All processes fit into a broad S-shaped envelope extending from the briefest to the most enduring biological events. For the first time, we have the first simple model that depicts the scope and scale of biology.
As biology is progressing into a digital age, it is creating new opportunities for discovery.
Increasingly, information from investigations into aspects of biology from ecology to molecular biology is available in a digital form. Older ‘legacy’ information is being digitized. Together, the digital information is accumulated in databases from which it can be harvested and examined with an increasing array of algorithmic and visualization tools.
That information also must make its way to trustworthy repositories to guarantee the permanent access to the data in a polished and fully suited for re-use state.
The first layer in the infrastructure is the one that gathers all old and new information, whether it be about the migrations of ocean mammals, the sequence of bases in ribosomal RNA, or the known locations of particular species of ciliated protozoa.
This is achieved by compiling information about the processes conducted by all living organisms. The processes occur at all levels of organization, from sub-molecular transactions, such as those that underpin nervous impulses, to those within and among plants, animals, fungi, protists and prokaryotes. Further, they are also the actions and reactions of individuals and communities; but also the sum of the interactions that make up an ecosystem; and finally, the consequences of the biosphere as a whole system.
In the Nature’s Envelope, information on sizes of participants and durations of processes from all levels of organization are plotted on a grid. The grid uses a logarithmic (base 10) scale, which has about 21 orders of magnitude of size and 35 orders of magnitude of time. Information on processes ranging from the subatomic, through molecular, cellular, tissue, organismic, species, communities to ecosystems is assigned to the appropriate decadal blocks.
The extremes of life processes are determined by the smallest and largest entities to participate, and the briefest and most enduring processes.
The briefest event to be included is the transfer of energy from a photon to a photosynthetic pigment as the photon passes through a chlorophyll molecule several nanometres in width at a speed of 300,000 km per second. That transaction is conducted in about 10-17 seconds. As it involves the smallest subatomic particles, it defines the lower left corner of the grid.
The most enduring is the process of evolution that has been progressing for almost 4 billion years. The influence of the latter has created the biosphere (the largest living object) and affects the gas content of the atmosphere. This process established the upper right extreme of the grid.
All biological processes fit into a broad S-shaped envelope that includes about half of the decadal blocks in the grid. The envelope drawn round the initial examples is Nature’s Envelope.
Eligible submissions enjoy a 50% discount off APCs in 2021
Since its launch in 2015, RIO Journal has been mapping its articles to the Sustainable Development Goals (SDGs) of the United Nations. The articles published so far span the entire research cycle, a broad range of research fields and all SDGs, which can also be used as a search filter. However, the distribution of RIO articles across SDGs is uneven, as detailed in a recent editorial: for instance, more than 100 articles addressed SDG9 (Industry, innovation & infrastructure), while only one publication has been mapped to SDG1 (No poverty) so far.
Even though there might be logical explanations for this phenomenon, including funding biases or specific scholarly communication tendencies in some research fields, RIO’s team remains dedicated to its role as a harbinger of innovative open science practices and socially engaged research, and is eager to support the open publication of research on all SDGs.
So, RIO Journal is now inviting research outcomes – early, interim or final – addressing the four least represented SDGs in RIO’s content to date (with the current number indicated in parentheses):
The call will remain open until the end of 2021, where all accepted papers will enjoy a 50% discount on their publication charges (APCs), regardless of how many contributions RIO receives in the meantime. Eligible submissions encompass all article types generally accepted in RIO, as long as the journal’s editorial team confirms that they belong to the assigned SDG category.
As also highlighted in the editorial, RIO is currently experimenting with a more fine-grained mapping of its publications to the individual targets under each SDG. This was piloted with SDG 14 (Life below water). For instance, Target 14.a (Marine Biodiversity contributes to Economic Development of small/developing nations) is currently covered by 17 RIO articles. If you would like to get involved with mapping RIO articles to the Targets under other SDGs, please get in touch.
You can find more about RIO’s rationale behind introducing the SDGs mapping in the latest editorial or in this earlier blog post.
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 ActionDNAqua-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).
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.
RIO updated its article collection approach to evolve into a “project-driven knowledge hub”, where a project coordinator, institution or conference organiser can create and centrally manage a collection under their own logo.
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.
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.
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.
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.
Hence, as a forward-looking, open science-driven journalResearch Ideas and Outcomes (RIO) took it as its own responsibility to encourage scientific project teams, conference organisers and research institutions to bring together unconventional research outputs (e.g. grant proposals, data management plans, project deliverables, policy briefs, conference materials) as well as traditional (e.g. research or review papers, monographs, etc.), including such published elsewhere. To do so, RIO now provides the platform ready to be used as a research knowledge hub, where published outcomes are preserved permanently and easier to share, disseminate, reference and reuse.
