Tag: research

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RIO Journal 5 years on: over 300 published outcomes from all around the research cycle

Five years on, the Open Science-driven journal Research Ideas and Outcomes (RIO) published an editorial that looks back on the 300 research ideas and research outcomes it has published so far.

Since its early days, RIO has enjoyed quite positive reactions from the open-minded academic community for its innovative approach to Open Science in practice: it provides a niche that had long been missing, namely the publication of early, intermediate and generally unconventional research outcomes from all around the research cycle (e.g. grant proposals, data management plans, project deliverables, reports, policy briefs, conference materials) in a cross-disciplinary scientific journal. In fact, several months after its launch, in 2016, the journal was acknowledged with the SPARC Innovator Award.

‘Alternative’ research publications

In times when posting a preprint was seen as a novel and rather bold practice across many fields, RIO facilitated much deeper dives into the research process, in order to unveil scientific knowledge and the process by which it is gathered, well before any final conclusions have been drawn. Long story short, to date, RIO has published 33 Research Ideas, 78 Grant Proposals, 16 Data Management Plans, 33 Workshop Reports and 5 PhD Project Plans, in addition to plenty of other early, interim and final non-traditional research outcomes, as well as conventional articles. Over time, RIO has kept adding additional article types to its list of publication types, with a few more expected in the near future.

What’s more, over the years, we’ve already observed how papers published in RIO successfully followed up on the continuity of the research process. For example, the Grant Proposal for the “Exploring the opportunities and challenges of implementing open research strategies within development institutions” project, funded by the International Development Research Centre (IDRC), was followed by the project’s Data Management Plan a year later.

Five years later, the figures reflecting the usage and engagement with the content published in RIO are evidently supportive of the value of having non-final and unconventional academic publications. For instance, the Grant Proposal for the COST Action DNAqua-Net, a still ongoing project dedicated to the development of novel genetic tools for bioassessment and monitoring of aquatic ecosystems, is the article with the most total views in RIO’s publication record to date. In the category of sub-article elements, whose usage is also tracked at the journal, the most viewed figure belongs to a Project Report and illustrates a sample code meant to be used in future neuroimaging studies. Similarly, the most viewed table ever published in RIO is part of a Workshop Report that summarises ASAPbio‘s third workshop, dedicated to the technical aspects of services related to the promotion of preprints in the biomedical and other life science communities.

Response to societal challenges

A unique and defining staple for RIO since the very beginning has also been the pronounced engagement with the Sustainable Development Goals (SDGs), as formulated by the United Nations right around the time of RIO’s launch. In order to highlight the societal impact of published research, RIO lets authors map their articles to the SDGs relevant to their paper. Once published, the article displays the associated badge(s) next to its title. Readers of the journal can even search RIO’s content by SDG, in the same way they would filter articles by subject, publication types, date or funding agency. Next on the list for RIO is to add another level of granularity to the SDGs mapping. The practice has already been piloted by mapping relevant RIO articles to the ten targets under SDG14 (Life below water).

Taking transparency, responsibility and collaboration in academia and scholarly publishing up another notch, RIO requires for reviews to be publicly available. In addition, the journal supports post-publication reviews, where peers are free to post their review anytime. In turn, RIO registers each review with its own DOI via CrossRef, in order to recognise the valuable input and let the reviewers easily refer to their contributions. A fine example is a Review Article exploring the biodiversity-related issues and challenges across Southeast Asia, which currently has a total of three public peer reviews, one of which is provided two years after the publication of the paper.

Public, transparent and perpetual peer review, pre- and/or post-publication

What’s more striking about peer review at RIO, however, is that it is not always mandatory. Given that the journal publishes many article types that have already been scrutinised by a legitimate authority – for instance, Grant Proposals that have previously been evaluated by a funder or defended PhD Theses – it only makes sense to avoid withholding these publications and duplicating associated evaluation efforts. On such occasions, all an author needs to do is provide a statement about the review status of their paper, which will be made public alongside the article.

On the other hand, where the article type of a manuscript requires pre-publication review, to avoid potential delays caused by the review process and editorial decisions, RIO encourages the authors to post their pre-review manuscript as a preprint on the recently launched ARPHA Preprints platform, subject to a quick editorial screening, which would only take a few days.

