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Practices, Challenges, and Prospects of Big Data Curation: a Case Study in Geoscience 大数据管理的实践、挑战和前景:以地球科学为例
Pub Date : 2020-01-06 DOI: 10.2218/ijdc.v14i1.669
Suzhen Chen, Bin Chen
Open and persistent access to past, present, and future scientifc data is fundamental for transparent and reproducible data-driven research. The scientifc community is now facing both challenges and opportunities caused by the growingly complex disciplinary data systems. Concerted efforts from domain experts, information professionals, and Internet technology experts are essential to ensure the accessibility and interoperability of the big data. Here we review current practices in building and managing big data within the context of large data infrastructure, using geoscience cyberinfrastructure such as Interdisciplinary Earth Data Alliance (IEDA) and EarthCube as a case study. Geoscience is a data-rich discipline with a rapid expansion of sophisticated and diverse digital data sets. Having started to embrace the digital age, the community have applied big data and data mining tools into the new type of research. We also identify current challenges, key elements, and prospects to construct a more robust and future-proof big data infrastructure for research and publication for the future, as well as the roles, qualifcations, and opportunities for librarians1information professionals in the data era. Received 06 May 2019 ~ Accepted 11 September 2019 Correspondence should be addressed to Suzhen Chen, Cataloging Department, University of Hawaiʻi at Mānoa Library, 2550 McCarthy Mall, Honolulu, Hawaii 96822. Email: suzhen@hawaii.edu The International Journal of Digital Curation is an international journal committed to scholarly excellence and dedicated to the advancement of digital curation across a wide range of sectors. The IJDC is published by the University of Edinburgh on behalf of the Digital Curation Centre. ISSN: 1746-8256. URL: http://www.ijdc.net/ Copyright rests with the authors. This work is released under a Creative Commons Attribution Licence, version 4.0. For details please see https://creativecommons.org/licenses/by/4.0/ International Journal of Digital Curation 2020, Vol. 14, Iss. 1, 275–291 275 http:11dx.doi.org110.22181ijdc.v14i1.669 DOI: 10.22181ijdc.v14i1.669 276 | Practices, Challenges and Prospects of Big Data Curation doi:10.2218/ijdc.v14i1.669
开放和持续地获取过去、现在和未来的科学数据是透明和可重复的数据驱动研究的基础。科学领域正面临着学科数据系统日益复杂所带来的挑战和机遇。确保大数据的可访问性和互操作性,领域专家、信息专家和互联网技术专家的共同努力至关重要。本文以跨学科地球数据联盟(IEDA)和EarthCube等地球科学网络基础设施为例,回顾了在大数据基础设施背景下构建和管理大数据的当前实践。地球科学是一门数据丰富的学科,复杂多样的数字数据集正在迅速扩展。随着数字时代的到来,学界开始将大数据和数据挖掘工具应用到新型研究中。我们还确定了当前的挑战、关键因素和前景,以便为未来的研究和出版构建一个更强大、更面向未来的大数据基础设施,以及数据时代图书馆员和信息专业人员的角色、资格和机会。信件应寄给夏威夷大学编目部Suzhen Chen,地址:Mānoa图书馆,2550 McCarthy Mall, Honolulu, Hawaii 96822。电子邮件:suzhen@hawaii.edu《国际数字策展杂志》是一本致力于学术卓越的国际期刊,致力于在各个领域推进数字策展。IJDC由爱丁堡大学代表数字策展中心出版。ISSN: 1746 - 8256。版权归作者所有。本作品在知识共享署名许可4.0版本下发布。详情请参见https://creativecommons.org/licenses/by/4.0/《国际数字策展杂志2020》Vol. 14, Iss. 1,275 - 291,275 http://11dx.doi.org110.22181ijdc.v14i1.669 DOI: 10.22181ijdc.v14i1.669 276 |大数据策展的实践、挑战与展望DOI: 10.2218/ijdc.v14i1.669
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引用次数: 3
Improving the Reproducibility of LaTeX Documents by Enriching Figures with Embedded Scripts and Data 通过嵌入脚本和数据丰富图形来提高LaTeX文档的再现性
Pub Date : 2020-01-06 DOI: 10.2218/ijdc.v14i1.656
C. Jacobs
