Tag: open science

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 at RIO

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.

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:

RIO shifts gears to serve as project-driven knowledge hub

RIO shifts gears to serve as project-driven knowledge hub

Research Ideas and Outcomes (RIO Journal) upgrades its unique concept to appeal to scientific projects, conference organisers and research institutions

Research Ideas and Outcomes (RIO Journal) upgrades its unique concept to appeal to scientific projects, conference organisers and research institutions

Over the last few years, we’ve been increasingly observing how major funders of research around the world, including the likes of the European Commission, Wellcome, U.S. National Institutes of Health (NIH), Deutsche Forschungsgemeinschaft (DFG) and the Japan Society for the Promotion of Science (JSPS) recognise the research cycle as a continuum, rather than scattered standalone conclusions and reports. 

Hence, as a forward-looking, open science-driven journal Research 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.

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). 

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: 

  1. Project, institution or conference branding and promotion.
  2. One-stop point for outputs of a research project, institution or conference.
  3. Free publication of author-formatted project outputs (i.e. grant proposals, deliverables, reports, policy briefs, conference materials and others).
  4. Inclusivity through adding articles, preprints and other documents published elsewhere as easy as entering the DOI number of the document.
  5. Credit and recognition for the Collection and Guest editors, who take care to organise and manage the article collection.
  6. Easier discoverability and usability of topically related studies to benefit both authors and readers.
  7. Increased visibility of related papers in a collection, even when these might otherwise not have much exposure.
  8. Simultaneous citation of multiple articles related to a certain subject.
  9. Citation and referencing of the whole collection as a complete entity.
  10.  DOI and citation details for collections and individual articles.

Furthermore, RIO Journal maps all publications to the Sustainable Development Goals  (SDGs), in order to emphasise the real-world impact of each published contribution, by displaying the corresponding badge within the article list. 

Last, but not least, both collections and individual publications in RIO enjoy the variety of default and on-demand science communication services, provided by Pensoft.  

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.

The Path2Integrity Project Outcomes collection demonstrates how research papers published elsewhere are featured in RIO Journal.

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.

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Find more information regarding the submission and review process, policies and pricing, visit RIO Journal’s website.

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Making the most of conferences with modern publishing and indexing practices

Given scientific conferences present academics with the fantastic opportunity to meet up and discuss their latest work, as well as share their vision for the future of their field, it’s no wonder that, historically, the majority of ground-breaking science can easily be traced back to a particular event.

This said, don’t you think that we need to do everything within our powers to ensure the visibility, dissemination and long-term accessibility of research presented and linked to these wonderful drivers of scientific progress that conferences are? Similarly to the care conference organisers take to make sure the event runs smoothly and the attendants are happy with the programme and enjoy themselves, the organisational committee should also be thinking how to preserve all those promising pieces of research well after the event is over.

Here at Pensoft, an open-access scholarly publisher, founded by scientists, we’ve been contemplating for a while now how to encourage and support the community to efficiently open up the valuable outputs to researchers and readers well beyond the publication of abstracts in an abstract book of the conference. 

As a result, we came up with several simple, yet efficient publishing solutions for scientific conferences to collect and contextualise various research outputs either presented at or resulting from the event.

Bear in mind that with any solution, all publications enjoy the benefits seen in conventional research papers, such as:

  • Crossref registration and individual DOI to ensure preservation;
  • Publication in PDF, semantically enhanced HTML and data-minable XML formats to improve readability, accessibility and findability;
  • Indexing and archiving at multiple, industry leading databases to increase visibility;
  • PR and social media promotion to boost outreach to various audiences.

Collections of conference abstracts, posters and presentations

Conference (video) abstracts, posters and presentations are easily the first to fall victims of the ephemerality of an event, yet these are too often the stepping stones to major scientific discoveries. This is why a few years back we launched ARPHA Conference Abstracts (ACA), where conference organisers can open their own collection and provide the participants with submission, review and publication of their abstracts ahead of the conference.

