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Gonzalesmalaverri Joanaesther ! "# $% & ' ( % ' ) % ' ' ' ' ! ** %) +,-.- --/00#- 1 ' 2' 2 ' 3 &4 5 '6 * $ ' ' '2 ' %) 72'%)2 &4- -,% '8 % &4( --3 ' '( -9- '' '-:-, & ;-"- ' '-7-' 2' 2 - 77- $ ' ' '2 ' %) - 72 ' %)2 &4- 777-<=2- 5%8% 6 <=2%(> ? 8 ' % (%8 ' @8 % @% . * ! %(>5A@B '6 (%8 % @%' @3 ; 3 2' - C ' &4 '3 ' <2 &4 %> ' %)2 &4 D % ' . 8 -3 - 2' 2 ' 57*$ %)6 . 8 -3 % E ' 5$-' '?6 . 8 -3 - 57*$ %)6 3 ' '8 :0:00# . ( % '.F* '2 &4 '%> ' %)2 &4 Instituto de Computa»c~ao Universidade Estadual de Campinas Um Servi»code Gerenciamento de Coletas para Sistemas de Biodiversidade Joana E. Gonzales Malaverri1 Abril de 2009 Banca Examinadora: ² Claudia M. Bauzer Medeiros Instituto de Computa»c~ao- Unicamp (Orientadora) ² Maria Camila Nardini Barioni Universidade Federal do ABC ² Eliane Martins Instituto de Computa»c~ao- Unicamp ² Rodolfo Jardim de Azevedo (Suplente) Instituto de Computa»c~ao- Unicamp ² Antonia Cec¶³liaZacagnini Amaral (Suplente) Instituto de Biologia - Unicamp 1Este trabalho teve o apoio ¯nanceiro da CAPES, 08/2007 `a03/2009, CNPq e Microsoft Research iv Resumo A pesquisa em biodiversidade requer correlacionar dados sobre seres vivos e seus habitats. Essas correla»c~oespodem ser de v¶ariostipos, integrando desde relacionamentos espaciais a especi¯ca»c~oesambientais (descri»c~oesdo habitat ou ecossistema). Sistemas de Biodiver- sidade s~aosistemas de software complexos que permitem aos pesquisadores realizar tais an¶alises. A complexidade desses sistemas varia com os dados manipulados, os usu¶arios visados e o ambiente em que s~aoexecutados. Um problema que deve ser enfrentado, es- pecialmente no ambiente Web, ¶ea heterogeneidade dos dados, agravado pela diversidade dos vocabul¶ariosdos usu¶arios. Esta disserta»c~aocontribui para resolver tal problema, apresentando um modelo de banco de dados que permite organizar informa»c~oesde biodiversidade a partir de padr~oes mundiais de dados. O modelo proposto combina informa»c~oescoletadas em campo com dados de cat¶alogosde museus. Para a especi¯ca»c~aodo modelo, contamos com a parti- cipa»c~aode ec¶ologose bi¶ologos. Para permitir o acesso e recupera»c~aode informa»c~aode forma transparente, o banco de dados foi encapsulado em um servi»co Web, que ¶einvo- cado por aplica»c~oescliente. A valida»c~aodo banco de dados e do servi»coutiliza dados reais fornecidos pelos parceiros do projeto BIO-CORE, um projeto de pesquisa que en- volve pesquisadores em Computa»c~aoe Biologia da UNICAMP e USP. v Abstract Biodiversity research requires correlations of data on living beings and their habitats. Such correlations can be of di®erent types, considering factors such as spatial relationships or environmental descriptions (e.g., description of habitat and ecossystems). Biodiversity information systems are complex pieces of software that allow researchers to perform these kinds of analysis. The complexity of these systems varies with the data used, the target users, and the environment where the systems are executed. One of the problems to be faced, especially on the Web, is the heterogeneity of the data aggravated by the diversity of user vocabularies. This research contributes