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Programmatic Retrieval of Small Molecule Information from PubChem Using PUG-REST

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Part of the book series: Methods in Pharmacology and Toxicology

Abstract

PubChem (https://pubchem.ncbi.nlm.nih.gov) is an open archive which contains information on small molecules as well as other chemical entities such as lipids, carbohydrates, and (chemically modified) amino acid and nucleic acid sequences (including siRNA and miRNA). Developed and maintained by the US National Institutes of Health, PubChem is a chemical information hub, collecting chemical information from various data sources and disseminating it to the public free of charge. PubChem provides multiple programmatic access routes, including E-Utilities, Power User Gateway (PUG), PUG-SOAP, and PUG-REST. This chapter describes how to access PubChem programmatically through PUG-REST. The syntax of the PUG-REST request URL is explained with many examples that cover various tasks and a series of Perl scripts are provided to demonstrate how these URLs can be included in actual programs.

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References

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Acknowledgments

This research was supported in part by the Intramural Research Program of the National Library of Medicine, National Institutes of Health, the US Department of Health and Human Services.

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Authors and Affiliations

  1. National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, US Department of Health and Human Services, Bethesda, MD, USA

    Sunghwan Kim, Paul A. Thiessen & Evan E. Bolton

Authors
  1. Sunghwan Kim
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  2. Paul A. Thiessen
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  3. Evan E. Bolton
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Corresponding author

Correspondence to Sunghwan Kim .

1 Electronic Supplementary Material

Data 1

pug-rest-scripts.zip: contains the Perl scripts shown in Figs. 7, 8, 9, 10, 11, 12, 13, and 14 (ZIP 5 kb)

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Kim, S., Thiessen, P.A., Bolton, E.E. (2018). Programmatic Retrieval of Small Molecule Information from PubChem Using PUG-REST. In: Methods in Pharmacology and Toxicology. Humana Press. https://doi.org/10.1007/7653_2018_30

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  • DOI: https://doi.org/10.1007/7653_2018_30

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  • Publisher Name: Humana Press

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