Database Integration toward Semantic Web:             Development of     Ontologies and RDF databases             Database...
Paradigm shift in biology   • Appearance of “High-throughput” devices      – Next-generation sequencer, Mass spectrometry ...
To make efficient use of data...• Sharing and integration of data are required for  knowledge mining from a sea of data   –...
History of the project          Survey	  study          in	  CSTP,	  CAO                                                 P...
Activities by NBDC1. Formulation of strategies related to coordination and    integration of databases(DBs), and internati...
10 programs for coordination toward      integration of related databases•   Glycobiology (JCGG-DB)•   Brain imaging (J-AD...
Activities by DBCLS1.Database integration using RDF technology  – TogoDB, Biohackathon2.Advanced search system using RDF  ...
Activities by DBCLS5.Development of large-scale data navigation  – SRA, GEO6.Support for curators  – natural language proc...
TogoDBhTp://semanRc.togodb.dbcls.jp/                                                                           9          ...
TogoDBhTp://semanRc.togodb.dbcls.jp/                                                                           10         ...
TogoTable                 hTp://togotable.dbcls.jp/• It is a tool that adds information (annotation)  extracted from RDF n...
TogoTable                 hTp://togotable.dbcls.jp/• It is a tool that adds information (annotation)  extracted from RDF n...
Biohackathon                  hTp://www.biohackathon.org/• Bio + Hack + Marathon = Biohackathon• Working-level meeting for...
AcknowledgmentNBDC  Prof. Michio Oishi, Director  Prof. Toshihisa Takagi, Deputy director/Research supervisor  Prof. Takes...
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Database Integration toward Semantic Web: Development of Ontologies and RDF databases

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The 3rd Asian Communications for Glycobiology and Glycotechnology Database Meeting at Okinawa on April 23 and 24, 2012

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Database Integration toward Semantic Web: Development of Ontologies and RDF databases

