Beware the Hype of Digital Publishing

2017 ◽  
Vol 39 (3) ◽  
Author(s):  
Martin G. Hicks ◽  
Carsten Kettner
Keyword(s):  
Open Access ◽  
Open Data ◽  
Digital Publishing ◽  
Scientific Publishing ◽  
Data Repositories

AbstractScientific publishing is changing; Open Access allows for published information to be freely shared, and Open Data repositories [

scholarly journals Open Data and Open Access Articles: Exploring Connections in the Life Sciences

2020 ◽  
Vol 9 (1) ◽  
Author(s):  
Sarah Williams
Keyword(s):  
Open Access ◽  
Life Sciences ◽  
Open Data ◽  
Data Bank ◽  
Data Availability ◽  
Research Articles ◽  
Future Research ◽  
Small Scale ◽  
Data Repositories ◽  
Current State

Objectives: This small-scale study explores the current state of connections between open data and open access (OA) articles in the life sciences. Methods: This study involved 44 openly available life sciences datasets from the Illinois Data Bank that had 45 related research articles. For each article, I gathered the OA status of the journal and the article on the publisher website and checked whether the article was openly available via Unpaywall and Research Gate. I also examined how and where the open data was included in the HTML and PDF versions of the related articles. Results: Of the 45 articles studied, less than half were published in Gold/Full OA journals, and while the remaining articles were published in Gold/Hybrid journals, none of them were OA. This study found that OA articles pointed to the Illinois Data Bank datasets similarly to all of the related articles, most commonly with a data availability statement containing a DOI. Conclusions: The findings indicate that Gold OA in hybrid journals does not appear to be a popular option, even for articles connected to open data, and this study emphasizes the importance of data repositories providing DOIs, since the related articles frequently used DOIs to point to the Illinois Data Bank datasets. This study also revealed concerns about free (not licensed OA) access to articles on publisher websites, which will be a significant topic for future research.

scholarly journals Crosswalk among Prominent Open Research Data Repositories

Webology ◽  
2021 ◽  
Vol 18 (2) ◽  
pp. 60-67
Author(s):  
Dr.M. Krishnamurthy ◽  
Dr. Bhalachandra S. Deshpande ◽  
Dr.C. Sajana
Keyword(s):  
Open Access ◽  
Open Data ◽  
Research Data ◽  
Data Repositories ◽  
Digital Repositories ◽  
Open Research ◽  
Global Movement ◽  
Access To Knowledge ◽  
Metadata Harvesting ◽  
Data Upload

Open Access is a synergised global movement using Internet to provide equal access to knowledge that once hid behind the subscription paywalls. Many new models for scholarly communication have emerged in recent past. One among them is institutional or digital repositories which archive the scholarly content of an organization. While the concept of Open Access opened new arena for institutional or digital repositories in the form of Open repositories. Likewise, the Open repositories for Research Data Management (RDM) are initiative to organize, store, cite, preserve, and share the collected data derived from the research. There are many multidisciplinary and subject specific open repositories for RDM offering exquisite features for perpetual management of research data. The objective of the present study is to evaluate features of popular Open Data Repositories-Zenodo, FigShare, Harvard Dataverse and Mendeley Data. The evaluation provided insights about the key features of the selected Open Data Repositories and which enable us to select the best among them. Zenodo provides maximum data upload limit. While the major features required by a researcher like DOI, File Types, citation support, licenses, search (metadata harvesting) are provided by all three repositories.

scholarly journals GigaByte: Publishing at the Speed of Research

2020 ◽  
Author(s):  
Scott C Edmunds ◽  
Laurie Goodman
Keyword(s):  
Open Access ◽  
Data Sharing ◽  
Review Process ◽  
Open Data ◽  
Software Tools ◽  
Cutting Edge ◽  
Data Sets ◽  
Scientific Publishing ◽  
Publication Process ◽  
Publishing Infrastructure

