KEGG WebLinks

This is an introductory document for retrieving html files from and creating links to KEGG at http://www.kegg.jp/.

[ Top | KEGG API | MEDICUS Extension | KEGG WebLinks | KEGG Database Entry Format ]

General form

REST-style URL

http://www.kegg.jp/<operation>/<argument> <operation> = entry | pathway | module | brite

Other URLs

<operation> = pathway mapping (get) | pathway mapping (post) | pathway mapping (post, webgl) | ssdb search

Database name

<database> = KEGG databases (Table 1) and KEGG MEDICUS extension databases (Table 2) = pathway | brite | module | ko | genome | <org> | vg | ag | compound | glycan | reaction | rclass | enzyme | disease | drug | dgroup | environ | genes | ligand | kegg | <medicus> <org> = KEGG organism code <medicus> = disease_ja | drug_ja | dgroup_ja | environ_ja | compound_ja

Database entry identifier

<dbentry> = <kid> | <org>:<gene> | <database>:<entry> <kid> = KEGG identifier <gene> = Gene entry name or accession <entry> = Database entry name or accession <dbentries> = <dbentry>1[+<dbentry>2...]

Naming conventions

KEGG is an integrated database consisting of fifteen databases (and one under development) shown in Table 1. Except for "genes" and "enzyme", each database entry is identified by the KEGG identifier <kid> consisting of a database-dependent prefix followed by a five-digit number (see KEGG Objects for more details), such as K number, C number and D numbers as identifiers of "ko", "compound" and "drug" databases, respectively.

A "genes" entry is identified by
<org>:<gene>
where <org> is the three- or four-letter KEGG organism code or the T number genome identifier and <gene> is the gene identifier, usually NCBI GeneID or INSDC Locus_tag (see KEGG GENES).

An "enzyme" entry or an entry of any outside database is identified by
<database>:<entry>
where <database> is the database name or its abbreviation defined in Tables 1-3 and <entry> is the entry name or the accession number given by the database.

Table 1. KEGG databases

DB name Abbrev Content Web page kid prefix
pathway path KEGG pathway maps KEGG PATHWAY map, ko, ec, rn, <org>
brite br BRITE functional hierarchies KEGG BRITE br, jp, ko, <org>
module md KEGG modules KEGG MODULE M, <org>_M
orthology ko KO functional orthologs KEGG ORTHOLOGY K
genome gn KEGG organisms KEGG GENOME T
genes <org>
vg
ag		 Genes in KEGG organisms
Genes in viruses category
Genes in addendum category		 KEGG GENES -
compound cpd Small molecules KEGG COMPOUND C
glycan gl Glycans KEGG GLYCAN G
reaction rn Biochemical reactions KEGG REACTION R
rclass rc Reaction class RC
enzyme ec Enzyme nomenclature KEGG ENZYME -
network nt Network variants (under development) N
disease ds Human diseases KEGG DISEASE H
drug dr Drugs KEGG DRUG D
dgroup dg Drug groups DG
environ ev Health-related substances KEGG ENVIRON E
  • "genes" is a composite database consisting of KEGG organisms with three- or four-letter <org> codes, and viruses (vg) and addendum (ag) categories (see KEGG GENES).
  • "pathway", "brite" and "module" consist of manually created reference datasets and computationally generated organism-specific datasets (see KEGG Pathway Maps).
  • "kegg" stands for the collection of all databases shown above.
  • "ligand" stands for the collection of chemical databases: compound, glycan, reaction and enzyme.

KEGG MEDICUS is a translational bioinformatics resource, both in English and Japanese, promoting use of genomic information in society. Table 2 shows KEGG MEDICUS extension databases that are available in KEGG WebLinks.

