Category: Partnering scientific projects

Pensoft joins EU-funded project SOLO, supporting the EU Mission “A Soil Deal for Europe”

Apart from communication, dissemination and data management tasks, within SOLO, Pensoft is also responsible for the development of the key project output: the SOLO platform

The issue at hand

As the foundation of our food systems, healthy soils are essential for life on Earth. They provide clean water and habitats for biodiversity while contributing to climate resilience and support our cultural heritage and landscapes and are the basis of our economy and prosperity.

Soils are under multiple pressures, including climate change, urbanisation, pollution, overexploitation, nutrient mining and biodiversity loss with the European Commission estimating that under current management practices, it’s between 60% and 70% of our soils that are unhealthy.

The ‘deal’ with soils

The EU Mission “A Soil Deal for Europe” aims to address these issues by:

  • funding an ambitious research and innovation programme with a strong social science component;

  •  putting in place an effective network of 100 living labs and lighthouses to co-create knowledge, test solutions and demonstrate their value in real-life conditions;

  • developing a harmonised framework for soil monitoring in Europe;

  •  raising people’s awareness on the vital importance of soils.

Achieving those objectives requires a direct involvement of a wide range of stakeholders, bringing together multiple perspectives in ecological, environmental, economic and social contexts.

The project

SOLO launched in December 2022 and will be running until November 2027 with the support of 5 million euros provided by the European Union’s Horizon Europe program. 

SOLO will identify current knowledge gaps, drivers, bottlenecks, and novel research and innovation approaches to be considered in the European Soil Mission research and innovation roadmap.

The project aims to create a knowledge hub for soil health research and innovation that will last beyond the project’s lifespan by establishing strategic partnerships and by implementing a participatory and transparent process.

The project will implement Think Tanks, one for each Mission objective, with the aim of co-creating knowledge and identifying the knowledge gaps, drivers, bottlenecks, and novel approaches in terms of research and innovation.

The Think Tanks will consist of groups of experts who will together tackle the issues regarding soil health, set out in the EU Mission ‘A Soil Deal for Europe’.
Together with an open digital platform, based on Pensoft’s ARPHA Writing Tool, the Think Tanks will function as an operational tool for implementing a participatory process that will last beyond SOLO’s lifespan.

The project will engage users at regional, national and European level to support the co-design of comprehensive research and innovation roadmaps for the Soil Mission and identify knowledge gaps and novel avenues for European soil research and innovation in the context of the Soil Mission objectives. 

Furthermore, SOLO will identify, describe and assess the drivers and barriers to soil health in Europe, develop dynamic roadmaps as effective research and innovation agendas for the Soil Mission with a particular focus on the integration and synthesis across sectors.

The 3rd Global Soil Biodiversity Conference (March 2023; Dublin, Ireland) saw several talks by researchers involved in the SOLO project, while communication materials provided additional information to the delegates who stopped by the Pensoft exhibition stand.

You can find out more about the project on the Soils for Europe (SOLO) website: soils4europe.eu. Stay up to date with the project’s progress on Twitter (@soils4europe) and LinkedIn (/Soils-for-Europe).

UPDATE: The Soils for Europe journal is NOW LIVE at: https://journal.soils4europe.eu/.


The innovative open-access digital publishing platform provides a forum for open review and co-creation of the European Mission Soil research and innovation roadmaps in support of more integrative and encompassing policies aiming to achieve improvements in soil health and a thriving environment for soil-related research in Europe.

The consortium

SOLO’s consortium comprises a European network of established professionals from the academic and non-academic fields from various backgrounds, who have agreed to work collaboratively to fulfil the objectives set by the EU Mission “A Soil Deal for Europe” which aims to create a shared research and innovation vision that will accelerate Europe’s trajectory towards sustainable soil management and restoration as part of a wider, green transition in rural and urban areas.

