Using Neo4J geospatial data storage and integration

Online geographic-databases have been growing increasingly as they have become a crucial source of information for both social networks and safety-critical systems. Since the quality of such applications is largely related to the richness and completeness of their data, it becomes imperative to develop adaptable and persistent storage systems, able to make use of several sources of information as well as enabling the fastest possible response from them. This work will create a shared and extensible geographic model, able to retrieve and store information from the major spatial sources available. A geographic-based system also has very high requirements in terms of scalability, computational power and domain complexity, causing several difficulties for a traditional relational database as the number of results increases. NoSQL systems provide valuable advantages for this scenario, in particular graph databases which are capable of modeling vast amounts of inter-connected data while providing a very substantial increase of performance for several spatial requests, such as finding shortestpath routes and performing relationship lookups with high concurrency. In this work, we will analyze the current state of geographic information systems and develop a unified geographic model, named GeoPlace Explorer (GE). GE is able to import and store spatial data from several online sources at a symbolic level in both a relational and a graph databases, where several stress tests were performed in order to find the advantages and disadvantages of each database paradigm.

Banco de dados relacional para cadastro, avaliação e manejo da arborização em vias públicas

A arborização urbana em calçadas é fundamental para manutenção da qualidade de vida, proporcionando conforto aos habitantes das cidades. Contudo, existem problemas causados principalmente pela falta de planejamento na implantação e no manejo da arborização. O objetivo do presente trabalho foi a criação de um banco de dados relacional para auxiliar no cadastro informatizado, na avaliação e no manejo da arborização de vias públicas. Apresenta resultados sobre a valoração de indivíduos cadastrados, cálculo da diversidade entre os bairros, introdução de fotos digitais e relatórios para manejo em interface amigável, podendo servir de instrumento à manutenção da arborização e de vetor de comunicação para educação ambiental.

Molecular models of protein targets from Mycobacterium tuberculosis

Structural characterization of enzymes that belong to microbial metabolic pathways is very important for structure-based drug design since some of these proteins may be present in the bacterial genome, but absent in humans. Thus, metabolic pathways became potential targets for drug design. The motivation of this work is the fact that Mycobacterium tuberculosis is the cause of the deaths of millions of people in the world, so that the structural characterization of protein targets to propose new drugs has become essential. DBMODELING is a relational database, created to highlight the importance of methods of molecular modeling applied to the Mycobacterium tuberculosis genome with the aim of proposing protein-ligand docking analysis. There are currently more than 300 models for proteins from Mycobacterium tuberculosis genome in the database. The database contains a detailed description of the reaction catalyzed by each enzyme and their atomic coordinates. Information about structures, a tool for animated gif image, a table with a specification of the metabolic pathway, modeled protein, inputs used in modeling, and analysis methods used in this project are available in the database for download. The search tool can be used for reseachers to find specific pathways or enzymes.

Perfil de beta talassemia heterozigota obtido a partir de análise data mining em banco de dados

Variations in the phenotypic expression of heterozygous beta thalassemia reflect the formation of different populations. To better understand the profile of heterozygous beta-thalassemia of the Brazilian population, we aimed at establishing parameters to direct the diagnosis of carriers and calculate the frequency from information stored in an electronic database. Using a Data Mining tool, we evaluated information on 10,960 blood samples deposited in a relational database. Over the years, improved diagnostic technology has facilitated the elucidation of suspected beta thalassemia heterozygote cases with an average frequency of 3.5% of referred cases. We also found that the Brazilian beta thalassemia trait has classic increases of Hb A2 and Hb F (60%), mainly caused by mutations in beta zero thalassemia, especially in the southeast of the country.

Knowledge extraction using visualization of hemoglobin parameters to identify thalassemia

The analysis of large amounts of data is better performed by humans when represented in a graphical format. Therefore, a new research area called the Visual Data Mining is being developed endeavoring to use the number crunching power of computers to prepare data for visualization, allied to the ability of humans to interpret data presented graphically.This work presents the results of applying a visual data mining tool, called FastMapDB to detect the behavioral pattern exhibited by a dataset of clinical information about hemoglobinopathies known as thalassemia. FastMapDB is a visual data mining tool that get tabular data stored in a relational database such as dates, numbers and texts, and by considering them as points in a multidimensional space, maps them to a three-dimensional space. The intuitive three-dimensional representation of objects enables a data analyst to see the behavior of the characteristics from abnormal forms of hemoglobin, highlighting the differences when compared to data from a group without alteration.

Development of an open case-based decision-support system for diagnosis in oral pathology

Making diagnoses in oral pathology are often difficult and confusing in dental practice, especially for the lessexperienced dental student. One of the most promising areas in bioinformatics is computer-aided diagnosis, where a computer system is capable of imitating human reasoning ability and provides diagnoses with an accuracy approaching that of expert professionals. This type of system could be an alternative tool for assisting dental students to overcome the difficulties of the oral pathology learning process. This could allow students to define variables and information, important to improving the decision-making performance. However, no current open data management system has been integrated with an artificial intelligence system in a user-friendly environment. Such a system could also be used as an education tool to help students perform diagnoses. The aim of the present study was to develop and test an open case-based decisionsupport system.Methods: An open decision-support system based on Bayes' theorem connected to a relational database was developed using the C++ programming language. The software was tested in the computerisation of a surgical pathology service and in simulating the diagnosis of 43 known cases of oral bone disease. The simulation was performed after the system was initially filled with data from 401 cases of oral bone disease.Results: the system allowed the authors to construct and to manage a pathology database, and to simulate diagnoses using the variables from the database.Conclusion: Combining a relational database and an open decision-support system in the same user-friendly environment proved effective in simulating diagnoses based on information from an updated database.