Furthermore, these abstracts can be handled editorially in sub-collections, e.g. the convenors of symposia or working groups within a conference will take care of the abstracts submitted to them, thus spreading the editorial workload across larger teams of editors and organisers.

Not only will conference organisers spare themselves the worries about providing a special platform for abstracts submissions, but this will also facilitate presenting authors, who will be able to easily point to their contribution before, during or after their presentations. On the contrary, the abstracts are assigned with DOIs, published in human-readable PDF and HTML and machine-actionable JATS XML, permanently preserved on ARPHA and Zenodo, and easy to find, access and cite, just like a conventional research paper, providing authors with full credit for their work early on.

Further, with ACA, the conference abstracts can be enhanced into what we call “extended abstracts”, meaning they can also include data, images, videos and multimedia. After the conferences, we can add video recordings of the presentations or graphic files of posters, so that these are visualised on the page of each abstract.

For example, take a look at the conference abstract collection of the Vth International Congress on Biodiversity: “Taxonomy, Speciation and Euro-Mediterranean Biodiversity”.

Conference proceedings

About the time we launched ACA, we also created ARPHA Proceedings, in order to also find a place for full-text conference papers. Similarly, the platform supports dedicated collections, where conference attendants are invited to submit and publish dynamically articles under the imprint of the event.

Conference papers in ARPHA Proceedings can also include data, figures and citations, and can also be updated with video recordings, posters and presentations following the conference.

Check out an example by the VI International Forum on Teacher Education.

Article topical collections and special issues resulting from conferences

Naturally, papers resulting from a particular conference are contextually linked, so a one-stop place to discover topical studies sharing one and the same topic would be greatly appreciated by readers and future researchers. In turn, this would lead to better viewership and citability of the papers in the collection.

With our user-friendly, dedicated workflow for special issues and permanent topical article collections, we’ve made it easy for guest editors across our journals to pitch and manage article collections, in order to bring together valuable and related studies. Using such a collection under the theme of your conference in a suitable journal, you can invite your conference’s participants or, better yet, all scientists working within the field, to submit their work in a nice package of topical science. We’d be happy to assist you with the identification of the most suitable journal for your conference, authors and goals.

See an example from One Ecosystem and the collection “Mapping and assessment of ecosystem condition and ecosystem services across different scales and domains in Europe”, the result from the “Mapping and assessment of ecosystem services – Science in action” conference, held in 2017.

Bringing together traditional and non-conventional research outputs, (e.g. research ideas, grant proposals, conference materials or workshop reports) with RIO Journal’s article collections

Undoubtedly, valuable research outcomes come in many shapes and sizes well beyond research papers, conference abstracts, posters and proceedings. We are firm supporters that every research item, even early and interim outputs, could be of value to the scientist next in line within a particular study.

This is why we launched the award-winning journal Research Ideas and Outcomes (RIO), where your collections can include both conventional and non-traditional research outputs, such as research ideas, posters, workshop reports, forum papers, policy briefs, software and data management plans to name a few. Furthermore, in RIO, you can even link articles or preprints published elsewhere to your collection via their metadata. Similarly to other Pensoft journals, in RIO, you will have the full control to whom you are opening your collection for submissions, allowing you to either limit it to the outcomes coming from your conference or welcome submissions from other researchers as well.

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). 

See the Brainhack 2016 Project Reports, whose aim is to collate reports from the 2016 Brainhack events. Also, check out the collection of the European Biodiversity Observation Network (EU BON) Project, providing a nice example for a wide range of publication types.

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Don’t hesitate to get in touch to discuss your own case and select the best option for your conference – we’ll be happy to hear from you!

