m o s a i c s mosaics brussels 5-6 october 2005 © 2005 belgian science policy. i virginie storms...
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© 2005 Belgian Science Policy.
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Virginie Storms Belgian Science Policy Office
Laboratory for Microbiology, University of Ghent
ORGANISING THE SYSTEM
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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
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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
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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
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In order to meet these options…
… there’s a need for unique identifiers
Examples from different fields: Accession numbers IPEN number barcodes patent number …
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Unique Identifiers for microbial resources
Present situation:Strain number: collection accronym followed by number
Problem:Synonym accronyms (homonym strains) and synonym strains WDCM ID acronym country institute
66 BTCC Bulgaria Bulgarian Type Culture Collection632 BTCC Indonesia Biotechnology Culture Collection Institution Pusat Penelitian dan Pengembangan Bioteknologi-LIPI117 CCDM China Culture Collection of Department of Microbiology878 CCDM Czech Culture Collection of Dairy Microorganisms Laktoflora770 CCF Cuba Colleccion de Cuttivos Finlay182 CCF Czech Culture Collection of Fungi95 CISM Mexico Verticillium dahliae from cotton75 CISM Thailand NifTAL Rhizobium Collection (Asia Center)
805 IFM Australia IFM Quality Services Pty Ltd60 IFM Japan Research Center for Pathogenic Fungi and Microbial Toxicoses, Chiba University
742 LCC Canada Labatt Culture Collection, Technology Development231 LCC Poland University of Warmia and Mazury in Olsztyn
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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
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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
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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
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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
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© 2005 Belgian Science Policy.
Jean Swings
Bernard De Baets
Peter Dawyndt
Xianhua Zhou
Juncai Ma
S T R A I N I N F O N E T
Holding a wealth of downstreaminformation on microbial resources
right in our hands
Illustration
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www.straininfo.net
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www.straininfo.net
Tracking of strains
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Data fusion: complete strain historyBacillus 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
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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)
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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
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Globally Unique Identifiers
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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
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Digital Object Identifier (DOI)
http://doi.org
© Norman Paskin (2005)
DOI
Numbering scheme
Internet resolutionData model
Policies
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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
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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
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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
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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
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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?