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 in IKRI Launch

Click here to watch a short explanatory video on IKRI.

The UNGA76 Science Summit is in full swing, and LifeWatch ERIC has already played an active part in several sessions, looking forward to the LifeWatch ERIC-convened session on SDGs 14 and 15 on 1 October 2021. On 23 September, LifeWatch ERIC CTO, Dr Juan Miguel González-Aranda, alongside Prof Vladislav Popov and Ms Karina Angelieva from LifeWatch Bulgaria, took part in an important session on the launch of the Indigenous Knowledge Research Infrastructure (IKRI), which approximately 140 people attended.

The UNFSS (UN Food Systems Summit) recommended five ongoing Action Areas where the UN will place a particular focus and take increased responsibility to link the local to the global and support implementation at country level to maximise impact on the 2030 Agenda.* These Action Areas will help to organise, guide, and direct the wealth of initiatives emerging from the Summit process to achieve the SDGs. Action area 5: “Support the Means of Implementation” covers the following: Finance; Governance; Science and Knowledge (Indigenous Food Systems); Innovation, Technology, & Data, Capacity; and Human Rights, and beyond).

The “Global Research Initiative and Knowledge Repository to integrate Indigenous Knowledge into Food Systems” was developed as part of the UN Food Systems Summit process, with the collective efforts of CANEUS, together with The Fund for the Development of Indigenous Peoples of Latin America and the Caribbean (FILAC), United Nations Office for Outer Space Affairs (UNOOSA), The International Center for Agricultural Research in the Dry Areas (ICARDA), The Africa-Europe Science and Innovation Platform (AERAP) and LifeWatch ERIC. It will contribute to action area 5: “Support Means of Implementation”, and was launched at the UN FSS Summit.

This Global research initiative aims to develop digital infrastructure to support more comprehensive R&D collaboration between the UN and the EU, AU, and other regions, creating partnerships and sustained access to data and information sources globally and lessening the regulatory burden associated with access to and use of public data. The initiative will function as a digital infrastructure known as IKRI, based on the EU Strategy Forum for Research infrastructures ESFRI. It will have a component of “Technology-based Repository” that utilises frontier Technologies (Earth observation and geospatial intelligence with 4th Industrial Revolution Technologies) for the development of a portal that captures, processes, analyses and presents Indigenous knowledge through multiple sources.

The IKRI is hoped to increase the level and range of partners who can bring Indigenous knowledge to collaborative research supported by the EU Horizon Europe Programme and other research programmes implemented at state level and committed to supporting the SDGs. It would further leverage the EU Neighbourhood, Development and International Cooperation Programme, known as the Global Europe Programme, to support Indigenous knowledge, ensuring that developing nations are considered within the context of enabling global policies and related regulations to ensure that the global regulatory environment does not become a barrier to knowledge exchange, but rather supports access to and use of patent data, knowledge and know-how.

*(1) Nourish All People, (2) Boost Nature-based Solutions, (3) Advance Equitable Livelihoods, Decent Work & Empowered Communities, (4) Build Resilience to Vulnerabilities, Shocks and Stresses, and (5) Support Means of Implementation.

Space and the Sustainable Development Goals 2030

UNGA 75

LifeWatch ERIC was represented on Friday 10 October, 2020, at another international online workshop by Chief Technology Officer Dr Juan Miguel González-Aranda. Entitled Space and SDG 2030, and organised by Science Digital @ UNGA 75, the forum discussed how to frame the contribution of space technologies to the attainment of the United Nations Sustainable Development Goals (SDGs), and featured contributions from Ireland, Germany, Spain, the Netherlands, Canada, Nicaragua, and the UN.
 
Dr González-Aranda’s presentation at UNGA 75 started from the premise that human well-being depends on healthy ecosystems and that LifeWatch ERIC’s work, in assessing and monitoring ecosystem functions to understand the underlying ecological processes of biodiversity, is critical to achieving the UN’s Sustainable Development Goals.
 
Using Tesseract VRE, the product-framework being deployed to build large-scale virtual research environments, and LifeBlock, the blockchain technology to guarantee the provenance and persistence of evidence, LifeWatch ERIC is using remote sensing information from space to providing science-based management frameworks, tools and mechanisms.  
 