The introduction of open access data policies by research councils, the enforcement of best practices, and the deployment of persistent online repositories have enabled datasets that support results in scientific papers to become more widely accessible. Unfortunately, despite this advancement in the curation/publishing workflow, the data-driven figures within a paper often remain difficult to reproduce. Plotting or analysis scripts rarely accompany the manuscript or any associated software release; and even if they do, it may be unclear exactly which version was used. Furthermore, the precise commands and parameters used to execute the scripts are often not included in a README file or in the paper itself. This paper introduces a new open source digital curation tool, Pynea, for improving the reproducibility of LaTeX documents. Each figure within a document is enriched by automatically embedding the plotting script and data files required to generate it, such that it can be regenerated by readers of the paper in the future. The command used to execute the plotting script is also added to the figure’s metadata, along with details of the specific version of the script used (if the script is tracked with the Git version control system). If the document is to be recompiled with a figure that has since changed, or had its plotting script or data files modified, the figure is regenerated such that the author can be confident that the latest version of the figure and its dependencies are included. Received 06 April 2019 | Revision received 30 June 2019 | Accepted 12 August 2019 Correspondence should be addressed to Dr Christian T. Jacobs, Defence Science and Technology Laboratory (Dstl), Porton Down, Salisbury, Wiltshire, SP4 0JQ, United Kingdom, Email: cjacobs@dstl.gov.uk The International Journal of Digital Curation is an international journal committed to scholarly excellence and dedicated to the advancement of digital curation across a wide range of sectors. The IJDC is published by the University of Edinburgh on behalf of the Digital Curation Centre. ISSN: 1746-8256. URL: http://www.ijdc.net/ Copyright rests with the authors. This work is released under a Creative Commons Attribution 4.0 International Licence. For details please see http://creativecommons.org/licenses/by/4.0/ International Journal of Digital Curation 2020, Vol. 14, Iss. 1, 292–302. 292 https://doi.org/10.2218/ijdc.v14i1.656 DOI: 10.2218/ijdc.v14i1.656 doi:10.2218/ijdc.v14i1.656 Christian T. Jacobs | 293
研究委员会引入的开放获取数据政策,最佳实践的实施,以及持久在线存储库的部署,使支持科学论文结果的数据集变得更广泛地可访问。不幸的是,尽管在管理/出版工作流程方面取得了进步,但论文中数据驱动的数字通常仍然难以复制。绘图或分析脚本很少伴随手稿或任何相关的软件发布;即使他们知道,可能也不清楚到底使用了哪个版本。此外,用于执行脚本的精确命令和参数通常不包括在README文件或论文本身中。本文介绍了一个新的开源数字管理工具Pynea,用于提高LaTeX文档的可再现性。通过自动嵌入生成所需的绘图脚本和数据文件,可以丰富文档中的每个图形,以便将来由论文的读者重新生成。用于执行绘图脚本的命令还被添加到图的元数据中,以及所使用的脚本的特定版本的详细信息(如果使用Git版本控制系统跟踪脚本)。如果文档要用一个已经更改过的图形重新编译,或者其绘图脚本或数据文件已被修改,则会重新生成该图形,以便作者可以确信包含了该图形及其依赖项的最新版本。收到2019年4月6日|修订收到2019年6月30日|接受2019年8月12日信件应发送给Christian T. Jacobs博士,国防科学与技术实验室(Dstl), Porton Down,索尔兹伯里,威尔特郡,SP4 0JQ,英国,电子邮件:cjacobs@dstl.gov.uk国际数字策展杂志是一本致力于学术卓越的国际期刊,致力于在各个领域推进数字策展。IJDC由爱丁堡大学代表数字策展中心出版。ISSN: 1746 - 8256。版权归作者所有。本作品采用知识共享署名4.0国际许可协议发布。详细信息请参见http://creativecommons.org/licenses/by/4.0/国际数字策展杂志2020,Vol. 14, Iss. 1,292 - 302。292 https://doi.org/10.2218/ijdc.v14i1.656 DOI: 10.2218/ijdc.v14i1.656 DOI: 10.2218/ijdc.v14i1.656 Christian T. Jacobs | 293
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引用次数: 0
Building an Aotearoa New Zealand-wide Digital Curation Community of Practice 建立一个新西兰范围内的数字策展实践社区
