Metadata Needs and Support
The caDSR (Cancer Data Standards Registry and Repository
a metadata repository based on the ISO/IEC 11179
Metadata is defined as "data about data" or "the description of a piece of information." Standardizing and registering metadata addresses a significant problem in biomedical data management: the wide variety of ways that similar data are collected and described.
The ISO/IEC 11179 standard defines a framework for how metadata can be specified, maintained in a consistent manner, shared, and used across diverse domains. The caDSR is a conforming implementation of the ISO/IEC 11179 metadata standard with NCI extensions. The caDSR has been designed to support creation, maintenance, registration, and use of metadata in accordance with the metadata standard; in addition, the NCI has extended the standard, most notably in the use of controlled terminology. This enables metadata consumers to register the descriptive information needed to render cancer research data reusable and interoperable.
The fundamental unit of data in the ISO/IEC 11179 standard is called a data element. According to the ISO metadata standard, any item represented by a data element has two distinct parts: an explicit definition that is independent of any particular implementation, and an explicit description of implementation--specific details regarding how the item is represented in computer storage. Capturing these two aspects makes it possible to compare data elements that describe the same thing across different applications, and to understand what data transformation may be necessary in order to make the data comparable.
caCORE-like systems follow an object-oriented paradigm where classes of data are described using UML models. A UML model, serialized into XMI, can then be used to transform the UML model objects into caDSR registered items. Once registered, the items in caDSR can be re-used in other systems' models. If different systems are using the same registered terms (metadata) for the data in their models, those systems can more easily communicate and share information.
The caDSR itself is a database that contains Administered Items. As defined in the ISO/IEC 11179 standard, an Administered Item is an item (a Data Element or one of the associated components that comprise a Data Element) for which administrative information must be recorded. caDSR administered items are supported by the use of externally defined terminologies and controlled vocabularies, such as the NCI Thesaurus.
To support the database, the caDSR also has a suite of tools for creating, sharing, and deploying data elements (also called common data elements or CDEs). These tools include a public CDE Browser that enables you to search for data elements, create forms, and download CDEs, and a UML Model Browser viewer that makes it easier to find CDEs that are registered as part of UML modeling projects. All of the caDSR tools and interfaces connect to the same central database. Links to further information regarding the caDSR tools appear in the section "caDSR Tools."
By complying with the ISO/IEC 11179 standard, caDSR provides, among other things, a semantic bridge between the data elements contained in registered data objects and standard vocabularies and ontologies. caDSR was originally designed to support the development and deployment of data elements as metadata descriptors for NCI-sponsored research, but now supports an ever-widening group of users and metadata consumers in caBIG®.
caDSR Database and Implementation
The caDSR is based on an Oracle database. All of the various tools and interfaces connect to the same central database.
The software applications that access caDSR content are based on open source standards and are freely available for use by other government agencies and for download and use by interested parties.
caDSR follows the ISO/IEC 11179 standard to harmonize, register and integrate user-defined UML information models with existing and new caDSR content and to represent the CDEs in the database. This standard is somewhat complex, but it offers a richly expressive model for metadata that does a good job of supporting the variations needed for biomedical applications. If you are interested in working with the caDSR, please review the background material on the way we have implemented the ISO/IEC 11179 standard.
In addition to implementing the ISO/IEC 11179 model, we have added a few additional types of content to the caDSR. The two most important additional items are Forms and Protocols.
A Form is a collection of CDEs, and a Protocol is a collection of Forms. For clinical trials applications, the Forms correspond to Case Report Forms (CRFs), and Protocols correspond to a clinical trial protocol.
Template forms are generic forms that can be used as the basis for creating the actual forms used in a Protocol. Templates are stored both as a collection of CDEs that comprise the form, and an MS Word or PDF file that shows the CDEs laid out.
The caDSR and semantic tools include the following.
Wiki home page
http://cadsradmin.nci.nih.gov/ (Login required)
http://cadsrsentinel.nci.nih.gov/cadsrsentinel/do/logon (Login required)
https://formbuilder.nci.nih.gov (Login required)
UML Model Browser
CDE Curation Tool
http://cdecurate.nci.nih.gov/cdecurate/ (Login required)
Semantic Integration Workbench (SIW)
Contact NCICB Application Support, email@example.com
Several tools perform various tasks in creating, managing, and deploying CDEs. There are also tools that support reviewing externally generated forms to see if they are CDE-compliant, that is, are comprised of approved CDEs found in the caDSR. The public CDE Browser lets you search for data elements, create forms and download CDEs. The UML Model Browser is specifically designed for browsing registered UML information models. Online help is available, but you will find that using the tools is easier if you have first read through the description of the caDSR implementation of the ISO/IEC 11179 Standard.
