{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,12,2]],"date-time":"2025-12-02T15:19:37Z","timestamp":1764688777692},"reference-count":11,"publisher":"Oxford University Press (OUP)","issue":"20","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2010,10,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: A standard systems-based approach to biomarker and drug target discovery consists of placing putative biomarkers in the context of a network of biological interactions, followed by different \u2018guilt-by-association\u2019 analyses. The latter is typically done based on network structural features. Here, an alternative analysis approach in which the networks are analyzed on a \u2018semantic similarity\u2019 space is reported. Such information is extracted from ontology-based functional annotations. We present SimTrek, a Cytoscape plugin for ontology-based similarity assessment in biological networks.<\/jats:p>\n               <jats:p>Availability: \u00a0http:\/\/rosalind.infj.ulst.ac.uk\/SimTrek.html<\/jats:p>\n               <jats:p>Contact: \u00a0francisco.azuaje@crp-sante.lu<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btq477","type":"journal-article","created":{"date-parts":[[2010,8,28]],"date-time":"2010-08-28T00:40:38Z","timestamp":1282956038000},"page":"2643-2644","source":"Crossref","is-referenced-by-count":14,"title":["Ontology- and graph-based similarity assessment in biological networks"],"prefix":"10.1093","volume":"26","author":[{"given":"Haiying","family":"Wang","sequence":"first","affiliation":[{"name":"1 Computer Science Research Institute, School of Computing and Mathematics, University of Ulster and 2Laboratory of Cardiovascular Research, Public Research Centre for Health (CRP-Sant\u00e9), L-1150, Luxembourg"}]},{"given":"Huiru","family":"Zheng","sequence":"additional","affiliation":[{"name":"1 Computer Science Research Institute, School of Computing and Mathematics, University of Ulster and 2Laboratory of Cardiovascular Research, Public Research Centre for Health (CRP-Sant\u00e9), L-1150, Luxembourg"}]},{"given":"Francisco","family":"Azuaje","sequence":"additional","affiliation":[{"name":"1 Computer Science Research Institute, School of Computing and Mathematics, University of Ulster and 2Laboratory of Cardiovascular Research, Public Research Centre for Health (CRP-Sant\u00e9), L-1150, Luxembourg"}]}],"member":"286","published-online":{"date-parts":[[2010,8,27]]},"reference":[{"key":"2023012507564122700_B1","doi-asserted-by":"crossref","first-page":"ra10","DOI":"10.1126\/scisignal.2000008","article-title":"Fault diagnosis engineering of digital circuits can identify vulnerable molecules in complex cellular pathways","volume":"1","author":"Abdi","year":"2008","journal-title":"Sci. Signal."},{"key":"2023012507564122700_B2","first-page":"114","article-title":"Predictive integration of gene ontology-driven similarity and functional interactions","volume-title":"Proceedings of the 6th IEEE International Conference on Data Mining, Hong Kong","author":"Azuaje","year":"2006"},{"key":"2023012507564122700_B3","doi-asserted-by":"crossref","first-page":"1172","DOI":"10.1002\/jcb.21829","article-title":"Mitogenic roles of Gab1 and Grb10 as direct cellular partners in the regulation of MAP kinase signaling","volume":"105","author":"Deng","year":"2008","journal-title":"J. Cell Biochem."},{"key":"2023012507564122700_B4","first-page":"19","article-title":"Semantic similarity based on corpus statistics and lexical taxonomy","volume-title":"Proceedings of International Conference on Research in Computational Linguistics","author":"Jiang","year":"1997"},{"key":"2023012507564122700_B5","doi-asserted-by":"crossref","first-page":"560","DOI":"10.1038\/379560a0","article-title":"A Grb2-associated docking protein in EGF- and insulin-receptor signaling","volume":"379","author":"Holgado-Madruga","year":"1996","journal-title":"Nature"},{"key":"2023012507564122700_B6","first-page":"296","article-title":"An information-theoretic definition of similarity","volume-title":"Proceedings of 15th International Conference on Machine Learning","author":"Lin","year":"1998"},{"key":"2023012507564122700_B7","doi-asserted-by":"crossref","first-page":"1078","DOI":"10.1126\/science.1108876","article-title":"Formation of regulatory patterns during signal propagation in a mammalian cellular network","volume":"309","author":"Ma'ayan","year":"2005","journal-title":"Science"},{"key":"2023012507564122700_B8","doi-asserted-by":"crossref","first-page":"921","DOI":"10.1038\/nbt.1567","article-title":"How to visually interpret biological data using networks","volume":"27","author":"Merico","year":"2009","journal-title":"Nat. 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Biol."},{"key":"2023012507564122700_B10","first-page":"448","article-title":"Using information content to evaluate semantic similarity in a taxonomy","volume-title":"Proceedings of the 14th International Joint Conference on Artificial Intelligence","author":"Resnik","year":"1995"},{"key":"2023012507564122700_B11","doi-asserted-by":"crossref","first-page":"2498","DOI":"10.1101\/gr.1239303","article-title":"Cytoscape: a software environment for integrated models of biomolecular interaction networks","volume":"13","author":"Shannon","year":"2003","journal-title":"Genome Res."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/26\/20\/2643\/48853486\/bioinformatics_26_20_2643.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/26\/20\/2643\/48853486\/bioinformatics_26_20_2643.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,25]],"date-time":"2023-01-25T07:57:19Z","timestamp":1674633439000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/26\/20\/2643\/194210"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2010,8,27]]},"references-count":11,"journal-issue":{"issue":"20","published-print":{"date-parts":[[2010,10,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btq477","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2010,10,15]]},"published":{"date-parts":[[2010,8,27]]}}}