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Biodiversity Informatics: CRIA’s Experience
Dora Ann Lange Canhos
dora@cria.org.br
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.
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.
datadata
informationinformation
knowledgeknowledge
actionaction
Challenge: increase the use of scientific data about biodiversity
real world real world
observationobservation
Decision making• conservation• managing• sustainable use• restoration, rehabilitation
Policies and Strategies
• government• industry• individuals
Building knowledge about biodiversity
Collective, multi and inter-disciplinary Requires a global cooperative environment Depends on a comparative data and knowledge base
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
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
BIOTA/FAPESPBIOTA/FAPESP
The Virtual Institute of The Virtual Institute of
BiodiversityBiodiversity
Overall aim: inventory and characterize the biodiversity of the State of São Paulo, and define the mechanisms for its conservation and sustainable use.
• SinBiota (Atlas)SinBiota (Atlas)• Biota NeotropicaBiota Neotropica• speciesspeciesLinkLink
April/2006
Projects 76 “Authors” 755
Users 219
Surveys 12,396 “names” 90,504 unique 10,386
“names”
Environmental Information System: field surveys
http://sinbiota.cria.org.br
Web Interface
Biota programresearcher
Database
Maps
User
Map service
Web server
Field records andassociated species list
Atlas SinBiota
Collections at Smithsonian, NMNH
Photos: Chip Clark
speciesLink site
Presentation Layer
speciesLink site
Presentation Layer
DiGIRPortal
DiGIRPortal
DataProvider
PHP
CollectionManagement
System
SQL
Collection ACollection A
DataPostgres
ProviderPHP
MirrorSOAP server
SQL
Regional ServerRegional Server
DataspLinker
Java
CollectionManagement
System
SQL
Collection BCollection B
DataRepository
DataspLinker
Java
CollectionManagement
System
SQL
Collection CCollection C
DataRepository
LibDiGir
LibDiGir
Slow or unstable connectivity
Fast and stable connectivity
Data Migration ClientData 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
Servidor Regional
Servidor Regional
Servidor Regional
Servidor Regional
Z M
MZB
B
Z
Z
Z
Z
B
B
B
B
B
M
M
Herbário do InstitutoAgronômico deCampinas
Herbário da UNICAMP,Campinas
Coleção de AcariMuseu de Zoologia,ESALQ, Piracicaba
Herbário do DepartamentoDe Ciências Biológicas daESALQ, Piracicaba
Herbário da USP,São Paulo
Coleção de PeixesMuseu de Zoologia da USP,São Paulo
Coleção de FungosInstituto de Botânica,São Paulo
Coleção de AlgasInstituto de Botânica,São Paulo
Coleção de FanerógamasHerbário do Instituto de Botânica,São Paulo
Coleção de PeixesDept. Zoologia e
Botânica, UNESP,São José do Rio Preto
Coleção de AcariDept. Zoologia e
Botânica, UNESP,São José do Rio Preto
Coleção de Peixes doLaboratório deIctiologia, USP,Ribeirão Preto
Col. Culturas de FitobactériasLab. De Bacteriologia Vegetal
Instituto Biológico,Campinas
SinBiotaSistema de InformaçãoAmbiental do Programa
Biota - Fapesp
Coleção de Microrganismos deAmbiente e Indústria, UNICAMPCampinas
ZColeção de Anfíbios
Dept. Zoologia eBotânica, UNESP,
São José do Rio Preto
ZColeção de Quirópteros
Dept. Zoologia eBotânica, UNESP,
São José do Rio Preto
Servidor Regional
Servidor Regional
BHerbário do Instituto de
Biociências, UNESP,Botucatu
Z
BHerbário do Instituto de Biociências, UNESPRio Claro
Coleção de Anfíbios doInstituto de BiociênciasUNESP, Rio Claro
BHerbário de Ilha Solteira, UNESPIlha Solteira
ZColeção do Museude Entomologia da FEIS/UNESPIlha Solteira
Coleção Científica de Aranhas do Dept. Zoologia
e Botânica, UNESP,Botucatu
Z
BHerbário Dom Bento Pickeldo Instituto Florestal,São Paulo
BHerbário do
Jardim Botânico doRio de Janeiro
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)
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
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
Centro de Referência em Informação Ambiental
Obrigada.
Dora Ann Lange Canhos
dora@cria.org.br
www.cria.org.br
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