ABI Development: Collaborative Research: The first open access digital archive for high fidelity 3D data on morphological phenomes

ABI 开发：协作研究：第一个开放存取数字档案，用于形态学现象的高保真 3D 数据

• 批准号: 1661132
• 负责人: Timothy Ryan
• 金额: $ 50.6万
• 依托单位: Pennsylvania State Univ University Park
• 依托单位国家: 美国
• 项目类别: Continuing Grant
• 财政年份: 2017
• 资助国家: 美国
• 起止时间: 2017-09-01 至 2021-08-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1661132&HistoricalAwards=false
• 关键词: ABI; Development; Collaborative; Research; first

People and societies thrive best when they understand how the social and physical dynamics of their environment work, allowing them to respond appropriately. Natural scientists have built our understanding of the physical world. The scientific understanding they built has contributed to the development of technologies and practices that benefit human economies. For example, genetic sequencing of DNA enables deeper understanding of biological organisms; the consequences for human health, food production, understanding of evolutionary adaptation, etc. have been revolutionary and are still unfolding. The DNA sequence is the blueprint for an organism's anatomical structure (morphology) and function, but images capturing morphology are now much less prevalent than genetic data. Museums and researchers have been creating 3D digital images of natural history collections, and there are extensive 3D image data sets for some model organisms, but these data are mostly in closed collections, and generally unavailable or very difficult to access. This project aims to provide infrastructure to increase the accessibility of anatomical information, with a focus on 3D images. The resource will create the first open access, web-enabled image archive accepting and serving high-resolution, 3D scans of all organisms, called MorphoSource. Standardized descriptive tags will allow scientists to use this database to easily combine genetic and anatomical datasets for the first time, supporting the formulation of novel research questions. MorphoSource will link to other databases (such as iDigBio [www.idigbio.org]) that aggregate information on museum specimens from around the world. Having a shared common resource will change the culture among researchers and museums, making collaborations between physically distant experts more feasible, but it will also open the linked research collections of museums to anyone with Internet access anywhere in the world. Large data sets are prerequisites for many statistical and machine learning methods, so the resource will enable innovations in computational image analysis methods, fostering new types of collaborations that advance field-wide scientific understanding. The resource will track data use, enhancing reproducibility and also providing an objective metric of the value of individual data elements. Open access to the data linked through MorphoSource will enable anyone with Internet access to see the detailed anatomical evidence for theories like evolution. Pilot work has shown that teachers and students eagerly consume this newly available information, with numbers already in the thousands. Positive results of this access include (1) providing a more intuitive type of raw data (compared to DNA sequence) for showing the public why some conclusions about evolutionary relationships were reached, (2) providing an 'interest metric' for the value of natural history museums and the collections they hold, (3) increasing the community of people (including citizen scientists) who have access to the data required to make important discoveries by studying biological variation. The specific plan for creating the repository for 3D data on all organisms is as follows. The primary goal is to restructure and improve a proof of concept database called MorphoSource. The restructuring will allow MorphoSource to meet the needs of a growing community of researchers and educators through massive upscaling, and to implement a novel approach for economically preserving data for the long term. To accomplish this, the MorphoSource server will be rebuilt to use the Fedora digital asset management architecture, which has been developed by library scientists to serve emerging needs related to the archiving and sharing of digital data. As part of this architecture upgrade, the data hosted on MorphoSource will be given an additional layer of protection through managing asynchronous copies in DuraCloud, a digital data preservation platform that leverages Amazon cloud. This restructuring will allow the MorphoSource server architecture to be integrated with the Duke University Libraries repository infrastructure. MorphoSource will also be able to invite institutional communities to be consortium partners in support of data storage and to enact data preservation techniques that guarantee integrity and readability for the foreseeable future. Additional tools will (1) allow for rapid, automated ingestion of dozens to hundreds of datasets at once, (2) link MorphoSource with major biodiversity archives, and (3) provide in-browser visualization of 3D series of image slices, such as those generated by CT and MRI scanners. The plan includes ingesting thousands of high quality legacy CT datasets from published studies, enabling their reuse, increasing the repeatability of studies. The project leaders plan to directly work with and design tools for K-12 educators and students to help them benefit from this resource. These datasets and educational tools will be available to researchers and the public through the updated MorphoSource website, available at www.morphosource.org.

