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 | ddiDatabase 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 | ykDatabase 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
An "enzyme" entry, a "variant" entry or an entry of any outside database is identified by
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).
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 1-2 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, 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
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Output
Output format
The output of all operations is in a text format:
Status code
- tab-delimited text returned from list, find, conv and link
- flat file database format returned from get
- text message returned from info
The HTTP status code can be used to check if the operation was successful.
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KEGG API Operations
INFO
Name
See also
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 | dgroupDescription
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 |
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 | dgroupDescription
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
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.
/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
See also
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 | nopDescription
This is a search operation. The first form searches entry identifier and associated fields shown below for matching keywords.
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
Database | Text search fields (see flat file format) |
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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.
/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 |
DBGET search interface such as in the KEGG Table of Contents page.
GET
Name
See also
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 | jsonDescription
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
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.
/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 |
KEGG WebLinks to retrieve entries in HTML.
CONV
Name
See also
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 | chebiDescription
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 |
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 | ndc | yk
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 | ndc | ykDescription
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
See also
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 | yjDescription
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 |
Drug Interaction Checker tool in KEGG MEDICUS.
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-tripleDescription
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: December 1, 2024
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