PubChem Data Usage

The PubChem database is designed to provide and encourage access within the scientific community to the most up to date and comprehensive source of chemical structures of small organic molecules and their biological activities. PubChem houses both compound information from the scientific literature as well as screening and probe data from the Molecular Libraries Program. Citing the original generators of the data sets (see below for how to cite) will ensure that the corresponding scientists will get credit and allow readers to locate the source.

PubChem Citation Guidelines
Citing Data that you find in PubChem

Citing Individual Records from a PubChem Database

When citing individual or multiple records from a PubChem database, please cite each record's identification number (for example, the AID or Summary AID for a BioAssay record, the SID for a PubChem Substance record or the CID for the associated PubChem Compound record) and the organization that deposited the data. Please also cite the chemical probe Molecular Libraries (ML) number when appropriate, along with the reference for the relevant PubChem database. If the database record has a corresponding publication, it is appropriate to cite that as well.

For example:

  Excerpt of text from the body of an article that cites PubChem records and a Molecular Libraries chemical probe:
  "We searched the PubChem BioAssay database for the biological activity and found one assay, AID: 2299 (1) from the Scripps Research Institute Molecular Screening Center, which reported the identification and development of chemical probe ML114 (2), a potent small molecule inhibitor against Retinoblastoma binding protein 9 (RBBP9). The chemical structure information for this probe is available in the PubChem Substance and Compound database through the substance identifier number SID: 85098567 (3) and/or the unique chemical structure identifier CID: 5934766 (4)."
  Excerpt of corresponding references from the article's bibliography:
  (1) National Center for Biotechnology Information. PubChem BioAssay Database; AID=2299, Source=Scripps Research Institute Molecular Screening Center, (accessed Feb. 22, 2011).
  (2) NIH Molecular Libraries. Probe Report for RBBP9 Inhibitors. Chapter ML114 IN Probe Reports from the Molecular Libraries Program [Internet], National Library of Medicine (US), National Center for Biotechnology Information, Bethesda, MD, 2010 (accessed 2011 Feb 22). Available from (or in Entrez Books (
  (3) National Center for Biotechnology Information. PubChem Substance Database; SID=85098567, Source=Scripps Research Institute Molecular Screening Center, (accessed Feb. 22, 2011).
  (4) National Center for Biotechnology Information. PubChem Compound Database; CID=5934766, (accessed Feb. 22, 2011).
Citing a PubChem Database

Database publications can cite either the PubChem Substance or Compound database or the PubChem BioAssay databases as appropriate.

  PubChem Substance and PubChem Compound
  Kim S, Thiessen PA, Bolton EE, Chen J, Fu G, Gindulyte A, Han L, He J, He S, Shoemaker BA, Wang J, Yu B, Zhang J, Bryant SH. PubChem Substance and Compound databases. Nucleic Acids Res. 2015 Sep 22. pii: gkv951. [Epub ahead of print] [PubMed PMID: 26400175] doi: 10.1093/nar/gkv951 [Free Full Text at Oxford Journals]
  PubChem BioAssay
  Wang Y, Suzek T, Zhang J, Wang J, He S, Cheng T, Shoemaker BA, Gindulyte A, Bryant SH. PubChem BioAssay: 2014 update. Nucleic Acids Res. 2014 Jan 1;42(1):D1075-82. doi:10.1093/nar/gkt978. Epub 2013 Nov 5 [PubMed PMID: 24198245] [Free Full Text at Oxford Journals]
 Revised 24 November 2015