Current practices in scientific publishing are unsuitable for rapidly changing fields and for presenting updatable data sets and software tools. In this regard, and as part of the need to push scientific publishing to match the needs of modern research, we would like to announce the upcoming launch of GigaByte, an online open-access, open data journal that aims to be a new way to publish research following the software paradigm: CODE, RELEASE, FORK, UPDATE and REPEAT. Following on the success of GigaScience in promoting data sharing and reproducibility of research, its new sister, GigaByte, will aim to take this even further. With a focus on short articles, using a questionnaire-style review process, and combining that with the custom built publishing infrastructure from River Valley Technologies, we now have a cutting edge, XML-first publishing platform designed specifically to make the entire publication process easier, quicker, more interactive, and better suited to the speed needed to communicate modern research.

scholarly journals Neighbourhood Modelling for Urban Sustainability Assessment

2021 ◽  
Vol 13 (9) ◽  
pp. 4654
Author(s):  
Javier Orozco-Messana ◽  
Milagro Iborra-Lucas ◽  
Raimon Calabuig-Moreno
Keyword(s):  
Sustainable Development ◽  
Impact Assessment ◽  
Urban Policy ◽  
Sustainability Assessment ◽  
Open Data ◽  
Policy Impact ◽  
Physical Parameters ◽  
Data Repositories ◽  
Digital Twins ◽  
Climate Action

Climate change is becoming a dominant concern for advanced countries. The Paris Agreement sets out a global framework whose implementation relates to all human activities and is commonly guided by the United Nations Sustainable Development Goals (UN SDGs), which set the scene for sustainable development performance configuring all climate action related policies. Fast control of CO2 emissions necessarily involves cities since they are responsible for 70 percent of greenhouse gas emissions. SDG 11 (Sustainable cities and communities) is clearly involved in the deployment of SDG 13 (Climate Action). European Sustainability policies are financially guided by the European Green Deal for a climate neutral urban environment. In turn, a common framework for urban policy impact assessment must be based on architectural design tools, such as building certification, and common data repositories for standard digital building models. Many Neighbourhood Sustainability Assessment (NSA) tools have been developed but the growing availability of open data repositories for cities, together with big-data sources (provided through Internet of Things repositories), allow accurate neighbourhood simulations, or in other words, digital twins of neighbourhoods. These digital twins are excellent tools for policy impact assessment. After a careful analysis of current scientific literature, this paper provides a generic approach for a simple neighbourhood model developed from building physical parameters which meets relevant assessment requirements, while simultaneously being updated (and tested) against real open data repositories, and how this assessment is related to building certification tools. The proposal is validated by real data on energy consumption and on its application to the Benicalap neighbourhood in Valencia (Spain).

scholarly journals Conservation: A New Open Access Journal for Rapid Dissemination of the Transdisciplinary Dimensions of Biodiversity Conservation

Conservation ◽  
2021 ◽  
Vol 1 (1) ◽  
pp. 17-20
Author(s):  
Antoni Margalida ◽  
Luca Luiselli ◽  
José L. Tella ◽  
Shuqing Zhao
Keyword(s):  
Open Access ◽  
Biodiversity Conservation ◽  
Case Reports ◽  
Digital Publishing ◽  
Open Access Journal ◽  
Research Articles ◽  
Original Research ◽  
Rapid Dissemination

We are pleased to launch the new peer-reviewed open access journal, Conservation, published by MDPI (Multidisciplinary Digital Publishing Institute), which offers an exciting new opportunity to publish comprehensive reviews, original research articles, communications, case reports, letters, commentaries, and other perspectives related to the biological, sociological, ethical, economic, methodological, and other transdisciplinary dimensions of conservation [...]

scholarly journals The effects of publishing processes on scientific thought: Typography and typology in prehistoric archaeology (1950s–1990s)

