The scholarly publisher and technology provider Pensoft and its self-developed publishing platform ARPHA welcome three journals to their distinguished and growing portfolio of biodiversity-themed journals. The international, peer-reviewed and open-access journals Acta Ichthyologica et Piscatoria, Caucasiana and Zitteliana are now fully operable and open for submissions through their new websites and technologically advanced user interfaces.
By moving to ARPHA, the three scholarly outlets will not only revamp their websites and technological backbone, but will also take advantage from ARPHA’s signature fast-track, end-to-end publishing system, which is to benefit all journal users: authors, reviewers and editors alike. In addition, the journals will use all unique services offered by ARPHA, such as data publishing, linked data tables, semantic markup and enhancements, automated export of sub-article elements and data to aggregators, web-service integrations with over 40 world-class indexing and archiving databases, sub-article-level usage metrics, and more. Published articles are to be available in PDF, machine-readable JATS XML formats and semantically enriched HTML, so that they guarantee better reader experience to ensure they are easy to discover, access, cite and reuse.
Acta Ichthyologica et Piscatoria
Launched in 1970, Acta Ichthyologica et Piscatoria (AIeP) publishes research about all aspects of ichthyology and fisheries, concerning true fishes (fin-fishes), including taxonomy, biology, morphology, anatomy, physiology, pathology, parasitology, reproduction and zoogeography. To be accepted, manuscripts need to be based on original experimental data or experimental methods, or new analyses of already existing data. The journal stands against the publication of “isolated” research, linked neither to the “past” nor the “future” of science. Likewise, “salami science” is also discouraged. AIeP is indexed by all major indexers, including Web of Science and Scopus. The journal’s first Impact Factor was released in 2010, and currently stands at 0.629 (2019).
Caucasiana
As a successor of the Proceedings of the Institute of Zoology of the Georgian Academy of Science, the Caucasiana is to give new life to the historical, print-only zoological by becoming a full-fledged, exclusively digital scholarly journal, focused on the still poorly known biodiversity in the Caucasus region and its adjacent areas. Caucasiana‘s aim is to accumulate primary biodiversity data urgently needed to understand the big picture of the biodiversity in the area: from individuals to ecosystems. To support the mission of uncovering the secrets of the Caucasus, the journal operates a no-APCs policy.
While the journal will be considering all biodiversity-related studies, based on their merits and quality of research, Caucasiana places special attention to taxonomic inventories and systematics. Thereby, in addition to traditional research outputs, the journal also publishes data papers, annotated checklists, monographs and conference proceedings, making use of the suite of biodiversity data publishing innovations, tools and know-how available from Pensoft.
Zitelliana
In 2021, Zitelliana is celebrating its 50th anniversary in a brand new gear in an excellent example of tradition working perfectly together with innovation and modernity. Since its launch in 1961, Zitelliana, a scholarly journal devoted to all fields of paleontology and geobiology, and owned by the Bavarian State Collection of Palaeontology and Geology (SNSB), has changed several names (i.e. Mitteilungen der Bayerischen Staatssammlung für Paläontologie und historische Geologie, Zitteliana A (Abhandlungen) and Zitteliana B (Mitteilungen)) and has extended its scope to cover research from outside Bavaria and adjacent regions or materials deposited in the SNSB’s collections.
Today, Zitteliana welcomes both modern and traditional research outputs, including palaeobiology, geobiology, palaeogenomics, biodiversity, stratigraphy, sedimentology, regional geology, systematics, phylogeny, and cross-disciplinary studies. Thanks to the support of the SNSB, authors in Zitteliana publish free of charge.
“At Pensoft, we take pride in our experience and achievements in the field of biodiversity research publishing and dissemination, so we’re particularly pleased to welcome these three wonderful journals and share our know-how with them at all levels: readership, editorship, publication and dissemination,” comments Prof. Lyubomir Penev, CEO and founder of Pensoft and ARPHA.
As another year is drawing to a close, it’s time for us to evaluate what we’ve achieved to better our services, or, as we’d rather refer to those, our mutual collaboration with our client journals and publishers, as well as their users: editors, reviewers, authors and readers alike.
Without a doubt, 2020 has been an extraordinary year that posed plenty of challenges at both personal and professional level to everyone, everywhere in the world. Having said that, at ARPHA, we’re proud that our perseverance and dedication to never let down those who have put their trust in us have pulled us through, while ensuring that we close the year with a positive outlook.
In 2020, we saw the move of a total of 14 international scientific journals to ARPHA Platform of diverse origin, background and scientific fields:
Some of them opted to use our white-label publishing solution, while others decided to sign up with Pensoft as a (co-)publisher. Browse the complete list of ARPHA-hosted journals on our website.
Naturally, we understand that each journal has its own needs and wants, in addition to its own short- and long-term plans and goals. This is why it is from day one that we assume responsibility to work closely together to ensure a personal, customer-centric approach at all times. One way to do this is by having our various services flexible and available as opt-in, mix-and-match features, so that journals can customise their own publishing solution.
Furthermore, based on our clients’ feedback, in addition to our in-house observations and know-how, we don’t cease to introduce new opportunities for journals to upgrade their functionality to the benefit of their own teams and users.
