pubchem.bio: Biologically Informed Metabolomic Databases from 'PubChem'

All 'PubChem' compounds are downloaded to a local computer, but for each compound, only partial records are used. The data are organized into small files referenced by 'PubChem' CID. This package also contains functions to parse the biologically relevant compounds from all 'PubChem' compounds, using biological database sources, pathway presence, and taxonomic relationships. Taxonomy is used to generate a lowest common ancestor taxonomy ID (NCBI) for each biological metabolite, which then enables creation of taxonomically specific metabolome databases for any taxon.

Version:	1.0.0
Depends:	R (≥ 3.5.0)
Imports:	foreach, doParallel, R.utils, data.table, dplyr, rcdk, stringr
Suggests:	utils, knitr, rmarkdown, formatR
Published:	2025-08-28
Author:	Corey Broeckling [aut, cre]
Maintainer:	Corey Broeckling <cbroeckl at colostate.edu>
License:	GPL-3
NeedsCompilation:	no
Materials:	NEWS
CRAN checks:	pubchem.bio results

Documentation:

Reference manual:	pubchem.bio.html , pubchem.bio.pdf
Vignettes:	pubchem.bio (source, R code)

Downloads:

Package source:	pubchem.bio_1.0.0.tar.gz
Windows binaries:	r-devel: not available, r-release: not available, r-oldrel: not available
macOS binaries:	r-release (arm64): not available, r-oldrel (arm64): not available, r-release (x86_64): pubchem.bio_1.0.0.tgz, r-oldrel (x86_64): pubchem.bio_1.0.0.tgz

Linking:

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