Étiquette : biomedical research

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Nanopublications: A Growing Resource of Provenance-Centric Scientific Linked Data

Authors : Tobias Kuhn, Albert Meroño-Peñuela, Alexander Malic, Jorrit H. Poelen, Allen H. Hurlbert, Emilio Centeno Ortiz, Laura I. Furlong, Núria Queralt-Rosinach, Christine Chichester, Juan M. Banda, Egon Willighagen, Friederike Ehrhart, Chris Evelo, Tareq B. Malas, Michel Dumontier

Nanopublications are a Linked Data format for scholarly data publishing that has received considerable uptake in the last few years. In contrast to the common Linked Data publishing practice, nanopublications work at the granular level of atomic information snippets and provide a consistent container format to attach provenance and metadata at this atomic level.

While the nanopublications format is domain-independent, the datasets that have become available in this format are mostly from Life Science domains, including data about diseases, genes, proteins, drugs, biological pathways, and biotic interactions.

More than 10 million such nanopublications have been published, which now form a valuable resource for studies on the domain level of the given Life Science domains as well as on the more technical levels of provenance modeling and heterogeneous Linked Data.

We provide here an overview of this combined nanopublication dataset, show the results of some overarching analyses, and describe how it can be accessed and queried.

URL : https://arxiv.org/abs/1809.06532

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Towards a culture of open science and data sharing in health and medical research

Author : Anisa Rowhani-Farid

This thesis investigated the factors that contribute to the cultural shift towards open science and data sharing in health and medical research, with a focus on the role health and medical journals play.

The findings of this research demonstrate that journal data sharing policies are not effective and that journals do not currently provide incentives for sharing.

This study contributed to the movement towards more reproducible research by providing empirical evidence for the strengthening of journal data sharing policies and the adoption of an incentive for open research.

DOI : https://doi.org/10.5204/thesis.eprints.119697

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Open Access E-Books in the Field of Health Sciences: A Scientometric Study

Authors : Fayaz Ahmad Loan, Ufaira Yaseen Shah

The Directory of Open Access Books (DOAB) is a discovery service for open access e-books. It provides a searchable index to peer-reviewed e-books published under an open access business model.

The present study aims to assess the scientometric trends of the open access e-books in the field of the Health Sciences available through the Directory of Open Access Books. In order to fulfil the set objectives, the relevant details of the Health Sciences e-books were collected.

The results reveal that 916 e-books are available in the field of the Health Sciences through the Directory of Open Access. The highest number of e-books is contributed in General Medicine (40.61%, 372) and in the English language (83.84%, 768). These e-books also contain current information as the majority (88.32%, 809) of these are published from 2011 onwards by the reputed publishers like Frontiers Media, SciELO, Springer, Palgrave Macmillan, and Oxford University Press etc.

The Directory of Open Access Books was selected as a source for data collection whereas the Health Sciences was selected as the field of study. Therefore, the finding can’t be generalised across directories and subjects.

URL : Open Access E-Books in the Field of Health Sciences: A Scientometric Study

Alternative location : https://ijism.ricest.ac.ir/index.php/ijism/article/view/1272

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Post-publication peer review in biomedical journals: overcoming obstacles and disincentives to knowledge sharing

Authors : Valerie Matarese, Karen Shashok

The importance of post-publication peer review (PPPR) as a type of knowledge exchange has been emphasized by several authorities in research publishing, yet biomedical journals do not always facilitate this type of publication.

Here we report our experience publishing a commentary intended to offer constructive feedback on a previously published article. We found that publishing our comment required more time and effort than foreseen, because of obstacles encountered at some journals.

Using our professional experience as authors’ editors and our knowledge of publication policies as a starting point, we reflect on the probable reasons behind these obstacles, and suggest ways in which journals could make PPPR easier. In addition, we argue that PPPR should be more explicitly valued and rewarded in biomedical disciplines, and suggest how these publications could be included in research evaluations.

Eliminating obstacles and disincentives to PPPR is essential in light of the key roles of post-publication analysis and commentary in drawing attention to shortcomings in published articles that were overlooked during pre-publication peer review.

