PubChem 2023 update

2022/10/28 by Sunghwan Kim, Jie Chen, Tiejun Cheng +10 · 61 citations
Biochemistry, Genetics and Molecular Biology · Computer Science · #Biomedical Text Mining and Ontologies #Computational Drug Discovery Methods #Metabolomics and Mass Spectrometry Studies

paper · pdf · doi:10.1093/nar/gkac956

openalex publication_date 2022/10/28 · openalex created_date 2025/10/10 · openalex updated_date 2026/07/31

Abstract

PubChem (https://pubchem.ncbi.nlm.nih.gov) is a popular chemical information resource that serves a wide range of use cases. In the past two years, a number of changes were made to PubChem. Data from more than 120 data sources was added to PubChem. Some major highlights include: the integration of Google Patents data into PubChem, which greatly expanded the coverage of the PubChem Patent data collection; the creation of the Cell Line and Taxonomy data collections, which provide quick and easy access to chemical information for a given cell line and taxon, respectively; and the update of the bioassay data model. In addition, new functionalities were added to the PubChem programmatic access protocols, PUG-REST and PUG-View, including support for target-centric data download for a given protein, gene, pathway, cell line, and taxon and the addition of the 'standardize' option to PUG-REST, which returns the standardized form of an input chemical structure. A significant update was also made to PubChemRDF. The present paper provides an overview of these changes.

Citations

• NCBI Taxonomy: a comprehensive update on curation, resources and tools
• PubChem in 2021: new data content and improved web interfaces
• UniProt: the universal protein knowledgebase in 2021
• The Gene Ontology resource: enriching a GOld mine

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