Collaborative Proposal: EarthCube Building Blocks: Planet Microbe: Enabling the discovery and integration of oceanographic 'omics, environmental and physiochemical data layers

合作提案：EarthCube 构建模块：行星微生物：实现海洋组学、环境和理化数据层的发现和整合

• 批准号: 1639588
• 负责人: Bonnie Hurwitz
• 金额: $ 87.3万
• 依托单位: University of Arizona
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2017
• 资助国家: 美国
• 起止时间: 2017-09-01 至 2020-08-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1639588&HistoricalAwards=false
• 关键词: Collaborative; Proposal; EarthCube; Building; Blocks

Oceanographic research expeditions provide a rich source of data comprised of next generation sequencing, microscopy, and physical/chemical environmental data to explore ocean biodiversity. As collection bottles and chemical sensors emerge from the depths of the ocean, research teams work through the night processing their key component of this oceanographic treasure. Despite careful efforts to share data among collaborators, the moment each sample emerges is often the last time these rich data sources are together. In this project the investigators will develop Planet Microbe, a federated resource of database connections to enable data discovery and open data sharing for historical and on-going oceanography and geobiology sequencing efforts. Planet Microbe will provide the community with a platform that partners -omics data and analyses with any relevant contextual and environmental data available.  To promote the use of Planet Microbe, adoption by the community, and a collaborative research paradigm, the project will leverage and continue development of ECOGEO Research Coordination Network workshop on bioinformatics protocols using open-source web-based Protocols.io software. These protocols will contain multimedia training videos, screenshots, and example datasets in a stepwise format that are cross-linked to specific commands, tools, or outside websites. The investigators will refine and extend these use-cases and protocols in early career workshops. They will adapt the protocols for broader use in high school curriculum in ocean sciences and cyberinfrastructure through an existing collaboration with a technical librarian and science teacher in a high school comprised of 70% minority students. The project will offer undergraduate students research opportunities to design and develop Apps in the existing CyVerse Cyberinfrastructure to address bioinformatic needs from the oceanographic community and participate in protocol development and teaching. Initially, the project will develop a prototype using data from Hawaii Ocean Time-series (HOT) and Bermuda Atlantic Time Series (BATS), both of which produce extensive "-omics" data sets (available via iMicrobe) and oceanographic data (available via the Biological and Chemical Oceanography Data Management Office (BCO-DMO)) and are of great value to the broader science community. Connections between data sets will be derived through automated distance-based algorithms, and refined through collaborative hand-curation. Once the prototype has been validated, additional -omics data sets from two NSF-funded Science and Technology Centers, the Centers for Dark Energy Biosphere Investigations (CDEBI) and Microbial Oceanography Research and Education (CMORE), will be retrieved from disparate -omic repositories (e.g., JGI/IMG, MG-RAST, NCBI, EBI) and queryable through a recommendation algorithm fueled and refined by scientific queries from past users. Finally, data in Planet Microbe will leverage existing EarthCube funded projects to expand beyond BCO-DMO such as: GeoLink, which also includes Rolling Deck to Repository (R2R) and International Ocean Discovery Program (IODP), SeaView to share collected resources and create a "microbe" user scenario, and GeoDeepDive to discover dark data in historical publications. Through this concerted effort, Planet Microbe will become the go-to site for oceanographic data discovery and integration. By reconnecting -omics data with environmental data from oceanographic cruises, Planet Microbe will enable biological inquiry into environmental changes that affect the distribution and abundance of microbes in the sea. Further, algorithms for connecting disparate data types and a robust search interface developed by Planet Microbe will enable the creation of virtual datasets through user-defined oceanographic measurements, features, and thresholds that can be used to synthesize and analyze global datasets in novel ways by the community. In particular, virtual datasets can be used broadly by the geosciences community to refine global ecological models, to inform citizen science efforts, and derive critical information on temporal and spatial data associated with ocean microbes that re important in disaster analysis. Taken together, Planet Microbe will provide a much needed resource for the geosciences community to unite -omics and environmental data toward unforeseen discovery in the Earth system.

