1. M O S A i C S MOSAICS Brussels 5-6 October 2005 © 2005 Belgian Science Policy. I Virginie Storms Belgian Science Policy Office Laboratory for Microbiology, University of Ghent ORGANISING THE SYSTEM C S

2. M O S A i C S © 2005 Belgian Science Policy Office. MOSAICS Brussels 5-6 October 2005 2 Necessary properties of an Integrated Conveyance System Compatibility with the political framework Easily applicable in most conditions Fulfilling the needs of users/providers Attractive system enforceable without constraints

3. M O S A i C S © 2005 Belgian Science Policy Office. MOSAICS Brussels 5-6 October 2005 3 Options ? Tracking rather than traceability Source rather than origin Electronic thread rather than paperwork path Built in system, which allows ex ante and ex post conveyance

4. M O S A i C S © 2005 Belgian Science Policy Office. MOSAICS Brussels 5-6 October 2005 4 Schematic view of the options Source of isolation Deposit in BRC User 1 TRACEABILITY through electronic path TRACKING User 2 User 3 Application … Link between final use and original provider

5. M O S A i C S © 2005 Belgian Science Policy Office. MOSAICS Brussels 5-6 October 2005 5 In order to meet these options… … there’s a need for unique identifiers Examples from different fields: Accession numbers IPEN number barcodes patent number …

6. M O S A i C S © 2005 Belgian Science Policy Office. MOSAICS Brussels 5-6 October 2005 6 Unique Identifiers for microbial resources Present situation: Strain number: collection accronym followed by number Problem: Synonym accronyms (homonym strains) and synonym strains

7. M O S A i C S © 2005 Belgian Science Policy Office. MOSAICS Brussels 5-6 October 2005 7 Unique Identifiers for microbial resources Local unique identifiers = LABEL Strain numbers are used as a link between different databases, however, in absence of a comprehensive database of synomyn numbers, individual databases lack an easy way of linking information

8. M O S A i C S © 2005 Belgian Science Policy Office. MOSAICS Brussels 5-6 October 2005 8 Persistent unique identifiers We need identifiers that are a combination of the traditional ‘LABEL’ and a globally unique identifier and PERSISTENT location where to retrieve the information

9. M O S A i C S © 2005 Belgian Science Policy Office. MOSAICS Brussels 5-6 October 2005 9 Persistent unique identifiers are: Actionable: with a single click from the identifier to a useful URL Persistent: located in a namespace where they can be reliable identifed, no matter what their current location may be Interoperable: ability to diffrentiate between copies and to access the most desired by the user

10. M O S A i C S © 2005 Belgian Science Policy Office. MOSAICS Brussels 5-6 October 2005 10 Persistent unique identifiers: first concept PURLs (1995) map a symbolic identifier to a network location, they can garuantee persistency of the name but not the perpetual access to the resource Client PURL server Resource server Redirection

11. M O S A i C S MOSAICS Brussels 5-6 October 2005 © 2005 Belgian Science Policy. Jean Swings Bernard De Baets Peter Dawyndt Xianhua Zhou Juncai Ma STRAIN INFO NET Holding a wealth of downstream information on microbial resources right in our hands Illustration

12. M O S A i C S © 2005 Belgian Science Policy Office. MOSAICS Brussels 5-6 October 2005 12 www.straininfo.net

13. M O S A i C S © 2005 Belgian Science Policy Office. MOSAICS Brussels 5-6 October 2005 13 www.straininfo.net Tracking of strains

14. M O S A i C S MOSAICS Brussels 5-6 October 2005 © 2005 Belgian Science Policy. www.straininfo.net

15. M O S A i C S MOSAICS Brussels 5-6 October 2005 © 2005 Belgian Science Policy. Data fusion: complete strain history Bacillus cereus type strain LMG 6923 <- 1985, DSM <- ATCC <- R.Gordon <- T.Gibson <- W.Ford JCM 2152 <-- IAM 12605 <-- NCIB 9373 <-- R. E. Gordon. CIP 66.24  1966, ATCC  R.E. Gordon: strain NRRL B-3711  T. Gibson: strain 971  W.W. Ford: strain 13 CCRC 11026 << IAM www.straininfo.net