Below you will find an overview of the top new features and services ARPHA introduced in 2020:
ARPHA Preprints
Dedicated editorial workflow for Special Issues and Topical article collections
Editor and reviewer application form
Journal performance statistics
Journal performance reports
Workload statistics for reviewers and subject editors
Review rating
Contributor roles for co-authors
Easy update of user expertise
Integration with the research discovery app Researcher
ARPHA Preprints
In October, we officially launched ARPHA’s preprint platform, aptly named ARPHA Preprints. Frankly speaking, we’ve been planning for our own preprint platform for quite a while now, as we were determined to ensure the feature is ultimately convenient and beneficial to our journals and their authors. Undeniably, 2020 proved the perfect timing to see this idea ripe, as we’ve been witnessing a significant rise in preprints use and demand.
So, what’s it in ARPHA Preprints that stands out?
Available to all ARPHA Platform-hosted journals as an opt-in and free of charge service, ARPHA Preprints provides authors with the opportunity to post a preprint at the mere ‘cost’ of several clicks while submitting their article manuscript.
Submission of preprints workflow at participating ARPHA-hosted journals
By doing so, their pre-review manuscripts appear on ARPHA Preprints in a matter of one to a few days’ time, subject to a quick screening performed at the journal’s editorial office, in order to verify the submission conforms with the journal’s scope and standards, and does not contain any unethical content or plagiarism. If the associated paper is published in the journal, a link between the article and preprint is provided to prompt the citation of the paper rather than the preprint. On the occasion that the article is rejected at the ARPHA-hosted journal, where it has been submitted, the preprint is disassociated from the journal.
Dedicated editorial workflow for Special Issues and Topical article collections
Following a series of meetings with the editorial boards of our client journals, where we discussed the next steps in their plans in terms of journal development, we came up with the decision that we need a dedicated workflow to facilitate guest editors, who wish to propose a special issue or a topical article collection. Naturally, this workflow had to work just as convenient for the journal’s managing editors and everyone further down the line. Similarly to the ARPHA Preprints integration, we made this feature available to all ARPHA-hosted journals as an opt-in, free of charge service.
Firstly, we provided a clear information note on the key specifics, advantages and requirements for each article collection type. These are now available on the websites of all participating journals, in addition to an easy to spot proposal form, located on the journal’s homepage, in order to ensure that guest editors won’t be dissuaded by any technicalities.
Manuscript handling workflow at special issues / article collections in ARPHA-hosted journals
Secondly, by implementing direct proposal forms delivered straight to the Editors-in-Chief’s inboxes and easily visible on the journal website, as well as our distinguished highly automated manuscript handling workflow, we ended up with a smooth process that avoids potential delays, misunderstandings and annoying issues for everyone.
Read more about ARPHA’s approach to article collections and special issues on our blog.
Editor and reviewer application form
Similarly, after receiving valuable feedback from our client’s editorial board members, we figured that we could provide an easier application for subject editors at ARPHA-hosted journals.
At the request of a journal’s managing editor, we are ready to add a convenient Become an Editor button on the homepage of the journal that takes the applicant to an exhaustive, yet simple to fill-in form. Upon submission, the application is delivered straight to the Editor-in-Chief’s inbox providing him/her with all necessary information to make a decision and reply to the applicant.
By opting to add the feature, journals can make a simple, yet efficient step towards expanding the journal’s editorial team, thus optimising and expediting the editorial process, and naturally improving user satisfaction and journal performance.
Journal performance statistics
As we’re talking about journal development and striving for progress and success, the logical question is: how do we know what needs to be improved, revised or built upon? As always in science, the answer is: we need data and insight.
While we have had plenty of statistics available to Editors-in-Chief and managing editors for years already, we recently introduced several extra ones to provide further insight into the journal’s performance and how the numbers fare against those of previous months, quartiles or years.
So far, the Editors-in-Chief and managing editors have had access to:
manuscript submissions at any moment and their status;
publications and submissions for any period of interest;
publications by article type for a period of choice;
international representation based on lead author’s country for a period of choice;
article views for a period of choice.
In 2020, we added statistics about turnaround times, so that the editors are aware of the average time submitted manuscripts spend at different stages (e.g. peer review or editorial decision). Also, they now have access to a record of all online mentions from across the Internet, including traditional and new media, blogs, Wikipedia, policy documents and many others, thanks to our partners at Altmetric.
Journal performance reports
Even though we already made all those data concerning a journal’s real-time performance readily available for Editors-in-Chief and managing editors, we knew we could do more. As open-research proponents, we are well aware that openness and free access is not quite the same as findability. So, we set up bi-annual reports to be delivered to the inboxes of Editors-in-Chief and managing editors as a convenient and regular reminder of the current progress of the journal compared to the last period.
In those reports, we point to the most recent statistics, concerning:
current submissions and their status;
submissions, publications and rejections;
acceptance rate;
turnaround times;
average review invitations, declines and review rounds;
authors by country;
article views;
online article mentions;
Journal Impact Factor and CiteScore trends.
Furthermore, for journals using ARPHA’s Standard and Premium reporting services, we have prepared an extended report for the end of the calendar year, where they will find even more insights into the citability, outreach, readership and scholarly impact of their journals and their content. For Premium customers, the report will also feature a review and recommendations provided by ARPHA’s journal development team.
Workload for reviewers and subject editors
We know that prolonged peer review time presents a frustrating stumbling block for many otherwise renowned for their high standards and academic rigour journals. Striving to further optimise this process at ARPHA-hosted journals, we developed workload statistics and record of past activity for reviewers and subject editors, visible to the editor at the stage of assignment. Thus, the editor is able to give priority to users who aren’t busy with editorial/review assignments at the moment, and/or those who have a good record of past activity at the journal and/or similar journals on ARPHA Platform.
