makes the inference of those who could not be collected. Multi-agent System for Environmental Monitoring of the Port Complex of the Island of São Luís-Maranhão- Brasil, therefore, is made up of the bio-ontology, sensor networking, mobile application collection and inference of data from environmental conditions, software agents to simulate biochemical analysis, calculation of GST activity and other staff related to the maintenance and security of the SMA. / Nesta dissertação é discutido o modelo conceitual de um sistema multiagente para monitoramento ambiental com uso de marcadores biológicos de organismos aquáticos presentes no complexo portuário de São Luís-MA, segundo mais importante do país em movimentação de carga. Situado na Baía de São Marcos, esse complexo possui um dos ecossistemas estuarinos que mais têm sofrido agressões no atual processo de desenvolvimento econômico, provocadas pela intensa movimentação portuária, despejo de água de lastro e lavagem dos navios, pesca predatória, introdução de espécies exóticas no meio, poluição por efluentes domésticos e industriais, sujeitando o ambiente a fortes impactos ambientais que devem ser monitorados. Metodologicamente, na modelagem da solução de monitoramento, utilizou-se o registro das condições ambientais e de organismos aquáticos capturados em dois pontos distintos do complexo portuário: o primeiro, em uma área potencialmente contaminada e o segundo em uma livre de contaminação (controle), propondo-se a criação de uma rede de sensores nesses locais. Empregou-se dados cedidos por Carvalho-Neta (2007) cuja pesquisa contou com a captura de peixes nesses perímetros, submetendo-os posteriormente a análise laboratorial para medição da atividade enzimática da Glutationa s- Transferase (GST) e Catalase (CAT), tendo todos os resultados processados e registrados em bio-ontologia. O núcleo da solução do Sistema Multiagente baseia-se nos resultados oriundos da análise bioquímica da GST, inspirando a modelagem de agente de software que simula o comportamento desta enzima. Todos esses dados foram registrados em bio-ontologia. A solução contempla também uma aplicação executada em dispositivos móveis que realiza a coleta das variáveis abióticas nos pontos selecionados, valida-as e realiza a inferência daquelas que não puderam ser coletadas. O Sistema Multiagente para Monitoramento Ambiental do Complexo Portuário da Ilha de São Luís, portanto, é constituído pelo conjunto da bio-ontologia, rede de sensores, aplicação móvel de coleta e inferência de dados das condições do meio ambiente, agentes de software para simulação de análise bioquímica, cálculo da atividade da GST e outros agentes relacionados à manutenção e segurança do SMA.

Made available in DSpace on 2016-08-17T14:53:06Z (GMT). No. of bitstreams: 1 Luciana Fortes Farias.pdf: 24712291 bytes, checksum: d8760f57e945d0cde298c31a44b38539 (MD5) Previous issue date: 2009-11-04 / This work is discussed the conceptual model of a multi-agent system for environmental monitoring with the use of biomarkers of aquatic organisms present in the port complex of São Luís-Maranhão-Brasil, second most important in the country in cargo handling. Located in the São Marcos Bay, this complex have an estuarine ecosystems which have suffered attacks in the current process of economic development, caused by intense port handling, dumping of ballast water and washing the vessels, overfishing, introduction of exotic species in the middle pollution in urban and industrial effluents, subject to severe environmental impacts that should be monitored. Methodologically, the modeling of the monitoring solution, we used the existing environmental conditions and aquatic life caught in two different sites of the port complex, the first in a potentially contaminated area and the second in a contamination-free (control), proposing the creation of a network of sensors in these locations. Invest conceded data by Carvalho-Neta (2007) whose research includes to catch fish in these perimeters, then submitting them for laboratory analysis to measure the enzyme activity of glutathione S-transferase (GST) and Catalase (CAT), the result was processed and recorded in bio-ontology . The core of the solution of Multi-agent system is based on the results derived from the biochemical analysis of GST, inspiring the modeling software agent that simulates the behavior of this enzyme. The solution also includes an application running on mobile devices that makes the collection of environmental variables in the selected points, validates them and makes the inference of those who could not be collected. Multi-agent System for Environmental Monitoring of the Port Complex of the Island of São Luís-Maranhão- Brasil, therefore, is made up of the bio-ontology, sensor networking, mobile application collection and inference of data from environmental conditions, software agents to simulate biochemical analysis, calculation of GST activity and other staff related to the maintenance and security of the SMA. / Nesta dissertação é discutido o modelo conceitual de um sistema multiagente para monitoramento ambiental com uso de marcadores biológicos de organismos aquáticos presentes no complexo portuário de São Luís-MA, segundo mais importante do país em movimentação de carga. Situado na Baía de São Marcos, esse complexo possui um dos ecossistemas estuarinos que mais têm sofrido agressões no atual processo de desenvolvimento econômico, provocadas pela intensa movimentação portuária, despejo de água de lastro e lavagem dos navios, pesca predatória, introdução de espécies exóticas no meio, poluição por efluentes domésticos e industriais, sujeitando o ambiente a fortes impactos ambientais que devem ser monitorados. Metodologicamente, na modelagem da solução de monitoramento, utilizou-se o registro das condições ambientais e de organismos aquáticos capturados em dois pontos distintos do complexo portuário: o primeiro, em uma área potencialmente contaminada e o segundo em uma livre de contaminação (controle), propondo-se a criação de uma rede de sensores nesses locais. Empregou-se dados cedidos por Carvalho-Neta (2007) cuja pesquisa contou com a captura de peixes nesses perímetros, submetendo-os posteriormente a análise laboratorial para medição da atividade enzimática da Glutationa s- Transferase (GST) e Catalase (CAT), tendo todos os resultados processados e registrados em bio-ontologia. O núcleo da solução do Sistema Multiagente baseia-se nos resultados oriundos da análise bioquímica da GST, inspirando a modelagem de agente de software que simula o comportamento desta enzima. Todos esses dados foram registrados em bio-ontologia. A solução contempla também uma aplicação executada em dispositivos móveis que realiza a coleta das variáveis abióticas nos pontos selecionados, valida-as e realiza a inferência daquelas que não puderam ser coletadas. O Sistema Multiagente para Monitoramento Ambiental do Complexo Portuário da Ilha de São Luís, portanto, é constituído pelo conjunto da bio-ontologia, rede de sensores, aplicação móvel de coleta e inferência de dados das condições do meio ambiente, agentes de software para simulação de análise bioquímica, cálculo da atividade da GST e outros agentes relacionados à manutenção e segurança do SMA.

