Biodiversity Informatics: CRIA’s Experience
Dora Ann Lange Canhos
[email protected]
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.
Decision making
•
•
•
•
conservation
managing
sustainable use
restoration, rehabilitation
Policies and
Strategies
action
knowledge
information
Challenge:
increase the use
of scientific data
about biodiversity
data
observation
real world
• 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/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.
April/2006
Projects
“Authors”
Users
Surveys
“names”
unique
“names”
Environmental Information System: field surveys
http://sinbiota.cria.org.br
76
755
219
12,396
90,504
10,386
Maps
Map service
User
Web server
Database
Biota program
researcher
Web Interface
Field records and
associated species list
Atlas SinBiota
Collections at Smithsonian, NMNH
Photos: Chip Clark
speciesLink site
DiGIR
Portal
Lib
DiGir
Presentation Layer
Fast and stable connectivity
Regional Server
Collection A
SQL
Data
Provider
PHP
Collection
Management
System
Data
Postgres
SQL
Provider
PHP
Mirror
SOAP server
Slow or unstable connectivity
Collection B
SQL
Data
Collection
Management
System
Collection C
spLinker
Java
Data
Repository
SQL
Data
Collection
Management
System
spLinker
Java
Data
Repository
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
SinBiota
B
Col. Culturas de Fitobactérias
Lab. De Bacteriologia Vegetal
Instituto Biológico,
Campinas
Herbário do
Jardim Botânico do
Rio de Janeiro
Coleção de Quirópteros
Dept. Zoologia e
Botânica, UNESP,
São José do Rio Preto
Herbário do Instituto
Agronômico de
Campinas
Z
Coleção de Anfíbios do
Instituto de Biociências
UNESP, Rio Claro
Z
Servidor
Regional
Coleção de Acari
Museu de Zoologia,
ESALQ, Piracicaba
Z
Servidor
Regional
Herbário do Departamento
De Ciências Biológicas da
ESALQ, Piracicaba
B
Z
Z
Servidor
Regional
Servidor
Regional
Z
Z
Servidor
Regional
Servidor
Regional
B
B
Z
Herbário do Instituto de
Biociências, UNESP,
Botucatu
B
Herbário da UNICAMP,
Campinas
B
M
B
Coleção de Peixes
Dept. Zoologia e
Botânica, UNESP,
São José do Rio Preto
Coleção de Anfíbios
Dept. Zoologia e
Botânica, UNESP,
São José do Rio Preto
B
Herbário do Instituto de Biociências, UNESP
Rio Claro
B
Coleção de Peixes do
Laboratório de
Ictiologia, USP,
Ribeirão Preto
Coleção de Acari
Dept. Zoologia e
Botânica, UNESP,
São José do Rio Preto
M
M
ZB
Sistema de Informação
Ambiental do Programa
Biota - Fapesp
Coleção de Microrganismos de
Ambiente e Indústria, UNICAMP
Campinas
Coleção Científica de
Aranhas do Dept. Zoologia
e Botânica, UNESP,
Botucatu
B
Z
Z
Herbário da USP,
São Paulo
Coleção de Peixes
Museu de Zoologia da USP,
São Paulo
M
Coleção de Fungos
Instituto de Botânica,
São Paulo
B
Coleção de Algas
Instituto de Botânica,
São Paulo
Coleção de Fanerógamas
Herbário do Instituto de Botânica,
São Paulo
Herbário Dom Bento Pickel
do Instituto Florestal,
São Paulo
Herbário de Ilha Solteira, UNESP
Ilha Solteira
Coleção do Museu
de Entomologia da FEIS/UNESP
Ilha Solteira
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
Partners in Brazil
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
[email protected]
www.cria.org.br