3 XML SPring-8 SPring-8 DNA DNA 4 XML BLAST)
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1 BioGrid
2 3 XML SPring-8 SPring-8 DNA DNA 4 XML BLAST)
3 5 (flat file) XML DB XML DB DDBJ 6 DNA (SWISS-PROT) (PDB)
4 XML 7 Common Format SWISS-PROT PIR PDB entry entry ProteinEntry PDBj ID entry/id entry/@name ProteinEntry/@id PDBj/@entry_ID entry/name entry/proteinname ProteinEntry/protein/name PDBj/main/entity/entity_item/desc iption entry/gene entry/genes/gene/@name ProteinEntry/genetics/gene/uid PDBj/main/entity/entity_item/src_g en/gene entry/organism/scientif PDBj/main/entity/entity_item/src_g entry/organisms/organism/name ProteinEntry/organism/formal ic en/scientific_name entry/organism/commo PDBj/main/entity/entity_item/src_g entry/organisms/organism/name ProteinEntry/organism/common n en/common_name entry/reference entry/references/reference ProteinEntry/reference/refinfo PDBj/main/citation/citation_item entry/function entry/comments EC# entry/ec_num entry/proteinname --- PDBj/main/entity/entity_item/EC entry/keyword entry/keywords/keyword ProteinEntry/keywords/keyword PDBj/main/struct/keywords entry/sequence entry/sequence ProteinEntry/sequence PDBj/main/entity/entity_item/seq_ one_letter_code entry/feature entry/features/feature ProteinEntry/feature PDBj/struct/site entry/feature/type entry/features/feature/@key ProteinEntry/feature/feature-type PDBj/struct/site/@id entry/feature/descriptio entry/features/feature/@descriptio ProteinEntry/feature/description n n PDBj/struct/site/site_gen/details XML <?xml version="1.0"?> <entry> <id> </id> <date> </date> <name db= pir acc=.. > </name> <gene db= sp acc=.. > </gene> <organism db="pir" acc=".."> <scientific db= pir acc=.. > </scientific> <common db= pir acc=.. > </common> </organism> <reference db= pir acc=.. > <author> </author> <citation> </citation> <volume></volume> <year> </year> <title> </title> <first_page> </first_page> <last_page> </last_page> </reference> <function db= sp acc=.. > <desc> </desc> </function> <keyword db= sp acc=.. > </keyword> <feature db= pir acc=.. > <type> </type> <desc> </desc> <start> </start> <end> </end> </feature> <sequence db= sp acc=.. length=.. > </sequence> </entry> 8
5 9 SOAP SOAP PC XML XML DB DB datagrid Web PIR SWISS PROT PDB XML SOAP
6 11 XML SWISS PROT PIR PDB 12
7 XML 13 XSLT HTML (1) 14
8 XSLT HTML (2) 15 XSLT HTML (3) 16
9 17 18 Local Disk 3. Error check 2Download Public DB BioDB-Updater 4. Post Processing 1 Pre-download check Mirror DB BLAST index Others Configuration File
10 HoCDB Homology-based Clustering DataBase 19 SwissProt(+TrEMBL) 85 BLAST HoCDB HoCDB Swiss-Prot PDB SCOP BLAST All Against All 20
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12 23 XML PRF XML 24 PRF WEB Server System Users Database System litquery.pl seqsrch.pl motsrch.pl synsrch.pl blast seqget.pl orgget.pl CGI (SyBase, Solaris) (Perl,) XML Query Server
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14 27 CGI HTML 28 CGI XML
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