LifeWatch ERIC in support of AgroEcology

LifeWatch ERIC in support of AgroEcology Communities of Practice

On 9 February 2021, LifeWatch ERIC Chief Technology Officer Juan Miguel González-Aranda participated as speaker and in the discussions at a workshop co-organised by ScienceDigital@UNGA75 and the European Research Area (ERA) Agenda 2021-2027 to present a vision for research and innovation in Agri-food systems and explore opportunities for universities and industry.

The meeting was organised as part of the United Nations General Assembly 75th Anniversary (UNGA75) events, in line with EU Green Deal objectives to achieve a green transition and digital transformation while delivering the United Nations Sustainable Development Goals, which require a full understanding of the Agri-Food context and, in particular, AgroEcology. 

Dr González-Aranda presented LifeWatch ERIC as a distributed ICT e-Infrastructure which is helping to address the primary challenges outlined in the European Commission’s comprehensive strategy on AgroEcology. It has already played a key role in the establishment of the European AgroEcology Living Lab and Research Infrastructure Network, as key partner of the homonymous H2020 Coordination Support Action, ALL-Ready.

LifeWatch ERIC offers expertise and e-Services in Data Management Platforms & Plans (DMPs), Virtual Research Environments (VREs), and Intellectual Property Rights and Global Data Protection Regulation (IPR & GDPR) technologies. Disruptive Blockchain technologies are also a unique feature of the applications available in LifeBlock – the LifeWatch ERIC Blockchain platform – which guarantee the integrity and provenance of data, and provide a model for the e-Services vital to European AgroEcology Communities of Practice. Structuring e-Tools to assess the socioeconomic valorization of ecosystem services and their impacts is another important aspect to be considered in supporting the complexities associated with the accomplishment of SDGs 2030.

Click here for the complete agenda of the Research and Innovation in Agri-food Systems workshop.

Life in the North Sea is becoming more exotic

VLIZ Alien Species Consortium

A recent study of 14 national and international institutions – the “VLIZ Alien Species Consortium” – revealed the presence of 79 exotic (alien) marine and brackish species in the Belgian part of the North Sea and the Scheldt estuary. This translates to a 15% increase in alien species in these areas over the past decade (2012-2020). An increase in intercontinental shipping, a better monitoring of these species, and movement of species for aquaculture purposes are all likely explanations.

The VLIZ Alien Species Consortium compiled their findings in a book, and factsheets for all 79 exotic species are available through their website (both book and website are only available in Dutch).

The taxonomic information and alien distributions of these 79 Belgian alien species are also available through the Belgian Register of Marine Species (BeRMS) and the World Register of Introduced Marine Species (WRiMS), both sub-registers of the World Register of Marine Species (WoRMS). WoRMS, WRiMS and BeRMS are all contributors to the LifeWatch Species Information Backbone.

By compiling taxonomic information, native and alien distributions, and other relevant information (such as e.g. invasiveness, impact, pathways of introduction), the LifeWatch Species Information Backbone offers scientists and policy makers the needed information to analyze the current situation and to work towards possible prevention measures to stop further introductions and spreading of these species. All of this – linked to the currently maintained ‘Watch-list’ that keeps track of potential new introductions in the area – can lead to the set-up of a fast detection system and the development of a control and management framework.

See the Complete Species List here.

ENVRI Community International Winter School 2021

ENVRI Winter School 2021

The 2021 ENVRI Community International Winter School from 11–22 January attracted 32 participants from all around the world, predominantly data centre staff, researchers and PhD candidates. Centred on the FAIR principles of data management, the online curriculum covered semantic navigation, Jupyter environments for visualisation and data discovery, resource access tools and cloud computing.

In recognition of the difficulties of distance learning, the organisers structured 40 hours of presence (including preparations) over a two-week period, with scheduled lectures and presentations in the mornings (09-11), followed by associated group and individual work time (11-12). The relevance of the content to the participants’ work ensured a high level of commitment and a great sense of camaraderie developed. 

