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 CatalogueData Download Toolboxweb services and IPT), the Ocean Biodiversity Information System (OBIS) and the Global Biodiversity Information Facility (GBIF).

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”).

ENVRI Community Winter School

The 2021 ENVRI Community International Winter School on Data FAIRness will be offered online from 11 – 22 January, 2021. Developed around the theme of “ENVRI-FAIR Resources: Access & Discoverability“, the programme will cover a range of topics including semantic navigation, Jupyter environments for visualisation and data discovery, resource access tools and cloud computing.

With a focus on supporting end users in making the best use of data, developing user-friendly interfaces and providing services to facilitate their interact with data, the curriculum will cover:

  • state-of-the-art technologies relevant to FAIRification of services
  • real-life use cases, to encourage adoption of new technology and enhance data centre functionality
  • enabling new knowledge-exchange networks for ENVRI data professionals.

Applications are invited, primarily, from ENVRI data centres staff, researchers and PhD candidates and offers will be restricted to a total of 30 participants, to ensure high quality outcomes. The selection process will be based on a mix of criteria motivation and use case descriptions.

The EU AgroEcology Living Lab & RI Network

The European AgroEcology Living Lab and Research Infrastructure Network CSA launched its preparatory phase online on 8–9 December, bringing together agricultural, land-use, ecological and research institutes, to prepare a framework that will enable the transition to an expansion of agroecology in Europe. 

Under the name of ALL-Ready, the project will address the multiple challenges that agricultural systems are facing today, including climate change, biodiversity loss, dwindling resources, and degradation of soil and water quality. Open Innovation Arrangements (OIAs), in particular Living Labs (LL), and Research infrastructures (RIs) are capable of showing the way to strengthen the sustainability and resilience of farming systems.

Chief Technology Officer Juan Miguel González-Aranda, is bringing to the table LifeWatch ERIC’s expertise in data management platforms, virtual research environments, and intellectual property rights technology – including LifeBlock, which guarantees the integrity and provenance of data – as a model of the e-Services vital to European AgroEcology Communities of Practice. 

ALL-Ready will follow a highly participatory and inclusive approach, using a living lab methodology based on experimentation in real life situations. Underpinned by principles of strong stakeholder engagement, the project has three phases: 

  1. this preparatory phase to define the vision, scope and mission for the Network, which will then enable the mapping of current and emerging LLs, RIs and OIAs across Europe and their characteristics, highlighting best practice 
  2. the preparation of different prerequisites/ activities for the Network regarding sustainability, funding, governance, capacity building, data and knowledge management, that will be tested in a small-scale pilot networks and refined, and
  3. communication of the outcomes of the work throughout Europe.

H2020 ALL-Ready CSA is supporting the co-design and establishment of the coming next EU DG-AGRI Programme on AgroEcology to be published by T4 2020-T1 2023, and granted by end 2023-early 2024.

The ALL-Ready partners are: 

  • Institut National de Recherche pour L’Agriculture, L’Alimentation et L’Environnement (INRAE)
  • Aarhus Universitet  (AU)
  • Ökológiai Mezógazdasági Kutatóintézet Közhasznú Nonprofit Kft (ÖMKi)
  • Johann Heinrich Von Thúnen-Institut, Bundesforschungsinstitut für Ländliche Räume, Wald und Fischerei  (TI)
  • European Network of Living Labs IVZW  (ENoLL)
  • Biosense Institute – Research and Development Institute for Information Technology in Biosystems  (BIOS)
  • Fibl Europe –  Forschungsinstitutfur Biologischen Landbau in Europa (FIBL)
  • Ecologic Institut Gemeinnützige (GmbH  Ecologic)
  • European Landowners Organization  (ELO)
  • Agriculture and Agri-Food Canada (AAFC)
  • Eigen Vermogen van het Institut voor Landbouw -En Visserijonderzoek   (EV ILVO)
  • The e-Science European Infrastructure for Biodiversity and Ecosystem Research (LifeWatch ERIC)
  • The University of Sheffield (UOS).

Biodiversity & ecosystem research survey

In a new initiative to engage the scientific community, LifeWatch ERIC has launched an online survey to better understand their needs and to elicit their views on the important topics that will shape biodiversity and ecosystem research in the next 10 years.  

Consisting of only six questions, the consultation seeks to gather researchers’ insights into the key topics, challenges and solutions that will need to be addressed in the decade 2021-2030. The results of the questionnaire will guide the infrastructure in further developing the services and tools deemed most essential to the scientific community.

LifeWatch ERIC already provides e-Science research facilities in pursuit of its mission of increasing knowledge and deepening understanding of biodiversity organisation and ecosystem functions and services in order to support civil society in addressing key planetary challenges. 

Have your say in this consultation by following this link. It only takes five minutes, none of the questions are mandatory and you can save the questionnaire and come back to it later. At the end of the questions, you will be taken to a collaborative space where you will be able to drop us your ideas after you completed the survey. 

