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ID/synonym lookup via ChEBI

Source: R/chebi_lookup_class.R
chebi_lookup.Rd

Uses the ChEBI REST API to look up a ChEBI identifier from a compound name/synonym, or a synonym from a ChEBI identifier, based on the input annotation column.

Usage

chebi_lookup(
  query_column,
  search_by = c("name", "chebi_id"),
  suffix = "_chebi",
  records = "best",
  max_records = "50",
  columns = ".all",
  delay = 1,
  ...
)

Arguments

query_column

(character) The name of a column in the annotation table containing the search terms. If search_by = "name" this should be a column of compound names/synonyms. If search_by = "chebi_id" this should be a column of ChEBI identifiers (e.g. "CHEBI:27732" or "27732"; any "CHEBI:" prefix is stripped automatically before querying the API).

search_by

(character) Search by. Allowed values are limited to the following:

  • "name": Search ChEBI by compound name/synonym and return the matching ChEBI ID(s).

  • "chebi_id": Search ChEBI by ChEBI ID and return the matching synonym(s)/name(s).

The default is c("name", "chebi_id").

suffix

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

records

(character) Returned record(s). Allowed values are limited to the following:

  • "": There can be multiple matches for a given search term (multiple ChEBI entities matching a name, or multiple synonyms for a ChEBI ID).

  • "best": Return only the single best/primary matching record.

  • "all": Return all matching records.

The default is "best".

max_records

(character) The maximum number of hits requested from the ChEBI search API when search_by = "name" (passed as the "size" query parameter). Has no effect when search_by = "chebi_id". The default is "50".

columns

(character) The columns to include in the result. One or more of "chebi_id", "name" (search_by = "name" only), "synonym" (search_by = "chebi_id" only), "inchikey", "smiles", "inchi", "formula", "mass", "monoisotopicmass", "charge", "stars" (ChEBI's own curation-quality rating, 3 = fully manually annotated). Keyword ".all" (the default) returns every column available for the chosen search_by direction. The default is ".all".

delay

(numeric, integer) Delay in seconds between API calls. ChEBI's REST API does not publish a specific rate limit, so this default is a conservative courtesy value; increase it if you see 429/503 responses, or decrease it if you have confirmed a higher rate is acceptable. The default is 1.

...

Additional slots and values passed to struct_class.

Value

A chebi_lookup object with the following output slots:

updated(annotation_source) The annotation_source after adding data returned by the API.

Inheritance

A chebi_lookup object inherits the following struct classes:

[chebi_lookup] -> [rest_api] -> [model] -> [struct_class]

References

Hastings, Janna, Owen, Gareth, Dekker, Adriano, Ennis, Marcus, Kale, Namrata, Muthukrishnan, Venkatesh, Turner, Steve, Swainston, Neil, Mendes, Pedro, Steinbeck, Christoph (2016). "ChEBI in 2016: Improved services and an expanding collection of metabolites." Nucleic Acids Research, 44(D1), D1214-D1219. doi:10.1093/nar/gkv1031 https://doi.org/10.1093/nar/gkv1031.

Examples

M <- chebi_lookup(
        search_by = "name",
        records = "best",
        max_records = "50",
        columns = ".all",
        base_url = "https://www.ebi.ac.uk/chebi/backend/api/public",
        url_template = "<base_url>/es_search?term=<query_column>&size=<max_records>",
        query_column = character(0),
        cache = NULL,
        cache_mode = "update",
        status_codes = list(),
        delay = 1,
        suffix = "_rest_api")