当人们和社会了解其环境的社会和物理动态如何运作时，他们才能最好地蓬勃发展，使他们能够做出适当的反应。 自然科学家建立了我们对物理世界的理解。他们建立的科学认识促进了有益于人类经济的技术和做法的发展。例如，DNA的基因测序使人们能够更深入地了解生物有机体;对人类健康、粮食生产、对进化适应的理解等的影响是革命性的，而且仍在不断发展。DNA序列是生物体解剖结构（形态学）和功能的蓝图，但捕获形态学的图像现在远不如遗传数据流行。博物馆和研究人员一直在创建自然历史收藏品的3D数字图像，并且存在一些模式生物的广泛3D图像数据集，但这些数据大多处于封闭收藏中，并且通常不可用或非常难以访问。该项目旨在提供基础设施以提高解剖信息的可访问性，重点是3D图像。该资源将创建第一个开放获取的、支持网络的图像存档，接受并提供所有生物体的高分辨率3D扫描，称为MorphoSource。标准化的描述性标签将使科学家能够使用该数据库首次轻松地将遗传和解剖数据集联合收割机结合起来，支持新研究问题的制定。MorphoSource将链接到其他数据库（如iDigBio [www.idigbio.org]），这些数据库汇集了来自世界各地的博物馆标本信息。拥有一个共享的共同资源将改变研究人员和博物馆之间的文化，使相距遥远的专家之间的合作更加可行，但它也将向世界上任何地方的任何人开放博物馆的相关研究收藏。 大型数据集是许多统计和机器学习方法的先决条件，因此该资源将实现计算图像分析方法的创新，促进新型合作，推动全领域的科学理解。该资源将跟踪数据使用情况，提高可重复性，并提供单个数据元素价值的客观度量。通过MorphoSource链接的数据的开放访问将使任何可以访问互联网的人都可以看到进化论等理论的详细解剖证据。 试点工作表明，教师和学生热切地消费这些新提供的信息，人数已经达到数千人。 这种访问的积极结果包括（1）提供更直观类型的原始数据（与DNA序列相比）向公众展示为什么得出了一些关于进化关系的结论，（2）为自然历史博物馆及其收藏品的价值提供了一个“兴趣度量”，（3）增加能够接触到通过研究生物变异作出重大发现所需数据的人（包括公民科学家）的群体。创建所有生物体3D数据库的具体计划如下。主要目标是重构和改进一个名为MorphoSource的概念数据库证明。重组将使MorphoSource能够通过大规模升级来满足不断增长的研究人员和教育工作者社区的需求，并实施一种新的方法来长期经济地保存数据。为了实现这一目标，MorphoSource服务器将被重建，以使用Fedora数字资产管理架构，该架构由图书馆科学家开发，以满足与数字数据归档和共享相关的新兴需求。作为此次架构升级的一部分，MorphoSource上托管的数据将通过在DuraCloud（一个利用亚马逊云的数字数据保存平台）中管理异步副本而获得额外的保护层。这一重组将允许MorphoSource服务器架构与杜克大学图书馆存储库基础设施集成。MorphoSource还将能够邀请机构社区成为支持数据存储的联盟伙伴，并制定数据保存技术，以保证可预见的未来的完整性和可读性。额外的工具将（1）允许快速，自动化地同时摄取数十到数百个数据集，（2）将MorphoSource与主要的生物多样性档案链接，以及（3）提供3D系列图像切片的浏览器可视化，例如CT和MRI扫描仪生成的切片。 该计划包括从已发表的研究中提取数千个高质量的遗留CT数据集，使其能够重复使用，提高研究的可重复性。项目负责人计划直接与K-12教育工作者和学生合作并为他们设计工具，以帮助他们从这一资源中受益。这些数据集和教育工具将通过更新的MorphoSource网站提供给研究人员和公众，网址是www.morphosource.org。