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1 KEGG API KEGG API KEGG KEGG KEGG API KEGG API Ruby SOAP WSDL Perl, Python, Java KEGG API KEGG API Ruby Perl Python Java KEGG API WSDL SSDBRelation, ArrayOfSSDBRelation MotifResult, ArrayOfMotifResult Definition, ArrayOfDefinition LinkDBRelation, ArrayOfLinkDBRelation list_databases, list_organisms, list_pathways DBGET binfo, bfind, bget, btit LinkDB get_linkdb_by_entry SSDB get_neighbors_by_gene, get_best_best_neighbors_by_gene, get_best_neighbors_by_gene, get_reverse_best_neighbors_by_gene, get_paralogs_by_gene, get_similarity_between_genes Motif get_motifs_by_gene, get_genes_by_motifs KO, OC, PC get_ko_by_gene, get_ko_members, get_oc_members_by_gene, get_pc_members_by_gene PATHWAY mark_pathway_by_objects, color_pathway_by_objects get_genes_by_pathway, get_enzymes_by_pathway, get_compounds_by_pathway, get_reactions_by_pathway get_pathways_by_genes, get_pathways_by_enzymes, get_pathways_by_compounds, get_pathways_by_reactions get_linked_pathways get_genes_by_enzyme, get_enzymes_by_gene get_enzymes_by_compound, get_enzymes_by_reaction, get_compounds_by_enzyme, get_compounds_by_reaction, get_reactions_by_enzyme, get_reactions_by_compound GENES get_genes_by_organism GENOME get_number_of_genes_by_organism HTTP XML Google HTTP XML XML SOAP WSDL SOAP Simple Object Access Method ( Service Oriented Access Protocol ) WSDL SOAP Web Service Description Language KEGG API KEGG KEGG API URL

2 <URL: KEGG API Ruby, Perl, Python, Java KEGG API SOAP WSDL Ruby Ruby SOAP Ruby SOAP4R, devel-logger, http-access2 Ruby SOAP4R (date2, uconv, XML ) SOAP4R b0002 Smith-Waterman 5 #!/usr/bin/env ruby require 'soap/wsdldriver' wsdl = " serv = SOAP::WSDLDriverFactory.new(wsdl).create_driver serv.generate_explicit_type = true # SOAP Ruby start = 1 max_results = 5 top5 = serv.get_best_neighbors_by_gene('eco:b0002', start, max_results) top5.each do hit print hit.genes_id1, " t", hit.genes_id2, " t", hit.sw_score, " n" end 'get_best_neighbors_by_gene' KEGG SSDB KEGG GENES API eco:b0002 eco:b eco:b0002 ecj:jw eco:b0002 sfx:s eco:b0002 sfl:sf eco:b0002 ecc:c serv = SOAP::WSDLDriverFactory.new(wsdl).create_driver serv.wiredump_dev = STDERR # serv.generate_explicit_type = true wiredump_dev STDERR KEGG API v3.0 start, max_results #!/usr/bin/env ruby require 'soap/wsdldriver' wsdl = " serv = SOAP::WSDLDriverFactory.new(wsdl).create_driver serv.generate_explicit_type = true start = 1 max_results = 100 loop do results = serv.get_best_neighbors_by_gene('eco:b0002', start, max_results) break unless results # results.each do hit print hit.genes_id1, " t", hit.genes_id2, " t", hit.sw_score, " n" end start += max_results end WSDL Ruby BioRuby

3 #!/usr/bin/env ruby require 'bio' serv = Bio::KEGG::API.new results = serv.get_all_best_neighbors_by_gene('eco:b0002') results.each do hit print hit.genes_id1, " t", hit.genes_id2, " t", hit.sw_score, " n" end BioRuby 'get_all_best_neighbors_by_gene' filter #!/usr/bin/env ruby require 'bio' serv = Bio::KEGG::API.new results = serv.get_all_best_neighbors_by_gene('eco:b0002') # SW fields = [:genes_id1, :genes_id2, :sw_score] results.each do hit puts hit.filter(fields).join(" t") end # fields1 = [:genes_id1, :start_position1, :end_position1, :best_flag_1to2] fields2 = [:genes_id2, :start_position2, :end_position2, :best_flag_2to1] results.each do hit print "> score: ", hit.sw_score, ", identity: ", hit.identity, " n" print "1: t", hit.filter(fields1).join(" t"), " n" print "2: t", hit.filter(fields2).join(" t"), " n" end (eco) KEGG #!/usr/bin/env ruby require 'bio' serv = Bio::KEGG::API.new list = serv.list_pathways("eco") list.each do path print path.entry_id, " t", path.definition, " n" end ArrayOfDefinition Definition entry_id (ID) definition ( ) SSDB SSDBRelation genes_id1 sw_score b1002 b2388 eco00010 #!/usr/bin/env ruby require 'bio' serv = Bio::KEGG::API.new genes = ["eco:b1002", "eco:b2388"] url = serv.mark_pathway_by_objects("path:eco00010", genes) puts url # BioRuby save_image serv.save_image(url, "filename.gif") Perl Perl SOAP::Lite

