Richard Horton, editor-in-chief of The Lancet (published by Elsevier), “suggested that journals like The Lancet “need to be advocates for open science — we need to believe in tearing down the barriers that stop people from accessing that information, generating that information and disseminating it. We need to be strong voices; in a sense, the moral conscious of our community, holding us accountable.” …”
“Extracting research evidence from publications Bioinformaticians are routinely handling big data, including DNA, RNA, and protein sequence information. It’s time to treat biomedical literature as a dataset and extract valuable facts hidden in the millions of scientific papers. This webinar demonstrates how to access text-mined literature evidence using Europe PMC Annotations API. We highlight several use cases, including linking diseases with potential treatment targets, or identifying which protein structures are cited along with a gene mutation.
This webinar took place on 5 March 2018 and is for wet-lab researchers and bioinformaticians who want to access scientific literature and data programmatically. Some prior knowledge of programmatic access and common programming languages is recommended.
The webinar covers: Available data (annotation types and sources) (1:50) API operations and parameters and web service outputs (8:08) Use case examples (16:56) How to get help (24:16)
You can download the slides from this webinar here. You can learn more about Europe PMC in our Europe PMC: Quick tour and our previous webinar Europe PMC, programmatically.
For documentation, help and support visit the Europe PMC help pages or download the developer friendly web service guide. For web service related question you can get in touch via the Google group or contact the helpdesk [at] europepmc.org”>help desk.”
“Preprints — versions of research papers made publicly available prior to formal publication in a peer reviewed journal — continue to be a topic of much discussion within the medical publications community. As the industry looks at ways to improve and advance the transparent and timely dissemination of research, preprints offer a potential route to achieving these aims. Already commonly used in fields such as physics, the launch of the medical publications preprint server medRxiv, expected later this year, is awaited with interest.
Meanwhile, Public Library of Science (PLOS) announced last month that all articles submitted to PLOS journals will now automatically be published on the biology preprint server bioRxiv as preprints, ahead of ‘traditional’ publication in a PLOS journal. Following initial top-line checks by PLOS, to ensure adherence to things like ethical standards and the journal’s scope, articles will be posted to bioRxiv while undergoing peer review at PLOS in parallel.
PLOS and Cold Spring Harbor Laboratory, which operates bioRxiv, hope this collaboration will help advance data dissemination and ultimately increase the speed of research. The potential of preprints has also been explored by other groups, including the possibility for preprints to improve online article engagement and for journals to use preprint servers to identify potential articles for publication.”
“The Montreal Neurological Institute and Hospital becomes the first Open Science Institute in the world.
Open Science is a no-barrier approach to scientific research that is gaining ground within the academic community. Its principles are simple: allow research data and materials to move freely from one research team to another, between disciplines and toward the creation of innovative businesses….
MNI researchers will render all positive and negative numerical data, models used, data sources, reagents, algorithms, software and other scientific resources publicly available no later than the publication date of the first article that relies on this data or resource….
Subject to patient confidentiality and informed consent given, neither the MNI nor its researchers in their capacity as employees or consultants of the McGill- MNI unit will obtain patent protection or assert data protection rights in respect of any of their research….”
“Along with a number of leading Danish industrial companies, Aarhus University has opted out of the rat race in a new collaboration on industrially relevant basic research. Researchers and companies from all over Denmark publish all their results and data on the innovative Open Science platform, where the information is available free of charge to everyone interested….
The Open Science platform is thus the source of a number of paradigm shifts. It not only breaks away from the focus of universities on patenting their research discoveries, but also constitutes a conscious rebellion against the business models used by scientific journals….”
“The data in electronic health records overlaps with the types of data collected for clinical research. This provides opportunities for data sharing and reuse without reentry or transcription, thus supporting open science and learning health systems. Building better bridges between research and health care offers limitless possibilities for facilitating research and improving health care delivery….”
Kohls, A.; Mele, S. Converting the Literature of a Scientific Field to Open Access Through Global Collaboration: the Experience of SCOAP3 in Particle Physics. Preprints 2018
“Abstract: Gigantic particle accelerators, incredibly complex detectors, an antimatter factory and the discovery of the Higgs boson – this is part of what makes CERN famous. Only a few know that CERN also hosts the world largest Open Access initiative: SCOAP3. The Sponsoring Consortium for Open Access Publishing in Particle Physics (SCOAP3) started operation in 2014 and has since supported the publication of 19,000 Open Access articles in the field of particle physics, at no direct cost, nor burden, for individual authors worldwide. SCOAP3 is made possible by a 3,000-institute strong partnership, where libraries re-direct funds previously used for subscriptions to ’flip’ articles to ’gold Open Access’. With its recent expansion, the initiative now covers about 90% of the journal literature of the field. This article describes the economic principles of SCOAP3, the collaborative approach of the partnership, and finally summarizes financial results after four years of successful operation.”
“Which successful company has benefited the most from basic science and technology, yet given the least back to it? The answer: Apple. It is so extreme, that the runners-up are not even close. Apple funds internal research galore, then locks it up, reportedly refusing to allow its own scientists to attend public and open research conferences. It does make some software open (sort of), but funds no accessible research to speak of that would help further the kind of basic computer science upon which others can build. You might think that such behavior is natural; how could Apple—or any company for that matter—be competitive otherwise? And yet there is a long history of precompetitive basic science that, for example, came from the likes of Bell Labs (like semi-conductors), later IBM, and more recently Microsoft. You cannot keep skimming the cream off the top, without doing some basic, open research that is widely shared. Open and shared are the key words….”