The Walking Dead: Status Report, Data Workflow and Best Practices of the oVert Thematic Collections Network
The Walking Dead: Status Report, Data Workflow and Best Practices of the oVert Thematic Collections Network
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DOI：
10.3897/biss.2.26078
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发表时间：
2018-06
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影响因子：
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通讯作者：
G. Watkins-Colwell
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作者：
G. Watkins-Colwell
2017年，美国国家科学基金会资助了“oVert（开放脊椎动物）：3D脊椎动物多样性的开放探索”，这是第一个完全致力于脊椎动物形态标本的专题收藏网络。oVert的主要目标是生成并提供高分辨率的数字三维数据，用于跨脊椎动物多样性的内部解剖。oVert公司将用ct扫描技术扫描2万份液体保存的脊椎动物标本，这些标本占脊椎动物现存属的80%，为所有主要脊椎动物类群的探索和研究提供了广泛的覆盖范围。对比增强扫描将产生，以显示软组织和器官的大多数活脊椎动物家族。这个数字图像和三维体积的集合将开放供探索、下载和使用。这些新媒体将提供前所未有的全球访问美国馆藏标本的宝贵形态学数据。oVert正在开发高通量ct扫描的最佳实践和指导方针，包括高效的工作流程、首选分辨率和存档格式，以优化各种下游应用程序。使用集成数字化生物采集（iDigBio） API，我们开发了一个工作流程，人们上传媒体文件到MorphoSource可以直接从iDigBio中搜索和导入标本的元数据。通过MorphoSource的富站点摘要（RSS）提要，可以检索描述给定科学集合的媒体文件的Audubon Core数据，并将其集成到机构IPT和数据库中。这种大型文件的数据迁移需要注意细节和数据工作流程的开发，以确保在所有步骤中正确绘制标本。MorphoSource的RSS提要还将整合来自每个科学收集标本的媒体文件的使用信息，以供报告。该项目的另一个目标是为创建图像许可/版权的最佳实践提供至关重要的信息。将提交一份关于最佳做法的现状报告和最新情况。
In 2017 NSF funded “oVert (openVertebrate): Open Exploration of Vertebrate Diversity in 3D,” which is the first Thematic Collections Network devoted entirely to vertebrate morphological specimens. The primary goal of oVert is to generate and serve high-resolution digital three-dimensional data for internal anatomy across vertebrate diversity. oVert will CT-scan >20,000 fluid-preserved specimens representing >80% of the living genera of vertebrates, providing broad coverage for exploration and research on all major groups of vertebrates. Contrast-enhanced scans will be generated to reveal soft tissues and organs for a majority of the living vertebrate families. This collection of digital imagery and three-dimensional volumes will be open for exploration, download, and use. These new media will provide unprecedented global access to valuable morphological data of specimens in US collections.oVert is developing best practices and guidelines for high-throughput CT-scanning, including efficient workflows, preferred resolutions, and archival formats that optimize the variety of downstream applications. Using the Integrated Digitized Biocollections (iDigBio) API, we have developed a workflow where people uploading media files to MorphoSource can search for and import metadata for specimens directly from iDigBio. Via a Rich Site Summary (RSS) feed from MorphoSource, Audubon Core data describing media files for a given scientific collection can be retrieved and integrated into institutional IPT and databases. Such data migration of large files requires attention to detail and the development of data workflows that ensure correct specimen mapping at all steps. The RSS feed from MorphoSource will also consolidate usage information for media files from specimens in each scientific collection for reporting. Additional goals of the project are to provide information vital to the creation of collection best practices for imaging permissions/copyright. A status report and update on best practices will be presented.