DTO-BioFlow: Building the biodiversity component of the Digital Twin of the Ocean

Funded through the EC Horizon Europe Programme and coordinated by the Flanders Marine Institute (VLIZ), DTO-BioFlow aims at incorporating previously unavailable or difficult-to-access marine-biodiversity data into the biodiversity component of the EU Digital Twin Ocean, ensuring sustainable data flows for marine biodiversity research.

When it comes to observing, mapping, and monitoring biodiversity in maritime ecosystems, marine habitats present specific and one-of-a-kind issues. In spite of the fact that significant advancement has been made in Europe to collect, harmonise, and make available data on marine biodiversity, particularly as a result of the efforts of European research infrastructure (such as EMODnet, Copernicus Marine, and other related European and international initiatives (MBON, OBIS, GOOS)), a large portion of the data that is currently being collected is unavailable and inaccessible; this type of data is referred to as “sleeping data.”

That’s the stage when DTO BioFlow Project steps in: its primary objective is to awaken sleeping biodiversity data, enabling a smooth integration of both existing and new data into the EU Digital Twin Ocean.

The project aligns with the EU’s Biodiversity Strategy and Nature Restoration Law and with the mission “Restore our oceans and waters by 2030”, both of which advocate for the protection and restoration of land and sea regions.

The DTO-BioFlow Kick off meeting

DTO-BioFlow project kicked off on September 27th in Ostend, Belgium. The meeting was hosted at the InnovOcean Campus and organised by the Flanders Marine Institute (VLIZ), the project’s coordinator, host and technical manager of the European Marine Observation and Data Network (EMODnet) portal.

LifeWatch ERIC is one of the 30 partners from 14 countries that make up DTO-BioFlow Consortium. The other project partners include research, infrastructures (e.g., EMBRC), networks (MBON), organisations (ICES), global aggregators and platforms (OBIS), and others.

The consortium partners bring together biological monitoring infrastructures and experts, data managers, and DTO developers, marine biodiversity-relevant policy development and implementation and enabling the Mission to meet its 2030 targets.

Revolutionizing Access to Ocean Biodiversity Data and Driving Sustainable Integration

“Between September 2023 and February 2027, DTO-Bioflow will come up with creative and long-term solutions that will make previously unavailable or difficult-to-access marine-biodiversity data available to the public. The ultimate goal of the project is to increase the flow of relevant biodiversity data by unlocking current barriers to assimilation and ingestion.”, explains Klaas Deneudt, manager of the VLIZ Marine Observation Centre and coordinator of the DTO BioFlow project.

Over the next four years DTO-BioFlow consortium will work on consolidating standards, quality control, communication protocols, harmonisation pipelines, data products, data models, ingestion procedures and incentives for sustainable connection to improve the interoperability and digitisation of biodiversity data. The project will also test out various technologies that are both affordable and adaptable to carry out species monitoring on a massive scale. The end-to-end approach will be demonstrated via a number of science-based use cases and via mechanisms to monitor, measure progress and drive community action towards increasing biodiversity data flows. To learn more about DTO-BioFlow, please visit the project website.

In Brussels to present the All-Ready project: meet the Agroecology Virtual Lab

Agroecology Living Labs & Research Infrastructures

In collaboration with AE4EU, ALL-Ready organised its final event in Brussels on 27 September 2023. The conference was hosted by the Committee of the Regions.

Our Agroecology Project Manager, Iria Soto Embodas, presented the All-Ready project in the panel “Practice Perspective: How to put Agroecology Living Labs and Research Infrastructures in practice? Q&A”. Within the project, one of the deliverables was to produce the Agroecology Virtual Lab, a collaboration platform to standardise collaboration for research and innovation. During the event, the steps to achieve this were presented.

The one-day conference highlighted two projects that have laid the foundation for a European Network of Living Labs and Research Infrastructures. The discussions focused on how these projects can best support the transition to agroecology and translate theoretical concepts into practical applications. The event explored the lessons learned from three years of project work and highlighted regions’ role in driving agroecology transitions.

The Agroecology Virtual Lab

The Agroecology Virtual Lab is a web platform designed to simplify, centralise, digitalise and streamline the creation of interdisciplinary innovation ecosystems and communities via collaboration with complementary partners that match your needs. This Agroecology Virtual Lab includes, among other functionalities, a marketplace, networking tools, a repository of resources for dissemination and knowledge sharing, geographical visualisation of innovation ecosystems available agroecology best practices and other data management functionalities.

The platform caters to individuals and organisations from various sectors, including research, innovation, public, and civil sectors. The main objective of Agroecology Virtual Labs is to assist scientists, academics, small and medium-sized businesses, farmers, authorities, public bodies, consumers, citizens, and anyone interested in agrifood systems. Additionally, it aims to bring together stakeholders from different sectors of society to foster collaboration and exchange of knowledge on real-world applications of agroecology, research questions, technological solutions, and any other innovative ideas.

