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

基本信息

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

项目摘要

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.

该项目旨在扩展海洋蛋白质门户 (OPP) 的功能，用于海洋生物化学的研究和教育。海洋蛋白质门户原型的设计目的是让广大科学家和学生找到以下问题的答案：1) “我感兴趣的蛋白质在海洋中在哪里”，2）“谁通过最不常见的祖先分析制造了蛋白质？”，以及 3）“有多少？”通过使海洋蛋白质数据集可供广泛的访问和搜索。领域社区，包括生物化学海洋学家、地球生物学家、微生物学家、生物化学家和生物无机化学家的帮助，我们对海洋和微生物生物化学的了解将得到提高。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，从而提高对环境变化的认识。门户致力于捕获、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为海洋宏蛋白质组社区内的社区建设做出贡献。将通过与教师和教授合作，为学生创建学习化学反应的教育模块，激励不断努力提高数据质量和标准。该项目的技术目标包括对海洋蛋白质门户的具体改进，例如扩展搜索功能，增加服务新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，为机器可访问的搜索创建API，进一步与外部数据连接并增强可视化功能，创建可重复和可引用的搜索OPP 向知识图谱的转变将进一步促进与海洋生态学以外领域的联系，因为该图谱还将链接到环境科学和生物学中的其他数据资源。，OPP 知识图还将提供对计算机科学领域有用的数据结构，因为该数据结构可立即用于机器学习和人工智能的应用，从而提高新型机器辅助科学发现的潜力。研究人员将开展教程。（虚拟或在人）让参与者了解海洋元蛋白质组学数据类型、如何使用 OPP 接口以及如何从 OPP 中提取数据并在 Jupyter Notebook 环境中绘制数据（使用 Python、Matplotlib、Bokeh 和 Binder）。该奖项反映了通过使用基金会的智力价值和更广泛的影响审查标准进行评估，NSF 的法定使命被认为值得支持。

项目成果

期刊论文数量（4）

专著数量（0）

科研奖励数量（0）

会议论文数量（0）

专利数量（0）

Development of an Ocean Protein Portal for Interactive Discovery and Education

开发用于互动发现和教育的海洋蛋白质门户

DOI：
10.1021/acs.jproteome.0c00382
发表时间：
2021-01
期刊：
Journal of Proteome Research
影响因子：
4.4
作者：
Saito, Mak A.;Saunders, Jaclyn K.;Chagnon, Michael;Gaylord, David A.;Shepherd, Adam;Held, Noelle A.;Dupont, Christopher;Symmonds, Nicholas;York, Amber;Charron, Matthew;et al
通讯作者：
et al

METATRYP v 2.0: Metaproteomic Least Common Ancestor Analysis for Taxonomic Inference Using Specialized Sequence Assemblies—Standalone Software and Web Servers for Marine Microorganisms and Coronaviruses

METATRYP v 2.0：使用专门的序列组件进行分类推理的元蛋白质组最不常见祖先分析——海洋微生物和冠状病毒的独立软件和网络服务器

DOI：
10.1021/acs.jproteome.0c00385
发表时间：
2020-11
期刊：
Journal of Proteome Research
影响因子：
4.4
作者：
Saunders, Jaclyn K.;Gaylord, David A.;Held, Noelle A.;Symmonds, Nicholas;Dupont, Christopher L.;Shepherd, Adam;Kinkade, Danie B.;Saito, Mak A.
通讯作者：
Saito, Mak A.

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

中层腺苷酸硫酸还原酶的宏蛋白质组谱：使用海洋蛋白质门户进行基于课程的发现

DOI：
10.1021/acs.jproteome.3c00152
发表时间：
2023-08
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

太平洋中部生物地球化学区的微生物功能多样性

DOI：
10.1073/pnas.2200014119
发表时间：
2022-09-13
期刊：
Proceedings of the National Academy of Sciences
影响因子：
0
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.