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面的所有生命变异，其中大部分源自基因组多样性。随着基因组技术在生物科学领域的广泛应用，生物多样性的全面表征需要基因组的全面表征。同样，整个生物多样性研究领域的数据合成需要数据交换标准的开发、实施、整合和协调。这种可互操作的信息学将彻底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。增加变革潜力的是，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，但对于传统的生物多样性研究来说仍然是不可见的和难以处理的。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，因此需要替代的信息学框架。EAGER 将改变两个以前独立的研究团体之间的合作：传统生物多样性界的信息学家，他们采用达尔文核心 (DwC) 作为标准，以及基因组标准联盟 (GSC) 的信息学家，他们采用达尔文核心 (DwC) 作为标准。 制定了基因组学、宏基因组学和标记基因的有关任何序列的最小信息 (MIxS) 标准。这些小组将共同致力于统一的信息学工作，以开发三层互操作性。 EAGER 将协调观察 (DwC) 和基因组 (MIxS) 标准，建立在 NSF 研究协调网络主持和建立的社区对话和跨学科网络的基础上。标准互操作性是接下来两层的基础。将支持句法互操作性（在互联网 API 和数据库参考模型的上下文中）。 EAGER 将聚集来自两个社区的专家来 (a) 设计一个集成了 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具体的实施方案以促进采用。在不同数据库系统上/针对不同数据库系统的参考模型的实际实现将首次允许对技术性能和用例进行系统的比较测试（例如，哪种实现最适合哪种复杂的数据查询）。 EAGER 将创建任务组来建立管理本体的基础设施，并在纯语义层面构建参考模型，以融合两个数据标准世界，这两个世界都足够先进，可以实现有用的互操作性。在开发跨学科信息基础设施以实现跨领域数据互操作性时，EAGER 将促进对复杂环境现象的理解，从而为未来的政策决策提供信息。事实上，通过建立一个信息学标准平台，为微生物“暗物质”世界构想一个新颖的概念和理论框架。 EAGER 将产生超越科学的变革性影响。