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.

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. English?
2

3. 日本語？
3

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. 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. http://biosciencedbc.jp/
2P-0220
6

7. DB Catalog
http://biosciencedbc.jp/ 7

8. http://biosciencedbc.jp/dbcatalog/ 8

9. DB Cross Search
http://biosciencedbc.jp/ 9

10. 2P-0240
http://biosciencedbc.jp/dbsearch/en/
10

11. DB Archive
http://biosciencedbc.jp/ 11

12. 12

13. What is DBCLS doing now?
http://biosciencedbc.jp/nbdc.cgi?lng=en&gg=projects_and_activities 13

14. Technology development
of database integration
1.Database integration with RDF
2.Development and maintenance of research
environment for accessing databases 2P-0978
3.Technology development of the integrated
database search
4.Maintenance and standardization of ontologies,
dictionaries, and corpus
5.Technology development of huge amount of
public biological data
6.Development and distribution of the system for
manual curation 2P-0269
7.Development and maintenance of contents
concerning the integrated database 1P-0881 14

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. BodyParts3D/Anatomography
d /
p 3
/b
. jp
d b
c e
ie n
s c
if e
/ l
p :/
t t
h 16

17. Wikimedia commons for circulation
17

18. RefEx: curated expression dataset
for circulation of knowledge obtained
http://refex.dbcls.jp/
• RefEx: Reference Expression dataset
‒GGRNA 2P-0131 2P-0113
‒Bodyparts3D
18

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. Digest of archived NGS data
• http://sra.dbcls.jp/
• Search by publications
• Search by diseases 2P-0133
20

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