Transcript 슬라이드 1 - Scientific Committee on Antarctic Research

KOPRI BioDB
A part of Korea Polar Data Center
Soon Gyu Hong1, Min Chul Lee1, Cheng-Dae Choe2 and Hong Kum Lee1
1
2
Korea Polar Research Institute
Newgex Co. (Boram Pharm. Bioinfo team)
Databases to manage Bioresources
Samples from Polar area
Soil, sediment, water, glacier, lichens, plants, animals
Strain DB
Microbial and
tissue culture
Metagenomic
DNA isolation
Genome
library
Sequence DB
Metagenome
library
Identification by
phylogenetic analysis
Selection
of clones
Polyphasic
classification
Characterization
Sample DB
Genomic
DNA DB
Genome
Library DB
Metagenome
Library DB
Clone DB
Enzyme DB
Polymer DB
Metabolite DB
Samples from Polar Areas
Ny-Ålesund
2006.7.14-2006.7.31
Locality
water
sedimen
t
soil
Sejong Station
21
Dasan Station
15
4
4
Barents/Cara
156
235
22
Okhotsk/Bering
g
129
426
glacier
plant
animal
1
biofilm
total
260
7
289
21
238
41
7
140
50
10
31
504
555
8
Austria
6
Fungi
(lichens)
7
15
44
Baikal
etc
10
total
331
44
82
665
34
14
135
17
513
92
28
1,73
7
Cultural strains
Microbial cultures
 Bacteria: 4,500 strains
 Molds: 30 strains
 Moss: 8 strains
Preservation
 Liquid nigrogen (-180C)
 deep freezer (-80C)
 Freeze-dry
Microbial Cultures
Crenarchaeota
1
Actinobacteria
113
Bacteroidetes
171
Gammaproteobacteria
534
1583 STRAINS
99 GENERA
Betaproteobacteria
10
Alphaproteobacteria
59
Firmicutes
688
Microbial Cultures
ACTINOBACTERIA
Agrococcus, 1
16 genera
113 strains
Subtercola, 1
Sanguibacter, 6
Salinibacterium, 17
Arthrobacter, 41
Rhodococcus, 5
Plantibacter, 1
Nocardioides, 1
Micrococcus, 16
Brachybacterium, 2
Brevibacterium, 3
Cellulomonas, 1
Microbacterium, 3
Leifsonia, 12
Curtobacterium, 1
Knoellia, 2
BACTEROIDETES
FIRMICUTES
Aequorivita, 1
Zobellia, 10
27 genera
171 strains
Algibacter, 1
Winogradskyella, 4
Algoriphagus, 9
Ulvibacter, 1
Aquimarina, 3
Tenacibaculum, 1
Arenibacter, 2
Pullulanibacillus, 1
Virgibacillus, 2
13 genera
688 strains
Planococcus, 11
Paenibacillus, 50
Bizionia, 1
Sejongia, 6
Cellulophaga, 26
Sediminicola, 2
Trichococcus, 1
Sporosarcina, 19
Planomicrobium, 3
Tamlana, 2
Sphingobacterium, 5
Terribacillus, 1
Staphylococcus, 2
Marinibacillus, 12
Listeria, 1
Halolactibacillus, 1
Polaribacter, 10
Halobacillus, 6
Persicivirga, 1
Pedobacter, 2
Flaviramulus, 6
Olleya, 9
Maribacter, 22
Flavobacterium, 35
Leeuwenhoekiella, 4
Bacillus, 578
Formosa, 2
Gillisia, 2
Gelidibacter, 2
Gaetbulibacter, 2
ALPHAPROTEOBACTERIA
16 genera
59 strains
Agrococcus, 1
Subtercola, 1
Stenotrophomonas,
6
Shewanella, 44
Rheinheimera, 1
Sanguibacter, 6
Psychromonas, 10
Salinibacterium, 17
15 genera
534 strains
GAMMAPROTEOBACTERIA
Arthrobacter, 41
Psychrobacter, 98
Alteromonas, 66
Colwellia, 5
Dasania, 1
Glaciecola, 8
Granulosicoccus, 1
Halomonas, 6
Marinomonas, 1
Photobacterium, 2
Rhodococcus, 5
Plantibacter, 1
Nocardioides, 1
Pseudomonas, 51
Micrococcus, 16
Brachybacterium, 2
Brevibacterium, 3
Cellulomonas, 1
Microbacterium, 3
Leifsonia, 12
Curtobacterium, 1
Knoellia, 2
Pseudoalteromonas,
234
Information for Culture Condition
Temperature : 4 – 37C
Media: R2A, ZB, MR2A, TSA, NA
Enzyme and polymer Production
Protease test on ZoBell or 0.1x NA with skim milk
Lipase test on ZoBell or 0.1x NA with TBA
Chitinase test on ZoBell or 0.1X NA with coloidal chitin
Polymer test on SZoBell with high glucose content
Tests at 10C and 20 C
Needs for KOPRI BioDB
 Management and sharing of bio-resources from
polar areas
 Sharing biodiversity information with national and
international organization
AMD: Antarctic Master Directory
 Central directory system containing all Antarctic data set descriptions
gathered by NADCs.