Table 2. KEGG MEDICUS extension databases

DB name Abbrev Entry ID Web page
disease_ja ds_ja H number KEGG DISEASE (in Japanese)
drug_ja dr_ja D number KEGG DRUG (in Japanese)
dgroup_ja dg_ja DG number
environ_ja ev_ja E number KEGG ENVIRON (in Japanese)
compound_ja cpd_ja C number

REST-style URL

ENTRY

Name

entry – retrieve database entries

URL form

http://www.kegg.jp/entry/<dbentries> <dbentries> = Entries of the following <database> <database> = pathway | module | ko | genome | <org> | vg | ag | compound | glycan | reaction | rclass | enzyme | disease | drug | dgroup | environ | <medicus>

Description

This URL returns the KEGG database entry page(s). It is equivalent to
    http://www.kegg.jp/dbget-bin/www_bget?<dbentries>
or its GenomNet mirror
    http://www.genome.jp/dbget-bin/www_bget?<dbentries>

Examples

http://www.kegg.jp/entry/K00873
http://www.kegg.jp/entry/C00022
http://www.kegg.jp/entry/map00010

See also

KEGG API get operation for obtaining database entries in flat-file text format.

PATHWAY

Name

pathway - retrieve pathway map with optional coloring of objects

URL form

http://www.kegg.jp/pathway/<mapid>[+<map_objects>] <mapid> = KEGG pathway map identifier <map_objects> = <dbentry>1[+<dbentry>2...]

Description

This URL returns the KEGG pathway map page. It is equivalent to
    http://www.kegg.jp/kegg-bin/show_pathway?<mapid>[+<map_objects>]
or its GenomNet mirror
    http://www.genome.jp/kegg-bin/show_pathway?<mapid>[+<map_objects>]

Examples

http://www.kegg.jp/pathway/map00010
http://www.kegg.jp/pathway/map00010+K00873+C00022
http://www.kegg.jp/pathway/hsa00010
http://www.kegg.jp/pathway/hsa00010+5315+C00022
http://www.kegg.jp/pathway/map00010+M00002 (KEGG module in pathway map)

See also

Search Pathway in KEGG Mapper for more details of map objects that can be specified.

MODULE

URL form

module - retrieve module map with optional coloring of objects

URL form

http://www.kegg.jp/module/<modid>[+<mod_objects>] <modid> = KEGG module identifier <mod_objects> = <dbentry>1[+<dbentry>2...]

Description

This URL returns the KEGG module page. It is equivalent to
    http://www.kegg.jp/kegg-bin/show_module?<modid>[+<mod_objects>]
or its GenomNet mirror
    http://www.genome.jp/kegg-bin/show_module?<modid>[+<mod_objects>]

Examples

http://www.kegg.jp/module/M00010
http://www.kegg.jp/module/hsa_M00095+3156

See also

Search Module in KEGG Mapper for more details of module objects that can be specified.

BRITE

Name

brite - retrieve brite hierarchy with optional coloring of objects

URL form

http://www.kegg.jp/brite/<brid>[+<br_objects>] <brid> = KEGG brite hierarchy identifier <br_objects> = <dbentry>1[+<dbentry>2...]

Description

This URL returns the KEGG BRITE hierarchy page. It is equivalent to
    http://www.kegg.jp/kegg-bin/get_htext?<brid>[+<br_objects>]
or its GenomNet mirror
    http://www.genome.jp/kegg-bin/get_htext?<brid>[+<br_objects>]

Examples

http://www.kegg.jp/brite/ko00001
http://www.kegg.jp/brite/br08303
http://www.kegg.jp/brite/br08601+hsa

See also

Search Brite in KEGG Mapper for more details of brite objects that can be specified.

Links to Analysis Tools

PATHWAY MAPPING (GET)

Name

pathway mapping (get) - KEGG pathway map coloring by HTTP GET method

URL form

http://www.kegg.jp/kegg-bin/show_pathway?<mapid>/<dataset>[/default%3d<dcolor>] <mapid> = KEGG pathway map identifier <dataset> = <dbentry>1%09<bgcolor>1,<fgcolor>1[/<dbentry>2%09<bgcolor>2,<fgcolor>2...] <bgcolor> = background color <fgcolor> = foreground color "%09" represents TAB in ASCII code <dcolor> = default background color "%3d" represents "=" in ASCII code

Description

This URL allows coloring of objects in a KEGG pathway map according to the color specification given in single-line, slash(/)-delimited <dataset>. Use "%23" in ASCII code instead of "#" for color specification.

