PubChem Substance and Compound databases
Open accessAbstract
PubChem (https://pubchem.ncbi.nlm.nih.gov) 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). For the past 11 years, PubChem has grown to a sizable system, serving as a chemical information resource for the scientific research community. PubChem consists of three inter-linked databases, Substance, Compound and BioAssay. 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. Biological activity data of chemical substances tested in assay experiments are contained in the BioAssay database. 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. It also gives a brief description of PubChem3D, a resource derived from theoretical three-dimensional structures of compounds in PubChem, as well as PubChemRDF, Resource Description Framework (RDF)-formatted PubChem data for data sharing, analysis and integration with information contained in other databases.
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The last ten years have seen a dramatic increase in the amount of public chemical and biological data in PubChem, ChEMBL, and other databases that include screening data.
“The last ten years have seen a dramatic increase in the amount of public chemical and biological data in PubChem16, ChEMBL17, and other databases that include screening data.”
From Exploiting machine learning for end-to-end drug discovery and development (2019) · cites this paper as [16]
Outside of the pharmaceutical industry, the availability of large volumes of published or otherwise public domain data in databases like ChEMBL and PubChem has transformed the field.
“Outside of the pharmaceutical industry, the availability of large volumes of published, or otherwise public domain data in databases like ChEMBL29 and PubChem 30 has transformed the field.”
From QSAR without borders (2020) · cites this paper as [30]
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Comparative Study of Multitask Toxicity Modeling on a Broad Chemical Space
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Artificial intelligence for drug discovery and development in Alzheimer's disease
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PerturbNet predicts single-cell responses to unseen chemical and genetic perturbations
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- Authors
- Kim, S., Thiessen, P. A., Bolton, E. E., Chen, J., Fu, G., Gindulyte, A., Han, L., He, J., He, S., Shoemaker, B. A., Wang, J., Yu, B., Zhang, J., & Bryant, S. H.
- Affiliations
- National Institutes of Health (US)
- Corresponding author
- Bolton, Evan E.
- ORCID
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2015-09-22
- Volume
- 44
- Issue
- D1
- Pages
- D1202-D1213
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- PMC
- PMC4702940
- OpenAlex
- W2177317049
- Cited by
- 5,436
- References
- 50
- Citations by year
- 2026: 407 · 2025: 644 · 2024: 624 · 2023: 586 · 2022: 554 · 2021: 611 · 2020: 562 · 2019: 499 · 2018: 497 · 2017: 281 · 2016: 159 · 2015: 3 · 2013: 3
- FWCI
- 323.86
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- public-domain
- Locations
- Nucleic Acids Research (publishedVersion, public-domain)
- Europe PMC (PubMed Central) (publishedVersion, public-domain)
- PubMed Central (publishedVersion, public-domain)
- PubMed (publishedVersion)
- HighWire Press Open Archive (submittedVersion)
- Funders
- National Institutes of Health
- U.S. 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 compound database, Resource Description Framework, chemical information resources, molecular libraries
- MeSH terms
- Pharmaceutical Preparations, Software, Molecular Structure, Internet, 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.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
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