scholarly journals Uniform resolution of compact identifiers for biomedical data

2017 ◽  
Author(s):  
Sarala M. Wimalaratne ◽  
Nick Juty ◽  
John Kunze ◽  
Greg Janée ◽  
Julie A. McMurry ◽  
...  

AbstractMost biomedical data repositories issue locally-unique accessions numbers, but do not provide globally unique, machine-resolvable, persistent identifiers for their datasets, as required by publishers wishing to implement data citation in accordance with widely accepted principles. Local accessions may however be prefixed with a namespace identifier, providing global uniqueness. Such “compact identifiers” have been widely used in biomedical informatics to support global resource identification with local identifier assignment.We report here on our project to provide robust support for machine-resolvable, persistent compact identifiers in biomedical data citation, by harmonizing the Identifiers.org and N2T.net (Name-To-Thing) meta-resolvers and extending their capabilities. Identifiers.org services hosted at the European Molecular Biology Laboratory – European Bioinformatics Institute (EMBL-EBI), and N2T.net services hosted at the California Digital Library (CDL), can now resolve any given identifier from over 600 source databases to its original source on the Web, using a common registry of prefix-based redirection rules.We believe these services will be of significant help to publishers and others implementing persistent, machine-resolvable citation of research data.

2020 ◽  
Author(s):  
Graham Smith ◽  
Andrew Hufton

<p>Researchers are increasingly expected by funders and journals to make their data available for reuse as a condition of publication. At Springer Nature, we feel that publishers must support researchers in meeting these additional requirements, and must recognise the distinct opportunities data holds as a research output. Here, we outline some of the varied ways that Springer Nature supports research data sharing and report on key outcomes.</p><p>Our staff and journals are closely involved with community-led efforts, like the Enabling FAIR Data initiative and the COPDESS 2014 Statement of Commitment <sup>1-4</sup>. The Enabling FAIR Data initiative, which was endorsed in January 2019 by <em>Nature</em> and <em>Scientific Data</em>, and by <em>Nature Geoscience</em> in January 2020, establishes a clear expectation that Earth and environmental sciences data should be deposited in FAIR<sup>5</sup> Data-aligned community repositories, when available (and in general purpose repositories otherwise). In support of this endorsement, <em>Nature</em> and <em>Nature Geoscience</em> require authors to share and deposit their Earth and environmental science data, and <em>Scientific Data</em> has committed to progressively updating its list of recommended data repositories to help authors comply with this mandate.</p><p>In addition, we offer a range of research data services, with various levels of support available to researchers in terms of data curation, expert guidance on repositories and linking research data and publications.</p><p>We appreciate that researchers face potentially challenging requirements in terms of the ‘what’, ‘where’ and ‘how’ of sharing research data. This can be particularly difficult for researchers to negotiate given that huge diversity of policies across different journals. We have therefore developed a series of standardised data policies, which have now been adopted by more than 1,600 Springer Nature journals. </p><p>We believe that these initiatives make important strides in challenging the current replication crisis and addressing the economic<sup>6</sup> and societal consequences of data unavailability. They also offer an opportunity to drive change in how academic credit is measured, through the recognition of a wider range of research outputs than articles and their citations alone. As signatories of the San Francisco Declaration on Research Assessment<sup>7</sup>, Nature Research is committed to improving the methods of evaluating scholarly research. Research data in this context offers new mechanisms to measure the impact of all research outputs. To this end, Springer Nature supports the publication of peer-reviewed data papers through journals like <em>Scientific Data</em>. Analysis of citation patterns demonstrate that data papers can be well-cited, and offer a viable way for researchers to receive credit for data sharing through traditional citation metrics. Springer Nature is also working hard to improve support for direct data citation. In 2018 a data citation roadmap developed by the Publishers Early Adopters Expert Group was published in <em>Scientific Data</em><sup>8</sup>, outlining practical steps for publishers to work with data citations and associated benefits in transparency and credit for researchers. Using examples from this roadmap, its implementation and supporting services, we outline how a FAIR-led data approach from publishers can help researchers in the Earth and environmental sciences to capitalise on new expectations around data sharing.</p><p>__</p><ol><li>https://doi.org/10.1038/d41586-019-00075-3</li> <li>https://doi.org/10.1038/s41561-019-0506-4</li> <li>https://copdess.org/enabling-fair-data-project/commitment-statement-in-the-earth-space-and-environmental-sciences/</li> <li>https://copdess.org/statement-of-commitment/</li> <li>https://www.force11.org/group/fairgroup/fairprinciples</li> <li>https://op.europa.eu/en/publication-detail/-/publication/d375368c-1a0a-11e9-8d04-01aa75ed71a1</li> <li>https://sfdora.org/read/</li> <li>https://doi.org/10.1038/sdata.2018.259</li> </ol>


