%1 services

Name	Description	ELIXIR Node
2015-2016 Beacon project	The goal of the project is to provide consent-based access to genomic data in the European Genome-phenome Archive (EGA, a joint project of EMBL-EBI and the CRG in Barcelona) as well as national resources in Finland, Sweden and the Netherlands by establishing GA4GH Beacons. The project is funded through ELIXIR Hub a series of Implementation Studies. The first of these focused on establishing Beacons within ELIXIR Nodes and resulted in six ELIXIR Beacons in: ELIXIR Belgium ELIXIR Finland (the first ELIXIR Beacon connected to the ELIXIR AAI to demonstrate registered data access level) ELIXIR France ELIXIR Switzerland: Beacon Array Map, DIPG Beacon ELIXIR Sweden European Genome-phenome Archive (EGA) Included within this was a Security Workshop held in Hinxton (31 May - 1 June 2016) (agenda & slides). The study is now completed, the details are available in the End report. This project helped established a close relationship between ELIXIR and GA4GH (see the news story). Webinar summarising the outcomes The work was picked up in further Implementation Studies (2017, 2018). The ongoing work on the Beacon Project is coordinated by the ELIXIR Human Data Community.	ELIXIR Finland, ELIXIR Spain, ELIXIR Sweden, ELIXIR Switzerland, ELIXIR Belgium , ELIXIR Netherlands, EMBL-EBI, ELIXIR France
2015-2016 Beacon project	The goal of the project is to provide consent-based access to genomic data in the European Genome-phenome Archive (EGA, a joint project of EMBL-EBI and the CRG in Barcelona) as well as national resources in Finland, Sweden and the Netherlands by establishing GA4GH Beacons. The project is funded through ELIXIR Hub a series of Implementation Studies. The first of these focused on establishing Beacons within ELIXIR Nodes and resulted in six ELIXIR Beacons in: ELIXIR Belgium ELIXIR Finland (the first ELIXIR Beacon connected to the ELIXIR AAI to demonstrate registered data access level) ELIXIR France ELIXIR Switzerland: Beacon Array Map, DIPG Beacon ELIXIR Sweden European Genome-phenome Archive (EGA) Included within this was a Security Workshop held in Hinxton (31 May - 1 June 2016) (agenda & slides). The study is now completed, the details are available in the End report. This project helped established a close relationship between ELIXIR and GA4GH (see the news story). Webinar summarising the outcomes The work was picked up in further Implementation Studies (2017, 2018). The ongoing work on the Beacon Project is coordinated by the ELIXIR Human Data Community.	ELIXIR Finland, ELIXIR Spain, ELIXIR Sweden, ELIXIR Switzerland, ELIXIR Belgium , ELIXIR Netherlands, EMBL-EBI, ELIXIR France
2015-2016 Beacon project	The goal of the project is to provide consent-based access to genomic data in the European Genome-phenome Archive (EGA, a joint project of EMBL-EBI and the CRG in Barcelona) as well as national resources in Finland, Sweden and the Netherlands by establishing GA4GH Beacons. The project is funded through ELIXIR Hub a series of Implementation Studies. The first of these focused on establishing Beacons within ELIXIR Nodes and resulted in six ELIXIR Beacons in: ELIXIR Belgium ELIXIR Finland (the first ELIXIR Beacon connected to the ELIXIR AAI to demonstrate registered data access level) ELIXIR France ELIXIR Switzerland: Beacon Array Map, DIPG Beacon ELIXIR Sweden European Genome-phenome Archive (EGA) Included within this was a Security Workshop held in Hinxton (31 May - 1 June 2016) (agenda & slides). The study is now completed, the details are available in the End report. This project helped established a close relationship between ELIXIR and GA4GH (see the news story). Webinar summarising the outcomes The work was picked up in further Implementation Studies (2017, 2018). The ongoing work on the Beacon Project is coordinated by the ELIXIR Human Data Community.	ELIXIR Finland, ELIXIR Spain, ELIXIR Sweden, ELIXIR Switzerland, ELIXIR Belgium , ELIXIR Netherlands, EMBL-EBI, ELIXIR France
2015-2016 Beacon project	The goal of the project is to provide consent-based access to genomic data in the European Genome-phenome Archive (EGA, a joint project of EMBL-EBI and the CRG in Barcelona) as well as national resources in Finland, Sweden and the Netherlands by establishing GA4GH Beacons. The project is funded through ELIXIR Hub a series of Implementation Studies. The first of these focused on establishing Beacons within ELIXIR Nodes and resulted in six ELIXIR Beacons in: ELIXIR Belgium ELIXIR Finland (the first ELIXIR Beacon connected to the ELIXIR AAI to demonstrate registered data access level) ELIXIR France ELIXIR Switzerland: Beacon Array Map, DIPG Beacon ELIXIR Sweden European Genome-phenome Archive (EGA) Included within this was a Security Workshop held in Hinxton (31 May - 1 June 2016) (agenda & slides). The study is now completed, the details are available in the End report. This project helped established a close relationship between ELIXIR and GA4GH (see the news story). Webinar summarising the outcomes The work was picked up in further Implementation Studies (2017, 2018). The ongoing work on the Beacon Project is coordinated by the ELIXIR Human Data Community.	ELIXIR Finland, ELIXIR Spain, ELIXIR Sweden, ELIXIR Switzerland, ELIXIR Belgium , ELIXIR Netherlands, EMBL-EBI, ELIXIR France
2015-2016 Beacon project	The goal of the project is to provide consent-based access to genomic data in the European Genome-phenome Archive (EGA, a joint project of EMBL-EBI and the CRG in Barcelona) as well as national resources in Finland, Sweden and the Netherlands by establishing GA4GH Beacons. The project is funded through ELIXIR Hub a series of Implementation Studies. The first of these focused on establishing Beacons within ELIXIR Nodes and resulted in six ELIXIR Beacons in: ELIXIR Belgium ELIXIR Finland (the first ELIXIR Beacon connected to the ELIXIR AAI to demonstrate registered data access level) ELIXIR France ELIXIR Switzerland: Beacon Array Map, DIPG Beacon ELIXIR Sweden European Genome-phenome Archive (EGA) Included within this was a Security Workshop held in Hinxton (31 May - 1 June 2016) (agenda & slides). The study is now completed, the details are available in the End report. This project helped established a close relationship between ELIXIR and GA4GH (see the news story). Webinar summarising the outcomes The work was picked up in further Implementation Studies (2017, 2018). The ongoing work on the Beacon Project is coordinated by the ELIXIR Human Data Community.	ELIXIR Finland, ELIXIR Spain, ELIXIR Sweden, ELIXIR Switzerland, ELIXIR Belgium , ELIXIR Netherlands, EMBL-EBI, ELIXIR France
2015-2016 Beacon project	The goal of the project is to provide consent-based access to genomic data in the European Genome-phenome Archive (EGA, a joint project of EMBL-EBI and the CRG in Barcelona) as well as national resources in Finland, Sweden and the Netherlands by establishing GA4GH Beacons. The project is funded through ELIXIR Hub a series of Implementation Studies. The first of these focused on establishing Beacons within ELIXIR Nodes and resulted in six ELIXIR Beacons in: ELIXIR Belgium ELIXIR Finland (the first ELIXIR Beacon connected to the ELIXIR AAI to demonstrate registered data access level) ELIXIR France ELIXIR Switzerland: Beacon Array Map, DIPG Beacon ELIXIR Sweden European Genome-phenome Archive (EGA) Included within this was a Security Workshop held in Hinxton (31 May - 1 June 2016) (agenda & slides). The study is now completed, the details are available in the End report. This project helped established a close relationship between ELIXIR and GA4GH (see the news story). Webinar summarising the outcomes The work was picked up in further Implementation Studies (2017, 2018). The ongoing work on the Beacon Project is coordinated by the ELIXIR Human Data Community.	ELIXIR Finland, ELIXIR Spain, ELIXIR Sweden, ELIXIR Switzerland, ELIXIR Belgium , ELIXIR Netherlands, EMBL-EBI, ELIXIR France
2015-2016 Beacon project	The goal of the project is to provide consent-based access to genomic data in the European Genome-phenome Archive (EGA, a joint project of EMBL-EBI and the CRG in Barcelona) as well as national resources in Finland, Sweden and the Netherlands by establishing GA4GH Beacons. The project is funded through ELIXIR Hub a series of Implementation Studies. The first of these focused on establishing Beacons within ELIXIR Nodes and resulted in six ELIXIR Beacons in: ELIXIR Belgium ELIXIR Finland (the first ELIXIR Beacon connected to the ELIXIR AAI to demonstrate registered data access level) ELIXIR France ELIXIR Switzerland: Beacon Array Map, DIPG Beacon ELIXIR Sweden European Genome-phenome Archive (EGA) Included within this was a Security Workshop held in Hinxton (31 May - 1 June 2016) (agenda & slides). The study is now completed, the details are available in the End report. This project helped established a close relationship between ELIXIR and GA4GH (see the news story). Webinar summarising the outcomes The work was picked up in further Implementation Studies (2017, 2018). The ongoing work on the Beacon Project is coordinated by the ELIXIR Human Data Community.	ELIXIR Finland, ELIXIR Spain, ELIXIR Sweden, ELIXIR Switzerland, ELIXIR Belgium , ELIXIR Netherlands, EMBL-EBI, ELIXIR France
2015-2016 Beacon project	The goal of the project is to provide consent-based access to genomic data in the European Genome-phenome Archive (EGA, a joint project of EMBL-EBI and the CRG in Barcelona) as well as national resources in Finland, Sweden and the Netherlands by establishing GA4GH Beacons. The project is funded through ELIXIR Hub a series of Implementation Studies. The first of these focused on establishing Beacons within ELIXIR Nodes and resulted in six ELIXIR Beacons in: ELIXIR Belgium ELIXIR Finland (the first ELIXIR Beacon connected to the ELIXIR AAI to demonstrate registered data access level) ELIXIR France ELIXIR Switzerland: Beacon Array Map, DIPG Beacon ELIXIR Sweden European Genome-phenome Archive (EGA) Included within this was a Security Workshop held in Hinxton (31 May - 1 June 2016) (agenda & slides). The study is now completed, the details are available in the End report. This project helped established a close relationship between ELIXIR and GA4GH (see the news story). Webinar summarising the outcomes The work was picked up in further Implementation Studies (2017, 2018). The ongoing work on the Beacon Project is coordinated by the ELIXIR Human Data Community.	ELIXIR Finland, ELIXIR Spain, ELIXIR Sweden, ELIXIR Switzerland, ELIXIR Belgium , ELIXIR Netherlands, EMBL-EBI, ELIXIR France
A Scalable approach to Personal FAIR Data Management and Analysis	Our aim is to extend myFAIR Analysis into a cloud based service that can be executed using the advanced INDIGO PaaS services on-top of any ELIXIR Compute Platform cloud resource. This approach will enable the advanced features provided by INDIGO to be made accessible to the whole of ELIXIR by porting them on the standard ECP cloud resource. The utility of this myFAIR cloud will be demonstrated using existing validated test case scenarios (e.g. Mothur-SOP and/or EGA), and building towards providing myFAIR Analysis as a research service CLOUD (myFAIR CLOUD Analysis) supporting single/multi-user and single/multi-center for FAIR data management and analysis. Impact of the Study: Extend myFAIR Analysis into a cloud based service, executed using advanced INDIGO PaaS services on-top of any ECP cloud resource. Enable INDIGO features to be accessible to the whole of ELIXIR by porting them on the standard ECP cloud resource. Demonstrate myFAIR cloud using existing validated test case scenarios (e.g. Mothur-SOP and/or EGA). Building towards providing myFAIR Analysis as a research service CLOUD (myFAIR CLOUD Analysis) supporting single/multi-user and single/multi-center for FAIR data management and analysis.	ELIXIR Netherlands, ELIXIR Italy, EMBL-EBI
A Scalable approach to Personal FAIR Data Management and Analysis	Our aim is to extend myFAIR Analysis into a cloud based service that can be executed using the advanced INDIGO PaaS services on-top of any ELIXIR Compute Platform cloud resource. This approach will enable the advanced features provided by INDIGO to be made accessible to the whole of ELIXIR by porting them on the standard ECP cloud resource. The utility of this myFAIR cloud will be demonstrated using existing validated test case scenarios (e.g. Mothur-SOP and/or EGA), and building towards providing myFAIR Analysis as a research service CLOUD (myFAIR CLOUD Analysis) supporting single/multi-user and single/multi-center for FAIR data management and analysis. Impact of the Study: Extend myFAIR Analysis into a cloud based service, executed using advanced INDIGO PaaS services on-top of any ECP cloud resource. Enable INDIGO features to be accessible to the whole of ELIXIR by porting them on the standard ECP cloud resource. Demonstrate myFAIR cloud using existing validated test case scenarios (e.g. Mothur-SOP and/or EGA). Building towards providing myFAIR Analysis as a research service CLOUD (myFAIR CLOUD Analysis) supporting single/multi-user and single/multi-center for FAIR data management and analysis.	ELIXIR Netherlands, ELIXIR Italy, EMBL-EBI
A Scalable approach to Personal FAIR Data Management and Analysis	Our aim is to extend myFAIR Analysis into a cloud based service that can be executed using the advanced INDIGO PaaS services on-top of any ELIXIR Compute Platform cloud resource. This approach will enable the advanced features provided by INDIGO to be made accessible to the whole of ELIXIR by porting them on the standard ECP cloud resource. The utility of this myFAIR cloud will be demonstrated using existing validated test case scenarios (e.g. Mothur-SOP and/or EGA), and building towards providing myFAIR Analysis as a research service CLOUD (myFAIR CLOUD Analysis) supporting single/multi-user and single/multi-center for FAIR data management and analysis. Impact of the Study: Extend myFAIR Analysis into a cloud based service, executed using advanced INDIGO PaaS services on-top of any ECP cloud resource. Enable INDIGO features to be accessible to the whole of ELIXIR by porting them on the standard ECP cloud resource. Demonstrate myFAIR cloud using existing validated test case scenarios (e.g. Mothur-SOP and/or EGA). Building towards providing myFAIR Analysis as a research service CLOUD (myFAIR CLOUD Analysis) supporting single/multi-user and single/multi-center for FAIR data management and analysis.	ELIXIR Netherlands, ELIXIR Italy, EMBL-EBI
Annotation and curation of human genomic variations (2018-Variations)	This implementation study aims to understand the existing infrastructure, resources and protocols for human genome variation annotation and curation. Work focuses on processes that can be automated to support interpretation of high-throughput genome sequencing results. The outcome will be a report that describes the current status within ELIXIR member states, identified requirements and potential solutions. The report will be part of the ELIXIR Human Genomics and Translational Data Services strategy and roadmap. This project coordinates with ELIXIR Data Platform on surveys regarding data archives and other resources. It also consults with Compute and Tools Platforms on potential models for resourcing, scaling and providing portable tools based on the identified requirements for running data analysis workflows. The aim is also to work in close collaboration with the ELIXIR Interoperability Platform to understand the future requirements on managing variation annotation and their interpretation. This implementation study will also aim to support the coordination between ELIXIR Human Genomics and Translational Data use case and the relevant GA4GH technical work streams. The expected outcome is a better alignment of ELIXIR activities with those in the GA4GH and direct communication with relevant resources outside of ELIXIR such as ClinVar.	ELIXIR Finland, EMBL-EBI, ELIXIR Switzerland, ELIXIR UK, ELIXIR Norway, ELIXIR Italy
Annotation and curation of human genomic variations (2018-Variations)	This implementation study aims to understand the existing infrastructure, resources and protocols for human genome variation annotation and curation. Work focuses on processes that can be automated to support interpretation of high-throughput genome sequencing results. The outcome will be a report that describes the current status within ELIXIR member states, identified requirements and potential solutions. The report will be part of the ELIXIR Human Genomics and Translational Data Services strategy and roadmap. This project coordinates with ELIXIR Data Platform on surveys regarding data archives and other resources. It also consults with Compute and Tools Platforms on potential models for resourcing, scaling and providing portable tools based on the identified requirements for running data analysis workflows. The aim is also to work in close collaboration with the ELIXIR Interoperability Platform to understand the future requirements on managing variation annotation and their interpretation. This implementation study will also aim to support the coordination between ELIXIR Human Genomics and Translational Data use case and the relevant GA4GH technical work streams. The expected outcome is a better alignment of ELIXIR activities with those in the GA4GH and direct communication with relevant resources outside of ELIXIR such as ClinVar.	ELIXIR Finland, EMBL-EBI, ELIXIR Switzerland, ELIXIR UK, ELIXIR Norway, ELIXIR Italy
Annotation and curation of human genomic variations (2018-Variations)	This implementation study aims to understand the existing infrastructure, resources and protocols for human genome variation annotation and curation. Work focuses on processes that can be automated to support interpretation of high-throughput genome sequencing results. The outcome will be a report that describes the current status within ELIXIR member states, identified requirements and potential solutions. The report will be part of the ELIXIR Human Genomics and Translational Data Services strategy and roadmap. This project coordinates with ELIXIR Data Platform on surveys regarding data archives and other resources. It also consults with Compute and Tools Platforms on potential models for resourcing, scaling and providing portable tools based on the identified requirements for running data analysis workflows. The aim is also to work in close collaboration with the ELIXIR Interoperability Platform to understand the future requirements on managing variation annotation and their interpretation. This implementation study will also aim to support the coordination between ELIXIR Human Genomics and Translational Data use case and the relevant GA4GH technical work streams. The expected outcome is a better alignment of ELIXIR activities with those in the GA4GH and direct communication with relevant resources outside of ELIXIR such as ClinVar.	ELIXIR Finland, EMBL-EBI, ELIXIR Switzerland, ELIXIR UK, ELIXIR Norway, ELIXIR Italy
Annotation and curation of human genomic variations (2018-Variations)	This implementation study aims to understand the existing infrastructure, resources and protocols for human genome variation annotation and curation. Work focuses on processes that can be automated to support interpretation of high-throughput genome sequencing results. The outcome will be a report that describes the current status within ELIXIR member states, identified requirements and potential solutions. The report will be part of the ELIXIR Human Genomics and Translational Data Services strategy and roadmap. This project coordinates with ELIXIR Data Platform on surveys regarding data archives and other resources. It also consults with Compute and Tools Platforms on potential models for resourcing, scaling and providing portable tools based on the identified requirements for running data analysis workflows. The aim is also to work in close collaboration with the ELIXIR Interoperability Platform to understand the future requirements on managing variation annotation and their interpretation. This implementation study will also aim to support the coordination between ELIXIR Human Genomics and Translational Data use case and the relevant GA4GH technical work streams. The expected outcome is a better alignment of ELIXIR activities with those in the GA4GH and direct communication with relevant resources outside of ELIXIR such as ClinVar.	ELIXIR Finland, EMBL-EBI, ELIXIR Switzerland, ELIXIR UK, ELIXIR Norway, ELIXIR Italy
Annotation and curation of human genomic variations (2018-Variations)	This implementation study aims to understand the existing infrastructure, resources and protocols for human genome variation annotation and curation. Work focuses on processes that can be automated to support interpretation of high-throughput genome sequencing results. The outcome will be a report that describes the current status within ELIXIR member states, identified requirements and potential solutions. The report will be part of the ELIXIR Human Genomics and Translational Data Services strategy and roadmap. This project coordinates with ELIXIR Data Platform on surveys regarding data archives and other resources. It also consults with Compute and Tools Platforms on potential models for resourcing, scaling and providing portable tools based on the identified requirements for running data analysis workflows. The aim is also to work in close collaboration with the ELIXIR Interoperability Platform to understand the future requirements on managing variation annotation and their interpretation. This implementation study will also aim to support the coordination between ELIXIR Human Genomics and Translational Data use case and the relevant GA4GH technical work streams. The expected outcome is a better alignment of ELIXIR activities with those in the GA4GH and direct communication with relevant resources outside of ELIXIR such as ClinVar.	ELIXIR Finland, EMBL-EBI, ELIXIR Switzerland, ELIXIR UK, ELIXIR Norway, ELIXIR Italy
Annotation and curation of human genomic variations (2018-Variations)	This implementation study aims to understand the existing infrastructure, resources and protocols for human genome variation annotation and curation. Work focuses on processes that can be automated to support interpretation of high-throughput genome sequencing results. The outcome will be a report that describes the current status within ELIXIR member states, identified requirements and potential solutions. The report will be part of the ELIXIR Human Genomics and Translational Data Services strategy and roadmap. This project coordinates with ELIXIR Data Platform on surveys regarding data archives and other resources. It also consults with Compute and Tools Platforms on potential models for resourcing, scaling and providing portable tools based on the identified requirements for running data analysis workflows. The aim is also to work in close collaboration with the ELIXIR Interoperability Platform to understand the future requirements on managing variation annotation and their interpretation. This implementation study will also aim to support the coordination between ELIXIR Human Genomics and Translational Data use case and the relevant GA4GH technical work streams. The expected outcome is a better alignment of ELIXIR activities with those in the GA4GH and direct communication with relevant resources outside of ELIXIR such as ClinVar.	ELIXIR Finland, EMBL-EBI, ELIXIR Switzerland, ELIXIR UK, ELIXIR Norway, ELIXIR Italy
Architecture for Software Containers at ELIXIR and its use by EXCELERATE Use Case Communities	The aim of this implementation study is to provide a stable infrastructure for unifying software containers solutions within ELIXIR. This infrastructure will provide an access point for end-users to find, generate, store, monitor, and even benchmark software containers solutions. Hardware infrastructure will be provided by an ELIXIR Node from the ELIXIR Compute Platform for software containers deployment while ELIXIR-ES will provide the backup system using EUDAT protocols and infrastructures. In the long-term this registry could become a relying service to the ELIXIR AAI allowing infrastructures to manage users accounts. The impact of this infrastructure will be demonstrated across ELIXIR Platforms and Use Cases. Software containers are a key technology which enables the rapid deployment of software resources including workflows across a variety of systems e.g. HPC, Cloud environments, and local computers; and the connection with existing database repositories. Additionally, this technology will be used to support training activities carried out by ELIXIR, where trainers will be able to focus on the training content rather than in the technological framework of the training, during face to face or remote sessions. Such a leading role on the development of this infrastructure will greatly increase ELIXIR's visibility across many domains of life sciences and even beyond. The coordinated effort to develop this infrastructure is similar to previous efforts carried out in ELIXIR, such as the Beacon Project and Bioschemas and will also link into work taking place in the ELIXIR Compute and Interoperability Platforms in coordination with the GA4GH.	EMBL-EBI, ELIXIR Germany, ELIXIR Spain, ELIXIR Belgium , ELIXIR France, ELIXIR Denmark, ELIXIR Italy
Architecture for Software Containers at ELIXIR and its use by EXCELERATE Use Case Communities	The aim of this implementation study is to provide a stable infrastructure for unifying software containers solutions within ELIXIR. This infrastructure will provide an access point for end-users to find, generate, store, monitor, and even benchmark software containers solutions. Hardware infrastructure will be provided by an ELIXIR Node from the ELIXIR Compute Platform for software containers deployment while ELIXIR-ES will provide the backup system using EUDAT protocols and infrastructures. In the long-term this registry could become a relying service to the ELIXIR AAI allowing infrastructures to manage users accounts. The impact of this infrastructure will be demonstrated across ELIXIR Platforms and Use Cases. Software containers are a key technology which enables the rapid deployment of software resources including workflows across a variety of systems e.g. HPC, Cloud environments, and local computers; and the connection with existing database repositories. Additionally, this technology will be used to support training activities carried out by ELIXIR, where trainers will be able to focus on the training content rather than in the technological framework of the training, during face to face or remote sessions. Such a leading role on the development of this infrastructure will greatly increase ELIXIR's visibility across many domains of life sciences and even beyond. The coordinated effort to develop this infrastructure is similar to previous efforts carried out in ELIXIR, such as the Beacon Project and Bioschemas and will also link into work taking place in the ELIXIR Compute and Interoperability Platforms in coordination with the GA4GH.	EMBL-EBI, ELIXIR Germany, ELIXIR Spain, ELIXIR Belgium , ELIXIR France, ELIXIR Denmark, ELIXIR Italy
Architecture for Software Containers at ELIXIR and its use by EXCELERATE Use Case Communities	The aim of this implementation study is to provide a stable infrastructure for unifying software containers solutions within ELIXIR. This infrastructure will provide an access point for end-users to find, generate, store, monitor, and even benchmark software containers solutions. Hardware infrastructure will be provided by an ELIXIR Node from the ELIXIR Compute Platform for software containers deployment while ELIXIR-ES will provide the backup system using EUDAT protocols and infrastructures. In the long-term this registry could become a relying service to the ELIXIR AAI allowing infrastructures to manage users accounts. The impact of this infrastructure will be demonstrated across ELIXIR Platforms and Use Cases. Software containers are a key technology which enables the rapid deployment of software resources including workflows across a variety of systems e.g. HPC, Cloud environments, and local computers; and the connection with existing database repositories. Additionally, this technology will be used to support training activities carried out by ELIXIR, where trainers will be able to focus on the training content rather than in the technological framework of the training, during face to face or remote sessions. Such a leading role on the development of this infrastructure will greatly increase ELIXIR's visibility across many domains of life sciences and even beyond. The coordinated effort to develop this infrastructure is similar to previous efforts carried out in ELIXIR, such as the Beacon Project and Bioschemas and will also link into work taking place in the ELIXIR Compute and Interoperability Platforms in coordination with the GA4GH.	EMBL-EBI, ELIXIR Germany, ELIXIR Spain, ELIXIR Belgium , ELIXIR France, ELIXIR Denmark, ELIXIR Italy
Architecture for Software Containers at ELIXIR and its use by EXCELERATE Use Case Communities	The aim of this implementation study is to provide a stable infrastructure for unifying software containers solutions within ELIXIR. This infrastructure will provide an access point for end-users to find, generate, store, monitor, and even benchmark software containers solutions. Hardware infrastructure will be provided by an ELIXIR Node from the ELIXIR Compute Platform for software containers deployment while ELIXIR-ES will provide the backup system using EUDAT protocols and infrastructures. In the long-term this registry could become a relying service to the ELIXIR AAI allowing infrastructures to manage users accounts. The impact of this infrastructure will be demonstrated across ELIXIR Platforms and Use Cases. Software containers are a key technology which enables the rapid deployment of software resources including workflows across a variety of systems e.g. HPC, Cloud environments, and local computers; and the connection with existing database repositories. Additionally, this technology will be used to support training activities carried out by ELIXIR, where trainers will be able to focus on the training content rather than in the technological framework of the training, during face to face or remote sessions. Such a leading role on the development of this infrastructure will greatly increase ELIXIR's visibility across many domains of life sciences and even beyond. The coordinated effort to develop this infrastructure is similar to previous efforts carried out in ELIXIR, such as the Beacon Project and Bioschemas and will also link into work taking place in the ELIXIR Compute and Interoperability Platforms in coordination with the GA4GH.	EMBL-EBI, ELIXIR Germany, ELIXIR Spain, ELIXIR Belgium , ELIXIR France, ELIXIR Denmark, ELIXIR Italy
Architecture for Software Containers at ELIXIR and its use by EXCELERATE Use Case Communities	The aim of this implementation study is to provide a stable infrastructure for unifying software containers solutions within ELIXIR. This infrastructure will provide an access point for end-users to find, generate, store, monitor, and even benchmark software containers solutions. Hardware infrastructure will be provided by an ELIXIR Node from the ELIXIR Compute Platform for software containers deployment while ELIXIR-ES will provide the backup system using EUDAT protocols and infrastructures. In the long-term this registry could become a relying service to the ELIXIR AAI allowing infrastructures to manage users accounts. The impact of this infrastructure will be demonstrated across ELIXIR Platforms and Use Cases. Software containers are a key technology which enables the rapid deployment of software resources including workflows across a variety of systems e.g. HPC, Cloud environments, and local computers; and the connection with existing database repositories. Additionally, this technology will be used to support training activities carried out by ELIXIR, where trainers will be able to focus on the training content rather than in the technological framework of the training, during face to face or remote sessions. Such a leading role on the development of this infrastructure will greatly increase ELIXIR's visibility across many domains of life sciences and even beyond. The coordinated effort to develop this infrastructure is similar to previous efforts carried out in ELIXIR, such as the Beacon Project and Bioschemas and will also link into work taking place in the ELIXIR Compute and Interoperability Platforms in coordination with the GA4GH.	EMBL-EBI, ELIXIR Germany, ELIXIR Spain, ELIXIR Belgium , ELIXIR France, ELIXIR Denmark, ELIXIR Italy
Architecture for Software Containers at ELIXIR and its use by EXCELERATE Use Case Communities	The aim of this implementation study is to provide a stable infrastructure for unifying software containers solutions within ELIXIR. This infrastructure will provide an access point for end-users to find, generate, store, monitor, and even benchmark software containers solutions. Hardware infrastructure will be provided by an ELIXIR Node from the ELIXIR Compute Platform for software containers deployment while ELIXIR-ES will provide the backup system using EUDAT protocols and infrastructures. In the long-term this registry could become a relying service to the ELIXIR AAI allowing infrastructures to manage users accounts. The impact of this infrastructure will be demonstrated across ELIXIR Platforms and Use Cases. Software containers are a key technology which enables the rapid deployment of software resources including workflows across a variety of systems e.g. HPC, Cloud environments, and local computers; and the connection with existing database repositories. Additionally, this technology will be used to support training activities carried out by ELIXIR, where trainers will be able to focus on the training content rather than in the technological framework of the training, during face to face or remote sessions. Such a leading role on the development of this infrastructure will greatly increase ELIXIR's visibility across many domains of life sciences and even beyond. The coordinated effort to develop this infrastructure is similar to previous efforts carried out in ELIXIR, such as the Beacon Project and Bioschemas and will also link into work taking place in the ELIXIR Compute and Interoperability Platforms in coordination with the GA4GH.	EMBL-EBI, ELIXIR Germany, ELIXIR Spain, ELIXIR Belgium , ELIXIR France, ELIXIR Denmark, ELIXIR Italy
Architecture for Software Containers at ELIXIR and its use by EXCELERATE Use Case Communities	The aim of this implementation study is to provide a stable infrastructure for unifying software containers solutions within ELIXIR. This infrastructure will provide an access point for end-users to find, generate, store, monitor, and even benchmark software containers solutions. Hardware infrastructure will be provided by an ELIXIR Node from the ELIXIR Compute Platform for software containers deployment while ELIXIR-ES will provide the backup system using EUDAT protocols and infrastructures. In the long-term this registry could become a relying service to the ELIXIR AAI allowing infrastructures to manage users accounts. The impact of this infrastructure will be demonstrated across ELIXIR Platforms and Use Cases. Software containers are a key technology which enables the rapid deployment of software resources including workflows across a variety of systems e.g. HPC, Cloud environments, and local computers; and the connection with existing database repositories. Additionally, this technology will be used to support training activities carried out by ELIXIR, where trainers will be able to focus on the training content rather than in the technological framework of the training, during face to face or remote sessions. Such a leading role on the development of this infrastructure will greatly increase ELIXIR's visibility across many domains of life sciences and even beyond. The coordinated effort to develop this infrastructure is similar to previous efforts carried out in ELIXIR, such as the Beacon Project and Bioschemas and will also link into work taking place in the ELIXIR Compute and Interoperability Platforms in coordination with the GA4GH.	EMBL-EBI, ELIXIR Germany, ELIXIR Spain, ELIXIR Belgium , ELIXIR France, ELIXIR Denmark, ELIXIR Italy
Beacon (2019-21)	This study follows on from a number of earlier activities that has established the ELIXIR Beacon Project. During 2019-21 the main aims are to: Extend the Beacon protocol to become the reference ELIXIR Data Discovery product, through expanding query options and providing richer responses, with view on biomedical applications, and in alignment with developing GA4GH standards Deliver ELIXIR Beacon Network as an established ELIXIR service Leverage ELIXIR Nodes to increase data flow through Beacon services Actively support the integration of the Beacon API with human data resources throughout ELIXIR, with particular view on National Genomics Initiatives, biobanks, and Human Data Communities (such as Rare Diseases and Human CNV) To achieve these goals it is imperative to continue a strategic partnership with the GA4GH Work Streams as a Driver Project and to increase coordination with the ELIXIR platforms. The focus is to prioritise and deliver future European requirements on Beacon and Beacon Network API development, continue to develop the overall security framework for this service type, and contribute to the GA4GH Discovery Work Stream goals towards a global genomic query language. Timeline: Q1 2019-21: Annual F2F meeting (7 March 2019, Sweden) Q2 2019-21: Annual training workshop @ ELIXIR All Hands (June 2019, Lisbon) Q4 2019-21: Annual workshop @ GA4GH Plenary (October 2019, TBC)	ELIXIR Switzerland, EMBL-EBI, ELIXIR Spain, ELIXIR Finland, ELIXIR Luxembourg, ELIXIR Sweden
Beacon (2019-21)	This study follows on from a number of earlier activities that has established the ELIXIR Beacon Project. During 2019-21 the main aims are to: Extend the Beacon protocol to become the reference ELIXIR Data Discovery product, through expanding query options and providing richer responses, with view on biomedical applications, and in alignment with developing GA4GH standards Deliver ELIXIR Beacon Network as an established ELIXIR service Leverage ELIXIR Nodes to increase data flow through Beacon services Actively support the integration of the Beacon API with human data resources throughout ELIXIR, with particular view on National Genomics Initiatives, biobanks, and Human Data Communities (such as Rare Diseases and Human CNV) To achieve these goals it is imperative to continue a strategic partnership with the GA4GH Work Streams as a Driver Project and to increase coordination with the ELIXIR platforms. The focus is to prioritise and deliver future European requirements on Beacon and Beacon Network API development, continue to develop the overall security framework for this service type, and contribute to the GA4GH Discovery Work Stream goals towards a global genomic query language. Timeline: Q1 2019-21: Annual F2F meeting (7 March 2019, Sweden) Q2 2019-21: Annual training workshop @ ELIXIR All Hands (June 2019, Lisbon) Q4 2019-21: Annual workshop @ GA4GH Plenary (October 2019, TBC)	ELIXIR Switzerland, EMBL-EBI, ELIXIR Spain, ELIXIR Finland, ELIXIR Luxembourg, ELIXIR Sweden
Beacon (2019-21)	This study follows on from a number of earlier activities that has established the ELIXIR Beacon Project. During 2019-21 the main aims are to: Extend the Beacon protocol to become the reference ELIXIR Data Discovery product, through expanding query options and providing richer responses, with view on biomedical applications, and in alignment with developing GA4GH standards Deliver ELIXIR Beacon Network as an established ELIXIR service Leverage ELIXIR Nodes to increase data flow through Beacon services Actively support the integration of the Beacon API with human data resources throughout ELIXIR, with particular view on National Genomics Initiatives, biobanks, and Human Data Communities (such as Rare Diseases and Human CNV) To achieve these goals it is imperative to continue a strategic partnership with the GA4GH Work Streams as a Driver Project and to increase coordination with the ELIXIR platforms. The focus is to prioritise and deliver future European requirements on Beacon and Beacon Network API development, continue to develop the overall security framework for this service type, and contribute to the GA4GH Discovery Work Stream goals towards a global genomic query language. Timeline: Q1 2019-21: Annual F2F meeting (7 March 2019, Sweden) Q2 2019-21: Annual training workshop @ ELIXIR All Hands (June 2019, Lisbon) Q4 2019-21: Annual workshop @ GA4GH Plenary (October 2019, TBC)	ELIXIR Switzerland, EMBL-EBI, ELIXIR Spain, ELIXIR Finland, ELIXIR Luxembourg, ELIXIR Sweden
Beacon (2019-21)	This study follows on from a number of earlier activities that has established the ELIXIR Beacon Project. During 2019-21 the main aims are to: Extend the Beacon protocol to become the reference ELIXIR Data Discovery product, through expanding query options and providing richer responses, with view on biomedical applications, and in alignment with developing GA4GH standards Deliver ELIXIR Beacon Network as an established ELIXIR service Leverage ELIXIR Nodes to increase data flow through Beacon services Actively support the integration of the Beacon API with human data resources throughout ELIXIR, with particular view on National Genomics Initiatives, biobanks, and Human Data Communities (such as Rare Diseases and Human CNV) To achieve these goals it is imperative to continue a strategic partnership with the GA4GH Work Streams as a Driver Project and to increase coordination with the ELIXIR platforms. The focus is to prioritise and deliver future European requirements on Beacon and Beacon Network API development, continue to develop the overall security framework for this service type, and contribute to the GA4GH Discovery Work Stream goals towards a global genomic query language. Timeline: Q1 2019-21: Annual F2F meeting (7 March 2019, Sweden) Q2 2019-21: Annual training workshop @ ELIXIR All Hands (June 2019, Lisbon) Q4 2019-21: Annual workshop @ GA4GH Plenary (October 2019, TBC)	ELIXIR Switzerland, EMBL-EBI, ELIXIR Spain, ELIXIR Finland, ELIXIR Luxembourg, ELIXIR Sweden
Beacon (2019-21)	This study follows on from a number of earlier activities that has established the ELIXIR Beacon Project. During 2019-21 the main aims are to: Extend the Beacon protocol to become the reference ELIXIR Data Discovery product, through expanding query options and providing richer responses, with view on biomedical applications, and in alignment with developing GA4GH standards Deliver ELIXIR Beacon Network as an established ELIXIR service Leverage ELIXIR Nodes to increase data flow through Beacon services Actively support the integration of the Beacon API with human data resources throughout ELIXIR, with particular view on National Genomics Initiatives, biobanks, and Human Data Communities (such as Rare Diseases and Human CNV) To achieve these goals it is imperative to continue a strategic partnership with the GA4GH Work Streams as a Driver Project and to increase coordination with the ELIXIR platforms. The focus is to prioritise and deliver future European requirements on Beacon and Beacon Network API development, continue to develop the overall security framework for this service type, and contribute to the GA4GH Discovery Work Stream goals towards a global genomic query language. Timeline: Q1 2019-21: Annual F2F meeting (7 March 2019, Sweden) Q2 2019-21: Annual training workshop @ ELIXIR All Hands (June 2019, Lisbon) Q4 2019-21: Annual workshop @ GA4GH Plenary (October 2019, TBC)	ELIXIR Switzerland, EMBL-EBI, ELIXIR Spain, ELIXIR Finland, ELIXIR Luxembourg, ELIXIR Sweden
Beacon (2019-21)	This study follows on from a number of earlier activities that has established the ELIXIR Beacon Project. During 2019-21 the main aims are to: Extend the Beacon protocol to become the reference ELIXIR Data Discovery product, through expanding query options and providing richer responses, with view on biomedical applications, and in alignment with developing GA4GH standards Deliver ELIXIR Beacon Network as an established ELIXIR service Leverage ELIXIR Nodes to increase data flow through Beacon services Actively support the integration of the Beacon API with human data resources throughout ELIXIR, with particular view on National Genomics Initiatives, biobanks, and Human Data Communities (such as Rare Diseases and Human CNV) To achieve these goals it is imperative to continue a strategic partnership with the GA4GH Work Streams as a Driver Project and to increase coordination with the ELIXIR platforms. The focus is to prioritise and deliver future European requirements on Beacon and Beacon Network API development, continue to develop the overall security framework for this service type, and contribute to the GA4GH Discovery Work Stream goals towards a global genomic query language. Timeline: Q1 2019-21: Annual F2F meeting (7 March 2019, Sweden) Q2 2019-21: Annual training workshop @ ELIXIR All Hands (June 2019, Lisbon) Q4 2019-21: Annual workshop @ GA4GH Plenary (October 2019, TBC)	ELIXIR Switzerland, EMBL-EBI, ELIXIR Spain, ELIXIR Finland, ELIXIR Luxembourg, ELIXIR Sweden
