{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,5,14]],"date-time":"2025-05-14T04:27:52Z","timestamp":1747196872567,"version":"3.40.5"},"reference-count":38,"publisher":"Springer Science and Business Media LLC","issue":"S5","content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Syst Biol"],"published-print":{"date-parts":[[2014,12]]},"DOI":"10.1186\/1752-0509-8-s5-s8","type":"journal-article","created":{"date-parts":[[2014,12,12]],"date-time":"2014-12-12T12:07:40Z","timestamp":1418386060000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":15,"title":["An integrative approach for measuring semantic similarities using gene ontology"],"prefix":"10.1186","volume":"8","author":[{"given":"Jiajie","family":"Peng","sequence":"first","affiliation":[]},{"given":"Hongxiang","family":"Li","sequence":"additional","affiliation":[]},{"given":"Qinghua","family":"Jiang","sequence":"additional","affiliation":[]},{"given":"Yadong","family":"Wang","sequence":"additional","affiliation":[]},{"given":"Jin","family":"Chen","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2014,12,12]]},"reference":[{"key":"1407_CR1","doi-asserted-by":"publisher","first-page":"D530","DOI":"10.1093\/nar\/gks1050","volume":"41","author":"GO Consortium","year":"2013","unstructured":"Consortium GO: Gene Ontology annotations and resources. Nucleic acids research. 2013, 41: D530-D535.","journal-title":"Nucleic acids research"},{"key":"1407_CR2","doi-asserted-by":"publisher","first-page":"e1003343","DOI":"10.1371\/journal.pcbi.1003343","volume":"9","author":"J Blake","year":"2013","unstructured":"Blake J: Ten quick tips for using the gene ontology. PLoS computational biology. 2013, 9: e1003343-10.1371\/journal.pcbi.1003343.","journal-title":"PLoS computational biology"},{"key":"1407_CR3","doi-asserted-by":"publisher","first-page":"22","DOI":"10.1186\/1752-0509-7-22","volume":"7","author":"F Vafaee","year":"2013","unstructured":"Vafaee F, Rosu D, Broackes-Carter F, Jurisica I: Novel semantic similarity measure improves an integrative approach to predicting gene functional associations. BMC systems biology. 2013, 7: 22-10.1186\/1752-0509-7-22.","journal-title":"BMC systems biology"},{"key":"1407_CR4","doi-asserted-by":"publisher","first-page":"e1002073","DOI":"10.1371\/journal.pcbi.1002073","volume":"7","author":"N Nehrt","year":"2011","unstructured":"Nehrt N, Clark W, Radivojac P, Hahn M: Testing the ortholog conjecture with comparative functional genomic data from mammals. PLoS computational biology. 2011, 7: e1002073-10.1371\/journal.pcbi.1002073.","journal-title":"PLoS computational biology"},{"key":"1407_CR5","doi-asserted-by":"publisher","first-page":"787","DOI":"10.1016\/S0092-8674(03)01018-3","volume":"115","author":"B Lewis","year":"2003","unstructured":"Lewis B, Shih I, Jones-Rhoades M, Bartel D, Burge C: Prediction of mammalian microRNA targets. Cell. 2003, 115: 787-798. 10.1016\/S0092-8674(03)01018-3.","journal-title":"Cell"},{"key":"1407_CR6","doi-asserted-by":"crossref","unstructured":"Lu Z, Hunter L: GO molecular function terms are predictive of subcellular localization. PSB. 151-","DOI":"10.1142\/9789812702456_0015"},{"key":"1407_CR7","doi-asserted-by":"publisher","first-page":"1275","DOI":"10.1093\/bioinformatics\/btg153","volume":"19","author":"P Lord","year":"2003","unstructured":"Lord P, Stevens R, Brass A, Goble C: Investigating semantic similarity measures across the Gene Ontology: the relationship between sequence and annotation. Bioinformatics. 2003, 19: 1275-1283. 10.1093\/bioinformatics\/btg153.","journal-title":"Bioinformatics"},{"key":"1407_CR8","doi-asserted-by":"publisher","first-page":"687","DOI":"10.1081\/BIP-200025659","volume":"14","author":"J Cheng","year":"2004","unstructured":"Cheng J, Cline M, Martin J, Finkelstein D, Awad T, Kulp D, Siani-Rose M: A knowledge-based clustering algorithm driven by gene ontology. Journal of biopharmaceutical statistics. 