{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,9]],"date-time":"2026-04-09T03:32:46Z","timestamp":1775705566342,"version":"3.50.1"},"reference-count":78,"publisher":"Public Library of Science (PLoS)","issue":"7","license":[{"start":{"date-parts":[[2009,7,31]],"date-time":"2009-07-31T00:00:00Z","timestamp":1248998400000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"DOI":"10.1371\/journal.pcbi.1000443","type":"journal-article","created":{"date-parts":[[2009,7,30]],"date-time":"2009-07-30T18:16:13Z","timestamp":1248977773000},"page":"e1000443","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":628,"title":["Semantic Similarity in Biomedical Ontologies"],"prefix":"10.1371","volume":"5","author":[{"given":"Catia","family":"Pesquita","sequence":"first","affiliation":[]},{"given":"Daniel","family":"Faria","sequence":"additional","affiliation":[]},{"given":"Andr\u00e9 O.","family":"Falc\u00e3o","sequence":"additional","affiliation":[]},{"given":"Phillip","family":"Lord","sequence":"additional","affiliation":[]},{"given":"Francisco M.","family":"Couto","sequence":"additional","affiliation":[]}],"member":"340","published-online":{"date-parts":[[2009,7,31]]},"reference":[{"key":"ref1","doi-asserted-by":"crossref","first-page":"D258","DOI":"10.1093\/nar\/gkh036","article-title":"The Gene Ontology (GO) database and informatics resource.","volume":"32","year":"2004","journal-title":"Nucleic Acids Research"},{"key":"ref2","doi-asserted-by":"crossref","first-page":"i169","DOI":"10.1093\/bioinformatics\/bth921","article-title":"The gene ontology categorizer.","volume":"20","author":"C Joslyn","year":"2004","journal-title":"Bioinformatics"},{"key":"ref3","first-page":"17","article-title":"Development and application of a metric on semantic nets.","author":"R Rada","year":"1989"},{"key":"ref4","first-page":"133","article-title":"Verb semantics and lexical selection.","author":"Z Wu","year":"1994"},{"key":"ref5","article-title":"Lexical semantic relatedness and its application in natural language processing.","author":"A Budanitsky","year":"1999"},{"key":"ref6","article-title":"Using WordNet as a knowledge base for measuring semantic similarity between words.","author":"R Richardson","year":"1994"},{"key":"ref7","first-page":"1089","article-title":"An intrinsic information content metric for semantic similarity in wordnet.","author":"N Seco","year":"2004"},{"key":"ref8","first-page":"448","article-title":"Using information content to evaluate semantic similarity in a taxonomy.","author":"P Resnik","year":"1995"},{"key":"ref9","article-title":"Semantic similarity over the gene ontology: Family correlation and selecting disjunctive ancestors.","author":"FM Couto","year":"2005"},{"key":"ref10","article-title":"Semantic distance in wordnet: An experimental, application-oriented evaluation of five measures.","author":"A Budanitsky","year":"2001"},{"key":"ref11","first-page":"529","article-title":"A genetic similarity algorithm for searching the gene ontology terms and annotating anonymous protein sequences.","volume":"23","author":"R Othman","year":"2007","journal-title":"J Biomed Inform"},{"key":"ref12","doi-asserted-by":"crossref","first-page":"1275","DOI":"10.1093\/bioinformatics\/btg153","article-title":"Investigating semantic similarity measures across the Gene Ontology: the relationship between sequence and annotation.","volume":"19","author":"P Lord","year":"2003","journal-title":"Bioinformatics"},{"key":"ref13","first-page":"296","article-title":"An information-theoretic definition of similarity.","author":"D Lin","year":"1998"},{"key":"ref14","article-title":"Semantic similarity based on corpus statistics and lexical taxonomy.","author":"J Jiang","year":"1997"},{"key":"ref15","first-page":"601","article-title":"Semantic