In a new integration, the Pensoft-developed innovative journal publishing platform ARPHA teams up with nonprofit, open-source annotation technology provider Hypothesis to further enable academic discussion and foster collaboration in the spirit of open science practices.
This partnership makes Pensoft the second publisher to implement this technology across its whole journal portfolio.
Upon opening an article published in any ARPHA journal, website visitors can now spot a dialog-box icon in the top-right of the screen showing the number of submitted annotations, which he/she can reply to at the click of a button. Annotations appear highlighted within the webpage whenever a user is logged into their account on Hypothesis.
Alternatively, the user can simply select some text and add a note to share his/her own idea, feedback, opinion or question inspired by the publication. Thus, the content of the research paper becomes alive, while readers could contribute to the study’s discourse.
“I am delighted to see ARPHA partnering with Hypothesis not only because this benefits our users and journals, but because it also works for the good of science and academia in general,” comments Pensoft’s and ARPHA’s founder and CEO Prof. Lyubomir Penev.
“What we’ve learned from implementing Open Science more and more vigorously in research practices is that striving for transparency and easier collaboration only stimulates scientific progress,” he adds. “One way to do this is definitely by providing the right platforms for giving and addressing feedback.”
Dan Whaley, CEO at Hypothesis, adds:
“We’re excited to see annotation brought to the many publications on the ARPHA platform. As an early member of the Annotating All Knowledge Coalition with a strong commitment to open research and transparent data, Pensoft shares Hypothesis’ commitment to facilitating conversations around scholarly content and improving researcher workflow. We look forward to working with the journal editors to integrate annotation into existing workflows to maximize the success of this initiative.”
Hypothesis is a US 501(c)3 nonprofit organization dedicated to the development and spread of open, standards-based annotation technologies and practices that enable anyone to annotate anywhere, helping humans reason more effectively together through a shared, collaborative discussion layer over all knowledge. Hypothesis is based in San Francisco, CA with a worldwide team. Learn more from <web.hypothes.is>.
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.
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).
The first issue in collaboration with Pensoft is live on the new journal’s website as of June 2017.
While preserving its attractive and well-known style and global expertise on the order Orthoptera and other closely allied insect orders, the journal now offers increased accessibility through a modernised design, intuitive interface, and many high-tech perks for authors, readers, reviewers and editors alike.
In continuous publication since 1992, Journal of Orthoptera Research is no newcomer to the arena of entomological peer-reviewed journals. It has enjoyed an esteemed place in the canon as the only global scientific publication dedicated to publishing work on the grasshoppers, crickets and bushcrickets. Now, the move to Pensoft ushers the journal to a new digital age by providing a modernised platform for showcasing fascinating research on these most charismatic and valuable of insects.
Among the innovative advantages is fast-track and convenient publishing thanks to ARPHA. Each manuscript is carried through all stages from submission and reviewing to dissemination and archiving on a single platform to facilitate and expedite the process using the best technological capabilities. Furthermore, this results in publications available in three formats (PDF, XML, HTML) with state-of-the-art semantic enhancements, so that articles can be easily found, accessed and harvested by both humans and machines.
Among the nine articles comprising the first Journal of Orthoptera Research issue since joining Pensoft [JOR Vol. 26(1)], there is a new species of bushcricket from China that sings an unusually complex tune when courting its potential partners; a curious experiment in the colour-shifting abilities of adult grasshoppers; and a description of a unique YouTube video showing two male bushcrickets engaging in previously unreported sexual activities.
“It’s pretty exciting to welcome Journal of Orthoptera Research to Pensoft’s family,” says Pensoft’s founder and CEO Prof. Lyubomir Penev. “We first started discussions on the possible publication of the journal by Pensoft back in 2010 and have resumed them a couple of times since. I am happy to see the journal now published in the modern design and format it really deserves!”
“I’m certain that ARPHA will secure the right place for Journal of Orthoptera Research among a whole portfolio of excellent zoological journals. Our journal will definitely feel at home next to the names of Journal of Hymenoptera Research, Nota Lepidopterologica, Zoologia, ZooKeysand many others,” says Editor-in-Chief Dr. Corinna Bazelet.
