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.

海洋学研究考察提供了丰富的数据来源，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浮出水面，研究团队彻夜工作，处理这一海洋宝藏的关键组成部分。尽管合作者努力共享数据，但每个样本出现的时刻往往是这些丰富的数据源最后一次在一起。在这个项目中，研究人员将开发Planet Microbe，这是一个数据库连接的联合资源，用于历史和正在进行的海洋学和地球生物学测序工作的数据发现和开放数据共享。 Planet Microbe将为社区提供一个平台，将组学数据和分析与任何相关的上下文和环境数据结合起来。 为了促进Planet Microbe的使用、社区的采用和协作研究范式，该项目将利用和继续发展ECOGEO研究协调网络关于生物信息学协议的讲习班，使用基于Protocols.io的开源网络软件。这些协议将包含多媒体培训视频、屏幕截图和逐步格式的示例数据集，这些数据集与特定命令、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。他们将通过与一所由70%少数民族学生组成的高中的技术图书管理员和科学教师的现有合作，将这些协议应用于海洋科学和网络基础设施的高中课程。该项目将为本科生提供研究机会，在现有的CyVerse网络基础设施中设计和开发应用程序，以满足海洋学社区的生物信息学需求，并参与协议开发和教学。 最初，该项目将利用来自夏威夷海洋时间序列和百慕大大西洋时间序列的数据开发一个原型，这两个数据库都产生了广泛的“组学”数据集（可通过iMicrobe获得）和海洋学数据（可通过生物和化学海洋学数据管理办公室获得），对更广泛的科学界具有重要价值。数据集之间的联系将通过自动化的基于距离的算法得出，并通过协作手工管理进行完善。一旦原型得到验证，将从不同的组学存储库（例如，JGI/IMG、MG-RAST、NCBI、EBI），并且可通过由来自过去用户的科学查询提供动力和细化的推荐算法进行查询。最后，Planet Microbe中的数据将利用现有的EarthCube资助项目扩展到BCO-DMO之外，例如：GeoLink，其中还包括Rolling Deck to Repository（R2 R）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，以及GeoDeepDive发现历史出版物中的暗数据。通过这一共同努力，Planet Microbe将成为海洋学数据发现和整合的首选网站。通过将组学数据与海洋学巡航的环境数据重新连接，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，Planet Microbe开发的用于连接不同数据类型的算法和强大的搜索界面将通过用户定义的海洋测量，功能和阈值创建虚拟数据集，这些数据集可用于以新颖的方式合成和分析全球数据集。特别是，虚拟数据集可以被地球科学界广泛用于完善全球生态模型，为公民科学工作提供信息，并获得与海洋微生物相关的时间和空间数据的关键信息，这些信息在灾害分析中非常重要。总之，Planet Microbe将为地球科学界提供一个急需的资源，以联合组学和环境数据，实现地球系统中不可预见的发现。

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