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.

Biomonitoring of aquatic ecosystems using genetic methods

Hand holding vial containing clear liquid

The second part of a DNAqua-Net workshop on “Biomonitoring of aquatic ecosystems using genetic methods”, was hosted virtually by the Cyprus University of Technology and the Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC) of the Hellenic Centre for Marine Research on Friday 12 March 2021. It presented to experts, and to the general public, the exciting potential of new, promising and rapidly developing genetic methods for assessing biodiversity, and their use as monitoring tools.

Throughout their lifetime, all organisms release DNA into the environment (environmental DNA or eDNA). New genetic methods, such as DNA metabarcoding, detect this eDNA that is released into the environment and can partially identify and quantify the existence of various organisms without necessarily collecting whole organisms. In aquatic ecosystems, for example, living species can be detected by filtering only a few litres of water and submitting them to genetic analysis.

In an age of great ecological challenges, eDNA methods will find applications in monitoring changes in biodiversity caused by factors such as ecosystem degradation and climate change, in the early detection of alien/invasive species, and in the identification of rare and endangered species. They therefore have the potential to substantially improve the procedures for assessing and monitoring the ecological status of aquatic ecosystems, in particular as part of national and European directives, such as the Water Framework Directive and the Marine Strategy Framework Directive.

The workshop provided in-depth information on the great potential of DNA and eDNA-based methods to experts involved in the practical implementation of these European Directives, and highlighted the status quo of the reference databases. The presentations by IMBBC and CUT were followed by a discussion which emphasised the need for collaborative action between stakeholders (scientists in the fields of genetics, ecology and bioinformatics, policy makers, management bodies, NGOs, etc.) in order to standardise the methods used at national level so as to be able to engage in formal bio-monitoring actions on the ecological quality of aquatic ecosystems right across Europe.

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. 

5th LifeWatch ERIC General Assembly

5th General Assembly

The Dirk Bouts Building in the Flemish Administrative Centre (VAC) in Leuven, Belgium, was the scene for the 5th LifeWatch ERIC General Assembly, from 11–12 December 2019, chaired by Gert Verreet. Composed of the representatives from all full Member States and observers, the purpose of General Assembly Meetings, the highest governing body of LifeWatch ERIC, is to set the overall direction and to supervise the development and operation of LifeWatch ERIC. 

At the heart of this 5th General Assembly lies the prototype of the LifeWatch ERIC Platform, an integrated initiative of LifeWatch ERIC Common Facilities presented by the CTO, Dr Juan Miguel González-Aranda. Thanks to its application layers and user-friendly interfaces, the prototype will enable the integration of all the resources, including web services developed by National Nodes over the years, as well as those resulting from Common Facilities and Joint Initiatives, like the recent investigation undertaken by the infrastructure members on the current and future challenges of NIS in Europe, into Virtual Research Environments (VREs). The prototype was adopted by the General Assembly, officially marking the beginning of the deployment and operational phase, with its implementation expected to continue until the end of next year.

With many other important issues on the agenda, this rich two-day meeting moved from a review of LifeWatch ERIC activities in 2019 to forward planning for 2020 and delivering general frameworks for implementation. Among these, the Assembly approved the general framework for Service Level Agreements (SLAs) to be used as the basis for a roll-out to national nodes in the course of the year, and an engagement policy to reinforce our dialogue with – and capacity to reach out to – external stakeholders. By finalising the rules and procedures for subsidiary bodies, and having established the selection committee to complete the recruitment of one of the most strategic positions, the Chief Financial Officer, LifeWatch ERIC will be in good shape to hit the ground running in 2020.

2nd Dahlem-Type Workshop

2nd Dahlem-Type Workshop

The LifeWatch ERIC Internal Joint Initiative was launched in October 2019 to design and construct a Virtual Research Environment capable of processing and modelling available data on one of the planet’s most burning biodiversity issues, the proliferation of Non-indigenous and Invasive Species (NIS), in order to help mitigate their impacts. 

