Posts tagged cohort
CINECA Poster - GA4GH 9th Plenary
CINECA Poster - GA4GH 9th Plenary

In collaboration with other GA4GH-associated projects, CINECA is developing infrastructure which will permit effective use of widely-dispersed data increasing the size and quality of datasets available for disease research. In alignment with community standards, using standardised interfaces, data analysis will be federated and migrated to the data, respecting data access restrictions.
Solutions CINECA is adopting from the Discovery Work Stream include the Data Connect and Beacon v2 API, while from the DURI and Data Security Work Streams the GA4GH Passports, AAI and DUO are being utilised.

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CINECA Short Reports, Blog, WP4Mamana MbiyavangaWP6, FAIR, wp4, federated analysis, GA4GH TES, TESK, Nextflow, cohort, pipeline Comments
Joint Variant genotyping use case
Joint Variant genotyping use case

Recently WP4 has delivered a simple demonstrator pipeline to perform a federated joint variant genotyping analysis. The goal of this use case is to demonstrate how a simple metric (in this case, allele frequency) can be computed in a federated manner, without requiring ever collecting the individual level data in a central location.

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CINECA Short Reports, Blog, WP4Elisa Cirillo, Álvaro González, Kirill TsukanovWP6, FAIR, wp4, federated analysis, GA4GH TES, TESK, Nextflow, cohort, pipeline Comment
Assigning standard descriptors to free text
Assigning standard descriptors to free text

This post is part of a series on a text-mining pipeline being developed by CINECA in Work Package 3. In previous instalments, first, Zooma and Curami pipelines were explained in "Uncovering metadata from semi-structured cohort data". Then, LexMapr was introduced in "LexMapr - A rule-based text-mining tool for ontology term mapping and classification". In this third instalment we are going to explain the normalisation pipeline developed at SIB/HES-SO.

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Text-mining series, CINECA Short Reports, WP3, BlogJenny Copara, SIB/HES-SOtext mining, zooma, metadata, cohort, ontology, WP3
LexMapr - A rule-based text-mining tool for ontology term mapping and classification
LexMapr - A rule-based text-mining tool for ontology term mapping and classification

The initial focus of LexMapr development has been on providing a text-mining tool to clean up the short free-text biosample metadata that contained inconsistent punctuation, abbreviations and typos, and to map the identified entities to standard terms from ontologies. This blog is the second in a series on text-mining in CINECA. For the previous instalment "Uncovering metadata from semi-structured cohort data" please click here.

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Text-mining series, CINECA Short Reports, WP3, BlogGurinder Gosal, University of British Columbiacohort, ontology, text mining, metadata, WP3
Uncovering metadata from semi-structured cohort data
Uncovering metadata from semi-structured cohort data

Harmonisation of attributes across different cohorts is very challenging and labour intensive, but critical to leverage the collective potential of the data. The CINECA text mining group aims to provide common tools and methods to extract additional metadata from structured and semi-structured fields in cohorts’ data.

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Text-mining series, CINECA Short Reports, WP3, BlogIsuru Liyanagetext mining, metadata, ontology, cohort, WP3
CINECA: Sharing patient genomic and biomolecular data across continents
CINECA: Sharing patient genomic and biomolecular data across continents

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.

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CINECA Short Reports, BlogElisa Cirillofederated, cohort, cloud, network, use-cases