Review rating
Similarly, to further encourage diligence and speed in peer review at ARPHA-hosted journals, we offer our clients an optional feature where subject editors can evaluate submitted reviews using a 5-star rating system. As a result, the next subject editors will be able to see the average score of a reviewer before they assign him/her for the manuscript they’re handling.
Contributor roles for co-authors
Determined to always give credit where credit is due, while promoting transparency in academia and scholarship, we enabled submitting authors to assign each co-author with a role, depending on his/her primary contribution to the preparation of the manuscript. Thus, once published, a paper will clearly indicate the author who has, for example, conceptualised the study, developed the utilised software or written the original draft.
The options available in the drop-down menu follow CRediT (Contributor Roles Taxonomy): a high-level taxonomy, which includes 14 roles typically assumed by contributors to scholarly output.
Easy update of user expertise
As everything is (hopefully!) moving quickly in academia, we figured it’s time to take extra care after ensuring the users profiles in our systems are as relevant as possible. This is important, because ARPHA uses the expertise listed in a user’s profile to suggest reviewers and subject editors for each manuscript. So, in order to facilitate our editors and, ultimately, further expedite the peer review process at ARPHA-hosted journals, we’ve scheduled a few reminders throughout the year to prompt users to have a look at their profiles and update them, if necessary.
Integration with the research discovery app Researcher
Well aware of the fact that Open Science is way more than cost-free access to scientific and publicly funded knowledge, we understand that in the digital reality of today, the question is much more about findability and discoverability, i.e. the probability that you stumble across a particular research paper while browsing. This is why we’re continuously integrating our platform and the journals hosted on ARPHA with additional research discovery platforms used by scientists around the world to inform themselves about the latest findings in their fields of interest.
So, we recently collaborated with Researcher: an innovative mobile and web application, currently used by 1.8 million people globally, which allows you to set up your own social media-style feed of research papers by following your favourite academic journals or research topics. Now, all articles published in Pensoft’s journals – as well as participating journals using ARPHA’s white-label publishing solution – are continuously fetched by the app and delivered to their right audiences.
Read more about our integration with Researcher on our blog.
We are always looking forward to hearing from our clients about what they like or dislike in ARPHA, as well as their recommendations on what we could do better! You are welcome to contact us with your feedback and questions at: info@arphahub.com.
Having long considered how to help authors at our client journals get their work out in the open as early as possible, and prompted by the current research ecosystem, we came up with a new landmark feature, the ARPHA Preprints, where the preparation and posting of a preprint would be as much of a hassle as ticking a couple of check-boxes. Posting a preprint is an optional service for both journals and authors.
ARPHA Preprints in short
ARPHA Preprints is a new platform designed by ARPHA and Pensoft to host pre-review manuscripts submitted to participating ARPHA-hosted journals. The key here is that it only takes a few clicks for the author to submit a preprint, and no more than a few days before the preprint becomes accessible on ARPHA Preprints, thus open to feedback and contribution by fellow scientists.
Once the associated manuscript successfully completes peer review in the ARPHA-hosted journal and gets published, the preprint will be conveniently linked to the formal paper, thus facilitating and prompting citation of peer-reviewed research.
ARPHA Preprints publication workflow in participating ARPHA-hosted journals.
Visit ARPHA Preprints website to see the growing list of ARPHA-hosted journals integrated with ARPHA Preprints to date.
Manuscript submitted to ZooKeys (currently under review) and posted as a preprint (DOI: 10.3897/arphapreprints.e69376) on ARPHA Preprints. If published in the journal, the text will change to “Published in ZooKeys”. If rejected, the preprint will be disassociated from the journal to prevent potential issues with future resubmission.
ARPHA Preprints in practice
During submission at any of the journals that have been integrated with ARPHA Preprints, an author will come to a question asking them whether they wish to post a preprint. If they check that box and agree to the terms and conditions of posting a preprint, the platform will use the files uploaded to compile a preprint in PDF format. Here, the author will be able to preview the file and either agree they are happy with how it looks, or, alternatively, replace it with their own copy. The bottom line is, the manuscript and the preprint are submitted simultaneously.
Having confirmed they wish to post a preprint while submitting to the journal, ARPHA lets the authors review and, if needed, replace the preprint with their own PDF file. This is the version that will be posted as a preprint on ARPHA Preprints in a few days’ time – once it successfully completes the in-house screening.
At this point, it is only one to a few days keeping the preprint away from public knowledge. This time is needed for the submission to undergo a basic screening, meant to verify that it complies with the journal’s focus and scope, and does not contain offensive language, pseudoscience, plagiarism or any other unethical content.
When posted, preprints indicate the name of the journal, where the associated manuscript has been submitted. If published in that journal, this status changes to Published, while a link and citation details to the formal publication are provided via DOI and the Citation tab, respectively. This means that whenever a reader finds information in the preprint he/she would like to cite in their own work, he/she will have easy to spot, intuitive access to the peer-reviewed paper. If the manuscript is rejected on this occasion, the preprint is disassociated from the journal to prevent potential issues with future resubmission.
Preprints are open to public as well as private comments, in order to encourage constructive feedback and contribution well before the formal publication sees the light of the day.
