News

The NCICB has a number of Center-wide activities that are developed and managed by the Core Infrastructure Group. Our main product is caCORE, the open-source foundation upon which the NCI builds its research information management systems. In addition, we support hardware systems at our data centers; software configuration management; change control; quality assurance; and project management. The Director of the Core Infrastructure Group, Peter Covitz, is a member of the NCICB Executive Committee.

caCORE

• Improved Common Data Element (CDE) Curation Tool
• New Form Builder application for creating CDE-compliant data collection forms
• Refactored software code for better correspondence between the APIs and the UML models
• Improved interfaces to vocabulary services
• ...many other fixes and improvements

Quick links:

• caCORE 2.1.1 Maintenance Release Notes
• caCORE 2.1 Major Release Notes
• caCORE Technical Guide
• Publications
• Downloads
• Support

The vision for caCORE is to provide a common data management framework that will support the consistency, clarity, and comparability of biomedical research data and information. The three major components of caCORE are:

Cancer Bioinformatics Infrastructure Objects (caBIO) We create UML models of biomedical objects to facilitate data integration and consistent representation. These UML models are then implemented in Java as middleware that is connected to various cancer research databases. Java, SOAP-XML and HTTP-XML programming interfaces to the NCICB-hosted data are available. You can also set up your own caBIO server for data at your own site. BIOgopher provides a flexible user interface to caBIO, and supports MS Excel format for queries and reports. The Quick Start guide can get you going right away.

Cancer Data Standards Repository (caDSR) NCICB supports a broad initiative to standardize the data elements used for cancer research. These Common Data Elements (CDEs) are developed by various NCI-sponsored organizations, then centrally stored and managed at NCICB in the Cancer Data Standards Repository. CDEs corresponding to widely adopted external standards such as ICD-O-3 are also made available. A number of tools are available for the caDSR, including a CDE Browser that lets you search for, retrieve and download CDEs.

Enterprise Vocabulary Services (EVS) At the foundation of the caCORE "standards stack" is controlled vocabulary. The NCI Enterprise Vocabulary Services, a collaborative effort of the NCI Center for Bioinformatics and the NCI Office of Communications, develops the NCI Thesaurus and the NCI Metathesaurus, two broadly used vocabulary sources for cancer research. EVS also hosts and contributes to other standards, and works with vendors to create and improve tools for vocabulary development, curation and deployment.

An open source platform
The NCICB has made a committment to open source software and open systems. We make most of our own caCORE technologies available under an open source licensing mechanism, and we use open source technologies wherever practical. caCORE is powered by a number of Apache projects, including: HTTP Server, Tomcat, Ant, Struts, OJB, Xalan, Xerces, XML-RPC, Jakarta Commons, and POI. We also use ZOPE for web site management and JUnit for unit testing.