BiCIKL Project supports article collection in Biodiversity Data Journal about use of linked data

Welcomed are taxonomic and other biodiversity-related research articles, which demonstrate the advantages and novel approaches in accessing and (re-)using linked biodiversity data.

The EU-funded project BiCIKL (Biodiversity Community Integrated Knowledge Library) will support free of charge publications submitted to the dedicated topical collection: “Linking FAIR biodiversity data through publications: The BiCIKL approach” in the Biodiversity Data Journal, demonstrating advanced publishing methods of linked biodiversity data, so that they can be easily harvested, distributed and re-used to generate new knowledge. 

BiCIKL is dedicated to building a new community of key research infrastructures, researchers and citizen scientists by using linked FAIR biodiversity data at all stages of the research lifecycle, from specimens through sequencing, imaging, identification of taxa, etc. to final publication in novel, re-usable, human-readable and machine-interpretable scholarly articles.

Achieving a culture change in how biodiversity data are being identified, linked, integrated and re-used is the mission of the BiCIKL consortium. By doing so, BiCIKL is to help increase the transparency, trustworthiness and efficiency of the entire research ecosystem.


The new article collection welcomes taxonomic and other biodiversity-related research articles, data papers, software descriptions, and methodological/theoretical papers. These should demonstrate the advantages and novel approaches in accessing and (re-)using linked biodiversity data.

In a cover letter to the manuscript submitted to this collection, the authors will need to confirm that their manuscripts comply with the requirements and expectations of the BiCIKL project, which are briefly outlined below.

Likewise, they will need to abide by the community-agreed standards for terms, ontologies and vocabularies used in biodiversity informatics. 


Here are several examples of research questions that might be explored using semantically enriched and linked biodiversity data: 

(1) How does linking taxon names or Operational Taxonomic Units (OTUs) to related external data (e.g. specimen records, sequences, distributions, ecological & bionomic traits, images) contribute to a better understanding of the functions and regional/local processes within faunas/floras/mycotas or biotic communities?

(2) How could the production and publication of taxon descriptions and inventories – including those based mostly on genomic and barcoding data – be streamlined? 

(3) How could general conclusions, assertions and citations in biodiversity articles be expressed in formal, machine-actionable language, either to update prior work or express new facts (e.g. via nanopublications)? 

(4) How could research data and narratives be re-used to support more extensive and data-rich studies? 

(5) Are there other taxon- or topic-specific research questions that would benefit from richer, semantically enhanced FAIR biodiversity data?


All manuscripts submitted to the Biodiversity Data Journal have their data audited by data scientists prior to the peer review stage.

Once published, specimen records data are being exported in Darwin Core Archive to GBIF.

The data and taxon treatments are also exported to several additional data aggregators, such as TreatmentBank, the Biodiversity Literature Repository, and SiBILS amongst others. The full-text articles are also converted to Linked Open Data indexed in the OpenBiodiv Knowledge Graph.


Conditions for publication in the article collection:

  • The authors are expected to use explicit Globally Unique Persistent and Resolvable Identifiers (GUPRI) or other persistent identifiers (PIDs), where such are available, for the different types of data they use and/or cite in the manuscripts (specimens IDs, sequence accession numbers, taxon name and taxon treatment IDs, image IDs, etc.)

  • Global taxon reviews in the form of “cyber-catalogues” are welcome if they contain links of the key data elements (specimens, sequences, taxon names, taxon treatments, images, literature references, etc.) to their respective records in external repositories.

  • Taxonomic papers (e.g. descriptions of new species or revisions) must contain persistent identifiers for the holotype, paratypes and at least most of the specimens used in the study.

  • Specimen records that are used for new taxon descriptions or taxonomic revisions and are associated with a particular Barcode Identification Number (BIN) or Species Hypothesis (SH) should be imported directly from BOLD or PlutoF, respectively, via the ARPHA Writing Tool data-import plugin.

  • More generally, individual specimen records used for various purposes in taxonomic descriptions and inventories should be imported directly into the manuscript from GBIF, iDigBio, or BOLD via the ARPHA Writing Tool data-import plugin. 

  • In-text citations of taxon treatments from Plazi’s TreatmentBank are highly welcome in any taxonomic revision. The in-text citations should be hyperlinked to the original treatment data at TreatmentBank.

  • Hyperlinking other terms of importance in the article text to their original external data sources or external vocabularies is encouraged.

  • Tables that list gene accession numbers, specimens and taxon names, should conform to the Biodiversity Data Journal’s linked data tables guidelines.

  • Theoretical or methodological papers on linking FAIR biodiversity data are eligible for the BiCIKL collection if they provide real examples and use cases.

  • Data papers or software descriptions are eligible if they use linked data from the BiCIKL’s partnering research infrastructures, or describe tools and services that facilitate access to and linking between FAIR biodiversity data.

  • Manuscripts that contain or describe any other novel idea or feature related to linked or semantically enhanced biodiversity data will be considered too.

We recommend authors to get acquainted with these two papers before they decide to submit a manuscript to the collection: 


The articles will be published for free.

All articles will need to acknowledge the BiCIKL project, Grant No 101007492 in the Acknowledgements section.

The submission deadline is 31st December 2023.

Follow the BiCIKL Project on Twitter and Facebook. Join the conservation on via #BiCIKL_H2020.

You can also follow Biodiversity Data Journal on Twitter and Facebook.