FAIR data are data which meet the principles of findability, accessibility, interoperability and reusability. The presentation of real-life use cases using state-of-the-art technologies demonstrated how essential it is to support end users in making the best use of the data, and to develop good user interfaces and services. The time the participants spent together created a new knowledge-exchange network for these data professionals. The team of teachers behind the “ENVRI-FAIR Resources: Access & Discoverability” Winter School was also international, with up-to-the-minute experience in the application of new technologies to enhance data centre functionality.
  • Dr Antonio José Sáenz-Albanés (ICT Infrastructure Operations Coordinator at LifeWatch ERIC) and Dr José Maria García-Rodriguez (Associate Professor of Applied Software Engineering at the University of Seville) dealt with how semantics enrich data resources and increase their FINDability by making them machine-actionable;
  • Dr Ute Karstens and Dr Claudio Onofrio, respectively researcher and data scientist at Lund University, Sweden, gave a presentation on a fully integrated VRE application at ICOS Carbon Portal, called the atmospheric transport model STILT, running through a full life cycle for an ‘on demand’ model and visualising results as an interactive map;
  • Dr Karolina Pantazatou and Ida Storm also work at ICOS Carbon Portal, Lund University, as scientific programmer and project assistant. Their workshop on using GIS-tools and Python-programming and user friendly Jupyter notebooks that process and analyse ICOS data products, had students tweeting in delight: “What a great workspace to document (text, images, links), write code & visualize data -all open and shareable!”;
  • ICT Coordinator at the LifeWatch ERIC Service Centre, Nicola Fiore, and Web Portal Officer at the LifeWatch ERIC Service Centre, Lucia Vaira, kicked off the second week with a presentation on the LifeWatch ERIC Metadata Catalogue, explaining the entire process behind the creation and publication of new resources and how to access them; and
  • Dr Zhiming Zhao, assistant professor at the University of Amsterdam, used examples from the ENVRIplus and ENVRI-FAIR projects to illustrate how to develop and operate data management services in cloud environments, from running a legacy and native cloud applications, to automating their deployment. Students were able to practice on the cloud infrastructures at EOSC and LifeWatch. One student tweeted a quote: “Users don’t care about the technology you use, but its quality and usefulness”. 

The final presentations allowed participants to demonstrate just how much they had learned in professional terms, but there was no sad goodbye at the end. Students had been given the recipe for pasticciotti, the characteristic Lecce pastry, the week before, and everyone cheered as the winner of the ENVRI Chef Challenge was announced. The final tweet? “I highly recommend @ENVRIcomm open training resources!”

EU-AFRICA e-Biodiversity & Ecosystem Sustainable Management in support of GeoScience

EU-Africa Geoscience Infrastructure

LifeWatch ERIC Chief Technology Officer Juan Miguel González-Aranda participated as speaker and in the discussions at a workshop co-organised on 22 January 2021 by The Science Foundation Ireland Research Centre for Applied Geosciences (iCRAG) and the Council for Geoscience of South Africa to present a vision for a shared EU-Africa Geoscience Infrastructure. 

The meeting was organised as part of the AERAP EU-Africa science collaboration platform, aimed at providing input for the forthcoming EU-Africa summit during the Portuguese Counsel Presidency. Although the summit date has yet to be finalised, the EU Strategy for Africa and the launch of Horizon Europe and the Neighbourhood, International Cooperation and Development Instrument (NDICI) can benefit from contributions from the EU and African geosciences communities. 

In line with UN Sustainable Development Goal 17, “partnerships for the goals”, the African Union’s Agenda 2063 for socio-economic transformation and the European Commission’s Africa Strategy call for partnerships to achieve common goals. The foundation for a strong and enduring partnership needs to be rooted in our shared Earth, and informed by the knowledge of what science and technology can deliver. Justly achieving the green transition and the digital transformation while delivering the United Nations Sustainable Development Goals requires a full understanding of our planet home. 