ARPHA Preprints extra perks
Preprints posted on ARPHA Preprints are:
Registered with CrossRef and assigned with their own digital object identifier (DOI) to ensure scientific record and permanent availability;
Indexed in several indexing services covering preprints to increase findability;
Easy to track for viewership (via ARPHA Platform-provided views counting tools), and citation (via integration with Dimensions) rates;
Recently, at Pensoft, we were delighted to report the positive trends and progress the majority of our journals demonstrated in terms of their citability for 2019. Moreover, this comes as an encouraging pattern where the results have been following the positive progression we’ve been enjoying in recent years.
New Impact Factors are out. @NeobiotaJournal had a slight increase since last year to now 2.64. Getting us almost to the top 1/3 in Ecology and within the top 20% in Biodiversity Conservation ?.
Below you can learn about our latest features that address the availability of transparent and dynamic information about the journal’s performance from various perspectives: from authorship and readership to trends in peer review time, and user activity.
Even more statistics to provide key insights into the journal’s performance
Our system already provides plenty of statistics, in order to inform the editors about:
manuscript submissions at any moment and their status;
publications and submissions for any period of interest;
publications by article type for a period of choice;
international representation based on lead author’s country for a period of choice;
article views for a period of choice.
Now, in the Statistics tab, the editors can find even more data, including the average time the manuscripts submitted over a defined period have spent at each stage (e.g. reviewer or editorial decision). Also, the editors have access to a record of all online mentions from across the Internet (data available from our partners at Altmetric), including traditional and new media, blogs, Wikipedia, policy documents and many others.
See how to access all available statistics on an ARPHA-host journal here.
… all of this brought straight to your inbox with our:
Biannual journal performance report
For further convenience for our managing editors, we will be emailing a journal performance report twice a year, starting in July 2020. In this report, the editors will be receiving graphics on the journal’s performance for the current year and how the results fare against the previous one. The statistics provided include:
current submissions and their status;
submissions, publications and rejections by quarter;
acceptance rate;
turnaround time at different processing stages;
average review invitations, declines and review rounds per article;
top 10 countries represented by lead authors;
article views by format (PDF, HTML and XML) and in total;
number of online article mentions (data available from Altmetric);
Journal Impact Factor and CiteScore trends over the last five years.
Extended annual journal performance report
Citations trends available from Dimensions are reported on an annual basis for journals using the Standard and Premium packages provided by ARPHA Platform.
An extended annual report will be emailed to those who have opted for the ARPHA’s Standard and Premium package of reporting services. There, the editors will also have access to further and more exhaustive insights into the citability, outreach, readership and scholarly impact of their journals and their content. For journals that benefit from the Premium package of reporting services, we will be providing reviews and analyses meant to support the future strategy and progress of their journal.
Statistics on reviewers’ and editors’ workload and activities
We know that it is the exception rather than the rule that a subject editor is certain about whom out of the lists of names in the system’s database will be most likely to provide a peer review at his request, especially when the task is due time. This is why before the editor selects a particular reviewer, he/she will be able to see the number of tasks (if any) the user is currently working on, in order to find out their current availability. In addition, the subject editor will be able to see how many reviews the user has provided so far, as well as how many times he/she has been invited to do so in the past.
Likewise, the same functionality is available for managing editors when they look to assign a manuscript to a subject editor.
Review ratings
To further assist subject editors in their choice of appropriate reviewer, and also motivate reviewers, we have also implemented a 5-star rating system, where upon editorial decision on the acceptance/rejection of a manuscript, a subject editor is able to rate each of the provided reviews. The average result for a particular user will be visible in the system for the next subject editor who considers to assign him/her as a reviewer.
It’s fully understandable that users seldom think of the personal information visible on their accounts once they’ve completed their registration, as they don’t normally need to go back to it afterwards. However, their expertise details determine whether their name will show up in the lists of suggested reviewers and/or subject editors whenever an editor considers an assignment to the manuscript he/she is managing.
Here’s why we’ve introduced a regular reminder for users to review and, where necessary, update their expertise on their ARPHA account. This system message will come up once a year upon login and will straight away offer users a text box, where they can update their saved expertise. By means of free text, they will also be able to narrow it down even further.
As a result, not only are users not going to be bothered by irrelevant invitations – such as those received on the basis of their saved expertise being too broad, thereby saving time to the editorial team, but will also ensure that manuscripts will be indeed handed into the right hands for the sake of quality science.
Subscribe to our blog’s newsletter and follow us on Twitter (@ARPHAPlatform and @Pensoft) to keep yourself posted about the next features and updates coming to ARPHA!
In a new editorial, Plant Sociology’s Editor-in-Chief Daniela Gigante and Co-editors Gianni Bacchetta, Simonetta Bagella and Daniele Viciani reflect on the current position and outlook of the official journal of the Italian Society of Vegetation Science (Società Italiana di Scienza della Vegetazione or SISV), now that it has completed its first issue since transitioning to the scientific publisher and technology provider Pensoft and ARPHA Platform earlier this year.
The Editorial board briefly analyses the issues around the inaccessibility to scholarly research and suitable scholarly outlets still persisting in our days that impede both readers and authors across branches of science. Naturally, they go on to focus on the situation in vegetation science, where, unfortunately, there are rather few outlets open to original research related to any aspect within vegetation science.