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All articles published in Pensoft journals at your fingertips with the Researcher app

Following a recent integration with the novel, social network-style research discovery app Researcher, the scholarly platform ARPHA has taken yet another step to ensure scholarly publications from across its open-access, peer-reviewed journal portfolio are as easy to find and read as possible. Now, research papers published in all Pensoft’s and all other journals hosted on ARPHA Platform can reach the 1.8 million current users of Researcher directly on their smartphones.

Following a recent integration with the novel, social network-style research discovery app Researcher, the scholarly publishing platform ARPHA has taken yet another step to ensure scholarly publications from across its open-access, peer-reviewed journal portfolio are as easy to find and read as possible. Now, research papers published in all Pensoft’s, as well as all other journals hosted on ARPHA, can reach the 1.8 million current users of Researcher directly on their screens.

Similarly to the world’s best known and used social media networks: Twitter, LinkedIn and Facebook, Researcher allows its users, scientists and academics, to follow their favourite scholarly journals and topics, in order to receive their content in a personalised newsfeed format, either on their phones or computers. Thus, they can stay up to date with the latest research in their scientific fields by simply scrolling down: much like what they are already used to in their everyday life outside academia. 

Similarly to the well-known social network apps, Researcher lets users bookmark papers to go back to later on and even invite friends to join the platform. Furthermore, the users can also synchronise their accounts with their ORCID iDs, in order to load their own papers on their profiles on Researcher. 

The Researcher app fetches new publications from all indexed journals several times a day, thus ensuring that a user’s newsfeed is updated in almost real time. Now, the ARPHA-hosted journals have joined the 17,000 academic outlets from across the sciences already sharing their publications on the app.

“At Pensoft, we are perfectly aware that good and open science practices go far beyond cost-free access to research articles. In reality, Open Science is also about easier findability and reusability, that is the probability one stumbles across a particular research publication, and consequently, cite and build on the findings in his/her own studies. By indexing our journals with Researcher, we’re further facilitating the discoverability of their content to the benefit of the authors who trust us with their work,”

says ARPHA’s and Pensoft’s founder and CEO Prof. Lyubomir Penev.

“We share ARPHA’s belief that Open Science means more than just free access – it means giving scholarly and scientific content the best chance to get in front the right reader at the right time. Our mission is to make sure that scientists and researchers never miss vital research. This partnership will ensure that distribution to our users across the world is built into the ARPHA platform – boosting discoverability and smoothing the path to impact,”

adds Olly Cooper, CEO of Researcher.

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Acta Biologica Sibirica signs with Pensoft and moves to ARPHA

Acta Biologica Sibirica, an open-access, peer-reviewed journal of Altai State University, with its content on original research in the field of experimental and field biology, moves to Pensoft and the publisher’s scholarly platform ARPHA. The journal has been published since 2015 and follows all the standards in modern biological research and Open Access policy. The first papers published in 2020 are already available on a brand new user-friendly website, running on ARPHA publishing platform.

Acta Biologica Sibirica Credit: Acta Biologica Sibirica and Pensoft License: CC-BY 4.0
The first papers in 2020 of Acta Biologica Sibirica, journal of Altai State University, are published on the innovative ARPHA publishing platform and already available online on a user-friendly brand new website
Credit:Acta Biologica Sibirica and Pensoft
License: CC-BY 4.0

Acta Biologica Sibirica is an open-access, peer-reviewed journal on the biodiversity of Siberia and the adjacent lands by Altai State University. Since 2015, it has been publishing  original research in the field of experimental and field biology. 

Starting from 2020, Acta Biologica Sibirica moves to the full-featured technologically advanced platform ARPHA and will be published in collaboration with the scholarly publisher and technology provider Pensoft.

Pensoft’s original publishing system ARPHA allows Acta Biologica Sibirica to publish original research papers, reviews, short communications, letters and discussion papers, book reviews and memorial articles. The scholarly platform was designed to facilitate authors in the manuscript writing, submission and review process as end-to-end experience, including publication of the data and multimedia content in the form, suitable for both enhanced high-tech human and machine discoverability of the scholarly outputs.