 Hosted by the Global Change Master Directory (GCMD)
Scientist
Metadata
entry
Scientist
Metadata
search
Global
Change
Master
Directory
Antarctic
Master
Directory
Metadata entry
ADMS
Antarctic Data Management System
National
Antarctic
Data
Centre
National
Antarctic
Data
Centre
Korea
Polar
Data
Centre
Data entry
Scientist
Data search
Scientist
Data Management
Public databases
• Data download (GenBank Taxonomy etc)
Public users
Contributors
Deposit of
resources
Delivery of
resources
• Metadata upload (AMD)
• Original data transfer (EBA, SCAR-Marbin etc)
search
KOPRI BioDB
(Culture Collection)
Public users
Data
download
Curators
•
•
•
•
Long-term preservation of bio-resources
Identification
Characterization
Data updates
DB Structure
Sample DB
Reference DB
Taxonomy DB
Nomenclature DB
Environmental data
Geographical data
References
Taxonomic hierarchy
Nomenclature (Authors, year, Korean name)
Strain DB
Media DB
Media composition
Schema
Sample Database
Sample Database
Sample Database
Sample Database
Sample Database
Schema for Strain DB
Strain DB
Strain DB
Strain DB
Strain DB
Workflow for delivery
Search
User
save
Selection
User
E-mail of order information
and strain information
Order
Shopping Cart
Sorting by curator (Work
order on the DB system
and E-mail alert)
Curator 1
Curator 2
User
When strains have problems
(no revival, contamination, misidentification etc)
Curator 3
Delivery
Receive Claim
Curator
Claim
Records for
Claim
Revival test
Purity check
Re-identification
Data Search : click next category for search or use boolean search option
Taxonomy
Geography
Habitats
Characteristics
Others
Taxonomy
AND / OR / NOT
AND / OR / NOT
AND / OR / NOT
AND / OR / NOT
AND / OR / NOT
AND / OR / NOT
AND / OR / NOT
AND / OR / NOT
Division
Kingdom
Phylum
Class
Order
Family
Genus
Species
Bacillus
subtilis
Boolean Search
Search
Bacillus [genus] AND subtilis [species]
Search History
Show results
Further Search
Show results
Further Search
1231 results from : Bacillus [genus]
153 results from : Bacillus [genus] AND subtilis [species]
Search Results
Select



Order
Strain
KOPRI 25231
KOPRI 22321
KOPRI 23215
Species
Bacillus subtilis
Bacillus subtilis
Bacillus subtilis
Shopping cart
Locality
Antarctic
Barents sea
Cara sea
Download Data
Habitat
marine
marine
marine
Characteristics
protease at 4˚C
lipase at 15, 20 and 25˚C
lipase at 20 and 25˚C
Availability
strain
none
strain
Welcome any advices and comments
Soon Gyu Hong (Korea Polar Research Institute)
[email protected]