Embedding Amnesia, OpenAIRE’s free and open-source software, in COVID-19 research workflows to enable secure processing and sharing of sensitive data

Background: Since the beginning of the pandemic, 'ΑΤΗΕΝΑ' Research Center has been active in communicating best practices and achievements from the national and European R&I ecosystems to the Greek academic and research communities. To maximize the impact of this effort for the benefit of researchers and health practitioners, the OpenAIRE Greek NOAD has been collaborating with national stakeholders and initiatives from different domains (e.g. SSH, Bioinformatics, Computer Science, Public Management) to both support diverse research endeavors and offer opportunities for discussion about strengths and weaknesses observed in the followed approaches.

Practical workshops: In continuation of the COVID-19 series, more practical workshops are foreseen to enhance community understanding of the use of available tools as well as to build capacity on specific aspects in the COVID-19 research data lifecycle.

The workshop that was held in June 2021 ran together with the OpenAIRE NOAD in Cyprus and concentrated on the processing of data that carry sensitive and personal information taking as a use case real data from medical records of a hospital in the United Kingdom. Moreover, OpenAIRE's anonymization tool "Amnesia" was demonstrated as a tool that can be embedded in COVID-19 research workflows to enable personal identifiers' removal with guarantees.

Presentation and demo: Guest speaker and trainer for the needs of the workshop was Manolis Terrovitis, who is the creator of the Amnesia tool. Manolis started with a presentation to set the basis of the legal framework pertaining to sensitive information (GDPR) and Open Access restrictions in Europe. The presentation went on to communicate data security and privacy methods, including encryption, and highlighted the two most commonly used anonymization techniques stating that they are usually misused by researchers:

  • Anonymization that transforms personal data into exploitable non-personal data so they can be re-used or exposed or given to third parties without limitations, e.g. GDPR. The anonymization process offers guaranties that original data cannot be retrieved,
  • Pseudo-anonymization that removes direct identifiers while retaining secondary information. The pseudo-anonymized data are partially protected, but they remain personal data and can lead to the recognition of a person when reverse engineering is applied.

In order to comply with Open Access principles, the preferred method is anonymization with guarantees, such as those characterizing k- and km- anonymity techniques.

Amnesia is a free and open-source software that can be downloaded and installed locally in all operating systems (Windows, Linux, etc). 

It is a unique tool for implementing anonymization to set-valued data. Despite its complexity and the different algorithms that it runs, its interface is simple and user-friendly.


The way Amnesia works is as follows:

  1. Researchers import their data in tabular formats (e.g. .csv, .xls)
  2. Researchers select from or create the generalization hierarchies, which are compiled following rules for generalizing values in a semi-automatic way. Hierarchies can be saved and re-used or they may also be imported from other sources.
  3. Researchers choose the most suitable method for their situation (e.g., k-anonymity or km-anonymity) and link the hierarchies with the respective attributes of the records.
  4. From the results of the data generalization, researchers can choose the solution(s) that fits their needs.
  5. The anonymized data can be saved locally or directly deposited to Zenodo!

Hands-on and discussion: During the workshop, Manolis answered all the questions posed by the participants and had one-on-one break out sessions with those who needed more assistance. The discussions mainly focused on understanding the proper use of Amnesia in the different contexts and domains represented by participants and how anonymization is integrated in third party systems. Clarifications and tips included specific steps of the anonymization process in Amnesia, like the rounding of continuous variables where Manolis suggested selecting the largest range in the data to achieve the major accuracy.

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The launch of the new Library of Science website in Poland

Over 320 people from Poland and around the world participated in the launch event of the Library of Science organized on June 15, 2021. The new website was inaugurated as part of the 'Platform of Polish Scientific Publications' project by the Interdisciplinary Centre for Mathematical and Computational Modelling, University of Warsaw (ICM UW).  The Library of Science - the new version of the platform An introductory speech was given by Marek Michalewicz, director of ICM UW, who presented the...

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National policy and support actions for research data skills - impact and experiences: outcomes from the FAIRsFAIR & OpenAIRE stakeholder Workshop

FAIRsFAIR and OpenAIRE organised a joint workshop on April 28th aimed to discuss the role of national-level initiatives to advance skills development for research data management. At a European level, the emerging European Open Science Cloud (EOSC) provides impetus for skills development. However, the recent report of the EOSC Working Group on Skills & Training finds that national skills policy is usually fragmented or underdeveloped when concerning skills for research data and data-intensiv...

