KEGG API Manual

KEGG API is a REST-style Application Programming Interface to the KEGG database resource.

General form

URL form

https://rest.kegg.jp/<operation>/<argument>[/<argument2[/<argument3> ...]]

<operation> = info | list | find | get | conv | link | ddi

Database name

<database> = KEGG databases (Table 1) and Outside databases integrated in KEGG (Table 2)

           = pathway | brite | module | ko | <org> | vg | vp | ag | genome | compound |
             glycan | reaction | rclass | enzyme | network | variant | disease |
             drug | dgroup | disease_ja | drug_ja | dgroup_ja | compound_ja |
             genes | ligand | kegg | <outside_db>

<org> = KEGG organism code

<outside_db> = pubmed | ncbi-geneid | ncbi-proteinid | uniprot | pubchem | chebi |
               atc | jtc | ndc | yj

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 sixteen databases (including four Japanese versions) 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

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

where <database> is the database name or its abbreviation defined in Tables 1-2 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
genes	<org> vg vp ag	Genes in KEGG organisms Genes in viruses category Mature peptides in viruses Genes in addendum category	KEGG GENES	-
genome	gn	KEGG organisms	KEGG GENOME	T
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	ne	Network elements	KEGG NETWORK	N
variant	hsa_var	Human gene variants		-
disease	ds	Human diseases	KEGG DISEASE	H
drug	dr	Drugs	KEGG DRUG	D
dgroup	dg	Drug groups		DG

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
compound_ja	cpd_ja	C number

"genes" is a composite database consisting of KEGG organisms with three- or four-letter <org> codes, and viruses (vg, vp) and addendum (ag) categories (see KEGG GENES).
"pathway", "brite" and "module" consist of manually created reference datasets and computationally generated organism-specific datasets.
"kegg" stands for the collection of all databases shown above.
"ligand" stands for the collection of chemical databases: compound, glycan, reaction and enzyme.

In addition to these databases, the NCBI PubMed database shown in Table 2 is tightly integrated in KEGG. Table 2 also contains databases used only for ID conversion (conv operation) or links (link operation).

Table 2. Outside databases integrated in KEGG

DB name	Abbrev	Entry ID	Web page	Remark

pubmed	pmid	PubMed ID	NCBI PubMed
ncbi-geneid		Gene ID	NCBI Gene	conv only
ncbi-proteinid		Protein ID	NCBI Protein	conv only
uniprot	up	UniProt Accession	UniProt	conv only
pubchem		PubChem SID	NCBI PubChem	conv only
chebi		ChEBI ID	ChEBI	conv only
	atc	7-letter ATC code	ATC classification	link only
	jtc	Therapeutic category code	Therapeutic category in Japan	link only
	ndc	National Drug Code	Drug products in the USA	ddi only
	yj	YJ code	Drug products in Japan	ddi only

Output

Output format

The output of all operations is in a text format:

tab-delimited text returned from list, find, conv and link
flat file database format returned from get
text message returned from info

Status code

The HTTP status code can be used to check if the operation was successful.

Code	Meaning
200	Success
400	Bad request (syntax error, wrong database name, etc.)
404	Not found (e.g., requesting amino acid sequence for RNA)

KEGG API Operations

INFO

Name

info – display database release information and linked db information

URL form

https://rest.kegg.jp/info/<database>

<database> = kegg | pathway | brite | module | ko | genes | <org> | vg | vp | ag |
             genome | ligand | compound | glycan | reaction | rclass | enzyme |
             network | variant | disease | drug | dgroup

Description

This operation displays the database release information with statistics for the databases shown in Table 1. Except for kegg, genes and ligand, this operation also displays the list of linked databases that can be used in the link operation.

Examples

/info/kegg		displays the current statistics of the KEGG database
/info/pathway		displays the number of pathway entries including both the reference and organism-specific pathways
/info/hsa		displays the number of gene entries for the KEGG organism Homo sapiens

See also

Current statistics in the KEGG website.

LIST

Name

list – obtain a list of entry identifiers and associated names

URL form

https://rest.kegg.jp/list/<database>

<database> = pathway | brite | module | ko | <org> | vg | vp | ag | genome | compound |
             glycan | reaction | rclass | enzyme | network | variant | disease |
             drug | dgroup | organism

https://rest.kegg.jp/list/pathway/<org>

https://rest.kegg.jp/list/brite/<option>

<option> = br | jp | ko | <org>

https://rest.kegg.jp/list/<dbentries>

<dbentries> = Entries of the following <database>
<database> = pathway | brite | module | ko | <org> | vg | vp | ag | genome | compound |
             glycan | reaction | rclass | enzyme | network | variant | disease |
             drug | dgroup

Description

This operation can be used to obtain a list of all entries in each database. The database names shown in Tables 1 and 2, excluding the composite database names of genes, ligand and kegg, may be given. The special database name "organism" is allowed only in this operation, which may be used to obtain a list of KEGG organisms with the three- or four-letter organism codes.

