Category: Partnering scientific projects

Nanopublications tailored to biodiversity data

Novel nanopublication workflows and templates for associations between organisms, taxa and their environment are the latest outcome of the collaboration between Knowledge Pixels and Pensoft.

First off, why nanopublications?

Nanopublications complement human-created narratives of scientific knowledge with elementary, machine-actionable, simple and straightforward scientific statements that prompt sharing, finding, accessibility, citability and interoperability. 

By making it easier to trace individual findings back to their origin and/or follow-up updates, nanopublications also help to better understand the provenance of scientific data. 

With the nanopublication format and workflow, authors make sure that key scientific statements – the ones underpinning their research work – are efficiently communicated in both human-readable and machine-actionable manner in line with FAIR principles. Thus, their contributions to science are better prepared for a reality driven by AI technology.

The machine-actionability of nanopublications is a standard due to each assertion comprising a subject, an object and a predicate (type of relation between the subject and the object), complemented by provenance, authorship and publication information. A unique feature here is that each of the elements is linked to an online resource, such as a controlled vocabulary, ontology or standards. 

Now, what’s new?

As a result of the partnership between high-tech startup Knowledge Pixels and open-access scholarly publisher and technology provider Pensoft, authors in Biodiversity Data Journal (BDJ) can make use of three types of nanopublications:

  1. Nanopublications associated with a manuscript submitted to BDJ. This workflow lets authors add a Nanopublications section within their manuscript while preparing their submission in the ARPHA Writing Tool (AWT). Basically, authors ‘highlight’ and ‘export’ key points from their papers as nanopublications to further ensure the FAIRness of the most important findings from their publications.
  1. Standalone nanopublication related to any scientific publication, regardless of its author or source. This can be done via the Nanopublications page accessible from the BDJ website. The main advantage of standalone nanopublication is that straightforward scientific statements become available and FAIR early on, and remain ready to be added to a future scholarly paper.
  1. Nanopublications as annotations to existing scientific publications. This feature is available from several journals published on the ARPHA Platform, including BDJ. By attaching an annotation to the entire paper (via the Nanopublication tab) or a text selection (by first adding an inline comment, then exporting it as a nanopublication), a reader can evaluate and record an opinion about any article using a simple template based on the Citation Typing Ontology (CiTO).

Nanopublications for biodiversity data?

At Biodiversity Data Journal (BDJ), authors can now incorporate nanopublications within their manuscripts to future-proof the most important assertions on biological taxa and organisms or statements about associations of taxa or organisms and their environments. 

On top of being shared and archived by means of a traditional research publication in an open-access peer-reviewed journal, scientific statements using the nanopublication format will also remain ‘at the fingertips’ of automated tools that may be the next to come looking for this information, while mining the Web.

Using the nanopublication workflows and templates available at BDJ, biodiversity researchers can share assertions, such as:

So far, the available biodiversity nanopublication templates cover a range of associations, including those between taxa and individual organisms, as well as between those and their environments and nucleotide sequences. 

Nanopublication template customised for biodiversity research publications available from Nanodash.

As a result, those easy-to-digest ‘pixels of knowledge’ can capture and disseminate information about single observations, as well as higher taxonomic ranks. 

The novel domain-specific publication format was launched as part of the collaboration between Knowledge Pixels – an innovative startup tech company aiming to revolutionise scientific publishing and knowledge sharing and the open-access scholarly publisher Pensoft.

… so, what exactly is a nanopublication?

General structure of a nanopublication:

“the smallest unit of publishable information”,

as explained on nanopub.net.

Basically, a nanopublication – unlike a research article – is a tiny snippet of a precise and structured scientific finding (e.g. medication X treats disease Y), which exists as a reusable and cite-able pieces of a growing knowledge graph stored on a decentralised server network in a format that it is readable for humans, but also “understandable” and actionable for computers and their algorithms.

These semantic statements expressed in community-agreed terms, openly available through links to controlled vocabularies, ontologies and standards, are not only freely accessible to everyone in both human-readable and machine-actionable formats, but also easy-to-digest for computer algorithms and AI-powered assistants.

