Posts tagged metadata
"How FAIR are You" webinar series and hackathon
"How FAIR are You" webinar series and hackathon

This month’s blog was written by Nicola Mulder, Professor and head of the Computational Biology division at the University of Cape Town, and Principal investigator of H3ABioNet, a Pan African bioinformatics network for H3Africa, and Mamana Mbiyavanga, a Bioinformatics Scientist and PhD student at UCT, who contribute to a diverse range of CINECA work packages. This blog is less of a technical report in our Global Alliance for Genomics and Health (GA4GH) standards series than the previous 4, and more of a report on how WP6 - ‘Outreach, training and dissemination’ is contributing to developing better implementation of GA4GH standards.

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CINECA Short Reports, Blog, WP6Nicola Mulder, Mamana Mbiyavanga (UCT)GA4GH, Data Access, metadata, Passport, authorisation, WP6, FAIR, FAIRness, Training materials, cohort data, software tools, FAIRsharing
Powering up data discovery and access using the Data Use Ontology
Powering up data discovery and access using the Data Use Ontology

This month’s blog was written by Melanie Courtot, metadata standards coordinator at EMBL-EBI and co-Work Package Lead of CINECA WP3 - Cohort Level Metadata Representation. This blog is the fourth in our Global Alliance for Genomics and Health (GA4GH) standards series, presenting an overview of how GA4GH standards are being developed and implemented by CINECA. In our April post about Passport, Mikael from CINECA WP2 explained the importance of controlled-access to protect sensitive data, federated data access in the cloud and how Passport enables researchers to authenticate - prove they are who they say they are.

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GA4GH standards series, CINECA Short Reports, Blog, WP3Melanie CourtotWP3, DUO, GA4GH, Data Access, Federated Data Sharing, metadata, Passport, authorisation, ontology, consent, data use ontology
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