Presentation is loading. Please wait.

Presentation is loading. Please wait.

Soon Gyu Hong 1, Min Chul Lee 1, Cheng-Dae Choe 2 and Hong Kum Lee 1 KOPRI BioDB A part of Korea Polar Data Center 1 Korea Polar Research Institute 2 Newgex.

Similar presentations


Presentation on theme: "Soon Gyu Hong 1, Min Chul Lee 1, Cheng-Dae Choe 2 and Hong Kum Lee 1 KOPRI BioDB A part of Korea Polar Data Center 1 Korea Polar Research Institute 2 Newgex."— Presentation transcript:

1 Soon Gyu Hong 1, Min Chul Lee 1, Cheng-Dae Choe 2 and Hong Kum Lee 1 KOPRI BioDB A part of Korea Polar Data Center 1 Korea Polar Research Institute 2 Newgex Co. (Boram Pharm. Bioinfo team)

2 Databases to manage Bio- resources Samples from Polar area Soil, sediment, water, glacier, lichens, plants, animals Samples from Polar area Soil, sediment, water, glacier, lichens, plants, animals Microbial and tissue culture Microbial and tissue culture Identification by phylogenetic analysis Identification by phylogenetic analysis Polyphasic classification Polyphasic classification Metagenomic DNA isolation Metagenomic DNA isolation Metagenome library Metagenome library Genome library Genome library Selection of clones Selection of clones Characterization Sample DB Strain DB Sequence DB Genomic DNA DB Genomic DNA DB Genome Library DB Genome Library DB Metagenome Library DB Metagenome Library DB Clone DB Enzyme DB Polymer DB Metabolite DB

3 Samples from Polar Areas Localitywater sedimen t soilglacierplantanimal Fungi (lichens) biofilmtotal Sejong Station Dasan Station Barents/Cara Okhotsk/Bering Austria 8715 Baikal 44 etc total ,73 7 Ny-Ålesund

4 Cultural strains Bacteria: 4,500 strains Molds: 30 strains Moss: 8 strains Microbial cultures Preservation Liquid nigrogen (-180 C) deep freezer (-80 C) Freeze-dry

5 1583 STRAINS 99 GENERA Microbial Cultures

6 ACTINOBACTERIA Microbial Cultures 16 genera 113 strains

7 BACTEROIDETESFIRMICUTES ALPHAPROTEOBACTERIAGAMMAPROTEOBACTERIA 27 genera 171 strains 13 genera 688 strains 16 genera 59 strains 15 genera 534 strains

8 Information for Culture Condition Temperature : 4 – 37C Media: R2A, ZB, MR2A, TSA, NA

9 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

10 Management and sharing of bio-resources from polar areas Sharing biodiversity information with national and international organization Needs for KOPRI BioDB

11 Central directory system containing all Antarctic data set descriptions gathered by NADCs. Hosted by the Global Change Master Directory (GCMD) AMD: Antarctic Master Directory Antarctic Master Directory Global Change Master Directory National Antarctic Data Centre Korea Polar Data Centre Scientist Metadata entry Scientist Metadata search National Antarctic Data Centre Metadata entry Scientist Data entryData search ADMS Antarctic Data Management System

12 Data Management KOPRI BioDB (Culture Collection) KOPRI BioDB (Culture Collection) Curators Public databases Public users search Data download Public users Contributors Public users Contributors Deposit of resources Delivery of resources Long-term preservation of bio-resources Identification Characterization Data updates Metadata upload (AMD) Original data transfer (EBA, SCAR-Marbin etc) Data download (GenBank Taxonomy etc)

13 DB Structure Sample DB Strain DB Reference DB Taxonomy DB Nomenclature DB Media DB Environmental data Geographical data Media composition References Taxonomic hierarchy Nomenclature (Authors, year, Korean name)

14 Schema

15 Sample Database

16

17

18

19

20 Schema for Strain DB

21 Strain DB

22

23

24

25 Workflow for delivery User Search Curator 1 Selection Shopping Cart Order Curator 2 Curator 3 Sorting by curator (Work order on the DB system and alert) save User of order information and strain information Delivery User Claim When strains have problems (no revival, contamination, misidentification etc) Curator Receive Claim Records for Claim Revival test Purity check Re-identification

26 TaxonomyGeographyHabitats Characteristic s Others Data Search : click next category for search or use boolean search option Taxonomy Species Genus Family Order Class Phylum Kingdom Division Boolean Search Bacillus subtilis Search History Search Results AND / OR / NOT Bacillus [genus] AND subtilis [species] Show results Further Search 1231 results from : Bacillus [genus] Show results Further Search 153 results from : Bacillus [genus] AND subtilis [species] SelectStrainSpeciesLocalityHabitatCharacteristicsAvailability KOPRI 25231Bacillus subtilisAntarctic marineprotease at 4˚Cstrain KOPRI 22321Bacillus subtilisBarents seamarinelipase at 15, 20 and 25˚Cnone KOPRI 23215Bacillus subtilisCara seamarinelipase at 20 and 25˚Cstrain Order Shopping cart Download Data Search

27 Welcome any advices and comments Soon Gyu Hong (Korea Polar Research Institute)


Download ppt "Soon Gyu Hong 1, Min Chul Lee 1, Cheng-Dae Choe 2 and Hong Kum Lee 1 KOPRI BioDB A part of Korea Polar Data Center 1 Korea Polar Research Institute 2 Newgex."

Similar presentations


Ads by Google