EarthCube Data Capabilities: Expanding the Ocean Protein Portal Capabilities for Use in Biochemical Research and Education

EarthCube 数据功能：扩展海洋蛋白质门户功能，用于生化研究和教育

• 批准号: 2026933
• 负责人: Mak Saito
• 金额: $ 60万
• 依托单位: Woods Hole Oceanographic Institution
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2020
• 资助国家: 美国
• 起止时间: 2020-09-01 至 2024-08-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=2026933&HistoricalAwards=false
• 关键词: EarthCube; Data; Capabilities; Expanding; Ocean

This project aims to expand the functionality of the Ocean Protein Portal (OPP) for use in research and education on ocean biochemistry. The Ocean Protein Portal prototype was designed to allow a broad range of scientists and students to discover answers to the questions: 1) “Where is my protein of interest in the oceans”, 2) “Who makes the protein?” through least common ancestor analysis, and 3) “How much is there?”. By making ocean protein datasets accessible and searchable to broad multi-domain communities including biological and chemical oceanographers, geobiologists, microbiologists, biochemists, and bioinorganic chemists, our understanding of the oceans and of microbial biochemistry will be improved. Moreover, these large datasets have the potential to provide future scientists with an important record of environmental change, and hence the portal is serving to capture, organize, and share these data to enable long term ocean change capabilities. Additional benefits of this project include contributing to community building within the ocean metaproteome community by providing a data repository and motivating ongoing efforts to improve data quality and standards. Educational use will be developed through collaborations with teachers and professors by the creation of educational modules for students learning about chemical reactions.Technical goals of this project include specific improvements to the Ocean Protein Portal such as expanding search capabilities, adding the ability to serve new metaproteomic data types, implementing a Knowledge Graph system for increased interoperability and sustainability, creating an API for machine accessible searches, furthering connections to external data and enhancing visualization capabilities, creating reproducible and citable search results, and development of automated ingestion with immediate QC capability. The transition of the OPP to a Knowledge Graph will further facilitate connections with domains outside marine ecology, as the graph will link out to other data resources in the environmental sciences and biology. In addition, an OPP Knowledge Graph would also provide a data structure useful to the field of computer science as this data structure is immediately available to applications of Machine Learning and Artificial Intelligence thus advancing the potential for novel machine-assisted scientific discovery. The researchers will conduct tutorials (virtual or in person) for participants to learn about the ocean metaproteomics datatype, how to use the OPP interface, and how to pull data from the OPP and plot it within the Jupyter notebook environment (using Python, Matplotlib, Bokeh, and Binder).This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.

该项目旨在扩大海洋蛋白质门户网站的功能，用于海洋生物化学的研究和教育。海洋蛋白质门户网站原型的设计是为了让广泛的科学家和学生发现问题的答案：1）“我感兴趣的蛋白质在海洋中的位置”，2）“谁制造蛋白质？”通过最小共同祖先分析，以及3）“有多少？"。通过使海洋蛋白质数据集可供包括生物和化学海洋学家、地质生物学家、微生物学家、生物化学家和生物无机化学家在内的广泛的多领域社区访问和搜索，我们对海洋和微生物生物化学的理解将得到改善。此外，这些大型数据集有可能为未来的科学家提供环境变化的重要记录，因此该门户网站可以捕获，组织和共享这些数据，以实现长期的海洋变化能力。该项目的其他好处包括通过提供数据存储库和激励持续努力提高数据质量和标准，为海洋元蛋白质组社区内的社区建设做出贡献。该项目的技术目标包括对海洋蛋白质门户网站进行具体改进，如扩大搜索功能，增加提供新的元蛋白质组数据类型的能力，实施知识图谱系统以提高互操作性和可持续性，创建机器可访问搜索的API，进一步连接外部数据并增强可视化功能，创建可复制和可引用的搜索结果，以及开发具有即时QC功能的自动摄取。将海洋生态学数据库转变为知识图谱将进一步促进与海洋生态学以外领域的联系，因为该图谱将与环境科学和生物学的其他数据资源相连接。此外，人工智能知识图谱还将提供对计算机科学领域有用的数据结构，因为这种数据结构可立即用于机器学习和人工智能的应用，从而推进新的机器辅助科学发现的潜力。研究人员将进行辅导（虚拟或亲自），让参与者了解海洋元蛋白质组学数据类型，如何使用数据库界面，以及如何从数据库中提取数据并在数据库笔记本环境中绘制（使用Python，Matplotlib，Bokeh，（Binder）该奖项反映了NSF的法定使命，并通过使用基金会的智力价值进行评估，更广泛的影响审查标准。

项目成果

Metaproteogenomic Profile of a Mesopelagic Adenylylsulfate Reductase: Course-Based Discovery Using the Ocean Protein Portal.

• DOI: 10.1021/acs.jproteome.3c00152
• 发表时间: 2023-09-01
• 期刊: JOURNAL OF PROTEOME RESEARCH
• 影响因子: 4.4
• 作者: Paoletti, Madeline M.;Fournier, Gregory P.;Dolan, Erin L.;Saito, Mak A.
• 通讯作者: Saito, Mak A.

Microbial functional diversity across biogeochemical provinces in the central Pacific Ocean.

• DOI: 10.1073/pnas.2200014119
• 发表时间: 2022-09-13
• 期刊: PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
• 影响因子: 11.1
• 作者: Saunders, Jaclyn K.;McIlvin, Matthew R.;Dupont, Chris L.;Kaul, Drishti;Moran, Dawn M.;Horner, Tristan;Laperriere, Sarah M.;Webb, Eric A.;Bosak, Tanja;Santoro, Alyson E.;Saito, Mak A.
• 通讯作者: Saito, Mak A.