Edentulous jaw is a condition where either the upper (maxilla) or the lower (mandible) jaw is missing all teeth. In medical practice, it could be treated by placement of a complete denture.
Previous research has already pointed that the application of a border molding procedure (or functional shaping) results in significantly fewer cases of pressure ulcers (decubitus) and soft tissues deformations, hence increased retention and stability of the prosthesis, both at rest and in function. Since there are many factors that affect the optimal treatment, such as anatomical structures (i.e. muscles, muscular and soft-tissue gripping) and the asymmetry between the left and right halves of upper and lower jaws, it is important that special care is taken to determine the depth, as well as the width of the tissue where the teeth would normally be nested (gingivobuccal sulcus). With border molding, it is possible to determine those, however, the accuracy of the impression would still largely depend on the materials used in the procedure.
In their study, published in the open-access, peer-reviewed scholarly journal Folia Medica, Dr Dobromira Shopova and Prof. Diyan Slavchev at the Plovdiv Medical University (Bulgaria) sought to evaluate and determine the accuracy of two different groups of impression materials for border molding: thermoplastic and elastomers. They examined four different brands: Detaseal function (additive silicone for border molding), Sta-seal F (condensation silicone for border molding), GC Iso functional sticks (synthetic resin for border molding), Kerr Impression compound green sticks for border molding.
To perform their research, the team applied Dr Dobromira Shopova’s clinical method to measure negative pressure after border molding procedure, referred to as the vacuum measurement technique on edentulous upper jaw. They also assembled a special custom tray from a light-curing base plate with a palatal adapter. This was a 900, 7-millimetre metal adapter, which was fixed to the midline on the palatal slope. To create and measure the negative pressure, they used a combined pressure pump. The maximum value was 3 bars for positive pressure and -1 bar for negative pressure.
Working protocol followed for all materials:
1. Apply the impression material along the edge of the individual tray;
2. Insert, position and perform Herbst functional tests;
3. Wait for the elasticity or hardening of the material;
4. Assemble the clinical unit for negative pressure measurement;
5. Measure the negative pressure that has been created between the custom tray and the prosthetic field, then record the result;
6. Release the individual impression tray from the patient’s mouth.
A statistically significant difference was observed between the two thermoplastic materials: the GC Iso functional sticks and the Impression compound green sticks. No statistically significant difference was observed between the other groups of materials.
The measured mean negative pressure values created between the prosthetic field and the custom tray showed close values for each patient – with a difference of -0,05 to -0,1 bar. This showed that the anatomical features of the prosthetic field were of great importance.
In conclusion, quantitative measurement of negative pressure is entirely possible under clinical conditions. Thermoplastic materials for border molding are retained and formed only along the edge of the custom tray. However, silicone impression materials do not spread only on the edge of the custom tray, but also on the alveolar ridge, demonstrating their superior manipulative qualities and accuracy for the purposes of border molding.
ARPHA is a full-featured publishing platform providing: an authoring tool, peer review, production, publishing, hosting, indexing, archiving and dissemination of content.
This means that journals or publishers moving to ARPHA will avoid the burden of dealing with various software or service vendors (e.g. one for submission and peer review, another for production and a third for publishing and hosting).
The benefits from this seamlessly integrated workflow is that all team members (editors, reviewers, authors, layout managers and linguistic editors) can work within a single environment, where they can benefit from:
one-stop entry and unified interface from the start to the end of the publishing process;
reduced manuscript turnaround times;
in-built tools for monitoring and control at all stages of the publishing process;
data security and GDPR compliance;
reduced costs and optimised cost/quality ratio.
Complementary to the integrated and user-friendly software platform, ARPHA offers afull range of servicesprovided by our team or external vendors. This gives journal editors the flexibility and freedom to outsource some processes to ARPHA’s team or continue using its own staff or vendors.Additionally, we offer advanced journal performance reporting services designed to assist the Editors-in-Chief and managing editors in keeping an eye on the journal’s development and management.
(2) White-label and (co-)publishing
ARPHA can be used as a white-label solution, meaning the platform will operate under a journal/publisher’s own logo and imprint.
In other cases, especially for starting journals, a (co-)publishing solution together with ARPHA’s developer Pensoft Publishers may bring additional benefits in terms of recognition, promotion, development and goodwill.
