Common Semantics: The goal of providing common semantics is provided by the Enterprise Vocabulary Services (EVS) and Common Data Element (CDE) Harmonization and Development Group. The Enterprise Vocabulary Services (EVS) project is an effort to create open, comprehensive terminology resources for the cancer research community. The primary purpose is to provide the semantics needed for shared coding, processing and exchange of all types of cancer-related information. This involves the creation and distribution of controlled biomedical termologies (see below). The EVS is an active service agency, providing near real-time support to a variety of internal and external stakeholders. EVS publishes two controlled vocabulary resources, the NCI Thesaurus and NCI Metathesaurus. The NCI Thesaurus is a biomedical vocabulary covering much of the cancer research domain, including human and mouse pathology, epidemiology, molecular biology, genetics, clinical trials, patient care, and various other biomedical and bioinformatics application areas. The EVS Project also produces the NCI Metathesaurus, which is a cancer oriented variant of the National Library of Medicines Unified Medical Language System Metathesaurus. In addition, the EVS Project licenses MedDRA, ICD-O-3, and other proprietary vocabularies for NCIs use. The EVS operates servers on which its products and licensed content are made publicly available. These resources provide terminology management and semantic 'raw material'from which data elements, classes and objects are constructed. The EVS supports CBIITs mission to enable advanced biomedical informatics computing across both clinical and basic scientific research domains. The role of EVS is to provide the base semantics for caCORE metadata and data, as well as being used more broadly by other caBIG components and external organizations (e.g. FDA, CDISC). EVS is used throughout CBIIT and caBIG community applications. If controlled biomedical terminology provides the foundation, then Common Data Elements (CDEs) provide the structure of semantic interoperability of data. A CDE is a representation of a question on a CRF or part of an information system created using a standardized set of syntax and semantics (provided by EVS), thus allowing for unambiguous reuse of data. Each CDE is created using an international metadata standard (ISO 11179) and is housed in the cancer Data Standards Repository (caDSR). A harmonization and development team of NCI stakeholders and contractor staff produces new CDEs as required to conduct NCI sponsored clinical trials or to annotate a new caBIG compatible information system. This team supports the harmonization of data collection across the NCI and has been a major force in the creation of data standards within the caBIG program. Supporting technology for common semantics: The caCORE program provides two major supporting technology components for common semantics. The first is the LexBIG terminology server and supporting components. These tools (built in cooperation with the Mayo Clinic and Stanford University) provide hosting, editing and viewing support for controlled biomedical terminology. During FY2008, these tools have been continually enhanced to ensure that they will meet the needs of a variety of internal and external stakeholders. The other supporting technology is the cancer Data Standards Repository (caDSR) to support development and deployment of Common Data Elements (CDEs), electronic case report forms, and data models in cancer research. The caDSR is comprised of a suite of tools for creating, sharing and deploying CDEs including a public CDE Browser that lets the user search for data elements, create forms and download CDEs. caCORE provides web services to access caDSR content programmatically. The caDSR, based on open source standards, is freely available for use by other government agencies and for download and use by interested parties. The caDSR toolset is comprised of: CDE Browser UML Model Browser Administration Tool Sentinel Tool and Sentinel API Curation Tool APIs for accessing caDSR content Form Builder CDE Comparison Matrix Enabling Technology for caBIG compatible software: The caCORE Software Development Kit is a set of open source software tools for the purposes of creating semantically aware software systems. The caCORE SDK consists of the following tools: Semantic Integration Workbench: A tool that aids in the binding of formal semantics to software systems. Code Generator: The code generator creates the actual software system based on a model created by a software developer. UML Loader: Creates the metadata used to ensure semantic interoperability Common Security Module: Provides a convenient, 21CFR Part 11 compatible module for authentication and authorization in systems developed with the caCORE Software Development Kit. Common Logging Module: Provides logging services (required by 21 CFR Part 11) for systems constructed using the caCORE SDK. The caCORE SDK is designed to allow a moderately experienced Java programmer to create a Silver compatible software system. Repositories of data utilized by a variety of other CBIIT/caBIG applications: The cancer Bioinformatics Infrastructure Objects (caBIO) system provides programmatic access to data utilized by a variety of other CBIIT/caBIG applications. caBIO provides a central repository of a variety of molecular biology/genomics data types (information related to genes, proteins, transcripts, array designs, biomarkers, etc.) in a service oriented architecture. The caBIO supports CBIITs mission to enable advanced biomedical informatics computing based on common data elements and common semantics across both clinical and basic scientific research domains. The caBIO is part of the NCI caCORE Foundational Infrastructure, along with caDSR and EVS. caBIO is used throughout CBIIT and caBIG community applications.
