PubChem Citation Guidelines

PubChem contains a wealth of chemical structures, bioactivity, health & safety, spectra data, and more. In addition to the web interface, PubChem provides direct data access via programmatic services and FTP downloads.

If you use data or services from PubChem, proper citation helps readers locate the original source of the work. Some records in PubChem are directly assembled from the contributing organization with attribution provided on the record. Other records, like Compound records, contain derived data in addition to collected annotations with attribution.

 

Contents

 

Primary PubChem Citation

Please use the following citation as a general reference for most PubChem data and services:

AMA

Kim S, Chen J, Cheng T, et al. PubChem in 2021: new data content and improved web interfaces. Nucleic Acids Res. 2021;49(D1):D1388–D1395. doi:10.1093/nar/gkaa971
 

MLA

Kim, Sunghwan et al. “PubChem in 2021: new data content and improved web interfaces.” Nucleic Acids Res. vol. 49,D1 (2021): D1388-D1395. doi:10.1093/nar/gkaa971
 

APA

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. (2019). PubChem in 2021: new data content and improved web interfaces. Nucleic Acids Res., 49(D1), D1388–D1395. https://doi.org/10.1093/nar/gkaa971
 

NLM

Kim S, Chen J, Cheng T, Gindulyte A, He J, He S, Li Q, Shoemaker BA, Thiessen PA, Yu B, Zaslavsky L, Zhang J, Bolton EE. PubChem in 2021: new data content and improved web interfaces. Nucleic Acids Res. 2019 Jan 8;47(D1):D1388-D1395. doi: 10.1093/nar/gkaa971. PMID: 33151290.
 

[Free Full Text at Oxford Journals] [Free Full Text at PubMed Central]

 

 

Specific Citation Scenarios

If you would like to reference something more specific in PubChem, either an individual data record or a particular service, browse the following topics.

 

Reference individual records with in-page Cite button

PubChem contains various types of records; on each page a Cite button exists in the upper-right corner to generate standard reference formats (APA, AMA, MLA, and NLM) for the record. 

 

Alternatively, the record URL provides a regular format including the data type and record identifier.

 

EXAMPLE: Derived PubChem Compound record for aspirin:

PubChem Identifier: CID 2244
URL: https://pubchem.ncbi.nlm.nih.gov/compound/2244

 

EXAMPLE: Contributed PubChem Substance record for aspirin from ChemIDplus:

PubChem Identifier: SID 134971785
URL: https://pubchem.ncbi.nlm.nih.gov/substance/134971785

 

EXAMPLE: Contributed PubChem BioAssay record from Genentech:

PubChem Identifier: AID 1224916
URL: https://pubchem.ncbi.nlm.nih.gov/bioassay/1224916

 

EXAMPLE: Derived PubChem Protein Target record for EGFR product:

PubChem Protein Target: P00533
URL: https://pubchem.ncbi.nlm.nih.gov/target/protein/P00533

 

Reference a particular data section within a record

 

PubChem collects and computes many pieces of information in each record. To reference a particular data section within a derived record, use the full record URL including the section name suffix. You can easily navigate to the section using the table of contents or scrolling within the page and then copying the URL.

 

Note: Do not use section numbers within a record as they differ between records and over time.

 

EXAMPLE: Clinical Trials involving the PubChem Compound record for aspirin:

PubChem Identifier: CID 2244
URL: https://pubchem.ncbi.nlm.nih.gov/compound/2244#section=Clinical-Trials

 

EXAMPLE: Chemical Probes identified in a PubChem Target record for EGFR:

PubChem Identifier: SID 134971785
URL: https://pubchem.ncbi.nlm.nih.gov/substance/134971785#section=Chemical-Probes

 

Reusing the 2D or 3D structure image of a compound or substance record

 

You can reuse in your own publication the 2D or 3D structure images presented on PubChem pages, without any special permission from PubChem.  Referencing the structure images is done in a similar manner to referencing a data section within a record (as described above).  Use the full record URL, followed by the section name suffix, "2D-Structure" or "3D-Conformer".

