Launching Transpose, a database of journal policies on preprinting & peer review – ASAPbio

“Today, we’re excited to announce the launch of Transpose (@TransposeSCI), a database of journal peer review, co-reviewing, and preprint policies relating to media coverage, licensing, versions, and citation.

These policies can often be difficult to find, unclear, or undefined. Our hope is to bring them to light so that authors, readers, reviewers, and other stakeholders can more easily find journals that align with their values. At the same time, editors can use this resource to draw inspiration from changing practices at other journals. (Read more user stories here.)

In addition to searching for individual journals, users can select up to three journals to compare side-by-side. For instance, when planning when to preprint, researchers may wish to look up the preprint policies for up to three journals they’re likely to submit to and check which are supportive of preprints and any conditions attached to this….”

New tool and dataset make permissions checking easier, faster, and clearer for libraries.

“Together with librarians, we’re building a new way to perform permissions checking that is backed by a modern approach and informed by a decade of experience and open, community-editable, machine-readable data. Today, we’re releasing a prototype of that system, a bulk automated permissions checker (and its data), which is specialized for use during mediated deposit and en masse outreach and built to check hundreds of articles and journals in seconds. It returns comprehensive permissions information, along with complete article metadata and links to open access versions. Try the tool today at: …”

OSAOS [Open Source Alliance for Open Scholarship] Handbook

Open source projects in the scholarly domain exist at the intersection of academia, technology, and the public interest. The diversity of the communities involved results in unique opportunities for financial support, but also potentially in the tragedy of the commons — a situation where multiple stakeholders use open scholarly resources but collectively fail to sufficiently support them.

There’s no one path to financial sustainability that is right for all projects. Many projects begin in academic contexts, run by students and volunteers, and eventually gain funding via donations and grants. Two examples are NumPy and the Dat Project, which were initially run by volunteers and have been supported by donations and private philanthropic funds. Other projects seek investment from venture capital firms to scale their work.

As the open scholarly ecosystem matures, the community is exploring how to maintain long-term sustainability to maintain operations while building the potential to scale….”

Enabling A Conversation Across Scholarly Monographs through Open Annotation

Abstract:  The digital format opens up new possibilities for interaction with monographic publications. In particular, annotation tools make it possible to broaden the discussion on the content of a book, to suggest new ideas, to report errors or inaccuracies, and to conduct open peer reviews. However, this requires the support of the users who might not yet be familiar with the annotation of digital documents. This paper will give concrete examples and recommendations for exploiting the potential of annotation in academic research and teaching. After presenting the annotation tool of Hypothesis, the article focuses on its use in the context of HIRMEOS (High Integration of Research Monographs in the European Open Science Infrastructure), a project aimed to improve the Open Access digital monograph. The general line and the aims of a post-peer review experiment with the annotation tool, as well as its usage in didactic activities concerning monographic publications are presented and proposed as potential best practices for similar annotation activities.

The IA Client – The Swiss Army Knife of Internet Archive | Internet Archive Blogs

“As someone who’s uploaded hundreds of thousands of items to the Internet Archive’s stacks and who has probably done a few million transactions with the materials over the years, I just “know” about the Internet Archive python client, and if you’re someone who wants to interact with the site as a power user (or were looking for an excuse to), it’ll help you to know about it too.

You might even be the kind of power user who is elbowing me out of the way saying “show me the code and show me the documentation”. Well, the documentation is here and the code is here. Have a great time….”

“Sharing should be simple. With, we’ll make sure that deposit into any repository is just that. We’re building a workflow that removes barriers we’ve seen after asking thousands of authors to self-archive, as well as easily upgrades the deposit workflow in thousands of repositories. For libraries, helps you fill your repository by offering the simplest possible deposit workflow for authors, while saving you time and requiring no migrations or upgrades to your current repository….”

Building to make self-archiving the simplest way to increase a paper’s impact.

“Self-archiving needs to be simpler to unleash its power as an equitable route to open access. Yet, it’s too hard for individual repositories to overhaul their existing user experience. We’re building to transform deposit from an often complicated, time-consuming process into one that’s possible in just a few clicks, for any repository without the need for complex integrations. is a tool that automates the deposit workflow?—?metadata entry, permissions and version checking?—?to require only the single manual step of uploading the paper itself. Libraries looking to fill their repositories can learn more and help us build the tool by signing up….

