Prepare merged structure organism pairs libraries

Description

This function merges all structure-organism pair libraries (LOTUS, HMDB, ECMDB, etc.) into a single comprehensive library. Can optionally filter by taxonomic level to create biologically-focused subsets. Also splits structures into separate metadata tables.

Usage

prepare_libraries_sop_merged(
  files = get_params(step = "prepare_libraries_sop_merged")\$files\$libraries\$sop\$prepared,
  filter = get_params(step = "prepare_libraries_sop_merged")\$organisms\$filter\$mode,
  level = get_params(step = "prepare_libraries_sop_merged")\$organisms\$filter\$level,
  value = get_params(step = "prepare_libraries_sop_merged")\$organisms\$filter\$value,
  cache = get_params(step =
    "prepare_libraries_sop_merged")\$files\$libraries\$sop\$merged\$structures\$processed,
  output_key = get_params(step =
    "prepare_libraries_sop_merged")\$files\$libraries\$sop\$merged\$keys,
  output_org_tax_ott = get_params(step =
    "prepare_libraries_sop_merged")\$files\$libraries\$sop\$merged\$organisms\$taxonomies\$ott,
  output_str_stereo = get_params(step =
    "prepare_libraries_sop_merged")\$files\$libraries\$sop\$merged\$structures\$stereo,
  output_str_met = get_params(step =
    "prepare_libraries_sop_merged")\$files\$libraries\$sop\$merged\$structures\$metadata,
  output_str_nam = get_params(step =
    "prepare_libraries_sop_merged")\$files\$libraries\$sop\$merged\$structures\$names,
  output_str_tax_cla = get_params(step =
    "prepare_libraries_sop_merged")\$files\$libraries\$sop\$merged\$structures\$taxonomies\$cla,
  output_str_tax_npc = get_params(step =
    "prepare_libraries_sop_merged")\$files\$libraries\$sop\$merged\$structures\$taxonomies\$npc
)

Arguments

files	Character vector or list of paths to prepared library files
filter	Logical whether to filter the merged library by taxonomy
level	Character string taxonomic rank for filtering (kingdom, phylum, family, genus, etc.)
value	Character string taxon name(s) to keep (can use | for multiple, e.g., ‘Gentianaceae|Apocynaceae’)
cache	Character string path to cache directory for processed SMILES
output_key	Character string path for output keys file
output_org_tax_ott	Character string path for organisms taxonomy (OTT) file
output_str_stereo	Character string path for structures stereochemistry file
output_str_met	Character string path for structures metadata file
output_str_nam	Character string path for structures names file
output_str_tax_cla	Character string path for ClassyFire taxonomy file
output_str_tax_npc	Character string path for NPClassifier taxonomy file

Details

Creates merged library by combining all available SOP sources, optionally filtering by taxonomic criteria (e.g., only Gentianaceae). Splits output into structures metadata, names, taxonomy, and organisms.

Value

Character string path to the prepared merged SOP library

Examples

library("tima")

copy_backbone()
go_to_cache()
github <- "https://raw.githubusercontent.com/"
repo <- "taxonomicallyinformedannotation/tima-example-files/main/"
dir <- paste0(github, repo)
files <- get_params(step = "prepare_libraries_sop_merged")$files$libraries$sop$prepared$lotus |>
  gsub(pattern = ".gz", replacement = "", fixed = TRUE)
get_file(url = paste0(dir, files), export = files)
prepare_libraries_sop_merged(files = files)
unlink("data", recursive = TRUE)