4 MIME-Base64 libwww-perl URI Ruby #!/usr/bin/env perl use SOAP::Lite; $wsdl = ' $serv = SOAP::Lite -> service($wsdl); $start = 1; $max_results = 5; $top5 = $serv->get_best_neighbors_by_gene('eco:b0002', $start, $max_results); foreach $hit (@{$top5}) { print "$hit->{genes_id1} t$hit->{genes_id2} t$hit->{sw_score} n"; } KEGG #!/usr/bin/env perl use SOAP::Lite; $wsdl = ' $results = SOAP::Lite -> service($wsdl) -> list_pathways("eco"); foreach $path (@{$result}) { print "$path->{entry_id} t$path->{definition} n"; } SOAP::Lite SOAP::Data->type(array => [value1, value2,.. ]) #!/usr/bin/env perl use SOAP::Lite; $wsdl = ' $serv = SOAP::Lite -> service($wsdl); $genes = SOAP::Data->type(array => ["eco:b1002", "eco:b2388"]); $result = $serv -> mark_pathway_by_objects("path:eco00010", $genes); print $result; Python Python SOAPpy SOAPpy (fpconst, PyXML ) KEGG/PATHWAY #!/usr/bin/env python from SOAPpy import WSDL wsdl = ' serv = WSDL.Proxy(wsdl)

5 results = serv.get_genes_by_pathway('path:eco00020') print results Java Java Apache Axis axis-1.2alpha (axis-1_1 jar Apache Axis Apache Axis axis-1_2beta axis-1_2beta/lib jar % cp axis-1_2beta/lib/* /path/to/lib/ WSDL KEGG API axisfix.pl % java -classpath /path/to/lib/axis.jar:/path/to/lib/jaxrpc.jar:/path/to/lib/commons-logging.jar % perl -i axisfix.pl keggapi/keggbindingstub.java % javac -classpath /path/to/lib/axis.jar:/path/to/lib/jaxrpc.jar:/path/to/lib/wsdl4j.jar:. kegga % jar cvf keggapi.jar keggapi/* % javadoc -classpath /path/to/lib/axis.jar:/path/to/lib/jaxrpc.jar -d keggapi_javadoc keggapi/*. javadoc javadoc -locale en_us Python KEGG/PATHWAY 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]); } SSDBRelation import keggapi.*; class GetBestNeighborsByGene { public static void main(string[] args) throws Exception { KEGGLocator locator = new KEGGLocator(); KEGGPortType serv = locator.getkeggport(); String query = args[0]; SSDBRelation[] results = null; results = serv.get_best_neighbors_by_gene(query, 1, 50); } } for (int i = 0; i < results.length; i++) { String gene1 = results[i].getgenes_id1(); String gene2 = results[i].getgenes_id2(); int score = results[i].getsw_score(); System.out.println(gene1 + " t" + gene2 + " t" + score); } -classpath keggapi.jar % javac -classpath /path/to/lib/axis.jar:/path/to/lib/jaxrpc.jar:/path/to/lib/wsdl4j.jar:/path/t % java -classpath /path/to/lib/axis.jar:/path/to/lib/jaxrpc.jar:/path/to/lib/commons-logging.jar CLASSPATH bash zsh

6 % for i in /path/to/lib/*.jar do CLASSPATH="${CLASSPATH}:${i}" done % export CLASSPATH tcsh % foreach i ( /path/to/lib/*.jar ) setenv CLASSPATH ${CLASSPATH}:${i} end WSDL2Java <URL: KEGG API KEGG API WSDL SOAP WSDL WSDL SOAP/WSDL KEGG API WSDL URL <URL: KEGG org KEGG eco sce <URL: db GenomeNet list_databases entry_id db_name ':' ID embl:j00231 EMBL J00231 entry_id genes_id, enzyme_id, compound_id, reaction_id, pathway_id, motif_id genes_id keggorg ':' KEGG ID eco:b0001 b0001 enzyme_id ec: ID ec: compound_id cpd: ID cpd:c00158 C00158 reaction_id REACTION rn:r00959 R00959 (cpd:c00103 cpd:00668 ) pathway_id KEGG/PATHWAY map keggorg path:map path:eco motif_id pf:dnaj Pfam DnaJ 'pf' 'ps' PROSITE, 'bl' BLOCS, 'pr' PRINTS, 'pd' PRODOM ko_id KO (KEGG Orthology) ko:k02598 KO K02598 nitrite transporter NirC start, max_results start max_results start = start + max_results fg_color_list fg_color_list KEGG API SSDBRelation SSDB genes_id1 genes_id2 sw_score bit_score identity overlap 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)

