LWGreece Research Infrastructure Data Services

Research Infrastructure Data Services

The Hellenic Centre for Marine Research (HCMR) is working on the enhancement of the LifeWatchGreece Research Infrastructure (LWGreece RI) Data Services. The purpose of these activities is to provide end-users with a user-friendly service, enabling them to search and access (meta)data from two sources, Micro-CT vLab and IPT MedOBIS.

The activities are divided into three major categories:

(a) design and implementation of facilities for harvesting data

(b) data modelling and semantic data transformation activities, and

(c) updates and enhancements of the Data Services of the LWGreece RI.

More details of these activities are given below:

A set of supporting services and tools have been designed and implemented, able to harvest resources from two databases: (a) the IPT MedOBIS database and (b) the Micro-CT vLab database. A harvesting mechanism has been implemented that exports information from the above-mentioned sources, which are subsequently transformed and added to LWGreece repositories (see point below). 

After harvesting data from the sources described above, they needed to be homogenised before depositing them in the repositories of the LWGreece infrastructure. To this end, a set of mappings was implemented, using X3ML Specification Language,[1] that describes the transition of the harvested resources from their original schemata, to a common target top-level ontology MarineTLO.[2] The result was a set of ontological-based descriptions regarding MarineTLO that were inserted into the LWGreece semantic repositories.

Several endpoints of the Data Services were updated, so that they can properly retrieve information from LWGreece semantic repositories. In addition, we have enhanced the services based on the findings and the updated modelling that emerged from the two new sources that were used (i.e., IPT MedOBIS, micro-CT vLab). 

It is worth mentioning that the Data Services (along with all the other available vLabs) is now available through the Metadata Catalogue of LifeWatch ERIC. Allowing this central catalogue to be machine-interoperable is necessary for the population of the catalogue, and implements the FAIR principles and EOSC-interoperability, promoted through ENVRI-FAIR WP9 and WP11.


[1] Marketakis, Y., Minadakis, N., Kondylakis, H., Konsolaki, K., Samaritakis, G., Theodoridou, M., Flouris, G. and Doerr, M., 2017. X3ML mapping framework for information integration in cultural heritage and beyond. International Journal on Digital Libraries, 18(4), pp. 301-319.

[2] Tzitzikas, Y., Allocca, C., Bekiari, C., Marketakis, Y., Fafalios, P., Doerr, M., Minadakis, N., Patkos, T. and Candela, L., 2016. Unifying heterogeneous and distributed information about marine species through the top level ontology MarineTLO. Program, 50(1), pp. 16-40.

Explainers: the Micro-CT vLab

Micro-CT vLab

The Micro-CT vLab is a virtual laboratory which is hosted in the Hellenic Centre for Marine Research (HCMR) and was initially established during the ESFRI LifeWatchGreece Research Infrastructure. This virtual lab offers users access to virtual galleries of various samples which can be displayed and downloaded through a web application. This tool has been updated over the Elixir-GR, BIOIMAGING-GR and Synthesys+ projects with the addition of several new features. Firstly, the Micro-CT vLab has now been upgraded to Drupal version 9. A series of micro-CT datasets from medical to biological studies can be uploaded in order to be stored and disseminated.

Furthermore, the Micro-CT vLab has now a REST API for creating new content. Through the API, the user has the ability to access micro-CT API endpoints, which can retrieve information about various micro-CT scans, species and metadata information related with the micro-CT datasets. A metadata catalogue has been also created in order to dynamically display the complete metadata available for each dataset which are published in the micro-CT. Finally, following registration, the user now has the ability to upload the original micro-CT datasets and the related metadata through a user-friendly form.

You can watch a short demonstration video of the Micro-CT vLab below.

Catalogue of Life turns 20

Catalogue of Life

The Catalogue of Life (COL) is the result of international collaboration, providing researchers, policymakers, environmental managers, and the wider public with a consistent and up-to-date index of the names of all the world’s known species. COL originated in 2001 as a partnership between the organisations Species 2000 and the Integrated Taxonomic Information System (ITIS), and is now curated by an international community of 165 taxonomic data sources. In 2021, the COL turned 20, and with the release of the 2021 Annual Checklist (Bánki et al. 2021, July, 2021), has reached just over 2 million accepted species names.