Beacon and Beacon Network as a Service	The GA4GH Discovery work stream is developing a data discovery platform which includes Beacons and MatchMaker Exchange (MME). To enhance the reusability of scientific data, ELIXIR aims to facilitate making data ‘findable’ (FAIR guiding principles). To date, GA4GH Beacons have been lit for genetic sequencing data that resides in 6 continents. To be of value to the community the scale of genetic sequencing data that is ‘findable’ needs to increase. ELIXIR can bring Europe’s data forward in particular via ELIXIR Nodes but can also develop tools to enable data to be brought forward from anywhere in the world. The endpoint will be that user communities can find data on an international scale and identify appropriate data to then access for research. The ELIXIR Beacon 2016 and 2017 Implementation studies initiated this work by providing consent-based access to genomic data in the European Genome-phenome Archive and national resources in Finland, Sweden, France and The Netherlands by establishing GA4GH standard based Beacons. The 2017 project developed new features including an ELIXIR Beacon Network and adding security measures that would identify re-identification attempts. The 2018 project aims evolve the ELIXIR Beacons into a GA4GH Driver project with full alignment to GA4GH Technical Work Streams and consolidate and establish a fully costed process of “Lighting a Beacon” for any ELIXIR Node and deliver Beacon/Beacon Network as an established ELIXIR infrastructure service. It is imperative to continue to synchronize with the GA4GH Beacon project as well as other GA4GH activities and so this plan defines who is responsible for the communication between ELIXIR and GA4GH to ensure strategic partnership is maintained. This study is broken down into 7 Work Packages: WP1 - Development of Beacon API specification with the GA4GH WP2 - Supporting new ELIXIR Beacon development and deployment across Europe WP3 - Implementation of an ELIXIR Beacon Network & Registry WP4 - Security of ELIXIR Beacon and Beacon Network WP5 - Developing Indicators to establish Registry and Beacon as an Emerging ELIXIR Service WP6 - Strategic partnerships with national data cohorts and biobanks WP7 - Project Management and Communication Other Implementation Studies: 2015-16 2017 2019 (in preparation) The ongoing work on the Beacon Project is coordinated by the ELIXIR Human Data Community	ELIXIR Finland, ELIXIR Switzerland, ELIXIR Spain, ELIXIR Belgium , ELIXIR France, ELIXIR Netherlands, ELIXIR Norway, ELIXIR Italy, EMBL-EBI
Beacon and Beacon Network as a Service	The GA4GH Discovery work stream is developing a data discovery platform which includes Beacons and MatchMaker Exchange (MME). To enhance the reusability of scientific data, ELIXIR aims to facilitate making data ‘findable’ (FAIR guiding principles). To date, GA4GH Beacons have been lit for genetic sequencing data that resides in 6 continents. To be of value to the community the scale of genetic sequencing data that is ‘findable’ needs to increase. ELIXIR can bring Europe’s data forward in particular via ELIXIR Nodes but can also develop tools to enable data to be brought forward from anywhere in the world. The endpoint will be that user communities can find data on an international scale and identify appropriate data to then access for research. The ELIXIR Beacon 2016 and 2017 Implementation studies initiated this work by providing consent-based access to genomic data in the European Genome-phenome Archive and national resources in Finland, Sweden, France and The Netherlands by establishing GA4GH standard based Beacons. The 2017 project developed new features including an ELIXIR Beacon Network and adding security measures that would identify re-identification attempts. The 2018 project aims evolve the ELIXIR Beacons into a GA4GH Driver project with full alignment to GA4GH Technical Work Streams and consolidate and establish a fully costed process of “Lighting a Beacon” for any ELIXIR Node and deliver Beacon/Beacon Network as an established ELIXIR infrastructure service. It is imperative to continue to synchronize with the GA4GH Beacon project as well as other GA4GH activities and so this plan defines who is responsible for the communication between ELIXIR and GA4GH to ensure strategic partnership is maintained. This study is broken down into 7 Work Packages: WP1 - Development of Beacon API specification with the GA4GH WP2 - Supporting new ELIXIR Beacon development and deployment across Europe WP3 - Implementation of an ELIXIR Beacon Network & Registry WP4 - Security of ELIXIR Beacon and Beacon Network WP5 - Developing Indicators to establish Registry and Beacon as an Emerging ELIXIR Service WP6 - Strategic partnerships with national data cohorts and biobanks WP7 - Project Management and Communication Other Implementation Studies: 2015-16 2017 2019 (in preparation) The ongoing work on the Beacon Project is coordinated by the ELIXIR Human Data Community	ELIXIR Finland, ELIXIR Switzerland, ELIXIR Spain, ELIXIR Belgium , ELIXIR France, ELIXIR Netherlands, ELIXIR Norway, ELIXIR Italy, EMBL-EBI
Beacon and Beacon Network as a Service	The GA4GH Discovery work stream is developing a data discovery platform which includes Beacons and MatchMaker Exchange (MME). To enhance the reusability of scientific data, ELIXIR aims to facilitate making data ‘findable’ (FAIR guiding principles). To date, GA4GH Beacons have been lit for genetic sequencing data that resides in 6 continents. To be of value to the community the scale of genetic sequencing data that is ‘findable’ needs to increase. ELIXIR can bring Europe’s data forward in particular via ELIXIR Nodes but can also develop tools to enable data to be brought forward from anywhere in the world. The endpoint will be that user communities can find data on an international scale and identify appropriate data to then access for research. The ELIXIR Beacon 2016 and 2017 Implementation studies initiated this work by providing consent-based access to genomic data in the European Genome-phenome Archive and national resources in Finland, Sweden, France and The Netherlands by establishing GA4GH standard based Beacons. The 2017 project developed new features including an ELIXIR Beacon Network and adding security measures that would identify re-identification attempts. The 2018 project aims evolve the ELIXIR Beacons into a GA4GH Driver project with full alignment to GA4GH Technical Work Streams and consolidate and establish a fully costed process of “Lighting a Beacon” for any ELIXIR Node and deliver Beacon/Beacon Network as an established ELIXIR infrastructure service. It is imperative to continue to synchronize with the GA4GH Beacon project as well as other GA4GH activities and so this plan defines who is responsible for the communication between ELIXIR and GA4GH to ensure strategic partnership is maintained. This study is broken down into 7 Work Packages: WP1 - Development of Beacon API specification with the GA4GH WP2 - Supporting new ELIXIR Beacon development and deployment across Europe WP3 - Implementation of an ELIXIR Beacon Network & Registry WP4 - Security of ELIXIR Beacon and Beacon Network WP5 - Developing Indicators to establish Registry and Beacon as an Emerging ELIXIR Service WP6 - Strategic partnerships with national data cohorts and biobanks WP7 - Project Management and Communication Other Implementation Studies: 2015-16 2017 2019 (in preparation) The ongoing work on the Beacon Project is coordinated by the ELIXIR Human Data Community	ELIXIR Finland, ELIXIR Switzerland, ELIXIR Spain, ELIXIR Belgium , ELIXIR France, ELIXIR Netherlands, ELIXIR Norway, ELIXIR Italy, EMBL-EBI
Beacon and Beacon Network as a Service	The GA4GH Discovery work stream is developing a data discovery platform which includes Beacons and MatchMaker Exchange (MME). To enhance the reusability of scientific data, ELIXIR aims to facilitate making data ‘findable’ (FAIR guiding principles). To date, GA4GH Beacons have been lit for genetic sequencing data that resides in 6 continents. To be of value to the community the scale of genetic sequencing data that is ‘findable’ needs to increase. ELIXIR can bring Europe’s data forward in particular via ELIXIR Nodes but can also develop tools to enable data to be brought forward from anywhere in the world. The endpoint will be that user communities can find data on an international scale and identify appropriate data to then access for research. The ELIXIR Beacon 2016 and 2017 Implementation studies initiated this work by providing consent-based access to genomic data in the European Genome-phenome Archive and national resources in Finland, Sweden, France and The Netherlands by establishing GA4GH standard based Beacons. The 2017 project developed new features including an ELIXIR Beacon Network and adding security measures that would identify re-identification attempts. The 2018 project aims evolve the ELIXIR Beacons into a GA4GH Driver project with full alignment to GA4GH Technical Work Streams and consolidate and establish a fully costed process of “Lighting a Beacon” for any ELIXIR Node and deliver Beacon/Beacon Network as an established ELIXIR infrastructure service. It is imperative to continue to synchronize with the GA4GH Beacon project as well as other GA4GH activities and so this plan defines who is responsible for the communication between ELIXIR and GA4GH to ensure strategic partnership is maintained. This study is broken down into 7 Work Packages: WP1 - Development of Beacon API specification with the GA4GH WP2 - Supporting new ELIXIR Beacon development and deployment across Europe WP3 - Implementation of an ELIXIR Beacon Network & Registry WP4 - Security of ELIXIR Beacon and Beacon Network WP5 - Developing Indicators to establish Registry and Beacon as an Emerging ELIXIR Service WP6 - Strategic partnerships with national data cohorts and biobanks WP7 - Project Management and Communication Other Implementation Studies: 2015-16 2017 2019 (in preparation) The ongoing work on the Beacon Project is coordinated by the ELIXIR Human Data Community	ELIXIR Finland, ELIXIR Switzerland, ELIXIR Spain, ELIXIR Belgium , ELIXIR France, ELIXIR Netherlands, ELIXIR Norway, ELIXIR Italy, EMBL-EBI
Beacon and Beacon Network as a Service	The GA4GH Discovery work stream is developing a data discovery platform which includes Beacons and MatchMaker Exchange (MME). To enhance the reusability of scientific data, ELIXIR aims to facilitate making data ‘findable’ (FAIR guiding principles). To date, GA4GH Beacons have been lit for genetic sequencing data that resides in 6 continents. To be of value to the community the scale of genetic sequencing data that is ‘findable’ needs to increase. ELIXIR can bring Europe’s data forward in particular via ELIXIR Nodes but can also develop tools to enable data to be brought forward from anywhere in the world. The endpoint will be that user communities can find data on an international scale and identify appropriate data to then access for research. The ELIXIR Beacon 2016 and 2017 Implementation studies initiated this work by providing consent-based access to genomic data in the European Genome-phenome Archive and national resources in Finland, Sweden, France and The Netherlands by establishing GA4GH standard based Beacons. The 2017 project developed new features including an ELIXIR Beacon Network and adding security measures that would identify re-identification attempts. The 2018 project aims evolve the ELIXIR Beacons into a GA4GH Driver project with full alignment to GA4GH Technical Work Streams and consolidate and establish a fully costed process of “Lighting a Beacon” for any ELIXIR Node and deliver Beacon/Beacon Network as an established ELIXIR infrastructure service. It is imperative to continue to synchronize with the GA4GH Beacon project as well as other GA4GH activities and so this plan defines who is responsible for the communication between ELIXIR and GA4GH to ensure strategic partnership is maintained. This study is broken down into 7 Work Packages: WP1 - Development of Beacon API specification with the GA4GH WP2 - Supporting new ELIXIR Beacon development and deployment across Europe WP3 - Implementation of an ELIXIR Beacon Network & Registry WP4 - Security of ELIXIR Beacon and Beacon Network WP5 - Developing Indicators to establish Registry and Beacon as an Emerging ELIXIR Service WP6 - Strategic partnerships with national data cohorts and biobanks WP7 - Project Management and Communication Other Implementation Studies: 2015-16 2017 2019 (in preparation) The ongoing work on the Beacon Project is coordinated by the ELIXIR Human Data Community	ELIXIR Finland, ELIXIR Switzerland, ELIXIR Spain, ELIXIR Belgium , ELIXIR France, ELIXIR Netherlands, ELIXIR Norway, ELIXIR Italy, EMBL-EBI
Beacon and Beacon Network as a Service	The GA4GH Discovery work stream is developing a data discovery platform which includes Beacons and MatchMaker Exchange (MME). To enhance the reusability of scientific data, ELIXIR aims to facilitate making data ‘findable’ (FAIR guiding principles). To date, GA4GH Beacons have been lit for genetic sequencing data that resides in 6 continents. To be of value to the community the scale of genetic sequencing data that is ‘findable’ needs to increase. ELIXIR can bring Europe’s data forward in particular via ELIXIR Nodes but can also develop tools to enable data to be brought forward from anywhere in the world. The endpoint will be that user communities can find data on an international scale and identify appropriate data to then access for research. The ELIXIR Beacon 2016 and 2017 Implementation studies initiated this work by providing consent-based access to genomic data in the European Genome-phenome Archive and national resources in Finland, Sweden, France and The Netherlands by establishing GA4GH standard based Beacons. The 2017 project developed new features including an ELIXIR Beacon Network and adding security measures that would identify re-identification attempts. The 2018 project aims evolve the ELIXIR Beacons into a GA4GH Driver project with full alignment to GA4GH Technical Work Streams and consolidate and establish a fully costed process of “Lighting a Beacon” for any ELIXIR Node and deliver Beacon/Beacon Network as an established ELIXIR infrastructure service. It is imperative to continue to synchronize with the GA4GH Beacon project as well as other GA4GH activities and so this plan defines who is responsible for the communication between ELIXIR and GA4GH to ensure strategic partnership is maintained. This study is broken down into 7 Work Packages: WP1 - Development of Beacon API specification with the GA4GH WP2 - Supporting new ELIXIR Beacon development and deployment across Europe WP3 - Implementation of an ELIXIR Beacon Network & Registry WP4 - Security of ELIXIR Beacon and Beacon Network WP5 - Developing Indicators to establish Registry and Beacon as an Emerging ELIXIR Service WP6 - Strategic partnerships with national data cohorts and biobanks WP7 - Project Management and Communication Other Implementation Studies: 2015-16 2017 2019 (in preparation) The ongoing work on the Beacon Project is coordinated by the ELIXIR Human Data Community	ELIXIR Finland, ELIXIR Switzerland, ELIXIR Spain, ELIXIR Belgium , ELIXIR France, ELIXIR Netherlands, ELIXIR Norway, ELIXIR Italy, EMBL-EBI
Beacon and Beacon Network as a Service	The GA4GH Discovery work stream is developing a data discovery platform which includes Beacons and MatchMaker Exchange (MME). To enhance the reusability of scientific data, ELIXIR aims to facilitate making data ‘findable’ (FAIR guiding principles). To date, GA4GH Beacons have been lit for genetic sequencing data that resides in 6 continents. To be of value to the community the scale of genetic sequencing data that is ‘findable’ needs to increase. ELIXIR can bring Europe’s data forward in particular via ELIXIR Nodes but can also develop tools to enable data to be brought forward from anywhere in the world. The endpoint will be that user communities can find data on an international scale and identify appropriate data to then access for research. The ELIXIR Beacon 2016 and 2017 Implementation studies initiated this work by providing consent-based access to genomic data in the European Genome-phenome Archive and national resources in Finland, Sweden, France and The Netherlands by establishing GA4GH standard based Beacons. The 2017 project developed new features including an ELIXIR Beacon Network and adding security measures that would identify re-identification attempts. The 2018 project aims evolve the ELIXIR Beacons into a GA4GH Driver project with full alignment to GA4GH Technical Work Streams and consolidate and establish a fully costed process of “Lighting a Beacon” for any ELIXIR Node and deliver Beacon/Beacon Network as an established ELIXIR infrastructure service. It is imperative to continue to synchronize with the GA4GH Beacon project as well as other GA4GH activities and so this plan defines who is responsible for the communication between ELIXIR and GA4GH to ensure strategic partnership is maintained. This study is broken down into 7 Work Packages: WP1 - Development of Beacon API specification with the GA4GH WP2 - Supporting new ELIXIR Beacon development and deployment across Europe WP3 - Implementation of an ELIXIR Beacon Network & Registry WP4 - Security of ELIXIR Beacon and Beacon Network WP5 - Developing Indicators to establish Registry and Beacon as an Emerging ELIXIR Service WP6 - Strategic partnerships with national data cohorts and biobanks WP7 - Project Management and Communication Other Implementation Studies: 2015-16 2017 2019 (in preparation) The ongoing work on the Beacon Project is coordinated by the ELIXIR Human Data Community	ELIXIR Finland, ELIXIR Switzerland, ELIXIR Spain, ELIXIR Belgium , ELIXIR France, ELIXIR Netherlands, ELIXIR Norway, ELIXIR Italy, EMBL-EBI
Beacon and Beacon Network as a Service	The GA4GH Discovery work stream is developing a data discovery platform which includes Beacons and MatchMaker Exchange (MME). To enhance the reusability of scientific data, ELIXIR aims to facilitate making data ‘findable’ (FAIR guiding principles). To date, GA4GH Beacons have been lit for genetic sequencing data that resides in 6 continents. To be of value to the community the scale of genetic sequencing data that is ‘findable’ needs to increase. ELIXIR can bring Europe’s data forward in particular via ELIXIR Nodes but can also develop tools to enable data to be brought forward from anywhere in the world. The endpoint will be that user communities can find data on an international scale and identify appropriate data to then access for research. The ELIXIR Beacon 2016 and 2017 Implementation studies initiated this work by providing consent-based access to genomic data in the European Genome-phenome Archive and national resources in Finland, Sweden, France and The Netherlands by establishing GA4GH standard based Beacons. The 2017 project developed new features including an ELIXIR Beacon Network and adding security measures that would identify re-identification attempts. The 2018 project aims evolve the ELIXIR Beacons into a GA4GH Driver project with full alignment to GA4GH Technical Work Streams and consolidate and establish a fully costed process of “Lighting a Beacon” for any ELIXIR Node and deliver Beacon/Beacon Network as an established ELIXIR infrastructure service. It is imperative to continue to synchronize with the GA4GH Beacon project as well as other GA4GH activities and so this plan defines who is responsible for the communication between ELIXIR and GA4GH to ensure strategic partnership is maintained. This study is broken down into 7 Work Packages: WP1 - Development of Beacon API specification with the GA4GH WP2 - Supporting new ELIXIR Beacon development and deployment across Europe WP3 - Implementation of an ELIXIR Beacon Network & Registry WP4 - Security of ELIXIR Beacon and Beacon Network WP5 - Developing Indicators to establish Registry and Beacon as an Emerging ELIXIR Service WP6 - Strategic partnerships with national data cohorts and biobanks WP7 - Project Management and Communication Other Implementation Studies: 2015-16 2017 2019 (in preparation) The ongoing work on the Beacon Project is coordinated by the ELIXIR Human Data Community	ELIXIR Finland, ELIXIR Switzerland, ELIXIR Spain, ELIXIR Belgium , ELIXIR France, ELIXIR Netherlands, ELIXIR Norway, ELIXIR Italy, EMBL-EBI
Beacon and Beacon Network as a Service	The GA4GH Discovery work stream is developing a data discovery platform which includes Beacons and MatchMaker Exchange (MME). To enhance the reusability of scientific data, ELIXIR aims to facilitate making data ‘findable’ (FAIR guiding principles). To date, GA4GH Beacons have been lit for genetic sequencing data that resides in 6 continents. To be of value to the community the scale of genetic sequencing data that is ‘findable’ needs to increase. ELIXIR can bring Europe’s data forward in particular via ELIXIR Nodes but can also develop tools to enable data to be brought forward from anywhere in the world. The endpoint will be that user communities can find data on an international scale and identify appropriate data to then access for research. The ELIXIR Beacon 2016 and 2017 Implementation studies initiated this work by providing consent-based access to genomic data in the European Genome-phenome Archive and national resources in Finland, Sweden, France and The Netherlands by establishing GA4GH standard based Beacons. The 2017 project developed new features including an ELIXIR Beacon Network and adding security measures that would identify re-identification attempts. The 2018 project aims evolve the ELIXIR Beacons into a GA4GH Driver project with full alignment to GA4GH Technical Work Streams and consolidate and establish a fully costed process of “Lighting a Beacon” for any ELIXIR Node and deliver Beacon/Beacon Network as an established ELIXIR infrastructure service. It is imperative to continue to synchronize with the GA4GH Beacon project as well as other GA4GH activities and so this plan defines who is responsible for the communication between ELIXIR and GA4GH to ensure strategic partnership is maintained. This study is broken down into 7 Work Packages: WP1 - Development of Beacon API specification with the GA4GH WP2 - Supporting new ELIXIR Beacon development and deployment across Europe WP3 - Implementation of an ELIXIR Beacon Network & Registry WP4 - Security of ELIXIR Beacon and Beacon Network WP5 - Developing Indicators to establish Registry and Beacon as an Emerging ELIXIR Service WP6 - Strategic partnerships with national data cohorts and biobanks WP7 - Project Management and Communication Other Implementation Studies: 2015-16 2017 2019 (in preparation) The ongoing work on the Beacon Project is coordinated by the ELIXIR Human Data Community	ELIXIR Finland, ELIXIR Switzerland, ELIXIR Spain, ELIXIR Belgium , ELIXIR France, ELIXIR Netherlands, ELIXIR Norway, ELIXIR Italy, EMBL-EBI
Best Practices for storing genomic data – compression and encryption workshop	Genomic data is immensely valuable for drug development and as a diagnostic tool in clinical settings. With the advent of next-generation sequencing instruments, the cost of data production was tremendously reduced. However, new challenges emerge as more population-scale genomics initiatives take off. Firstly, the sheer volume of data means that a large proportion of budgets will have to be diverted towards storage hardware for these data. Secondly, these data are highly identifiable and must be stored securely in order to meet strict national and regional compliance regulations. This project will offer industry and academics the opportunity to learn about best practices for storing genomic and other data. Key areas that will be addressed include how to reduce the cost of storage by leveraging state of the art genomic compression tools and how to achieve compliance by leveraging software that is architected to encrypt NGS and other data in a secure yet accessible approach. Impact Statement By attending this one-day course, attendees will be equipped with knowledge of the best practices for securely storing NGS and other data in a cost-effective manner. This knowledge will benefit projects across the ELIXIR Nodes and their national stakeholders, in both academia and industry by ensuring that budgets are designed more optimally, ensuring resources can be allocated towards research purposes while making the cost of storage manageable. ELIXIR Luxembourg’s services are mainly centred around repositories for translational medicine data as well as data access and computing. An example would be the storage of data generated in the IMI Oncotrack project. Therefore, it would be invaluable for the Node to exchange knowledge in this area with Petagene, who is a leader in the area of cost-effective data compression and encryption. This workshop will be the basis for future collaboration between Petagene and ELIXIR Luxembourg, with a scope to expand to other ELIXIR Nodes.	ELIXIR Luxembourg
Data Resource Implementations for the GA4GH Data Schema	The aim of this Implementation Study was to use the existing, genome related datasets from the areas of clinical and population genetics, cancer genomics and nonhuman genome analysis to drive the refinement of the Global Alliance for Genomics and Health (GA4GH) data schema (documents) as well as to implement compatible example resources. A GA4GH compatible version of the arrayMap resource, a large repository of genomic copy number aberration data in human malignancies, will be created. BioSamples and Ontology Lookup Service (OLS) supply data-ontology mapping services and ontology access via a new version of OLS. This task interacts with and supports the ELIXIR Beacon project, especially regarding the design and technical implementation of extended Beacon query and report formats (including quantitative return and metadata enrichment). This study is now completed, the work is outlined in the end report and was presented at a number of meetings (see the slides). Webinar summarising the outcomes	EMBL-EBI, ELIXIR France, ELIXIR Switzerland
Data Resource Implementations for the GA4GH Data Schema	The aim of this Implementation Study was to use the existing, genome related datasets from the areas of clinical and population genetics, cancer genomics and nonhuman genome analysis to drive the refinement of the Global Alliance for Genomics and Health (GA4GH) data schema (documents) as well as to implement compatible example resources. A GA4GH compatible version of the arrayMap resource, a large repository of genomic copy number aberration data in human malignancies, will be created. BioSamples and Ontology Lookup Service (OLS) supply data-ontology mapping services and ontology access via a new version of OLS. This task interacts with and supports the ELIXIR Beacon project, especially regarding the design and technical implementation of extended Beacon query and report formats (including quantitative return and metadata enrichment). This study is now completed, the work is outlined in the end report and was presented at a number of meetings (see the slides). Webinar summarising the outcomes	EMBL-EBI, ELIXIR France, ELIXIR Switzerland
Data Resource Implementations for the GA4GH Data Schema	The aim of this Implementation Study was to use the existing, genome related datasets from the areas of clinical and population genetics, cancer genomics and nonhuman genome analysis to drive the refinement of the Global Alliance for Genomics and Health (GA4GH) data schema (documents) as well as to implement compatible example resources. A GA4GH compatible version of the arrayMap resource, a large repository of genomic copy number aberration data in human malignancies, will be created. BioSamples and Ontology Lookup Service (OLS) supply data-ontology mapping services and ontology access via a new version of OLS. This task interacts with and supports the ELIXIR Beacon project, especially regarding the design and technical implementation of extended Beacon query and report formats (including quantitative return and metadata enrichment). This study is now completed, the work is outlined in the end report and was presented at a number of meetings (see the slides). Webinar summarising the outcomes	EMBL-EBI, ELIXIR France, ELIXIR Switzerland
Data Validation	The aim of this Implementation Study is to determine the requirements for validation with ELIXIR partners, to build prototype open validation services for archetype archival databases and knowledge bases, in particular: Content validation according to minimum information checklists. Syntactic format validation according to a standard format in conjunction with the GA4GH file formats team as part of the Large Scale Genomics Workstream. Syntactic format validation for Phenotyping data. Semantic validation according to a publicly available ontology.	ELIXIR Belgium , ELIXIR France, EMBL-EBI, ELIXIR UK
Data Validation	The aim of this Implementation Study is to determine the requirements for validation with ELIXIR partners, to build prototype open validation services for archetype archival databases and knowledge bases, in particular: Content validation according to minimum information checklists. Syntactic format validation according to a standard format in conjunction with the GA4GH file formats team as part of the Large Scale Genomics Workstream. Syntactic format validation for Phenotyping data. Semantic validation according to a publicly available ontology.	ELIXIR Belgium , ELIXIR France, EMBL-EBI, ELIXIR UK
Data Validation	The aim of this Implementation Study is to determine the requirements for validation with ELIXIR partners, to build prototype open validation services for archetype archival databases and knowledge bases, in particular: Content validation according to minimum information checklists. Syntactic format validation according to a standard format in conjunction with the GA4GH file formats team as part of the Large Scale Genomics Workstream. Syntactic format validation for Phenotyping data. Semantic validation according to a publicly available ontology.	ELIXIR Belgium , ELIXIR France, EMBL-EBI, ELIXIR UK
Data Validation	The aim of this Implementation Study is to determine the requirements for validation with ELIXIR partners, to build prototype open validation services for archetype archival databases and knowledge bases, in particular: Content validation according to minimum information checklists. Syntactic format validation according to a standard format in conjunction with the GA4GH file formats team as part of the Large Scale Genomics Workstream. Syntactic format validation for Phenotyping data. Semantic validation according to a publicly available ontology.	ELIXIR Belgium , ELIXIR France, EMBL-EBI, ELIXIR UK
ELIXIR Federated Human Data (2019-21)	Over the last forty years, we have seen the emergence of large cohorts of human samples from research and national healthcare initiatives. Many countries in Europe now have nascent personalised medicine programmes meaning that human genomics is undergoing a step change from being a predominantly research-driven activity to one funded through healthcare. This is evidenced by the recent Declaration of 19 European countries to sequence and share transnationally at least 1M human genomes by 2022. This initiative will catalyse the transition of genomics from the bench to bedside in Europe. We envisage that a significant subset of these data will be made available for secondary research. However genetic data generated through healthcare is not likely to be shared as widely as research data. Healthcare is subject to national laws, and it is often unacceptable for health data from one country to be exported outside regional or national jurisdictions. Our vision for the ELIXIR Federated Human Data Community is to create a federated ecosystem of interoperable services that enables population scale genomic and biomolecular data to be accessible across international borders accelerating research and improving the health of individuals resident across Europe. This project will coordinate the delivery of FAIR compliant metadata standards, interfaces, and reference implementation to support the federated ELIXIR network of human data resources. The overall goal is to provide secure, standardized, documented and interoperable services under the framework of the European Genome-phenome Archive (EGA). This three year plan includes a structured roadmap for ELIXIR Nodes to join the EGA federated network by providing the necessary technical, logistical, and training coordination across the network. This project builds on earlier work in the ELIXIR-EXCELERATE, CORBEL and Tryggve projects. It will be led by the European Genome-phenome Archive (EGA) to ensure work described in this proposal is aligned with the policies, legal agreements, and governance model for establishing the Federated EGA. WP3 will build on work in EXCELERATE WP9 to create a reference software implementation, the Local EGA, that Nodes can use to operate their federated node. The work is divided between five Work Packages (WPs): WP1: Coordination of metadata standards for sensitive human data WP2: Architecture and interfaces to support ELIXIR federated human data infrastructure WP3: Coordination of interface implementation WP4: Coordination of operational nodes as part of the federated services WP5: Project overall coordination, outreach and training WP1: Coordination of metadata standards for sensitive human data Lead: Ilkka Lappalainen (ELIXIR FI) The overall objective of this work package is to coordinate a clearly defined, documented and maintained set of metadata standards for data collected from human samples. The data and metadata collected by disparate cohorts varies widely from the type of biomaterials collected from participants (e.g. blood, DNA, tissue samples), lifestyle information by participant questionnaires and molecular measurements used to record phenotypes. The cohorts are also assembled for different purposes - population longitudinal studies vs. disease progress for example. Cohort variables are considered separately, and in groups where they may be grouped to represent a diagnosis e.g. those measured variables related to metabolic syndrome or risk factors for stroke. Standardisation and interoperability of these data are critical for this project and application of the FAIR principles brings benefits to cohort owners and the wider community. The work package partners are actively involved in both global and European standards bodies (e.g. Global Alliance for Genomics and Health - GA4GH, and the International Nucleotide Sequence Database Collaboration - INSDC), infrastructure coordination projects (e.g. CORBEL, EXCELERATE, dbGap/DATS, BioCADDIE, CINECA), and disease specific resources (e.g. ICGC, rare diseases RD-Connect, Solve-RD). This work package provides the necessary coordination activity from existing forums as the basis for deciding which metadata standards will be adopted by the ELIXIR federated human data network and provides documentation on how to apply these standards across the Federated EGA nodes. The work package will not create new standards nor provide coordination to harmonise national patient registries, clinical use of ontologies or vocabularies for example. WP2: Architecture and interfaces to support ELIXIR federated human data infrastructure Lead: Thomas Keane (EMBL-EBI) One of the fundamental requirements for creating an interoperable federated network is to determine what information needs to be communicated between the nodes, and to translate these requirements into a technical specification and protocol for sending/receiving messages. This work package will deliver the overall architecture and define interfaces for the federated human data services. Maintaining architectural integrity is essential for developing the federation in controlled fashion and ensuring interoperability between the locally run services. This work package will focus on interfaces for data discovery, metadata exchange, data dissemination, access and authorisation. This work package will align with emerging international standards (where possible) to promote interoperability between the Federated EGA nodes and similar international initiatives. For discovery, we will align with the ELIXIR Beacon and the GA4GH Discovery Work Stream, data dissemination will align with GA4GH Large Scale Genomics Work Stream (e.g. htsget, GA4GH file formats, encryption container format, and reference retrieval API), and access and authorisation will use the ELIXIR AAI which is aligned with the DURI Work Stream of GA4GH. The overall goal is to achieve unified user experience, ensure security across the ecosystem while maintaining flexibility to cater local requirements. We envisage two levels of engagement from federation partners: Nodes that have an existing operational human data sharing platform with deep investment in existing IT infrastructure and data security infrastructure solutions. These nodes would join the federated network by implementing the APIs recommended by WP2 as a layer over their existing infrastructure. Nodes with less well mature human data sharing infrastructure (but with resources and competence) that would want to contribute via WP3 to the joint development effort and deploy it locally for their Node. We will provide foundation for data analysis by providing suitable access (e.g. streaming) to data. However implementation of analysis protocols to be used is out of the scope for this work. WP3: Coordination of interface implementation Lead: Jordi Rambla (ELIXIR ES) This work package will coordinate the software development work that provides an implementation of the WP2 defined interfaces to support the federated services for human data. This task will leverage the work done as Local EGA in the context of EXCELERATE, extending it whenever is necessary. WP3 will support Nodes by coordinating through: Hosting periodic coordination calls and facilitate the interface implementation work. Use of a shared code repository and coordination of relevant documentation. Coordinating maintenance, development on WP2 defined interfaces. Providing relevant documentation together with WP5 describing software and deployment processes to assist capacity building in other Nodes. While the priorities of the implemented interfaces will be decided during the project we have already identified the following important development tasks based on the preceding work on EXCELERATE tasks on sensitive human data: (1) unified data deposition interface that enables submission in uniform fashion to any of the federated archives, (2) support shared user authentication and authorization framework (e.g. ELIXIR AAI and EGA AAI) to ease submitter authentication and re-use of archived data for authorized researchers, (3) quality control processes for submitted data files and (4) validation processes for submitted phenotypic attributes for the samples. As the majority of the funding for implementation will need to be provided by the participating Nodes, the main risk to this work package is alignment of delivery times with other relevant projects that also fund the development of this infrastructure. During the project it may also become necessary to implement interfaces to services that are not part of the federation and may need to be adapted to support required information exchange. WP4: Coordination of operational nodes as part of the federated services Lead: Ilkka Lappalainen (ELIXIR FI) This work package provides a mechanism for ELIXIR Node services to become part of the federated interoperable services for human data. The process of a Node transitioning from an expression of interest through to becoming a fully operational EGA federated instance requires coordination and support in the form of training, documentation, and advice on best practices. It is designed to offer support especially to those Nodes that have signed the Declaration to share one million human genomes cross-border by 20221. Importantly, each Node is responsible for their own infrastructure, security and operational legal framework. The specific objectives of WP4 are to: Coordinate relevant training material for new staff members within the Nodes together with WP5. Coordinate workshops for interested Nodes on how to become operational partner of the federated EGA services. Development, coordination, and organisation of best practices for security incident practices (aligned with the GA4GH Data Security work stream recommendations). Define and monitor relevant KPIs together with WP2 and WP3 for monitoring successful service delivery. This work will be done in close collaboration with the ELIXIR Beacon project and the ELIXIR Compute platform. This work package will not fund the local infrastructure, software deployment processes or operational staff members to manage the local services. Furthermore, it will not provide the legal framework for the Federated EGA. The risks include lack of resources to solve infrastructure dependent issues on software deployment or management of local dependencies such as availability of staff members for training. WP5: Project overall coordination, outreach and training This work package will provide the project management and coordination for this project. The specific objectives of WP5 are to: Establish a project management team that ensures effective communication and timely delivery through the project life time. Coordination of calls, workshops and meetings. Development and implementation of contingency and risk management plan. Development and implementation of outreach strategy. Coordination and delivery of training material for WP1-WP4 in collaboration with the ELIXIR Training Platform ensuring that materials are accessible via ELIXIR’s Training Portal.	ELIXIR Finland, EMBL-EBI, ELIXIR Spain, ELIXIR Switzerland, ELIXIR Netherlands, ELIXIR Sweden, ELIXIR Luxembourg, ELIXIR Norway, ELIXIR Czech Republic, ELIXIR Portugal, ELIXIR Estonia, ELIXIR Belgium , ELIXIR Slovenia
