{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,26]],"date-time":"2026-02-26T20:34:11Z","timestamp":1772138051831,"version":"3.50.1"},"reference-count":35,"publisher":"Oxford University Press (OUP)","issue":"9","license":[{"start":{"date-parts":[[2022,3,11]],"date-time":"2022-03-11T00:00:00Z","timestamp":1646956800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Swiss Personalized Health Network"},{"name":"BioMedIT infrastructure"},{"name":"SIBiLS"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,4,28]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>Identification and interpretation of clinically actionable variants is a critical bottleneck. Searching for evidence in the literature is mandatory according to ASCO\/AMP\/CAP practice guidelines; however, it is both labor-intensive and error-prone. We developed a system to perform triage of publications relevant to support an evidence-based decision. The system is also able to prioritize variants. Our system searches within pre-annotated collections such as MEDLINE and PubMed Central.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>We assess the search effectiveness of the system using three different experimental settings: literature triage; variant prioritization and comparison of Variomes with LitVar. Almost two-thirds of the publications returned in the top-5 are relevant for clinical decision-support. Our approach enabled identifying 81.8% of clinically actionable variants in the top-3. Variomes retrieves on average +21.3% more articles than LitVar and returns the same number of results or more results than LitVar for 90% of the queries when tested on a set of 803 queries; thus, establishing a new baseline for searching the literature about variants.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>Variomes is publicly available at https:\/\/candy.hesge.ch\/Variomes. Source code is freely available at https:\/\/github.com\/variomes\/sibtm-variomes. SynVar is publicly available at https:\/\/goldorak.hesge.ch\/synvar.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Supplementary information<\/jats:title>\n                    <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btac146","type":"journal-article","created":{"date-parts":[[2022,3,10]],"date-time":"2022-03-10T07:14:28Z","timestamp":1646896468000},"page":"2595-2601","source":"Crossref","is-referenced-by-count":10,"title":["Variomes: a high recall search engine to support the curation of genomic variants"],"prefix":"10.1093","volume":"38","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-9118-5762","authenticated-orcid":false,"given":"Emilie","family":"Pasche","sequence":"first","affiliation":[{"name":"SIB Text Mining Group, Swiss Institute of Bioinformatics , 1206 Geneva, Switzerland"},{"name":"BiTeM Group, Information Sciences, HES-SO\/HEG , 1227 Carouge, Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0080-9451","authenticated-orcid":false,"given":"Ana\u00efs","family":"Mottaz","sequence":"additional","affiliation":[{"name":"SIB Text Mining Group, Swiss Institute of Bioinformatics , 1206 Geneva, Switzerland"},{"name":"BiTeM Group, Information Sciences, HES-SO\/HEG , 1227 Carouge, Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0800-544X","authenticated-orcid":false,"given":"D\u00e9borah","family":"Caucheteur","sequence":"additional","affiliation":[{"name":"SIB Text Mining Group, Swiss Institute of Bioinformatics , 1206 Geneva, Switzerland"},{"name":"BiTeM Group, Information Sciences, HES-SO\/HEG , 1227 Carouge, Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9809-7741","authenticated-orcid":false,"given":"Julien","family":"Gobeill","sequence":"additional","affiliation":[{"name":"SIB Text Mining Group, Swiss Institute of Bioinformatics , 1206 Geneva, Switzerland"},{"name":"BiTeM Group, Information Sciences, HES-SO\/HEG , 1227 Carouge, Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Pierre-Andr\u00e9","family":"Michel","sequence":"additional","affiliation":[{"name":"SIB Text Mining Group, Swiss Institute of Bioinformatics , 1206 Geneva, Switzerland"},{"name":"BiTeM Group, Information Sciences, HES-SO\/HEG , 1227 Carouge, Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3374-2962","authenticated-orcid":false,"given":"Patrick","family":"Ruch","sequence":"additional","affiliation":[{"name":"SIB Text Mining Group, Swiss Institute of Bioinformatics , 1206 Geneva, Switzerland"},{"name":"BiTeM Group, Information Sciences, HES-SO\/HEG , 1227 Carouge, Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2022,3,11]]},"reference":[{"key":"2023041402563081400_","doi-asserted-by":"crossref","first-page":"W530","DOI":"10.1093\/nar\/gky355","volume":"46","author":"Allot","year":"2018","journal-title":"Nucleic Acids Res"},{"key":"2023041402563081400_","doi-asserted-by":"crossref","first-page":"W352","DOI":"10.1093\/nar\/gkab326","volume":"49","author":"Allot","year":"2021","journal-title":"Nucleic Acids Res"},{"key":"2023041402563081400_","first-page":"276","author":"Aslam","year":"2001"},{"key":"2023041402563081400_","doi-asserted-by":"crossref","first-page":"431","DOI":"10.1016\/0306-4573(94)00057-A","volume":"31","author":"Belkin","year":"1995","journal-title":"Inf. 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