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

从复杂的数据集中提取生物学知识，比如现在正在汇编的那些，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来源为整合海量生物数据提供了新的机会。这场新数据的完美风暴以及先进的数据获取、管理和集成为推动发现新的、复杂的生物学模式提供了独特的机会。该项目将利用NSF在生物多样性工具方面的大量投资，这些工具由Open Tree of Life(该项目的框架)、Lifemapper(处理地理空间数据)、iDigBio(来自携带当地数据及其生态信息的约10亿个博物馆标本的数据)和Arbor(允许从所述来源进行新的分析的计算机工具)提供。它将在这些工具之间建立亟需的计算连接。然后，它将建立在这些新的联系和工具上，使生物多样性方面的新研究成为可能。这些联系将为研究人员提供快速合成数据集并使用它们来解决各种进化问题的机会。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。该项目将改变未来对生物多样性的研究；它将提供强大工具的全球集成，使“下一代”生物多样性科学中的新数据驱动发现成为可能。它将提供生物信息学、数字化标本数据的使用和复杂分析(例如生态分析)方面的跨学科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妇女，并开发一门本科生课程，帮助培养学生具备劳动力所需的综合技能(从田野生物学到计算生物学)。我们将进一步开发此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，介绍如何使用所开发的资源。该项目将与密歇根大学的教育专家一起制作视频材料，并向普通观众协调展示数字化标本数据的重要性及其对气候变化研究的作用。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、生态学、化石、地理和气候树)联系起来，包括开放生命树，这将作为连接所有其他生物数据--特征、基因、基因组，特别是标本--以及Lifemapper、iDigBio和Arbor的框架。使用大型、超多样化的植物群Saxifradales将准确地提供推动这些工具开发所需的东西--一个涵盖形态、生态、地理、化石和气候的综合数据集，为完善该项目将开发的工具及其集成提供了测试案例。该项目将：1.促进在系统发生学、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具有广泛实用价值的新的协同研究，使科学家能够解决与表型和生态生物多样性、空间和时间变化、群落聚集以及不同景观和时间的多样性有关的新问题。2.将iDigBio、Open Tree of Life、Arbor和Lifemapper资源链接在一起，并以各种适当的格式通过多个接入点(例如，与Arbor和Lifemapper相关的现有工具)提供，从而提高iDigBio、Open Tree of Life、Arbor和Lifemapper资源的可见性和可及性。3.开发一套完整的、多方面的物种级大型分支数据集(Saxifradales)，这不仅将填补TOL上的这一分支，而且将产生一个非常有用的资源，供科学界探索。4.通过使用近乎完整的虎耳目样本进行全面分析，展示iDigBio、Open Tree、Lifemapper和Arbor资源的效用，我们将为其添加以下数据层：DNA序列、形态、化石、本体、地理空间和环境数据、数字化凭证样本，以及到生命百科全书(EOL)的链接。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树后分析(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)招募代表性不足的学生和妇女；3)开发一个使用实地采集、标本标本馆标本、数字化数据(IDigBio)和生态位建模(与气候变化有关)的本科生课程；4)为学生和博士后引入为期一周的年度课程(UF)，介绍如何利用所产生的资源；5)制作视频材料，并向普通观众协调展示数字化标本数据的重要性、其对模拟生态位随时间演变的作用以及对气候变化的影响。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取相同的综合方法。它还将建立到EOL的网络链接，并1)建立物种页面；2)将形态和其他特征数据放在TraitBank上，使其广泛可用；3)与EOL和iNaturist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.