Full list of partners:
  1. National Resources Institute Finland
  2. University of Leipzig
  3. Pesticide Action Network
  4. Agroecology Europe
  5. Leitat Technological Centre
  6. Netherlands Institute of Ecology
  7. Leibniz Centre for Agricultural Landscape Research
  8. Lund University
  9. Pensoft Publishers
  10. University of Évora
  11. Institute of Advanced Studies Kőszeg
  12. National Observatory of Athens
  13. Norwegian University of Life Sciences
  14. University of Antwerp
  15. University of Trento
  16. Fraunhofer Society
  17. ICLEI European Secretariat GMBH

Redefining nature-based decision-making: Pensoft joins EU project SELINA

“Ecosystem services is one of the topics that Pensoft has been involved in for over 10 years,” points out COO Prof Pavel Stoev.

Ambitious goals have been set by the European Union, in order to tackle the biodiversity conservation challenges over the coming decade. No less ambitious are the goals of the Horizon Europe project SELINA, which is one of the current major initiatives looking in the same direction. 

SELINA (Science for Evidence-based and Sustainable Decisions about Natural Capital) is a transdisciplinary project aimed at promoting the conservation of biodiversity, enhancing ecosystem conditions, and supporting the sustainable use of the environment through evidence-based decision-making.

As an experienced science communicator and open-science publisher, Pensoft will be leading the project’s communication and dissemination activities.

“Ecosystem services is one of the topics that Pensoft has been involved in for more than 10 years, so it was only natural for us to continue our work as a communicator of scientific information in the ambitious SELINA project as well,”

says Prof Pavel Stoev, COO at Pensoft.

“We have already collaborated with many of the partners within the earlier EC Horizon 2020 project ESMERALDA, which concluded with the launch of a pan-European network of scientific institutions engaged with biodiversity conservation and ecosystem services.

In addition, Pensoft has been strongly connected to the community through the scholarly journal One Ecosystem, which is supported by Ecosystem Services Partnership, and offers an opportunity for scientists in the field to publish their results in a new and innovative way.”

he adds.

The project

SELINA was launched in July 2022 and will run for 5 years. Having received EUR 13 million in funding, the project is seen as an unprecedented opportunity for smart, cost-effective, and nature-based solutions to historic societal challenges such as climate change, biodiversity loss, and food security. 

One of the project’s main objectives is to identify biodiversity, ecosystem condition, and ecosystem service factors that can be successfully integrated into decision-making processes in both the public and private sectors. 

To achieve this objective, SELINA will develop, test, and integrate new and existing knowledge, including methodological approaches to improve biodiversity, ecosystem condition, and ecosystem service information uptake by decision-makers. 

In addition, the project will utilise EU-wide workshops and multi-disciplinary Communities of Practice involving a wide range of stakeholders, including scientists, policymakers, business leaders, and civil society organisations. 

The project will also organise Demonstration Projects on biodiversity, ecosystem condition, and ecosystem service integration in decision-making and co-create a Compendium of Guidance that will allow stakeholders to make full use of the project’s results and fit-for-purpose recommendations with real-world applications in policy-making and business decisions. 

International consortium

SELINA project brings together experts from 50 partnering organisations across all European Union member states, Norway, Switzerland, Israel, and the United Kingdom.

The project comprises a Pan-European and transdisciplinary network of professionals from the academic and non-academic sectors with various (inter)disciplinary backgrounds – including ecologists, economists, social scientists – who have agreed to work collaboratively to support transformative change based on evidence-based decision-making related to the management of natural resources.

Find out more about the project on the SELINA website: project-selina.eu/.

Stay up to date with the project’s progress on Twitter, Facebook, Linkedin and YouTube.

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.

To be eligible for the collection, a manuscript must comply with at least two of the conditions listed below. In the submission form, the author needs to specify the condition(s) applicable to the manuscript. The author should provide the explanation in a cover letter, using the Notes to the editor field.

All submissions must abide by the community-agreed standards for terms, ontologies and vocabularies used in biodiversity informatics. 

