Linking FAIR biodiversity data, NEW article collection in BDJ

Supported by the EU-funded Biodiversity Community Integrated Knowledge Library (BiCIKL) project, the collection at Biodiversity Data Journal will provide APC waivers for up to 100 publications

A new article collection, dedicated to linked FAIR biodiversity data was announced by the EU-funded Biodiversity Community Integrated Knowledge Library (BiCIKL) project.

The BiCIKL project is dedicated to building new communities of key research infrastructures, researchers, citizen scientists and other stakeholders by using linked and FAIR biodiversity data at all stages of the research lifecycle, from specimens through sequencing and identification of taxa, to final publication in advanced, human- and machine-readable, reusable scholarly articles.

Supported by BiCIKL, the upcoming collection at BDJ will provide an exciting opportunity for biodiversity researchers to enjoy free and technologically advanced publication for up to 100 scholarly articles.

The collection will welcome research articles, data papers, software descriptions, and methodological/theoretical papers that demonstrate the advantages and novel approaches in accessing and (re-)using linked biodiversity data.

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The journal is still looking for guest editors to join the core team. If you are interested, please let us know at bdj@pensoft.net.

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In this collection, the authors will need to ensure that their narratives comply with the community-agreed standards for terms, ontologies and vocabularies. Additionally, they will be required to use explicit persistent identifiers, where such are available. 

Here are several examples of research questions concerning semantically enriched biodiversity data: 

  1. How linking taxa or OTUs to external data in my study will contribute to a better understanding of the functions and regional/local processes within faunas/floras/mycotas or biotic communities?
  2. How mine and other researchers’ data and narratives (e.g. specimen records, sequences, traits, biotic interactions etc.) can be re-used to support more extensive and data-rich studies? 
  3. How to streamline taxon descriptions and inventories, including such based on genomic and barcoding data? 
  4. How general conclusions, assertions and citations in my article can be expressed in a formal, machine-actionable language? 
  5. Other taxon- or topic-specific research questions that would benefit from richer, semantically enhanced FAIR data.

Conditions for publication and types of articles:

  • Manuscripts must use data from at least two of the BiCIKL’s partnering research infrastructures. Highly welcome are also submissions that include data from research infrastructures that are not part of BiCIKL.
  • Taxonomic papers (e.g. descriptions of new species) must contain persistent identifiers for the holotype, paratypes and the majority of the specimens used in the study.
  • New species descriptions using data associated with a particular Barcode Identification Number (BIN) imported directly from BOLD via the ARPHA Writing Tool are encouraged.
  • Individual specimen records imported directly from BOLD, GBIF or iDigBio into the manuscript are strongly encouraged.
  • Hyperlinked in-text citations of taxon treatments from Plazi’s TreatmentBank are highly welcome.
  • Other terms of value hyperlinked to external resources are encouraged.
  • Tables that list gene accession numbers, specimens and taxon names, should conform to the Biodiversity Data Journal’s guidelines.
  • Theoretical or methodological papers on linking of FAIR biodiversity data are eligible for the BiCIKL collection if they provide examples and use cases.
  • Data papers or software descriptions are eligible if they use data from the BiCIKL’s partnering research infrastructures, or describe tools and services that facilitate access to and linking between FAIR biodiversity data.


You can find full information about the eligibility criteria in the Open Call published on the BiCIKL’s website, or can contact us at bdj@pensloft.net.

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Digitising the Natural History Museum London’s entire collection could contribute over £2 billion to the global economy

In a world first, the Natural History Museum, London, has collaborated with economic consultants, Frontier Economics Ltd, to explore the economic and societal value of digitising natural history collections and concluded that digitisation has the potential to see a seven to tenfold return on investment. Whilst significant progress is already being made at the Museum, additional investment is needed in order to unlock the full potential of the Museum’s vast collections – more than 80 million objects. The project’s report is published in the open science scientific journal Research Ideas and Outcomes (RIO Journal).

One of the Museum’s digitisers imaging a butterfly to join the 4.93 million specimens already available online. 
© The Trustees of the Natural History Museum, London

The societal benefits of digitising natural history collections extends to global advancements in food security, biodiversity conservation, medicine discovery, minerals exploration, and beyond. Brand new, rigorous economic report predicts investing in digitising natural history museum collections could also result in a tenfold return. The Natural History Museum, London, has so far made over 4.9 million digitised specimens available freely online – over 28 billion records have been downloaded over 429,000 download events over the past six years. 