The journal will continue being released biannually. Traditionally, it publishes research on the insect order Orthoptera, as well as its close allies – Blattodea, Mantodea, Phasmatodea, Grylloblattodea, Mantophasmatodea and Dermaptera. The range of biological studies of these insects includes diversity, conservation, and control and management of pest species. As for the article types accepted in the journal, in addition to original research, editors will be considering review articles, short communications, and articles focusing on policy and management of Orthoptera.
Academic publisher Pensoft strengthens partnership with Dryad by adding its latest five journals to the list integrated with the digital repository. From now on, all authors who choose any of the journals published under Pensoft’s imprint will be able to opt for uploading their datasets on Dryad. At the click of a button, the authors will have their data additionally discoverable, reusable, and citable.
Started in 2011 as one of the first ever integrated data deposition workflows between a repository (Dryad) and a publisher (Pensoft), the partnership has now been reinforced to cover publications submitted to any of Pensoft’s 21 journals, including recently launched Research Ideas and Outcomes (RIO) and One Ecosystem, as well as BioDiscovery, African Invertebrates and Zoologia, which all moved to Pensoft within the last year.
By agreeing to deposit their datasets to Dryad, authors take advantage of a specialised and highly acknowledged platform to easily showcase and, hence, take credit for their data. On the other hand, the science community, including educators and students, can readily access the data, facilitating verification, citability and even potential collaborations.
“Dedicated to open and reproducible science, at Pensoft we have always strived to encourage our authors to make their research as transparent and, hence, trustworthy as possible, by providing the right infrastructure and support,” says Pensoft’s founder and CEO Prof. Lyubomir Penev. “By strengthening our long-year partnership with Dryad, I envision more and more authors, who publish in our journals, adding open data to their list of best practices.”
“Dryad works to promote data that are openly available, integrated with the scholarly literature, and routinely re-used to create knowledge,” said Dryad’s Executive Director, Meredith Morovati. “We are encouraged by the growth of our partnership with Pensoft, one of our earliest supporters. We are honored to provide services to Pensoft authors to ensure their data is openly available, linked to the article, and preserved for future use and for the future of science.”
Vilnius Gediminas Technical University and Pensoft launch a new joint pilot project for the open access peer-reviewed journal BTP
In a new joint pilot project, the open access peer-reviewed journal Business: Theory and Practice (BTP), issued by VGTU Press since 2000, runs on the new journal publishing platform ARPHA, developed by Pensoft. ARPHA provides end-to-end technological solution for all peer-review stages starting from submission to fully functional dedicated new website. Publications are also available in semantically enriched HTML and XML formats, as well as the traditional PDF. The journal’s authors and editors enjoy easily manageable peer-review workflow in ARPHA.
Business: Theory and Practice publishes original research articles and reviews that integrate economic development and globalization, interpretations and consequences of entrepreneurship, strategic management and organizational behavior, theoretical questions and empirical questions of industrial organizations. It covers a variety of fields, including business environment, economic development and globalization, entrepreneurial finance, interpretations and consequences of entrepreneurship, strategic management, organizational behavior, theoretical questions and empirical questions of industrial organization, and case studies.
BTP has opted for the ARPHA-DOC publishing workflow, which provides an individually designed website under the imprint and logo of VGTU Press, a document-based article submission, as well as peer review, publication, hosting and dissemination. The manuscripts submitted to BTP will be subject to double-blind peer review.
“It is a great pleasure to work with the Pensoft team on establishing an innovative publishing platform for Business: Theory and Practice. I am sure the new platform will exceed the expectations of all – the authors, the editors and the readers,” says VGTU Press Director Eleonora Dagiene.
“Academic publishing is in a process of disruptive transition. As a result, small journal publishers and society journals are strongly affected and threatened with decline and even extinction. This is because access to high-level publishing technologies is not easy and, in most cases, not affordable. So, we developed ARPHA specially for them! ARPHA is not only an end-to-end journal publishing platform, covering the whole process from website design, authoring, editorial management and peer-review to publishing and dissemination – it also delivers a wide range of easily customizable end-to-end services, on the choice of the journal. I am glad to see Business: Theory and Practice published by VGTU Press as the first Lithuanian journal coming to the ARPHA platform and becoming a member of ARPHA’s growing family of international partners,” says Pensoft’s founder and CEO Prof. Lyubomir Penev.
The articles accepted for the current issue of 2016 in BTP, published via ARPHA, are already available on the journal’s new website.
ARPHA is open to journals looking for a technologically advanced publishing platform plus all associated services, which can be customized to the journal’s preferences.
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.