{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,4,27]],"date-time":"2024-04-27T13:58:22Z","timestamp":1714226302218},"reference-count":21,"publisher":"Oxford University Press (OUP)","license":[{"start":{"date-parts":[[2023,4,1]],"date-time":"2023-04-01T00:00:00Z","timestamp":1680307200000},"content-version":"vor","delay-in-days":90,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100010661","name":"Horizon 2020 Framework Programme","doi-asserted-by":"publisher","award":["825775"],"id":[{"id":"10.13039\/100010661","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Elixir Data Platform"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,3,31]]},"abstract":"Abstract<\/jats:title>The curation of genomic variants requires collecting evidence not only in variant knowledge bases but also in the literature. However, some variants result in no match when searched in the scientific literature. Indeed, it has been reported that a significant subset of information related to genomic variants are not reported in the full text, but only in the supplementary materials associated with a publication. In the study, we present an evaluation of the use of supplementary data (SD) to improve the retrieval of relevant scientific publications for variant curation. Our experiments show that searching SD enables to significantly increase the volume of documents retrieved for a variant, thus reducing by \u223c63% the number of variants for which no match is found in the scientific literature. SD thus represent a paramount source of information for curating variants of unknown significance and should receive more attention by global research infrastructures, which maintain literature search engines.<\/jats:p>Database URL https:\/\/www.expasy.org\/resources\/variomes<\/jats:p>","DOI":"10.1093\/database\/baad017","type":"journal-article","created":{"date-parts":[[2023,4,1]],"date-time":"2023-04-01T06:08:35Z","timestamp":1680329315000},"source":"Crossref","is-referenced-by-count":1,"title":["Assessing the use of supplementary materials to improve genomic variant discovery"],"prefix":"10.1093","volume":"2023","author":[{"ORCID":"http:\/\/orcid.org\/0000-0002-9118-5762","authenticated-orcid":false,"given":"Emilie","family":"Pasche","sequence":"first","affiliation":[{"name":"BiTeM Group, Information Sciences, HES-SO\/HEG Geneva , rue de la Tambourine 17, Geneva, Carouge 1227, Switzerland"},{"name":"SIB Text Mining Group, Swiss Institute of Bioinformatics , rue de la Tambourine 17, Geneva, Carouge 1227, Switzerland"}]},{"ORCID":"http:\/\/orcid.org\/0000-0003-0080-9451","authenticated-orcid":false,"given":"Ana\u00efs","family":"Mottaz","sequence":"additional","affiliation":[{"name":"BiTeM Group, Information Sciences, HES-SO\/HEG Geneva , rue de la Tambourine 17, Geneva, Carouge 1227, Switzerland"},{"name":"SIB Text Mining Group, Swiss Institute of Bioinformatics , rue de la Tambourine 17, Geneva, Carouge 1227, Switzerland"}]},{"ORCID":"http:\/\/orcid.org\/0000-0001-9809-7741","authenticated-orcid":false,"given":"Julien","family":"Gobeill","sequence":"additional","affiliation":[{"name":"BiTeM Group, Information Sciences, HES-SO\/HEG Geneva , rue de la Tambourine 17, Geneva, Carouge 1227, Switzerland"},{"name":"SIB Text Mining Group, Swiss Institute of Bioinformatics , rue de la Tambourine 17, Geneva, Carouge 1227, Switzerland"}]},{"given":"Pierre-Andr\u00e9","family":"Michel","sequence":"additional","affiliation":[{"name":"BiTeM Group, Information Sciences, HES-SO\/HEG Geneva , rue de la Tambourine 17, Geneva, Carouge 1227, Switzerland"},{"name":"SIB Text Mining Group, Swiss Institute of Bioinformatics , rue de la Tambourine 17, Geneva, Carouge 1227, Switzerland"}]},{"ORCID":"http:\/\/orcid.org\/0000-0003-0800-544X","authenticated-orcid":false,"given":"D\u00e9borah","family":"Caucheteur","sequence":"additional","affiliation":[{"name":"BiTeM Group, Information Sciences, HES-SO\/HEG Geneva , rue de la Tambourine 17, Geneva, Carouge 1227, Switzerland"},{"name":"SIB Text Mining Group, Swiss Institute of Bioinformatics , rue de la Tambourine 17, Geneva, Carouge 1227, Switzerland"}]},{"ORCID":"http:\/\/orcid.org\/0000-0002-1272-7640","authenticated-orcid":false,"given":"Nona","family":"Naderi","sequence":"additional","affiliation":[{"name":"BiTeM Group, Information Sciences, HES-SO\/HEG Geneva , rue de la Tambourine 17, Geneva, Carouge 1227, Switzerland"},{"name":"SIB Text Mining Group, Swiss Institute of Bioinformatics , rue de la Tambourine 17, Geneva, Carouge 1227, Switzerland"}]},{"ORCID":"http:\/\/orcid.org\/0000-0002-3374-2962","authenticated-orcid":false,"given":"Patrick","family":"Ruch","sequence":"additional","affiliation":[{"name":"BiTeM Group, Information Sciences, HES-SO\/HEG Geneva , rue de la Tambourine 17, Geneva, Carouge 1227, Switzerland"},{"name":"SIB Text Mining Group, Swiss Institute of Bioinformatics , rue de la Tambourine 17, Geneva, Carouge 1227, Switzerland"}]}],"member":"286","published-online":{"date-parts":[[2023,3,31]]},"reference":[{"key":"2023040106083207200_","doi-asserted-by":"crossref","first-page":"D941","DOI":"10.1093\/nar\/gky1015","article-title":"COSMIC: the Catalogue Of Somatic Mutations In Cancer","volume":"47","author":"Tate","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"2023040106083207200_","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1200\/PO.17.00011","article-title":"OncoKB: a precision oncology knowledge base","volume":"2017","author":"Chakravarty","year":"2017","journal-title":"JCO Precis. 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