{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,12,18]],"date-time":"2025-12-18T19:41:28Z","timestamp":1766086888701},"reference-count":8,"publisher":"Oxford University Press (OUP)","issue":"22","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":1123,"URL":"http:\/\/creativecommons.org\/licenses\/by\/3.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2013,11,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: The Web Ontology Language (OWL) provides a sophisticated language for building complex domain ontologies and is widely used in bio-ontologies such as the Gene Ontology. The Prot\u00e9g\u00e9-OWL ontology editing tool provides a query facility that allows composition and execution of queries with the human-readable Manchester OWL syntax, with syntax checking and entity label lookup. No equivalent query facility such as the Prot\u00e9g\u00e9 Description Logics (DL) query yet exists in web form. However, many users interact with bio-ontologies such as chemical entities of biological interest and the Gene Ontology using their online Web sites, within which DL-based querying functionality is not available. To address this gap, we introduce the OntoQuery web-based query utility.<\/jats:p>\n               <jats:p>Availability and implementation:\u2003The source code for this implementation together with instructions for installation is available at http:\/\/github.com\/IlincaTudose\/OntoQuery. OntoQuery software is fully compatible with all OWL-based ontologies and is available for download (CC-0 license). The ChEBI installation, ChEBI OntoQuery, is available at http:\/\/www.ebi.ac.uk\/chebi\/tools\/ontoquery.<\/jats:p>\n               <jats:p>Contact: hastings@ebi.ac.uk<\/jats:p>","DOI":"10.1093\/bioinformatics\/btt514","type":"journal-article","created":{"date-parts":[[2013,9,6]],"date-time":"2013-09-06T00:39:36Z","timestamp":1378427976000},"page":"2955-2957","source":"Crossref","is-referenced-by-count":11,"title":["OntoQuery: easy-to-use web-based OWL querying"],"prefix":"10.1093","volume":"29","author":[{"given":"Ilinca","family":"Tudose","sequence":"first","affiliation":[{"name":"1 Cheminformatics and Metabolism, European Bioinformatics Institute, Cambridge, UK, 2Swiss Center for Affective Sciences, University of Geneva, Geneva, Switzerland and 3Evolutionary Bioinformatics, Swiss Institute of Bioinformatics, Lausanne, Romandy, Switzerland"}]},{"given":"Janna","family":"Hastings","sequence":"additional","affiliation":[{"name":"1 Cheminformatics and Metabolism, European Bioinformatics Institute, Cambridge, UK, 2Swiss Center for Affective Sciences, University of Geneva, Geneva, Switzerland and 3Evolutionary Bioinformatics, Swiss Institute of Bioinformatics, Lausanne, Romandy, Switzerland"},{"name":"1 Cheminformatics and Metabolism, European Bioinformatics Institute, Cambridge, UK, 2Swiss Center for Affective Sciences, University of Geneva, Geneva, Switzerland and 3Evolutionary Bioinformatics, Swiss Institute of Bioinformatics, Lausanne, Romandy, Switzerland"},{"name":"1 Cheminformatics and Metabolism, European Bioinformatics Institute, Cambridge, UK, 2Swiss Center for Affective Sciences, University of Geneva, Geneva, Switzerland and 3Evolutionary Bioinformatics, Swiss Institute of Bioinformatics, Lausanne, Romandy, Switzerland"}]},{"given":"Venkatesh","family":"Muthukrishnan","sequence":"additional","affiliation":[{"name":"1 Cheminformatics and Metabolism, European Bioinformatics Institute, Cambridge, UK, 2Swiss Center for Affective Sciences, University of Geneva, Geneva, Switzerland and 3Evolutionary Bioinformatics, Swiss Institute of Bioinformatics, Lausanne, Romandy, Switzerland"}]},{"given":"Gareth","family":"Owen","sequence":"additional","affiliation":[{"name":"1 Cheminformatics and Metabolism, European Bioinformatics Institute, Cambridge, UK, 2Swiss Center for Affective Sciences, University of Geneva, Geneva, Switzerland and 3Evolutionary Bioinformatics, Swiss Institute of Bioinformatics, Lausanne, Romandy, Switzerland"}]},{"given":"Steve","family":"Turner","sequence":"additional","affiliation":[{"name":"1 Cheminformatics and Metabolism, European Bioinformatics Institute, Cambridge, UK, 2Swiss Center for Affective Sciences, University of Geneva, Geneva, Switzerland and 3Evolutionary Bioinformatics, Swiss