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Metabolomics Workbench RefMet lookup

Source: R/mwb_refmet_lookup_class.R
mwb_refmet_lookup.Rd

Matches a reported compound name (which may be a synonym, conjugate acid/base form, or otherwise non-canonical name) to its RefMet standardised name and identifiers, using the Metabolomics Workbench RefMet REST API. Intended as a substitute for the (now defunct) Chemical Translation Service (CTS): the original 'PubChem Identifier Exchange + CTS' translation route described by some published metabolite-merging methods can no longer be reproduced, since CTS has been shut down and its replacement, CTS-Lite, does not support name-based lookups. RefMet's match endpoint plays a similar synonym-resolution role, and its curated picks (e.g. preferring the biologically-relevant stereoisomer/protonation state over a generic entry) often differ usefully from a plain PubChem name search.

Usage

mwb_refmet_lookup(query_column, suffix = "_refmet", ...)

Arguments

query_column

(character) The name of a column in the annotation table containing values to search in the api call.

suffix

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

...

Additional slots and values passed to struct_class.

Value

A mwb_refmet_lookup object with the following output slots:

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

Details

This object makes use of functionality from the following packages:

  • httr

Inheritance

A mwb_refmet_lookup object inherits the following struct classes:

[mwb_refmet_lookup] -> [rest_api] -> [model] -> [struct_class]

References

Wickham H (2026). httr: Tools for Working with URLs and HTTP. doi:10.32614/CRAN.package.httr https://doi.org/10.32614/CRAN.package.httr. R package version 1.4.9, https://CRAN.R-project.org/package=httr.

See also

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

Examples

M <- mwb_refmet_lookup(
        base_url = "https://www.metabolomicsworkbench.org/rest/refmet",
        url_template = "<base_url>/match/<query_column>/name",
        query_column = character(0),
        cache = NULL,
        cache_mode = "update",
        status_codes = list(),
        delay = 0.5,
        suffix = "_refmet")