 

EXAMPLE: 2D structure image of CID 2244 (aspirin):

PubChem Identifier: CID 2244
URL: https://pubchem.ncbi.nlm.nih.gov/compound/2244#section=2D-Structure

 

EXAMPLE: 3D structure image of CID 2244 (aspirin)

PubChem Identifier: CID 2244
URL: https://pubchem.ncbi.nlm.nih.gov/compound/2244#section=3D-Conformer

 

EXAMPLE: 3D structure image of SID 381317591 (atorvastatin)

PubChem Identifier: SID 381317591
URL: https://pubchem.ncbi.nlm.nih.gov/substance/381317591#section=3D-Conformer

 

 

Cite a paper focused on a particular aspect or service of PubChem

PUG-REST

Kim S, Thiessen PA, Cheng T, Yu B, Bolton EE. An update on PUG-REST: RESTful interface for programmatic access to PubChem. Nucleic Acids Res. 2018 July 2; 46(W1):W563-570. [PubMed PMID: 29718389] doi: 10.1093/nar/gky294.

[Free Full Text in PubMed Central] - includes ability to cite in different formats (AMA, MLA, APA), etc.

 

PUG-View

Kim S, Thiessen PA, Cheng T, Zhang J, Gindulyte A, Bolton EE. PUG-View: programmatic access to chemical annotations integrated in PubChem. J Cheminform. 2019 Aug 9; 11(1):56. [PubMed PMID: 31399858] doi: 10.1186/s13321-019-0375-2.

[Free Full Text in PubMed Central] - includes ability to cite in different formats (AMA, MLA, APA), etc.

 

PUG and PUG-SOAP

Kim S, Thiessen PA, Bolton EE, Bryant SH. PUG-SOAP and PUG-REST: web services for programmatic access to chemical information in PubChem. Nucleic Acids Res. 2015 Jul 1;43(W1):W605-611. [PubMed PMID: 25934803] doi: 10.1093/nar/gkv396.

[Free Full Text in PubMed Central] - includes ability to cite in different formats (AMA, MLA, APA), etc.

 

PubChem Sketcher

Ihlenfeldt WD, Bolton EE, Bryant SH. The PubChem chemical structure sketcher. J Cheminform. 2009 Dec 17;1(1):20. [PubMed PMID: 20298522] doi: 10.1186/1758-2946-1-20. 

[Free Full Text in PubMed Central] - includes ability to cite in different formats (AMA, MLA, APA), etc.

 

PubChemRDF

Fu G, Batchelor C, Dumontier M, Hastings J, Willighagen E, Bolton E. PubChemRDF: towards the semantic annotation of PubChem compound and substance databases. J Cheminform. 2015 July 14; 7:34. eCollection 2015. [PubMed PMID: 26175801] doi: 10.1186/s13321-015-0084-4.

[Free Full Text in PubMed Central] - includes ability to cite in different formats (AMA, MLA, APA), etc.

 

PubChem3D

Bolton EE, Chen J, Kim S, Han L, He S, Shi W, Simonyan V, Sun Y, Thiessen PA, Wang J, Yu B, Zhang J, Bryant SH. PubChem3D: A new resource for scientists. J Cheminform. 2011 Sep 20; 3(1):32. [PubMed PMID: 21933373] doi: 10.1186/1758-2946-3-32.

[Free Full Text in PubMed Central] - includes ability to cite in different formats (AMA, MLA, APA), etc.

[PubChem3D thematic series at Journal of Cheminformatics]

 

PubChem Fingerprint

National Center for Biotechnology Information. PubChem Subgraph Fingerprint [Internet]. Bethesda, MD: National Institutes of Health; 2009 May 1 [cited 2022 February 1]. Available from: https://ftp.ncbi.nlm.nih.gov/pubchem/specifications/pubchem_fingerprints.pdf.

 

Other

Please see the PubChem Publications for other services or technology not mentioned here.

 

 

Find original sources of data

 

To cite an original source of PubChem data use one of the following:

  • Refer to attribution on the PubChem record
  • Cite publication linked to record, if present
  • Navigate to the source using our PubChem Data Sources page.

 

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