Pub Date : 2020-01-03 DOI: 10.2218/ijdc.v14i1.638
Jessica Moran, Floran Feltham, Valerie Love
How do you build awareness and capability for digital curation knowledge and experience across a country? The National Library of New Zealand has a statutory role in supporting and advancing the work of Aotearoa New Zealand libraries to ensure documentary heritage and taonga is collected and preserved across the country’s memory system. This role includes supporting the collecting and curation of born-digital content. Aotearoa New Zealand’s Gallery Library Archive Museum (GLAM) sector is small but varied and diverse, so requires a flexible and adaptive plan to grow experience and capability in this area. This paper will describe the background research undertaken to gain a better understanding of the current environment, describe the development and delivery of pilot training in managing born-digital archival content, and outline our next steps. Driving this effort has been two foundational principles: 1) theory and practice are always in conversation with each other and practical hands-on experience is as important as theoretical knowledge and understanding; and 2) the work of growing capability should be done in a spirt of collaboration and partnership, meeting each other as equals and learning from each other.
你如何在全国范围内建立数字策展知识和经验的意识和能力?新西兰国家图书馆的法定职责是支持和推进新西兰图书馆的工作,以确保文献遗产和汤加语在全国的记忆系统中得到收集和保存。这个角色包括支持收集和管理原生数字内容。新西兰的画廊图书馆档案博物馆(GLAM)部门很小,但种类繁多,因此需要一个灵活和适应性的计划来增加这一领域的经验和能力。本文将描述为更好地了解当前环境而进行的背景研究,描述管理原生数字档案内容的试点培训的开发和交付,并概述我们的下一步工作。推动这一努力的两个基本原则是:1)理论和实践总是相互联系的,实践经验与理论知识和理解同样重要;二是坚持合作伙伴精神,平等相待、互学互鉴。
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引用次数: 0
A Class Focused Approach to Research Outputs and Policy Literature Metadata 研究成果和政策文献元数据的班级聚焦方法
Pub Date : 2020-01-02 DOI: 10.2218/ijdc.v14i1.640
Les Kneebone
Successful research object sharing requires that systems and users understand the structure, semantics and rules that govern a given research object collection. A number of metadata standards define ontologies and vocabularies for consistent expression of research object semantics. Supporting, clarifying and sometimes extending these standards are metadata application profiles (MAPs). MAPs play a key role defining metadata element cardinality and data types. MAPs may also mandate or recommend controlled vocabularies, where metadata standards have not already mentioned these in formal range declarations, encoding schemes and semantics that are to be consumed by external systems. MAPs also guide design options for in-house systems and workflows. In this paper, development of a draft MAP for grey-literature policy and research collections is discussed. A focus of the discussion is the considerations around selection and adoption of metadata standards given the research data and literature communities in the APO stakeholder map. This paper presents a work-in-progress version of a Dublin Core Application Profile (DCAP) candidate. The Analysis & Policy Observatory Metadata Application Profile (APO-MAP) takes research object class structure as a starting point and considers class model options, especially given the availability of registry services and Persistent Indenter (PID) systems. The discussion finds that MAP development progresses towards a best fit that balances the need to adopt widely supported standards, local business drivers, and community acceptance.