Working with other Research Institutes, and offering expertise on cross-border initiatives, as in EU-LAC and EU-AFRICA, LifeWatch ERIC is applying Artificial Intelligence and Big Data services to enable faster and more accurate detection and identification of species. This helps the United Nations Office for Outer Space Affairs -UNOOSA-, for example, to link space and wildlife communities and understand what is going on. By assisting international agencies and building citizen awareness, these operations contribute critically to preserving the planet.

Towards a Comprehensive & Integrated Strategy of the European Marine Research Infrastructures for Ocean Observations

Strategy European Marine Research Infrastructures

LifeWatch ERIC Service Centre Director Alberto Basset and CTO Juan Miguel González-Aranda have contributed to a recently-published paper that addresses today’s environmental challenges, entitled “Towards a Comprehensive & Integrated Strategy of the European Marine Research Infrastructures for Ocean Observations”, published in Frontiers in Marine Science.

Addressing environmental challenges is crucial for humanity and for life on Earth, and will depend on accurate information about fundamental processes in the geosphere, hydrosphere, biosphere and atmosphere, and their interactions. Marine Research Infrastructures (RIs) are key tools for understanding these complexities and interrelationships through multi-, inter-disciplinary approaches, because they constitute a dynamic long-term infrastructure framework, supported by European and national funds, to facilitate research, and provide highly accurate data and services.

Collaboration is essential to provide solutions to complex issues that cannot be solved by one partner alone. Europe has the resources and capacity to make comprehensive ocean observations for the benefit of society, and collaboration between RIs is emphasizing the development of multi-sensor technologies and the adoption of multi-parameter and interoperable methodologies for integrated and sustained marine observations. Click here to download the article.

Leading. Pioneering. Inspiring. | Inaugural address by LifeWatch ERIC CEO

LifeWatch CEO

Today is a very humbling day for me. It reminds me of my very first days with LifeWatch, when the idea of such a Research Infrastructure (RI) was conceived and then announced to the marine biodiversity community during the kick-off meeting of the MarBEF Network of Excellence, back in 2004. Like all of you, I was an enthusiast of LifeWatch (LW) RI and since then, I have been involved in the design, the development and operation of this great RI. The vision of this perpetual process of construction, operation and evolution of such an RI, where people meet and collaborate in cyberspace in order to test their hypotheses on biodiversity and ecosystem research, has never stopped fascinating and inspiring me.

Since the early times of LW, I saw clearly how we can empower people to do and achieve things never attempted before with our creations and ultimately make the LW RI a better place to work. By analyzing, understanding and modelling Biodiversity and Ecosystem functioning, we provide science-based evidence to preserve and sustainably use our resources, our biodiversity, our ecosystems and the services they provide to our common planet. I felt there was no better RI to join if I wanted to try to make a difference to this discipline. This is the very same inspiration that continues to drive me today. It is, therefore, an incredible honour for me to lead and serve LifeWatch ERIC (LW ERIC) and above all the community interested in this discipline. I’ve been fortunate to lead the construction and operation phase of LifeWatchGreece RI and work closely with all members of the LW ERIC Executive Board and General Assembly over the last five years. I have, therefore, gained a good knowledge of what has been done so far but I’m also looking forward to working with the members of the broader LW ERIC community. This community has achieved, so far, a great success, but we are all so hungry to do a lot more. As we depart on this new journey of LifeWatch ERIC together, I wanted to share some background on myself and what inspires and motivates me. 

What has been achieved so far at LifeWatch?

LifeWatch has undergone a remarkable evolution during the three years of its existence as an ERIC: (a) the legal entities and bodies that are absolutely necessary for its operation have been established; (b) both the headquarters and the distributed components of the ERIC have been hosted in physical installations; (c) a lot of the machinery to be used has been purchased and is already in operation; (d) currently, we’re on the process of the integration of all the technology (e.g. data, tools and services) that has been developing over the past years by the national nodes of LW ERIC. I feel extremely grateful to all those who have worked hard for LW ERIC to become a reality, those pioneers who have laid the foundations of LW ERIC.

