PubChem (https://pubchem.ncbi.nlm.nih.gov) is a public chemical database at the U.S. National Institutes of Health. It contains a large corpus of chemical information, collected from hundreds of data sources. Especially, it has 300+ million experimental bioactivity data from 1.5 million bioassays, covering tens of thousands of target genes and proteins. This bioactivity data is organized into multiple target-centric data collections in PubChem, called Protein, Gene, Pathway, Cell Line, and Taxonomy. Records in these collections contain information on chemicals related to a given biological target (i.e., protein, gene, pathway, cell line, or taxon), along with annotations about the target, collected from authoritative and curated data sources. These collections assist users in quickly accessing, analyzing, and interpreting the bioactivity data of chemicals. This presentation provides a brief overview of these target-centric data collections in PubChem. In addition, for demonstration purposes, bioactivity data in the PubChem Cell Line collection is used to analyze the similarity between the National Cancer Institute (NCI)-60 cell lines in terms of their response to chemicals.

Target-centric bioactivity data in PubChem and its application for the analysis of chemical-response similarity among the NCI-60 cell lines

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