Acta Biologica Sibirica accepts for publication papers in taxonomy, phylogeny, biogeography, faunistics, floristics, biological systematics, nature conservation and protected areas. In the fields of faunistics and floristics there are several types of articles, available for submission: floral and faunal lists on any region of the world, faunal and floral discoveries (e.g. species newly recorded in a particular region, additions to previously published inventories), papers on methodology of faunal and floral studies.

«Our basic task is to turn our journal into a high-quality world-class publication. Without the help of modern publishers, this is almost impossible. The choice of the publisher was perfectly logical – the reputation of Pensoft Publishers and its founder, the famous Bulgarian zoologist Lubomir Penev, is impeccable. To stand in one cohort with powerful publications with a long history is an honor for us. High standards of editing and reviewing manuscripts, the absolute level of originality and scientific novelty – these are the criteria on which we will rely»,

comments the Editor-in-Chief of the journal, Professor of Altai University Roman Yakovlev.

«At Pensoft, we are delighted to initiate this wonderful partnership with yet another renowned research institution in Russia, namely Altai State University. With our long-year experience in zoological and biodiversity research publishing and dissemination, I am certain that the journal has found a fitting place in the family of Pensoft and ARPHA»,

comments Prof. Lyubomir Penev, CEO and founder of Pensoft and ARPHA.

The first papers of 2020 are already available online on the new website of Acta Biologica Sibirica.

Within the pioneering papers published in the renewed journal, there is a research article about the first result of DNA-studies on the Central Asiatic owlet moths in the genus Euchalcia. The studied specimens were collected in Kyrgyzstan and Kazakhstan during the expeditions of the Russian Entomological Society in 2017-2019. When comparing a specific mitochondrial gene (cytochrome C oxidase subunit I or COI) between various species, the scientists revealed that the difference amongst European Euchalcia species is smaller than the one amongst high-mountainous Central Asiatic species.

Another study records the first occurrence of the moorland clouded yellow in Altai Region. The butterfly was found to share a mitochondrial barcode with some specimens from mountain populations from the Alps and the Czech Republic.

Colias palaeno, male, vicinity of Ozerki village, Talmenskiy district, Altai region, Russia Credit: Nazar A. Shapoval License: CC-BY 4.0
Colias palaeno, male, vicinity of Ozerki village, Talmenskiy district, Altai region, Russia
Credit: Nazar A. Shapoval
License: CC-BY 4.0

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Additional information

About Altai State University:

Altai State University is one of the leading Russian classical higher education institutions established in 1973. It is a major educational, research and cultural center located in the Asian part of the country, integrated into the international academic community, training the intellectual elite and conducting high-impact research.

The unique geographical position of Altai region, located in the center of Asia predestinates the University’s mission – to appear as an international research and educational center that integrates, develops and spreads the modern Western, Russian and Asian knowledge in education, science and culture within the Asian region.

About ARPHA:

ARPHA is the first end-to-end, narrative- and data-integrated publishing solution that supports the full life cycle of a manuscript, from authoring to reviewing, publishing and dissemination. ARPHA provides accomplished and streamlined production workflows that can be customized according to the journal’s needs. The platform enables a variety of publishing models through a number of options for branding, production and revenue models to choose from.

About Pensoft:

Pensoft is an independent academic publishing company, well-known worldwide for its innovations in the field of semantic publishing, as well as for its cutting-edge publishing tools and workflows. In 2013, Pensoft launched the first ever end to end XML-based authoring, reviewing and publishing workflow, as demonstrated by the Pensoft Writing Tool (PWT) and the Biodiversity Data Journal (BDJ), now upgraded to the ARPHA Publishing Platform. Flagship titles include: Research Ideas and Outcomes (RIO), One Ecosystem, ZooKeys, Biodiversity Data Journal, PhytoKeys, MycoKeys and many more.

