GLOBAL BIODIVERSITY

1. GLOBALBIODIVERSITY INFORMATIONFACILITY GBIF - From Prototype towards Full Operation Éamonn Ó Tuama, Vishwas Chavan, Markus Döring, Samy Gaiji, David Remsen, Tim Robertson GBIF Secretariat

2. What does GBIF do? • - emphasises participation and working through partners • - mobilises biodiversity data • - promotes standards to enable interoperability • - builds an informatics architecture • data provider / aggregator • - promotes capacity building • - catalyses development of analytical tools

3. GBIF Themes & Work Areas Nodes, Training, Communications, Outreach Participation GBIF Secretariat Informatics IDA1, DIGIT, ECAT, IIP2 1Inventory, Discovery, Access 2Informatics Infrastructure and Data Portal

4. GBIF Informatics Thematic Area Area Focus IDA 1 Standards, metadata, interoperability DIGIT Mobilisation of primary biodiversity data ECAT Global Names Architecture IIP 2 Integrated data publishing tools, GBIF portal, web services, decentralisation 1 Inventory, Discovery, Access 2 Informatics Infrastructure and Portal

5. GBIF Task Groups - New modus operandi - Replacement for standing Science Sub Committees - Time limited, defined task with report as outcome - Draw on broader community of experts - Examples: - Observational Data Task Group - Multimedia Resources Task Group Vishwas Chavan

6. Proof of Concept Demonstrated • - First five-year phase: 2002-2006 • - A global network is feasible • - Barriers: social rather than technical • - Key requirement: well designed informatics architecture • - Key requirement: enabled, committed Participants • - All benefit from contributing to “common good”

7. http:/data.gbif.org

9. http://data.gbif.org/countries/datasharing

10. Rich Internet Application

11. occurrence record data http://data.gbif.org/ws/rest/occurrence taxon data occurrence density data http://data.gbif.org/ws/rest/taxon http://data.gbif.org/ws/rest/density GBIF Web Services 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 Web Services Software applications that run over the internet and use a standardised message passing system to handle request and response, usually based on XML. GBIF's web services are based on the REST architecture style.

12. data data data Web Map Service Web Feature Service Web Coverage Service national and thematic portals The Geospatial Web - OGC1 Web Services Occurrences, Names Meteorological, Oceanographic Coastlines, Boundaries, Remote sensing imagery Prototype OGC web services developed by GBIF: • Web Map Service • Web Feature Service (TDWG GML2 application schema)‏ 1Open Geospatial Consortium 2Geography Markup Language

14. Species Response to Climate Change The range of the common roadside skipper (Amblyscirtes vialis) will move about 300 km northwards by 2050 under the most conservative IPCC climate change scenario (B1)‏ Ref: 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”

15. Number of Occurrence Records Indexed

16. Poster A scalable, distributed network of Participants Challenge • Meeting requirements of Participants in terms of growth, scalability, capacity, visibility Strategy • Developing a full suite of IT infrastructure, architecture, services and tools Key components • GBRDS, IPT, GNA, Harvesting Indexing Toolkit, Nodes Portal Toolkit

17. Key Informatics Components • - Global Biodiversity Resources Discovery System (GBRDS) • - Integrated Publishing Toolkit (IPT) • - Global Names Architecture (GNA) • - Harvesting Indexing Tool • - Node Portal Toolkit

18. Global Biodiversity Resources Discovery System • (GBRDS) Poster

19. Integrated Publishing Toolkit • (IPT)

20. IPT: publishing data to the world • - Easy hosting and sharing of data • - Focus on specific data types for richer environment • - Data cache based on embedded or external database • - Link to existing relational DBs; import text files; assign • GUIDs; detect changes for incremental harvesting • Each data type has core entity; one-to-many relation to extension tables

22. Interface for mapping from local database schema to Darwin Core

23. Interface for events logging

24. IPT: multiple interfaces to data • Publishes data to web; statistics and maps via Google Chart API; fulltext search via Lucene • - Serves compressed archive of tab delimited files • - Incremental harvesting via OAI PMH • - TAPIR for Darwin Core and ABCD • - REST web services delivering XML and JSON records • - TCS for taxonomic checklists (also tab delimited archives) • - GeoServer for OGC Web Map and Web Feature services • - RSS feed announcing new or modified resources

25. Interfaces to Data

27. Poster Demo Markus Döring

28. “The key to modern biological information are the scientific names of organisms, and the electronic catalogue of the names that GBIF is building is fundamental to searching within and among the types of data indicated.”- GBIF Strategic Plan p.17 Fundamental as a “taxonomic backbone”

29. Information about Names Semantic and syntactic information that is focus of ECAT and its sources

30. Global Names Architecture • Mobilise, index and cross reference nomenclatural and taxonomic resources • - Common registration system (GBRDS) • - Standard exchange formats and GUIDs • - Assign GUIDS to normalised and stable nomenclature • - Map nomenclatural components of taxon concepts • - Reconcile names usages within data objects • Enhanced discovery and access methods by which objects can be linked to taxon concepts

31. Poster David Remsen Integrate taxonomic, nomenclatural resources with indexes of biodiversity content

32. Harvesting Indexing Toolkit Key Features Use to facilitate fast development of data portals • - Use of existing TDWG protocols • - Scheduling of data source harvesting • - Web based console to view progress and errors • - Cached copy of complete “raw” data held on disk • - Synchronising with UDDI registries • - Fully internationalised web application Could this be a tool to Certify provider installations? • - Role based security model • - Simple codebase, easy to extend (Java)

33. Harvesting Indexing Toolkit Early development screenshot [Protocol selection]

34. Harvesting Indexing Toolkit Early development screenshot [Datasource creation]

35. demo Tim Robertson Harvesting Indexing Toolkit Early development screenshot [Internationalised web based log console]

36. Node Portal Toolkit Goal • To provide a simple-to-use, simple-to-extend ‘core features’-only portal toolkit as the basis for development of customised portals tailored to particular needs. • Will leverage functionality already developed for the Integrated Publishing Toolkit and Harvsting/Indexing Toolkit.

37. GBIF and TDWG • - GBIF: representing needs of broader biodiversity community • TDWG standards process • Supported by GBIF task groups • Involving the wider community • - GBIF Informatics Advisory Group

38. How to contact GBIF: Web site:www.gbif.org Data portal:data.gbif.org GBIF Secretariat Universitetsparken 15DK-2100 Copenhagen ØDenmark E-mail: info@gbif.org Phone: +45 3532 1470 Fax: +45 3532 1480 GBIF Secretariat building, supported by a grant from the Aage V. Jensens Fonde