Prepare libraries of structure organism pairs ECMDB

Description

This function prepares ECMDB (E. coli Metabolome Database) structure-organism pairs by parsing JSON data, extracting metabolite information, and formatting for TIMA workflows. Handles E. coli metabolite data with structures.

Usage

prepare_libraries_sop_ecmdb(
  input = get_params(step = "prepare_libraries_sop_ecmdb")\$files\$libraries\$sop\$raw\$ecmdb,
  output = get_params(step =
    "prepare_libraries_sop_ecmdb")\$files\$libraries\$sop\$prepared\$ecmdb
)

Arguments

input	character Character string path to ECMDB JSON zip file
output	character Character string path for prepared ECMDB library output

Value

Character string path to prepared ECMDB structure-organism pairs

See Also

Other preparation: prepare_annotations_gnps(), prepare_annotations_mzmine(), prepare_annotations_sirius(), prepare_annotations_spectra(), prepare_features_components(), prepare_features_edges(), prepare_features_tables(), prepare_libraries_rt(), prepare_libraries_sop_bigg(), prepare_libraries_sop_closed(), prepare_libraries_sop_hmdb(), prepare_libraries_sop_lotus(), prepare_libraries_sop_merged(), prepare_libraries_spectra(), prepare_params(), prepare_taxa()

Examples

library("tima")

copy_backbone()
go_to_cache()
prepare_libraries_sop_ecmdb()
unlink("data", recursive = TRUE)