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

基本信息

批准号：
1661386
负责人：
Douglas Boyer
金额：
$ 136.09万
依托单位：
Duke University
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=1661386&HistoricalAwards=false
关键词：
ABI Development Collaborative Research first

项目摘要

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.

当人们了解环境的社会和物理动态如何工作时，他们可以做出适当的反应时，就可以最好地蓬勃发展。自然科学家已经建立了我们对物理世界的理解。他们建立的科学理解为有利于人类经济的技术和实践的发展做出了贡献。例如，DNA的遗传测序可以更深入地了解生物生物体。人类健康，粮食生产，对进化适应的理解的后果是革命性的，并且仍在发展。 DNA序列是生物体解剖结构（形态）和功能的蓝图，但是捕获形态的图像现在不如遗传数据流行得多。博物馆和研究人员一直在创建自然历史收藏的3D数字图像，某些模型有机体有广泛的3D图像数据集，但是这些数据主要是在封闭的集合中，通常不可用或很难访问。该项目旨在提供基础架构以增加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式访问，启用网络的图像存档，接受并提供所有生物体的3D扫描，称为Morphosource。标准化的描述性标签将使科学家首次使用该数据库轻松地结合遗传和解剖学数据集，从而支持新的研究问题的提出。 Morphosource将链接到其他数据库（例如IDIGBIO [www.idigbio.org]），该数据库汇总了来自世界各地的博物馆标本的信息。拥有共同的共同资源将改变研究人员和博物馆之间的文化，使身体遥远的专家之间的合作更加可行，但它还将向世界上任何地方的任何人都开放链接的博物馆研究集。大型数据集是许多统计和机器学习方法的先决条件，因此资源将使计算图像分析方法的创新能够创新，从而促进新型的合作类型，以提高范围内的范围内科学理解。资源将跟踪数据使用，增强可重复性，并提供单个数据元素价值的客观指标。通过Morphosource链接的数据的开放访问将使任何具有Internet访问的人都可以查看诸如Evolution之类的理论的详细解剖学证据。飞行员工作表明，老师和学生热切地消费这些新的信息，数千个数字已经存在。此访问的积极结果包括（1）提供更直观的原始数据（与DNA序列相比），以向公众展示为什么要达到有关进化关系的一些结论，（（2）为自然历史博物馆的价值及其持有的收藏的价值提供“兴趣指标”，（3）增加了人们（包括公民科学家）（包括公民科学家），以使数据访问需要研究重要的数据。为所有生物体创建3D数据存储库的特定计划如下。主要目标是重组和改善称为Morphosource的概念数据库证明。重组将使Morphosource能够通过大规模的升级来满足不断增长的研究人员和教育者社区的需求，并实施一种新颖的方法来长期保存经济上的数据。为此，将重建Morphosource服务器以使用Fedora Digital Asset Manchatecture，图书馆科学家已经开发了与数字数据的归档和共享有关的新兴需求。作为此体系结构升级的一部分，通过管理杜拉克洛德（Duracloud）中的异步副本（一个利用Amazon Cloud的数字数据保存平台）中的异步副本，将为Morphosource上托管的数据提供额外的保护层。这种重组将使Morphosource服务器体系结构与杜克大学库存储库基础架构集成在一起。 Morphosource还将能够邀请机构社区成为联盟合作伙伴，以支持数据存储并制定数据保存技术，以确保可预见的未来的完整性和可读性。其他工具将（1）允许一次快速自动摄入数十个数据集，（2）将Mormphosource与主要的生物多样性档案联系起来，（3）（3）提供3D级别的图像切片的浏览器可视化，例如由CT和MRI扫描仪生成的图像切片。该计划包括从已发表的研究中摄入数千个高质量的旧版CT数据集，使其重复使用，从而提高了研究的重复性。项目负责人计划直接使用并为K-12教育者和学生设计工具，以帮助他们从该资源中受益。这些数据集和教育工具将通过更新的Morphosource网站向研究人员和公众使用，网站可在www.morphosource.org上找到。