PubChem Substance and Compound databases

PubChem is a public repository for information on chemical substances and their biological activities, launched in 2004 as a component of the Molecular Libraries Roadmap Initiatives of the US National Institutes of Health and grown over eleven years into a sizable chemical information resource for the research community. It consists of three inter-linked databases: the Substance database, containing chemical information deposited by individual contributors; the Compound database, storing unique chemical structures extracted from Substance; and the BioAssay database, holding biological activity data of substances tested in assay experiments.

The paper provides an overview of the Substance and Compound databases, including data sources and contents, data organization, submission using PubChem Upload, chemical structure standardization, web-based interfaces for textual and non-textual searches, and programmatic access. It also briefly describes PubChem3D, derived from theoretical three-dimensional structures of compounds, and PubChemRDF, Resource Description Framework-formatted data supporting sharing, analysis and integration with other databases.