Recently, we held a series of meetings with the editorial boards of our client journals, where we focused on journal development and how we, as a publisher and services provider, can further chip in in the ultimate editorial task: quality content acquisition. One thing that we reaffirmed was a longstanding notion: academics are deeply fond of special issues and topical collections (collectively referred to as “article collections”).
So, there’s a good reason why this remains to be the case, even in the high-tech era of today where everything changes and evolves day by day. Come to think about it, it’s several of them:
Good for the editors: guest editors receive highly valued credit and recognition for bringing together extensive quantities of thematic content, where the topic is usually a pressing and highly appreciated amongst fellow academics. Showcasing that you have pitched and taken the responsibility of managing an article collection is a wonderful way to sprinkle some sparkle in your academic resume!
Good for the readers: collated content makes it easier to discover and, in turn, use relevant studies, thereby saving precious time for the next research team looking to develop the topic.
Good for the authors: it’s the bitter truth that many research papers fall short on academic and/or public attention for no reason other than the fact they haven’t gone viral on Twitter, nor have their titles been made artificially appealing. Getting your paper next to a highly attractive publication, however, can give your study that delicate boost of first-sight appeal!
Good for the journal: having multiple papers conveniently grouped together by topic and relevance prompts their simultaneous use and citation, naturally increasing the overall impact of the journal hosting the article collection. As a bonus, the issue as an entity is likely to receive references, further aiding the journal’s outstanding reputation.
Having acknowledged all of this, we found ourselves contemplating how we could possibly help our client journals and their users pitch and manage article collections.
Firstly, we refined the concepts for both special issues and topical collections. Then, we developed a dedicated editorial management system to allow for a smooth and efficient workflow all the way from the moment the collection’s proposal is submitted to its successful conclusion.
Special issue vs. Topical collection
While both types of article collections overlap considerably, we shall start by explaining what are the key differences between a special issue and a topical collection:
Available* only at journals published in consequent numbered issues
Available* at all journals
Deadline for manuscript submission and publication of the issue
No deadline for manuscript submission (until the collection is announced to be closing soon)
Possible limits in the volume and/or number of articles in the special issue
No limits for volume or number of articles
Pre-scheduled (approximate) date of publication announced with the initial call for papers
Collection editors need to provide a timely notice when/if the collection is planned to close for submission
Papers wait for publication until completion of the special issue and the set publication date
Papers are published on a rolling basis as soon as ready
All papers published in a separately numbered issue within the yearly journal’s volume
Papers in the collection normally published in different journal issues, depending on time of publication
Normally published within a year from the initial call for papers
Can be published across many years, depending on the Collection editor’s commitment and journal’s decision
*Availability is subject to request by the journal.
How it works
Each submission meant for the collection will be first delivered to the editorial office and/or Editor-in-Chief (depending on the journal’s policy), in order to ensure that the manuscript is compatible with the journal’s scope, focus and standards.
If approved, the manuscript is forwarded to the Collection editor who assigns it to either himself/herself or another Guest editor to take care after the peer review process and make the editorial decision on its acceptance or rejection.
Once the Collection editor submits the decision, the submission’s processing will be finalised at the journal’s editorial office.
As a result, ARPHA’s automated journal management system, in combination with our experienced editorial team, provides an efficient and convenient service that balances out user interface intuitivity, time-efficiency and quality.
The editor’s point of view
To provide an efficient organisation and balance in the workload, we’ve designated two roles for the guest editors of an article collection: a Collection editor and a Guest editor(s). While both are able to handle manuscripts as handling (subject) editors (i.e. manage the peer review process and make a final decision on the manuscript’s acceptance or rejection), the Collection editor is the one who pitches the collection, appoints the Guest editors and works with the journal’s editorial office on matters regarding the collection, including its appearance on the journal’s website. It’s also the responsibility of the Collection editor to ensure that the collection meets any applicable requirements.
Thanks to the refined ARPHA workflow, all the Collection editor needs to do is fill in an application form on the journal’s website, then wait to be contacted by the journal’s editorial office and/or Editor-in-Chief. If the collection is approved, the editorial office will set up the collection and grant the Collection editor with the necessary rights and provide instructions for ARPHA’s comprehensive journal management system, where he/she will be able to track and perform the actions needed to handle the manuscript. Similarly to the regular editorial workflow at ARPHA-hosted journals, the platform will be automatically notifying the editors each time they need to take an action.