Further, RIO has now abandoned the practice of burdening the journal’s editors with the time-consuming task of finding reviewers, and instead requiring the submitting author to invite suitable reviewers upon submission, who are then immediately and automatically invited by the system. While significantly expediting the editorial work on a manuscript, this practice doesn’t compromise the quality of peer review in the slightest, since the reviews go public, while the final decision about the acceptance of the paper lies with the editor, who is also overlooking the process and able to intervene and invite additional reviewers anytime, if necessary.

Project-driven knowledge hub

The most significant novelty at RIO, however, is perhaps the newly assumed role of the journal as “a project-driven knowledge hub“, targeting specifically the needs of research projects, conference organisers and institutions. For them, RIO provides a one-stop source for the outputs of their scientists, in order to comply with the requirements of their funders or management, or simply to facilitate the discoverability, reusability and citability of their academic outputs and to highlight their interconnectedness.

Unlike typical permanent article collections, already widely used in scholarly publishing, with RIO, collection owners can take advantage of the unique opportunity to add a wide range of research outputs, including such published elsewhere, in order to provide even greater context to the assembled research outputs in their project- or institution-branded article collection (see the Horizon 2020 Project Path2Integrity‘s project collection as an example).

A permanent topical collection in RIO Journal may include a diverse range of both traditional and unconventional research outputs, as well as links to publications from outside the journal (see What can I publish on the journal’s website). 

For example, a project coordinator could open a collection under the brand of the project, and start by publishing the Grant Proposal, followed shortly by Data and Software Management Plans and Workshop Reports. Thus, even at this early point in the project’s development, the funder – and with them everyone else – would already have strong evidence of the project’s dedication to transparency and active science communication. Later on, the project’s participants would all be able to easily add to the project’s collection by either submitting their diverse research outputs straight to RIO and having it accepted by the collection lead editor, or providing metadata and link to their publication from elsewhere, even preprints. If the document is published outside of RIO, its metadata, i.e. author names and affiliations, article title and publication date, show up in the collection, while a click on the item will lead to the original publication. As the project progresses, the team behind it could add more and more outputs (e.g. Project Reports, Guidelines and Policy Briefs), continuously updating the public and the relevant stakeholders about the development of their work. Eventually, the collection will be able to provide a comprehensive and fully transparent report of the project from start to finish.

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Centrally-managed collections & Peer review flexibility: what’s new at RIO

In 2015, Research Ideas and Outcomes (RIO) was launched to streamline dissemination of scientific knowledge throughout the research process, recognised to begin with the inception of a research idea, followed by the submission of a grant proposal and progressing to, for example, data / software management plans and mid-stage project reports, before concluding with the well-known research and review paper.

In order to really expedite and facilitate access to scientific knowledge, the hurdles for engagement with the process need to be minimized for readers, authors, reviewers and editors alike. RIO aims to lay the groundwork for constructive scientific feedback and dialogue that would then lead to the elaboration and refinement of the research work well in its early stage. 

Recently, RIO published its 300th article – about a software for analyzing time series data from a microclimate research site in the Alps – and at that occasion, the RIO team wrote an editorial summarizing how the articles published in RIO so far facilitate engagement with the respective research processes. One of the observations in this regard was that while providing access to the various stages of the research cycle is necessary for meaningful engagement, there is a need for the various outcomes to be packed together, so that we can provide a more complete context for individual published outcomes.

Read the new editorial celebrating RIO’s 5th anniversary and looking back on 300 publications.

RIO introduced updates to its article collection approach to evolve into a “project-driven knowledge hub”, where a project coordinator, research institution or conference organiser can create and centrally manage a collection under their own logo, so that authors can much more easily contribute. Further, research outputs published elsewhere – including preprints – are also allowed, so that the collection displays each part of the ‘puzzle’ within its context. In this case, the metadata of the paper, i.e. title, authors and publication date, are displayed in the article list within the collection, and link to the original source.

