Open Science Infrastructure Research Articles

*READ**THIS*!! Spam as a threat for open science

Drawing on multiple sources of qualitative data, I describe a case of open science infrastructure (OSI) abuse. The case illustrates how developers navigated scholarly value tensions and issues of epistemic and platform legitimacy while battling spam on their open science webapp. Notably, their struggle used precious financial resources and drew attention away from other development tasks like feature expansion. This research makes evident that not only is OSI abuse like spam a financial burden, but it puts scholarly information security—specifically, the legitimacy of open science content—at risk. However, protecting against such abuse is not a trivial matter; it raises questions of who is responsible for defining and enforcing scholarly values. The urgency of this issue is magnified by OSI’s relationship to public trust in science.

From Deep Mutational Mapping of Allosteric Protein Landscapes to Deep Learning of Allostery and Hidden Allosteric Sites: Zooming in on "Allosteric Intersection" of Biochemical and Big Data Approaches.

The recent advances in artificial intelligence (AI) and machine learning have driven the design of new expert systems and automated workflows that are able to model complex chemical and biological phenomena. In recent years, machine learning approaches have been developed and actively deployed to facilitate computational and experimental studies of protein dynamics and allosteric mechanisms. In this review, we discuss in detail new developments along two major directions of allosteric research through the lens of data-intensive biochemical approaches and AI-based computational methods. Despite considerable progress in applications of AI methods for protein structure and dynamics studies, the intersection between allosteric regulation, the emerging structural biology technologies and AI approaches remains largely unexplored, calling for the development of AI-augmented integrative structural biology. In this review, we focus on the latest remarkable progress in deep high-throughput mining and comprehensive mapping of allosteric protein landscapes and allosteric regulatory mechanisms as well as on the new developments in AI methods for prediction and characterization of allosteric binding sites on the proteome level. We also discuss new AI-augmented structural biology approaches that expand our knowledge of the universe of protein dynamics and allostery. We conclude with an outlook and highlight the importance of developing an open science infrastructure for machine learning studies of allosteric regulation and validation of computational approaches using integrative studies of allosteric mechanisms. The development of community-accessible tools that uniquely leverage the existing experimental and simulation knowledgebase to enable interrogation of the allosteric functions can provide a much-needed boost to further innovation and integration of experimental and computational technologies empowered by booming AI field.

Open Science Infrastructure as a key component of Open Science

The Open Science movement is a response to the accumulated problems in scholarly communication, like the "reproducibility crisis", "serials crisis", and "peer review crisis". The European Commission defines priorities of Open Science as Findable, Accessible, Interoperable and Reproducible (FAIR) data, infrastructure and services in the European Open Science Cloud (EOSC), Next generation metrics, altmetrics and rewards, the future of scientific communication, research integrity and reproducibility, education and skills and citizen science. Open Science Infrastructure is also one of four key components of Open Science defined by UNESCO. Mainly represented among Open Science Infrastructures are institutional and thematic repositories for publications, research data, software and code. Furthermore, the Open Science Infrastructure services range may include discovery, mining, publishing, the peer review process, archiving and preservation, social networking tools, training, high-performance computing, and tools for processing and analysis. Successful Open Science Infrastructure should be based on community values and responsive to needed changes. Preferably the Open Science Infrastructure should be distributed, enabling machine-actionable tools and services, supporting reusability and reproducibility, quality FAIR data, interoperability, sustainability, long-term preservation and funding.

Open Science-friendly national R&D knowledge and information infrastructure

This paper outlines the functionality of the South Korea’s National Science and Technology Information Service (NTIS), maintained by the Korea Institute of Science and Technology Information (KISTI). NTIS is a “one-stop shop” portal federating information on national R&D projects from multiple databases and metadata aggregators, including links to downloadable Open Access outputs and raw data. Among other functions, it provides a range of services based on R&D information analysis to facilitate open collaboration and knowledge co-development (e.g., providing network maps visualising collaboration among researchers and research institutes based on the field of research interest). In addition, some challenges associated with NTIS are outlined, including a lack of explicit Open Science mandates in national legislation and policies. We also suggest some opportunities for further development of the NTIS platform so that it can better support Open Science. These include, for example, alternative research impact metrics and a virtual laboratory service to be embedded into the NTIS functionality. Insights offered in this paper regarding the Korean experience of building an Open Science infrastructure could be useful to anyone planning to establish an R&D knowledge and information infrastructure, including various Open Science building blocks, in other contexts and countries.