By telling their own experience, but also citing the stories of other similarly positioned society journals, including other journals that have moved to Pensoft’s self-developed ARPHA Platform over the past several years (e.g. Journal of Hymenoptera Research, European Science Editing, Italian Botanist, Vegetation Classification and Survey, Nota Lepidopterologica), the editors present an example how to address the challenges of securing the long-term sustainability and quality for a journal used to being run by a small editorial staff in what they refer to as a “home made” method.
Other society journals that have moved to Pensoft’s self-developed ARPHA Platform over the past several years
In this process, the SISV supported its official scholarly outlet to be published as a “gold open access” journal and ensured that the APCs are kept to a reasonable low in line with its non-profit international business model. Further discounts are available for the members of the Society.
Then, the journal management also reorganised its Editorial Board and welcomed a dedicated Social media team responsible for the increased outreach of published research in the public domain through the channels of Twitter and Facebook.
Besides making the publications publicly available as soon as they see the light of day, the journal strongly supports other good open science practices, such as open data dissemination. In Plant Sociology, authors are urged to store their vegetation data in the Global Index of Vegetation-Plot Databases (GIVD). Additionally, the journal is integrated with the Dryad Digital Repository to make it easier for authors to publish, share and, hence, have their data re-used and cited.
The team behind Plant Sociology is perfectly aware of the fact that it is only through easy to find and access knowledge about life on Earth that the right information can reach the right decision-makers, before making the right steps towards mitigating and preventing future environmental catastrophes.
“A journal focusing on all aspects of natural, semi-natural and anthropic plant systems, from basic investigation to their modelisation, assessment, mapping, management, conservation and monitoring, is certainly a precious tool to detect environmental unbalances, understand processes and outline predictive scenarios that support decision makers. In this sense, we believe that more and more OA journals focused on biodiversity should find space in the academic editorial world, because only through deep knowledge of processes and functions of a complex planet, humankind can find a way to survive healthy,”
elaborate the editors.
To take the burden of technical journal management off the shoulders of Plant Sociology’s own editorial team, the journal has entrusted Pensoft to provide a user-friendly and advanced submission system, in addition to the production, online publishing and archiving of the accepted manuscripts. Thus, the editorial team is able to focus entirely on the scientific quality of the journal’s content.
“The renewal of Plant Sociology is a challenge that we have undertaken with conviction, aware of the difficulties and pitfalls that characterize the life of a scientific journal today. Entrusting the technical management of the journal to a professional company aims to improve its dissemination and attractiveness, but also to focus our efforts only on scientific content,”
explain the editors.
***
About Plant Sociology:
Plant Sociology publishes articles dealing with all aspects of vegetation, from plant community to landscape level, including dynamic processes and community ecology. It favours papers focusing on plant sociology and vegetation survey for developing ecological models, vegetation interpretation, classification and mapping, environmental quality assessment, plant biodiversity management and conservation, EU Annex I habitats interpretation and monitoring, on the ground of rigorous and quantitative measures of physical and biological components. The journal is open to territorial studies at different geographic scale and accepts contributes dealing with applied research, provided they offer new methodological perspectives and a robust, updated vegetation analysis.
By Mariya Dimitrova, Raïssa Meyer, Pier Luigi Buttigieg, Lyubomir Penev
Data papers are scientific papers which describe a dataset rather than present and discuss research results. The concept was introduced to the biodiversity community by Chavan and Penev in 2011 as the result of a joint project of GBIF and Pensoft.
Since then, Pensoft has implemented the data paper in several of its journals (Fig. 1). The recognition gained through data papers is an important incentive for researchers and data managers to author better quality metadata and to make it Findable, Accessible, Interoperable and Re-usable (FAIR). High quality and FAIRness of (meta)data are promoted through providing peer review, data audit, permanent scientific record and citation credit as for any other scholarly publication. One can read more on the different types of data papers and how they help to achieve these goals in the Strategies and guidelines for scholarly publishing of biodiversity data (https://doi.org/10.3897/rio.3.e12431).
Fig. 1 Number of data papers published in Pensoft’s journals since 2011.
The data paper concept was initially based on the standard metadata descriptions, using the Ecological Metadata Language (EML). Apart from distinguishing a specialised place for dataset descriptions by creating a data paper article type, Pensoft has developed multiple workflows for streamlined import of metadata from various repositories and their conversion into data paper a manuscripts in Pensoft’s ARPHA Writing Tool (AWT). You can read more about the EML workflow in this blogpost.
Similarly, we decided to create a specialised data paper article type for the omics community within Pensoft’s Biodiversity Data Journal to reflect the specific nature of omics data. We established a manuscript template to help standardise the description of such datasets and their most important features. This initiative was supported in part by the IGNITE project.
How can authors publish omics data papers?
There are two ways to do publish omics data papers – (1) to write a data paper manuscript following the respective template in the ARPHA Writing Tool (AWT) or (2) to convert metadata describing a project or study deposited in EMBL-EBI’s European Nucleotide Archive (ENA) into a manuscript within the AWT.