similarity measures as tools for exploring the gene ontology.","author":"P Lord","year":"2003"},{"key":"ref16","doi-asserted-by":"crossref","DOI":"10.1186\/1471-2105-7-302","article-title":"A new measure for functional similarity of gene products based on gene ontology.","volume":"7","author":"A Schlicker","year":"2006","journal-title":"BMC Bioinformatics"},{"key":"ref17","first-page":"91","article-title":"Non-lexical approaches to identifying associative relations in the gene ontology.","author":"O Bodenreider","year":"2005","journal-title":"Pac Symp Biocomput"},{"key":"ref18","first-page":"99","article-title":"Xoa: Web-enabled cross-ontological analytics.","author":"RM Riensche","year":"2007"},{"key":"ref19","first-page":"1","article-title":"Taxonomy learning: factoring the structure of a taxonomy into a semantic classification decision.","author":"V Pekar","year":"2002"},{"key":"ref20","doi-asserted-by":"crossref","first-page":"75","DOI":"10.1016\/j.gene.2005.03.033","article-title":"Broadly predicting specific gene functions with expression similarity and taxonomy similarity.","volume":"352","author":"H Yu","year":"2005","journal-title":"Gene"},{"key":"ref21","doi-asserted-by":"crossref","first-page":"687","DOI":"10.1081\/BIP-200025659","article-title":"A knowledge-based clustering algorithm driven by gene ontology.","volume":"14","author":"J Cheng","year":"2004","journal-title":"Journal of Biopharmaceutical Statistics"},{"key":"ref22","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":"H Wu","year":"2005","journal-title":"Nucleic Acids Res"},{"key":"ref23","doi-asserted-by":"crossref","first-page":"2137","DOI":"10.1093\/nar\/gkl219","article-title":"Prediction of yeast proteinprotein interaction network: insights from the gene ontology and annotations.","volume":"34","author":"X Wu","year":"2006","journal-title":"Nucleic Acids Research"},{"key":"ref24","article-title":"Defining functional distances over gene ontology.","volume":"9","author":"AD Pozo","year":"2008","journal-title":"BMC Bioinformatics"},{"key":"ref25","article-title":"A new method to measure the semantic similarity of go terms.","author":"JZZ Wang","year":"2007","journal-title":"Bioinformatics"},{"key":"ref26","doi-asserted-by":"crossref","DOI":"10.1109\/TCBB.2005.50","article-title":"Correlation between gene expression and go semantic similarity.","author":"JL Sevilla","year":"2005"},{"key":"ref27","article-title":"Ontology-driven similarity approaches to supporting gene functional assessment.","author":"F Azuaje","year":"2005"},{"key":"ref28","doi-asserted-by":"crossref","first-page":"529","DOI":"10.1093\/bioinformatics\/btm195","article-title":"Information theory applied to the sparse gene ontology annotation network to predict novel gene function.","volume":"23","author":"Y Tao","year":"2007","journal-title":"Bioinformatics"},{"key":"ref29","article-title":"Assessing protein similarity with gene ontology and its use in subnuclear localization prediction.","volume":"7","author":"Z Lei","year":"2006","journal-title":"BMC Bioinformatics"},{"key":"ref30","doi-asserted-by":"crossref","first-page":"1085","DOI":"10.1101\/gr.1910904","article-title":"Coexpression analysis of human genes across many microarray data sets.","volume":"14","author":"HK Lee","year":"2004","journal-title":"Genome Res"},{"key":"ref31","doi-asserted-by":"crossref","DOI":"10.1186\/1471-2105-9-327","article-title":"Gene ontology term overlap as a measure of gene functional similarity.","volume":"9","author":"M Mistry","year":"2008","journal-title":"BMC Bioinformatics"},{"key":"ref32","doi-asserted-by":"crossref","DOI":"10.1186\/gb-2004-5-12-r101","article-title":"Gotoolbox: functional analysis of gene datasets based on gene ontology.","volume":"5","author":"D