CGI DB REST --- URI REpresentational State Transfer SOAP --- RPC, XML RPC XML Remote Procedure Call SOAP Service Oriented Architecture Protocol SOAP +

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1 2005/3/3

2 CGI DB REST --- URI REpresentational State Transfer SOAP --- RPC, XML RPC XML Remote Procedure Call SOAP Service Oriented Architecture Protocol SOAP + WSDL Web Service Description Language SOAP + WSDL + UDDI Universal Description, Discovery, and Integration

3 CGI DB REST --- URI REpresentational State Transfer SOAP --- RPC, XML RPC XML Remote Procedure Call SOAP Service Oriented Architecture Protocol SOAP + WSDL Web Service Description Language SOAP + WSDL + UDDI Universal Description, Discovery, and Integration

4 DBGET, dbfetch (SRS), BioFetch --- REST Entrez E-Utilities (NCBI) --- REST BioDAS (WormBase, Ensembl ) --- REST XML Central of DDBJ ( ) --- SOAP/WSDL KEGG API ( ) --- SOAP/WSDL EBI Web Services --- SOAP/WSDL ESOAP (SOAP E-Utils) --- SOAP/WSDL

5 REST BioFetch EMBL FASTA BioDAS WormBase WormBase

6 WormBase DAS <?xml version="1.0" standalone="yes"?> <!DOCTYPE DASGFF SYSTEM " <DASGFF> <GFF version="1.01" href=" <SEGMENT id="i" start="1" stop="20000" version="1.0"> <FEATURE id="sequence:yk582g6.5/241592" label="yk582g6.5"> <TYPE id="est_match:blat_est_other" category="miscellaneous">est_match:blat_est_other</type> <METHOD id="est_match">est_match</method> <START>1</START> <END>22</END> <SCORE>14.2</SCORE> <ORIENTATION>+</ORIENTATION> <PHASE>0</PHASE> <LINK href=" <TARGET id="yk582g6.5" start="284" stop="305" /> <GROUP id="sequence:yk582g6.5" type="sequence" /> </FEATURE> <FEATURE id="sequence:yk585b5.5/722458" label="yk585b5.5"> <TYPE id="est_match:blat_est_other" category="miscellaneous">est_match:blat_est_other</type> <METHOD id="est_match">est_match</method> <START>1</START> <END>50</END> <SCORE>12.8</SCORE> <ORIENTATION>-</ORIENTATION> <PHASE>0</PHASE> <LINK href=" <TARGET id="yk585b5.5" start="119" stop="168" /> <GROUP id="sequence:yk585b5.5" type="sequence" /> </FEATURE> <FEATURE id="161762" label="inverted_repeat:inverted"> <TYPE id="inverted_repeat:inverted" category="miscellaneous">inverted_repeat:inverted</type> <METHOD id="inverted_repeat">inverted_repeat</method>

7 DAS Distributed Annotation System REST URI XML (DTD) Ensembl UCSC WormBase FlyBase KEGG DAS etc.

8 KEGG DAS - GBrowse GMOD/GBrowse DAS KEGG 237 KEGG

9 KEGG DAS DAS <?xml version="1.0" standalone="yes"?> <!DOCTYPE DASGFF SYSTEM " <DASGFF> <GFF version="1.01" href=" <SEGMENT id="eco" start="205563" stop="255562" version="1.0"> <FEATURE id="ec: /649" label=" "> <TYPE id="enzyme:kegg" category="enzyme">enzyme:kegg</type> <METHOD id="enzyme">enzyme</method> <START>229167</START> <END>229970</END> <SCORE>-</SCORE> <ORIENTATION>+</ORIENTATION> <PHASE>0</PHASE> <LINK href=" <GROUP id="ec: " type="ec" /> </FEATURE> <FEATURE id="ec: /700" label=" "> <TYPE id="enzyme:kegg" category="enzyme">enzyme:kegg</type> <METHOD id="enzyme">enzyme</method> <START>240859</START>

