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

Piotr Kraj, Richard A. McIndoe

Research output: Contribution to journalArticle

5 Citations (Scopus)

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. Although 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.

Original languageEnglish (US)
Pages (from-to)3456-3458
Number of pages3
JournalBioinformatics
Volume21
Issue number16
DOIs
StatePublished - Aug 15 2005

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Wrapper
National Cancer Institute (U.S.)
Bioinformatics
Computational Biology
Application programming interfaces (API)
XML
Genomics
Cancer
HTTP
Software
Databases
Data Streams
Java
2,5-Dimethoxy-4-Methylamphetamine
Management Information Systems
Object-oriented Programming
Object oriented programming
Chromosomes
Data Management
Information Systems

ASJC Scopus subject areas

  • Statistics and Probability
  • Biochemistry
  • Molecular Biology
  • Computer Science Applications
  • Computational Theory and Mathematics
  • Computational Mathematics

Cite this

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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. Although 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.",
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