Contacts:

Prof. Lyubomir Penev, founder and CEO at ARPHA and Pensoft
Email: penev@pensoft.net

Prof. Alex Matsyura, Editor-in-Chief of Acta Biologica Sibirica
Email: amatsyura@gmail.com

Prof. Roman Yakovlev, Editor-in-Chief of Acta biologica sibirica 
Email: yakovlev_asu@mail.ru


Open Science RIO Journal invites early research outcomes for the free-to-publish collection “Observations, prevention and impact of COVID-19”

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.

Why publish in RIO Journal? 

Launched in 2015, RIO Journal has since proved its place at the forefront of Open Science, which resulted in the SPARC’s Innovator Award in 2016. Supported by a renowned advisory board and subject editors, today the journal stands as a leading Open Science proponent. 

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.

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More info about RIO’s globally unique features, visit the journal’s website. Follow RIO Journal on Twitter and Facebook.

Plazi and Pensoft join forces to let biodiversity knowledge of coronaviruses hosts out

Pensoft’s flagship journal ZooKeys invites free-to-publish research on key biological traits of SARS-like viruses potential hosts and vectors; Plazi harvests and brings together all relevant data from legacy literature to a reliable FAIR-data repository

To bridge the huge knowledge gaps in the understanding of how and which animal species successfully transmit life-threatening diseases to humans, thereby paving the way for global health emergencies, scholarly publisher Pensoft and literature digitisation provider Plazi join efforts, expertise and high-tech infrastructure. 

By using the advanced text- and data-mining tools and semantic publishing workflows they have developed, the long-standing partners are to rapidly publish easy-to-access and reusable biodiversity research findings and data, related to hosts or vectors of the SARS-CoV-2 or other coronaviruses, in order to provide the stepping stones needed to manage and prevent similar crises in the future.

Already, there’s plenty of evidence pointing to certain animals, including pangolins, bats, snakes and civets, to be the hosts of viruses like SARS-CoV-2 (coronaviruses), hence, potential triggers of global health crises, such as the currently ravaging Coronavirus pandemic. However, scientific research on what biological and behavioural specifics of those species make them particularly successful vectors of zoonotic diseases is surprisingly scarce. Even worse, the little that science ‘knows’ today is often locked behind paywalls and copyright laws, or simply ‘trapped’ in formats inaccessible to text- and data-mining performed by search algorithms. 

This is why Pensoft’s flagship zoological open-access, peer-reviewed scientific journal ZooKeys recently announced its upcoming, special issue, titled “Biology of pangolins and bats”, to invite research papers on relevant biological traits and behavioural features of bats and pangolins, which are or could be making them efficient vectors of zoonotic diseases. Another open-science innovation champion in the Pensoft’s portfolio, Research Ideas and Outcomes (RIO Journal) launched another free-to-publish collection of early and/or brief outcomes of research devoted to SARS-like viruses.

Due to the expedited peer review and publication processes at ZooKeys, the articles will rapidly be made public and accessible to scientists, decision-makers and other experts, who could then build on the findings and eventually come up with effective measures for the prevention and mitigation of future zoonotic epidemics. To further facilitate the availability of such critical research, ZooKeys is waiving the publication charges for accepted papers.

Meanwhile, the literature digitisation provider Plazi is deploying its text- and data-mining expertise and tools, to locate and acquire publications related to hosts of coronaviruses – such as those expected in the upcoming “Biology of pangolins and bats” special issue in ZooKeys – and deposit them in a newly formed Coronavirus-Host Community, a repository hosted on the Zenodo platform. There, all publications will be granted persistent open access and enhanced with taxonomy-specific data derived from their sources. Contributions to Plazi can be made at various levels: from sending suggestions of articles to be added to the Zotero bibliographic public libraries on virus-hosts associations and hosts’ taxonomy, to helping the conversion of those articles into findable, accessible, interoperable and reusable (FAIR) knowledge.

