Literature Associated with PubChem Records

Many PubChem records have information about scientific articles related to chemicals.  This page provides a brief overview of the literature information in PubChem.  To learn more about this topic, read the following paper:

Kim S, Thiessen PA, Cheng T, Yu B, Shoemaker BA, Wang J, Bolton EE, Wang Y, Bryant SH. Literature information in PubChem: associations between PubChem records and scientific articles. J Cheminform 2016 Jun 10; 8:32. doi: 10.1186/s13321-016-0142-6. eCollection 2016.
[PubMed PMID: 27293485] [Free Full Text on J Cheminform]


As an example, take a look at the Literature section of the Compound Summary of CID 2244 (aspirin):


The associations between compounds and scientific papers are derived in three different ways:


  • Data submission by individual contributors

    • SID/CID-PMID associations: Individual data contributors provide PubChem with cross-references between chemical substances and PubMed articles that contain information on that substance. From these SID-PMID cross-references, PubChem generates cross-references between the corresponding compound and the PubMed articles (i.e., CID-PMID cross-references).

    • AID-PMID associations: Data contributors can also supply a list of PMIDs for scientific articles that have information relevant to a given assay record. These articles may contain various kinds of information related to the assay, including experimental protocols, assay targets, diseases associated with the targets, and known ligands that bind the targets. Of particular interest, some data contributors provide bioactivity data extracted from literature through manual curation or data mining and are an important source of bioactivity information in PubChem that complement HTS data from the now-concluded NIH Molecular Libraries Program and other HTS projects.

  • Annotations collected directly by PubChem

    The PubChem team also collects annotations from reputable sources if it believes they are valuable to PubChem users.  Among these annotations, there are reference articles that provide general information about a particular compound (for example, how to synthesize it, how it is metabolized, etc.)

  • Automated cross link generation via MeSH

    PubChem generates Entrez links between PubChem records and PubMed articles that share the same MeSH annotation. This automated process allows PubChem users to leverage the biomedical literature and its MeSH indexing for search and analysis purposes.


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