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Networking Biodiversity Data – Online Access to Distributed Data Sources in GBIF-D

Networking Biodiversity Data – Online Access to Distributed Data Sources in GBIF-D. Andrea Hahn , A. Kirchhoff & W.G. Berendsohn Botanic Garden and Botanical Museum Berlin-Dahlem, FU Berlin, Dept. of Biodiversity Informatics and Laboratories. Nov 29, 2004. Invertebrates I.

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Networking Biodiversity Data – Online Access to Distributed Data Sources in GBIF-D

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  1. Networking Biodiversity Data – Online Access to Distributed Data Sources in GBIF-D Andrea Hahn, A. Kirchhoff & W.G. Berendsohn Botanic Garden and Botanical Museum Berlin-Dahlem, FU Berlin, Dept. of Biodiversity Informatics and Laboratories Nov 29, 2004

  2. Invertebrates I Invertebrates II Fungi and Lichens Invertebrates III Vertebrates The German GBIF "National Nodes" Plants and Protists Prokaryotes and Viruses

  3. VIRTUAL HERBARIUM GBIF-D Botany The Portal of the German botanical node combines five "Areas of Expertise" Phyto-Taxonomy GeneticResources GBIF.de /botanik Phytodiversity(in-situ) Herbaria Botanical Gardens

  4. ? ! : "Wrapper Technology" Database Access DB 1 DB 4 DB 2 DB 5 etc. DB 3

  5. Technical Approach: BioCASE Separation of transfer protocol and content • protocol: BioCASe • content schema: ABCD • covers all types of biological collections • allows for a high degree of detail • uses variable atomization www.biocase.org

  6. The BioCASe Protocol (1) • XML based specification for communication between providers and consumers • Works with any content schema • Defines three basic operations: • capabilities • scan • search

  7. Internet Portal Client Meta-data Request XML Unit Wrapper http JDBC SQL BioCASe Protocol User Interface Client (Servlet) ? Java API ResponseXML UnitLoader UnitLoader http ! Data Flow, simplified Data Provider Unit wrapper Config.Files Unit data Unit data C

  8. AccesstoBiologicalCollectionData an XML Schema for: • collection information – unit data • scientific names from identifications • data on the collection as such • data origin, IPR etc. www.bgbm.org/TDWG/CODATA/Schema/default.htm

  9. Datasets Dataset (admin. & tech. contacts, other networks, expiry date) Metadata Units (observation or specimen records) Dataset ..... ABCD Structure – Overview v.1.49

  10. Metadata RevisionData Creators DateCreated Contributors DateModified ABCD - CollectionMetadata Description IconURI Scope (geographical and taxonomic keywords) Version Owners IPRStatements v.1.49

  11. Datasets Dataset (admin. & tech. contacts, other networks, expiry date) Metadata Units (observation or specimen records) Dataset ..... ABCD Structure – Overview v.1.49

  12. Units/Unit Identifications Unit state domain (physical state-specific subtypes) Gathering event and site characteristics Specimen unit Observation unit Unit collection domain (domain-specific subtypes) IDs, content contact, editor, IPR,... References, digital images, associations, assemblages, measurements and facts, sequences, notes ABCD - Unit Data Unit extension v.1.49

  13. Integration into GBIF • Software components (portal / provider) freely available • GBIF portal understands DiGIR and BioCASe protocol • Darwin Core and ABCD records integrated into user interface

  14. Thank you! • BioCASE: www.biocase.org • GBIF-International: www.gbif.org • GBIF-D: www.gbif.de ABCD:www.bgbm.org/TDWG/CODATA/Schema/default.htm Open Review Process – Comments Welcome! Contact: w.berendsohn@bgbm.org

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