caCORE: A common infrastructure for cancer informatics
caCORE: A common infrastructure for cancer informatics
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DOI：
10.1093/bioinformatics/btg335
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发表时间：
2003-12-12
期刊：
影响因子：
5.8
通讯作者：
Buetow, KH
中科院分区：
文献类型：
--
作者：
Covitz, PA;Hartel, F;Buetow, KH
动机：具有实质性生物信息学操作的站点面临着建立数据处理和交付基础设施的挑战，这些基础设施提供可靠的访问并实现数据集成。必须处理和存储本地生成的数据，以便能够显示与外部数据源的关系。数据集之间的一致性和可比性需要使用受控词汇表进行注释，并且需要数据表示的元数据标准。应该支持对处理过的数据的编程访问，以确保提取最大可能的值。面对国家癌症研究所生物信息学中心的这些挑战，我们决定开发一个强大的基础设施，用于数据管理和集成，以支持先进的生物医学应用。结果：我们开发了一套相互关联的软件和服务，称为caCORE。企业词汇服务（EVS）提供受控词汇、字典和同义词库服务。癌症数据标准存储库（caDSR）为公共数据元素提供元数据注册表。癌症生物信息学基础设施对象（caBIO）实现了生物医学领域的面向对象模型，并提供Java、简单对象访问协议和HTTP-XML应用程序编程接口。caCORE已被用于开发科学应用程序，这些应用程序汇集了来自不同基因组和临床科学来源的数据。
Motivation:Sites with substantive bioinformatics operations are challenged to build data processing and delivery infrastructure that provides reliable access and enables data integration. Locally generated data must be processed and stored such that relationships to external data sources can be presented. Consistency and comparability across data sets requires annotation with controlled vocabularies and, further, metadata standards for data representation. Programmatic access to the processed data should be supported to ensure the maximum possible value is extracted. Confronted with these challenges at the National Cancer Institute Center for Bioinformatics, we decided to develop a robust infrastructure for data management and integration that supports advanced biomedical applications.Results: We have developed an interconnected set of software and services called caCORE. Enterprise Vocabulary Services (EVS) provide controlled vocabulary, dictionary and thesaurus services. The Cancer Data Standards Repository (caDSR) provides a metadata registry for common data elements. Cancer Bioinformatics Infrastructure Objects (caBIO) implements an object-oriented model of the biomedical domain and provides Java, Simple Object Access Protocol and HTTP-XML application programming interfaces. caCORE has been used to develop scientific applications that bring together data from distinct genomic and clinical science sources.