to solve this problem by presenting a database model that organizes the biodiversity information using consensual data standards. The proposed model combines information collected in the ¯eld with that from museum data catalogues. The model was speci¯ed with the assistance of biologists and ecologists. The database was encapsulated in a Web service to ensure transparency in using, accessing and recovering the information. The service is invoked by client applications. The database and service were validated using real data, provided by the BIO-CORE project partners. BIO-CORE is a research project that involves computer and biology researchers from UNICAMP and USP. vi Agradecimentos A Deus pelo amor in¯nito, por ter me acompanhado e iluminado sempre a cada passo e por tudo que eu tenho recebido dele. A professora Claudia Bauzer Medeiros, pelo privil¶egiode t^e-lacomo orientadora. Obri- gada pela con¯an»ca,aten»c~aoe paci^enciaao longo de todo o meu mestrado. Agrade»copelos ensinamentos e as cr¶³ticasque permitiram explorar melhor meu pot^encial. A toda minha fam¶³lia, por sempre ter me oferecido todo o seu apoio e carinho. Agrade»coem especial a minha m~aee irm~aspor todo o amor, for»ca,e por sempre ter acreditado em mim. Aos meus tios Lucho, Gladys e fam¶³liaque estiveram presentes desde os in¶³ciosda minha carreira. Obrigada por todo o carinho e compreens~ao. A todos os meus amigos, deste maravilhoso pais, Brasil, que me acolheram com carinho e compartilharam comigo momentos inesquec¶³veis. Por toda sua bondade, amizade e paci^encia,muito obrigada. Aos meus amigos e colegas do Laborat¶oriode Sistemas de Informa»c~ao(LIS), pelas contribui»c~oes,sugest~oese inumeras corre»c~oes,que ajudaram no desenvolvimento desta disserta»c~ao. Aos meus amigos que est~aodistantes, que mesmo `adist^anciasouberam me motivar e ofereceram sempre o melhor dos seus conselhos. Aos bi¶ologosparceiros do projeto BioCORE, que contribu¶³ram com informa»c~oese sugest~oesno decorrer deste trabalho. As ag^enciasde fomento CAPES, CNPq e Microsoft Research, pelo suporte ¯nanceiro no desenvolvimento deste trabalho. vii Lista de Abrevia»c~oes ABCD: Access Biological Colections Data. BIO-CORE: Biodiversity and Computing Research. BioCase: Biological Collection Access Services. DiGIR: Distributed Generic Information Retrieval. EML: Ecological Metadata Language. FGDC: Federal Geographic Data Committee. GBIF: Global Biodiversity Information Facility. ITIS: Integrated Taxonomic Information System. NBII: National Biological Information Infrastructure. OBIS-SEAMAP: Ocean Biogeographic Information System Spatial Ecological Analysis of Megavertebrate Populations. OGC: Open Geospatial Consortium. TAPIR: TDWG Access Protocol for Information Retrieval. TDWG: Taxonomic Database Working Group. WeBIOS: Web Service Multimodal Tools for Biodiversity Research, Assessment and Monitoring. WOODS: WOrkflOw-based Spatial Decision Support System. viii Sum¶ario Resumo v Abstract vi Agradecimentos vii 1 Introdu»c~ao 1 2 Trabalhos Correlatos 4 2.1 Aplica»c~oespara o gerenciamento de informa»c~aoem Biodiversidade . 5 2.2 Mecanismos para dissemina»c~aoe compartilhamento de informa»c~aona In- ternet . 