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

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

dora@cria.org.br

www.cria.org.br