M O S A i C S MOSAICS Brussels 5-6 October 2005 © 2005 Belgian Science Policy. I Virginie Storms...

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MOSAICS Brussels 5-6 October 2005

© 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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© 2005 Belgian Science Policy Office.


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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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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www.straininfo.net

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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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http://doi.org

© Norman Paskin (2005)

DOI

Numbering scheme

Internet resolutionData model

Policies

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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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• 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?

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