Over the past years LifeWatch Belgium, as part of the COL governance, has been overhauling its digital infrastructure. The new infrastructure, powered by GBIF, functions more efficiently, is on the path to better facilitate the work of the taxonomic community, and provides a more sustainable service for users at all scales. It consists of a public portal, a ChecklistBank, and a new API. Another of its new features is that it provides stable taxon name identifiers. The intent is to create more opportunities to address taxonomic and scientific name gaps associated with the COL Checklist, which will enable the transformation of the COL Checklist to serve as the GBIF Backbone Taxonomy in the future. In the next few years, together with the taxonomic community at large, COL would like to address the apparent taxonomic gaps that still exist in the Checklist. 

COL is a wonderful example of a cost effective, functional research infrastructure that was brought to life by true international collaboration, focus, and persistence of dedicated people offering their time to make it work. COL invites everyone who has an interest to become part of the effort!

The full article can be found on the LifeWatch Belgium website.

European Tracking Network for fish reaches 500 million detections

ETN

In recent years, fish tracking technology has revolutionised our knowledge on fish migration and behaviour. The LifeWatch initiative, the European Tracking Network (ETN), integrates the European efforts of hundreds of users, dealing with thousands of tagged fish from a multitude of species. It is powered by LifeWatch Belgium through VLIZ and INBO, and supported by numerous partners throughout Europe. These combined efforts have culminated in a striking milestone: 500 million detections have been reached, imparting invaluable information on fish species such as the Atlantic bluefin tuna, European seabass and sturgeon.

There is a large and growing number of researchers using biotelemetry to study aquatic animals, such as fish, and answer management-related questions (stock management, impact of climate change, etc.). Large scale nationally and regionally managed fish tagging initiatives were implemented around the globe in recent years. The ETN aims at encouraging collaboration in the field of aquatic animal tracking in Europe and ensuring a transition from a loosely-coordinated set of existing regional telemetry initiatives to an open, sustainable, efficient, and integrated pan-European biotelemetry network embedded in the international context. In animal tracking research, electronic tags are attached to the animal, allowing us to track its movements. On land, GPS technology can be used, but in the aquatic environment we have to rely on other technologies, one of the most commonly applied techniques being acoustic telemetry. This technology uses tags that emit a sound signal that is recognised by receivers placed at strategic locations.

ETN is celebrating over 500 million detections, with 8710 tags applied to 81 species. Biotelemetry has proven its value in species research, often with a scope on pressing scientific as well as policy-driven questions. For vulnerable species such as the Atlantic Bluefin tuna for instance, biotelemetry enables researchers to fine-tune their long-distance migration patterns in support of protective management plans. In the case of critically endangered species such as the European sturgeon, tagging is a crucial element in reintroduction programmes. And for several species, including the European seabass, biotelemetry facilitates the study of a species’ migration and population structure beyond the individual stock level.

The full article, including information on individual species, is available on the LifeWatch Belgium website.

Source Image: © Exeter University

WoRMS endorsed as ‘Project Action’ for the Ocean Decade

Ocean Decade Project Action

The World Register of Marine Species (WoRMS) aims to provide an authoritative and comprehensive list of names of marine organisms, including information on synonymy. This register, which is hosted by VLIZ, a member of LifeWatch Belgium, has received endorsement by the Ocean Decade as a ‘Project Action’. In early October 2021, the UN Decade of Ocean Science for Sustainable Development (‘Ocean Decade’), endorsed 94 new Decade Actions across all ocean basins, all of them contributing in some way to the central vision of “the science we need for the ocean we want”.

Earlier in 2021, the WoRMS Steering Committee and the WoRMS Data Management Team submitted a proposal under the first Call for Actions, entitled “Above and Beyond – Completing the World Register of Marine Species (ABC WoRMS)”, which has been recently accepted, together with 93 other Actions. These actions all build on the global momentum for ocean knowledge-based solutions ahead of major upcoming global summits on climate and biodiversity. In total, there are now 335 endorsed Decade Actions.

As an Ocean Decade Project, WoRMS is being linked to the earlier endorsed Action Programme Marine Life 2030: A Global Integrated Marine Biodiversity Information Management and Forecasting System for Sustainable Development and Conservation. The Data Management Team has recently initiated conversation with the coordinators of the Marine Life 2030 Programme, to discuss the optimal ways to connect WoRMS to their goals.