In fact, Earth sciences provide solutions for many aspects underpinning the European Green Deal and the circular economy, including water security, agricultural sustainability, energy security, raw materials availability, especially as regards the critical minerals necessary for decarbonisation, the blue economy, and community safety from geohazards including climate change. The revolution in earth sciences brought about by the Big Data generated through AU-EU research partnerships will require additional distributed ICT e-Infrastructures in Africa and Europe, and the development of data analysis and management skills, especially for younger generations and particularly women. 

An AU-EU partnership in earth sciences is being leveraged by expanding the existing cooperation between the Organization of African Geological Surveys (OAGS) and the European Geological Surveys (EGS), such as PanAfGeo which has been ongoing since 2016. At Friday’s meeting, Dr González-Aranda presented LifeWatch ERIC as a distributed ICT e-Infrastructure which is already providing support to address the primary challenges outlined in the European Commission’s comprehensive strategy with Africa, based on the essential relationship between Geodiversity and e-Biodiversity.

EcoLogicaMente

EcoLogicaMente

The EcoLogicaMente platform, developed by LifeWatch Italy in partnership with the Italian Society of Ecology (SItE) and University of Salento (UniSalento), is a web-based tool launched in 2021 to allow visitors to explore a broad range of issues in the field of ecology. 

Primarily addressed to Italian school students and teachers, from Primary through to High School, the in-depth topics contain various types of material including texts, videos, presentations, live lessons, games, questionnaires, and practical activity sheets for work in the field or in the laboratory.

The EcoLogicaMente study topics and materials have been compiled by university professors and experts on ecological issues and are divided into five macro-areas: Ecosystem goods and services, Sustainability, Resource Management, Climate Change, and Biodiversity. 

The courses are divided into different levels all of which require a login, and it is possible to receive a certificate of participation, after completing all the lessons and passing a final test. Support is available through an FAQ page and users can leave a rating of the material available and write reviews. Click here to navigate the platform.

Data Archaeology: 90 new datasets for EurOBIS

EurOBIS datasets

The Flanders Marine Institute (VLIZ), founded in 1999, promotes marine knowledge creation and excellence through sound interdisciplinary research about the ocean, seas, coasts and tidal estuaries. Since 2012, the LifeWatch team at VLIZ has processed and digitised over 100 historical biodiversity datasets that were created by, or collected in close collaboration with, Belgian marine scientists.

Over the last year, 90 of these datasets were further refined to become part of the European Ocean Biodiversity Information System (EurOBIS). EurOBIS is an important building block of the LifeWatch Species Information Backbone, a central contribution from LifeWatch Flanders to LifeWatch ERIC, the purpose of which is to centralise biodiversity data and fill the gaps in our knowledge.

Although these data refer to observations made in the twentieth century, investing time in making them available through online systems is highly valuable, as looking at the past will help us to better understand the future. Data archaeology fills in a historical data gap and provides the necessary baseline information for inter alia species distribution and climate change models.

The 90 newly-available datasets mainly cover the North Sea and provide the historical context for present observations, thereby facilitating the process of setting reference conditions for monitoring and management activities in this area. They comprise 305,529 occurrence records of 3,758 different taxa from small meiofauna as well as bigger macrobenthos communities, with the earliest occurrence record dating back to 1903. 

The datasets conform to FAIR data principles, ensuring the findability, accessibility, interoperability and reusability of the (meta)data, and have been formatted to the internationally accepted DarwinCore format (DwC), and BODC vocabularies. They are available through the Belgian LifeWatch e-Lab, the EMODnet Biology project (through its Data Catalogue, Data Download Toolbox, web services and IPT), the Ocean Biodiversity Information System (OBIS) and the Global Biodiversity Information Facility (GBIF).

Crowdsourcing platform for Coimbra Herbarium

EXPLORATOR

The Herbarium of the University of Coimbra, Portugal, celebrated its 140th anniversary in 2020, but it is only since 2002 that the collection has been moving online to make sure that these priceless resources will be available to future generations. As the digitisation is a painstakingly slow process, the University has developed a platform to enable citizen scientists to contribute to the transcription of information to the database. The COI Catalogue, as it is known internationally, contains approximately 800,000 specimens, many of which are of great historical interest. The new crowdsourcing platform – EXPLORATOR – allows registered citizens to update the descriptive labels within the database workflow, with which it is fully integrated. The data validated by the platform is progressively added to the master database and therefore made available through the online catalogue. 