The author’s point of view
The only thing authors, who wish to submit their paper to an article collection within an ARPHA-hosted journal, will have to do differently in comparison to the regular submission process, is to select the name of the collection in a dropdown menu during the submission process.
On the occasion that the manuscript complies with the scope and standards of the journal, meaning it successfully passes the pre-review evaluation, however, is declined from the collection by the Collection editor prior to peer review, the submission will be processed through the journal’s standard editorial process, and if accepted for publication, the article will appear as a regular article in the journal.
Find more information about the article collections workflow and requirements in the About space at the website of the journal you’re interested in (see example from ZooKeys).
We’re open to feedback and further information requests. You can contact us on email: firstname.lastname@example.org
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;
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.
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!
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.
Already bracing ourselves for another goodbye in a few weeks, it’s time to look back at 12 months of ceaseless efforts to further advance the user experience for authors, reviewers, editors and readers alike.
What’s in it for ARPHA that keeps us motivated all year round? Well, it’s a win-win: we get to stay at the top of our game within the scholarly publishing and technological landscape, while honouring our word to client journals, publishers and platforms to provide a state-of-the-art publishing solution sewn with the genuine understanding of a fellow scholar.
Frankly speaking, having observed a rapid expansion in our journal portfolio – which currently counts over 50 peer-reviewed and exclusively open-access scholarly titles – over the past few years we’ve never been so enthusiastic to draw the line of another “most successful year” and set sights on our 2020 targets.
Without further ado, here are the key innovations and milestones achieved by ARPHA in 2019.
ORCID integration to connect researchers to research
Would a researcher trust a journal with his/her manuscript if it said the research paper will not be assigned with a Digital Object Identifier (DOI) upon publication?
Likewise, thanks to ORCID, researchers are also provided with a unique digital identifier to provide a persistent link between their identity and their work across platforms. Apart from papers, the latter includes various professional activities such as grant applications as well as links to external profiles, for example, Web of Science ResearcherID or LinkedIn.
To ensure that their work published in an ARPHA-hosted journal is automatically logged on their ORCID account, the platform allows users to sign in using their ORCID credentials. Alternatively, they can add them to their existing profile and merge the two to avoid potential duplicate records and confusion.
Look out for the exclamation mark next to your user name: it reminds you that you haven’t taken full advantage of the ARPHA-ORCID integration just yet.
Visit ORCID’s website to learn more about their mission to connect researchers to research.
Now on display: ORCID ID, Web of Science ResearcherID and Scopus Author ID
In addition to their ORCID IDs, users at any ARPHA-hosted journal can add their Web of Science ResearcherID and SCOPUS ID to their user profiles to ensure further seamless connectivity between their identity and professional activities. Once they do so, the corresponding icon(s) will show up next to their names every time they appear in an authors list across ARPHA-associated journals.
While ORCID IDs automatically link users to their work published on ORCID-integrated platforms (records can also be added manually), a Web of Science ResearcherID – which of recently is managed by Publons – creates a link between a researcher’s peer review and editorial contributions and their Web of Science Core Collection-indexed publications. Similarly, Scopus Author IDs connect Scopus-indexed publications with their authors’ profiles, including references, citations, h-index and subject areas.
Pending tasks visualised for each reviewer and Subject editor to facilitate and speed up the editorial process
Even though the high-tech and user-friendly infrastructure available from ARPHA Platform substantially reduces the time between a manuscript’s acceptance, publication, dissemination, archiving and indexing, we do realise that, technology-wise, there is little to be done in order to expedite the manual labour performed by overburdened editors and reviewers.
This is why we’ve made it possible for an editor to see how many tasks any Subject editor or reviewer is currently handling whenever he/she gets to assign a manuscript.
Multilingualism on a journal AND platform level
Despite the ceaseless globalisation in the scholarly landscape, we can’t fail to recognise that there are, and perhaps will always be, academic journals whose specific scope and readership would do best if the content is also available in additional languages apart from English.
