Conference homepage – Singapore Open Research Conference 2022 – LibGuides at Nanyang Technological University

“Open Research, or Open Science is the movement to make the scientific process and research outputs more transparent, inclusive and accessible. 

It supports validation, reproducibility and reduces cases of academic misconduct.

It helps to maximise the impact of one’s research and provides the foundations for others to build upon. 

Held in conjunction with the International Open Access Week, the inaugural Singapore Open Research Conference, “Accelerating Research with Responsible Open Science”, will provide a great opportunity to interact with drivers and practitioners about their experiences and suggestions on Open Science/Open Research.

Though the discussions will be based on the bioscience field, researchers from various institutions are most welcome….”

Analysis of Harvard Medical School Countway Library’s MOOC Course, Best Practices for Biomedical Research Data Management: Learner Demographics and Motivations

Abstract:  The Harvard Medical School Countway Library’s Massive Open Online Course (MOOC) Best Practices for Biomedical Research Data Management launched on Canvas in January 2018. This report analyzes learner reported data and course generated analytics from March 2020 through June 2021 for the course. This analysis focuses on three subsets of participant data during the pandemic to understand global learner demographics and interest in biomedical research data management. 

Recognizing Our Collective Responsibility in the Prioritization of Open Data Metrics · Issue 4.3, Summer 2022

Abstract:  With the rise in data-sharing policies, development of supportive infrastructure, and the amount of data published over the last decades, evaluation and assessment are increasingly necessary to understand the reach, impact, and return on investment of data-sharing practices. As biomedical research stakeholders prepare for the implementation of the updated National Institutes of Health (NIH) Data Management and Sharing Policy in 2023, it is essential that the development of responsible, evidence-based open data metrics are prioritized. If the community is not mindful of our responsibility in building for assessment upfront, there are prominent risks to the advancement of open data-sharing practices: failing to live up to the policy’s goals, losing community ownership of the open data landscape, and creating disparate incentive systems that do not allow for researcher reward. These risks can be mitigated if the community recognizes data as its own scholarly output, resources and leverages open infrastructure, and builds broad community agreement around approaches for open data metrics, including using existing standards and resources. In preparation for the NIH policy, the community has an opportune moment to build for researchers’ best interests and support the advancement of biomedical sciences, including assessment, reward, and mechanisms for improving policy resources and supportive infrastructure as the space evolves.

FASEB DataWorks!

“FASEB DataWorks! is our new initiative that brings the biological and biomedical research communities together to advance human health through data sharing and reuse.

DataWorks! features four components:

DataWorks! Salons are conversation spaces for the biological and biomedical research community to exchange ideas and design effective practices for data sharing and reuse;
DataWorks! Help Desk provides guidance for the biological and biomedical research community to navigate and adopt data sharing and reuse policies and practices;
DataWorks! Prize recognizes biological and biomedical research teams that integrate data sharing and reuse to advance human health; and
DataWorks! Community enables biological and biomedical researchers and teams to hone skills and mentor peers in data management and sharing….”

Oxford University Press and Bibliosan sign major Read & Publish agreement

“Oxford University Press (OUP) and the Italian consortium of Biomedical Research Libraries (BIBLIOSAN) have announced a new Read & Publish agreement. As OUP’s first Read & Publish deal with an Italian consortium, the deal is significant in that it will provide online access for Bibliosan’s network, which includes 68 institutions and their researchers, to OUP’s full journal collection of peer-reviewed journals….”

DataWorks! Challenge | HeroX

“Share your story of how you reused or shared data to further your biological and/or biomedical research effort and get recognized!…

The Federation of American Societies for Experimental Biology (FASEB) and the National Institutes of Health (NIH) are championing a bold vision of data sharing and reuse. The DataWorks! Prize fuels this vision with an annual challenge that showcases the benefits of research data management while recognizing and rewarding teams whose research demonstrates the power of data sharing or reuse practices to advance scientific discovery and human health. We are seeking new and innovative approaches to data sharing and reuse in the fields of biological and biomedical research. 

To incentivize effective practices and increase community engagement around data sharing and reuse, the 2022 DataWorks! Prize will distribute up to 12 monetary team awards. Submissions will undergo a two-stage review process, with final awards selected by a judging panel of NIH officials. The NIH will recognize winning teams with a cash prize, and winners will share their stories in a DataWorks! Prize symposium.”

The Rise of Open Access Journals in Radiation Oncology: Are We Paying for Impact? – ScienceDirect

Purpose/Objective(s)

We aimed to examine how the rise of open access (OA) journals in biomedicine has impacted resident research in radiation oncology.

Materials/Methods

We built a comprehensive database of first-author, PubMed-searchable articles published by US radiation oncology residents who graduated between 2015 and 2019. We then classified each journal in which these manuscripts appeared as either OA or non-OA, and obtained the current article processing charge (APC) for every publication that appeared in an OA journal. Lastly, we performed a secondary analysis to identify the factors associated with publishing an article in an OA journal.

Results

The US radiation oncology residents in this study published 2,637 first-author, PubMed-searchable manuscripts, 555 (21.0%) of which appeared in 138 OA journals. The number of publications in OA journals increased from 0.47 per resident for the class of 2015 to 0.79 per resident for the class of 2019. Likewise, the number of publications in OA journals with a 2019 impact factor of zero increased from 0.14 per resident for the class of 2015 to 0.43 per resident for the class of 2019. Publications in OA journals garnered fewer citations than those in non-OA journals (8.9 versus 14.9, P < 0.01). 90.6% of OA journals levy an APC for original research reports (median $1,896), which is positively correlated with their 2019 impact factor (r?=?0.63, P < 0.01). Aggregate APCs totaled $900,319.21 for all US radiation oncology residency programs and appeared to increase over the study period.

