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Collaborative Research: ABI Innovation: FuTRES, an Ontology-Based Functional Trait Resource for Paleo- and Neo-biologists

合作研究：ABI 创新：FuTRES，为古生物学家和新生物学家提供的基于本体的功能性状资源

基本信息

批准号：
1759882
负责人：
Raymond Bernor
金额：
$ 27.47万
依托单位：
Howard University
依托单位国家：
美国
项目类别：
Standard Grant
财政年份：
2018
资助国家：
美国
起止时间：
2018-06-01 至 2024-05-31
项目状态：
已结题

来源：
https://www.nsf.gov/awardsearch/showAward?AWD_ID=1759882&HistoricalAwards=false
关键词：
Collaborative Research ABI Innovation FuTRES

项目摘要

Physical characteristics of animals can help determine which ones survive and flourish, especially in a changing environment. These characteristics, also known as functional traits, include features such as length, height, shape, weight, growth rate, sex, and reproductive state. Studying these traits provides insights into how communities of different types of animals come together and how species and communities respond to changes in their environment over time, which is critical for conservation efforts. However, very little information about functional traits is available, and what is available is difficult to combine with other data. How these traits are influenced by environmental changes - such as climate change, pollution, urbanization and human predation - and how they shift over longer timescales are poorly understood, and the need for this information is outstripping the speed with which scientists can collect these data. Digitized collections of animals representing life from the past two million years contain a treasure trove of information about these individuals' functional traits, but these data are stored in multiple places and in different formats. Researchers may have recorded dates differently, for example, or used a variety of terms to describe a single physical feature. Making these data widely available in standardized formats could help scientists study changes in functional traits through time, linking their observations of traits of modern animals to those from fossil and archaeological records. The Functional Trait Resource for Environmental Studies (FuTRES) project will gather trait data from digitized records; to engage communities of researchers to make these data available, standardized, and useable; and to develop a more complete workflow for using these data in research. Functional trait data have revolutionized ecology and are transforming paleontology, but acquiring them requires extensive labor, not only in measuring traits but in managing and communicating the resulting data. When trait data are lacking, researchers substitute average values, or other characteristics like behavioral or dietary categories. These substitutes - assigned at the species level - obscure intraspecific changes in traits. FuTRES fills the clear need for informatics tools that give researchers access to existing trait data and a place to store new data as they are generated. FuTRES is assembling a varied collection of existing trait data, building a pipeline that converts data to an integrated, semantically enriched form, and developing an Application Programming Interface (API) and web platform to serve the data. One of the key innovations of FuTRES is the use of ontologies, an information science approach that creates computer-readable definitions of traits and describes the interrelationships of traits, organisms, collecting events, and other entities. In this way, FuTRES will make functional trait data searchable through reference to time, space, and vertebrate anatomy. FuTRES will also provide access to trait data via popular data portals (e.g., VertNet) and software such as R, opening the data to scientists in biodiversity and other domains. The toolkit will be tested with mammalian use cases that leverage the massive scale of the unlocked data. In sum, newly created access mechanisms and tools will provide novel approaches for analyses of trait variation across space and time, providing researchers in disparate fields discovery capabilities for relevant data that would otherwise have been invisible to them.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.

动物的身体特征可以帮助决定哪些动物存活和繁衍，特别是在不断变化的环境中。这些特征也称为功能特征，包括长度、身高、形状、体重、生长速度、性别和生殖状态等特征。研究这些特征可以深入了解不同类型动物的群落是如何聚集在一起的，以及物种和群落如何随着时间的推移对环境的变化做出反应，这对保护工作至关重要。然而，关于功能特征的信息很少，而且现有的信息很难与其他数据结合起来。这些特征如何受到气候变化、污染、城市化和人类捕食等环境变化的影响，以及它们如何在更长的时间尺度上发生变化，人们还知之甚少，而且对这些信息的需求正在超过科学家收集这些数据的速度。过去200万年来代表生命的动物的数字化集合包含了关于这些人的功能特征的宝贵信息，但这些数据存储在多个地方，并以不同的格式存储。例如，研究人员可能记录了不同的日期，或者使用了不同的术语来描述单一的物理特征。以标准化格式广泛提供这些数据，可以帮助科学家研究功能特征随时间的变化，将他们对现代动物特征的观察与化石和考古记录中的观察联系起来。环境研究功能特性资源(FuTRES)项目将从数字化记录中收集特性数据；让研究人员社区参与，使这些数据可用、标准化和可用；并为在研究中使用这些数据开发更完整的工作流程。功能特征数据彻底改变了生态学，并正在改变古生物学，但获取这些数据需要大量的劳动，不仅是在测量特征方面，而且在管理和交流由此产生的数据方面。当缺乏特征数据时，研究人员会替换平均值，或行为或饮食类别等其他特征。这些替代品--在物种层面上分配--掩盖了种内性状的变化。FuTRES满足了对信息学工具的明显需求，这些工具使研究人员能够访问现有的特征数据，并在生成新数据时提供存储它们的位置。FuTRES正在汇集各种现有的性状数据，建立一条将数据转换为集成的、语义丰富的形式的管道，并开发应用程序编程接口(API)和网络平台来提供数据。FuTRES的关键创新之一是使用本体论，这是一种信息科学方法，创建了计算机可读的特征定义，并描述了特征、有机体、收集事件和其他实体之间的相互关系。通过这种方式，FuTRES将通过参考时间、空间和脊椎动物解剖学来搜索功能特征数据。FuTRES还将通过流行的数据门户(如VertNet)和R等软件提供对特征数据的访问，向生物多样性和其他领域的科学家开放数据。该工具包将通过利用海量解锁数据的哺乳动物用例进行测试。总之，新创建的访问机制和工具将为分析跨空间和时间的特征变异提供新的方法，为不同领域的研究人员提供发现原本看不见的相关数据的能力。这一奖项反映了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。

项目成果

期刊论文数量（12）

专著数量（0）

科研奖励数量（0）

会议论文数量（0）

专利数量（0）

Mammal Biochronology (Land Mammal Ages) Around the World From Late Miocene to Middle Pleistocene and Major Events in Horse Evolutionary History

DOI：
10.3389/fevo.2019.00278
发表时间：
2019-07
期刊：
Frontiers in Ecology and Evolution
影响因子：
3
作者：
L. Rook;R. Bernor;L. Avilla;O. Cirilli;L. Flynn;A. Jukar;William H. Sanders;E. Scott;Xiao-Mei Wang
通讯作者：
L. Rook;R. Bernor;L. Avilla;O. Cirilli;L. Flynn;A. Jukar;William H. Sanders;E. Scott;Xiao-Mei Wang

Evolution of Early Equus in Italy, Georgia, the Indian Subcontinent, East Africa and the Origins of African Zebras. Frontiers in Ecology and Evolution

意大利、格鲁吉亚、印度次大陆、东非早期马科动物的进化和非洲斑马的起源。