Last data update: 2014.03.03

 R: Finds entries with matching query keywords or other query...
keggFindR Documentation

Finds entries with matching query keywords or other query data in a given database

Description

Finds entries with matching query keywords or other query data in a given database.

Usage

keggFind(database, query, option = c("formula", "exact_mass", 
    "mol_weight"))

Arguments

database

Either the name of a single KEGG database (list available via listDatabases(), a "T number" genome identifier, or a KEGG organism code (lists of both available via keggList("organism")).

query

One or more keywords, or a range of integers representing molecular weights. If query includes identifiers not known to KEGG, the results will not contain any information about those identifiers.

option

Optional. If database is compound or drug, option can be formula, exact_mass, or weight. Chemical formula search is a partial match irrespective of the order of atoms given. The exact mass (or molecular weight) is checked by rounding off to the same decimal place as the query data.

Value

A named character vector.

Author(s)

Dan Tenenbaum

References

http://www.kegg.jp/kegg/docs/keggapi.html

Examples

keggFind("genes", c("shiga", "toxin")) ## for keywords "shiga" and "toxin"
keggFind("genes", "shiga toxin") ## for keywords "shiga toxin"
keggFind("compound", "C7H10O5", "formula") ## for chemical formula "C7H10O5"
keggFind("compound", "O5C7", "formula") ## for chemical formula containing
                                        ## "O5" and "C7"
keggFind("compound", 174.05, "exact_mass") ## for 174.045
                                           ## =< exact mass < 174.055
keggFind("compound", 300:310, "mol_weight") ## for 300 =<
                                            ## molecular weight =< 310