Martin","year":"2004","journal-title":"Genome Biol"},{"key":"ref33","article-title":"Visualizing and Distances Using GO.","author":"R Gentleman","year":"2005"},{"key":"ref34","article-title":"Evaluating gobased semantic similarity measures.","author":"C Pesquita","year":"2007"},{"key":"ref35","first-page":"msb4100034\u2013E1","article-title":"Gene function prediction from congruent synthetic lethal interactions in yeast.","volume":"1","author":"P Ye","year":"2005","journal-title":"Molecular Systems Biology"},{"key":"ref36","doi-asserted-by":"crossref","first-page":"265+","DOI":"10.1186\/1471-2105-8-265","article-title":"Semantic integration to identify overlapping functional modules in protein interaction networks.","volume":"8","author":"YR Cho","year":"2007","journal-title":"BMC Bioinformatics"},{"key":"ref37","article-title":"Information assessment on predicting protein-protein interactions.","volume":"5","author":"N Lin","year":"2004","journal-title":"BMC Bioinformatics"},{"key":"ref38","article-title":"Developing a similarity measure in biological function space.","author":"H Yu","year":"2007","journal-title":"Bioinformatics"},{"key":"ref39","doi-asserted-by":"crossref","DOI":"10.1186\/1471-2105-9-468","article-title":"A relation based measure of semantic similarity for gene ontology annotations.","volume":"9","author":"B Sheehan","year":"2008","journal-title":"BMC Bioinformatics"},{"key":"ref40","doi-asserted-by":"crossref","first-page":"R183+","DOI":"10.1186\/gb-2007-8-9-r183","article-title":"David gene functional classification tool: A novel biological modulecentric algorithm to functionally analyze large gene list.","volume":"8","author":"DW Huang","year":"2007","journal-title":"Genome Biology"},{"key":"ref41","doi-asserted-by":"crossref","first-page":"235","DOI":"10.1186\/1471-2105-8-235","article-title":"A transversal approach to predict gene product networks from ontology-based similarity.","volume":"2","author":"J Chabalier","year":"2007","journal-title":"BMC Bioinformatics"},{"key":"ref42","first-page":"25","article-title":"Gene expression correlation and gene ontology-based similarity: an assessment of quantitative relationships.","author":"H Wang","year":"2004"},{"key":"ref43","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":"X Guo","year":"2006","journal-title":"Bioinformatics"},{"key":"ref44","doi-asserted-by":"crossref","DOI":"10.1186\/1471-2105-9-S5-S4","article-title":"Metrics for go based protein semantic similarity: a systematic evaluation.","volume":"9","author":"C Pesquita","year":"2008","journal-title":"BMC Bioinformatics"},{"key":"ref45","article-title":"Evaluation of go-based functional similarity measures using s. cerevisiae protein interaction and expression profile data.","volume":"9","author":"T Xu","year":"2008","journal-title":"BMC Bioinformatics"},{"key":"ref46","article-title":"Implementation of a functional semantic similarity measure between gene-products.","author":"F Couto","year":"2003"},{"key":"ref47","article-title":"Proteinon: A web tool for protein semantic similarity.","author":"D Faria","year":"2007"},{"key":"ref48","first-page":"gkm806+","article-title":"Funsimmat: a comprehensive functional similarity database.","author":"A Schlicker","year":"2007","journal-title":"Nucl Acids Res"},{"key":"ref49","article-title":"Dyngo: a tool for visualizing and mining of gene ontology and its associations.","volume":"6","author":"H Liu","year":"2005","journal-title":"BMC bioinformatics"},{"key":"ref50","doi-asserted-by":"crossref","DOI":"10.1186\/1756-0381-1-11","article-title":"Fast gene ontology based clustering for microarray experiments.","volume":"1","author":"K Ovaska","year":"2008","journal-title":"BioData mining"},{"key":"ref51","doi-asserted-by":"crossref","first-page":"225","DOI":"10.1093\/bib\/bbl004","article-title":"Automated