2004, 14: 687-700. 10.1081\/BIP-200025659.","journal-title":"Journal of biopharmaceutical statistics"},{"key":"1407_CR9","doi-asserted-by":"crossref","first-page":"343","DOI":"10.1145\/1099554.1099658","volume-title":"CIKM","author":"F Couto","year":"2005","unstructured":"Couto F, Silva M, Coutinho P: Semantic similarity over the gene ontology: family correlation and selecting disjunctive ancestors. CIKM. 2005, 343-344."},{"key":"1407_CR10","first-page":"91","volume-title":"PSB","author":"O Bodenreider","year":"2005","unstructured":"Bodenreider O, Aubry M, Burgun A: Non-lexical approaches to identifying associative relations in the gene ontology. PSB. 2005, 91-"},{"key":"1407_CR11","doi-asserted-by":"publisher","first-page":"2822","DOI":"10.1093\/nar\/gki573","volume":"33","author":"H Wu","year":"2005","unstructured":"Wu H, Su Z, Mao F, Olman V, Xu Y: Prediction of functional modules based on comparative genome analysis and Gene Ontology application. Nucleic acids research. 2005, 33: 2822-2837. 10.1093\/nar\/gki573.","journal-title":"Nucleic acids research"},{"key":"1407_CR12","doi-asserted-by":"publisher","first-page":"75","DOI":"10.1016\/j.gene.2005.03.033","volume":"352","author":"H Yu","year":"2005","unstructured":"Yu H, Gao L, Tu K, Guo Z: Broadly predicting specific gene functions with expression similarity and taxonomy similarity. Gene. 2005, 352: 75-81.","journal-title":"Gene"},{"key":"1407_CR13","doi-asserted-by":"publisher","first-page":"302","DOI":"10.1186\/1471-2105-7-302","volume":"7","author":"A Schlicker","year":"2006","unstructured":"Schlicker A, Domingues F, Rahnenfhrer J, Lengauer T: A new measure for functional similarity of gene products based on Gene Ontology. BMC bioinformatics. 2006, 7: 302-10.1186\/1471-2105-7-302.","journal-title":"BMC bioinformatics"},{"key":"1407_CR14","first-page":"99","volume-title":"IEEE Congress on Services","author":"R Riensche","year":"2007","unstructured":"Riensche R, Baddeley B, Sanfilippo A, Posse C, Gopalan B: Xoa: Web-enabled cross-ontological analytics. IEEE Congress on Services. 2007, 99-105."},{"key":"1407_CR15","doi-asserted-by":"publisher","first-page":"1274","DOI":"10.1093\/bioinformatics\/btm087","volume":"23","author":"J Wang","year":"2007","unstructured":"Wang J, Du Z, Payattakool R, Philip S, Chen C: A new method to measure the semantic similarity of GO terms. Bioinformatics. 2007, 23: 1274-1281. 10.1093\/bioinformatics\/btm087.","journal-title":"Bioinformatics"},{"key":"1407_CR16","doi-asserted-by":"publisher","first-page":"2163","DOI":"10.1093\/bioinformatics\/btm291","volume":"23","author":"H Yu","year":"2007","unstructured":"Yu H, Jansen R, Stolovitzky G, Gerstein M: Total ancestry measure: quantifying the similarity in tree- like classification, with genomic applications. Bioinformatics. 2007, 23: 2163-2173. 10.1093\/bioinformatics\/btm291.","journal-title":"Bioinformatics"},{"key":"1407_CR17","doi-asserted-by":"publisher","first-page":"50","DOI":"10.1186\/1471-2105-9-50","volume":"9","author":"A del Pozo","year":"2008","unstructured":"del Pozo A, Pazos F, Valencia A: Defining functional distances over Gene Ontology. BMC bioinformatics. 2008, 9: 50-10.1186\/1471-2105-9-50.","journal-title":"BMC bioinformatics"},{"key":"1407_CR18","doi-asserted-by":"publisher","first-page":"e1000443","DOI":"10.1371\/journal.pcbi.1000443","volume":"5","author":"C Pesquita","year":"2009","unstructured":"Pesquita C, Faria D, Falcao A, Lord P, Couto F: Semantic similarity in biomedical ontologies. PLoS computational biology. 2009, 5: e1000443-10.1371\/journal.pcbi.1000443.","journal-title":"PLoS computational biology"},{"key":"1407_CR19","doi-asserted-by":"publisher","first-page":"65","DOI":"10.1016\/j.jbi.2007.05.010","volume":"41","author":"R Othman","year":"2008","unstructured":"Othman R, Deris S, Illias R: A genetic similarity algorithm for searching the Gene Ontology terms and annotating anonymous protein sequences. Journal of biomedical informatics. 