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Integrating Biodiversity Datasets - the case of GBIF

Integrating Biodiversity Datasets - the case of GBIF. Éamonn Ó Tuama GBIF Secretariat, Universitetsparken 15 DK-2100 Copenhagen Ø Denmark email: eotuama@gbif.org. gbif.data.org. Outline. Role of GBIF in biodiversity informatics. The GBIF architecture.

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Integrating Biodiversity Datasets - the case of GBIF

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  1. Integrating Biodiversity Data – the Case of GBIF EIONET, Oct 30, 2007, Copenhagen Integrating Biodiversity Datasets - the case of GBIF Éamonn Ó Tuama GBIF Secretariat, Universitetsparken 15 DK-2100 Copenhagen Ø Denmark email: eotuama@gbif.org gbif.data.org

  2. Integrating Biodiversity Data – the Case of GBIF EIONET, Oct 30, 2007, Copenhagen Outline Role of GBIF in biodiversity informatics The GBIF architecture GBIF web services & geospatial web Using GBIF mediated data - Indicators of Compliance with 2010 Target Assessment of Climate Change Impact

  3. Integrating Biodiversity Data – the Case of GBIF EIONET, Oct 30, 2007, Copenhagen 4 Themes Informatics Content Participation Campaigns Digitisation of natural history collections (DIGIT) Electronic catalogue of names of known organisms (ECAT) Outreach and capacity building (OCB) Building regional and local infrastructure (NODES) Data access and database interoperability (DADI) GBIF has five main programmes of work GBIF Secretariat, Universitetsparken 15, DK-2100 Copenhagen Ø

  4. Integrating Biodiversity Data – the Case of GBIF EIONET, Oct 30, 2007, Copenhagen

  5. Integrating Biodiversity Data – the Case of GBIF EIONET, Oct 30, 2007, Copenhagen http://www.tdwg.org/

  6. Integrating Biodiversity Data – the Case of GBIF EIONET, Oct 30, 2007, Copenhagen • Taxon names • Taxon occurrence information • specimen records from natural history collections • observational records Core data types on GBIF network • Mandatory • Scientific name • Institutional code • Collection code • Catalogue number • Highly desirable • Geospatial location • Collection date • Higher taxon info • Date last modified Fields used in indexing records

  7. Integrating Biodiversity Data – the Case of GBIF EIONET, Oct 30, 2007, Copenhagen

  8. Integrating Biodiversity Data – the Case of GBIF EIONET, Oct 30, 2007, Copenhagen index metadata data cache logging Components of GBIF Architecture data portal request handling web services query engine registry institutions providers services name providers data providers datasets datasets metadata metadata

  9. Integrating Biodiversity Data – the Case of GBIF EIONET, Oct 30, 2007, Copenhagen

  10. Integrating Biodiversity Data – the Case of GBIF EIONET, Oct 30, 2007, Copenhagen http:/data.gbif.org

  11. Integrating Biodiversity Data – the Case of GBIF EIONET, Oct 30, 2007, Copenhagen

  12. Integrating Biodiversity Data – the Case of GBIF EIONET, Oct 30, 2007, Copenhagen

  13. Integrating Biodiversity Data – the Case of GBIF EIONET, Oct 30, 2007, Copenhagen Web Services Software applications that run over the internet and use some kind of standardised message passing system to handle request and response, usually based on XML.

  14. Integrating Biodiversity Data – the Case of GBIF EIONET, Oct 30, 2007, Copenhagen occurrence record data http://data.gbif.org/ws/rest/occurrence occurrence density data taxon data http://data.gbif.org/ws/rest/taxon http://data.gbif.org/ws/rest/density http://data.gbif.org/ws/rest/resource http://data.gbif.org/ws/rest/provider dataset metadata data provider metadata http://data.gbif.org/ws/rest/network data network metadata GBIF Data Portal Web Services

  15. Integrating Biodiversity Data – the Case of GBIF EIONET, Oct 30, 2007, Copenhagen GBIF Occurrence Web Service http://data.gbif.org/ws/rest/occurrence/ <action>?<parameter_list> Main actions: Get, List, Count Parameter list: key-value pairs http://data.gbif.org/ws/rest/occurrence/list? scientificname=Ensis+ensis&format=darwin-1.2 http://data.gbif.org/ws/rest/occurrence/get/801914

