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Integrated database biology    with well-curated and well-circulated knowledge        Dr. Hidemasa Bono    Database Center...
English?           2
日本語?       3
DBCLS: Database Center for Life Science• Since 2007               バイオDB7-8• Located at Hongo campus(Asano area)  of the Un...
NBDC• National Bioscience Database Center• Since 2011                                                     バイオDB1-3• Affiliat...
http://biosciencedbc.jp/                  2P-0220                            6
DB Cataloghttp://biosciencedbc.jp/   7
http://biosciencedbc.jp/dbcatalog/   8
DB Cross Searchhttp://biosciencedbc.jp/   9
2P-0240http://biosciencedbc.jp/dbsearch/en/                                   10
DB Archivehttp://biosciencedbc.jp/   11
12
What is DBCLS doing now?    http://biosciencedbc.jp/nbdc.cgi?lng=en&gg=projects_and_activities   13
Technology development of database integration1.Database integration with RDF2.Development and maintenance of research env...
統合TV (TogoTV)•Curated tutorial movies for DB&tools ‒Freely available from YouTube & iTunes Store ‒Lectures from various cl...
BodyParts3D/Anatomography                                            d /                                         p 3      ...
Wikimedia commons for circulation                                    17
RefEx: curated expression datasetfor circulation of knowledge obtained  http://refex.dbcls.jp/ • RefEx: Reference Expressi...
How to deal with big data                      2P-0132        from NGS• Before publication                             SRR...
Digest of archived NGS data• http://sra.dbcls.jp/• Search by publications• Search by diseases     2P-0133                 ...
Conclusion★   Curation and circulation of data required.    ✴ So many raw data, so little curated data and      circulated...
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Integrated database biology with well-curated and circulated knowledge

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In Database Center for Life Science (DBCLS), we have been tackling the problem how to organize various types of database in life science under the MEXT Integrated Database Project. Currently, we are developing database integration technologies to utilize huge amount of public data in collaboration with various sectors of biologists including National Bioscience Database Center (NBDC) newly founded in Japan Science and Technology Agency (JST). We will present current status of the project and how to use data produced and maintained in the system.

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Transcript of "Integrated database biology with well-curated and circulated knowledge"

  1. 1. Integrated database biology with well-curated and well-circulated knowledge Dr. Hidemasa Bono Database Center for Life Science(DBCLS)Research Organization of Information and Systems © ライフサイエンス統合データベースセンター/大学共同利用機関法人 情報・システム研究機構
  2. 2. English? 2
  3. 3. 日本語? 3
  4. 4. DBCLS: Database Center for Life Science• Since 2007 バイオDB7-8• Located at Hongo campus(Asano area) of the University of Tokyo(UT)• Not affiliated to UT http://dbcls.rois.ac.jp/ 4
  5. 5. NBDC• National Bioscience Database Center• Since 2011 バイオDB1-3• Affiliated to Japan Science and Technology Agency (JST) http://biosciencedbc.jp/nbdc.cgi?lng=en&gg=projects_and_activities 5
  6. 6. http://biosciencedbc.jp/ 2P-0220 6
  7. 7. DB Cataloghttp://biosciencedbc.jp/ 7
  8. 8. http://biosciencedbc.jp/dbcatalog/ 8
  9. 9. DB Cross Searchhttp://biosciencedbc.jp/ 9
  10. 10. 2P-0240http://biosciencedbc.jp/dbsearch/en/ 10
  11. 11. DB Archivehttp://biosciencedbc.jp/ 11
  12. 12. 12
  13. 13. What is DBCLS doing now? http://biosciencedbc.jp/nbdc.cgi?lng=en&gg=projects_and_activities 13
  14. 14. Technology development of database integration1.Database integration with RDF2.Development and maintenance of research environment for accessing databases 2P-09783.Technology development of the integrated database search4.Maintenance and standardization of ontologies, dictionaries, and corpus5.Technology development of huge amount of public biological data6.Development and distribution of the system for manual curation 2P-02697.Development and maintenance of contents concerning the integrated database 1P-0881 14
  15. 15. 統合TV (TogoTV)•Curated tutorial movies for DB&tools ‒Freely available from YouTube & iTunes Store ‒Lectures from various classes Kawano S, Ono H, Takagi T, Bono H ‒ over 500 contents Brief Bioinform. Jul 29 (2011) 15
  16. 16. BodyParts3D/Anatomography d / p 3 /b . jp d b c e ie n s c if e / l p :/ t t h 16
  17. 17. Wikimedia commons for circulation 17
  18. 18. RefEx: curated expression datasetfor circulation of knowledge obtained http://refex.dbcls.jp/ • RefEx: Reference Expression dataset ‒GGRNA 2P-0131 2P-0113 ‒Bodyparts3D 18
  19. 19. How to deal with big data 2P-0132 from NGS• Before publication SRR001356.1 2023DAAXX:5:1:123:563 length=33 TGTCGGTCCAGCTCGGCCTTGGGCTCCGTTTTC FASTQ +SRR001356.1 2023DAAXX:5:1:123:563 length=33 -IIIIIIII8IIIIIIIIIII6IIIIIIIII9I @SRR001356.2 2023DAAXX:5:1:123:476 length=33 TCTGAACCCGACTCCCTTTCGATCGGCCGCGGG +SRR001356.2 2023DAAXX:5:1:123:476 length=33 ‒TogoTV: How to... IIIIIIIIIIIIIIIIIIIIIGIIIIIII-III @SRR001356.3 2023DAAXX:5:1:121:746 length=33 GTGGCAGCGTTTTTGGGCCCGCCGCTTGCCGTT +SRR001356.3 2023DAAXX:5:1:121:746 length=33 IIIII&IIIIIIIIIIIIIIIIHI1IIIIIIII •Make use of available tools •Handle huge amount of data •Submit to DDBJ Sequence Read Archive(DRA)• After publication ‒Promote recycle of archived data •Metadata(Experimental condition etc) 19 © 2011 DBCLS Licensed under CC 表示 2.1 日本
  20. 20. Digest of archived NGS data• http://sra.dbcls.jp/• Search by publications• Search by diseases 2P-0133 20
  21. 21. Conclusion★ Curation and circulation of data required. ✴ So many raw data, so little curated data and circulated knowledge. ✴ 「さらさらで、知の巡りのよい分子生物学」★ Sharing information needed. ✴ Join our forum tomorrow! 3F5 ✴ 「もし分子生物学者がGoogle+の招待を受けたら」 ✴ Join tutorial online and offline(統合DB講習会)★ For information in Japanese. ✴ バイオDB7-8 Visit our booth ʻバイオDB7-8ʻ 21
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