Bridging fields and expanding research opportunities with the timescale of life

生命的时间尺度，描绘了物种何时与共同祖先背道而驰，是理解生物学的框架，也是其他科学领域(如地质学、化学和生物医学)的基本背景。基因组学和计算机技术的进步完善了这一时间尺度，导致了数千棵随时间变化的进化树的出版，这些进化树被称为时间表。该项目支持TimeTree的开发和扩展，TimeTree是一个开放源码的统一数据库，将这些数据综合成全球生命时间表。用户可以获得任何两个物种的分化时间，显示所有进化分裂的时间线，以及任何群体或自定义物种列表的可输出时间表。地质学和天文学历史上的事件，如小行星撞击、氧气水平和太阳光度，与物种时间表和时间线整合到同一时间尺度中，促进了分子生物学、环境保护和医学等领域的跨学科研究和应用。新的TimeTree资源将实施新的算法、工具和应用程序编程接口，以加快、改进和提高时间表管理和数据挖掘的效率。它将有一个为K-12和大学生设计的新的在线教育部分，包括演示制定时间表的原则、模型和方法的作业。其新的图形界面将得到改进，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，允许更多用户反馈。这一扩展的TimeTree资源旨在刺激和加速跨不同科学学科的研究和发现，同时也是一种简单易用的教育和推广工具。TimeTree的增强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，从而帮助形成假设，并增加基础生物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时间表。采用一种新的超级时刻表估计方法将产生更快速和更精确的综合，从而更频繁地自动汇编超级时刻表和更新数据库。例如，将采用深度学习方法来确定新公布的时间表研究，并将其迅速纳入数据库。除了这些核心功能之外，TimeTree的目标是通过开发和集成用于数据分析和挖掘的新工具，简化复杂时间表数据的使用，从而在科学学科之间架起一座桥梁。一个专门的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。应用程序编程接口的进步将提供更广泛的功能，例如服务于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，为它们提供分歧时间和派生指标。Timetree还将包括分析工具，如随时间推移的谱系和多样化曲线图，因此研究人员可以立即看到任何群体的结果。为确保长期可持续性，同时限制维护费用，将整合处理和管理已公布时间表的自动化工具。Timetree将保持完全开放获取，超级时间表、相关研究数据和源代码随时可供下载。该奖项反映了NSF的法定使命，并通过使用基金会的智力优势和更广泛的影响审查标准进行评估，被认为值得支持。

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.