BiCIKL keeps on adding project outcomes in own collection in RIO Journal

The publications so far include the grant proposal; conference abstracts, a workshop report, guidelines papers and deliverables submitted to the Commission.

The dynamic open-science project collection of BiCIKL, titled “Towards interlinked FAIR biodiversity knowledge: The BiCIKL perspective” (doi: 10.3897/rio.coll.105), continues to grow, as the project progresses into its third year and its results accumulate ever so exponentially. 

Following the publication of three important BiCIKL deliverables: the project’s Data Management Plan, its Visual identity package and a report, describing the newly built workflow and tools for data extraction, conversion and indexing and the user applications from OpenBiodiv, there are currently 30 research outcomes in the BiCIKL collection that have been shared publicly to the world, rather than merely submitted to the European Commission.

Shortly after the BiCIKL project started in 2021, a project-branded collection was launched in the open-science scholarly journal Research Ideas and Outcomes (RIO). There, the partners have been publishing – and thus preserving – conclusive research papers, as well as early and interim scientific outputs.

The publications so far also include the BiCIKL grant proposal, which earned the support of the European Commission in 2021; conference abstracts, submitted by the partners to two consecutive TDWG conferences; a project report that summarises recommendations on interoperability among infrastructures, as concluded from a hackathon organised by BiCIKL; and two Guidelines papers, aiming to trigger a culture change in the way data is shared, used and reused in the biodiversity field. 

In fact, one of the Guidelines papers, where representatives of the Consortium of European Taxonomic Facilities (CETAF), the Society for the Preservation of Natural History Collections (SPNHC) and the Biodiversity Heritage Library (BHL) came together to publish their joint statement on best practices for the citation of authorities of scientific names, has so far generated about 4,000 views by nearly 3,000 unique readers.

At the time of writing, the top three of the most read papers in the BiCIKL collection is completed by the grant proposal and the second Guidelines paper, where the partners – based on their extensive and versatile experience – present recommendations about the use of annotations and persistent identifiers in taxonomy and biodiversity publishing. 

Access to data and services along the entire data and research life cycle in biodiversity science.
The figure was featured in the BiCIKL grant proposal, now made available from the BiCIKL project collection in RIO Journal.

What one might find quite odd when browsing the BiCIKL collection is that each publication is marked with its own publication source, even though all contributions are clearly already accessible from RIO Journal

So, we can see many project outputs marked as RIO publications, but also others that have been published in the likes of F1000Research, the official journal of TDWG: Biodiversity Information Science and Standards, and even preprints servers, such as BiohackrXiv

This is because one of the unique features of RIO allows for consortia to use their project collection as a one-stop access point for all scientific results, regardless of their publication venue, by means of linking to the original source via metadata. Additionally, projects may also upload their documents in their original format and layout, thanks to the integration between RIO and ARPHA Preprints. This is in fact how BiCIKL chose to share their latest deliverables using the very same files they submitted to the Commission.

“In line with the mission of BiCIKL and our consortium’s dedication to FAIRness in science, we wanted to keep our project’s progress and results fully transparent and easily accessible and reusable to anyone, anywhere,” 

explains Prof Lyubomir Penev, BiCIKL’s Project Coordinator and founder and CEO of Pensoft. 

“This is why we opted to collate the outcomes of BiCIKL in one place – starting from the grant proposal itself, and then progressively adding workshop reports, recommendations, research papers and what not. By the time BiCIKL concludes, not only will we be ready to refer back to any step along the way that we have just walked together, but also rest assured that what we have achieved and learnt remains at the fingertips of those we have done it for and those who come after them,” he adds.

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You can keep tabs on the BiCIKL project collection in RIO Journal by subscribing to the journal newsletter or following @RIOJournal on Twitter and Facebook.

Boosting the reproducibility of research: Pensoft joins the EU-funded project TIER2

As an experienced science communicator and open-science publisher, Pensoft is joining this promising project on its mission within its acronym: Trust, Integrity, and Efficiency in Research, through next-level Reproducibility

Recent years have seen perceptions of a “reproducibility crisis” grow in various disciplines. Scientists see poor levels of reproducibility as a severe threat to scientific self-correction, the efficiency of research processes, and societal trust in research results. 

Now, a newly launched Horizon Europe-funded project: TIER2 brings together 10 major European organisations and proponents of open science to dig deeper into the issues surrounding reproducibility in research work with the aim to improve practices and policies across diverse scientific fields. 

In its capacity as an experienced science communicator and open-science publisher, Pensoft is joining this promising project on its mission within its acronym: Trust, Integrity, and Efficiency in Research, through next-level Reproducibility (TIER2).

TIER2’s interdisciplinary, expert project team will use co-creative methods to work with researchers in social, life and computer sciences, research funders, and publishers to further understand and address the causes of poor reproducibility. 

The project will produce and test new tools, connect initiatives, engage communities, and test novel interventions to increase reuse and overall quality of research results. 

“It is very exciting to take part in such significant work for the benefit of scientific rigor and integrity. As an open-access publisher, the goals of Pensoft and TIER2 are very much aligned – increasing the trust and efficiency of the research apparatus on a large scale. We are looking forward to collaborating on this mutual goal.”

said Teodor Metodiev, TIER2 Principal Investigator for Pensoft.
The project

TIER2 launched in early January 2023 and will be running until December 2025 with the support of EUR 2 millions in funding, provided by the European Union’s Horizon Europe program and the United Kingdom’s Research & Innovation

TIER2 will study reproducibility in diverse contexts by selecting three broad research areas (i.e. social, life and computer sciences) and two cross-disciplinary stakeholder groups (i.e. research publishers and funders). Reaching different contexts will allow the project team to systematically investigate the causes and implications of the lack of reproducibility across the research spectrum. Together with curated co-creation communities of these groups, the project will design, implement, and assess systematic interventions – addressing critical levers of change (tools, skills, communities, incentives, and policies) in the process.

