A Stable Isotope Data Repository as Part of Neotoma, a Paleoecological Database
A Stable Isotope Data Repository as Part of Neotoma, a Paleoecological Database
复制标题
作为古生态数据库 Neotoma 一部分的稳定同位素数据存储库
DOI：
--
复制
发表时间：
2015
期刊：
影响因子：
--
通讯作者：
R. Graham
中科院分区：
文献类型：
--
作者：
S. P. Birch;R. Graham
http://bioscience.oxfordjournals.org October 2015 / Vol. 65 No. 10 · BioScience 953稳定同位素数据库作为Neotoma的一部分，一个古生态数据库我们同意Pauli和同事的观点，现在是建立一个存储和服务稳定同位素数据的综合数据库的时候了。正如他们所指出的，稳定同位素数据的用途很多，在生物学、生态学、生理学、法医学、气候学、古生物学和考古学中都有应用。也许作者最重要的观察是，限制进展的不是数据获取，而是数据交换。我们认为，不仅能够交换稳定同位素数据，而且能够可视化它们与其他类型的生物、生态和古考古数据的交叉，这将极大地促进这些学科研究的进步（例如，Pilaar Birch 2013）。为此，我们在这里讨论了Neotoma古生态数据库（www.neotomadb.org）中IsoBank的潜力，该数据库已经是美国国家科学基金会认可的数据库联盟，存储和服务于从中新世到现在的子古生物学数据库，包括花粉，脊椎动物，植物宏体化石，硅藻和介形虫数据。目前正在Neotoma内建立一个稳定同位素数据库，并将提供按年代和地理参考的同位素数据。因此，它为作者引用的数据交换类型提供了完美的格式，并提供了实现两个额外目标的方法：数据标准化和集成。Neotoma有一个集中的结构，便于使用特定学科的数据集进行跨学科的多代理分析（Graham 2012）。每个组成数据库由一个顾问小组管理，该小组制定标准，格式和质量控制。指定的数据管理员使用程序Tilia上传数据，该程序自动检查错误以防止数据库损坏。数据通过Neotoma Explorer访问，它允许同时提供多种数据组合。有可能绘制个别参数图，例如特定哺乳动物分类群在特定时间间隔的地理分布，沿着海拔和植被覆盖图。这些数据的显示可以被动画化以显示随时间的变化。数值地层数据可以基于内部年龄模型以连续曲线或离散不连续条形图的形式绘制。数据可以下载到各种软件包中进行分析和操作，Neotoma也有R模块来帮助下载和导入数据（Goring et al. 2015）。Pauli及其同事指出的同位素数据的特殊性导致了同位素数据分析，管理和传播缺乏标准化。通过建立一个标准化的数据库格式，如已经存在的Neotoma和Tilia，我们希望稳定同位素研究中的数据实践变得更有凝聚力。数据共享的统一结构应促进数据记录和分析的标准，提高再现性和与其他数据集整合的可能性。Neotoma旨在直接存储元数据和数据，并可与GenBank和Arctos等存储库链接，其格式易于在时间和空间上可视化和交叉引用多个数据集。我们设想它完全准备好服务于对强大的，多代理的，链接的，标准化的数据库的需求，这将使开创性的综合生态和生物研究在未来成为可能。
http://bioscience.oxfordjournals.org October 2015 / Vol. 65 No. 10 • BioScience 953 A Stable Isotope Data Repository as Part of Neotoma, a Paleoecological Database We agree with Pauli and colleagues that the time is right for a comprehensive database that stores and serves stable isotope data. As they point out, the uses of stable isotope data are many, with applications in biology, ecology, physiology, forensic sciences, climatology, paleontology, and archaeology. Perhaps the authors’ most important observation is that limits to progress are not in data acquisition but rather in data exchange. We suggest that the ability to not only exchange stable isotope data but also to visualize their intersection with other types of biological, ecological, and paleoor archaeological data will add immeasurably to the advancement of research in these disciplines (e.g., Pilaar Birch 2013). To that end, we discuss here the potential of an IsoBank within the Neotoma Paleoecological Database (www.neotomadb.org), already a National Science Foundation– recognized database consortium, which stores and serves subsidiary paleobiological databases spanning the Miocene to the present day, including pollen, vertebrate, plant macrofossil, diatom, and ostracod data. A stable isotope database is currently being created within Neotoma and will provide open access to chronologically and geographically referenced isotopic data. Therefore, it provides the perfect format for the type of data exchange cited by the authors and offers a means toward two additional goals: data standardization and integration. Neotoma has a centralized structure that facilitates interdisciplinary multiproxy analyses using discipline-specific data sets (Graham 2012). Each constituent database is administered by an advisory panel that sets standards, format, and quality controls. Appointed data stewards upload data using the program Tilia, which automatically checks for errors in order to prevent database corruption. Data is accessed through the Neotoma Explorer, which allows for multiple combinations of data to be served at one time. It is possible to map individual parameters, such as the geographic distribution of a given mammalian taxa at a specific time interval, along with elevation and vegetation overlays. These displays of data can be animated to show change through time. Numerical stratigraphic data can be graphed based on an internal age model in either continuous curves or discrete discontinuous bar graphs. Data can be downloaded into various software packages for analysis and manipulation, and Neotoma also has R modules to assist with downloading and importing data (Goring et al. 2015). The idiosyncratic nature of isotope data noted by Pauli and colleagues contributes to a lack of standardization in isotopic data analysis, curation, and dissemination. By instituting a standardized database format, such as already exists in Neotoma and Tilia, it is our hope that data practices in stable isotope research become more cohesive. A unified structure in data sharing should foster standards in data recording and analysis, increasing reproducibility and the potential for integration with other data sets. Neotoma is designed for the direct storage of metadata with data and can be linked with repositories such as GenBank and Arctos, and its format makes it easy to visualize and crossreference multiple data sets in time and space. We envision it as perfectly poised to serve the need for robust, multiproxy, linked, standardized databases that will make groundbreaking integrated ecological and biological research possible in the future.