In short, nanopublications allow us to browse and aggregate such findings as part of a complex scientific knowledge graph. Therefore, nanopublications bring us one step closer to the next revolution in scientific publishing, which started with the emergence and increasing adoption of knowledge graphs. 

“As pioneers in the semantic open access scientific publishing field for over a decade now, we at Pensoft are deeply engaged with making research work actually available at anyone’s fingertips. What once started as breaking down paywalls to research articles and adding the right hyperlinks in the right places, is time to be built upon,”

said Prof. Lyubomir Penev, founder and CEO at Pensoft, which had published the very first semantically enhanced research article in the biodiversity domain back in 2010 in the ZooKeys journal.

Why are nanopublications necessary?

By letting computer algorithms access published research findings in a structured format, nanopublications allow for the knowledge snippets that they are intended to communicate to be fully understandable and actionable. With nanopublications, each of those fragments of scientific information is interconnected and traceable back to its author(s) and scientific evidence. 

A nanopublication is a tiny snippet of a precise and structured scientific finding (e.g. medication X treats disease Y), which exists within a growing knowledge graph stored on a decentralised server network in a format that it is readable for humans, but also “understandable” and actionable for computers and their algorithms. Illustration by Knowledge Pixels. 

By building on shared knowledge representation models, these data become Interoperable (as in the I in FAIR), so that they can be delivered to the right user, at the right time, in the right place , ready to be reused (as per the R in FAIR) in new contexts. 

Another issue nanopublications are designed to address is research scrutiny. Today, scientific publications are produced at an unprecedented rate that is unlikely to cease in the years to come, as scholarship embraces the dissemination of early research outputs, including preprints, accepted manuscripts and non-conventional papers.

A network of interlinked nanopublications could also provide a valuable forum for scientists to test, compare, complement and build on each other’s results and approaches to a common scientific problem, while retaining the record of their cooperation each step along the way. 

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We encourage you to try the nanopublications workflow yourself when submitting your next biodiversity paper to Biodiversity Data Journal. 

Community feedback on this pilot project and suggestions for additional biodiversity-related nanopublication templates are very welcome!

This Nanopublications for biodiversity workflow was created with a partial support of the European Union’s Horizon 2020 BiCIKL project under grant agreement No 101007492 and in collaboration with Knowledge Pixels AG.The tool uses data and API services of ChecklistBank, Catalogue of Life, GBIF, GenBank/ENA, BOLD, Darwin Core, Environmental Ontology (ENVO), Relation Ontology (RO), NOMEN, ZooBank, Index Fungorum, MycoBank, IPNI, TreatmentBank, and other resources. 

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On the journal website: https://bdj.pensoft.net/, you can find more about the unique features and workflows provided by the Biodiversity Data Journal (BDJ), including innovative research paper formats (e.g. Data Paper, OMICS Data Paper, Software Description, R Package, Species Conservation Profiles, Alien Species Profile), expert-provided data audit for each data paper submission, automated data export and more.

Don’t forget to also sign up for the BDJ newsletter via the Email alert form on the journal’s homepage and follow it on Twitter and Facebook.

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How it works: Nanopublications linked to articles in RIO Journal

Earlier this year, Knowledge Pixels and Pensoft presented several routes for readers and researchers to contribute to research outputs – either produced by themselves or by others – through nanopublications generated through and visualised in Pensoft’s cross-disciplinary Research Ideas and Outcomes (RIO) journal, which uses the same nanopublication workflows.

New way to browse interlinked biodiversity data: Biodiversity Knowledge Hub NOW ONLINE!

The Biodiversity Knowledge Hub is a one-stop portal that allows users to access FAIR and interlinked biodiversity data and services in a few clicks.

The Horizon 2020 BiCIKL Project is proud to announce that the Biodiversity Knowledge Hub (BKH) is now online.

BKH is a one-stop portal that allows users to access FAIR and interlinked biodiversity data and services in a few clicks. BKH was designed to support a new emerging community of users over time and across the entire biodiversity research cycle providing its services to anybody, anywhere and anytime.

The Knowledge Hub is the main product from our BiCIKL consortium, and we are delighted with the result!