The original and still a major purpose of ontologies in computer and information sciences is to serve for the semantic integration of represented content, facilitating information system interoperability. Content can be data, information, and knowledge, and it can be distributed within or across these categories. A myriad of languages is available for representation. Ontologies themselves are artifacts which are expressed in various languages. Different such languages are utilized today, including, as well-known representatives, predicate logic, subsuming first-order (predicate) logic (FOL), in particular, and higher-order (predicate) logic (HOL); the Web Ontology Language (OWL) on the basis of description logics (DL); and the Unified Modeling Language (UML). We focus primarily on languages with formally defined syntax and semantics. This overall picture immediately suggests questions of the following kinds: What is the relationship between an ontology and the language in which it is formalized? Especially, what is the impact of the formal semantics of the language on the formalized ontology? How well understood is the role of ontologies in semantic integration? Can the same ontology be represented in multiple languages and/or in distinct ways within one language? Is there an adequate understanding of whether two expressions are intensionally/conceptually equivalent and whether two ontologies furnish the same ontological commitments? One may assume that these questions are resolved. Indeed, the development and adoption of ontologies is widespread today. Ontologies are authored in a broad range of different languages, including offering equally named ontologies in distinct languages. Much research is devoted to techniques and technologies that orbit ontologies, for example, ontology matching, modularization, learning, and evolution, to name a few. Ontologies have found numerous beneficial applications, and hundreds of ontologies have been created, considering solely the context of biomedical research. For us, these observations increase the relevance of the stated questions and close relatives thereof, and raise the desire for solid theoretical underpinnings. In the literature of computer and information sciences, we have found only few approaches that tackle the foundations of ontologies and their representation to allow for answering such questions or that actually answer them. We elaborate an analysis of the subject as the first item of central contributions within this thesis. It mainly results in the identification of a vicious circularity in (i) the intended use of ontologies to mediate between formal representations and (ii) solely exploiting formal semantic notions in representing ontologies and defining ontology-based equivalence as a form of intensional/conceptual equivalence. On this basis and in order to overcome its identified limitations, we contribute a general model-theoretic semantic account, named \\\"ontological semantics\\\". This kind of semantics takes the approach of assigning arbitrary entities as referents of atomic symbols and to link syntactic constructions with corresponding ontological claims and commitments. In particular, ontological semantics targets the avoidance of encoding effects in its definition. Therefore we argue that this semantic account is well suited for interpreting formalized ontologies and for defining languages for the representation of ontologies. It is further proposed as a fundament for envisioned novel definitions of the intensional equivalence of expressions, in potential deviation from only being formally equivalent under set-theoretic semantics. The thesis is defended that a particular usage of a formalism and its respective vocabulary should be accompanied by establishing an ontological semantics that is tailored to that use of the formalism, in parallel to the formal semantics of the language, in order to capture the ontological content of the formal representation for adequate reuse in other formalisms. Accordingly, we advocate ontological semantics as a useful framework for justifying translations on an intensional basis. Despite all deviations of ontological semantics from its set-theoretic blueprint, close relationships between the two can be shown, which allow for using established FOL and DL reasoners while assuming ontological semantics.

