Transcript Diapositive 1 - Indentifying Species with DNA Barcoding

BARCODE DATA, MUSEUM
CATALOGS AND GBIF
Simon Tillier
CBoL
Taipei, 17-22 september 2007
Vouchering is a necessity for
Barcode in the long term
virtual world
real world
species name
species
concept
barcode sequence
barcode
voucher
organisms
CBoL
Taipei, 17-22 september 2007
Vouchering is a necessity for
Barcode in the long term
virtual world
real world
species
concept 1
species name
barcode sequence
species
concept 2
WITHOUT VOUCHERS, BARCODE IDENTIFICATION WILL BECOME SECOND
LIFE TAXONOMY INSTEAD OF BIODIVERSITY TAXONOMY
CBoL
Taipei, 17-22 september 2007
From catalogues to collections
databases
• traditional catalogues
number
(or date, or code + number)
taxon name
= key to location of the
specimen in the collection
origin
donor, region of origin
– 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
CBoL
Taipei, 17-22 september 2007
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
CBoL
Taipei, 17-22 september 2007
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)
CBoL
Taipei, 17-22 september 2007
Looking forward: Barcode as a
collection management tool
•
“classical” collection processing
–
–
–
–
–
•
EDIT (Moorea?) processing
–
–
–
•
1. collection event
2. sorting, naming and labelling
3. databasing info accumulated so far
4. barcoding
Barcoding = additional secondary information
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
CBoL
Taipei, 17-22 september 2007
Acknowledgements
Nicolas Bailly
Walter Berendsohn
Markus Doring
Sarah Samadi
... and collection curators who have
tried to manage since four centuries
CBoL
Taipei, 17-22 september 2007
GBIF Scope
DIGIT:
References
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 Life
Data systems
Species Banks:
GSIS: Global Species Information System
EoL: Encyclopedia of Life
SpeciesBase
GSDs, RSDs, TSDs, …
CBoL
DADI: Data Access and DatabaseTaipei,
Interoperability:
GBIF/TDWG schemas and protocols
17-22 september 2007
USERS
Institution
Institutions
Institutions
Institutions
Institutions
Bold/Genebank
Taxon name
Sequencing facility
Collection
Taxonomist
Voucher
CBoL
Taipei, 17-22 september 2007
Extraction facility