Molecular modeling databases: A new way in the search of protein targets for drug development

DBMODELING is a relational database of annotated comparative protein structure models and their metabolic, pathway characterization. It is focused on enzymes identified in the genomes of Mycobacterium tuberculosis and Xylella fastidiosa. The main goal of the present database is to provide structural models to be used in docking simulations and drug design. However, since the accuracy of structural models is highly dependent on sequence identity between template and target, it is necessary to make clear to the user that only models which show high structural quality should be used in such efforts. Molecular modeling of these genomes generated a database, in which all structural models were built using alignments presenting more than 30% of sequence identity, generating models with medium and high accuracy. All models in the database are publicly accessible at http://www.biocristalografia.df.ibilce.unesp.br/tools. DBMODELING user interface provides users friendly menus, so that all information can be printed in one stop from any web browser. Furthermore, DBMODELING also provides a docking interface, which allows the user to carry out geometric docking simulation, against the molecular models available in the database. There are three other important homology model databases: MODBASE, SWISSMODEL, and GTOP. The main applications of these databases are described in the present article. © 2007 Bentham Science Publishers Ltd.

A clinical decision support system for cancer diseases

The second main cause of death in Brazil is cancer, and according to statistics disclosed by National Cancer Institute from Brazil (INCA) 466,730 new cases of cancer are forecast for 2008. The analysis of tumour tissues of various types and patients' clinical data, genetic profiles, characteristics of diseases and epidemiological data may lead to more precise diagnoses, providing more effective treatments. In this work we present a clinical decision support system for cancer diseases, which manages a relational database containing information relating to the tumour tissue and their location in freezers, patients and medical forms. Furthermore, it is also discussed some problems encountered, as database integration and the adoption of a standard to describe topography and morphology. It is also discussed the dynamic report generation functionality, that shows data in table and graph format, according to the user's configuration. © ACM 2008.

Mineração multirrelacional de regras de associação em grandes bases de dados

Pós-graduação em Ciência da Computação - IBILCE

Bioinformática estrutural aplicada ao estudo de enzimas da via metabólica do ácido chiquímico

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Bioinformática estrutural aplicada ao estudo de proteínas alvo do genoma do Mycobacterium tuberculosis

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Subsídio à gestão ambiental hidroviária: o empreendimento hídrico Santa Maria da Serra

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Desenvolvimento de um sistema de alerta de enchente aplicado aos planos de defesa civil em áreas de risco no estado do Pará utilizando Sistema de Informações Geográficas (SIG), caso: cidade de Marabá

A presente dissertação desenvolveu um Sistema de Alerta de Enchentes para a Cidade de Marabá, localizada na confluência dos rios Itacaiúnas e Tocantins, a 440 km da cidade de Belém, capital do Estado do Pará. O Sistema de Alerta de Enchentes foi desenvolvido com base no modelo hidrológico MOD-4B incorporado a um Sistema de Informações Geográficas. Esse sistema permite prever as variações do nível do Rio Tocantins ao longo do ano, de modo a acompanhar a evolução da cheia com antecedência de 4 dias, o que torna possível uma ação eficiente da defesa civil. O modelo de previsão utilizou como referência as réguas linimétricas localizadas nos rios Tocantins e Araguaia nas cidades de Carolina e Conceição do Araguaia, distantes aproximadamente 225 e 270 km, respectivamente, da cidade de Marabá. O sistema utiliza o software de geoprocessamento ArcView 3.3, que teve implementada uma interface desenvolvida através da linguagem de programação orientada a objetos Avenue, com a finalidade de rodar o aplicativo do modelo hidrológico. O uso de menus e janelas customizados do sistema possibilitou o acesso a dados espaciais e tabelas de dados relacionais e/ou banco de dados cadastral, além de módulos de análise espacial e de visualização de dados geográficos em um Sistema de Informações Geográficas (SIG), possibilitando a previsão de enchentes na forma de mapas, tabelas e relatórios com a indicação das áreas inundadas para os períodos de 4, 3, 2 e 1 dia de antecedência do evento de enchente. O Sistema permitiu identificar os imóveis e as ruas atingidos, e possibilitará através de levantamentos futuros quantificar a população afetada e os prejuízos causados pelo desastre, facilitando que a defesa civil execute planos de ação para enfrentamento eficiente antes, durante e depois da ocorrência da enchente.

Planejamento integrado dos recursos hídricos na microbacia do córrego Três Barras no município de Marinópolis-SP

Pós-graduação em Agronomia - FEIS

Sensoriamento remoto e Sistemas de Informações Geográficas (SIG) na análise dos impactos referentes à cultura canavieira e reflorestamento: a subtração dos biomas nativos no município de Itirapina-SP

The main objective of this study was to perform a temporal analysis of land use and cover of Itirapina – São Paulo estate, Brazil, for 1962, 2000 and 2008 scenarios, indicating the rate of change in native vegetation and contextualizing its modifications. Based on photointerpretation performed by supervised classification using the method of Bhattacharya, the thematic classes were mapped and characterized in an area equivalent to 56400 hectares. Using remote sensing technologies and geographic information systems, was structured and implemented a georeferenced and relational database, allowing the analysis of the size of the area occupied. The results showed that the expansion of cultivation of cane sugar and reforestation in the past 45 years has been conditioned the fragmentation of natural vegetation cover in the city, which fell by 34793 ha (61,7%) in 1962 to 9765,2 ha (17,3%) in 2008, with the loss of 25027,8 hectares.