10 BioRuby DAS #!/usr/bin/env ruby require 'bio' serv = Bio::DAS.new(" # (eco) segment = Bio::DAS::SEGMENT.region("eco", , ) # DNA results = serv.get_dna("eco", segment) results.each do dna puts dna.sequence end # results = serv.get_features("eco", segment) results.segments.each do segment segment.features.each do feature puts feature.entry_id puts feature.start end end

11 REST URI

12 REST XML

13 SOAP KEGG API DBGET, GENES, XML Central of DDBJ DDBJ,, GIB, GTOP, PML etc. EBI Web Services DBFetch, WU-BLAST, FASTA, InterProScan NCBI ESOAP Entrez (EFetch, ESearch )

14 SOAP XML SOAP get_genes_by_pathway("path:eco00010") "eco:b0114", "eco:b0115", "eco:b0116",...

15 WSDL XML  <message name="color_pathway_by_objectsrequest"> <part name="pathway_id" type="xsd:string"/> <part name="object_id_list" type="typens:arrayofstring"/> <part name="fg_color_list" type="typens:arrayofstring"/> <part name="bg_color_list" type="typens:arrayofstring"/> </message> <message name="color_pathway_by_objectsresponse"> <part name="return" type="xsd:string"/> </message>   <message name="get_genes_by_pathwayrequest"> <part name="pathway_id" type="xsd:string"/> </message> <message name="get_genes_by_pathwayresponse"> <part name="return" type="typens:arrayofstring"/> </message>  <message name="get_enzymes_by_pathwayrequest"> <part name="pathway_id" type="xsd:string"/>

16 SOAP + WSDL (1) WSDL Perl, Python, Ruby, PHP, Java, C#

17 Ruby #!/usr/bin/env ruby require "soap/wsdldriver" wsdl = " serv = SOAP::WSDLDriverFactory.new(wsdl).create_driver # (eco) puts serv.get_genes_by_pathway("path:eco00010") # (eco) list = serv.list_pathways("eco") list.each do path end puts "#{path.entry_id} t#{path.definition} n"

18 Perl #!/usr/bin/env perl use SOAP::Lite; $wsdl = " $serv = SOAP::Lite -> service($wsdl); # (eco) $list = $serv -> list_pathways("eco"); foreach $path (@{$list}) { } print "$path->{entry_id} t$path->{definition} n";

19 # (eco) get_genes_by_pathway("path:eco00010") eco:b0114 eco:b0115 eco:b0116 eco:b0356 eco:b0688 : # (eco) list_pathways("eco") path:eco00010 path:eco00020 path:eco00030 path:eco00040 path:eco00051 path:eco00052 path:eco00053 path:eco00061 : Glycolysis / Gluconeogenesis - Escherichia coli K-12 MG1655 Citrate cycle (TCA cycle) - Escherichia coli K-12 MG1655 Pentose phosphate pathway - Escherichia coli K-12 MG1655 Pentose and glucuronate interconversions - Escherichia coli K-12 MG1655 Fructose and mannose metabolism - Escherichia coli K-12 MG1655 Galactose metabolism - Escherichia coli K-12 MG1655 Ascorbate and aldarate metabolism - Escherichia coli K-12 MG1655 Fatty acid biosynthesis (path 1) - Escherichia coli K-12 MG1655

20 SOAP Ruby Ruby 1.8 Ruby Perl CPAN SOAP::Lite

21 Java Apache Axis WSDL org.apache.axis.wsdl.wsdl2java jar CLASSPATH

22 Java import keggapi.*; class GetGenesByPathway { public static void main(string[] args) throws Exception { KEGGLocator locator = new KEGGLocator(); KEGGPortType serv = locator.getkeggport(); String query = args[0]; String[] results = serv.get_genes_by_pathway(query); for (int i = 0; i < results.length; i++) { System.out.println(results[i]); } } } Axis CLASSPATH % javac -classpath keggapi.jar GetGenesByPathway.java % java -classpath keggapi.jar:. GetGenesByPathway path:eco00010 eco:b0114 eco:b0115 eco:b0116 :