成功的研究对象共享要求系统和用户理解管理给定研究对象集合的结构、语义和规则。许多元数据标准定义了本体和词汇表,以实现研究对象语义的一致表达。支持、澄清并有时扩展这些标准的是元数据应用程序概要文件(MAPs)。MAPs在定义元数据元素基数和数据类型方面起着关键作用。MAPs还可能强制要求或推荐受控词汇表,而元数据标准尚未在正式范围声明、编码模式和外部系统使用的语义中提到受控词汇表。MAPs还指导内部系统和工作流程的设计选项。本文讨论了灰色文献政策和研究收集的MAP草案的开发。讨论的重点是考虑到APO利益相关者地图中的研究数据和文献社区,围绕选择和采用元数据标准的考虑。本文介绍了都柏林核心应用程序配置文件(DCAP)候选人的正在进行的版本。分析与政策观察站元数据应用程序概要(APO-MAP)以研究对象类结构为起点,并考虑类模型选项,特别是考虑到注册服务和持久缩表(PID)系统的可用性。讨论发现,MAP开发朝着最合适的方向发展,平衡了采用广泛支持的标准、本地业务驱动因素和社区接受度的需要。
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引用次数: 0
Research Data Management in a cultural heritage organisation 文化遗产组织的研究数据管理
Pub Date : 2020-01-02 DOI: 10.2218/ijdc.v14i1.647
T. Drysdale
Research is a core function of cultural heritage organisations. Inevitably, the undertaking of research by galleries, libraries, archives and museums (the GLAM sector) leads to the creation of vast quantities of research data. Yet despite growing recognition that research data must be managed if it is to be exploited effectively, and in spite of increasing understanding of research data management practices and needs, particularly in the higher education sector, knowledge of research data management in cultural heritage organisations remains extremely limited. This paper represents an attempt to address the limited awareness of research data management in the cultural heritage sector. It presents the results of a data management audit conducted at Historic Royal Palaces (HRP) in 2018. The study reveals that research data management at HRP is underdeveloped, while highlighting some causes for optimism. The results of the study are compared to the results of similar studies conducted in UK higher education institutions (HEIs), highlighting the many discrepancies in the ways that research data is managed at HRP and in the HE sector. Recognition of these differences and similarities, it is argued, is necessary for the development of better research data management practices and tools for the heritage sector. Received 15 January 2019 ~ Revision received 09 August 2019 ~ Accepted 09 August 2019 Correspondence should be addressed to Tom Drysdale, 4B The Casemates, HM Tower of London, EC3N 4AB. Email: tom.drysdale@hrp.org.uk The International Journal of Digital Curation is an international journal committed to scholarly excellence and dedicated to the advancement of digital curation across a wide range of sectors. The IJDC is published by the University of Edinburgh on behalf of the Digital Curation Centre. ISSN: 1746-8256. URL: http://www.ijdc.net/ Copyright rests with the authors. This work is released under a Creative Commons Attribution Licence, version 4.0. For details please see https://creativecommons.org/licenses/by/4.0/ International Journal of Digital Curation 2019, Vol. 14, Iss. 1, 199–227 199 http://dx.doi.org/10.2218/ijdc.v14i1.647 DOI: 10.2218/ijdc.v14i1.647 200 | Research Data Management in a Cultural Heritage Organisation doi:10.2218/ijdc.v14i1.647
研究是文化遗产组织的核心职能。不可避免地,画廊、图书馆、档案馆和博物馆(GLAM部门)的研究工作导致了大量研究数据的产生。然而,尽管越来越多的人认识到,如果要有效地利用研究数据,就必须对其进行管理,并且尽管对研究数据管理实践和需求的理解越来越多,特别是在高等教育部门,文化遗产组织的研究数据管理知识仍然非常有限。本文试图解决文化遗产部门对研究数据管理的有限认识。它介绍了2018年在历史悠久的皇家宫殿(HRP)进行的数据管理审计结果。该研究表明,HRP的研究数据管理还不发达,同时也突出了一些乐观的理由。该研究的结果与在英国高等教育机构(HEIs)进行的类似研究的结果进行了比较,突出了HRP和高等教育部门在管理研究数据的方式上的许多差异。有人认为,认识到这些差异和相似之处对于为遗产部门开发更好的研究数据管理实践和工具是必要的。收到2019年1月15日~修改收到2019年8月9日~接受2019年8月9日信件应发送给Tom Drysdale, 4B The Casemates,伦敦HM Tower, EC3N 4AB。电子邮件:tom.drysdale@hrp.org.uk《国际数字策展杂志》是一本致力于学术卓越的国际期刊,致力于在各个领域推进数字策展。IJDC由爱丁堡大学代表数字策展中心出版。ISSN: 1746 - 8256。版权归作者所有。本作品在知识共享署名许可4.0版本下发布。详情请参见https://creativecommons.org/licenses/by/4.0/国际数字策展杂志2019,Vol. 14, Iss. 1,199 - 227 199 http://dx.doi.org/10.2218/ijdc.v14i1.647 DOI: 10.2218/ijdc.v14i1.647 200 |文化遗产组织的研究数据管理DOI: 10.2218/ijdc.v14i1.647