Pensoft’s and Plazi’s collaboration once again aligns with the efforts of the biodiversity community, after the natural science collections consortium DiSSCo (Distributed System of Scientific Collections) and the Consortium of European Taxonomic Facilities (CETAF), recently announced the COVID-19 Task Force with the aim to create a network of taxonomists, collection curators and other experts from around the globe.

Viticulture Data Journal: Non-conventional papers foster Open Science & sustainability

Non-conventional, yet pivotal research results: data, models, methods, software, data analytics pipelines and visualisation methods, related to the field of viticulture, find a place in a newly launched, open-access and peer-reviewed Viticulture Data Journal.

Non-conventional, yet pivotal research results: data, models, methods, software, data analytics pipelines and visualisation methods, related to the field of viticulture, find a place in a newly launched, open-access and peer-reviewed Viticulture Data Journal (VDJ). The journal went live with the publication of an introductory editorial and a data paper.

The publishing venue is one of the fruits borne during the collaboration between scholarly publisher and technology provider Pensoft, its self-developed ARPHA Platform and the EU project AGINFRA+, whose mission is to provide a sustainable channel and data infrastructure for the use of cooperating, but not fully connected user communities working within the agricultural and food sciences. 

The novel journal brings together a wide range of topics related to the field of viticulture: from genetic research, food safety of viticultural products to climate change adaptation of grapevine varieties through grape specific research. Amongst these are:

  • Phenotyping and genotyping
  • Vine growth and development
  • Vine ecophysiology
  • Berry yield and composition
  • Genetic resources and breeding
  • Vine adaptation to climate change, abiotic and biotic stress
  • Vine propagation
  • Rootstock and clonal evaluation
  • Effects of field practices (pruning, fertilization etc.) on vine growth and quality
  • Sustainable viticulture and environmental impact
  • Ampelography
  • Plant pathology, diseases and pests of grapevine
  • Microbiology and microbiological risk assessment
  • Food safety related to table grapes, raisins, wine, etc.

With the help of the ARPHA Platform’s signature writing tool, authors are able to use a set of pre-defined, yet flexible manuscript templates: Data Paper, Methods, Emerging Techniques, Applied Study, Software Description, R Package and Commentary. Furthermore, thanks to the advanced collaborative virtual environment provided by the tool, authors, but also reviewers, editors and other invited contributors enjoy the convenience of working within the same consolidated online file all the way from the authoring and peer review stages to copy editing and publication.

“The Viticulture Data Journal was created to respond to the major technological and sociological changes that have influenced the entire process of scholarly communication towards Open Science,”

explain the editors.

“The act of scientific publishing is actually the moment when the long effort of researchers comes to light and can be assessed and used by other researchers and the wider public. Therefore, it is little wonder that the main arena of transition from Open Access to Open Science was actually the field of academic publishing,”

they add.

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The first research publication made available in VDJ is a data paper by the research team from Agricultural University of Athens: Dr Katerina Biniari, Ioannis Daskalakis, Despoina Bouza and Dr Maritina Stavrakaki. In their study, they assess and compare both the qualitative and quantitative characters of the grape cultivars ‘Mavrodafni’ and ‘Renio’, grown in different regions of the Protected Designation of Origin Mavrodafni Patras (Greece). The associated dataset, containing the mechanical properties, the polyphenolic content and the antioxidant capacity of skin extracts and must of berries of the two cultivars, is available to download as supplementary material from the article.  

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During the AGINFRA+ project, ARPHA has been extended to be used from the AGINFRA+ Virtual Research Environment (VRE), which would allow the authors to use the VRE as an additional gate to the AWT and the journal, as well as to benefit from the integration of AWT with several other services offered by the AGINFRA+ platform. The AGINFRA+ platform has been designed as a Gateway providing online access through a one-stop endpoint to services, aiming at the integration of the traditional narrative of research articles with their underlying data, software code and workflows.

