Authors - Romain Tanzer (HES-SO), Nona Naderi (HES-SO), Douglas Teodoro (HES-SO), Anais Mottaz (HES-SO), Patrick Ruch (HES-SO), Jonathan Dursi (SickKids), Jordi Rambla de Argila (CRG)

CINECA aims to support federated queries and analyses of distributed cohorts across continents. But human health datasets are extremely diverse; many different types of data are collected for many different kinds of health studies by many different health research communities. As a result, different cohort datasets often use different ontologies to describe similar kinds of entities, or represent concepts, such as genomic variation differently.

CINECA must span this diversity of data representations in order to achieve its goals of connecting health research cohort data. The work of WP3 partially addresses discoverability of datasets by defining a standard minimal cohort-level data representation which will be common across all cohorts; but that does not address cohort-level data that falls outside of the minimal common data model, nor does it address the representation of patient-level data. WP1’s role is to design and deploy API access to both cohort- and patient-level data, and a fundamental functionality of the infrastructure is to allow the user to find the appropriate dataset independently of the ontology used to map locally the different cohorts or indifferently of the format and syntax used to describe the variants.

This report describes the work done on query expansion, by implementing and demonstrating a query expansion service API that improves findability and searchability of distributed cohort data. Multiple kinds of query expansions are available for enabling further data integration and interoperability, including horizontal expansion, i.e., across ontological systems, and vertical expansion, i.e., within sublevels of the same ontological resource.

https://doi.org/10.5281/zenodo.4609335

DeliverablesLeslie GlassDecember 15, 2020WP1

Cohort minimal metadata model - D3.1

Authors - Vivian Jin, Fiona Brinkman (SFU)

To support human cohort genomic and other “omic” data discovery and analysis across jurisdictions, basic data such as cohort participant age, sex, etc needs to be harmonised. Developing a key “minimal metadata model” of these basic attributes which should be recorded with all cohorts is critical to aid initial querying across jurisdictions for suitable dataset discovery. We describe here the creation of a minimal metadata model, the specific methods used to create the minimal metadata model, and this model’s utility and impact.

A first version of the metadata model was built based on a review of Maelstrom research data standards and a manual survey of cohort data dictionaries, which identified and incorporated overlapping core variables across CINECA cohorts. The model was then converted to Genomics Cohorts Knowledge Ontology (GECKO) format and further expanded with additional terms. The minimal metadata model is being made broadly available to aid any project or projects, including those outside of CINECA interested in facilitating cross-jurisdictional data discovery and analysis.

https://doi.org/10.5281/zenodo.4575460

Deliverables, WP3Leslie GlassDecember 15, 2020WP3, deliverables, cohort data

Training Programme, Detailed D6.4

In this deliverable document, we report on the activities in task 6.4 - Training Programme, describe the CINECA training activities in the first 24 months of the project and provide the Training Plan for the next 12-24 months. For training interventions targeted at a broader audience, we have set up a webinar series, providing quarterly online learning interventions. We ran a total of 6 webinars (3 of these webinars in 2019, and 3 in 2020), with 23 attendees on average, 68% on average of those who registered. In addition, a series of short training videos (https://www.cineca-project.eu/short-videos) was created to facilitate the uptake of CINECA outputs. Eight short videos were produced by work packages on different topics. The short videos were submitted to ELIXIR’s training portal to increase engagement and disseminated via CINECA’s various communication channels.

https://doi.org/10.5281/zenodo.6223125

Deliverables, WP4December 15, 2020deliverables, wp4

Catalogue of Canadian, European and African ethical and legal gaps - D7.2

Authors - Éloïse Gennet, Melanie Goisauf, Delphine Pichereau, Emmanuelle Rial-Sebbag

Remaining liberties that GDPR provides to EU Member States, as well as remaining ambiguities on GDPR interpretation, continue to feed debates in the ethical and legal literature. Projects like CINECA, which is seeking to facilitate health data exchanges between cohorts in Europe, Canada and Africa, offer valuable experience and input on essential ethical and legal gaps between countries and cohorts on questions such as the ethical lawful basis for international health data sharing and secondary processing for research purposes.