The data used in the articles must comply with the Data Quality Checklist and Fair Data Checklist available in the Authors’ instructions of the journal.

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 treatments, images, literature references, etc.) to their respective records in external repositories. Taxon names in the text should not be hyperlinked. Instead, under each taxon name in the catalogue, the authors should add external links to, for example, Catalogue of Life, nomenclators (e.g. IPNI, MycoBank, Index Fungorum, ZooBank), taxon treatments in Plazi’s TreatmentBank or other relevant trusted resources.

  • 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 or catalogue. 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.

  • Articles that contain nanopublications created or added during the authoring process in Biodiversity Data Journal. A nanopublication is a scientifically meaningful assertion about anything that can be uniquely identified and attributed to its author and serve to communicate a single statement, for example biotic relationship between taxa, or habitat preference of a taxon. The in-built workflow ensures the linkage and its persistence, while the information is simultaneously human-readable and machine-interpretable.
  • 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: 

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.

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

* The publication fee (APC) is waived for standard-sized manuscripts (up to 40,000 characters, including spaces) normally charged by BDJ at € 650. Authors of larger manuscripts will need to cover the surplus charge (€10 for each 1,000 characters above 40,000). See more about the APC policy at Biodiversity Data Journal, or contact the journal editorial team at: bdj@pensoft.net.

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.

***

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.

Towards a climate-neutral society: Pensoft takes part in the Horizon project ForestPaths

Apart from science communication, Pensoft is also tasked with the development and maintenance of the CANOPY platform, whose aim is to support policymakers and national and regional authorities

Dedicated to bridging the gap between science, policy, industry and society, Pensoft is striving to maximise ForestPaths’ impact in meeting Europe’s climate and biodiversity targets
The backdrop

The European Union (EU) has set ambitious targets to reduce greenhouse gas emissions by at least 55% in 2030 and to become climate neutral by 2050, which require urgent and major societal and economic reforms. 

In the meantime, the EU also aims to protect biodiversity and reverse the degradation of ecosystems, while using natural resources to mitigate climate change. 

ForestPaths – a recently started Horizon Europe project will help meet Europe’s climate and biodiversity targets by providing clear policy options that enable European forests and the forest-based sector to contribute to climate change mitigation, while conserving their biodiversity and sustaining the services they provide to people.

As an experienced science communicator, Pensoft is dedicated to maximising ForestPaths’ impact. The team will do so by means of tailored communication, dissemination and exploitation strategies aimed at sharing the project’s results with relevant stakeholder groups.

Furthermore, Pensoft is tasked with the development and long-term maintenance of the CANOPY platform, whose aim is to support policymakers and national and regional authorities by granting them access to the knowledge and scientific evidence acquired within ForestPaths long after the project is finalised.

The ForestPaths approach

ForestPaths will work with practitioners through four demo cases to determine climate- and biodiversity-smart forest management options. 

Building on these options, the project will collaborate with policymakers and key authorities through a series of Policy labs, where the partners will co-design policy pathways, which will then be analysed with next-generation integrated assessment techniques. 

Lastly, ForestPaths will apply this framework for an all-round assessment of the climate mitigation potential of European forests and the forest-based sector.

Aerial view of a forest road.
The ForestPaths legacy

ForestPaths’ policy pathways – as well as their supporting information and evidence – will be made openly available through the project’s policy-support platform CANOPY, hosted on the ForestPaths website. 

The platform, whose launch is scheduled for 2026, will feature an interactive policy analysis tool explaining the policy pathways and showcasing their implications, as well as providing detailed assessment results and policy recommendations in an easily accessible manner. Its long-term mission is to become the go-to place for easily accessible assessment results and policy recommendations.

“We are excited to be doing our part for Europe’s fight for climate neutrality by extending ForestPaths reach to policy, industry and society at large! As an open-access scientific publisher engaged in about 50 environmental research projects, Pensoft echoes ForestPaths’ aim to support the EU’s climate neutrality transition through what we are sure will be a prolific international research collaboration,” says ForestPaths’ WP7 leader Anna Sapundzhieva.