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(KEGGREST)
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/KEGGREST/keggFind.Rd_%03d_medium.png", width=480, height=480)
> ### Name: keggFind
> ### Title: Finds entries with matching query keywords or other query data
> ###   in a given database
> ### Aliases: keggFind
> ### Keywords: find
> 
> ### ** Examples
> 
> keggFind("genes", c("shiga", "toxin")) ## for keywords "shiga" and "toxin"
                                                                                                                              ece:Z1464 
                                  "stx2A; shiga-like toxin II A subunit encoded by bacteriophage BP-933W; K11006 shiga toxin subunit A" 
                                                                                                                              ece:Z1465 
                                  "stx2B; shiga-like toxin II B subunit encoded by bacteriophage BP-933W; K11007 shiga toxin subunit B" 
                                                                                                                              ece:Z3343 
                                    "stx1B; shiga-like toxin 1 subunit B encoded within prophage CP-933V; K11007 shiga toxin subunit B" 
                                                                                                                              ece:Z3344 
                                    "stx1A; shiga-like toxin 1 subunit A encoded within prophage CP-933V; K11006 shiga toxin subunit A" 
                                                                                                                            ecs:ECs1205 
                                                                                "Shiga toxin 2 subunit A; K11006 shiga toxin subunit A" 
                                                                                                                            ecs:ECs1206 
                                                                                "Shiga toxin 2 subunit B; K11007 shiga toxin subunit B" 
                                                                                                                            ecs:ECs2973 
                                                                                "Shiga toxin I subunit B; K11007 shiga toxin subunit B" 
                                                                                                                            ecs:ECs2974 
                                                                                "Shiga toxin I subunit A; K11006 shiga toxin subunit A" 
                                                                                                                      ecf:ECH74115_2905 
                                                                                "shigatoxin 2, subunit B; K11007 shiga toxin subunit B" 
                                                                                                                      ecf:ECH74115_2906 
                                                                                  "shiga toxin subunit A; K11006 shiga toxin subunit A" 
                                                                                                                      ecf:ECH74115_3532 
                                                                                "shiga toxin 2 B subunit; K11007 shiga toxin subunit B" 
                                                                                                                      ecf:ECH74115_3533 
                                                                                  "shiga toxin subunit A; K11006 shiga toxin subunit A" 
                                                                                                                          etw:ECSP_2722 
                                                        "stx2cB; Shiga-like toxin II subunit B precursor; K11007 shiga toxin subunit B" 
                                                                                                                          etw:ECSP_2723 
                                                        "stx2A1; Shiga-like toxin II subunit A precursor; K11006 shiga toxin subunit A" 
                                                                                                                          etw:ECSP_3252 
                                                                        "stx2B; shiga toxin II subunit B; K11007 shiga toxin subunit B" 
                                                                                                                          etw:ECSP_3253 
                                                                       "stx2A2; shiga toxin II subunit A; K11006 shiga toxin subunit A" 
                                                                                                                       elx:CDCO157_1154 
                                                                                "Shiga toxin 2 subunit A; K11006 shiga toxin subunit A" 
                                                                                                                       elx:CDCO157_1155 
                                                                                "Shiga toxin 2 subunit B; K11007 shiga toxin subunit B" 
                                                                                                                       elx:CDCO157_2738 
                                                                      "Shiga toxin I subunit B precursor; K11007 shiga toxin subunit B" 
                                                                                                                       elx:CDCO157_2739 
                                                                      "Shiga toxin I subunit A precursor; K11006 shiga toxin subunit A" 
                                                                                                                         eoj:ECO26_1599 
                                                                                "Shiga toxin 1 subunit A; K11006 shiga toxin subunit A" 
                                                                                                                         eoj:ECO26_1600 
                                                                                "Shiga toxin 1 subunit B; K11007 shiga toxin subunit B" 
                                                                                                                        eoi:ECO111_2429 
                                                                                "Shiga toxin 2 subunit B; K11007 shiga toxin subunit B" 
                                                                                                                        eoi:ECO111_2430 
                                                                                "Shiga toxin 2 subunit A; K11006 shiga toxin subunit A" 
                                                                                                                        eoi:ECO111_3361 
                                                                                "Shiga toxin 1 subunit A; K11006 shiga toxin subunit A" 
                                                                                                                        eoi:ECO111_3362 
                                                                                "Shiga toxin 1 subunit B; K11007 shiga toxin subunit B" 
                                                                                                                        eoh:ECO103_2844 
                                                                                "Shiga toxin 2 subunit B; K11007 shiga toxin subunit B" 
                                                                                                                        eoh:ECO103_2845 
                                                                                "Shiga toxin 2 subunit A; K11006 shiga toxin subunit A" 
                                                                                                                        eoh:ECO103_5197 
                                                                                "Shiga toxin 1 subunit A; K11006 shiga toxin subunit A" 
                                                                                                                        eoh:ECO103_5198 
                                                                                "Shiga toxin 1 subunit B; K11007 shiga toxin subunit B" 
                                                                                                                          eso:O3O_09170 
                                                                                "Shiga toxin 2 subunit B; K11007 shiga toxin subunit B" 
                                                                                                                          eso:O3O_09165 
                                                                                "Shiga toxin 2 subunit A; K11006 shiga toxin subunit A" 
                                                                                                                          esm:O3M_16105 
                                                                                "Shiga toxin 2 subunit B; K11007 shiga toxin subunit B" 
                                                                                                                          esm:O3M_16110 
                                                                                "Shiga toxin 2 subunit A; K11006 shiga toxin subunit A" 