BKH can easily be seen as the beginning of the major shift in the way we search interlinked biodiversity information.”

Biodiversity researchers, research infrastructures and publishers interested in fields ranging from taxonomy to ecology and bioinformatics can now freely use BKH as a compass to navigate the oceans of biodiversity data. BKH will do the linkages.

says Prof. Lyubomir Penev, BiCIKL’s Project coordinator and Founder of Pensoft Publishers. 
The BKH is designed to serve a new emerging community of users over time and across the entire biodiversity research cycle. 

We have invested our best energies and resources in the development of BKH and the Fair Data Place (FDP), which is the beating heart of the portal,”

BKH has been designed to support a new emerging community of users across the entire biodiversity research cycle.

Its purpose goes beyond the BiCIKL project itself: we are thrilled to say that BKH is meant to stay, aiming to reshape the way biodiversity knowledge is accessed and used.

says Dr Christos Arvanitidis, CEO of LifeWatch ERIC.

The BKH outlines how users can navigate and access the linked data, tools and services of the infrastructures cooperating in BiCIKL.

By revealing how they harvest, liberate and reuse data, these increasingly integrated sources enable researchers in the natural sciences to move more seamlessly between specimens and material samples, genomic and metagenomic data, scientific literature, and taxonomic names and units.

said Dr Joe Miller, Executive Secretary of GBIF—the Global Biodiversity Information Facility.

A training programme on how to best utilise the platform is currently being developed by the Consortium of European Taxonomic Facilities (CETAF), Pensoft Publishers, Plazi, Meise Botanic Garden, EMBL’s European Bioinformatics Institute (EMBL-EBI), ELIXIR Hub, GBIF – the Global Biodiversity Information Facility, and LifeWatch ERIC and will be finalised in the coming months.

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A detailed description of the BKH tools and services provided by its contributing organisations is available at: https://biodiversityknowledgehub.eu.

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Find more information about the BiCIKL consortium partners on the project’s website.

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

Pensoft turns up ‘the voice’ of two strategic EU projects aiming to safeguard nature

CO-OP4CBD & BioAgora are among the latest Horizon Europe projects to benefit from Pensoft’s expertise in science communication and dissemination

Here we are, on our way to wave goodbye the first quarter of the 21st century, and the Earth is still experiencing its largest loss of life and biodiversity since the demise of the dinosaurs. 

One million plant and animal species are threatened with extinction, many within decades, admits the global Convention on Biological Diversity (CBD) on the eve of the adoption of its boldest plan ever, the New Global Agreement to Safeguard Nature.

Europe is a major player in the political response to this global crisis mobilised through its own Biodiversity Strategy for 2030. In recognition of its global responsibilities, the EU has taken bold steps towards global leadership in setting policies and commitments. 

However, political commitments are not sufficient to mitigate and reverse biodiversity loss. To secure the future of the planet and society politicians, business leaders, scientists and society leaders must all prioritise the conservation and restoration of ecosystems through strong legislation and smart decisions. 

The recently adopted by the CBD Global Biodiversity Framework (GBF) provides the basis for the instruments for conservation and sustainable use of biodiversity and for equitable sharing of their benefits, including the genetic resources.

About the projects

The new Horizon Europe-funded projects CO-OP4CBD (abbreviation for Co-operation for the Convention on Biological Diversity) and BioAgora (or Bio Knowledge Agora) unite experts from renowned European organisations to enhance the coordination and strengthen the EU support for the implementation of the Convention. 

Both projects will make more effective use of existing networks of experts with the aim to transform the EU policy-making process by supplying decision-makers with access to top European scientific expertise on biodiversity and social transformation.

CO-OP4CBD
Logo of the Horizon Europe project CO-OP4CBD
(abbreviation for Co–operation for the Convention on Biological Diversity).

CO-OP4CBD kicked-off in December 2022 and will be running until 2026 with the grant of EUR 4 million, provided by the European Union’s Horizon Europe programme. 

The project will put in place a mechanism for mobilising, engaging and sharing expertise necessary for effective participation of EU member States and bodies in the CBD policy and decision-making processes. 