Hence, RIO stepped up its game by turning permanent article collections into a one-stop source of diverse research items, where project coordinators, conference organisers or research institutions can not only publish early, interim and conclusive research items as they emerge within a research project, a series of events or the continuous scientific efforts at their lab, but also link relevant publications (i.e. preprints, articles or other documents, published elsewhere) available elsewhere through their metadata. As a result, they will receive a one-stop source under their own branding for every piece of scientific contribution ready to present to funding bodies or prospective collaborators and future research teams.
Apart from bringing contextually linked research outcomes together, thus prompting findability, readership and citability en masse, RIO’s approach to collections ensures further accessibility by not only having RIO-published articles available in traditional PDF, semantically enriched HTML and minable XML format. The open-science journal has now made it possible for users to add to their collections preprints from ARPHA Preprints, as well as author-formatted PDFs (e.g. project deliverables, reports, policy briefs, etc.) and linked metadata to documents published elsewhere. Thanks to the integration of the journal with the general-purpose open-access repository Zenodo, all items in a collection are archived, and additionally indexed, disseminated and cited.
By focusing on article and preprint collections coming out from a research project, institution or conference, RIO provides a quite specific and unique combination of benefits to all actors of the research process: scientists, project coordinators, funders and institutions:
Project, institution or conference branding and promotion.
One-stop point for outputs of a research project, institution or conference.
Free publication of author-formatted project outputs (i.e. grant proposals, deliverables, reports, policy briefs, conference materials and others).
Inclusivity through adding articles, preprints and other documents published elsewhere as easy as entering the DOI number of the document.
Credit and recognition for the Collection and Guest editors, who take care to organise and manage the article collection.
Easier discoverability and usability of topically related studies to benefit both authors and readers.
Increased visibility of related papers in a collection, even when these might otherwise not have much exposure.
Simultaneous citation of multiple articles related to a certain subject.
Citation and referencing of the whole collection as a complete entity.
DOI and citation details for collections and individual articles.
How do project coordinators, funders and institutions benefit from a collection in RIO?
At the time a grant proposal is submitted to a research funder for evaluation, the team behind the proposed project has already put in considerable efforts, resulting in a unique idea with the potential to make a great stride towards the resolution of an outstanding problem in science, if only given the chance. However, too many of these ideas are bound to remain locked away in the archives of those funders, not because they are lacking in scientific value, but due to limited funds.
So, with its launch back in 2015, RIO Journal made it possible to publish and shed light on grant proposals and research ideas in general, similar early research outputs regardless of whether they are eventually funded or not, a novelty in scholarly publishing which earned RIO the SPARC Innovator Award Winner in 2016. To date, the journal has already published 75 grant proposals.
Then, imagine what a contribution to science it would make to bring together the whole continuum of knowledge and scientific work all the way from the grant proposal to data and software management plans, workshop reports, policy briefs and all interim and final deliverables produced within the span of the project!
On the other hand, funders are increasingly evaluating a prospective project’s impact based on its communication strategy. So, why not publish a grant proposal at the time of the submission of your proposal, in order to prove to the funding body that your project is serious about optimising its outreach to both the public and academia? Furthermore, by having an academic journal host any subsequent project deliverable, as a coordinator, you can rest assured that the communication activities of your project remain consistent and efficient.
In an excellent example of a project collection, the EU-funded ICEDIG (Innovation and Consolidation for Large Scale Digitisation of Natural Heritage), led by several major natural history institutions, including the Natural History Museum of London, Naturalis Biodiversity Center (the Netherlands), the French National Museum of Natural History and Helsinki University, brought together policy briefs, project reports, research articles and review papers, in order to provide a fantastic overview of their own research continuum. As a result, future researchers and various stakeholders can easily piece together the key components within the project, in order to learn from, recreate or even build on the experience of ICEDIG.
Similarly, conference organisers can make use of their own branded collections to overcome the ephemerality of presented research by collating virtually all valuable conference outputs, including abstracts, posters, presentations, datasets and full-text conference talks. For further convenience, a collection can be divided into subcollections, in order to organise the contribution by type or symposium. What particularly appeals to conference participants is the ARPHA Writing Tool, an intuitive collaborative online environment, which practically guides the user through each step: authoring, submission and pre-submission review, within a set of pre-designed, yet flexible templates available for each type of a conference output, thus sparing them the hassle to familiarise themselves with specific and perplexing formatting requirements
For institutions, RIO offers the opportunity to continuously provide evidence of the scholarly impact of their organisation. To better serve the needs of different labs or research teams, an institution can easily organise their outputs into various subcollections, and also customise their own article types, as well as the available usage tracking systems. Furthermore, by making use of the available pre-paid plans, institutions can support their researchers by covering fully or partially the publication charges at a discounted rate.
Find more information regarding the submission and review process, policies and pricing, visit RIO Journal’s website.
Looking at today’s ravaging COVID-19 (Coronavirus) pandemic, which, at the time of writing, has spread to over 220 countries; its continuously rising death toll and widespread fear, on the outside, it may feel like scientists and decision-makers are scratching their heads more than ever in the face of the unknown. In reality, however, we get to witness an unprecedented global community gradually waking up to the realisation of the only possible solution: collaboration.