The first method is straightforward but the second one deserves more attention. We focused on metadata published in ENA, which is part of the International Nucleotide Sequence Database Collaboration (INSDC) and synchronises its records with these of the other two members (DDBJ and NCBI). ENA is linked to the ArrayExpress and BioSamples databases, which describe sequencing experiments and samples, and follow the community-accepted metadata standards MINSEQE and MIxS. To auto populate a manuscript with a click of a button, authors can provide the accession number of the relevant ENA Study of Project and our workflow will automatically retrieve all metadata from ENA, as well as any available ArrayExpress or BioSamples records linked to it (Fig. 2). After that, authors can edit any of the article sections in the manuscript by filling in the relevant template fields or creating new sections, adding text, figures, citations and so on.
An important component of the OMICS data paper manuscript is a supplementary table containing MIxS-compliant metadata imported from BioSamples. When available, BioSamples metadata is automatically converted to a long table format and attached to the manuscript. The authors are not permitted to edit or delete it inside the ARPHA Writing Tool. Instead, if desired, they should correct the associated records in the sourced BioSamples database. We have implemented a feature allowing the automatic re-import of corrected BioSamples records inside the supplementary table. In this way, we ensure data integrity and provide a reliable and trusted source for accessing these metadata.
Fig. 2 Automated generation of omics data paper manuscripts through import and conversion of metadata associated with the Project ID or Study ID at ENA
Here is a step-by-step guide for conversion of ENA metadata into a data paper manuscript:
The author has published a dataset to any of the INSDC databases. They copy its ENA Study or Project accession number.
The author goes to the Biodiversity Data Journal (BDJ) webpage, clicks the “Start a manuscript” buttоn and selects OMICS Data Paper template in the ARPHA Writing Tool (AWT). Alternatively, the author can also start from the AWT website, click “Create a manuscript”, and select “OMICS Data Paper” as the article type, the Biodiversity Data Journal will be automatically marked by the system. The author clicks the “Import a manuscript” button at the bottom of the webpage.
The author pastes the ENA Study or Project accession number inside the relevant text box (“Import an European Nucleotide Archive (ENA) Study ID or Project ID”) and clicks “Import”.
The Project or Study metadata is converted into an OMICS data paper manuscript along with the metadata from ArrayExpress and BioSamples if available. The author can start making changes to the manuscript, invite co-authors and then submit it for technical evaluation, peer review and publication.
Our innovative workflow makes authoring omics data papers much easier and saves authors time and efforts when inserting metadata into the manuscript. It takes advantage of existing links between data repositories to unify biodiversity and omics knowledge into a single narrative. This workflow demonstrates the importance of standardisation and interoperability to integrate data and metadata from different scientific fields.
We have established a special collection for OMICS data papers in the Biodiversity Data Journal. Authors are invited to describe their omics datasets by using the novel streamlined workflow for creating a manuscript at a click of a button from metadata deposited in ENA or by following the template to create their manuscript via the non-automated route.
To stimulate omics data paper publishing, the first 10 papers will be published free of charge. Upon submission of an omics data paper manuscript, do not forget to assign it to the collection Next-generation publishing of omics data.
Following the recent contract between the State Natural History Collection of Bavaria (Staatliche Naturwissenschaftliche Sammlungen Bayerns or SNSB) and the scholarly publisher and technology provider Pensoft, the scholarly peer-reviewed, open-access journal on paleontology and geobiology Zitteliana will be published on the technologically advanced scholarly publishing platform ARPHA.
Expected later in 2020, Zitteliana will not only benefit from its own sleek-looking and user-friendly website, but will also enjoy a long list of services and high-tech features and human-provided services delivered from ARPHA’s signature fast-track, end-to-end publishing system.
One thing that will greatly appeal to submitting authors, editors and reviewers is that the collaboration-focused ARPHA Platform supports manuscripts all the way from submission, peer review, editing, publication, dissemination and archiving within its online environment. On the other hand, to the benefit of readers, after publication, the articles are made available in PDF, machine-readable JATS XML formats, and semantically enriched HTML, which prompts discoverability, accessibility, citability and reusability. In addition, the journals will use all unique services offered by ARPHA, such as data publishing, linked data tables, semantic markup and enhancements, automated export of sub-article elements and data to aggregators, web-service integrations with more than 40 world-class indexing and archiving databases, sub-article-level usage metrics, and more.
Zitteliana is a scholarly journal covering all fields of paleontology and geobiology by the Bavarian State Collection of Palaeontology and Geology (SNSB): a research institution for natural history in Bavaria, comprising five State Collections. Initially limited to publications studying either the materials deposited in SNSB’s own collections, or topics related to the geology and palaeontology of Bavaria and adjacent regions, these days, Zitteliana welcomes articles in all fields of paleontology and geobiology. Encouraged are submissions on paleobiology, numerical paleontology, paleobiogeography, paleogenomics, palaeooceanography, biosedimentology, multiproxy and sequential stratigraphy, biodiversity research, and actuopaleontology, as well as contributions to the journal’s traditionally well-represented topics, such as paleontological taxonomy, systematics, phylogeny, and regional geology.
“It’s a great delight for Pensoft to be partnering such a prominent natural history institution like the SNSB and publish this particular journal of theirs. With our joint expertise and devotion, I am certain that we will successfully address major needs of the research community: readers, authors and their affiliates alike.”
says Pensoft and ARPHA’s founder and CEO Prof. Lyubomir Penev.
The Bavarian Natural History Collections (Staatliche Naturwissenschaftliche Sammlungen Bayerns, SNSB) are a research institution for natural history in Bavaria. They encompass five State Collections (zoology, botany, paleontology and geology, mineralogy, anthropology and paleoanatomy), the Botanical Garden Munich-Nymphenburg and eight museums with public exhibitions in Munich, Bamberg, Bayreuth, Eichstätt and Nördlingen.