  16. Integrating Biodiversity Data – the Case of GBIF EIONET, Oct 30, 2007, Copenhagen

  17. Integrating Biodiversity Data – the Case of GBIF EIONET, Oct 30, 2007, Copenhagen GBIF Occurrence Web Service Parameter list: keys minlongitude maxlongitude cellid georeferencedonly hostisocountrycode originisocountrycode startdate enddate scientificname taxonconceptkey dataproviderkey datasourcekey resourcenetworkkey basisofrecord minlatitude maxlatitude modifiedsince startindex maxresults format icon mode stylesheet http://data.gbif.org/ws/rest/occurrence

  18. Integrating Biodiversity Data – the Case of GBIF EIONET, Oct 30, 2007, Copenhagen Open Geospatial Consortium (OGC) Web Services Web Map Service Web Feature Service (TDWG GML1 application schema) Web Coverage Service 1Geography Markup Language

  19. Integrating Biodiversity Data – the Case of GBIF EIONET, Oct 30, 2007, Copenhagen data data data Web Map Service Web Feature Service Web Coverage Service integrating national and thematic portals Coastlines, Marine areas, Remote sensing imagery Occurrences, Names Meteorological, Oceanographic The Geospatial Web

  20. Integrating Biodiversity Data – the Case of GBIF EIONET, Oct 30, 2007, Copenhagen • Ecological Niche Modelling • a modelling technique for defining the ecological requirements of a species – its ecological niche • many different algorithms in use (e.g. Maxent, GARP) • an algorithm uses a set of environmental variables (e.g. topographic, climatic) to define the ecological niche • once the ecological niche is defined it can then be used to query a set of environmental conditions (e.g. as predicted by a climate change model) to determine the potential distribution of the species • outputs as maps, statistics • Source:http://www.gbif.org/GBIF/zdepot/ReportonTarget2010Oct27.pdf

  21. Integrating Biodiversity Data – the Case of GBIF EIONET, Oct 30, 2007, Copenhagen • GBIF mediated data can, in principle, be used, in pursuit of CBD 2010 objectives - • to provide indices of “trends in the abundance and distribution of selected species” • to develop indices of any kind of “selected species” • to develop indices at national, regional or global levels • Source:http://www.gbif.org/GBIF/zdepot/ReportonTarget2010Oct27.pdf

  22. Integrating Biodiversity Data – the Case of GBIF EIONET, Oct 30, 2007, Copenhagen GBIF mediated data can be used to develop temporally-organised indicators to measure the effects of land-use change on the distribution of species Change in distributional area of species over time • Source:http://www.gbif.org/GBIF/zdepot/ReportonTarget2010Oct27.pdf

  23. Integrating Biodiversity Data – the Case of GBIF EIONET, Oct 30, 2007, Copenhagen Source: Predicting the impact of climate change on biodiversity – a GEOSS scenario. Nativi et al. In “The Full Picture, A publication for the GEO Ministerial Summit, ‘Earth Observation for Sustainable Growth and Development’ Cape Town, 30 November 2007” Climate Change Using GBIF mediated data can be used to measure the impact of climate change on species distributions Working within the GEOSS / GMES framework

  24. Integrating Biodiversity Data – the Case of GBIF EIONET, Oct 30, 2007, Copenhagen The species has expanded its range over time Species can be highly responsive to climate change Source: Predicting the impact of climate change on biodiversity – a GEOSS scenario. Nativi et al. In “The Full Picture, A publication for the GEO Ministerial Summit, ‘Earth Observation for Sustainable Growth and Development’ Cape Town, 30 November 2007” Climate Change Distribution of Vanessa atalanta a) distribution derived from historical observations of climate, land use, and species location from 1900-1930 b) distribution derived from models run on the same data from 1960-1990 a b Vanessa atalanta; Photo by Jeremy T.Kerr – August 1, 2005. Ottawa, Ontario

  25. Integrating Biodiversity Data – the Case of GBIF EIONET, Oct 30, 2007, Copenhagen Acknowledgements The modelling scenarios in this presentation are based on publications by Peterson & Soberón1 and Nativi et al.2 Development of indicators of compliance with the 2010 target of the convention on biological diversity using primary biodiversity data provided by GBIF. A.T.Peterson & J. Soberón. http://www.gbif.org/GBIF/zdepot/ReportonTarget2010Oct27.pdf 1 data.gbif.org Predicting the impact of climate change on biodiversity – a GEOSS scenario. Nativi et al. In “The Full Picture, A publication for the GEO Ministerial Summit, ‘Earth Observation for Sustainable Growth and Development’ Cape Town, 30 November 2007” 2 Thank you

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