When the organism code is known, the second form can be used to obtain a list of organism-specific pathways.

The third form is a similar option for brite hierarchies.

The fourth form may be used to obtain a list of definitions for a given set of database entry identifiers. The maximum number of identifiers that can be given is 10.

Examples

/list/pathway		returns the list of reference pathways
/list/pathway/hsa		returns the list of human pathways
/list/organism		returns the list of KEGG organisms with taxonomic classification
/list/hsa		returns the entire list of human genes with gene types and chromosomal positions
/list/T01001		same as above
/list/hsa:10458+ece:Z5100		returns the list of a human gene and an E.coli O157 gene
/list/C01290+G00092		returns the list of a compound entry and a glycan entry

FIND

Name

find – find entries with matching query keyword or other query data

URL form

https://rest.kegg.jp/find/<database>/<query>

<database> = pathway | brite | module | ko | genes | <org> | vg | vp | ag | genome |
             ligand | compound | glycan | reaction | rclass | enzyme | network |
             variant | disease | drug | dgroup

https://rest.kegg.jp/find/<database>/<query>/<option>

<database> = compound | drug
<option> = formula | exact_mass | mol_weight | nop

Description

This is a search operation. The first form searches entry identifier and associated fields shown below for matching keywords.

Database	Text search fields (see flat file format)
pathway	ENTRY and NAME
brite	ENTRY and NAME
module	ENTRY and NAME
ko	ENTRY, SYMBOL and NAME
genes (<org>, vg, vp, ag)	ENTRY, SYMBOL, NAME and KO
genome	ENTRY, ORG_CODE and NAME
compound	ENTRY and NAME
glycan	ENTRY, NAME and COMPOSITION
reaction	ENTRY, NAME and DEFINITION
rclass	ENTRY and DEFINITION
enzyme	ENTRY and NAME
network	ENTRY and NAME
variant	ENTRY and NAME
disease	ENTRY and NAME
drug	ENTRY and NAME
dgroup	ENTRY and NAME

In the second form the 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. A range of values may also be specified with the minus(-) sign.

Examples

/find/genes/shiga+toxin		for keywords "shiga" and "toxin" (use nop option to disable this processing)
/find/genes/"shiga toxin"		for keywords "shiga toxin"

/find/compound/C7H10O5/formula		for chemical formula "C7H10O5"
/find/compound/O5C7/formula		for chemical formula containing "O5" and "C7"
/find/compound/174.05/exact_mass		for 174.045 =< exact mass < 174.055
/find/compound/300-310/mol_weight		for 300 =< molecular weight =< 310

See also

DBGET search interface such as in the KEGG Table of Contents page.

GET

Name

get – retrieve given database entries

URL form

https://rest.kegg.jp/get/<dbentries>[/<option>]

<dbentries> = KEGG database entries of the following <database>
<database> = pathway | brite | module | ko | <org> | vg | vp | ag | genome | compound |
             glycan | reaction | rclass | enzyme | network | variant | disease |
             drug | dgroup | disease_ja | drug_ja | dgroup_ja | compound_ja

<option> = aaseq | ntseq | mol | kcf | image | conf | kgml | json

Description

This operation retrieves given database entries in a flat file format or in other formats with options. Flat file formats are available for all KEGG databases except brite. The input is limited up to 10 entries.

Options allow retrieval of selected fields, including sequence data from genes entries, chemical structure data or gif image files from compound, glycan and drug entries, png image files or kgml files from pathway entries. The input is limited to one compound/glycan/drug entry with the image option, and to one pathway entry with the image or kgml option.

Examples

/get/C01290+G00092		retrieves a compound entry and a glycan entry
/get/hsa:10458+ece:Z5100		retrieves a human gene entry and an E.coli O157 gene entry
/get/hsa:10458+ece:Z5100/aaseq		retrieves amino acid sequences of a human gene and an E.coli O157 gene
/get/C00002/image		retrieves the gif image file of a compound
/get/hsa00600/image		retrieves the png image file of a pathway map
/get/map00600/image2x		retrieves the doubled-sized png image file of a reference pathway map New!
/get/hsa00600/conf		retrieves the conf file of a pathway map
/get/hsa00600/kgml		retrieves the kgml file of a pathway map
/get/br:br08301		retrieves the htext file of a brite hierarchy
/get/br:br08301/json		retrieves the json file of a brite hierarchy

See also

KEGG WebLinks to retrieve entries in HTML.

