Collaborative Research: Aggregating and Repurposing Phylogeographic Data

合作研究：系统发育地理学数据的汇总和重新利用

• 批准号: 1911293
• 负责人: Tara Pelletier
• 金额: $ 12.88万
• 依托单位: Radford University
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2019
• 资助国家: 美国
• 起止时间: 2019-07-01 至 2024-06-30
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1911293&HistoricalAwards=false
• 关键词: Collaborative; Research; Aggregating; Repurposing; Phylogeographic

Patterns of genetic diversity within species contain information about the history of the species, including how it responded to historical climate change and the degree of isolation of its populations. For this reason, thousands of scientific projects have been funded by federal agencies with the goal of investigating the genetic diversity within a particular focal species. The data from these efforts, including the genetic data collected from a given specimen and the physical location from which that specimen was collected, are a valuable resource and typically are made available to other researchers upon publication of the study. However, since different types of data are stored in different databases, it can be difficult to access and assemble these data for reanalysis. This project will build a database that (i) aggregates data from different sources, (ii) connects these data at the specimen level, and (iii) includes customized web-based apps that will enable these data to be analyzed in a variety of ways. This project will benefit the public by increasing an understanding of conservation risks that may be faced by species in particular habitats and by facilitating comparisons across species. This project will facilitate two types of scientific research: large meta-analyses of thousands of species that can address classic questions in evolutionary biology, ecology, and conservation biology on a global scale, and student- or citizen- science based investigations that will introduce a broad range of people to the analysis of genetic data for species of interest.More than 40,000 phylogeographic investigations have been published to date, each collecting genetic data from hundreds of samples. Despite millions of data points, few meta-analyses have been conducted because the synthesis of results across hundreds of studies, each using different methods and forms of analysis, is a daunting and time-consuming task. It is more efficient to proceed by repurposing existing data and using automated data analysis. While the editorial policies of most journals now require data to be made available upon publication, the utility of these data are limited because genetic data and geographic sampling localities are typically published in separate databases that are not easily linked. This project will: (i) provide a series of web-based tools to connect accessions in genetic databases such as GenBank with geographic information on databases such as GBIF; (ii) expand data analysis pipelines that can be used to automate phylogeographic analyses from thousands of species on a global scale; (iii) promote these tools to the broader community of organismal biologists; and (iv) work with High School teachers and undergraduate students to develop educational modules that utilize this project's software. The primary deliverable will be Phylogatr, a database and web application built by professional software engineers via a partnership with the Ohio Supercomputer Center. The project will enhance the value of existing data via the creation of software and web-based tools that enable these data to be recycled and reanalyzed.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.

物种内遗传多样性的模式包含有关该物种历史的信息，包括它对历史气候变化的反应以及其种群的隔离程度。因此，成千上万的科学项目是由联邦机构资助的，目的是研究特定焦点物种内的遗传多样性。这些努力的数据，包括从给定标本收集的遗传数据以及收集该标本的物理位置，是一种宝贵的资源，通常在发表研究后向其他研究人员提供。但是，由于不同类型的数据存储在不同的数据库中，因此很难访问和组装这些数据进行重新分析。该项目将构建一个数据库，该数据库（i）从不同来源汇总数据，（ii）在样品级别连接这些数据，并且（iii）包括自定义的基于Web的应用程序，这些应用程序将使这些数据能够以多种方式进行分析。该项目将通过增加对特定栖息地物种可能面临的保护风险的了解并促进跨物种的比较来使公众受益。该项目将促进两种类型的科学研究：数千种物种的大型荟萃分析可以在全球范围内解决进化生物学，生态学和保护生物学中的经典问题，以及基于学生或公民科学的研究，这些研究将向遗传学的遗传数据分析，以分析属于遗传学的遗传数据的遗传数据，以分析遗传学的数量超过遗传学的研究，以收集遗传学的数据。尽管有数百万个数据点，但很少进行荟萃分析，因为数百种研究的结果的综合，每种研究都使用不同的方法和分析形式，这是一项令人生畏且耗时的任务。通过重新利用现有数据并使用自动数据分析来进行更有效的效率。尽管现在大多数期刊的编辑策略都需要在出版时提供数据，但这些数据的实用性受到限制，因为遗传数据和地理采样位置通常在不容易链接的单独数据库中发布。该项目将：（i）提供一系列基于Web的工具，以将GenBank等基因数据库中的配件与GBIF等数据库中的地理信息联系起来； （ii）扩展数据分析管道，可用于在全球范围内从数千种物种中自动化植物地理分析； （iii）将这些工具推广到更广泛的有机生物学家社区； （iv）与高中教师和本科生一起开发利用该项目软件的教育模块。主要可交付的是PhyloGATR，这是专业软件工程师通过与俄亥俄州超级计算机中心的合作伙伴关系构建的数据库和Web应用程序。该项目将通过创建软件和基于Web的工具来增强现有数据的价值，从而使这些数据被回收并重新分析。该奖项反映了NSF的法定任务，并被认为是值得通过基金会的智力优点和更广泛影响的评估来通过评估来支持的。