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2 DNA 87 ( ) Nucleic Acids ResearchDB RNA : 511 Bio DB Catalog (DBCAT) 2

3 GenBank MB SRS) DAS) 3

4 4

5 5

6 A A A 6

7 OGSA-DAI 7

9 9

10 DB Medical Encyclopedia 3K entries PRF DB () KEGG 18K entries SwissProt 163K entries, 60M amino acids PIR 283K entries, 96M amino acids PDB 28K protein structures Ensembl, DDBJ Human 24K genes 3.3G nucleotides MDDR 150K compounds PubChem, Ligand Info 1.8M compounds ENZYME GPCR-DB NucleaRDB LGIC DB 10

11 Ligand.Info ChemBank subset 2,344 ChemPDB subset 4,009 KEGG subset 10,005 Anti-HIV NCE subset 42,689 Drug-likeness NCI subset 192,323 Not annotated NCI subset 15,237 AKos GmbH subset 544,391 Ligand.InfoAsinex Ltd. subset 348,276 Tim Tec subset 7,500 1,159,274 PubChem 711,361 High Thorough Screening 344Bio Assay Drug Bank(

12 (Gene Ontology) Nuclear Receptor NR (MDL Drug Data Report) Endocrine Agents Glucocorticoid receptor Glucocorticoid like Estrogen like Hormones and agents affecting hormone mechanisms Estrogen receptor ER alpha Androgen receptor ER beta Estrogen agonist Estrogen receptor modulator 12

BLAST Query: 1 MSVMYKKILYPTDFSETAEIALKHVKAFKTLKAEEVILLHVIDEREIKKRDIFSLLLGVA 60 M M++K+L+PTDFSE A A++ + ++ EVILLHVIDE +++ L+ G + Sbjct: 1 MIFMFRKVLFPTDFSEGAYRAVEVFEKRNKMEVGEVILLHVIDEGTLEE-----LMDGYS

13 BLAST Query: 1 MSVMYKKILYPTDFSETAEIALKHVKAFKTLKAEEVILLHVIDEREIKKRDIFSLLLGVA 60 M M++K+L+PTDFSE A A EVILLHVIDE +++ L+ G + Sbjct: 1 MIFMFRKVLFPTDFSEGAYRAVEVFEKRNKMEVGEVILLHVIDEGTLEE-----LMDGYS 55 Query: 61 GLNKSVEEFENELKNKLTEEAKNKMENIKKELEDV--GFKVKDIIVVGIPHEEIVKIAED E ++K KL EEA K++ +E++ V+ II GIP +EIVK+AE+ Sbjct: 56 FFYDNAEIELKDIKEKLKEEASRKLQEKAEEVKRAFRAKNVRTIIRFGIPWDEIVKVAEE OG NH1 NE NH2 NZ OE2 NH3 ND2 13

14 MLBGGATSGKRC (4) 14

15 Web OGSA-DAI OGSA-DAI DB DB DB SwissProt, PIR, PDB, DDBJ ENZYME, GPCRDB MDL, ChemBank, Ligand KEGG, Ensembl NucleaRDB ChemPDB 15

16 ID ID

17 OGSA-DAI Open Grid Services Architecture Data Access and Integration Discover Registry GDSR SOAP/HTTP service creation API interactions Client Request Bind Create Factory GDSF Receiver File Transfer Grid Data Service GDS (RDB, XML DB 17

18 Tomcat HTTPS () SOAP Factory Factory Factory Factory Factory (BLAST) (OGSA-DAI) GDSF GDS GDSF GDS BLAST GDS: B MDDR DB (Enzyme, GPCR-DB, NucleaRDB, LGIC-DB) DB SwissProt DB PIR DB PDB (Globus Toolkit 3) 18

Category Database Amount Disease Medical Encyclopedia 3079 entries

2,932,352,227 bases 163,235 entries, 59,631,787 amino acids 283,416

19 Category Database Amount Disease Medical Encyclopedia 3079 entries Genome Protein Compound Ensembl DDBJ Swiss-Prot PIR PDB MDL Drug Data Report (MDDR-3D) Ver Human 24,195 genes, 3,272,187,692 bases Mouse 28,055 genes, 2,932,352,227 bases 163,235 entries, 59,631,787 amino acids 283,416 entries, 96,216,763 amino acids 27,969 structures entries Interaction Ligand Ontology ENZYME, GPCR-DB, NucleaRDB, LGIC-DB BioDataGrid 19

20 Medical Encyclopedia at USA SwissProt, EnsEMBL at UK DDBJ, KEGG, LIT-DB PDBj MDDR at Japan DataGrid at Pittsburgh, USA 20

21 DDBJ Web Processing Time (msec.) SuperComputing Data Size (bytes) 21

22 EBI Web SuperComputing Processing Time (msec.) Data Size (bytes) 22

23 OGSA-DAI SC PRF LITDB, Medical Encyclopedia, KEGG, DDBJ, EnsEMBL, SwissProt, PIR, PDB, Enzyme, GPCR-DB, NucleaRDB, LGIC-DB, MDDR, ChemBank, ChemPDB, NCI 23

DDBJ Ei-ji Nakama nakama at com-one.com COM-ONE Ltd. DDBJ p. 1

DDBJ Ei-ji Nakama nakama at com-one.com COM-ONE Ltd. DDBJ p. 1 DDBJ - 2007-06-18 - Ei-ji Nakama nakama at com-one.com COM-ONE Ltd. DDBJ p. 1 R XML R[6] XML XML[1]. R XML[1] libxml(http://xmlsoft.org/). R XML, libxml. XML-1.9.0 encoding. Omegahat a, CRAN. a http://www.omegahat.org/