Category Archives: oa.specimens

A global approach for natural history museum collections | Science

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Abstract:  Over the past three centuries, people have collected objects and specimens and placed them in natural history museums throughout the world. Taken as a whole, this global collection is the physical basis for our understanding of the natural world and our place in it, an unparalleled source of information that is directly relevant to issues as diverse as wildlife conservation, climate change, pandemic preparedness, food security, invasive species, rare minerals, and the bioeconomy (1). Strategic coordination and use of the global collection has the potential to focus future collecting and guide decisions that are relevant to the future of humanity and biodiversity. To begin to map the aggregate holdings of the global collection, we describe here a simple and fast method to assess the contents of any natural history museum, and report results based on our assessment of 73 of the world’s largest natural history museums and herbaria from 28 countries.

From the body of the article:

“Natural history museums have generally operated independently, and no interoperable data structure exists to provide open access to their collective holdings. Because most natural history museum data are not digitally discoverable, the networks of data aggregators have not been able to access these “dark data” …”

 

The Netherlands Heart Tissue Bank : Strengthening the cardiovascular research infrastructure with an open access Cardiac Tissue Repository – PubMed

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Abstract:  Aim: Cardiac diseases remain a leading cause of cardiovascular disease (CVD) related hospitalisation and mortality. That is why research to improve our understanding of pathophysiological processes underlying cardiac diseases is of great importance. There is a strong need for healthy and diseased human cardiac tissue and related clinical data to accomplish this, since currently used animal and in vitro disease models do not fully grasp the pathophysiological processes observed in humans. This design paper describes the initiative of the Netherlands Heart Tissue Bank (NHTB) that aims to boost CVD-related research by providing an open-access biobank.

Methods: The NHTB, founded in June 2020, is a non-profit biobank that collects and stores biomaterial (including but not limited to myocardial tissue and blood samples) and clinical data of individuals with and without previously known cardiac diseases. All individuals aged ? 18 years living in the Netherlands are eligible for inclusion as a potential future donor. The stored samples and clinical data will be available upon request for cardiovascular researchers.

Conclusion: To improve the availability of cardiac tissue for cardiovascular research, the NHTB will include extensive (cardiac) biosamples, medical images, and clinical data of donors with and without a previously known cardiac disease. As such, the NHTB will function as a translational bridge to boost a wide range of cardiac disease-related fundamental and translational studies.

decade of GigaScience: What can be learned from half a million RRIDs in the scientific literature? | GigaScience | Oxford Academic

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Abstract:  Research resource identifiers (RRIDs) are persistent unique identifiers for scientific resources used to conduct studies such as reagents and tools. Inclusion of these identifiers into the scientific literature has been demonstrated to improve the reproducibility of papers because resources, like antibodies, are easier to find, making methods easier to reproduce. RRIDs also dramatically reduce the use of problematic resources, such as contaminated cell lines. The addition of RRIDs into a manuscript means that authors have to look up information that they may have previously omitted or confront information about problems that may have been reported about their resources. The use of RRIDs is primarily driven by champion journals, such as GigaScience and others. Although still nascent, this practice lays important groundwork for citation types that can cover non-traditional scholarly output, such as software tools and key reagents; giving authors of various types of tools scholarly credit for their contributions.

 

The Pandemic Response Box?Accelerating Drug Discovery Efforts after Disease Outbreaks | ACS Infectious Diseases

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Abstract:  The current Covid-19 pandemic has underlined the need for a more coordinated and forward-looking investment in the search for new medicines targeting emerging health care threats. Repositioning currently approved drugs is a popular approach to any new emerging disease, but it represents a first wave of response. Behind this would be a second wave of more specifically designed therapies based on activities against specific molecular targets or in phenotypic assays. Following the successful deployment and uptake of previous open access compound collections, we assembled the Pandemic Response Box, a collection of 400 compounds to facilitate drug discovery in emerging infectious disease. These are based on public domain information on chemotypes currently in discovery and early development which have been shown to have useful activities and were prioritized by medicinal chemistry experts. They are freely available to the community as a pharmacological test set with the understanding that data will be shared rapidly in the public domain.

Biodiversity Community Integrated Knowledge Library (BiCIKL)

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Abstract:  BiCIKL is an European Union Horizon 2020 project that will initiate and build a new European starting community of key research infrastructures, establishing open science practices in the domain of biodiversity through provision of access to data, associated tools and services at each separate stage of and along the entire research cycle. BiCIKL will provide new methods and workflows for an integrated access to harvesting, liberating, linking, accessing and re-using of subarticle-level data (specimens, material citations, samples, sequences, taxonomic names, taxonomic treatments, figures, tables) extracted from literature. BiCIKL will provide for the first time access and tools for seamless linking and usage tracking of data along the line: specimens > sequences > species > analytics > publications > biodiversity knowledge graph > re-use.

 

NIH-Wide Strategic Plan: Fiscal Years 2021-2025

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“NIH is committed to making findings from the research that it funds accessible and available in a timely manner, while also providing safeguards for privacy, intellectual property, security, and data management. For instance, NIH-funded investigators are expected to make the results and accomplishments of their activities freely available within 12 months of publication. NIH also encourages investigators to share results prior to peer review, such as through preprints, to speed the dissemination of their findings and enhance the rigor of their work through informal peer review. A robust culture of data sharing is critical to continued progress in science, maximizing NIH’s investment in research, and assurance of the highest levels of transparency and rigor. To this end, NIH will continue to promote opportunities for data management and sharing while allowing flexibility for various data types, sharing platforms, and strategies. Additionally, NIH is implementing a policy requiring that all applications include data sharing and management plans that consider input from stakeholders….”