Use case II: Alternatively, the Museum für Naturkunde (Natural History Museum), Berlin, took a decision to flip to open access and modernise their historical journals Deutsche Entomologische Zeitschrift (since 1859) and (since 1890, journal name changed) on ARPHA under the strong publishing brand of the platform’s mother company, Pensoft Publishers.
(3) Operational flexibility
The software modules or human-provided services can be selected on choice, so that they align with the journal’s existing workflows, future needs and budgetary requirements.
Use case I: Where journals already maintain their own editorial and/or production staff, they can opt to use ARPHA’s software platform in part and keep some of the work (e.g. editorial management and production) in-house. For example, the Plant Sociology journal of the Italian Society for Vegetation Science (SISV) decided to go for ARPHA’s ADVANCED pricing model, while continuing to use their own copy editing and typesetting services, leaving to ARPHA the building and maintenance of the entire editorial management and publishing platform, along with the highly specialised work on XML tagging and semantically-enhanced publishing. As a result, the journal achieved a quick technological modernisation, while significantly optimising its operational costs, allowing authors to publish with APC as low as €350 (€250 for society members).
Use case II: When the European Science Editing (ESE) journal, published by the European Association for Science Editing (EASE), enquired about ARPHA for possible use of its software and services, we decided to provide the platform for free, given the importance of the Society’s activities for increasing the quality and integrity of science publishing in Europe. During the negotiation phase, it appeared that the Society found its own way to typeset the articles to PDF, while the XML services had to be provided by ARPHA. At the very end, ARPHA and EASE decided to publish the journal as PDF only and move to HTML/XML later on, possibly after the second or third year. The result of this was an entirely free publishing in the ESE journal, while the transition to HTML/XML can happen at any point selected by the Society.
(4) Affordable and flexible pricing models
ARPHA publicly offers a transparent cost structure for its services. Each pricing plan contains a detailed account of the software modules and human-provided services. A journal can select from four pricing models that, depending on the publication volume, may amount to the following exemplary yearly costs:
EXAMPLES OF APPROXIMATE YEARLY COSTS (€)
2 issues 20 articles / year
4 issues 40 articles / year
Use case I: Check List is a large international journal operating mostly in the Global South, which sought an inexpensive publishing venue for its authors, while providing them with a modernised and technologically-advanced platform. ARPHA elaborated a custom business model for Check List based on PDF-only publishing, but providing distribution of metadata in XML and HTML, thus allowing the Article Processing Charges (APCs) for authors to be reduced to €120-€150.
Use case II: The journal Evolutionary Systematics of the University of Hamburg is published on ARPHA under the conditions of a fixed yearly budget which does not need to be calculated on the basis of the number of articles published per year. ARPHA customised a business model, based on a fixed number of pages published each year, which allowed for flexibility in publication of articles of different size within the yearly limit, while keeping the costs in accordance with the planned budget.
Use case III: The journal Alpine Entomology inherited the historical journal Mitteilungen der Schweizerischen Entomologischen Gesellschaft, which has been published by the Swiss Entomological Society since the middle of the 19th Century in black-and-white printed format only. In an open discussion with the journal’s editorial board, ARPHA was able to offer a model that allowed the building of a new website, publishing of the journal at the highest possible technological standards in semantic XML, HTML and PDF, printing 300 full-colour copies for distribution to society members and still allowed the saving of a small part of the journal pre-ARPHA budget!
(5) Various business models
A journal can operate on ARPHA using a wide variety of business models, for example:
Diamond open access – all costs are covered by an institution, society or third parties and the authors publish for free. The benefit of using ARPHA is that the costs of maintaining diamond open access for the journal owner will be FAIR, LOW and TRANSPARENT.
Mixed model – part of the costs can be covered by an institution, society or third parties and part from author’s APCs. The benefit of using ARPHA is that, with this model, the APCs for the authors can be kept as low as to be considered symbolic, in comparison even to average market standards.
APC-based income model – a society or institution may set APC that cover the production costs or add a surplus on the top of ARPHA’s prices. The benefit would be financial sustainability through generation and sharing of income.
Differentiated groups model – some authors can publish for free (e.g. staff or society members), others can benefit from discounts or waivers (e.g. from low-income countries) and a third group of authors can pay full APCs. The benefit of using ARPHA is that its accounting and online payment modules can be tuned to cater for administration of fees for different user groups.
