{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,14]],"date-time":"2026-04-14T20:54:28Z","timestamp":1776200068579,"version":"3.50.1"},"reference-count":12,"publisher":"Oxford University Press (OUP)","issue":"10","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2007,5,15]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Motivation: Although controlled biochemical or biological vocabularies, such as Gene Ontology (GO) (http:\/\/www.geneontology.org), address the need for consistent descriptions of genes in different data sources, there is still no effective method to determine the functional similarities of genes based on gene annotation information from heterogeneous data sources.<\/jats:p><jats:p>Results: To address this critical need, we proposed a novel method to encode a GO term's semantics (biological meanings) into a numeric value by aggregating the semantic contributions of their ancestor terms (including this specific term) in the GO graph and, in turn, designed an algorithm to measure the semantic similarity of GO terms. Based on the semantic similarities of GO terms used for gene annotation, we designed a new algorithm to measure the functional similarity of genes. The results of using our algorithm to measure the functional similarities of genes in pathways retrieved from the saccharomyces genome database (SGD), and the outcomes of clustering these genes based on the similarity values obtained by our algorithm are shown to be consistent with human perspectives. Furthermore, we developed a set of online tools for gene similarity measurement and knowledge discovery.<\/jats:p><jats:p>Availability: The online tools are available at: http:\/\/bioinformatics.clemson.edu\/G-SESAME<\/jats:p><jats:p>Contact: \u00a0jzwang@cs.clemson.edu<\/jats:p><jats:p>Supplementary information: \u00a0http:\/\/bioinformatics.clemson.edu\/Publication\/Supplement\/gsp.htm<\/jats:p>","DOI":"10.1093\/bioinformatics\/btm087","type":"journal-article","created":{"date-parts":[[2007,3,8]],"date-time":"2007-03-08T01:12:41Z","timestamp":1173316361000},"page":"1274-1281","source":"Crossref","is-referenced-by-count":1103,"title":["A new method to measure the semantic similarity of GO terms"],"prefix":"10.1093","volume":"23","author":[{"given":"James Z.","family":"Wang","sequence":"first","affiliation":[{"name":"1 School of Computing, Clemson University, Clemson, SC 29634, USA, 2IBM T. J. Watson Research Center, 19 Skyline Drive, Hawthorne, NY 10532, USA and 3Department of Genetics and Biochemistry, Clemson University, Clemson, SC 29634, USA"}]},{"given":"Zhidian","family":"Du","sequence":"additional","affiliation":[{"name":"1 School of Computing, Clemson University, Clemson, SC 29634, USA, 2IBM T. J. Watson Research Center, 19 Skyline Drive, Hawthorne, NY 10532, USA and 3Department of Genetics and Biochemistry, Clemson University, Clemson, SC 29634, USA"}]},{"given":"Rapeeporn","family":"Payattakool","sequence":"additional","affiliation":[{"name":"1 School of Computing, Clemson University, Clemson, SC 29634, USA, 2IBM T. J. Watson Research Center, 19 Skyline Drive, Hawthorne, NY 10532, USA and 3Department of Genetics and Biochemistry, Clemson University, Clemson, SC 29634, USA"}]},{"given":"Philip S.","family":"Yu","sequence":"additional","affiliation":[{"name":"1 School of Computing, Clemson University, Clemson, SC 29634, USA, 2IBM T. J. Watson Research Center, 19 Skyline Drive, Hawthorne, NY 10532, USA and 3Department of Genetics and Biochemistry, Clemson University, Clemson, SC 29634, USA"}]},{"given":"Chin-Fu","family":"Chen","sequence":"additional","affiliation":[{"name":"1 School of Computing, Clemson University, Clemson, SC 29634, USA, 2IBM T. J. Watson Research Center, 19 Skyline Drive, Hawthorne, NY 10532, USA and 3Department of Genetics and Biochemistry, Clemson University, Clemson, SC 29634, USA"}]}],"member":"286","published-online":{"date-parts":[[2007,3,7]]},"reference":[{"key":"2023041104475921600_","doi-asserted-by":"crossref","first-page":"77","DOI":"10.1093\/nar\/28.1.77","article-title":"Integrating functional genomic information into the Saccharomyces Genome Database","volume":"28","author":"Ball","year":"2000","journal-title":"Nucleic Acids Res."