Experts will provide advice to the European Commission, Member States and associated countries’ delegations of negotiators and technical experts.

CO-OP4CBD kick off meeting in Brussels (Belgium), February 2023.

Furthermore, the project will increase access to European expertise through enhanced mechanisms for promoting technical and scientific cooperation not only for negotiations, but also for implementation, monitoring and review of the efforts of the Parties towards the Post-2020 Global Biodiversity Framework and the Convention on Biological Diversity.

You can visit COOP4CBD on coop4cbd.eu and follow the project on Twitter (@coop4cbd) and LinkedIn (/COOP4CBD).

Consortium:

The consortium of CO-OP4CBD comprises 9 universities and research centers from across Europe. Together, they bring together experts from various backgrounds with extensive experience in EU projects in the field of biodiversity.

Full list of partners:

BioAgora
Logo of the Horizon Europe project BioAgora
(abbreviation for Bio Knowledge Agora).

BioAgora was launched in July 2022 and is a five-year project with nearly EUR 12 million granted from the European Union’s Horizon Europe programme. 

The project is tasked to build the Science Service for Biodiversity platform (SSBD) as the scientific pillar of the EU Knowledge Centre for Biodiversity (KCBD).

The KCBD, the European Commission’s initiative on better knowledge management for policy-making on biodiversity, plays a central role in the EU biodiversity policy landscape, and therefore BioAgora will support orchestrating a harmonious dialogue among scientists, other knowledge holders and policy actors in the biodiversity policy arena.

The project partners believe that science, policy, and society need to work closer together, if they wish to enable the sustainability transformation in Europe.

BioAgora kick-off meeting, Helsinki (Finland), November 2022.

A key part of this transformation will depend on a stronger role of knowledge, whether from science or practitioner experience in decision-making and implementation of decisions on the ground. BioAgora aims to facilitate this interaction. 

“Biodiversity and natural capital have to be integrated into public and business decision-making at all levels.
Collective actions and pluralistic principles have to be at the core of biodiversity policy-making efforts, which is why the Science Service for Biodiversity is envisioned as a bridge between science, policy, and society.”

comments project coordinator Kati Vierikko from the Finnish Environment Institute (SYKE).

Visit BioAgora on https://bioagora.eu/. You can also follow the project on Twitter (@BioAgoraEU), LinkedIn (BioAgora Project) and YouTube (@BioAgoraProject).

Consortium:

The consortium of BioAgora consists of 22 partnering organisations from thirteen European countries, all of which bring their extensive knowledge of biodiversity policy and decision-making. 

Full list of partners:

  • SYKE: Finnish Environment Institute
  • UB: The University of Bucharest
  • UniTrento: The University of Trento
  • INRAE: National Research Institute for Agriculture, Food and Environment
  • EV INBO: Research Institute of Nature and Forest
  • PBL: Ministry of Infrastructure and Water Management
  • NINA: Norwegian Institute for Nature Research
  • UFZ: Helmholtz Centre for Environmental Research
  • DC: Delbaere Consulting
  • FVB-IGB: Leibniz-Institute of Freshwater Ecology and Inland Fisheries
  • CREAF: Ecological and Forestry Applications Research Centre
  • ESSRG: Environmental social science research group
  • PENSOFT: Pensoft Publishers
  • ERCE PAN: European Regional Centre for Ecohydrology
  • Euronovia
  • WR: Wageningen University & Research
  • ECSA: European Citizen Science Association
  • AWI: Alfred Wegener Institute for Polar and Marine Research
  • UNEP-WCMC
  • UK CEH: UK Centre For Ecology & Hydrology
  • Alternet Europe
  • OPPLA

Transformative changes for biodiversity and climate protection: Pensoft partners with EU project TRANSPATH

As an expert in science communication, dissemination and exploitation, Pensoft joins TRANSPATH for transformative changes at consumer, producer and organisational levels.

As an expert in science communication, dissemination and exploitation, Pensoft joins the Horizon-funded project TRANSPATH to identify leverage points and interventions for triggering transformative changes at consumer, producer and organisational levels.

Why TRANSPATH?

