DNA 87 ( ) Nucleic Acids ResearchDB RNA 29 94 58 29 18 43 153 : 511 Bio DB Catalog (DBCAT) http://www.infobiogen.fr/services/dbcat/ 2
GenBank MB SRS) DAS) 3
4
5
A A A 6
OGSA-DAI 7
9
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
Ligand.Info http://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 http://pubchem.ncbi.nlm.nih.gov/ 711,361 High Thorough Screening 344Bio Assay Drug Bank(http://redpoll.pharmacy.ualberta.ca/drugbank) 256 11
(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 55 Query: 61 GLNKSVEEFENELKNKLTEEAKNKMENIKKELEDV--GFKVKDIIVVGIPHEEIVKIAED 118 + E ++K KL EEA K++ +E++ V+ II GIP +EIVK+AE+ Sbjct: 56 FFYDNAEIELKDIKEKLKEEASRKLQEKAEEVKRAFRAKNVRTIIRFGIPWDEIVKVAEE 115 2. OG NH1 NE NH2 NZ OE2 NH3 ND2 13
MLBGGATSGKRC (4) 14
Web OGSA-DAI OGSA-DAI DB DB DB SwissProt, PIR, PDB, DDBJ ENZYME, GPCRDB MDL, ChemBank, Ligand KEGG, Ensembl NucleaRDB ChemPDB 15
ID ID
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
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 Genome Protein Compound Ensembl DDBJ Swiss-Prot PIR PDB MDL Drug Data Report (MDDR-3D) Ver. 2004.1 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 147969 entries Interaction Ligand Ontology ENZYME, GPCR-DB, NucleaRDB, LGIC-DB BioDataGrid 19
Medical Encyclopedia at USA SwissProt, EnsEMBL at UK DDBJ, KEGG, LIT-DB PDBj MDDR at Japan DataGrid at Pittsburgh, USA 20
DDBJ Web Processing Time (msec.) 7000 6000 5000 4000 3000 2000 SuperComputing 1000 0 0 10000 20000 30000 40000 50000 60000 70000 80000 Data Size (bytes) 21
EBI Web 70000 60000 SuperComputing Processing Time (msec.) 50000 40000 30000 20000 10000 0 0 100000 200000 300000 400000 500000 600000 700000 800000 Data Size (bytes) 22
OGSA-DAI SC2004 16 PRF LITDB, Medical Encyclopedia, KEGG, DDBJ, EnsEMBL, SwissProt, PIR, PDB, Enzyme, GPCR-DB, NucleaRDB, LGIC-DB, MDDR, ChemBank, ChemPDB, NCI 23