Bridging fields and expanding research opportunities with the timescale of life

弥合不同领域并扩大研究机会与生命的时间尺度

• 批准号: 2318917
• 负责人: Stephen Hedges
• 金额: $ 100万
• 依托单位: Temple University
• 依托单位国家: 美国
• 项目类别: Continuing Grant
• 财政年份: 2024
• 资助国家: 美国
• 起止时间: 2024-02-15 至 2027-01-31
• 项目状态: 未结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=2318917&HistoricalAwards=false
• 关键词: Bridging; fields; expanding; research; opportunities

The timescale of life, delineating when species diverged from common ancestors, serves as a framework for understanding biology and is fundamental context for other fields of science such as geology, chemistry, and biomedicine. The advancements in genomics and computing have refined this timescale, resulting in the publication of thousands of evolutionary trees scaled to time, known as timetrees. This project supports the development and expansion of TimeTree, an open-source and unified database that synthesizes these data into a global timetree of life. Users can obtain the divergence time of any two species, a timeline showing all evolutionary splits back in time, and exportable timetrees of any group or from a custom list of species. Events in geological and astronomical history, such as asteroid impacts, oxygen levels, and solar luminosity, are integrated into the same timescale with species timetrees and timelines, facilitating interdisciplinary research and applications in areas like molecular biology, conservation, and medicine. The new TimeTree resource will implement new algorithms, tools, and application programming interfaces to speed, improve, and increase the efficiency of timetree curation and data mining. It will have a new online educational component designed for K-12 and college students, including assignments that demonstrate the principles, models, and methods for building timetrees. Its new graphical interface will be enhanced specifically for use by non-scientists and will include training tools to engage stakeholder communities, allowing for more user feedback. This expanded TimeTree resource aims to stimulate and accelerate research and discovery across diverse scientific disciplines while also serving as a simple-to-use tool for education and outreach. The enhancements in TimeTree will enable researchers worldwide to query, retrieve, visualize, and explore evolutionary patterns, thus aiding hypothesis formulation and augmenting both scientific and societal returns on investments in basic biological research. The newly developed approaches and computational infrastructure will have greater efficiency that will result in the largest timetree of life ever assembled. The incorporation of a novel super-timetree estimation method will yield a more rapid and precise synthesis, affording greater and frequent automated assembly of the super-timetree and updates of the database. For example, a deep-learning approach will be employed to identify and incorporate newly published timetree studies quickly into the database. Beyond these core functionalities, TimeTree aims to bridge scientific disciplines by developing and integrating new tools for data analytics and mining, streamlining the use of complex timetree data. A specialized tool will allow users to access all associated study data for the node of interest, perform analyses on those data, and retrieve the data and results for further offline analyses. Advances in the application programming interface will offer a broader array of functionalities, such as serving commonly used biodiversity metrics. Innovative widgets will interface with other databases to provide them with divergence times and derivative metrics. TimeTree also will also include analytical utilities, such as lineages-through-time and diversification plots, so researchers may immediately see the results for any group. To ensure long-term sustainability while limiting maintenance costs, automated tools for processing and curating published timetrees will be integrated. TimeTree will remain fully open access, with the super-timetree, associated study data, and source code being readily downloadable.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.

生命的时间尺度，描绘了物种从共同祖先分化出来的时间，是理解生物学的框架，也是地质学、化学和生物医学等其他科学领域的基本背景。基因组学和计算技术的进步已经完善了这个时间尺度，导致成千上万的进化树按时间缩放，称为时间树。该项目支持TimeTree的开发和扩展，TimeTree是一个开源且统一的数据库，可将这些数据合成为全球生命时间表。用户可以获得任何两个物种的分歧时间，显示所有进化分裂的时间轴，以及任何群体或自定义物种列表的可导出时间树。地质和天文历史上的事件，如小行星撞击，氧气水平和太阳光度，被整合到同一个时间尺度与物种时间树和时间线，促进跨学科的研究和应用领域，如分子生物学，保护和医学。新的TimeTree资源将实现新的算法、工具和应用程序编程接口，以加速、改进和提高数据树管理和数据挖掘的效率。它将为K-12和大学生设计一个新的在线教育组件，包括演示构建时间树的原理，模型和方法的作业。其新的图形界面将得到加强，专门供非科学家使用，并将包括培训工具，以吸引利益攸关方社区的参与，从而获得更多的用户反馈。这个扩展的TimeTree资源旨在刺激和加速跨不同科学学科的研究和发现，同时也作为教育和推广的简单易用的工具。TimeTree的增强功能将使世界各地的研究人员能够查询、检索、可视化和探索进化模式，从而帮助提出假设，并增加基础生物学研究投资的科学和社会回报。新开发的方法和计算基础设施将具有更高的效率，这将导致有史以来最大的生命树组装。一种新的超级树估计方法的结合将产生一个更快速和精确的合成，提供更大和更频繁的自动组装的超级树和数据库的更新。例如，将采用深度学习方法来识别新发表的研究成果并将其快速纳入数据库。除了这些核心功能之外，TimeTree还旨在通过开发和集成新的数据分析和挖掘工具，简化复杂数据树数据的使用，从而弥合科学学科。专用工具将允许用户访问感兴趣节点的所有相关研究数据，对这些数据进行分析，并检索数据和结果以进行进一步的离线分析。应用程序编程接口方面的进展将提供更广泛的功能，例如提供常用的生物多样性指标。创新的小部件将与其他数据库接口，为他们提供分歧时间和衍生指标。TimeTree还将包括分析实用程序，例如时间线和多样化图，因此研究人员可以立即看到任何组的结果。为了确保长期可持续性，同时限制维护成本，将整合用于处理和管理已发布时间树的自动化工具。TimeTree将保持完全开放访问，超级时间表、相关研究数据和源代码均可随时下载。该奖项反映了NSF的法定使命，并通过使用基金会的知识价值和更广泛的影响力进行评估而被认为值得支持。审查标准。