ELIXIR Federated Human Data (2019-21)	Over the last forty years, we have seen the emergence of large cohorts of human samples from research and national healthcare initiatives. Many countries in Europe now have nascent personalised medicine programmes meaning that human genomics is undergoing a step change from being a predominantly research-driven activity to one funded through healthcare. This is evidenced by the recent Declaration of 19 European countries to sequence and share transnationally at least 1M human genomes by 2022. This initiative will catalyse the transition of genomics from the bench to bedside in Europe. We envisage that a significant subset of these data will be made available for secondary research. However genetic data generated through healthcare is not likely to be shared as widely as research data. Healthcare is subject to national laws, and it is often unacceptable for health data from one country to be exported outside regional or national jurisdictions. Our vision for the ELIXIR Federated Human Data Community is to create a federated ecosystem of interoperable services that enables population scale genomic and biomolecular data to be accessible across international borders accelerating research and improving the health of individuals resident across Europe. This project will coordinate the delivery of FAIR compliant metadata standards, interfaces, and reference implementation to support the federated ELIXIR network of human data resources. The overall goal is to provide secure, standardized, documented and interoperable services under the framework of the European Genome-phenome Archive (EGA). This three year plan includes a structured roadmap for ELIXIR Nodes to join the EGA federated network by providing the necessary technical, logistical, and training coordination across the network. This project builds on earlier work in the ELIXIR-EXCELERATE, CORBEL and Tryggve projects. It will be led by the European Genome-phenome Archive (EGA) to ensure work described in this proposal is aligned with the policies, legal agreements, and governance model for establishing the Federated EGA. WP3 will build on work in EXCELERATE WP9 to create a reference software implementation, the Local EGA, that Nodes can use to operate their federated node. The work is divided between five Work Packages (WPs): WP1: Coordination of metadata standards for sensitive human data WP2: Architecture and interfaces to support ELIXIR federated human data infrastructure WP3: Coordination of interface implementation WP4: Coordination of operational nodes as part of the federated services WP5: Project overall coordination, outreach and training WP1: Coordination of metadata standards for sensitive human data Lead: Ilkka Lappalainen (ELIXIR FI) The overall objective of this work package is to coordinate a clearly defined, documented and maintained set of metadata standards for data collected from human samples. The data and metadata collected by disparate cohorts varies widely from the type of biomaterials collected from participants (e.g. blood, DNA, tissue samples), lifestyle information by participant questionnaires and molecular measurements used to record phenotypes. The cohorts are also assembled for different purposes - population longitudinal studies vs. disease progress for example. Cohort variables are considered separately, and in groups where they may be grouped to represent a diagnosis e.g. those measured variables related to metabolic syndrome or risk factors for stroke. Standardisation and interoperability of these data are critical for this project and application of the FAIR principles brings benefits to cohort owners and the wider community. The work package partners are actively involved in both global and European standards bodies (e.g. Global Alliance for Genomics and Health - GA4GH, and the International Nucleotide Sequence Database Collaboration - INSDC), infrastructure coordination projects (e.g. CORBEL, EXCELERATE, dbGap/DATS, BioCADDIE, CINECA), and disease specific resources (e.g. ICGC, rare diseases RD-Connect, Solve-RD). This work package provides the necessary coordination activity from existing forums as the basis for deciding which metadata standards will be adopted by the ELIXIR federated human data network and provides documentation on how to apply these standards across the Federated EGA nodes. The work package will not create new standards nor provide coordination to harmonise national patient registries, clinical use of ontologies or vocabularies for example. WP2: Architecture and interfaces to support ELIXIR federated human data infrastructure Lead: Thomas Keane (EMBL-EBI) One of the fundamental requirements for creating an interoperable federated network is to determine what information needs to be communicated between the nodes, and to translate these requirements into a technical specification and protocol for sending/receiving messages. This work package will deliver the overall architecture and define interfaces for the federated human data services. Maintaining architectural integrity is essential for developing the federation in controlled fashion and ensuring interoperability between the locally run services. This work package will focus on interfaces for data discovery, metadata exchange, data dissemination, access and authorisation. This work package will align with emerging international standards (where possible) to promote interoperability between the Federated EGA nodes and similar international initiatives. For discovery, we will align with the ELIXIR Beacon and the GA4GH Discovery Work Stream, data dissemination will align with GA4GH Large Scale Genomics Work Stream (e.g. htsget, GA4GH file formats, encryption container format, and reference retrieval API), and access and authorisation will use the ELIXIR AAI which is aligned with the DURI Work Stream of GA4GH. The overall goal is to achieve unified user experience, ensure security across the ecosystem while maintaining flexibility to cater local requirements. We envisage two levels of engagement from federation partners: Nodes that have an existing operational human data sharing platform with deep investment in existing IT infrastructure and data security infrastructure solutions. These nodes would join the federated network by implementing the APIs recommended by WP2 as a layer over their existing infrastructure. Nodes with less well mature human data sharing infrastructure (but with resources and competence) that would want to contribute via WP3 to the joint development effort and deploy it locally for their Node. We will provide foundation for data analysis by providing suitable access (e.g. streaming) to data. However implementation of analysis protocols to be used is out of the scope for this work. WP3: Coordination of interface implementation Lead: Jordi Rambla (ELIXIR ES) This work package will coordinate the software development work that provides an implementation of the WP2 defined interfaces to support the federated services for human data. This task will leverage the work done as Local EGA in the context of EXCELERATE, extending it whenever is necessary. WP3 will support Nodes by coordinating through: Hosting periodic coordination calls and facilitate the interface implementation work. Use of a shared code repository and coordination of relevant documentation. Coordinating maintenance, development on WP2 defined interfaces. Providing relevant documentation together with WP5 describing software and deployment processes to assist capacity building in other Nodes. While the priorities of the implemented interfaces will be decided during the project we have already identified the following important development tasks based on the preceding work on EXCELERATE tasks on sensitive human data: (1) unified data deposition interface that enables submission in uniform fashion to any of the federated archives, (2) support shared user authentication and authorization framework (e.g. ELIXIR AAI and EGA AAI) to ease submitter authentication and re-use of archived data for authorized researchers, (3) quality control processes for submitted data files and (4) validation processes for submitted phenotypic attributes for the samples. As the majority of the funding for implementation will need to be provided by the participating Nodes, the main risk to this work package is alignment of delivery times with other relevant projects that also fund the development of this infrastructure. During the project it may also become necessary to implement interfaces to services that are not part of the federation and may need to be adapted to support required information exchange. WP4: Coordination of operational nodes as part of the federated services Lead: Ilkka Lappalainen (ELIXIR FI) This work package provides a mechanism for ELIXIR Node services to become part of the federated interoperable services for human data. The process of a Node transitioning from an expression of interest through to becoming a fully operational EGA federated instance requires coordination and support in the form of training, documentation, and advice on best practices. It is designed to offer support especially to those Nodes that have signed the Declaration to share one million human genomes cross-border by 20221. Importantly, each Node is responsible for their own infrastructure, security and operational legal framework. The specific objectives of WP4 are to: Coordinate relevant training material for new staff members within the Nodes together with WP5. Coordinate workshops for interested Nodes on how to become operational partner of the federated EGA services. Development, coordination, and organisation of best practices for security incident practices (aligned with the GA4GH Data Security work stream recommendations). Define and monitor relevant KPIs together with WP2 and WP3 for monitoring successful service delivery. This work will be done in close collaboration with the ELIXIR Beacon project and the ELIXIR Compute platform. This work package will not fund the local infrastructure, software deployment processes or operational staff members to manage the local services. Furthermore, it will not provide the legal framework for the Federated EGA. The risks include lack of resources to solve infrastructure dependent issues on software deployment or management of local dependencies such as availability of staff members for training. WP5: Project overall coordination, outreach and training This work package will provide the project management and coordination for this project. The specific objectives of WP5 are to: Establish a project management team that ensures effective communication and timely delivery through the project life time. Coordination of calls, workshops and meetings. Development and implementation of contingency and risk management plan. Development and implementation of outreach strategy. Coordination and delivery of training material for WP1-WP4 in collaboration with the ELIXIR Training Platform ensuring that materials are accessible via ELIXIR’s Training Portal.	ELIXIR Finland, EMBL-EBI, ELIXIR Spain, ELIXIR Switzerland, ELIXIR Netherlands, ELIXIR Sweden, ELIXIR Luxembourg, ELIXIR Norway, ELIXIR Czech Republic, ELIXIR Portugal, ELIXIR Estonia, ELIXIR Belgium , ELIXIR Slovenia
ELIXIR Federated Human Data (2019-21)	Over the last forty years, we have seen the emergence of large cohorts of human samples from research and national healthcare initiatives. Many countries in Europe now have nascent personalised medicine programmes meaning that human genomics is undergoing a step change from being a predominantly research-driven activity to one funded through healthcare. This is evidenced by the recent Declaration of 19 European countries to sequence and share transnationally at least 1M human genomes by 2022. This initiative will catalyse the transition of genomics from the bench to bedside in Europe. We envisage that a significant subset of these data will be made available for secondary research. However genetic data generated through healthcare is not likely to be shared as widely as research data. Healthcare is subject to national laws, and it is often unacceptable for health data from one country to be exported outside regional or national jurisdictions. Our vision for the ELIXIR Federated Human Data Community is to create a federated ecosystem of interoperable services that enables population scale genomic and biomolecular data to be accessible across international borders accelerating research and improving the health of individuals resident across Europe. This project will coordinate the delivery of FAIR compliant metadata standards, interfaces, and reference implementation to support the federated ELIXIR network of human data resources. The overall goal is to provide secure, standardized, documented and interoperable services under the framework of the European Genome-phenome Archive (EGA). This three year plan includes a structured roadmap for ELIXIR Nodes to join the EGA federated network by providing the necessary technical, logistical, and training coordination across the network. This project builds on earlier work in the ELIXIR-EXCELERATE, CORBEL and Tryggve projects. It will be led by the European Genome-phenome Archive (EGA) to ensure work described in this proposal is aligned with the policies, legal agreements, and governance model for establishing the Federated EGA. WP3 will build on work in EXCELERATE WP9 to create a reference software implementation, the Local EGA, that Nodes can use to operate their federated node. The work is divided between five Work Packages (WPs): WP1: Coordination of metadata standards for sensitive human data WP2: Architecture and interfaces to support ELIXIR federated human data infrastructure WP3: Coordination of interface implementation WP4: Coordination of operational nodes as part of the federated services WP5: Project overall coordination, outreach and training WP1: Coordination of metadata standards for sensitive human data Lead: Ilkka Lappalainen (ELIXIR FI) The overall objective of this work package is to coordinate a clearly defined, documented and maintained set of metadata standards for data collected from human samples. The data and metadata collected by disparate cohorts varies widely from the type of biomaterials collected from participants (e.g. blood, DNA, tissue samples), lifestyle information by participant questionnaires and molecular measurements used to record phenotypes. The cohorts are also assembled for different purposes - population longitudinal studies vs. disease progress for example. Cohort variables are considered separately, and in groups where they may be grouped to represent a diagnosis e.g. those measured variables related to metabolic syndrome or risk factors for stroke. Standardisation and interoperability of these data are critical for this project and application of the FAIR principles brings benefits to cohort owners and the wider community. The work package partners are actively involved in both global and European standards bodies (e.g. Global Alliance for Genomics and Health - GA4GH, and the International Nucleotide Sequence Database Collaboration - INSDC), infrastructure coordination projects (e.g. CORBEL, EXCELERATE, dbGap/DATS, BioCADDIE, CINECA), and disease specific resources (e.g. ICGC, rare diseases RD-Connect, Solve-RD). This work package provides the necessary coordination activity from existing forums as the basis for deciding which metadata standards will be adopted by the ELIXIR federated human data network and provides documentation on how to apply these standards across the Federated EGA nodes. The work package will not create new standards nor provide coordination to harmonise national patient registries, clinical use of ontologies or vocabularies for example. WP2: Architecture and interfaces to support ELIXIR federated human data infrastructure Lead: Thomas Keane (EMBL-EBI) One of the fundamental requirements for creating an interoperable federated network is to determine what information needs to be communicated between the nodes, and to translate these requirements into a technical specification and protocol for sending/receiving messages. This work package will deliver the overall architecture and define interfaces for the federated human data services. Maintaining architectural integrity is essential for developing the federation in controlled fashion and ensuring interoperability between the locally run services. This work package will focus on interfaces for data discovery, metadata exchange, data dissemination, access and authorisation. This work package will align with emerging international standards (where possible) to promote interoperability between the Federated EGA nodes and similar international initiatives. For discovery, we will align with the ELIXIR Beacon and the GA4GH Discovery Work Stream, data dissemination will align with GA4GH Large Scale Genomics Work Stream (e.g. htsget, GA4GH file formats, encryption container format, and reference retrieval API), and access and authorisation will use the ELIXIR AAI which is aligned with the DURI Work Stream of GA4GH. The overall goal is to achieve unified user experience, ensure security across the ecosystem while maintaining flexibility to cater local requirements. We envisage two levels of engagement from federation partners: Nodes that have an existing operational human data sharing platform with deep investment in existing IT infrastructure and data security infrastructure solutions. These nodes would join the federated network by implementing the APIs recommended by WP2 as a layer over their existing infrastructure. Nodes with less well mature human data sharing infrastructure (but with resources and competence) that would want to contribute via WP3 to the joint development effort and deploy it locally for their Node. We will provide foundation for data analysis by providing suitable access (e.g. streaming) to data. However implementation of analysis protocols to be used is out of the scope for this work. WP3: Coordination of interface implementation Lead: Jordi Rambla (ELIXIR ES) This work package will coordinate the software development work that provides an implementation of the WP2 defined interfaces to support the federated services for human data. This task will leverage the work done as Local EGA in the context of EXCELERATE, extending it whenever is necessary. WP3 will support Nodes by coordinating through: Hosting periodic coordination calls and facilitate the interface implementation work. Use of a shared code repository and coordination of relevant documentation. Coordinating maintenance, development on WP2 defined interfaces. Providing relevant documentation together with WP5 describing software and deployment processes to assist capacity building in other Nodes. While the priorities of the implemented interfaces will be decided during the project we have already identified the following important development tasks based on the preceding work on EXCELERATE tasks on sensitive human data: (1) unified data deposition interface that enables submission in uniform fashion to any of the federated archives, (2) support shared user authentication and authorization framework (e.g. ELIXIR AAI and EGA AAI) to ease submitter authentication and re-use of archived data for authorized researchers, (3) quality control processes for submitted data files and (4) validation processes for submitted phenotypic attributes for the samples. As the majority of the funding for implementation will need to be provided by the participating Nodes, the main risk to this work package is alignment of delivery times with other relevant projects that also fund the development of this infrastructure. During the project it may also become necessary to implement interfaces to services that are not part of the federation and may need to be adapted to support required information exchange. WP4: Coordination of operational nodes as part of the federated services Lead: Ilkka Lappalainen (ELIXIR FI) This work package provides a mechanism for ELIXIR Node services to become part of the federated interoperable services for human data. The process of a Node transitioning from an expression of interest through to becoming a fully operational EGA federated instance requires coordination and support in the form of training, documentation, and advice on best practices. It is designed to offer support especially to those Nodes that have signed the Declaration to share one million human genomes cross-border by 20221. Importantly, each Node is responsible for their own infrastructure, security and operational legal framework. The specific objectives of WP4 are to: Coordinate relevant training material for new staff members within the Nodes together with WP5. Coordinate workshops for interested Nodes on how to become operational partner of the federated EGA services. Development, coordination, and organisation of best practices for security incident practices (aligned with the GA4GH Data Security work stream recommendations). Define and monitor relevant KPIs together with WP2 and WP3 for monitoring successful service delivery. This work will be done in close collaboration with the ELIXIR Beacon project and the ELIXIR Compute platform. This work package will not fund the local infrastructure, software deployment processes or operational staff members to manage the local services. Furthermore, it will not provide the legal framework for the Federated EGA. The risks include lack of resources to solve infrastructure dependent issues on software deployment or management of local dependencies such as availability of staff members for training. WP5: Project overall coordination, outreach and training This work package will provide the project management and coordination for this project. The specific objectives of WP5 are to: Establish a project management team that ensures effective communication and timely delivery through the project life time. Coordination of calls, workshops and meetings. Development and implementation of contingency and risk management plan. Development and implementation of outreach strategy. Coordination and delivery of training material for WP1-WP4 in collaboration with the ELIXIR Training Platform ensuring that materials are accessible via ELIXIR’s Training Portal.	ELIXIR Finland, EMBL-EBI, ELIXIR Spain, ELIXIR Switzerland, ELIXIR Netherlands, ELIXIR Sweden, ELIXIR Luxembourg, ELIXIR Norway, ELIXIR Czech Republic, ELIXIR Portugal, ELIXIR Estonia, ELIXIR Belgium , ELIXIR Slovenia
ELIXIR Federated Human Data (2019-21)	Over the last forty years, we have seen the emergence of large cohorts of human samples from research and national healthcare initiatives. Many countries in Europe now have nascent personalised medicine programmes meaning that human genomics is undergoing a step change from being a predominantly research-driven activity to one funded through healthcare. This is evidenced by the recent Declaration of 19 European countries to sequence and share transnationally at least 1M human genomes by 2022. This initiative will catalyse the transition of genomics from the bench to bedside in Europe. We envisage that a significant subset of these data will be made available for secondary research. However genetic data generated through healthcare is not likely to be shared as widely as research data. Healthcare is subject to national laws, and it is often unacceptable for health data from one country to be exported outside regional or national jurisdictions. Our vision for the ELIXIR Federated Human Data Community is to create a federated ecosystem of interoperable services that enables population scale genomic and biomolecular data to be accessible across international borders accelerating research and improving the health of individuals resident across Europe. This project will coordinate the delivery of FAIR compliant metadata standards, interfaces, and reference implementation to support the federated ELIXIR network of human data resources. The overall goal is to provide secure, standardized, documented and interoperable services under the framework of the European Genome-phenome Archive (EGA). This three year plan includes a structured roadmap for ELIXIR Nodes to join the EGA federated network by providing the necessary technical, logistical, and training coordination across the network. This project builds on earlier work in the ELIXIR-EXCELERATE, CORBEL and Tryggve projects. It will be led by the European Genome-phenome Archive (EGA) to ensure work described in this proposal is aligned with the policies, legal agreements, and governance model for establishing the Federated EGA. WP3 will build on work in EXCELERATE WP9 to create a reference software implementation, the Local EGA, that Nodes can use to operate their federated node. The work is divided between five Work Packages (WPs): WP1: Coordination of metadata standards for sensitive human data WP2: Architecture and interfaces to support ELIXIR federated human data infrastructure WP3: Coordination of interface implementation WP4: Coordination of operational nodes as part of the federated services WP5: Project overall coordination, outreach and training WP1: Coordination of metadata standards for sensitive human data Lead: Ilkka Lappalainen (ELIXIR FI) The overall objective of this work package is to coordinate a clearly defined, documented and maintained set of metadata standards for data collected from human samples. The data and metadata collected by disparate cohorts varies widely from the type of biomaterials collected from participants (e.g. blood, DNA, tissue samples), lifestyle information by participant questionnaires and molecular measurements used to record phenotypes. The cohorts are also assembled for different purposes - population longitudinal studies vs. disease progress for example. Cohort variables are considered separately, and in groups where they may be grouped to represent a diagnosis e.g. those measured variables related to metabolic syndrome or risk factors for stroke. Standardisation and interoperability of these data are critical for this project and application of the FAIR principles brings benefits to cohort owners and the wider community. The work package partners are actively involved in both global and European standards bodies (e.g. Global Alliance for Genomics and Health - GA4GH, and the International Nucleotide Sequence Database Collaboration - INSDC), infrastructure coordination projects (e.g. CORBEL, EXCELERATE, dbGap/DATS, BioCADDIE, CINECA), and disease specific resources (e.g. ICGC, rare diseases RD-Connect, Solve-RD). This work package provides the necessary coordination activity from existing forums as the basis for deciding which metadata standards will be adopted by the ELIXIR federated human data network and provides documentation on how to apply these standards across the Federated EGA nodes. The work package will not create new standards nor provide coordination to harmonise national patient registries, clinical use of ontologies or vocabularies for example. WP2: Architecture and interfaces to support ELIXIR federated human data infrastructure Lead: Thomas Keane (EMBL-EBI) One of the fundamental requirements for creating an interoperable federated network is to determine what information needs to be communicated between the nodes, and to translate these requirements into a technical specification and protocol for sending/receiving messages. This work package will deliver the overall architecture and define interfaces for the federated human data services. Maintaining architectural integrity is essential for developing the federation in controlled fashion and ensuring interoperability between the locally run services. This work package will focus on interfaces for data discovery, metadata exchange, data dissemination, access and authorisation. This work package will align with emerging international standards (where possible) to promote interoperability between the Federated EGA nodes and similar international initiatives. For discovery, we will align with the ELIXIR Beacon and the GA4GH Discovery Work Stream, data dissemination will align with GA4GH Large Scale Genomics Work Stream (e.g. htsget, GA4GH file formats, encryption container format, and reference retrieval API), and access and authorisation will use the ELIXIR AAI which is aligned with the DURI Work Stream of GA4GH. The overall goal is to achieve unified user experience, ensure security across the ecosystem while maintaining flexibility to cater local requirements. We envisage two levels of engagement from federation partners: Nodes that have an existing operational human data sharing platform with deep investment in existing IT infrastructure and data security infrastructure solutions. These nodes would join the federated network by implementing the APIs recommended by WP2 as a layer over their existing infrastructure. Nodes with less well mature human data sharing infrastructure (but with resources and competence) that would want to contribute via WP3 to the joint development effort and deploy it locally for their Node. We will provide foundation for data analysis by providing suitable access (e.g. streaming) to data. However implementation of analysis protocols to be used is out of the scope for this work. WP3: Coordination of interface implementation Lead: Jordi Rambla (ELIXIR ES) This work package will coordinate the software development work that provides an implementation of the WP2 defined interfaces to support the federated services for human data. This task will leverage the work done as Local EGA in the context of EXCELERATE, extending it whenever is necessary. WP3 will support Nodes by coordinating through: Hosting periodic coordination calls and facilitate the interface implementation work. Use of a shared code repository and coordination of relevant documentation. Coordinating maintenance, development on WP2 defined interfaces. Providing relevant documentation together with WP5 describing software and deployment processes to assist capacity building in other Nodes. While the priorities of the implemented interfaces will be decided during the project we have already identified the following important development tasks based on the preceding work on EXCELERATE tasks on sensitive human data: (1) unified data deposition interface that enables submission in uniform fashion to any of the federated archives, (2) support shared user authentication and authorization framework (e.g. ELIXIR AAI and EGA AAI) to ease submitter authentication and re-use of archived data for authorized researchers, (3) quality control processes for submitted data files and (4) validation processes for submitted phenotypic attributes for the samples. As the majority of the funding for implementation will need to be provided by the participating Nodes, the main risk to this work package is alignment of delivery times with other relevant projects that also fund the development of this infrastructure. During the project it may also become necessary to implement interfaces to services that are not part of the federation and may need to be adapted to support required information exchange. WP4: Coordination of operational nodes as part of the federated services Lead: Ilkka Lappalainen (ELIXIR FI) This work package provides a mechanism for ELIXIR Node services to become part of the federated interoperable services for human data. The process of a Node transitioning from an expression of interest through to becoming a fully operational EGA federated instance requires coordination and support in the form of training, documentation, and advice on best practices. It is designed to offer support especially to those Nodes that have signed the Declaration to share one million human genomes cross-border by 20221. Importantly, each Node is responsible for their own infrastructure, security and operational legal framework. The specific objectives of WP4 are to: Coordinate relevant training material for new staff members within the Nodes together with WP5. Coordinate workshops for interested Nodes on how to become operational partner of the federated EGA services. Development, coordination, and organisation of best practices for security incident practices (aligned with the GA4GH Data Security work stream recommendations). Define and monitor relevant KPIs together with WP2 and WP3 for monitoring successful service delivery. This work will be done in close collaboration with the ELIXIR Beacon project and the ELIXIR Compute platform. This work package will not fund the local infrastructure, software deployment processes or operational staff members to manage the local services. Furthermore, it will not provide the legal framework for the Federated EGA. The risks include lack of resources to solve infrastructure dependent issues on software deployment or management of local dependencies such as availability of staff members for training. WP5: Project overall coordination, outreach and training This work package will provide the project management and coordination for this project. The specific objectives of WP5 are to: Establish a project management team that ensures effective communication and timely delivery through the project life time. Coordination of calls, workshops and meetings. Development and implementation of contingency and risk management plan. Development and implementation of outreach strategy. Coordination and delivery of training material for WP1-WP4 in collaboration with the ELIXIR Training Platform ensuring that materials are accessible via ELIXIR’s Training Portal.	ELIXIR Finland, EMBL-EBI, ELIXIR Spain, ELIXIR Switzerland, ELIXIR Netherlands, ELIXIR Sweden, ELIXIR Luxembourg, ELIXIR Norway, ELIXIR Czech Republic, ELIXIR Portugal, ELIXIR Estonia, ELIXIR Belgium , ELIXIR Slovenia
ELIXIR Federated Human Data (2019-21)	Over the last forty years, we have seen the emergence of large cohorts of human samples from research and national healthcare initiatives. Many countries in Europe now have nascent personalised medicine programmes meaning that human genomics is undergoing a step change from being a predominantly research-driven activity to one funded through healthcare. This is evidenced by the recent Declaration of 19 European countries to sequence and share transnationally at least 1M human genomes by 2022. This initiative will catalyse the transition of genomics from the bench to bedside in Europe. We envisage that a significant subset of these data will be made available for secondary research. However genetic data generated through healthcare is not likely to be shared as widely as research data. Healthcare is subject to national laws, and it is often unacceptable for health data from one country to be exported outside regional or national jurisdictions. Our vision for the ELIXIR Federated Human Data Community is to create a federated ecosystem of interoperable services that enables population scale genomic and biomolecular data to be accessible across international borders accelerating research and improving the health of individuals resident across Europe. This project will coordinate the delivery of FAIR compliant metadata standards, interfaces, and reference implementation to support the federated ELIXIR network of human data resources. The overall goal is to provide secure, standardized, documented and interoperable services under the framework of the European Genome-phenome Archive (EGA). This three year plan includes a structured roadmap for ELIXIR Nodes to join the EGA federated network by providing the necessary technical, logistical, and training coordination across the network. This project builds on earlier work in the ELIXIR-EXCELERATE, CORBEL and Tryggve projects. It will be led by the European Genome-phenome Archive (EGA) to ensure work described in this proposal is aligned with the policies, legal agreements, and governance model for establishing the Federated EGA. WP3 will build on work in EXCELERATE WP9 to create a reference software implementation, the Local EGA, that Nodes can use to operate their federated node. The work is divided between five Work Packages (WPs): WP1: Coordination of metadata standards for sensitive human data WP2: Architecture and interfaces to support ELIXIR federated human data infrastructure WP3: Coordination of interface implementation WP4: Coordination of operational nodes as part of the federated services WP5: Project overall coordination, outreach and training WP1: Coordination of metadata standards for sensitive human data Lead: Ilkka Lappalainen (ELIXIR FI) The overall objective of this work package is to coordinate a clearly defined, documented and maintained set of metadata standards for data collected from human samples. The data and metadata collected by disparate cohorts varies widely from the type of biomaterials collected from participants (e.g. blood, DNA, tissue samples), lifestyle information by participant questionnaires and molecular measurements used to record phenotypes. The cohorts are also assembled for different purposes - population longitudinal studies vs. disease progress for example. Cohort variables are considered separately, and in groups where they may be grouped to represent a diagnosis e.g. those measured variables related to metabolic syndrome or risk factors for stroke. Standardisation and interoperability of these data are critical for this project and application of the FAIR principles brings benefits to cohort owners and the wider community. The work package partners are actively involved in both global and European standards bodies (e.g. Global Alliance for Genomics and Health - GA4GH, and the International Nucleotide Sequence Database Collaboration - INSDC), infrastructure coordination projects (e.g. CORBEL, EXCELERATE, dbGap/DATS, BioCADDIE, CINECA), and disease specific resources (e.g. ICGC, rare diseases RD-Connect, Solve-RD). This work package provides the necessary coordination activity from existing forums as the basis for deciding which metadata standards will be adopted by the ELIXIR federated human data network and provides documentation on how to apply these standards across the Federated EGA nodes. The work package will not create new standards nor provide coordination to harmonise national patient registries, clinical use of ontologies or vocabularies for example. WP2: Architecture and interfaces to support ELIXIR federated human data infrastructure Lead: Thomas Keane (EMBL-EBI) One of the fundamental requirements for creating an interoperable federated network is to determine what information needs to be communicated between the nodes, and to translate these requirements into a technical specification and protocol for sending/receiving messages. This work package will deliver the overall architecture and define interfaces for the federated human data services. Maintaining architectural integrity is essential for developing the federation in controlled fashion and ensuring interoperability between the locally run services. This work package will focus on interfaces for data discovery, metadata exchange, data dissemination, access and authorisation. This work package will align with emerging international standards (where possible) to promote interoperability between the Federated EGA nodes and similar international initiatives. For discovery, we will align with the ELIXIR Beacon and the GA4GH Discovery Work Stream, data dissemination will align with GA4GH Large Scale Genomics Work Stream (e.g. htsget, GA4GH file formats, encryption container format, and reference retrieval API), and access and authorisation will use the ELIXIR AAI which is aligned with the DURI Work Stream of GA4GH. The overall goal is to achieve unified user experience, ensure security across the ecosystem while maintaining flexibility to cater local requirements. We envisage two levels of engagement from federation partners: Nodes that have an existing operational human data sharing platform with deep investment in existing IT infrastructure and data security infrastructure solutions. These nodes would join the federated network by implementing the APIs recommended by WP2 as a layer over their existing infrastructure. Nodes with less well mature human data sharing infrastructure (but with resources and competence) that would want to contribute via WP3 to the joint development effort and deploy it locally for their Node. We will provide foundation for data analysis by providing suitable access (e.g. streaming) to data. However implementation of analysis protocols to be used is out of the scope for this work. WP3: Coordination of interface implementation Lead: Jordi Rambla (ELIXIR ES) This work package will coordinate the software development work that provides an implementation of the WP2 defined interfaces to support the federated services for human data. This task will leverage the work done as Local EGA in the context of EXCELERATE, extending it whenever is necessary. WP3 will support Nodes by coordinating through: Hosting periodic coordination calls and facilitate the interface implementation work. Use of a shared code repository and coordination of relevant documentation. Coordinating maintenance, development on WP2 defined interfaces. Providing relevant documentation together with WP5 describing software and deployment processes to assist capacity building in other Nodes. While the priorities of the implemented interfaces will be decided during the project we have already identified the following important development tasks based on the preceding work on EXCELERATE tasks on sensitive human data: (1) unified data deposition interface that enables submission in uniform fashion to any of the federated archives, (2) support shared user authentication and authorization framework (e.g. ELIXIR AAI and EGA AAI) to ease submitter authentication and re-use of archived data for authorized researchers, (3) quality control processes for submitted data files and (4) validation processes for submitted phenotypic attributes for the samples. As the majority of the funding for implementation will need to be provided by the participating Nodes, the main risk to this work package is alignment of delivery times with other relevant projects that also fund the development of this infrastructure. During the project it may also become necessary to implement interfaces to services that are not part of the federation and may need to be adapted to support required information exchange. WP4: Coordination of operational nodes as part of the federated services Lead: Ilkka Lappalainen (ELIXIR FI) This work package provides a mechanism for ELIXIR Node services to become part of the federated interoperable services for human data. The process of a Node transitioning from an expression of interest through to becoming a fully operational EGA federated instance requires coordination and support in the form of training, documentation, and advice on best practices. It is designed to offer support especially to those Nodes that have signed the Declaration to share one million human genomes cross-border by 20221. Importantly, each Node is responsible for their own infrastructure, security and operational legal framework. The specific objectives of WP4 are to: Coordinate relevant training material for new staff members within the Nodes together with WP5. Coordinate workshops for interested Nodes on how to become operational partner of the federated EGA services. Development, coordination, and organisation of best practices for security incident practices (aligned with the GA4GH Data Security work stream recommendations). Define and monitor relevant KPIs together with WP2 and WP3 for monitoring successful service delivery. This work will be done in close collaboration with the ELIXIR Beacon project and the ELIXIR Compute platform. This work package will not fund the local infrastructure, software deployment processes or operational staff members to manage the local services. Furthermore, it will not provide the legal framework for the Federated EGA. The risks include lack of resources to solve infrastructure dependent issues on software deployment or management of local dependencies such as availability of staff members for training. WP5: Project overall coordination, outreach and training This work package will provide the project management and coordination for this project. The specific objectives of WP5 are to: Establish a project management team that ensures effective communication and timely delivery through the project life time. Coordination of calls, workshops and meetings. Development and implementation of contingency and risk management plan. Development and implementation of outreach strategy. Coordination and delivery of training material for WP1-WP4 in collaboration with the ELIXIR Training Platform ensuring that materials are accessible via ELIXIR’s Training Portal.	ELIXIR Finland, EMBL-EBI, ELIXIR Spain, ELIXIR Switzerland, ELIXIR Netherlands, ELIXIR Sweden, ELIXIR Luxembourg, ELIXIR Norway, ELIXIR Czech Republic, ELIXIR Portugal, ELIXIR Estonia, ELIXIR Belgium , ELIXIR Slovenia