The magnitude of biodiversity loss and climate crisis has grown exponentially in recent years, which will inevitably lead to serious consequences at a global scale. Although reversing the degradation of ecosystems and reducing greenhouse gas emissions are top priorities for the European Union, science and policy communities are united in the belief that conventional policies alone are not enough to halt biodiversity loss or mitigate climate change.

In order to achieve climate neutrality by 2050, whilst simultaneously reshaping people’s relations with nature, we need transformative changes in our economies and societies urgently. 

How?

TRANSPATH (short for TRANSformative PATHways for synergising just biodiversity and climate actions) – a new European Union-funded project, plans to satisfy this need by accelerating diverse transformative pathways towards biodiversity-positive and climate-proofed societies, with sensitivity to social-cultural contexts and rights.

TRANSPATH will identify leverage points and interventions for triggering transformative changes at consumer, producer and organisational levels. A research team, consisting of leading academics, science-policy experts, and early-career professionals, will directly engage with diverse stakeholders, who affect and are affected by trade regimes and associated ‘greening’ mechanisms.

As a leader of WP5: Dissemination, outreach and catalysing transformative pathways, Pensoft is responsible for providing a dissemination and communication strategy, as well as taking care of the project branding and website. In addition, the Pensoft team is to organise joint activities with other projects or initiatives on transformative change and related topics.

What?

Funded by the European Union’s Horizon Europe research and innovation programme, TRANSPATH was launched on 1st November 2022 and will be running until October 2026. The official kick-off of the project took place online and was followed by an in-person kick-off meeting of all consortium members on the 2nd and 3rd February 2023 in Wageningen, the Netherlands.

For the next four years TRANSPATH will be focussing on the design and integrated assessment of a suite of transformative pathways that hold potential to accelerate shifts in unsustainable patterns of extraction, production, consumption and trade. The project’s mission will be achieved by four objectives:

  1. Set up a Policy Board and Science-policy-practitioner Labs at multiple scales to engage and jointly deliberate on implications of diverse visions and pathways of change.
  2. Identify and characterise leverage points for diverse contexts that lead to positive synergies between biodiversity, climate and trade domains.
  3. Integrate and customise European and global pathways by considering coupled biodiversity-climate actions and critical leverage points.
  4. Identify and test alternative interventions at global and European scales that can trigger transformative change at the level of consumers, producers and organisations.

TRANSPATH will bring together and advance several strands of recent research, which hold potential for triggering and accelerating transformative changes that can restrain biodiversity loss and climate change. 

The project will draw on diverse contexts in Eastern and Western Europe, Africa and Latin America, to engage with policy makers and practitioners, individuals, Civil Society Organisations (CSOs), small- and medium-sized enterprises (SMEs) and multinational corporations.

In addition, policy packages and other interventions will be designed to facilitate the emergence of leverage points at different scales of action in ways that change the decision-making framework of everyday choices.

These interventions take into account the synergies and trade-offs of actions across multiple individuals and locations, as well as the role of incentives and political obstacles to implementation.

The EU project will provide a suite of Transformative Pathways along with a Toolbox of Transformative Interventions to trigger and enable these pathways. The Transformative Navigation Toolkit assists practitioners in enabling and navigating these pathways, acknowledging that determining what constitutes a ‘transformative pathway’ is also a product of an iterative and adaptive process that emerges and evolves over time.

Whom?

The TRANSPATH project brings together leading academics, science-policy experts, and young professionals from different social-cultural origins across Eastern and Western Europe, Africa and Latin America. Represented by nine countries and twelve nationalities, the consortium comprises a diverse range of scientific disciplines in environments, economics, and social sciences.

Dedicated to ensuring sufficient engagement from local to global levels in this project, the experts are focused on integrated and inclusive deliberation that is essential for identifying, legitimising, and navigating transformative pathways.

Full list of partners

You can find more about the project on the TRANSPATH website: transpath.eu. Stay up to date with the project’s progress on Twitter (@TRANSPATH_EU) and Linkedin (/transpath-project).

