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变化，其中大多数源于基因组多样性。随着基因组技术在整个生物科学中都可以使用，生物多样性的完整表征需要完全表征基因组。同样，整个生物多样性研究领域的数据综合都需要数据交换标准的开发，实施，集成和协调。这种可互操作的信息学对于我们对生物学的理解将是转变的，因此对环境和保护政策有影响。加上变革潜力的是，微生物世界代表了世界上生物量的一半及其几乎所有的生物多样性，但仍然有效地看不见且对传统生物多样性研究的可靠性。 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 tr​​ansform 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开发了有关基因组学，宏基因组学和标记基因的任何序列（混合）标准的最小信息。这些团体将共同进行统一的信息学努力，以开发三层互操作性。渴望将观察性（DWC）和基因组（MIX）标准统一，并建立在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。标准互操作性是接下来两层的基础。将支持句法互操作性（在Internet API和数据库参考模型的上下文中）。渴望将两个社区的专家组装成（a）设计一个集成DWC和GSC混合标准的数据库参考模型； （b）为了有效的数据管理，请为不同的数据库平台创建特定的实现，以促进采用。在/对于不同数据库系统上的参考模型的实际实现将首次允许对技术性能和用例的系统比较测试（例如，实施最佳地提供哪些复杂的数据查询）。急切的工作组将创建任务组，以建立管理本体论的基础架构，并在纯语义级别上构建参考模型，以融合两个数据标准世界，这两个世界都足够先进，可以进行有用的互操作性。开发跨学科的信息基础设施，以实现跨越域的数据互动性，以实现该领域的数据互动，以实现EAGER的范围，即将实现复杂的环境，未来的环境能够实现未来的现象。的确，通过导致信息标准平台，以构想微生物世界的新颖概念和理论框架？渴望将在科学之外产生变革性的影响。