In 3 years’ time, TIER2-led activities will have significantly boosted knowledge on reproducibility, created valuable tools, engaged communities, and implemented interventions and policies across science. As a result, the reuse of resources and the quality of research results in the European research landscape and beyond will be improved and increased, and so will trust, integrity, and efficiency in research overall.

You can read more about the project’s plans, rationale and mission in the full project proposal, recently published in the open-science journal Research Ideas and Outcomes (RIO).

You can also browse the project’s website at https://tier2-project.eu/.

The website – including its design and software development – is itself one of Pensoft’s communication contributions to TIER2.

Stay up to date with the project’s activities and progress on Twitter: @TIER2Project.

International consortium

The interdisciplinary TIER2 consortium comprises ten members from universities and research centers across Europe to bring together a range of expertise spanning open science, research integrity, AI, data analytics, policy research, science infrastructures, stakeholder engagement, and core knowledge in social, life, and computational sciences. They share a long history of successful cooperation and have extensive experience in completed EU projects, especially in the fields of Open Science, Research Integrity, and Science Policy.

Full list of partners:
  1. Know Center
  2. Athena Research Center
  3. Amsterdam University Medical Center
  4. Aarhus University 
  5. Pensoft Publishers
  6. GESIS Leibniz Institute for the Social Sciences 
  7. OpenAIRE
  8. Charité – University of Medicine Berlin
  9. Oxford University
  10. Alexander Fleming Biomedical Sciences Research Center

Pensoft among the first 27 publishers to share prices & services via the Journal Comparison Service by Plan S

All journals published by Pensoft – each using the publisher’s self-developed ARPHA Platform – provide extensive and transparent information about their costs and services in line with the Plan S principles.

In support of transparency and openness in scholarly publishing and academia, the scientific publisher and technology provider Pensoft joined the Journal Comparison Service (JCS) initiative by cOAlition S, an alliance of national funders and charitable bodies working to increase the volume of free-to-read research. 

As a result, all journals published by Pensoft – each using the publisher’s self-developed ARPHA Platform – provide extensive and transparent information about their costs and services in line with the Plan S principles.

The JCS was launched to aid libraries and library consortia – the ones negotiating and participating in Open Access agreements with publishers – by providing them with everything they need to know in order to determine whether the prices charged by a certain journal are fair and corresponding to the quality of the service. 

According to cOAlition S, an increasing number of libraries and library consortia from Europe, Africa, North America, and Australia have registered with the JCS over the past year since the launch of the portal in September 2021.

While access to the JCS is only open to librarians, individual researchers may also make use of the data provided by the participating publishers and their journals. 

This is possible through an integration with the Journal Checker Tool, where researchers can simply enter the name of the journal of interest, their funder and affiliation (if applicable) to check whether the scholarly outlet complies with the Open Access policy of the author’s funder. A full list of all academic titles that provide data to the JCS is also publicly available. By being on the list means a journal and its publisher do not only support cOAlition S, but they also demonstrate that they stand for openness and transparency in scholarly publishing.

“We are delighted that Pensoft, along with a number of other publishers, have shared their price and service data through the Journal Comparison Service. Not only are such publishers demonstrating their commitment to open business models and cultures but are also helping to build understanding and trust within the research community.”

said Robert Kiley, Head of Strategy at cOAlition S. 

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About cOAlition S:

On 4 September 2018, a group of national research funding organisations, with the support of the European Commission and the European Research Council (ERC), announced the launch of cOAlition S, an initiative to make full and immediate Open Access to research publications a reality. It is built around Plan S, which consists of one target and 10 principles. Read more on the cOAlition S website.

About Plan S:

Plan S is an initiative for Open Access publishing that was launched in September 2018. The plan is supported by cOAlition S, an international consortium of research funding and performing organisations. Plan S requires that, from 2021, scientific publications that result from research funded by public grants must be published in compliant Open Access journals or platforms. Read more on the cOAlition S website.

New BiCIKL project to build a freeway between pieces of biodiversity knowledge

Within Biodiversity Community Integrated Knowledge Library (BiCIKL), 14 key research and natural history institutions commit to link infrastructures and technologies to provide flawless access to biodiversity data.

In a recently started Horizon 2020-funded project, 14 European institutions from 10 countries, representing both the continent’s and global key players in biodiversity research and natural history, deploy and improve their own and partnering infrastructures to bridge gaps between each other’s biodiversity data types and classes. By linking their technologies, they are set to provide flawless access to data across all stages of the research cycle.

Three years in, BiCIKL (abbreviation for Biodiversity Community Integrated Knowledge Library) will have created the first-of-its-kind Biodiversity Knowledge Hub, where a researcher will be able to retrieve a full set of linked and open biodiversity data, thereby accessing the complete story behind an organism of interest: its name, genetics, occurrences, natural history, as well as authors and publications mentioning any of those.

Ultimately, the project’s products will solidify Open Science and FAIR (Findable, Accessible, Interoperable and Reusable) data practices by empowering and streamlining biodiversity research.

