CBoL Taipei, 17-22 september 2007 BARCODE DATA, MUSEUM CATALOGS AND GBIF Simon Tillier.

CBoLTaipei, 17-22 september 2007

BARCODE DATA, MUSEUM CATALOGS AND GBIF

Simon Tillier


Vouchering is a necessity for Barcode in the long term virtual world real world

species name

barcode sequence

speciesconcept

organisms

barcode voucher


Vouchering is a necessity for Barcode in the long term virtual world real world

species name

barcode sequence

speciesconcept 1

speciesconcept 2

WITHOUT VOUCHERS, BARCODE IDENTIFICATION WILL BECOME SECOND LIFE TAXONOMY INSTEAD OF BIODIVERSITY TAXONOMY


From catalogues to collections databases

• traditional catalogues

– other precise information on the label stored with the specimen (successive identifications, precise location etc)

• databasing – transfer of all this information (label + catalogue) on

virtual support

number (or date, or code + number)

taxon name = key to location of the specimen in the collection

origin donor, region of origin


Present and further implementation of the GBIF concept

• once the support of the info is virtual, the info can circulate and there is no need to have it in the same physical location

– GBIF starting concept• we can make the collection databases interoperable

– Extension / further implementation of the GBIF concept• we can have the various pieces of species and specimen information in many

homogenous databases (ontological categories) in many places in the world:– names in one database system (CoL)– sequences in one database system (Genbank/BOLD)– localities– ID numbers of specimens giving access to physical location and real specimens and linking

with other databases – (however experience suggests wise to print the information on a label with permanent ink!).

• needed : a common model which will allow linking databases whichever way they are split in whatever locations (the ABCD model already has a section for sequences)

• TDWG, Genbank, BOLD, Zoobank (and EoL?) should urgently agree on a common model under the overarching GBIF framework


Barcode curation challenge

• management of fragmented specimens = makeshift job in museums (eg organism + slides)

• tissue and DNA collections create fragmented units– whole organism – tissue of the same– DNA from the same (IMAGENE)

• problem = workflow, info management, change in curatorial culture

• first step = creation of curation standards (eg SYNTHESYS ) and implementation of standards (EDIT)


Looking forward: Barcode as a collection management tool

• “classical” collection processing– 1. collection event – 2. sorting, naming and labelling – 3. databasing info accumulated so far– 4. barcoding – Barcoding = additional secondary information

• EDIT (Moorea?) processing– 1. databasing collection event – 2. progressive expansion of the database following the same steps as above– Barcoding = additional secondary information

• Future process– 1. databasing collecting events – 2. sorting + barcoding = provides name and creates a link between the virtual catalogue and

an unique material property of the specimen

– Barcode sequence = an intrinsic label of the specimen linking to other DBs for collection management


AcknowledgementsNicolas BaillyWalter BerendsohnMarkus DoringSarah Samadi

... and collection curators who have tried to manage since four centuries


GBIF Scope

DIGIT:Digitization of Natural History Collections

Collection and Observation databases

ECAT:Electronic Catalogue of Names of Known Organisms[+ Management Classification]

Catalog of Life (Species 2000, ITIS, WoRMS)GSDs and RSDs: Global and Regional Sp. DBs

ZooBank, uBio, …Other names

BIS:Biodiversity Information System

BoL:Barcode of Life

BoLD:

Barcode of LifeData systems

Ref

eren

ces

Species Banks:GSIS: Global Species Information System

EoL: Encyclopedia of LifeSpeciesBase

GSDs, RSDs, TSDs, …

DADI: Data Access and Database Interoperability: GBIF/TDWG schemas and protocols


Taxonomist

Taxon name

Voucher

Extraction facility

Sequencing facility

Collection

Bold/Genebank

InstitutionInstitutionsInstitutionsInstitutionsInstitutions

USERS

CBoL Taipei, 17-22 september 2007 BARCODE DATA, MUSEUM CATALOGS AND GBIF Simon Tillier.

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