Late this year, we plan to launch for anyone, everywhere, to deposit wherever they are in the publishing process. It’ll be free, built on open-source code, community-curated open data, simple documented APIs, library values, and resources that enable others to do even better. If you’d like to learn more or contribute in any way, please express your interest.…”

The Rise of Open Science in Psychology, a Preliminary Report

Open science is on the rise. Across disciplines, there are increasing rates of sharing data, making available underlying materials and protocols, and preregistering studies and analysis plans.  Hundreds of services have emerged to support open science behaviors at every stage of the research lifecycle.  But, what proportion of the research community is practicing open science? Where is penetration of these behaviors strongest and weakest?  Answers to these questions are important for evaluating progress in culture reform and for strategic planning of where to invest resources next.  


The hardest part of getting meaningful answers to these questions is quantifying the population that is NOT doing the behaviors.  For example, in a recent post, Nici Pfeiffer summarized the accelerating growth of OSF users on the occasion of hitting 150,000 registered users.  That number and non-linear growth suggests cultural movement associated with this one service, but how much movement?…”

Analyzing the DOAJ – Delta Think

“The Directory of Open Access Journals (DOAJ) is increasingly being used as a benchmark to determine whether a journal is fully OA, most notably as part of both the original and recently revised Plan S guidelines. This month we take a look at the DOAJ and consider how it compares to other sources for evaluating fully OA status.

The draft Plan S Implementation guidelines suggested that a listing in the DOAJ is mandatory if a journal is to be considered fully OA. This led to commentators raising concerns that many DOAJ Journals do not meet other Plan S criteria, and are therefore not compliant.

In an open letter on its blog, the DOAJ team addressed concerns about its coverage, journal quality, promotion of APC-charging journals, and Plan S compliance. The DOAJ is not (at the time of writing) a formal partner of Plan S. The team do not claim it offers exhaustive coverage and remain neutral to whether journals charge APCs. In 2014 it tightened its acceptance criteria and made all of its 10,000+ indexed journals reapply to remain indexed, which led to a shrinkage in its coverage. The team is now taking active steps to ensure that lost ground in arts & social sciences coverage (in particular) is made up and they have ambitions to keep it updated at least annually.

Whatever its shortcomings, the DOAJ is used as a benchmark by academic studies as it’s a convenient data set to analyze. ImpactStory uses a journal’s presence in the DOAJ as a key indicator of its fully OA (gold) status,* which means that products which consume ImpactStory data (such as Web of Science and Dimensions) do so as well. Following its recent consultation exercise, the latest implementation guidelines from cOAlition S restate the DOAJ as being the de facto index of compliant fully OA journals. cOAlition S also hints at further work to be done, stating that it “will work with the…DOAJ…and other potential partners to establish mechanisms for identifying and signalling whether journals…fulfil [its] requirements.” …

The DOAJ is now being used as an ipso facto source which feeds a number of services and is a core part in OA compliance policies (even allowing for caveats). However, if the DOAJ is being used as a sole indicator of journals’ fully OA status, then their coverage will be incomplete.

Much of this discrepancy may be due to omitted journals not meeting the DOAJ inclusion criteria. It ultimately remains the responsibility of publishers to make sure that their (eligible) DOAJ data are up to date. If publishers fail to do this, then their journals may not appear – or not appear correctly – in some widely-used discovery services….”

Kopernio, Lean Library, Anywhere Access & other “Access Broker” browser extensions – a roundup & update of current state of play | Musings about librarianship

It has been over a year in April 2018 since I had the opportunity to present at two panels in  conferences alongside experts such  as Lisa Hinchliffe, Johan Tilstra (Founder Lean Library), Jason Priem (Cofounder Unpaywall), Ben Kaube (Cofounder Kopernio) on the topic of browser extensions that help users gain quick access to the full text of articles while browsing the web. 

They would typically be installed as a browser extension in the user’s web browser, and would activate when they detected the user was on a page with article details and would typically popup a message with a link to where the article full text was available or offer to download the PDF directly for the user.

These browser extensions can be divided into two main categories. Early on many  of these extensions such as Unpaywall and Open Access Button focused only on discovery of free to read text only

We eventually started to see the rise of browser extensions (many of which were commerical) such as Kopernio and Lean Library, that extended the idea to finding copies available via institutional subscriptions.

Such extensions aimed to help users conveniently get one-click access to the best verson of the article available to them.  This could be very helpful if you didn’t start off your search from a library discovery service or page and was off campus. …”