The caCORE Software Development Kit: streamlining construction of interoperable biomedical information services.
The caCORE Software Development Kit: streamlining construction of interoperable biomedical information services.
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DOI：
10.1186/1472-6947-6-2
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发表时间：
2006-01-06
影响因子：
3.5
通讯作者：
Covitz, Peter A
中科院分区：
文献类型：
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作者：
Phillips, Joshua;Chilukuri, Ram;Covitz, Peter A
背景技术背景：健壮的，可编程访问的生物医学信息服务，与其他资源的语法和语义互操作是具有挑战性的建设。这种系统需要采用共同的信息模型、数据表示和术语标准以及有文件记录的应用程序编程接口。美国国家癌症研究所（NCI）开发了癌症通用本体表示环境（caCORE），以提供实现其开发或赞助的系统之间互操作性所需的基础设施。caCORE软件开发工具包（SDK）的目的是为NCI内部和外部的开发人员提供所需的工具，以构建这样的互操作的软件systems.Results：caCORE SDK需要一个统一建模语言（UML）工具，开始开发工作流程与建设的领域信息模型的UML类图的形式。使用语义连接器组件，用来自描述逻辑术语源的概念和定义来注释模型。使用UML加载器组件在癌症数据标准库（caDSR）中注册带注释的模型。系统软件是使用Codegen组件自动生成的，该组件生成在应用服务器上运行的中间件。caCORE SDK最初使用七类UML模型进行了测试和验证，并已用于生成caCORE生产系统，其中包括具有数十个类的模型。所部署的系统支持通过面向对象的API进行访问，这些API具有一致的语法，可以跨原始UML模型中的所有类检索任何类型的数据对象。caCORE SDK目前被多个开发团队使用，包括癌症生物医学信息网格（caBIG）计划的参与者，以创建兼容的数据服务。caBIG兼容性标准基于caCORE资源，因此caCORE SDK已成为caBIG.CONCLUSION的关键使能技术：caCORE SDK通过提供标准化和加速建模、开发和部署的工作流和自动化工具，大大降低了实现在语法和语义上可互操作的系统的障碍。它已经得到了caBIG程序开发人员的认可，并有望为正在开发的数据网格上创建数据服务节点提供一种通用机制。
BACKGROUND: Robust, programmatically accessible biomedical information services that syntactically and semantically interoperate with other resources are challenging to construct. Such systems require the adoption of common information models, data representations and terminology standards as well as documented application programming interfaces (APIs). The National Cancer Institute (NCI) developed the cancer common ontologic representation environment (caCORE) to provide the infrastructure necessary to achieve interoperability across the systems it develops or sponsors. The caCORE Software Development Kit (SDK) was designed to provide developers both within and outside the NCI with the tools needed to construct such interoperable software systems.RESULTS: The caCORE SDK requires a Unified Modeling Language (UML) tool to begin the development workflow with the construction of a domain information model in the form of a UML Class Diagram. Models are annotated with concepts and definitions from a description logic terminology source using the Semantic Connector component. The annotated model is registered in the Cancer Data Standards Repository (caDSR) using the UML Loader component. System software is automatically generated using the Codegen component, which produces middleware that runs on an application server. The caCORE SDK was initially tested and validated using a seven-class UML model, and has been used to generate the caCORE production system, which includes models with dozens of classes. The deployed system supports access through object-oriented APIs with consistent syntax for retrieval of any type of data object across all classes in the original UML model. The caCORE SDK is currently being used by several development teams, including by participants in the cancer biomedical informatics grid (caBIG) program, to create compatible data services. caBIG compatibility standards are based upon caCORE resources, and thus the caCORE SDK has emerged as a key enabling technology for caBIG.CONCLUSION: The caCORE SDK substantially lowers the barrier to implementing systems that are syntactically and semantically interoperable by providing workflow and automation tools that standardize and expedite modeling, development, and deployment. It has gained acceptance among developers in the caBIG program, and is expected to provide a common mechanism for creating data service nodes on the data grid that is under development.