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PubChem IDs in MEDLINE®/PubMed®

Demsey, A. PubChem IDs in MEDLINE®/PubMed®. NLM Tech Bull. 2007 Jan-Feb;(354):e2.

January 26, 2007 [posted]

Unique Identifiers for records in the PubChem databases [PubChem: An Entrez Database of Small Molecules. NLM Tech Bull. 2005 Jan-Feb;(342):e2.] are now being included in MEDLINE/PubMed records when publishers send the IDs as part of their electronic citation submission to MEDLINE/PubMed. The databases (PubChem Substance, PubChem Compound, and PubChem BioAssay) provide information on the biological activities of small molecules, including substance information, standardized and validated chemical structures, and bioactivity screens.

In PubMed records, the PubChem IDs will display in the Secondary Source Identifier (SI) field in the Citation (see Figure 1) and MEDLINE display formats and in the <DataBankList> area of the XML format. The database name prefixes each ID number. The unique IDs in the Citation display of PubMed records also link directly to the associated records in PubChem.

Screen capture of Citation display in PubMed with PubChem IDs.
Figure 1: PubMed's Citation Display showing PubChem IDs.


PubChem IDs can be searched in PubMed using the [si] search tag.

  1. To retrieve a specific ID:
       pubchem-substance/17424970 [si]
           or
       17424970 [si]

  2. To retrieve all IDs for a PubChem database, search the database name:
       pubchem-substance [si]

NLM began to accept PubChem IDs in electronic XML citation data submissions from publishers on January 11, 2007. PubChem IDs for a number of articles from the journal Nature Chemical Biology have also been added retrospectively to those citations. PubChem-Substance is the first PubChem ID data to be received. NLM itself will not capture PubChem ID data from articles.

PubChem was developed and is maintained by the National Center for Biotechnology (NCBI) and additional information is available at //pubchem.ncbi.nlm.nih.gov.