Digitisation at the Natural History Museum, London 

Digitisation is the process of creating and sharing the data associated with Museum specimens. To digitise a specimen, all its related information is added to an online database. This typically includes where and when it was collected and who found it, and can include photographs, scans and other molecular data if available. Natural history collections are a unique record of biodiversity dating back hundreds of years, and geodiversity dating back millennia. Creating and sharing data this way enables science that would have otherwise been impossible, and we accelerate the rate at which important discoveries are made from our collections.  

The Natural History Museum’s collection of 80 million items is one of the largest and most historically and geographically diverse in the world. By unlocking the collection online, the Museum provides free and open access for global researchers, scientists, artists and more. Since 2015, the Museum has made 4.9 million specimens available on the Museum’s Data Portal, which have seen more than 28 billion downloads over 427,000 download events. 

This means the Museum has digitised  about 6% of its collections to date. Because digitisation is expensive, costing tens of millions of pounds, it is difficult to make a case for further investment without better understanding the value of this digitisation and its benefits. 

In 2021, the Museum decided to explore the economic impacts of collections data in more depth, and commissioned Frontier Economics to undertake modelling, resulting in this project report, now made publicly available in the open-science journal Research Ideas and Outcomes (RIO Journal), and confirming benefits in excess of £2 billion over 30 years. While the methods in this report are relevant to collections globally, this modelling focuses on benefits to the UK, and is intended to support the Museum’s own digitisation work, as well as a current scoping study funded by the Arts & Humanities Research Council about the case for digitising all UK natural science collections as a research infrastructure.

Sharing data from our collections can transform scientific research and help find solutions for nature and from nature. Our digitised collections have helped establish the baseline plant biodiversity in the Amazon, find wheat crops that are more resilient to climate change and support research into potential zoonotic origins of Covid-19. The research that comes from sharing our specimens has immense potential to transform our world and help both people and the planet thrive,

says Helen Hardy, Science Digital Programme Manager at the Natural History Museum.

How digitisation impacts scientific research?

The data from museum collections accelerates scientific research, which in turn creates benefits for society and the economy across a wide range of sectors. Frontier Economics Ltd have looked at the impact of collections data in five of these sectors: biodiversity conservation, invasive species, medicines discovery, agricultural research and development and mineral exploration. 

The Natural History Museum’s collection is a real treasure trove which, if made easily accessible to scientists all over the world through digitisation, has the potential to unlock ground-breaking research in any number of areas. Predicting exactly how the data will be used in future is clearly very uncertain. We have looked at the potential value that new research could create in just five areas focussing on a relatively narrow set of outcomes. We find that the value at stake is extremely large, running into billions,”

says Dan Popov, Economist at Frontier Economics Ltd.

The new analyses attempt to estimate the economic value of these benefits using a range of approaches, with the results in broad agreement that the benefits of digitisation are at least ten times greater than the costs. This represents a compelling case for investment in museum digital infrastructure without which the many benefits will not be realised.

This new analysis shows that the data locked up in our collections has significant societal and economic value, but we need investment to help us release it,

adds Professor Ken Norris, Head of the Life Sciences Department at the Natural History Museum.

Other benefits could include improvements to the resilience of agricultural crops by better understanding their wild relatives, research into invasive species which can cause significant damage to ecosystems and crops, and improving the accuracy of mining.  

Finally, there are other impacts that such work could have on how science is conducted itself. The very act of digitising specimens means that researchers anywhere on the planet can access these collections, saving time and money that may have been spent as scientists travelled to see specific objects.

The value of research enabled by digitisation of natural history collections can be estimated by looking at specific areas where the Museum’s collections contribute towards scientific research and subsequently impact the wider economy. 
© Frontier Economics Ltd.

Original source: 

Popov D, Roychoudhury P, Hardy H, Livermore L, Norris K (2021) The Value of Digitising Natural History Collections. Research Ideas and Outcomes 7: e78844. https://doi.org/10.3897/rio.7.e78844

The S.L.E.E.P.ing Beauty: new Research Idea suggests sedation-led chemotherapy to avoid pain

Photo by National Cancer Institute (NIH, USA) on Unsplash.

Blog post by Dr. Marco Cirillo, Heart Failure Surgery Unit Director at the Cardiovascular Department in Poliambulanza Foundation Hospital (Brescia, Italy)

Good morning, madam,” said the doctor greeting the patient who was entering his office. 