                                                                                                                          esl:O3K_16130 
                                                                                "Shiga toxin 2 subunit B; K11007 shiga toxin subunit B" 
                                                                                                                          esl:O3K_16135 
                                                                                "Shiga toxin 2 subunit A; K11006 shiga toxin subunit A" 
                                                                                                                    ecoo:ECRM13514_3144 
                                                         "stx2B; Shiga-like toxin II subunit B precursor; K11007 shiga toxin subunit B" 
                                                                                                                    ecoo:ECRM13514_3145 
                                           "stx2A; Shiga-like toxin II subunit A precursor (EC:3.2.2.22); K11006 shiga toxin subunit A" 
                                                                                                                    ecoh:ECRM13516_2315 
                                                         "stx2B; Shiga-like toxin II subunit B precursor; K11007 shiga toxin subunit B" 
                                                                                                                    ecoh:ECRM13516_2316 
                                           "stx2A; Shiga-like toxin II subunit A precursor (EC:3.2.2.22); K11006 shiga toxin subunit A" 
                                                                                                                            stm:STM0284 
                                                                                                           "shiga-like toxin A subunit" 
                                                                                                                         seo:STM14_0332 
                                                                                                  "putative Shiga-like toxin A subunit" 
                                                                                                                        sev:STMMW_02891 
                                                                                                  "putative shiga-like toxin A subunit" 
                                                                                                                     sem:STMDT12_C02790 
                                                                                                  "putative Shiga-like toxin A subunit" 
                                                                                                                         sej:STMUK_0287 
                                                                                                  "putative Shiga-like toxin A subunit" 
                                                                                                                      setu:STU288_13325 
                                                                                                  "putative shiga-like toxin A subunit" 
                                                                                                                 setc:CFSAN001921_15985 
                                                                                                                "Shiga toxin A subunit" 
                                                                                                                       send:DT104_02831 
                                             "sciR; shiga-like toxin a subunit, type VI secretion system SciR protein flags: precursor" 
                                                                                                                        seni:CY43_01420 
                                                                                                                "Shiga toxin A subunit" 
                                                                                                                    seen:SE451236_07435 
                                                                                                                "Shiga toxin A subunit" 
                                                                                                                            spt:SPA2480 
                                                                                                  "putative shiga-like toxin A subunit" 
                                                                                                                           sek:SSPA2315 
                                                                                                  "putative shiga-like toxin A subunit" 
                                                                                                                           sei:SPC_0292 
                                                                                                  "putative shiga-like toxin A subunit" 
                                                                                                                           sec:SCH_0277 
                                                                                                  "putative shiga-like toxin A subunit" 
                                                                                                                           shb:SU5_0926 
                                                                                                      "SciR Shiga-like toxin A subunit" 
                                                                                                                 senh:CFSAN002069_07720 
                                                                                                                "Shiga toxin A subunit" 
                                                                                                                    seeh:SEEH1578_10515 
                                                                                                  "putative shiga-like toxin A subunit" 
                                                                                                                 seec:CFSAN002050_07960 
                                                                                                                "Shiga toxin A subunit" 
                                                                                                                         sene:IA1_01505 
                                                                                                                "Shiga toxin A subunit" 
                                                                                                                    senc:SEET0819_08350 
                                                                                                                "Shiga toxin A subunit" 
                                                                                                                           sdy:SDY_1389 
                                                                            "stxA; Shiga toxin subunit A; K11006 shiga toxin subunit A" 
                                                                                                                           sdy:SDY_1390 
                                                                            "stxB; Shiga toxin subunit B; K11007 shiga toxin subunit B" 
                                                                                                                      sdz:Asd1617_01826 
                                                                    "Shiga toxin subunit A (EC:3.2.2.22); K11006 shiga toxin subunit A" 
                                                                                                                          ebi:EbC_13780 
                                                                                                  "Putative shiga-like toxin A subunit" 
                                                                                                                        psos:POS17_2009 
                                                                                          "P9; putative Shiga-like toxin alpha subunit" 
                                                                                                                    ssab:SSABA_v1c03870 
                                                                                   "hypothetical protein; K11006 shiga toxin subunit A" 
                                                                                                                    ssab:SSABA_v1c09020 
                                                                                   "hypothetical protein; K11006 shiga toxin subunit A" 
                                                                                                                      calt:Cal6303_2132 
                                                                          "ribosome-inactivating protein; K11006 shiga toxin subunit A" 
                                                                                                                            vg:22277199 
                          "PI30_gp34; Shigella phage POCJ13; shiga toxin A-chain precursor (EC:3.2.2.22); K11006 shiga toxin subunit A" 
                                                                                                                            vg:22277200 
                                    "PI30_gp35; Shigella phage POCJ13; shiga toxin I subunit B precursor; K11007 shiga toxin subunit B" 