23 SOAP + WSDL (2) XML XML

24 XML #!/usr/bin/env ruby require 'soap/wsdldriver' wsdl = " serv = SOAP::WSDLDriverFactory.new(wsdl).create_driver # serv.wiredump_dev = STDERR # (eco) puts serv.get_genes_by_pathway("path:eco00010")

25 SOAP XML Wire dump: opening connection to soap.genome.jp... opened <- "POST /keggapi/request_v3.2.cgi HTTP/1.1\r\nAccept: */*\r\ncontent-type: text/xml; charset=utf-8\r\nuser-agent: SOAP4R/1.5.3-ruby1.8.2\r\nSoapaction: \"SOAP/KEGG#get_genes_by_pathway\"\r\nContent-Length: 336\r\nHost: soap.genome.jp\r\n\r\n" <- "<?xml version=\"1.0\" encoding=\"utf-8\"?>\n<env:envelope xmlns:env=\" xmlns:xsi=\" <env:body>\n <n1:get_genes_by_pathway xmlns:n1=\"soap/kegg\">\n <pathway_id>path:eco00010</pathway_id>\n </n1:get_genes_by_pathway>\n </env:body>\n</env:envelope>" -> "HTTP/ OK\r\n" -> "Date: Thu, 03 Mar :02:19 GMT\r\n" -> "Server: Apache/ (Unix)\r\n" -> "SOAPServer: SOAP::Lite/Perl/0.55\r\n" -> "Content-Length: 2422\r\n" -> "Content-Type: text/xml; charset=utf-8\r\n" -> "\r\n" reading 2422 bytes... -> "<?xml version=\"1.0\" encoding=\"utf-8\"?><soap-env:envelope xmlns:soap- ENC=\" SOAP- ENV:encodingStyle=\" xmlns:soap- ENV=\" xmlns:xsi=\" xmlns:xsd=\" xmlns:namesp1=\"soap/kegg\"><return SOAP-ENC:arrayType=\"xsd:string[42]\" xsi:type=\"soap-enc:array\"><item xsi:type=\"xsd:string\">eco:b0114</item><item xsi:type=\"xsd:string\">eco:b0115</item><item xsi:type=\"xsd:string\">eco:b0116</item><item xsi:type=\"xsd:string\">eco:b0356</item><item xsi:type=\"xsd:string\">eco:b0688</item><item xsi:type=\"xsd:string\">eco:b0755</item><item

26 SOAP + WSDL (3) Java Ruby SOAP

27 # (eco) list = serv.list_pathways("eco") # => ArrayOfDefinition list.each do path # => Definition puts "#{path.entry_id} t#{path.definition} n" end Definition entry_id definition ID (string) (string) <SOAP-ENV:Body><namesp1:list_pathwaysResponse xmlns:namesp1=\"soap/kegg\"> <return SOAP-ENC:arrayType=\"namesp2:SOAPStruct[111]\" xsi:type=\"soap-enc:array\"> <item xsi:type=\"namesp2:soapstruct\"> <definition xsi:type=\"xsd:string\"> Glycolysis / Gluconeogenesis - Escherichia coli K-12 MG1655 </definition> <entry_id xsi:type=\"xsd:string\">path:eco00010</entry_id> </item> <item xsi:type=\"namesp2:soapstruct\"> <definition xsi:type=\"xsd:string\"> Citrate cycle (TCA cycle) - Escherichia coli K-12 MG1655 </definition> <entry_id xsi:type=\"xsd:string\">path:eco00020</entry_id> </item> : path:eco00010 Glycolysis / Gluconeogenesis - Escherichia coli K-12 MG1655 path:eco00020 Citrate cycle (TCA cycle) - Escherichia coli K-12 MG1655 path:eco00030 Pentose phosphate pathway - Escherichia coli K-12 MG1655 :