The focus of this deliverable will be on answering, both from a legal and an ethical point of view, two priority questions: How to choose a legal basis for CINECA’s data processing? And how should CINECA apprehend broad consent to further data processing? The goal will be to study how the CINECA project could be efficiently conducted (especially data sharing) while being legally compliant with relevant laws and regulations across all member states, and most of all, being compliant with established ethical guidelines and practices across three continents.

https://doi.org/10.5281/zenodo.4298450

DeliverablesLeslie GlassNovember 30, 2020wp4

CanDIG and ELIXIR AAI interoperability demonstration - D2.1

This deliverable demonstrates authentication and authorisation interoperability between the ELIXIR and CanDIG infrastructures. Users from one infrastructure can access services from the other. The interoperability covers user identification and authentication as well as the transfer of the authorisation claims following the GA4GH Passport and AAI OpenID Connect protocol (OIDC) profile specifications.

https://doi.org/10.5281/zenodo.3938916

Deliverables, WP2Leslie GlassJuly 29, 2020WP2

Discovery Service Catalog - D1.1

CINECA aims to support the federated queries and analyses of distributed cohorts across continents. A vital component of this work is building a machine readable catalogue of cohorts and sites that support the efforts of Work Package 1 discovery and analysis APIs, which can be programmatically queried so that API calls can be made to relevant sites and results gathered and presented to the researcher.

Deliverable D1.1, Discovery Service Catalogue, supports the work of dependent work packages by implementing and demonstrating an open-source extended implementation of the Service Registry standard of the Global Alliance for Genomics and Health (GA4GH) for WP1’s discovery queries, the GA4GH Beacon queries. The Service Registry standard is now supported by the ELIXIR Beacon Network that CINECA WP1 uses to federate discovery queries across cohorts, and this demonstrator deliverable demonstrates the use of the service registry and its open source implementation.

https://doi.org/10.5281/zenodo.3908397

DeliverablesLeslie GlassJune 30, 2020WP1

Report of the CINECA Kick-off Meeting - D8.1

The CINECA consortium was formed in response to the EU call ‘Better Health and care, economic growth and sustainable health systems’ (H2020-SC1-BHC-2018-2020) with a proposal for an international collaboration with Canada and Africa for a federated cloud enabled infrastructure making population scale genomic and biomolecular data accessible across international borders. The CINECA consortium will create one of the largest cross-continental implementations of human genetic and phenotypic data federation and interoperability with a focus on common (complex) disease, one of the world’s most significant health burdens.

The CINECA Kick off meeting was held on January 24th-25th 2019 at the Wellcome Genome Campus Conference Centre, Hinxton UK. The key objective of the meeting was to bring together consortium members to facilitate discussion on the project’s goals and action plan. The report focuses on an overview of the Work Packages as presented to the consortium (focusing on deliverables due in the first reporting period), the cohorts included in the project, and the decisions made by the Executive Board for actions to implement in year 1 of the project.

https://doi.org/10.5281/zenodo.3908145

Deliverables, WP8Leslie GlassMay 30, 2020

Report on trust model for partner sites, and between sites and controlled-access researchers - D4.1

In this deliverable, we report on the activities for Deliverable 4.1 - Report on trust model for partner sites, and between sites and controlled-access researchers. The Work Package 4 (WP4) goals concern the development of a set of tools that can facilitate federated analyses of new and diverse genetic and genomic datasets, based on specific use cases. The tools selected will be using the common federated infrastructure established in WP1 and WP2, and the datasets will be described with metadata standards identified in WP3.

In our report we considered trust as the extent to which one party is willing to depend on the other party in a given situation with a feeling of relative security, even though negative consequences are possible. This work has contributed towards establishing a description of the trust model and four different levels of data access concerning specific cohort’s data, identifying use cases for the development of federated analysis workflows and describing existing data access models to inspire subsequent WP4 deliverables related to the implementation of the federated analysis workflow. Active communication and engagement of several WP4 members in other CINECA work packages enabled the inclusion in this document of other aspects of the CINECA cohort data access model. Examples include the WP2 cohort survey, the Data Use Ontology framework that was adopted by WP3 and by WP1, and WP5 provided input on the harmonisation and formalisation of clinical use cases.

https://doi.org/10.5281/zenodo.3909521

Deliverables, WP4Leslie GlassJanuary 31, 2020

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