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

ECOGEO RCN的网络元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的不同群体，并将建立新的跨学科联系。尽管拟议的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，可以确定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，因为丰富的基因组数据集的挑战在土壤科学、海洋学、地理生物学和人类微生物组研究等不同领域具有共性。本项目开发的最佳实践和用例场景将整合不同科学领域的挑战，并为基因组数据管理和分析提供良好的文档化方法，这些方法将作为新的网络基础设施系统的模型和测试用例。这些努力不仅会影响海洋科学家和地球生物学家，还会影响使用同样方法的其他相关领域，从环境评估到人类健康。低成本的测序技术促进了数十亿个环境DNA序列的生成，同时相关的基因表达（超转录组学）和蛋白质表达（宏蛋白质组学）调查技术也在不断发展。庞大而复杂的环境经济数据集现在对海洋和地球科学社区提出了重大挑战。这些组学数据集多样、复杂且呈指数级增长，需要构建、管理和查询不同的联邦数据库，以及开发共享的、可互操作的、具有大数据能力的分析工具。为了帮助应对当前的这些大数据挑战，该项目建立了一个名为EarthCube海洋学和地球生物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界在组学数据管理和分析方面的合作、交流、创新和教育。这项工作将在更广泛的海洋和地球科学领域确定和交流所需的数据标准、共享和获取机制以及分析策略。ECOGEO RCN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协作和交流；2)在快速发展的环境组学和生物信息学领域培养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)确定和阐述环境数据标准、本体、共享机制和分析策略；4)开发用例场景，激发创建新的用户友好的互操作社区数据管理调色板，分析和可视化工具，用于海洋学和地球生物组学科学等。ECOGEO RCN的建立将提供一系列在线资源，以实现海洋和地理生物组学数据、元数据、分析工具、方法和其他用户驱动需求的访问、管理和发现。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存储库、模型和工具的开放论坛。ECOGEO集中网络和基于网络的门户网站将促进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更好的交流。这将使更大的访问和组织大型和异构数据集，提高科学发现的效率，以及基于调查和实验数据的更广泛合作成为可能。总体结果将有助于为广泛的海洋科学和地球科学用户访问和使用现有的和快速积累的新组学数据集，以观察、测量和模拟从海洋表层水到深层地下的群落组成、生物和生物地球化学活动以及生态系统结构和功能。

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.