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TDWG
EDIT Platform for Cybertaxonomy – An Overview
Andreas Müller, Andreas Kohlbecker, Pepe Ciardelli, Julius Welby, Pere Roca, Niels Hoffmann, Patricia Kelbert, Lutz Suhrbier and Edit co-workers
Conference 2008
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Andreas Müller, Botanical Garden Botanic Museum Berlin, TDWG 2008
What’s that ??
Platform
for
Cybertaxonomy
Taxonomy, Computer, Web
… taxonomist
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Andreas Müller, Botanical Garden Botanic Museum Berlin, TDWG 2008
Platform
Train platform
(station)
Travel faster
Trains (tools)
Trac system
Adapter
Cache machine
Bookshop
McDonalds
Photoshop
Show it
Feedback Police
don’t loose anything
Timetable
reusable
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Andreas Müller, Botanical Garden Botanic Museum Berlin, TDWG 2008
Platform Architecture
YES• Independent components (desktop or web applications or
services for machines) • Old (existing) & new developments • Service oriented (SOA)• Adaptable to individual institutional IT preconditions• Gradual migration • Adaptable to new challenges
NO• Monolithic, single user interface application• Everything new
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Andreas Müller, Botanical Garden Botanic Museum Berlin, TDWG 2008
Platform Components
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Andreas Müller, Botanical Garden Botanic Museum Berlin, TDWG 2008
Data Domain
ABCD, DC, wmf, wfs TCS SDD
?
ABCD, DC
• No common standard/model exists
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Andreas Müller, Botanical Garden Botanic Museum Berlin, TDWG 2008
Common Data Model (CDM)
• New development• Covering all relevant
areas• Leans on existing
standards/ models (TCS, SDD, TDWG Ontology, Berlin Model, …)
• Exchange format• Expandabel
http://wp5.e-taxonomy.eu/cdm/v1/
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Andreas Müller, Botanical Garden Botanic Museum Berlin, TDWG 2008
CDM Library
• To access, persist & query CDM data
• Database independent
• Includes taxonomic business logic (Parsing, Validation,…)
• JAVA / Hibernate / Spring / Eclipse
• Local and remote API (Web Services)
• Bulk import/export
• Collaboration with other projects (e.g. CATE)
IO
(Bulk) Import/ Export
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Andreas Müller, Botanical Garden Botanic Museum Berlin, TDWG 2008
New Platform Components
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Andreas Müller, Botanical Garden Botanic Museum Berlin, TDWG 2008
http://search.biocase.org/edit
Patricia Kelbert, BGBM
Uses GBIF dataAdvanced search by using taxonomic thesauriLarger resultHigh quality result
Specimen and Observation Explorer for Taxonomists
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Andreas Müller, Botanical Garden Botanic Museum Berlin, TDWG 2008
Geo Services
Online GIS Client & Map services
Taxonomically relevant layers
Multi species symbolization
Occurrence points
Distribution per region presence/absence
Publication ready quality
…
http://edit.csic.es/edit_geo/prototype/edit_project.htmlPere Roca, CSIC, Madrid; Frank Theeten, RMCA, Tervuren
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Andreas Müller, Botanical Garden Botanic Museum Berlin, TDWG 2008
ViTaL - Virtual Taxonomic Library
Meta Data Search (MetaLib)
OpenURL (SFX)
Harvester for known data sources (Falx)
Web UI & Web Service
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Andreas Müller, Botanical Garden Botanic Museum Berlin, TDWG 2008
Single Sign-On (Shibboleth)
EDIT Federation
Shibboleth Proxy
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Andreas Müller, Botanical Garden Botanic Museum Berlin, TDWG 2008
Drupal basedconfiguration
themeing
Data from CDM via web-service
Taxonomic treemultiple trees
filter
flattening
On-the-fly maps from GeoServer
…
Dataportals
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Andreas Müller, Botanical Garden Botanic Museum Berlin, TDWG 2008
Taxonomic Editor
Freetext ~ Word
↔ forms
Nameparser
Copy & Paste
Drag & Drop
Eclipse RCP
Warning & Errors
…
http://dev.e-taxonomy.eu/trac/wiki/TaxonomicEditorPepe Ciardelli, BGBM, Berlin
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Andreas Müller, Botanical Garden Botanic Museum Berlin, TDWG 2008
Descriptive Data
Use existing Tools
SDD import/export functionalities for the Common Data Model
Problem with different dialects
Elise Kunzelmann, Hélène Fradin; MNHN; Paris
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Andreas Müller, Botanical Garden Botanic Museum Berlin, TDWG 2008
Other Tools
http://www.bdtracker.net/
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Andreas Müller, Botanical Garden Botanic Museum Berlin, TDWG 2008
EDIT Platform Cybergate
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Andreas Müller, Botanical Garden Botanic Museum Berlin, TDWG 2008
Integrated Workflow (Example)
CDMCDM
CDM ServerCDM Server
Geo-server
Geo-server
Data-portal- Drupal
VitalVital
BCIBCI
DeltaLucidExpert²
Tax Editor
uBiouBioSpObET
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Andreas Müller, Botanical Garden Botanic Museum Berlin, TDWG 2008
Where are we ?
DONE– CDM v1.0 (v1.3)– CDM Library (v1.3)– Pilot implementations
• ViTaL, MapViewer, GeoService,Editor, Dataportals, Shibboleth, Taxonomic Editor
– Specimen & Observation Explorer is ready
TODOs: – Import-/Export– Cybergate– Tools: Full functionality– CDM / Library: Roles, Versioning, (Synchronisation)– Feedback from users
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Andreas Müller, Botanical Garden Botanic Museum Berlin, TDWG 2008
Thank you !