URL : Post-publication peer review in biomedical journals: overcoming obstacles and disincentives to knowledge sharing

DOI : https://dx.doi.org/10.31229/osf.io/8kxyz

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Health Sciences Libraries Advancing Collaborative Clinical Research Data Management in Universities

Authors : Tania P. Bardyn, Emily F. Patridge, Michael T. Moore, Jane J. Koh

Purpose

Medical libraries need to actively review their service models and explore partnerships with other campus entities to provide better-coordinated clinical research management services to faculty and researchers. TRAIL (Translational Research and Information Lab), a five-partner initiative at the University of Washington (UW), explores how best to leverage existing expertise and space to deliver clinical research data management (CRDM) services and emerging technology support to clinical researchers at UW and collaborating institutions in the Pacific Northwest.

Methods

The initiative offers 14 services and a technology-enhanced innovation lab located in the Health Sciences Library (HSL) to support the University of Washington clinical and research enterprise.

Sharing of staff and resources merges library and non-library workflows, better coordinating data and innovation services to clinical researchers. Librarians have adopted new roles in CRDM, such as providing user support and training for UW’s Research Electronic Data Capture (REDCap) instance.

Results

TRAIL staff are quickly adapting to changing workflows and shared services, including teaching classes on tools used to manage clinical research data. Researcher interest in TRAIL has sparked new collaborative initiatives and service offerings. Marketing and promotion will be important for raising researchers’ awareness of available services.

Conclusions

Medical librarians are developing new skills by supporting and teaching CRDM. Clinical and data librarians better understand the information needs of clinical and translational researchers by being involved in the earlier stages of the research cycle and identifying technologies that can improve healthcare outcomes.

At health sciences libraries, leveraging existing resources and bringing services together is central to how university medical librarians will operate in the future.

DOI : https://doi.org/10.7191/jeslib.2018.1130

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Clinical Trial Participants’ Views of the Risks and Benefits of Data Sharing

Authors : Michelle M. Mello, Van Lieou, Steven N. Goodman

Background

Sharing of participant-level clinical trial data has potential benefits, but concerns about potential harms to research participants have led some pharmaceutical sponsors and investigators to urge caution. Little is known about clinical trial participants’ perceptions of the risks of data sharing.

Methods

We conducted a structured survey of 771 current and recent participants from a diverse sample of clinical trials at three academic medical centers in the United States. Surveys were distributed by mail (350 completed surveys) and in clinic waiting rooms (421 completed surveys) (overall response rate, 79%).

Results

Less than 8% of respondents felt that the potential negative consequences of data sharing outweighed the benefits. A total of 93% were very or somewhat likely to allow their own data to be shared with university scientists, and 82% were very or somewhat likely to share with scientists in for-profit companies.

Willingness to share data did not vary appreciably with the purpose for which the data would be used, with the exception that fewer participants were willing to share their data for use in litigation.

The respondents’ greatest concerns were that data sharing might make others less willing to enroll in clinical trials (37% very or somewhat concerned), that data would be used for marketing purposes (34%), or that data could be stolen (30%). Less concern was expressed about discrimination (22%) and exploitation of data for profit (20%).

Conclusions

In our study, few clinical trial participants had strong concerns about the risks of data sharing. Provided that adequate security safeguards were in place, most participants were willing to share their data for a wide range of uses. (Funded by the Greenwall Foundation.)

URL : https://www.nejm.org/doi/full/10.1056/NEJMsa1713258

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Data management and sharing in neuroimaging: Practices and perceptions of MRI researchers

Authors : John A. Borghi, Ana E. Van Gulick

Neuroimaging methods such as magnetic resonance imaging (MRI) involve complex data collection and analysis protocols, which necessitate the establishment of good research data management (RDM). Despite efforts within the field to address issues related to rigor and reproducibility, information about the RDM-related practices and perceptions of neuroimaging researchers remains largely anecdotal.

To inform such efforts, we conducted an online survey of active MRI researchers that covered a range of RDM-related topics. Survey questions addressed the type(s) of data collected, tools used for data storage, organization, and analysis, and the degree to which practices are defined and standardized within a research group.

Our results demonstrate that neuroimaging data is acquired in multifarious forms, transformed and analyzed using a wide variety of software tools, and that RDM practices and perceptions vary considerably both within and between research groups, with trainees reporting less consistency than faculty.

Ratings of the maturity of RDM practices from ad-hoc to refined were relatively high during the data collection and analysis phases of a project and significantly lower during the data sharing phase.

Perceptions of emerging practices including open access publishing and preregistration were largely positive, but demonstrated little adoption into current practice.

URL : Data management and sharing in neuroimaging: Practices and perceptions of MRI researchers

DOI : https://doi.org/10.1371/journal.pone.0200562