Custom-fit models that can be elaborated together by the journal and ARPHA.
Use case: The International Association for Vegetation Science (IASV) decided to add a new journal Vegetation Classification and Survey to their portfolio, aiming at not-for-profit financial sustainability of the journal achieved over a period of three years. ARPHA supported a quite complex and highly-automated APCs model, ranging from free publication during the first year, low APCs during the second and below market average APCs during the third year and beyond, with different levels of discounts and waivers for society members, journal editors and authors from different groups of low-income countries, based on the World Bank classification. As a result, the journal is expected to become cost-neutral for the Society or even to bring in a small income for it, while offering APCs that are two to three times lower than those charged by large commercial publishers.
(6) Language flexibility
The majority of journals on ARPHA are published exclusively in English. Still, some journals prefer to operate in other languages, depending on their audience of authors and readers. ARPHA supports bilingual solutions at interface, metadata and content levels.
Use case I: The journal Maandblad voor Accountancy en Bedrijfseconomie of the Amsterdam University Press transitioned to open access and XML publishing on ARPHA in 2017. The journal wanted to keep the metadata and website interface exclusively in English, so that it is generally understandable to the international audience, but at the same time, the main content and journal’s news announcements to be published exclusively in Dutch. The result was more than satisfactory for the editors, authors and readers, especially after ARPHA uploaded the journal’s historical content (since 1924) and made it searchable and discoverable at article level on MAB’s new website.
Use case II: The journal Population and Economics, published by the Moscow State University, was established as an international journal publishing exclusively in English, while also offering its content in Russian to the vast community of Russian economists and population geographers. ARPHA created a special solution for formatting and publication of a Russian version of all articles, identical to the primary English text and formatted according to the journal’s design standards. The Russian version is published as PDF under the same DOI as the English version and under English Language metadata only; a special statement is included in the Russian version to be cited with its original English metadata to avoid splitting the citation counts between the two language communities.
(7) Multi-purpose platform
ARPHA can be used for publication of journals, books, conference abstracts or full-text papers, preprints and institutional documents.
For all these different products, ARPHA can create multifunctional platforms for institutions and societies operating under the customer’s logo and branding.
Use case: The Bulgarian Society of Cardiology transferred its 25-years old journal Bulgarian Cardiology on ARPHA in 2019. The journal is multilingual and publishes articles in English, Bulgarian and occasionally in other European languages. The new ARPHA-designed website of Bulgarian Cardiology provides a bilingual interface and the possibility to publish both English and Bulgarian language metadata and articles in either of the two languages. Shortly after the journal’s launch, the Society commissioned a new society website following the journal’s corporate design, yet providing a wide variety of other features to present the Society’s activities, publication of various documents, news items and so on. Both websites are available through a platform built on the Society’s domain address bgcardio.org.
(8) Technological innovation and relevance
ARPHA provides the highest technological publishing and dissemination standards, including several innovations, for example:
Amongst the most prominent technological innovations of the platform is the advanced semantics publishing module, which allows tagging and enhancement of content and the development of multiple interactive tools linked to the article’s content. This module is now fully operational for the domain of Biology, but can be developed for any field on demand of the client.
Another useful feature of the platform is the fully-automated indexing and archiving module. All content is instantaneously distributed on the day of its publication via web services, saving valuable time and effort in the editorial office.
Use case I: One of the most remarkable and well-known innovations of ARPHA was the 2013 launch of the first ever entirely XML-based and fully-integrated authoring, peer review and publishing workflow, exemplified by the highly successful Biodiversity Data Journal (BDJ). The ARPHA-XML workflow offered a number of globally-unique features, most of which are still unrivalled by other platforms, for example, import of data from data aggregators directly into the manuscripts via web services or the automated conversion and submission of metadata from data repositories into data paper manuscripts.
Use case II: In 2015, the ARPHA-XML workflow was used to establish the Research Ideas and Outcomes (RIO Journal) as the first open science journal aiming at publication of all outputs from the research cycle: from research ideas and grant proposals to methods, data, software, project reports, research articles and many more. The unique features of RIO resulted in the winning of the SPARC Innovator AWARD for 2016.