                                                                                                                             vg:1262301 
                                                               "APSE-1_07; Endosymbiont phage APSE-1; P7; K11007 shiga toxin subunit B" 
                                                                                                                            vg:26228052 
               "AS349_gp84; Escherichia phage PA2; shiga-like toxin II subunit A precursor (EC:3.2.2.22); K11006 shiga toxin subunit A" 
                                                                                                                            vg:26228100 
                             "AS349_gp83; Escherichia phage PA2; shiga-like toxin II subunit B precursor; K11007 shiga toxin subunit B" 
                                                                                                                            vg:26516496 
                            "stx2A, AU085_gp42; Enterobacteria phage VT2phi_272; Shiga toxin 2 A subunit; K11006 shiga toxin subunit A" 
                                                                                                                            vg:26516448 
                            "stx2B, AU085_gp41; Enterobacteria phage VT2phi_272; Shiga toxin 2 B subunit; K11007 shiga toxin subunit B" 
                                                                                                                            vg:26516283 
              "stxB, phi191_00011, AU083_gp11; Escherichia phage phi191; shiga toxin subunit B precursor; K11007 shiga toxin subunit B" 
                                                                                                                            vg:26516284 
"stxA, phi191_00012, AU083_gp12; Escherichia phage phi191; shiga toxin subunit A precursor (EC:3.2.2.22); K11006 shiga toxin subunit A" 
                                                                                                                            vg:26519429 
                                                     "AU154_gp39; Shigella phage Ss-VASD; Stx1 A subunit; K11006 shiga toxin subunit A" 
                                                                                                                            vg:26519430 
                                                     "AU154_gp40; Shigella phage Ss-VASD; Stx1 B subunit; K11007 shiga toxin subunit B" 
                                                                                                                             vg:1481767 
                                   "stx2A, Stx2II_p143; Stx2 converting phage II; Shiga toxin2 subunit A; K11006 shiga toxin subunit A" 
                                                                                                                             vg:1481768 
                                   "stx2B, Stx2II_p144; Stx2 converting phage II; Shiga toxin2 subunit B; K11007 shiga toxin subunit B" 
                                                                                                                            vg:26798065 
                                    "AXI88_gp33; Shigella phage 75/02 Stx; shiga toxin A-chain precursor; K11006 shiga toxin subunit A" 
                                                                                                                            vg:26798066 
                                "AXI88_gp34; Shigella phage 75/02 Stx; shiga toxin I subunit B precursor; K11007 shiga toxin subunit B" 
                                                                                                                             vg:1481747 
                            "stx1A, Stx1_p142; Escherichia Stx1 converting phage; Shiga toxin1 subunit A; K11006 shiga toxin subunit A" 
                                                                                                                             vg:1481748 
                            "stx1B, Stx1_p143; Escherichia Stx1 converting phage; Shiga toxin1 subunit B; K11007 shiga toxin subunit B" 
                                                                                                                             vg:1261950 
               "stxA2, L0103, sltIIA, stx2A, 933Wp40; Enterobacteria phage 933W; Shiga toxin 2 subunit A; K11006 shiga toxin subunit A" 
                                                                                                                             vg:1262010 
               "stxB2, L0104, sltIIB, stx2B, 933Wp41; Enterobacteria phage 933W; Shiga toxin 2 subunit B; K11007 shiga toxin subunit B" 
                                                                                                                             vg:2641645 
                "stxA1, phi4795p38, PBV4795_ORF40; Enterobacteria phage BP-4795; Shiga toxin 1 subunit A; K11006 shiga toxin subunit A" 
                                                                                                                             vg:2641657 
                "stxB1, phi4795p39, PBV4795_ORF41; Enterobacteria phage BP-4795; Shiga toxin 1 subunit B; K11007 shiga toxin subunit B" 
                                                                                                                              vg:929695 
                                  "stxA2e, P27p25; Enterobacteria phage phiP27; shiga toxin 2e A-subunit; K11006 shiga toxin subunit A" 
                                                                                                                              vg:929727 
                                  "stxB2e, P27p26; Enterobacteria phage phiP27; shiga toxin 2e B-subunit; K11007 shiga toxin subunit B" 
                                                                                                                             vg:4397483 
                                 "stx2A, Stx2-86_gp01; Stx2-converting phage 86; shiga toxin 2 subunit A; K11006 shiga toxin subunit A" 
                                                                                                                             vg:4397484 
                                 "stx2B, Stx2-86_gp02; Stx2-converting phage 86; shiga toxin 2 subunit B; K11007 shiga toxin subunit B" 
                                                                                                                             vg:6159405 
                                                    "stx2A, pMIN27_41; Enterobacteria phage Min27; ORF44; K11006 shiga toxin subunit A" 
                                                                                                                             vg:6159351 
                                                    "stx2B, pMIN27_42; Enterobacteria phage Min27; ORF45; K11007 shiga toxin subunit B" 
                                                                                                                             vg:6973138 
                       "Stx2-1717_gp41; Stx2-converting phage 1717; verocytotoxin 2 variant 2c subunit A; K11006 shiga toxin subunit A" 
                                                                                                                             vg:6972909 
               "stx2cB, Stx2-1717_gp42; Stx2-converting phage 1717; verocytotoxin 2 variant 2c subunit B; K11007 shiga toxin subunit B" 
                                                                                                                             vg:6973079 
                                       "YYZ_gp39; Enterobacteria phage YYZ-2008; Shiga toxin 1 subunit A; K11006 shiga toxin subunit A" 
                                                                                                                             vg:6973080 
                                       "YYZ_gp40; Enterobacteria phage YYZ-2008; Shiga toxin 1 subunit B; K11007 shiga toxin subunit B" 
                                                                                                                            vg:13828571 
                                    "stx2A, D300_gp43; Escherichia phage P13374; shiga toxin 2 subunit A; K11006 shiga toxin subunit A" 
                                                                                                                            vg:13828535 
                                    "stx2B, D300_gp42; Escherichia phage P13374; shiga toxin 2 subunit B; K11007 shiga toxin subunit B" 
                                                                                                                            vg:14005228 
                                         "F366_gp36; Escherichia phage TL-2011c; Shiga toxin 2 subunit A; K11006 shiga toxin subunit A" 
                                                                                                                            vg:14005229 
                                         "F366_gp37; Escherichia phage TL-2011c; Shiga toxin 2 subunit B; K11007 shiga toxin subunit B" 
                                                                                                                             vg:1262249 
                              "stx2A, VT2-Sap42; Enterobacteria phage VT2-Sakai; Shiga toxin 2 subunit A; K11006 shiga toxin subunit A" 
                                                                                                                             vg:1262250 
                              "stx2B, VT2-Sap43; Enterobacteria phage VT2-Sakai; Shiga toxin 2 subunit B; K11007 shiga toxin subunit B" 
> keggFind("genes", "shiga toxin") ## for keywords "shiga toxin"
                                                                                                                              ec


Created & Maintained by Osamu Ogasawara (osamu.ogasawara@gmail.com) and IMSBIO