The original and still a major purpose of ontologies in computer and information sciences is to serve for the semantic integration of represented content, facilitating information system interoperability. Content can be data, information, and knowledge, and it can be distributed within or across these categories. A myriad of languages is available for representation. Ontologies themselves are artifacts which are expressed in various languages. Different such languages are utilized today, including, as well-known representatives, predicate logic, subsuming first-order (predicate) logic (FOL), in particular, and higher-order (predicate) logic (HOL); the Web Ontology Language (OWL) on the basis of description logics (DL); and the Unified Modeling Language (UML). We focus primarily on languages with formally defined syntax and semantics. This overall picture immediately suggests questions of the following kinds: What is the relationship between an ontology and the language in which it is formalized? Especially, what is the impact of the formal semantics of the language on the formalized ontology? How well understood is the role of ontologies in semantic integration? Can the same ontology be represented in multiple languages and/or in distinct ways within one language? Is there an adequate understanding of whether two expressions are intensionally/conceptually equivalent and whether two ontologies furnish the same ontological commitments? One may assume that these questions are resolved. Indeed, the development and adoption of ontologies is widespread today. Ontologies are authored in a broad range of different languages, including offering equally named ontologies in distinct languages. Much research is devoted to techniques and technologies that orbit ontologies, for example, ontology matching, modularization, learning, and evolution, to name a few. Ontologies have found numerous beneficial applications, and hundreds of ontologies have been created, considering solely the context of biomedical research. For us, these observations increase the relevance of the stated questions and close relatives thereof, and raise the desire for solid theoretical underpinnings. In the literature of computer and information sciences, we have found only few approaches that tackle the foundations of ontologies and their representation to allow for answering such questions or that actually answer them. We elaborate an analysis of the subject as the first item of central contributions within this thesis. It mainly results in the identification of a vicious circularity in (i) the intended use of ontologies to mediate between formal representations and (ii) solely exploiting formal semantic notions in representing ontologies and defining ontology-based equivalence as a form of intensional/conceptual equivalence. On this basis and in order to overcome its identified limitations, we contribute a general model-theoretic semantic account, named \\\"ontological semantics\\\". This kind of semantics takes the approach of assigning arbitrary entities as referents of atomic symbols and to link syntactic constructions with corresponding ontological claims and commitments. In particular, ontological semantics targets the avoidance of encoding effects in its definition. Therefore we argue that this semantic account is well suited for interpreting formalized ontologies and for defining languages for the representation of ontologies. It is further proposed as a fundament for envisioned novel definitions of the intensional equivalence of expressions, in potential deviation from only being formally equivalent under set-theoretic semantics. The thesis is defended that a particular usage of a formalism and its respective vocabulary should be accompanied by establishing an ontological semantics that is tailored to that use of the formalism, in parallel to the formal semantics of the language, in order to capture the ontological content of the formal representation for adequate reuse in other formalisms. Accordingly, we advocate ontological semantics as a useful framework for justifying translations on an intensional basis. Despite all deviations of ontological semantics from its set-theoretic blueprint, close relationships between the two can be shown, which allow for using established FOL and DL reasoners while assuming ontological semantics.:* Preface ** Abstract ** Contents ** Acknowledgments ** Foreword 1 Introduction 1.1 Background 1.2 Motivations 1.3 Theses, Objectives and Scope 1.4 Outline and Contributions 1.5 Formal Preliminaries 2 Foundations on Languages, Semantics, and Ontology 2.1 Formal Syntax and Formal Semantics 2.2 The Role of Ontologies in Semantic Integration 2.3 Ontological Analysis and Meta-Ontological Architecture 2.4 Conceptualization of Categories and Relations - CR 2.5 Summary of the Analysis and Next Steps 3 Views on Set-Theoretic Semantics of Classical Predicate Logics 3.1 Tarskian Model Theory and Set-Theoretic Superstructure 3.2 Formal Semantics and Choices for Entity Postulation 3.3 Theory View of Semantics 3.4 Aims for an Ontologically Neutral Semantic Account 4 Ontological Semantics 4.1 Definition of Ontological Structures by Analogy to the Set-Theoretic Approach 4.2 Properties and Further Background for Ontological Structures in General 4.3 Ontological Models & Signature Aspects 4.4 Semantics of Predication 4.5 Semantics of Connectives and Quantifiers & Semantic Notions 4.6 Relations between Ontological and Set-Theoretic Semantics 4.7 Ontological Neutrality 5 Ontological Engineering and Applications 5.1 Formalization Method for Ontology Representation in FOL 5.2 Ontological Usage Schemes 5.3 Glimpse on Characterizing Modular Representation 5.4 Applications in the Biomedical Domain 6 Contributions to Ontologies 6.1 Formalizations of Categories and Relations - CR 6.2 Remarks on Further Contributions 6.3 Ontologies of Time 7 Conclusion and Continuation 7.1 Resume 7.2 Related Work 7.3 Conclusions 7.4 Beginnings of Future Work Appendix A Additional Preliminaries A.1 Logical Notions A.2 Axiomatic Systems of Set and Number Theory B Axioms of the CR Taxonomy in OWL B.1 Asserted OWL Class Axioms B.2 Asserted OWL Object Property Axioms C Lists of Figures and Tables C.1 List of Figures C.2 List of Tables D Abbreviations, Acronyms and Names D.1 Abbreviations D.2 Acronyms and Names E References E.1 Literature References E.2 Web References/List of URLs F Work and Author Information ** Selbständigkeitserklärung (Declaration of Authorship) ** Bibliographic Data ** Scientific Record