Advancing Biodiversity Databases with Mash-Up Technology

1. 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

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

3. 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 Biology Resource Centre

4. http://www.wfcc.info/ 501 culture collections in 66 countries 175 culture collections publish catalogues 154 culture collections have Web pages Biology Resource Centre

5. http://www.wdcm.org/ Registration of culture collections and their holdings WDCM assigns culture collections WDCM numbers, cf. accession number of sequence data assgined by INSDC Search engines Biology Resource Centre

6. 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 Biology Resource Centre

7. Web services provide more sophisticated way to aggregate biological data resources User Web services client RDB schema A <result> RDB schema B <request> Web services provide human interface (Web browsing) and programmatic interface as well. XML EXCEL Biology Resource Centre

8. Web services expands beyond BRCs GBIF International Nucleotide Sequence Databases GBRCN Bibliographical databases Environmental data GIS 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. Biology Resource Centre

9. XML Central of DDBJ XML Central of DDBJ XML Central of DDBJ XML Central of DDBJ INSDC taxonomy DB INSD 生物分類DB INSDC taxonomy DB INSD 生物分類DB TxSearch Web service TxSearch Web service TxSearch Web service TxSearch Web service INSD 配列DB INSD 配列DB INSDC sequence DB INSDC sequence DB SRS Web service SRS Web service SRS Web service SRS Web service GBIF GBIF GBIF GBIF 標本DB 標本DB Specimen DB Specimen DB GBIF Providers GBIF Providers GBIF Providers GBIF Providers Specimen DB 標本DB 標本DB Specimen DB GBIF Providers GBIF Providers GBIF Providers GBIF Providers Specimen DB 標本DB 標本DB Specimen DB GBIF Providers GBIF Providers GBIF Providers GBIF Providers Exampls of mash-up: INSDC and GBIF INSDC taxonomy DB TxSearch Web service SOAP INSDC sequence DB SRS Web service Specimen DB GBIF Providers DiGIR Specimen DB GBIF Providers Specimen DB GBIF Providers Biology Resource Centre 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 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 SOAP SOAP SOAP SOAP 複数のプロトコール を組合せ 複数のプロトコール を組合せ http://bioportal.ddbj.nig.ac.jp/gbif_tx/ http://bioportal.ddbj.nig.ac.jp/gbif_tx/ http://bioportal.ddbj.nig.ac.jp/gbif_tx/ http://bioportal.ddbj.nig.ac.jp/gbif_tx/ DiGIR DiGIR DiGIR DiGIR

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

11. Example of mash-up: GBIF and mapping tool Google map Biology Resource Centre

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

13. With MapServer Biology Resource Centre

14. Display richness of species in Google earth Specimen data were from a plant data file in Japan GBIF node. Biology Resource Centre

15. 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 Biology Resource Centre

16. 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. Biology Resource Centre