2020 ◽  
Vol 33 (3) ◽  
pp. 273-297
Author(s):  
Sébastien Plutniak
Keyword(s):  
Twentieth Century ◽  
Scientific Production ◽  
Support Networks ◽  
Scientific Publishing ◽  
Prehistoric Archaeology ◽  
Data Repositories ◽  
Editorial Policies ◽  
Publication Data ◽  
File Formats ◽  
Wide Scale

ArgumentIn the last decades, many changes have occurred in scientific publishing, including online publication, data repositories, file formats and standards. The role played by computers in this process rekindled the argument on forms of technical determinism. This paper addresses this old debate by exploring the case of publishing processes in prehistoric archaeology during the second part of the twentieth century, prior to the wide-scale adoption of computers. It investigates the case of a collective and international attempt to standardize the typological analysis of prehistoric lithic objects, coined typologie analytique by Georges Laplace and developed by a group of French, Italian, and Spanish researchers. The aim of this paper is to: 1) present a general bibliometric scenario of prehistoric archaeology publishing in continental Europe; 2) report on the little-known typologie analytique method in archaeology, using publications, archives, and interviews; 3) show how the publication of scientific production was shaped by social (editorial policies, support networks) and material (typography features and publication formats) constraints; and 4) highlight how actors founded resources to control and counterbalance these effects, namely by changing and improving publishing formats.

scholarly journals Critérios para avaliação de ferramentas para repositório conforme a Ciência Aberta

2017 ◽  
Vol 6 (2) ◽  
Author(s):  
Angélica Conceição Dias Miranda ◽  
Milton Shintaku ◽  
Simone Machado Firme
Keyword(s):  
Open Access ◽  
Evaluation Criteria ◽  
Open Data ◽  
Open Science ◽  
Scientific Production ◽  
Open File ◽  
Research Institutes ◽  
Criteria For Evaluation ◽  
Science Movement ◽  
Bibliographic Study

Resumo: Os repositórios têm se tornado comum nas universidades e institutos de pesquisa, como forma de ofertar acesso à produção científica e, com isso, dar visibilidade à instituição. Entretanto, em muitos casos ainda estão restritos aos conceitos do movimento do arquivo aberto e acesso aberto, sendo que já se discute o Movimento da Ciência Aberta, revelando certo descompasso, requerendo estudos que apoiem a atualização dessa importante ferramenta. Nesse sentido, o presente estudo verifica os requisitos envolvidos nos movimentos abertos, de forma a apoiar a discussão técnica e tecnológica. Um estudo bibliográfico, que transforma as informações sobre os movimentos em critérios para avaliação de ferramentas para criação de repositórios, apresentando a implementação da interação como um novo desafio. Nas considerações procura-se contribuir com a discussão sobre a Ciência Aberta, de forma mais aplicada bem como o ajuste dos repositórios a esse movimento.Palavras-chave: Repositórios.  Critérios de avaliação. Arquivo aberto. Acesso aberto. Dados abertos. Ciência aberta.SURVEY OF CRITERIA FOR EVALUATION OF REPOSITORY TOOLS ACCORDING TO OPEN SCIENCE Abstract: Repositories have become common in universities and research institutes, as a way of offering access to scientific production, thereby giving visibility to the institution. Meanwhile, in many cases, repositories are restricted to the concepts of open movement and open access considering that the Open Science Movement is already being discussed. Regarding this matter, this study verifies the requirements involved in the open movements, in order to support a technical and technological discussion.  A bibliographic study that transforms information about movements into criteria to evaluate tools used to create repositories, presenting an implementation of interaction as a new challenge. In the considerations, we contribute with a discussion about an Open Science, in a more applied way, as well as the adjustment of the repositories to this movement.Keywords: Repositories. Evaluation Criteria. Open File. Open Access. Open Data. Open Science.

scholarly journals Estimating the reproducibility & transparency of smoking cessation behaviour change interventions

