EAGER: An Interoperable Information Infrastructure for Biodiversity Research (I3BR)

EAGER：生物多样性研究的可互操作信息基础设施 (I3BR)

• 批准号: 1255035
• 负责人: Mark Ellisman
• 金额: $ 30万
• 依托单位: University of California-San Diego
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2012
• 资助国家: 美国
• 起止时间: 2012-10-01 至 2018-09-30
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1255035&HistoricalAwards=false
• 关键词: EAGER; Interoperable; Information; Infrastructure; Biodiversity

Biodiversity comprises all variations of life at all levels of biological organization, most of which arise from genomic diversity. As genomic technologies become available across the biological sciences, a full characterization of biodiversity demands a full characterization of genomes. Similarly, data synthesis across the full range of biodiversity research domains demands development, implementation, integration and harmonization of data exchange standards. Such interoperable informatics would be transformational for our understanding of biology, with consequent impact on environmental and conservation policy. Adding to the transformational potential is the fact that the microbial world represents half of the world's biomass and nearly all of its biodiversity, yet is still effectively invisible and intractable to traditional biodiversity research. Metagenomic data are not amenable to the concepts, standards, semantics, and methods of traditional eukaryotic biodiversity, and therefore, require an alternate informatics framework.The EAGER will transform the collaborations between two previously separate research communities: the informaticists of the traditional biodiversity community, who employ the Darwin Core (DwC) as a standard, and the informaticists of the Genomic Standards Consortium (GSC), who have developed the Minimal Information about any Sequence (MIxS) standard for genomics, metagenomics and marker genes. Together, these groups will engage in a unified informatics effort to develop three layers of interoperability. The EAGER will harmonize the observational (DwC) and genomic (MIxS) standards, building on a community dialogue and interdisciplinary networking hosted and established under an NSF Research Coordination Network. Standards interoperability is the basis for the next two layers. Syntactic interoperability (in the context of Internet APIs and a database Reference Model) will be supported. The EAGER will assemble experts from the two communities to (a) devise a database Reference Model that integrates the DwC and GSC MIxS standards; and (b) for effective data management, create specific implementations for different database platforms to foster adoption. The practical implementation of the reference model on/for different database systems will allow, for the first time, systematic comparative testing of technical performance and of use cases (e.g., which implementation best serves which complex data query). The EAGER will create task groups to establish the infrastructure for managing ontologies, and to construct a reference model on the purely semantic level in order to fuse the two worlds of data standards, both of which are advanced enough to engage in useful interoperability.In developing an interdisciplinary information infrastructure to achieve data interoperability across domains, this EAGER would advance understanding of complex environmental phenomena and, thereby, inform future policy decisions. Indeed, by leading to an informatics standards platform to conceive a novel conceptual and theoretical framework for the world of microbial ?dark matter,? the EAGER would have a transformational impact beyond science.

生物多样性包括生物组织各个层次的所有生命变异，其中大部分来自基因组多样性。随着基因组技术在生物科学中的应用，生物多样性的全面表征需要基因组的全面表征。同样，在生物多样性研究的所有领域进行数据综合，需要制定、执行、整合和统一数据交换标准。这种可互操作的信息学将改变我们对生物学的理解，从而对环境和保护政策产生影响。微生物世界代表了世界生物量的一半和几乎所有的生物多样性，但传统的生物多样性研究仍然是有效的无形和棘手的。宏基因组数据不符合传统真核生物多样性的概念、标准、语义和方法，因此，需要一个替代的信息学框架。EAGER将改变两个以前独立的研究社区之间的合作：传统生物多样性社区的信息学家，他们使用达尔文核心（DwC）作为标准，以及基因组标准联盟（GSC）的信息学家，他们开发了用于基因组学、宏基因组学和标记基因的关于任何序列的最小信息（MIxS）标准。这些小组将共同参与统一的信息学工作，以开发三个层次的互操作性。EAGER将协调观察（DWC）和基因组（MIxS）标准，建立在NSF研究协调网络下托管和建立的社区对话和跨学科网络的基础上。标准互操作性是下两层的基础。语法互操作性（在互联网API和数据库参考模型的背景下）将得到支持。EAGER将召集来自两个社区的专家，以（a）设计一个集成DwC和GSC MIxS标准的数据库参考模型;（B）为了有效的数据管理，为不同的数据库平台创建特定的实现，以促进采用。在不同数据库系统上/为不同数据库系统实际实施参考模型将首次允许对技术性能和用例进行系统的比较测试（例如，哪个实现最好地服务于哪个复杂数据查询）。EAGER将创建任务组，以建立管理本体的基础设施，并在纯语义层面上构建参考模型，以融合两个世界的数据标准，这两个世界都足够先进，可以进行有用的互操作性。在开发跨学科信息基础设施以实现跨领域的数据互操作性方面，EAGER将促进对复杂环境现象的理解，从而为未来的政策决定提供信息。事实上，通过建立一个信息学标准平台，为微生物的世界构思一个新的概念和理论框架？暗物质？EAGER将产生超越科学的变革性影响。