(9) High-level integration via web services & data exchange
ARPHA is fully integrated with more than 60 industry leading indexing and archiving services. Our partners include CrossRef, DOAJ, Clarivate Analytics, Scopus, Zenodo, OpenAIRE and PubMed Central, to name just a few.
The full automation of processes within ARPHA means that all content is directly exported upon publication without any extra human effort. This means that publishers and Editors-in-Chief can sit back and relax after pressing the “publish-an-article button”, while ARPHA makes sure that all their content is safely archived and successfully disseminated.
Use case: The journal Neotropical Biology and Conservation (NBC) was established and published by the University of Rio dos Sinos (UNISINOS), Brazil, by a team of motivated scientists. The journal was quite well-known and was indexed in Scopus and several other resources. At some point the editors realised that modern journal publishing requires much more than good scientific expertise and motivation, due to the rapidly evolving and highly competing science publishing market. In 2019, NBC was transferred to Pensoft and hosted on ARPHA. Particularly useful in the whole process proved to be the automated indexing and archiving functionality that is in-built with each plan of ARPHA. Previously submitted “by hand” by the Editor-in-Chief following each indexer’s specific requirements, this task used to be burdensome for the editorial office and results were prone to errors. After the move, all metadata was not only submitted automatically to all services previously used by the journal, but NBC could take advantage of disseminating their content to a package of more than 50 indexers and archivers (listed on the journal’s homepage) that automatically comes with the platform.
(10) Personal approach in technical support and consultancy
Journals joining ARPHA will enjoy a personal, reply-within-a-business-day, approach from a designated team member and benefit from operational training and technical support included in all pricing plans.
Use case I:ARPHA is built on the principle of transparency and openness and the platform even offers options for open peer review and annotations. However, when the newly-established journal Rethinking Ecology expressed a strong case for the need of a double-blind peer review functionality for the specifics of their work, the feature was developed and introduced on the platform and it is now available as an option for all users on ARPHA.
Use case II:When the journals Russian Journal of Economics and Population and Economics moved to ARPHA, the editorial boards wanted to make the most of the new platform and its features, with the shortest possible uptake time for their in-house staff. As a result, a two-day training was organised for the editorial teams in their Moscow offices, where they received an induction to the platform’s technical features, insights on how to make the most of its workflows and complementary training in journals’ promotion and PR. This induction has led to the requirements of the Editorial Board for these journals being met and successful adoption of the ARPHA platform.
The first 2020 issue of the journal by the Academy’s Forest Research Institute is already online on a brand new and user-friendly website
The scholarly publisher and technology provider Pensoft welcomes the open-access, peer-reviewed international journal in forest science concerning the Balkan Peninsula, Central and Southern Europe Silva Balcanica to its self-developed publishing platform ARPHA. Having become the latest addition to the lengthy portfolio of scholarly outlets dedicated to the fields of ecology and biology for Pensoft and ARPHA, Silva Balcanica is now offering a wide range of benefits and services to its readers, authors, reviewers and editors alike.
Having already acquired its own glossy and user-friendly website provided by ARPHA, Silva Balcanica also takes advantage of the platform’s signature fast-track, end-to-end publishing system. In addition, the published content enjoys automated export of data to aggregators, as well as web-service integrations with major global indexing and archiving databases.
Silva Balcanica invites scientific analysis of practical results, as well as investigations, in the forest sciences, including forest ecology; forest soil science; forest genetics, tree breeding and plantation forestry; biometry and sylviculture; forest economy and management; forest entomology and pathology; ecology and management of game fauna, urban forestry and green infrastructure. Constructive critique addressing scientific publications or events in the field of forestry and forest science are also accepted.
In the first 2020 issue of Silva Balcanica, we can find a total of eight research papers, dealing with a range of various topics, including studies on local plant diversity, genetics, application of experimental designs for forestry research, ecosystem services, population dynamics, invasive pathogens and previously unknown populations of forest-dwelling insects. It brings together single-authored research contributions as well as international collaborative projects, with input from authors from Bulgaria, Greece, Northern Macedonia and Italy.
CEO and founder of both Pensoft and ARPHA Platform Prof. Lyubomir Penev comments:
“Silva Balcanica is an important scholarly outlet and also a remarkable example of international cooperation, inspired and maintained by curiosity, care and responsibility towards the unique, but fragile ecosystems this part of Europe hosts. This is why we take pride in having this particular journal joining our portfolio.”
