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. 2016 Jun 10:8:32.
doi: 10.1186/s13321-016-0142-6. eCollection 2016.

Literature information in PubChem: associations between PubChem records and scientific articles

Sunghwan Kim  1 , Paul A Thiessen  1 , Tiejun Cheng  1 , Bo Yu  1 , Benjamin A Shoemaker  1 , Jiyao Wang  1 , Evan E Bolton  1 , Yanli Wang  1 , Stephen H Bryant  1
Affiliations

Literature information in PubChem: associations between PubChem records and scientific articles

Sunghwan Kim et al. J Cheminform. .

Abstract

Background: PubChem is an open archive consisting of a set of three primary public databases (BioAssay, Compound, and Substance). It contains information on a broad range of chemical entities, including small molecules, lipids, carbohydrates, and (chemically modified) amino acid and nucleic acid sequences (including siRNA and miRNA). Currently (as of Nov. 2015), PubChem contains more than 150 million depositor-provided chemical substance descriptions, 60 million unique chemical structures, and 225 million biological activity test results provided from over 1 million biological assay records.

Description: Many PubChem records (substances, compounds, and assays) include depositor-provided cross-references to scientific articles in PubMed. Some PubChem contributors provide bioactivity data extracted from scientific articles. Literature-derived bioactivity data complement high-throughput screening (HTS) data from the concluded NIH Molecular Libraries Program and other HTS projects. Some journals provide PubChem with information on chemicals that appear in their newly published articles, enabling concurrent publication of scientific articles in journals and associated data in public databases. In addition, PubChem links records to PubMed articles indexed with the Medical Subject Heading (MeSH) controlled vocabulary thesaurus.

Conclusion: Literature information, both provided by depositors and derived from MeSH annotations, can be accessed using PubChem's web interfaces, enabling users to explore information available in literature related to PubChem records beyond typical web search results.

Graphical abstract: Graphical abstractLiterature information for PubChem records is derived from various sources.

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Figures

Graphical abstract
Graphical abstract
Literature information for PubChem records is derived from various sources
Fig. 1
Fig. 1
The substance record page for SID 85856310 (warfarin), with a link to the source article published in Nature Chemical Biology. The original article has a link to SID 85856310 in PubChem, allowing article readers to access comprehensive information on warfarin available in the PubChem Compound database, by clicking a link to the Compound Summary page for CID 54678486
Fig. 2
Fig. 2
Retrieving compound records annotated with MeSH terms using the Advanced Search Builder. Clicking the “Advanced” link under the “Compound” tab on the PubChem Homepage directs users to the PubChem Compound Advanced Search Builder. Selecting the “MeSHTerm” from the dropdown menu and providing a MeSH term in the search box will retrieve compounds annotated with that MeSH term
Fig. 3
Fig. 3
The document summary (DocSum) page that shows the results for a search for “warfarin”. Scientific articles associated with the returned compound records can be accessed via the Entrez Links, which are available under the “Find related data” menu (for multiple records) or from a link for individual compound records
Fig. 4
Fig. 4
The literature section of the Compound Summary page (DocSum) for CID 5288826 (morphine). Clicking the “Literature” section in the Table of Contents allows users to jump to the literature section, which consists of two subsections: depositor-provided and NLM-curated PubMed citations
Fig. 5
Fig. 5
Retrieving compound records with a particular property using the Entrez filters. Selecting the “Filter” option under the drop-down menu on the PubChem Compound Advanced Search Builder allows you to retrieve compounds with a particular property or annotation. Available filters can be shown or hidden by clicking the “Show/Hide index list” button
Fig. 6
Fig. 6
Distribution of PMIDs per CID and CIDs per PMID for three types of Entrez links. Distributions of a PMIDs per CID and b CIDs per PMID are shown for three Entrez links between PubChem Compound and PubMed: “pccompound_pubmed”, “pccompound_pubmed_mesh”, and “pccompound_pubmed_publisher”. See texts for the description of these links
Fig. 7
Fig. 7
Venn diagrams for depositor-provided CID-PMID associations and those generated via MeSH. The Venn diagrams compare depositor-provided CID-PMID associations and automated annotations via MeSH in terms of a the number of CID-PMID associations, and b CIDs and c PMIDs involved in these associations
See this image and copyright information in PMC

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