2020 ◽  
Author(s):  
Emma Norris ◽  
Yiwei He ◽  
Rachel Loh ◽  
Robert West ◽  
Susan Michie
Keyword(s):  
Open Access ◽  
Behaviour Change ◽  
Conflict Of Interest ◽  
Open Data ◽  
Smoking Behaviour ◽  
Funding Source ◽  
Behaviour Change Intervention ◽  
Behaviour Change Interventions ◽  
Replication Studies ◽  
Randomised Controlled

Introduction: Activities promoting research reproducibility and transparency are crucial for generating trustworthy evidence. Evaluation of smoking interventions is one area where vested interests may motivate reduced reproducibility and transparency. Aims: Assess markers of transparency and reproducibility in smoking behaviour change intervention evaluation reports.Methods: One hundred evaluation reports of smoking behaviour change intervention randomised controlled trials published in 2018-2019 were identified. Reproducibility markers of pre-registration, protocol sharing, data-, materials- and analysis script-sharing, replication of a previous study and open access publication were coded in identified reports. Transparency markers of funding and conflict of interest declarations were also coded. Coding was performed by two researchers, with inter-rater reliability calculated using Krippendorff’s alpha.Results: Seventy-one percent of reports were open access and 73% pre-registered. However, only 13% provided accessible materials, 7% accessible data and 1% accessible analysis scripts. No reports were replication studies. Ninety-four percent of reports provided a funding source statement and eighty-eight percent of reports provided a conflict of interest statement.Conclusions: Open data, materials, analysis and replications are rare in smoking behaviour change interventions, whereas funding source and conflict of interest declarations are common. Future smoking research should be more reproducible to enable knowledge accumulation.

scholarly journals TaxoNERD: deep neural models for the recognition of taxonomic entities in the ecological and evolutionary literature

2021 ◽  
Author(s):  
Nicolas Le Guillarme ◽  
Wilfried Thuiller
Keyword(s):  
Information Extraction ◽  
High Performance ◽  
Named Entity Recognition ◽  
Open Data ◽  
Entity Recognition ◽  
Data Repositories ◽  
Biodiversity Crisis ◽  
Domain Specific ◽  
Ecological Information ◽  
Gold Standard Corpus

1. Given the biodiversity crisis, we more than ever need to access information on multiple taxa (e.g. distribution, traits, diet) in the scientific literature to understand, map and predict all-inclusive biodiversity. Tools are needed to automatically extract useful information from the ever-growing corpus of ecological texts and feed this information to open data repositories. A prerequisite is the ability to recognise mentions of taxa in text, a special case of named entity recognition (NER). In recent years, deep learning-based NER systems have become ubiqutous, yielding state-of-the-art results in the general and biomedical domains. However, no such tool is available to ecologists wishing to extract information from the biodiversity literature. 2. We propose a new tool called TaxoNERD that provides two deep neural network (DNN) models to recognise taxon mentions in ecological documents. To achieve high performance, DNN-based NER models usually need to be trained on a large corpus of manually annotated text. Creating such a gold standard corpus (GSC) is a laborious and costly process, with the result that GSCs in the ecological domain tend to be too small to learn an accurate DNN model from scratch. To address this issue, we leverage existing DNN models pretrained on large biomedical corpora using transfer learning. The performance of our models is evaluated on four GSCs and compared to the most popular taxonomic NER tools. 3. Our experiments suggest that existing taxonomic NER tools are not suited to the extraction of ecological information from text as they performed poorly on ecologically-oriented corpora, either because they do not take account of the variability of taxon naming practices, or because they do not generalise well to the ecological domain. Conversely, a domain-specific DNN-based tool like TaxoNERD outperformed the other approaches on an ecological information extraction task. 4. Efforts are needed in order to raise ecological information extraction to the same level of performance as its biomedical counterpart. One promising direction is to leverage the huge corpus of unlabelled ecological texts to learn a language representation model that could benefit downstream tasks. These efforts could be highly beneficial to ecologists on the long term.

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