species species Link & openModeller: Link & openModeller: network and tool enabling network and tool enabling biodiversity research biodiversity research Renato De Giovanni, Alexandre Marino, Sidnei de Souza, Dora A.L. Canhos, Marinez F. de Siqueira, Vanderlei P. Canhos TDWG 2008
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species Link & openModeller : network and tool enabling biodiversity research
Renato De Giovanni, Alexandre Marino, Sidnei de Souza, Dora A.L. Canhos, Marinez F. de Siqueira, Vanderlei P. Canhos TDWG 2008. species Link & openModeller : network and tool enabling biodiversity research. Reference Center on Environmental Information. - PowerPoint PPT Presentation
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speciesspeciesLink & openModeller:Link & openModeller:network and tool enabling biodiversity researchnetwork and tool enabling biodiversity research
Renato De Giovanni, Alexandre Marino, Sidnei de Souza, Dora A.L. Canhos,
Marinez F. de Siqueira,
Vanderlei P. Canhos
TDWG 2008
Reference Center on Environmental InformationReference Center on Environmental Information
Brazilian not-for-profit, non-governmental organization that aims to contribute towards a more sustainable use of Brazil's biodiversity through dissemination of high quality information.
Develop a distributed information system to retrieve primary
biodiversity data from biological collections. Develop mapping, data cleaning and niche modelling tools using data
from the network.
Support from the projectSupport from the project Basic equipment and network infrastructure. Scholarships to help digitizing specimen data. Assistance to choose collection management software, install it, train
users and import data.
speciesspeciesLink evolutionLink evolution
TDWG 2003
~100k records
12 collections
TDWG 2008
~3M records
~150 collections and
subcollections
speciesspeciesLink evolutionLink evolution
~45% of the records with coordinates
speciesspeciesLink statisticsLink statistics
66% Plants
28% Animals
5% “broad scope”
1% microorganisms 85% from Brazilian collections
15% from foreign collections
RegionalServer
RegionalServer
RegionalServer
RegionalServer
Evolution of network designEvolution of network design
spLinker – uploading data to regional serversspLinker – uploading data to regional servers
Original features: Platform independent (Java). Database independent (no particular data model required - RDBMS
accessible through JDBC, CSV files supported). Complete control over data. After initial upload, only updates are sent. Possibility to filter sensitive data.
New features: Automatic updates. Mappings for most collection management software are available.
Additional tools – data cleaningAdditional tools – data cleaning
openModelleropenModeller
Open source C++ framework for
potential distribution modelling. First prototype developed as part of
the speciesLink project. Basis of a new thematic project
funded by Fapesp (2006 – 2009)
involving CRIA, INPE, Poli-USP. Also developed in collaboration with other institutions: University of
Kansas and University of Reading. Used by the GBIF portal, Life Mapper, GEOSS, BDWorld, Species
Population Loss Meter.
Potential distribution modelling – model creationPotential distribution modelling – model creation
Occurrence data
Distribution model(environmental space)
Tem
pera
ture
Precipitation
Environmental layers
algorithm
Potential distribution modelling – model projectionPotential distribution modelling – model projection
Environmental layers Potential Distribution map
Tem
pera
ture
Precipitation
Distribution model
Potential distribution modelling can be used to...Potential distribution modelling can be used to...
Search for rare or endangered species. Plan conservation areas. Predict the impact of climate change on biodiversity. Prevent the spread of invasive species. Identify disease vectors. Increase agricultural productivity. Others...
Work with multiple algorithms. Allow different interfaces on top of the same library. Support different input formats (for both points and rasters). Platform independent (runs on GNU/Linux, Mac OSX and
Windows).
Multiple algorithmsMultiple algorithms
Minimum distance
Bioclim
Distance to average
GARP Best Subsets
openModeller interfacesopenModeller interfaces
local files GBIF local files
Occurrence data (points) Environmental data (rasters)
openModeller
Algorithm 1
Algorithm 2
Algorithm n
Interfaces (desktop, command line, web service, etc.)