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Open Science course for CHIST-ERA researchers

Background: Towards the end of 2020, CHIST-ERA organized a set of training events for its researchers network in light of their newly adopted Open Science policy. The courses were prepared and run in partnership with OpenAIRE that has been advising CHIST-ERA on Open Access and Research Data Management (RDM) issues to develop and implement policies and services (CHIST-ERA Open Science Advisory Board). CHIST-ERA is a pan european consortium of national funders supporting research on Information an...

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University approaches to Citizen Science in the transition to Open Science - Institutional opportunities and challenges for creating an open and inclusive environment for Research

EUA and OpenAIRE organized a two-day, online workshop "University approaches to Citizen Science in the transition to Open Science" on December 9th and 10th. It provided a place to discuss Citizen Science (CS) in an era of Open Science (OS) and showcased a range of Citizen Science  projects combining the two movements. A particular focus was on support and opportunities for CS in universities and institutions, with ample attention to the analysis of current practice and the challenges for institutions and projects.


It will be key to provide support and incentives to encourage institutions and academic staff to pursue citizen science.

by Alexander Refsum Jensenius

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Belgian Online Open Science Webinars – skills and training

During Open Access Week, Open Science staff from Belgian universities teamed up to organize a series of 4 webinars aimed at research support staff to provide information on Open Science skills and offer the opportunity to discuss approaches to Open Science literacy and training. The first webinar 'Skills development for Open Science' introduced two EOSC related talks. Sadia Vancauwenbergh (EOSC, UHasselt) talked about the EOSC – skills and training working group which is working on building comp...

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What the future holds for OpenAIRE? German National Workshop at Open Access Tage

Virtual environment, perfect organization: On September 15th, Germany, as an OpenAIRE partner, teamed up with the organizers of the Open Access Tage 2020 at Bielefeld University for the national workshop on OpenAIRE initiatives and the EOSC. Due to the pandemic, the Open Access Tage 2020 was transferred to the digital world under the perfect organization of the team from Bielefeld University of Applied Sciences and Bielefeld University Library. Speakers at the event were Ilaria Fava and Najko Ja...

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New Handbook on research data management for Croatian researchers

The University Computing Centre of the University of Zagreb SRCE has published a Handbook on research data management entitled "Research data - what to do with it?" that provides instructions on how to manage research data for efficient sharing and reuse in accordance with FAIR (Findable, Accessible, Interoperable, Reusable) principles. The handbook is suitable for students, librarians and anyone interested in the topic of research data management, and it is publicly available (in Croatian).&nbs...

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OpenAIRE for repository managers: interoperability, metadata enrichment and usage statistics in Greece and Cyprus

The webinar: The National Open Access Desks in Greece and Cyprus, in collaboration with NI4OS-Europe project, organised a webinar entitled "Interoperability in EOSC: OpenAIRE Guidelines for repositories". NI4OS-Europe supports onboarding of national infrastructures and services of Southeast European countries, including the Balkans, to the European Open Science Cloud (EOSC) and uses OpenAIRE to assist repositories in complying with OpenAIRE Guidelines and to increase information exchange be...

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Declining Open Science into specific disciplines. The webinar series for Earth and Environmental Sciences

No doubt Open Science is a cross-cutting movement, touching all fields of knowledge and scholarly communication. And adopting a more open and transparent approach in science has broad and transversal motivations. But there are many aspects that are specific for different disciplines and research areas. In particular when looking at practical aspects on how to concretely realize open science and open access. When practically applying OS, at a certain point discipline-specific resources - such as ...

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Webinar “NARCIS PID Graph - PID graph of the Dutch research landscape”

  Connecting and enriching information in the national portal NARCIS The National Academic Research and Collaborations Information System (NARCIS) hosted by Data Archiving and Networked Services (DANS) is a portal that collects and disseminates information about scientific work in the Netherlands. Within the EU-funded FREYA project, the use of persistent identifiers (PIDs) in NARCIS has been extended and innovated to connect and integrate research information making it more visible to ...

