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
Other URLs
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 | network | variant | 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 seventeen databases shown in Table 1. Except for "genes", "enzyme" and "variant", 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
An "enzyme" entry, a "variant" entry or an entry of any outside database is identified by
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.
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, a "variant" 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
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- "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
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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 | brite | module | ko | genome | <org> | vg | ag | compound |
glycan | reaction | rclass | enzyme | network | variant | 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>
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
http://www.kegg.jp/entry/br:01002
http://www.kegg.jp/entry/C00022
http://www.kegg.jp/entry/map00010
http://www.kegg.jp/entry/br:01002
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>]
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)
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>]
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
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>]
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
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>
<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
C00118+pink
See also
Search&Color Pathway 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
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: December 1, 2017