protein function prediction-the genomic challenge.","volume":"7","author":"I Friedberg","year":"2006","journal-title":"Briefings in Bioinformatics"},{"key":"ref52","first-page":"76","article-title":"The relationship between protein sequences and their gene ontology functions.","author":"ZH Duan","year":"2006"},{"key":"ref53","first-page":"msb4100034\u2013E1","article-title":"Gene function prediction from congruent synthetic lethal interactions in yeast.","volume":"1","author":"P Ye","year":"2005","journal-title":"Molecular Systems Biology"},{"key":"ref54","doi-asserted-by":"crossref","first-page":"113","DOI":"10.1016\/j.gene.2006.12.008","article-title":"Globally predicting protein functions based on co-expressed protein-protein interaction networks and ontology taxonomy similarities.","volume":"391","author":"M Zhu","year":"2007","journal-title":"Gene"},{"key":"ref55","article-title":"Predicting gene ontology functions from protein's regional surface structures.","volume":"8","author":"ZP Liu","year":"2007","journal-title":"BMC Bioinformatics"},{"key":"ref56","article-title":"Evaluation of highthroughput functional categorization of human disease genes.","volume":"8","author":"JL Chen","year":"2007","journal-title":"BMC Bioinformatics"},{"key":"ref57","doi-asserted-by":"crossref","first-page":"19","DOI":"10.1186\/1747-5333-1-19","article-title":"Goannotator: linking protein go annotations to evidence text.","volume":"1","author":"F Couto","year":"2006","journal-title":"Journal of Biomedical Discovery and Collaboration"},{"key":"ref58","doi-asserted-by":"crossref","first-page":"2739","DOI":"10.1093\/bioinformatics\/bti406","article-title":"Modularized learning of genetic interaction networks from biological annotations and mrna expression data.","volume":"21","author":"PH Lee","year":"2005","journal-title":"Bioinformatics"},{"key":"ref59","doi-asserted-by":"crossref","first-page":"2076","DOI":"10.1093\/bioinformatics\/bti273","article-title":"Online predicted human interaction database.","volume":"21","author":"KR Brown","year":"2005","journal-title":"Bioinformatics"},{"key":"ref60","article-title":"Choosing negative examples for the prediction of protein-protein interactions.","volume":"7","author":"AB Hur","year":"2006","journal-title":"BMC Bioinformatics"},{"key":"ref61","doi-asserted-by":"crossref","DOI":"10.1186\/1471-2105-8-262","article-title":"False positive reduction in protein-protein interaction predictions using gene ontology annotations.","volume":"8","author":"MA Mahdavi","year":"2007","journal-title":"BMC Bioinformatics"},{"key":"ref62","doi-asserted-by":"crossref","first-page":"5","DOI":"10.1109\/TSMCB.2007.908912","article-title":"Integration of genomic data for inferring protein complexes from global protein-protein interaction networks.","volume":"38","author":"H Zheng","year":"2008","journal-title":"IEEE Trans Syst Man Cybern B Cybern"},{"key":"ref63","article-title":"B.: Gosap: Gene ontology based semantic alignment of biological pathways.","author":"J Gamalielsson","year":"2005"},{"key":"ref64","doi-asserted-by":"crossref","first-page":"948","DOI":"10.1002\/prot.21071","article-title":"Combining functional and topological properties to identify core modules in protein interaction networks.","volume":"64","author":"Z Lubovac","year":"2006","journal-title":"Proteins: Structure, Function, and Bioinformatics"},{"key":"ref65","article-title":"Dynamic modularity in protein interaction networks predicts breast cancer outcome.","author":"IWW Taylor","year":"2009","journal-title":"Nature biotechnology"},{"key":"ref66","first-page":"252","article-title":"A memetic clustering algorithm for the functional partition of genes based on the gene ontology.","author":"N