9 2.2.1 Padr~oesde Metadados para biodiversidade . 9 2.2.2 Protocolos para compartilhamento de dados de biodiversidade . 10 2.3 O projeto BIO-CORE . 13 2.4 Resumo . 15 3 Modelo Proposto para Armazenamento de Dados de Biodiversidade 16 3.1 Vis~aoGeral . 16 3.1.1 Cen¶arioGen¶ericopara o Modelo . 17 3.1.2 Cen¶ariosde Trabalho dos usu¶ariosde BioCore . 18 3.2 O Modelo de Banco de Dados proposto para o BioCore . 21 3.3 Exemplos de Consultas . 27 3.4 Exemplo da informa»c~aoarmazenada pelos usu¶arios . 28 3.5 Resumo . 36 4 O Servi»code Coletas 38 4.1 Vis~aoGeral . 38 4.2 Especi¯ca»c~aodo Servi»co . 39 4.2.1 Opera»c~oesde prop¶ositogeral . 40 ix 4.2.2 Opera»c~oesespec¶³¯cas . 41 4.3 Descri»c~aodos tipos de usu¶ariosque interagem com o Servi»co . 43 4.4 Descri»c~aodo Funcionamento do Servi»co. 44 4.5 Resumo . 49 5 Aspectos de Implementa»c~ao 50 5.1 Implementa»c~aodo Banco de Dados Proposto . 50 5.2 Implementa»c~aodas Consultas . 51 5.2.1 Consultas simples . 52 5.2.2 Consultas complexas . 53 5.3 Implementa»c~aodo Servi»co . 57 5.4 Resumo . 59 6 Conclus~oese Extens~oes 60 Bibliogra¯a 63 A Dicion¶ariode Dados 68 x Lista de Tabelas 2.1 Tabela das principais caracter¶³sticasdas aplica»c~oesde biodiversidade . 8 2.2 Exemplos de campos do padr~aoDarwin Core, retirado de [30] . 10 3.1 Elementos de interesse do padr~aoDarwin Core . 22 3.2 Informa»c~aodas Amostras coletadas . 29 3.3 Informa»c~aodo Substrato da Amostra - no banco de dados as especializa»c~oes da entidade Substrato s~aotratadas em uma s¶otabela . 29 3.4 Taxonomia da Planta, substrato da amostra (taxonomia retirada do ITIS [28]) . 30 3.5 Informa»c~aodo lote de esp¶eciesretirado da amostra . 31 3.6 Taxonomia do lote de insetos (taxonomia retirada do ITIS [28]) . 31 3.7 Informa»c~aodo Habitat do local onde foi coletada a amostra . 31 3.8 Informa»c~aoda localiza»c~aoda amostra coletada . 32 3.9 Informa»c~aogeral relacionada `alocaliza»c~aoda amostra . 32 3.10 Informa»c~aodos pesquisadores que realizaram a coleta . 32 3.11 Informa»c~aodo cat¶alogo. 33 3.12 Informa»c~aoda taxonomia da esp¶ecie(taxonomia retirada do ITIS [28]) . 34 3.13 Informa»c~aoda localiza»c~aoda esp¶eciecatalogada . 35 3.14 Informa»c~aogeral relacionada `alocaliza»c~ao . 35 3.15 Informa»c~aodo habitat da esp¶eciecatalogada . 35 3.16 Informa»c~aodo projeto ao qual pertence a esp¶eciecatalogada . 36 3.17 Informa»c~aoda metodologia adotada para coletar esp¶ecie . 36 3.18 Informa»c~aodo pesquisador que realizou a coleta . 36 4.1 Resultado parcial da consulta (a) . 46 4.2 Continua»c~ao:Resultado parcial da consulta (a) . 47 4.3 Resultado parcial da consulta (b) . 48 5.1 Resultado da consulta . 53 5.2 Continua»c~ao:Resultado da consulta . 53 5.3 Resultado da consulta . 54 xi 5.4 Resultado da consulta . 55 5.5 Resultado da consulta . 56 5.6 M¶etodos de prop¶ositogeral do servi»code Coletas . 58 5.7 M¶etodos de prop¶ositoespec¶³¯codo servi»code Coletas . 58 xii Lista de Figuras 2.1 Mapeamento da Fonte de Dados para a Camada de Abstra»c~ao,inspirado em [53] . 12 2.2 Arquitetura do Sistema BIO-CORE, retirado de [1] . 14 3.1 Representa»c~aodo cen¶ariogeral dos procedimentos de coleta e cataloga»c~ao - c¶opiade tela do WOODSS [47] .
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