Following the launch of our self-developed journal publishing platform ARPHA (standing for Authoring, Reviewing, Publishing, Hosting and Archiving, all happening at one place), we were so happy with the outcome, that we couldn’t help sharing it with the world. Therefore, it’s on offer not only to our own journals and authors, but it’s also at hand to journals looking for their new home. Just let us know you’re interested!
On these lines, what could be a better place to have a chat about the transition in scholarly publishing, open science, research reproducibility and, of course, the advantages of having a journal published on ARPHA, than Frankfurt Book Fair 2016? Between 18th and 23rd October, this immense event will be all about unveiling and celebrating the evolution in the publishing industry, with exhibitors, trade and private visitors from across the globe, gathering together, led by their common expertise and passion.
Meet us at HotSpot Professional and Scientific Information Stage, Hall 4.2, Stand M90, during the Fair, and make sure you don’t miss the “ARPHA: Next-Generation Journal Publishing” presentation at 11:30 AM (local time) on Friday, 21st October, where Pensoft’s Founder and Managing Director Prof Lyubomir Penev will shed more light on the first end-to-end publishing solution, providing everything a journal needs in a technologically advanced, highly efficient and user-friendly manner.
ARPHA in a few notes:
With ARPHA you can choose between two journal publishing workflows: ARPHA-DOC and ARPHA-XML. The former provides document-based submission for the articles in a journal, as well as peer review and publication. The latter makes use of the ARPHA Writing Tool, which takes all processes, including authoring, peer review and post-publication updates, to an online environment, created with collaboration and openness in mind.
ARPHA takes care of all the steps that go along with academic publishing and its efficient dissemination, so that it provides a long list of perks to make it easier for the scientific community to bring research to light. Website design, online editorial management system, linguistic editing, semantic markup, promotion and (sub-)article usage metrics are only a part of the services the platform has to offer.
The publishing models
ARPHA basically lets users mix-and-match services and features to create the publishing model that’s the best fit for their journals. How do you envision your imprint / web-design look / manuscript input / peer review process / publication output / revenue model? ARPHA understands your journal’s individual needs and works around them.
Find out more about ARPHA at our talk, or come and meet us at our stand in HotSpot Professional and Scientific Information (Hall 4.2, M90).
In the heat of this year’s Peer Review Week, themed “Recognition for Review”, we would like to express how and why we are so proud to be part of it and Publons’ initiative Sentinels of Science, meant to recognize the true guardians of quality science, or in other words, the peer reviewers.
Being a high-tech and modern publishing solution, developed by Pensoft with the mindset that to adapt to the future, means to innovate, ARPHA itself was set to take the quite stagnant current peer review practice forward from day one.
Author-organised, pre-submission review, available to all journals that make use of our ARPHA Writing Tool, which is our way to take the common get-a-friend-to-proofread-your-work practice to a whole new, transparent and technologically facilitated level. The review happens in real time with the author and the reviewers being able to work together in the ARPHA online environment. It is not mandatory, but we encourage it strongly. All pre-submission reviews provided on authors’ request in RIO can be published along with the article, bearing DOI and citation details.
Pre-submission technical and editorial check is another benefit, provided by the journal’s editorial office to those who are using the ARPHA Writing Tool. If necessary, it can take up several rounds, until the manuscript is improved to the level appropriate for direct submission to the journal.
The community-sourced, post-publication, open peer review is the next review stage provided to all articles published in RIO and all other ARPHA journals.
In addition, RIO also provides journal-organised, post-publication open peer review upon author’s request. In all other ARPHA journals this review stage happens mandatory before publication.
To facilitate peer review in any journal published on the platform, ARPHA consolidates every review automatically into a single online file, which makes it possible for reviewers to comment in real time, even during the authoring process. Once posted, the whole peer review history is archived along with the associated files.
To recognize peer review even further, ARPHA registers automatically each of our peer reviewers, along with their work, on Publons, thanks to the integration of all Pensoft journals with the platform, created to credit reviewers and their contributions.
With this vision of peer review, we simply could not stay clear of the aspiring Sentinels of Science initiative, started by Publons. It only made sense for us to step in, which logically led to the ARPHA logo appearing in the Gold star sponsors list.
With what already sounds like an annual tradition at this time of the year, we are delighted to announce yet another milestone that ZooKeysjust reached. Our 600th issue is now out and we are just as proud with it as we were exactly five years and a month ago, when we printed out our first three-digit issue number on a ZooKeys cover.