海洋学研究探险提供了丰富的数据源，包括下一代测序、显微镜和物理/化学环境数据，以探索海洋生物多样性。随着收集瓶和化学传感器从海洋深处出现，研究团队通宵达旦地处理他们的数据。尽管努力在合作者之间共享数据，但每个样本出现的那一刻往往是这些丰富的数据源最后一次聚集在一起。在这个项目中，研究人员将开发 Planet Microbe，这是一个与数据库连接的联合资源。启用数据发现并开放历史和正在进行的海洋学和地球生物学测序工作的数据共享将为社区提供一个平台，该平台可以与任何相关的背景和环境数据进行组学数据和分析，以促进对微生物星球的使用。社区和协作研究范式，该项目将利用基于开源网络的 Protocols.io 软件，利用并继续开发 ECOGEO 研究协调网络研讨会的生物信息学协议。这些协议将包含多媒体培训视频、屏幕截图和内容。逐步格式的示例数据集与特定命令、工具或外部网站交叉链接，研究人员将在早期职业研讨会中完善和扩展这些用例和协议，他们将调整这些协议以在高中课程中更广泛地使用。通过与一所由 70% 少数族裔学生组成的高中的技术图书馆员和科学教师现有合作，该项目将为本科生提供在现有 CyVerse 网络基础设施中设计和开发应用程序的研究机会，以解决海洋科学和网络基础设施方面的问题。最初，该项目将使用夏威夷海洋时间序列（HOT）和百慕大大西洋时间序列（BATS）的数据开发原型，这两个数据都产生广泛的“组学”。 “数据集（通过 iMicrobe 提供）和海洋学数据（通过生物和化学海洋学数据管理办公室 (BCO-DMO) 提供）对于更广泛的科学界具有重要价值。数据集之间的连接将通过自动基于距离的算法导出，并通过协作手工管理进行完善。一旦原型得到验证，来自两个 NSF 资助的科学技术中心、暗能量生物圈研究中心 (CDEBI) 和微生物中心的额外组学数据集。海洋学研究和教育 (CMORE)，将从不同的组学存储库（例如 JGI/IMG、MG-RAST、NCBI、EBI）中检索，并可通过推荐算法进行查询最后，Planet Microbe 中的数据将利用现有的 EarthCube 资助的项目来扩展到 BCO-DMO 之外，例如：GeoLink，其中还包括 Rolling Deck to Repository (R2R) 和国际海洋发现计划 (IODP)。 ) )、SeaView 共享收集的资源并创建“微生物”用户场景，GeoDeepDive 发现历史出版物中的暗数据通过这种共同努力，Planet Microbe 将成为海洋学数据发现和分析的首选网站。通过将组学数据与海洋学巡游的环境数据重新连接起来，Planet Microbe 将能够对影响海洋微生物分布和丰度的环境变化进行生物学调查。此外，还开发了用于连接不同数据类型的算法和强大的搜索界面。 Planet Microbe 将能够通过用户定义的海洋学测量、特征和阈值创建虚拟数据集，社区可使用这些测量、特征和阈值以新颖的方式综合和分析全球数据集，特别是，虚拟数据集可被地球科学广泛使用。地球科学界将致力于完善全球生态模型，为公民科学工作提供信息，并获取与海洋微生物相关的时空数据的关键信息，这些数据在灾害分析中非常重要。总而言之，Planet Microbe 将为地球科学界团结起来提供急需的资源。 -针对地球系统中不可预见的发现的组学和环境数据。

项目成果

The Promises and Pitfalls of Machine Learning for Detecting Viruses in Aquatic Metagenomes

• DOI: 10.3389/fmicb.2019.00806
• 发表时间: 2019-04-16
• 期刊: FRONTIERS IN MICROBIOLOGY
• 影响因子: 5.2
• 作者: Ponsero, Alise J.;Hurwitz, Bonnie L.
• 通讯作者: Hurwitz, Bonnie L.

iMicrobe: Tools and data-driven discovery platform for the microbiome sciences

iMicrobe：微生物组科学的工具和数据驱动的发现平台

• DOI: 10.1093/gigascience/giz083
• 发表时间: 2019
• 期刊: GigaScience
• 影响因子: 9.2
• 作者: Youens-Clark, Ken;Bomhoff, Matt;Ponsero, Alise J;Wood-Charlson, Elisha M;Lynch, Joshua;Choi, Illyoung;Hartman, John H;Hurwitz, Bonnie L
• 通讯作者: Hurwitz, Bonnie L