PubChem 2023 update
Open accessAbstract
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.
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Mathematical modeling of multi-objective decision-making has been prevalent since the 1960s.
“Mathematical modeling of multi-objective decision-making has been prevalent since the 1960s (99).”
From Artificial Intelligence for Drug Discovery: Are We There Yet? (2024) · cites this paper as [99]
The BIOASSAY DATA MODEL CHANGE section discusses updates to PubChem’s bioactivity data, while the References section lists work on chemical modeling. Neither addresses the history of mathematical modeling of multi-objective decision-making. Searches for that topic and for the 1960s found no supporting passage in our copy. (LLM, conf=0.76)
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- Authors
- Kim, S., Chen, J., Cheng, T., Gindulyte, A., He, J., He, S., Li, Q., Shoemaker, B. A., Thiessen, P. A., Yu, B., Zaslavsky, L., Zhang, J., & Bolton, E. E.
- Affiliations
- National Institutes of Health (US)
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Department of Health and Human Services , Bethesda , MD, 20894, USA
- Corresponding author
- Bolton, Evan E
- ORCID
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2022-10-28
- Volume
- 51
- Issue
- D1
- Pages
- D1373-D1380
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- PMC
- PMC9825602
- OpenAlex
- W4307468223
- Cited by
- 3,443
- References
- 58
- Citations by year
- 2026: 811 · 2025: 1150 · 2024: 1094 · 2023: 379 · 2022: 2 · 2021: 4 · 2020: 2 · 2012: 1
- FWCI
- 356.78
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- other-oa
- Locations
- Nucleic Acids Research (publishedVersion, other-oa)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Funders
- National Center for Biotechnology Information of the National Library of Medicine
- Topics
- Physical Sciences › Computer Science › Computational Theory and Mathematics › Computational Drug Discovery Methods
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Biomedical Text Mining and Ontologies
- Physical Sciences › Computer Science › Information Systems › Research Data Management Practices
- Keywords
- PubChem, chemical information resources, patent information
- MeSH terms
- Cheminformatics, Biological Assay, Proteins, Drug Discovery, Databases, Chemical
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
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