However, we feel nowhere near getting tired of counting pages, covers and issues, nor do we believe this will ever going to happen. Quite the contrary, every year we take more and more pleasure in adding new achievements next to the name of ZooKeys and Pensoft.
Last year was no exception. During the past 13 months, we published a total of 673 articles, including research findings spectacular enough to reach out to not only the zoological fellowship, but to the wide audience from around the world. While our Impact Factor keeps on increasing, according to the figures Thomson Reuters released last week, we are gratified to observe our progressively growing impact on both the scholarly and the popular-science front.
Last June, we introduced you to the Hades centipede, known to be the world’s deepest-dwelling species of its kind. Who knew that the entrance to the Underworld is located in a Croatian cave?
Later on, in November, published with us snail species Acmella nanabroke the World record for the tiniest land snail. Moreover, this happened only about a month after we published the previous ‘prizewinner’Angustopila dominikae, and that one was already tiny enough to fit 10 of its shells within the eye of a needle at the very same time!
About two months ago, graduate student Madhu Chetri spotted the ancient Himalayan woolly wolf in Nepal. The new knowledge about the beautiful and, sadly, Critically Endangered carnivore, which he acquired, will hopefully help in preventing its otherwise imminent extinction.
While being in the spotlight is definitely a gratifying feeling, we also indulge in our successes achieved far from the eyes of the public, although we are certain that our authors will be just as excited to hear about. Such an accomplishment is our recently sealed partnership with open digital repository Zenodo, who are helping us, along with the rest of the journals, published by Pensoft, to keep our research findings safe and easily accessible by archiving all our articles in both PDF and XML format on the date of publication.
However, let’s not forget that nothing of all the above would be what it is without our authors, editors and reviewers, who have always done their best to keep ZooKeys at the World’s top open access academic journals. We’d especially like to thank our Most active authors, editors and reviewers for being substantial part of ZooKeys.
We want to stress at this point that the import functionality itself is agnostic of the data source and any metadata file in EML 2.1.1 or 2.1.0 can be imported. We have listed these three most likely sources of metadata to illustrate the workflow.
In the remainder of the post, we will go through the original post from October 13, 2015 and highlight the latest updates.
At the time of the writing of the original post, the Biodiversity Information Standards conference, TDWG 2015, was taking place in Kenya. Data sharing, data re-use, and data discovery were being brought up in almost every talk. We might have entered the age of Big Data twenty years ago, but it is now that scientists face the real challenge – storing and searching through the deluge of data to find what they need.
As the rate at which we exponentially generate data exceeds the rate at which data storage technologies improve, the field of data management seems to be greatly challenged. Worse, this means the more new data is generated, the more of the older ones will be lost. In order to know what to keep and what to delete, we need to describe the data as much as possible, and judge the importance of datasets. This post is about a novel way to automatically generate scientific papers describing a dataset, which will be referred to as data papers.
The common characters of the records, i.e. descriptions of the object of study, the measurement apparatus and the statistical summaries used to quantify the records, the personal notes of the researcher, and so on, are called metadata. Major web portals such as DataONE, the Global Biodiversity Information Facility(GBIF), or the Long Term Ecological Research Network store metadata in conjunction with a given dataset as one or more text files, usually structured in special formats enabling the parsing of the metadata by algorithms.
To make the metadata and the corresponding datasets discoverable and citable, the concept of the data paper was introduced in the early 2000’s by the Ecological Society of America. This concept was brought to the attention of the biodiversity community by Chavan and Penev (2011) with the introduction of a new data paper concept, based on a metadata standard, such as the Ecological Metadata Language, and derived from metadata content stored at large data platforms, in this case the Global Biodiversity Information Facility (GBIF). You can read this article for an in-depth discussion of the topic.
Therefore, in the remainder of this post we will explain how to use an automated approach to publish a data paper describing an online dataset in Biodiversity Data Journal. The ARPHA system will convert the metadata describing your dataset into a manuscript for you after reading in the metadata. We will illustrate the workflow on the previously mentioned DataONE and GBIF.
As you can notice, this resource has two objects associated with it: metadata, which has been highlighted, and the dataset itself. Let’s download the metadata from the cloud! The resulting text file, “Blandy.235.1.xml”, or whatever you want to call it, can be read by humans, but is somewhat cryptic because of all the XML tags. Now, you can import this file to the ARPHA writing platform and the information stored in it would be used to create a data paper!Go to the ARPHA web-site, and click on “Start a manuscript,” then scroll all the way down and click on “Import manuscript”.
