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Bioinformatics Advance Access published online on June 16, 2005
Bioinformatics, doi:10.1093/bioinformatics/bti545
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© The Author (2005). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oupjournals.org
Received January 28, 2005
Revised March 15, 2005
Accepted June 14, 2005

Applications note

caBIONet - a .NET wrapper to access and process genomic data stored at the National Cancer Institute's Center for Bioinformatics databases

Piotr Kraj 1 and Richard A. McIndoe 2*

1 Medical College of Georgia, Institute of Molecular Medicine and Genetics, Augusta, GA 30912, USA
2 Medical College of Georgia, Center for Biotechnology and Genomic Medicine, Augusta, GA 30912, USA

* To whom correspondence should be addressed.
Richard A. McIndoe, E-mail: rmcindoe{at}mail.mcg.edu


  Abstract

Motivation: The National Cancer Institute's Center for Bioinformatics (NCICB) has developed a java based data management and information system called caCORE. One component of this software suite is the object oriented API (caBIO) used to access the rich biological datasets collected at the NCI. This API can access the data using native java classes, SOAP requests or HTTP calls. Non-java based clients wanting to use this API have to use the SOAP or HTTP interfaces with the data being returned from the NCI servers as an XML data stream. While the XML can be read and manipulated using DOM or SAX parsers, one loses the convenience and usability of an object oriented programming paradigm. caBIONet is a set of .NET wrapper classes (managers, genes, chromosomes, sequences, etc.) capable of serializing the XML data stream into local .NET objects. The software is able to search NCICB databases and provide local objects representing the data that can be manipulated and used by other .NET programs. The software was written in C# and compiled as a .NET DLL.

Availability: The program is freely available to academics and non-profit organizations from www.amdcc.org. The source code is available from the authors upon request.


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