species link & openmodeller : network and tool enabling biodiversity research

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