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引用次数: 0
Embedding Analytics within the Curation of Scientific Workflows. 在科学工作流管理中嵌入分析。
Pub Date : 2020-01-01 DOI: 10.2218/ijdc.v15i1.709
Gerard Weatherby, Michael R Gryk

This paper reports on the ongoing activities and curation practices of the National Center for Biomolecular NMR Data Processing and Analysis. Over the past several years, the Center has been developing and extending computational workflow management software for use by a community of biomolecular NMR spectroscopists. Previous work had been to refactor the workflow system to utilize the PREMIS framework for reporting retrospective provenance as well as for sharing workflows between scientists and to support data reuse. In this paper, we report on our recent efforts to embed analytics within the workflow execution and within provenance tracking. Important metrics for each of the intermediate datasets are included within the corresponding PREMIS intellectual object, which allows for both inspection of the operation of individual actors as well as visualization of the changes throughout a full processing workflow. These metrics can be viewed within the workflow management system or through standalone metadata widgets. Our approach is to support a hybrid approach of both automated, workflow execution as well as manual intervention and metadata management. In this combination, the workflow system and metadata widgets encourage the domain experts to be avid curators of the data which they create, fostering both computational reproducibility and scientific data reuse.

本文报告了国家生物分子核磁共振数据处理与分析中心的持续活动和管理实践。在过去的几年里,该中心一直在开发和扩展计算工作流管理软件,供生物分子核磁共振波谱学家社区使用。以前的工作是重构工作流系统,以利用PREMIS框架报告追溯的来源,以及在科学家之间共享工作流,并支持数据重用。在本文中,我们报告了我们最近在工作流执行和溯源跟踪中嵌入分析的努力。每个中间数据集的重要指标都包含在相应的PREMIS智能对象中,它既可以检查单个参与者的操作,也可以在整个处理工作流中可视化更改。这些指标可以在工作流管理系统中查看,也可以通过独立的元数据小部件查看。我们的方法是支持自动化、工作流执行以及人工干预和元数据管理的混合方法。在这种组合中,工作流系统和元数据小部件鼓励领域专家成为他们创建的数据的热心管理者,从而促进计算再现性和科学数据重用。
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引用次数: 1
Finding a Repository with the Help of Machine-Actionable DMPs: Opportunities and Challenges 在机器可操作的dmp的帮助下寻找存储库:机遇与挑战
Pub Date : 2020-01-01 DOI: 10.2218/ijdc.v15i1.704
Simon Oblasser, Tomasz Miksa, A. Kitamoto
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引用次数: 2
Out of the Jar into the World! A Case Study on Storing and Sharing Vertebrate Data 走出罐子,走进世界!脊椎动物数据存储与共享的案例研究
Pub Date : 2020-01-01 DOI: 10.2218/ijdc.v15i1.700
S. Borda
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引用次数: 0
A Review of the History, Advocacy and Efficacy of Data Management Plans 数据管理计划的历史、倡导和功效综述
Pub Date : 2020-01-01 DOI: 10.2218/ijdc.v15i1.525
Nicholas Andrew Smale, Kathryn Unsworth, G. Denyer, Elise Magatova, Daniel Barr
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引用次数: 12
Piloting a Community of Student Data Consultants that Supports and Enhances Research Data Services 试点学生数据顾问社区,支持和加强研究数据服务
Pub Date : 2020-01-01 DOI: 10.2218/ijdc.v15i1.723
Jonathan S. Briganti, A. Ogier, Anne-Marie Brown