Open science in China: Openness, economy, freedom & innovation

Taking credit for digitalization and platformization, China has initiated its open science infrastructure implementation and made an effort to focus on open access (OA) journals and data sharing over the past two decades. With the continuous development need, issues and concerns have caught in attention, including data accessibility, research transparency, general population awareness and communication of science, public trust in science, and scientific research and innovation efficiency. This paper has unfolded the maze of open science stance in China and elaborated on its current economy, openness and freedom extents, and future innovation potential towards a global open science community, within depth and scope of both the Chinese and Western scholars’ interpretations.

Open Science for Accelerating the Sustainable Development Goals: Status and Prospects in Asia and the Pacific

Achieving the United Nations Sustainable Development Goals is increasingly challenging due to widening inequality in access to scientific and technological knowledge and resources. With science remaining too discipline based, and policymakers too often science averse, there is a need for greater understanding of the opportunities and challenges of open science for science practitioners, policy makers and communities. Acknowledging that open science can be a powerful tool to reduce inequalities, UNESCO has been supporting the shift to open science. Following global multistakeholder consultation, the UNESCO Recommendation on Open Science was adopted in November 2021, establishing a universal definition, common standards and shared set of values and principles. In 2021, the UNESCO Regional Science Bureau for Asia and the Pacific partnered with the Institute for Study and Development Worldwide on local and national mapping to identify implementation strategies and mechanisms already in place to enable open science in Asia and the Pacific, and to identify what more is needed. Focused on Malaysia, Republic of Korea, Pakistan, Samoa and Uzbekistan, the study showed that while there are many examples of good practice in aspects of open science, none of the focus countries currently has in place all the policies, infrastructure, awareness and capacity building needed. Typically, clear policies on open science have not yet been articulated and funding mechanisms not yet established. Trust is a key pre-requisite for open science. Current inequities in access to open science infrastructure will need to be addressed or implementation may be unbalanced, exacerbating existing inequities at national, regional, and global scales. There are many opportunities to learn from existing efforts toward open science, but there will be no generic model; each country will need to design an open science model and implementation pathway suited to its context. A predominant message from this research was that the convening power of UNESCO should continue to be harnessed to engage countries on open science implementation. Further, those committed to open science will need to work hard, with UNESCO, to democratize science and encourage an ethos of “policy for science, science for policy - science for society and society for science”.

The global environmental agenda urgently needs a semantic web of knowledge

Progress in key social-ecological challenges of the global environmental agenda (e.g., climate change, biodiversity conservation, Sustainable Development Goals) is hampered by a lack of integration and synthesis of existing scientific evidence. Facing a fast-increasing volume of data, information remains compartmentalized to pre-defined scales and fields, rarely building its way up to collective knowledge. Today's distributed corpus of human intelligence, including the scientific publication system, cannot be exploited with the efficiency needed to meet current evidence synthesis challenges; computer-based intelligence could assist this task. Artificial Intelligence (AI)-based approaches underlain by semantics and machine reasoning offer a constructive way forward, but depend on greater understanding of these technologies by the science and policy communities and coordination of their use. By labelling web-based scientific information to become readable by both humans and computers, machines can search, organize, reuse, combine and synthesize information quickly and in novel ways. Modern open science infrastructure—i.e., public data and model repositories—is a useful starting point, but without shared semantics and common standards for machine actionable data and models, our collective ability to build, grow, and share a collective knowledge base will remain limited. The application of semantic and machine reasoning technologies by a broad community of scientists and decision makers will favour open synthesis to contribute and reuse knowledge and apply it toward decision making.

We Can Make a Better Use of ORCID: Five Observed Misapplications

Since 2012, the “Open Researcher and Contributor ID” organisation (ORCID) has been successfully running a worldwide registry, with the aim of “providing a unique, persistent identifier for individuals to use as they engage in research, scholarship, and innovation activities”. Any service in the scholarly communication ecosystem (e.g., publishers, repositories, CRIS systems, etc.) can contribute to a non-ambiguous scholarly record by including, during metadata deposition, referrals to iDs in the ORCID registry. The OpenAIRE Research Graph is a scholarly knowledge graph that aggregates both records from the ORCID registry and publication records with ORCID referrals from publishers and repositories worldwide to yield research impact monitoring and Open Science statistics. Graph data analytics revealed “anomalies” due to ORCID registry “misapplications”, caused by wrong ORCID referrals and misexploitation of the ORCID registry. Albeit these affect just a minority of ORCID records, they inevitably affect the quality of the ORCID infrastructure and may fuel the rise of detractors and scepticism about the service. In this paper, we classify and qualitatively document such misapplications, identifying five ORCID registrant-related and ORCID referral-related anomalies to raise awareness among ORCID users. We describe the current countermeasures taken by ORCID and, where applicable, provide recommendations. Finally, we elaborate on the importance of a community-steered Open Science infrastructure and the benefits this approach has brought and may bring to ORCID.