EXPLORATOR was developed by the Herbarium COI team within the framework of PORBIOTA, the Portuguese e-Infrastructure for information and research on biodiversity, which manages LifeWatch Portugal. It provides each user with an image and a form to be completed one field at a time. A help icon is available for each field to provide support at every stage of the process. When a value is submitted, the platform verifies whether different values have been submitted for that field and issues an alert for discrepancies.

This validation function allows less experienced citizen scientists working in EXPLORATOR to start with fields that are easily identified and helps them become familiar with the herbarium specimens and the type of information required. When a given number of responses are validated as correct, the user is given access to the next levels which unlock more complex fields.  The architecture therefore encourages learning and greater proficiency, as well as avoiding inadvertent errors.

User proficiency levels determine the assignation of confidence values to the data entered. Validation occurs when the sum of points for a value reaches 60. Answers from an expert user are worth 50 points and those from a basic user are only worth 10, so the same value would have to be submitted by six basic users to equal the work of one expert. As an additional safeguard, manual validation by an administrator is also possible. 

The EXPLORATOR platform currently accounts for 300 registered users and a total of 140,000 submissions, which relate to 36,000 validated fields. As only 12 percent of the catalogue materials have been processed so far, it is hoped that more citizen scientists will step forward and help speed up the work of the PORBIOTA e-infrastructure consortium in storing and managing biodiversity data that is essential for the national agenda for biodiversity research.

Metabarcoding and Metagenomics Conference

The 10th edition of the Trends in Biodiversity and Evolution Conference (TiBE2020), organised by the Research Centre in Biodiversity and Genetic Resources CIBIO- InBIO Associate Laboratory, at the University of Porto, Portugal, was conducted online from 9-11 December, with a focus on Metabarcoding and Metagenomics. 

The availability of ever more powerful DNA sequencing technologies has made possible exploration of the living world in ways that were beyond our imagination just ten years ago. Researchers at all levels came together to discuss the application of metabarcoding and metagenomics to foster new and more cost-efficient environmental assessment and monitoring programs in ecological and environmental research. 

Staged over three afternoons, the programme was divided into three sections: Molecular surveys of biodiversity and invasive species; Next generation biomonitoring of aquatic and terrestrial ecosystems; and Understanding species interactions in complex ecosystems. Keynote speakers from France, UK and USA as well as 24 other communications selected from received abstracts. The conference was attended by nearly 200 participants from 24 different countries, and representing over 60 research institutions.

TiBE2020 was also the closing event of the ERA Chair in Environmental Metagenomics – ENVMETAGEN, funded by the European Commission’s H2020 Framework Program, an initiative that enhanced the capacity of InBIO to tackle societal challenges related to the loss of biodiversity, degradation of ecosystem services and sustainable development, at regional, national and international levels.

CIBIO InBIO is part of LifeWatch Portugal. 

World Conference on Marine Biodiversity 2020

The World Conference on Marine Biodiversity 2020 was successfully presented online between Sunday 13 – Wednesday 15 December 2020, by the University of Auckland, New Zealand. A state-of-the-art virtual conference platform, that facilitated interactive plenary sessions, live panel discussions, filmed presentations, e-posters, a meeting hub and virtual exhibition areas, attracted over 400 participants.  

LifeWatch ERIC was privileged to be able to support the international event as platinum sponsor. Chief Executive Officer Christos Arvanitidis, in a pre-recorded video message broadcast at the start of proceedings, warmly welcomed the participants, wishing them good luck and a great remote conference, inviting them to support the United Nations decade of ocean science for sustainable development and to become part of the LifeWatch ERIC global community.