7 start_position1 end_position1 start_position2 end_position2 best_flag_1to2 best_flag_2to1 definition1 definition2 length1 length2 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) ArrayOfSSDBRelation SSDBRelation MotifResult motif_id definition genes_id start_position end_position score evalue ID (string) (string) genes_id (string) (int) (int) (PROSITE Profile, TIGRFAM) (float) (Pfam) E-value (double) score evalue -1 ArrayOfMotifResult MotifResult Definition entry_id definition ID (string) (string) ArrayOfDefinition Definitioin LinkDBRelation entry_id1 entry_id2 type path ID (string) ID (string) "direct" "indirect" (string) (string) ArrayOfLinkDBRelation LinkDBRelation KEGG API KEGG KEGG API SSDB, PATHWAY, GENES, LIGAND Ruby list_databases KEGG

8 ArrayOfDefinition list_organisms KEGG (org) ArrayOfDefinition list_pathways(org) KEGG 'map' ArrayOfDefinition DBGET DBGET DBGET <URL: binfo(string) 'all' binfo string # GenBank binfo('gb') # binfo('all') bfind(string) DBGET bfind 100 string # E-cadherin human GenBank bfind("gb E-cadherin human") bget(string) entry_id GENES DBGET (list_databases ) bget 100 string # bget("eco:b0002 bsu:bg10065 cpd:c00209") # FASTA bget("-f -n a eco:b0002 bsu:bg10065") # FASTA bget("-f -n n eco:b0002 hin:trna-cys-1") btit(string)

9 DBGET btit ID 100 string # btit("hsa:1798 mmu:13478 dme:cg5287-pa cel:y60a3a.14") LinkDB get_linkdb_by_entry(entry_id, db, start, max_results) entry_id db ArrayOfLinkDBRelation # E. coli b0002 KEGG/PATHWAY get_linkdb_by_entry('eco:b0002', 'pathway', 1, 10) get_linkdb_by_entry('eco:b0002', 'pathway', 11, 10) SSDB SSDB SSDB KEGG/GENES ssearch Smith-Waterman KEGG Smith- Waterman SSDB <URL: get_neighbors_by_gene(genes_id, org, start, max_results) genes_id org 'all' ArrayOfSSDBRelation # b0002 # get_neighbors_by_gene('eco:b0002', 'all' 1, 10) # start = start + max_results get_neighbors_by_gene('eco:b0002', 'all' 11, 10) get_best_best_neighbors_by_gene(genes_id, start, max_results) best-best ArrayOfSSDBRelation # b0002 best-best get_best_best_neighbors_by_gene('eco:b0002', 1, 10) get_best_best_neighbors_by_gene('eco:b0002', 11, 10) get_best_neighbors_by_gene(genes_id, start, max_results)

10 ArrayOfSSDBRelation # b0002 best neighbor get_best_neighbors_by_gene('eco:b0002', 1, 10) get_best_neighbors_by_gene('eco:b0002', 11, 10) get_reverse_best_neighbors_by_gene(genes_id, start, max_results) ArrayOfSSDBRelation # b0002 reverse best neighbor get_reverse_best_neighbors_by_gene('eco:b0002', 1, 10) get_reverse_best_neighbors_by_gene('eco:b0002', 11, 10) get_paralogs_by_gene(genes_id, start, max_results) ArrayOfSSDBRelation # b0002 get_paralogs_by_gene('eco:b0002', 1, 10) get_paralogs_by_gene('eco:b0002', 11, 10) get_similarity_between_genes(genes_id1, genes_id2) Smith-Waterman SSDBRelation # b0002 b3940 get_similarity_between_genes('eco:b0002', 'eco:b3940') Motif get_motifs_by_gene(genes_id, db) Pfam (pfam), TIGRFAM (tfam), PROSITE pattern (pspt), PROSITE profile (pspf) (all) ArrayOfMotifResult # b0002 Pfam get_motifs_by_gene('eco:b0002', 'pfam') get_genes_by_motifs(motif_id_list, start, max_results)