CloudRT: A Chinese example of open science infrastructure and services

As the backbone of the open science campaign, open science infrastructures (OSIs) play an increasingly important role in scientific innovation and the digital transformation of society. Nevertheless, OSIs still have a range of issues to contend with, particularly as they move towards more openness and a sustainable future. In this paper, as a case study of OSIs in China, we present the experience of operating CloudRT—the first and only open-access cloud-native high-performance computing ray-tracing platform in the world. Quantitative analysis demonstrates how such an OSI can produce an interdisciplinary impact beyond expectations. Moreover, the value of CloudRT is also shown through its acknowledgement by participants across the whole innovation chain, from pure science and engineering to applications in vertical industries. Both inspirations from this practice and its open challenges are discussed. Suggestions are put forward to guide the future efforts of stakeholders to develop a fruitful OSI ecosystem.

Open access repositories: Functions and trends

Open access repositories are an integral part of open science infrastructure that ensures the accessibility and findability of research results. This article is based on the analysis of the various types of repositories. The authors attempted to identify main functions of these platforms, their features and development trends. The sample includes 11 repositories, both institutional and thematic projects, and also general-purpose platforms. The main function of repositories is the storage of publications, although over time the role of these services as the publication priority registrators is increasing. Projects typically feature pre-moderation procedures, as well as a rather careful attitude to the metadata and its accuracy. Only one repository charges publication fee, their revenue come from sponsorship funds, donations, advertising, additional paid services (in various combinations). The possibilities of social interaction as a rule are quite limited: neither reviewing, nor even commenting are built-in functions of the reviewed projects. Collective work on the manuscript is also impossible. The trends of repositories future development are the diversification of formats and types of works exchanged by scientists, as well as the increasing of the importance of non-profit projects for the scientific communication infrastructure.

The Changing Nature of Data: Sociality, Relationality, and Implications for Organizing

This symposium showcases recent research projects on the changing nature of data and its implications for organizations, online communities, and platforms. The era of “big” data, and the algorithms they feed, is underway. Scholars across the disciplines of information science, human–computer interaction, sociology, communication, legal studies, and computer-supported cooperative work have discussed the implications for society of the new forms of data, the categories they bring about, or the new ways of knowing they enable. Yet significant questions for scholars of work, technology, and organizations remain. We will present fresh insights into three aspects of the changing nature of data — sociality, relationality, and organizing consequences — and discuss the implications of these changes for organizations, online communities, and platforms. The contexts in which we will explore the changing nature of data are diverse and include organizations (high technology firm and hospital), online communities (firm-sponsored open-source software development) and platforms (online music discovery, open science infrastructure). Overall, the symposium will address these goals: (1) highlighting new findings and theory with the goal of contributing to richer understanding of the changing nature of data in organizations and fields; (2) comparing and contrasting the challenges of development and use of data, emerging technologies, and algorithms in various settings among different kinds of actors; (3) providing a forum for discussion of the changing nature of data and its implications for organizations, fields, and society. Governing the Open Science Commons Through Digital Infrastructures Presenter: Paolo Vincenzo Leone; McGill U. Presenter: Samer Faraj; McGill U. Presenter: Arvind Karunakaran; McGill U. Emergent Group Diversity in Open Knowledge Evaluation: Evidence from Online Communities Presenter: Shiko M. Ben-Menahem; ETH Zurich Presenter: Yash Raj Shrestha; ETH Zurich Presenter: Georg von Krogh; ETH Zurich The Data Work of Algorithmic Recommendation Systems Presenter: Katherine C. Kellogg; MIT Basic Objects, Categorization, and Organizing Presenter: Cristina Alaimo; Luiss U. Presenter: Jannis Kallinikos; London School of Economics

