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SPARClink:一个用于可视化 SPARC 计划影响的交互式工具。

SPARClink: an interactive tool to visualize the impact of the SPARC program.

机构信息

Fair Data Innovations Hub, California Medical Innovations Institute, San Diego, California, USA.

Auckland Bioengineering Institute, University of Auckland, Auckland, New Zealand.

出版信息

F1000Res. 2022 Jan 31;11:124. doi: 10.12688/f1000research.75071.1. eCollection 2022.


DOI:10.12688/f1000research.75071.1
PMID:36816808
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC9936100/
Abstract

The National Institutes of Health (NIH) Stimulating Peripheral Activity to Relieve Conditions (SPARC) program seeks to accelerate the development of therapeutic devices that modulate electrical activity in nerves to improve organ function. SPARC-funded researchers are generating rich datasets from neuromodulation research that are curated and shared according to FAIR (Findable, Accessible, Interoperable, and Reusable) guidelines and are accessible to the public on the SPARC data portal. Keeping track of the utilization of these datasets within the larger research community is a feature that will benefit data-generating researchers in showcasing the impact of their SPARC outcomes. This will also allow the SPARC program to display the impact of the FAIR data curation and sharing practices that have been implemented. This manuscript provides the methods and outcomes of SPARClink, our web tool for visualizing the impact of SPARC, which won the Second prize at the 2021 SPARC FAIR Codeathon. With SPARClink, we built a system that automatically and continuously finds new published SPARC scientific outputs (datasets, publications, protocols) and the external resources referring to them. SPARC datasets and protocols are queried using publicly accessible REST application programming interfaces (APIs, provided by Pennsieve and Protocols.io) and stored in a publicly accessible database. Citation information for these resources is retrieved using the NIH reporter API and National Center for Biotechnology Information (NCBI) Entrez system. A novel knowledge graph-based structure was created to visualize the results of these queries and showcase the impact that the FAIR data principles can have on the research landscape when they are adopted by a consortium.

摘要

美国国立卫生研究院(NIH)刺激外周活动以缓解疾病(SPARC)计划旨在加速开发治疗性设备,以调节神经中的电活动,从而改善器官功能。SPARC 资助的研究人员正在从神经调节研究中生成丰富的数据集,这些数据集根据 FAIR(可发现、可访问、可互操作和可重复使用)指南进行管理和共享,并可在 SPARC 数据门户上供公众访问。跟踪这些数据集在更大的研究社区中的使用情况是一个功能,它将使产生数据的研究人员受益,展示他们的 SPARC 结果的影响。这也将使 SPARC 计划能够展示已经实施的 FAIR 数据管理和共享实践的影响。本文提供了我们的 SPARClink 方法和结果,这是我们的可视化工具,用于展示 SPARC 的影响,该工具在 2021 年 SPARC FAIR 代码挑战赛中获得了二等奖。使用 SPARClink,我们构建了一个系统,该系统可以自动和持续地找到新发布的 SPARC 科学成果(数据集、出版物、方案)以及引用它们的外部资源。使用公共可访问的 REST 应用程序编程接口(API,由 Pennsieve 和 Protocols.io 提供)查询 SPARC 数据集和方案,并将其存储在公共可访问的数据库中。使用 NIH 报告 API 和国家生物技术信息中心(NCBI)Entrez 系统检索这些资源的引文信息。创建了一个基于知识图的新结构,以可视化这些查询的结果,并展示当一个联盟采用 FAIR 数据原则时,它们对研究领域的影响。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/6b6b/9936100/b3c5c586c1c5/f1000research-11-78888-g0005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/6b6b/9936100/4e0e5941144b/f1000research-11-78888-g0000.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/6b6b/9936100/90e7ab6440f8/f1000research-11-78888-g0001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/6b6b/9936100/9af2a96e5438/f1000research-11-78888-g0002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/6b6b/9936100/bc68b0010757/f1000research-11-78888-g0003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/6b6b/9936100/4e4e3533cd22/f1000research-11-78888-g0004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/6b6b/9936100/b3c5c586c1c5/f1000research-11-78888-g0005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/6b6b/9936100/4e0e5941144b/f1000research-11-78888-g0000.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/6b6b/9936100/90e7ab6440f8/f1000research-11-78888-g0001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/6b6b/9936100/9af2a96e5438/f1000research-11-78888-g0002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/6b6b/9936100/bc68b0010757/f1000research-11-78888-g0003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/6b6b/9936100/4e4e3533cd22/f1000research-11-78888-g0004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/6b6b/9936100/b3c5c586c1c5/f1000research-11-78888-g0005.jpg

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本文引用的文献

[1]
The SPARC DRC: Building a Resource for the Autonomic Nervous System Community.

Front Physiol. 2021-6-24

[2]
The FAIR Guiding Principles for scientific data management and stewardship.

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