Are huge genetic databases leaving marginalized people out of their data? | Salon.com

“However, as promising as biobanks might seem, the data may tell only partial or even misleading stories. Criticisms of the project include that the research coming out of the UK Biobank will only benefit certain people, and even then, the usefulness of the health associations found are under question.

Compared to the 2011 UK census, Black, Indian, Pakistani and Chinese participants are all underrepresented in the Biobank by at least one third. David Curtis, at University College London, tested whether this under-representation of ethnic minority groups has any impact on schizophrenia genetics research….”

Are huge genetic databases leaving marginalized people out of their data? | Salon.com

“However, as promising as biobanks might seem, the data may tell only partial or even misleading stories. Criticisms of the project include that the research coming out of the UK Biobank will only benefit certain people, and even then, the usefulness of the health associations found are under question.

Compared to the 2011 UK census, Black, Indian, Pakistani and Chinese participants are all underrepresented in the Biobank by at least one third. David Curtis, at University College London, tested whether this under-representation of ethnic minority groups has any impact on schizophrenia genetics research….”

How to add academic journal articles to PubMed: An overview for publishers

“If you work with journals in the biomedical or life sciences, getting the articles you publish added to PubMed to make them more discoverable is likely one of your top goals. But, you may be wondering how to go about it.

We caught up with PubMed Central (PMC) Program Manager Kathryn Funk to get answers to some of the most common questions that we hear from journal publishers about PubMed and the related literature databases at the National Library of Medicine (NLM), MEDLINE and PMC. Read on to learn more about how the PubMed database works and how to apply to have a journal included in MEDLINE or PMC in order to make its articles searchable via PubMed….”

Reflections on Global Community Biology of the Future: It is Open, Diverse, and Thriving | PLOS Synthetic Biology Community

“Community biology—a  movement that seems to democratize life sciences through access and diversity—has grown over the last decades.  This is reflected in a thriving population of community labs, like Genspace and BioCurious in the US, and Freak Lab in Thailand and Kumasi Hive in Ghana, and Co-Lab in Denmark—to name a few—that are popping up across the world. I’m reminded that community labs may be to 2019  what computer clubhouses were to the 1980s, when computers were becoming accessible to private citizens and shifting the way we interacted and communicated with technology. Community labs, too, provide an entry point for everyday people—the community—to access, tinker, and play with biology!

 

Recognizing the potential of community labs to democratize scientific knowledge on a global scale—from what I’ve heard—folks like David Kong, Maria Chavez, JJ Hastings, Scott Pownall, and other global leaders in the field, sought in different ways to convene the community as a way to network, share, and connect.  This may have sparked the first Global Community Bio Summit in 2017 and that brought together hundreds (me included) of biology enthusiasts, educators, and researchers from a number of countries collectively striving to share in the responsibility of building an open and diverse movement for community science. I attended again a few weeks ago as the Bio Summit convened for the third time and, from my experience, the event continues to grow as it draws hundreds of participants across the globe and from every continent….”

bioRxiv: the preprint server for biology | bioRxiv

Abstract:  The traditional publication process delays dissemination of new research, often by months, sometimes by years. Preprint servers decouple dissemination of research papers from their evaluation and certification by journals, allowing researchers to share work immediately, receive feedback from a much larger audience, and provide evidence of productivity long before formal publication. Launched in 2013 as a non-profit community service, the bioRxiv server has brought preprint practice to the life sciences and recently posted its 64,000th manuscript. The server now receives more than four million views per month and hosts papers spanning all areas of biology. Initially dominated by evolutionary biology, genetics/genomics and computational biology, bioRxiv has been increasingly populated by papers in neuroscience, cell and developmental biology, and many other fields. Changes in journal and funder policies that encourage preprint posting have helped drive adoption, as has the development of bioRxiv technologies that allow authors to transfer papers easily between the server and journals. A bioRxiv user survey found that 42% of authors post their preprints prior to journal submission whereas 37% post concurrently with journal submission. Authors are motivated by a desire to share work early; they value the feedback they receive, and very rarely experience any negative consequences of preprint posting. Rapid dissemination via bioRxiv is also encouraging new initiatives that experiment with the peer review process and the development of novel approaches to literature filtering and assessment.