ELIXIR Federated Human Data (2019-21)	Over the last forty years, we have seen the emergence of large cohorts of human samples from research and national healthcare initiatives. Many countries in Europe now have nascent personalised medicine programmes meaning that human genomics is undergoing a step change from being a predominantly research-driven activity to one funded through healthcare. This is evidenced by the recent Declaration of 19 European countries to sequence and share transnationally at least 1M human genomes by 2022. This initiative will catalyse the transition of genomics from the bench to bedside in Europe. We envisage that a significant subset of these data will be made available for secondary research. However genetic data generated through healthcare is not likely to be shared as widely as research data. Healthcare is subject to national laws, and it is often unacceptable for health data from one country to be exported outside regional or national jurisdictions. Our vision for the ELIXIR Federated Human Data Community is to create a federated ecosystem of interoperable services that enables population scale genomic and biomolecular data to be accessible across international borders accelerating research and improving the health of individuals resident across Europe. This project will coordinate the delivery of FAIR compliant metadata standards, interfaces, and reference implementation to support the federated ELIXIR network of human data resources. The overall goal is to provide secure, standardized, documented and interoperable services under the framework of the European Genome-phenome Archive (EGA). This three year plan includes a structured roadmap for ELIXIR Nodes to join the EGA federated network by providing the necessary technical, logistical, and training coordination across the network. This project builds on earlier work in the ELIXIR-EXCELERATE, CORBEL and Tryggve projects. It will be led by the European Genome-phenome Archive (EGA) to ensure work described in this proposal is aligned with the policies, legal agreements, and governance model for establishing the Federated EGA. WP3 will build on work in EXCELERATE WP9 to create a reference software implementation, the Local EGA, that Nodes can use to operate their federated node. The work is divided between five Work Packages (WPs): WP1: Coordination of metadata standards for sensitive human data WP2: Architecture and interfaces to support ELIXIR federated human data infrastructure WP3: Coordination of interface implementation WP4: Coordination of operational nodes as part of the federated services WP5: Project overall coordination, outreach and training WP1: Coordination of metadata standards for sensitive human data Lead: Ilkka Lappalainen (ELIXIR FI) The overall objective of this work package is to coordinate a clearly defined, documented and maintained set of metadata standards for data collected from human samples. The data and metadata collected by disparate cohorts varies widely from the type of biomaterials collected from participants (e.g. blood, DNA, tissue samples), lifestyle information by participant questionnaires and molecular measurements used to record phenotypes. The cohorts are also assembled for different purposes - population longitudinal studies vs. disease progress for example. Cohort variables are considered separately, and in groups where they may be grouped to represent a diagnosis e.g. those measured variables related to metabolic syndrome or risk factors for stroke. Standardisation and interoperability of these data are critical for this project and application of the FAIR principles brings benefits to cohort owners and the wider community. The work package partners are actively involved in both global and European standards bodies (e.g. Global Alliance for Genomics and Health - GA4GH, and the International Nucleotide Sequence Database Collaboration - INSDC), infrastructure coordination projects (e.g. CORBEL, EXCELERATE, dbGap/DATS, BioCADDIE, CINECA), and disease specific resources (e.g. ICGC, rare diseases RD-Connect, Solve-RD). This work package provides the necessary coordination activity from existing forums as the basis for deciding which metadata standards will be adopted by the ELIXIR federated human data network and provides documentation on how to apply these standards across the Federated EGA nodes. The work package will not create new standards nor provide coordination to harmonise national patient registries, clinical use of ontologies or vocabularies for example. WP2: Architecture and interfaces to support ELIXIR federated human data infrastructure Lead: Thomas Keane (EMBL-EBI) One of the fundamental requirements for creating an interoperable federated network is to determine what information needs to be communicated between the nodes, and to translate these requirements into a technical specification and protocol for sending/receiving messages. This work package will deliver the overall architecture and define interfaces for the federated human data services. Maintaining architectural integrity is essential for developing the federation in controlled fashion and ensuring interoperability between the locally run services. This work package will focus on interfaces for data discovery, metadata exchange, data dissemination, access and authorisation. This work package will align with emerging international standards (where possible) to promote interoperability between the Federated EGA nodes and similar international initiatives. For discovery, we will align with the ELIXIR Beacon and the GA4GH Discovery Work Stream, data dissemination will align with GA4GH Large Scale Genomics Work Stream (e.g. htsget, GA4GH file formats, encryption container format, and reference retrieval API), and access and authorisation will use the ELIXIR AAI which is aligned with the DURI Work Stream of GA4GH. The overall goal is to achieve unified user experience, ensure security across the ecosystem while maintaining flexibility to cater local requirements. We envisage two levels of engagement from federation partners: Nodes that have an existing operational human data sharing platform with deep investment in existing IT infrastructure and data security infrastructure solutions. These nodes would join the federated network by implementing the APIs recommended by WP2 as a layer over their existing infrastructure. Nodes with less well mature human data sharing infrastructure (but with resources and competence) that would want to contribute via WP3 to the joint development effort and deploy it locally for their Node. We will provide foundation for data analysis by providing suitable access (e.g. streaming) to data. However implementation of analysis protocols to be used is out of the scope for this work. WP3: Coordination of interface implementation Lead: Jordi Rambla (ELIXIR ES) This work package will coordinate the software development work that provides an implementation of the WP2 defined interfaces to support the federated services for human data. This task will leverage the work done as Local EGA in the context of EXCELERATE, extending it whenever is necessary. WP3 will support Nodes by coordinating through: Hosting periodic coordination calls and facilitate the interface implementation work. Use of a shared code repository and coordination of relevant documentation. Coordinating maintenance, development on WP2 defined interfaces. Providing relevant documentation together with WP5 describing software and deployment processes to assist capacity building in other Nodes. While the priorities of the implemented interfaces will be decided during the project we have already identified the following important development tasks based on the preceding work on EXCELERATE tasks on sensitive human data: (1) unified data deposition interface that enables submission in uniform fashion to any of the federated archives, (2) support shared user authentication and authorization framework (e.g. ELIXIR AAI and EGA AAI) to ease submitter authentication and re-use of archived data for authorized researchers, (3) quality control processes for submitted data files and (4) validation processes for submitted phenotypic attributes for the samples. As the majority of the funding for implementation will need to be provided by the participating Nodes, the main risk to this work package is alignment of delivery times with other relevant projects that also fund the development of this infrastructure. During the project it may also become necessary to implement interfaces to services that are not part of the federation and may need to be adapted to support required information exchange. WP4: Coordination of operational nodes as part of the federated services Lead: Ilkka Lappalainen (ELIXIR FI) This work package provides a mechanism for ELIXIR Node services to become part of the federated interoperable services for human data. The process of a Node transitioning from an expression of interest through to becoming a fully operational EGA federated instance requires coordination and support in the form of training, documentation, and advice on best practices. It is designed to offer support especially to those Nodes that have signed the Declaration to share one million human genomes cross-border by 20221. Importantly, each Node is responsible for their own infrastructure, security and operational legal framework. The specific objectives of WP4 are to: Coordinate relevant training material for new staff members within the Nodes together with WP5. Coordinate workshops for interested Nodes on how to become operational partner of the federated EGA services. Development, coordination, and organisation of best practices for security incident practices (aligned with the GA4GH Data Security work stream recommendations). Define and monitor relevant KPIs together with WP2 and WP3 for monitoring successful service delivery. This work will be done in close collaboration with the ELIXIR Beacon project and the ELIXIR Compute platform. This work package will not fund the local infrastructure, software deployment processes or operational staff members to manage the local services. Furthermore, it will not provide the legal framework for the Federated EGA. The risks include lack of resources to solve infrastructure dependent issues on software deployment or management of local dependencies such as availability of staff members for training. WP5: Project overall coordination, outreach and training This work package will provide the project management and coordination for this project. The specific objectives of WP5 are to: Establish a project management team that ensures effective communication and timely delivery through the project life time. Coordination of calls, workshops and meetings. Development and implementation of contingency and risk management plan. Development and implementation of outreach strategy. Coordination and delivery of training material for WP1-WP4 in collaboration with the ELIXIR Training Platform ensuring that materials are accessible via ELIXIR’s Training Portal.	ELIXIR Finland, EMBL-EBI, ELIXIR Spain, ELIXIR Switzerland, ELIXIR Netherlands, ELIXIR Sweden, ELIXIR Luxembourg, ELIXIR Norway, ELIXIR Czech Republic, ELIXIR Portugal, ELIXIR Estonia, ELIXIR Belgium , ELIXIR Slovenia
ELIXIR Federated Human Data (2019-21)	Over the last forty years, we have seen the emergence of large cohorts of human samples from research and national healthcare initiatives. Many countries in Europe now have nascent personalised medicine programmes meaning that human genomics is undergoing a step change from being a predominantly research-driven activity to one funded through healthcare. This is evidenced by the recent Declaration of 19 European countries to sequence and share transnationally at least 1M human genomes by 2022. This initiative will catalyse the transition of genomics from the bench to bedside in Europe. We envisage that a significant subset of these data will be made available for secondary research. However genetic data generated through healthcare is not likely to be shared as widely as research data. Healthcare is subject to national laws, and it is often unacceptable for health data from one country to be exported outside regional or national jurisdictions. Our vision for the ELIXIR Federated Human Data Community is to create a federated ecosystem of interoperable services that enables population scale genomic and biomolecular data to be accessible across international borders accelerating research and improving the health of individuals resident across Europe. This project will coordinate the delivery of FAIR compliant metadata standards, interfaces, and reference implementation to support the federated ELIXIR network of human data resources. The overall goal is to provide secure, standardized, documented and interoperable services under the framework of the European Genome-phenome Archive (EGA). This three year plan includes a structured roadmap for ELIXIR Nodes to join the EGA federated network by providing the necessary technical, logistical, and training coordination across the network. This project builds on earlier work in the ELIXIR-EXCELERATE, CORBEL and Tryggve projects. It will be led by the European Genome-phenome Archive (EGA) to ensure work described in this proposal is aligned with the policies, legal agreements, and governance model for establishing the Federated EGA. WP3 will build on work in EXCELERATE WP9 to create a reference software implementation, the Local EGA, that Nodes can use to operate their federated node. The work is divided between five Work Packages (WPs): WP1: Coordination of metadata standards for sensitive human data WP2: Architecture and interfaces to support ELIXIR federated human data infrastructure WP3: Coordination of interface implementation WP4: Coordination of operational nodes as part of the federated services WP5: Project overall coordination, outreach and training WP1: Coordination of metadata standards for sensitive human data Lead: Ilkka Lappalainen (ELIXIR FI) The overall objective of this work package is to coordinate a clearly defined, documented and maintained set of metadata standards for data collected from human samples. The data and metadata collected by disparate cohorts varies widely from the type of biomaterials collected from participants (e.g. blood, DNA, tissue samples), lifestyle information by participant questionnaires and molecular measurements used to record phenotypes. The cohorts are also assembled for different purposes - population longitudinal studies vs. disease progress for example. Cohort variables are considered separately, and in groups where they may be grouped to represent a diagnosis e.g. those measured variables related to metabolic syndrome or risk factors for stroke. Standardisation and interoperability of these data are critical for this project and application of the FAIR principles brings benefits to cohort owners and the wider community. The work package partners are actively involved in both global and European standards bodies (e.g. Global Alliance for Genomics and Health - GA4GH, and the International Nucleotide Sequence Database Collaboration - INSDC), infrastructure coordination projects (e.g. CORBEL, EXCELERATE, dbGap/DATS, BioCADDIE, CINECA), and disease specific resources (e.g. ICGC, rare diseases RD-Connect, Solve-RD). This work package provides the necessary coordination activity from existing forums as the basis for deciding which metadata standards will be adopted by the ELIXIR federated human data network and provides documentation on how to apply these standards across the Federated EGA nodes. The work package will not create new standards nor provide coordination to harmonise national patient registries, clinical use of ontologies or vocabularies for example. WP2: Architecture and interfaces to support ELIXIR federated human data infrastructure Lead: Thomas Keane (EMBL-EBI) One of the fundamental requirements for creating an interoperable federated network is to determine what information needs to be communicated between the nodes, and to translate these requirements into a technical specification and protocol for sending/receiving messages. This work package will deliver the overall architecture and define interfaces for the federated human data services. Maintaining architectural integrity is essential for developing the federation in controlled fashion and ensuring interoperability between the locally run services. This work package will focus on interfaces for data discovery, metadata exchange, data dissemination, access and authorisation. This work package will align with emerging international standards (where possible) to promote interoperability between the Federated EGA nodes and similar international initiatives. For discovery, we will align with the ELIXIR Beacon and the GA4GH Discovery Work Stream, data dissemination will align with GA4GH Large Scale Genomics Work Stream (e.g. htsget, GA4GH file formats, encryption container format, and reference retrieval API), and access and authorisation will use the ELIXIR AAI which is aligned with the DURI Work Stream of GA4GH. The overall goal is to achieve unified user experience, ensure security across the ecosystem while maintaining flexibility to cater local requirements. We envisage two levels of engagement from federation partners: Nodes that have an existing operational human data sharing platform with deep investment in existing IT infrastructure and data security infrastructure solutions. These nodes would join the federated network by implementing the APIs recommended by WP2 as a layer over their existing infrastructure. Nodes with less well mature human data sharing infrastructure (but with resources and competence) that would want to contribute via WP3 to the joint development effort and deploy it locally for their Node. We will provide foundation for data analysis by providing suitable access (e.g. streaming) to data. However implementation of analysis protocols to be used is out of the scope for this work. WP3: Coordination of interface implementation Lead: Jordi Rambla (ELIXIR ES) This work package will coordinate the software development work that provides an implementation of the WP2 defined interfaces to support the federated services for human data. This task will leverage the work done as Local EGA in the context of EXCELERATE, extending it whenever is necessary. WP3 will support Nodes by coordinating through: Hosting periodic coordination calls and facilitate the interface implementation work. Use of a shared code repository and coordination of relevant documentation. Coordinating maintenance, development on WP2 defined interfaces. Providing relevant documentation together with WP5 describing software and deployment processes to assist capacity building in other Nodes. While the priorities of the implemented interfaces will be decided during the project we have already identified the following important development tasks based on the preceding work on EXCELERATE tasks on sensitive human data: (1) unified data deposition interface that enables submission in uniform fashion to any of the federated archives, (2) support shared user authentication and authorization framework (e.g. ELIXIR AAI and EGA AAI) to ease submitter authentication and re-use of archived data for authorized researchers, (3) quality control processes for submitted data files and (4) validation processes for submitted phenotypic attributes for the samples. As the majority of the funding for implementation will need to be provided by the participating Nodes, the main risk to this work package is alignment of delivery times with other relevant projects that also fund the development of this infrastructure. During the project it may also become necessary to implement interfaces to services that are not part of the federation and may need to be adapted to support required information exchange. WP4: Coordination of operational nodes as part of the federated services Lead: Ilkka Lappalainen (ELIXIR FI) This work package provides a mechanism for ELIXIR Node services to become part of the federated interoperable services for human data. The process of a Node transitioning from an expression of interest through to becoming a fully operational EGA federated instance requires coordination and support in the form of training, documentation, and advice on best practices. It is designed to offer support especially to those Nodes that have signed the Declaration to share one million human genomes cross-border by 20221. Importantly, each Node is responsible for their own infrastructure, security and operational legal framework. The specific objectives of WP4 are to: Coordinate relevant training material for new staff members within the Nodes together with WP5. Coordinate workshops for interested Nodes on how to become operational partner of the federated EGA services. Development, coordination, and organisation of best practices for security incident practices (aligned with the GA4GH Data Security work stream recommendations). Define and monitor relevant KPIs together with WP2 and WP3 for monitoring successful service delivery. This work will be done in close collaboration with the ELIXIR Beacon project and the ELIXIR Compute platform. This work package will not fund the local infrastructure, software deployment processes or operational staff members to manage the local services. Furthermore, it will not provide the legal framework for the Federated EGA. The risks include lack of resources to solve infrastructure dependent issues on software deployment or management of local dependencies such as availability of staff members for training. WP5: Project overall coordination, outreach and training This work package will provide the project management and coordination for this project. The specific objectives of WP5 are to: Establish a project management team that ensures effective communication and timely delivery through the project life time. Coordination of calls, workshops and meetings. Development and implementation of contingency and risk management plan. Development and implementation of outreach strategy. Coordination and delivery of training material for WP1-WP4 in collaboration with the ELIXIR Training Platform ensuring that materials are accessible via ELIXIR’s Training Portal.	ELIXIR Finland, EMBL-EBI, ELIXIR Spain, ELIXIR Switzerland, ELIXIR Netherlands, ELIXIR Sweden, ELIXIR Luxembourg, ELIXIR Norway, ELIXIR Czech Republic, ELIXIR Portugal, ELIXIR Estonia, ELIXIR Belgium , ELIXIR Slovenia
ELIXIR Federated Human Data (2019-21)	Over the last forty years, we have seen the emergence of large cohorts of human samples from research and national healthcare initiatives. Many countries in Europe now have nascent personalised medicine programmes meaning that human genomics is undergoing a step change from being a predominantly research-driven activity to one funded through healthcare. This is evidenced by the recent Declaration of 19 European countries to sequence and share transnationally at least 1M human genomes by 2022. This initiative will catalyse the transition of genomics from the bench to bedside in Europe. We envisage that a significant subset of these data will be made available for secondary research. However genetic data generated through healthcare is not likely to be shared as widely as research data. Healthcare is subject to national laws, and it is often unacceptable for health data from one country to be exported outside regional or national jurisdictions. Our vision for the ELIXIR Federated Human Data Community is to create a federated ecosystem of interoperable services that enables population scale genomic and biomolecular data to be accessible across international borders accelerating research and improving the health of individuals resident across Europe. This project will coordinate the delivery of FAIR compliant metadata standards, interfaces, and reference implementation to support the federated ELIXIR network of human data resources. The overall goal is to provide secure, standardized, documented and interoperable services under the framework of the European Genome-phenome Archive (EGA). This three year plan includes a structured roadmap for ELIXIR Nodes to join the EGA federated network by providing the necessary technical, logistical, and training coordination across the network. This project builds on earlier work in the ELIXIR-EXCELERATE, CORBEL and Tryggve projects. It will be led by the European Genome-phenome Archive (EGA) to ensure work described in this proposal is aligned with the policies, legal agreements, and governance model for establishing the Federated EGA. WP3 will build on work in EXCELERATE WP9 to create a reference software implementation, the Local EGA, that Nodes can use to operate their federated node. The work is divided between five Work Packages (WPs): WP1: Coordination of metadata standards for sensitive human data WP2: Architecture and interfaces to support ELIXIR federated human data infrastructure WP3: Coordination of interface implementation WP4: Coordination of operational nodes as part of the federated services WP5: Project overall coordination, outreach and training WP1: Coordination of metadata standards for sensitive human data Lead: Ilkka Lappalainen (ELIXIR FI) The overall objective of this work package is to coordinate a clearly defined, documented and maintained set of metadata standards for data collected from human samples. The data and metadata collected by disparate cohorts varies widely from the type of biomaterials collected from participants (e.g. blood, DNA, tissue samples), lifestyle information by participant questionnaires and molecular measurements used to record phenotypes. The cohorts are also assembled for different purposes - population longitudinal studies vs. disease progress for example. Cohort variables are considered separately, and in groups where they may be grouped to represent a diagnosis e.g. those measured variables related to metabolic syndrome or risk factors for stroke. Standardisation and interoperability of these data are critical for this project and application of the FAIR principles brings benefits to cohort owners and the wider community. The work package partners are actively involved in both global and European standards bodies (e.g. Global Alliance for Genomics and Health - GA4GH, and the International Nucleotide Sequence Database Collaboration - INSDC), infrastructure coordination projects (e.g. CORBEL, EXCELERATE, dbGap/DATS, BioCADDIE, CINECA), and disease specific resources (e.g. ICGC, rare diseases RD-Connect, Solve-RD). This work package provides the necessary coordination activity from existing forums as the basis for deciding which metadata standards will be adopted by the ELIXIR federated human data network and provides documentation on how to apply these standards across the Federated EGA nodes. The work package will not create new standards nor provide coordination to harmonise national patient registries, clinical use of ontologies or vocabularies for example. WP2: Architecture and interfaces to support ELIXIR federated human data infrastructure Lead: Thomas Keane (EMBL-EBI) One of the fundamental requirements for creating an interoperable federated network is to determine what information needs to be communicated between the nodes, and to translate these requirements into a technical specification and protocol for sending/receiving messages. This work package will deliver the overall architecture and define interfaces for the federated human data services. Maintaining architectural integrity is essential for developing the federation in controlled fashion and ensuring interoperability between the locally run services. This work package will focus on interfaces for data discovery, metadata exchange, data dissemination, access and authorisation. This work package will align with emerging international standards (where possible) to promote interoperability between the Federated EGA nodes and similar international initiatives. For discovery, we will align with the ELIXIR Beacon and the GA4GH Discovery Work Stream, data dissemination will align with GA4GH Large Scale Genomics Work Stream (e.g. htsget, GA4GH file formats, encryption container format, and reference retrieval API), and access and authorisation will use the ELIXIR AAI which is aligned with the DURI Work Stream of GA4GH. The overall goal is to achieve unified user experience, ensure security across the ecosystem while maintaining flexibility to cater local requirements. We envisage two levels of engagement from federation partners: Nodes that have an existing operational human data sharing platform with deep investment in existing IT infrastructure and data security infrastructure solutions. These nodes would join the federated network by implementing the APIs recommended by WP2 as a layer over their existing infrastructure. Nodes with less well mature human data sharing infrastructure (but with resources and competence) that would want to contribute via WP3 to the joint development effort and deploy it locally for their Node. We will provide foundation for data analysis by providing suitable access (e.g. streaming) to data. However implementation of analysis protocols to be used is out of the scope for this work. WP3: Coordination of interface implementation Lead: Jordi Rambla (ELIXIR ES) This work package will coordinate the software development work that provides an implementation of the WP2 defined interfaces to support the federated services for human data. This task will leverage the work done as Local EGA in the context of EXCELERATE, extending it whenever is necessary. WP3 will support Nodes by coordinating through: Hosting periodic coordination calls and facilitate the interface implementation work. Use of a shared code repository and coordination of relevant documentation. Coordinating maintenance, development on WP2 defined interfaces. Providing relevant documentation together with WP5 describing software and deployment processes to assist capacity building in other Nodes. While the priorities of the implemented interfaces will be decided during the project we have already identified the following important development tasks based on the preceding work on EXCELERATE tasks on sensitive human data: (1) unified data deposition interface that enables submission in uniform fashion to any of the federated archives, (2) support shared user authentication and authorization framework (e.g. ELIXIR AAI and EGA AAI) to ease submitter authentication and re-use of archived data for authorized researchers, (3) quality control processes for submitted data files and (4) validation processes for submitted phenotypic attributes for the samples. As the majority of the funding for implementation will need to be provided by the participating Nodes, the main risk to this work package is alignment of delivery times with other relevant projects that also fund the development of this infrastructure. During the project it may also become necessary to implement interfaces to services that are not part of the federation and may need to be adapted to support required information exchange. WP4: Coordination of operational nodes as part of the federated services Lead: Ilkka Lappalainen (ELIXIR FI) This work package provides a mechanism for ELIXIR Node services to become part of the federated interoperable services for human data. The process of a Node transitioning from an expression of interest through to becoming a fully operational EGA federated instance requires coordination and support in the form of training, documentation, and advice on best practices. It is designed to offer support especially to those Nodes that have signed the Declaration to share one million human genomes cross-border by 20221. Importantly, each Node is responsible for their own infrastructure, security and operational legal framework. The specific objectives of WP4 are to: Coordinate relevant training material for new staff members within the Nodes together with WP5. Coordinate workshops for interested Nodes on how to become operational partner of the federated EGA services. Development, coordination, and organisation of best practices for security incident practices (aligned with the GA4GH Data Security work stream recommendations). Define and monitor relevant KPIs together with WP2 and WP3 for monitoring successful service delivery. This work will be done in close collaboration with the ELIXIR Beacon project and the ELIXIR Compute platform. This work package will not fund the local infrastructure, software deployment processes or operational staff members to manage the local services. Furthermore, it will not provide the legal framework for the Federated EGA. The risks include lack of resources to solve infrastructure dependent issues on software deployment or management of local dependencies such as availability of staff members for training. WP5: Project overall coordination, outreach and training This work package will provide the project management and coordination for this project. The specific objectives of WP5 are to: Establish a project management team that ensures effective communication and timely delivery through the project life time. Coordination of calls, workshops and meetings. Development and implementation of contingency and risk management plan. Development and implementation of outreach strategy. Coordination and delivery of training material for WP1-WP4 in collaboration with the ELIXIR Training Platform ensuring that materials are accessible via ELIXIR’s Training Portal.	ELIXIR Finland, EMBL-EBI, ELIXIR Spain, ELIXIR Switzerland, ELIXIR Netherlands, ELIXIR Sweden, ELIXIR Luxembourg, ELIXIR Norway, ELIXIR Czech Republic, ELIXIR Portugal, ELIXIR Estonia, ELIXIR Belgium , ELIXIR Slovenia
ELIXIR Federated Human Data (2019-21)	Over the last forty years, we have seen the emergence of large cohorts of human samples from research and national healthcare initiatives. Many countries in Europe now have nascent personalised medicine programmes meaning that human genomics is undergoing a step change from being a predominantly research-driven activity to one funded through healthcare. This is evidenced by the recent Declaration of 19 European countries to sequence and share transnationally at least 1M human genomes by 2022. This initiative will catalyse the transition of genomics from the bench to bedside in Europe. We envisage that a significant subset of these data will be made available for secondary research. However genetic data generated through healthcare is not likely to be shared as widely as research data. Healthcare is subject to national laws, and it is often unacceptable for health data from one country to be exported outside regional or national jurisdictions. Our vision for the ELIXIR Federated Human Data Community is to create a federated ecosystem of interoperable services that enables population scale genomic and biomolecular data to be accessible across international borders accelerating research and improving the health of individuals resident across Europe. This project will coordinate the delivery of FAIR compliant metadata standards, interfaces, and reference implementation to support the federated ELIXIR network of human data resources. The overall goal is to provide secure, standardized, documented and interoperable services under the framework of the European Genome-phenome Archive (EGA). This three year plan includes a structured roadmap for ELIXIR Nodes to join the EGA federated network by providing the necessary technical, logistical, and training coordination across the network. This project builds on earlier work in the ELIXIR-EXCELERATE, CORBEL and Tryggve projects. It will be led by the European Genome-phenome Archive (EGA) to ensure work described in this proposal is aligned with the policies, legal agreements, and governance model for establishing the Federated EGA. WP3 will build on work in EXCELERATE WP9 to create a reference software implementation, the Local EGA, that Nodes can use to operate their federated node. The work is divided between five Work Packages (WPs): WP1: Coordination of metadata standards for sensitive human data WP2: Architecture and interfaces to support ELIXIR federated human data infrastructure WP3: Coordination of interface implementation WP4: Coordination of operational nodes as part of the federated services WP5: Project overall coordination, outreach and training WP1: Coordination of metadata standards for sensitive human data Lead: Ilkka Lappalainen (ELIXIR FI) The overall objective of this work package is to coordinate a clearly defined, documented and maintained set of metadata standards for data collected from human samples. The data and metadata collected by disparate cohorts varies widely from the type of biomaterials collected from participants (e.g. blood, DNA, tissue samples), lifestyle information by participant questionnaires and molecular measurements used to record phenotypes. The cohorts are also assembled for different purposes - population longitudinal studies vs. disease progress for example. Cohort variables are considered separately, and in groups where they may be grouped to represent a diagnosis e.g. those measured variables related to metabolic syndrome or risk factors for stroke. Standardisation and interoperability of these data are critical for this project and application of the FAIR principles brings benefits to cohort owners and the wider community. The work package partners are actively involved in both global and European standards bodies (e.g. Global Alliance for Genomics and Health - GA4GH, and the International Nucleotide Sequence Database Collaboration - INSDC), infrastructure coordination projects (e.g. CORBEL, EXCELERATE, dbGap/DATS, BioCADDIE, CINECA), and disease specific resources (e.g. ICGC, rare diseases RD-Connect, Solve-RD). This work package provides the necessary coordination activity from existing forums as the basis for deciding which metadata standards will be adopted by the ELIXIR federated human data network and provides documentation on how to apply these standards across the Federated EGA nodes. The work package will not create new standards nor provide coordination to harmonise national patient registries, clinical use of ontologies or vocabularies for example. WP2: Architecture and interfaces to support ELIXIR federated human data infrastructure Lead: Thomas Keane (EMBL-EBI) One of the fundamental requirements for creating an interoperable federated network is to determine what information needs to be communicated between the nodes, and to translate these requirements into a technical specification and protocol for sending/receiving messages. This work package will deliver the overall architecture and define interfaces for the federated human data services. Maintaining architectural integrity is essential for developing the federation in controlled fashion and ensuring interoperability between the locally run services. This work package will focus on interfaces for data discovery, metadata exchange, data dissemination, access and authorisation. This work package will align with emerging international standards (where possible) to promote interoperability between the Federated EGA nodes and similar international initiatives. For discovery, we will align with the ELIXIR Beacon and the GA4GH Discovery Work Stream, data dissemination will align with GA4GH Large Scale Genomics Work Stream (e.g. htsget, GA4GH file formats, encryption container format, and reference retrieval API), and access and authorisation will use the ELIXIR AAI which is aligned with the DURI Work Stream of GA4GH. The overall goal is to achieve unified user experience, ensure security across the ecosystem while maintaining flexibility to cater local requirements. We envisage two levels of engagement from federation partners: Nodes that have an existing operational human data sharing platform with deep investment in existing IT infrastructure and data security infrastructure solutions. These nodes would join the federated network by implementing the APIs recommended by WP2 as a layer over their existing infrastructure. Nodes with less well mature human data sharing infrastructure (but with resources and competence) that would want to contribute via WP3 to the joint development effort and deploy it locally for their Node. We will provide foundation for data analysis by providing suitable access (e.g. streaming) to data. However implementation of analysis protocols to be used is out of the scope for this work. WP3: Coordination of interface implementation Lead: Jordi Rambla (ELIXIR ES) This work package will coordinate the software development work that provides an implementation of the WP2 defined interfaces to support the federated services for human data. This task will leverage the work done as Local EGA in the context of EXCELERATE, extending it whenever is necessary. WP3 will support Nodes by coordinating through: Hosting periodic coordination calls and facilitate the interface implementation work. Use of a shared code repository and coordination of relevant documentation. Coordinating maintenance, development on WP2 defined interfaces. Providing relevant documentation together with WP5 describing software and deployment processes to assist capacity building in other Nodes. While the priorities of the implemented interfaces will be decided during the project we have already identified the following important development tasks based on the preceding work on EXCELERATE tasks on sensitive human data: (1) unified data deposition interface that enables submission in uniform fashion to any of the federated archives, (2) support shared user authentication and authorization framework (e.g. ELIXIR AAI and EGA AAI) to ease submitter authentication and re-use of archived data for authorized researchers, (3) quality control processes for submitted data files and (4) validation processes for submitted phenotypic attributes for the samples. As the majority of the funding for implementation will need to be provided by the participating Nodes, the main risk to this work package is alignment of delivery times with other relevant projects that also fund the development of this infrastructure. During the project it may also become necessary to implement interfaces to services that are not part of the federation and may need to be adapted to support required information exchange. WP4: Coordination of operational nodes as part of the federated services Lead: Ilkka Lappalainen (ELIXIR FI) This work package provides a mechanism for ELIXIR Node services to become part of the federated interoperable services for human data. The process of a Node transitioning from an expression of interest through to becoming a fully operational EGA federated instance requires coordination and support in the form of training, documentation, and advice on best practices. It is designed to offer support especially to those Nodes that have signed the Declaration to share one million human genomes cross-border by 20221. Importantly, each Node is responsible for their own infrastructure, security and operational legal framework. The specific objectives of WP4 are to: Coordinate relevant training material for new staff members within the Nodes together with WP5. Coordinate workshops for interested Nodes on how to become operational partner of the federated EGA services. Development, coordination, and organisation of best practices for security incident practices (aligned with the GA4GH Data Security work stream recommendations). Define and monitor relevant KPIs together with WP2 and WP3 for monitoring successful service delivery. This work will be done in close collaboration with the ELIXIR Beacon project and the ELIXIR Compute platform. This work package will not fund the local infrastructure, software deployment processes or operational staff members to manage the local services. Furthermore, it will not provide the legal framework for the Federated EGA. The risks include lack of resources to solve infrastructure dependent issues on software deployment or management of local dependencies such as availability of staff members for training. WP5: Project overall coordination, outreach and training This work package will provide the project management and coordination for this project. The specific objectives of WP5 are to: Establish a project management team that ensures effective communication and timely delivery through the project life time. Coordination of calls, workshops and meetings. Development and implementation of contingency and risk management plan. Development and implementation of outreach strategy. Coordination and delivery of training material for WP1-WP4 in collaboration with the ELIXIR Training Platform ensuring that materials are accessible via ELIXIR’s Training Portal.	ELIXIR Finland, EMBL-EBI, ELIXIR Spain, ELIXIR Switzerland, ELIXIR Netherlands, ELIXIR Sweden, ELIXIR Luxembourg, ELIXIR Norway, ELIXIR Czech Republic, ELIXIR Portugal, ELIXIR Estonia, ELIXIR Belgium , ELIXIR Slovenia
