The Journal of the Bulgarian Geographical Society is an international scientific journal dedicated to all fields of geography and interrelated fields of earth, ecological, social, economic and geoinformation sciences. It has a global geographical scope with a focus on Southeastern Europe and the Balkans, and its first issue dates back to 1933.
Having already acquired its own glossy and user-friendly website provided by ARPHA, the journal also takes advantage of the platform’s signature fast-track publishing system, which offers an end-to-end solution from submission to publication, distribution and archiving.
With features such as machine-readable XML format for papers, automated data export to aggregators, automated email notifications and reminders, and web-service integrations with major global indexing databases, the easy-to-use, open-access platform ensures that published research is easy to discover, access, cite and reuse by both humans and machines all over the world. The journal is now indexed in the likes of Crossref, Google Scholar, OpenCitations, Publons and Scibey, and archived in CLOCKSS, Portico and Zenodo.
The very first publications for 2021 (vol. 44) are out now. An opening editorial presents the background, the new mission and perspectives of the journal. A paper, authored by Stanley D. Brunn, communicates the mapping morality and its visible and invisible geographies. The rest of the issue’s articles will be published upon approval, following a “flow publishing” schedule.
“In the autumn of 2020, the editorial team and the executive committee of the Bulgarian Geographical Society agreed upon a new mission of the journal. It aims to respond and to adapt to the newest developments in scholarly publishing by providing a platform for high quality and innovative papers in all fields of geography and interrelated fields of earth, ecological, social, economic, and geoinformation sciences. The geographical scope of the journal will cover the entire world with special attention to Southeastern Europe and the Balkans,”
comment the journal’s editors.
“In these days of continuous speeding up of paces of work and life, the idea of facilitating the sharing of existing knowledge in order to create synergies, new knowledge, and innovation is more than timely and our journal can join the efforts to achieve these goals. That is why we are excited by the launch of JBGS on the ARPHA platform – a next-generation publishing solution that supports the full life cycle of a manuscript, from authoring and reviewing to publishing and dissemination.”
Arthropod Systematics & Phylogeny, Vertebrate Zoology and Geologica Saxonica are the latest historic titles to select the various services and advanced technology provided by the OA-born scholarly publishing platform
One of the largest natural research associations in Germany, the Senckenberg Nature Research Society moved three of its international, open-access scholarly journals to the publishing platform ARPHA, following a recent contract with the scientific publisher and technology provider Pensoft.
Having opted for the white-label publishing solution, the journals remain under the brand of the Society and the Senckenberg Natural History Collections Dresden, one of the oldest natural-science museums in the world. Despite transitioning to a new platform, the past volumes of the journals remain accessible from a link on their website homepages.
Following their recent move to the Pensoft-developed publishing platform, Arthropod Systematics & Phylogeny, Vertebrate Zoology and Geologica Saxonica have not only acquired their own glossy and user-friendly websites, but have also taken 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 are already using many of the unique services offered by ARPHA, including publication in PDF, semantically enhanced HTML and machine-readable XML formats; advanced data publishing; sub-article-level usage metrics; automated export of sub-article elements and data to key aggregators; web-service integrations with major indexing and archiving databases; and others.
In particular, to the appeal of the authors, editors and reviewers, the ARPHA’s collaboration-centred online environment takes care after each submitted manuscript during the review, editing, publication, dissemination and archiving stages, so that no one needs to deal with locally stored files and their transfer by email or third-party cloud storages. Additionally, the platform is designed to regularly notify the users about any required action, thus sparing the burden of unnecessary communication and ensuring the speedy processing of manuscripts.
All three journals operate a Diamond Open Access policy, thanks to the support of the Senckenberg Nature Research Society, making the journals free to publish for all authors.
Arthropod Systematics & Phylogeny
Arthropod Systematics & Phylogeny is the successor of the historical Entomologische Abhandlungen, formerly published by the Museum of Zoology at Dresden.
Its scope covers the taxonomy, morphology, anatomy, phylogeny, historical biogeography and palaeontology of arthropod taxa, but excludes faunistics and research with a strong regional focus. Descriptions of new taxa are only welcome when embedded in a wider context, for example, a phylogenetic, evolutionary, or biogeographical framework.