2008, 41: 65-81. 10.1016\/j.jbi.2007.05.010.","journal-title":"Journal of biomedical informatics"},{"key":"1407_CR20","doi-asserted-by":"publisher","first-page":"1383","DOI":"10.1093\/bioinformatics\/bts129","volume":"28","author":"H Yang","year":"2012","unstructured":"Yang H, Nepusz T, Paccanaro A: Improving GO semantic similarity measures by exploring the ontology beneath the terms and modelling uncertainty. Bioinformatics. 2012, 28: 1383-1389. 10.1093\/bioinformatics\/bts129.","journal-title":"Bioinformatics"},{"key":"1407_CR21","doi-asserted-by":"publisher","first-page":"1424","DOI":"10.1093\/bioinformatics\/btt160","volume":"29","author":"Z Teng","year":"2013","unstructured":"Teng Z, Guo M, Liu X, Dai Q, Wang C, Xuan P: Measuring gene functional similarity based on group- wise comparison of GO terms. Bioinformatics. 2013, 29: 1424-1432. 10.1093\/bioinformatics\/btt160.","journal-title":"Bioinformatics"},{"key":"1407_CR22","doi-asserted-by":"publisher","first-page":"e66745","DOI":"10.1371\/journal.pone.0066745","volume":"8","author":"X Wu","year":"2013","unstructured":"Wu X, Pang E, Lin K, Pei Z: Improving the measurement of semantic similarity between gene ontology terms and gene products: Insights from an edge-and ic-based hybrid method. PloS one. 2013, 8: e66745-10.1371\/journal.pone.0066745.","journal-title":"PloS one"},{"key":"1407_CR23","doi-asserted-by":"publisher","first-page":"S5","DOI":"10.1186\/1471-2105-15-S2-S5","volume":"15","author":"J Peng","year":"2014","unstructured":"Peng J, Wang Y, Chen J: Towards integrative gene functional similarity measurement. BMC bioinformatics. 2014, 15: S5-","journal-title":"BMC bioinformatics"},{"key":"1407_CR24","doi-asserted-by":"crossref","first-page":"95","DOI":"10.1613\/jair.514","volume":"11","author":"P Resnik","year":"1999","unstructured":"Resnik P: Semantic similarity in a taxonomy: An information-based measure and its application to problems of ambiguity in natural language. Journal of Artificial Intelligence Research. 1999, 11: 95-130.","journal-title":"Journal of Artificial Intelligence Research"},{"key":"1407_CR25","first-page":"9008","volume-title":"ROCLING","author":"J Jiang","year":"1997","unstructured":"Jiang J, Conrath D: Semantic similarity based on corpus statistics and lexical taxonomy. ROCLING. 1997, 9008-"},{"key":"1407_CR26","first-page":"296","volume":"98","author":"D Lin","year":"1998","unstructured":"Lin D: An information-theoretic definition of similarity. CM. 1998, 98: 296-304.","journal-title":"CM"},{"key":"1407_CR27","doi-asserted-by":"publisher","first-page":"330","DOI":"10.1109\/TCBB.2005.50","volume":"2","author":"J Sevilla","year":"2005","unstructured":"Sevilla J, Segura V, Podhorski A, Guruceaga E, Mato J, Martinez-Cruz L, Rubio A: Correlation between gene expression and GO semantic similarity. Computational Biology and Bioinformatics, IEEE\/ACM Transactions on. 2005, 2: 330-338. 10.1109\/TCBB.2005.50.","journal-title":"Computational Biology and Bioinformatics, IEEE\/ACM Transactions on"},{"key":"1407_CR28","doi-asserted-by":"publisher","first-page":"853","DOI":"10.1007\/s00158-009-0460-7","volume":"41","author":"R Marler","year":"2010","unstructured":"Marler R, Arora J: The weighted sum method for multi-objective optimization: new insights. Structural and multidisciplinary optimization. 2010, 41: 853-862. 10.1007\/s00158-009-0460-7.","journal-title":"Structural and multidisciplinary optimization"},{"key":"1407_CR29","doi-asserted-by":"publisher","first-page":"533","DOI":"10.1016\/0305-0548(86)90048-1","volume":"13","author":"F Glover","year":"1986","unstructured":"Glover F: Future paths for integer programming and links to artificial intelligence. Computers & Operations Research. 