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.

LifeWatch ERIC CEO at the Ionian University

Ionian University

On 23–24 November 2021, LifeWatch ERIC CEO, Christos Arvanitidis, travelled to the Ionian University in Zakynthos (Greece) to deliver three lectures to Bachelor’s degree students at the University’s Department of the Environment.

Dr Arvanitidis gave three in-person lectures; the first presented the research infrastructure LifeWatch ERIC and its unique position at the service of the biodiversity and ecosystem research community, the second covered examples on the international, European and national legal framework of the sea, whilst the third demonstrated  how LifeWatch ERIC can help scientists working on lagoonal biodiversity and ecosystem dynamics. Dr Arvanitidis himself is a marine scientist and Research Director at the Hellenic Centre for Marine Research, where he helped to form the national node LifeWatchGreece before becoming LifeWatch ERIC CEO.

LifeWatch ERIC already has strong ties with the Ionian University, which will soon be offering the same LifeWatch ERIC-developed e-Biodiversity and Ecosystem Sciences (EBES) MSc programme already available at the University of Salento (host of LifeWatch Italy). Once activated there, the course will give enrolled students the opportunity to obtain a “Joint Degree” with an exchange programme between the two countries.

You can view the EBES Master’s brochure here.

COP26: A New Hope? – LifeWatch ERIC CTO in Lecture Series on Climate Change

cumbre del clima COP26
An expert-led Lecture Series on the topic of Climate Change (La cumbre del clima COP26: ¿Una nueva esperanza?) is taking place at the University of Navarra, in light of COP26, which came to a close last week.

The Conference brought together representatives from many countries with a common goal: to implement measures to reduce global temperature below 1.5 ºC compared to pre-industrial levels, in a bid to reduce the negative effects of climate change. The aim of the Lecture Series is to present a multidisciplinary exploration of this topic, touching on themes of biodiversity, circular economy, ecology, energy sources or sustainable building, hearing from a range of topic-specific experts.

One of these such experts was LifeWatch ERIC’s own Juan Miguel González-Aranda, Chief Technology Officer and ICT-Core Director, who was called on to present on Sustainable Development Goal 15 Life on Earth. The lecture took place on 12 November 2021 with an in-person audience at the University of Navarra, as well as being livestreamed on YouTube.

His lecture followed the following structure, and was followed by a Q&A session with the audience:

Part 1: Approaching ecosystem services in the context of climate change

Part 2: e-pan-European distributed research infrastructures to strengthen communities working in the realms of science, technology and innovation 

Part 3: Let’s be FAIR: Addressing the challenges of the heterogeneity and scale of biodiversity data, and providing ecosystem services in a sustainable manner through the use of disruptive ICT

Part 4: Tesseract and LifeBlock (tools developed by LifeWatch ERIC)

Part 5: Conclusions

The full PowerPoint presentation (in Spanish) can be downloaded here.

You can watch the full lecture here (in Spanish).

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!

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:

LifeWatch ERIC at the 1st International Congress of Equinology and Equestrian Tourism

e-Horse: International Congress of Equinology and Equestrian Tourism

Dr Juan Miguel González-Aranda, CTO, represented LifeWatch ERIC yesterday at the 1st International Congress of Equinology and Equestrian Tourism. The interdisciplinary event took place at the Polytechnic Institute of Viana do Castelo on the northern Portuguese coast. It was held in the Professor Lima de Carvalho Auditorium and co-organised by Dr Enrique Alonso-García, one of the founders of LifeWatch ERIC, who gave a presentation entitled “The International ‘Wild/feral horses in National Parks’ initiative: the case of the Iberian Peninsula”.

The aim of the Congress was to investigate a range of research themes based on the scientific studies of equines, as research on equine social behaviour and cognition is still scarce, despite horses having traditionally been the most-researched animals in Europe due to their major role in the dynamics of human societies. In fact, the event was split between both social and scientific aspects of equine research, which the project behind the event maintains requires the creation of an independent and holistic scientific discipline.

Dr González-Aranda gave a scientific intervention as part of the panel “Language, Intelligence and Cognition”, with his presentation: “e-Horse: the EU LifeWatch ERIC initiative on digital transformation and the role of equids in biodiversity conservation and sustainable use” (e-Horse: a iniciativa EU LifeWatch ERIC sobre transformação digital e o papel dos equídeos na conservação da biodiversidade e uso sustentável).  