Leveraging Concepts in Open Access Publications

This paper addresses the integration of a Named Entity Recognition and Disambiguation (NERD) service within a group of open access (OA) publishing digital platforms and considers its potential impact on both research and scholarly publishing. The software powering this service, called entity-fishing, was initially developed by Inria in the context of the EU FP7 project CENDARI and provides automatic entity recognition and disambiguation using the Wikipedia and Wikidata data sets. The application is distributed with an open-source licence, and it has been deployed as a web service in DARIAH's infrastructure hosted by the French HumaNum. In the paper, we focus on the specific issues related to its integration on five OA platforms specialized in the publication of scholarly monographs in the social sciences and humanities (SSH), as part of the work carried out within the EU H2020 project HIRMEOS (High Integration of Research Monographs in the European Open Science infrastructure). In the first section, we give a brief overview of the current status and evolution of OA publications, considering specifically the challenges that OA monographs are encountering. In the second part, we show how the HIRMEOS project aims to face these challenges by optimizing five OA digital platforms for the publication of monographs from the SSH and ensuring their interoperability. In sections three and four we give a comprehensive description of the entity-fishing service, focusing on its concrete applications in real use cases together with some further possible ideas on how to exploit the annotations generated. We show that entity-fishing annotations can improve both research and publishing process. In the last chapter, we briefly present further possible application scenarios that could be made available through infrastructural projects.

Implementation of Open Science in Lithuania

The number of open science policies being adopted in Europe by universities and research institutions is constantly increasing, however many European countries face difficulties while implementing open science practically. This publication reveals the Lithuanian landscape of open science policies and institutional involvement in open science practices. Prerequisites for sustainable and consistent open science implementation such as open science infrastructure, incentives for researchers, research assessment, and repositories' compliance with EC requirements on a national level are discussed.

Enabling A Conversation Across Scholarly Monographs through Open Annotation

The digital format opens up new possibilities for interaction with monographic publications. In particular, annotation tools make it possible to broaden the discussion on the content of a book, to suggest new ideas, to report errors or inaccuracies, and to conduct open peer reviews. However, this requires the support of the users who might not yet be familiar with the annotation of digital documents. This paper will give concrete examples and recommendations for exploiting the potential of annotation in academic research and teaching. After presenting the annotation tool of Hypothesis, the article focuses on its use in the context of HIRMEOS (High Integration of Research Monographs in the European Open Science Infrastructure), a project aimed to improve the Open Access digital monograph. The general line and the aims of a post-peer review experiment with the annotation tool, as well as its usage in didactic activities concerning monographic publications are presented and proposed as potential best practices for similar annotation activities.

The open science infrastructure in Russia and the world

The article gives an overview of open access projects that form the new infrastructure for scientific communication. It provides information on initiatives and programs contributing to the development of open science in Russia and in the world. The paper also describes innovative scientific projects and platforms that significantly accelerate exchange of information and communication between scientists and create new opportunities for their cooperation and for society.The scientific novelty of the article consists in the distinction between the notions of ‘publication’ and ‘article’ or ‘edition’ in the context of scientific communication and the work of libraries, the description of the challenges that the new media era puts behind the system of scientific communications and libraries, and Russian projects, which aim to solve the described problems.The system of scientific communication has transformed significantly over the past two decades, alternative channels of information exchange are beginning to play a leading role and become the competitors of the traditional media (scientific journals), which have converted into electronic form, but still remain rooted in the past, supported by the inertia of administration of science.In Russia the achievements of open science are still much too modest compared to Europe, but the necessary background has already been created by libraries and non-for-profit organizations. Further development of such projects will depend on whether government, libraries and universities could use these instruments and the capabilities of the new media, reorienting to a new paradigm of access to scientific information.

With open science gaining traction, do we need an Australasia PubMed Central (PMC)? A qualitative investigation.

Open biomedical repositories, such as PubMed Central (PMC), are a means to make research discoverable and permanently accessible. Assessing the potential interest of key stakeholders in an Australasia PubMed Central was the objective of this research. The investigation is novel, assisting in the development of open science infrastructure through its systematic analysis of the potential interest in, and viability of a biomedical repository for managing openly accessible research outputs for the Australasia region. The research adopted a qualitative approach based on semi-structured interviews and a focus group. Forty-four stakeholders located throughout Australia and New Zealand participated in the research. Participants expanded upon their experience of PubMed, MEDLINE, PMC and their use of information resources for research and clinical practice. The Evidence Based Healthcare (EBHC) pyramid was the theoretical model adopted to explain open biomedical repository processes. A strengths, weaknesses, opportunities and threats (SWOT) analysis identified support for exploring membership of an international PMC system, in particular Europe PMC. Lessons learnt from PMC US, Europe PMC and PMC Canada (collectively known as PubMed Central International) informed the investigation. A major strength identified was that PubMed Central International has been able to achieve high levels of compliance way beyond that of most institutional repositories. A great threat faced is overcoming the difficulties of working together with other major world bodies and financially sustaining an Australasia PMC. Improving Australasian biomedical knowledge management processes may be possible from adopting a PMC for retrieving and transferring research, linked to the data underlying the research. This in turn could help put regional research under a brighter spotlight, potentially leading to improvements in research quality. There is an opportunity for a potential Australasia PMC to harvest biomedical research from the National Library of Australia’s aggregator database, Trove and work closely with Europe PMC to avoid duplication of effort. Overall, establishment of an Australasia permanent biomedical digital open repository is perceived as important, with significant potential flow-on benefits to healthcare, industry and society.