Institute of Bioinformatics, Lausanne, Romandy, Switzerland"}]},{"given":"Adriano","family":"Dekker","sequence":"additional","affiliation":[{"name":"1 Cheminformatics and Metabolism, European Bioinformatics Institute, Cambridge, UK, 2Swiss Center for Affective Sciences, University of Geneva, Geneva, Switzerland and 3Evolutionary Bioinformatics, Swiss Institute of Bioinformatics, Lausanne, Romandy, Switzerland"}]},{"given":"Namrata","family":"Kale","sequence":"additional","affiliation":[{"name":"1 Cheminformatics and Metabolism, European Bioinformatics Institute, Cambridge, UK, 2Swiss Center for Affective Sciences, University of Geneva, Geneva, Switzerland and 3Evolutionary Bioinformatics, Swiss Institute of Bioinformatics, Lausanne, Romandy, Switzerland"}]},{"given":"Marcus","family":"Ennis","sequence":"additional","affiliation":[{"name":"1 Cheminformatics and Metabolism, European Bioinformatics Institute, Cambridge, UK, 2Swiss Center for Affective Sciences, University of Geneva, Geneva, Switzerland and 3Evolutionary Bioinformatics, Swiss Institute of Bioinformatics, Lausanne, Romandy, Switzerland"}]},{"given":"Christoph","family":"Steinbeck","sequence":"additional","affiliation":[{"name":"1 Cheminformatics and Metabolism, European Bioinformatics Institute, Cambridge, UK, 2Swiss Center for Affective Sciences, University of Geneva, Geneva, Switzerland and 3Evolutionary Bioinformatics, Swiss Institute of Bioinformatics, Lausanne, Romandy, Switzerland"}]}],"member":"286","published-online":{"date-parts":[[2013,9,5]]},"reference":[{"key":"2023012810491769300_btt514-B1","article-title":"Smart: A web-based, ontology-driven, semantic web query answering application","volume-title":"Semantic Web Challenge, Vol. 295 of CEUR Workshop Proceedings","author":"Battista","year":"2007"},{"key":"2023012810491769300_btt514-B2","doi-asserted-by":"crossref","first-page":"D249","DOI":"10.1093\/nar\/gkp886","article-title":"Chemical entities of biological interest: an update","volume":"38","author":"de Matos","year":"2010","journal-title":"Nucleic Acids Res."},{"key":"2023012810491769300_btt514-B3","doi-asserted-by":"crossref","first-page":"D456","DOI":"10.1093\/nar\/gks1146","article-title":"The ChEBI reference database and ontology for biologically relevant chemistry: enhancements for 2013","volume":"41","author":"Hastings","year":"2013","journal-title":"Nucleic Acids Res."},{"key":"2023012810491769300_btt514-B4","article-title":"The OWL API: a Java API for working with OWL 2 ontologies","volume-title":"Proceedings of OWL Experiences and Directions 2009 (OWLED 2009)","author":"Horridge","year":"2009"},{"key":"2023012810491769300_btt514-B5","volume-title":"OWL 2 web ontology language manchester syntax","author":"Horridge","year":"2009"},{"key":"2023012810491769300_btt514-B6","first-page":"129","article-title":"Ontologies in bioinformatics and systems biology","volume-title":"Artificial Intelligence Methods And Tools For Systems Biology, volume 5 of Computational Biology","author":"Lambrix","year":"2004"},{"key":"2023012810491769300_btt514-B7","doi-asserted-by":"crossref","first-page":"187","DOI":"10.4137\/BBI.S451","article-title":"Ontologies for bioinformatics","volume":"2","author":"Schuurman","year":"2008","journal-title":"Bioinform. Biol. Insights"},{"key":"2023012810491769300_btt514-B8","doi-asserted-by":"crossref","first-page":"25","DOI":"10.1038\/75556","article-title":"Gene ontology: tool for the unification of biology","volume":"25","author":"The Gene Ontology Consortium","year":"2000","journal-title":"Nat. Genet."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/29\/22\/2955\/48898296\/bioinformatics_29_22_2955.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/29\/22\/2955\/48898296\/bioinformatics_29_22_2955.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,28]],"date-time":"2023-01-28T12:50:43Z","timestamp":1674910243000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/29\/22\/2955\/316713"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2013,9,5]]},"references-count":8,"journal-issue":{"issue":"22","published-print":{"date-parts":[[2013,11,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btt514","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2013,11,15]]},"published":{"date-parts":[[2013,9,5]]}}}