Upload the “blandy” file and you will see an “Authors’ page,” where you can select which of the authors mentioned in the metadata must be included as authors of the data paper itself. Note that the user of ARPHA uploading the metadata is added to the list of the authors even if they are not included in the metadata. After the selection is done, a scholarly article is created by the system with the information from the metadata already in the respective sections of the article:
Now, the authors can add some description, edit out errors, tell a story, cite someone – all of this without leaving ARPHA – i.e. do whatever it takes to produce a high-quality scholarly text. After they are done, they can submit their article for peer-review and it could be published in a matter of hours. Voila!
Let’s look at GBIF. Go to “Data -> Explore by country” and select “Saint Vincent and the Grenadines,” an English-speaking Caribbean island. There are, as of the time of writing of this post, 166 occurrence datasets containing data about the islands. Select the dataset from the Museum of Comparative Zoology at Harvard. If you scroll down, you will see the GBIF annotated EML. Download this as a separate text file (if you are using Chrome, you can view the source, and then use Copy-Paste). Do the exact same steps as before – go to “Import manuscript” in ARPHA and upload the EML file. The result should be something like this, ready to finalize:
To finish it up, we want to leave you with some caveats and topics for further discussion. Till today, useful and descriptive metadata has not always been present. There are two challenges: metadata completeness and metadata standards. The invention of the EML standard was one of the first efforts to standardize how metadata should be stored in the field of ecology and biodiversity science.
Currently, our import system supports the last two versions of the EML standard: 2.1.1 and 2.1.0, but we hope to further develop this functionality. In an upcoming version of their search interface, DataONE will provide infographics on the prevalence of the metadata standards on their site (as illustrated below), so there is still work to be done, but if there is a positive feedback from the community, we will definitely keep elaborating this feature.
Regarding metadata completeness, our hope is that by enabling scientists to create scholarly papers from their metadata with a single-step process, they will be incentivized to produce high-quality metadata.
Now, allow us to give a disclaimer here: the authors of this blog post have nothing to do with the two datasets. They have not contributed to any of them, nor do they know the authors. The datasets have been chosen more or less randomly since the authors wanted to demonstrate the functionality with a real-world example. You should only publish data papers if you know the authors or you are the author of the dataset itself. During the actual review process of the paper, the authors that have been included will get an email from the journal.
This project has received funding from the European Union’s FP7 project EU BON (Building the European Biodiversity Observation Network), grant agreement No 308454, and Horizon 2020 research and innovation project BIG4 (Biosystematics, informatics and genomics of the big 4 insect groups: training tomorrow’s researchers and entrepreneurs) under the Marie Sklodovska-Curie grant agreement No. 642241 for a PhD project titled Technological Implications of the Open Biodiversity Knowledge Management System.
Established in the distant 1888, the Italian Botanical Society has gone a long way towards publishing its achievements and research. Originated as a bulletin within an Italian journal, they have been growing ever since to now form a new international journal in its own right. Covering both Italian and international research in botany and mycology, the online open access journal Italian Botanist, published by Pensoft, is now officially launched via its first papers.
Although what was later to become Italian Botanist, published its first issue as an independent journal, called Informatore Botanico Italiano in 1969, the publications were still rather bulletin-style. It consisted of a mixture of administrative and scientific proceedings of the Society, the yearbook of the members, as well as scientific notes.
Nevertheless, such a major transition has been set to change everything fundamentally. Establishing its name, the journal started picking up, so that it was not long before the scientific contributions were prevailing. Impressively, for the Society’s centenary the journal published a celebratory 331-page contribution.
Gradually, its scope was expanded to cover several scientific fields. It hosted several themed columns, including cytotaxonomic contributions on the Italian flora, relevant new floristic records for Italy, conservational issues concerning the Italian flora and mycology.
However, the Directive Council of the Italian Botanical Society has not seemed to be ready to give up on their journal’s evolution. Last year, the botanists decided that they need to transform the journal to an an online, open access journal written in English and called Italian Botanist, in order to boost the scientific value and international visibility of Informatore Botanico Italiano.
Under the name Italian Botanist, the journal has now joined Pensoft’s portfolio of peer-reviewed open access journals, all of which take advantage of the advanced technologies and innovations developed by the publisher.
The new journal’s scope ranges from molecular to ecosystem botany and mycology. The geographical coverage of Italian Botanist is specially focused on the Italian territory, but studies from other areas are also welcome.