During the full span of the Ocean Decade, WoRMS will continue its endeavors to provide a full taxonomic overview of all marine life, not only supporting scientists, but everyone who makes use of species names, including policymakers, industry and the public at large. Although already fairly complete, taxonomic gaps still need to be addressed, in terms of both space and time. New challenges in the field of taxonomy – such as temporary names – need to be explored, thereby looking for the best suitable solution for all WoRMS users. The documentation of species traits which are of critical importance for ecological marine research will be encouraged, as will there be increased efforts to link these with other global databases, infrastructures and initiatives such as the LifeWatch Species Information BackboneOBISGOOSCOLBoLD & GenBank.

The full article is available on the LifeWatch Belgium website.

Celebrating European Researchers’ Night 2021

European Researchers' Night 2021

Friday 24 September marked the 2021 edition of European Researchers’ Night (ERN), the Europe-wide event which takes place every year on the last Friday of September. The aim of the initiative is to bring research and researchers closer to the public, displaying the diversity of science and its impact on citizens’ daily lives.

The LifeWatch ERIC Common Facility in Spain celebrated the occasion by taking part in ERN Seville (Spain), setting up its own designated area in the Plaza de San Francisco. Here it presented the SUMHAL Project (Sustainability for Mediterranean Hotspots in Andalusia integrating LifeWatch ERIC), which is supported by the European Regional Development Fund. The core objective of this project is biodiversity conservation in sustainable natural/semi-natural systems of the Western Mediterranean, using high-tech infrastructures. Speakers included Christos Arvanitidis, LifeWatch ERIC CEO, Margarita Paneque, National Research Council of Spain and Delegate for Andalusia and Extremadura, and Juan Miguel González-Aranda, LifeWatch ERIC CTO and ICT-Core Director, in the left-hand photo above.

In Portugal, on the other hand, ERN2021 saw activities taking place in 20 cities, with the active involvement of PORBIOTA, which coordinates LifeWatch Portugal. The Researchers for European Green Growth and Education Consortium, coordinated by the Ciência Viva Agency, together with the Institute for Research & Innovation in Health and the Institute of Chemical and Biological Technology ‘António Xavier’, mobilised 18 science centres, which promoted 78 build-up activities and over 100 activities. Altogether, around 7000 participants of all ages were engaged in the programme.
In turn, Science for Climate, coordinated by the Portuguese National Museum of Natural History and Science of the University of Lisbon, brought together the Universities of Minho, Coimbra and Évora, the University Institute of Lisbon, the Faculty of Sciences and Technology of the Universidade Nova de Lisboa, the Estoril Higher Institute for Tourism and Hotel Studies, and the International Iberian Nanotechnology Laboratory. The partners, several of which belong to PORBIOTA, promoted 7 build-up activities, including a bioblitz, and an open day for school groups, which set up 13 activities in various scientific fields. In addition, an online programme with 90 different activities was promoted, and on the 24 September, an onsite programme with 156 activities took place in Évora, Lisbon, Coimbra and Braga, mobilising a total of 4581 participants. The right-hand photo shows the open night at the Portuguese National Museum of Natural History and Science of the University of Lisbon.

Recapping the ENVRI Community International School “Services for FAIRness”

Services for FAIRness

The ENVRI Community International School 2021 “Services for FAIRness”, organised by LifeWatch ERIC and ENVRI Community, was held online from 27 September – 8 October. Centred on the FAIR principles (Findability, Accessibility, Interoperability and Reusability), the School covered the design, development and publishing of FAIR webservices: the full programme can be found here. The initiative attracted 19 participants from all around the world, predominantly academics, policymakers and ICT experts, with 13 nations represented –from Italy, to Senegal, to Sweden– making it a truly international School, with a near 50:50 gender balance.

As well as the participants, the team of trainers and experts was also international, listed below in alphabetical order:


• Alessandro Spinuso – Data Technology Researcher at The Royal Netherlands Meteorological Institute
• Andreas Petzold – Head of Group Global Observation Forschungszentrum Jülich
• Antoni Huguet-Vives – Front-end architect for the LifeWatch ERIC ICT-Core team
• Antonio José Sáenz-Albanés – ICT Infrastructure Operations Coordinator at LifeWatch ERIC
• Luca Cervone – Executive Technologist at CREA-AA
• Malcom Atkinson – Professor of e-Science at Edinburgh University
• Nicola Fiore – ICT Coordinator of the LifeWatch ERIC Service Centre
• Oleg Mirzov – System Architect at ICOS Carbon Portal
• Rita Gomes – Software Engineer at Forschungszentrum Jülich
• Zhiming Zhao – Assistant Professor at the University of Amsterdam

The School included trainer-led sessions (24 hours), group work and self-study, for a total of 50 learning hours over a two-week period, with lessons taking place on Monday, Wednesday and Friday mornings. Participants appreciated the day-on–day-off approach, which allowed them time to process and elaborate the contents of the live sessions and read the provided study materials. On the last day, all the participants had the chance to show and share what that they learned during the School through group work presentations, in which they illustrated their respective projects to the rest of the class and the trainers.