On one hand, we have nationwide collective actions, including cancelled travel plans and mass gatherings; social distancing; and lockdowns, that have already proved successful at changing what the World Health Organisation (WHO) has determined as “the course of a rapidly escalating and deadly epidemic” in Hong Kong, Singapore and China. On the other hand, we have the world’s best scientists and laboratories all steering their expertise and resources towards the better understanding of the virus and, ultimately, developing a vaccine for mass production as quickly as possible.
While there is little doubt that the best specialists in the world will eventually invent an efficient vaccine – just like they did following the Western African Ebola virus epidemic (2013–2016) and on several other similar occasions in the years before – the question at hand is rather when this is going to happen and how many human lives it is going to cost?
Again, it all comes down to collective efforts. It only makes sense that if research teams and labs around the globe join their efforts and expertise, thereby avoiding duplicate work, their endeavours will bear fruit sooner rather than later. Similarly to employees from across the world, who have been demonstrating their ability to perform their day-to-day tasks and responsibilities from the safety of their homes just as efficiently as they would have done from their conventional offices, in today’s high-tech, online-friendly reality, no more should scientists be restricted by physical and geographical barriers either.
“Observations, prevention and impact of COVID-19”: Special Collection in RIO Journal
To inspire and facilitate collaboration across the world, the SPARC-recognised Open Science innovator Research Ideas and Outcomes(RIO Journal) decided to bring together scientific findings in an easy to discover, read, cite and build on collection of publications.
Furthermore, due to its revolutionary approach to publishing, where early and brief research outcomes (i.e. ideas, raw data, software descriptions, posters, presentations, case studies and many others) are all considered as precious scientific gems, hence deserving a formal publication in a renowned academic journal, RIO places a special focus on these contributions.
Accepted manuscripts that shall deal with research relevant to the COVID-19 pandemic across disciplines, including medicine, ethics, politics, economics etc. at a local, regional, national or international scale; and also meant to encourage crucial discussions, will be published free of charge in recognition of the emergency of the current situation. Especially encouraged are submissions focused on the long-term effects of COVID-19.
Furthermore, thanks to the technologically advanced infrastructure and services it provides, in addition to a long list of indexers and databases where publications are registered, the manuscripts submitted to RIO Journal are not only rapidly processed and published, but once they get online, they immediately become easy to discover, cite and built on by any researcher, anywhere in the world.
On top of that, Pensoft’s targeted and manually provided science communication services make sure that published research of social value reaches the wider audience, including key decision-makers and journalists, by means of press releases and social media promotion.
More info about RIO’s globally unique features, visit the journal’s website. Follow RIO Journal on Twitter and Facebook.
Research Ideas & Outcomes (RIO), a new open access journal, is formally announced. The new journal represents a paradigm shift in academic publishing: for the first time, RIO will publish research from all stages of the research cycle, across a broad suite of disciplines, from humanities to science.
Traditional journals accept only articles produced at the end of the research continuum, long after the core work has been completed. RIO will publish ideas and outputs from all stages of the research cycle: proposals, experimental designs, data, software, research articles, project reports, policy briefs, project management plans and more.
The journal takes another step ahead with a collaborative platform that allows all ideas and outputs to be labelled with Impact Categories based upon UN Millennium Development Goals(MDGs) and EU Societal Challenges. These categories provide social impact-based labelling to help funders, journalists and the wider public discover and finance relevant research as well as to foster interdisciplinary collaboration around societal challenges.
These game-changing ideas come packed with technical innovation and unique features. The journal is published through ARPHA, the first publishing platform ever to support the full life cycle of a manuscript: from authoring to submission, public peer review, publication and dissemination, within a single, fully-integrated online collaborative environment. The new platform will also allow for RIO to offer one of the most transparent, open and public peer review processes, thus building trust in the reviewed outcomes.
These features come à la carte: RIO will offer flexible pricing where authors can choose exactly which publishing services fit their needs and budget. All its contents – including reviews and comments, data and code – will receive a persistent unique identifier, will be permanently archived and made available under open licenses without any access embargo.
“RIO is not just about different kinds of submissions, though that is a crucial feature and certainly unique for publishing ongoing or even proposed research: it is also about linking those submissions together across the research cycle, about reducing the time from submission to publication, about collaborative authoring and reviewing, about mapping to societal challenges, about technical innovation, about enabling reuse and about giving authors more choice in what features they actually want from the journal.” said Dr. Daniel Mietchen, a founding editor of RIO.
“I’m proud to pioneer the first journal which can publish research from all stages of the research process,” said Prof. Lyubomir Penev, Co-Founder of RIO and Pensoft. “For the first time, researchers can get formal publication credit for previously ‘hidden’ parts of their work like written research proposals. We can publish all outputs in one journal; the same journal – RIO.”
RIO is scheduled to start accepting manuscripts in November 2015.