Our ERIC respects three things: (a) science, the driving force for the production of new knowledge; (b) innovation, an essential aspect for the RI to make a difference not only to science but also to the attitude of the community involved; and (c) community, the most critical of all the ingredients for the successful development and implementation of an RI.

Who am I?

I am 53. I’ve been a humble servant of biodiversity and ecosystem research discipline for almost a quarter of a century now. And like anyone else, a lot of what I do and how I think has been shaped by my research family and my overall life experiences. I’ve spent many thousands of hours digging in mudflats and lagoons, sampling the ports, the coastal substrates by SCUBA diving or from a scientific vessel or inflatable and so many more hours at the microscope, conducting traditional taxonomy on countless thousands of creatures, and on computer screens, trying to analyse the data. I have been running the Biodiversity laboratory in the Institute of Marine Biology, Biotechnology and Aquaculture (HCMR) for more than fifteen years now. This laboratory conducts research on the cutting edge of ecology, genetics/genomics and cyber-taxonomy, using the institute’s state-of-the-art heavy instrumentation such as micro-CT scanners and next generation sequencers. I have worked with people in the field, in the laboratory, with people at all levels of investigation, from the technicians to computer scientists, and stakeholders and policy makers at local, regional, national and European (international) levels. My special drive in my scientific life is an insatiable thirst for learning new things, doing new things, wondering, discovering, reading, writing, training, teaching. That’s me, that’s how I think, what I do and how I live my life.

Why am I here?

I am right here for the same reason I think most members of this wonderful research (and not only) community: to change the current way scientists conduct biodiversity and ecosystem research through the ever-growing Research Infrastructure of LW ERIC; to work hard in order that LW ERIC provide them with Virtual Research Environments (VREs) where they can carry out almost the entire process of research making, from the conception of the idea and formulation of the hypotheses to test, all the way to the interpretation of the results and the production of knowledge. Over the next decade we shall witness that power- and cloud-computing will become even more ubiquitous and that artificial intelligence and intelligence from machine learning will prevail in our discipline. We will also witness a faster co-evolution of hardware, software and scientific thinking. All these create a wonderful challenge for us to achieve our mission.

Why is LifeWatch ERIC here?

When we started this journey of the RIs foundation, our mission was to create machine-to-machine readable data and to develop software (web tools and services) for data analysis, a task which over the last couple of decades has created a big ecosystem of both data and services. The opportunity ahead requires us to re-imagine and re-think a lot of what we have done in the past for this community and to create new things.

Our big challenges require VREs where both data and software can be combined, integrated and used to: (a) test complex hypotheses on biodiversity and ecosystem patterns and processes at multiple levels of the biological organization and scales of observation; (b) explore and model the consequences from possible alterations in these patterns and processes as a result of multiple drivers of change. We are the only ones who can harness the power of such VREs through devices and web services that truly empower every researcher or any other type of user in doing biodiversity and ecosystem research. We are the only RI with a past history and a continuing focus on laying the foundations for building those VREs that create great opportunities. What we do empowers our community to do more of what they care about, that is, to accomplish great things and in so doing, also to have fun and real enjoyment. Ultimately, this is what makes the hard core of who we are, and meeting our future great challenges and achieving our goals is why we are here.

What do we do next?

We’re fortunate to have a clear vision and sense of mission that leads us to imagine, design and deliver our next generation of biodiversity and ecosystem research products and services. Our mission for the next period of LW ERIC is to turn scientists’ attitude from working in isolation in a single-core PC and with licensed software into using and benefiting from an ecosystem of web services publicly available on the web site of the LW RI with huge data management effort and support, storage capacity and computational power, which provides them not only with the capability to scale up their research interests and work on global hypotheses but it also ensures transparency, repeatability and attribution for their endeavour. All of the above constitute the very fundamentals of the scientific method and production of knowledge. Therefore, the vision for LW ERIC should be to achieve this groundbreaking change in the way most scientists on biodiversity and ecosystem research currently work: to change their everyday habits by opening the LW RI web page as they turn on their PCs and use their preferred operational platforms. This change would direct most of the scientific effort from a single-core brain (SCBs) operation or “brain-etics” to high-performance brain network synthesis (HPBNs) or “brain-omics”. This is a cultural change we have to drive our community. 