16. M O S A i C S MOSAICS Brussels 5-6 October 2005 © 2005 Belgian Science Policy. T. Gibson (971) W.W. Ford (13) original isolate GUID: new isolate GUID: NCTC 2599 GUID: NRRL B-3711 GUID: ATCC 14579 GUID: Gibson 971 GUID: Ford 13 GUID: NCIMB 9373 first BRC deposit NCIMB 9373 NCTC 2599 NRRL B-3711 ATCC 14579 isolate entities culture entities new isolate Dawyndt P, Vancanneyt M, De Meyer H, Swings J. Knowledge Accumulation and Resolution of Data Inconsistencies during the Integration of Microbial Information Sources. IEEE Transactions on Knowledge and Data Engineering, 17(8), pp. 1111-1126, 2005. registration authority strain number equivalence relation strain deposit history relation strain number resolution (disambiguation) BRC resolution (online catalogues)

17. M O S A i C S MOSAICS Brussels 5-6 October 2005 © 2005 Belgian Science Policy. T. Gibson (971) W.W. Ford (13) original isolate GUID: new isolate GUID: NCTC 2599 GUID: NRRL B-3711 GUID: ATCC 14579 GUID: Gibson 971 GUID: Ford 13 GUID: NCIMB 9373 first BRC deposit NCIMB 9373 NCTC 2599 NRRL B-3711 ATCC 14579 culture entities new isolate isolate entities Dawyndt P, Vancanneyt M, De Meyer H, Swings J. Knowledge Accumulation and Resolution of Data Inconsistencies during the Integration of Microbial Information Sources. IEEE Transactions on Knowledge and Data Engineering, 17(8), pp. 1111-1126, 2005. registration authority

18. M O S A i C S © 2005 Belgian Science Policy Office. MOSAICS Brussels 5-6 October 2005 18 Globally Unique Identifiers

19. M O S A i C S © 2005 Belgian Science Policy Office. MOSAICS Brussels 5-6 October 2005 19 Digital Object Identifier (DOI) Developed by the international DOI foundation in 1998 originating from publishing sector as an identification system for intellectual property in the digital environment A name for an entity on digital networks and a system for persistent and actionable identification and interoperable exchange

20. M O S A i C S © 2005 Belgian Science Policy Office. MOSAICS Brussels 5-6 October 2005 20 Digital Object Identifier (DOI) http://doi.org © Norman Paskin (2005) DOI Numbering scheme Internet resolution Data model Policies

21. M O S A i C S © 2005 Belgian Science Policy Office. MOSAICS Brussels 5-6 October 2005 21 Digital Object Identifier (DOI) Made up of two components: prefix assigned by a registration agency, suffix assigned by the publisher to the specific content. The suffix can follow any system of the publisher choosing and be assigned to objects of any size. An object eg strain may have one DOI and a component of that object eg gene another DOI Can include any existing ‘label’ eg 10.6756/LMG10567 NUMBERING SCHEME

22. M O S A i C S © 2005 Belgian Science Policy Office. MOSAICS Brussels 5-6 October 2005 22 Digital Object Identifier (DOI) DOI’s are widespread used, core technology for main- taining cross-reference Some sectors have developed their own identifier, e.g. LSID, these can be incorporated into a DOI (or vice versa) Based on the Handle system: comprehensive system for assigning, managing and resolving persistent identifiers, can be used as URN Internet resolution allows a DOI to link to any & multiple pieces of current data e.g. Model for assigning DOI’s to prokaryotic taxa: Garrity & Lyons

23. M O S A i C S © 2005 Belgian Science Policy Office. MOSAICS Brussels 5-6 October 2005 23 Life Science Identifier LSID e.g. urn:lsid:ncbi.nlm.nig.gov:GenBank:T4685:3 Developed by I3C (Interoperable Informatics Infra- structure Consortium and OMG (Object Managing Group) (2003) for uniform naming (URN) and access to life science data Young standard

24. M O S A i C S © 2005 Belgian Science Policy Office. MOSAICS Brussels 5-6 October 2005 24 Options facilitating ABS Tracking rather than traceability Source rather than origin Electronic thread rather than paperwork path Built in system, which allows ex ante and ex post conveyance

25. M O S A i C S © 2005 Belgian Science Policy Office. MOSAICS Brussels 5-6 October 2005 25 Appropriate management Culture collections system is deposit procedure with attribution of an identifier transfer procedure based on registration of movements between culture collections and attribution of identifier distribution management to non culture collections well established, efficient documented (standard forms and procedures) world wide (for public collections / BRC) Culture collections system is based on Role for WFCC and WDCM?