ELIXIR Federated Human Data (2019-21)	Over the last forty years, we have seen the emergence of large cohorts of human samples from research and national healthcare initiatives. Many countries in Europe now have nascent personalised medicine programmes meaning that human genomics is undergoing a step change from being a predominantly research-driven activity to one funded through healthcare. This is evidenced by the recent Declaration of 19 European countries to sequence and share transnationally at least 1M human genomes by 2022. This initiative will catalyse the transition of genomics from the bench to bedside in Europe. We envisage that a significant subset of these data will be made available for secondary research. However genetic data generated through healthcare is not likely to be shared as widely as research data. Healthcare is subject to national laws, and it is often unacceptable for health data from one country to be exported outside regional or national jurisdictions. Our vision for the ELIXIR Federated Human Data Community is to create a federated ecosystem of interoperable services that enables population scale genomic and biomolecular data to be accessible across international borders accelerating research and improving the health of individuals resident across Europe. This project will coordinate the delivery of FAIR compliant metadata standards, interfaces, and reference implementation to support the federated ELIXIR network of human data resources. The overall goal is to provide secure, standardized, documented and interoperable services under the framework of the European Genome-phenome Archive (EGA). This three year plan includes a structured roadmap for ELIXIR Nodes to join the EGA federated network by providing the necessary technical, logistical, and training coordination across the network. This project builds on earlier work in the ELIXIR-EXCELERATE, CORBEL and Tryggve projects. It will be led by the European Genome-phenome Archive (EGA) to ensure work described in this proposal is aligned with the policies, legal agreements, and governance model for establishing the Federated EGA. WP3 will build on work in EXCELERATE WP9 to create a reference software implementation, the Local EGA, that Nodes can use to operate their federated node. The work is divided between five Work Packages (WPs): WP1: Coordination of metadata standards for sensitive human data WP2: Architecture and interfaces to support ELIXIR federated human data infrastructure WP3: Coordination of interface implementation WP4: Coordination of operational nodes as part of the federated services WP5: Project overall coordination, outreach and training WP1: Coordination of metadata standards for sensitive human data Lead: Ilkka Lappalainen (ELIXIR FI) The overall objective of this work package is to coordinate a clearly defined, documented and maintained set of metadata standards for data collected from human samples. The data and metadata collected by disparate cohorts varies widely from the type of biomaterials collected from participants (e.g. blood, DNA, tissue samples), lifestyle information by participant questionnaires and molecular measurements used to record phenotypes. The cohorts are also assembled for different purposes - population longitudinal studies vs. disease progress for example. Cohort variables are considered separately, and in groups where they may be grouped to represent a diagnosis e.g. those measured variables related to metabolic syndrome or risk factors for stroke. Standardisation and interoperability of these data are critical for this project and application of the FAIR principles brings benefits to cohort owners and the wider community. The work package partners are actively involved in both global and European standards bodies (e.g. Global Alliance for Genomics and Health - GA4GH, and the International Nucleotide Sequence Database Collaboration - INSDC), infrastructure coordination projects (e.g. CORBEL, EXCELERATE, dbGap/DATS, BioCADDIE, CINECA), and disease specific resources (e.g. ICGC, rare diseases RD-Connect, Solve-RD). This work package provides the necessary coordination activity from existing forums as the basis for deciding which metadata standards will be adopted by the ELIXIR federated human data network and provides documentation on how to apply these standards across the Federated EGA nodes. The work package will not create new standards nor provide coordination to harmonise national patient registries, clinical use of ontologies or vocabularies for example. WP2: Architecture and interfaces to support ELIXIR federated human data infrastructure Lead: Thomas Keane (EMBL-EBI) One of the fundamental requirements for creating an interoperable federated network is to determine what information needs to be communicated between the nodes, and to translate these requirements into a technical specification and protocol for sending/receiving messages. This work package will deliver the overall architecture and define interfaces for the federated human data services. Maintaining architectural integrity is essential for developing the federation in controlled fashion and ensuring interoperability between the locally run services. This work package will focus on interfaces for data discovery, metadata exchange, data dissemination, access and authorisation. This work package will align with emerging international standards (where possible) to promote interoperability between the Federated EGA nodes and similar international initiatives. For discovery, we will align with the ELIXIR Beacon and the GA4GH Discovery Work Stream, data dissemination will align with GA4GH Large Scale Genomics Work Stream (e.g. htsget, GA4GH file formats, encryption container format, and reference retrieval API), and access and authorisation will use the ELIXIR AAI which is aligned with the DURI Work Stream of GA4GH. The overall goal is to achieve unified user experience, ensure security across the ecosystem while maintaining flexibility to cater local requirements. We envisage two levels of engagement from federation partners: Nodes that have an existing operational human data sharing platform with deep investment in existing IT infrastructure and data security infrastructure solutions. These nodes would join the federated network by implementing the APIs recommended by WP2 as a layer over their existing infrastructure. Nodes with less well mature human data sharing infrastructure (but with resources and competence) that would want to contribute via WP3 to the joint development effort and deploy it locally for their Node. We will provide foundation for data analysis by providing suitable access (e.g. streaming) to data. However implementation of analysis protocols to be used is out of the scope for this work. WP3: Coordination of interface implementation Lead: Jordi Rambla (ELIXIR ES) This work package will coordinate the software development work that provides an implementation of the WP2 defined interfaces to support the federated services for human data. This task will leverage the work done as Local EGA in the context of EXCELERATE, extending it whenever is necessary. WP3 will support Nodes by coordinating through: Hosting periodic coordination calls and facilitate the interface implementation work. Use of a shared code repository and coordination of relevant documentation. Coordinating maintenance, development on WP2 defined interfaces. Providing relevant documentation together with WP5 describing software and deployment processes to assist capacity building in other Nodes. While the priorities of the implemented interfaces will be decided during the project we have already identified the following important development tasks based on the preceding work on EXCELERATE tasks on sensitive human data: (1) unified data deposition interface that enables submission in uniform fashion to any of the federated archives, (2) support shared user authentication and authorization framework (e.g. ELIXIR AAI and EGA AAI) to ease submitter authentication and re-use of archived data for authorized researchers, (3) quality control processes for submitted data files and (4) validation processes for submitted phenotypic attributes for the samples. As the majority of the funding for implementation will need to be provided by the participating Nodes, the main risk to this work package is alignment of delivery times with other relevant projects that also fund the development of this infrastructure. During the project it may also become necessary to implement interfaces to services that are not part of the federation and may need to be adapted to support required information exchange. WP4: Coordination of operational nodes as part of the federated services Lead: Ilkka Lappalainen (ELIXIR FI) This work package provides a mechanism for ELIXIR Node services to become part of the federated interoperable services for human data. The process of a Node transitioning from an expression of interest through to becoming a fully operational EGA federated instance requires coordination and support in the form of training, documentation, and advice on best practices. It is designed to offer support especially to those Nodes that have signed the Declaration to share one million human genomes cross-border by 20221. Importantly, each Node is responsible for their own infrastructure, security and operational legal framework. The specific objectives of WP4 are to: Coordinate relevant training material for new staff members within the Nodes together with WP5. Coordinate workshops for interested Nodes on how to become operational partner of the federated EGA services. Development, coordination, and organisation of best practices for security incident practices (aligned with the GA4GH Data Security work stream recommendations). Define and monitor relevant KPIs together with WP2 and WP3 for monitoring successful service delivery. This work will be done in close collaboration with the ELIXIR Beacon project and the ELIXIR Compute platform. This work package will not fund the local infrastructure, software deployment processes or operational staff members to manage the local services. Furthermore, it will not provide the legal framework for the Federated EGA. The risks include lack of resources to solve infrastructure dependent issues on software deployment or management of local dependencies such as availability of staff members for training. WP5: Project overall coordination, outreach and training This work package will provide the project management and coordination for this project. The specific objectives of WP5 are to: Establish a project management team that ensures effective communication and timely delivery through the project life time. Coordination of calls, workshops and meetings. Development and implementation of contingency and risk management plan. Development and implementation of outreach strategy. Coordination and delivery of training material for WP1-WP4 in collaboration with the ELIXIR Training Platform ensuring that materials are accessible via ELIXIR’s Training Portal.	ELIXIR Finland, EMBL-EBI, ELIXIR Spain, ELIXIR Switzerland, ELIXIR Netherlands, ELIXIR Sweden, ELIXIR Luxembourg, ELIXIR Norway, ELIXIR Czech Republic, ELIXIR Portugal, ELIXIR Estonia, ELIXIR Belgium , ELIXIR Slovenia
ELIXIR Federated Human Data (2019-21)	Over the last forty years, we have seen the emergence of large cohorts of human samples from research and national healthcare initiatives. Many countries in Europe now have nascent personalised medicine programmes meaning that human genomics is undergoing a step change from being a predominantly research-driven activity to one funded through healthcare. This is evidenced by the recent Declaration of 19 European countries to sequence and share transnationally at least 1M human genomes by 2022. This initiative will catalyse the transition of genomics from the bench to bedside in Europe. We envisage that a significant subset of these data will be made available for secondary research. However genetic data generated through healthcare is not likely to be shared as widely as research data. Healthcare is subject to national laws, and it is often unacceptable for health data from one country to be exported outside regional or national jurisdictions. Our vision for the ELIXIR Federated Human Data Community is to create a federated ecosystem of interoperable services that enables population scale genomic and biomolecular data to be accessible across international borders accelerating research and improving the health of individuals resident across Europe. This project will coordinate the delivery of FAIR compliant metadata standards, interfaces, and reference implementation to support the federated ELIXIR network of human data resources. The overall goal is to provide secure, standardized, documented and interoperable services under the framework of the European Genome-phenome Archive (EGA). This three year plan includes a structured roadmap for ELIXIR Nodes to join the EGA federated network by providing the necessary technical, logistical, and training coordination across the network. This project builds on earlier work in the ELIXIR-EXCELERATE, CORBEL and Tryggve projects. It will be led by the European Genome-phenome Archive (EGA) to ensure work described in this proposal is aligned with the policies, legal agreements, and governance model for establishing the Federated EGA. WP3 will build on work in EXCELERATE WP9 to create a reference software implementation, the Local EGA, that Nodes can use to operate their federated node. The work is divided between five Work Packages (WPs): WP1: Coordination of metadata standards for sensitive human data WP2: Architecture and interfaces to support ELIXIR federated human data infrastructure WP3: Coordination of interface implementation WP4: Coordination of operational nodes as part of the federated services WP5: Project overall coordination, outreach and training WP1: Coordination of metadata standards for sensitive human data Lead: Ilkka Lappalainen (ELIXIR FI) The overall objective of this work package is to coordinate a clearly defined, documented and maintained set of metadata standards for data collected from human samples. The data and metadata collected by disparate cohorts varies widely from the type of biomaterials collected from participants (e.g. blood, DNA, tissue samples), lifestyle information by participant questionnaires and molecular measurements used to record phenotypes. The cohorts are also assembled for different purposes - population longitudinal studies vs. disease progress for example. Cohort variables are considered separately, and in groups where they may be grouped to represent a diagnosis e.g. those measured variables related to metabolic syndrome or risk factors for stroke. Standardisation and interoperability of these data are critical for this project and application of the FAIR principles brings benefits to cohort owners and the wider community. The work package partners are actively involved in both global and European standards bodies (e.g. Global Alliance for Genomics and Health - GA4GH, and the International Nucleotide Sequence Database Collaboration - INSDC), infrastructure coordination projects (e.g. CORBEL, EXCELERATE, dbGap/DATS, BioCADDIE, CINECA), and disease specific resources (e.g. ICGC, rare diseases RD-Connect, Solve-RD). This work package provides the necessary coordination activity from existing forums as the basis for deciding which metadata standards will be adopted by the ELIXIR federated human data network and provides documentation on how to apply these standards across the Federated EGA nodes. The work package will not create new standards nor provide coordination to harmonise national patient registries, clinical use of ontologies or vocabularies for example. WP2: Architecture and interfaces to support ELIXIR federated human data infrastructure Lead: Thomas Keane (EMBL-EBI) One of the fundamental requirements for creating an interoperable federated network is to determine what information needs to be communicated between the nodes, and to translate these requirements into a technical specification and protocol for sending/receiving messages. This work package will deliver the overall architecture and define interfaces for the federated human data services. Maintaining architectural integrity is essential for developing the federation in controlled fashion and ensuring interoperability between the locally run services. This work package will focus on interfaces for data discovery, metadata exchange, data dissemination, access and authorisation. This work package will align with emerging international standards (where possible) to promote interoperability between the Federated EGA nodes and similar international initiatives. For discovery, we will align with the ELIXIR Beacon and the GA4GH Discovery Work Stream, data dissemination will align with GA4GH Large Scale Genomics Work Stream (e.g. htsget, GA4GH file formats, encryption container format, and reference retrieval API), and access and authorisation will use the ELIXIR AAI which is aligned with the DURI Work Stream of GA4GH. The overall goal is to achieve unified user experience, ensure security across the ecosystem while maintaining flexibility to cater local requirements. We envisage two levels of engagement from federation partners: Nodes that have an existing operational human data sharing platform with deep investment in existing IT infrastructure and data security infrastructure solutions. These nodes would join the federated network by implementing the APIs recommended by WP2 as a layer over their existing infrastructure. Nodes with less well mature human data sharing infrastructure (but with resources and competence) that would want to contribute via WP3 to the joint development effort and deploy it locally for their Node. We will provide foundation for data analysis by providing suitable access (e.g. streaming) to data. However implementation of analysis protocols to be used is out of the scope for this work. WP3: Coordination of interface implementation Lead: Jordi Rambla (ELIXIR ES) This work package will coordinate the software development work that provides an implementation of the WP2 defined interfaces to support the federated services for human data. This task will leverage the work done as Local EGA in the context of EXCELERATE, extending it whenever is necessary. WP3 will support Nodes by coordinating through: Hosting periodic coordination calls and facilitate the interface implementation work. Use of a shared code repository and coordination of relevant documentation. Coordinating maintenance, development on WP2 defined interfaces. Providing relevant documentation together with WP5 describing software and deployment processes to assist capacity building in other Nodes. While the priorities of the implemented interfaces will be decided during the project we have already identified the following important development tasks based on the preceding work on EXCELERATE tasks on sensitive human data: (1) unified data deposition interface that enables submission in uniform fashion to any of the federated archives, (2) support shared user authentication and authorization framework (e.g. ELIXIR AAI and EGA AAI) to ease submitter authentication and re-use of archived data for authorized researchers, (3) quality control processes for submitted data files and (4) validation processes for submitted phenotypic attributes for the samples. As the majority of the funding for implementation will need to be provided by the participating Nodes, the main risk to this work package is alignment of delivery times with other relevant projects that also fund the development of this infrastructure. During the project it may also become necessary to implement interfaces to services that are not part of the federation and may need to be adapted to support required information exchange. WP4: Coordination of operational nodes as part of the federated services Lead: Ilkka Lappalainen (ELIXIR FI) This work package provides a mechanism for ELIXIR Node services to become part of the federated interoperable services for human data. The process of a Node transitioning from an expression of interest through to becoming a fully operational EGA federated instance requires coordination and support in the form of training, documentation, and advice on best practices. It is designed to offer support especially to those Nodes that have signed the Declaration to share one million human genomes cross-border by 20221. Importantly, each Node is responsible for their own infrastructure, security and operational legal framework. The specific objectives of WP4 are to: Coordinate relevant training material for new staff members within the Nodes together with WP5. Coordinate workshops for interested Nodes on how to become operational partner of the federated EGA services. Development, coordination, and organisation of best practices for security incident practices (aligned with the GA4GH Data Security work stream recommendations). Define and monitor relevant KPIs together with WP2 and WP3 for monitoring successful service delivery. This work will be done in close collaboration with the ELIXIR Beacon project and the ELIXIR Compute platform. This work package will not fund the local infrastructure, software deployment processes or operational staff members to manage the local services. Furthermore, it will not provide the legal framework for the Federated EGA. The risks include lack of resources to solve infrastructure dependent issues on software deployment or management of local dependencies such as availability of staff members for training. WP5: Project overall coordination, outreach and training This work package will provide the project management and coordination for this project. The specific objectives of WP5 are to: Establish a project management team that ensures effective communication and timely delivery through the project life time. Coordination of calls, workshops and meetings. Development and implementation of contingency and risk management plan. Development and implementation of outreach strategy. Coordination and delivery of training material for WP1-WP4 in collaboration with the ELIXIR Training Platform ensuring that materials are accessible via ELIXIR’s Training Portal.	ELIXIR Finland, EMBL-EBI, ELIXIR Spain, ELIXIR Switzerland, ELIXIR Netherlands, ELIXIR Sweden, ELIXIR Luxembourg, ELIXIR Norway, ELIXIR Czech Republic, ELIXIR Portugal, ELIXIR Estonia, ELIXIR Belgium , ELIXIR Slovenia
ELIXIR Federated Human Data (2019-21)	Over the last forty years, we have seen the emergence of large cohorts of human samples from research and national healthcare initiatives. Many countries in Europe now have nascent personalised medicine programmes meaning that human genomics is undergoing a step change from being a predominantly research-driven activity to one funded through healthcare. This is evidenced by the recent Declaration of 19 European countries to sequence and share transnationally at least 1M human genomes by 2022. This initiative will catalyse the transition of genomics from the bench to bedside in Europe. We envisage that a significant subset of these data will be made available for secondary research. However genetic data generated through healthcare is not likely to be shared as widely as research data. Healthcare is subject to national laws, and it is often unacceptable for health data from one country to be exported outside regional or national jurisdictions. Our vision for the ELIXIR Federated Human Data Community is to create a federated ecosystem of interoperable services that enables population scale genomic and biomolecular data to be accessible across international borders accelerating research and improving the health of individuals resident across Europe. This project will coordinate the delivery of FAIR compliant metadata standards, interfaces, and reference implementation to support the federated ELIXIR network of human data resources. The overall goal is to provide secure, standardized, documented and interoperable services under the framework of the European Genome-phenome Archive (EGA). This three year plan includes a structured roadmap for ELIXIR Nodes to join the EGA federated network by providing the necessary technical, logistical, and training coordination across the network. This project builds on earlier work in the ELIXIR-EXCELERATE, CORBEL and Tryggve projects. It will be led by the European Genome-phenome Archive (EGA) to ensure work described in this proposal is aligned with the policies, legal agreements, and governance model for establishing the Federated EGA. WP3 will build on work in EXCELERATE WP9 to create a reference software implementation, the Local EGA, that Nodes can use to operate their federated node. The work is divided between five Work Packages (WPs): WP1: Coordination of metadata standards for sensitive human data WP2: Architecture and interfaces to support ELIXIR federated human data infrastructure WP3: Coordination of interface implementation WP4: Coordination of operational nodes as part of the federated services WP5: Project overall coordination, outreach and training WP1: Coordination of metadata standards for sensitive human data Lead: Ilkka Lappalainen (ELIXIR FI) The overall objective of this work package is to coordinate a clearly defined, documented and maintained set of metadata standards for data collected from human samples. The data and metadata collected by disparate cohorts varies widely from the type of biomaterials collected from participants (e.g. blood, DNA, tissue samples), lifestyle information by participant questionnaires and molecular measurements used to record phenotypes. The cohorts are also assembled for different purposes - population longitudinal studies vs. disease progress for example. Cohort variables are considered separately, and in groups where they may be grouped to represent a diagnosis e.g. those measured variables related to metabolic syndrome or risk factors for stroke. Standardisation and interoperability of these data are critical for this project and application of the FAIR principles brings benefits to cohort owners and the wider community. The work package partners are actively involved in both global and European standards bodies (e.g. Global Alliance for Genomics and Health - GA4GH, and the International Nucleotide Sequence Database Collaboration - INSDC), infrastructure coordination projects (e.g. CORBEL, EXCELERATE, dbGap/DATS, BioCADDIE, CINECA), and disease specific resources (e.g. ICGC, rare diseases RD-Connect, Solve-RD). This work package provides the necessary coordination activity from existing forums as the basis for deciding which metadata standards will be adopted by the ELIXIR federated human data network and provides documentation on how to apply these standards across the Federated EGA nodes. The work package will not create new standards nor provide coordination to harmonise national patient registries, clinical use of ontologies or vocabularies for example. WP2: Architecture and interfaces to support ELIXIR federated human data infrastructure Lead: Thomas Keane (EMBL-EBI) One of the fundamental requirements for creating an interoperable federated network is to determine what information needs to be communicated between the nodes, and to translate these requirements into a technical specification and protocol for sending/receiving messages. This work package will deliver the overall architecture and define interfaces for the federated human data services. Maintaining architectural integrity is essential for developing the federation in controlled fashion and ensuring interoperability between the locally run services. This work package will focus on interfaces for data discovery, metadata exchange, data dissemination, access and authorisation. This work package will align with emerging international standards (where possible) to promote interoperability between the Federated EGA nodes and similar international initiatives. For discovery, we will align with the ELIXIR Beacon and the GA4GH Discovery Work Stream, data dissemination will align with GA4GH Large Scale Genomics Work Stream (e.g. htsget, GA4GH file formats, encryption container format, and reference retrieval API), and access and authorisation will use the ELIXIR AAI which is aligned with the DURI Work Stream of GA4GH. The overall goal is to achieve unified user experience, ensure security across the ecosystem while maintaining flexibility to cater local requirements. We envisage two levels of engagement from federation partners: Nodes that have an existing operational human data sharing platform with deep investment in existing IT infrastructure and data security infrastructure solutions. These nodes would join the federated network by implementing the APIs recommended by WP2 as a layer over their existing infrastructure. Nodes with less well mature human data sharing infrastructure (but with resources and competence) that would want to contribute via WP3 to the joint development effort and deploy it locally for their Node. We will provide foundation for data analysis by providing suitable access (e.g. streaming) to data. However implementation of analysis protocols to be used is out of the scope for this work. WP3: Coordination of interface implementation Lead: Jordi Rambla (ELIXIR ES) This work package will coordinate the software development work that provides an implementation of the WP2 defined interfaces to support the federated services for human data. This task will leverage the work done as Local EGA in the context of EXCELERATE, extending it whenever is necessary. WP3 will support Nodes by coordinating through: Hosting periodic coordination calls and facilitate the interface implementation work. Use of a shared code repository and coordination of relevant documentation. Coordinating maintenance, development on WP2 defined interfaces. Providing relevant documentation together with WP5 describing software and deployment processes to assist capacity building in other Nodes. While the priorities of the implemented interfaces will be decided during the project we have already identified the following important development tasks based on the preceding work on EXCELERATE tasks on sensitive human data: (1) unified data deposition interface that enables submission in uniform fashion to any of the federated archives, (2) support shared user authentication and authorization framework (e.g. ELIXIR AAI and EGA AAI) to ease submitter authentication and re-use of archived data for authorized researchers, (3) quality control processes for submitted data files and (4) validation processes for submitted phenotypic attributes for the samples. As the majority of the funding for implementation will need to be provided by the participating Nodes, the main risk to this work package is alignment of delivery times with other relevant projects that also fund the development of this infrastructure. During the project it may also become necessary to implement interfaces to services that are not part of the federation and may need to be adapted to support required information exchange. WP4: Coordination of operational nodes as part of the federated services Lead: Ilkka Lappalainen (ELIXIR FI) This work package provides a mechanism for ELIXIR Node services to become part of the federated interoperable services for human data. The process of a Node transitioning from an expression of interest through to becoming a fully operational EGA federated instance requires coordination and support in the form of training, documentation, and advice on best practices. It is designed to offer support especially to those Nodes that have signed the Declaration to share one million human genomes cross-border by 20221. Importantly, each Node is responsible for their own infrastructure, security and operational legal framework. The specific objectives of WP4 are to: Coordinate relevant training material for new staff members within the Nodes together with WP5. Coordinate workshops for interested Nodes on how to become operational partner of the federated EGA services. Development, coordination, and organisation of best practices for security incident practices (aligned with the GA4GH Data Security work stream recommendations). Define and monitor relevant KPIs together with WP2 and WP3 for monitoring successful service delivery. This work will be done in close collaboration with the ELIXIR Beacon project and the ELIXIR Compute platform. This work package will not fund the local infrastructure, software deployment processes or operational staff members to manage the local services. Furthermore, it will not provide the legal framework for the Federated EGA. The risks include lack of resources to solve infrastructure dependent issues on software deployment or management of local dependencies such as availability of staff members for training. WP5: Project overall coordination, outreach and training This work package will provide the project management and coordination for this project. The specific objectives of WP5 are to: Establish a project management team that ensures effective communication and timely delivery through the project life time. Coordination of calls, workshops and meetings. Development and implementation of contingency and risk management plan. Development and implementation of outreach strategy. Coordination and delivery of training material for WP1-WP4 in collaboration with the ELIXIR Training Platform ensuring that materials are accessible via ELIXIR’s Training Portal.	ELIXIR Finland, EMBL-EBI, ELIXIR Spain, ELIXIR Switzerland, ELIXIR Netherlands, ELIXIR Sweden, ELIXIR Luxembourg, ELIXIR Norway, ELIXIR Czech Republic, ELIXIR Portugal, ELIXIR Estonia, ELIXIR Belgium , ELIXIR Slovenia
ELIXIR Federated Human Data (2019-21)	Over the last forty years, we have seen the emergence of large cohorts of human samples from research and national healthcare initiatives. Many countries in Europe now have nascent personalised medicine programmes meaning that human genomics is undergoing a step change from being a predominantly research-driven activity to one funded through healthcare. This is evidenced by the recent Declaration of 19 European countries to sequence and share transnationally at least 1M human genomes by 2022. This initiative will catalyse the transition of genomics from the bench to bedside in Europe. We envisage that a significant subset of these data will be made available for secondary research. However genetic data generated through healthcare is not likely to be shared as widely as research data. Healthcare is subject to national laws, and it is often unacceptable for health data from one country to be exported outside regional or national jurisdictions. Our vision for the ELIXIR Federated Human Data Community is to create a federated ecosystem of interoperable services that enables population scale genomic and biomolecular data to be accessible across international borders accelerating research and improving the health of individuals resident across Europe. This project will coordinate the delivery of FAIR compliant metadata standards, interfaces, and reference implementation to support the federated ELIXIR network of human data resources. The overall goal is to provide secure, standardized, documented and interoperable services under the framework of the European Genome-phenome Archive (EGA). This three year plan includes a structured roadmap for ELIXIR Nodes to join the EGA federated network by providing the necessary technical, logistical, and training coordination across the network. This project builds on earlier work in the ELIXIR-EXCELERATE, CORBEL and Tryggve projects. It will be led by the European Genome-phenome Archive (EGA) to ensure work described in this proposal is aligned with the policies, legal agreements, and governance model for establishing the Federated EGA. WP3 will build on work in EXCELERATE WP9 to create a reference software implementation, the Local EGA, that Nodes can use to operate their federated node. The work is divided between five Work Packages (WPs): WP1: Coordination of metadata standards for sensitive human data WP2: Architecture and interfaces to support ELIXIR federated human data infrastructure WP3: Coordination of interface implementation WP4: Coordination of operational nodes as part of the federated services WP5: Project overall coordination, outreach and training WP1: Coordination of metadata standards for sensitive human data Lead: Ilkka Lappalainen (ELIXIR FI) The overall objective of this work package is to coordinate a clearly defined, documented and maintained set of metadata standards for data collected from human samples. The data and metadata collected by disparate cohorts varies widely from the type of biomaterials collected from participants (e.g. blood, DNA, tissue samples), lifestyle information by participant questionnaires and molecular measurements used to record phenotypes. The cohorts are also assembled for different purposes - population longitudinal studies vs. disease progress for example. Cohort variables are considered separately, and in groups where they may be grouped to represent a diagnosis e.g. those measured variables related to metabolic syndrome or risk factors for stroke. Standardisation and interoperability of these data are critical for this project and application of the FAIR principles brings benefits to cohort owners and the wider community. The work package partners are actively involved in both global and European standards bodies (e.g. Global Alliance for Genomics and Health - GA4GH, and the International Nucleotide Sequence Database Collaboration - INSDC), infrastructure coordination projects (e.g. CORBEL, EXCELERATE, dbGap/DATS, BioCADDIE, CINECA), and disease specific resources (e.g. ICGC, rare diseases RD-Connect, Solve-RD). This work package provides the necessary coordination activity from existing forums as the basis for deciding which metadata standards will be adopted by the ELIXIR federated human data network and provides documentation on how to apply these standards across the Federated EGA nodes. The work package will not create new standards nor provide coordination to harmonise national patient registries, clinical use of ontologies or vocabularies for example. WP2: Architecture and interfaces to support ELIXIR federated human data infrastructure Lead: Thomas Keane (EMBL-EBI) One of the fundamental requirements for creating an interoperable federated network is to determine what information needs to be communicated between the nodes, and to translate these requirements into a technical specification and protocol for sending/receiving messages. This work package will deliver the overall architecture and define interfaces for the federated human data services. Maintaining architectural integrity is essential for developing the federation in controlled fashion and ensuring interoperability between the locally run services. This work package will focus on interfaces for data discovery, metadata exchange, data dissemination, access and authorisation. This work package will align with emerging international standards (where possible) to promote interoperability between the Federated EGA nodes and similar international initiatives. For discovery, we will align with the ELIXIR Beacon and the GA4GH Discovery Work Stream, data dissemination will align with GA4GH Large Scale Genomics Work Stream (e.g. htsget, GA4GH file formats, encryption container format, and reference retrieval API), and access and authorisation will use the ELIXIR AAI which is aligned with the DURI Work Stream of GA4GH. The overall goal is to achieve unified user experience, ensure security across the ecosystem while maintaining flexibility to cater local requirements. We envisage two levels of engagement from federation partners: Nodes that have an existing operational human data sharing platform with deep investment in existing IT infrastructure and data security infrastructure solutions. These nodes would join the federated network by implementing the APIs recommended by WP2 as a layer over their existing infrastructure. Nodes with less well mature human data sharing infrastructure (but with resources and competence) that would want to contribute via WP3 to the joint development effort and deploy it locally for their Node. We will provide foundation for data analysis by providing suitable access (e.g. streaming) to data. However implementation of analysis protocols to be used is out of the scope for this work. WP3: Coordination of interface implementation Lead: Jordi Rambla (ELIXIR ES) This work package will coordinate the software development work that provides an implementation of the WP2 defined interfaces to support the federated services for human data. This task will leverage the work done as Local EGA in the context of EXCELERATE, extending it whenever is necessary. WP3 will support Nodes by coordinating through: Hosting periodic coordination calls and facilitate the interface implementation work. Use of a shared code repository and coordination of relevant documentation. Coordinating maintenance, development on WP2 defined interfaces. Providing relevant documentation together with WP5 describing software and deployment processes to assist capacity building in other Nodes. While the priorities of the implemented interfaces will be decided during the project we have already identified the following important development tasks based on the preceding work on EXCELERATE tasks on sensitive human data: (1) unified data deposition interface that enables submission in uniform fashion to any of the federated archives, (2) support shared user authentication and authorization framework (e.g. ELIXIR AAI and EGA AAI) to ease submitter authentication and re-use of archived data for authorized researchers, (3) quality control processes for submitted data files and (4) validation processes for submitted phenotypic attributes for the samples. As the majority of the funding for implementation will need to be provided by the participating Nodes, the main risk to this work package is alignment of delivery times with other relevant projects that also fund the development of this infrastructure. During the project it may also become necessary to implement interfaces to services that are not part of the federation and may need to be adapted to support required information exchange. WP4: Coordination of operational nodes as part of the federated services Lead: Ilkka Lappalainen (ELIXIR FI) This work package provides a mechanism for ELIXIR Node services to become part of the federated interoperable services for human data. The process of a Node transitioning from an expression of interest through to becoming a fully operational EGA federated instance requires coordination and support in the form of training, documentation, and advice on best practices. It is designed to offer support especially to those Nodes that have signed the Declaration to share one million human genomes cross-border by 20221. Importantly, each Node is responsible for their own infrastructure, security and operational legal framework. The specific objectives of WP4 are to: Coordinate relevant training material for new staff members within the Nodes together with WP5. Coordinate workshops for interested Nodes on how to become operational partner of the federated EGA services. Development, coordination, and organisation of best practices for security incident practices (aligned with the GA4GH Data Security work stream recommendations). Define and monitor relevant KPIs together with WP2 and WP3 for monitoring successful service delivery. This work will be done in close collaboration with the ELIXIR Beacon project and the ELIXIR Compute platform. This work package will not fund the local infrastructure, software deployment processes or operational staff members to manage the local services. Furthermore, it will not provide the legal framework for the Federated EGA. The risks include lack of resources to solve infrastructure dependent issues on software deployment or management of local dependencies such as availability of staff members for training. WP5: Project overall coordination, outreach and training This work package will provide the project management and coordination for this project. The specific objectives of WP5 are to: Establish a project management team that ensures effective communication and timely delivery through the project life time. Coordination of calls, workshops and meetings. Development and implementation of contingency and risk management plan. Development and implementation of outreach strategy. Coordination and delivery of training material for WP1-WP4 in collaboration with the ELIXIR Training Platform ensuring that materials are accessible via ELIXIR’s Training Portal.	ELIXIR Finland, EMBL-EBI, ELIXIR Spain, ELIXIR Switzerland, ELIXIR Netherlands, ELIXIR Sweden, ELIXIR Luxembourg, ELIXIR Norway, ELIXIR Czech Republic, ELIXIR Portugal, ELIXIR Estonia, ELIXIR Belgium , ELIXIR Slovenia
ELIXIR Human Data	This brochure presents ELIXIR activities, resources and projects in human genomics and translational data.
ELIXIR Portugal as a case-study for the deployment of Local EGA/Beacon v2 instances	The European Genome-phenome Archive (EGA) is a repository for all types of sequence and genotype experiments, including case-control, population, and family studies. The EGA will serve as a permanent archive that will archive several levels of data including the raw data (which could, for example, be re-analysed in the future by other algorithms) as well as the genotype calls provided by the submitters. In spite of EGA accepting data from all Europe, due to regulations over data and other constraints, it is desirable that ELIXIR Nodes deploy and operate Local EGA instances. Beacon is an API (sometimes extended with a user interface) that allows for data discovery of genomic and phenoclinic data. The version 2 (v2) of the Beacon protocol has been accepted as GA4GH standard in Spring 2022 and brings many new query possibilities including metadata filters, and facilitates the access to the data owners. The Portuguese Node has been testing and providing feedback for the Local EGA and Beacon v2 repositories. We have successfully deployed a prototype of the LocalEGA with some of the components of these systems, namely the connection to the Central EGA and the Ingestion system and the validation and upload components of Beacon. In spite of these milestones already achieved, we are facing difficulties with the implementation of the data distribution system of the Local EGA and the API of the Beacon v2. We are working closely with the ELIXIR Spain node and could benefit from short stays of the Portuguese team at CRG and from the Spanish team at INESC-ID to overcome current hurdles in these implementations. In addition to enhancing the delivery by the ELIXIR PT, this staff exchange will serve as a case-study to define such hurdles and troubleshooting measures that can be extended to other nodes in the form of recommendations and tutorials, thus lowering the effort required for other nodes to achieve their implementations.	ELIXIR Portugal, ELIXIR Spain, EMBL-EBI
ELIXIR Portugal as a case-study for the deployment of Local EGA/Beacon v2 instances	The European Genome-phenome Archive (EGA) is a repository for all types of sequence and genotype experiments, including case-control, population, and family studies. The EGA will serve as a permanent archive that will archive several levels of data including the raw data (which could, for example, be re-analysed in the future by other algorithms) as well as the genotype calls provided by the submitters. In spite of EGA accepting data from all Europe, due to regulations over data and other constraints, it is desirable that ELIXIR Nodes deploy and operate Local EGA instances. Beacon is an API (sometimes extended with a user interface) that allows for data discovery of genomic and phenoclinic data. The version 2 (v2) of the Beacon protocol has been accepted as GA4GH standard in Spring 2022 and brings many new query possibilities including metadata filters, and facilitates the access to the data owners. The Portuguese Node has been testing and providing feedback for the Local EGA and Beacon v2 repositories. We have successfully deployed a prototype of the LocalEGA with some of the components of these systems, namely the connection to the Central EGA and the Ingestion system and the validation and upload components of Beacon. In spite of these milestones already achieved, we are facing difficulties with the implementation of the data distribution system of the Local EGA and the API of the Beacon v2. We are working closely with the ELIXIR Spain node and could benefit from short stays of the Portuguese team at CRG and from the Spanish team at INESC-ID to overcome current hurdles in these implementations. In addition to enhancing the delivery by the ELIXIR PT, this staff exchange will serve as a case-study to define such hurdles and troubleshooting measures that can be extended to other nodes in the form of recommendations and tutorials, thus lowering the effort required for other nodes to achieve their implementations.	ELIXIR Portugal, ELIXIR Spain, EMBL-EBI
