{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,7,30]],"date-time":"2025-07-30T11:43:44Z","timestamp":1753875824045,"version":"3.41.2"},"reference-count":25,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2022,12,13]],"date-time":"2022-12-13T00:00:00Z","timestamp":1670889600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"BICKL Research Project","award":["H2020-EU.1.4"],"award-info":[{"award-number":["H2020-EU.1.4"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,1,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Since early 2020, the coronavirus disease 2019 (COVID-19) pandemic has confronted the biomedical community with an unprecedented challenge. The rapid spread of COVID-19 and ease of transmission seen worldwide is due to increased population flow and international trade. Front-line medical care, treatment research and vaccine development also require rapid and informative interpretation of the literature and COVID-19 data produced around the world, with 177\u00a0500 papers published between January 2020 and November 2021, i.e. almost 8500 papers per month. To extract knowledge and enable interoperability across resources, we developed the COVID-19 Vocabulary (COVoc), an application ontology related to the research on this pandemic. The main objective of COVoc development was to enable seamless navigation from biomedical literature to core databases and tools of ELIXIR, a European-wide intergovernmental organization for life sciences.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>This collaborative work provided data integration into SIB Literature services, an application ontology (COVoc) and a triage service named COVTriage and based on annotation processing to search for COVID-related information across pre-defined aspects with daily updates. Thanks to its interoperability potential, COVoc lends itself to wider applications, hopefully through further connections with other novel COVID-19 ontologies as has been established with Coronavirus Infectious Disease Ontology.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>The data at https:\/\/github.com\/EBISPOT\/covoc and the service at https:\/\/candy.hesge.ch\/COVTriage.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btac800","type":"journal-article","created":{"date-parts":[[2022,12,13]],"date-time":"2022-12-13T13:17:15Z","timestamp":1670937435000},"source":"Crossref","is-referenced-by-count":3,"title":["COVoc and COVTriage: novel resources to support literature triage"],"prefix":"10.1093","volume":"39","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-0800-544X","authenticated-orcid":false,"given":"D\u00e9borah","family":"Caucheteur","sequence":"first","affiliation":[{"name":"SIB Text Mining Group, Swiss Institute of Bioinformatics , Geneva 1206, Switzerland"},{"name":"BiTeM Group, Information Sciences, HES-SO\/HEG Gen\u00e8ve , Carouge 1227, Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Zo\u00eb","family":"May Pendlington","sequence":"additional","affiliation":[{"name":"European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus , Cambridge CB10 1SD, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Paola","family":"Roncaglia","sequence":"additional","affiliation":[{"name":"European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus , Cambridge CB10 1SD, UK"}],"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 , Geneva 1206, Switzerland"},{"name":"BiTeM Group, Information Sciences, HES-SO\/HEG Gen\u00e8ve , Carouge 1227, Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9614-9293","authenticated-orcid":false,"given":"Luc","family":"Mottin","sequence":"additional","affiliation":[{"name":"SIB Text Mining Group, Swiss Institute of Bioinformatics , Geneva 1206, Switzerland"},{"name":"BiTeM Group, Information Sciences, HES-SO\/HEG Gen\u00e8ve , Carouge 1227, Switzerland"},{"name":"Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva , Geneva 1205, Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Nicolas","family":"Matentzoglu","sequence":"additional","affiliation":[{"name":"European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus , Cambridge CB10 1SD, UK"},{"name":"Semanticly Ltd , London, WC2H 9JQ, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Donat","family":"Agosti","sequence":"additional","affiliation":[{"name":"SIB Text Mining Group, Swiss Institute of Bioinformatics , Geneva 1206, Switzerland"},{"name":"Plazi , Bern 3007, Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7073-9172","authenticated-orcid":false,"given":"David","family":"Osumi-Sutherland","sequence":"additional","affiliation":[{"name":"European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus , Cambridge CB10 1SD, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Helen","family":"Parkinson","sequence":"additional","affiliation":[{"name":"European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus , Cambridge CB10 1SD, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Patrick","family":"Ruch","sequence":"additional","affiliation":[{"name":"SIB Text Mining Group, Swiss Institute of Bioinformatics , Geneva 1206, Switzerland"},{"name":"BiTeM Group, Information Sciences, HES-SO\/HEG Gen\u00e8ve , Carouge 1227, Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2022,12,13]]},"reference":[{"key":"2023010805401222300_btac800-B1","doi-asserted-by":"crossref","first-page":"25","DOI":"10.7171\/jbt.18-2902-002","article-title":"The cellosaurus, a cell-line knowledge resource","volume":"29","author":"Bairoch","year":"2018","journal-title":"J. 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