CINECA Virtual Platform

Learning Pathway
Federated Analysis
     Platform

Federated Data Discovery

CINECA aims to accelerate disease research and improve health by facilitating transcontinental human data exchange, empowering researchers to analyse data across cohorts. A key first step is to have a platform that enables discovery queries across all of these cohorts to enable researchers to discover relevant samples, patient data, and cohorts which merit closer examination for their particular research questions.

Once discovered, simple interactive analyses on those subsets of data (extended queries) should be enabled, so that researchers can ask questions such as "what fraction of these patients that underwent this treatment had that outcome?”. Then, researchers must be able to hand off these subsets to services which allow batch-mode computationally intensive workflows to run on the data subsets.

Finally, underlying the ability to connect these queries across all of the cohorts, datasets, and services provided by CINECA sites and cohorts, there must be a Service Catalog of available datasets and services available to the platform, which can be queried directly (“what cohorts of population size larger than 1000 are available?”) or indirectly (powering the federated Discovery or Extended queries).

  • Beacon is a genomics discovery tool that allows the search of genomic variants and associated information without jeopardising the privacy of the dataset. CINECA has been involved in the creation of 4 Beacon endpoints at the European Genome-Phenome Archive (EGA) in UK, at the Center for Scientific Computing (CSC) in Finland, at the Canadian Centre for Computational Genomics (C3G) in Canada, and at the Human Heredity and Health in Africa (H3Africa) in Africa.

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  • CINECA has implemented a Query Expansion Service in the Beacon query, a system to expand the Beacon user’s search by using ontologies and a data driven approach, where search terms are expanded to similar concepts in other ontologies.

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  • The Federated Discovery Portal is a user Interface to facilitate the user’s Beacon queries, which includes a search box to perform Beacon queries, the Query Expansion Services to improve the results obtained, and allows users to fine-tune several parameters to shape the desired response.

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