Mapping our ecosystems: Pensoft joined the Horizon Europe project MAMBO

With expertise in science communication, dissemination and exploitation, Pensoft is involved in this project set to develop new technologies for monitoring species and their habitats across Europe

With expertise in science communication, dissemination and exploitation, Pensoft became part of this project dedicated to new technologies for species and habitat monitoring across Europe

Background 

The European Union puts a great value in monitoring the health of ecosystems, as comprehensive mapping can aid policy makers’ work in adopting appropriate legislation for nature conservation. It allows for understanding the impact of human activities and making informed decisions for effective management of nature’s resources. This is particularly important for the EU, as it has set ambitious goals to halt biodiversity loss and restore degraded ecosystems by 2030, as outlined in the EU Biodiversity Strategy for 2030. 

Effective biodiversity monitoring can help the EU track progress towards these goals, assess the effectiveness of conservation policies and initiatives, and identify emerging threats to biodiversity. 

Despite this awareness, efforts to monitor animals and plants remain spatially and temporally fragmented. This lack of integration regarding data and methods creates a gap in biodiversity monitoring, which can negatively impact policy-making. Today, modern technologies such as drones, artificial intelligence algorithms, or remote sensing are still not widely used in biodiversity monitoring. 

MAMBO project (Modern Approaches to the Monitoring of BiOdiversity) recognises this need and aims to develop, test, and implement enabling tools for monitoring conservation status and ecological requirements of species and habitats. Having started in late 2022, the project is set to run for four years until September 2026.

Pensoft – with its proven expertise in communicating scientific results – is committed to amplifying the impact of MAMBO. Pensoft supports the project through tailored approaches to communication, dissemination and exploitation so as to reach the most appropriate target audience and achieve maximum visibility of the project.

Deep-dive into the project

In order to enrich the biodiversity monitoring landscape, MAMBO will implement a multi-disciplinary approach by utilising the technical expertise in the fields of computer science, remote sensing, and social science expertise on human-technology interactions, environmental economy, and citizen science. This will be combined with knowledge on species, ecology, and conservation biology. 

More specifically, the project will develop, evaluate and integrate image and sound recognition-based AI solutions for EU biodiversity monitoring from species to habitats as well as promote the standardised calculation and automated retrieval of habitat data using deep learning and remote sensing.

“Classification algorithms have matured to an extent where it is possible to identify organisms automatically from digital data, such as images or sound,”

comments project coordinator Prof. Toke T. Høye, Aarhus University. 

“Technical breakthroughs in the realm of high spatial resolution remote sensing set the future of ecological monitoring and can greatly enrich traditional approaches to biodiversity monitoring.” 

In order to achieve its goals, the project will test existing tools in combination with MAMBO-developed new technologies at the project’s demonstration sites geographically spread across Europe. This will contribute to an integrated European biodiversity monitoring system with potential for dynamic adaptations.

Pensoft is part of MAMBO’s Work Package 7 (WP7): “Science-policy interface and dissemination”, led by Helmholtz Centre for Environmental Research (UFZ). The work package is dedicated to providing a distinct identity of the project and its services through branding, visualisation and elaborated dissemination and communication strategy.

Within WP7, Pensoft will also be taking care after the launch of an open-science collection of research outputs in the scholarly journal Research Ideas and Outcomes (RIO). 

Amongst the tasks of the partners in WP7 is also the development of different pathways for integrating new technologies and innovations into the EU Pollinators Monitoring Scheme (EU PoMS; SPRING). 

Full list of partners
  1. Aarhus University (AU)
  2. Naturalis Biodiversity Centre (Naturalis)
  3. Helmholtz Centre for Environmental Research (UFZ)
  4. National Institute for Research in Digital Science and Technology (INRIA)
  5. University of Amsterdam (UvA)
  6. The French Agricultural Research Centre for International Development (CIRAD)
  7. Pensoft Publishers (Pensoft)
  8. Ecostack Innovations Limited (EcoINN)
  9. University of Reading (UREAD)
  10. UK Centre For Ecology & Hydrology (UKCEH) 

You can find more about the project on the MAMBO website: mambo-project.eu. Stay up to date with the project’s progress on Twitter (@MAMBO_EU) and Linkedin (/MAMBO Project).

