EarthCubeIA: Collaborative Proposal: Building Interoperable Cyberinfrastructure (CI) at the Interface between Paleogeoinformatics and Bioinformatics

EarthCubeIA：协作提案：在古地理信息学和生物信息学之间的接口处构建可互操作的网络基础设施 (CI)

• 批准号: 1540994
• 负责人: Alison Smith
• 金额: $ 7.8万
• 依托单位: Kent State University
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2015
• 资助国家: 美国
• 起止时间: 2015-09-01 至 2017-08-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1540994&HistoricalAwards=false
• 关键词: EarthCubeIA; Collaborative; Proposal; Building; Interoperable

Paleontologists provide data about the past distribution and diversity of life. These data are useful both to geologists, because they can help determine the age of rocks, reconstruct past environments, and constrain models of the Earth system; and to biologists interested in the evolutionary history of organisms and the behavior of ecological systems during past global changes. Currently, data about fossils are dispersed across thousands of scientific publications, and dozens of small to large databases, only some of which are publicly available via the Internet. Even publicly available databases can be difficult to access because each stores different kinds of data with different conventions, requiring researchers to individually harmonize searches and their outputs. This project brings together six paleobiological databases so that they share a single set of Internet-based commands by which researchers and the public can easily access fossil records from all of Earth history. By coordinating with other emerging efforts in geological and biological data sharing, best practices, and protocols, we ensure that data will be freely available to all, enabling new scientific syntheses and discovery, more powerful educational opportunities, and general exploration of the history of life on Earth.The paleobiological sciences sit at the nexus between geosciences and the biosciences, with close interdependencies in both domains. Within the geosciences, information about the past spatiotemporal distribution of organisms, species, and assemblages of species is essential to a wide array of allied disciplines: to sedimentologists and economic geologists studying facies relationships and employing biostratigraphic controls for correlating rock strata, to structural geologists and geophysicists seeking biogeographic constraints on reconstructions of former tectonic plate positions, to paleoclimatologists extracting paleoclimatic signals from paleoecological data, and to earth system modelers seeking to understand how biospheric dynamics have shaped, and continue to shape, the history of the Earth-Life system. Within the biosciences, the fossil record is essential for understanding how contemporary ecological systems are shaped by historical legacies of slow-acting processes, for testing climate-driven models of species distribution and diversity that are being used to project the impacts of 21st century climate change, for constraining phylogenetic models of species divergence and rates of evolution, and for understanding the fundamental drivers of biodiversity (i.e. species extinctions and originations). In an era of global change, when stewarding biodiversity is an urgent societal concern, conservation biologists, global change ecologists, and earth system scientists are all looking to the past to study the behavior of the Earth-Life system during rapid transitions. Paleobiological data are currently served by a wide array of databases that vary in structure, composition, temporal scales, types of data and metadata. To conduct ?global? or holistic analyses of the paleobiological record it is necessary to retrieve data from a variety of these databases - requiring queries of each database to retrieve the types of data needed. The purpose of this project is to make six different paleobiological databases interoperable so that they can be accessed via a common Application Programming Interface (API) to query the data from these and other databases. Towards that end, five key records of North American Pleistocene lakes will be uploaded and become available through this integrative project. This project also will increase the interoperability between these paleobiological resources and contemporary databases of species distributions and diversity, enabling continuous time-series analyses (e.g., of biodiversity) from the beginning of life on earth to today. Integration of the paleobiological databases with databases of the stratigraphic record (Macrostrat) will enhance the value of both types of data. New R packages will facilitate retrieval and analysis of data from all of the databases. Finally, this proposal establishes a Paleobiological Data Consortium, consisting of leaders of cyberinfrastructure resources in the paleobiosciences and allied disciplines, with the goal of sharing best practices and protocols among the geoinformatic and bioinformatic communities.

古生物学家提供有关生命过去的分布和多样性的数据。这些数据对于地质学家来说都很有用，因为它们可以帮助确定岩石的年龄，重建过去的环境，并约束地球系统的模型；以及对过去全球变化期间生物体进化史和生态系统行为感兴趣的生物学家。目前，有关化石的数据分散在数千种科学出版物和数十个大大小小的数据库中，其中只有一些可以通过互联网公开获取。即使是公开可用的数据库也可能很难访问，因为每个数据库都存储具有不同约定的不同类型的数据，需要研究人员单独协调搜索及其输出。该项目汇集了六个古生物学数据库，以便它们共享一套基于互联网的命令，研究人员和公众可以通过这些命令轻松访问整个地球历史的化石记录。通过与地质和生物数据共享、最佳实践和协议方面的其他新兴努力协调，我们确保所有人都能免费获得数据，从而实现新的科学综合和发现、更强大的教育机会以及对生命历史的普遍探索古生物学是地球科学和生物科学的纽带，两个领域之间有着密切的相互依存关系。在地球科学中，有关生物体、物种和物种组合过去时空分布的信息对于一系列相关学科至关重要：对于研究相关系并利用生物地层控制来关联岩层的沉积学家和经济地质学家，对于构造地质学家和地球物理学家寻求对重建前构造板块位置的生物地理限制，古气候学家从古生态数据中提取古气候信号，以及寻求了解生物圈动力学如何塑造并继续塑造地球生命系统历史的地球系统建模者。在生物科学领域，化石记录对于理解缓慢作用过程的历史遗产如何塑造当代生态系统至关重要，对于测试气候驱动的物种分布和多样性模型（用于预测 21 世纪气候变化的影响）至关重要，用于限制物种分化和进化速率的系统发育模型，并了解生物多样性的基本驱动因素（即物种灭绝和起源）。在全球变化的时代，当管理生物多样性成为一个紧迫的社会问题时，保护生物学家、全球变化生态学家和地球系统科学家都在回顾过去，研究地球生命系统在快速转变期间的行为。目前，古生物学数据由各种数据库提供，这些数据库在结构、组成、时间尺度、数据类型和元数据方面各不相同。进行“全球”？或对古生物学记录进行整体分析，有必要从各种数据库中检索数据 - 需要查询每个数据库以检索所需的数据类型。该项目的目的是使六个不同的古生物学数据库具有互操作性，以便可以通过通用应用程序编程接口（API）访问它们，以查询这些数据库和其他数据库的数据。为此，北美更新世湖泊的五个关键记录将通过这个综合项目上传并提供。该项目还将提高这些古生物学资源与物种分布和多样性的当代数据库之间的互操作性，从而实现从地球生命诞生到今天的连续时间序列分析（例如生物多样性）。古生物学数据库与地层记录数据库（Macrostrat）的整合将提高两种类型数据的价值。新的 R 包将有助于从所有数据库中检索和分析数据。最后，该提案建立了一个古生物学数据联盟，由古生物科学和相关学科的网络基础设施资源的领导者组成，其目标是在地理信息学和生物信息学社区之间共享最佳实践和协议。