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Different Preservation Levels: The Case of Scholarly Digital Editions

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Authors : Elias Oltmanns, Tim Hasler, Wolfgang Peters-Kottig, Heinz-Günter Kuper

Ensuring the long-term availability of research data forms an integral part of data management services. Where OAIS compliant digital preservation has been established in recent years, in almost all cases the services aim at the preservation of file-based objects.

In the Digital Humanities, research data is often represented in highly structured aggregations, such as Scholarly Digital Editions. Naturally, scholars would like their editions to remain functionally complete as long as possible.

Besides standard components like webservers, the presentation typically relies on project specific code interacting with client software like webbrowsers. Especially the latter being subject to rapid change over time invariably makes such environments awkward to maintain once funding has ended.

Pragmatic approaches have to be found in order to balance the curation effort and the maintainability of access to research data over time. A sketch of four potential service levels aiming at the long-term availability of research data in the humanities is outlined: (1) Continuous Maintenance, (2) Application Conservation, (3) Application Data Preservation, and (4) Bitstream Preservation.

The first being too costly and the last hardly satisfactory in general, we suggest that the implementation of services by an infrastructure provider should concentrate on service levels 2 and 3. We explain their strengths and limitations considering the example of two Scholarly Digital Editions.

URL : Different Preservation Levels: The Case of Scholarly Digital Editions

DOI : http://doi.org/10.5334/dsj-2019-051

Research integrity: environment, experience, or ethos?

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Authors : Bjørn Hofmann, Søren Holm

Background

Research integrity has gained attention in the general public as well as in the
research community. We wanted to investigate knowledge, attitudes, and practices amongst researchers that have recently finished their PhD and compare this to their responses during their PhD fellowship. In particular, we wanted to investigate whether their attitudes are related to their experiences of their immediate research environment.

Material and method

Researchers (n = 86) awarded the PhD degree at the Faculty of Medicine at the University of Oslo in 2016 were invited to answer a questionnaire about knowledge, attitudes, and actions related to scientific dishonesty. Seventy-two responded (83.7%). The results were compared with results among first-year doctoral students who responded to the same questionnaire during 2010–2017.

Results

Overall, 13% of PhDs reported that they knew of people in their immediate research environment who had committed serious forms of scientific dishonesty. A small percentage of PhDs (1.4%) indicated that they themselves had committed such acts. About 3% of the candidates had experienced pressure to commit serious forms of dishonesty and nearly a third of respondents had experienced unethical pressure with respect to authorship during the course of their fellowship.

Thirteen percent reported that they had experienced unethical pressure in relation to other forms of dishonesty and 11% had experienced the consequences of some form of scientific dishonesty. Eighteen percent of the respondents believed that one or more actions, which in the literature were perceived as scientific misconduct, were not wrong. We find a connection between attitudes and the perceived research integrity of their research environment.

The results also show a difference between PhD students and graduated PhDs in terms of scientific dishonesty. In some areas, the PhDs’ norms are stricter, such as for the use of statistical analysis methods, while there is little change in others, such as in misconduct in order to expedite publications.

Conclusion

Many PhDs knew about serious forms of scientific misconduct from the research environment in which they are trained, and some also report misconduct themselves.

Some experienced pressure to serious forms of misconduct and a large proportion of the respondents had experienced unethical pressure with respect to authorship during their fellowship. Attitudes change during the PhD studies, but ambiguously. Scientific misconduct seems to be an environmental issue as much as a matter of personal integrity.

URL : Research integrity: environment, experience, or ethos?

DOI : https://doi.org/10.1177%2F1747016119880844

 

Public Microbial Resource Centers: Key Hubs for Findable,Accessible, Interoperable, and Reusable (FAIR) Microorganismsand Genetic Materials

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Authors : P. Becker, M. Bosschaerts, P. Chaerle, H.-M. Daniel, A. Hellemans, A. Olbrechts, L. Rigouts, A. Wilmotte, M. Hendrickx

In the context of open science, the availability of research materials is essential for knowledge accumulation and to maximize the impact of scientific research. In microbiology, microbial domain biological resource centers (mBRCs) have long-standing experience in preserving and distributing authenticated microbial strains and genetic materials (e.g., recombinant plasmids and DNA libraries) to support new discoveries and follow-on studies.

These culture collections play a central role in the conservation of microbial biodiversity and have expertise in cultivation, characterization, and taxonomy of microorganisms. Information associated with preserved biological resources is recorded in databases and is accessible through online catalogues.

Legal expertise developed by mBRCs guarantees end users the traceability and legality of the acquired material, notably with respect to the Nagoya Protocol. However, awareness of the advantages of depositing biological materials in professional repositories remains low, and the necessity of securing strains and genetic resources for future research must be emphasized.

This review describes the unique position of mBRCs in microbiology and molecular biology through their history, evolving roles, expertise, services, challenges, and international collaborations. It also calls for an increased deposit of strains and genetic resources, a responsibility shared by scientists, funding agencies, and publishers.

Journal policies requesting a deposit during submission of a manuscript represent one of the measures to make more biological materials available to the broader community, hence fully releasing their potential and improving openness and reproducibility in scientific research.