When we welcomed Population and Economics in April, the renowned Moscow State University’s journal became the first ARPHA-hosted scholarly title to accommodate our bilingual approach allowing for the reader to download a PDF copy of an article in Russian straight from its webpage. To avoid potential confusion in references, citations etc., both the Russian- and the English-language articles are using the same DOI.
Happy with the positive feedback from our clients and motivated by the soaring number of similar requests coming from potential client journals, we continued investing in the full transformation of ARPHA into a multilingual platform.
As a result, clients of ARPHA can now opt for our bilingual solution, where it is entirely up to the individual user to toggle between the English and Russian interface of the journal.
We’ve already started working on adding more languages to make sure that ARPHA is truly multilingual and international-friendly!
ARPHA-Proceedings inaugural issue
Recently, we also saw the publication of the inaugural issue of conference proceedings submitted to our self-titled innovative platform.
Aimed at conference organisers from across all scientific fields, ARPHA Proceedings allows for the publication of dedicated issues, where conference papers are published along associated data, figures and citations. Additionally, video recordings, posters and presentations can be uploaded in bulk once the conference is over.
Individual conference papers as well as complete volumes are assigned with their own DOIs, which are registered by ARPHA in full compliance with CrossRef’s metadata requirements for conference materials.
Historical issues of Dutch journal of Accountancy & Business Economics (MAB) republished by modern standards
As a result, not only are all papers published in MAB in the last 95 years openly accessible from a single online source, but they also take full advantage of the technology normally available to modern research outputs. These include a DOI assignment and CrossRef registration of metadata for each individual study. A full-text search of an article’s content is available with the PDF copy.
MAB, a journal by Amsterdam University Press, moved to our platform using ARPHA’s white label publishing solution last year. ARPHA’s white label publishing is targeted primarily to university presses, independent publishers and societies seeking to retain their identity in an increasingly competitive high-tech environment.
A whole new batch of web integrations available to clients
Most recently, Pensoft and ARPHA signed a strategic collaboration agreement with the research discovery platform ScienceOpen, which means that content from all ARPHA-hosted journals will be indexed in the ScienceOpen’s research and discovery environment and added within the thematic context of over 60 million articles and books.
Earlier in 2019, ARPHA was integrated with several other research databases, including Portico, EBSCO and Transpose, so that content published across the journals is even easier to discover and access and ultimately facilitating the citability, reusability and reproducibility of scientific research.
One size to fit them all? At ARPHA, we are well aware that it does not work like that in academia, let alone when it comes to accommodating individual scholarly journals from across the tremendously varied publishing landscape.
This is why we have prepared four options to account for the specific aims and needs of ARPHA’s potential clients, while bearing in mind their resources and sustainability.
In the spirit of transparency and openness, along with a comprehensive list of services that clarifies how each plan compares with the rest, we have provided the associated pricing ranges, where the total expenditure is easy to calculate, as it is based solely on the volume of published content. To support emerging publishers and prolific institutions, and express gratitude for their trust, we offer discounts for multiple journals joining ARPHA’s community.
While Open Science initiatives, including OA2020 and Plan S, have clearly become the major talking points, academic institutions, societies and small-to-medium publishers from around the world are increasingly looking to chip in the growing community and make their own stand for science becoming truly efficient, responsible and inclusive by ensuring openness, transparency and FAIRness. But how do they do that when capped budgets, scarce human resources and lack of know-how in specific areas come into play?
While one may be struggling with bringing together the right in-house expertise, another might be unable to keep track of the ‘top wanted’ integrations and services required for any state-of-the-art publication venue, and yet another might be encountering difficulties in communicating their otherwise ground-breaking published research to the public. In our experience, all of them are most likely experiencing difficulties with either the development of an advanced and user-friendly technological backbone or covering the associated costs.
Here are the good news! ALL journals published on ARPHA Platform take advantage of our signature high-tech and easy-to-operate full-featured platform by default. What we mean, is that any journal benefits from an end-to-end, entirely online publishing solution, which takes care of the manuscripts all the way from submission and peer review to editing, publication, dissemination, indexing and archiving (see “The 5 Most Distinct Features of ARPHA”), while the annual maintenance could easily costas little as a few thousands euros.
