From the World Directory of Collections of Cultures of Microorganisms towards Mash-up of Biodiversity and Sequence Databases Director, WFCC-MIRCEN World Data Centre for Microorganisms V ice-chair, Governing Board of Global Biodiversity Information Facility (GBIF) Center for Information Biology and DNA Data Bank of Japan (DDBJ) National Institute of Genetics Hideaki Sugawara

2006/10/23Biology Resource Centre2 Evolution of Culture Collections to BRC Culture collections (low sustainability) OECD BRC report -Underpinning the future of life sciences and biotechnology Genomic Biodiversity Informatics Biosecurity MTA/IPR Legislation Quality of services- accreditation/certification The World Directory to federate culture collections Global BRC Network (GBRCN) for harmonization, efficiency and sustaibability

2006/10/23Biology Resource Centre3 Prototypes of information network for GBRCN.  Global networks, e.g. WFCC-MIRCEN* World Data Centre for Microorganisms (WDCM) Global Biodiversity Information Facility (GBIF)  Regional networks, e.g. EBRCN  National networks, e.g. CCCM, JSCC, TNCC, UKNCC * WFCC: World Federation for Culture Collections MIRCEN: Microbial Resources Centers Network

2006/10/23Biology Resource Centre4 501 culture collections in 66 countries 175 culture collections publish catalogues 154 culture collections have Web pages

2006/10/23Biology Resource Centre5 Registration of culture collections and their holdings Search engines WDCM assigns culture collections WDCM numbers, cf. accession number of sequence data assgined by INSDC

2006/10/23Biology Resource Centre6 WDCN wrapped several databases for one-stop query for a search engine named AHMII  AHMII call CGIs of the member Web sites.  AHMII requires neither change nor expansion of the member Web sites.  AHMII counts on query functions of the member Web sites.  AHMII does not display results in a standardized format.  WDCM has to maintain the program and the list of the member Web sites. More sophisticated system than AHMII is now feasible

2006/10/23Biology Resource Centre7 Web services provide more sophisticated way to aggregate biological data resources RDB schema A XML RDB schema B EXCEL Web services User client Web services provide human interface (Web browsing) and programmatic interface as well.

2006/10/23Biology Resource Centre8 Web services expands beyond BRCs GBIF International Nucleotide Sequence Databases GIS Environmental data Aggregation of taxonomy, phenotypes, sequence data, environmental condition, location, references and even socio-econimcal data will the base of the problem solving environment for R&D and decision makers. Bibliographical databases GBRCN

2006/10/23Biology Resource Centre9 Exampls of mash-up: INSDC and GBIF TxSearch Web service INSD 生物分類 DB SRS Web service INSD 配列 DB XML Central of DDBJ GBIF Providers 標本 DB GBIF Providers 標本 DB GBIF Providers 標本 DB GBIF DiGIR SOAP GBIF のデータベース群と国際塩基配列データベース（ DDBJ ）との連携 複数のプロトコー ル を組合せ TxSearch Web service INSD 生物分類 DB SRS Web service INSD 配列 DB XML Central of DDBJ GBIF Providers 標本 DB GBIF Providers 標本 DB GBIF Providers 標本 DB GBIF DiGIR SOAP GBIF のデータベース群と国際塩基配列データベース（ DDBJ ）との連携 複数のプロトコー ル を組合せ TxSearch Web service INSDC taxonomy DB SRS Web service INSDC sequence DB XML Central of DDBJ GBIF Providers Specimen DB GBIF Providers Specimen DB GBIF Providers Specimen DB GBIF DiGIR SOAP TxSearch Web service INSDC taxonomy DB SRS Web service INSDC sequence DB XML Central of DDBJ GBIF Providers Specimen DB GBIF Providers Specimen DB GBIF Providers Specimen DB GBIF DiGIR SOAP TxSearch Web service INSDC taxonomy DB SRS Web service INSDC sequence DB GBIF Providers Specimen DB GBIF Providers Specimen DB GBIF Providers Specimen DB SOAP DiGIR

2006/10/23Biology Resource Centre10 More fine linkage of specimen including miroorganisms cultures and sequence data by “structured vouchers” - abbreviation of the archiving institution - collection within the institution (possibly null) <specimen-id- specimen identifier within the collection /specimen_voucher=“ | | ”  museums  herbaria  culture collections  stock centers  germplasm repositories (seed banks)  frozen tissue banks  zoos/aquaria/botanical gardens  DNA banks  personal collections  e-voucher archives

2006/10/23Biology Resource Centre11 Example of mash-up: GBIF and mapping tool Google map

2006/10/23Biology Resource Centre12 Example of mash-up: GBIF, data analysis tool and mapping tool BAT has been implemented in NIG based on collaborative work with Australia.

2006/10/23Biology Resource Centre13 With MapServer

2006/10/23Biology Resource Centre14 Display richness of species in Google earth Specimen data were from a plant data file in Japan GBIF node.

2006/10/23Biology Resource Centre15 Display richness of species in Google earth Specimen data were from a plant data file in Japan GBIF node. Grids and color codes are diplayed based on outputs from BAT system

2006/10/23Biology Resource Centre16 Summary  The next generation WDCM will depend on a distributed system based on standard data schema and data transfer protocol.  The question is who designs and maintains the standards.  The next generation WDCM will provide a stable database that supports LSID (Life Science IDentifier) for the linkage of cultures ant their data on genetypes and phenotypes.  The question is who funds these acitivities for a long term.