You can find out more about the project on the ForestPath website: forestpaths.eu. Stay up to date with the project’s progress on Twitter (@forestpaths_eu) and LinkedIn (/forestpaths-project).

Full list of project partners:
  1. European Forest Institute
  2. Lund University
  3. Technical University of Munich
  4. Karlsruhe Institute of Technology
  5. Natural Resources Institute Finland
  6. Wageningen Research
  7. Flemish Institute for Technological Research
  8. PBL Netherlands Environmental Assessment Agency
  9. Oeko-Institut
  10. Euro-Mediterranean Center on Climate Change
  11. Prospex Institute
  12. Transilvania University of Brasov
  13. Pensoft Publishers
  14. Joint Research Centre – European Commission
  15. University of Edinburgh
  16. Teesside University

Interoperable biodiversity data extracted from literature through open-ended queries

OpenBiodiv is a biodiversity database containing knowledge extracted from scientific literature, built as an Open Biodiversity Knowledge Management System. 

The OpenBiodiv contribution to BiCIKL

Apart from coordinating the Horizon 2020-funded project BiCIKL, scholarly publisher and technology provider Pensoft has been the engine behind what is likely to be the first production-stage semantic system to run on top of a reasonably-sized biodiversity knowledge graph.

OpenBiodiv is a biodiversity database containing knowledge extracted from scientific literature, built as an Open Biodiversity Knowledge Management System. 

As of February 2023, OpenBiodiv contains 36,308 processed articles; 69,596 taxon treatments; 1,131 institutions; 460,475 taxon names; 87,876 sequences; 247,023 bibliographic references; 341,594 author names; and 2,770,357 article sections and subsections.

In fact, OpenBiodiv is a whole ecosystem comprising tools and services that enable biodiversity data to be extracted from the text of biodiversity articles published in data-minable XML format, as in the journals published by Pensoft (e.g. ZooKeys, PhytoKeys, MycoKeys, Biodiversity Data Journal), and other taxonomic treatments – available from Plazi and Plazi’s specialised extraction workflow – into Linked Open Data.

“I believe that OpenBiodiv is a good real-life example of how the outputs and efforts of a research project may and should outlive the duration of the project itself. Something that is – of course – central to our mission at BiCIKL.”

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

“The basics of what was to become the OpenBiodiv database began to come together back in 2015 within the EU-funded BIG4 PhD project of Victor Senderov, later succeeded by another PhD project by Mariya Dimitrova within IGNITE. It was during those two projects that the backend Ontology-O, the first versions of RDF converters and the basic website functionalities were created,”

he adds.

At the time OpenBiodiv became one of the nine research infrastructures within BiCIKL tasked with the provision of virtual access to open FAIR data, tools and services, it had already evolved into a RDF-based biodiversity knowledge graph, equipped with a fully automated extraction and indexing workflow and user apps.

Currently, Pensoft is working at full speed on new user apps in OpenBiodiv, as the team is continuously bringing into play invaluable feedback and recommendation from end-users and partners at BiCIKL. 

As a result, OpenBiodiv is already capable of answering open-ended queries based on the available data. To do this, OpenBiodiv discovers ‘hidden’ links between data classes, i.e. taxon names, taxon treatments, specimens, sequences, persons/authors and collections/institutions. 

Thus, the system generates new knowledge about taxa, scientific articles and their subsections, the examined materials and their metadata, localities and sequences, amongst others. Additionally, it is able to return information with a relevant visual representation about any one or a combination of those major data classes within a certain scope and semantic context.

Users can explore the database by either typing in any term (even if misspelt!) in the search engine available from the OpenBiodiv homepage; or integrating an Application Programming Interface (API); as well as by using SPARQL queries.

On the OpenBiodiv website, there is also a list of predefined SPARQL queries, which is continuously being expanded.

