SinBIOTA 2.0: Planning a New Generation Environmental Information System

Prof. Carlos A. Joly & Prof.João Meidanis

University of Campinas & Scylla Bioinformatics

250,000 Km2

97,656 sq.m

720 km coast

Sao Paulo State

Sao Paulo State• Development rates close to Spain,

France, Germany, Italy, UK• 41,541,191 inhabitants (22% of Brazil)• US$ 450 billion GDP (33,4% of Brazil)• US$ 10,800.00/year per capita income• 42% of Brazilian exports• Brazilian’s biggest sugar cane producer:

270 million t/y = US$ 5.65 billion/2007 (expected to increase 50% in five years)

www.biota.org.br

Based on the Convention of Biological Diversity

MARCH 1999

Taxonomic group

Number of records

Number of species

Higher plants 62600 5463

Mammals 8062 149

Reptiles 431 74

Birds 19742 520

Amphibians 17531 168

Fish 11620 349

Sample of BIOTA Data Records

Guidelines for biodiversity conservation and restoration in the State of São Paulo.

The map produced by the BIOTA/FAPESP Program was adopted by the State Secretary of Agriculture to prohibit sugar cane expansion in the areas prioritize by the program for biodiversity conservation and

restoration.

Database of geo-referenced Sao

Paulo’s Biodiversity

102.704 records 11.820 species

SinBIOTA

SinBIOTA: shortcomings

• hard to expanded with new modules• not portable• hard to replicate for other states or

regions• need to check geographic coordinates

for species occurrences• need to check spelling of species names

SinBIOTA 2.0: Plan for evolution

• Reference Document - Specification• Public call for implementation groups• Implementation (possibly one module at

a time)

Community Meeting: 2009

• 300+ researchers and students• discussion of future directions for the

BIOTA Program• 2 full days• resulted in “Science Plan & Strategies

for the Next decade”• suppl. material of Science paper

Community requirements

• Import all data from current system• Must be easily replicable and portable,

to allow use in other states and regions• Must be easily expandable, to allow

future inclusion of new modules

Community requirements (cont.)

• Built in dictionary of species names, to avoid mistakes due to misspeling

• Built in mechanism of data auditory, to avoid mistakes due to wrong geographic coordinates

• Import/export mechanisms to/from specialized tools (species distribution, niche modeling, etc.)

TOOLS

MaxEnt

Open Modeler

DIV

A G

is

Expand carthographic base

Full interoperability

Fapesp/Microsoft Research

• Two-year, jointly funded project• Started Decembro 2009• Goals:

– Reference Document (specification) for SinBIOTA 2.0

– Implementation of prototype for SinBIOTA 2.0

• Visits to users to get feedback• Study of GBIF, OBIS, ALA, EOL, etc.• Scalability and security of large DBs• Multimodal data and search• Survey of map systems• Specialized tools (sp. distribution, etc.)• Data mining, knowledge discovery• Use of mobile clients• Cloud computing• Social networks

Reference Document: topics

Current Database Schema

• Lack of integrity constraints

• Each taxon rank as individual table

Class Modeling + Object-Relational Mapping

New Database Schema

Each taxon group is a row in Taxon tableRank is attribute of taxon groupExplicit parent / child relationship

Taxonomy Class/Table

System architecture: prototype

Implementation with Bing Maps

Heat Map with Population

Color Map

United Nations' Human Development Index

Auto-complete

Cited links• www.biota.org.br• www.biotaneotropica.org.br• sinbiota.cria.org.br• bioenfapesp.org• biota.cna.unicamp.br/bioprospecta• DOI: 10.1126/science.1188639

www.mp.sp.gov.br/portal/page/portal/cao_urbanismo_e_meio_ambiente/atos/Ato-PGJ-565-09-metas-GAEMA.doc

www.cetesb.sp.gov.br/licenciamentoo/legislacao/estadual/resolucoes/2009_Res_SMA_15.pdf

www.ambiente.sp.gov.br/zoneamentoagroambientalcana.pdf

DankeschönThank you !Thank you !