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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Cypriot NI4OS-Europe event and OpenAIRE contribution

About: On April 23, 2021 the University of Cyprus Library organized an Open Science event to update on the latest developments of European Research and Innovation actions, mainly focusing around the European Open Science Cloud (EOSC) developments. The event welcomed 65 participants spanning from academics, researchers to policy makers, funders, librarians and Open Science enthusiasts. Agenda: The Cypriot Open Science event was organized in the context of the National Initiatives for Open Science...

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European Commission introduces the Open Research Europe platform to the Greek and Cypriot scientific communities

Focus: In April, the Greek and Cypriot OpenAIRE NOADs, in collaboration also with the Scholarly Communication Unit of HEAL-Link, organized an event to inform their scientific communities and individual researchers about the newly launched European platform for open access publications, namely the Open Research Europe (ORE). The event welcomed Victoria Tsoukala, Policy Officer-Seconded National Expert- Open Access-Science Cloud - European Commission (EC), who presented key features of ORE as well...

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OpenAIRE and EOSC in national settings: the Greek and Cypriot paradigms

About: In the framework of established collaboration between OpenAIRE NOADs in Greece and Cyprus, and in support of the NI4OS-Europe project where they both contribute, a webinar was organized to update the Greek and Cypriot scientific community about news from the evolving European Research and Innovation (R&I) area. In brief: Data intensive scientific demands and emerging technologies that are progressively embedded in scientific practices, such as artificial intelligence, significantly af...

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3rd webinar series in Greek: season finale with Intellectual Property Rights

The focus: Research has different interpretations by stakeholders. Most tend to focus mainly on the research output and neglect in-between processes leading to it. This webinar of the OpenAIRE National Open Access Desks in Greece and Cyprus perceived research as a process and analysed the implementation of intellectual property practices in all the steps of a research lifecycle. In his presentation, invited speaker Prodromos Tsiavos, legal adviser at Athena Research Center and an expert on Open ...

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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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Open Data Day 2020 in Cyprus

OpenAIRE was presented in the event dedicated to the International Open Data Day 2020, held in Cyprus on the 5th of March 2020. The event was organised in Nicosia, by the Cyprus Ministry of Finance, Public Administration and Personnel Department and the Library of the University of Cyprus which acts as the Cyprus National Open Access Desk of OpenAIRE and partner of NI4OS Europe project. ️1 "Opening our data is providing an unlimited perspective on research, innovation, political accoun...

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Open Science: From Theory to practice

A great event was organised during Open Access Week 2019 in Nicosia, Cyprus. On the 24th of October 2019, the Cyprus OpenAIRE NOAD hosted in the newly built premises of the Learning-Resource Centre Stelios Ioannou of the University of Cyprus, the National OpenAIRE workshop. Experts presented various aspects of Open Science. Issues like Citizen Science, Innovative metrics, practical aspects of Open Science in research, business development and innovation and legal aspects were addressed. Almost 1...

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Setting up a data stewardship programme - an institutional perspective

Background and importance: Part of the Open Science webinar series running in collaboration of the Greek and Cypriot OpenAIRE NOADs, this webinar focused on Data Stewardship. With data management services and practices to be at a primary stage of developments at the University level in Greece and Cyprus, it seemed as a good opportunity to introduce the concept/role of data stewards to the library and to the research community, providing an understanding of duties and position within the Universi...

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Webinar on GDPR literacy

The occasion: The series of the Greek and Cypriot NOADs webinars on Open Science aim to keep the academic and research community in Greece and Cyprus up-to-date and in sync with European developments and trends as well as support their open research endeavours. The need for GDPR literacy: The webinars have proven to be a good practice also for getting a better understanding of national community needs. Of the most popular areas where researchers, innovators and libraries seek advise is the Gener...

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OpenAIRE webinars in the Greek language:
Webinar on Research Data Management and Data Management Plans

 ⏪Flashback: A series of OpenAIRE webinars on vital Open Science issues was initiated last year in collaboration between the Greek and Cypriot NOADs. The specificity of these webinars is that they are conducted in the greek language in an attempt to engage more librarians and researchers with particular aspects of open and responsible research conduct. This activity is expected to, and has actually had already a positive effect, in cultivating change in research culture and in familiarising...

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OpenAIRE national webinars in the Greek language – a collaborative effort between the Greek and the Cypriot NOADs

📖 NOADship in Greece and Cyprus: Athena Research and Innovation Center acts as the National Open Access Desk (NOAD) for Greece, a position evolving stakeholders’ engagement and supporting research activities, currently run jointly with the Hellenic Academic Libraries Link (HEAL-Link) as third partner to the OpenAIRE Advance project. NOADship in Cyprus falls under the responsibility and management of the University of Cyprus Library. 💡 The idea: Recognising the need of a disruptive move to spread...

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Cyprus adopts National Open Access policy

On the 25th of February 2016, the Council of ministers of the Republic of Cyprus, approved the adoption of the National policy for Open Access in Cyprus. The document's approval was the outcome of a tremendous collaboration between the different stakeholders involved in the Working Group for Open Access (consisting of the NPR for OA, local Academic institutions and national funders), coordinated by the OPENAIRE2020 Cyprus NOAD (University of Cyprus Library) and highly supported by the coord...

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Cyprus working group for Open Access: setting up a national mandate and OA coordinating body

On the 22nd of April 2015 the first meeting of the Working Group for Open Access took place in the University of Cyprus, in Nicosia, Cyprus. The local National Points of Reference for Open Access, the main funding institutions for research in Cyprus, and representatives from almost all the academic institutions of Cyprus, were present.The event was organized by the OpenAIRE2020 Cyprus NOAD, which is also the Key node organization of Pasteur4OA project in Cyprus. At the meeting, project Pasteur4O...

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