Together, the project partners will redesign the way biodiversity data is found, linked, integrated and re-used across the research cycle. By the end of the project, BiCIKL will provide the community with a more transparent, trustworthy and efficient highly automated research ecosystem, allowing for scientists to access, explore and put into further use a wide range of data with only a few clicks.

“In recent years, we’ve made huge progress on how biodiversity data is located, accessed, shared, extracted and preserved, thanks to a vast array of digital platforms, tools and projects looking after the different types of data, such as natural history specimens, species descriptions, images, occurrence records and genomics data, to name a few. However, we’re still missing an interconnected and user-friendly environment to pull all those pieces of knowledge together. Within BiCIKL, we all agree that it’s only after we puzzle out how to best bridge our existing infrastructures and the information they are continuously sourcing that future researchers will be able to realise their full potential,” 

explains BiCIKL’s project coordinator Prof. Lyubomir Penev, CEO and founder of Pensoft, a scholarly publisher and technology provider company.

Continuously fed with data sourced by the partnering institutions and their infrastructures, BiCIKL’s key final output: the Biodiversity Knowledge Hub, is set to persist with time long after the project has concluded. On the contrary, by accelerating biodiversity research that builds on – rather than duplicates – existing knowledge, it will in fact be providing access to exponentially growing contextualised biodiversity data.

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Learn more about BiCIKL on the project’s website at: bicikl-project.eu

Follow BiCIKL Project on Twitter and Facebook. Join the conversation on Twitter at #BiCIKL_H2020.

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The project partners:

Call for research outcomes addressing four UN Sustainable Development Goals in RIO Journal

Eligible submissions enjoy a 50% discount off APCs in 2021

Since its launch in 2015, RIO Journal has been mapping its articles to the Sustainable Development Goals (SDGs) of the United Nations. The articles published so far span the entire research cycle, a broad range of research fields and all SDGs, which can also be used as a search filter. However, the distribution of RIO articles across SDGs is uneven, as detailed in a recent editorial: for instance, more than 100 articles addressed SDG9 (Industry, innovation & infrastructure), while only one publication has been mapped to SDG1 (No poverty) so far.

Even though there might be logical explanations for this phenomenon, including funding biases or specific scholarly communication tendencies in some research fields, RIO’s team remains dedicated to its role as a harbinger of innovative open science practices and socially engaged research, and is eager to support the open publication of research on all SDGs.

So, RIO Journal is now inviting research outcomes – early, interim or final – addressing the four least represented SDGs in RIO’s content to date (with the current number indicated in parentheses):

  • SDG1: No poverty (1)
  • SDG7: Affordable & clean energy (2)
  • SDG5: Gender equality (4)
  • SDG2: Zero hunger (4)
All publications in RIO Journal are mapped to one or more SDGs.

The call will remain open until the end of 2021, where all accepted papers will enjoy a 50% discount on their publication charges (APCs), regardless of how many contributions RIO receives in the meantime. Eligible submissions encompass all article types generally accepted in RIO, as long as the journal’s editorial team confirms that they belong to the assigned SDG category.

As also highlighted in the editorial, RIO is currently experimenting with a more fine-grained mapping of its publications to the individual targets under each SDG. This was piloted with SDG 14 (Life below water). For instance, Target 14.a (Marine Biodiversity contributes to Economic Development of small/developing nations) is currently covered by 17 RIO articles. If you would like to get involved with mapping RIO articles to the Targets under other SDGs, please get in touch.

You can find more about RIO’s rationale behind introducing the SDGs mapping in the latest editorial or in this earlier blog post.

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Follow RIO Journal on Twitter, Facebook and LinkedIn.

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Further reading:

RIO Journal 5 years on: over 300 published outcomes from all around the research cycle

Five years on, the Open Science-driven journal Research Ideas and Outcomes (RIO) published an editorial that looks back on the 300 research ideas and research outcomes it has published so far.

Since its early days, RIO has enjoyed quite positive reactions from the open-minded academic community for its innovative approach to Open Science in practice: it provides a niche that had long been missing, namely the publication of early, intermediate and generally unconventional research outcomes from all around the research cycle (e.g. grant proposals, data management plans, project deliverables, reports, policy briefs, conference materials) in a cross-disciplinary scientific journal. In fact, several months after its launch, in 2016, the journal was acknowledged with the SPARC Innovator Award.

‘Alternative’ research publications

In times when posting a preprint was seen as a novel and rather bold practice across many fields, RIO facilitated much deeper dives into the research process, in order to unveil scientific knowledge and the process by which it is gathered, well before any final conclusions have been drawn. Long story short, to date, RIO has published 33 Research Ideas78 Grant Proposals16 Data Management Plans33 Workshop Reports and 5 PhD Project Plans, in addition to plenty of other early, interim and final non-traditional research outcomes, as well as conventional articles. Over time, RIO has kept adding additional article types to its list of publication types, with a few more expected in the near future.

What’s more, over the years, we’ve already observed how papers published in RIO successfully followed up on the continuity of the research process. For example, the Grant Proposal for the “Exploring the opportunities and challenges of implementing open research strategies within development institutions” project, funded by the International Development Research Centre (IDRC), was followed by the project’s Data Management Plan a year later.