This is the only way to ensure that the research effort goes far beyond the personal interests of each scientist and delivers a synthetic view of the phenomena and processes we explore, trying to understand and provide prognosis in the discipline of biodiversity and ecosystem research. Delivering such a science-based synthetic knowledge is the best way to address current and urgent societal demands and assist the EU efforts for growth and job creation.

Our new LifeWatch tagline: Leading. Pioneering. Inspiring.

During the next period of LW ERIC, every one of us needs to do our best and try to make this cultural change happen. What is clearer than ever before, though, is that we cannot achieve any degree of success if we choose to pursue the above goals independently. We need to do this, together and with our community.

Many Research Infrastructures aspire to bring about cultural changes, changes to the current landscape, and to achieve the de-fragmentation of their communities. Very few though have all the elements required: physical installations, hardware, software, data and data observatories, resources, and above all, the right people to do the job. LifeWatch ERIC RI has proven that it has all of them and in abundance.

As the new CEO, I can’t ask for a better foundation.

Let’s build on this foundation together.

Christos Arvanitidis.

Acknowledgements:

I’m very grateful to the former CEO Jesús Miguel Santamaría Ulecia, the interim CTO Juan Miguel González-Aranda and the members of the Executive Board, Prof. Alberto Basset and Prof. Peter van Tienderen, for their Herculean work to make this ERIC operational; also Prof. Jesus Marco de Lucas vice-President of CSIC and Prof. Enrique Alonso Council of State for the Kingdom of Spain for their continuous support at all levels and phases; the former Chair of the General Assembly Prof. Benjamin Sánchez Gimeno, our deceased Chair Mr Marc de Jong, our current acting Chair Mr Gert Verreet and the members of the General Assembly for laying the foundations of this ERIC; the LifeWatch ERIC staff for all the hard work and dedication they put in daily; the national coordinators and their teams for their massive support and for building the components of this wonderful Research Infrastructure and finally our scientific community for being the soul of LifeWatch ERIC. I’m much indebted to all of you and I hope my service here will meet your expectations.

Welcome, LifeWatch ERIC!

Deepening biodiversity and ecosystem related issues has become a crucial value in contemporary society, which is tackling global scale challenges on capital elements, such as resource supply, economic development, environmental security and human well-being. The European Commission recognises research in this area as a priority, moving further from the punctual programmes funding the many fixed-term projects, to the institution of a European Research Infrastructure Consortium, as a long term strategy to ensure sustainability of research. Welcome, LifeWatch ERIC!

LifeWatch ERIC is the 14th European research infrastructure to be granted this important status, and it is composed by eight founding member states and three common facilities. Through the use of the ICT, the infrastructure guarantees the access to big sets of data on biodiversity, ensuring their standardisation and interoperability, and providing researchers and institutions with tools and services allowing the creation of customised virtual research environments, supporting policy making.

Italy, through its Ministry for Education, University and Research (MIUR) and its National Research Council (CNR), plays a key role in LifeWatch ERIC, hosting its Service Centre, one of the three common facilities, at the University of Salento, and contributing with its e-Biodiversity Research Institute, powered by a Joint Research Unit counting more than 30 among top level universities, national institutes, regional agencies and academies of the country.

On 8 and 9  May 2017, the first General Assembly of LifeWatch ERIC took place in Seville (Spain), and elected the interim members of the statutory bodies which will manage the Consortium until the formal ones will be appointed. Prof. Alberto Basset has been named interim Director of the Service Centre and interim Member of the Executive Board.

On 23 May 2017, European Commission Director-General for Research & Innovation, Robert Jan-Smits, awarded the LifeWatch ERIC Plate to the Spanish Secretary of State for Research, Development & Innovation, Carmen Vela, who received it on behalf of the entire LifeWatch ERIC community.

Welcome, LifeWatch ERIC!

To see the LifeWatch ERIC statutes, please click here.

You can find the Communication of the European Commission here.