},{"key":"2023041104475921600_","article-title":"Implementation of a Functional Semantic Similarity Measure between Gene-Products","volume-title":"DI\/FCUL TR 03-29","author":"Coute","year":"2003"},{"key":"2023041104475921600_","doi-asserted-by":"crossref","first-page":"967","DOI":"10.1093\/bioinformatics\/btl042","article-title":"Assessing semantic similarity measures for the characterization of human regulatory pathways","volume":"22","author":"Guo","year":"2006","journal-title":"Bioinformatics"},{"key":"2023041104475921600_","article-title":"Semantic Similarity Based on Corpus Statistics and Lexical Taxonomy","author":"Jiang","year":"1997"},{"key":"2023041104475921600_","doi-asserted-by":"crossref","first-page":"33","DOI":"10.1093\/nar\/29.1.33","article-title":"CluSTr: a database of clusters of SWISS-PROT+TrEMBL proteins","volume":"29","author":"Kriventseva","year":"2001","journal-title":"Nucleic Acids Res"},{"key":"2023041104475921600_","article-title":"Statistical hypothesis testing of associa-tion between two reporter lists within the GO-hierarchy","volume-title":"Technical report.","author":"Langaas","year":"2005"},{"key":"2023041104475921600_","doi-asserted-by":"crossref","first-page":"381","DOI":"10.1093\/bioinformatics\/btg420","article-title":"A graph-theoretic modeling on GO space for biological interpretation of gene clusters","volume":"20","author":"Lee","year":"2004","journal-title":"Bioinformatics"},{"key":"2023041104475921600_","first-page":"296","article-title":"An information-theoretic definition of similarity, Semantic Similarity Based on Corpus Statistics and Lexical Taxonomy","volume-title":"fifteenth International Conference on Machine Learning","author":"Lin","year":"1998"},{"key":"2023041104475921600_","doi-asserted-by":"crossref","first-page":"95","DOI":"10.1613\/jair.514","article-title":"Semantic similarity in a taxonomy: an information-based measure and its application to problems of ambiguity in natural language","volume":"11","author":"Resnik","year":"1999","journal-title":"J. Artificial Intelligence Res."},{"key":"2023041104475921600_","doi-asserted-by":"crossref","first-page":"330","DOI":"10.1109\/TCBB.2005.50","article-title":"Correlation between Gene Expression and GO Semantic Similarity","volume":"2","author":"Sevilla","year":"2005","journal-title":"IEEE\/ACM Transactions on Computational Biology and Bioinformatics"},{"key":"2023041104475921600_","first-page":"25","article-title":"Gene Expression Correlation and Gene Ontology-Based Similarity: An Assessment of Quantitative Relationships","author":"Wang","year":"2004"},{"key":"2023041104475921600_","doi-asserted-by":"crossref","first-page":"2822","DOI":"10.1093\/nar\/gki573","article-title":"Prediction of functional modules based on comparative genome analysis and Gene Ontology application","volume":"33","author":"Wu","year":"2005","journal-title":"Nucleic Acids Res."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/23\/10\/1274\/49812526\/bioinformatics_23_10_1274.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/23\/10\/1274\/49812526\/bioinformatics_23_10_1274.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,2,11]],"date-time":"2024-02-11T14:17:47Z","timestamp":1707661067000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/23\/10\/1274\/197095"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2007,3,7]]},"references-count":12,"journal-issue":{"issue":"10","published-print":{"date-parts":[[2007,5,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btm087","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2007,5,15]]},"published":{"date-parts":[[2007,3,7]]}}}