{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,6]],"date-time":"2026-06-06T00:25:34Z","timestamp":1780705534553,"version":"3.54.1"},"reference-count":44,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2015,1,16]],"date-time":"2015-01-16T00:00:00Z","timestamp":1421366400000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2015,12]]},"DOI":"10.1186\/s12859-014-0430-y","type":"journal-article","created":{"date-parts":[[2015,1,15]],"date-time":"2015-01-15T10:34:22Z","timestamp":1421318062000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":327,"title":["Predicting protein functions using incomplete hierarchical labels"],"prefix":"10.1186","volume":"16","author":[{"given":"Guoxian","family":"Yu","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hailong","family":"Zhu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Carlotta","family":"Domeniconi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2015,1,16]]},"reference":[{"issue":"8","key":"430_CR1","doi-asserted-by":"publisher","first-page":"1551","DOI":"10.1038\/nprot.2013.092","volume":"8","author":"H Mi","year":"2013","unstructured":"Mi H, Muruganujan A, Casagrande JT, Thomas PD. Large-scale gene function analysis with the PANTHER classification system. Nat Protoc. 2013; 8(8):1551\u20131566.","journal-title":"Nat Protoc"},{"issue":"S2","key":"430_CR2","doi-asserted-by":"publisher","first-page":"S2","DOI":"10.1186\/1752-0509-6-S2-S2","volume":"6","author":"H Zhou","year":"2012","unstructured":"Zhou H, Jin J, Zhang H, Yi B, Wozniak M, Wong L. IntPath\u2013an integrated pathway gene relationship database for model organisms and important pathogens. BMC Syst Biol. 2012; 6(S2):S2.","journal-title":"BMC Syst Biol"},{"issue":"9","key":"430_CR3","doi-asserted-by":"publisher","first-page":"1236","DOI":"10.1093\/bioinformatics\/btu031","volume":"30","author":"P Jones","year":"2014","unstructured":"Jones P, Binns D, Chang HY, Fraser M, Li W, McAnulla C, et al.InterProScan 5 genome-scale protein function classification. Bioinformatics. 2014; 30(9):1236\u20131240.","journal-title":"Bioinformatics"},{"issue":"7","key":"430_CR4","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 AO, Lord P, Couto FM. Semantic similarity in biomedical ontologies. PLoS Comput Biol. 2009; 5(7):e1000443.","journal-title":"PLoS Comput Biol"},{"key":"430_CR5","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/1745-6150-9-5","volume":"9","author":"H Zhou","year":"2014","unstructured":"Zhou H, Gao S, Nguyen NN, Fan M, Jin J, Liu B, et al. Stringent homology-based prediction of H. sapiens-M tuberculosis H37Rv protein-protein interactions. Biol Direct. 2014; 9:1\u201330.","journal-title":"Biol Direct"},{"key":"430_CR6","volume-title":"Computational Approaches to Protein Function Prediction","author":"G Pandey","year":"2012","unstructured":"Pandey G, Kumar V, Steinbach M, Meyers CL. Computational Approaches to Protein Function Prediction. New York, NY, USA: Wiley-Interscience; 2012."},{"issue":"3","key":"430_CR7","doi-asserted-by":"publisher","first-page":"832","DOI":"10.1109\/TCBB.2010.38","volume":"8","author":"G Valentini","year":"2011","unstructured":"Valentini G. True Path Rule hierarchical ensembles for genome-wide gene function prediction. IEEE\/ACM Trans Comput Bi. 2011; 8(3):832\u2013847.","journal-title":"IEEE\/ACM Trans Comput Bi"},{"key":"430_CR8","doi-asserted-by":"publisher","first-page":"209","DOI":"10.1007\/s10994-011-5271-6","volume":"88","author":"N Cesa-Bianchi","year":"2012","unstructured":"Cesa-Bianchi N, Re M, Valentini G. Synergy of multi-label hierarchical ensembles, data fusion, and cost-sensitive methods for gene functional inference. Mach Learn. 