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.

生命的时间尺度描述了物种从共同祖先分化的时间，它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。基因组学和计算的进步完善了这个时间尺度，导致发布了数千个按时间缩放的进化树，称为时间树。该项目支持TimeTree的开发和扩展，TimeTree是一个开源的统一数据库，可将这些数据合成为全球生命时间树。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线以及任何群体或自定义物种列表的可导出时间树。地质和天文历史中的事件，例如小行星撞击、氧气水平和太阳光度，与物种时间树和时间线整合到同一时间尺度中，促进分子生物学、保护和医学等领域的跨学科研究和应用。新的时间树资源将实现新的算法、工具和应用程序编程接口，以加速、改进和提高时间树管理和数据挖掘的效率。它将包含一个专为 K-12 和大学生设计的新在线教育组件，包括展示构建时间树的原理、模型和方法的作业。其新的图形界面将专门针对非科学家使用进行增强，并将包括吸引利益相关者社区参与的培训工具，从而获得更多用户反馈。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，同时也作为一种易于使用的教​​育和推广工具。 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，从而有助于假设的制定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，这将产生有史以来最大的生命时间树。新颖的超级时间树估计方法的结合将产生更快速和精确的合成，提供更频繁和更频繁的超级时间树自动组装和数据库更新。例如，将采用深度学习方法来识别新发表的时间树研究并将其快速合并到数据库中。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来连接科学学科，简化复杂时间树数据的使用。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。应用程序编程接口的进步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交互，为它们提供分歧时间和衍生指标。 TimeTree 还将包括分析实用程序，例如随时间变化的谱系和多样化图，因此研究人员可以立即看到任何群体的结果。为了确保长期可持续性，同时限制维护成本，将集成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，超级时间树、相关研究数据和源代码均可轻松下载。该奖项反映了 NSF 的法定使命，并通过使用基金会的智力优点和更广泛的影响审查标准进行评估，被认为值得支持。