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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.

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species Link & openModeller : network and tool enabling biodiversity research

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  1. Renato De Giovanni, Alexandre Marino, Sidnei de Souza, Dora A.L. Canhos, Marinez F. de Siqueira, Vanderlei P. Canhos TDWG 2008 speciesLink & openModeller:network and tool enabling biodiversity research

  2. Reference 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

  3. The speciesLink network Project started in 2002 with funding from Fapesp. splink.cria.org.br

  4. speciesLink 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 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.

  5. speciesLink evolution TDWG 2003 ~100k records 12 collections TDWG 2008 ~3M records ~150 collections and subcollections

  6. speciesLink evolution ~45% of the records with coordinates

  7. speciesLink statistics 66% Plants 28% Animals 5% “broad scope” 1% microorganisms 85% from Brazilian collections 15% from foreign collections

  8. Evolution of network design RegionalServer RegionalServer RegionalServer RegionalServer

  9. speciesLink regional servers

  10. spLinker – 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.

  11. Search interface

  12. Search results

  13. Search results

  14. Additional tools – collection's profile

  15. Additional tools – data cleaning

  16. openModeller • 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.

  17. Potential distribution modelling – model creation Temperature Precipitation Occurrence data Distribution model (environmental space)‏ algorithm Environmental layers

  18. Potential distribution modelling – model projection Temperature Precipitation Environmental layers Distribution model Potential Distribution map

  19. 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...

  20. openModeller 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).

  21. Multiple algorithms Minimum distance Distance to average GARP Best Subsets Bioclim

  22. openModeller interfaces

  23. openModeller architecture Interfaces (desktop, command line, web service, etc.)‏ plugins modelling, pre-analysis, post-analysis API Algorithm 1 data cleaning georeferencing openModeller Algorithm 2 occurrence data reader environmental data reader Algorithm n Environmental data (rasters)‏ Occurrence data (points)‏ GBIF TAPIR & DarwinCore local files local files TerraLib WCS

  24. Example 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

  25. Future 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.

  26. Thank you http:// splink . cria . org . br http:// openmodeller . sf . net renato (at) cria . org . br

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