dma-pubchem-db: SQLite database of PubChem CID compounds merged by InChIKey for Deep Metabolome Annotation (DMA)

PubChem CID SQLite Database (Extracted 27 August 2019) This SQLite database contains PubChem compound information (CID-based) extracted on 27 August 2019. Compounds sharing the same InChIKey have been merged into single entries. Use in Deep Metabolome Annotation (DMA) of Daphnia magna This database was used for Deep Metabolome Annotation (DMA) of D. magna in the following tools and packages: msPurity (R package)Repository: https://github.com/computational-metabolomics/msPurityFunction: combineAnnotation msPurity Galaxy toolsRepository: https://github.com/computational-metabolomics/msPurity-galaxyTool: msPurity.combineAnnotation LC Fractionation Galaxy toolRepository: https://github.com/computational-metabolomics/lcfrac-galaxyUsed for: combine-annotation functionality within the workflow The database was applied in the DMA workflows available in the Galaxy instance:https://dma.galaxy.bham.ac.uk/ HMDB similarity comparisons The database includes precomputed structural similarity between PubChem compounds and a curated subset of endogenous HMDB compounds (HMDB entries were filtered to remove clearly exogenous metabolites, such as drug metabolites). Molecular fingerprints were compared using Tanimoto similarity. This provides a simple structural proxy for assessing whether a given PubChem compound can be considered biologically relevant.