About the project

Agricultural systems face multiple challenges today, such as climate change, biodiversity loss, dwindling resources, and soil and water quality degradation. To address these challenges, Open Innovation Arrangements, including Living Labs and Research Infrastructures, can pave the way to enhance the sustainability and resilience of farming systems.

There is great potential to promote agroecology in Europe. The main objective of ALL-Ready is to establish AgroEcoLLNet, the framework for a future European network of LLs and RI that will facilitate the transition towards agroecology throughout Europe. To learn more about All-Ready, please visit the project website.

Community coding: discover the Ontoportal Alliance Workshop

Ontoportal Alliance Group picture

Hosted by LifeWacth ERIC, the Ontoportal Alliance workshop took place in Lecce from September 27 to 29, parallel with the Semantic Academy, the 5-days intensive school designed to boost research with semantic artefacts. The two events overlapped the topic of best practices in managing ontologies and relative data, learning from experts worldwide and sharing knowledge inside the research community. The Ontoportal Alliance workshop included two public sessions: the first focused on the Ontology Development Lifecycle, showing examples of integrating ontology development with the OntoPortal platform. The second session focused on the FAIR-IMPACT EOSC project. The two events were publicly accessible to those interested in the topic. In this framework, LifeWatch ERIC Service Centre ICT Coordinator presented EcoPortal, the LifeWatch ERIC repository of semantic resources for ecology and related domains

What is Ontoportal

The number of ontologies and semantic artefacts produced in science is rapidly increasing. To make these ontologies FAIR (Findable, Accessible, Interoperable, and Reusable), it’s essential to have ontology repositories and semantic artefact catalogues. OntoPortal is a resource that offers a platform for hosting and serving ontologies and semantic artefacts, complete with rich metadata extracted from source files. The user interface helps users quickly find the ontologies they need by using faceted search based on metadata.OntoPortal allows users to easily visualise a class or a concept within its hierarchy and retrieve related information since semantic content is indexed. To learn more about Ontoportal, you can check the official website.

The Ontoportal Alliance

The OntoPortal Alliance is a group of research and infrastructure teams, along with a company, that focuses on developing ontology repositories across various disciplines. The goal of the Alliance is to create and maintain numerous openly accessible ontology repositories and semantic artefact catalogues that make it easier for people to share knowledge and information. The community is encouraged to contribute to the development, dissemination, and documentation of OntoPortal. The Alliance is responsible for planning software improvements, adoption strategies, long-term growth and sustainability.

Global Dimension and Sustainability of Research Infrastructure

Global Dimension and Sustainability of Research Infrastructure

Under the Spanish presidency of the European Union, the high-level conference “Global Dimension and Sustainability of Research Infrastructure” was held on the island of Tenerife on 25-26 September 2023. LifeWatch ERIC Chief Executive Officer Christos Arvanitidis was among the dignitaries present in person, and the events of the two days were all available in streaming. 

The event was inaugurated on Monday afternoon by Rafael Rebolo López, Director of the Instituto di Astrofisica de Canarias (which hosted the event); Radka Wildovà, Director General for Higher Education, Science and Research, Czech Republic; Martin Balbackewski, adviser to the vice-president of Wallonia; Ana Arana Antelo, from the European Commission’s Directorate General for Research and Innovation; and Gonzalo Arévalo, from the Spanish Ministry for Science and Innovation.

Collaboration and the creation of synergies between such various players will contribute much to understanding what the sustainability challenges – including resilience and financial factors – are likely to be in the coming years, while discussion of the global dimensions of European Research Infrastructures demonstrated how much the European Commission’s policies have already contributed to Open Science worldwide. 

The international nature of discussions was also reflected in the topics addressed in the opening session of the second day of the Global Dimension and Sustainability of Research Infrastructure conference: ‘The sky needs to be protected’, ‘Energy crisis’, Environmental footprint of Research Infrastructures in the polar regions’, ‘Greening of Research Infrastructures’, and ‘Best practice exchange in remote access’. A statement is expected to be issued at the conclusion of the conference on International cooperation between Research Infrastructures in a changing context. See the website for more details.

The Semantic Academy: five days in Lecce dive deep into semantic artefacts

The participants of the Semantic academy Intensive School in Lecce

Over twenty researchers from multiple countries, including Algeria, Zimbabwe, Iran, Türkiye, and several European countries, gathered in Lecce this week to participate in the first edition of the “Semantic Academy – Intensive School: Boost your research with semantic artefacts“. In addition to the school, there were two workshops for experts in ontologies, providing a platform for the community to share their software knowledge and best practices.

The Semantic Academy Intensive School builds on the successful experience of six summer and winter schools. Since 2018, LifeWatch ERIC has co-organised them with ENVRI FAIR and the ENVRI Community on data and service FAIRness (Findable, Accessible, Interoperable, Reusable).