Examples

<dataset>
1.14.16.1<TAB>,blue/C00079<TAB>,red/C00166/default=pink
http://www.kegg.jp/kegg-bin/show_pathway?map00400/1.14.16.1%09,blue/C00079%09,red/C00166/default%3dpink

<dataset>
1.14.16.1<TAB>,blue/C00079<TAB>,red/C00166<TAB>#005050
http://www.kegg.jp/kegg-bin/show_pathway?map00400/1.14.16.1%09,blue/C00079%09,red/C00166%09%23005050

See also

Search&Color Pathway in KEGG Mapper for more details of KEGG identifier specification.

PATHWAY MAPPING (POST)

Name

pathway mapping (post) - KEGG pathway map coloring by HTTP POST method

URL form

http://www.kegg.jp/kegg-bin/show_pathway?map=<mapid>&multi_query=<dataset>[&nocolor=1] <mapid> = KEGG pathway map identifier <dataset> = <dbentry>1+<bgcolor>1,<fgcolor>1[%0d%0a<dbentry>2+<bgcolor>2,<fgcolor>2...] <bgcolor> = background color "%0d" represents CR in ASCII code <fgcolor> = foreground color "%0a" represents LF in ASCII code

Description

This URL allows coloring of objects in a KEGG pathway map according to the color specification given in multiple-line <dataset>, which corresponds to the textarea in KEGG Mapper Search&Color Pathway. To use uncolored diagram (rather than colored organism-specific diagram, for example) specify the nocolor option.

Examples

<dataset>
7167+red,blue
C00118+pink
http://www.kegg.jp/kegg-bin/show_pathway?map=hsa00010&multi_query=7167+red,blue%0d%0aC00118+pink

See also

Search&Color Pathway in KEGG Mapper for more details of KEGG identifier specification.

PATHWAY MAPPING (POST, WEBGL)

Name

pathway mapping (post, webgl) - KEGG pathway map coloring by HTTP POST method using WebGL

URL form

http://www.kegg.jp/kegg-bin/show_pathway_webgl?map=<mapid>&multi_query=<dataset> <mapid> = KEGG pathway map identifier <dataset> = <dbentry>1+<bgcolor>1,<fgcolor>1[%0d%0a<dbentry>2+<bgcolor>2,<fgcolor>2...] <bgcolor> = background color "%0d" represents CR in ASCII code <fgcolor> = foreground color "%0a" represents LF in ASCII code

Description

This URL allows bar chart drawing on a KEGG pathway map according to the numerical value specification given in multiple-line <dataset>, which corresponds to the textarea in KEGG Mapper Color Pathway WebGL.

Examples

<dataset>
#dbentry<TAB>wild-type<TAB>delta-Hik33
syn:sll0337<TAB>0.72<TAB>1.29
syn:slr0081<TAB>0.49<TAB>0.49
http://www.kegg.jp/kegg-bin/show_pathway_webgl?map=syn02020&multi_query=%23dbentry%09wild-type%09delta-Hik33%0d%0asyn:sll0337%090.72%091.29%0d%0asyn:slr0081%090.49%090.49

See also

Color Pathway WebGL in KEGG Mapper for more details of KEGG identifier specification.

SSDB SEARCH

Name

ssdb search - SSDB search for orthologs, paralogs and gene clusters

URL form

(ortholog) http://www.kegg.jp/ssdb-bin/ssdb_best?org_gene=<org>:<gene> (paralog) http://www.kegg.jp/ssdb-bin/ssdb_paralog?org_gene=<org>:<gene> (gene cluster) http://www.kegg.jp/ssdb-bin/ssdb_glcust?org_gene=<org>:<gene>

Description

These URLs retrieve data from the KEGG SSDB database containing amino acid similarity scores and best-hit relations in genome pairs among all genes in the KEGG GENES database.

Examples

http://www.kegg.jp/ssdb-bin/ssdb_best?org_gene=syn:sll1450
http://www.kegg.jp/ssdb-bin/ssdb_paralog?org_gene=syn:sll1450
http://www.kegg.jp/ssdb-bin/ssdb_gclust?org_gene=syn:sll1450

See also

KEGG SSDB web interface.

Last updated: June 1, 2017