Five years later, the figures reflecting the usage and engagement with the content published in RIO are evidently supportive of the value of having non-final and unconventional academic publications. For instance, the Grant Proposal for the COST Action DNAqua-Net, a still ongoing project dedicated to the development of novel genetic tools for bioassessment and monitoring of aquatic ecosystems, is the article with the most total views in RIO’s publication record to date. In the category of sub-article elements, whose usage is also tracked at the journal, the most viewed figure belongs to a Project Report and illustrates a sample code meant to be used in future neuroimaging studies. Similarly, the most viewed table ever published in RIO is part of a Workshop Report that summarises ASAPbio‘s third workshop, dedicated to the technical aspects of services related to the promotion of preprints in the biomedical and other life science communities.

Response to societal challenges

A unique and defining staple for RIO since the very beginning has also been the pronounced engagement with the Sustainable Development Goals (SDGs), as formulated by the United Nations right around the time of RIO’s launch. In order to highlight the societal impact of published research, RIO lets authors map their articles to the SDGs relevant to their paper. Once published, the article displays the associated badge(s) next to its title. Readers of the journal can even search RIO’s content by SDG, in the same way they would filter articles by subject, publication types, date or funding agency. Next on the list for RIO is to add another level of granularity to the SDGs mapping. The practice has already been piloted by mapping relevant RIO articles to the ten targets under SDG14 (Life below water).

Taking transparency, responsibility and collaboration in academia and scholarly publishing up another notch, RIO requires for reviews to be publicly available. In addition, the journal supports post-publication reviews, where peers are free to post their review anytime. In turn, RIO registers each review with its own DOI via CrossRef, in order to recognise the valuable input and let the reviewers easily refer to their contributions. A fine example is a Review Article exploring the biodiversity-related issues and challenges across Southeast Asia, which currently has a total of three public peer reviews, one of which is provided two years after the publication of the paper.

Public, transparent and perpetual peer review, pre- and/or post-publication

What’s more striking about peer review at RIO, however, is that it is not always mandatory. Given that the journal publishes many article types that have already been scrutinised by a legitimate authority – for instance, Grant Proposals that have previously been evaluated by a funder or defended PhD Theses – it only makes sense to avoid withholding these publications and duplicating associated evaluation efforts. On such occasions, all an author needs to do is provide a statement about the review status of their paper, which will be made public alongside the article.

On the other hand, where the article type of a manuscript requires pre-publication review, to avoid potential delays caused by the review process and editorial decisions, RIO encourages the authors to post their pre-review manuscript as a preprint on the recently launched ARPHA Preprints platform, subject to a quick editorial screening, which would only take a few days.

Further, RIO has now abandoned the practice of burdening the journal’s editors with the time-consuming task of finding reviewers, and instead requiring the submitting author to invite suitable reviewers upon submission, who are then immediately and automatically invited by the system. While significantly expediting the editorial work on a manuscript, this practice doesn’t compromise the quality of peer review in the slightest, since the reviews go public, while the final decision about the acceptance of the paper lies with the editor, who is also overlooking the process and able to intervene and invite additional reviewers anytime, if necessary.

Project-driven knowledge hub

The most significant novelty at RIO, however, is perhaps the newly assumed role of the journal as “a project-driven knowledge hub“, targeting specifically the needs of research projects, conference organisers and institutions. For them, RIO provides a one-stop source for the outputs of their scientists, in order to comply with the requirements of their funders or management, or simply to facilitate the discoverability, reusability and citability of their academic outputs and to highlight their interconnectedness.

Unlike typical permanent article collections, already widely used in scholarly publishing, with RIO, collection owners can take advantage of the unique opportunity to add a wide range of research outputs, including such published elsewhere, in order to provide even greater context to the assembled research outputs in their project- or institution-branded article collection (see the Horizon 2020 Project Path2Integrity‘s project collection as an example).

A permanent topical collection in RIO Journal may include a diverse range of both traditional and unconventional research outputs, as well as links to publications from outside the journal (see What can I publish on the journal’s website). 

For example, a project coordinator could open a collection under the brand of the project, and start by publishing the Grant Proposal, followed shortly by Data and Software Management Plans and Workshop Reports. Thus, even at this early point in the project’s development, the funder – and with them everyone else – would already have strong evidence of the project’s dedication to transparency and active science communication. Later on, the project’s participants would all be able to easily add to the project’s collection by either submitting their diverse research outputs straight to RIO and having it accepted by the collection lead editor, or providing metadata and link to their publication from elsewhere, even preprints. If the document is published outside of RIO, its metadata, i.e. author names and affiliations, article title and publication date, show up in the collection, while a click on the item will lead to the original publication. As the project progresses, the team behind it could add more and more outputs (e.g. Project Reports, Guidelines and Policy Briefs), continuously updating the public and the relevant stakeholders about the development of their work. Eventually, the collection will be able to provide a comprehensive and fully transparent report of the project from start to finish.

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Follow RIO Journal on TwitterFacebook and LinkedIn.

Centrally-managed collections & Peer review flexibility at RIO

RIO updated its article collection approach to evolve into a “project-driven knowledge hub”, where a project coordinator, institution or conference organiser can create and centrally manage a collection under their own logo.

In 2015, Research Ideas and Outcomes (RIO) was launched to streamline dissemination of scientific knowledge throughout the research process, recognised to begin with the inception of a research idea, followed by the submission of a grant proposal and progressing to, for example, data / software management plans and mid-stage project reports, before concluding with the well-known research and review paper.


In order to really expedite and facilitate access to scientific knowledge, the hurdles for engagement with the process need to be minimized for readers, authors, reviewers and editors alike. RIO aims to lay the groundwork for constructive scientific feedback and dialogue that would then lead to the elaboration and refinement of the research work well in its early stage. 