2012; 88:209\u2013241.","journal-title":"Mach Learn"},{"issue":"3","key":"430_CR9","doi-asserted-by":"publisher","first-page":"221","DOI":"10.1038\/nmeth.2340","volume":"10","author":"P Radivojac","year":"2013","unstructured":"Radivojac P, Wyatt TC, Oron TR, Tal RO, Alexandra MS, Tobias W, Artem S, et al.A large-scale evaluation of computational protein function prediction. Nat Methods. 2013; 10(3):221\u2013227.","journal-title":"Nat Methods"},{"issue":"Article ID 9014","key":"430_CR10","first-page":"34","volume":"2014","author":"G Valentini","year":"2014","unstructured":"Valentini G. Hierarchical ensemble methods for protein function prediction. ISRN Bioinformatics. 2014; 2014(Article ID 901419):34. doi:10.1155\/2014\/901419.","journal-title":"ISRN Bioinformatics"},{"issue":"7","key":"430_CR11","doi-asserted-by":"publisher","first-page":"830","DOI":"10.1093\/bioinformatics\/btk048","volume":"22","author":"Z Barutcuoglu","year":"2006","unstructured":"Barutcuoglu Z, Schapire RE, Troyanskaya OG. Hierarchical multi-label prediction of gene function. Bioinformatics. 2006; 22(7):830\u2013836.","journal-title":"Bioinformatics"},{"issue":"4","key":"430_CR12","doi-asserted-by":"publisher","first-page":"1045","DOI":"10.1109\/TCBB.2013.111","volume":"10","author":"G Yu","year":"2013","unstructured":"Yu G, Rangwala H, Domeniconi C, Zhang G, Yu Z. Protein function prediction using multi-label ensemble classification. IEEE\/ACM Trans Comput Bi. 2013; 10(4):1045\u20131057.","journal-title":"IEEE\/ACM Trans Comput Bi"},{"issue":"99","key":"430_CR13","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1109\/TNET.2013.2296614","volume":"99","author":"J Wu","year":"2014","unstructured":"Wu J, Huang S, Zhou Z. Genome-Wide Protein Function Prediction through Multi-instance Multi-label Learning. IEEE\/ACM Trans Comput Bi. 2014; 99(99):1\u201310.","journal-title":"IEEE\/ACM Trans Comput Bi"},{"key":"430_CR14","volume-title":"Proc of Int Joint Conf on Artificial Intelligence (IJCAI)","author":"G Yu","year":"2013","unstructured":"Yu G, Rangwala H, Domeniconi C, Zhang G, Zhang Z. Protein function prediction by integrating multiple kernels. In: Proc of Int Joint Conf on Artificial Intelligence (IJCAI). Beijing, China: AAAI Press: 2013. p. 1869\u20131875."},{"issue":"S3","key":"430_CR15","doi-asserted-by":"publisher","first-page":"S1","DOI":"10.1186\/1471-2105-14-S3-S1","volume":"14","author":"D Cozzetto","year":"2013","unstructured":"Cozzetto D, Buchan DW, Bryson K, Jones DT. Protein function prediction by massive integration of evolutionary analyses and multiple data sources. BMC Bioinformatics. 2013; 14(S3):S1.","journal-title":"BMC Bioinformatics"},{"issue":"12","key":"430_CR16","doi-asserted-by":"publisher","first-page":"i219","DOI":"10.1093\/bioinformatics\/btu263","volume":"30","author":"M Cao","year":"2014","unstructured":"Cao M, Pietras CM, Feng X, Doroschak KJ, Schaffner T, Park J, Zhang H, Cowen LJ, Hescott BJ. New directions for diffusion-based network prediction of protein function: incorporating pathways with confidence. Bioinformatics. 