SinBIOTA 2.0: Planning a New Generation Environmental Information System
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Transcript of SinBIOTA 2.0: Planning a New Generation Environmental Information System
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SinBIOTA 2.0: Planning a New Generation Environmental Information System
Prof. Carlos A. Joly & Prof.João Meidanis
University of Campinas & Scylla Bioinformatics
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250,000 Km2
97,656 sq.m
720 km coast
Sao Paulo State
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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)
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www.biota.org.br
Based on the Convention of Biological Diversity
MARCH 1999
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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
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Guidelines for biodiversity conservation and restoration in the State of São Paulo.
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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.
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Database of geo-referenced Sao
Paulo’s Biodiversity
102.704 records 11.820 species
SinBIOTA
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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
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SinBIOTA 2.0: Plan for evolution
• Reference Document - Specification• Public call for implementation groups• Implementation (possibly one module at
a time)
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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
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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
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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.)
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Expand carthographic base
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Full interoperability
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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
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• 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
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Current Database Schema
• Lack of integrity constraints
• Each taxon rank as individual table
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Class Modeling + Object-Relational Mapping
New Database Schema
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Each taxon group is a row in Taxon tableRank is attribute of taxon groupExplicit parent / child relationship
Taxonomy Class/Table
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System architecture: prototype
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Implementation with Bing Maps
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Heat Map with Population
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Color Map
United Nations' Human Development Index
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Auto-complete
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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
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DankeschönThank you !Thank you !
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