Good morning, Doctor,” she replied. 

So, how are you?” he asked her, motioning for her to sit in one of the two chairs in front of his desk. 

Well, it’s not bad.” 

The doctor looked at her carefully. 

So, this first dose of chemo… Did you tolerate it well, right?” 

“Yes, Doctor. I passed it…” 

Troubles? Nausea? Vomiting? Other problems?” 

No, Doctor. Nothing,” she replied. 

The doctor continued to watch her carefully. After her last answer he got up and went to sit next to her in the other chair that was in front of his desk. He took her hand and asked her again: 

So, madam: how are you?

The patient shook his hand as if in silent thanks. 

Doctor, you are a good doctor.” 

I’m here to understand what you need, madam, what can I do for you.” 

The patient thought a little longer before speaking. 

So, Doctor: the chemo didn’t bother me much, maybe because it’s the first one. Except that… In short, what was difficult was waiting together with the others, all talking about their tumor, where they have it, what chemo they are at, what happened to them, then the hairless ones with the turban on their heads, and how much hemoglobin you have, and what your husband said, and if they recognized you without hair…” 

I understand, madam. But it’s also a way to exorcise it, isn’t it? A way to share this bad experience, to not feel alone…” 

She looked him directly in the eyes.

Doctor, we are not all the same. These things bother me. Seeing how I will be in a month scares me. It doesn’t solace me to know that someone is sicker than me. And knowing that someone is better terrifies me…” 

The doctor nodded his head. 

I don’t want to think about my illness and when I come here, I necessarily think about it. I have to think about it. At home I do many things, I see many people, I may not think about it. But when I come here… Then for days I see these scenes in front of me, as if I’ve never left… Believe me, I do not simply ignore the disease, I know what I have and what awaits me. But if I could, I would avoid everything in between, between me and my illness. Do you understand?

Of course, madam. I understand. For others it is the same thing.” 

They went silent for a while. 

Then, the doctor said: 

If you had a choice, ma’am, what would you want? What would make you bear it all better?” 

She answered immediately, as if she had the answer ready. 

If I could, I would like to fall asleep and wake up when it’s all over! Don’t see the others, don’t even see the hospital, don’t hear what the nurses say, don’t see the drip, don’t feel the needle entering, don’t see the drop of poison that I have to let into my body to try to survive… Don’t feel the time passing so slowly, as slow as the drop of the drip, a time ‘lost’ that is part of the little time I still have left… I am forced to hope that this time will pass quickly, but at the same time I know that it is not convenient for me to pass quickly, because even this time of treatment is taken away from my life. From what remains of it…

The doctor released her hand and leaned back in his chair. 

The lady asked him: 

Did I say something wrong?” 

No, madam, on the contrary,” said the doctor. “You told me something wonderful.” 

Ah, really? It sounds trivial to me…” 

No, what a patient says when he talks about himself and his illness is never trivial. You gave me a very good idea, madam.” 

Indeed?” 

Sure! What you ask can be done.” 

That is…” 

I can set up a study in which to administer chemo during sleep and analyze the results,” the doctor said, then corrected himself by translating his words into more direct language. “Sorry: I can make you sleep during the treatment, maybe set the treatment during night, so it doesn’t alter your days. And then you will wake up when it’s all over. That wouldn’t prevent some side effects…” 

…but it would prevent me from living consciously at the time of treatment,” the patient completed. 

Sure,” the doctor confirmed. 

Like the Sleeping Beauty…” the patient said. “You know the tale, don’t you?” 

Sure, who doesn’t know it.” 

The fairy godmothers cannot avoid the evil witch’s curse, so they make her fall asleep instead of die. Waiting for a solution,” the patient sighed deeply. “So, Doctor, if you can eliminate the evil that hangs over me, do it. Otherwise, let me sleep before the spinning wheel stings me.” 

The doctor looked at her with a grateful look. He had always felt that not only did he do something for the patients every day, but the patients also did something for him every day. 

Would you do this for me, Doctor?” 

The doctor smiled. 

Of course, ma’am. For you and for all the people who want it. Just give me some time to organize this.” 

Take your time” the lady said enthusiastically, but soon after she added with a wink: “No, on the contrary: hurry up, I wouldn’t want to waste any more time…” 

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Every doctor’s job is to heal diseases. When it is not possible to heal them, the best cure is to relieve the suffering. In Oncology, this second option is still extremely important. The psychological aspect of dealing with something that is often not guaranteed to heal is crucial. 