Apart from allowing the inclusion of the whole diversity of research outcomes published in RIO or elsewhere, what particularly appeals to projects, conferences and institutions is the simplicity of opening and managing a self-branded collection at RIO. All they need to do is pay a one-time fee to cover the setup and maintenance of the collection, whereas an option with an unlimited number of publications is also available. Then, authors can add their work – subject to approval by the collection’s editor and the journal’s editorial office – by either starting a new manuscript at RIO and then assigning it to an existing collection; pasting the DOI of a publication available from elsewhere; or posting an author-formatted PDF document to ARPHA Preprints, as it has been submitted to the external evaluator (e.g. funding agency). In the latter two cases, the authors are charged nothing, in order to support greater transparency and contextuality within the research process.

Buttons on RIO Journal’s homepage allow users to create a new collection or add a document to an existing collection by either submitting a new manuscript via RIO Journal or pasting a DOI link of a publication from elsewhere, thus allowing for the collection to link to the original source and display the article’s metadata, i.e. title, authors and publication date.

Find more information about how to edit a collection at RIO and the associated benefits and responsibilities on RIO’s website.

Another thing we have revised at RIO is the peer review policy and workflow, which are now further clarified and tailored to the specificity of each type of research outcome.

Having moved to entirely author-initiated peer review, where the system automatically invites reviewers suggested by the author upon submission of a paper, RIO has also clearly defined which article types are subject to mandatory pre-publication peer review or not (see the full list). In the latter case, RIO no longer prompts the invitation of reviewers. Within their collections, owners and guest editors can decide on the peer review mode, guided by RIO’s existing policies.

While pre-publication peer review is not always mandatory, all papers are subject to editorial evaluation and also remain available in perpetuity for post-submission review. In both cases, reviews are public and disclose the name of their author by default. In turn, RIO registers each review with its own DOI via CrossRef, in order to recognise the valuable input and let the reviewers easily refer to their contributions. 

Both pre- and post-publication reviews at RIO are openly published alongside the paper and bear their own DOI. All papers in RIO remain available for post-publication review in perpetuity (see example).

For article types where peer review is mandatory (e.g. Research Idea, Review article, Research Article, Data Paper), authors are requested to invite a minimum of three suitable reviewers upon the submission of the paper, who are then automatically invited by the system. While significantly expediting the editorial work on a manuscript, this practice doesn’t compromise the quality of peer review in the slightest, since the editor is still overlooking the process and able to invite additional reviewers anytime, if necessary. 

For article types where peer review is not mandatory (e.g. Grant Proposal, Data Management Plan, Project Report and various conference materials), all an author needs to do is provide a statement about the review status of their paper, which will be made public alongside the article. Given that such papers have usually already been scrutinised by a legitimate authority (e.g. funding agency or conference committee), it only makes sense to not withhold their publication and duplicate academic efforts.

By the time it is submitted to RIO, a Grant Proposal like this one has often already been assessed by a legitimate funder, so it only makes sense to not undergo the process again at RIO and thereby slowing down its public dissemination.

Additionally, where the article type of a manuscript requires pre-publication review, RIO encourages the authors to click a checkbox during the submission and post their pre-review manuscript as a preprint on ARPHA Preprints, subject to a quick editorial screening, which would only take a few days.

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Further reading:

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In a nutshell: The four peer review stages in RIO explained

Having received a number of requests to further clarify our peer review process, we hereby provide a concise summary of the four author- and journal-organised peer review stages applicable to all research article publications submitted to RIO. 

 

Stage 1: Author-organised pre-submission review

Optional. This review process can take place in the ARPHA Writing Tool (AWT) during the authoring process BEFORE the manuscript is submitted to the journal. It works much like discussion of a manuscript within an institutional department, akin to soliciting comments and changes on a collaborate Google Doc file. The author can invite reviewers via the “+Reviewers” button located on the upper horizontal bar of the AWT. Then, the author(s) and the reviewers are able to work together in the ARPHA online environment through an inline comment/reply interface. The reviewers are then expected to submit a concise evaluation form and a final statement.