  1. 1. Database Integration toward Semantic Web: Development of Ontologies and RDF databases Database Center for Life Science (DBCLS), Research Organization of Information and Systems (ROIS) Shin Kawano kawano@dbcls.rois.ac.jp 3rd ACGG-DB meeting@Okinawa, 23-24 Apr. 2012 2012 Shin Kawano Licensed Under CC-BY-SA 2.1 Japan license
  2. 2. Paradigm shift in biology • Appearance of “High-throughput” devices – Next-generation sequencer, Mass spectrometry • Large scale projects are prompted – 1000 Genome Project, Human Proteome Project • Data explosion – SRA: 1.9 trillions sequences, 211.6 trillions bases, 1.68 PB disk spacesFrom hypothesis-driven research to data-driven research 2 2012 Shin Kawano Licensed Under CC-BY-SA 2.1 Japan license
  3. 3. To make efficient use of data...• Sharing and integration of data are required for knowledge mining from a sea of data – only data publication is insufficient – data “sharing” is needed for reuse, diversion, mashup, and integration of the data• To facilitate data sharing, – standardization of terminology – standardization of data exchange format – clarification of rules regarding data exchange (copyright, personal information, etc...) 3 2012 Shin Kawano Licensed Under CC-BY-SA 2.1 Japan license
  4. 4. History of the project Survey  study in  CSTP,  CAO Pilot  project 1st  phase  project 2nd  phase  project (2005  -­‐  2007) in  DBCLS,  ROIS in  NBDC,  JST (2014  -­‐   (2007  -­‐  2010) (2011  -­‐  2013) BIRD  project  in  JST (2001  -­‐  2011)CSTP:   the  Council  for  Science  and  Technology  policy  within  the  Cabinet  Office  (CAO)DBCLS:   Database  Center  for  Life  Science  within  Research  OrganizaRon  of  InformaRon  and                           Systems  (ROIS)  NBDC:   NaRonal  Bioscience  Database  Center  within  Japan  Science  and  Technology  Agency  (JST)BIRD:   InsRtute  for  BioinformaRcs  Research  and  Development  within  JST 4 2012 Shin Kawano Licensed Under CC-BY-SA 2.1 Japan license
  5. 5. Activities by NBDC1. Formulation of strategies related to coordination and integration of databases(DBs), and international cooperation2. Creation and management of a portal website from which users access existing life science DBs http://biosciencedbc.jp/?lng=en3. Funding of R&D of new technology necessary for organizing and linking life science DBs (Program Concerning Technology Development for DB Integration) DBCLS won this budget4. Funding of R&D that coordinate existing and emerging DBs in specific research fields (Program for Coordination Toward Integration of Related DBs) 10 fields won this budget Including JCGG-DB (PI: Hisashi Narimatsu)
  6. 6. 10 programs for coordination toward integration of related databases• Glycobiology (JCGG-DB)• Brain imaging (J-ADNI)• Metabolome• Drug (KEGG)• Meta-genome• Plant• Human genome variations• Phenome• Protein structures (PDBj)• Nagahama cohort 6 2012 Shin Kawano Licensed Under CC-BY-SA 2.1 Japan license
  7. 7. Activities by DBCLS1.Database integration using RDF technology – TogoDB, Biohackathon2.Advanced search system using RDF – TogoTable, RDF genome3.Development of platform for analytical workflows – DBCLS Galaxy4.Standardization of ontology, corpus, dictionary – OntoFinder/OntoFactory, PubCorpus 7 2012 Shin Kawano Licensed Under CC-BY-SA 2.1 Japan license
  8. 8. Activities by DBCLS5.Development of large-scale data navigation – SRA, GEO6.Support for curators – natural language processing (NLP) services – computer supported cooperative work (CSCW)7.Creating original contents – TogoTV, First Author’s, BodyParts3D/Anatomography 8 2012 Shin Kawano Licensed Under CC-BY-SA 2.1 Japan license
  9. 9. TogoDBhTp://semanRc.togodb.dbcls.jp/ 9 2012 Shin Kawano Licensed Under CC-BY-SA 2.1 Japan license
  10. 10. TogoDBhTp://semanRc.togodb.dbcls.jp/ 10 2012 Shin Kawano Licensed Under CC-BY-SA 2.1 Japan license
  11. 11. TogoTable hTp://togotable.dbcls.jp/• It is a tool that adds information (annotation) extracted from RDF network to tabulated data 11 2012 Shin Kawano Licensed Under CC-BY-SA 2.1 Japan license
  12. 12. TogoTable hTp://togotable.dbcls.jp/• It is a tool that adds information (annotation) extracted from RDF network to tabulated data 12 2012 Shin Kawano Licensed Under CC-BY-SA 2.1 Japan license
  13. 13. Biohackathon hTp://www.biohackathon.org/• Bio + Hack + Marathon = Biohackathon• Working-level meeting for data standardization and integration• Attendees from foreign countries are invited (All travel expenses are supported)• 2 - 7 Sep. 2012 in Toyama city• A few slots are available for glyco-informaticians 13 2012 Shin Kawano Licensed Under CC-BY-SA 2.1 Japan license
  14. 14. AcknowledgmentNBDC Prof. Michio Oishi, Director Prof. Toshihisa Takagi, Deputy director/Research supervisor Prof. Takeshi Nagasu, Research supervisorDBCLS Prof.Yuji Kohara, Director Prof. Shoko Kawamoto,Vice directorProgram for Coordination Toward Integration of Related Databases Directors Prof. Hisashi Narimatsu, AIST Prof. Tetsushi Tabata, KDRI Prof. Takeshi Iwatsubo, U. of Tokyo Prof. Katsushi Tokunaga, U. of Tokyo Prof. Shigehiko Kanaya, NAIST Prof. Tetsuro Toyoda, RIKEN Prof. Minoru Kanehisa, Kyoto U. Prof. Haruki Nakamura, Osaka U. Prof. Ken Kurokawa, TITECH Prof. Fumihiko Matsuda, Kyoto U. And all members who contribute the Life Science Database Integration Project 14 2012 Shin Kawano Licensed Under CC-BY-SA 2.1 Japan license

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