Introduction
Bio Browser is a desktop application facilitating the searching and browsing of the Cancer Bioinformatics Infrastructure Objects (caBIO) domain model made available via a web service from the National Cancer Institute Centre for Bioinformatics (NCICB).
Features
- Ability to search for !caBIO domain model objects
- View search results as an interactive tree and static XML document
- Navigate to related object by following xlinks embedded in the search result document
- Open pathway diagrams rendered from underlying SVG document
History
The Bio Browser project started life as a teaching tool designed to illustrate the use of web services, domain models and XML based data transfer within bioinformatics. However, it proved useful as a general tool for searching and examining the data provided by the !caBIO web services, and was released via a Web Start application and source code download in 2003. This current project is a complete rewrite of the original with the following goals: Update to use the current !caBIO domain model and remote services. This was essential since the original services were no longer available. As a example application for both Spring RCP and the JIDE-Spring RCP integration project.
Motivation
The !caBIO domain model objects represent entities found in biomedical research such as Gene, Chromosome, Sequence, SNP, Library, Clone, and Pathways. The instances of these entities, and their relationships, are constructed from an extensive collection of primarily molecular biology data-sources such as: NCBI UniGene Cancer Gene Anatomy Project (CGAP) UCSC Genome Project BioCarta Proteomics Pathway Project NCI Cancer Molecular Analysis Project (CMAP) Affymetrix, Illumina and Agilent human microarray annotation dnSNP NCI Cancer Therapeutics Evaluation Program (CTEP)
The following quote, from the !caBIO technical guide, best describes both the motivation underlying the !caBIO project and its border interest: "examining the relationship between these objects can reveal biomedical knowledge that was previously buried in the various primary data sources."
Development Resources
The project uses a Subversion source code repository with Trac for repository browsing: Subversion source code repository: http://svn2.assembla.com/svn/biobrowser Trac: Source code browser * Trac: Timeline