PubChemSR

Infobox Software
name = PubChemSR



caption =
author = Junguk Hur
developer =
released =
latest release version = 3.4.2
latest release date = 2008-10-06
latest preview version =
latest preview date =
programming language =
operating system = Microsoft Windows
platform = .NET
language = English
status = Active
genre =
license =
website = [http://cheminfo.informatics.indiana.edu/PubChemSR/ PubChemSR] [http://sourceforge.net/projects/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.

New Version Release

Version 3.4.2 is now available as of 10/06/2008.
* Update) BioAssay retriever has been modified to accommodate changes in the NCBI querying system.
* Update) Field data has been updated. Users can do this by This can also be done by
* Update) Default for the number of document per retrieval (internal not the total number) is now set t0 100. (previously it was 50)
* New) New version check of PubChemSR has been added.

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 [http://pubchem.ncbi.nlm.nih.gov/search/ 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.
* 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.

Reference

*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

* [http://cheminfo.informatics.indiana.edu/PubChemSR/ PubChemSR Indiana Homepage]
* [http://pubchemsr.sourceforge.net PubChemSR Sourceforge.net Homepage]
* [http://sourceforge.net/projects/pubchemsr Sourceforge Download Page]
* [http://www-personal.umich.edu/~juhur Junguk Hur's Homepage]