PubChemSR
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| Original author(s) | Junguk Hur |
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| Stable release | 3.5.0 / 2009-02-28 |
| Development status | Active |
| Operating system | Microsoft Windows |
| Platform | .NET |
| Available in | English |
| Website | PubChemSR Sourceforge.net-Download |
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.
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[edit] New Version Release
Version 3.5.0 is now available as of 28 February 2009.
- Enhancement: Automatic update check can be disabled/enabled through Tools/Preferences.
- Bug fix: The structure search is now available again.
- Enhancement: Missing figure sub directories (cis/sid) are further checked.
- Enhancement: The result directory names of the BatchSearch will automatically have data and time.
- Bug fix: Opening BatchSearch twice crashes the PubChemSR.
See PubChemSR homepage for more detail.
[edit] Platform
- PubChemSR is written in MS Visual Basic .Net
- PubChemSR is implemented by using NCBI's Entrez via SOAP interface.
[edit] Search Methods
- simple text based search as you would do at Entrez, e.g. acetaminophen
- structure search as you would do 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
- Screenshots
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PubChemSR main
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PubChemSR BatchSearch
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BioAssay Data Retriever
[edit] Features
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.
[edit] References
- 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
