Biodiversity Informatics: CRIA

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Biodiversity Informatics CRIAs Experience

• Dora Ann Lange Canhos
• dora_at_cria.org.br

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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.

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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.

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action
knowledge
information
Challenge increase the use of scientific data
about biodiversity
data
observation
real world
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Building knowledge about biodiversity

• Collective, multi and inter-disciplinary
• Requires a global cooperative environment
• Depends on a comparative data and knowledge base

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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

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CRIAs 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

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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.
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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
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Maps
Map service
User
Web server
Database
Biota program researcher
Field records and associated species list
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Atlas SinBiota
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DiGIRPortal
speciesLink site Presentation Layer
Lib DiGir
Fast and stable connectivity
Regional Server
Collection A
SQL
DataPostgres
ProviderPHP
SQL
ProviderPHP
Data
CollectionManagementSystem
MirrorSOAP server
Slow or unstable connectivity
Collection B
Collection C
Data
spLinkerJava
SQL
Data
spLinkerJava
SQL
Data Repository
Data Repository
CollectionManagementSystem
CollectionManagementSystem
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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

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Herbário do Instituto de Biociências, UNESP Rio
Claro
Coleção de Microrganismos de Ambiente e
Indústria, UNICAMP Campinas
B
M
SinBiota Sistema de Informação Ambiental do
Programa Biota - Fapesp
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
Coleção de Acari Museu de Zoologia, ESALQ,
Piracicaba
Z
Herbário do Jardim Botânico do Rio de Janeiro
B
Herbário do Departamento De Ciências Biológicas
da ESALQ, Piracicaba
B
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
M
Coleção de Acari Dept. Zoologia e Botânica,
UNESP, São José do Rio Preto
Z
Coleção de Algas Instituto de Botânica, São Paulo
B
Coleção de Anfíbios Dept. Zoologia e Botânica,
UNESP, São José do Rio Preto
Z
Servidor Regional
Coleção de Fanerógamas Herbário do Instituto de
Botânica, São Paulo
B
Servidor Regional
Herbário Dom Bento Pickel do Instituto
Florestal, São Paulo
B
Coleção de Quirópteros Dept. Zoologia e Botânica,
UNESP, São José do Rio Preto
Z
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
Coleção do Museu de Entomologia da
FEIS/UNESP Ilha Solteira
Z
Z
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speciesLink splink.cria.org.br

• data providers (collections) have full control
  over their data (add, modify, remove)
• curators dont 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)

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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

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Partners in Brazil
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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

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Centro de Referência em Informação Ambiental

• Obrigada.
• Dora Ann Lange Canhos
• dora_at_cria.org.br
• www.cria.org.br