Recently, RIO published its 300th article – about a software for analyzing time series data from a microclimate research site in the Alps – and at that occasion, the RIO team wrote an editorial summarizing how the articles published in RIO so far facilitate engagement with the respective research processes. One of the observations in this regard was that while providing access to the various stages of the research cycle is necessary for meaningful engagement, there is a need for the various outcomes to be packed together, so that we can provide a more complete context for individual published outcomes.

Read the new editorial celebrating RIO’s 5th anniversary and looking back on 300 publications. 

RIO introduced updates to its article collection approach to evolve into a “project-driven knowledge hub”, where a project coordinator, research institution or conference organiser can create and centrally manage a collection under their own logo, so that authors can much more easily contribute. Further, research outputs published elsewhere – including preprints – are also allowed, so that the collection displays each part of the ‘puzzle’ within its context. In this case, the metadata of the paper, i.e. title, authors and publication date, are displayed in the article list within the collection, and link to the original source.

Apart from allowing the inclusion of the whole diversity of research outcomes published in RIO or elsewhere, what particularly appeals to projects, conferences and institutions is the simplicity of opening and managing a self-branded collection at RIO. All they need to do is pay a one-time fee to cover the setup and maintenance of the collection, whereas an option with an unlimited number of publications is also available. Then, authors can add their work – subject to approval by the collection’s editor and the journal’s editorial office – by either starting a new manuscript at RIO and then assigning it to an existing collection; pasting the DOI of a publication available from elsewhere; or posting an author-formatted PDF document to ARPHA Preprints, as it has been submitted to the external evaluator (e.g. funding agency). In the latter two cases, the authors are charged nothing, in order to support greater transparency and contextuality within the research process.

Buttons on RIO Journal’s homepage allow users to create a new collection or add a document to an existing collection by either submitting a new manuscript via RIO Journal or pasting a DOI link of a publication from elsewhere, thus allowing for the collection to link to the original source and display the article’s metadata, i.e. title, authors and publication date.

Find more information about how to edit a collection at RIO and the associated benefits and responsibilities on RIO’s website.

Another thing we have revised at RIO is the peer review policy and workflow, which are now further clarified and tailored to the specificity of each type of research outcome.

Having moved to entirely author-initiated peer review, where the system automatically invites reviewers suggested by the author upon submission of a paper, RIO has also clearly defined which article types are subject to mandatory pre-publication peer review or not (see the full list). In the latter case, RIO no longer prompts the invitation of reviewers. Within their collections, owners and guest editors can decide on the peer review mode, guided by RIO’s existing policies.

While pre-publication peer review is not always mandatory, all papers are subject to editorial evaluation and also remain available in perpetuity for post-submission review. In both cases, reviews are public and disclose the name of their author by default. In turn, RIO registers each review with its own DOI via CrossRef, in order to recognise the valuable input and let the reviewers easily refer to their contributions. 

Both pre- and post-publication reviews at RIO are openly published alongside the paper and bear their own DOI. All papers in RIO remain available for post-publication review in perpetuity (see example).

For article types where peer review is mandatory (e.g. Research Idea, Review article, Research Article, Data Paper), authors are requested to invite a minimum of three suitable reviewers upon the submission of the paper, who are then automatically invited by the system. While significantly expediting the editorial work on a manuscript, this practice doesn’t compromise the quality of peer review in the slightest, since the editor is still overlooking the process and able to invite additional reviewers anytime, if necessary. 

For article types where peer review is not mandatory (e.g. Grant Proposal, Data Management Plan, Project Report and various conference materials), all an author needs to do is provide a statement about the review status of their paper, which will be made public alongside the article. Given that such papers have usually already been scrutinised by a legitimate authority (e.g. funding agency or conference committee), it only makes sense to not withhold their publication and duplicate academic efforts.

By the time it is submitted to RIO, a Grant Proposal like this one has often already been assessed by a legitimate funder, so it only makes sense to not undergo the process again at RIO and thereby slowing down its public dissemination.

Additionally, where the article type of a manuscript requires pre-publication review, RIO encourages the authors to click a checkbox during the submission and post their pre-review manuscript as a preprint on ARPHA Preprints, subject to a quick editorial screening, which would only take a few days.

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Further reading:

RIO shifts gears to serve as project-driven knowledge hub

Research Ideas and Outcomes (RIO Journal) upgrades its unique concept to appeal to scientific projects, conference organisers and research institutions

Research Ideas and Outcomes (RIO Journal) upgrades its unique concept to appeal to scientific projects, conference organisers and research institutions

Over the last few years, we’ve been increasingly observing how major funders of research around the world, including the likes of the European Commission, Wellcome, U.S. National Institutes of Health (NIH), Deutsche Forschungsgemeinschaft (DFG) and the Japan Society for the Promotion of Science (JSPS) recognise the research cycle as a continuum, rather than scattered standalone conclusions and reports. 

Hence, as a forward-looking, open science-driven journal Research Ideas and Outcomes (RIO) took it as its own responsibility to encourage scientific project teams, conference organisers and research institutions to bring together unconventional research outputs (e.g. grant proposals, data management plans, project deliverables, policy briefs, conference materials) as well as traditional (e.g. research or review papers, monographs, etc.), including such published elsewhere. To do so, RIO now provides the platform ready to be used as a research knowledge hub, where published outcomes are preserved permanently and easier to share, disseminate, reference and reuse.