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Report: OpenAIRE Legal Policy webinars

This blog is an adaptation of a blogpost first published on the CREATe (UK Copyright and Creative Economy Centre, University of Glasgow) blog. Thanks to CREATe's PhD students Methinee Suwannakit, Zihao Li and Jiarong Zhang for collecting the notes used to prepare this blog.                                                                &n...

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Citizen Science through seismology: School Seismograph Network WEBEX

On Tuesday, the 5th of May 2020, Greek teachers were invited to an inspirational presentation of the School Seismograph Network. During the event Dr. Gerasimos Chouliaras, who is responsible for the technical features regarding the network, presented in detail the basics of seismology and the value of society's interaction with that field of science. Later, two teachers who host seismographs in the premises of their schools presented good practices of involving the use of seismograph and the sei...

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Joint Nordic Policy Workshop

Recently, a Nordic Policy workshop was held to discuss the state of play of open data policy,barriers and opportunities and the implementation of the EOSC at the Nordic level. The workshop was co-organized by EOSC Nordic and the Nordic OpenAIRE group, and took place at the Danish National Archive in Copenhagen on the 6th of February. Stakeholders invited were Research and academic institution representatives, research communities, e-Infrastructure service providers, policymakers, and funding age...

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Third series of OpenAIRE webinars in greek launched with a “train the trainer” webinar

The new series: The National Open Access Desks for Greece and Cyprus are back with yet another series of informative and training webinars in the greek language! In 2020, webinars focus on Open Science advocacy, use of Research Data Management (RDM) services, understanding GDPR from the perspective of researchers, writing Data Management Plans and identifying areas to collaborate with each other. Hence, target groups for the webinars are librarians, repository managers, researchers and european ...

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'Monitoring OA publishing costs and revenues of publishing initiatives' - Workshop successfully

Colocated with the OpenAIRE General Assembly we organized the workshop "Monitoring OA publishing costs and revenues of publishing initiatives" on Dec-11-2019. Despite all the adverse circumstances of the general strike in Paris, the seminar room was well filled.​ Objectives of the workshop The monitoring of cost information on Open Access publishing is a crucial task in the course of the Open Access transition. The latter can only succeed if sustainable business models can be found acknowledging...

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OpenAIRE people, services and webinars during the International Open Access Week 2019

In the week of October 21st-27th 2019, OpenAIRE has organized a series of activities to highlight its continuous engagement with Open Access and Open science. Over 700 viewers participated in our Webinar Series, where specialists talked about RDM, H2020 policies, the OpenAPC project, Inclusive Science and a primer for open access journals on how to become Plan S compliant. We much appreciate the special participation and contribution of S.Venkataraman, Thomas Margoni, Emilie Hermans, Christoph B...

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The spirit of openness in Belgrade during the Open Access Week: Conference The Application of Free Software and Open Hardware

The second conference The Application of Free Software and Open Hardware (Primena slobodnog softvera i otvorenog hardvera – PSSOH) was certainly the most vibrant event organized in Serbia on the occasion of the 2019 Open Access Week. The conference was held on 26 October 2019 at the Faculty of Electrical Engineering, University of Belgrade. The conference programme, divided into five sessions, featured invited presentations on a wide range of topics, including open-source culture and local free-...

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Open Access Week in Slovakia

During Open Access week in Slovakia we organized two events. On 22.10 we had webinar "Open science is here for you" on the basics of open science and how to get involved. Around 40 people attended from all over Slovakia.  On 24.10.2019 we organized OpenAIRE workshop "Open Access: its opportunities and challenges" with 4 speakers. During the workshop participants could play a quiz about Open Science (topics were Open Access, CC Licenses, Open Data, Predatory Publishing and Plan S). ​Time ​​O...

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Services to Support FAIR Data: From Recommendations to Actions

The recommendations from previous workshops can be organised in 7 categories: CertificationEssential infrastructure componentsStewardshipCostsRewardsCollaboration and supportData Management The full draft report, provided by OpenAIRE, FAIRsFAIR, RDA Europe, FREYA, EOSC-hub can be found here. Earlier this year, two workshops were held to formulate recommendations on how services and infrastructures can better support the implementation of the FAIR data principles1. The input and conclusions from ...

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