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|Original author(s)||Junguk Hur|
|Stable release||3.5.0 / 2009-02-28|
|Operating system||Microsoft Windows|
|License||GNU GPL 2.0|
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
Version 3.5.0 became available as of 28 February 2009.
- Enhancement: automatic update check can be disabled and enabled through tools/preferences
- Bug fix: the structure search is 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
- PubChemSR is written in MS Visual Basic .Net
- PubChemSR is implemented by using NCBI's Entrez via SOAP interface.
- 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.
- 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