CONV

Name

conv – convert KEGG identifiers to/from outside identifiers

URL form

https://rest.kegg.jp/conv/<target_db>/<source_db>

(<target_db> <source_db>) = (<kegg_db> <outside_db>) | (<outside_db> <kegg_db>)

For gene identifiers:
<kegg_db> = <org>
<org> = KEGG organism code or T number
<outside_db> = ncbi-geneid | ncbi-proteinid | uniprot

For chemical substance identifiers:
<kegg_db> = compound | glycan | drug
<outside_db> = pubchem | chebi

https://rest.kegg.jp/conv/<target_db>/<dbentries>

For gene identifiers:
<dbentries> = database entries of the following <database>
<database> = <org> | genes | ncbi-geneid | ncbi-proteinid | uniprot
<org> = KEGG organism code or T number

For chemical substance identifiers:
<dbentries> = database entries of the following <database>
<database> = compound | glycan | drug | pubchem | chebi

Description

This operation can be used to convert entry identifiers (accession numbers) of outside databases to KEGG identifiers, and vice versa. The first form allows database to database mapping, while the second form allows conversion of a selected number of entries. The database name "genes" may be used only in the second form.

Examples

/conv/eco/ncbi-geneid		conversion from NCBI GeneID to KEGG ID for E. coli genes
/conv/ncbi-geneid/eco		opposite direction
/conv/ncbi-proteinid/hsa:10458+ece:Z5100		conversion from KEGG ID to NCBI ProteinID
/conv/genes/ncbi-geneid:948364		conversion from NCBI GeneID to KEGG ID when the organism code is not known

See also

Convert ID tool in KEGG Mapper.

LINK

Name

link – find related entries by using database cross-references

URL form

https://rest.kegg.jp/link/<target_db>/<source_db>

<target_db> = <database>
<source_db> = <database>

<database> = pathway | brite | module | ko | <org> | vg | vp | ag | genome | compound |
             glycan | reaction | rclass | enzyme | network | variant | disease |
             drug | dgroup | <outside_db>
<outside_db> = pubmed | atc | jtc

https://rest.kegg.jp/link/<target_db>/<dbentries>

<dbentries> = KEGG database entries of the following <database>
<database> = pathway | brite | module | ko | <org> | vg | vp | ag | genome | compound |
             glycan | reaction | rclass | enzyme | network | variant | disease |
             drug | dgroup | <outside_db>
<outside_db> = pubmed | atc | jtc

Description

This operation allows retrieval of cross-references within all KEGG databases, as well as between KEGG databases and outside databases. It is useful for finding various relationships, such as relationships between genes and pathways. The first form allows retrieval of database to database cross-references, while the second form allows retrieval for a selected number of entries. The database name "genes" may be used only for "ko" entries in the second form.

Examples

/link/pathway/hsa		KEGG pathways linked from each of the human genes
/link/hsa/pathway		human genes linked from each of the KEGG pathways
/link/pathway/hsa:10458+ece:Z5100		KEGG pathways linked from a human gene and an E. coli O157 gene
/link/genes/K00500		List of genes with the KO assignment of K00500
/link/hsa/hsa00010		List of human genes in pathway hsa00010
/link/ko/map00010 or /link/ko/ko00010		List of KO entries in pathway map00010 or ko00010
/link/rn/map00010 or /link/rn/rn00010		List of reaction entries in pathway map00010 or rn00010
/link/ec/map00010 or /link/ec/ec00010		List of EC number entries in pathway map00010 or ec00010
/link/cpd/map00010		List of compound entries in pathway map00010

DDI

Name

ddi – find adverse drug-drug interactions

URL form

https://rest.kegg.jp/ddi/<dbentry>

<dbentry> = Single entry of the following <database>
<database> = drug | ndc | yj

https://rest.kegg.jp/ddi/<dbentries>

<dbentries> = Multiple entries in one of the following <database>
<database> = drug | ndc | yj

Description

This operation searches against the KEGG drug interaction database, where drug-drug interactions designated as contraindication (CI) and precaution (P) in Japanese drug labels are extracted, standardized by KEGG identifiers and annotated with any possible molecular mechanims. The first form reports all known interactions, while the second form can be used to check if any drug pair in a given set of drugs is CI or P.

Examples

/ddi/D00564		drugs that are known to interact with a given drug
/ddi/D00564+D00100+D00109		check if drug-drug interactions are present among given drugs
/ddi/ndc:0078-0401		drug products that are known to interact with Gleevec

LINK (with RDF option)

Name

link – find related entries by using database cross-references

URL form

https://rest.kegg.jp/link/<target_db>/<source_db>[/<option>]

<target_db> = <database>
<source_db> = <database>

<database> = drug | atc | jtc

<option> = turtle | n-triple

https://rest.kegg.jp/link/<target_db>/<dbentries>[/<option>]

<dbentries> = KEGG database entries of the following <database>
<database> = drug | atc | jtc

<option> = turtle | n-triple

Description

This operation allows retrieval of cross-references within a few selected databases. The first form allows retrieval of database to database cross-references, while the second form allows retrieval for a selected number of entries.

Examples

/link/atc/D01441/n-triple		ATC code of a given KEGG DRUG entry in N-Triples format
/link/jtc/D01441/turtle		Japanese therapeutic category of a given KEGG DRUG entry in Turtle format

Last updated: May 26, 2023

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