database integration toward semantic web: development of ontologies and rdf databases

2012 Shin Kawano Licensed Under CC-BY-SA 2.1 Japan license

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 [email protected]

3rd ACGG-DB meeting@Okinawa, 23-24 Apr. 2012


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 spaces

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From hypothesis-driven research to data-driven research


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


History of the project

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Survey studyin CSTP, CAO(2005 -‐ 2007)

Pilot projectin DBCLS, ROIS(2007 -‐ 2010)

1st phase projectin NBDC, JST(2011 -‐ 2013)

2nd phase project(2014 -‐

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

Activities by NBDC

1. Formulation of strategies related to coordination and integration of databases(DBs), and international cooperation

2. Creation and management of a portal website from which users access existing life science DBs http://biosciencedbc.jp/?lng=en

3. Funding of R&D of new technology necessary for organizing and linking life science DBs (Program Concerning Technology Development for DB Integration)

4. 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 budgetIncluding JCGG-DB (PI: Hisashi Narimatsu)

DBCLS won this budget

• Glycobiology (JCGG-DB)• Brain imaging (J-ADNI)• Metabolome• Drug (KEGG)• Meta-genome• Plant• Human genome variations• Phenome• Protein structures (PDBj)• Nagahama cohort


10 programs for coordination toward integration of related databases

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Activities by DBCLS1.Database integration using RDF technology

– TogoDB, Biohackathon

2.Advanced search system using RDF– TogoTable, RDF genome

3.Development of platform for analytical workflows– DBCLS Galaxy

4.Standardization of ontology, corpus, dictionary– OntoFinder/OntoFactory, PubCorpus

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Activities by DBCLS

5.Development of large-scale data navigation– SRA, GEO

6.Support for curators– natural language processing (NLP) services– computer supported cooperative work (CSCW)

7.Creating original contents– TogoTV, First Author’s, BodyParts3D/Anatomography

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TogoDB

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hTp://semanRc.togodb.dbcls.jp/


TogoDB

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hTp://semanRc.togodb.dbcls.jp/


TogoTable

• It is a tool that adds information (annotation) extracted from RDF network to tabulated data

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hTp://togotable.dbcls.jp/

hTp://togotable.dbcls.jp/


TogoTable

• It is a tool that adds information (annotation) extracted from RDF network to tabulated data

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• 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


Biohackathon

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hTp://www.biohackathon.org/


Acknowledgment

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NBDCProf. Michio Oishi, DirectorProf. Toshihisa Takagi, Deputy director/Research supervisorProf. Takeshi Nagasu, Research supervisor

DBCLSProf. Yuji Kohara, DirectorProf. Shoko Kawamoto, Vice director

Program for Coordination Toward Integration of Related Databases DirectorsProf. Hisashi Narimatsu, AIST Prof. Tetsushi Tabata, KDRIProf. Takeshi Iwatsubo, U. of Tokyo Prof. Katsushi Tokunaga, U. of TokyoProf. Shigehiko Kanaya, NAIST Prof. Tetsuro Toyoda, RIKENProf. 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