Networking Biodiversity Data Online Access to Distributed Data Sources in GBIFD

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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
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The German GBIF "National Nodes"
Plants and Protists
Prokaryotes and Viruses
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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
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Database Access
"Wrapper Technology"
DB 1
DB 4
DB 2
DB 5 etc.
DB 3
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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
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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

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The BioCASe Protocol (2)

• ltrequest xmlns"http//www.biocase.org/schemas/pro
  tocol/1.3" gt
• ltheadergt
• ltversiongt0.93lt/versiongt
• ltsendTimegt2001-09-11T093047-0500lt/sendTimegt
  
• ltsourcegt192.168.1.105lt/sourcegt
• ltdestinationgthttp//www.collection.org/myColle
  ction.pylt/destinationgt
• lttypegtsearchlt/typegt
• lt/headergt
• ltsearchgt
• ltrequestFormatgthttp//www.tdwg.org/schemas/abc
  d/1.2lt/requestFormatgt
• ltresponseFormat start"0" limit"10"gt/abcd/
  1.2lt/responseFormatgt
• ltfiltergt
• ltlike path"//TaxonIdentified/NameAuthorY
  earString"gtAstlt/likegt
• lt/filtergt
• ltcountgtfalselt/countgt
• lt/searchgt
• lt/requestgt

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Data Flow, simplified
Data Provider
Unit wrapper
Config.Files
Unit data
Unit data
C
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Access to Biological Collection Data

• 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
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ABCD Structure Overview
v.1.49
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ABCD - Collection Metadata
Description
IconURI
Scope (geographical and taxonomic keywords)
Version
Owners
IPRStatements
v.1.49
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ABCD Structure Overview
v.1.49
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ABCD - Unit Data
Unit extension
v.1.49
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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

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Thank you!

• BioCASE www.biocase.org
• GBIF-International www.gbif.org
• GBIF-D www.gbif.de

ABCD www.bgbm.org/TDWG/CODATA/Schema/default.ht
m Open Review Process Comments
Welcome! Contact w.berendsohn_at_bgbm.org