The pre-submission review is not mandatory, but we strongly encourage it. Pre-submission reviews will be published along with the article and will bear a DOI and citation details. Articles reviewed before submission are labelled “Reviewed” when published. Manuscripts that have not been peer-reviewed before submission can be published on the basis of in-house editorial and technical checks, and will be labelled “Reviewable”.

If there is no pre-submission review, the authors have to provide a public statement explaining why they do not have, or need a pre-submission review for this work (e.g. a manuscript has been previously reviewed; a grant proposal has already been accepted for funding, etc.).

 

Stage 2: Pre-submission technical and editorial check with in-house editors or relevant members of RIO’s editorial board

Mandatory. Provided by the journal’s editorial office within the ARPHA Writing Tool when a manuscript is submitted to the journal. If necessary, it can take several rounds, until the manuscript is improved to the level appropriate for direct submission and publication in the journal. This stage ensures format compliance with RIO’s requirements, as well as relevant funding-body and discipline-specific requirements.

 

Stage 3: Community-sourced post-publication peer review

Continuously available. All articles published in RIO are available for post-publication review, regardless of them being subject to a pre-submission review or not, or their review status (Reviewable, Reviewed, or RIO-validated). The author may decide to publish a revised version of an article anytime based on feedback received from the community. Putatively, even years after publication of the original work our system allows a review to be published alongside the paper.  

 

Stage 4: Journal-organized post-publication peer review

Optional. If the author(s) request it, the journal can additionally organize a formal peer review from discipline-specific researchers in a timely manner. Authors may suggest reviewers during the submission process, but RIO may not necessarily invite suggested reviewers.

Once an editor and reviewers are invited by the journal, the review process happens much like the conventional peer review in many other journals, but is entirely open and transparent. It is also subject to a small additional fee, in order to cover the management of this process. When this review stage is successfully completed and the editors have decided to validate the article, the revised article version is labelled “RIO-validated”.

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Guiding EU researchers along the ‘last mile’ to Open Digital Science

Striving to address societal challenges in sectors including Health, Energy and the Environment, the European Union is developing the European Open Science Cloud, a complete socio-technical environment, including robust e-infrastructures capable of providing data and computational solutions where publicly funded research data are Findable, Accessible, Interoperable and Re-usable (FAIR).

Since 2007 The European Commission (EC) has invested more than €740 million in e-infrastructures through Horizon 2020 (the European Union Research and Innovation programme 2014-2020) and FP7 (the European Union’s Seventh Framework Programme for Research and Technological Development). They want to see this exploited in full.

Many research communities are, however, struggling to benefit from this investment. The authors call for greater emphasis on Virtual Research Environments (VREs) as the only way for researchers to capitalise on EC advances in networking and high performance computing. The authors characterise this as a “last mile” problem, a term borrowed from telecommunications networks and once coined to emphasise the importance (and difficulty) of connecting the broader network to each customer’s home or office. Without the last mile of connectivity, a network won’t generate a cent of value.

Some concerns around the transition to Open Digital Science refer to attribution and quality assurance, as well as limited awareness of open science and its implications to research. However, most difficulties relate to many e-infrastructure services being too technical for most users, not providing easy-to-use interfaces and not easily integrated into the majority of day-to-day research practices.

Trustworthy and interoperable Virtual Research Environments (VREs) are layers of software that hide technical details and facilitate communication between scientists and computer infrastructures. They serve as friendly environments for the scientists to work with complicated computer infrastructures, while being able to use their own set of concepts, ways of doing things and working protocols.

Helping them to solve the difficulties noted above, VREs could guide the skeptical research communities along the ‘last mile’ towards Open Digital Science, according to an international team of scientists who have published their Policy Brief in the open access journal Research Ideas and Outcomes (RIO).

The authors state “These domain-specific solutions can support communities in gradually bridging technical and socio-cultural gaps between traditional and open digital science practice, better diffusing the benefits of European e-infrastructures”. They also recognise that “different e-infrastructure audiences require different approaches.”

“Intuitive user interface experience, seamless data ingestion, and collaboration capabilities are among the features that could empower users to better engage with provided services,” stress the authors.