URL : https://orbi.uliege.be/bitstream/2268/240381/1/Applied%20and%20Environmental%20Microbiology-2019-Becker-e01444-19.full-1.pdf

The institutional repository landscape in medical schools and academic health centers: a 2018 snapshot view and analysis

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Authors : Daniel G. Kipnis, Lisa A. Palmer, Ramune K. Kubilius

Objective

This study uses survey research methods to gain a deeper understanding of the institutional repository (IR) landscape in medical schools and academic health centers.

Methods

Members of the Association of Academic Health Sciences Libraries (AAHSL) were surveyed about their IRs. The authors used a mixed-methods approach of a survey and qualitative content analysis to identify common themes.

Results

Survey results indicate that a large majority of responding medical schools and academic health centers have or are implementing an IR (35 out of 50, 70%). Of these, 60% (21 institutions) participate in an institution-wide IR rather than administer their own repositories.

Much of the archived content is grey literature that has not already been published, but the percentage of original content varies greatly among institutions. The majority (57.1%) of respondent institutions are not considering an open access policy or mandate. Most institutions (71.4%) reported that repository staff are depositing materials on behalf of users.

DSpace and bepress Digital Commons are the most popular repository platforms in this community. The planned enhancements that were most frequently reported were implementing a discovery layer and ORCID integration. The majority of respondents (54.3%) do not plan to migrate to a different platform in the foreseeable future.

Analysis of respondent comments identified the following themes: integration, redundancy, and reporting; alternatives and exploration; uniqueness; participation; and funding and operations.

Conclusions

The study results capture a view of the IR landscape in medical schools and academic health centers and help readers understand what services their peers have in place as well as their plans for future developments.

URL : The institutional repository landscape in medical schools and academic health centers: a 2018 snapshot view and analysis

DOI : https://dx.doi.org/10.5195%2Fjmla.2019.653

From Academia to Software Development: Publication Citations in Source Code Comments

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Authors : Akira Inokuchi, Yusuf Sulistyo Nugroho, Fumiaki Konishi, Hideaki Hata, Akito Monden, Kenichi Matsumoto

Academic publications have been evaluated with the impact on research communities based on the number of citations. On the other hand, the impact of academic publications on industry has been rarely studied.

This paper investigates how academic publications contribute to software development by analyzing publication citations in source code comments in open source software repositories.

We propose an automated approach of detecting academic publications based on Named Entity Recognition, and achieve 0.90 in F1 as detection accuracy. We conduct a large-scale study of publication citations with 319,438,977 comments collected from active 25,925 repositories written in seven programming languages.

Our findings indicate that academic publications can be knowledge sources of software development, and there can be potential issues of obsoleting knowledge.

URL : https://arxiv.org/abs/1910.06932

The NIH Open Citation Collection: A public access, broad coverage resource

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Authors : B. Ian Hutchins, Kirk L. Baker, Matthew T. Davis, Mario A. Diwersy, Ehsanul Haque, Robert M. Harriman, Travis A. Hoppe, Stephen A. Leicht, Payam Meyer, George M. Santangelo

Citation data have remained hidden behind proprietary, restrictive licensing agreements, which raises barriers to entry for analysts wishing to use the data, increases the expense of performing large-scale analyses, and reduces the robustness and reproducibility of the conclusions.

For the past several years, the National Institutes of Health (NIH) Office of Portfolio Analysis (OPA) has been aggregating and enhancing citation data that can be shared publicly. Here, we describe the NIH Open Citation Collection (NIH-OCC), a public access database for biomedical research that is made freely available to the community.

This dataset, which has been carefully generated from unrestricted data sources such as MedLine, PubMed Central (PMC), and CrossRef, now underlies the citation statistics delivered in the NIH iCite analytic platform.

We have also included data from a machine learning pipeline that identifies, extracts, resolves, and disambiguates references from full-text articles available on the internet. Open citation links are available to the public in a major update of iCite (https://icite.od.nih.gov).

URL : The NIH Open Citation Collection: A public access, broad coverage resource

DOI : https://doi.org/10.1371/journal.pbio.3000385

 

The diverse niches of megajournals: Specialism within generalism

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Authors: Kyle Siler, Vincent Larivière, Cassidy R. Sugimoto

Over the past decade, megajournals have expanded in popularity and established a legitimate niche in academic publishing. Leveraging advantages of digital publishing, megajournals are characterized by large publication volume, broad interdisciplinary scope, and peer‐review filters that select primarily for scientific soundness as opposed to novelty or originality.

These publishing innovations are complementary and competitive vis‐à‐vis traditional journals. We analyze how megajournals (PLOS One, Scientific Reports) are represented in different fields relative to prominent generalist journals (Nature, PNAS, Science) and “quasi‐megajournals” (Nature Communications, PeerJ).

Our results show that both megajournals and prominent traditional journals have distinctive niches, despite the similar interdisciplinary scopes of such journals.

These niches—defined by publishing volume and disciplinary diversity—are dynamic and varied over the relatively brief histories of the analyzed megajournals. Although the life sciences are the predominant contributor to megajournals, there is variation in the disciplinary composition of different megajournals.

The growth trajectories and disciplinary composition of generalist journals—including megajournals—reflect changing knowledge dissemination and reward structures in science.

URL : The diverse niches of megajournals: Specialism within generalism

DOI : https://doi.org/10.1002/asi.24299