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

EarthCube IA：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: 1541002
• 负责人: John Williams
• 金额: $ 22.88万
• 依托单位: University of Wisconsin-Madison
• 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 2018-08-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1541002&HistoricalAwards=false
• 关键词: EarthCube; IA; Collaborative; Proposal; Building

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过去生命分布和多样性的数据。这些数据对地质学家和生物学家都很有用，因为它们可以帮助确定岩石的年龄，重建过去的环境，并限制地球系统的模型;生物学家对生物的进化历史和生态系统在过去全球变化中的行为感兴趣。目前，有关化石的数据分散在数千种科学出版物和数十个小型到大型的数据库中，其中只有一部分是通过互联网公开的。即使是公开的数据库也很难访问，因为每个数据库都存储不同类型的数据，使用不同的约定，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，使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地球历史上的化石记录。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，我们确保数据将免费提供给所有人，从而实现新的科学综合和发现，更强大的教育机会，以及对地球生命历史的全面探索。古生物科学位于地球科学和生物科学之间的纽带，在这两个领域中相互依存。在地球科学中，关于生物、物种和物种组合的过去时空分布的信息对广泛的相关学科至关重要：对于研究相关系和使用生物地层控制来关联岩层的沉积学家和经济地质学家，对于寻求对以前构造板块位置的重建的地理限制的构造地质学家和地质学家，从古生态数据中提取古气候信号的古气候学家，以及试图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。在生物科学中，化石记录对于理解当代生态系统是如何被缓慢作用过程的历史遗产所塑造，对于测试气候驱动的物种分布和多样性模型（用于预测21世纪世纪气候变化的影响），对于限制物种分化和进化速率的系统发育模型，以及理解生物多样性的基本驱动因素（即物种的灭绝和起源）。在一个全球变化的时代，当管理生物多样性是一个紧迫的社会问题，保护生物学家，全球变化生态学家和地球系统科学家都在寻找过去研究地球生命系统在快速转变过程中的行为。古生物学数据目前由各种各样的数据库提供服务，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。指挥？全球化？或古生物学记录的整体分析，有必要从各种各样的这些数据库中检索数据-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，以便可以通过一个通用的应用程序编程接口（API）访问这些数据库和其他数据库中的数据。为此，将通过这一综合项目上传并提供北美更新世湖泊的五个关键记录。该项目还将提高这些古生物资源与当代物种分布和多样性数据库之间的互操作性，从而能够进行连续的时间序列分析（例如，生物多样性（从地球上生命的开始到今天）。将古生物学数据库与地层记录数据库（Macrostrat）结合起来将提高这两类数据的价值。新的R软件包将有助于从所有数据库检索和分析数据。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领导人组成，其目标是在地球信息学和生物信息学社区之间分享最佳实践和协议。

项目成果

The EarthLife Consortium API: an extensible, open-source service for accessing fossil data and taxonomies from multiple community paleodata resources

EarthLife Consortium API：一种可扩展的开源服务，用于从多个社区古数据资源访问化石数据和分类法

• DOI: 10.21425/f5fbg50711
• 发表时间: 2021
• 期刊: Frontiers of Biogeography
• 作者: Uhen, Mark D.;Buckland, Philip I.;Goring, Simon J.;Jenkins, Julian P.;Williams, John W.
• 通讯作者: Williams, John W.