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.

Text-mining series, CINECA Short Reports, WP3, BlogJenny Copara, SIB/HES-SONovember 3, 2020text mining, zooma, metadata, cohort, ontology, WP3

NanoGalaxy: Nanopore long-read sequencing data analysis in Galaxy

Willem de Koning, Milad Miladi, Saskia Hiltemann, Astrid Heikema, John P Hays, Stephan Flemming, Marius van den Beek, Dana A Mustafa, Rolf Backofen, Björn Grüning, Andrew P Stubbs

In this paper, de Koning, et al describe “NanoGalaxy", a Galaxy-based toolkit for analysing long-read sequencing data, suitable for diverse applications, including de novo genome assembly from genomic, metagenomic, and plasmid sequence reads.Read the full publication here.

https://doi.org/10.1093/gigascience/giaa105

Publications, WP5October 17, 2020

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.

CanDIG and ELIXIR AAI interoperability demonstration - CanDIG user accessing ELIXIR service

This video demonstrates the CanDIG and ELIXIR AAI interoperability.

CINECA Short Videos, WP2Guest UserSeptember 21, 2020WP2

CanDIG and ELIXIR AAI interoperability demonstration - ELIXIR user accessing CanDIG service

This video demonstrates the CanDIG and ELIXIR AAI interoperability..

CINECA Short Videos, WP2Guest UserSeptember 21, 2020WP2

CINECA Discovery Service Catalog - Technical Walkthrough - Beacon Integration

This video demonstrates how a service registry can operate with additional functionality when integrated more closely with the services providing queries (here, Beacon queries).

CINECA Short VideosGuest UserSeptember 21, 2020training materials, WP1

CINECA Discovery Service Catalog - Technical Walkthrough - Standalone Service

This video demonstrates how a standalone service registry operates, and our extensions to the service info and service registry standards to include cohort-level metadata.

CINECA Short VideosGuest UserSeptember 21, 2020WP1, training materials