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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. Invertebrates I. - PowerPoint PPT Presentation
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Networking Biodiversity Data – Online Access to Distributed
Data Sources in GBIF-D
Andrea Hahn, A. Kirchhoff & W.G. BerendsohnBotanic Garden and Botanical Museum
Berlin-Dahlem, FU Berlin, Dept. of Biodiversity Informatics and Laboratories
Nov 29, 2004
A.Hahn: Networking Distributed Data Sources in GBIF-D
The German GBIF "National Nodes"Plants
and Protists
Fungi and Lichens
Prokaryotesand Viruses
Invertebrates IVertebrates
Invertebrates II Invertebrates III
GBIF-D Botany
The Portal of the German botanical node combines five "Areas of Expertise"
GeneticResources
Phytodiversity(in-situ)
Botanical Gardens Herbaria
Phyto-Taxonomy
GBIF.de/botanik
VIRTUAL HERBARIUM
A.Hahn: Networking Distributed Data Sources in GBIF-D
Database Access
DB 2
DB 5 etc.
DB 1
DB 4
DB 3
?!
: "Wrapper Technology"
A.Hahn: Networking Distributed Data Sources in GBIF-D
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
A.Hahn: Networking Distributed Data Sources in GBIF-D
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
A.Hahn: Networking Distributed Data Sources in GBIF-D
User Interface Client (Servlet)
Portal
UnitLoader
Java API
Meta-data
JDBC
Data Provider
Data Flow, simplified
Config.Files
SQL
Unit wrapper
Unit Wrapper
Unit data
UnitLoader
Internet
http
BioCASe
Protocol
Request XML
http
ResponseXML
?
Client
!
Unit data
A.Hahn: Networking Distributed Data Sources in GBIF-D
an XML Schema for:
collection information – unit data scientific names from identifications data on the collection as such data origin, IPR etc.
Access to Biological Collection Data
www.bgbm.org/TDWG/CODATA/Schema/default.htm
A.Hahn: Networking Distributed Data Sources in GBIF-D
Datasets
ABCD Structure – Overview
Dataset
Units(observation or specimen records)
Dataset.....
(admin. & tech. contacts, other networks, expiry date)
Metadata
v.1.49
A.Hahn: Networking Distributed Data Sources in GBIF-D
ABCD - Collection MetadataMetadata
Description
IconURI
Scope (geographical and taxonomic keywords)
Version
Owners
IPRStatements
RevisionData Creators
Contributors
DateCreated
DateModified
v.1.49
A.Hahn: Networking Distributed Data Sources in GBIF-D
Datasets
ABCD Structure – Overview
Dataset
Metadata
Units(observation or specimen records)
Dataset.....
(admin. & tech. contacts, other networks, expiry date)
v.1.49
A.Hahn: Networking Distributed Data Sources in GBIF-D
Units/Unit
ABCD - Unit Data
Unit extension
References, digital images, associations, assemblages, measurements and facts, sequences, notes
IDs, content contact, editor, IPR,...
v.1.49
Observation unit
Specimen unit Unit state domain (physical state-specific subtypes)
Identifications
Gathering event and site characteristics
Unit collection domain (domain-specific subtypes)
A.Hahn: Networking Distributed Data Sources in GBIF-D
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
A.Hahn: Networking Distributed Data Sources in GBIF-D
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: [email protected]
