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PubChemSR main.jpg
Original author(s) Junguk Hur
Stable release
3.6.2 / 2017-06-22
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 Dr. Junguk Hur at the University of North Dakota.

New version release[edit]

Version 3.6.2 became available as of June 22, 2017.

  • Fixed: Batch Search not functional.
  • Fixed: Long records (such as some compound synonyms) with more than 37260 characters result in undesirable linebreak in Excel


  • 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]