Silva Balcanica’s Editorial Board says:
“The Scientific Council of the Forest Research Institute at the Bulgarian Academy of Sciences decided to begin publishing Silva Balcanica as an international series in 2001 and since 2014, Silva Balcanica has been published as an international journal.
We are honored to have as members of our Editorial Advisory Board eminent European professors and researchers in forestry and related sciences that join our efforts in pursuit of high quality scientific publishing.
We are confident that Silva Balcanica will unite the research of scientists and specialists in forestry from Southeastern, Central and Eastern Europe and beyond, and will help them in the processes of their European integration.”
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.
With its first 2020 issue, Bulgarian Cardiology pioneers the Bulgarian-English bilingual publishing solution from ARPHA, the open-access scholarly publishing platform, developed by the publisher and technology provider Pensoft. Thanks to this, authors will be able to publish their papers either in Bulgarian, or in Bulgarian and English. In the latter case, the article will be displayed in both languages side by side, as exemplified in the paper “Novel approaches to treat resistant hypertension” by Dr Alexandra Cherneva (Acibadem City Clinic – Cardiovascular center, Bulgaria) and Prof Ivo Petrov (Sofia University and Acibadem City Clinic – Cardiovascular center, Bulgaria).
Even though bilingual Russian-English publishing was first introduced by ARPHA in late 2019 to coincide with the move of the Lomonosov Moscow State University’s journal Population and Economics to the platform, this time around, it is not mandatory for authors to translate their manuscript in English. On the occasion that the authors deem their work relevant exclusively for the medical researchers and practitioners on a national level, they are welcome to only submit in Bulgarian. However, they will still need to provide the paper’s metadata, including the abstract, in English, so that their findings remain findable and accessible to foreign users, in line with the best Open Science practices.
Having already acquired its own glossy and user-friendly website provided by ARPHA, Bulgarian Cardiology also takes advantage of the platform’s signature fast-track, end-to-end publishing system, which is to benefit all journal users: authors, reviewers and editors alike. In addition, the published content enjoys automated export of data to aggregators, as well as web-service integrations with major global indexing and archiving databases.
The first issue of Bulgarian Cardiology was published in 1995 to provide a scholarly outlet for the Bulgarian Society of Cardiology. Ever since then, it has been serving as an essential forum to bring together the cardiology community in the country. Its aim is to publish both the academic achievements of the Bulgarian medical experts and the key practical guidelines of the European Society of Cardiology.
Bulgarian Cardiology accepts for publication research and review articles, clinical cases, editorials, letters to the Editor, European Society of Cardiology guidelines, announcements from the Bulgarian Society of Cardiology and materials presented at their meetings, and others.
“It’s a pleasure to all of us at ARPHA to welcome the Bulgarian Society of Cardiology’s journal. It’s a fantastic win-win situation for both parties: while we managed to customise and provide the necessary services the Society asked us for, they offered us the opportunity to further push our capabilities and know-how, in order to launch our first top-to-bottom bilingual publishing solution,”
says Prof. Lyubomir Penev, founder and CEO at ARPHA and Pensoft.
The journal will continue to be published also in print with four issues a year.
От създаването си насам, журналът изпълнява роля на своеобразен форум обединяващ кардиолозите в страната, като целта на „Българска кардиология” остава разпространението както на постиженията на българските медици, така и на ключовите практически указания на Европейското дружество.
С издаването на първия си брой за 2020, „Българска кардиология” е първото академично издание, което ползва новата двуезична услуга на ARPHA, платформа за академично публикуване, създадена от научното издателство и технологичен иноватор Pensoft.
Въпреки че подобна двуезична услуга бе въведена от ARPHA в края на 2019 за списанието на Московския държавен университет „М. В. Ломоносов”, Population and Economics, в „Българска кардиология” авторите не са задължени да предоставят версия на ръкописа си на английски. От редакторския екип на българския журнал преценяват, че автори, които смятат трудовете си от интерес конкретно за учени и професионалисти на национално ниво, следва да имат възможността да публикуват статиите си единствено на български. Въпреки това, за тях е необходимо да предоставят метаданните на ръкописа си, включително заглавие, имена на авторския екип, адрес за кореспонденция и резюме на английски за целите на международни агрегатори и бази данни. Откриваемостта на научни трудове през подобни дигитални портали, които да са достъпни от всяка точка на света, е фундаментално изискване за осигуряването на пълноценна достъпност на научното познание в глобален мащаб.