On top of ARPHA’s user- and collaboration-friendly platform that allows for authors, reviewers and editors to easily and conveniently manage and track the progress of manuscripts, thereby ensuring that no technological pitfalls stand in the way to rapid and efficient distribution of scientific knowledge, our platform is continuously expanding its suite of services and features. This is also where one can find the major differences between the four plans offered by ARPHA.
As you can notice, even the lowest-priced LITEPlan features a plenty of useful and advanced perks, including a one-stop API end-point for distribution to 30+ international databases, metadata export to 12+ machine-readable formats, article sharing and usage statistics tools.
At the other end of the spectrum, ARPHA’s PREMIUMPlan adds top-notch features, such as assignment of Digital Object Identifiers (DOIs) to individual images, which in turn allows for the delivery of real-time usage metrics for each one of those.
Curious about how ARPHA could accommodate your journal(s)?
Scroll down our pricing plans and operating models, and fill out the Get a Quote form. Shortly, we will be back in touch to discuss the best options for ARPHA to fit the specificity of your publishing project.
Monitoring the progress of your manuscript has never been easier!
The eagerly anticipated Track changes feature is now available in ARPHA Writing Tool to further facilitate collaborative authoring in the five academic journals* which currently make use of the ARPHA-XML publishing workflow.
Having tapped into ARPHA’s users constructive feedback, we have also updated our Revision History feature. Now, not only can authors access any past version, as created by their co-authors and collaborators, but they can also compare any two of these at the click of a button.
To let co-authors and collaborators easily see any changes they have made, a user needs to simply switch on the Track changes mode. From now on, each individual author’s input will be highlighted to draw the attention of the next user.
Logically, any newly inserted text will appear in green, while the deleted one will be coloured in red. A hover over a highlighted text will show the user who has made the edit.
To make overseeing even a single edit impossible, ARPHA Writing Tool has made it mandatory for a user to resolve all suggested changes before either submitting the manuscript or switching off the Track changes mode.
Not overlooking any new input, regardless of the length and complexity of a manuscript, is made even easier thanks to the Prev and Next buttons allowing a user to go through the changes one by one.
But what shall you do if you or your co-authors/collaborators happen to forget to switch on the Track changes mode?
Compare Manuscript Versions
Our latest update to the Revision history button lets users compare any two past manuscript versions, so that they can see at a glance what has changed between any two set points in time.
Just like before, clicking the Revision history button delivers a list of all manuscript versions along with the users who have created them in a chronological order. Now, however, a tick box next to each of these allows the user to select any two versions and see all edits that have taken place in between.
Again, newly added text shows in green, while the deleted text is crossed over and appears in red.
Creating, reviewing, editing and publishing of collections of proceedings from conferences, symposia and workshops is now available with the ARPHA-Proceedings module via the publishing platform ARPHA.
Designed as a venue for conference organisers to streamline proceedings publications, while simultaneously giving credit to the authors and preserving their contributions in a format that makes them easy to find and read by both humans and machines, the ARPHA-Proceedings module can be regarded as a simplified and straightforward journal publishing process specialised for conference abstracts.
The workflow supports multiple proceedings collections. For instance, a proceedings publishing platform could be created for a particular conference taking place on a regular basis or for a number of conferences organised by an institution or a society. A fine example is the Proceedings of TDWG dedicated to the yearly Biodiversity Information Standards (TDWG) conference.
Within the platform, hierarchical article collections could also be established. Abstracts can be submitted to sub-collections dedicated to various workshops/symposia within a larger event. The different sub-collections can be handled by different editors, normally the workshop/symposia conveners.
The workflow used in the ARPHA-Proceedings module includes ARPHA Writing Tool, editorial/technical evaluation, publication and dissemination.
At any point and at no additional costs, the platform can be modified to feature additional article types (e.g. full-text papers, posters, talks etc.). It is for the conference organisers to decide whether these submissions are to undergo a conventional peer review process.
Abstracts can be enriched with citations, figures, tables, data and multimedia if the conference organisers decide to allow it.
Abstracts can be published straight on the platform as soon as an editor approves them, so that the publication is available online ahead of the conference.
Abstracts published in this way have all features common for regular articles published via ARPHA, including Digital Object Identifier (DOI); publication in HTML, PDF and machine-readable and harvestable XML; citation, indexing and archiving in various databases; dissemination and others.