Research conducted by over 30 permanent and 30 third-party funded scientists, currently employed at the SNSB, focuses mainly on the past and present bio- and geodiversity and the evolution of animals and plants. To achieve this, the institution keeps large scientific collections (more than 30,000,000 specimens). The collections and museums also play an instrumental role in public and academic education.
Expected to move to the Pensoft-developed technologically advanced scholarly publishing platform ARPHA later in 2020, the three academic outlets will not only acquire their own glossy and user-friendly websites, but will also take advantage from ARPHA’s signature fast-track, end-to-end publishing system, which is to benefit all journal users: authors, reviewers and editors alike. In addition, the journals will use all unique services offered by ARPHA, such as data publishing, linked data tables, semantic markup and enhancements, automated export of sub-article elements and data to aggregators, web-service integrations with more than 40 world-class indexing and archiving databases, sub-article-level usage metrics, and more.
Thereby, each submitted manuscript will be carried through the review, editing, publication, dissemination and archiving stages without leaving ARPHA’s collaboration-centred online environment. The articles are to be available in PDF, machine-readable JATS XML formats, and semantically enriched HTML for better reader experience to ensure they are easy to discover, access, cite and reuse.
Arthropod Systematics & Phylogeny succeeded the historical Entomologische Abhandlungen, formerly published by the Museum of Zoology, Dresden, in 2006. Its scope covers the taxonomy, morphology, anatomy, phylogeny, historical biogeography and palaeontology of arthropod taxa.
Similarly, Vertebrate Zoology was preceded by Zoologische Abhandlungen, also formerly published by the Museum of Zoology, Dresden. It deals with research on the taxonomy, morphology, anatomy, phylogeny, historical biogeography and palaeontology of vertebrates.
Meanwhile, Geologica Saxonica – Journal of Central European Geology, began its life in distant 1876, when it was founded under the name Mitteilungen aus dem Koniglichen Mineralogisch-Geologischen und Prahistorischen Museum by German geologist Hanns Bruno Geinitz, renowned for his work on the Carboniferous and Cretaceous rocks and fossils of Saxony.
“At Pensoft, we take pride in our latest partnership with the world-renowned natural history association of Senckenberg. “We are certain that our collaboration will bring many advantages to the research community: readers, authors and their affiliates alike,”
comments Pensoft and ARPHA’s founder and CEO Prof. Lyubomir Penev.
Senckenberg, Research Institutes and Natural History Museums, conduct research in bio- and geoscience. Major research fields are biodiversity and ecosystem research and the research on the entire Earth-Human-Earth system. Senckenberg headquarters are located in Frankfurt am Main, but research on marine, terrestrial and climate systems is also housed at additional nine locations throughout Germany: in Dresden, Gelnhausen, Gorlitz, Hamburg, Messel, Muncheberg, Tubingen, Weimar and Wilhelmshaven. Senckenberg employs about 1,000 people, including 300 scientists. Senckenberg scientists are active in projects worldwide, most of which are international collaborations with universities and other research institutions. Senckenberg hosts biological and geological research collections with more than 35 million series.
Acta Biologica Sibirica is an open-access, peer-reviewed journal on the biodiversity of Siberia and the adjacent lands by Altai State University. Since 2015, it has been publishing original research in the field of experimental and field biology.
Starting from 2020, Acta Biologica Sibirica moves to the full-featured technologically advanced platform ARPHA and will be published in collaboration with the scholarly publisher and technology provider Pensoft.
Pensoft’s original publishing system ARPHA allows Acta Biologica Sibirica to publish original research papers, reviews, short communications, letters and discussion papers, book reviews and memorial articles. The scholarly platform was designed to facilitate authors in the manuscript writing, submission and review process as end-to-end experience, including publication of the data and multimedia content in the form, suitable for both enhanced high-tech human and machine discoverability of the scholarly outputs.
Acta Biologica Sibirica accepts for publication papers in taxonomy, phylogeny, biogeography, faunistics, floristics, biological systematics, nature conservation and protected areas. In the fields of faunistics and floristics there are several types of articles, available for submission: floral and faunal lists on any region of the world, faunal and floral discoveries (e.g. species newly recorded in a particular region, additions to previously published inventories), papers on methodology of faunal and floral studies.
«Our basic task is to turn our journal into a high-quality world-class publication. Without the help of modern publishers, this is almost impossible. The choice of the publisher was perfectly logical – the reputation of Pensoft Publishers and its founder, the famous Bulgarian zoologist Lubomir Penev, is impeccable. To stand in one cohort with powerful publications with a long history is an honor for us. High standards of editing and reviewing manuscripts, the absolute level of originality and scientific novelty – these are the criteria on which we will rely»,
comments the editor-in-chief of the journal, Professor of Altai University Roman Yakovlev.
«At Pensoft, we are delighted to initiate this wonderful partnership with yet another renowned research institution in Russia, namely Altai State University. With our long-year experience in zoological and biodiversity research publishing and dissemination, I am certain that the journal has found a fitting place in the family of Pensoft and ARPHA»,
comments Prof. Lyubomir Penev, CEO and founder of Pensoft and ARPHA.