Hence, RIO stepped up its game by turning permanent article collections into a one-stop source of diverse research items, where project coordinators, conference organisers or research institutions can not only publish early, interim and conclusive research items as they emerge within a research project, a series of events or the continuous scientific efforts at their lab, but also link relevant publications (i.e. preprints, articles or other documents, published elsewhere) available elsewhere through their metadata. As a result, they will receive a one-stop source under their own branding for every piece of scientific contribution ready to present to funding bodies or prospective collaborators and future research teams.

A permanent topical collection in RIO Journal may include a diverse range of both traditional and unconventional research outputs, as well as links to publications from outside the journal (see What can I publish on the journal’s website). 

Apart from bringing contextually linked research outcomes together, thus prompting findability, readership and citability en masse, RIO’s approach to collections ensures further accessibility by not only having RIO-published articles available in traditional PDF, semantically enriched HTML and minable XML format. The open-science journal has now made it possible for users to add to their collections preprints from ARPHA Preprints, as well as author-formatted PDFs (e.g. project deliverables, reports, policy briefs, etc.) and linked metadata to documents published elsewhere. Thanks to the integration of the journal with the general-purpose open-access repository Zenodo, all items in a collection are archived, and additionally indexed, disseminated and cited.

By focusing on article and preprint collections coming out from a research project, institution or conference, RIO provides a quite specific and unique combination of benefits to all actors of the research process: scientists, project coordinators, funders and institutions: 

  1. Project, institution or conference branding and promotion.
  2. One-stop point for outputs of a research project, institution or conference.
  3. Free publication of author-formatted project outputs (i.e. grant proposals, deliverables, reports, policy briefs, conference materials and others).
  4. Inclusivity through adding articles, preprints and other documents published elsewhere as easy as entering the DOI number of the document.
  5. Credit and recognition for the Collection and Guest editors, who take care to organise and manage the article collection.
  6. Easier discoverability and usability of topically related studies to benefit both authors and readers.
  7. Increased visibility of related papers in a collection, even when these might otherwise not have much exposure.
  8. Simultaneous citation of multiple articles related to a certain subject.
  9. Citation and referencing of the whole collection as a complete entity.
  10.  DOI and citation details for collections and individual articles.

Furthermore, RIO Journal maps all publications to the Sustainable Development Goals  (SDGs), in order to emphasise the real-world impact of each published contribution, by displaying the corresponding badge within the article list. 

Last, but not least, both collections and individual publications in RIO enjoy the variety of default and on-demand science communication services, provided by Pensoft.  

How do project coordinators, funders and institutions benefit from a collection in RIO?

At the time a grant proposal is submitted to a research funder for evaluation, the team behind the proposed project has already put in considerable efforts, resulting in a unique idea with the potential to make a great stride towards the resolution of an outstanding problem in science, if only given the chance. However, too many of these ideas are bound to remain locked away in the archives of those funders, not because they are lacking in scientific value, but due to limited funds.

So, with its launch back in 2015, RIO Journal made it possible to publish and shed light on grant proposals and research ideas in general, similar early research outputs regardless of whether they are eventually funded or not, a novelty in scholarly publishing which earned RIO the SPARC Innovator Award Winner in 2016. To date, the journal has already published 75 grant proposals

Then, imagine what a contribution to science it would make to bring together the whole continuum of knowledge and scientific work all the way from the grant proposal to data  and software management plans, workshop reports, policy briefs and all interim and final deliverables produced within the span of the project!

On the other hand, funders are increasingly evaluating a prospective project’s impact based on its communication strategy. So, why not publish a grant proposal at the time of the submission of your proposal, in order to prove to the funding body that your project is serious about optimising its outreach to both the public and academia? Furthermore, by having an academic journal host any subsequent project deliverable, as a coordinator, you can rest assured that the communication activities of your project remain consistent and efficient.

In an excellent example of a project collection, the EU-funded ICEDIG (Innovation and Consolidation for Large Scale Digitisation of Natural Heritage), led by several major natural history institutions, including the Natural History Museum of London, Naturalis Biodiversity Center (the Netherlands), the French National Museum of Natural History and Helsinki University, brought together policy briefs, project reports, research articles and review papers, in order to provide a fantastic overview of their own research continuum. As a result, future researchers and various stakeholders can easily piece together the key components within the project, in order to learn from, recreate or even build on the experience of ICEDIG.

The Path2Integrity Project Outcomes collection demonstrates how research papers published elsewhere are featured in RIO Journal.

Similarly, conference organisers can make use of their own branded collections to overcome the ephemerality of presented research by collating virtually all valuable conference outputs, including abstracts, posters, presentations, datasets and full-text conference talks. For further convenience, a collection can be divided into subcollections, in order to organise the contribution by type or symposium. What particularly appeals to conference participants is the ARPHA Writing Tool, an intuitive collaborative online environment, which practically guides the user through each step: authoring, submission and pre-submission review, within a set of pre-designed, yet flexible templates available for each type of a conference output, thus sparing them the hassle to familiarise themselves with specific and perplexing formatting requirements

For institutions, RIO offers the opportunity to continuously provide evidence of the scholarly impact of their organisation. To better serve the needs of different labs or research teams, an institution can easily organise their outputs into various subcollections, and also customise their own article types, as well as the available usage tracking systems. Furthermore, by making use of the available pre-paid plans, institutions can support their researchers by covering fully or partially the publication charges at a discounted rate.

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Find more information regarding the submission and review process, policies and pricing, visit RIO Journal’s website.