Sample of predefined SPARQL queries at OpenBiodiv.

“OpenBiodiv is an ambitious project of ours, and it’s surely one close to Pensoft’s heart, given our decades-long dedication to biodiversity science and knowledge sharing. Our previous fruitful partnerships with Plazi, BIG4 and IGNITE, as well as the current exciting and inspirational network of BiCIKL are wonderful examples of how far we can go with the right collaborators,”

concludes Prof Lyubomir Penev.

***

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

You can also follow Pensoft on Twitter, Facebook and Linkedin and use #OpenBiodiv on Twitter.

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

Experts in insect taxonomy “threatened by extinction” reveals the first European Red List of Taxonomists

While insect populations continue to decline, taxonomic expertise in Europe is at serious risk, confirms data obtained within the European Red List of Insect Taxonomists, a recent study commissioned by the European Union. 

Expertise tends to be particularly poor in the countries with the richest biodiversity, while taxonomists are predominantly male and ageing

While insect populations continue to decline, taxonomic expertise in Europe is at serious risk, confirms data obtained within the European Red List of Insect Taxonomists, a recent study commissioned by the European Union. 

Scientists who specialise in the identification and discovery of insect species – also known as insect taxonomists – are declining across Europe, highlights the newly released report by CETAF, International Union for Conservation of Nature (IUCN) and Pensoft. The authors of this report represent different perspectives within biodiversity science, including natural history and research institutions, nature conservation, academia and scientific publishing.

Despite the global significance of its taxonomic collections, Europe has been losing taxonomic expertise at such a rate that, at the moment nearly half (41.4%) of the insect orders are not covered by a sufficient number of scientists. If only EU countries are counted, the number looks only slightly more positive (34.5%). Even the four largest insect orders: beetles (Coleoptera), moths and butterflies (Lepidoptera), flies (Diptera) and wasps, bees, ants and sawflies (Hymenoptera) are only adequately ‘covered’ in a fraction of the countries.

To obtain details about the number, location and productivity of insect taxonomists, the team extracted information from thousands of peer-reviewed research articles published in the last decade, queried the most important scientific databases and reached out to over fifty natural science institutions and their networks. Furthermore, a dedicated campaign reached out to individual researchers through multiple communication channels. As a result, more than 1,500 taxonomists responded by filling in a self-declaration survey to provide information about their personal and academic profile, qualification and activities. 

Then, the collected information was assessed against numerical criteria to classify the scientists into categories similar to those used by the IUCN Red List of Threatened SpeciesTM. In the European List of Insect Taxonomists, these range from Eroded Capacity (equivalent to Extinct) to Adequate Capacity (equivalent to Least Concern). The assessment was applied to the 29 insect orders (i.e. beetles, moths and butterflies etc.) to figure out which insect groups the society, conservation practitioners and decision-makers need not be concerned at this point.

Overview of the taxonomic capacity in European countries based upon the Red List Index (colour gradient goes from red (Eroded Capacity) to green (Adequate Capacity).
Image by the European Red List of Taxonomists consortium.

On a country level, the results showed that Czechia, Germany and Russia demonstrate the most adequate coverage of insect groups. Meanwhile, Albania, Azerbaijan, Belarus, Luxembourg, Latvia, Ireland and Malta turned out to be the ones with insufficient number of taxonomists.

In most cases, the availability of experts seems to correlate to GDP, as wealthiest countries tend to invest more in their scientific institutions.

What is particularly worrying is that the lack of taxonomic expertise is more evident in the countries with the greatest species diversity. This trend may cause even more significant problems in the knowledge and conservation of these species, further aggravating the situation. Thus, the report provides further evidence about a global pattern where the countries richest in biodiversity are also the ones poorest in financial and human resources. 

The research team also reminds that it is European natural history museums that host the largest scientific collections – including insects – brought from all over the globe. As such, Europe is responsible to the world for maintaining taxonomic knowledge and building adequate expert capacity.

