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

EDIT needs biodiversity information standards

The BGBM Berlin-Dahlem EDIT Team

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


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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


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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


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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


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Platform Components

Community components


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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)


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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


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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


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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


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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


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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


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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

Central(ised) components


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Platform Components


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Central Components: Converter Services

• CDM to/from– TDWG Ontology RDF– NEXUS– TaxonX– Special Word format– Checklists as CSV– …

• Needs thinking of services standard


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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


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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


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Central Component: Experts DB

• Taxonomic Expertise in Europe– Personal data– Institutional links– Geographic focus– Taxonomic focus

• Drupal website• TDWG standard?


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Central: Service & Application Tracker

• Find applications, services and courses

• Categorised reviews– tax, bib, geo, etc.

• Open for comments


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Central Component: Security

• Common security framework– secures webservices & applications

• EDIT Identity Provider installation– central Authentication / SSO– serves user data from ExpertsDB incl.

metadata• Drupal auth module developed

“Personal“ Components


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Platform Components


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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


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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

Thank you

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

Documents

tdwg annual meeting

tdwg ontology

team slide

tdwg rdf annotations

biodiversity informatics

single user slide

community components

tdwg rdf ontology closest