NCI Enterprise caCORE

公共语义：提供公共语义的目标是由企业词汇服务(EVS)和公共数据元素(CDE)协调和开发小组提供的。 企业词汇服务(EVS)项目致力于为癌症研究社区创建开放、全面的术语资源。其主要目的是提供共享编码、处理和交换所有类型的癌症相关信息所需的语义。这涉及到受控生物医学术语的创建和分发(见下文)。电动汽车是一个积极的服务机构，为各种内部和外部利益攸关方提供近乎实时的支持。 EVS发布了两个受控词汇资源，NCI主题词表和NCI元主题词表。NCI主题词库是一种生物医学词汇，涵盖了癌症研究领域的大部分内容，包括人类和小鼠病理学、流行病学、分子生物学、遗传学、临床试验、患者护理以及各种其他生物医学和生物信息学应用领域。EVS项目还产生了NCI Metathesaurus，这是国家医学图书馆统一医学语言系统Metathesaurus的一个面向癌症的变体。此外，EVS项目还授权MedDRA、ICD-O-3和其他专有词汇表供NCIS使用。EVS运营着服务器，其产品和授权内容在这些服务器上公开可用。这些资源提供术语管理和语义“原材料”，数据元素、类和对象都是从这些“原材料”中构造出来的。 EVS支持CBIITs的使命，即在临床和基础科学研究领域实现先进的生物医学信息学计算。EVS的作用是为caCORE元数据和数据提供基本语义，并被其他caBIG组件和外部组织(例如FDA、CDISC)更广泛地使用。EVS在CBIIT和CABIG社区应用程序中使用。 如果说受控生物医学术语提供了基础，那么公共数据元素(CDE)则提供了数据语义互操作性的结构。CDE是使用一组标准化的语法和语义(由EVS提供)创建的CRF或部分信息系统上的问题的表示，从而允许明确地重复使用数据。每个CDE都使用国际元数据标准(国际标准化组织11179)创建，并存放在癌症数据标准储存库(CADSR)中。 由NCI利益相关者和承包商员工组成的协调和开发团队根据需要制作新的CDE，以进行NCI赞助的临床试验或注释新的caBIG兼容信息系统。该小组支持协调整个NCI的数据收集，并一直是在caBIG计划内创建数据标准的主要力量。 常见语义的支持技术： CaCORE程序为常见语义提供了两个主要的支持技术组件。第一个是LexBIG术语服务器和支持组件。这些工具(与梅奥诊所和斯坦福大学合作建立)为受控生物医学术语提供托管、编辑和查看支持。在2008财年期间，这些工具不断得到增强，以确保它们将满足各种内部和外部利益攸关方的需求。 另一项支持技术是癌症数据标准存储库(CaDSR)，用于支持癌症研究中通用数据元素(CDE)、电子病例报告表格和数据模型的开发和部署。CaDSR由一套用于创建、共享和部署CDE的工具组成，其中包括一个公共CDE浏览器，允许用户搜索数据元素、创建表单和下载CDE。CaCORE提供Web服务来以编程方式访问caDSR内容。基于开源标准的caDSR可供其他政府机构免费使用，也可供感兴趣的各方下载和使用。 CaDSR工具集包括： CDE浏览器 统一建模语言模型浏览器 管理工具 哨兵工具和哨兵API 管理工具 访问caDSR内容的API 表单生成器 CDE对比表 支持与caBIG兼容的软件的技术： CaCORE软件开发工具包是一组开源软件工具，用于创建语义感知的软件系统。CaCORE SDK由以下工具组成： 语义集成工作台：帮助将形式语义绑定到软件系统的工具。 代码生成器：代码生成器根据软件开发人员创建的模型创建实际的软件系统。 UML Loader：创建用于确保语义互操作性的元数据 通用安全模块：提供与21CFR Part 11兼容的便捷模块，用于在使用caCORE软件开发工具包开发的系统中进行身份验证和授权。 通用日志记录模块：为使用caCORE SDK构建的系统提供日志记录服务(21CFR第11部分要求)。 CaCORE SDK旨在允许中等经验的Java程序员创建与Silver兼容的软件系统。 各种其他CBIIT/caBIG应用程序使用的数据存储库： 癌症生物信息学基础设施对象(CaBIO)系统提供对各种其他CBIIT/caBIG应用程序使用的数据的程序化访问。CaBIO提供各种分子生物学/基因组学数据类型(与基因、蛋白质、转录本、阵列设计、生物标记物等相关的信息)的中央存储库。在面向服务的体系结构中。 CaBIO支持CBIITs的使命，即在临床和基础科学研究领域实现基于公共数据元素和公共语义的高级生物医学信息学计算。CaBIO与caDSR和EVS一起，是NCI caCORE基础架构的一部分。CaBIO在整个CBIIT和caBIG社区应用程序中使用。

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.