Discovery – GO FAIR

“The main purpose of the Discovery IN is to provide interfaces and other user-facing services for data discovery across disciplines. We explore new and innovative ways of enabling discovery, including visualizations, recommender systems, semantics, content mining, annotation, and responsible metrics. …”

Reply to Kiley and Smits: Meeting Plan S’s goal of maximizing access to research | PNAS

“Thank you for recognizing the value that scholarly societies bring to the research ecosystem and the scientific enterprise as a whole—and for recognizing the importance of their financial viability (1).

And thank you for clearly stating your goal for Plan S (2). A much simpler route toward achieving your goal of maximizing access to research and allowing for artificial intelligence and text and data mining is Plan U, in which funders require that grantees deposit manuscripts on a preprint server under a Creative Commons Attribution license (CC BY) before submission and peer review in a journal.* Plan U avoids the tremendous overhead and infrastructure needed to implement, monitor, and enforce Plan S—which entails vetting thousands of individual journals, various journal platforms, and repositories—and eliminates the need to further refine Plan S implementation guidelines, which have to date raised more questions than they answer.

Plan U would establish a far more uniform policy across a much larger group of researchers, while avoiding the need to cap article processing charges or ban hybrid journals. Such a policy is not only more inclusive, but more likely to achieve global buy-in….”

Open Research Data Task Force: final report – GOV.UK

“It is in this context that a new paradigm of “open science” has developed, that is more efficient, open to all, integrated across disciplines and societally engaged. Its necessary bedrock is:

• that published scientific results should be open access – digital, online, free of charge, and free of most copyright and licensing restrictions; and

• that the data acquired by individual scientists and scientific groups should be subject to a default position whereby it is made findable, accessible, interoperable and re-useable (FAIR);

The second of these aims forms the focus of this report and offers profound opportunities. Open research data (ORD) have the potential not only to deliver greater efficiencies in research, but to improve its rigour and reproducibility, to enhance its impact, and to increase public trust in its results….”

Solving global challenges starts with open data — new report launched today | EurekAlert! Science News

Better incentives for researchers and fewer barriers between technological systems are key to kickstarting a revolution in open data, according to Realising Potential, a report released today by the Open Research Data Task Force (ORDTF) – a group of senior professors and UK higher education and research organisations and Chaired by Professor Pam Thomas, Pro-Vice-Chancellor for Research at the University of Warwick

Open Research Data (ORD) or data which is FAIR (findable, accessible, interoperable and re-useable) dramatically increases the capacity of science to infer patterns and identify solutions in the complex systems that are at the heart of global issues such as climate change or antibiotic resistance. This transparency in the process and outcomes also increases the public’s trust in scientific research, enhances its impact and delivers greater efficiencies.

Realising The Potential, the final report of the Open Research Data Task Force, examines the opportunities presented though ORD and responds to a technological evolution in research, where machine-learning and Artificial intelligence are becoming more commonplace in mining open data….”

PRESS RELEASE: Researchers Respond to Implementation of Plan S | Eurodoc

joint response to the implementation guidance for Plan S has today been issued by three organisations representing early-career and senior researchers in Europe. The response by the European Council of Doctoral Candidates and Junior Researchers (Eurodoc), the Marie Curie Alumni Association (MCAA), and the Young Academy of Europe (YAE) offers concrete recommendations on the proposed guidance for implementing Open Access via Plan S.

Our three organisations represent a broad spectrum of researchers in Europe: Eurodoc represents 100000+ doctoral candidates and postdoctoral researchers from 29 national associations across Europe; MCAA has 10000+ members who are alumni fellows of the Marie Sk?odowska-Curie Actions (MSCA); YAE consists of 200+ outstanding and recognised researchers in Europe. We all strongly support the main goals of Open Science and Plan S.

The joint response builds upon previous recommendations by our organisations on the principles of Plan S and aims to ensure its realistic implementation from the perspective of European researchers. Eurodoc President Gareth O’Neill: “Plan S has shaken the academic community awake and created a lively discussion on Open Access publishing. cOAlition S has addressed some key concerns from researchers in the technical guidance but still leaves other issues open and sets too strict standards for the desired broad adoption of Plan S.” …”

Joint Statement on Implementation Guidance for Plan S

“Plan S is an initiative by cOAlition S to achieve full and immediate Open Access to scientific publications after 01 January 2020 in Europe. At the heart of the plan are 10 principles currently being developed into a set of implementation guidelines. We, representatives of early-career and senior researchers across Europe, have already commented on Plan S and hereby reaffirm our general support and offer our views on the implementation guidance….”

Plan S: how important is open access publishing? | Times Higher Education (THE)

Dislike of gold open access is also partly responsible for researchers’ opposition to Plan S. Lynn Kamerlin, professor of structural biology at Uppsala University, is one of the instigators of the open letter against it. While she pledges strong support for open access, she is happy with the current rate of progress and sees the recent “explosion” in the use of preprint servers as illustrative of the range of routes towards it. She fears that the details of Plan S’ “embargo requirements and repository technical requirements…are so draconian that paid-for gold becomes the easiest way to fulfil them”. This will convert the “nudges” towards gold in existing funder mandates (which she supports) into a “shove”, which will be “a disaster for the research community” because it will disadvantage those unable to pay article processing charges and “seriously jeopardise the much more rigorous quality control standards provided by high-quality society journals compared to the high-volume for-profit business model, which has an inbuilt conflict of interest”.

Nor is Kamerlin alone in expressing a concern that the allegedly lower standards of peer review practised by fully open access journals have compromised quality. But, for Suber, debating quality rather misses the point. “Yes, there is some low-quality open access work, but there’s also low-quality subscription journal work, and people who step back [to see the bigger picture] always acknowledge that,” he says. “Quality and access are completely independent of each other. Open access isn’t a kind of peer review, it’s a kind of dissemination.”

However, he agrees with Kamerlin that the “green” form of open access, whereby academics post work that is in subscription journals on their institutional repositories or elsewhere…is another good option….”

rOpenSci | pubchunks: extract parts of scholarly XML articles

“The goal of pubchunks is to fetch sections out of XML format scholarly articles. Users do not need to know about XML and all of its warts. They only need to know where their files or XML strings are and what sections they want of each article. Then the user can combine these sections and do whatever they wish downstream; for example, analysis of the text structure or a meta-analysis combining p-values or other data.

 

The other major format, and more common format, that articles come in is PDF. However, PDF has no structure other than perhaps separate pages, so it’s not really possible to easily extract specific sections of an article. Some publishers provide absolutely no XML versions (cough, Wiley) while others that do a good job of this are almost entirely paywalled (cough, Elsevier). There are some open access publishers that do provide XML (PLOS, Pensoft, Hindawi) – so you have the best of both worlds with those publishers….”