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Convert to or from kegg identifiers

Source: R/kegg_lookup_class.R
kegg_lookup.Rd

Searches the Kegg database to obtain external identifiers. KEGG compound, drug and glycan databases can be queried for pubchem and chebi identifiers, and vice-versa.

Usage

kegg_lookup(
  get = "pubchem_sid",
  from = "compound",
  query_column,
  suffix = "_kegg",
  cache = NULL,
  cache_mode = "update",
  ...
)

Arguments

get

(character) Get identifier. Allowed values are limited to the following:

  • "compound": KEGG small molecule database.

  • "glycan": KEGG glycan database.

  • "drug": KEGG drug database.

  • "chebi": Chemical Entities of Biological Interest (ChEBI) database.

  • "pubchem_sid": PubChem Substance Identifier.

The default is "pubchem_sid".

from

(character) From identifier. Allowed values are limited to the following:

  • "compound": KEGG small molecule database.

  • "glycan": KEGG glycan database.

  • "drug": KEGG drug database.

  • "chebi": Chemical Entities of Biological Interest (ChEBI) database.

  • "pubchem_sid": PubChem Substance Identifier.

The default is "compound".

query_column

(character) The name of the column containing identifiers to search the database for. They should be identifiers of the type selected for the "from" slot.

suffix

(character) A suffix appended to all column names in the returned result. The default is "_kegg".

cache

(annotation_database, NULL) A struct cache object (e.g. rds_cache()) that stores results of previous KEGG conversions, keyed by query value. Values already present in the cache are not requeried. If not using a cache then set to NULL. The default is NULL.

cache_mode

(character) Cache mode. Allowed values are limited to the following:

  • "update": The normal mode: values already in cache are used as-is, anything missing is queried live and the result added to the cache.

  • "offline": Never query the live KEGG API. Only values already present in cache are returned, and everything else is left as NA.

  • "rebuild": Ignore any existing cached value and query the live KEGG API for every value, overwriting the corresponding entry in cache. Useful when cached results are known to be stale.

The default is "update".

...

Additional slots and values passed to struct_class.

Value

A kegg_lookup object with the following output slots:

updated(annotation_source) An annotation_source object with a new column of compound identifiers.

Details

This object makes use of functionality from the following packages:

  • KEGGREST

  • dplyr

Inheritance

A kegg_lookup object inherits the following struct classes:

[kegg_lookup] -> [model] -> [struct_class]

References

Tenenbaum D, Maintainer B (2026). KEGGREST: Client-side REST access to the Kyoto Encyclopedia of Genes and Genomes (KEGG). doi:10.18129/B9.bioc.KEGGREST https://doi.org/10.18129/B9.bioc.KEGGREST. R package version 1.52.2, https://bioconductor.org/packages/KEGGREST.

Wickham H, François R, Henry L, Müller K, Vaughan D (2026). dplyr: A Grammar of Data Manipulation. doi:10.32614/CRAN.package.dplyr https://doi.org/10.32614/CRAN.package.dplyr. R package version 1.2.1, https://CRAN.R-project.org/package=dplyr.

See also

Other REST API's: classyfire_batch_lookup(), classyfire_lookup(), cts_lite_lookup(), lipidmaps_lookup(), mwb_compound_lookup(), mwb_refmet_lookup(), pubchem_id_exchange(), rest_api()

Examples

M <- kegg_lookup(
        get = "pubchem_sid",
        from = "compound",
        query_column = "V1",
        suffix = "_kegg",
        cache = NULL,
        cache_mode = "update")