Development of a new Virtual Research Environment (VRE) is essential to further integrate the tools and services available in the LifeWatch ERIC web portal. The process will allow stakeholders greater ability to develop their research activities within the e-Science Infrastructure, whilst also clearly demonstrating the added value that LifeWatch ERIC’s advanced technologies can bring not only to the biodiversity and ecosystem scientific community, but to policymaking and human wellbeing around the globe. 

The conceptual paper and workflow-timeline developed at the 1st Dahlem-type workshop in Seville, Spain, 14-18 October, formed the basis of this 2nd Dahlem-type Workshop, organised in Rome, Italy, from 2-6 December, this time coordinated by the LifeWatch ERIC CTO, Juan Miguel González-Aranda. This 2nd Dahlem-type workshop delivered the first prototype of the new LifeWatch ERIC Non-indigenous and Invasive Species Virtual Research Environment. The collaborative construction and deployment approach and the intense interaction between ICT and NIS experts made it possible to achieve definition of the requirements and needs of the scientific community and of the main architecture layers (application, e-Services composition, e-infrastructure integration, and resources) that underpin the VRE. 

1st Dahlem-type Workshop

LifeWatch ERIC just launched an Internal Joint Initiative (IJI) focusing on the topic of Non-indigenous and Invasive Species (NIS) with the aim of developing new dedicated Virtual Research Environments. The IJI kicked off with the organisation of the LifeWatch ERIC 1st Dahlem-type Workshop: Current and future challenges of NIS in Europe, which took place from 14th to 18th October, in the Casa de la Ciencia, and the V. De Madariaga Foundation, in Seville, Spain. 

The choice of the Dahlem-type1 workshop stems from the desire of the infrastructure to use the most participative interdisciplinary approach in the search for new perspectives to drive the international research agenda on NIS and to involve relevant communities in the development of validation cases. For this reason, experts from different domains – from scientists working in the field of NIS, to ICT specialists and bio-informaticians – gathered in Seville to select the most promising research and management questions, identify the resources and tools available and specify those to be developed.

As a first step, participants identified and clustered the main issues related to NIS and discussed two macro topics, 1) risks and impacts of NIS, and 2) long-term responses of both the NIS and the native communities after invasion. Participants agreed on the development of a general framework to describe and estimate both risks and impacts of NIS (Topic one) and responses from the perspective of both NIS and native communities (Topic two) in the context of climate change. Several validation cases were proposed for each topic to apply this new framework.

On topic one, the suggested validation cases focus on the EU-scale assessment of ecosystem and habitat-type vulnerability to NIS in the context of climate change, including an assessment of sink source dynamics for specific, model, ecosystem types such as harbour ecosystems. On topic two, the chosen validation cases are based on the availability of long-term data series on a number of relevant invaders: (1) Caulerpa taxifolia and racemose; (2) Callinectes sapidus & other Crustaceans; (3) freshwater fishes at a global scale; (4) Mnemiopsis; (5) Rugulopteryx; (6) Ailanthus invasion and response monitoring with satellite images; (7) Metagenomics for invasive species; and (8) early detection of NIS with the metagenomic approach. An additional validation case was also proposed for later collaboration dealing with the risk for human health of NIS as vectors of pathogens.

The  LifeWatch ERIC ICT team’s contribution was to highlight those data resources and services required for the development of the validation cases and to suggest the implementation of an innovative approach, LifeBlock, a LifeWatch ERIC service that for the first time ever applies blockchain technology to biodiversity science. 

As an immediate result of this collaboration, scientists and ICT experts jointly outlined a conceptual paper and designed a workflow that will serve as an organised timeline along which different e-tools have to be developed to help address relevant issues related to NIS for scientists, managers, decision-makers and society.

The next Dahlem-type workshop will take place in Rome from 2nd to 6th December 2019, this time driven and coordinated by the ICT community, to produce a second technical paper and pave the way towards developing the required Virtual Research Environments.