Conclusion

The number of first-author, PubMed-searchable manuscripts published by graduating US radiation oncology residents in OA journals rose significantly over the study period. US radiation oncology residency programs appear to be investing increasing and significant sums of money to publish the work of their residents in these journals. A more substantive discussion about the proper role of OA journals in resident research is needed.

Blog – Europe PMC: Europe PMC adopts the Principles of Open Scholarly Infrastructure

“As a long-standing service and infrastructure provider in the open science ecosystem, Europe PMC supports the Principles of Open Scholarly Infrastructure (POSI). We welcome the momentum gathering behind this initiative to promote the need to support and sustain the open infrastructure.

Europe PMC has been a part of the public and open infrastructure for over 15 years and is run and managed by EMBL-EBI (which is part of the pan-European organisation of EMBL). It is funded by 34 international funders and is community-driven, open infrastructure, set in the context of key global open data resources such as the European Nucleotide Archive (INSDC), the wwPDB and the European Genome-Phenome Archive. All of these resources exist for the public good, led by scientific need and international collaborations, and have open governance structures and a commitment to long-term sustainability. Together with PMC USA, Europe PMC is a part of the PubMed Central International archive network, which plays an integral part in fulfilling shared goals to enable international open science. Europe PMC has been selected as an ELIXIR Core Data Resource, which means that it is of fundamental importance to the wider life-science community and the long-term preservation of biological data….”

Investigating the replicability of preclinical cancer biology

Abstract:  Replicability is an important feature of scientific research, but aspects of contemporary research culture, such as an emphasis on novelty, can make replicability seem less important than it should be. The Reproducibility Project: Cancer Biology was set up to provide evidence about the replicability of preclinical research in cancer biology by repeating selected experiments from high-impact papers. A total of 50 experiments from 23 papers were repeated, generating data about the replicability of a total of 158 effects. Most of the original effects were positive effects (136), with the rest being null effects (22). A majority of the original effect sizes were reported as numerical values (117), with the rest being reported as representative images (41). We employed seven methods to assess replicability, and some of these methods were not suitable for all the effects in our sample. One method compared effect sizes: for positive effects, the median effect size in the replications was 85% smaller than the median effect size in the original experiments, and 92% of replication effect sizes were smaller than the original. The other methods were binary – the replication was either a success or a failure – and five of these methods could be used to assess both positive and null effects when effect sizes were reported as numerical values. For positive effects, 40% of replications (39/97) succeeded according to three or more of these five methods, and for null effects 80% of replications (12/15) were successful on this basis; combining positive and null effects, the success rate was 46% (51/112). A successful replication does not definitively confirm an original finding or its theoretical interpretation. Equally, a failure to replicate does not disconfirm a finding, but it does suggest that additional investigation is needed to establish its reliability.

 

NIH issues a seismic mandate: share data publicly

“In January 2023, the US National Institutes of Health (NIH) will begin requiring most of the 300,000 researchers and 2,500 institutions it funds annually to include a data-management plan in their grant applications — and to eventually make their data publicly available.

Researchers who spoke to Nature largely applaud the open-science principles underlying the policy — and the global example it sets. But some have concerns about the logistical challenges that researchers and their institutions will face in complying with it. Namely, they worry that the policy might exacerbate existing inequities in the science-funding landscape and could be a burden for early-career scientists, who do the lion’s share of data collection and are already stretched thin….

Such a seismic shift in practice has left some researchers worried about the amount of work that the mandate will require when it becomes effective….

Others worry that data-management activities will further sap funds from under-resourced labs. Although the policy outlines certain fees that researchers can add to their proposed budgets to offset the costs of compliance with the mandate, it doesn’t specify what criteria the NIH will use to grant these requests….

Despite its potential pitfalls, Ross thinks that the policy will have a ripple effect that will persuade smaller funding agencies and industry to adopt similar changes. “This policy establishes what people expect from clinical research,” he says. “It’s essentially saying the culture of research needs to change.” ”

Making Biomedical Sciences publications more accessible for machines | SpringerLink

Abstract:  With the rapidly expanding catalogue of scientific publications, especially within the Biomedical Sciences field, it is becoming increasingly difficult for researchers to search for, read or even interpret emerging scientific findings. PubMed, just one of the current biomedical data repositories, comprises over 33 million citations for biomedical research, and over 2500 publications are added each day. To further strengthen the impact biomedical research, we suggest that there should be more synergy between publications and machines. By bringing machines into the realm of research and publication, we can greatly augment the assessment, investigation and cataloging of the biomedical literary corpus. The effective application of machine-based manuscript assessment and interpretation is now crucial, and potentially stands as the most effective way for researchers to comprehend and process the tsunami of biomedical data and literature. Many biomedical manuscripts are currently published online in poorly searchable document types, with figures and data presented in formats that are partially inaccessible to machine-based approaches. The structure and format of biomedical manuscripts should be adapted to facilitate machine-assisted interrogation of this important literary corpus. In this context, it is important to embrace the concept that biomedical scientists should also write manuscripts that can be read by machines. It is likely that an enhanced human–machine synergy in reading biomedical publications will greatly enhance biomedical data retrieval and reveal novel insights into complex datasets.