Software

PubChemSR: A search and retrieval tool for PubChem

Junguk Hur¹ and David J Wild²

¹  Bioinformatics Program, University of Michigan, Ann Arbor, MI 48109, USA

²  Indiana University School of Informatics, 901 E. 10^th Street, Bloomington, IN 47406, USA

author email corresponding author email

Chemistry Central Journal 2008, 2:11doi:10.1186/1752-153X-2-11

Published:	15 May 2008

Abstract

Background

Recent years have seen an explosion in the amount of publicly available chemical and related biological information. A significant step has been the emergence of PubChem, which contains property information for millions of chemical structures, and acts as a repository of compounds and bioassay screening data for the NIH Roadmap. There is a strong need for tools designed for scientists that permit easy download and use of these data. We present one such tool, PubChemSR.

Implementation

PubChemSR (Search and Retrieve) is a freely available desktop application written for Windows using Microsoft .NET that is designed to assist scientists in search, retrieval and organization of chemical and biological data from the PubChem database. It employs SOAP web services made available by NCBI for extraction of information from PubChem.

Results and Discussion

The program supports a wide range of searching techniques, including queries based on assay or compound keywords and chemical substructures. Results can be examined individually or downloaded and exported in batch for use in other programs such as Microsoft Excel. We believe that PubChemSR makes it straightforward for researchers to utilize the chemical, biological and screening data available in PubChem. We present several examples of how it can be used.