The CEO’s emphasis on open access data, reproducible analytics and mobilised communities was reinforced by a dedicated webpage offering details of those LifeWatch ERIC products of greatest interest to marine biologists, with the Metadata Catalogue in prime position. National Nodes contributed materials on Micro-CTvLab, RvLab and MedOBIS (Greece), the LifeWatch Species Information Backbone, the Marine Observatory and three Antarctic services (Belgium), and EcoPortal (Italy).

LifeWatch ERIC staff from these member countries were also on hand at the virtual stand during the coffee breaks to maximise human interaction, in spite of the 12-hour time zone difference. The booth created considerable interest, with over 200 visitors overall and 85 downloads of brochures and other links. 

Castelporziano Estate Species Checklist

Castelporziano Biodiversity

The Castelporziano Presidential Estate, just outside Rome, Italy, is one of the three residences of the President of the Italian Republic. Dating from the fifth century, and declared a State Nature Reserve in 1999, the grounds at Castelporziano cover nearly 6000 hectares and are home to majestic oaks, laurel groves and free-roaming deer, foxes, badgers and wild boar. 

The Estate has now made its biodiversity dataset of 6329 taxa accessible through the LifeWatch Italy data portal and the LifeWatch ERIC metadata catalogue. The dataset is the result of the “Systematisation and geospatial analysis of the environmental monitoring data of the Castelporziano Estate” project, funded by the National Academy of Sciences (known as the XL), under the scientific supervision of Prof. Alberto Basset (University of Salento) and Prof. Emilia Chiancone (President of the Academy of XL). In parallel a series of 4 serious games were designed to support citizens and students in discovering the Castelporziano Presidential Estate, its biodiversity and ecosystem richness, and to further disseminate the species checklist (Check the dedicated minisite).

The first phase of creating the dataset involved the digitization of two checklists relating to the species found on the Estate from 1885 to 2006, with the integration in 2013 for the Insecta class. Subsequently, a literature search was carried out regarding all the publications on Castelporziano biodiversity from 2006 to 2019 and the data obtained were integrated into the dataset. All the observation records have been validated by botanical experts, wildlife specialists and entomologists of the Technical Scientific Commission of Castelporziano – Professors Sandro Pignatti, Carlo Blasi, Paolo Audisio and Marco Apollonio, who also provided unpublished data that were integrated into the dataset.

In the second stage, the data standardization and care/maintenance procedures were carried out using the services made available by the LifeWatch Italy platform. The dataset has been structured according to the LifeWatch Italy Data Schema which is based on the Darwin Core standard and on controlled vocabularies. For the dataset, 23 fields were selected that include information of a geographical, taxonomic nature, of the conservation status of the species according to the IUCN Red List and the Habitats and Birds Directives, as well as the alien trait and bibliographic references.

The dataset was subsequently screened for digitization errors and duplicate values removed. A taxonomic check was performed using the LifeWatch ITA nomenclatural reference system (Global Name Architecture; GNA). The GNA uses as its main Taxonomic Authority File the names present in PESI (Pan European Species directories Infrastructure; www.eu-.‐nomen.eu/portal), and for supplementary and subordinate purposes, two other nomenclators: WoRMS (www.marinespecies.org ) and the Catalogue of Life (www.catalogueoflife.org).

At the end of the standardisation and validation procedures, the dataset obtained presents 6329 taxa of which 6117 are species, 3073 genera, 801 families, 242 orders, 72 classes, 28 phyla, and 6 kingdoms.

The best represented of the latter is the animal kingdom with 3488 species, of which 2922 belong to the Insecta class. 0.77% of the species surveyed, or 49 species, are classified as alien. As for the conservation status, 492 species are present in the red lists of the IUCN (7.8%), 44 (0.7%) in the Habitat Directive 92/43 / EEC and 98 (1.55%) in the Birds Directive 2009/409 / EC. Overall, this represents 10% of the species present on the Estate and in particular 40% of the sedentary or migratory avifauna in the area.

The dataset and its metadata are accessible through the LifeWatch Italy data portal and the LifeWatch ERIC metadata catalogue. The metadata is freely available, while access and use of the dataset is guaranteed by a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International license (“CC BY-NC-SA 4.0 International”).