Other concerning trends revealed in the new report are that the community of taxonomists is also ageing and – especially in the older groups – male-dominated (82%). 

“One reason to have fewer young taxonomists could be due to limited opportunities for professional training (…), and the fact that not all professional taxonomists provide it, as a significant number of taxonomists are employed by museums and their opportunities for interaction with university students is probably not optimal. Gender bias is very likely caused by multiple factors, including fewer opportunities for women to be exposed to taxonomic research and gain an interest, unequal offer of career opportunities and hiring decisions. A fair-playing field for all genders will be crucial to address these shortcomings and close the gap.”

comments Ana Casino, CETAF’s Executive Director.

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Entomologist examining a small insect under a microscope.
Photo by anton_shoshin/stockadobe.com.
The European Red List of Taxonomists concludes with practical recommendations concerning strategic, science and societal priorities, addressed to specific decision-makers.

The authors give practical examples and potential solutions in support of their call to action.

For instance, in order to develop targeted and sustainable funding mechanisms to support taxonomy, they propose the launch of regular targeted Horizon Europe calls to study important insect groups for which taxonomic capacity has been identified to be at a particularly high risk of erosion.

To address specific gaps in expertise – such as the ones reported in the publication from Romania – a country known for its rich insect diversity, yet poor in taxonomic expertise – the consortium proposes the establishment of a natural history museum or entomological research institute that is well-fitted to serve as a taxonomic facility.

Amongst the scientific recommendations, the authors propose measures to ensure better recognition of taxonomic work at a multidisciplinary level. The scientific community, including disciplines that use taxonomic research, such as molecular biology, medicine and agriculture – need to embrace universal standards and rigorous conduct for the correct citation of scientific publications by insect taxonomists.

Societal engagement is another important call. “It is pivotal to widely raise awareness of the value and impact of taxonomy and the work of taxonomists. We must motivate young generations to join the scientific community” points Prof. Lyubomir Penev, Managing Director of Pensoft.

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“Understanding taxonomy is a key to understanding the extinction risk of species. If we strategically target the gaps in expert capacity that this European Red List identifies, we can better protect biodiversity and support the well-being and livelihoods of our societies. With the climate crisis at hand, there is no time left to waste,”

added David Allen from the IUCN Red List team.

“As a dedicated supporter of the IUCN Red List, I am inspired by this call to strengthen the capacity, guided by evidence and proven scientific methods. However, Europe has much more scientific capacity than most biodiversity-rich regions of the world. So, what this report particularly highlights is the need for massively increasing investment in scientific discovery, and building taxonomic expertise, around the world,”  

said Jon Paul Rodríguez, Chair of the IUCN Species Survival Commission.

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Follow and join the conversation on Twitter using the #RedListTaxonomists hashtag. 

BiCIKL partners sign the Leiden Declaration on FAIR Digital Objects

Key figures from Naturalis Biodiversity Center, Plazi and Pensoft were amongst the first to sign the Declaration at the closing session of the First International Conference on FAIR Digital Objects (FDO2022)

Several of the BiCIKL partners signed the Leiden Declaration on FAIR Digital Objects, thereby committing to “a new environment that works as a truly meaningful data space,” as framed by the organisers of the conference, whose first instalment turned out to be the perfect occasion for the formal publication of the pact. 

Key figures from Naturalis Biodiversity Center, Plazi and Pensoft were amongst the first to sign the Declaration at the closing session of the First International Conference on FAIR Digital Objects (FDO2022), which took place in October 2022 in Leiden, the Netherlands, where it was hosted by the Naturalis Biodiversity Center.

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The conference brought together key international technical, scientific, industry and science-policy stakeholders with the aim to boost the development and implementation of FAIR Digital Objects (FDOs) worldwide. It was organised by the FDO Forum, an initiative supported by major global initiatives and by a variety of regional and national initiatives with the shared goal to achieve a better coherence amongst the increasing number of initiatives working on FDO-based designs and implementations.  

