Collaborative Research: ABI Innovation: Connecting resources to enable large-scale biodiversity analyses

从复杂的数据集中提取生物知识，比如现在正在编译的数据集，需要集成强大的计算工具。计算生物学的最新发展以及丰富的新数据源为整合大量生物数据提供了新的机会。这种新数据和先进数据采集、管理和集成的完美风暴，为推动发现生物学中新的、复杂的模式提供了独特的机会。该项目将利用美国国家科学基金会在生物多样性工具上的可观投资，这些工具包括开放生命之树（该项目的框架）、Lifemapper（处理地理空间数据）、iDigBio（来自约10亿个博物馆标本的数据，这些标本携带了当地数据及其生态信息）和Arbor（允许从所提到的来源进行新的分析的计算机工具）。它将在这些工具之间创建急需的计算连接。然后，它将以这些新的联系和工具为基础，使生物多样性的新研究成为可能。这些联系将为研究人员提供快速合成数据集的机会，并利用它们来解决各种进化问题。该项目将建立的工具和基础设施将把物种关系与物种分布模型、气候预测、基因和特征联系起来。该项目将改变未来的生物多样性研究；它将提供强大工具的全球整合，这将允许在“下一代”生物多样性科学中发现新的数据驱动的发现。它将在生物信息学、数字化标本数据的使用和复杂分析（如生态分析）方面提供跨学科的博士后和研究生培训，为未来的生物多样性科学家做好准备。该项目将招收代表性不足的学生和女性，并开发一门本科课程，帮助培养学生掌握劳动力所需的综合技能（从野外生物学到计算生物学）。我们将进一步开发该模块，以供更广泛的课堂使用。我们将在佛罗里达大学（UF）为学生和博士后开设为期一周的年度课程，介绍所开发资源的使用。该项目将与佛罗里达大学的教育专家合作，制作视频材料，并为普通观众展示数字化标本数据的重要性，以及它们在气候变化研究中的应用。该项目将开发一个计算框架，将生物界使用的研究工具中的各种数据（物种关系树、形态学、生态学、化石、地理和气候）连接起来，包括开放生命之树，它将作为所有其他生物数据（特征、基因、基因组，特别是标本）连接的框架，以及Lifemapper、iDigBio和Arbor。使用大型的、高度多样化的植物群萨克斯花蒿将提供驱动这些工具开发所需的准确信息——一个涵盖形态学、生态学、地理学、化石和气候的综合数据集，为改进项目将开发的工具及其集成提供了一个测试案例。该项目将：1；在系统发育学、生态学、进化生物学、生物地理学和生物多样性科学的界面上促进具有广泛效用的新协同研究，使科学家能够解决有关表型和生态生物多样性、时空变化、群落聚集和跨景观和时间多样化的新问题。2. 通过将iDigBio、Open Tree of Life、Arbor和Lifemapper资源链接在一起，并通过多个访问点（例如，与Arbor和Lifemapper相关的现有工具）以各种适当的格式提供这些资源，从而提高它们的可见性和可访问性。3. 为大型进化支（Saxifragales）开发一个完整的、多方面的物种水平数据集，这不仅将填补ToL上的这一分支，而且将为科学界探索提供巨大的实用资源。4. 演示iDigBio， Open Tree， Lifemapper和Arbor资源的实用性，使用接近完整的Saxifragales采样进行全面分析，为此我们将添加以下数据层：DNA序列，形态学，化石，本体，地理空间和环境数据，数字化代金券标本，并链接到生命百科全书（EOL）。该项目将：1)在生物信息学、大规模系统发育重建、数字化标本数据的使用和复杂的后树分析（如生态位建模、生态位多样化）方面提供跨学科的博士后和研究生培训，为未来的综合生物多样性科学家做好准备；2)招收代表性不足的学生和女性；3)开发利用野外采集、植物标本馆标本、数字化数据（iDigBio）和生态位模型（气候变化）的本科课程；4)每年为学生和博士后开设为期一周的课程（UF），学习如何利用所产生的资源；5)制作视频材料，并为普通观众协调展示数字化标本数据的重要性，它们在模拟生态位随时间演变和对气候变化的影响方面的效用。该项目将提供一个平台，使其他研究人员能够在其他小组中采用同样的综合方法。它还将建立与EOL的网络链接，并1)建立物种页面；2)将形态和其他性状数据放在TraitBank上，使这些数据广泛可用；3)与EOL和iNaturalist合作，吸引公民科学家。

Extracting biological knowledge from complex datasets such as those now being compiled requires integration of powerful computational tools. Recent developments in computational biology as well as rich new data sources provide novel opportunities for integrating massive amounts of biological data. This perfect storm of new data and advanced data acquisition, management, and integration afford the unique opportunity to drive the discovery of new, complex patterns in biology. The project will leverage NSF's considerable investment in biodiversity tools provided by Open Tree of Life (the framework for the project), Lifemapper (which handles geospatial data), iDigBio (data from ~1 billion museum specimens that carry locality data and their ecological information), and Arbor (computer tools that permit new analyses from the sources noted). It will create much needed computational connections among these tools. It will then build upon these new linkages and tools, enabling novel research in biodiversity. These linkages will provide researchers the opportunity to rapidly synthesize datasets and use them to address diverse evolutionary questions. The tools and infrastructure the project will build will connect species relationships with species distribution models, climate projections, genes and traits. The project will transform future studies of biodiversity; it will provide a global integration of powerful tools that will permit new data-driven discovery in "next generation" biodiversity science. It will provide interdisciplinary post-doc and graduate student training in bioinformatics, use of digitized specimen data, and complex analyses (e.g. ecological analyses), preparing the biodiversity scientists of the future. The project will recruit underrepresented students and women and develop an undergrad course that will