This paper provides an overview of the PubChem Substance and Compound databases, including data sources and contents, data organization, data submission using PubChem Upload, chemical structure standardization, web-based interfaces for textual and non-textual searches, and programmatic access.

Biological activity data of chemical substances tested in assay experiments are contained in the BioAssay database.

The Substance database contains chemical information deposited by individual data contributors to PubChem, and the Compound database stores unique chemical structures extracted from the Substance database. PubChem consists of three inter-linked databases, Substance, Compound and BioAssay. For the past 11 years, PubChem has grown to a sizable system, serving as a chemical information resource for the scientific research community. 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 (NIH).

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