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Viticulture Data Journal is indexed by Altmetric, CrossRef, Dimensions, EBSCOhost, Google Scholar, Mendeley, Microsoft Academic, Naviga (Suweco), OCLC WorldCat, OpenAIRE, OpenCitations, ReadCube, Ulrichsweb™, Unpaywall; and archived at CLOCKSS and Zenodo

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Follow Viticulture Data Journal on Twitter and Facebook.

Seven journals moving to ARPHA in early 2020 showcase the versatility of the publishing platform

Seven journals of diverse backgrounds, scopes and geographies are moving to Pensoft-developed open access publishing platform ARPHA.

A full-featured, open access publishing platform for journals, books and data, which comes with an extensive list of services and features – both automated and human-provided – to adapt to the individual needs of any client journal. But how does that translate into practice? 

The latest scholarly titles to join the ranks of ARPHA might just provide a perfect example of the capabilities of the platform to accommodate the specificity of scholarly journal across sciences, audiences, geographies and languages.

Amsterdam University Press strengthens partnership with ARPHA by launching two brand new journals

Journal of European Landscapes (JEL) and Heritage, Memory and Conflict Journal (HMC) add up to the partnership between ARPHA and Amsterdam University Press (AUP), which started in early 2018 with the transfer of the only Dutch-language open-access journal focussing on accountancy, business economics and related areas: Accountancy and Business Economics, or Maandblad voor Accountancy en Bedrijfseconomi (MAB).

Homepage of Amsterdam University’s journal Accountancy and Business Economics (Maandblad voor Accountancy en Bedrijfseconomi), using the white-label publishing solution of ARPHA Platform.

Not only was MAB the first journal on the platform that publishes articles exclusively in a language other than English, but also became an impressive precedent with its nearly 100-year content that got successfully dusted off and fitted into the user-friendly digital environment of today. All papers ever issued in MAB since its launch in 1923, were re-published, so that each could be assigned with a DOI; have its metadata registered on CrossRef; and its article content fully searchable within the PDF copy.

All three make use of ARPHA’s white-label publishing solution, which allows for AUP to carry its recognisable logo through a unified banner across the websites of the journals. Unlike MAB, however, JEL and HMC are to have their articles published exclusively in English to further promote their international scope and focus.

Heritage, Memory and Conflict Journal (HMC)

Homepage of the new Heritage, Memory and Conflict Journalpublished by Amsterdam University Press via ARPHA Platform.

Heritage, Memory and Conflict Journal is a brand new journal launched to trace back the remnants of the past – be it physical or anecdotal – back to their roots in the days of old. How do memory sites and discourses operate as vehicles at local, national and transnational levels and what indeed is the ‘cargo’ they carry? This is the type of questions authors from across disciplines – academic, artistic and industrial – will be trying to answer when preparing their manuscripts for HMC. 

Journal of European Landscapes (JEL) 

Homepage of the new Journal of European Landscapes published by Amsterdam University Press via ARPHA Platform.

Similarly, the second newly launched Journal of European Landscapes is to turn to history and cultural heritage, in order to understand the present use of the past when it comes to landscape. JEL’s founders point out that while Europe’s landscapes have so far enjoyed quite a lot of scientific attention, there isn’t a journal to address its indisputable and critical connection to heritage, even though the latter is what connects historical research with modern planning and management.

Vegetation Classification and Survey (VCS)

Homepage of the new Vegetation Classification and Survey journal published by the International Association for Vegetation Science via ARPHA Platform.

Adding up to the landscape topic is the Vegetation Classification and Survey (VCS) journal. This is the latest outlet launched by the International Association for Vegetation Science (IAVS): a worldwide union of scientists and other aficionados of theory and practice concerning the study of vegetation. 

With its transfer to ARPHA, VCS fulfils the mission of the union to move to Open Access. Interestingly, the journal supports two permanent sections: Ecoinformatics and Phytosociological Nomenclature. There, authors can submit certain unique article types: Review and Synthesis and Short/Long Database Reports. 

