caBIONet – A .NET wrapper to access and process genomic data stored at the
National Cancer Institute’s Center for Bioinformatics databases
Authors Piotr Kraj and Richard A. McIndoe
Submitted By Richard McIndoe on 3/14/2005
Status Published
Journal Bioinformatics (Oxford, England)
Year 2005
Date Published 8/15/2005
Volume : Pages 21 : 3456 - 3458
PubMed Reference 15961441
Abstract Motivation: The National Cancer Institute’s Center for Bioin-formatics (NCICB)
has developed a java based data man-agement 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 pro-vide local objects representing the
data that can be manipu-lated 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 The source code is available from the authors
upon request.