So, the big question is: was the School useful? The statistics and the participants’ feedback speak for themselves: even though the participants’ prior knowledge of the topic varied widely, 80% of them self-evaluated strengthened skill levels in all three categories from the start to the end of the course – designing, developing and publishing FAIR data services. LifeWatch ERIC and the ENVRI Community are very pleased with the outcome of the School and look forward to future editions to continue enhancing the knowledge of FAIR principles, hoping in the meantime that the School can go back to in-person delivery!

LifeWatch ERIC Executive Board members to speak at the ‘XXX° Rassegna del mare’

Rassegna del mare

From 21 – 24 October, the Italian city of Gallipoli will host the XXX° Rassegna del mare (30th Festival of the Sea), organised by MareAmico, with the patronage of the Italian National Research Council and the contribution of several LifeWatch ERIC experts, scientists and representatives. This edition, which will be held in-person in compliance with anti-Covid regulations, will be based on the topic “Recognition and protection of the sea and marine resource management”.

With a range of activities taking place, the goal of the event is to raise awareness among institutions (the EU, competent ministries, the Puglia Region and local authorities) on the importance of ocean resources and their management. The round tables will be attended by international experts, who will participate in debates on this edition’s issues and topics.


Among the moderators of the event is Alberto Basset, Director of LifeWatch ERIC’s Service Centre, Manager of the LifeWatch Italy JRU (Joint Research Unit), and member of the Festival’s Organising Committee. On Saturday 23 October, during the round table “Alien Species: from threat to opportunity, the case studies of LifeWatch ERIC on the invasive blue crab (Callinectes sapidus)”, Christos Arvanitidis, LifeWatch ERIC CEO, and Juan Miguel González-Aranda, LifeWatch ERIC CTO, will present the results of the infrastructure’s Internal Joint Initiative on the theme of non-indigenous and invasive species. The work will be summed up in a report, which is going to be discussed in plenary assemblies and further worked on by the MareAmico Scientific Committee. This final document should represent the groundwork for subsequent deliberative and operational decisions.


Recreational and educational areas will be set up for younger participants, who will have the opportunity to participate in activities aimed at raising awareness on environmental issues, mainly concerning marine resources and fishing. Participants and tourists gathering at the stands will get the chance to witness the fish landing, and will be invited to enjoy the show’s cooking events, using local products.

You can read the programme here (in Italian).

Keeping up with LifeWatch Belgium

LifeWatch Belgium News

There’s been a lot going on at LifeWatch Belgium recently, so please flick through some of our favourite news stories from the LifeWatch Belgium website, where you can find the full versions of these featured articles. Source images: CATREIN, PBARN & Alvesgaspar.

 

PhD research reveals wild boar behaviour

Jolien Wevers successfully defended her PhD research on wild boar and roe deer ecology in a human-dominated landscape at Hasselt University

Jolien used the LifeWatch camera trap infrastructure (CATREIN) to investigate how wild boar and roe deer cope with human disturbance in a strongly urbanised environment at different temporal and geographical scales, and at different levels of intensity of human disturbance. 40 cameras registered wildlife presence and behaviour in the National Park Hoge Kempen in a collaborative effort between Hasselt UniversityINBO and LifeWatch Flanders. 4 years and millions of images later, the PhD research is finished.

The findings of the doctoral thesis implicate that at large scales the space use of both wild boar and roe deer is mainly driven by environmental variables (such as forest availability) rather than being driven by human activities. At smaller scales and high anthropogenic disturbance levels, wild boar display clever and opportunistic behaviour and avoid human contact by adapting their time use. At sunset, they are active in quiet areas without disturbance. Areas with many hiking trails or where hunting is allowed are only visited in the middle of the night. Roe deer on the other hand, do not actively avoid areas with human disturbance, but they do adjust their activity pattern. Instead of being very active at dawn and dusk, they are more active at night.