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Original source:

Koureas D, Arvanitidis C, Belbin L, Berendsohn W, Damgaard C, Groom Q, Güntsch A, Hagedorn G, Hardisty A, Hobern D, Marcer A, Mietchen D, Morse D, Obst M, Penev L, Pettersson L, Sierra S, Smith V, Vos R (2016) Community engagement: The ‘last mile’ challenge for European research e-infrastructures. Research Ideas and Outcomes 2: e9933. doi: 10.3897/rio.2.e9933>

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Open Science environment Unicorn allows researchers and decision makers to work together

Given that the most important societal needs require multidiscipli­nary collaboration between researchers and decision makers, a suitable environment has to be provided in the first place. A proposal, prepared by a Finnish consortium and published in the open access journal Research Ideas and Outcomes, suggests a new, open virtual work and modeling platform to support evidence-based decision making in a number of areas, while also abiding by the principles of openness, criticism and reuse.

The Finnish consortium, led by Prof. Pekka Neittaanmäki, University of Jyväskylä, and bringing together Timo Huttula and Janne Ropponen, Finnish Environment Institute, Juha Karvanen and Tero Tuovinen, University of Jyväskylä, Tom Frisk, Pirkanmaa Centre for Economic Development, Transport and the Environment, Jouni Tuomisto, National Institute for Health and Welfare, and Antti Simola, VATT Institute for Economic Research, acknowledge that, “it is not enough that experts push data to politicians.”

“There must be practices for mutual communication: experts must answer policy questions in a defendable and useful way; decision makers must more clearly explain their views using evidence; and there must be ICT tools to support this exchange,” the authors explain. “The focus is on end-users.”

Unicorn is to combine shared practices, tools, data, working environments and concerted actions in order to aggregate open information from multiple databases, and create tools for efficient policy studies.

The consor­­tium have already developed and tested prototypes of such practices and tools in several projects, and insist that they are now ready to apply their experience and knowledge on a larger scale. They are also certain that open data and models are deservedly the “mega trend” nowadays.

“Unicorn directs this trend to paths that are the most beneficial for societal decision making by providing quick, reliable and efficient decision support,” they say.

“Significant saving of resources will be mani­fested with improved data collection, analyses and modeling. Also, the quality and amount of assessments that can be done to support work.”

“The major challenges related to evidence-based decision making actually are about changing the practices of researchers and dec­­ision makers,” according to the authors. Therefore, they see their project as a demonstration of the needed shifts.

Although the approach is applicable in all areas, the researchers are to initially implement them in environment, human health, and regional economy, “as they are com­plex and chal­lenging enough to offer a good test bed for general development.”

Having already been submitted to the Strategic Funds of Academy of Finland in 2015, the Unicorn environment proposal has been rejected due to overambitiousness and low commercial potential. However, the authors are confident that the Unicorn environment along with its growing community of developers can, in fact, meet a great success. They are currently looking for further funding suggestions and forming new consortiums.

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Original source:

Neittaanmäki P, Huttula T, Karvanen J, Frisk T, Tuomisto J, Simola A, Tuovinen T, Ropponen J (2016) Unicorn-Open science for assessing environmental state, human health and regional economy. Research Ideas and Outcomes 2: e9232. doi: 10.3897/rio.2.e9232

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PART 2: The ARPHA Writing Tool: Adding Value to RIO

Last week, we presented some basic features of the ARPHA Writing Tool (AWT), focusing on the collaborative authoring process. This post will add the novelties that ARPHA has adopted when it comes to submission and post-submission processes.

arpha-validation

   

Two-step VALIDATION:

Checks are a must whenever high-quality, professional writing is concerned. Shortly before submitting their manuscripts via ARPHA, the authors are free to initiate the first step of the validation process at any time. As a result, an automated technical check runs through the manuscript to verify its consistency and compliance with the JATS (Journal Article Tag Suite) standard as well as key elements of the journal’s policy.

After the automated checks, there is a second-layer of human checks made by RIO editorial assistants in order to bring the manuscript to a pre-publication level. They check compliance with further elements of the journal’s policy as well as linguistic consistency and work with the authors before finalising it altogether.