ELIXIR Portugal as a case-study for the deployment of Local EGA/Beacon v2 instances	The European Genome-phenome Archive (EGA) is a repository for all types of sequence and genotype experiments, including case-control, population, and family studies. The EGA will serve as a permanent archive that will archive several levels of data including the raw data (which could, for example, be re-analysed in the future by other algorithms) as well as the genotype calls provided by the submitters. In spite of EGA accepting data from all Europe, due to regulations over data and other constraints, it is desirable that ELIXIR Nodes deploy and operate Local EGA instances. Beacon is an API (sometimes extended with a user interface) that allows for data discovery of genomic and phenoclinic data. The version 2 (v2) of the Beacon protocol has been accepted as GA4GH standard in Spring 2022 and brings many new query possibilities including metadata filters, and facilitates the access to the data owners. The Portuguese Node has been testing and providing feedback for the Local EGA and Beacon v2 repositories. We have successfully deployed a prototype of the LocalEGA with some of the components of these systems, namely the connection to the Central EGA and the Ingestion system and the validation and upload components of Beacon. In spite of these milestones already achieved, we are facing difficulties with the implementation of the data distribution system of the Local EGA and the API of the Beacon v2. We are working closely with the ELIXIR Spain node and could benefit from short stays of the Portuguese team at CRG and from the Spanish team at INESC-ID to overcome current hurdles in these implementations. In addition to enhancing the delivery by the ELIXIR PT, this staff exchange will serve as a case-study to define such hurdles and troubleshooting measures that can be extended to other nodes in the form of recommendations and tutorials, thus lowering the effort required for other nodes to achieve their implementations.	ELIXIR Portugal, ELIXIR Spain, EMBL-EBI
ELIXIR – IMI OncoTrack scoping study on long-term data handling	The aim of this project was to deposit relevant subsets of data from the IMI OncoTrack project into a data discovery service in the European Genome-phenome Archive (EGA) or as part of other ELIXIR Node resources (e.g. for long-term hosting of TranSMART instances). It also assessed the cost and complexity of ex-post data sharing efforts for IMI translational research projects. The results of the scoping study show that the upload of the OncoTrack data to the EGA for long-term storage is technically feasible. The main recommendations of the Implementation study are: Export of OncoTrack data to the EGA should be done from the OncoTrack database and standard file submission terminologies need to be defined to explain the data types. To maximise the future use of OncoTrack data and help generalising the results of this scoping study, extensive work has been carried out to establish the optimal mapping of the OncoTrack meta-data to existing EGA objects and attributes. From the governance point of view, to make the OncoTrack data available from the EGA, a Data Access Committee has been formed and will be funded by the owners of the OncoTrack data. A Data and Sample Transfer Agreement defining the terms of access to data and biological samples for research use has been drafted and is under review by the OncoTrack data owners. A draft Data Processing Agreement between the OncoTrack data owners, ELIXIR and the EGA, defining the terms and conditions for the storage of the OncoTrack data is in preparation. Final report: Henderson D, Yildirimman R, Almeida-King J et al. The ELIXIR-IMI OncoTrack Scoping Study on Long-term Data Handling [version 1; not peer reviewed]. News Item ELIXIR and OncoTrack examine solutions for long-term management of translational data Webinar summarising the outcome	ELIXIR Spain, EMBL-EBI
ELIXIR – IMI OncoTrack scoping study on long-term data handling	The aim of this project was to deposit relevant subsets of data from the IMI OncoTrack project into a data discovery service in the European Genome-phenome Archive (EGA) or as part of other ELIXIR Node resources (e.g. for long-term hosting of TranSMART instances). It also assessed the cost and complexity of ex-post data sharing efforts for IMI translational research projects. The results of the scoping study show that the upload of the OncoTrack data to the EGA for long-term storage is technically feasible. The main recommendations of the Implementation study are: Export of OncoTrack data to the EGA should be done from the OncoTrack database and standard file submission terminologies need to be defined to explain the data types. To maximise the future use of OncoTrack data and help generalising the results of this scoping study, extensive work has been carried out to establish the optimal mapping of the OncoTrack meta-data to existing EGA objects and attributes. From the governance point of view, to make the OncoTrack data available from the EGA, a Data Access Committee has been formed and will be funded by the owners of the OncoTrack data. A Data and Sample Transfer Agreement defining the terms of access to data and biological samples for research use has been drafted and is under review by the OncoTrack data owners. A draft Data Processing Agreement between the OncoTrack data owners, ELIXIR and the EGA, defining the terms and conditions for the storage of the OncoTrack data is in preparation. Final report: Henderson D, Yildirimman R, Almeida-King J et al. The ELIXIR-IMI OncoTrack Scoping Study on Long-term Data Handling [version 1; not peer reviewed]. News Item ELIXIR and OncoTrack examine solutions for long-term management of translational data Webinar summarising the outcome	ELIXIR Spain, EMBL-EBI
Empowering ELIXIR PT capabilities to deploy and operate Local EGA instances	The European Genome-phenome Archive (EGA) is designed to be a repository for all types of sequence and genotype experiments, including case-control, population, and family studies. The EGA will serve as a permanent archive that will archive several levels of data including the raw data (which could, for example, be re-analysed in the future by other algorithms) as well as the genotype calls provided by the submitters. In spite of EGA accepting data from all Europe, due to regulations over data and other constraints, it is desirable that ELIXIR Nodes deploy and operate Local EGA instances. The aim of this project is then to empower ELIXIR PT Node, and not only, with required expertise to deploy and operate Local EGA instances and related data processing procedures and pipelines. We will leverage ELIXIR PT efforts on designing and deploying pipelines for genomic data processing and ELIXIR ES expertise on Local EGA deployment and on the operation and use of HPC infrastructures.	ELIXIR Portugal, ELIXIR Spain
Empowering ELIXIR PT capabilities to deploy and operate Local EGA instances	The European Genome-phenome Archive (EGA) is designed to be a repository for all types of sequence and genotype experiments, including case-control, population, and family studies. The EGA will serve as a permanent archive that will archive several levels of data including the raw data (which could, for example, be re-analysed in the future by other algorithms) as well as the genotype calls provided by the submitters. In spite of EGA accepting data from all Europe, due to regulations over data and other constraints, it is desirable that ELIXIR Nodes deploy and operate Local EGA instances. The aim of this project is then to empower ELIXIR PT Node, and not only, with required expertise to deploy and operate Local EGA instances and related data processing procedures and pipelines. We will leverage ELIXIR PT efforts on designing and deploying pipelines for genomic data processing and ELIXIR ES expertise on Local EGA deployment and on the operation and use of HPC infrastructures.	ELIXIR Portugal, ELIXIR Spain
FAIRification of Genomic Tracks	We propose to advance the application of FAIR principles to metadata for human genomic tracks by developing recommendations for metadata as well as algorithmic tools, to apply the recommendations to tracks from selected hubs associated with the Ensembl TrackHub Registry, to implement a track search service that integrates metadata from different track hubs, and to test the implementation with selected track-oriented analytical tools. The recommendations will form a basis for developing a standard for metadata on genomic tracks. Currently ChIP-seq, RNAseq, variant, and epigenetic tracks lack standardisation. This Study will generate a set of published recommendations that will result in a published minimum standard for such tracks. This will be applied to Ensembl TrackHub tracks and GSuite HyperBrowser (NO).	ELIXIR Norway, EMBL-EBI, ELIXIR Spain
FAIRification of Genomic Tracks	We propose to advance the application of FAIR principles to metadata for human genomic tracks by developing recommendations for metadata as well as algorithmic tools, to apply the recommendations to tracks from selected hubs associated with the Ensembl TrackHub Registry, to implement a track search service that integrates metadata from different track hubs, and to test the implementation with selected track-oriented analytical tools. The recommendations will form a basis for developing a standard for metadata on genomic tracks. Currently ChIP-seq, RNAseq, variant, and epigenetic tracks lack standardisation. This Study will generate a set of published recommendations that will result in a published minimum standard for such tracks. This will be applied to Ensembl TrackHub tracks and GSuite HyperBrowser (NO).	ELIXIR Norway, EMBL-EBI, ELIXIR Spain
FAIRification of Genomic Tracks	We propose to advance the application of FAIR principles to metadata for human genomic tracks by developing recommendations for metadata as well as algorithmic tools, to apply the recommendations to tracks from selected hubs associated with the Ensembl TrackHub Registry, to implement a track search service that integrates metadata from different track hubs, and to test the implementation with selected track-oriented analytical tools. The recommendations will form a basis for developing a standard for metadata on genomic tracks. Currently ChIP-seq, RNAseq, variant, and epigenetic tracks lack standardisation. This Study will generate a set of published recommendations that will result in a published minimum standard for such tracks. This will be applied to Ensembl TrackHub tracks and GSuite HyperBrowser (NO).	ELIXIR Norway, EMBL-EBI, ELIXIR Spain
Genomic data management for TraIT using the EGA	This TraIT-EGA project allowed Dutch research projects in translational medicine submit, store and access their data, using the European Genome Archive (EGA). TraIT (Translational research IT) is a project by the Dutch Center for Translational Molecular Medicine (CTMM) to implement an IT infrastructure for translational biomedical research. It facilitates the collection, storage, analysis, sharing, and securing of the data generated in large multi-center translational research projects all across the Netherlands. The goal of the project was to connect TraIT's platform - TranSMART - with the European Genome-phenome Archive (EGA), and enable the Dutch researchers to use EGA as the long-term storage for raw data from all TraIT projects. The TraIT data stored in EGA will then be available on demand to the TraIT researchers for further analysis in a cloud service (using Galaxy workflow). The project also ensured that the researchers accessing the data though the cloud have the necessary EGA Data Access Committee (DAC) authorisation. This study was one of the Pilot Actions for 2015 and is now finished, the results are outlined in the end report. There was some alignment with the BILS-ProteomeXchange Implementation Study, developing a single point of entry for users to access and query data. There was a significant contribution for rare disease researchers, where the very nature of the data means it is spread across a number of instititues or countries. Publications: Zhang C, Bijlard J, Staiger C et al. Systematically linking tranSMART, Galaxy and EGA for reusing human translational research data. F1000Research 2017, 6:1488 doi: 10.12688/f1000research.12168.1 Hoogstrate Y, Zhang C, Senf A et al. Integration of EGA secure data access into Galaxy. F1000Research 2016, 5(ELIXIR):2841 doi: 10.12688/f1000research.10221.1 Webinar summarising the outcomes	EMBL-EBI, ELIXIR Spain, ELIXIR Netherlands
Genomic data management for TraIT using the EGA	This TraIT-EGA project allowed Dutch research projects in translational medicine submit, store and access their data, using the European Genome Archive (EGA). TraIT (Translational research IT) is a project by the Dutch Center for Translational Molecular Medicine (CTMM) to implement an IT infrastructure for translational biomedical research. It facilitates the collection, storage, analysis, sharing, and securing of the data generated in large multi-center translational research projects all across the Netherlands. The goal of the project was to connect TraIT's platform - TranSMART - with the European Genome-phenome Archive (EGA), and enable the Dutch researchers to use EGA as the long-term storage for raw data from all TraIT projects. The TraIT data stored in EGA will then be available on demand to the TraIT researchers for further analysis in a cloud service (using Galaxy workflow). The project also ensured that the researchers accessing the data though the cloud have the necessary EGA Data Access Committee (DAC) authorisation. This study was one of the Pilot Actions for 2015 and is now finished, the results are outlined in the end report. There was some alignment with the BILS-ProteomeXchange Implementation Study, developing a single point of entry for users to access and query data. There was a significant contribution for rare disease researchers, where the very nature of the data means it is spread across a number of instititues or countries. Publications: Zhang C, Bijlard J, Staiger C et al. Systematically linking tranSMART, Galaxy and EGA for reusing human translational research data. F1000Research 2017, 6:1488 doi: 10.12688/f1000research.12168.1 Hoogstrate Y, Zhang C, Senf A et al. Integration of EGA secure data access into Galaxy. F1000Research 2016, 5(ELIXIR):2841 doi: 10.12688/f1000research.10221.1 Webinar summarising the outcomes	EMBL-EBI, ELIXIR Spain, ELIXIR Netherlands
Genomic data management for TraIT using the EGA	This TraIT-EGA project allowed Dutch research projects in translational medicine submit, store and access their data, using the European Genome Archive (EGA). TraIT (Translational research IT) is a project by the Dutch Center for Translational Molecular Medicine (CTMM) to implement an IT infrastructure for translational biomedical research. It facilitates the collection, storage, analysis, sharing, and securing of the data generated in large multi-center translational research projects all across the Netherlands. The goal of the project was to connect TraIT's platform - TranSMART - with the European Genome-phenome Archive (EGA), and enable the Dutch researchers to use EGA as the long-term storage for raw data from all TraIT projects. The TraIT data stored in EGA will then be available on demand to the TraIT researchers for further analysis in a cloud service (using Galaxy workflow). The project also ensured that the researchers accessing the data though the cloud have the necessary EGA Data Access Committee (DAC) authorisation. This study was one of the Pilot Actions for 2015 and is now finished, the results are outlined in the end report. There was some alignment with the BILS-ProteomeXchange Implementation Study, developing a single point of entry for users to access and query data. There was a significant contribution for rare disease researchers, where the very nature of the data means it is spread across a number of instititues or countries. Publications: Zhang C, Bijlard J, Staiger C et al. Systematically linking tranSMART, Galaxy and EGA for reusing human translational research data. F1000Research 2017, 6:1488 doi: 10.12688/f1000research.12168.1 Hoogstrate Y, Zhang C, Senf A et al. Integration of EGA secure data access into Galaxy. F1000Research 2016, 5(ELIXIR):2841 doi: 10.12688/f1000research.10221.1 Webinar summarising the outcomes	EMBL-EBI, ELIXIR Spain, ELIXIR Netherlands
Health data anonymization, synthetic data and pseudonymization service technology	Life science and healthcare stakeholders need to use sensitive data in several ways. Sensitive data needs to be protected against unauthorized access. Protection of data may be required for legal or ethical reasons, for issues pertaining to personal privacy, or for proprietary considerations. Especially important but complicated this is when sensitive data comes from several sources and countries. CSC (ELIXIR Finland) has recently launched open beta sensitive data (SD) services to support secure data management through web-user interfaces accessible from the user's own computer. The services include Sensitive Data Connect (SD Connect) and Sensitive Data Desktop (SD Desktop). VEIL.AI, a University of Helsinki spinout, specializes in health data privacy protection powered by AI-driven technologies. These new technologies enable high-quality row-level anonymized data production with secure and easier data interoperability and federation for better research, education and innovation opportunities in life sciences. The data privacy protection technologies include: Pseudonymization and consent management: VEIL.AI ensures compliance with GDPR through data pseudonymization and consent management. This enables safe distributed identifier management in research collaborations and biobanking. Privacy protection through anonymization: The VEIL.AI Anonymization Engine provides automated tools for producing high quality row-level anonymized data for research collaborations. Other unique characteristics of VEIL.AI Anonymization Engine include continuous data collection, and multi-party data collaboration with automated quality optimization and high performance. Data Synthetization: In addition to anonymization, VEIL.AI de-identification technologies also support data synthetization for e.g. stress testing and assessing risk measures for healthcare technology developments and innovations. Purpose of this project is to validate use of VEIL.AI technologies as part of the CSC SD solutions delivered for researchers, organizations and educational purposes, and negotiate for a licencing model for technology that would allow long-term sustainability of the technology collaboration and exchange. Individual technology interests for knowledge exchange include: Deployment of VEIL.AI service stack and APIs in ELIXIR-FI, CSC SD environment Production of de-identified data (pseudonymized, anonymized, or synth data) using VEIL.AI APIs Pooling de-identified data (data lake; delta-lake?) Sharing of de-identified data (delta sharing) Access control to the de-identification resources (API) and results (data) Licencing of technology from an SME to support service infrastructure building of an ELIXIR node is a broad target. In this scheme CSC and VEIL.AI will produce a focused example of a collaboration scheme. We will first identify technology components, and then discuss what kind of agreement would be necessary, with the intention for a sustainable, long-term collaboration. Outcome will be know-how on how to build and formalise public infrastructure partnering with a (ICT) technology start-up. Optimally, lessons learned could be applicable for other similar arrangements.	ELIXIR Finland
Increasing Interoperability between ELIXIR Protein Structure and Sequence Resources and Expanding these Resources with 3D-Models of CATH Domains, built by SWISS-MODEL	This project will increase interoperability between four ELIXIR resources (CATH, SWISS-MODEL, InterPro and PDBe), three of which are Core Resources, by building APIs that facilitate the import and export of data between them. The ultimate goal is to improve provision of 3D-Models for protein domain sequences via CATH, SWISS-MODEL and InterPro. Less than 10% of known sequences have experimentally characterised 3D structural information and yet this data is often essential for understanding the protein’s molecular function and biological role and for determining whether residue mutations could damage the protein and lead to disease. So this integration is very timely as it will enhance links between sequence and structure data. APIs will be built using well-established protocols and as well as promoting interoperability, and therefore sustainability, we will expand the data in each resource to ensure they serve a wider community of biologists.	ELIXIR UK, ELIXIR Switzerland, EMBL-EBI
Increasing Interoperability between ELIXIR Protein Structure and Sequence Resources and Expanding these Resources with 3D-Models of CATH Domains, built by SWISS-MODEL	This project will increase interoperability between four ELIXIR resources (CATH, SWISS-MODEL, InterPro and PDBe), three of which are Core Resources, by building APIs that facilitate the import and export of data between them. The ultimate goal is to improve provision of 3D-Models for protein domain sequences via CATH, SWISS-MODEL and InterPro. Less than 10% of known sequences have experimentally characterised 3D structural information and yet this data is often essential for understanding the protein’s molecular function and biological role and for determining whether residue mutations could damage the protein and lead to disease. So this integration is very timely as it will enhance links between sequence and structure data. APIs will be built using well-established protocols and as well as promoting interoperability, and therefore sustainability, we will expand the data in each resource to ensure they serve a wider community of biologists.	ELIXIR UK, ELIXIR Switzerland, EMBL-EBI
Increasing Interoperability between ELIXIR Protein Structure and Sequence Resources and Expanding these Resources with 3D-Models of CATH Domains, built by SWISS-MODEL	This project will increase interoperability between four ELIXIR resources (CATH, SWISS-MODEL, InterPro and PDBe), three of which are Core Resources, by building APIs that facilitate the import and export of data between them. The ultimate goal is to improve provision of 3D-Models for protein domain sequences via CATH, SWISS-MODEL and InterPro. Less than 10% of known sequences have experimentally characterised 3D structural information and yet this data is often essential for understanding the protein’s molecular function and biological role and for determining whether residue mutations could damage the protein and lead to disease. So this integration is very timely as it will enhance links between sequence and structure data. APIs will be built using well-established protocols and as well as promoting interoperability, and therefore sustainability, we will expand the data in each resource to ensure they serve a wider community of biologists.	ELIXIR UK, ELIXIR Switzerland, EMBL-EBI
Integrating ELIXIR Italy into ELIXIR activities	The implementation study project plan of ELIXIR Italy consists of six activities that aim to boost the cooperation with existing ELIXIR activities and are expected to deepen the interaction between ELIXIR-IIB, the Joint Research Unit embodying the Italian Node, and ELIXIR. The partners involved have already established contacts with other ELIXIR Nodes and the relevant ELIXIR Platforms and Services in order to ensure an advantageous outcome for all the involved parties. The goal of the proposed activities is to create and/or reinforce collaborations based on concrete measures. With this implementation study the Italian ELIXIR Node will achieve greater integration within ELIXIR service infrastructures and data interoperability policies. The topics of the selected activities and an additional coordination task are summarized below: Integration in ELIXIR Bioschemas activities. Integration in ELIXIR Data Curation activities. Integration in ELIXIR Galaxy activities through a project on practical feasibility of creating and running large-scale Galaxy-based variant calling pipelines on microservice infrastructures. Integration in ELIXIR Human Data activities through Beacons. Integration in ELIXIR Marine Metagenomics activities through a web-service supporting ITS1-based survey of marine communities. Integration in ELIXIR Rare Diseases activities. Coordination of the Italian ELIXIR Node Implementation study project.	ELIXIR Italy
Integrating ELIXIR Luxembourg into ELIXIR activities	The ELIXIR Luxembourg Node focuses on the development of a European repository of integrated molecular and clinical/translational data, and providing high-performance oriented data access, computing services and long-term sustainability. In this Implementation Study, we will take part in ELIXIR Beacon, Local EGA, ELIXIR AAI and RD-Connect topics under ELIXIR Use Cases - ‘Human Genomics and Translational Data’, ‘Rare Disease’ and the ‘Compute Platform’ . ELIXIR Luxembourg will provide Beacon data-discovery services for genomics data deposited in the Node and ensure a balance between efficient data sharing and data protection. The local EGA facilitates federated data environment, while the ELIXIR AAI provides flexible yet secure authentication and authorisation layer, so that the users from Luxembourg and all ELIXIR Nodes can access all the services in the Luxembourg Node through a single sign-on. ELIXIR Luxembourg also has good working experience with tranSMART, thus this knowledge will be brough to RD-Connect and other similar projects in EXCELERATE and ELIXIR. This study is associated with a number of ELIXIR Platforms, Communities and Projects: Human Data Rare Diseases	ELIXIR Luxembourg
Interoperable controlled-access big data transfer for ELIXIR - expanding EGA collaboration	Building upon the existing ELIXIR based collaboration within the EMBL-EBI in the UK and the Center for Genomic Regulation (CRG) in Spain, this project addressed limitations on computing, network bandwidth, and storage buffer areas that affected the EGA data delivery, and developed a protocol for secure data transfer from the EGA archive to CRG. The project tested a number of data transfer protocols, (FTP, UDT, Aspera and Globus), optimised the EBI hardware and network access to the archive in support of large scale re-encryption processes, and created necessary monitoring tools for validating data integrity at the CRG storage. In total, the project successfully transferred one petabyte of data using Aspera. The new protocol now allows us to further optimise each step with the aim of automating the entire process by the end of 2015. The study is now finished, the end report is available here. Further Implementation Studies Genomic data management for TraIT using the EGA Visualization of aligned genomics data for rare diseases (RD-Connect) as a driver for real-time access of controlled data at the EGA Webinar on the Local EGA demo setup (See also the related documents)	EMBL-EBI, ELIXIR Spain
Interoperable controlled-access big data transfer for ELIXIR - expanding EGA collaboration	Building upon the existing ELIXIR based collaboration within the EMBL-EBI in the UK and the Center for Genomic Regulation (CRG) in Spain, this project addressed limitations on computing, network bandwidth, and storage buffer areas that affected the EGA data delivery, and developed a protocol for secure data transfer from the EGA archive to CRG. The project tested a number of data transfer protocols, (FTP, UDT, Aspera and Globus), optimised the EBI hardware and network access to the archive in support of large scale re-encryption processes, and created necessary monitoring tools for validating data integrity at the CRG storage. In total, the project successfully transferred one petabyte of data using Aspera. The new protocol now allows us to further optimise each step with the aim of automating the entire process by the end of 2015. The study is now finished, the end report is available here. Further Implementation Studies Genomic data management for TraIT using the EGA Visualization of aligned genomics data for rare diseases (RD-Connect) as a driver for real-time access of controlled data at the EGA Webinar on the Local EGA demo setup (See also the related documents)	EMBL-EBI, ELIXIR Spain
Life-cycle long data management and handling of sensitive data	The roadmap of the Institut Français de Bioinformatique (IFB, ELIXIR-FR) includes several actions that are tightly related to data management: storage, secure access, FAIRification, DMPs. However, France is facing many challenges to answer an increasing demands of our user communities. One of the most important bottlenecks in the French context concerns the access to and FAIRification of sensitive biomedical data, in order to enable its exploitation for research and transnational projects. Since several years, the Norwegian ELIXIR node developed a strong experience with notable achievements regarding the management, storage and sharing of biomedical data, with operational solutions at the national level through TSD (Services for sensitive data operated by UiO partner) and national coordination with data generating platforms (BioMedData), as well as involvement in Nordic and international projects for analysing and archiving sensitive data (Tryggve2 and Federated Human data/EGA respectively). The goal of this staff exchange is to organize exchanges of knowledge, experiences and solutions for data management. In particular, France would greatly benefit from the strong experience of ELIXIR-NO to develop solutions that would comply with the rather strict national regulations (e.g. obligation to obtain a national certification in order to handle human data). Reciprocally, to anticipate international data management policies that might be adopted in the near future by E.U., coordinated actions could be taken to extend the machine-actionable DMP project beyond France, to generalize the concepts and to evaluate the applicability and portability of the technical solutions to other ELIXIR Nodes.	ELIXIR France, ELIXIR Norway
Life-cycle long data management and handling of sensitive data	The roadmap of the Institut Français de Bioinformatique (IFB, ELIXIR-FR) includes several actions that are tightly related to data management: storage, secure access, FAIRification, DMPs. However, France is facing many challenges to answer an increasing demands of our user communities. One of the most important bottlenecks in the French context concerns the access to and FAIRification of sensitive biomedical data, in order to enable its exploitation for research and transnational projects. Since several years, the Norwegian ELIXIR node developed a strong experience with notable achievements regarding the management, storage and sharing of biomedical data, with operational solutions at the national level through TSD (Services for sensitive data operated by UiO partner) and national coordination with data generating platforms (BioMedData), as well as involvement in Nordic and international projects for analysing and archiving sensitive data (Tryggve2 and Federated Human data/EGA respectively). The goal of this staff exchange is to organize exchanges of knowledge, experiences and solutions for data management. In particular, France would greatly benefit from the strong experience of ELIXIR-NO to develop solutions that would comply with the rather strict national regulations (e.g. obligation to obtain a national certification in order to handle human data). Reciprocally, to anticipate international data management policies that might be adopted in the near future by E.U., coordinated actions could be taken to extend the machine-actionable DMP project beyond France, to generalize the concepts and to evaluate the applicability and portability of the technical solutions to other ELIXIR Nodes.	ELIXIR France, ELIXIR Norway
Local/Federated EGA	The Local / Federated EGA (European Genome-phenome Archive) is a distributed solution for sharing and exchange of human -omics data across national borders. Local EGA collects metadata of -omics data collections stored in national or regional archives and make them available for search through the main EGA portal. The EGA systems development is coordinated by the ELIXIR Spain but with large contributions from the Nordic countries, partly funded through the Nordic Tryggve project. This Staff Exchange project allowed experienced software engineers from the Swedish and Finnish ELIXIR Nodes to work in Barcelona, Spain, to intensify the systems development work by working side-by-side with the Spanish systems developers team. The project shortened the development time for those aspects of the federated EGA where there are strong interdependencies between Central EGA and Local EGA instances. This is instrumental for establishing a unified EGA ecosystem that can offer a seamless user experience for data submitters and requestors. Outcomes Code to support key processes that go across the Central/Local EGA boundary Automatic submitter account creation - when Central EGA creates an account it is automatically available to all local EGA instances Portable solution working across different instances with different infrastructures Documentation for customisation and deployment	ELIXIR Sweden, ELIXIR Spain
Local/Federated EGA	The Local / Federated EGA (European Genome-phenome Archive) is a distributed solution for sharing and exchange of human -omics data across national borders. Local EGA collects metadata of -omics data collections stored in national or regional archives and make them available for search through the main EGA portal. The EGA systems development is coordinated by the ELIXIR Spain but with large contributions from the Nordic countries, partly funded through the Nordic Tryggve project. This Staff Exchange project allowed experienced software engineers from the Swedish and Finnish ELIXIR Nodes to work in Barcelona, Spain, to intensify the systems development work by working side-by-side with the Spanish systems developers team. The project shortened the development time for those aspects of the federated EGA where there are strong interdependencies between Central EGA and Local EGA instances. This is instrumental for establishing a unified EGA ecosystem that can offer a seamless user experience for data submitters and requestors. Outcomes Code to support key processes that go across the Central/Local EGA boundary Automatic submitter account creation - when Central EGA creates an account it is automatically available to all local EGA instances Portable solution working across different instances with different infrastructures Documentation for customisation and deployment	ELIXIR Sweden, ELIXIR Spain
The ELIXIR Beacon - 2017	In January 2017, ELIXIR extended its collaboration with GA4GH to further drive the development and implementation of the Beacon technology across ELIXIR Nodes. This study complated a number of tasks: Establish the network of ELIXIR Beacons Development of new features Tiered access (Open, Registered, Controlled) Handover directly to the data resource Added security measures to attract stakeholders with more sensitive data sets while minimising risks to individual privacy, Increaseed strategic partnering with national data owners to enable data flow to the Beacon service This work is coordinated by the ELIXIR Human Data Community which has seen Beacon v1.0 adopted as a GA4GH Standard. This Implementation Study is now complere, there are full details in the end report, which forms part of an ongoing series of Studies: 2015-16 2018 2019 (in preparation)	ELIXIR Belgium , EMBL-EBI, ELIXIR Spain, ELIXIR Switzerland, ELIXIR Netherlands, ELIXIR Finland, ELIXIR Sweden, ELIXIR France
The ELIXIR Beacon - 2017	In January 2017, ELIXIR extended its collaboration with GA4GH to further drive the development and implementation of the Beacon technology across ELIXIR Nodes. This study complated a number of tasks: Establish the network of ELIXIR Beacons Development of new features Tiered access (Open, Registered, Controlled) Handover directly to the data resource Added security measures to attract stakeholders with more sensitive data sets while minimising risks to individual privacy, Increaseed strategic partnering with national data owners to enable data flow to the Beacon service This work is coordinated by the ELIXIR Human Data Community which has seen Beacon v1.0 adopted as a GA4GH Standard. This Implementation Study is now complere, there are full details in the end report, which forms part of an ongoing series of Studies: 2015-16 2018 2019 (in preparation)	ELIXIR Belgium , EMBL-EBI, ELIXIR Spain, ELIXIR Switzerland, ELIXIR Netherlands, ELIXIR Finland, ELIXIR Sweden, ELIXIR France
The ELIXIR Beacon - 2017	In January 2017, ELIXIR extended its collaboration with GA4GH to further drive the development and implementation of the Beacon technology across ELIXIR Nodes. This study complated a number of tasks: Establish the network of ELIXIR Beacons Development of new features Tiered access (Open, Registered, Controlled) Handover directly to the data resource Added security measures to attract stakeholders with more sensitive data sets while minimising risks to individual privacy, Increaseed strategic partnering with national data owners to enable data flow to the Beacon service This work is coordinated by the ELIXIR Human Data Community which has seen Beacon v1.0 adopted as a GA4GH Standard. This Implementation Study is now complere, there are full details in the end report, which forms part of an ongoing series of Studies: 2015-16 2018 2019 (in preparation)	ELIXIR Belgium , EMBL-EBI, ELIXIR Spain, ELIXIR Switzerland, ELIXIR Netherlands, ELIXIR Finland, ELIXIR Sweden, ELIXIR France
The ELIXIR Beacon - 2017	In January 2017, ELIXIR extended its collaboration with GA4GH to further drive the development and implementation of the Beacon technology across ELIXIR Nodes. This study complated a number of tasks: Establish the network of ELIXIR Beacons Development of new features Tiered access (Open, Registered, Controlled) Handover directly to the data resource Added security measures to attract stakeholders with more sensitive data sets while minimising risks to individual privacy, Increaseed strategic partnering with national data owners to enable data flow to the Beacon service This work is coordinated by the ELIXIR Human Data Community which has seen Beacon v1.0 adopted as a GA4GH Standard. This Implementation Study is now complere, there are full details in the end report, which forms part of an ongoing series of Studies: 2015-16 2018 2019 (in preparation)	ELIXIR Belgium , EMBL-EBI, ELIXIR Spain, ELIXIR Switzerland, ELIXIR Netherlands, ELIXIR Finland, ELIXIR Sweden, ELIXIR France
The ELIXIR Beacon - 2017	In January 2017, ELIXIR extended its collaboration with GA4GH to further drive the development and implementation of the Beacon technology across ELIXIR Nodes. This study complated a number of tasks: Establish the network of ELIXIR Beacons Development of new features Tiered access (Open, Registered, Controlled) Handover directly to the data resource Added security measures to attract stakeholders with more sensitive data sets while minimising risks to individual privacy, Increaseed strategic partnering with national data owners to enable data flow to the Beacon service This work is coordinated by the ELIXIR Human Data Community which has seen Beacon v1.0 adopted as a GA4GH Standard. This Implementation Study is now complere, there are full details in the end report, which forms part of an ongoing series of Studies: 2015-16 2018 2019 (in preparation)	ELIXIR Belgium , EMBL-EBI, ELIXIR Spain, ELIXIR Switzerland, ELIXIR Netherlands, ELIXIR Finland, ELIXIR Sweden, ELIXIR France
The ELIXIR Beacon - 2017	In January 2017, ELIXIR extended its collaboration with GA4GH to further drive the development and implementation of the Beacon technology across ELIXIR Nodes. This study complated a number of tasks: Establish the network of ELIXIR Beacons Development of new features Tiered access (Open, Registered, Controlled) Handover directly to the data resource Added security measures to attract stakeholders with more sensitive data sets while minimising risks to individual privacy, Increaseed strategic partnering with national data owners to enable data flow to the Beacon service This work is coordinated by the ELIXIR Human Data Community which has seen Beacon v1.0 adopted as a GA4GH Standard. This Implementation Study is now complere, there are full details in the end report, which forms part of an ongoing series of Studies: 2015-16 2018 2019 (in preparation)	ELIXIR Belgium , EMBL-EBI, ELIXIR Spain, ELIXIR Switzerland, ELIXIR Netherlands, ELIXIR Finland, ELIXIR Sweden, ELIXIR France
The ELIXIR Beacon - 2017	In January 2017, ELIXIR extended its collaboration with GA4GH to further drive the development and implementation of the Beacon technology across ELIXIR Nodes. This study complated a number of tasks: Establish the network of ELIXIR Beacons Development of new features Tiered access (Open, Registered, Controlled) Handover directly to the data resource Added security measures to attract stakeholders with more sensitive data sets while minimising risks to individual privacy, Increaseed strategic partnering with national data owners to enable data flow to the Beacon service This work is coordinated by the ELIXIR Human Data Community which has seen Beacon v1.0 adopted as a GA4GH Standard. This Implementation Study is now complere, there are full details in the end report, which forms part of an ongoing series of Studies: 2015-16 2018 2019 (in preparation)	ELIXIR Belgium , EMBL-EBI, ELIXIR Spain, ELIXIR Switzerland, ELIXIR Netherlands, ELIXIR Finland, ELIXIR Sweden, ELIXIR France
The ELIXIR Beacon - 2017	In January 2017, ELIXIR extended its collaboration with GA4GH to further drive the development and implementation of the Beacon technology across ELIXIR Nodes. This study complated a number of tasks: Establish the network of ELIXIR Beacons Development of new features Tiered access (Open, Registered, Controlled) Handover directly to the data resource Added security measures to attract stakeholders with more sensitive data sets while minimising risks to individual privacy, Increaseed strategic partnering with national data owners to enable data flow to the Beacon service This work is coordinated by the ELIXIR Human Data Community which has seen Beacon v1.0 adopted as a GA4GH Standard. This Implementation Study is now complere, there are full details in the end report, which forms part of an ongoing series of Studies: 2015-16 2018 2019 (in preparation)	ELIXIR Belgium , EMBL-EBI, ELIXIR Spain, ELIXIR Switzerland, ELIXIR Netherlands, ELIXIR Finland, ELIXIR Sweden, ELIXIR France
The Federated EGA framework: supporting sensitive data management across the ELIXIR Nodes (2022-23)	Background Sensitive human data management, access, and analysis is delivering advancements in discovery and application of therapies to treat human disease. The generation and management of the majority of these data is transitioning from the research setting to the healthcare systems across Europe, and therefore is often subject to national/regional legislation that means these data are unable to leave local jurisdictions. As a result, the access to sensitive data that is consented for research use and/or the application of these data to the healthcare field is posed with new challenges to ensure that these data can be accessed in secure, effective, and efficient ways locally, and transnationally, in a federated manner - where the data remains in local jurisdictions but can be accessed across international borders. The main goal for the ELIXIR Federated Human Data (FHD) Community is to position the Federated EGA (FEGA) framework as the core infrastructure driver to support human data sharing for research use-cases from nationally, European Commission, and/or internationally funded human health data sharing projects. Purpose The Deliverables from this project will be incorporated by the FEGA governance framework to roadmap the maturity of the service, enabling FEGA to meet the needs of the sensitive human data management use cases from the ELIXIR Nodes. To accomplish this goal, the project will act as a coordination hub to establish contact points with Nodes and projects to gather existing and emerging use-cases, map the engagement with the projects and Federated EGA, identify areas for collaboration on common goals (e.g. synthetic cohorts for infrastructure testing purposes; cohort harmonisation - a huge task shared across many projects; and the identification and mapping of, shared use-cases), and act as a convening group to communicate the Federated EGA project status to the wider ELIXIR community. This broad alignment role across Nodes and existing key projects will strategically place the Federated EGA infrastructure at the centre of European transnational sharing of sensitive human data.	EMBL-EBI, ELIXIR Spain, ELIXIR Finland, ELIXIR Belgium , ELIXIR Switzerland, ELIXIR Czech Republic, ELIXIR Germany, ELIXIR Estonia, ELIXIR Greece, ELIXIR Hungary, ELIXIR Italy, ELIXIR Netherlands, ELIXIR Luxembourg, ELIXIR Norway, ELIXIR Portugal, ELIXIR Sweden, ELIXIR Slovenia, ELIXIR UK
