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TDWG Annual Meeting, Bratislava, September 17, 2007
WP 5
EDIT
• Network of Excellence in the 6th Framework Programme of the European Commission
• 21 major natural history institutions (incl. 2 from the US and 2 from Russia) and several organisations
• 5 year project, started 2006, 11.9 Mio Euro• Reduce fragmentation, encourage durable
integration of institutions, promote collaborative research using biodiversity informatics
TDWG Annual Meeting, Bratislava, September 17, 2007
WP 5
EDIT and biodiversity informatics
• Creating the Internet Platform for Cybertaxonomy
• The platform is to support the taxonomic work process by means of applications and services
• Institutional integration through communication and specialisation of IT departments and formal agreements
TDWG Annual Meeting, Bratislava, September 17, 2007
WP 5
Practical focal points
• Revisionary taxonomy– Collaborative and individual taxonomic research
• Inventories and monitoring– Taxonomist’s field work
• Infrastructures– Taxonomic backbone (European and local
checklists) – Use of specimens– Literature access– Geographic services
TDWG Annual Meeting, Bratislava, September 17, 2007
WP 5
Building the platform
Build on existing applications and services vs.designing a new architecture
• Towards decoupled components• Full interoperability through the use of standard
interfaces• Multiple components varying in complexity acc. to
user needs• Every component may be an (desktop or web)
Application for human users or a (web) Service for machines
• No single user interface
TDWG Annual Meeting, Bratislava, September 17, 2007
WP 5
Community Components
• A community is delimited by – taxonomic groups, e.g. Diptera– geographic focus, e.g. an ATBI site– applied focus, e.g. invasive species
• Collaboratively managing data(but also may be a single user)
TDWG Annual Meeting, Bratislava, September 17, 2007
WP 5
Common Data Model (CDM)
• UML class model covering all core data areas
• Semantically aligns with TDWG ontology and standards like TCS, SDD, ABCD & DarwinCore
• Offers versioning of data• Use of Enterprise Architect to create
Java source code
TDWG Annual Meeting, Bratislava, September 17, 2007
WP 5
Community CDM Store
• Central datastore for a community• Webservices on top of CDM library
– remote API– sync API– RSS search feeds
• Other services– Converter services to/from TDWG Ontonlogy
(LSID Vocabularies) – Community CDM Store exposes data through
LSIDs as TDWG RDF– Annotations
TDWG Annual Meeting, Bratislava, September 17, 2007
WP 5
Why Yet Another Model ?
• No integrated standard available. TDWG RDF ontology closest to our needs,but lacks cardinality
• Implementation model provides– Application logic & constraints– Strongly typed data & interfaces– Operations
TDWG Annual Meeting, Bratislava, September 17, 2007
WP 5
CDM Java Library
• Persistent domain model– Hibernate & Spring framework– Domain POJOs– XML marshalling– Validation logic
• Several APIs• Flexible RDBMS backend
– Including embedded DBs
• Versatile use in many apps– Community store– Taxonomic editor– Converter services
TDWG Annual Meeting, Bratislava, September 17, 2007
WP 5
CDM Roadmap
• 4Q/2007 - frozen UML model– feed results into TDWG– new CDM release not before end of 2008
• 1Q/2008 - Software release– CDM library– Community store
TDWG Annual Meeting, Bratislava, September 17, 2007
WP 5
Community Webtools
• Customisable Drupal website– Webpages, forum, blog, calendar– Flexible design through themes– Simple image & document hosting
• Dataportal– Publishes CDM store– Concurrent concepts– Allows annotations– Drupal module
TDWG Annual Meeting, Bratislava, September 17, 2007
WP 5
Central Components: Converter Services
• CDM to/from– TDWG Ontology RDF– NEXUS– TaxonX– Special Word format– Checklists as CSV– …
• Needs thinking of services standard
TDWG Annual Meeting, Bratislava, September 17, 2007
WP 5
Central Components: Geo Services
• Map services– Occurrence points– Distribution per region
presence/absence
• Online GIS Client– Multi species– Targeted at ATBI sites
• Occurrence2Distribution transformation service
• Input for Geospatial IG
TDWG Annual Meeting, Bratislava, September 17, 2007
WP 5
Central Components: RSS Search Feeds
• Search for– Occurrences in GBIF– References in ViTaL– Taxa in Species2000– Agents in ExpertsDB
• Subscribe to searches
• Use any RSS clientor the webtools
TDWG Annual Meeting, Bratislava, September 17, 2007
WP 5
Central Component: Experts DB
• Taxonomic Expertise in Europe– Personal data– Institutional links– Geographic focus– Taxonomic focus
• Drupal website• TDWG standard?
TDWG Annual Meeting, Bratislava, September 17, 2007
WP 5
Central: Service & Application Tracker
• Find applications, services and courses
• Categorised reviews– tax, bib, geo, etc.
• Open for comments
TDWG Annual Meeting, Bratislava, September 17, 2007
WP 5
Central Component: Security
• Common security framework– secures web- services & applications
• EDIT Identity Provider installation– central Authentication / SSO– serves user data from ExpertsDB incl.
metadata• Drupal auth module developed
TDWG Annual Meeting, Bratislava, September 17, 2007
WP 5
Taxonomic Editor
• Eclipse Rich Client Platform– powerful GUI widgets– richer than web2.0– Bioclipse plugins for
genetics & biochemistry
• Uses local CDM library– embedded or network
database
• Offline work possible through syncing with CDM Store
TDWG Annual Meeting, Bratislava, September 17, 2007
WP 5
EDIT @ TDWG 2007
• Andreas Kohlbecker• Andreas Müller• Dave Roberts• Dave Taylor• Elise Kuntzelmann• Franck Theeten• Eduard Stloukal• Graham Higley• Julius Welby• Lutz Suhrbier• Malte Ebach
• Markus Döring• Neil Thomson• Patricia Mergen• Pepe Ciardelli• Pere Roca• Walter Berendsohn• Yde de Jong
• Anna Weitzman• Chuck Miller• Martin Pullan