Email List Servers
Following are the Email List Server addresses specific to the caDSR and the primary audience of each.
Content users, e.g. Curators
Developers using the caDSR Metadata
Adopters of the open source projects
About the caDSR Wiki
This is the wiki home page for caDSR. You may edit pages if you are working on them with the authors. You are welcome to leave comments. The content is grouped in several major categories:
Metadata Registry standard. It supports a broad community of users both inside and outside of NCI that have requirements to ensure the longevity and consistency of biomedical research data by registering metadata standards in caDSR.
What is a metadata standard? A metadata standard is a high level document which establishes a common way of structuring and understanding data, and includes principles and implementation issues for utilizing the standard. There are many metadata standards purposed for specific disciplines.
Content owners and end users include NCI and its partners in clinical trials, academic institutions (including NCI Designated Cancer Centers, SPOREs and NCTN/ETCTN), other NIH institutes (including NICHD, NHLBI, NCATS and NIDCR), other federal agencies (in particular the FDA), pharmaceutical companies, standards development organizations (e.g. CDISC) and a range of international biomedical organizations. For more information see the caDSR Collaborations and Use.
Requirements from researchers and/or their supporting informatics groups drive the creation of metadata in the caDSR. Metadata content development usually starts with a request for assistance by a researcher planning clinical or research data collection. Metadata curators work with the user and EVS to identify appropriate vocabulary while identifying a mix of new and existing CDE content to support the scientific requirement. Curators always attempt to reuse existing metadata (where that content supports the scientific requirement) as a way to help scientists ensure the compatibility of their data with other data collected across the enterprise, and sometimes researchers request that their content be harmonized with specific existing projects.
The word cloud that follows illustrates the broad variety of collections of data elements that are reposited in the caDSR for various communities and types of studies.
CBIIT’s management of metadata began as part of an effort to support CTEP’s reporting for breast cancer trials, and from a need to develop and disseminate standards that would ensure consistency and accuracy in reporting across the NCI Clinical Trial Network (NCTN/ETCTN) and Lead Protocol Organizations (LPOs). This led to the establishment of a centralized resource and associated web-based tools for creating, clearly documenting, and sharing human- and machine-readable data descriptions. The need to maintain and share data about data, or metadata, became the basis for the NCI’s repository of CDEs, metadata, and data standards, what is now known as the caDSR. A CDE Steering Committee was formed to define what kind of metadata was needed for the repository. Driven by the needs from community to create, share, and manage CDEs over time, a set of metadata attributes was established, which included attributes such as human friendly name(s), text definition(s), valid values, unique identifiers, and workflow status. Consultation with appropriate experts identified ISO 11179, an international standard for metadata registries, as meeting the needs identified by the CDE Steering committee. As time went on, more groups wanted to record their data elements and share them via the caDSR, so additional features were added, including extensions of ISO 11179 to enable storage of metadata describing Case Report Forms (CRFs) that use CDE metadata as the basis for questions on the CRFs.
As more groups recorded their data elements in caDSR, the difficulty in creating high-quality names and definitions for data elements became recognized as a best practice for clarifying the meaning of the data, but also a challenge for data-element curators. Consequently, ISO 11179-5 Naming Principles were used to establish naming conventions that could be applied across groups. The same naming conventions are used in the National Information Exchange Model (NIEM). Since NCI had the EVS terminology services available, this was seen as a reasonable means by which to aid this task by giving curators access to well-formed and NCI-preferred names for concepts that form the name of the CDEs. At present, curators find concepts in EVS based on synonym or concept id searches, and the EVS preferred-term name and definition streamline their task. The challenge of ensuring that duplicate CDEs were not created led to leveraging the parts of the ISO 11179 metamodel along with a preference for the use of NCIt concepts so the system could semi-automatically recognize and promote reuse of existing content. NCIt is a specialized cancer terminology that includes additional knowledge from the literature about these concepts and is modeled as an OWL ontology were concepts have various types of relationships and mappings defined to other concepts. It also includes mappings to the UMLS where they exist. Therefore, a link to NCIt concepts from caDSR content can help test similarity between CDEs. Links to NCIt concepts can also provide access to researchers for exploring the meaning of a data that conforms to a given CDE in greater depth.
Although this activity began as a means to support CTEPs trials networks, the caDSR now supports a much wider audience. This includes clinical trials run by the NCI intramural program, the Center for Cancer Research (CCR), and Division of Cancer Prevention (DCP); Specialized programs of Research Excellence (SPOREs), Cancer Centers and other academic medical centers, other NIH institutes and centers as well as standards groups such as CDISC and a variety of international partners.