The e-Horse Initiative

e-Horse is the LifeWatch ERIC initiative on digital transformation to understand the role of equids in biodiversity conservation and sustainability. As a distributed e-Infrastructure, LifeWatch ERIC provides state-of-art ICT in the form of outstanding analysis techniques such as Geodesign to support decision and policy makers in addressing societal challenges. It takes a transdisciplinary scientific evidence-based knowledge approach, applied in key sectors such as Agroecology, Invasive Alien Species impacts, and more. The work LifeWatch ERIC does in integrating micro-, meso- and macro- scales (which presents a challenge in terms of data heterogeneity) contributes towards the accomplishment of the EU Biodiversity Strategy 2030 & the Green Deal, as well as the SDG 2030 objectives

The e-Horse initiative involves other world regions besides Europe, among which Latin-America and the Caribbean, the USA, Africa, Japan, etc. It is therefore seen as an international referent in the holistic approach to horse livestock and ecosystem sustainable management. Together with the provision of advance services dealing with topics such as genetics, ethology, cultural heritage, etc., it fosters sustainable socioeconomic development beyond preservation activities. So far, two areas of e-Horse activity are of note: (a) Feasibility study of grassland monitoring for wild and domestic horse habitat mapping, making use of the EU-Copernicus programme for operational monitoring applications based on high resolution and acquisition frequency of Sentinel-1 (radar) and Sentinel-2 (optical) satellites, and (b) Development of equestrian sustainable ecotourism activities in the Portugal-Spain transboundary ecosystems corridor through cultural heritage trails.

Overall, e-Horse supports the provision of proper ecosystem sustainable services by demonstrating the essential role that horses play in recovering ecosystems worldwide. A concrete example of this is the case of mitigating the “drying of the oaks” disease in the “dehesas-montados”, with e-Horse linking cultural and biodiversity policies in instances of private sector involvement, through the development of citizen science activities.

Keeping up with LifeWatch Belgium

Keeping up with LifeWatch Belgium: a hand displaying Wormsina specimens, a still from a MarineRegions map, and the cover of the UN's World Oceans Assessment.

LifeWatch Belgium has been busy over the last few months, so enjoy a round-up of some of their best stories. You can read more news from LifeWatch Belgium, including the full versions of these featured articles, on their websiteSource images: Alice Schumacher (Natural History Museum Vienna), MarineRegions.org & UN.org.

 

WoRMS honoured with new genus

The World Register of Marine Species, better known as WoRMS, is hosted by VLIZ, which is a member of LifeWatch Belgium. For the first time, in recognition of the platform’s contribution to taxonomy research, a genus has been named after the Register: Wormsina. Harzhauser & Landau established the genus for a Miocene Paratethyan Mitridae, noting: “We all are frequently using and consulting WoRMS and this is [our] contribution to make this important platform even more visible.”
The full paper is available on ZooTaxa & ZooBank. Be sure to check out the Wormsina monograph on page 49! You can view the genus on WoRMS and MolluscaBase. Click here for the original article.

 

MarineRegions’ Exclusive Economic Zones featured on MarineTraffic.com

An important dataset from MarineRegions, (funded partly by LifeWatch Belgium) has now been featured as a map on MarineTraffic.com, helping to improve the experience of millions of users. Since 31 March 2021, vessel locations can be plotted against the global Exclusive Economic Zones (EEZs), a dataset provided by MarineRegions. EEZ was originally published in 2006 and shows the ocean and seas belonging to coastal states. The EEZ dataset and its derived products are increasingly being adopted by a wide range of users, from industry over researchers to journalists.
Read the full article here.    

 

VLIZ research data infrastructures played key role in UN Ocean report

On 21 April 2021, the United Nations launched the Second World Ocean Assessment (WOA II) on the state of the ocean, covering environmental, economic and social aspects. Staff from the data centre of VLIZ, a member of LifeWatch Belgium, were among the 300 selected from a pool of 780 experts around the world who contributed to this landmark document. The first cycle (WOA I) focused on establishing baselines, whereas WOA II, which ran from 2016 until 2020, extended the scope to evaluating trends and identifying gaps.
The contributions of VLIZ to WOA II were made possible through the support received from the Research Foundation – Flanders as part of the Belgian contribution to LifeWatch. Click here to learn more about the details of these contributions.

The 2021 ENVRI Community International School

The official banner for the ENVRI Community International School - Services for FAIRness

The 2021 edition of the ENVRI Community International School has been launched!

Organised by ENVRI-FAIR and LifeWatch ERIC, the ENVRI Community International School is at its fourth edition, having established itself as an unmissable opportunity to learn about FAIRness in the framework of Research Infrastructures. Having gone into depth on data FAIRness and data management during previous editions, this year the School will focus on Services for FAIRness, from their design to their development and publication.

Further information on the programme and teachers will soon be available.

SAVE THE DATE | The school will take place online from 27 September to 8 October 2021.

Do you want to know more about the School? Check out the previous editions at the following links:

The 2020 Winter School on DATA FAIRness

The 2019 Summer School on DATA FAIRness