Mining clinical attributes of genomic variants through assisted literature curation in Egas.
The veritable deluge of biological data over recent years has led to the establishment of a considerable number of knowledge resources that compile curated information extracted from the literature and store it in structured form, facilitating its use and exploitation. In this article, we focus on the curation of inherited genetic variants and associated clinical attributes, such as zygosity, penetrance or inheritance mode, and describe the use of Egas for this task. Egas is a web-based platform for text-mining assisted literature curation that focuses on usability through modern design solutions and simple user interactions. Egas offers a flexible and customizable tool that allows defining the concept types and relations of interest for a given annotation task, as well as the ontologies used for normalizing each concept type. Further, annotations may be performed on raw documents or on the results of automated concept identification and relation extraction tools. Users can inspect, correct or remove automatic text-mining results, manually add new annotations, and export the results to standard formats. Egas is compatible with the most recent versions of Google Chrome, Mozilla Firefox, Internet Explorer and Safari and is available for use at https://demo.bmd-software.com/egas/Database URL: https://demo.bmd-software.com/egas/.
IEETA/DETI, University of Aveiro, Aveiro, 3810-193, Portugal aleixomatos@ua.pt.
Sérgio
S
Matos
BMD Software, Aveiro, Portugal.
David
D
Campos
IEETA/DETI, University of Aveiro, Aveiro, 3810-193, Portugal.
Renato
R
Pinho
IEETA/DETI, University of Aveiro, Aveiro, 3810-193, Portugal Department of Medical Sciences, iBiMED, University of Aveiro, Aveiro, 3810-193, Portugal.
Raquel M
RM
Silva
Matthew
M
Mort
Institute of Medical Genetics, Cardiff University, Heath Park, Cardiff, UK.
David N
DN
Cooper
IEETA/DETI, University of Aveiro, Aveiro, 3810-193, Portugal.
José Luís
JL
Oliveira
D000818:Animals; D066289:Data Curation / Q000379:methods*; D057225:Data Mining / Q000379:methods*; D006801:Humans; D020407:Internet; D014584:User-Computer Interface; D064878:Web Browser