1 / 35

species Link A System for integrating distributed primary biodiversity data Vanderlei Perez Canhos

species Link A System for integrating distributed primary biodiversity data Vanderlei Perez Canhos Centro de Referência em Informação Ambiental, CrIA. Overview. CRIA SinBiota and The Species Analyst speciesLink Type of collections involved Number of records Technical features

frey
Download Presentation

species Link A System for integrating distributed primary biodiversity data Vanderlei Perez Canhos

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  1. speciesLink A System for integrating distributed primary biodiversity data Vanderlei Perez Canhos Centro de Referência em Informação Ambiental,CrIA

  2. Overview • CRIA • SinBiota and The Species Analyst • speciesLink • Type of collections involved • Number of records • Technical features • Future plans

  3. Focus on Biodiversity Informatics • Open source software • Standards and protocols • Systems interoperability • Partnerships CrIAReference Center on Environmental Informationhttp://www.cria.org.br

  4. http://speciesanalyst.net/ Location of participant collections:mainly United States Taxonomic groups:several taxa Protocol:Z39.50 (migration to DiGIR on process) Number of records:~ 50.000.000

  5. Paris British Museum KU – Natural History Museum Field Museum Importance of data sharing

  6. The main goal ofspeciesLinkwas to build a distributed system integrating several biological collections and making their primary data available on the Internet. speciesLinkDistributed Information System for Biological Collections http://splink.cria.org.br

  7. São Paulo State Collections fish: 3 mites: 2 herbaria: 4 microorganisms: 3 inventories: SinBiota Geographic distribution of the participant collections – phase I

  8. Number of Records

  9. Collection Management Software

  10. Support to collections • Providing basic equipment and network infrastructure • Helping to choose a management system, when needed • Helping to train and to import data, when needed

  11. Protocol and Content Schema • DiGIR protocol (Distributed Generic Information Retrieval) Potential to be globally accepted • DiGIR software (Java Portal & PHP Provider) Collaborative development • DarwinCore v.2 Covers the basic content elements (taxonomic identification, location and date of collecting event)

  12. Simple Search Interface

  13. Collection A Regional Server Data Postgres PHP Provider PHP Provider SQL SQL Collection Management System SOAP Server Collection B Collection C Data Data SOAP client SOAP client SQL SQL CollectionManagementSystem CollectionManagementSystem Data Repository Data Repository DiGIRPortal (Java) speciesLink site Presentation Layer System’s Architecture Perl Fast and stable connectivity Slow or unstable connectivity

  14. Network Design RegionalServer RegionalServer RegionalServer RegionalServer

  15. Regional Server Collection A Data Postgres PHP Provider PHP Provider SQL SQL Collection Management System SOAP Server DiGIRPortal (Java) speciesLink site Presentation Layer System’s Architecture Perl Fast and stable connectivity Slow or unstable connectivity Collection B Collection C Data SOAP client Data SOAP client SQL SQL CollectionManagementSystem CollectionManagementSystem Data Repository Data Repository

  16. Data Migration Client • Platform independent (java) • Connects to any database accessible via JDBC (simple text files are also supported) • Complete control over data • Low traffic • Possibility to filter sensitive data using a regular expression

  17. Collection A Data PHP Provider SQL Collection Management System DiGIRPortal (Java) speciesLink site Presentation Layer System’s Architecture Perl Fast and stable connectivity Regional Server Postgres PHP Provider SQL SOAP Server Slow or unstable connectivity Collection B Collection C Data SOAP client Data SOAP client SQL SQL CollectionManagementSystem CollectionManagementSystem Data Repository Data Repository

  18. Postgres Provider PHP SQL SOAP Server (perl) Regional server Features • perl / PostgreSQL combination • Can hold data from several collections • Interpretation rules can be applied to specific data

  19. Query Result (brief)

  20. speciesLink – phase II

  21. >35 collections available

  22. Future plans • Mapping tools

  23. Future plans • Mapping tools • Data cleaning tools

  24. Future plans • Mapping tools • Data cleaning tools • Modelling framework

  25. Neural Net Bioclim Vegetation GARP ACME DiGIR Portal BioCASE Portal Precipitation Temperature Modelling algoritms Environmental layers specimens Infrastructure for Species Distribution Modelling

  26. Acknowledgements (phase I) Instituto de Botânica Universidade Estadual de Campinas Universidade Estadual Paulista Instituto Agronômico de Campinas Escola Superior de Agricultura “Luiz de Queiroz” Instituto Biológico Universidade de São Paulo

  27. Fellowships • Visiting researchers • Andrew Townsend Peterson (3 months) • Arthur Chapman (1 year) • Pos-doctor • Ingrid Koch • Technical training (6 TT fellowships)

  28. Summing up • Achieved proof of concept • Data is already available • Low cost for connecting new collections • Triggered off a movement within the collections to improve the quality of data and to increase the amount of available information • Adoption of standards and protocols • International partnerships: DiGIR, modelling framework • Interoperability with similar initiatives

  29. Thank you! http://splink.cria.org.br vcanhos@cria.org.br

More Related