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Biodiversity Informatics: CRIA’s Experience

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Apresentação em tema: "Biodiversity Informatics: CRIA’s Experience"— Transcrição da apresentação:

1 Biodiversity Informatics: CRIA’s Experience
Dora Ann Lange Canhos

2 Institutional Mission
Dissemination of scientific and technological information and the promotion of education with a view of contributing towards a more sustainable use of Brazil's natural resources.

3 Aim Make scientific data and information useful and “useable” in a way that it can be incorporated in the definition of local, regional and national strategies for conservation and sustainable use of natural resources.

4 Decision making Policies and Strategies conservation managing
sustainable use restoration, rehabilitation Policies and Strategies government industry individuals action knowledge information Challenge: increase the use of scientific data about biodiversity data The real world - The natural and modified landscape Observations of the real world - Measurements, occurrences, photographs Collections from the real world - Herbarium specimens, living specimens Collated into datasets which are analysed in various ways to develop information and results which are interpreted and through that knowledge we can take decisions, we can implement and take actions Analysis of observations Visualization of analyses Interpretation of results observation real world

5 Building knowledge about biodiversity
Collective, multi and inter-disciplinary Requires a global cooperative environment Depends on a comparative data and knowledge base

6 Challenges for biodiversity informatics
Technical standardization, integration, validation, storage, recovery, analysis, synthesis, and dissemination of environmental data and information “usefulness” to non specialist communities Social help to promote “cultural” changes concerning data sharing establish partnerships promote open and free access to data on the Internet Sustainability project based versus long term support

7 CRIA’s Focus: biodiversity informatics
Data Focus on species and specimen data Content: through partnerships Freely and openly available information systems Tools: data providers Interoperability Data cleaning Data visualization Monitoring Tools: use Species distribution modeling




11 BIOTA/FAPESP The Virtual Institute of Biodiversity SinBiota (Atlas)
Biota Neotropica speciesLink Overall aim: inventory and characterize the biodiversity of the State of São Paulo, and define the mechanisms for its conservation and sustainable use.

12 April/2006 Projects 76 “Authors” 755 Users 219 Surveys 12,396
“names” ,504 unique 10,386 “names” Environmental Information System: field surveys

13 Freshwater Marine Terrestrial

14 associated species list
Maps Map service User Web server Web Interface Database Biota program researcher Field records and associated species list

15 Atlas SinBiota





20 Collections at Smithsonian, NMNH
Photos: Chip Clark Biodiversity collections form the best information available to assist in: supporting systematic and taxonomic research, understanding what lives where on the planet for a variety of purposes, e.g.: controlling invasive alien and pest spp., protecting endangered species, enabling countries to document, their biota and implement the CBD (Convention on Biological Diversity), understanding the anthropogenic impact on species distribution over the past 200+ years, and predict future distributions of species in light of different climate change models. The main mission of the NMNH is twofold: the caring for and improving the collections and passing along of these collections, in better condition that we received them, to the next generation of scientists, and research on the collections and the dissemination of the results of that research.


22 Regional Server Collection A Collection B Collection C DiGIR Portal
speciesLink site Presentation Layer DiGIR Portal Lib DiGir Fast and stable connectivity Regional Server Collection A Data SQL Provider PHP Data Postgres SQL Provider PHP Collection Management System Mirror SOAP server Slow or unstable connectivity Collection B Collection C Data SQL spLinker Java Data SQL spLinker Java Data Repository Data Repository Collection Management System Collection Management System

23 Platform independent (java)
Data Migration Client Platform independent (java) Connects to any database accessible via JDBC (simple text files are also supported) Complete control over data Low traffic Possibility to filter sensitive data using a regular expression

24 B M Z B B M Z B B Z B Z Z Z M B Z B Z B B B Z Z
Coleção de Microrganismos de Ambiente e Indústria, UNICAMP Campinas Herbário do Instituto de Biociências, UNESP Rio Claro B SinBiota Sistema de Informação Ambiental do Programa Biota - Fapesp M M ZB Coleção de Anfíbios do Instituto de Biociências UNESP, Rio Claro Herbário do Instituto Agronômico de Campinas Z B Herbário da UNICAMP, Campinas B Col. Culturas de Fitobactérias Lab. De Bacteriologia Vegetal Instituto Biológico, Campinas M Servidor Regional Z Coleção de Acari Museu de Zoologia, ESALQ, Piracicaba Herbário do Jardim Botânico do Rio de Janeiro B B Herbário do Departamento De Ciências Biológicas da ESALQ, Piracicaba Coleção de Peixes do Laboratório de Ictiologia, USP, Ribeirão Preto Z Servidor Regional Herbário da USP, São Paulo B Coleção de Peixes Dept. Zoologia e Botânica, UNESP, São José do Rio Preto Z Coleção de Peixes Museu de Zoologia da USP, São Paulo Z Servidor Regional Servidor Regional Coleção de Fungos Instituto de Botânica, São Paulo Coleção de Acari Dept. Zoologia e Botânica, UNESP, São José do Rio Preto Z M B Coleção de Algas Instituto de Botânica, São Paulo Coleção de Anfíbios Dept. Zoologia e Botânica, UNESP, São José do Rio Preto Z Servidor Regional B Coleção de Fanerógamas Herbário do Instituto de Botânica, São Paulo Servidor Regional Coleção de Quirópteros Dept. Zoologia e Botânica, UNESP, São José do Rio Preto Z B Herbário Dom Bento Pickel do Instituto Florestal, São Paulo Herbário de Ilha Solteira, UNESP Ilha Solteira B Herbário do Instituto de Biociências, UNESP, Botucatu B Coleção Científica de Aranhas do Dept. Zoologia e Botânica, UNESP, Botucatu Z Z Coleção do Museu de Entomologia da FEIS/UNESP Ilha Solteira

25 speciesLink – splink.cria.org.br
data providers (collections) have full control over their data (add, modify, remove) curators don’t have to change their routine or system because of the network and have complete liberty in selecting the software they want to use filters were developed to enable curators to block sensitive data tools were developed to help curators with data cleaning, visualization, ... a monitoring system accessible on the internet was developed study cases with ecological niche modeling were developed (data use)

26 Information management
Biological collections: what, where, who, when Tools: Managers (system, project, data): monitoring, indicators Provider: data cleaning; spatial visualization, collection profile, distribution, ... User: search, geographic distribution, modeling










36 Partners in Brazil

37 International Partners
Global Biodiversity Information Facility (GBIF) Kansas University California Academy of Science Museum of Vertebrate Zoology, Berkeley Biodiversity World Research groups from Australia and Europe

38 Centro de Referência em Informação Ambiental
Obrigada. Dora Ann Lange Canhos

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