A note on the term “Common Data Element” (CDE). While originally intended to mean a data element that was reused across groups, the term has come to mean any description of a variable and its valid values. In this document, we will use the standard NCI version of this definition, which is to say a variable description (including valid values) described in the caDSR using its implementation of the ISO 11179 variable, regardless of whether the element in question has been used more than once.
Information about caDSR Initiatives and Tools
This is the wiki home page for caDSR. You may edit pages if you are working on them with the authors. You are welcome to leave comments. This wiki includes the following.
- caDSR Content
Focuses on the Metadata Content within the caDSR and is most useful for consumers. The pages include Data Standards, Harmonization, Reuse and Business Rules that establish the capabilities of the caDSR Tools.
- caDSR Database and Tools
Provides access to caDSR tools and links to the tool summary page for current user documentation and technical information like release notes.
- caDSR for Application Developers
Focuses on the software interfaces to the caDSR available to programmers and software developers. The pages include details on the caDSR API, XML messages produced and consumed by the caDSR products and the caDSR UML Model.
- caDSR Installation and Implementation
Focuses on Open Source adoption of the caDSR Database and Tools. The pages include ISO 11179 implementation extensions, software implementation architectures and Downloads.
caDSR Future Requirements
We continually look at new requirements and have an initiative begun in 2014 to replace the aging software and infrastructure currently supporting caDSR end users. This is an opportunity to link our efforts more broadly with NIH wide CDE and metadata initiatives. Please see the caDSR Requirements pages for more information.
For a complete list of current caDSR Tool user documentation, application guides, release notes, and FAQs, see the caDSR Documentation wiki page.
Email Lists and Forums
Email address or URL
For end user issues regarding the caDSR tools and content
For developer issues regarding the caDSR APIs and use of caDSR Metadata
Archive for content users such as Curators
Archive for developers using caDSR Metadata, such as UML Model owners (subscription required)
Index of all NIH mail lists
How to Cite caDSR
To cite the NCI Semantic Infrastructure, use the following reference.
Komatsoulis, G.A., Warzel, D.B., Hartel, F.W., Shanbhag, K, Chilukuri, R, Fragoso, G., de Coronado, S, Reeves, D.M., Hadfield, J.B., Ludet, C., and P.A. Covitz (2007) "caCORE version 3: Implementation of a model driven, service-oriented architecture for semantic interoperability." Journal of Biomed Informatics. 2008 February; 41(1): 106--123. Published online 2007 April 2. doi: 10.1016/j.jbi.2007.03.009.
To cite the caDSR Form Builder general software, use the following reference.
NCI caDSR Form Builder. <https://formbuilder.nci.nih.gov/FormBuilder/formSearchAction.do> National Cancer Institute, Center for Biomedical Informatics and Information Technology, 01 Oct. 2010. Web. 17 Jan. 2013.
To cite a specific collection of forms in caDSR, use a reference like the following.
"[Protocol or Classification Scheme Name]." [Context name], [Node name], NCI caDSR Form Builder. <https://formbuilder.nci.nih.gov> National Cancer Institute, Center for Biomedical Informatics and Information Technology, 01 Oct. 2010. Web. 17 Jan. 2013
Example: " CALGB: 10603 Treatment Form ." CTEP, Protocol Forms, NCI caDSR Form Builder. <https://formbuilder.nci.nih.gov> National Cancer Institute, Center for Biomedical Informatics and Information Technology, 01 Oct. 2010. Web. 17 Jan. 2013
To cite caDSR CDE Browser software, use a reference like the following.
NCI caDSR CDE Browser. <https://cdebrowser.nci.nih.gov> National Cancer Institute, Center for Biomedical Informatics and Information Technology, 01 Oct. 2010. Web. 17 Jan. 2013.
To cite caDSR CDEs in a particular collection or group, use a reference like the following.
"[Classification Scheme Name]." [Context name], [Node name], NCI caDSR CDE Browser. <https://cdebrowser.nci.nih.gov> National Cancer Institute, Center for Biomedical Informatics and Information Technology, 01 Oct. 2010. Web. 17 Jan. 2013.
Example: "NAACCR 11.1." PS & CC (NCI Population Sciences & Cancer Control), Classifications, Division of Population Cancer Control and Population Sciences, NCI caDSR CDE Browser. <https://cdebrowser.nci.nih.gov> National Cancer Institute, Center for Biomedical Informatics and Information Technology, 01 Oct. 2010. Web. 17 Jan. 2013