Post on 09-Feb-2016
description
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.
www.cria.org.br
The The speciesspeciesLink networkLink network
Project started in 2002 with funding from Fapesp.
splink.cria.org.br
speciesspeciesLink project goalsLink project goals
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
speciesspeciesLink regional serversLink regional servers
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.
Search interfaceSearch interface
Search resultsSearch results
Search resultsSearch results
Additional tools – collection's profileAdditional tools – collection's profile
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...
openModeller basic requirementsopenModeller basic requirements
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.)
data cleaninggeoreferencing
modelling, pre-analysis, post-analysis API
occurrencedata
reader
environmentaldata
reader
WCSTerraLib
openModeller architectureopenModeller architecture
plugins
TAPIR &DarwinCore
Example generated using the TAPIR driverExample generated using the TAPIR driver Selected a TAPIR service listed on GBIF's UDDI registry:
ECOCEAN Whale Shark Photo-identification Library. Used openModeller command line interface to generate a model
using all available points directly from the service.
Rhincodon typus
Future plansFuture plans
speciesLink: Migrate all data providers to use TAPIR. Expand the network to other Brazilian states.
openModeller: Include more algorithms (artificial neural networks). Develop a full featured web interface.
Thank youThank you
http:// splink . cria . org . brhttp:// openmodeller . sf . net
renato (at) cria . org . br