By joining the Declaration’s signees, the BiCIKL partners formally committed to:

  • Support the FAIR guiding principles to be applied (ultimately) to each digital object in a web of FAIR data and services;  
  • Support open standards and protocols;
  • Support data and services to be as open as possible, and only as restricted as necessary;
  • Support distributed solutions where useful to achieve robustness and scalability, but recognise the need for centralised approaches where necessary;
    • Support the restriction of standards and protocols to the absolute minimum;
    • Support freedom to operate wherever possible;
    • Help to avoid monopolies and provider lock-in wherever possible.

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During the event, Plazi and Pensoft held a presentation demonstrating how their Biodiversity Literature Repository turns taxonomic treatments ‘locked’ in legacy scientific literature into FAIR Digital Objects. As a result of the collaboration between Plazi and Pensoft – a partnership long-preceding their involvement in BiCIKL – this workflow has also been adapted to modern-day publishing, in order to FAIRify data as soon as it is published.

A slide from the Plazi presentation at the FDO2022, Leiden, the Netherlands. Credit: Plazi.

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Ahead of FDO2022, all submitted conference abstracts – including the one associated with Plazi’s presentation – were made publicly available in a collection of their own in Pensoft’s open-science journal Research Ideas and Outcomes (RIO). Thus, not only did the organisers make the conference outputs available to the participants early on, so that they can familiarise themselves with the upcoming talks and topics in advance, but they also ensure that the contributions are permanently preserved and FAIR in their own turn. 

The conference collection, guest edited by Tina Loo (Naturalis Biodiversity Center), contains a total of 51 conference abstracts, where each is published in HTML, XML and PDF formats, and assigned with its own persistent identifier (DOI) just like the collection in its entirety (10.3897/rio.coll.190).

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Read more about the declaration and sign it yourself from this link. You can also follow the FDO Forum on Twitter (@FAIRDOForum).

One Biodiversity Knowledge Hub to link them all: BiCIKL 2nd General Assembly

The FAIR Data Place – the key and final product of the partnership – is meant to provide scientists with all types of biodiversity data “at their fingertips”

The Horizon 2020 – funded project BiCIKL has reached its halfway stage and the partners gathered in Plovdiv (Bulgaria) from the 22nd to the 25th of October for the Second General Assembly, organised by Pensoft. 

The BiCIKL project will launch a new European community of key research infrastructures, researchers, citizen scientists and other stakeholders in the biodiversity and life sciences based on open science practices through access to data, tools and services.

BiCIKL’s goal is to create a centralised place to connect all key biodiversity data by interlinking 15 research infrastructures and their databases. The 3-year European Commission-supported initiative kicked off in 2021 and involves 14 key natural history institutions from 10 European countries.

BiCIKL is keeping pace as expected with 16 out of the 48 final deliverables already submitted, another 9 currently in progress/under review and due in a few days. Meanwhile, 21 out of the 48 milestones have been successfully achieved.

Prof. Lyubomir Penev (BiCIKL’s project coordinator Prof. Lyubomir Penev and CEO and founder of Pensoft) opens the 2nd General Assembly of BiCIKL in Plovdiv, Bulgaria.

The hybrid format of the meeting enabled a wider range of participants, which resulted in robust discussions on the next steps of the project, such as the implementation of additional technical features of the FAIR Data Place (FAIR being an abbreviation for Findable, Accessible, Interoperable and Reusable).

This FAIR Data Place online platform – the key and final product of the partnership and the BiCIKL initiative – is meant to provide scientists with all types of biodiversity data “at their fingertips”.

This data includes biodiversity information, such as detailed images, DNA, physiology and past studies concerning a specific species and its ‘relatives’, to name a few. Currently, the issue is that all those types of biodiversity data have so far been scattered across various databases, which in turn have been missing meaningful and efficient interconnectedness.

Additionally, the FAIR Data Place, developed within the BiCIKL project, is to give researchers access to plenty of training modules to guide them through the different services.

