PubChemLite for Exposomics: Curated Chemical Data for Metabolite Identification

Regular updates of the PubChemLite for Exposomics data collection, a subset of PubChem compiled from 11 major categories. The repository, maintained by Emma Schymanski at the University of Luxembourg, provides a curated list of PubChem Compound Identifiers collapsed by InChIKey first block and filtered for compatibility with metabolite identification tools. The collection is described in a 2021 publication (DOI:10.1186/s13321-021-00489-0).

Use Cases

• Metabolite identification based on curated chemical structures and annotations.
• Exposomics research based on aggregated chemical safety and toxicity information.
• Chemical database filtering based on categories like AgroChemInfo, FoodRelated, and DisorderDisease.
• Structure annotation workflows based on InChIKey-collapsed PubChem entries.

Strengths

• Curated from 11 specific annotation categories within PubChem, including ToxicityInfo and SafetyInfo.
• Entries incompatible with MetFrag (e.g., salts, transition metals) have been removed, enhancing tool compatibility.
• Includes counts for Patent and PubMed IDs, providing context for annotation richness.

Limitations

• Column-level documentation is absent; field semantics must be inferred after download.
• Row count is unknown, which may limit suitability assessment for large-scale projects.
• Last update date is unknown; freshness unverified.

Provenance

Source

PubChem, via the University of Luxembourg.

Collection Method

Subset selected from major categories of the PubChem Classification Browser, with CIDs collapsed by InChIKey first block.