11 ArrayOfDefinition # Pfam DnaJ Prosite DNAJ_2 list = ['pf:dnaj', 'ps:dnaj_2'] get_genes_by_motifs(list, 1, 10) get_genes_by_motifs(list, 11, 10) KO, OC, PC KO (KEGG orthology), OC (KEGG ortholog cluster), PC (KEGG paralog cluster) KO OC PC get_ko_by_gene(genes_id) KO # eco:b0002 KO get_ko_by_gene('eco:b0002') get_ko_members(ko_id) ko_id KO # KO K02208 get_ko_by_gene('ko:k02598') get_oc_members_by_gene(genes_id, start, max_results) OC # eco:b0002 get_oc_members_by_gene('eco:b0002', 1, 10) get_oc_members_by_gene('eco:b0002', 11, 10) get_pc_members_by_gene(genes_id, start, max_results) PC # eco:b0002 get_pc_members_by_gene('eco:b0002', 1, 10) get_pc_members_by_gene('eco:b0002', 11, 10) PATHWAY PATHWAY PATHWAY <URL:

12 mark_pathway_by_objects(pathway_id, object_id_list) URL string # path:eco00260 eco:b0002 Homoserine # cpd:c00263 URL obj_list = ['eco:b0002', 'cpd:c00263'] mark_pathway_by_objects('path:eco00260', obj_list) color_pathway_by_objects(pathway_id, object_id_list, fg_color_list, bg_color_list) fg_color_list bg_color_list URL object_id_list fg_color_list, bg_color_list string # path:eco00053 eco:b0207 # eco:b1300 # URL obj_list = ['eco:b0207', 'eco:b1300'] fg_list = ['blue', '#00ff00'] bg_list = ['#ff0000', 'yellow'] color_pathway_by_objects('path:eco00053', obj_list, fg_list, bg_list) get_genes_by_pathway(pathway_id) pathway_id keggorg # get_genes_by_pathway('path:eco00020') get_enzymes_by_pathway(pathway_id) # get_enzymes_by_pathway('path:eco00020') get_compounds_by_pathway(pathway_id)

13 # get_compounds_by_pathway('path:eco00020') get_reactions_by_pathway(pathway_id) # get_reactions_by_pathways('path:map00260') get_pathways_by_genes(genes_id_list) # b0077 b0078 get_pathways_by_genes(['eco:b0077', 'eco:b0078']) get_pathways_by_enzymes(enzyme_id_list) # get_pathways_by_enzymes(['ec: ']) get_pathways_by_compounds(compound_id_list) # C00033 C00158 get_pathways_by_compounds(['cpd:c00033', 'cpd:c00158']) get_pathways_by_reactions(reaction_id_list) # rn:r00959, rn:r02740, rn:r00960, rn:r01786 # get_pathways_by_reactions(['rn:r00959', 'rn:r02740', 'rn:r00960', 'rn:r01786'])

14 get_linked_pathways(pathway_id) # path:eco00620 get_linked_pathways('path:eco00620') get_genes_by_enzyme(enzyme_id, org) # get_genes_by_enzyme('ec: ', 'eco') get_enzymes_by_gene(genes_id) # 'eco:b0002' get_enzymes_by_gene(eco:b0002) get_enzymes_by_compound(compound_id) # 'cpd:c00345' get_enzymes_by_compound('cpd:c00345') get_enzymes_by_reaction(reaction_id) # R00100 get_enzymes_by_reaction('rn:r00100') get_compounds_by_enzyme(enzyme_id)

15 # 'ec: ' get_compounds_by_enzyme('ec: ') get_compounds_by_reaction(reaction_id) # 'rn:r00100' get_compounds_by_reaction('rn:r00100') get_reactions_by_enzyme(enzyme_id) # 'ec: ' get_reactions_by_enzyme('ec: ') get_reactions_by_compound(compound_id) # 'cpd:c00199' get_reactions_by_compound('cpd:c00199') GENES GENES GENES <URL: get_genes_by_organism(org, start, max_results) GENES start max_results # 100 get_genes_by_organism('hin', 1, 100) get_genes_by_organism('hin', 101, 100) GENOME GENOMES GENOME

16 <URL: get_number_of_genes_by_organism(org) int # get_number_of_genes_by_organism('eco') Notes Last updated: July 12, 2004 This document is written and maintained by Toshiaki Katayama. Copyright (C) 2003, 2004 Toshiaki Katayama <k@bioruby.org>

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未踏成果報告会-fix.key BioRuby/ChemRuby http://www.tmd.ac.jp/artsci/biol/textbook/celltop.htm 350 280 210 140 2000 / 1 / 27 70 0 1995 96 97 98 99 2000 01 02 03 04 05 RefSeq PDB PubMed PubChem GenPept EMBL UniProt GenBank