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Cancer Data Standards Registry and Repository (caDSR) —
National Cancer Institute   U.S. National Institutes of Health www.cancer.gov

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Cancer Data Standards Registry and Repository (caDSR)

 
 

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caDSR is a database and a set of APIs and tools to create, edit, control, deploy, and find common data elements (CDEs) for use by metadata consumers, and information about the UML models and Forms containing CDEs for use in software development.

The common data elements are developed by the National Cancer Institute Center for Biomedical Informatics and Information Technology (NCI CBIIT) and caBIG® partners in the research community, to be used as metadata descriptors for research and caCORE-like applications.

The UML models represent information domains and are developed by research partners in collaboration with CBIIT. The semantics of the data elements used in the models are extracted and transformed into administered components in the caDSR database. When a UML model is registered in caDSR, the collection of related CDEs are classified as part of the UML Model and visible as a collection in the UML Model Browser.

The Forms are developed by data managers supporting a variety of research projects and visible using the Form Builder tool or via the "Catalog of Published Forms" in the caBIG Context.

Use of CDEs addresses a biomedical data management problem, namely the many and varied ways in which similar or identical concepts have been collected and stored in databases. This inconsistency in data representation makes it nearly impossible to aggregate and manage even modest-sized data sets in order to ask basic questions and obtain meaningful answers. Common information building blocks or "common data elements," used for capture of data and for reporting, facilitate understanding and sharing of cancer research information. Using registered metadata facilitates interoperability of the data collected by disparate applications developed in research centers and deployed on caGrid.

For in depth information about caDSR, including links to documentation and contacts as well as technical background and product status, visit the caDSR wiki.

Implementation of caDSR

The caDSR database is an Oracle database. All of the caDSR tools and interfaces connect to the same central database.

NCI chose an international standard to represent the CDEs in the database, the ISO/IEC 11179 Standard for Metadata Registries. This somewhat complex standard offers a richly expressive model for metadata that does a good job of supporting the variations needed for biomedical applications.

In implementing the ISO/IEC 11179 model, NCI has included extensions, among them two important additional types of content in the caDSR, Forms and UML Model associations. For clinical trials applications, a Form corresponds to a Case Report Form (CRF). CDEs can be grouped together for use in Modules on Case Report Forms (CRF). Modules are grouped together to make a CRF. A Protocol, which corresponds to a clinical trial protocol, is made up of a collection of CRFs. UML Model class associations are recorded as a new kind of administered item, with key semantic attributes of the association stored as an Object Class Relationship.

If you are interested in working with the caDSR, review the background information on the way NCI has implemented the ISO/IEC 11179 standard.

caDSR Tools

The caDSR tools include web tools and services to perform various tasks associated with managing and deploying CDEs and CRFs in user systems, such as downloads of content in Excel and XML format. APIs are also included.

To make using the tools easier, review the description of the CBIIT implementation of the ISO/IEC 11179 Standard. When you are using the tools, online help is available for reference.

If you would like an account for any of the caDSR tools, send a request describing the nature of your interest in the system to Application Support.

The caDSR Tools include the following:

  • CDE Browser: Start with this tool to explore the contents of the caDSR. The tool supports browsing, searching, and exporting CDEs within or across contexts. You do not need an account to use the CDE Browser.
  • UML Model Browser: Use this tool to browse and search UML Models loaded in the caDSR. This allows users to find Administered Items that are part of registered UML models. You do not need an account to use the UML Model Browser.
  • caDSR Freestyle Search: Use this tool to perform weighted semantic searches on the content of Administered Items in the caDSR. The search terms and phrases need not exactly match items in the database. Information about items searched and results is available on the Freestyle Search wiki page.
  • CDE Curation Tool: Context administrators use this tool to create and edit Data Element Concepts, Value Domains, and Data Elements. An account is required to create and edit, and you must have curatorial authority for your Context. No login is required to query CDEs and their components. Searching for CDEs using a concept is now supported.
  • Form Builder: Use this tool to organize CDEs in forms that replicate the content of Case Report Forms and other forms.
  • Semantic Integration Workbench (SIW): Use SIW to help in adding consistent metadata to a UML model by matching its concepts with similar items from the NCI Thesaurus. This is a prerequisite to running the UML Loader.
  • caDSR Sentinel Tool: Use this tool to create and manage Alert Definitions for the caDSR database, in order to receive email alerts and thus monitor changes to Administered Items. Information about what is monitored and reported and how reports may be set up is available on the caDSR Sentinel Tool wiki page.
  • caDSR Administration Tool: Context and central caDSR administrators use this tool as the main administrative interface to all caDSR features and components. You must have an account to use this tool and appropriate privileges for each function. This tool is accessible only within the NIH intranet.
last modified 04-17-2013 10:04 PM