PubChem 2023 update

PubChem 2023 update

2022 | Sunghwan Kim, Jie Chen, Tiejun Cheng, Asta Gindulyte, Jia He, Siqian He, Qingliang Li, Benjamin A. Shoemaker, Paul A. Thiessen, Bo Yu, Leonid Zaslavsky, Jian Zhang and Evan E. Bolton
PubChem, a public chemical database, has undergone significant updates in the past two years. Over 120 new data sources have been integrated, expanding its chemical information coverage. Key updates include the integration of Google Patents data, the creation of Cell Line and Taxonomy data collections, and an updated bioassay data model. New functionalities have been added to PUG-REST and PUG-View, including support for target-centric data downloads and a 'standardize' option for chemical structure standardization. PubChemRDF has also been significantly updated, now containing 120 billion triples and including a new Pathway subdomain. The Cell Line and Taxonomy data collections provide quick access to chemical information for specific cell lines and taxa. The new bioassay data model improves data management by storing panel assay data in rows rather than columns and includes endpoint qualifiers for accurate interpretation. The use of NCBI accessions has replaced GI numbers for protein identifiers. Programmatic access to PubChem has been enhanced, with new features allowing users to retrieve target-centric data and standardized chemical structures. PubChem continues to improve data quality, expand its data breadth, and integrate high-quality information from authoritative sources. It also aims to modernize interfaces and enhance handling of complex chemical data, including polymers and mixtures. The database is freely accessible and provides tools for researchers in the biomedical community. Future improvements will focus on enhancing data quality, modernizing interfaces, and improving access to information.PubChem, a public chemical database, has undergone significant updates in the past two years. Over 120 new data sources have been integrated, expanding its chemical information coverage. Key updates include the integration of Google Patents data, the creation of Cell Line and Taxonomy data collections, and an updated bioassay data model. New functionalities have been added to PUG-REST and PUG-View, including support for target-centric data downloads and a 'standardize' option for chemical structure standardization. PubChemRDF has also been significantly updated, now containing 120 billion triples and including a new Pathway subdomain. The Cell Line and Taxonomy data collections provide quick access to chemical information for specific cell lines and taxa. The new bioassay data model improves data management by storing panel assay data in rows rather than columns and includes endpoint qualifiers for accurate interpretation. The use of NCBI accessions has replaced GI numbers for protein identifiers. Programmatic access to PubChem has been enhanced, with new features allowing users to retrieve target-centric data and standardized chemical structures. PubChem continues to improve data quality, expand its data breadth, and integrate high-quality information from authoritative sources. It also aims to modernize interfaces and enhance handling of complex chemical data, including polymers and mixtures. The database is freely accessible and provides tools for researchers in the biomedical community. Future improvements will focus on enhancing data quality, modernizing interfaces, and improving access to information.
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