Search

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.

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.

euCanSHare deliverable D4.1 reporting on the opal software integration to euCanSHare Executive Summary: In order to support the data harmonization process to be achieved within euCanSHare as well as proper documentation of the harmonized datasets generated, it is essential to implement a data and metadata documentation, processing and management system. The OBiBa software suite (Opal, Mica and Agate) and harmonization and cataloguing resources (harmonization guidelines and metadata standards) developed by Maelstrom Research are used as key elements of the EuCanSHare system. OBiBa software infrastructures are implemented in Spain, Finland, Germany and Canada to form the EuCanSHare harmonization platform. The platform will be pilot tested in 2019-2020 and, where required, the software will be customized to serve the evolving needs of EuCanSHare. The deliverable is a software and this report is the written description and presentation of the software and its implementation in different environments to support EuCanSHare activities., This deliverable has been produced in the context of the euCanSHare ("An EU-Canada joint infrastructure for next-generation multi-Study Heart research") Research and Innovation Action, funded by the European Union's Horizon 2020 programme (grant agreement No 825903), the Canadian Institutes of Health Research (CIHR) and the Fonds de recherche du Québec – Santé under the framework of Canada‐EU Commission Flagship Collaboration for Human data storage, integration and sharing.