1986, 13: 533-549. 10.1016\/0305-0548(86)90048-1.","journal-title":"Computers & Operations Research"},{"key":"1407_CR30","doi-asserted-by":"publisher","first-page":"401","DOI":"10.1186\/gb-2004-5-8-401","volume":"5","author":"P Karp","year":"2004","unstructured":"Karp P: Call for an enzyme genomics initiative. Genome biology. 2004, 5: 401-10.1186\/gb-2004-5-8-401.","journal-title":"Genome biology"},{"key":"1407_CR31","doi-asserted-by":"publisher","first-page":"R26","DOI":"10.1186\/gb-2007-8-2-r26","volume":"8","author":"J D\u00edaz-Mej\u00eda","year":"2007","unstructured":"D\u00edaz-Mej\u00eda J, P\u00e9rez-Rueda E, Segovia L: A network perspective on the evolution of metabolism by gene duplication. Genome biology. 2007, 8: R26-10.1186\/gb-2007-8-2-r26.","journal-title":"Genome biology"},{"key":"1407_CR32","doi-asserted-by":"publisher","first-page":"55","DOI":"10.1038\/nrg1749","volume":"7","author":"D Allison","year":"2006","unstructured":"Allison D, Cui X, Page G, Sabripour M: Microarray data analysis: from disarray to consolidation and consensus. Nature Reviews Genetics. 2006, 7: 55-65. 10.1038\/nrg1749.","journal-title":"Nature Reviews Genetics"},{"key":"1407_CR33","doi-asserted-by":"publisher","first-page":"509","DOI":"10.1038\/nrg2363","volume":"9","author":"S Rhee","year":"2008","unstructured":"Rhee S, Wood V, Dolinski K, Draghici S: Use and misuse of the gene ontology annotations. Nature Reviews Genetics. 2008, 9: 509-515. 10.1038\/nrg2363.","journal-title":"Nature Reviews Genetics"},{"key":"1407_CR34","unstructured":"Gentleman R: Visualizing and distances using GO URL. [http:\/\/www.bioconductor.org\/docs\/vignettes.html]"},{"key":"1407_CR35","doi-asserted-by":"publisher","first-page":"1085","DOI":"10.1101\/gr.1910904","volume":"14","author":"H Lee","year":"2004","unstructured":"Lee H, Hsu A, Sajdak J, Qin J, Pavlidis P: Coexpression analysis of human genes across many microarray data sets. Genome research. 2004, 14: 1085-1094. 10.1101\/gr.1910904.","journal-title":"Genome research"},{"key":"1407_CR36","first-page":"37","volume-title":"Annual Bio-Ontologies Meeting","author":"C Pesquita","year":"2007","unstructured":"Pesquita C, Faria D, Bastos H, Falcao A, Couto F: Evaluating GO-based semantic similarity measures. Annual Bio-Ontologies Meeting. 2007, 37-40."},{"key":"1407_CR37","doi-asserted-by":"publisher","first-page":"403","DOI":"10.1016\/S0022-2836(05)80360-2","volume":"215","author":"S Altschul","year":"1990","unstructured":"Altschul S, Gish W, Miller W, Myers E, Lipman D: Basic local alignment search tool. Journal of molecular biology. 1990, 215: 403-410. 10.1016\/S0022-2836(05)80360-2.","journal-title":"Journal of molecular biology"},{"key":"1407_CR38","doi-asserted-by":"publisher","first-page":"70","DOI":"10.1021\/tx700079z","volume":"21","author":"F Guengerich","year":"2007","unstructured":"Guengerich F: Cytochrome p450 and chemical toxicology. Chemical research in toxicology. 2007, 21: 70-83.","journal-title":"Chemical research in toxicology"}],"container-title":["BMC Systems Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/1752-0509-8-S5-S8.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,5,14]],"date-time":"2025-05-14T01:10:21Z","timestamp":1747185021000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcsystbiol.biomedcentral.com\/articles\/10.1186\/1752-0509-8-S5-S8"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2014,12]]},"references-count":38,"journal-issue":{"issue":"S5","published-print":{"date-parts":[[2014,12]]}},"alternative-id":["1407"],"URL":"https:\/\/doi.org\/10.1186\/1752-0509-8-s5-s8","relation":{},"ISSN":["1752-0509"],"issn-type":[{"type":"electronic","value":"1752-0509"}],"subject":[],"published":{"date-parts":[[2014,12]]},"assertion":[{"value":"12 December 2014","order":1,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"S8"}}