Speer","year":"2004"},{"key":"ref67","first-page":"389","article-title":"An ontology-driven clustering method for supporting gene expression analysis.","author":"H Wang","year":"2005"},{"key":"ref68","first-page":"555","article-title":"Incorporating gene ontology in clustering gene expression data.","author":"R Kustra","year":"2006"},{"key":"ref69","doi-asserted-by":"crossref","DOI":"10.1186\/1471-2105-7-338","article-title":"Cluster analysis of protein array results via similarity of gene ontology annotation.","volume":"7","author":"C Wolting","year":"2006","journal-title":"BMC Bioinformatics"},{"key":"ref70","doi-asserted-by":"crossref","first-page":"566","DOI":"10.1093\/bioinformatics\/btk019","article-title":"Improving missing value estimation in microarray data with gene ontology.","volume":"22","author":"J Tuikkala","year":"2006","journal-title":"Bioinformatics"},{"key":"ref71","doi-asserted-by":"crossref","first-page":"228","DOI":"10.1109\/TNB.2005.853657","article-title":"Multiple svm-rfe for gene selection in cancer classification with expression data.","volume":"4","author":"KB Duan","year":"2005","journal-title":"IEEE Trans Nanobioscience"},{"key":"ref72","doi-asserted-by":"crossref","first-page":"1213","DOI":"10.1016\/j.str.2005.05.009","article-title":"Connecting the protein structure universe by using sparse recurring fragments.","volume":"13","author":"I Friedberg","year":"2005","journal-title":"Structure"},{"key":"ref73","doi-asserted-by":"crossref","first-page":"103","DOI":"10.1186\/1471-2164-7-103","article-title":"Transcriptome coexpression map of human embryonic stem cells.","volume":"7","author":"H Li","year":"2006","journal-title":"BMC Genomics"},{"key":"ref74","doi-asserted-by":"crossref","first-page":"911","DOI":"10.1016\/j.jmb.2005.08.067","article-title":"Domain rearrangements in protein evolution.","volume":"353","author":"AK Bjorklund","year":"2005","journal-title":"Journal of Molecular Biology"},{"key":"ref75","doi-asserted-by":"crossref","first-page":"365","DOI":"10.1093\/abbs\/36.5.365","article-title":"Semantic search among heterogeneous biological databases based on gene ontology.","volume":"36","author":"S Cao","year":"2004","journal-title":"Acta Biochim Biophys Sin (Shanghai)"},{"key":"ref76","doi-asserted-by":"crossref","DOI":"10.1186\/1471-2164-9-S1-S10","article-title":"Semantically linking and browsing pubmed abstracts with gene ontology.","volume":"9","author":"B Vanteru","year":"2008","journal-title":"BMC Genomics"},{"key":"ref77","doi-asserted-by":"crossref","first-page":"D262","DOI":"10.1093\/nar\/gkh021","article-title":"The gene ontology annotation (goa) database: sharing knowledge in uniprot with gene ontology.","volume":"32","author":"E Camon","year":"2004","journal-title":"Nucleic Acids Research"},{"key":"ref78","doi-asserted-by":"crossref","DOI":"10.1186\/1471-2105-6-S1-S17","article-title":"An evaluation of go annotation retrieval for biocreative and goa.","volume":"6","author":"EB Camon","year":"2005","journal-title":"BMC Bioinformatics"}],"container-title":["PLoS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pcbi.1000443","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2018,10,23]],"date-time":"2018-10-23T10:32:02Z","timestamp":1540290722000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1000443"}},"subtitle":[],"editor":[{"given":"Philip E.","family":"Bourne","sequence":"first","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2009,7,31]]},"references-count":78,"journal-issue":{"issue":"7","published-online":{"date-parts":[[2009,7,31]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1000443","relation":{"has-review":[{"id-type":"doi","id":"10.3410\/f.720907669.793528728","asserted-by":"object"}]},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2009,7,31]]}}}