Animal Research, Accountability, Openness and Public Engagement: Report from an International Expert Forum

Abstract:  In November 2013, a group of international experts in animal research policy (n = 11) gathered in Vancouver, Canada, to discuss openness and accountability in animal research. The primary objective was to bring together participants from various jurisdictions (United States, Sweden, Australia, New Zealand, Germany, Canada and the United Kingdom) to share practices regarding the governance of animals used in research, testing and education, with emphasis on the governance process followed, the methods of community engagement, and the balance of openness versus confidentiality. During the forum, participants came to a broad consensus on the need for: (a) evidence-based metrics to allow a “virtuous feedback” system for evaluation and quality assurance of animal research, (b) the need for increased public access to information, together with opportunities for stakeholder dialogue about animal research, (c) a greater diversity of views to be represented on decision-making committees to allow for greater balance and (d) a standardized and robust ethical decision-making process that incorporates some sort of societal input. These recommendations encourage aspirations beyond merely imparting information and towards a genuine dialogue that represents a shared agenda surrounding laboratory animal use.

Animal Research, Accountability, Openness and Public Engagement: Report from an International Expert Forum

Abstract:  In November 2013, a group of international experts in animal research policy (n = 11) gathered in Vancouver, Canada, to discuss openness and accountability in animal research. The primary objective was to bring together participants from various jurisdictions (United States, Sweden, Australia, New Zealand, Germany, Canada and the United Kingdom) to share practices regarding the governance of animals used in research, testing and education, with emphasis on the governance process followed, the methods of community engagement, and the balance of openness versus confidentiality. During the forum, participants came to a broad consensus on the need for: (a) evidence-based metrics to allow a “virtuous feedback” system for evaluation and quality assurance of animal research, (b) the need for increased public access to information, together with opportunities for stakeholder dialogue about animal research, (c) a greater diversity of views to be represented on decision-making committees to allow for greater balance and (d) a standardized and robust ethical decision-making process that incorporates some sort of societal input. These recommendations encourage aspirations beyond merely imparting information and towards a genuine dialogue that represents a shared agenda surrounding laboratory animal use.

New database enhances genomics research collaboration | EurekAlert! Science News

“Sharing datasets that reveal the function of genomic variants in health and disease has become easier, with the launch of a new, open-source database developed by Australian and North American researchers.

The MaveDB database is a repository for data from experiments – called multiplex assays of variant effect (MAVEs) – that systematically measure the impact of thousands of individual sequence variants on a gene’s function. These experiments can provide valuable information about how proteins produced by that gene function, how variants in that gene may contribute to disease, and how to engineer synthetic versions of naturally occurring proteins that are more effective than the original protein.

MaveDB is the first publicly accessible database for this data….”

bioRxiv: Trends and analysis of five years of preprints – Anderson – – Learned Publishing – Wiley Online Library

Abstract:  bioRxiv was founded on the premise that publicly posting preprints would allow authors to receive feedback and submit improved papers to journals. This paper analyses a number of trends against this stated purpose, namely, the timing of preprint postings relative to submission to accepting journals; trends in the rate of unpublished preprints over time; trends in the timing of publication of preprints by accepting journals; and trends in the concentration of published, reviewed preprints by publisher. Findings show that a steady c.30% of preprints remain unpublished and that the majority is posted onto bioRxiv close to or after submission – therefore giving no time for feedback to help improve the articles. Four publishers (Elsevier, Nature, PLOS, and Oxford University Press) account for the publication of 47% of bioRxiv preprints. Taken together, it appears that bioRxiv is not accomplishing its stated goals and that authors may be using the platform more to establish priority, as a marketing enhancement of papers, and as functional Green OA, rather than as a community?driven source of prepublication review.

 

OPEN SCHOLARSHIP position statement from the Biochemical Society and Portland Press

“Currently: ? We publish two fully-OA journals, and one of these is currently sustained by article publishing charges (APC) at an article-by-article level; in addition, we publish five hybrid journals where authors may opt to pay an APC to have their article published OA. ? For titles on the hybrid model we avoid ‘double dipping’ (charging twice for the same articles) through two routes: APCs are discounted for corresponding authors based at subscribing institutions; in addition, subscription prices are set, each year, based on the number of paywalled articles in the preceding years to account for OA content published in hybrid titles. ? There are a variety of mechanisms employed by different publishers to avoid double-dipping. We are supportive of efforts to standardize and agree common principles around transparent pricing of hybrid journals that demonstrate, objectively, the avoidance of double dipping….

Looking ahead: ? We are seeking to transition our hybrid journals to full-OA in a way that supports researchers and keeps the Society financially viable. ? We strongly believe that the ability to publish research should not be linked to individual researchers’ ability to pay; we are enthusiastic about all opportunities to remove author-facing invoices from OA publishing. To enable a transition away from paywalls, we seek to offer as much APC-free OA as possible that will be supported though continuing and new partnerships with institutions, consortia and funders….