Below you can find a practical guide to the submission process of a conference abstract and assigning it to a collection via the ARPHA-Proceedings module.
1. Log in at the platform’s website or ARPHA Writing Tool.
2. Click Start a manuscript to see the platform and article type options.
3. Select a venue and article type for your manuscript.
4. Click Collections on the navigation bar at the top. This is where you select the conference track to which you are assigning your manuscript (this does not guarantee acceptance in that track).
5. Fill in your abstract’s metadata by hovering over a category, and then clicking on the pencil icon. The fields Title, Abstract, “Keywords”, and Presenting Author are mandatory. The submitting author and affiliation are taken from the profile of the logged-in user. More authors can be added by clicking the icon beside Authors on the left-hand side. The corresponding author and the authors’ order can be changed from the same menu. The corresponding author must be available to communicate about the abstract until final acceptance for publication. The presenting author is the person who will actually be giving the talk/demonstration.
6. You may add references, figures, tables (if allowed on the particular platform) by clicking on the appropriate icon. You may also upload supplementary materials associated with the abstract.
7. Click Validate. An automated check will ensure that all mandatory fields are filled in and the abstract is assigned to a collection.
8. When you are ready to submit your abstract, click Submit for technical review. This will send the manuscript to the track editors, who will review it for relevance to the track. The button will be visible as soon as the validation has been successful.
9. The editors of the track to which you have submitted your abstract may accept or reject your submission, send feedback requesting changes or suggest submission to a different track.
10. Once the abstract is accepted, the Submit to the journal button becomes visible in ARPHA Writing Tool. You need to click this button and go through a checklist of submission steps. The fourth and final step asks you to assign categories to your submission (optional). When the submission process is finalised, the abstract goes directly to production and publication, a DOI is assigned and the abstract cannot be further revised.
11. To see your manuscripts, go to the ARPHA Writing Tool’s website, log in and click the See more button, so that you can access your ARPHA dashboard.
On the right-hand side, you can see the stage each manuscript is currently at, along with the collection it has been assigned to (note that this does not mean that it has been approved for this collection).
If an abstract is at the Draft stage, it means that it is still being authored. Once submitted for Technical Review, it reaches the In pre-submission review stage where it stays until a Collection editor approves it for addition to a particular collection. In layout means that a manuscript is successfully submitted to the journal and awaiting publication.
12. If at any time you feel in need for further assistance, you can send an email to the journal’s technical staff via the system. Click Helpdesk on the top navigation bar to open a new window with an email form for you to fill in.
Please keep in mind that the stepwise instructions displayed are subject to slight modifications per request. Feel welcome to contact us with your personal platform’s needs!
Only a couple of months ago, we announced a whole set of exciting features newly applied to ARPHA Writing Tool, based on the feedback we received from our users. Now, we are delighted to announce that we are back with a fresh batch of updates.
We have become faster. ARPHA has been optimised, so that it is even easier to prepare your manuscript. Enjoy your references and whole datasets being delivered straight into your draft in the blink of an eye!
Speaking of references, we have updated our Reference Parser. Simply copy-paste a reference in the box and click Parse – ARPHA Writing Tool will have it ready to go on your list momentarily!
Yet, there’s even more to the reference-related updates! To double-check an in-text citation in your manuscript, all you need to do is hover over it to see the full-text reference it is linked to.
Our new toolbar and re-arranged functionalities make up for the better intuitivity of the ARPHA Writing Tool that welcomes you the moment you open a new manuscript.
Hover over the new toolbar and you will notice another new perk we have added for your convenience. Keyboard shortcuts are now implemented to the ARPHA Writing Tool to let you add smart objects as you type.
Get a stronger grip on your figures! Two new buttons let you re-order your figures either by number, or by order of appearance. Alternatively, enter editing mode and simply drag and drop any figure wherever you wish.
We thank you for your continuous feedback which helps us focus on tailoring the ARPHA Writing Tool according to the needs and taste of our clients.
We are already working hard on the next updates, so keep an eye on us!
In the meantime, please feel welcome to test our new features and let us know what you think. We will be happy to address any comments and requests on email@example.com.