Author(s):  
Martin Fenner ◽  
Daniella Lowenberg ◽  
Matt Jones ◽  
Paul Needham ◽  
Dave Vieglais ◽  
...  

The Code of Practice for Research Data Usage Metrics standardizes the generation and distribution of usage metrics for research data, enabling for the first time the consistent and credible reporting of research data usage. This is the first release of the Code of Practice and the recommendations are aligned as much as possible with the COUNTER Code of Practice Release 5 that standardizes usage metrics for many scholarly resources, including journals and books. With the Code of Practice for Research Data Usage Metrics data repositories and platform providers can report usage metrics following common best practices and using a standard report format. This is an essential step towards realizing usage metrics as a critical component in our understanding of how publicly available research data are being reused. This complements ongoing work on establishing best practices and services for data citation.


2018 ◽  
Author(s):  
Martin Fenner ◽  
Daniella Lowenberg ◽  
Matt Jones ◽  
Paul Needham ◽  
Dave Vieglais ◽  
...  

The Code of Practice for Research Data Usage Metrics standardizes the generation and distribution of usage metrics for research data, enabling for the first time the consistent and credible reporting of research data usage. This is the first release of the Code of Practice and the recommendations are aligned as much as possible with the COUNTER Code of Practice Release 5 that standardizes usage metrics for many scholarly resources, including journals and books. With the Code of Practice for Research Data Usage Metrics data repositories and platform providers can report usage metrics following common best practices and using a standard report format. This is an essential step towards realizing usage metrics as a critical component in our understanding of how publicly available research data are being reused. This complements ongoing work on establishing best practices and services for data citation.


2021 ◽  
pp. 016555152199863
Author(s):  
Ismael Vázquez ◽  
María Novo-Lourés ◽  
Reyes Pavón ◽  
Rosalía Laza ◽  
José Ramón Méndez ◽  
...  

Current research has evolved in such a way scientists must not only adequately describe the algorithms they introduce and the results of their application, but also ensure the possibility of reproducing the results and comparing them with those obtained through other approximations. In this context, public data sets (sometimes shared through repositories) are one of the most important elements for the development of experimental protocols and test benches. This study has analysed a significant number of CS/ML ( Computer Science/ Machine Learning) research data repositories and data sets and detected some limitations that hamper their utility. Particularly, we identify and discuss the following demanding functionalities for repositories: (1) building customised data sets for specific research tasks, (2) facilitating the comparison of different techniques using dissimilar pre-processing methods, (3) ensuring the availability of software applications to reproduce the pre-processing steps without using the repository functionalities and (4) providing protection mechanisms for licencing issues and user rights. To show the introduced functionality, we created STRep (Spam Text Repository) web application which implements our recommendations adapted to the field of spam text repositories. In addition, we launched an instance of STRep in the URL https://rdata.4spam.group to facilitate understanding of this study.


2017 ◽  
Vol 49 (6) ◽  
pp. 816-819 ◽  
Author(s):  
Lucila Ohno-Machado ◽  
Susanna-Assunta Sansone ◽  
George Alter ◽  
Ian Fore ◽  
Jeffrey Grethe ◽  
...  

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