Similarly, Vertebrate Zoology was preceded by Zoologische Abhandlungen, also formerly published by the Museum of Zoology at Dresden. Its first publications since the move to ARPHA Platform and part of the first journal volume for 2021 are already a fact.
The journal deals with research on taxonomy, morphology, anatomy, phylogeny, historical biogeography and palaeontology of vertebrates. Again, descriptions of new taxa should be integrated into a proper context, for example, a complete revision of a taxon. To support accountability and reproducibility in science and academia, the journal requires that studied specimens have to be deposited in a public scientific collection.
Vertebrate Zoology’s Impact Factor is currently standing at 1.167, while its last Scopus CiteScore reached 2.1 (2019).
Geologica Saxonica – Journal of Central European Geology, began its life in distant 1876, when it was founded under the name Mitteilungen aus dem Königlichen Mineralogisch-Geologischen und Prähistorischen Museum by German geologist Hanns Bruno Geinitz, renowned for his work on the Carboniferous and Cretaceous rocks and fossils of Saxony.
The journal’s scope ecompasses geology, paleontology, stratigraphy, petrography, mineralogy and geoscience history with focus on Central Europe.
“At Pensoft, we are delighted to support a world-renowned natural history association like Senckenberg in carrying its legacy and treasure of knowledge into our days and well beyond. Now, with ARPHA’s white-label solution, we’re certain that the journals will simultaneously preserve their identity and enjoy all perks of modern and technologically advanced publishing,”
comments Pensoft and ARPHA’s founder and CEO Prof. Lyubomir Penev.
“We are very pleased to have found reliable partners in Pensoft and the ARPHA platform for our three publications to further increase their visibility. Senckenberg’s scientific publications have a long – almost 200-year tradition – and are now shown in a new and innovative design with unprecedented information retrieval options!”
says Prof. Dr. Uwe Fritz, Editor-in-Chief of the journal Vertebrate Zoology and head of the Department of Zoology at Senckenberg Natural History Collections in Dresden.
Given scientific conferences present academics with the fantastic opportunity to meet up and discuss their latest work, as well as share their vision for the future of their field, it’s no wonder that, historically, the majority of ground-breaking science can easily be traced back to a particular event.
This said, don’t you think that we need to do everything within our powers toensure the visibility, dissemination and long-term accessibility of research presented and linked to these wonderful drivers of scientific progress that conferences are? Similarly to the care conference organisers take to make sure the event runs smoothly and the attendants are happy with the programme and enjoy themselves, the organisational committee should also be thinking how to preserve all those promising pieces of research well after the event is over.
Here at Pensoft, an open-access scholarly publisher, founded by scientists, we’ve been contemplating for a while now how to encourage and support the community to efficiently open up the valuable outputs to researchers and readers well beyond the publication of abstracts in an abstract book of the conference.
As a result, we came up with several simple, yet efficient publishing solutions for scientific conferences to collect and contextualise various research outputseither presented at or resulting from the event.
Bear in mind that with any solution, all publications enjoy the benefits seen in conventional research papers, such as:
Crossref registration and individual DOI to ensure preservation;
Publication in PDF, semantically enhanced HTML and data-minable XML formats to improve readability, accessibility and findability;
Indexing and archiving at multiple, industry leading databases to increase visibility;
PR and social media promotion to boost outreach to various audiences.
Collections of conference abstracts, posters and presentations
Conference (video) abstracts, posters and presentations are easily the first to fall victims of the ephemerality of an event, yet these are too often the stepping stones to major scientific discoveries. This is why a few years back we launched ARPHA Conference Abstracts (ACA), where conference organisers can open their own collection and provide the participants with submission, review and publication of their abstracts ahead of the conference.
Furthermore, these abstracts can be handled editorially in sub-collections, e.g. the convenors of symposia or working groups within a conference will take care of the abstracts submitted to them, thus spreading the editorial workload across larger teams of editors and organisers.