Within the pioneering papers published in the renewed journal, there is a research article about the first result of DNA-studies on the Central Asiatic owlet moths in the genus Euchalcia. The studied specimens were collected in Kyrgyzstan and Kazakhstan during the expeditions of the Russian Entomological Society in 2017-2019. When comparing a specific mitochondrial gene (cytochrome C oxidase subunit I or COI) between various species, the scientists revealed that the difference amongst European Euchalcia species is smaller than the one amongst high-mountainous Central Asiatic species.
Another study records the first occurrence of the moorland clouded yellow in Altai Region. The butterfly was found to share a mitochondrial barcode with some specimens from mountain populations from the Alps and the Czech Republic.
Colias palaeno, male, vicinity of Ozerki village, Talmenskiy district, Altai region, Russia Credit: Nazar A. Shapoval License: CC-BY 4.0
Altai State University is one of the leading Russian classical higher education institutions established in 1973. It is a major educational, research and cultural center located in the Asian part of the country, integrated into the international academic community, training the intellectual elite and conducting high-impact research.
The unique geographical position of Altai region, located in the center of Asia predestinates the University’s mission – to appear as an international research and educational center that integrates, develops and spreads the modern Western, Russian and Asian knowledge in education, science and culture within the Asian region.
About ARPHA:
ARPHA is the first end-to-end, narrative- and data-integrated publishing solution that supports the full life cycle of a manuscript, from authoring to reviewing, publishing and dissemination. ARPHA provides accomplished and streamlined production workflows that can be customized according to the journal’s needs. The platform enables a variety of publishing models through a number of options for branding, production and revenue models to choose from.
About Pensoft:
Pensoft is an independent academic publishing company, well-known worldwide for its innovations in the field of semantic publishing, as well as for its cutting-edge publishing tools and workflows. In 2013, Pensoft launched the first ever end to end XML-based authoring, reviewing and publishing workflow, as demonstrated by the Pensoft Writing Tool (PWT) and the Biodiversity Data Journal (BDJ), now upgraded to the ARPHA Publishing Platform. Flagship titles include: Research Ideas and Outcomes (RIO), One Ecosystem, ZooKeys, Biodiversity Data Journal, PhytoKeys, MycoKeys and many more.
Contacts:
Prof. Lyubomir Penev, founder and CEO at ARPHA and Pensoft Email: penev@pensoft.net
Prof. Alex Matsyura, Editor-in-Chief of Acta Biologica Sibirica Email: amatsyura@gmail.com
Prof. Roman Yakovlev, Editor-in-Chief of Acta Biologica Sibirica Email: yakovlev_asu@mail.ru
This move is part of a strategic relaunch of the journal to provide greater focus on research and expert commentary that will inform and support editors working in the scholarly environment. The relaunch comes after several months of planning by a small working group of EASE Council members and ESE editors. Much of the non-research content previously published in the journal will now be published in the newly-created member magazine, the EASE Digest; for example, News notes, The editor’s bookshelf, Resources, and interviews.
The journal is being relaunched with a new editorial board, but retaining the same Chief Editor, Ksenija Bazdaric, managing editor Dado Cakalo and associate editor associate editors Hrvoje Jakovac, Tom Lang and Joan Marsh. An introductory editorial published in the journal explains the changes.
Introductory editorial by ESE’s Chief Editor, Ksenija Bazdaric. Openly available from https://doi.org/10.3897/ese.2020.e50566.
The new editorial board comprises distinguished members from all over the world: Eva Baranyiova (Czech Republic), Lisa Colledge (UK), Moira Hudson (UK), Olga Kirillova (Russia), Zafer Kocak (Turkey), Rachael Lammey (UK), Vladimir S Lazarev (Belarus), John Loadman (Australia), Herve Maisonneuve (France), Ana Marusic (Croatia), Arjan Polderman (The Netherlands), Maria del Carmen Ruiz Alcocer (Mexico), Karen Shashok (Spain), Cem Uzun (Turkey), and Quan Hoang Vuong (Vietnam).
Ever dedicated to be a source of peer-reviewed information on all aspects of scholarly editing and publishing (i.e. research integrity, peer review, scientometrics, open science, predatory publishing, statistics), writing, translation and ethics, ESE welcomes editorials, original research articles, reviews, viewpoints and correspondence items.
ESE has moved to its new website, provided by the open-access scholarly publishing platform ARPHA (developed by scientific publisher and technology provider Pensoft), for all new articles, although the archive content will remain on the old website. This new website provides better delivery of the journal content and will help to make the journal easier to discover.
“I am happy to be working with the ARPHA team and that ESE has moved to a completely new platform which will raise the profile of editorial research and topics,”
Ksenija Bazdaric, ESE’s Chief Editor.
“At EASE we are delighted to be working with ARPHA and Pensoft to publish the journal in its new format. There has been considerable work invested in relaunching the journal with a new focus so that we can raise the profile of research about editing and the value that editors provide in the scholarly environment. An important part of the relaunch was ensuring greater visibility of the journal content and we are confident that ARPHA can help us achieve this,”
Pippa Smart, President, EASE.
“It could only make us proud at ARPHA that such a pillar in the world of scholarly communication has chosen our publishing platform to make the crucial step towards Open Access. I am certain that by opening up and digitalising its content right away, EASE will greatly facilitate and expedite the improvement of quality and integrity of science on the global scene,”
ARPHA’s and Pensoft’s founder and CEO Prof. Lyubomir Penev. “