Staying faithful to its spirit and philosophy, it keeps its column-format, with each issue to contain five columns, namely Chromosome numbers for the Italian flora, Global and Regional IUCN Red List Assessments, Notulae to the Italian flora of algae, briophytes, fungi and lichens, Notulae to the Italian native vascular flora and Notulae to the Italian alien vascular flora.
“Our hope is that this renewed version of the journal will serve the Italian – and foreign – botanical community more efficiently and provide readers worldwide with an easier access to knowledge concerning the Italian flora,” says Italian Botanist‘s Editor-in-Chief Lorenzo Peruzzi.
Peruzzi L, Siniscalco C (2016) From Bullettino della Società Botanica Italiana to Italian Botanist, passing through Informatore Botanico Italiano. A 128 years-long story. Italian Botanist 1: 1-4. doi: 10.3897/italianbotanist.1.8646
This integration between two innovative platforms, striving to modernize the publishing industry, provides authors with the possibility not only to receive fast-track high-quality peer review of their manuscripts, but also to have a choice between a pool of journals, when it comes to publication.
“Pensoft is a special partner for us, because they were the first publisher to start an official collaboration with Peerage of Science years ago, when we had just launched. Also, Pensoft is in many ways a pioneering publisher seeking to make the world a better place for scientists, with initiatives like the ARPHA writing tool and the RIO Journal,” explains Janne-Tuomas Seppänen, Co-Founder and Managing Director at Peerage of Science.
“I am particularly happy that Pensoft is continuing and expanding its support for our solutions for peer review, and brings more journals to the author’s destination menu in Peerage of Science. We warmly welcome the 10 new titles and their editors, and look forward to a long and productive partnership.” he adds.
The idea behind Peerage of Science was inspired by the real-world struggles a young scientist is bound to face in the traditional peer-review system. The average peer review process takes more than 160 days and could easily conclude with the paper being rejected.
The initiative applies an out-of-the-box approach to the problem, providing a collaborative platform, where peer review takes place before the actual submission to a journal. Thus the process is significantly shortened, while at the same time it secures high quality manuscripts at the end.
Similarly, Pensoft journals provide open access, new generation publishing to scientists with an emphasis of online dissemination, data re-use and semantic linking of contents. With its latest projects — RIO Journal and the ARPHA writing tool — the publisher has introduced a new generation of pre-submission and post publication peer review possibilities.
Additional benefit for the reviewers is that their reviews will be registered at Publons automatically by Pensoft, if the manuscript is published in a Pensoft journal. Reviewers will be asked for approval of the review registration before it appears in their Publons profiles.
“This collaboration works well both for us and for Peerage of Science, but most of all, it empowers the authors to set the deadlines for peer review and choose between publication offers. From the very inception of Pensoft we have striven to provide a fast, reliable and innovative service to our authors, and this new move is yet another building block in this vision.” comments Prof. Lyubomir Penev, Founder and Managing Director at Pensoft.
With both Pensoft and Publons aiming to facilitate scientific research and its introduction to the wide world, it only makes sense for the two to join efforts in a campaign to speed up publications, while giving the rightful credit to reviewers. From now on, anyone who makes this contribution to any of the 15 Pensoft journals will be able to opt-in to get credit for their peer reviews on Publons.
As for the moment, there are already 32 Pensoft reviewers who have added a total of 58 reviews to their Publons personal accounts and already started to receive recognition for their peer input – a kind of contribution that traditionally tends to be largely overlooked in academia. However, you can get a head start by signing-up to Publons and joining the 50,000 peer reviewers that are getting credit for their peer reviews.
The only exception to this rule is Pensoft’s next generation Research Ideas and Outcomes (RIO) journal, where the policy of ultimate transparency and openness requires all peer reviews and their authors to be made public. It is also the only Pensoft journal whose article titles will be available on a Publons profile by default. Another distinctive feature of RIO’s – an assigned DOI for each peer review, is also supported in Publons to ensure reviewers get the most out of their contribution.
“Pensoft has a strong history of innovation and we’re excited to be working together to reward the efforts of peer reviewers,” comments the new partnership Publons co-founder Andrew Preston. “It’s also great to see that many Pensoft editors are already Publons users.”
“Crediting reviewers’ voluntary contributions to the quality of scientific publications has always been a problem, especially with the current tremendous increase in the volume of published research outputs. We are happy that Publons has found such a solution and that we can credit our reviewers through recording their activity in an entirely automated way,” added founder and CEO of Pensoft Prof. Lyubomir Penev.