caCORE--美国癌症研究的生物信息核心框架

近十年来基因组学和蛋白质组学的快速发展为医学生物学的研究提供了前所未有的机遇.一方面,大规模、高通量的基因和蛋白质的测定工作产生了大量有价值的各类数据;而另一方面,因数据标准的缺乏、数据兼容和整合的艰难而妨碍了人们去充分有效地共享数据,进而更好地促进各自领域的发展.生物信息学也因此成为当今生物医学研究发展必不可少的一个手段.本文就美国国家癌症研究所(National Cancer Institute,NCI)以癌症研究为试点所建立的一个生物信息核心框架caCORE(cancer Common Ontologic Reference Environment)作一简短介绍.

caCORE: Core architecture of bioinformation on cancer research in America

A critical factor in the advancement of biomedical research is the ease with which data can be integrated, redistributed and analyzed both within and across domains. This paper summarizes the Biomedical Information Core Infrastructure built by National Cancer Institute Center for Bioinformatics in America (NCICB). The main product from the Core Infrastructure is caCORE-cancer Common Onto-logic Reference Environment, which is the infrastructure backbone supporting data management and application development at NCICB. The paper explains the structure and function of caCORE: ( 1 ) Enterprise Vocabulary Services ( EVS) . They provide controlled vocabulary, dictionary and thesaurus services, and EVS produces the NCI Thesaurus and the NCI Metathesaurus; ( 2 ) The Cancer Data Standards Repository (caDSR) . It provides a metadata registry for common data elements. (3) Cancer Bioinformatics Infrastructure Objects ( caBIO). They provide Java, Simple Object Access Protocol and HTTP-XML application programming interfaces. The vision for caCORE is to provide a common data management framework that will support the consistency, clarity, and comparability of biomedical research data and information. In addition to providing facilities for data management and redistribution, caCORE helps solve problems of data integration. All NCICB-developed caCORE components are distributed under open-source licenses that support unrestricted usage by both non-profit and commercial entities, and caCORE has laid the foundation for a number of scientific and clinical applications. Based on it, the paper expounds caCORE-base applications simply in several NCI projects,of whic one is CMAP (Cancer Molecular Analysis Project ) , and the other is caBIG ( Cancer Biomedical Informatics Grid). In the end, the paper also gives good prospects of caCORE, and while caCORE was born out of the needs of the cancer research community, it is intended to serve as a general resource. Cancer research has historically contributed to many areas beyond tumor biology. At the same time, the paper makes some suggestions about the study at the present time on biomedical informatics in China.