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.

LifeWatch ERIC Takes the Baton: Final Meeting of LIFE AdaptaMED Project

LIFE Adaptmed

On Thursday 19 November, LifeWatch ERIC CTO, Dr Juan Miguel González-Aranda, delivered a keynote speech a the Adaptamed Symposium in Málaga, which marked the end of the LIFE Adaptamed project. His speeh was entitled “LifeWatch ERIC in a nutshell”, and showed the main goals and e-services provided by LifeWatch ERIC in the context of the ENVRI cluster. The presentation took place during the session named “New technologies for monitoring – ecosystem management and visualisation” together with Dr Regino Zamora, Professor of Ecology from Granada University, Dr Antonio Ortiz, from the Water and Environment Agency of Junta de Andalusia (AMAYA), chaired by Dr Francisco-Javier Cano-Manuel, Chief of the Environmental Management Department of Junta de Andalusia in Granada.

The LIFE Adaptamed Project has as main goal obtaining recommendations for the protection of Ecosystem Services in the Mediterranean area. These recommendations would be carried out through the development of adaptive management actions, focusing on the goods and services provided by their natural spaces: for example, those addressed to soil protection, the regulation of water resources and climate itself, the prevention of desertification, the maintenance of fundamental ecological functions to favour the self-organisation of ecosystems (e.g., pollination or seed dispersal), in a global climate change scenario in which socio-economics impacts should also be taken into consideration.

You can watch the recording of the event here (in Spanish). For Dr González-Aranda’s presentation, skip to 7:03:00.

LifeWatch ERIC CEO and CTO Inspire at ‘Inspirational Event 2021’

Inspirational Event

Inspirational Event 2021, powered by Advance Services, took place at Heraklion (Crete) on 15 and 16 November. Its purpose was to bring together successful and distinguished professionals to give half-hour talks, passing on their knowledge, experiences and advice to an audience consisting of executives and entrepreneurs of the local community.

Alongside LifeWatch ERIC Executive Board members, Dr Juan Miguel Gonzalez-Aranda (LifeWatch ERIC CTO & Head of its ICT-Core) and Dr Christos Arvanitidis (LifeWatch ERIC CEO), spoke Dr George Bruseker (Takin Solutions CEO), Dr George Caridakis (Professor at the Aegean University), Mr Yannis Lidakis (Harvard University Representative & SkyExpress Commercial Director) and Dr Armando Stellato (Professor at the University of Rome). The event was chaired by Nikos Minadakis, CEO of Advance Services, which provides Technical & Operations Consultancy to LifeWatch ERIC.

The audience was thrilled with the professional experiences, tips, suggestions and ideas of the speakers, and actively participated with comments and questions. A total of fifty people who had received invitations said they would gladly attend the event each year and were looking forward to returning. The executives of Advance Services expressed their enthusiasm in repeating the event, next time with even more speakers, listeners and a wider range of topics.

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.

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.