 

After SUBMISSION:

Even after submission, collaboration continues. With the peer-review stage being as transparent and open as the whole vision of RIO is, this step is no less straightforward and organised. All peer reviews are automatically consolidated into a single online file that makes the editorial process simple and pleasant. This is made possible by the XML-based workflow in the AWT.

arpha-review-

PEER-REVIEW evolution:

Last week, we mentioned that an author can invite reviewers during the authoring stage itself. Let us elaborate here by saying that the ARPHA Writing Tool provides a functionality for pre-submission peer review(s) performed during the authoring process. These peer reviews are submitted together with the manuscript, so that the editorial evaluation and publication can be significantly sped up.

Post-publication UPDATES:

Even after an article is brought to life, ARPHA continues to play a role in it. Because of the XML workflow, authors are able to publish updated versions of their articles at any time. Once they request such an update, their work is returned to the ARPHA Writing Tool, where authors and peers are to collaborate once again. Eventually, the two versions are linked via CrossMark, so that nothing is lost.   

As you might have already noticed, just like RIO, the new ARPHA Writing Tool is constructed entirely around the needs of its authors. Why not find out yourself by giving ARPHA & RIO a try when they open for submission early next month?

 

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Counting days and tweets: What’s happened to RIO Journal so far?

So, here we are, counting days and Twitter impressions since Research Ideas & Outcomes (or, RIO for short) our new open access journal was officially announced on 1st September 2015. As much as we were excited to take this long-prepared and anticipated stand in the spotlight, we are still holding our breath ahead of the big event – the launch itself, scheduled for November 2015.

In the meantime, when not busy welcoming our very first subject editors, we have our ear to the ground, so that we can make sure to provide everyone with the best services and insight. The truth is, we don’t only value attention, we deeply appreciate your opinion and respect your needs and concerns.

So, here below we provide a short summary of the eventful first week of RIO Journal:

It all started on 1st September on Twitter. Among the constantly growing list of our first followers, there were a lot of welcoming retweets, sounding just as excited as we were:

Then, the time came for the world media to give its verdict:

This week sees the birth of a new type of scientific journal, one that will publish not only study results and data, but also research ideas and proposals. It’s called Research Ideas and Outcomes (RIO).
/The Scientist, 3rd September/

With so many science journals already in existence, it is rare for a new title to draw attention. But researchers and publishing experts are taking notice of Research Ideas and Outcomes, or RIO, an open-access journal that launched on 1 September.
/Nature, 3rd September/

Understandably, the hottest discussion points were RIO’s initiatives:

> To present openly the whole process of the research cycle especially including research proposals
> To publish such ideas regardless of them being eventually approved or rejected for funding
> To apply a transparent, public, and open peer-review policy

Stephen Curry, a structural biologist at Imperial College London shared on Twitter that in his opinion RIO is “bringing a new sense of transparency and collaboration to research”, while he voiced his strong support for preprint publications and open feedback in his Guardian blog. “Preprints can help to refocus attention where it matters – on the work itself, not where it is published. In so doing, they have the potential to revitalize the scientific enterprise”, his column reads.

“I like the idea of getting “publishing-credit” for my research proposals and other research output. Roughly speaking for every proposal I write, I write one paper less”, points out computational chemist at the University of Copenhagen Jan Jansen on explaining why he accepted the invitation to become one of RIO’s subject editors.

At the end of the day, some of RIO’s innovations couldn’t escape being challenged by some criticisms. A librarian and known extreme critic of open access journals, Jeffrey Beall questioned the freedom given to RIO’s authors to make their own choice of reviewers.

One of the RIO’s own subject editors, Ivo Grigorov, a marine scientist at the Technical University of Denmark also raised his concerns on the matter. Yet, he and our ever growing list of editors and advisory board are sticking with us:

In his turn, Ross Mounce, a postdoc at the Natural History Museum, London and a founding editor of RIO, explained how the new open access journal seeks to improve the “immensely wasteful” traditional research process in his piece on the popular LSE Impact blog.

Ross also gave a podcast interview for Beta Pleated Chic, he spoke in detail about the whole list of innovative tools and strategies.

If you know of any other press mentions or blogs about RIO Journal, please don’t hesitate to forward them to us on Twitter @RIOJournal.