Novel tech for research & protection of marine biodiversity: Pensoft joins EU project ANERIS

Pensoft joins the ANERIS consortium as an expert in science communication with the goal to engage stakeholders and build an active community

Coastal and marine biodiversity has been declining at an alarming rate in recent years due to anthropogenic activity, climate change, ocean acidification and other factors. 

To help protect and preserve these precious ecosystems, the new research project under the name of ANERIS (operAtional seNsing lifE technologies for maRIne ecosystemS) and coordinated by the Institute of Marine Sciences (ICM-CSIC) was launched under the Horizon Europe program.

ANERIS aims to contribute to improving the understanding, monitoring and protection of these ecosystems through technological, scientific and methodological innovation in the fields of marine life-sensing and monitoring.

Pensoft is joining the ANERIS consortium as a leader of WP6 Exploitation, Communication and Networking. The Pensoft team is to develop and implement sustainable communication and dissemination strategies, which will ensure the impactful knowledge exchange between partners and external stakeholders.

In addition, Pensoft is responsible for the development of a long-lasting brand identity of the project, which shall be reached by establishing and maintaining a user-friendly and eye-appealing public website. The overall visual identity of ANERIS will be supported by a set of innovatively-designed promotional materials. 

The project

ANERIS launched in January 2023 and will be running until December 2026 with the support of EUR 10 million of funding provided by the European Union’s Horizon Europe program and the work on the project officially kicked off with the project’s first consortium meeting, which took place on the 8th and 9th of March 2023 in Barcelona, Spain. 

The joint mission of the ANERIS partners for the next four years is to build the next generation of marine-sensing instruments and infrastructure for systematic routine measurements and monitoring of oceanic and coastal life, and their rapid interpretation and dissemination to all interested stakeholders.

In total, ANERIS aims to pioneer 11 novel technologies rerelated to marine ecosystem monitoring, data processing and dissemination:

  • NANOMICS – NAnopore sequeNcing for Operational Marine genomICS
  • MARGENODAT – workflows for the MARine GENOmics DAta managemenT
  • SLIM-2.0 – A Virtual Environment for genomic data analysis (ANERIS extended version)
  • EMUAS – Expandable Multi-imaging Underwater Acquisition System
  • AIES-ZOO – Automatic Information Extraction System for ZOOplankton images
  • AIES-PHY – Automatic Information Extraction System for PHYtoplankton images
  • ATIRES – Automatic underwaTer Image REstoration System
  • AIES-MAC – Automatic Information Extraction System for MACroorganisms
  • AMAMER – Advanced Multiplatform App for Marine lifE Reporting
  • AMOVALIH – Advanced Marine Observations VALidation-Identification system based on Hybrid intelligence
  • AWIMAR – Adaptive Web Interfaces for MARine life reporting, sharing and consulting

These technologies will be validated across four ANERIS case studies which aim to bridge the gaps between existing technologies and incorporate them into a functional technological framework:

  • High-temporal resolution marine life monitoring in research infrastructure observatories;
  • Improved spatial and temporal resolution of marine life monitoring based on genomics;
  • Large scale marine participatory actions;
  • Merging imaging and genomic information in different monitoring scenarios.

The final goal of the project through the creation and validation of these novel technologies and involving academia, industry, governments and civil society, is to build up the concept of Operational Marine Biology (OMB) to provide faster, higher quality, reliable, and accessible marine and coastal life data. OMB opens the door for near-real-time marine observations, data interpretation and decision making based on that data.

International Consortium

The interdisciplinary ANERIS consortium consists of 25 partnering organisations from 13 countries around Europe, the Mediterranean basin and Israel, bringing diverse expertise spanning from robotics, biooptics, marine biology and genomics, to programming and sustainability.

Many partners represent acclaimed scientific institutions with rich experience in collaboration in EU projects, specifically in the fields of marine research.

Full list of partners:

Visit the ANERIS website on https://www.aneris.eu/. You can also follow the project on Twitter (@ANERISproject), LinkedIn (/ANERIS Project) and Instagram (@aneris_project).

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).

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.

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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.