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Making the most of conferences with modern publishing and indexing practices

Given scientific conferences present academics with the fantastic opportunity to meet up and discuss their latest work, as well as share their vision for the future of their field, it’s no wonder that, historically, the majority of ground-breaking science can easily be traced back to a particular event.

This said, don’t you think that we need to do everything within our powers to ensure the visibility, dissemination and long-term accessibility of research presented and linked to these wonderful drivers of scientific progress that conferences are? Similarly to the care conference organisers take to make sure the event runs smoothly and the attendants are happy with the programme and enjoy themselves, the organisational committee should also be thinking how to preserve all those promising pieces of research well after the event is over.

Here at Pensoft, an open-access scholarly publisher, founded by scientists, we’ve been contemplating for a while now how to encourage and support the community to efficiently open up the valuable outputs to researchers and readers well beyond the publication of abstracts in an abstract book of the conference. 

As a result, we came up with several simple, yet efficient publishing solutions for scientific conferences to collect and contextualise various research outputs either presented at or resulting from the event.

Bear in mind that with any solution, all publications enjoy the benefits seen in conventional research papers, such as:

  • Crossref registration and individual DOI to ensure preservation;
  • Publication in PDF, semantically enhanced HTML and data-minable XML formats to improve readability, accessibility and findability;
  • Indexing and archiving at multiple, industry leading databases to increase visibility;
  • PR and social media promotion to boost outreach to various audiences.

Collections of conference abstracts, posters and presentations

Conference (video) abstracts, posters and presentations are easily the first to fall victims of the ephemerality of an event, yet these are too often the stepping stones to major scientific discoveries. This is why a few years back we launched ARPHA Conference Abstracts (ACA), where conference organisers can open their own collection and provide the participants with submission, review and publication of their abstracts ahead of the conference.

Furthermore, these abstracts can be handled editorially in sub-collections, e.g. the convenors of symposia or working groups within a conference will take care of the abstracts submitted to them, thus spreading the editorial workload across larger teams of editors and organisers.

Not only will conference organisers spare themselves the worries about providing a special platform for abstracts submissions, but this will also facilitate presenting authors, who will be able to easily point to their contribution before, during or after their presentations. On the contrary, the abstracts are assigned with DOIs, published in human-readable PDF and HTML and machine-actionable JATS XML, permanently preserved on ARPHA and Zenodo, and easy to find, access and cite, just like a conventional research paper, providing authors with full credit for their work early on.

Further, with ACA, the conference abstracts can be enhanced into what we call “extended abstracts”, meaning they can also include data, images, videos and multimedia. After the conferences, we can add video recordings of the presentations or graphic files of posters, so that these are visualised on the page of each abstract.

For example, take a look at the conference abstract collection of the Vth International Congress on Biodiversity: “Taxonomy, Speciation and Euro-Mediterranean Biodiversity”.

Conference proceedings

About the time we launched ACA, we also created ARPHA Proceedings, in order to also find a place for full-text conference papers. Similarly, the platform supports dedicated collections, where conference attendants are invited to submit and publish dynamically articles under the imprint of the event.

Conference papers in ARPHA Proceedings can also include data, figures and citations, and can also be updated with video recordings, posters and presentations following the conference.

Check out an example by the VI International Forum on Teacher Education.

Article topical collections and special issues resulting from conferences

Naturally, papers resulting from a particular conference are contextually linked, so a one-stop place to discover topical studies sharing one and the same topic would be greatly appreciated by readers and future researchers. In turn, this would lead to better viewership and citability of the papers in the collection.

With our user-friendly, dedicated workflow for special issues and permanent topical article collections, we’ve made it easy for guest editors across our journals to pitch and manage article collections, in order to bring together valuable and related studies. Using such a collection under the theme of your conference in a suitable journal, you can invite your conference’s participants or, better yet, all scientists working within the field, to submit their work in a nice package of topical science. We’d be happy to assist you with the identification of the most suitable journal for your conference, authors and goals.

See an example from One Ecosystem and the collection “Mapping and assessment of ecosystem condition and ecosystem services across different scales and domains in Europe”, the result from the “Mapping and assessment of ecosystem services – Science in action” conference, held in 2017.

Bringing together traditional and non-conventional research outputs, (e.g. research ideas, grant proposals, conference materials or workshop reports) with RIO Journal’s article collections

Undoubtedly, valuable research outcomes come in many shapes and sizes well beyond research papers, conference abstracts, posters and proceedings. We are firm supporters that every research item, even early and interim outputs, could be of value to the scientist next in line within a particular study.

This is why we launched the award-winning journal Research Ideas and Outcomes (RIO), where your collections can include both conventional and non-traditional research outputs, such as research ideas, posters, workshop reports, forum papers, policy briefs, software and data management plans to name a few. Furthermore, in RIO, you can even link articles or preprints published elsewhere to your collection via their metadata. Similarly to other Pensoft journals, in RIO, you will have the full control to whom you are opening your collection for submissions, allowing you to either limit it to the outcomes coming from your conference or welcome submissions from other researchers as well.

A permanent topical collection in RIO Journal may include a diverse range of both traditional and unconventional research outputs, as well as links to publications from outside the journal (see What can I publish on the journal’s website). 

See the Brainhack 2016 Project Reports, whose aim is to collate reports from the 2016 Brainhack events. Also, check out the collection of the European Biodiversity Observation Network (EU BON) Project, providing a nice example for a wide range of publication types.

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Don’t hesitate to get in touch to discuss your own case and select the best option for your conference – we’ll be happy to hear from you!

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