Освен на красивия и интуитивен за потребителите нов уебсайт, „Българска кардиология” вече се радва и на пословичните за ARPHA технически нововъведения, създадени за удобството както на читателите на списанието, така и на авторите, рецензентите и редакторите, по време на целия издателски процес: от подаването на ръкописа до неговото публикуване, архивиране и разпространение. Благодарение на ARPHA, публикуваното в журнала съдържание също така ползва автоматизиран пренос на данни до международни агрегатори и други полезни онлайн интеграции.
„Българска кардиология” публикува оригинални статии, обзори, клинични случаи, редакционни коментари, писма до редактора, ръководства на Европейското дружество по кардиология, съобщения на Дружеството на кардиолозите в България и Европейското дружество по кардиология, материали, изнесени на техни заседания, обяви за симпозиуми, конгреси и др.
“Удоволствие е за всички ни в екипа на ARPHA да посрещнем журнала на Дружеството на кардиолозите в България в нашето портфолио. Смятам, че партньорството ни е страхотен успех и за двете страни. Докато ние успяхме да персонализираме и осигурим необходимите за Дружеството услуги, те ни предоставиха възможността да проверим и надградим уменията си, за да създадем една цялостна двуезична платформа”,
коментира проф. Любомир Пенев, основател и управител на ARPHA и Pensoft.
Списанието ще продължи да бъде издавано и в печатно издание четири пъти в годината.
Учредено през 1952 година, целта на Дружеството на кардиолозите в България (ДКБ) е да популяризира най-новите постижения в областта на кардиологията, да съдейства за издигане на професионалното равнище на кардиолозите в страната и да подпомага международните контакти на своите членове. Основната дейност на ДКБ е насочена към организиране на множество международни и национални прояви, конгреси, курсове, семинари, свързани с проблемите на кардиологията.
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.
Following recent API integration with ReviewerCredits, Pensoft – the scholarly publisher and technology provider – has launched a pilot phase with one of its peer-reviewed, open-access journal: Biodiversity Data Journal(BDJ). Reviewers, who create an account on ReviewerCredits,will automatically record their peer review contributions, which will be certified via the platform and receive rewards and recognition within the scholarly community and fellow scientists.
Apart from a seamless system to showcase their peer review activity, reviewers will also be assigned virtual credits, which can be redeemed for benefits provided by selected partners, including discounted APCs.
The registration on ReviewerCredits is free. While a reviewer can register any of his/her peer reviews on the platform, reviews for journals partnering with ReviewerCredits earn additional redeemable credits.
Once a reviewer signs in BDJ using their own reviewer account, a pop-up window will recommend that an account on ReviewerCredits is created by using an ORCID ID or an email address. Once the registration is complete, each completed peer review contributionwill automatically appear as certified on ReviewerCredits, as soon as the editor submits a final decision on the reviewed manuscript. In line with peer-review confidentiality, the entry displayed on ReviewerCredits will not contain the content of the review, nor the particular paper it is associated with.
“We are happy to partner with ReviewerCredits to further recognise, encourage and reward the contribution of reviewers in BDJ. No one should forget that, at the end of the day, it is up to reviewers to ensure that only good and quality science makes its way in the world. Unfortunately, though, their role in scholarship has traditionally been overlooked and we all need to put in effort to change the status quo,”
comments Prof. Lyubomir Penev, founder and CEO of Pensoft.
“We are excited by the collaboration with Pensoft on this project and to acknowledge BDJ among our prestigious partner journals. Pensoft has proved an extremely competent partner, well aware of the importance for journals to state the value of their peer review process. We work together to strengthen the collaboration between journals and reviewers and we are looking forward to a growing collaboration with Pensoft publications,”
Prof. Giacomo Bellani, co-founder and president of ReviewerCredits, underlines the value and enthusiasm for this new partnership.
ReviewerCredits is a startup company, accredited to the University of Milan Bicocca, launched in 2017 by enthusiastic active researchers and scientists. ReviewerCredits is an independent platform dedicated to scientists, Journals and Publishers addressing the peer review process.