Halfway through the duration of BiCIKL, the project is at a turning point, where crucial discussions between the partners are playing a central role in the refinement of the FAIR Data Place design. Most importantly, they are tasked with ensuring that their technologies work efficiently with each other, in order to seamlessly exchange, update and share the biodiversity data every one of them is collecting and taking care of.

By Year 3 of the BiCIKL project, the partners agree, when those infrastructures and databases become efficiently interconnected to each other, scientists studying the Earth’s biodiversity across the world will be in a much better position to build on existing research and improve the way and the pace at which nature is being explored and understood. At the end of the day, knowledge is the stepping stone for the preservation of biodiversity and humankind itself.

“Needless to say, it’s an honour and a pleasure to be the coordinator of such an amazing team spanning as many as 14 partnering natural history and biodiversity research institutions from across Europe, but also involving many global long-year collaborators and their infrastructures, such as Wikidata, GBIF, TDWG, Catalogue of Life to name a few,”

said BiCIKL’s project coordinator Prof. Lyubomir Penev, CEO and founder of Pensoft.

“I see our meeting in Plovdiv as a practical demonstration of our eagerness and commitment to tackle the long-standing and technically complex challenge of breaking down the silos in the biodiversity data domain. It is time to start building freeways between all biodiversity data, across (digital) space, time and data types. After the last three days that we spent together in inspirational and productive discussions, I am as confident as ever that we are close to providing scientists with much more straightforward routes to not only generate more biodiversity data, but also build on the already existing knowledge to form new hypotheses and information ready to use by decision- and policy-makers. One cannot stress enough how important the role of biodiversity data is in preserving life on Earth. These data are indeed the groundwork for all that we know about the natural world”  

Prof. Lyubomir Penev added.
Christos Arvanitidis (CEO of LifeWatch ERIC) at the 2nd General Assembly of the BiCIKL project.

Christos Arvanitidis, CEO of LifeWatch ERIC, added:

“The point is: do we want an integrated structure or do we prefer federated structures? What are the pros and cons of the two options? It’s essential to keep the community united and allied because we can’t afford any information loss and the stakeholders should feel at home with the Project and the Biodiversity Knowledge Hub.”

Joe Miller, Executive Secretary and Director at GBIF, commented:

“We are a brand new community, and we are in the middle of the growth process. We would like to already have answers, but it’s good to have this kind of robust discussion to build on a good basis. We must find the best solution to have linkages between infrastructures and be able to maintain them in the future because the Biodiversity Knowledge Hub is the location to gather the community around best practices, data and guidelines on how to use the BiCIKL services… In order to engage even more partners to fill the eventual gaps in our knowledge.”

Joana Pauperio (biodiversity curator at EMBL-EBI) at the 2nd General Assembly of the BiCIKL project.

“BiCIKL is leading data infrastructure communities through some exciting and important developments”  

said Dr Guy Cochrane, Team Leader for Data Coordination and Archiving and Head of the European Nucleotide Archive at EMBL’s European Bioinformatics Institute (EMBL-EBI).

“In an era of biodiversity change and loss, leveraging scientific data fully will allow the world to catalogue what we have now, to track and understand how things are changing and to build the tools that we will use to conserve or remediate. The challenge is that the data come from many streams – molecular biology, taxonomy, natural history collections, biodiversity observation – that need to be connected and intersected to allow scientists and others to ask real questions about the data. In its first year, BiCIKL has made some key advances to rise to this challenge,”

he added.

Deborah Paul, Chair of the Biodiversity Information Standards – TDWG said:

“As a partner, we, at the Biodiversity Information Standards – TDWG, are very enthusiastic that our standards are implemented in BiCIKL and serve to link biodiversity data. We know that joining forces and working together is crucial to building efficient infrastructures and sharing knowledge.”

The project will go on with the first Round Table of experts in December and the publications of the projects who participated in the Open Call and will be founded at the beginning of the next year.

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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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All BiCIKL project partners: