1 / 27

EDIT needs biodiversity information standards

EDIT needs biodiversity information standards. The BGBM Berlin-Dahlem EDIT Team. 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

hagen
Download Presentation

EDIT needs biodiversity information standards

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  1. EDIT needs biodiversity information standards The BGBM Berlin-Dahlem EDIT Team

  2. 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

  3. 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

  4. 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

  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

  6. Platform Components TDWG Annual Meeting, Bratislava, September 17, 2007

  7. Community components

  8. 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

  9. 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

  10. 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

  11. 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

  12. 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

  13. 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

  14. 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

  15. Central(ised) components

  16. Platform Components TDWG Annual Meeting, Bratislava, September 17, 2007

  17. 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

  18. 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

  19. 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

  20. 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

  21. 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

  22. 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

  23. “Personal“ Components

  24. Platform Components TDWG Annual Meeting, Bratislava, September 17, 2007

  25. 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

  26. 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 EDIT @ TDWG 2007 TDWG Annual Meeting, Bratislava, September 17, 2007

  27. WP 5 Thank you

More Related