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caArray database is a standards based open source repository developed for managing, sharing and publishing of microarray data produced by NCI supported programs. caArray v1.0 will be released in January 2005, with technical documentation and the source code to facilitate local caArray installations. The goals of the project are to make microarray data publicly available, and to develop and bring together open source tools to analyze these data. The caArray database and analysis tools were developed in compliance with caBIG (Cancer Bioinformatics Grid) principles that include open source, open access, open development, and federated data with a key focus on syntactic and semantic interoperability. caArray database features MIAME 1.1 compliant data annotation forms, MAGE-ML import and export, and controlled vocabularies (MGED ontology) from a shared, publicly accessible metadata repository (caDSR) and enterprise vocabulary services (EVS) from the National Cancer Institute. caArray database also features Application Programming Interfaces (APIs) that provide programmatic access to microarray data. Available data analysis tools include caWorkbench, a suite of data annotation, analysis and visualization functions; and webCGH to view DNA copy number measurements relative to genome locations and annotated genome features. Both of these tools connect to the NCICB’s cancer Bioinformatics Infrastructure Objects (caBIO) model, permitting access to a variety of genomic, cancer models, and clinical trials information. CaArray datasets and open source tools are publicly available and can be accessed at http://caArray.nci.nih.gov.

[Proc Amer Assoc Cancer Res, Volume 46, 2005]