This project aims to extend the concept of “care” by approaching the patient and his/her needs: it is not the patient who has to adapt to the hospital’s schemes, its timing, its protocols, but it is the hospital that must serve the patients, to “take care” after their problem in its multidimensionality.  

The disease derails the life of the patient in a decisive way. We must as far as possible try to “sew in” the disease element into their everyday life,  if we want them to experience it as something that is part of normal life. This can make them tolerate it better and perhaps improve the chances of overcoming it. 

Here, this is the concept behind my research idea.

The study could be initially applied to a selected series of patients, and then extended, if the results are promising. 

Certainly, there are some practical limitations related to this study. Arranging the administration during sleep requires many “beds”; it requires specialized nursing staff; if it is carried at home, it also needs allocating specialists for home visits.

It is true, however, that home care for cancer patients is already very common in advanced healthcare systems. Economic investment and funding of cancer research and treatment remain at the top, along with cardiovascular diseases, in all healthcare systems. 

Cancer Centers nowadays abound around the world and are increasing in numbers. Comprehensive Cancer Centers, which are the largest in America, carry out transdisciplinary research, recognizing the importance of integrating different knowledge together for more effective treatment. The assistance and therapeutic network, the shared protocols, the sector research in Oncology already boast a very high level today. The coordination between centers makes use of all that assistance know-how. If I have to think of a medical field in which research, assistance, network of knowledge and uniformity of treatment are the most coordinated and efficient, this field is undoubtedly the oncology one. 

I would gladly give my scientific contribution by collaborating with centers of Excellence and their teams, who would like to join me on this research project. I would also readily share some organizational ideas by integrating them with the specific knowledge of colleague oncologists. Let’s fight the curse and help people to bear it with the least physical and psychological suffering!

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Read the full Research Idea in Research Ideas and Outcomes (RIO Journal) at: https://doi.org/10.3897/rio.7.e71271

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Full citation:
Cirillo M (2021) Sedation-Led chEmotherapy Evades Pain (S.L.E.E.P.). Research Ideas and Outcomes 7: e71271. https://doi.org/10.3897/rio.7.e71271

Call for research outcomes addressing four UN Sustainable Development Goals in RIO Journal

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):

  • SDG1: No poverty (1)
  • SDG7: Affordable & clean energy (2)
  • SDG5: Gender equality (4)
  • SDG2: Zero hunger (4)
All publications in RIO Journal are mapped to one or more SDGs.

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.

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Further reading:

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:

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 websiteFollow RIO Journal on Twitter and Facebook.

Strategic collaboration agreement signed between ScienceOpen and Pensoft

The research discovery platform ScienceOpen and Pensoft Publishers have entered into a strategic collaboration partnership with the aim of strengthening the companies’ identities as the leaders of innovative content dissemination.

The research discovery platform ScienceOpen and Pensoft Publishers have entered into a strategic collaboration partnership with the aim of strengthening the companies’ identities as the leaders of innovative content dissemination. The new cooperation will focus on the unified indexation, the integration of Pensoft’s ARPHA Platform content into ScienceOpen and the utilization of novel streams of scientific communication for the published materials.

Pensoft is an independent academic publishing company, well known worldwide for bringing novelty through its cutting-edge publishing tools and for its commitment to open access practices. In 2013, Pensoft launched the first ever, end-to-end, XML-based, authoring, reviewing and publishing workflow, now upgraded to the ARPHA Publishing Platform. As of today, ARPHA hosts over 50 open access, peer-reviewed scholarly journals: the whole Pensoft portfolio in addition to titles owned by learned societies, university presses and research institutions.

As part of the strategic collaboration, all Pensoft content and journals hosted on ARPHA are indexed in the ScienceOpen’s research and discovery environment, which puts them into thematic context of over 60 million articles and books. In addition, thousands of articles across more than 20 journals were integrated into a “Pensoft Biodiversity” Collection. Combined this way, the content benefits from the special infrastructure of ScienceOpen Collections, which supports thematic groups of articles and books equipped with a unique landing page, a built-in search engine and an overview of the featured content. The Collections can be reviewed, recommended and shared by users, which facilitates academic debate and increases the discoverability of the research.

