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PubChemSR main.jpg
Original author(s) Junguk Hur
Stable release 3.5.3 / 2013-08-27
Development status Active
Operating system Microsoft Windows
Platform .NET
Available in English
License GNU GPL 2.0
Website PubChemSR

PubChemSR is a MS-Windows-based data search and retrieval tool for the NCBI's public chemical database PubChem. This tool is under active development by Junguk Hur, a bioinformatics Ph.D. student at University of Michigan, Ann Arbor.

New version release[edit]

Version 3.5.3 became available as of 27 August 2013.

  • Bugfix: BatchSearch failure.


  • PubChemSR is written in MS Visual Basic .Net
  • PubChemSR is implemented by using NCBI's Entrez via SOAP interface.

Search methods[edit]

  • simple text based search at Entrez, e.g. acetaminophen
  • structure search at PubChem's structure search page, e.g. CC(=O)NC1=CC=C(C=C1)O
  • batch search for multiple queries available in 'BatchSearch' mode, e.g., acetaminophen, isatin, aspirin


PubChemSR supports a bulk download of selected data fields for multiple chemicals.

  • Users can easily select only the fields of interest.
  • UIDs (unique identifier) can be manually entered or copied after simple text or structure search.
  • Retrieved data can be shown in doc-format, tab-delimited format, or HTML page.
  • Retrieved data can be exported to the MS EXCEL program or to a simple text file for further use.
  • BatchSearch supports extract specific data field (like SMILES) for multiple queries.
  • BioAssayRetriever can automatically retrieve actual bioassay data and be merged into bulk download data files.

Additional features:

  • Typos can be automatically corrected via NCBI's eSpell
  • Structure images are displayed after simple search.
  • The number of maximum results per each query can be adjusted.


  • Junguk Hur, David J Wild: PubChemSR: A search and retrieval tool for PubChem, Chemistry Central Journal 2008, 2:11 doi:10.1186/1752-153X-2-11

External links[edit]