1. BioCASE – A Biological Collection Access Service for Europe BioCASE programme – metadata and computing methods The Irish National Node Workshop: October 13 th, 2003. The Royal Irish Academy, Dublin. Chris Emblow Ecological Consultancy Services Ltd. (EcoServe)

2. BioCASE – A Biological Collection Access Service for Europe BioCASE Methodology This development of an advanced electronic access system is based on: 1.National nodes - standardised input through meta-information 2.Enhancement of key metadata using indexing tools and an extendible thesaurus…a WWW-based user interface 3.Applications implemented at the central access node to combine meta-information with specimen or observation-level data 4.A User Panel to channel user feedback throughout the project period 5.A business model to sustain the service after the project period and IPR issues addressed in collaboration with other FP5 projects

3. BioCASE – A Biological Collection Access Service for Europe Collection Level Unit Level BioCASE data methodology: all levels

4. BioCASE – A Biological Collection Access Service for Europe Collection Level BioCASE data methodology: collection level

5. BioCASE – A Biological Collection Access Service for Europe Stage 1: Metadata collection

6. BioCASE – A Biological Collection Access Service for Europe Stage 2: Data capture and storage

7. BioCASE – A Biological Collection Access Service for Europe Collection Level BioCASE data methodology: central node data harvesting

8. BioCASE – A Biological Collection Access Service for Europe BioCASE: National Node Network 31 National Nodes Core Meta Database is updated every night

9. BioCASE – A Biological Collection Access Service for Europe Stage 3: central node data harvesting

10. BioCASE – A Biological Collection Access Service for Europe Collection Level BioCASE data methodology: thesaurus and indexing

11. BioCASE – A Biological Collection Access Service for Europe Thesaurus and indexing Initially, the institution co-ordinating BioCASE will house the Central Node, however, it is envisaged that it will become a virtual facility, which can be accessed transparently through a number of servers on the network. The Central Node will integrate the data provided by national nodes with the thesaurus module by means of the indexing module.

12. BioCASE – A Biological Collection Access Service for Europe Collection Level BioCASE data methodology: user interface

13. BioCASE – A Biological Collection Access Service for Europe BioCASE: Preliminary User Interface A preliminary user interface displaying information collected by EcoServe to date is available at: www.biocase.org/biocasesimple/Default.cfm

14. BioCASE – A Biological Collection Access Service for Europe BioCASE: Preliminary Access Interface

15. BioCASE – A Biological Collection Access Service for Europe BioCASE: Preliminary Access Interface

16. BioCASE – A Biological Collection Access Service for Europe BioCASE: Preliminary Access Interface

17. BioCASE – A Biological Collection Access Service for Europe BioCASE: Preliminary Access Interface

18. BioCASE – A Biological Collection Access Service for Europe Advanced user interface – under developemnt

19. BioCASE – A Biological Collection Access Service for Europe Collection versus Unit Level Number of nodes –National node network: 31 nodes + SINs –Unit-level network: several hundreds to thousands of provider nodes in Europe Complexity of data profile (and query processes) –BioCASE MetaProfile: about 60 elements –ABCD unit-level schema: several hundreds of elements Control –Collection level: national nodes exert some control –Unit-level: providers to retain full control

20. BioCASE – A Biological Collection Access Service for Europe BioCASE: all data levels

21. BioCASE – A Biological Collection Access Service for Europe Unit level data standard: a history 1990 Accessions subgroup of the Taxonomic Databases Working Group Trying to provide field list for data exchange Botany: Types, ITF, Names, HISPID ASC model 1992, CDEFD 1995, BioCISE 1998 CODATA/TDWG Working Group 2000: Access to biological collection data, aim: ABCD XML Schema

22. BioCASE – A Biological Collection Access Service for Europe Unit-level data standard: ABCD Support: collection networking initiatives in the Americas, Australia, Europe, Japan, and New Zealand ENHSIN and BioCASE have driven the unit-level data specification process 2001/2002, investing substantial resources 2002 ABCD Schema accepted by GBIF 2003 GBIF declares to support and integrate BioCASE Network

23. BioCASE – A Biological Collection Access Service for Europe ABCD Schema design principles Common data definition for all biological collec- tions (living, dead, and sets of observations) Not a minimal common denominator approach; looking beyond the obvious questions Full support for statements of provider rights, IPR, copyright etc. Variable atomisation to support wide range of provider database structures

24. BioCASE – A Biological Collection Access Service for Europe ABCD Schema

25. BioCASE – A Biological Collection Access Service for Europe The BioCASE unit-level network Dynamic network, data held by providers Unit-level data provider (collection holders) are connected directly to BioCASE network Standard http Internet protocol Wrapper technology to produce standard output from any SQL database Output and query standard ABCD (XML)

26. BioCASE – A Biological Collection Access Service for Europe Unit data Use concepts as defined in ABCD Very flexible because of variable atomisation Not all information ABCD defines is needed –Geo-referenced taxa desired, but even just an object identifier (e.g. collectors field number) and a name or the location is sufficient

27. BioCASE – A Biological Collection Access Service for Europe The provider software Works on Windows and Unix derivates (Linux, Mac OS X) Works with many relational SQL databases –Currently: Access, Filemaker, MySQL, Oracle, PostgreSQL, SQL Server Generic software design, therefore supports any other concept definition, e.g. Darwin Core, if additionally configured for this

28. BioCASE – A Biological Collection Access Service for Europe Provider software installation Requirements: –SQL Database with unit-level data –Webserver connected to the Internet Install Python scripting language as CGI –available as open source: http://www.python.org Installation & configuration user guide: –http://www.biocase.org/dev/provider/index.shtml Report wrapper URL to BioCASE secretariat