With the Semantic Academy, LifeWatch ERIC wants to enhance its training offer in the field, exploring the significant challenge of collecting, organising and making sense of vast amounts of data from various sources and disciplines, with a focus on data FAIRness and semantic research.

For five days, students had the opportunity to build their skills. They navigated the complex landscape of environmental data and advancing scientific understanding. The Semantic Academy’s primary objective was to provide students with comprehensive knowledge about developing and managing semantic artefacts such as ontologies, vocabularies, and thesauri. The approach alternated between theoretical lectures and practical group activities, ensuring the students gained hands-on experience.

Lecturers from some of the most active universities in this field made possible an intensive programme. Naouel Karam (Leipzig University) held a session on Semantic Web, Ontology Engineering. Clement Jonquet (INRAE – MISTEA – University of Montpellier) and Mark Musen (Standford University – BMIR) focused on the ontologies repository. Yifang Shi and Zhiming Zhao (both from LifeWatch ERIC – University of Amsterdam) and Gabriel Pelouze (LifeWatch ERIC) explored AI, Jupyter Notebooks, and other tools to support the research. Armando Stellato and Manuel Fiorelli (University of Roma Tor Vergata) gave the students insights into managing ontologies with different tools.

Over the years, various standards, approaches, and tools have been developed to facilitate the data lifecycle, from data collection to curation, publication, processing, and utilisation. In particular, contemporary semantic technologies offer a promising approach to describe and connect various data sources precisely. This method reduces obstacles to data discovery, integration, and exchange among biodiversity and ecosystem resources and researchers.

The Semantic Academy ushered in participants on Monday, 25th September, in the afternoon, with the presentation of the programme, introduction of LifeWatch ERIC and some ice-breaking activities. The curricular program ran from Tuesday to Friday and concluded with the awarding of participation certificates on the last day.

Calling All Scientists: Submit Your Abstracts for the 7th International Zooplankton Production Symposium Workshop

On 17th of March, the workshop “Approaches towards findable, accessible, interoperable and reusable (FAIR) zooplankton trait data as stepping stones to improved functional ecology” will take place, organised by Jessica Titocci e Ilaria Rosati, from CNR-IRET and LifeWatch Italy, in collaboration with Dr. Kieran Murphy (ARC Australian Centre for Excellence in Antarctic Science), Dr. Brian Hunt (University of British Columbia), Dr. Patrick Pata (University of British Columbia).

In the current era of the Anthropocene, both marine and freshwater ecosystems are undergoing significant changes that are disrupting their delicate balance. Zooplankton plays a key role in the trophic dynamics, productivity and functioning of all aquatic ecosystems. As grazers of phytoplankton and food sources for higher trophic levels, zooplankton organisms represent a key link in the transfer of energy and nutrients in food webs and strongly influence global biogeochemical processes.

Therefore, in light of the current crisis of biodiversity loss and climate change, it is of paramount importance to study the dynamics and distribution of zooplankton populations and communities and to understand the role of zooplankton functional diversity in food web dynamics and ecosystem processes.

To achieve a comprehensive understanding of the impacts and consequences of these changing ecosystems, and to raise awareness of the importance of zooplankton communities in sustaining marine and freshwater environments in these changing times, the 7th International Symposium on Zooplankton Production will be held in Hobart, Australia, from 17 to 22 March 2024. The symposium will provide a global framework for zooplankton researchers to share the latest advances in the field and discuss key issues such as the impact of climate change and biodiversity loss, innovative zooplankton sampling methods, biochemical perspectives, advanced modelling and other related topics. The event is organised by the International Council for the Exploration of the Sea (ICES) in collaboration with the North Pacific Marine Science Organisation (PICES).

Submit your abstract

The workshop will discuss the challenges of implementing FAIR principles and analysing zooplankton trait data. To achieve this goal, researchers in this field are invited to submit their abstracts for presentation at the workshop before 30 September 2023.

The workshop’s main objective is to assess the current status of trait-based research on zooplankton and explore future possibilities. The workshop will also focus on sharing and implementing FAIR principles and best practices to ensure that zooplankton trait-based data are findable, accessible, interoperable and reusable.

 The preferred abstract topics for this workshop are:

  • Zooplankton functional ecology
  •  FAIRness of zooplankton trait based data
  •  Trait data collection and management
  •  Novel frameworks and analytical methods and e-science tools in zooplankton trait-based studies

The event will begin with informative presentations and interactive, hands-on sessions. During these sessions, the speakers will present various digital services and semantic resources developed to promote the harmonisation and interoperability of zooplankton functional trait data.

Finally, participants will have the opportunity to explore a global database of zooplankton traits and create a species trait matrix. For more information on the workshop, please visit the dedicated page and use this page to submit your abstract.