______________________

1 A Dahlem-type Workshop is defined as a quest for knowledge through an interdisciplinary communication process aimed at expanding the boundaries of current knowledge, addressing high-priority problems, identifying gaps in knowledge, posing questions aimed at directing future inquiries, and suggesting innovative approaches for solutions. 

European Researchers’ Night

September is a busy month in the LifeWatch ERIC calendar, not only for the many scientific congresses, but also because of the increased outreach to the general public, students and families in particular, to interest them in the science behind biodiversity and ecosystem research. Within the framework of the European Researchers’ Night, on 27 September 2019, events were staged in member countries to highlight the impact of research on our daily lives.

As a record 7.6 million people took to the streets in Climate Strike protests around the world, universities, laboratories and museums across Europe were opening their doors to promote how scientific researchers contribute to society by displaying their work in interactive and engaging ways, with the ultimate aim of motivating young people to embark on research careers of their own. 

The LifeWatch Greece team participated in a European Researchers’ Night in the Hellenic Centre for Marine Research, Heraklion. Hundreds of people attended and had the opportunity to learn about marine research and aquatic biodiversity in different thematic pavilions and hands-on activities, including Virtual Reality, interactive games and demonstrations.

In Lecce, Italy, professors Alberto Basset (LifeWatch ERIC) and Giuseppe Corriero (LifeWatch Italy) joined “A Pint with Science”, an open event in a popular bar, talking about ‘Biodiversity Emergency, Objective Sustainability’ to a responsive crowd of followers on Thursday. 

The following day, LifeWatch ERIC Service Centre at the University of Salento opened its premises to young people and families, to play dedicated serious games on biodiversity and make enquiries about the infrastructure and its activities. Listening to videos of key scientists explaining how ecological science builds an understanding of the issues we face globally, visitors were guided to learn more about the key challenges ahead in the field of biodiversity and ecosystem research 

In the midst of popular calls to deal with current climate issues, these outreach events showcase the diversity of research, bring researchers closer to the public, mobilise citizens, and increase general awareness and understanding of how important research and innovation are in addressing societal challenges.

LifeWatch ERIC Internal Joint Initiative

Non-indigenous and Invasive species (NIS) are considered a major threat to biodiversity around the globe: they can impact ecosystems in many ways by outcompeting or predating on native species. Who has not heard of the Burmese pythons in Florida that eat alligators? The negative impact of imported rats and cats that have decimated island fauna populations? However, the long-term impacts of NIS on ecosystem integrity are poorly explored, and policy-makers are often left without sufficient information to make wise management decisions.

In the belief that the first steps in tackling biodiversity loss must be to improve our knowledge by developing better inter-disciplinary paradigms, LifeWatch ERIC is launching an exciting new Internal Joint Initiative (IJI), involving the scientific communities of National Nodes and other European Research Infrastructures, that will thoroughly describe the issues involved in ecosystem and habitat type vulnerability, and produce future scenarios under changing vectors to help decision-makers combat the impacts of climate change. 

The LifeWatch ERIC Internal Joint Initiative will combine data, semantic resources, data management services, and data analysis and modelling from its seven member countries – Belgium, Greece, Italy, the Netherlands, Portugal, Slovenia and Spain – to bring together national assets on a scale never attempted before. This integration of Common Facilities and National Nodes will provide the comprehensive and synthetic knowledge so much needed by institutions and administrators.

By deploying and publishing on the LifeWatch ERIC web portal the federated resources and e-Tools and e-Resources, the Internal Joint Initiative will also define the requirements and architecture of the LifeWatch ERIC virtual research environments, and provide a clear demonstration of the Infrastructure’s added value for researchers in addressing specific biodiversity and ecosystem management issues. 

Non-indigenous and Invasive Species are a global problem. They are distributed among most plant and animal taxa, and present a number of key issues that remain challenging for both researchers and policy-makers. The knowledge produced by the Internal Joint Initiative will thus be of global significance. It is to be hoped that this demonstration case will be seen to have scientific and socio-economic implications for many different fields of investigation over the coming decades.