LifeWatch ERIC Metadata Catalogue

The release of the new LifeWatch ERIC Metadata Catalogue was announced on Friday, 20 November 2020, heralding an enormous step forward in the infrastructure’s capacity to offer researchers the innovative tools and services required to tackle the scientific challenges of today and into the future. 

LifeWatch ERIC resources and services, Virtual Research Environments, originally released by different member states, have now been united into a single catalogue equipped with descriptive metadata that allow users to retrieve and manage information in much greater quantities and at greater speed. It now consists of one unified VRE, workflows, datasets, services, and a research site.

The LifeWatch ERIC Metadata Catalogue is informed by extensive ontologies and thesauri that make the records findable, accessible, interoperable and reusable, according to the FAIR principles of data management. The architecture is based on GeoNetwork 3.10 and allows users to manage metadata related to five kinds of resources:

  • Datasets, by using the EML 2.2.0 standard (60 metadata attributes)
  • Research Site, by using a customised ISO19139 standard (36 metadata attributes)
  • Services, by using a customized ISO19139 standard (40 metadata attributes)
  • Virtual Research Environments, by using a customized ISO19139 standard (25 metadata attributes), and
  • Workflows, by using a customized ISO19139 standard (25 metadata attributes).

Not only can metadata attributes be optional/mandatory and require single/multiple values, the LifeWatch ERIC metadata catalogue also enables, upon validation and verification, the creation of Digital Object Identifiers (DOIs) for resources that do not already have one, by exploiting the GeoNetwork – DataCite connection. 

This combination of features will allow scientists and researchers, wherever they are in the world, to access data from multiple records and elaborate future models of biodiversity and ecosystem services and functioning under complex vectors of climate change, in a way that has never been possible before. 

As nations around the globe realise the need to change humanity’s relationship with Nature, it is timely that the LifeWatch ERIC Metadata Catalogue provides the computing power and access to historical records to facilitate the examination of scenarios of change across vast spatial and temporal scales. Access the catalogue here.

TiBE2020 Metabarcoding and Metagenomics

Trends in Biodiversity and Evolution

9-11 December 2020, online. The tenth edition of the Trends in Biodiversity and Evolution (TiBE) conference will be virtual this year and focus on Metabarcoding and Metagenomics. The meeting, held over three afternoons, will discuss exciting developments associated with the advent of ever more powerful DNA sequencing technologies, which are opening possibilities to explore the living world in ways that were unimaginable just a decade ago.

This annual Trends inn Biodiversity and Evolution event is organised by CIBIO-InBIO, the Research Centre in Biodiversity and Genetic Resources, connected through PORBIOTA with LifeWatch Portugal. It brings together senior researchers, post-graduate and graduate students working in the fields of biodiversity and evolutionary biology, to discuss cutting-edge findings in topics related to metabarcoding and metagenomic techniques, and their application in ecological and environmental research. The TiBE2020 conference is jointly organised by the CompBio and ApplEcol research groups. It will be hosted on an online platform that will facilitate networking opportunities and allow poster presentations. The programme, including both plenary and short presentations from selected abstracts, is divided into three sessions:

• Molecular surveys of biodiversity and invasive species

• Next generation biomonitoring of aquatic and terrestrial ecosystems

• Understanding species in interactions in complex ecosystems.

Abstracts are invited either as 15-minute oral presentations, or as 2-minute poster videos. Please note that only registered participants will be accepted as presenting authors. Abstract submission deadline is 27 October, 2020. Click here to download the abstract submission template

WCMB 2020 Virtual Conference

WCMB 2020

The World Conference on Marine Biodiversity 2020, Sunday 13-Wednesday 16 December 2020, will be fully virtual because of uncertainties in participants’ ability to travel to Auckland. To accommodate an expected increase in participants, the deadline for submission of abstracts for e-posters has been extended to 1 October.

The conference programme will be designed to accommodate varying timezones. It will enable all participants to view all talks and posters, even those in parallel sessions, at a time of their choosing. All materials, abstracts, programme, posters, talks, keynote presentations, and ‘breakout rooms’ for live discussion between participants, will be organised through one website. Side events to encourage live interactions between participants will be organised.

Conference fees for WCMB 2020 have been greatly reduced, earlybird prices apply up to 1 November, and sponsorship has been obtained to cover over 100 participants from Developing Countries. Virtual registration includes:

• Access to the virtual platform and all sessions during the conference 

• Access to recorded session content for up to three weeks after the conference has ended

• Access to view e-posters and chat with e-poster presenters

• Access to the Meeting Hub to connect with other virtual attendees. 

WCMB 2020 welcomes presentations on all aspects of marine biodiversity, both fundamental and applied sciences. The year 2020 is significant in being a deadline for both Convention on Biological Diversity Aichi Targets and UN Sustainable Development Goals, including SDG 14 on the oceans, and is a starting point for 2030 goals and the UN Decade of the Oceans. Thus, contributors are asked to link their talks and posters to these events where possible. The focus will be to prioritise contributions that are of general appeal and wide interest and, to minimise the number of parallel sessions and maximise inclusivity, participants can expect to be restricted to one presentation per speaker.