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Published June 27, 2022 | Version 1.11.0
Dataset Open

PubChemLite for Exposomics

  • 2. LCSB, University of Luxembourg


This is the repository for regular updates of the PubChemLite for Exposomics data collection. PubChemLite for Exposomics is a subset of PubChem selected from major categories of the Table of Contents page at the PubChem Classification Browser, described in DOI:10.1186/s13321-021-00489-0.

PubChemLite for Exposomics is 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.


These files can be used "as is" for MetFrag (command line) and other high throughput workflows.

Please do NOT upload these files directly to the MetFrag web interface, they are too large. The latest updates will be available in a drop-down menu.



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Additional details


  • Schymanski, E.L., Kondić, T., Neumann, S. et al. Empowering large chemical knowledge bases for exposomics: PubChemLite meets MetFrag. J Cheminform 13, 19 (2021).