Making Software FAIR: A machine-assisted workflow for the research software lifecycle

阻碍开放研究软件的可发现性、归属和可重用性的一个关键问题是，它的存在往往隐藏在研究论文的手稿中。为了使这些资源成为一流的书目记录，首先需要对它们进行标识，然后用持久标识符（pid）进行注册，使其成为FAIR（可查找、可访问、可互操作和可重用）。直到今天，许多开放的研究软件都不符合FAIR原则，软件资源大多没有从介绍它们或使用它们的手稿中明确链接起来。该项目将扩展由联盟合作伙伴运营的关键和广泛使用的开放学术基础设施（CORE、Software Heritage、HAL）和工具（GROBID）的能力，为研究软件生命周期的管理提供和部署有效的解决方案，包括：1)机器学习辅助识别学术论文手稿中的研究软件资产，2)作者对识别的资产进行验证，3)使用pid对软件资产进行注册及其存档。该解决方案将针对开放内容的部署进行优化，这些开放内容可通过由CORE （CORE .ac）聚合的开放存储库的全球网络获得。英国)，其中包含超过3200万全文和2.5亿元数据记录，来自超过1万个存储库，是目前世界上最大的开放获取文档集合。我们用于提取和消除软件资产歧义的机器学习软件将作为最先进的GROBID工具的扩展而实现。我们将建立在现有协议的基础上，如openaire指南v4.0、RIOXX v3和Codemeta，对软件资产及其与研究手稿的链接进行编码，建立一个可互操作和可扩展的工作流，连接开放存储库（以HAL为代表）、聚合器（以CORE为代表）和软件存档（以software Heritage为代表）。开发的工具和工作流程的有效性将在三个用例中得到验证：1)生命科学演示（针对欧洲PMC）， 2)机构存储库的多学科演示（以HAL为代表）和3)数字人文案例研究（与DARIAH和EOSC链接）。

A key issue hindering the discoverability, attribution and reusability of open research software is that its existence often remains hidden within the manuscript of research papers. For these resources to become first-class bibliographic records, they first need to be identified and subsequently registered with persistent identifiers (PIDs) to be made FAIR (Findable, Accessible, Interoperable and Reusable). To this day, much open research software fails to meet FAIR principles and software resources are mostly not explicitly linked from the manuscripts that introduced them or used them.This project will extend the capabilities of critical and widely used open scholarly infrastructures (CORE,Software Heritage, HAL) and tools (GROBID) operated by the consortium partners, delivering and deploying an effective solution for the management of the research software lifecycle, including: 1)ML-assisted identification of research software assets from within the manuscripts of scholarly papers, 2)validation of the identified assets by authors, 3) registration of software assets with PIDs and their archival. The solution will be optimised for deployment over open content available through the global network of open repositories aggregated by CORE (core.ac.uk), which constitutes with over 32 million full texts and250m+ metadata records from over 10k repositories currently the world's largest collection of open access documents. Our ML software for extraction and disambiguation of software assets will be realised as an extension of the state-of-the-art GROBID tool. We will build on established protocols, such as asOpenAIRE Guidelines v4.0, RIOXX v3 and Codemeta, to encode information about software assets and their links to research manuscripts establishing an interoperable and extensible workflow connecting open repositories (represented by HAL), aggregators (represented by CORE) and software archives(represented by Software Heritage). The efficacy of the developed tools and workflow will be validated in three use cases: 1) a life sciences demonstrator (for Europe PMC), 2) a multi-disciplinary demonstrator for institutional repositories (represented by HAL) and a 3) digital humanities case study (with links to DARIAH and EOSC).