28 SSDBRelation genes_id1 genes_id2 sw_score bit_score identity overlap start_position1 end_position1 start_position2 end_position2 best_flag_1to2 best_flag_2to1 definition1 definition2 length1 length2 genes_id (string) genes_id (string) genes_id1 genes_id2 Smith-Waterman (int) genes_id1 genes_id2 bit (float) genes_id1 genes_id2 (float) genes_id1 genes_id2 (int) genes_id1 (int) genes_id1 (int) genes_id2 (int) genes_id2 (int) genes_id1 genes_id2 (boolean) genes_id2 genes_id1 (boolean) genes_id1 (string) genes_id2 (string) genes_id1 (int) genes_id2 (int) # b0002 list = serv.get_best_best_neighbors_by_gene("eco:b0002", 1, 100) list.each do hit puts hit.genes_id1 # => eco:b0002 eco:b0002 puts hit.genes_id2 # => ecj:jw0001 bsu:bg10350 puts hit.sw_score # => end

29 SOAP WSDL SAX REST

30 (1) # serv.options["protocol.http.connect_timeout"] = 60 serv.options["protocol.http.receive_timeout"] = 600 # begin results = serv.send(*arg) rescue Timeout::Error retry end

31 (2) Proxy http_proxy # Ruby (SOAP4R) setenv SOAP_USE_PROXY on setenv HTTP_PROXY my.proxy.server:8080 #!/usr/bin/env perl use strict; use SOAP::Lite; my $wsdl = " my $results = SOAP::Lite -> proxy("$wsdl", proxy => " -> get_pathways_by_enzymes( SOAP::Data->name(data=>['ec: '])); foreach (@{$results}) { print $_,"\n"; }

32 : #!/usr/bin/env ruby require 'bio' serv = Bio::KEGG::API.new # hsa:7368 homologs = serv.get_all_best_neighbors_by_gene("hsa:7368") homologs.each do hit gene = hit.genes_id2 # if motifs = serv.get_motifs_by_gene(gene, "pfam") motifs.each do motif name = motif.motif_id desc = motif.definition puts "#{gene}: #{name} #{desc}" end end end

33 : 㐿ఎᏄ 䜘䝕䜽䜪䜫䜨䛱䝢䝇䝘䝷䜴 serv = Bio::KEGG::API.new list = serv.get_genes_by_pathway("path:bsu00020") fg_colors = Array.new bg_colors = Array.new list.each do gene fg_colors << "black" bg_colors << ratio2rgb(gene) # 遺伝子名と色の対応 end url = serv.color_pathway_by_objects( "path:bsu00020", list, fg_colors, bg_colors)

34 PDB #!/usr/bin/env ruby require 'bio' serv = Bio::KEGG::API.new # path = ARGV.shift "path:eco00010" genes = serv.get_genes_by_pathway(path) # PDB results = Hash.new genes.each do gene if pdb_links = serv.get_all_linkdb_by_entry(gene, "pdb") pdb_links.each do link results[gene] = true end end end # url = serv.mark_pathway_by_objects(path, results.keys) # serv.save_image(url, "pdb.gif")

35 #!/usr/bin/env ruby require 'bio' ### KEGG API kegg = Bio::KEGG::API.new list = kegg.get_all_paralogs_by_gene("eco:b0002") genes = Array.new list.each do hit genes << hit.genes_id2 end seqs = kegg.get_aaseqs(genes) ### DDBJ XML ddbj = Bio::DDBJ::XML::ClustalW.new puts ddbj.analyzesimple(seqs)

36 ID DDBJ KEGG LSID

37 BioMOBY UDDI

38 HTML XML

39 KEGG API KEGG HTML Oracle SQL HTML/CGI Perl SOAP::Lite

40 KEGG API PATHWAY GENES/SSDB pre-calc Pfam DBGET

41 KEGG API HTML RDB KEGG

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