KEGG API

Database	Name	Abbrev	kid	Remark
KEGG PATHWAY	pathway	path	map number
KEGG BRITE	brite	br	br number
KEGG MODULE	module	md	M number
KEGG DISEASE	disease	ds	H number	Japanese version: disease_ja ds_ja
KEGG DRUG	drug	dr	D number	Japanese version: drug_ja dr_ja
KEGG ENVIRON	environ	ev	E number	Japanese version: environ_ja ev_ja
KEGG ORTHOLOGY	orthology	ko	K number
KEGG GENOME	genome	genome	T number
KEGG GENOMES	genomes	gn	T number	Composite database: genome + egenome + mgenome
KEGG GENES	genes	-	-	Composite database: consisting of KEGG organisms
KEGG LIGAND	ligand	ligand	-	Composite database: compound + glycan + reaction + rpair + rclass + enzyme
KEGG COMPOUND	compound	cpd	C number	Japanese version: compound_ja cpd_ja
KEGG GLYCAN	glycan	gl	G number
KEGG REACTION	reaction	rn	R number
KEGG RPAIR	rpair	rp	RP number
KEGG RCLASS	rclass	rc	RC number
KEGG ENZYME	enzyme	ec	-

Auxiliary databases, dgenes, egenes, mgenes, egenome and mgenome, may also be used.

Database entry

Each database entry is identified by:

db:entry

where

"db" is the database name or its abbreviation shown above and
"entry" is the entry name or the accession number that is uniquely assigned within the database.

In reality "db" may be omitted, for the entry name called the KEGG object identifier (kid) is unique across KEGG.

kid = database-dependent prefix + five-digit number

In the KEGG GENES database the db:entry combination must be specified. This is more specifically written as:

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 locus_tag or ncbi GeneID, or the primary gene name.

Output

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)

Operations

Database information

Operation

info – displays the current statistics of a given database

URL form

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

<database> = pathway | brite | module | disease | drug | environ | ko | genome |
             <org> | compound | glycan | reaction | rpair | rclass | enzyme |
             genomes | genes | ligand | kegg
<org> = KEGG organism code or T number

Examples

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

Entry list

Operation

list – returns a list of entry identifiers and associated definition for a given database or a given set of database entries

URL form

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

<database> = pathway | brite | module | disease | drug | environ | ko | genome |
             <org> | compound | glycan | reaction | rpair | rclass | enzyme |
             organism
<org> = KEGG organism code or T number

http://rest.kegg.jp/list/<database>/<org>

<database> = pathway | module
<org> = KEGG organism code

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

<dbentries> = KEGG database entries involving the following <database>
<database> = pathway | brite | module | disease | drug | environ | ko | genome |
             <org> | compound | glycan | reaction | rpair | rclass | enzyme
<org> = KEGG organism code or T number

Notes

The special keyword "organism" for the database name is applicable only to this operation.
In the second form an organism-specific version of pathway/module list is returned.
In the third form the maximun number of database entries that can be given is 100.

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
/list/T01001		same as above
/list/hsa:10458+ece:Z5100		returns the list of a human gene and an E.coli O157 gene
/list/cpd:C01290+gl:G00092		returns the list of a compound entry and a glycan entry
/list/C01290+G00092		same as above

Data search

Operation

find – finds entries with matching query keywords or other query data in a given database

URL form

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

<database> = pathway | module | disease | drug | environ | ko | genome |
             <org> | compound | glycan | reaction | rpair | rclass | enzyme |
             genes | ligand
<org> = KEGG organism code or T number

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

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

Notes

The first form searches entry identifier and associated fields shown below for matching keywords.

Database	Search fields (see flat file format)
pathway module disease drug environ ko genome <org> compound glycan reaction rpair rclass enzyme	ENTRY and NAME ENTRY and NAME ENTRY and NAME ENTRY and NAME ENTRY and NAME ENTRY, NAME and DEFINITION ENTRY, NAME and DEFINITION ENTRY, NAME, DEFINITION and ORTHOLOGY ENTRY and NAME ENTRY, NAME, COMPOSITION and CLASS ENTRY, NAME and DEFINITION ENTRY and NAME ENTRY, NAME and DEFINITION ENTRY and NAME

Keyword search against brite is not supported. Use /list/brite to retrieve a short list.

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"
/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

Data retrieval

Operation

get – retrieves given database entries

URL form

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

<dbentries> = KEGG database entries involving the following <database>
<database> = pathway | brite | module | disease | drug | environ | ko | genome |
             <org> | compound | glycan | reaction | rpair | rclass | enzyme
<org> = KEGG organism code or T number

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

Notes

The input is limited up to 10 entries.
The input is limited to one pathway entry with the image or kgml option.

Examples

/get/cpd:C01290+gl:G00092		retrieves a compound entry and a glycan entry
/get/C01290+G00092		same as above
/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/hsa05130/image		retrieves the image file of a pathway map
/get/hsa05130/kgml		retrieves the kgml file of a pathway map New!

Operation

conv – convert KEGG identifiers to/from outside identifiers

URL form

http://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-gi | ncbi-geneid | uniprot

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

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

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

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

Note

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-gi/hsa:10458+ece:Z5100		conversion from KEGG ID to NCBI GI
/conv/genes/ncbi-gi:3113320		conversion from NCBI GI to KEGG ID when the organism code is not known New!

Linked entries

Operation

link – find related entries by using database cross-references

URL form

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

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

<database> = pathway | brite | module | disease | drug | environ | ko | genome |
             <org> | compound | glycan | reaction | rpair | rclass | enzyme

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

<dbentries> = KEGG database entries involving the following <database>
<database> = pathway | brite | module | disease | drug | environ | ko | genome |
             <org> | compound | glycan | reaction | rpair | rclass | enzyme |
             genes

Note

The database name "genes" may be used only 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 New!
/link/genes/hsa00010 or /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

KEGG API

General form of the URL

URL form

Database

Database entry

Output

Status code

Operations

Database information

Operation

URL form

Examples

Entry list

Operation

URL form

Notes

Examples

Data search

Operation

URL form

Notes

Examples

Data retrieval

Operation

URL form

Notes

Examples

See also

ID conversion

Operation

URL form

Note

Examples

Linked entries

Operation

URL form

Note

Examples

See also