Research ecosystems within university environments are continuously evolving and requiring more resources and domain specialists to assist with the data lifecycle. Typically, academic researchers and professionals are overcommitted, making it challenging to be up-to-date on recent developments in best practices of data management, curation, transformation, analysis, and visualization. Recently, research groups, university core centers, and Libraries are revitalizing these services to fill in the gaps to aid researchers in finding new tools and approaches to make their work more impactful, sustainable, and replicable. In this paper, we report on a student consultation program built within the University Libraries, that takes an innovative, student-centered approach to meeting the research data needs in a university environment while also providing students with experiential learning opportunities. This student program, DataBridge, trains students to work in multi-disciplinary teams and as student consultants to assist faculty, staff, and students with their real-world, data-intensive research challenges. Centering DataBridge in the Libraries allows students the unique opportunity to work across all disciplines, on problems and in domains that some students may not interact with during their college careers. To encourage students from multiple disciplines to participate, we developed a scaffolded curriculum that allows students from any discipline and skill level to quickly develop the essential data science skill sets and begin contributing their own unique perspectives and specializations to the research consultations. These students, mentored by Informatics faculty in the Libraries, provide research support that can ultimately impact the entire research process. Through our pilot phase, we have found that DataBridge enhances the utilization and openness of data created through research, extends the reach and impact of the work beyond the researcher’s specialized community, and creates a network of student “data champions” across the University who see the value in working with the Library. Here, we describe the evolution of the DataBridge program and outline its unique role in both training the data stewards of the future with regard to FAIR data practices, and in contributing significant value to research projects at Virginia Tech. Ultimately, this work highlights the need for innovative, strategic programs that encourage and enable real-world experience of data curation, data analysis, and data publication for current researchers, all while training the next generation of researchers in these best practices.
大学环境中的研究生态系统不断发展,需要更多的资源和领域专家来协助数据生命周期。通常情况下,学术研究人员和专业人员的工作量过大,这使得他们很难跟上数据管理、管理、转换、分析和可视化最佳实践的最新发展。最近,研究小组、大学核心中心和图书馆正在振兴这些服务,以填补空白,帮助研究人员找到新的工具和方法,使他们的工作更具影响力、可持续性和可复制性。在本文中,我们报告了在大学图书馆内建立的学生咨询计划,该计划采用创新的,以学生为中心的方法来满足大学环境中的研究数据需求,同时也为学生提供体验式学习机会。这个名为DataBridge的学生项目训练学生在多学科团队中工作,并作为学生顾问协助教师、员工和学生应对现实世界中数据密集型的研究挑战。以图书馆为中心的DataBridge让学生有独特的机会跨学科工作,解决一些学生在大学生涯中可能不会接触的问题和领域。为了鼓励来自多个学科的学生参与,我们开发了一个框架课程,允许来自任何学科和技能水平的学生快速发展基本的数据科学技能集,并开始为研究咨询贡献自己独特的观点和专业知识。这些学生在图书馆信息学教师的指导下,提供研究支持,最终影响整个研究过程。通过我们的试点阶段,我们发现DataBridge提高了通过研究创造的数据的利用率和开放性,扩展了研究工作的范围和影响,超出了研究人员的专业社区,并在整个大学建立了一个学生“数据冠军”网络,他们看到了与图书馆合作的价值。在这里,我们描述了DataBridge计划的演变,并概述了它在培训未来的数据管理员方面的独特作用,以及在为弗吉尼亚理工大学的研究项目做出重大贡献方面的作用。最终,这项工作强调了创新的战略计划的必要性,这些计划鼓励并使当前研究人员能够获得数据管理、数据分析和数据出版的实际经验。同时在这些最佳实践方面培训下一代研究人员。
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引用次数: 0
期刊
International journal of digital curation
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