EarthCube RCN: An EarthCube Oceanography and Geobiology Environmental Omics Research Coordination Network (ECOGEO RCN)

EarthCube RCN：EarthCube 海洋学和地球生物学环境组学研究协调网络 (ECOGEO RCN)

• 批准号: 1440066
• 负责人: Edward DeLong
• 金额: $ 30万
• 依托单位: University of Hawaii
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2014
• 资助国家: 美国
• 起止时间: 2014-09-01 至 2017-02-28
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1440066&HistoricalAwards=false
• 关键词: EarthCube; RCN; Oceanography; Geobiology; Environmental

The network elements of the ECOGEO RCN reach across diverse communities of ocean scientists, geoscientists, computer scientists and bioinformaticians, and will forge new cross-disciplinary connections. Although the scientific goals of the proposed ECOGEO community network are diverse, common challenges and requirements for big data analyses be identified across this broad community. This project will provide new solutions and ideas that reach beyond disciplinary boundaries, since the challenges of rich omic datasets share commonalities across areas as diverse as soil science, oceanography, geobiology and studies of the human microbiome. Best practices and use case scenarios developed in this project will integrate across challenges of diverse science domains, and provide well documented approaches for omic data management and analyses, that will serve as models and test cases for new cyberinfrascructure systems. These efforts will impact not only ocean scientists and geobiologists, but also other allied areas that use the same approaches, that range from environmental assessment to human health. Inexpensive sequencing has facilitated the generation of billions of environmental DNA sequences, and allied techniques to survey gene expression (metatranscriptomics) and protein expression (metaproteomics) are advancing as well. The large and complex environmental omic datasets now present major challenges to the ocean and geoscience communities. These omic datasets are diverse, complex, and exponentially expanding, and require the construction, curation, and query of diverse federated databases, as well as development of shared interoperable, big-data capable analytical tools. To help address these current big data challenges, this project establishes a virtual network called EarthCube Oceanography and Geobiology Environmental Omics Research Coordination Network (ECOGEO RCN), that will foster collaborations, communication, innovation, and education in omic data management and analyses in the oceanography and geobiology communities. The effort will identify and communicate needed data standards, sharing and access mechanisms and analytical strategies across the broader community of ocean and geosciences. Major outcomes of ECOGEO RCN will be: 1)Establishment of a virtual network that coordinates collaboration and communication in omics, data sharing and analyses; 2)Training of a cyber-savvy generation of ocean and geo science graduate students, postdocs and young professionals in the rapidly evolving environmental omics and bioinformatics field. 3)Identification and elaboration of environmental omic data standards, ontologies, sharing mechanisms, and analytical strategies; 4)Development of use case scenarios that will inspire creation of a new palette of user friendly inter-operative community data management, analytical and visualization tools for oceanography and geobiology omic science and beyond.The establishment of the ECOGEO RCN will provide a collection of online resources to enable the access, management and discovery of oceanographic and geobiology omic data, metadata, analysis tools, methodologies, and other user-driven needs. An EarthCube hosted ECOGEO-Wiki will serve as open forum for network participants to share content and link to data repositories, models, and tools. The ECOGEO centralized network and web-based portal will promote better communication within and between ECOGEO microbial oceanography and geobiology scientists and the broader scientific community. This will enable greater access and organization of large and heterogeneous datasets, greater efficiencies in scientific discovery, and broader collaborations based on both survey and experimental data. The overall result will be to facilitate access and use of existing and rapidly accumulating new omic datasets for a wide range of ocean science and geoscience users, to observe measure and model community composition, biological and biogeochemical activities and ecosystem structure and function from ocean surface waters to the deep subsurface.

ECOGEO区域网络的网络要素覆盖了海洋科学家、地球科学家、计算机科学家和生物信息学家等不同群体，并将建立新的跨学科联系。虽然拟议的ECOGEO社区网络的科学目标是多种多样的，但在这个广泛的社区中确定了大数据分析的共同挑战和要求。该项目将提供超越学科界限的新解决方案和想法，因为丰富的组学数据集的挑战在土壤科学，海洋学，地球生物学和人类微生物组研究等不同领域具有共性。该项目中开发的最佳实践和用例场景将整合不同科学领域的挑战，并为组学数据管理和分析提供有据可查的方法，这些方法将作为新的网络基础架构系统的模型和测试用例。这些努力不仅将影响海洋科学家和地球生物学家，而且还将影响从环境评估到人类健康等使用相同方法的其他相关领域。廉价的测序促进了数十亿环境DNA序列的产生，并且调查基因表达（元转录组学）和蛋白质表达（元蛋白质组学）的相关技术也在进步。大型和复杂的环境组学数据集现在对海洋和地球科学界提出了重大挑战。这些组学数据集是多样的，复杂的，呈指数级增长，需要构建，管理和查询不同的联合数据库，以及开发共享的可互操作的，大数据的分析工具。为了帮助解决这些当前的大数据挑战，该项目建立了一个名为EarthCube海洋学和地球生物学环境组学研究协调网络（ECOGEO RCN）的虚拟网络，该网络将促进海洋学和地球生物学社区在组学数据管理和分析方面的合作，交流，创新和教育。这项工作将确定和传播所需的数据标准、共享和访问机制以及整个海洋和地球科学界的分析战略。ECOGEO区域网络的主要成果将是：1）建立一个虚拟网络，协调组学、数据共享和分析方面的合作和交流; 2）在迅速发展的环境组学和生物信息学领域培训精通网络的一代海洋和地球科学研究生、博士后和年轻专业人员。3)确定和制定环境组学数据标准、本体、共享机制和分析战略; 4）开发用例场景，这将激励创建一个新的用户友好的社区数据管理，分析和可视化工具，用于海洋学和地球生物学和经济学等领域。ECOGEO RCN的建立将提供一系列在线资源，以实现访问，管理和发现海洋学和地球生物学组学数据、元数据、分析工具、方法和其他用户驱动的需求。一个由EarthCube托管的ECOGEO-Wiki将作为网络参与者共享内容和链接到数据库、模型和工具的开放论坛。ECOGEO的中央网络和网络门户将促进ECOGEO微生物海洋学和地球生物学科学家与更广泛的科学界之间的更好沟通。这将使大型和异构数据集的访问和组织更方便，科学发现的效率更高，以及基于调查和实验数据的更广泛的合作。总体结果将是促进广大海洋科学和地球科学用户获取和使用现有的和迅速积累的新的组学数据集，以观测和模拟从海洋表面沃茨到深层次表面的群落组成、生物和地球化学活动以及生态系统结构和功能。