Microarray Data Standards and Supporting Applications

描述(由申请人提供)：本申请建议获得正式资金，为功能基因组学社区提供工具和资源，以使用标准格式和实践来交流他们的数据。我们的组织，微阵列基因表达数据协会(MGED)，是一个由生物学家、计算机科学家和数据分析师组成的国际组织，其目标是通过提供共享微阵列和其他大规模生物数据的基础设施和资源来促进和扩大实验科学。这一基础设施包括这些数据的交换和注释标准，以及为根据这些标准开发数据库和数据获取、管理和分析工具提供共同基础的支持软件。MGED资源(MIAME、MAGE-ML、MAGE-STK和MGED Ontology)已经被广泛使用，因此这项赠款申请寻求资金来改进它们，开发新功能，并使用MGED资源为研究和计算社区提供可靠的支持。每一个具体的目标都与至少一个其他目标密切相关，继续密切合作，这一直是 MGED。此外，每个目标都需要与更大的研究界进行沟通，以获得批评和反馈，并提供使用资源的途径和协助。所有生产的软件将继续在麻省理工学院开放源码许可证下免费使用，其他人的共同开发将因频繁的软件开发“jumberrees”而得到促进。 我们建议扩展和改进MAGE对象模型，开发和传播先进的MAGE软件工具包，研究和创建微阵列数据的数据质量度量，扩展和交流描述微阵列实验的本体，开发和提供用于验证MIAME合规性和MAGE格式化的文档的工具，以及开发允许我们共享数据的免费工具。

DESCRIPTION (provided by applicant): This application proposes to obtain formal funding to provide the functional genomics community with tools and resources to use standard formats and practices to communicate their data. Our group, the Microarray Gene Expression Data Society (MGED), is an international organization of biologist, computer scientists and data analysts whose aim is to promote and extend experimental science by providing the infrastructure and resources for sharing microarray and other large-scale biological data. This infrastructure includes standards for exchange and annotation of these data and supporting software that provides a common ground for the development of databases and data acquisition, management and analysis tools based on these standards. MGED resources (MIAME, MAGE-ML, MAGE-stk and the MGED Ontology) are already in widespread use, so this grant application seeks funding to improve them, develop new features and to provide dependable support to the research and computational communities using MGED resources. Each specific aim is closely tied to at least one other aim, continuing the close and collaborative work that has been the hallmark of MGED. In addition, each of the aims will require communication with the larger research community, both to obtain criticism and feedback, as well as to provide access to resources and assistance in using them. All software produced will continue to be freely available under the MIT Open Source license, and co-development by others will be facilitated by frequent software development "jamborees." We propose to extend and improve the MAGE Object Model, develop and disseminate an advanced MAGE software toolkit, research and create data quality metrics for microarray data, extend and communicate ontologies for describing microarray experiments, develop and provide tools for validating documents for MIAME compliance and MAGE formatting and to develop freely available tools that allow us to share data.