The Pensoft Biodiversity collection is available from: https://www.scienceopen.com/collection/PensoftBiodiversity

“It is certainly great news and a much-anticipated milestone for Pensoft, ARPHA and our long-year partners and supporters from ScienceOpen to have brought our collaboration to a new level by indexing the whole ARPHA-hosted content at ScienceOpen,” comments Pensoft’s and ARPHA’s CEO and founder Prof. Lyubomir Penev. “Most of all, the integration between ARPHA and ScienceOpen at an infrastructural level means that we will be able to offer this incredible service and increased visibility to newcoming journals right away. On the other hand, by streaming fresh and valuable publicly accessible content to the ScienceOpen database, these journals will be further adding to the growth of science in the open.”

Stephanie Dawson, CEO of ScienceOpen says, “I am particularly excited to add new high-quality, open access biodiversity content from Pensoft Publishers to the ScienceOpen discovery environment as we have a very active community of researchers on ScienceOpen creating and sharing Collections in this field. We are looking forward to working with Pensoft’s innovative journals to support their open science goals.”

The collaboration reflects not only the commitment of both Pensoft and ScienceOpen to new methods of knowledge dissemination, but also the joint mission to champion open science through innovation. The two companies will cooperate at a strategic level in order to increase the international outreach of their content and services, and to make them even more accessible to the broad community.

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About ScienceOpen:

From promotional collections to Open Access hosting and full publishing packages, ScienceOpen provides next-generation services to academic publishers embedded in an interactive discovery platform. ScienceOpen was founded in 2013 in Berlin and Boston by Alexander Grossmann and Tibor Tscheke to accelerate research communication.

New partnership between Pensoft and BEXIS 2 encourages Data Paper publications

Following the new partnership between the German open source platform BEXIS 2 and the academic publisher Pensoft, scientists are now able to publish data papers in three of the most innovative Pensoft journals: Biodiversity Data Journal (BDJ)One Ecosystem and Metabarcoding and Metagenomics (MBMG), using EML data packs from BEXIS 2.

In order to encourage and facilitate high-quality data publication, the collaboration allows for researchers to easily store, analyse and manage their data via BEXIS 2, before sharing it with the scientific community in a creditable format.

The newly implemented workflow requires researchers to first download their data from the free open source BEXIS 2 software and, then, upload the data pack on Pensoft’s ARPHA Journal Publishing Platform where the data can be further elaborated to comply to the established Data Paper standards. Within the software, they can work freely on these data.

Having selected a journal and a data paper article template, a single click at an ‘Import a manuscript’ button transfers the data into a manuscript in ARPHA Authoring Tool. Within the collaborative writing tool, the data owner can invite co-authors and peers to help him/her finalise the paper.

Once submitted to a journal, the article undergoes a peer review and data auditing and, if accepted for publication, is published to take advantage of all perks available at any Pensoft journal, including easy discoverability and increased citability.

“I am delighted to have this new partnership between Pensoft and BEXIS 2 announced,” says Pensoft’s founder and CEO Prof. Lyubomir Penev.

“I believe that workflows like ours do inspire scientists to, firstly, refine their data to the best possible quality, and, secondly, make them available to the world, so that these data can benefit the society much faster and more efficiently through collaborative efforts and constructive feedback.”

“With scientists becoming more and more eager to publish research data in data journals like Pensoft’s BDJ, it is important to provide comprehensive and easy workflows for the transition of data from a data management platform like BEXIS 2 to the repository of the data journal without losing or re-entering any information. So we are absolutely delighted that a first version of such data publication workflow is now available to users of BEXIS 2.” says Prof. Birgitta König-Ries, Principle Investigator of BEXIS 2.

The collaboration between Pensoft and BEXIS 2 is set to strengthen in the next few months, when a new import workflow is expected to provide an alternative way to publish datasets.

In 2015, Pensoft launched similar workflows for DataONE, the Global Biodiversity Information Facility (GBIF) and the Long Term Ecological Research Network (LTER).

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Additional information:

About BEXIS 2:

BEXIS 2 is a free and open source software supporting researchers in managing their data throughout the entire data lifecycle from data collection, documentation, processing, analyzing, to sharing and publishing research data.

BEXIS 2 is a modular scalable platform suitable for working groups and collaborative project consortia with up to several hundred researchers. It has been designed to meet the requirements of researchers in the field of biodiversity, but it is generic enough to serve other communities as well.

