PubChemLite for Exposomics

PubChemLite is a subset of PubChem (https://pubchem.ncbi.nlm.nih.gov/) selected from major categories of the Table of Contents page at the PubChem Classification Browser (https://pubchem.ncbi.nlm.nih.gov/classification/#hid=72). With this release, there is now just one "exposomics" flavour, which is the former tier1 plus two new categories (Associated Disorders & Diseases and Identification):

PubChemLite "exposomics" is 371,663 compounds (31 Oct 2020) compiled from 10 categories: AgroChemInfo, BioPathway, DrugMedicInfo, FoodRelated, PharmacoInfo, SafetyInfo, ToxicityInfo, KnownUse, DisorderDisease, Identification.

PubChemCIDs have been collapsed by InChIKey first block, reporting the structure from the most annotated CID, plus related CIDs. Entries that will be ignored by MetFrag (salts, disconnected substances) or cause errors (e.g. transition metals) have been removed. The Patent and PubMed ID counts are extracted from files on the PubChem FTP site. The "AnnoTypeCount" term counts how many of the categories are represented, the subsequent column (named per category) counts the number of annotation categories available in the next sub-category of the TOC entry.

These files can be used "as is" as localCSV for MetFrag Command Line (https://ipb-halle.github.io/MetFrag/) - please do NOT upload these files directly to the web interface, they are too large and will instead be available in a drop-down menu.

Further details are described in Schymanski et al. (2021) DOI:10.1186/s13321-021-00489-0.

NOTE: The latest PubChemLite for Exposomics version can be downloaded at DOI:10.5281/zenodo.5995885 (currently updating monthly).