Publications:

Contact persons:

UHasselt : Natalie.Beenaerts@uhasselt.be
INBO : jim.casaer@inbo.be 

 

Big Five conservation measures for diadromous fish

Five years of fish tracking research using the LifeWatch fish acoustic receiver network has generated key insights into how to save diadromous fish species from historic decline 

Population numbers of diadromous fish species have reached an all-time low. Diadromous fish migrate between the sea and rivers to complete their lifecycle, such as salmon, which spawn in rivers, but grow at sea. Or eels, which do the exact opposite. However, due to water regulating obstacles in rivers like dams and hydropower stations, their migration is blocked. On top of that, many rivers have been degraded substantially by human activities, leading to the disappearance of essential spawning and growing habitats.

Researchers from Ghent University (UGent), Flanders Marine Institute (VLIZ) and the Research Institute for Nature and Forest (INBO) have come up with five actions (the ‘Big Five’) to restore diadromous fish populations:

  1. Check the functionality of a migration barrier and whether it can be removed
  2. Adjust the barrier to allow for the passage of fish, both upstream and downstream
  3. Restore spawning and growing habitats to a good state to permit species recolonisation
  4. Restock juvenile fish from nearby populations in the event of the complete eradication of source populations
  5. Ensure sustainable fishing is carried out on relevant species only once their populations are fully restored

You can read the whole article here.

For more information on the difficult migration of the eel, a diadromous species:

 

First Detections of Culiseta longiareolata (Diptera: Culicidae) in Belgium and the Netherlands 

Between 2017 and 2020, Culiseta longiareolata specimens were found at distinct locations in Belgium and the Netherlands­ – a potential vector of bird pathogens

Collected mosquitoes were morphologically identified and the identification was then validated by LifeWatch BopCo using COI DNA barcoding. These are the first records for this species, which might be a potential vector of bird pathogens (e.g., West Nile virus), in Belgium and the Netherlands. More information on the mosquito monitoring project, during which the Cs. longiareolata specimens were collected, can be found on the MEMO project page

The Barcoding Facility for Organisms and Tissues of Policy Concern (BopCo) is financed by the Belgian Science Policy Office (Belspo) as Belgian federal in-kind contribution to LifeWatch ERIC.

Publication:

Completion of RI-SI-LifeWatch Project

RI-SI-LifeWatch

In December 2019, the “Development of research infrastructure for the international competitiveness of the Slovenian RRI space – RI-SI-LifeWatch” project was granted by the Slovenian Ministry of Education, Science and Sport and the European Regional Development Fund. The aim of the project was for the LifeWatch Slovenia consortium to build a network for monitoring and collecting biodiversity and environmental data obtained and processed through the acquisition of high-performance research equipment. 

With the help of the new research equipment from the RI-SI-LifeWatch project, the Slovenian consortium is now collecting a large amount of research data in digital form, which will be included in the national Karst database, harmonised with FAIR principles and designed to provide a temporal and spatial link between specific sites.

The LifeWatch Slovenia Data Centre has also been established and consists of very powerful server and computer units. Although it is still in an early stage of development, the current functionality of LifeWatch Slovenia Data Centre is beginning to collect the various large datasets obtained with the new instruments and catalogue their metadata within a GeoNetwork portal to build a standardised database with system management and user interface for data mining and access to data products. The architecture of the new data centre proposes to replicate the functionality and standards of LifeWatch ERIC to be compliant with FAIR data principles and data lifecycle. Data collected by RI-SI-LifeWatch’s equipment will support the development of data and services planned and/or already developed and operating within the LifeWatch Slovenia consortium.

In addition, LifeWatch Slovenia is now providing new ecological research measurements and observations leading to scientific publications, as well as new datasets for the Bird Ringing database (BRDbase), for the FOR-PLAT forest database and for the Buoy VIDA marine database

With the new equipment we will develop two virtual labs in the near future: ProteusWatch vLabKarst Groundwater Habitats vLab to assess and monitor the inaccessible and unique karst groundwater biodiversity hotspots (e.g. Proteus anguinus and various cave invertebrates).

The RI-SI-LifeWatch project has also enriched the international research infrastructure LifeWatch ERIC with new research opportunities and incentives. The project has helped to:

  1. conduct modern biodiversity research for marine, freshwater, and terrestrial ecosystems
  2. establish open access to Big Data related to various databases and observatories
  3. conduct data visualisation from virtual labs with modelling tools and enhance the LifeWatch RI by developing new analytical capacity for open research data
  4. support targeted user training and collaboration to monitor and predict the impacts of global change on biodiversity

A national hub of distributed biodiversity and ecosystem research data centres will be implemented at individual national partners. The RI-SI-LifeWatch project was successfully completed on 31 August 2021.