Internet of Samples: iSamples | home

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“The Internet of Samples (iSamples) is a multi-disciplinary and multi-institutional project funded by the National Science Foundation to design, develop, and promote service infrastructure to uniquely, consistently, and conveniently identify material samples, record metadata about them, and persistently link them to other samples and derived digital content, including images, data, and publications….”

VACANCY: SENIOR GLOBAL HEALTH ADVOCATE ON ACCESS TO MEDICINES

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“As global health advocate at Wemos you will be part of the Access to Medicines team to realise the operational and policy aims of our Access to Medicines programme. You will build and strengthen coalitions on Access to Medicines, gather relevant knowledge and work to implement an effective advocacy strategy towards (inter)national stakeholders. Your objective? To advocate that everyone, everywhere, has access to high-quality, affordable medicines and other medical products that meet their medical needs….

Health is a human right and commodities like vaccines should be considered a global public good, especially considering the high amount of public money invested in the R&D of the vaccines. We are concerned about the lack of 1) transparency of pricing and R&D costs, 2) conditions for public funding, 3) fair regulations, and 4) cooperation between countries….”

Actives from MMV Open Access Boxes? A suggested way forward

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Abstract:  It is estimated that more than 1 billion people across the world are affected by a neglected tropical disease (NTD) that requires medical intervention. These diseases tend to afflict people in areas with high rates of poverty and cost economies billions of dollars every year. Collaborative drug discovery efforts are required to reduce the burden of these diseases in endemic regions. The release of “Open Access Boxes” is an initiative launched by Medicines for Malaria Venture (MMV) in collaboration with its partners to catalyze new drug discovery in neglected diseases. These boxes are mainly requested by biology researchers across the globe who may not otherwise have access to compounds to screen nor knowledge of the workflow that needs to be followed after identification of actives from their screening campaigns. Here, we present guidelines on how to move such actives beyond the hit identification stage, to help in capacity strengthening and enable a greater impact of the initiative.

 

 

Principles of open, transparent and reproducible science in author guidelines of sleep research and chronobiology journals

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Abstract:  Background: “Open science” is an umbrella term describing various aspects of transparent and open science practices. The adoption of practices at different levels of the scientific process (e.g., individual researchers, laboratories, institutions) has been rapidly changing the scientific research landscape in the past years, but their uptake differs from discipline to discipline. Here, we asked to what extent journals in the field of sleep research and chronobiology encourage or even require following transparent and open science principles in their author guidelines.

Methods: We scored the author guidelines of a comprehensive set of 27 sleep and chronobiology journals, including the major outlets in the field, using the standardised Transparency and Openness (TOP) Factor. The TOP Factor is a quantitative summary of the extent to which journals encourage or require following various aspects of open science, including data citation, data transparency, analysis code transparency, materials transparency, design and analysis guidelines, study pre-registration, analysis plan pre-registration, replication, registered reports, and the use of open science badges.

Results: Across the 27 journals, we find low values on the TOP Factor (median [25 th, 75 th percentile] 3 [1, 3], min. 0, max. 9, out of a total possible score of 29) in sleep research and chronobiology journals.

Conclusions: Our findings suggest an opportunity for sleep research and chronobiology journals to further support recent developments in transparent and open science by implementing transparency and openness principles in their author guidelines.

Inside An Effort To Put Millions Of Biological Specimens Online : Shots – Health News : NPR

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“For scientists to pull out detailed information like that, however, they first have to know that a particular specimen even exists. In 2011, the National Science Foundation started handing out grants as part of a ten-year push to bring old-fashioned collections into the Internet age. One of the goals was to put specimen records online and into a searchable portal called iDigBio….

Now, as that program winds down, he and other experts are pondering what needs to happen over the next decade so that biological collections can continue to become more accessible. That’s why the NSF recently asked for some advice from an expert panel convened by the National Academies of Sciences, Engineering, and Medicine.

One of its recommendations was simple: create a national registry of all collections, so experts know who’s got plants, microbes, or animals of interest.

The U.S. is thought to possess about 1,800 natural history collections, which is about a third of those that exist worldwide. In addition, the country has at least 2,800 “living stock” collections, such as microbe collections, which continually maintain living organisms for research….”

Leveraging Open Science to Accelerate Research | NEJM

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The United States has mobilized the full force of its clinical research enterprise to address the Covid-19 pandemic, allocating billions of dollars to support timely research. As of January 2021, for example, the National Institutes of Health (NIH) had issued nearly a thousand awards cumulatively worth roughly $2 billion to support Covid-19 projects ranging from the development of medical products (including diagnostics and vaccines) to evaluations of population-specific risk factors and outcomes.1 Such initiatives, which have yielded new technologies and important evidence, illustrate the value of robust scientific infrastructure.

Finding equipoise: CEPI revises its equitable access policy – ScienceDirect

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“Both the original policy and the revised one recommended that CEPI not take ownership in IP, particularly with regard to patents….

Awardees may choose to obtain intellectual property rights (such as patents or copyrights) for inventions, research materials, data bases and the like developed using funding from CEPI. If they seek such intellectual property protection, it will be at their own cost and they must promptly notify CEPI….

CEPI has committed to “Open Access” for project data, requiring that any final manuscripts of the research results must be publicly available and published in accordance with globally accepted standards, in particular the principles of “Plan S” (https://www.scienceeurope.org/wp-content/uploads/2018/09/Plan_S.pdf), an initiative developed by Science Europe regarding open access publishing.
CEPI has committed to “Open Data” for project data….”

Addgene: COVID-19 Resources

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“The global research community is moving quicky to expand the knowledge and understanding of COVID-19 and related coronaviruses. To assist with this effort Addgene will maintain this plasmid collection page, which outlines various plasmids available and those coming soon. Additionally, we have linked to collections of open-access articles, protocols, and other resource collections related to COVID-19 that may be of use to scientists….”