Text-mining services of the Swiss variant interpretation platform for oncology

Caucheteur, Déborah (Haute école de gestion de Genève, HES-SO // Haute Ecole Spécialisée de Suisse Occidentale ; SIB Swiss Institute of Bioinformatics, Geneva, Switzerland) ; Gobeill, Julien (Haute école de gestion de Genève, HES-SO // Haute Ecole Spécialisée de Suisse Occidentale ; SIB Swiss Institute of Bioinformatics, Geneva, Switzerland) ; Mottaz, Anaïs (Haute école de gestion de Genève, HES-SO // Haute Ecole Spécialisée de Suisse Occidentale ; SIB Swiss Institute of Bioinformatics, Geneva, Switzerland) ; Pasche, Emilie (Haute école de gestion de Genève, HES-SO // Haute Ecole Spécialisée de Suisse Occidentale ; SIB Swiss Institute of Bioinformatics, Geneva, Switzerland) ; Michel, Pierre-André (Haute école de gestion de Genève, HES-SO // Haute Ecole Spécialisée de Suisse Occidentale ; SIB Swiss Institute of Bioinformatics, Geneva, Switzerland) ; Mottin, Luc (Haute école de gestion de Genève, HES-SO // Haute Ecole Spécialisée de Suisse Occidentale ; SIB Swiss Institute of Bioinformatics, Geneva, Switzerland) ; Stekhoven, Daniel J. (SIB Swiss Institute of Bioinformatics, Geneva, Switzerland ; ETHZ, Zürich, Switzerland) ; Barbié, Valérie (SIB Swiss Institute of Bioinformatics, Geneva, Switzerland) ; Ruch, Patrick (Haute école de gestion de Genève, HES-SO // Haute Ecole Spécialisée de Suisse Occidentale ; SIB Swiss Institute of Bioinformatics, Geneva, Switzerland)

The Swiss Variant Interpretation Platform for Oncology is a centralized, joint and curated database for clinical somatic variants piloted by a board of Swiss healthcare institutions and operated by the SIB Swiss Institute of Bioinformatics. To support this effort, SIB Text Mining designed a set of text analytics services. This report focuses on three of those services. First, the automatic annotations of the literature with a set of terminologies have been performed, resulting in a large annotated version of MEDLINE and PMC. Second, a generator of variant synonyms for single nucleotide variants has been developed using publicly available data resources, as well as patterns of non-standard formats, often found in the literature. Third, a literature ranking service enables to retrieve a ranked set of MEDLINE abstracts given a variant and optionally a diagnosis. The annotation of MEDLINE and PMC resulted in a total of respectively 785,181,199 and 1,156,060,212 annotations, which means an average of 26 and 425 annotations per abstract and full-text article. The generator of variant synonyms enables to retrieve up to 42 synonyms for a variant. The literature ranking service reaches a precision (P10) of 63%, which means that almost two-thirds of the top-10 returned abstracts are judged relevant. Further services will be implemented to complete this set of services, such as a service to retrieve relevant clinical trials for a patient and a literature ranking service for full-text articles.


Keywords:
Faculty:
Economie et Services
School:
HEG - Genève
Institute:
CRAG - Centre de Recherche Appliquée en Gestion
Subject(s):
Sciences de l'information
Publisher:
Amsterdam, The Netherlands, IOS Press
Date:
2020-01
Amsterdam, The Netherlands
IOS Press
Pagination:
Pp. 884-888
Published in:
Digital personalized health and medicine
Series Statement:
Studies in Health Technology and Informatics, vol. 270
Author of the book:
Pape-Haugaard, Louise B. ; Aalborg University, Denmark
DOI:
ISSN:
0926-9630
ISBN:
978-1-64368-082-8
Appears in Collection:



 Record created 2020-07-20, last modified 2020-07-24

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