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.

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Platform

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

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

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.

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.