Biologically Informed Metabolomic Databases from 'PubChem'
build.cid.lca
build.primary.metabolome
build.pubchem.bio
build.taxon.metabolome
cid.monoisotopic.mass.rda
export.msfinder
export.pubchem.bio
export.sirius
get.pubchem.ftp
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.