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dc.contributor.author
Caucheteur, Déborah
dc.contributor.author
Gobeill, Julien
dc.contributor.author
Mottaz, Anaïs
dc.contributor.author
Pasche, Emilie
dc.contributor.author
Michel, Pierre-André
dc.contributor.author
Mottin, Luc
dc.contributor.author
Stekhoven, Daniel J.
dc.contributor.author
Barbié, Valérie
dc.contributor.author
Ruch, Patrick
dc.contributor.editor
Pape-Haugaard, Louise B.
dc.contributor.editor
Lovis, Christian
dc.contributor.editor
Cort Madsen, Inge
dc.contributor.editor
Weber, Patrick
dc.contributor.editor
Hostrup Nielsen, Per
dc.contributor.editor
Scott, Philip
dc.date.accessioned
2021-01-26T14:52:46Z
dc.date.available
2020-07-02T02:49:42Z
dc.date.available
2020-07-07T09:43:43Z
dc.date.available
2020-07-07T09:51:07Z
dc.date.available
2020-07-07T12:03:35Z
dc.date.available
2021-01-26T14:52:46Z
dc.date.issued
2020
dc.identifier.isbn
978-1-64368-082-8
en_US
dc.identifier.isbn
978-1-64368-083-5
en_US
dc.identifier.issn
0926-9630
dc.identifier.issn
1879-8365
dc.identifier.other
10.3233/SHTI200288
en_US
dc.identifier.uri
http://hdl.handle.net/20.500.11850/424123
dc.identifier.doi
10.3929/ethz-b-000424123
dc.description.abstract
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.
en_US
dc.format
application/pdf
en_US
dc.language.iso
en
en_US
dc.publisher
IOS Press
en_US
dc.rights.uri
http://creativecommons.org/licenses/by-nc/4.0/
dc.subject
Precision medicine
en_US
dc.subject
Literature
en_US
dc.subject
Variant
en_US
dc.subject
Terminology
en_US
dc.subject
Text-mining
en_US
dc.title
Text-Mining Services of the Swiss Variant Interpretation Platform for Oncology
en_US
dc.type
Conference Paper
dc.rights.license
Creative Commons Attribution-NonCommercial 4.0 International
ethz.book.title
Digital Personalized Health and Medicine
en_US
ethz.journal.title
Studies in Health Technology and Informatics
ethz.journal.volume
270
en_US
ethz.journal.abbreviated
Stud. health technol. inform.
ethz.pages.start
884
en_US
ethz.pages.end
888
en_US
ethz.version.deposit
publishedVersion
en_US
ethz.event
30th Medical Informatics Europe Conference (MIE 2020) (cancelled)
en_US
ethz.event.location
Geneva, Switzerland
en_US
ethz.event.date
April 28 - May 1, 2020
en_US
ethz.notes
Conference cancelled due to Corona virus (COVID-19).
en_US
ethz.identifier.wos
ethz.identifier.scopus
ethz.publication.place
Amsterdam
en_US
ethz.publication.status
published
en_US
ethz.date.deposited
2020-07-02T02:49:51Z
ethz.source
SCOPUS
ethz.eth
yes
en_US
ethz.availability
Open access
en_US
ethz.rosetta.installDate
2020-07-07T09:43:59Z
ethz.rosetta.lastUpdated
2022-03-29T04:58:47Z
ethz.rosetta.versionExported
true
ethz.COinS
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