help train students with the integrative skills (field biology to computational biology) needed in the workforce. We will further develop this module for wider classroom use. We will introduce an annual week-long course at University of Florida (UF) for students and post-docs on the use of the resources developed. With education specialists at UF, the project will produce video materials and a coordinated display for general audiences on the importance of digitized specimen data, and their utility for studies of climate change. The project will develop a computational framework linking diverse data (trees of species relationships, morphology, ecology, fossils, geography, and climate) across research tools used by the biological community, including Open Tree of Life, which will serve as the framework to which all other biological data - traits, genes, genomes, and especially specimens - will be linked, as well as Lifemapper, iDigBio, and Arbor. Use of the large, hyper-diverse plant group Saxifragales will provide precisely what is needed to drive the development of these tools--a comprehensive dataset that covers morphology, ecology, geography, fossils, and climate provides a test case for refining the tools the project will develop and their integration. The project will: 1. Facilitate new synergistic research of broad utility at the interface of phylogenetics, ecology, evolutionary biology, biogeography and biodiversity science, enabling scientists to address novel questions relating phenotypic and ecological biodiversity, spatial and temporal variation, community assembly, and diversification across landscapes and through time. 2. Increase visibility and accessibility of iDigBio, Open Tree of Life, Arbor, and Lifemapper resources by linking them together and making them available through multiple access points (e.g., pre-existing tools associated with Arbor and Lifemapper) in a variety of appropriate formats. 3. Develop a complete, multifaceted species-level dataset for a large clade (Saxifragales), which will not only fill in this branch on the ToL, but will produce a resource of great utility for the scientific community to explore. 4. Demonstrate the utility of iDigBio, Open Tree, Lifemapper, and Arbor resources with a comprehensive analysis using near complete sampling of Saxifragales, for which we will add the following data layers: DNA sequences, morphology, fossils, ontologies, geospatial and environmental data, digitized voucher specimens, and link to the Encyclopedia of Life (EOL). The project will: 1) provide interdisciplinary post-doc and graduate student training in bioinformatics, large-scale phylogeny reconstruction, use of digitized specimen data, and complex post-tree analyses (e.g. niche modeling, niche diversification), preparing the integrative biodiversity scientists of the future; 2) recruit underrepresented students and women; 3) developed an undergrad course that uses field collection, herbarium specimens, digitized data (iDigBio), and niche modeling (with climate change; 4) introduce an annual week-long course (UF) for students and post-docs on the use of the resources produced; 5) produce video materials and a coordinated display for general audiences on the importance of digitized specimen data, their utility for modeling niche evolution through time and implications for climate change. The project will provide a platform that will enable other researchers to take the same integrated approach in other groups. It will also establish web links to EOL and 1) build species pages; 2) place morphological and other trait data on TraitBank, making these widely available; 3) work with EOL and iNaturalist to engage citizen scientists.