The Federated EGA framework: supporting sensitive data management across the ELIXIR Nodes (2022-23)	Background Sensitive human data management, access, and analysis is delivering advancements in discovery and application of therapies to treat human disease. The generation and management of the majority of these data is transitioning from the research setting to the healthcare systems across Europe, and therefore is often subject to national/regional legislation that means these data are unable to leave local jurisdictions. As a result, the access to sensitive data that is consented for research use and/or the application of these data to the healthcare field is posed with new challenges to ensure that these data can be accessed in secure, effective, and efficient ways locally, and transnationally, in a federated manner - where the data remains in local jurisdictions but can be accessed across international borders. The main goal for the ELIXIR Federated Human Data (FHD) Community is to position the Federated EGA (FEGA) framework as the core infrastructure driver to support human data sharing for research use-cases from nationally, European Commission, and/or internationally funded human health data sharing projects. Purpose The Deliverables from this project will be incorporated by the FEGA governance framework to roadmap the maturity of the service, enabling FEGA to meet the needs of the sensitive human data management use cases from the ELIXIR Nodes. To accomplish this goal, the project will act as a coordination hub to establish contact points with Nodes and projects to gather existing and emerging use-cases, map the engagement with the projects and Federated EGA, identify areas for collaboration on common goals (e.g. synthetic cohorts for infrastructure testing purposes; cohort harmonisation - a huge task shared across many projects; and the identification and mapping of, shared use-cases), and act as a convening group to communicate the Federated EGA project status to the wider ELIXIR community. This broad alignment role across Nodes and existing key projects will strategically place the Federated EGA infrastructure at the centre of European transnational sharing of sensitive human data.	EMBL-EBI, ELIXIR Spain, ELIXIR Finland, ELIXIR Belgium , ELIXIR Switzerland, ELIXIR Czech Republic, ELIXIR Germany, ELIXIR Estonia, ELIXIR Greece, ELIXIR Hungary, ELIXIR Italy, ELIXIR Netherlands, ELIXIR Luxembourg, ELIXIR Norway, ELIXIR Portugal, ELIXIR Sweden, ELIXIR Slovenia, ELIXIR UK
The Federated EGA framework: supporting sensitive data management across the ELIXIR Nodes (2022-23)	Background Sensitive human data management, access, and analysis is delivering advancements in discovery and application of therapies to treat human disease. The generation and management of the majority of these data is transitioning from the research setting to the healthcare systems across Europe, and therefore is often subject to national/regional legislation that means these data are unable to leave local jurisdictions. As a result, the access to sensitive data that is consented for research use and/or the application of these data to the healthcare field is posed with new challenges to ensure that these data can be accessed in secure, effective, and efficient ways locally, and transnationally, in a federated manner - where the data remains in local jurisdictions but can be accessed across international borders. The main goal for the ELIXIR Federated Human Data (FHD) Community is to position the Federated EGA (FEGA) framework as the core infrastructure driver to support human data sharing for research use-cases from nationally, European Commission, and/or internationally funded human health data sharing projects. Purpose The Deliverables from this project will be incorporated by the FEGA governance framework to roadmap the maturity of the service, enabling FEGA to meet the needs of the sensitive human data management use cases from the ELIXIR Nodes. To accomplish this goal, the project will act as a coordination hub to establish contact points with Nodes and projects to gather existing and emerging use-cases, map the engagement with the projects and Federated EGA, identify areas for collaboration on common goals (e.g. synthetic cohorts for infrastructure testing purposes; cohort harmonisation - a huge task shared across many projects; and the identification and mapping of, shared use-cases), and act as a convening group to communicate the Federated EGA project status to the wider ELIXIR community. This broad alignment role across Nodes and existing key projects will strategically place the Federated EGA infrastructure at the centre of European transnational sharing of sensitive human data.	EMBL-EBI, ELIXIR Spain, ELIXIR Finland, ELIXIR Belgium , ELIXIR Switzerland, ELIXIR Czech Republic, ELIXIR Germany, ELIXIR Estonia, ELIXIR Greece, ELIXIR Hungary, ELIXIR Italy, ELIXIR Netherlands, ELIXIR Luxembourg, ELIXIR Norway, ELIXIR Portugal, ELIXIR Sweden, ELIXIR Slovenia, ELIXIR UK
The Federated EGA framework: supporting sensitive data management across the ELIXIR Nodes (2022-23)	Background Sensitive human data management, access, and analysis is delivering advancements in discovery and application of therapies to treat human disease. The generation and management of the majority of these data is transitioning from the research setting to the healthcare systems across Europe, and therefore is often subject to national/regional legislation that means these data are unable to leave local jurisdictions. As a result, the access to sensitive data that is consented for research use and/or the application of these data to the healthcare field is posed with new challenges to ensure that these data can be accessed in secure, effective, and efficient ways locally, and transnationally, in a federated manner - where the data remains in local jurisdictions but can be accessed across international borders. The main goal for the ELIXIR Federated Human Data (FHD) Community is to position the Federated EGA (FEGA) framework as the core infrastructure driver to support human data sharing for research use-cases from nationally, European Commission, and/or internationally funded human health data sharing projects. Purpose The Deliverables from this project will be incorporated by the FEGA governance framework to roadmap the maturity of the service, enabling FEGA to meet the needs of the sensitive human data management use cases from the ELIXIR Nodes. To accomplish this goal, the project will act as a coordination hub to establish contact points with Nodes and projects to gather existing and emerging use-cases, map the engagement with the projects and Federated EGA, identify areas for collaboration on common goals (e.g. synthetic cohorts for infrastructure testing purposes; cohort harmonisation - a huge task shared across many projects; and the identification and mapping of, shared use-cases), and act as a convening group to communicate the Federated EGA project status to the wider ELIXIR community. This broad alignment role across Nodes and existing key projects will strategically place the Federated EGA infrastructure at the centre of European transnational sharing of sensitive human data.	EMBL-EBI, ELIXIR Spain, ELIXIR Finland, ELIXIR Belgium , ELIXIR Switzerland, ELIXIR Czech Republic, ELIXIR Germany, ELIXIR Estonia, ELIXIR Greece, ELIXIR Hungary, ELIXIR Italy, ELIXIR Netherlands, ELIXIR Luxembourg, ELIXIR Norway, ELIXIR Portugal, ELIXIR Sweden, ELIXIR Slovenia, ELIXIR UK
The Federated EGA framework: supporting sensitive data management across the ELIXIR Nodes (2022-23)	Background Sensitive human data management, access, and analysis is delivering advancements in discovery and application of therapies to treat human disease. The generation and management of the majority of these data is transitioning from the research setting to the healthcare systems across Europe, and therefore is often subject to national/regional legislation that means these data are unable to leave local jurisdictions. As a result, the access to sensitive data that is consented for research use and/or the application of these data to the healthcare field is posed with new challenges to ensure that these data can be accessed in secure, effective, and efficient ways locally, and transnationally, in a federated manner - where the data remains in local jurisdictions but can be accessed across international borders. The main goal for the ELIXIR Federated Human Data (FHD) Community is to position the Federated EGA (FEGA) framework as the core infrastructure driver to support human data sharing for research use-cases from nationally, European Commission, and/or internationally funded human health data sharing projects. Purpose The Deliverables from this project will be incorporated by the FEGA governance framework to roadmap the maturity of the service, enabling FEGA to meet the needs of the sensitive human data management use cases from the ELIXIR Nodes. To accomplish this goal, the project will act as a coordination hub to establish contact points with Nodes and projects to gather existing and emerging use-cases, map the engagement with the projects and Federated EGA, identify areas for collaboration on common goals (e.g. synthetic cohorts for infrastructure testing purposes; cohort harmonisation - a huge task shared across many projects; and the identification and mapping of, shared use-cases), and act as a convening group to communicate the Federated EGA project status to the wider ELIXIR community. This broad alignment role across Nodes and existing key projects will strategically place the Federated EGA infrastructure at the centre of European transnational sharing of sensitive human data.	EMBL-EBI, ELIXIR Spain, ELIXIR Finland, ELIXIR Belgium , ELIXIR Switzerland, ELIXIR Czech Republic, ELIXIR Germany, ELIXIR Estonia, ELIXIR Greece, ELIXIR Hungary, ELIXIR Italy, ELIXIR Netherlands, ELIXIR Luxembourg, ELIXIR Norway, ELIXIR Portugal, ELIXIR Sweden, ELIXIR Slovenia, ELIXIR UK
The Federated EGA framework: supporting sensitive data management across the ELIXIR Nodes (2022-23)	Background Sensitive human data management, access, and analysis is delivering advancements in discovery and application of therapies to treat human disease. The generation and management of the majority of these data is transitioning from the research setting to the healthcare systems across Europe, and therefore is often subject to national/regional legislation that means these data are unable to leave local jurisdictions. As a result, the access to sensitive data that is consented for research use and/or the application of these data to the healthcare field is posed with new challenges to ensure that these data can be accessed in secure, effective, and efficient ways locally, and transnationally, in a federated manner - where the data remains in local jurisdictions but can be accessed across international borders. The main goal for the ELIXIR Federated Human Data (FHD) Community is to position the Federated EGA (FEGA) framework as the core infrastructure driver to support human data sharing for research use-cases from nationally, European Commission, and/or internationally funded human health data sharing projects. Purpose The Deliverables from this project will be incorporated by the FEGA governance framework to roadmap the maturity of the service, enabling FEGA to meet the needs of the sensitive human data management use cases from the ELIXIR Nodes. To accomplish this goal, the project will act as a coordination hub to establish contact points with Nodes and projects to gather existing and emerging use-cases, map the engagement with the projects and Federated EGA, identify areas for collaboration on common goals (e.g. synthetic cohorts for infrastructure testing purposes; cohort harmonisation - a huge task shared across many projects; and the identification and mapping of, shared use-cases), and act as a convening group to communicate the Federated EGA project status to the wider ELIXIR community. This broad alignment role across Nodes and existing key projects will strategically place the Federated EGA infrastructure at the centre of European transnational sharing of sensitive human data.	EMBL-EBI, ELIXIR Spain, ELIXIR Finland, ELIXIR Belgium , ELIXIR Switzerland, ELIXIR Czech Republic, ELIXIR Germany, ELIXIR Estonia, ELIXIR Greece, ELIXIR Hungary, ELIXIR Italy, ELIXIR Netherlands, ELIXIR Luxembourg, ELIXIR Norway, ELIXIR Portugal, ELIXIR Sweden, ELIXIR Slovenia, ELIXIR UK
The Federated EGA framework: supporting sensitive data management across the ELIXIR Nodes (2022-23)	Background Sensitive human data management, access, and analysis is delivering advancements in discovery and application of therapies to treat human disease. The generation and management of the majority of these data is transitioning from the research setting to the healthcare systems across Europe, and therefore is often subject to national/regional legislation that means these data are unable to leave local jurisdictions. As a result, the access to sensitive data that is consented for research use and/or the application of these data to the healthcare field is posed with new challenges to ensure that these data can be accessed in secure, effective, and efficient ways locally, and transnationally, in a federated manner - where the data remains in local jurisdictions but can be accessed across international borders. The main goal for the ELIXIR Federated Human Data (FHD) Community is to position the Federated EGA (FEGA) framework as the core infrastructure driver to support human data sharing for research use-cases from nationally, European Commission, and/or internationally funded human health data sharing projects. Purpose The Deliverables from this project will be incorporated by the FEGA governance framework to roadmap the maturity of the service, enabling FEGA to meet the needs of the sensitive human data management use cases from the ELIXIR Nodes. To accomplish this goal, the project will act as a coordination hub to establish contact points with Nodes and projects to gather existing and emerging use-cases, map the engagement with the projects and Federated EGA, identify areas for collaboration on common goals (e.g. synthetic cohorts for infrastructure testing purposes; cohort harmonisation - a huge task shared across many projects; and the identification and mapping of, shared use-cases), and act as a convening group to communicate the Federated EGA project status to the wider ELIXIR community. This broad alignment role across Nodes and existing key projects will strategically place the Federated EGA infrastructure at the centre of European transnational sharing of sensitive human data.	EMBL-EBI, ELIXIR Spain, ELIXIR Finland, ELIXIR Belgium , ELIXIR Switzerland, ELIXIR Czech Republic, ELIXIR Germany, ELIXIR Estonia, ELIXIR Greece, ELIXIR Hungary, ELIXIR Italy, ELIXIR Netherlands, ELIXIR Luxembourg, ELIXIR Norway, ELIXIR Portugal, ELIXIR Sweden, ELIXIR Slovenia, ELIXIR UK
The Federated EGA framework: supporting sensitive data management across the ELIXIR Nodes (2022-23)	Background Sensitive human data management, access, and analysis is delivering advancements in discovery and application of therapies to treat human disease. The generation and management of the majority of these data is transitioning from the research setting to the healthcare systems across Europe, and therefore is often subject to national/regional legislation that means these data are unable to leave local jurisdictions. As a result, the access to sensitive data that is consented for research use and/or the application of these data to the healthcare field is posed with new challenges to ensure that these data can be accessed in secure, effective, and efficient ways locally, and transnationally, in a federated manner - where the data remains in local jurisdictions but can be accessed across international borders. The main goal for the ELIXIR Federated Human Data (FHD) Community is to position the Federated EGA (FEGA) framework as the core infrastructure driver to support human data sharing for research use-cases from nationally, European Commission, and/or internationally funded human health data sharing projects. Purpose The Deliverables from this project will be incorporated by the FEGA governance framework to roadmap the maturity of the service, enabling FEGA to meet the needs of the sensitive human data management use cases from the ELIXIR Nodes. To accomplish this goal, the project will act as a coordination hub to establish contact points with Nodes and projects to gather existing and emerging use-cases, map the engagement with the projects and Federated EGA, identify areas for collaboration on common goals (e.g. synthetic cohorts for infrastructure testing purposes; cohort harmonisation - a huge task shared across many projects; and the identification and mapping of, shared use-cases), and act as a convening group to communicate the Federated EGA project status to the wider ELIXIR community. This broad alignment role across Nodes and existing key projects will strategically place the Federated EGA infrastructure at the centre of European transnational sharing of sensitive human data.	EMBL-EBI, ELIXIR Spain, ELIXIR Finland, ELIXIR Belgium , ELIXIR Switzerland, ELIXIR Czech Republic, ELIXIR Germany, ELIXIR Estonia, ELIXIR Greece, ELIXIR Hungary, ELIXIR Italy, ELIXIR Netherlands, ELIXIR Luxembourg, ELIXIR Norway, ELIXIR Portugal, ELIXIR Sweden, ELIXIR Slovenia, ELIXIR UK
The Federated EGA framework: supporting sensitive data management across the ELIXIR Nodes (2022-23)	Background Sensitive human data management, access, and analysis is delivering advancements in discovery and application of therapies to treat human disease. The generation and management of the majority of these data is transitioning from the research setting to the healthcare systems across Europe, and therefore is often subject to national/regional legislation that means these data are unable to leave local jurisdictions. As a result, the access to sensitive data that is consented for research use and/or the application of these data to the healthcare field is posed with new challenges to ensure that these data can be accessed in secure, effective, and efficient ways locally, and transnationally, in a federated manner - where the data remains in local jurisdictions but can be accessed across international borders. The main goal for the ELIXIR Federated Human Data (FHD) Community is to position the Federated EGA (FEGA) framework as the core infrastructure driver to support human data sharing for research use-cases from nationally, European Commission, and/or internationally funded human health data sharing projects. Purpose The Deliverables from this project will be incorporated by the FEGA governance framework to roadmap the maturity of the service, enabling FEGA to meet the needs of the sensitive human data management use cases from the ELIXIR Nodes. To accomplish this goal, the project will act as a coordination hub to establish contact points with Nodes and projects to gather existing and emerging use-cases, map the engagement with the projects and Federated EGA, identify areas for collaboration on common goals (e.g. synthetic cohorts for infrastructure testing purposes; cohort harmonisation - a huge task shared across many projects; and the identification and mapping of, shared use-cases), and act as a convening group to communicate the Federated EGA project status to the wider ELIXIR community. This broad alignment role across Nodes and existing key projects will strategically place the Federated EGA infrastructure at the centre of European transnational sharing of sensitive human data.	EMBL-EBI, ELIXIR Spain, ELIXIR Finland, ELIXIR Belgium , ELIXIR Switzerland, ELIXIR Czech Republic, ELIXIR Germany, ELIXIR Estonia, ELIXIR Greece, ELIXIR Hungary, ELIXIR Italy, ELIXIR Netherlands, ELIXIR Luxembourg, ELIXIR Norway, ELIXIR Portugal, ELIXIR Sweden, ELIXIR Slovenia, ELIXIR UK
The Federated EGA framework: supporting sensitive data management across the ELIXIR Nodes (2022-23)	Background Sensitive human data management, access, and analysis is delivering advancements in discovery and application of therapies to treat human disease. The generation and management of the majority of these data is transitioning from the research setting to the healthcare systems across Europe, and therefore is often subject to national/regional legislation that means these data are unable to leave local jurisdictions. As a result, the access to sensitive data that is consented for research use and/or the application of these data to the healthcare field is posed with new challenges to ensure that these data can be accessed in secure, effective, and efficient ways locally, and transnationally, in a federated manner - where the data remains in local jurisdictions but can be accessed across international borders. The main goal for the ELIXIR Federated Human Data (FHD) Community is to position the Federated EGA (FEGA) framework as the core infrastructure driver to support human data sharing for research use-cases from nationally, European Commission, and/or internationally funded human health data sharing projects. Purpose The Deliverables from this project will be incorporated by the FEGA governance framework to roadmap the maturity of the service, enabling FEGA to meet the needs of the sensitive human data management use cases from the ELIXIR Nodes. To accomplish this goal, the project will act as a coordination hub to establish contact points with Nodes and projects to gather existing and emerging use-cases, map the engagement with the projects and Federated EGA, identify areas for collaboration on common goals (e.g. synthetic cohorts for infrastructure testing purposes; cohort harmonisation - a huge task shared across many projects; and the identification and mapping of, shared use-cases), and act as a convening group to communicate the Federated EGA project status to the wider ELIXIR community. This broad alignment role across Nodes and existing key projects will strategically place the Federated EGA infrastructure at the centre of European transnational sharing of sensitive human data.	EMBL-EBI, ELIXIR Spain, ELIXIR Finland, ELIXIR Belgium , ELIXIR Switzerland, ELIXIR Czech Republic, ELIXIR Germany, ELIXIR Estonia, ELIXIR Greece, ELIXIR Hungary, ELIXIR Italy, ELIXIR Netherlands, ELIXIR Luxembourg, ELIXIR Norway, ELIXIR Portugal, ELIXIR Sweden, ELIXIR Slovenia, ELIXIR UK
The Federated EGA framework: supporting sensitive data management across the ELIXIR Nodes (2022-23)	Background Sensitive human data management, access, and analysis is delivering advancements in discovery and application of therapies to treat human disease. The generation and management of the majority of these data is transitioning from the research setting to the healthcare systems across Europe, and therefore is often subject to national/regional legislation that means these data are unable to leave local jurisdictions. As a result, the access to sensitive data that is consented for research use and/or the application of these data to the healthcare field is posed with new challenges to ensure that these data can be accessed in secure, effective, and efficient ways locally, and transnationally, in a federated manner - where the data remains in local jurisdictions but can be accessed across international borders. The main goal for the ELIXIR Federated Human Data (FHD) Community is to position the Federated EGA (FEGA) framework as the core infrastructure driver to support human data sharing for research use-cases from nationally, European Commission, and/or internationally funded human health data sharing projects. Purpose The Deliverables from this project will be incorporated by the FEGA governance framework to roadmap the maturity of the service, enabling FEGA to meet the needs of the sensitive human data management use cases from the ELIXIR Nodes. To accomplish this goal, the project will act as a coordination hub to establish contact points with Nodes and projects to gather existing and emerging use-cases, map the engagement with the projects and Federated EGA, identify areas for collaboration on common goals (e.g. synthetic cohorts for infrastructure testing purposes; cohort harmonisation - a huge task shared across many projects; and the identification and mapping of, shared use-cases), and act as a convening group to communicate the Federated EGA project status to the wider ELIXIR community. This broad alignment role across Nodes and existing key projects will strategically place the Federated EGA infrastructure at the centre of European transnational sharing of sensitive human data.	EMBL-EBI, ELIXIR Spain, ELIXIR Finland, ELIXIR Belgium , ELIXIR Switzerland, ELIXIR Czech Republic, ELIXIR Germany, ELIXIR Estonia, ELIXIR Greece, ELIXIR Hungary, ELIXIR Italy, ELIXIR Netherlands, ELIXIR Luxembourg, ELIXIR Norway, ELIXIR Portugal, ELIXIR Sweden, ELIXIR Slovenia, ELIXIR UK
The Federated EGA framework: supporting sensitive data management across the ELIXIR Nodes (2022-23)	Background Sensitive human data management, access, and analysis is delivering advancements in discovery and application of therapies to treat human disease. The generation and management of the majority of these data is transitioning from the research setting to the healthcare systems across Europe, and therefore is often subject to national/regional legislation that means these data are unable to leave local jurisdictions. As a result, the access to sensitive data that is consented for research use and/or the application of these data to the healthcare field is posed with new challenges to ensure that these data can be accessed in secure, effective, and efficient ways locally, and transnationally, in a federated manner - where the data remains in local jurisdictions but can be accessed across international borders. The main goal for the ELIXIR Federated Human Data (FHD) Community is to position the Federated EGA (FEGA) framework as the core infrastructure driver to support human data sharing for research use-cases from nationally, European Commission, and/or internationally funded human health data sharing projects. Purpose The Deliverables from this project will be incorporated by the FEGA governance framework to roadmap the maturity of the service, enabling FEGA to meet the needs of the sensitive human data management use cases from the ELIXIR Nodes. To accomplish this goal, the project will act as a coordination hub to establish contact points with Nodes and projects to gather existing and emerging use-cases, map the engagement with the projects and Federated EGA, identify areas for collaboration on common goals (e.g. synthetic cohorts for infrastructure testing purposes; cohort harmonisation - a huge task shared across many projects; and the identification and mapping of, shared use-cases), and act as a convening group to communicate the Federated EGA project status to the wider ELIXIR community. This broad alignment role across Nodes and existing key projects will strategically place the Federated EGA infrastructure at the centre of European transnational sharing of sensitive human data.	EMBL-EBI, ELIXIR Spain, ELIXIR Finland, ELIXIR Belgium , ELIXIR Switzerland, ELIXIR Czech Republic, ELIXIR Germany, ELIXIR Estonia, ELIXIR Greece, ELIXIR Hungary, ELIXIR Italy, ELIXIR Netherlands, ELIXIR Luxembourg, ELIXIR Norway, ELIXIR Portugal, ELIXIR Sweden, ELIXIR Slovenia, ELIXIR UK
The Federated EGA framework: supporting sensitive data management across the ELIXIR Nodes (2022-23)	Background Sensitive human data management, access, and analysis is delivering advancements in discovery and application of therapies to treat human disease. The generation and management of the majority of these data is transitioning from the research setting to the healthcare systems across Europe, and therefore is often subject to national/regional legislation that means these data are unable to leave local jurisdictions. As a result, the access to sensitive data that is consented for research use and/or the application of these data to the healthcare field is posed with new challenges to ensure that these data can be accessed in secure, effective, and efficient ways locally, and transnationally, in a federated manner - where the data remains in local jurisdictions but can be accessed across international borders. The main goal for the ELIXIR Federated Human Data (FHD) Community is to position the Federated EGA (FEGA) framework as the core infrastructure driver to support human data sharing for research use-cases from nationally, European Commission, and/or internationally funded human health data sharing projects. Purpose The Deliverables from this project will be incorporated by the FEGA governance framework to roadmap the maturity of the service, enabling FEGA to meet the needs of the sensitive human data management use cases from the ELIXIR Nodes. To accomplish this goal, the project will act as a coordination hub to establish contact points with Nodes and projects to gather existing and emerging use-cases, map the engagement with the projects and Federated EGA, identify areas for collaboration on common goals (e.g. synthetic cohorts for infrastructure testing purposes; cohort harmonisation - a huge task shared across many projects; and the identification and mapping of, shared use-cases), and act as a convening group to communicate the Federated EGA project status to the wider ELIXIR community. This broad alignment role across Nodes and existing key projects will strategically place the Federated EGA infrastructure at the centre of European transnational sharing of sensitive human data.	EMBL-EBI, ELIXIR Spain, ELIXIR Finland, ELIXIR Belgium , ELIXIR Switzerland, ELIXIR Czech Republic, ELIXIR Germany, ELIXIR Estonia, ELIXIR Greece, ELIXIR Hungary, ELIXIR Italy, ELIXIR Netherlands, ELIXIR Luxembourg, ELIXIR Norway, ELIXIR Portugal, ELIXIR Sweden, ELIXIR Slovenia, ELIXIR UK
The Federated EGA framework: supporting sensitive data management across the ELIXIR Nodes (2022-23)	Background Sensitive human data management, access, and analysis is delivering advancements in discovery and application of therapies to treat human disease. The generation and management of the majority of these data is transitioning from the research setting to the healthcare systems across Europe, and therefore is often subject to national/regional legislation that means these data are unable to leave local jurisdictions. As a result, the access to sensitive data that is consented for research use and/or the application of these data to the healthcare field is posed with new challenges to ensure that these data can be accessed in secure, effective, and efficient ways locally, and transnationally, in a federated manner - where the data remains in local jurisdictions but can be accessed across international borders. The main goal for the ELIXIR Federated Human Data (FHD) Community is to position the Federated EGA (FEGA) framework as the core infrastructure driver to support human data sharing for research use-cases from nationally, European Commission, and/or internationally funded human health data sharing projects. Purpose The Deliverables from this project will be incorporated by the FEGA governance framework to roadmap the maturity of the service, enabling FEGA to meet the needs of the sensitive human data management use cases from the ELIXIR Nodes. To accomplish this goal, the project will act as a coordination hub to establish contact points with Nodes and projects to gather existing and emerging use-cases, map the engagement with the projects and Federated EGA, identify areas for collaboration on common goals (e.g. synthetic cohorts for infrastructure testing purposes; cohort harmonisation - a huge task shared across many projects; and the identification and mapping of, shared use-cases), and act as a convening group to communicate the Federated EGA project status to the wider ELIXIR community. This broad alignment role across Nodes and existing key projects will strategically place the Federated EGA infrastructure at the centre of European transnational sharing of sensitive human data.	EMBL-EBI, ELIXIR Spain, ELIXIR Finland, ELIXIR Belgium , ELIXIR Switzerland, ELIXIR Czech Republic, ELIXIR Germany, ELIXIR Estonia, ELIXIR Greece, ELIXIR Hungary, ELIXIR Italy, ELIXIR Netherlands, ELIXIR Luxembourg, ELIXIR Norway, ELIXIR Portugal, ELIXIR Sweden, ELIXIR Slovenia, ELIXIR UK
The Federated EGA framework: supporting sensitive data management across the ELIXIR Nodes (2022-23)	Background Sensitive human data management, access, and analysis is delivering advancements in discovery and application of therapies to treat human disease. The generation and management of the majority of these data is transitioning from the research setting to the healthcare systems across Europe, and therefore is often subject to national/regional legislation that means these data are unable to leave local jurisdictions. As a result, the access to sensitive data that is consented for research use and/or the application of these data to the healthcare field is posed with new challenges to ensure that these data can be accessed in secure, effective, and efficient ways locally, and transnationally, in a federated manner - where the data remains in local jurisdictions but can be accessed across international borders. The main goal for the ELIXIR Federated Human Data (FHD) Community is to position the Federated EGA (FEGA) framework as the core infrastructure driver to support human data sharing for research use-cases from nationally, European Commission, and/or internationally funded human health data sharing projects. Purpose The Deliverables from this project will be incorporated by the FEGA governance framework to roadmap the maturity of the service, enabling FEGA to meet the needs of the sensitive human data management use cases from the ELIXIR Nodes. To accomplish this goal, the project will act as a coordination hub to establish contact points with Nodes and projects to gather existing and emerging use-cases, map the engagement with the projects and Federated EGA, identify areas for collaboration on common goals (e.g. synthetic cohorts for infrastructure testing purposes; cohort harmonisation - a huge task shared across many projects; and the identification and mapping of, shared use-cases), and act as a convening group to communicate the Federated EGA project status to the wider ELIXIR community. This broad alignment role across Nodes and existing key projects will strategically place the Federated EGA infrastructure at the centre of European transnational sharing of sensitive human data.	EMBL-EBI, ELIXIR Spain, ELIXIR Finland, ELIXIR Belgium , ELIXIR Switzerland, ELIXIR Czech Republic, ELIXIR Germany, ELIXIR Estonia, ELIXIR Greece, ELIXIR Hungary, ELIXIR Italy, ELIXIR Netherlands, ELIXIR Luxembourg, ELIXIR Norway, ELIXIR Portugal, ELIXIR Sweden, ELIXIR Slovenia, ELIXIR UK
The Federated EGA framework: supporting sensitive data management across the ELIXIR Nodes (2022-23)	Background Sensitive human data management, access, and analysis is delivering advancements in discovery and application of therapies to treat human disease. The generation and management of the majority of these data is transitioning from the research setting to the healthcare systems across Europe, and therefore is often subject to national/regional legislation that means these data are unable to leave local jurisdictions. As a result, the access to sensitive data that is consented for research use and/or the application of these data to the healthcare field is posed with new challenges to ensure that these data can be accessed in secure, effective, and efficient ways locally, and transnationally, in a federated manner - where the data remains in local jurisdictions but can be accessed across international borders. The main goal for the ELIXIR Federated Human Data (FHD) Community is to position the Federated EGA (FEGA) framework as the core infrastructure driver to support human data sharing for research use-cases from nationally, European Commission, and/or internationally funded human health data sharing projects. Purpose The Deliverables from this project will be incorporated by the FEGA governance framework to roadmap the maturity of the service, enabling FEGA to meet the needs of the sensitive human data management use cases from the ELIXIR Nodes. To accomplish this goal, the project will act as a coordination hub to establish contact points with Nodes and projects to gather existing and emerging use-cases, map the engagement with the projects and Federated EGA, identify areas for collaboration on common goals (e.g. synthetic cohorts for infrastructure testing purposes; cohort harmonisation - a huge task shared across many projects; and the identification and mapping of, shared use-cases), and act as a convening group to communicate the Federated EGA project status to the wider ELIXIR community. This broad alignment role across Nodes and existing key projects will strategically place the Federated EGA infrastructure at the centre of European transnational sharing of sensitive human data.	EMBL-EBI, ELIXIR Spain, ELIXIR Finland, ELIXIR Belgium , ELIXIR Switzerland, ELIXIR Czech Republic, ELIXIR Germany, ELIXIR Estonia, ELIXIR Greece, ELIXIR Hungary, ELIXIR Italy, ELIXIR Netherlands, ELIXIR Luxembourg, ELIXIR Norway, ELIXIR Portugal, ELIXIR Sweden, ELIXIR Slovenia, ELIXIR UK
The Federated EGA framework: supporting sensitive data management across the ELIXIR Nodes (2022-23)	Background Sensitive human data management, access, and analysis is delivering advancements in discovery and application of therapies to treat human disease. The generation and management of the majority of these data is transitioning from the research setting to the healthcare systems across Europe, and therefore is often subject to national/regional legislation that means these data are unable to leave local jurisdictions. As a result, the access to sensitive data that is consented for research use and/or the application of these data to the healthcare field is posed with new challenges to ensure that these data can be accessed in secure, effective, and efficient ways locally, and transnationally, in a federated manner - where the data remains in local jurisdictions but can be accessed across international borders. The main goal for the ELIXIR Federated Human Data (FHD) Community is to position the Federated EGA (FEGA) framework as the core infrastructure driver to support human data sharing for research use-cases from nationally, European Commission, and/or internationally funded human health data sharing projects. Purpose The Deliverables from this project will be incorporated by the FEGA governance framework to roadmap the maturity of the service, enabling FEGA to meet the needs of the sensitive human data management use cases from the ELIXIR Nodes. To accomplish this goal, the project will act as a coordination hub to establish contact points with Nodes and projects to gather existing and emerging use-cases, map the engagement with the projects and Federated EGA, identify areas for collaboration on common goals (e.g. synthetic cohorts for infrastructure testing purposes; cohort harmonisation - a huge task shared across many projects; and the identification and mapping of, shared use-cases), and act as a convening group to communicate the Federated EGA project status to the wider ELIXIR community. This broad alignment role across Nodes and existing key projects will strategically place the Federated EGA infrastructure at the centre of European transnational sharing of sensitive human data.	EMBL-EBI, ELIXIR Spain, ELIXIR Finland, ELIXIR Belgium , ELIXIR Switzerland, ELIXIR Czech Republic, ELIXIR Germany, ELIXIR Estonia, ELIXIR Greece, ELIXIR Hungary, ELIXIR Italy, ELIXIR Netherlands, ELIXIR Luxembourg, ELIXIR Norway, ELIXIR Portugal, ELIXIR Sweden, ELIXIR Slovenia, ELIXIR UK
The Federated EGA framework: supporting sensitive data management across the ELIXIR Nodes (2022-23)	Background Sensitive human data management, access, and analysis is delivering advancements in discovery and application of therapies to treat human disease. The generation and management of the majority of these data is transitioning from the research setting to the healthcare systems across Europe, and therefore is often subject to national/regional legislation that means these data are unable to leave local jurisdictions. As a result, the access to sensitive data that is consented for research use and/or the application of these data to the healthcare field is posed with new challenges to ensure that these data can be accessed in secure, effective, and efficient ways locally, and transnationally, in a federated manner - where the data remains in local jurisdictions but can be accessed across international borders. The main goal for the ELIXIR Federated Human Data (FHD) Community is to position the Federated EGA (FEGA) framework as the core infrastructure driver to support human data sharing for research use-cases from nationally, European Commission, and/or internationally funded human health data sharing projects. Purpose The Deliverables from this project will be incorporated by the FEGA governance framework to roadmap the maturity of the service, enabling FEGA to meet the needs of the sensitive human data management use cases from the ELIXIR Nodes. To accomplish this goal, the project will act as a coordination hub to establish contact points with Nodes and projects to gather existing and emerging use-cases, map the engagement with the projects and Federated EGA, identify areas for collaboration on common goals (e.g. synthetic cohorts for infrastructure testing purposes; cohort harmonisation - a huge task shared across many projects; and the identification and mapping of, shared use-cases), and act as a convening group to communicate the Federated EGA project status to the wider ELIXIR community. This broad alignment role across Nodes and existing key projects will strategically place the Federated EGA infrastructure at the centre of European transnational sharing of sensitive human data.	EMBL-EBI, ELIXIR Spain, ELIXIR Finland, ELIXIR Belgium , ELIXIR Switzerland, ELIXIR Czech Republic, ELIXIR Germany, ELIXIR Estonia, ELIXIR Greece, ELIXIR Hungary, ELIXIR Italy, ELIXIR Netherlands, ELIXIR Luxembourg, ELIXIR Norway, ELIXIR Portugal, ELIXIR Sweden, ELIXIR Slovenia, ELIXIR UK
Visit to prepare & coordinate genomic data infrastructure project in Europe	This project is to improve the coordination between the Beyond 1 Million Genomes project and the Federated Human Data / ELIXIR CONVERGE projects. All three projects are based around Federated EGA, or its technology, to support cross border access to human controlled access genetic and phenotypic data. Objective 1: Strengthen the collaboration and coordination between the Hub and ELIXIR-FI, especially the Beyond 1 Million Genomes (B1MG) project and prospective Digital Europe Genomic Data Call, and the Federated Human Data Communities, ELIXIR Converge, and CINECA. Additionally leverage ELIXIR-Hub contacts with other nodes to explore new collaboration opportunities. The project lead is a Senior Coordinator at ELIXIR-FI on the B1MG project and co-lead of the Federated Human Data Community. Objective 2: Maximise adoption of GA4GH standards, and existing or developing services, such as Federated EGA and Beacon, throughout Europe by identifying and exploiting parallels between the deployment of Federated EGA nodes and B1MG data hubs. As Senior Coordinator for the B1MG project the project lead is tasked with driving adoption of the proposed infrastructure and subsequent deployment of data hubs by the 1+MG signatory member states. Objective 3: Identify and utilise additional collaborations within other European Projects, such as European Health Data Space 2 (EHDS2), to ensure both the genomic and phenotypic or clinical data is as interoperable as possible. The project lead was on the GA4GH product review committee for the version 2 of the Phenopacket standard which enables linking of genetic and phenotypic data. Objective 4: Align the deployment, ELSI, and governance procedures of B1MG data hubs with the B1MG Maturity Models. Ensure that these procedures are compatible with Federated EGA deployment ELSI procedures. The project lead has lead the Security work package for the Beacon project since 2017.	ELIXIR Finland, EMBL-EBI
Visit to prepare & coordinate genomic data infrastructure project in Europe	This project is to improve the coordination between the Beyond 1 Million Genomes project and the Federated Human Data / ELIXIR CONVERGE projects. All three projects are based around Federated EGA, or its technology, to support cross border access to human controlled access genetic and phenotypic data. Objective 1: Strengthen the collaboration and coordination between the Hub and ELIXIR-FI, especially the Beyond 1 Million Genomes (B1MG) project and prospective Digital Europe Genomic Data Call, and the Federated Human Data Communities, ELIXIR Converge, and CINECA. Additionally leverage ELIXIR-Hub contacts with other nodes to explore new collaboration opportunities. The project lead is a Senior Coordinator at ELIXIR-FI on the B1MG project and co-lead of the Federated Human Data Community. Objective 2: Maximise adoption of GA4GH standards, and existing or developing services, such as Federated EGA and Beacon, throughout Europe by identifying and exploiting parallels between the deployment of Federated EGA nodes and B1MG data hubs. As Senior Coordinator for the B1MG project the project lead is tasked with driving adoption of the proposed infrastructure and subsequent deployment of data hubs by the 1+MG signatory member states. Objective 3: Identify and utilise additional collaborations within other European Projects, such as European Health Data Space 2 (EHDS2), to ensure both the genomic and phenotypic or clinical data is as interoperable as possible. The project lead was on the GA4GH product review committee for the version 2 of the Phenopacket standard which enables linking of genetic and phenotypic data. Objective 4: Align the deployment, ELSI, and governance procedures of B1MG data hubs with the B1MG Maturity Models. Ensure that these procedures are compatible with Federated EGA deployment ELSI procedures. The project lead has lead the Security work package for the Beacon project since 2017.	ELIXIR Finland, EMBL-EBI