Not only will conference organisers spare themselves the worries about providing a special platform for abstracts submissions, but this will also facilitate presenting authors, who will be able to easily point to their contribution before, during or after their presentations. On the contrary, the abstracts are assigned with DOIs, published in human-readable PDF and HTML and machine-actionable JATS XML, permanently preserved on ARPHA and Zenodo, and easy to find, access and cite, just like a conventional research paper, providing authors with full credit for their work early on.
Further, with ACA, the conference abstracts can be enhanced into what we call “extended abstracts”, meaning they can also include data, images, videos and multimedia. After the conferences, we can add video recordings of the presentations or graphic files of posters, so that these are visualised on the page of each abstract.
About the time we launched ACA, we also created ARPHA Proceedings, in order to also find a place for full-text conference papers. Similarly, the platform supports dedicated collections, where conference attendants are invited to submit and publish dynamically articles under the imprint of the event.
Conference papers in ARPHA Proceedings can also include data, figures and citations, and can also be updated with video recordings, posters and presentations following the conference.
Article topical collections and special issues resulting from conferences
Naturally, papers resulting from a particular conference are contextually linked, so a one-stop place to discover topical studies sharing one and the same topic would be greatly appreciated by readers and future researchers. In turn, this would lead to better viewership and citability of the papers in the collection.
With our user-friendly, dedicated workflow for special issues and permanent topical article collections, we’ve made it easy for guest editors across our journals to pitch and manage article collections, in order to bring together valuable and related studies. Using such a collection under the theme of your conference in a suitable journal, you can invite your conference’s participants or, better yet, all scientists working within the field, to submit their work in a nice package of topical science. We’d be happy to assist you with the identification of the most suitable journal for your conference, authors and goals.
Bringing together traditional and non-conventional research outputs, (e.g. research ideas, grant proposals, conference materials or workshop reports) with RIO Journal’s article collections
Undoubtedly, valuable research outcomes come in many shapes and sizes well beyond research papers, conference abstracts, posters and proceedings. We are firm supporters that every research item, even early and interim outputs, could be of value to the scientist next in line within a particular study.
This is why we launched the award-winning journal Research Ideas and Outcomes(RIO), where your collections can include both conventional and non-traditional research outputs, such as research ideas, posters, workshop reports, forum papers, policy briefs, software and data management plans to name a few. Furthermore, in RIO,you can even link articles or preprints published elsewhere to your collection via their metadata. Similarly to other Pensoft journals, in RIO, you will have the full control to whom you are opening your collection for submissions, allowing you to either limit it to the outcomes coming from your conference or welcome submissions from other researchers as well.
A permanent topical collection in RIO Journal may include a diverse range of both traditional and unconventional research outputs, as well as links to publications from outside the journal (see What can I publish on the journal’s website).
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).
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.
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.
The open-access, peer-reviewed International Journal of Heritage, Memory and Conflict (HMC) aims to offer an interdisciplinary space for the rich scholarship within a wide range of studies by crossing academic, artistic and professional boundaries; while also contributing to the better understanding of the extent to which memory sites and discourses operate as vehicles at local, national and transnational levels.
The HMC covers the fields of memory studies, cultural studies, museum studies, Arts and media and performative studies, postcolonial studies, ethnology, Holocaust and genocide studies, conflict and identity studies, archaeology, material culture and landscapes, conservation and restoration, cultural, public and oral history, critical and digital heritage studies.
Likewise, HMC will also benefit not only from the signature glossy and intuitive user interface provided by ARPHA, but also from the platform’s distinguished fast-track, end-to-end publishing experience available to the use of authors, reviewers and editors. Within ARPHA’s seamless environment, each manuscript submitted to HMC is carried through the review, editing, publication, dissemination and archiving stages without ever leaving ARPHA’s collaboration-centred online environment.
Furthermore, in order to ensure that HMC’s content is as easy to find, access, cite and reuse as possible, the articles are published in three formats: traditional PDF, machine-readable JATS XML formats, and semantically enriched HTML. The journal is also indexed at major indexers and archivers.
*** More information on submission and article processing charges can be found on the journal’s website here.
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.
Visit ARPHA Preprints website to see the growing list of ARPHA-hosted journals integrated with ARPHA Preprints to date.
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.
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;
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.
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;
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
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.
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!
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.
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).
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.
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.