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Oralcard: Web Information System for Oral Health

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Oralcard: Web Information System for Oral Health Universidade de Aveiro Departamento de Electrónica, Telecomunicações e 2011 Informática José Manuel OralCard: Sistema de Informação Web para a Saúde Santos Melo Oral OralCard: Web Information System for Oral Health Universidade de Aveiro Departamento de Electrónica, Telecomunicações e 2011 Informática José Manuel OralCard: Web Information System for Oral Health Santos Melo OralCard: Sistema de Informação Web para a Saúde Oral Dissertação apresentada à Universidade de Aveiro para cumprimento dos requisitos necessários à obtenção do grau de Mestre em Engenharia de Computadores e Telemática (M.I.E.C.T.), realizada sob a orientação científica do Professor Doutor José Luís Guimarães Oliveira, Professor Associado do Departamento de Electrónica, Telecomunicações e Informática da Universidade de Aveiro. Dedico este trabalho à minha família. o júri presidente Professor Doutor Armando José Formoso de Pinho Professor Associado com Agregação do Departamento de Electrónica, Telecomunicações e Informática da Universidade de Aveiro vogais Professor Doutor António Manuel de Jesus Pereira Professor Coordenador do Departamento de Engenharia Informática da Escola Superior de Tecnologia e Gestão do Instituto Politécnico de Leiria Professor Doutor José Luís Guimarães Oliveira Professor Associado do Departamento de Electrónica, Telecomunicações e Informática da Universidade de Aveiro agradecimentos Um obrigado especial ao Professor José Luís Oliveira pela minha integração no grupo de trabalho de Bioinformática, no Instituto de Engenharia Electrónica e Telemática de Aveiro (IEETA). Um obrigado especial ao Pedro Lopes e ao Joel P. Arrais, que me ajudaram com grande dedicação no desenvolvimento deste trabalho. Um obrigado ao Nuno Rosa pela ajuda na parte biológica e científica do trabalho. Este projecto não estaria concluído sem reconhecer a ajuda prestada pelos meus pais e irmãs, não só na dissertação como em todo o percurso académico na Universidade de Aveiro. palavras-chave Sistema informação web, Saúde oral, Integração de dados, doenças, proteínas, ontologias resumo Os sistemas de informação na web assumem-se cada vez mais como um recurso indispensável para os que estudam as ciências biomédicas. Uma das áreas de estudo destas ciências incide na cavidade oral e nas proteínas que nela residem. Existem variadas plataformas online que permitem a pesquisa de dados específicos a microorganismos e a proteínas associadas, mas estes dados são genéricos e não são desenhados para casos de estudo específicos. Este trabalho tem como objectivo desenvolver uma estratégia e um protótipo para o armazenamento de informação relacionada com a cavidade oral, visando a sua utilização em investigação. Uma preocupação diferenciadora prende-se com o objectivo de integrar dados obtidos experimentalmente com referências existentes na web e estudadas por outras entidades. O protótipo desenvolvido permite aos investigadores na área das ciências biomédicas, sem conhecimentos específicos em bases de dados, pesquisar proteínas, doenças e genes, e integrar novos resultados de ensaios na base de dados existente. keywords Web information system, Oral health, Data integration, Diseases, Proteins, Gene Ontologies abstract Information systems on the web are becoming important resources for those studying biomedical sciences. One area of study of these sciences focuses on the oral cavity and on proteins that reside in it. Several online platforms provide specific knowledge on multiple microorganisms and associated proteins, but these are generic and are not designed for specific case studies. This work aims to develop a strategy and a prototype for the storage of information related to the oral cavity, aiming their use in research. It will integrate data collected from experimental results with existing references on the web and explored by other entities. The prototype allows researchers in the biomedical sciences, without particular expertise in databases, searching for proteins, genes and diseases, and integrating new test results in the existing database. Contents List of Acronyms .............................................................................................................. v List of Figures .................................................................................................................. ix List of Tables ................................................................................................................... xi 1. Introduction ............................................................................................................. 1 1.1 Motivation and Context ................................................................................. 1 1.2 Objectives ...................................................................................................... 2 1.3 Dissertation structure ..................................................................................... 3 2. Background Concepts and State of the Art ............................................................. 5 2.1 The emergence of data integration ................................................................ 5 2.1.1 Database Abstraction Layer ............................................................... 5 2.1.2 Object-relational Mapping.................................................................. 8 2.2 Software Architectural Patterns ................................................................... 10 2.2.1 Model-View-Controller .................................................................... 11 2.3 Software Development Methodology .......................................................... 13 2.3.1 Rapid Application Development ...................................................... 13 2.4 Web Application Frameworks (Full-stack) ................................................. 14 2.4.1 Ruby on Rails ................................................................................... 15 2.4.2 Symfony – Open Source PHP Web Framework .............................. 16 2.4.3 Liferay – Open Source Enterprise Portal.......................................... 18 2.4.4 Molgenis ........................................................................................... 19 2.4.5 Conclusions ...................................................................................... 20 i José Melo 2.5 Presentation Frameworks for Web Applications (Frontend) ....................... 22 2.5.1 Stripes ............................................................................................... 23 2.5.2 Google Web Toolkit ......................................................................... 24 2.5.3 ZK – Open Source AJAX ................................................................. 25 2.5.4 Conclusions ...................................................................................... 27 3. Context of the Problem ......................................................................................... 29 3.1 Data Integration ........................................................................................... 29 3.1.1 Data Warehousing ............................................................................ 30 3.1.2 Data Integration Alternatives ........................................................... 32 3.1.3 Conclusions ...................................................................................... 35 3.2 The Oral Cavity ........................................................................................... 35 3.2.1 Proteins ............................................................................................. 37 3.2.2 Diseases ............................................................................................ 38 3.2.3 Pathways ........................................................................................... 39 3.2.4 Gene Ontology.................................................................................. 40 3.3 Summary ...................................................................................................... 41 4. Work Implementation ........................................................................................... 43 4.1 Backend Development ................................................................................. 43 4.2 Database Architecture .................................................................................. 46 4.3 Importing Data ............................................................................................. 49 4.4 Frontend Development ................................................................................ 55 4.5 Summary ...................................................................................................... 61 5. Results ................................................................................................................... 63 5.1 Importing Data ............................................................................................. 63 5.2 Frontend ....................................................................................................... 65 5.2.1 The Home Page ................................................................................ 65 5.2.2 Protein Search and Details................................................................ 67 5.2.3 Disease Search and Details ............................................................... 75 5.2.1 Direct access using URL Bindings ................................................... 77 5.3 Summary .....................................................................................................
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