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Webinar summarising the outcomes

Webinar summarising the outcomes

Webinar summarising the outcomes

Webinar summarising the outcomes

Webinar summarising the outcomes

Webinar summarising the outcomes

Webinar summarising the outcomes

Webinar summarising the outcomes

Impact Statement

Webinar summarising the outcomes

Webinar summarising the outcomes

Webinar summarising the outcomes

WP1: Coordination of metadata standards for sensitive human data

WP2: Architecture and interfaces to support ELIXIR federated human data infrastructure

WP3: Coordination of interface implementation

WP4: Coordination of operational nodes as part of the federated services

WP5: Project overall coordination, outreach and training

WP1: Coordination of metadata standards for sensitive human data

WP2: Architecture and interfaces to support ELIXIR federated human data infrastructure

WP3: Coordination of interface implementation

WP4: Coordination of operational nodes as part of the federated services

WP5: Project overall coordination, outreach and training

WP1: Coordination of metadata standards for sensitive human data

WP2: Architecture and interfaces to support ELIXIR federated human data infrastructure

WP3: Coordination of interface implementation

WP4: Coordination of operational nodes as part of the federated services

WP5: Project overall coordination, outreach and training

WP1: Coordination of metadata standards for sensitive human data

WP2: Architecture and interfaces to support ELIXIR federated human data infrastructure

WP3: Coordination of interface implementation

WP4: Coordination of operational nodes as part of the federated services

WP5: Project overall coordination, outreach and training

WP1: Coordination of metadata standards for sensitive human data

WP2: Architecture and interfaces to support ELIXIR federated human data infrastructure

WP3: Coordination of interface implementation

WP4: Coordination of operational nodes as part of the federated services

WP5: Project overall coordination, outreach and training

WP1: Coordination of metadata standards for sensitive human data

WP2: Architecture and interfaces to support ELIXIR federated human data infrastructure

WP3: Coordination of interface implementation

WP4: Coordination of operational nodes as part of the federated services

WP5: Project overall coordination, outreach and training

WP1: Coordination of metadata standards for sensitive human data

WP2: Architecture and interfaces to support ELIXIR federated human data infrastructure

WP3: Coordination of interface implementation

WP4: Coordination of operational nodes as part of the federated services

WP5: Project overall coordination, outreach and training

WP1: Coordination of metadata standards for sensitive human data

WP2: Architecture and interfaces to support ELIXIR federated human data infrastructure

WP3: Coordination of interface implementation

WP4: Coordination of operational nodes as part of the federated services

WP5: Project overall coordination, outreach and training

WP1: Coordination of metadata standards for sensitive human data

WP2: Architecture and interfaces to support ELIXIR federated human data infrastructure

WP3: Coordination of interface implementation

WP4: Coordination of operational nodes as part of the federated services

WP5: Project overall coordination, outreach and training

WP1: Coordination of metadata standards for sensitive human data

WP2: Architecture and interfaces to support ELIXIR federated human data infrastructure

WP3: Coordination of interface implementation

WP4: Coordination of operational nodes as part of the federated services

WP5: Project overall coordination, outreach and training

WP1: Coordination of metadata standards for sensitive human data

WP2: Architecture and interfaces to support ELIXIR federated human data infrastructure

WP3: Coordination of interface implementation

WP4: Coordination of operational nodes as part of the federated services

WP5: Project overall coordination, outreach and training

WP1: Coordination of metadata standards for sensitive human data

WP2: Architecture and interfaces to support ELIXIR federated human data infrastructure

WP3: Coordination of interface implementation

WP4: Coordination of operational nodes as part of the federated services

WP5: Project overall coordination, outreach and training

WP1: Coordination of metadata standards for sensitive human data

WP2: Architecture and interfaces to support ELIXIR federated human data infrastructure

WP3: Coordination of interface implementation

WP4: Coordination of operational nodes as part of the federated services

WP5: Project overall coordination, outreach and training

Final report:

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