BEXIS 2 is developed at Friedrich-Schiller-University Jena together with partners from Max-Planck Institute of Biogeochemistry Jena, Technical University Munich and GWDG Göttingen. The development is funded by the German Science Foundation (DFG).

Journal publishing platform ARPHA partners with content recommendation engine TrendMD

Thanks to the new collaboration between content recommendation engine TrendMD and journal publishing platform ARPHA, readers of all journals under Pensoft’s imprint, as well as those using the white-label publishing solution provided by the platform, will be given a useful list of recommended articles related to the study they are reading. The new widget is to save the users a great amount of time, by simply pointing them to the most relevant papers on the topic from across a constantly expanding network of of peer-reviewed articles and research news.

While nearly 8,000 new scholarly articles are published each day, it is basically impossible staying up-to-date with the news from a single scientific field, let alone doing cross-disciplinary research. Furthermore, sifting out the quality literature is another painstaking activity no academic is looking forward to. Hence, TrendMD comes as the sensible solution to help a reader find the most relevant and fine studies on a particular topic. The widget’s recommendations are based on the topic a user is currently reading, what papers they have read in the past, and the articles others with similar interests have sought out – all available from the most authoritative and quality journals in the world.

“TrendMD is excited to welcome Pensoft, a highly innovative, open access, online publishing platform, to the TrendMD network! This partnership will bring over 5,000 open access articles and books in the field of natural history, predominantly taxonomy and organismal biology, to TrendMD’s ever expanding network,” says Paul Kudlow, CEO and co-founder of TrendMD.

“In our continuing effort to develop and implement the most novel tools and workflows in academic publishing, at Pensoft we are pleased to have integrated our journal publishing platform ARPHA with the new-age scholarly innovation that is TrendMD’s tool, so that our readers have an easy and constant access to the most relevant and best-quality research,” says Pensoft’s CEO and founder Prof. Lyubomir Penev.

Publishing platform ARPHA partners with Altmetric to track online attention to research

With a research output mentioned online every 1.8 seconds, it only makes sense for the science community to grow curious of how they could access the knowledge of this public interest to better and build on their work.

Journal publishing platform ARPHA, developed by academic publisher Pensoft, has partnered with Altmetric to enable authors, readers and other users to track the online shares and discussions relating to each research output in journals published on ARPHA.

Thanks to the integration, a single click in the top menu of an article reveals the Altmetric donut visualisation, which provides an at-a-glance summary of the attention the item has received. The colours of the donut reflect the source of the attention, and the user can click on the image to be taken to the Altmetric details page, which provides a record of all of the mentions. Data is updated in real-time to provide insight into how the item is being received and shared.

To deliver such detailed information, Altmetric follows 2,000 mainstream media outlets in over 30 languages, social networks, public policy documents, post-publication peer-review forums, online reference managers, blogs, and Wikipedia.

As a result, all authors, readers, editors and funders can easily and immediately track the popularity, reception and impact of each of their studies.

“Having built an extensive portfolio of innovations as a technological provider, we are always looking forward to making yet another effort at providing our users with the best-quality experience. The integration of Altmetric data provides us with another opportunity to do exactly this,” says Pensoft’s founder and CEO Prof Lyubomir Penev.

“Furthermore, the science community has long been in need of a more adequate measure of the influence and engagement of individual research outputs, and Altmetric provides this.”

Altmetric’s Founder Euan Adie adds, “We’re excited to see the Altmetric badges being implemented across the ARPHA platform. Helping researchers get credit for their work and demonstrate its reach and influence is a core part of what we do, and this integration provides new opportunities to do so.”

The Altmetric badges and associated details pages are now available for all articles within Pensoft’s journals, as well as the journals using the white-label publishing available from ARPHA.

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Additional information:

About Altmetric:

Altmetric was founded in 2011 and has made it a mission to track and analyze the online activity around scholarly literature. Altmetric tracks what people are saying about research outputs online and works with some of the biggest publishers, funders, and institutions around the world to deliver this data in an accessible and reliable format. Altmetric is supported by Digital Science. Visit http://www.altmetric.com for more information, and follow on Twitter @altmetric.

About ARPHA:

ARPHA is the first end-to-end journal publishing solution that supports the full life cycle of a manuscript, from authoring through submission, peer review, publication and dissemination. With ARPHA, journals and publishers enjoy a complete set of services, which enable tailored, technologically advanced publishing solutions. The platform enables a variety of publishing models through a number of options for branding, production and revenue models to choose from.