HIRMEOS – High Integration of Research Monographs in the European Open Science infrastructure

Open Access has matured for journals, but open access uptake in the book market is still delayed, despite the fact that books continue to be the leading publishing format for qualitative social sciences and humanities. HIRMEOS, High Integration of Research Monographs in the European Open Science infrastructure, is a 30-month EU-funded project and tackles the main obstacles of the full integration of important platforms supporting open access monographs and their contents.HIRMEOS will work on innovative services on identification, entities recognition, annotation, and altmetrics, using when possible common standards. These standards are well established in journal publishing, however not common enough yet in book publishing to pave the way for deeper linking of book and journal content or crosslinking of references, entities or usage. HIRMEOS is based upon 5 Open Access book-publishing platforms, OpenEdition Books, OAPEN Library, EKT Open Book Press, Ubiquity Press and Göttingen University Press. During the run of the project these platforms integrate tools for identification, authentication and interoperability (DOI, ORCID, Fundref), for additional information and entity extraction (INRIA (N)ERD), the ability to annotate monographs (Hypothes.is), and gather usage and alternative metric data. HIRMEOS will also enrich the technical capacities of the Directory of Open Access Books (DOAB), a most significant indexing service for open access monographs globally, to receive automated information for ingestion, while it will also develop a structured certification system to document monograph peer-review. The project consortium will develop shared minimum standards for their monograph publications, such that allow the full embedding of technologies and content in the European Science Cloud. Finally, the project will have a catalyst effect in including more disciplines into the Open Science paradigm, widening its boundaries towards the SSH.The poster will give facts and figures aboutthe involved platforms and their catalogues,the types of services to be implemented and the used standards,the expected benefit for the Social Sciences and Humanities playersthe global benefits for the Open Science environment

SCOSS: A global Sustainability Coalition for Open Science Services

Watch the VIDEO here.The transition to a more far-reaching OA and Open Science is often very much dependent on services and on an infrastructure embedded in workflows to deliver on policy. However, the sustainability of Open Access or Open Science services is often a long way from being assured. A relatively new global coalition called SCOSS will enable the international research community, through its institutions and funding organisations, to take responsibility for sustaining those services. It will do this by providing a new co-ordinated cost-sharing framework to ensure that non-commercial OS services that underpin the development of wider global Open Access and Open Science are sustained in the future.The SCOSS group makes recommendations on what to fund and why based on a rigorous evaluation procedure where services are invited to apply and provide extensive information to the SCOSS group. Applicants provide information on the service’s value to communities such as funders, universities, libraries, authors, research managers, repositories, etc.; information on the governance structure, the technical solution, costs, sustainability measures, and their plans for the future.SCOSS is currently in the middle of a pilot to test the concept. Current SCOSS members include the Australasian Open Access Strategy Group (AOASG), the Council of the Australian University Librarians (CAUL), LIBER, EIFL and SPARC Europe with other organisations following the pilot and advising such as the Confederation of Open Access Repositories (COAR), the European Research Council (ERC), the European University Association (EUA), and others. This presentation will outline the Terms of Reference of the coalition, the case, the SCOSS governance structure, experience with the pilot and challenges to date. This session is of interest to those who are interested in helping the user community to sustain an Open Access and Open Science infrastructure to help implement policy goals, and finding out how they can contribute to making that happen.

A Data Infrastructure for Digital Cultural Heritage: Characteristics, Requirements and Priority Services

The European amount of digitized material is growing very rapidly, as national, regional and European programmes support the digitization processes by museums, libraries, archives, archaeological sites, and audiovisual repositories. The generation of digital cultural heritage is accelerated also by the impulse of Europeana that is fostering the European cultural institutions to produce even more digital content. Moreover digital cultural heritage content are complex and interlinked through many relations. European countries are working for the future, in order to create a data infrastructure devoted to cultural heritage research. Currently, Europe have twin projects (DC-NET and INDICATE) ongoing and a new international coordination action is under preparation to design a validated roadmap for the preservation of digital cultural content. These initiatives are contributing to smooth the way to the Open Science Infrastructure for Digital Cultural Heritage, which is foreseen in 2020.