LIPID MAPS database

Imports the full LIPID MAPS Structure Database (LMSD) bulk compound export (~50,000 lipids), cached locally with BiocFileCache so it is only downloaded once rather than queried per-row. Columns include lm_id, name, abbrev, core, main_class, sub_class, formula, inchi, inchi_key, kegg_id, hmdb_id, chebi_id, pubchem_cid and smiles – a single database_lookup() against this table can replace many individual lipidmaps_lookup() REST queries.

Usage

lipidmaps_database(
  bfc_path = NULL,
  resource_name = "MetMashR_lipidmaps",
  source = paste0("https://www.lipidmaps.org/rest/compound/lm_id/LM/all/download"),
  ...
)

Arguments

bfc_path: (character, NULL) BiocFileCache is used to cache the database locally and prevent unnecessary downloads. If a path is provided then BiocFileCache will use this location. If NULL it will use the default location (see BiocFileCache::BiocFileCache() for details). The default is NULL.
resource_name: (character) The name given to this resource in the cache. (see BiocFileCache::BiocFileCache() for details). The default is "MetMashR_lipidmaps".
source: (ANY) The source of annotation data. The default is paste0("https://www.lipidmaps.org/rest/compound/lm_id/LM/all/download").
...: Additional slots and values passed to struct_class.

Value

A lipidmaps_database object. This object has no output slots.

Details

This object makes use of functionality from the following packages:

BiocFileCache

Inheritance

A lipidmaps_database object inherits the following struct classes:

[lipidmaps_database] -> [BiocFileCache_database] -> [annotation_database] -> [annotation_source] -> [struct_class]

References

Shepherd L, Morgan M (2026). BiocFileCache: Manage Files Across Sessions. R package version 3.2.0.

Examples

M <- lipidmaps_database(
        bfc_path = NULL,
        resource_name = "bfc",
        bfc_fun = function(){},
        import_fun = function(){},
        offline = FALSE,
        tag = character(0),
        data = data.frame(),
        source = "ANY")