Devoted to plant community ecology, VCS publishes original research that works toward the development of novel vegetation classifications, as well as applied studies that use such typologies. Particularly encouraged are methodological studies that design and compare tools for vegetation classification and mapping. 

Plant Sociology 

Homepage of the new Plant Sociology journal published by Società Italiana di Scienza della Vegetazione via ARPHA Platform.

Another modern botany journal still awaiting its first issue since its transfer to ARPHA, is Plant Sociology, brought to life by the “Società Italiana di Scienza della Vegetazione” (SISV) with the aim to succeed the historical journals of the society: Fitosociologia (1990-2011) and Notiziario della Società Italiana di Fitosociologia (1964-1989).

The editorial management opted to have the journal co-published with Pensoft: the academic publisher and technology provider standing behind ARPHA. Thus, by default, the journal receives some extra perks as a result of Pensoft’s partnerships with leading innovators in the scholarly communication domain.  An excellent example would be the indexing and addition of each Plant Sociology article by the research discovery platform ScienceOpen in the “Pensoft Biodiversity” collection, following a recent strategic collaboration between the two Open Science champions.

With a wide scope covering vegetation studies from plant community to landscape level, Plant Sociology puts a special focus on topics such as plant sociology and vegetation survey for developing ecological models, as well as plant classification, monitoring, assessment, management and conservation, as long as the studies are based on rigorous and quantitative measures of physical and biological components.

Caucasiana

Adding up to the well-pronounced biodiversity theme in ARPHA’s and Pensoft’s journal portfolios, as well as the “Pensoft Biodiversity” collection on ScienceOpen, is the first Georgian journal to join the lines of the publishing platform. Caucasiana is to be co-published by the top biodiversity research centre in the region: Ilia State University in Tbilisi and Pensoft.

The scholarly outlet that we’ll soon see on ARPHA Platform is in fact a successor of an earlier journal launched by the Institute of Zoology of the Georgian Academy of Science that has been revamped top-to-bottom. Transformed into a technologically advanced publishing venue, Caucasiana’s task is to handle the growing research interest in the incredible, yet surprisingly overlooked animal, plant and fungal life of Caucasus and adjacent regions. 

Research published in Caucasiana will be well-positioned to bring this hotspot of biodiversity and endemism into focus for the global conservation movement.

The EASE Journal: European Science Editing (ESE)

The quarterly journal of the European Association of Science Editors (EASE): European Science Editing (ESE) is a key news source for all actors involved in scholarly publishing.

For the first time, ESE will open up its content to the public from day one of its publication, thanks to its move to ARPHA. While digital and print subscriptions used to be included as part of the association’s membership packages, other readers would have had to wait six months after print publication to receive free access.

Launched in 2003, ESE’s aim has been to keep editors posted about everything they need to know concerning scholarly communication. To do so, the journal publishes research articles, meeting reports, essays and viewpoints, as well as book and website reviews. Especially for members of the association, ESE takes care to highlight upcoming events and provide resources and publications, considered to be of their interest. 

Bulgarian Journal of Cardiology

In 2020, ARPHA will also welcome the third Bulgarian-born academic journal and the fourth covering the field of Medical Sciences to its open-access portfolio: the journal of Bulgaria’s National Cardiac Society, which is part of the European Society of Cardiology (ESC).

For the first time, the Bulgarian Journal of Cardiology will make use of the soon-to-be-released English-Bulgarian bilingual publishing solution from ARPHA. Similarly to the English-Russian approach to journal publishing, which was presented in Moscow in early December, ARPHA will allow for users of the Bulgarian Journal of Cardiology to not only publish papers in both English and Bulgarian, but also enjoy a top-to-bottom Bulgarian user interface.

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Learn more about ARPHA’s key features and achievements from 2019 in our yearly recap.