integrated database biology with well-curated and circulated knowledge
DESCRIPTION
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.TRANSCRIPT
© 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
Integrated database biology with well-curated and
well-circulated knowledge
Dr. Hidemasa BonoDatabase Center for Life Science(DBCLS)
Research Organization of Information and Systems
English?
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日本語？
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DBCLS: Database Center for Life Science•Since 2007•Located at Hongo campus(Asano area) of the University of Tokyo(UT)•Not affiliated to UT
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http://dbcls.rois.ac.jp/
バイオDB7-8
NBDC•National Bioscience Database Center•Since 2011•Affiliated to Japan Science and Technology Agency (JST)
5http://biosciencedbc.jp/nbdc.cgi?lng=en&gg=projects_and_activities
バイオDB1-3
8http://biosciencedbc.jp/dbcatalog/
10http://biosciencedbc.jp/dbsearch/en/2P-0240
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What is DBCLS doing now?
13http://biosciencedbc.jp/nbdc.cgi?lng=en&gg=projects_and_activities
Technology development of database integration1.Database integration with RDF2.Development and maintenance of research environment for accessing databases3.Technology development of the integrated database search4.Maintenance and standardization of ontologies, dictionaries, and corpus 5.Technology development of huge amount of public biological data6.Development and distribution of the system for manual curation7.Development and maintenance of contents concerning the integrated database 14
2P-0269
2P-0978
1P-0881
統合TV (TogoTV)•Curated tutorial movies for DB&tools‒Freely available from YouTube & iTunes Store‒Lectures from various classes‒over 500 contents
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Kawano S, Ono H, Takagi T, Bono H Brief Bioinform. Jul 29 (2011)
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p://lif
escien
cedb.jp
/bp3d/
BodyParts3D/Anatomography
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Wikimedia commons for circulation
RefEx: curated expression dataset for circulation of knowledge obtained
•RefEx: Reference Expression dataset‒GGRNA‒Bodyparts3D
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http://refex.dbcls.jp/ 2P-0131 2P-0113
How to deal with ‘big data’ from NGS
•Before publication‒TogoTV: How to...•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)
© 2011 DBCLS Licensed under CC 表示 2.1 日本
SRR001356.1 2023DAAXX:5:1:123:563 length=33TGTCGGTCCAGCTCGGCCTTGGGCTCCGTTTTC+SRR001356.1 2023DAAXX:5:1:123:563 [email protected] 2023DAAXX:5:1:123:476 length=33TCTGAACCCGACTCCCTTTCGATCGGCCGCGGG+SRR001356.2 2023DAAXX:5:1:123:476 [email protected] 2023DAAXX:5:1:121:746 length=33GTGGCAGCGTTTTTGGGCCCGCCGCTTGCCGTT+SRR001356.3 2023DAAXX:5:1:121:746 length=33IIIII&IIIIIIIIIIIIIIIIHI1IIIIIIII
FASTQ
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2P-0132
Digest of archived NGS data•http://sra.dbcls.jp/ •Search by publications
•Search by diseases20
2P-0133
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! ✴「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.✴Visit our booth ʻバイオDB7-8ʻ 21
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バイオDB7-8