2014; 30(12):i219\u2013i227.","journal-title":"Bioinformatics"},{"issue":"S3","key":"430_CR17","doi-asserted-by":"publisher","first-page":"S5","DOI":"10.1186\/1471-2105-14-S3-S5","volume":"14","author":"R Rentzsch","year":"2013","unstructured":"Rentzsch R, Orengo CA. Protein function prediction using domain families. BMC Bioinformatics. 2013; 14(S3):S5.","journal-title":"BMC Bioinformatics"},{"issue":"6","key":"430_CR18","doi-asserted-by":"publisher","first-page":"e1003644","DOI":"10.1371\/journal.pcbi.1003644","volume":"10","author":"N Youngs","year":"2014","unstructured":"Youngs N, Penfold-Brown D, Bonneau R, Shasha D. Negative Example Selection for Protein Function Prediction: The NoGO Database. PLoS Comput Biol. 2014; 10(6):e1003644.","journal-title":"PLoS Comput Biol"},{"issue":"30","key":"430_CR19","doi-asserted-by":"publisher","first-page":"2091","DOI":"10.1093\/bioinformatics\/btu117","volume":"14","author":"MN Wass","year":"2014","unstructured":"Wass MN, Mooney SD, Linial M, Radivojac P, Friedberg I. The automated function prediction SIG looks back at 2013 and prepares for 2014. Bioinformatics. 2014; 14(30):2091\u20132092.","journal-title":"Bioinformatics"},{"issue":"4","key":"430_CR20","doi-asserted-by":"publisher","first-page":"1059","DOI":"10.1109\/TCBB.2011.156","volume":"9","author":"JQ Jiang","year":"2012","unstructured":"Jiang JQ, McQuay LJ. Predicting protein function by multi-label correlated semi-supervised learning. IEEE\/ACM Trans Comput Bi. 2012; 9(4):1059\u20131069.","journal-title":"IEEE\/ACM Trans Comput Bi"},{"issue":"8","key":"430_CR21","doi-asserted-by":"publisher","first-page":"1819","DOI":"10.1109\/TKDE.2013.39","volume":"26","author":"ML Zhang","year":"2014","unstructured":"Zhang ML, Zhou ZH. A Review On Multi-Label Learning Algorithms. IEEE Trans Knowl Data En. 2014; 26(8):1819\u20131837.","journal-title":"IEEE Trans Knowl Data En"},{"key":"430_CR22","doi-asserted-by":"publisher","first-page":"142","DOI":"10.1186\/1471-2105-10-142","volume":"10","author":"G Pandey","year":"2009","unstructured":"Pandey G, Myers CL, Kumar V. Incorporating functional inter-relationships into protein function prediction algorithms. BMC Bioinformatics. 2009; 10:142.","journal-title":"BMC Bioinformatics"},{"key":"430_CR23","volume-title":"Proc of Int Conf on Machine Learning (ICML)","author":"D Lin","year":"1998","unstructured":"Lin D. An Information-Theoretic Definition of Similarity. In: Proc of Int Conf on Machine Learning (ICML). Madison, Wisconsin, USA: Morgan Kaufmann: 1998. p. 296\u2013304."},{"issue":"3","key":"430_CR24","doi-asserted-by":"publisher","first-page":"740","DOI":"10.1109\/TCBB.2011.148","volume":"9","author":"XF Zhang","year":"2012","unstructured":"Zhang XF, Dai DQ. A framework for incorporating functional interrelationships into protein function prediction algorithms. IEEE\/ACM Trans Comput Bi. 2012; 9(3):740\u2013753.","journal-title":"IEEE\/ACM Trans Comput Bi"},{"issue":"4","key":"430_CR25","doi-asserted-by":"publisher","first-page":"322","DOI":"10.1089\/cmb.2012.0272","volume":"20","author":"H Wang","year":"2013","unstructured":"Wang H, Huang H, Ding C. Function\u2013function correlated multi-label protein function prediction over interaction networks. J Comput Biol. 2013; 20(4):322\u2013343.","journal-title":"J Comput Biol"},{"key":"430_CR26","doi-asserted-by":"publisher","first-page":"437","DOI":"10.1186\/1471-2105-12-437","volume":"12","author":"X Chi","year":"2011","unstructured":"Chi X, Hou J. An iterative approach of protein function prediction. BMC Bioinformatics. 2011; 12:437.","journal-title":"BMC Bioinformatics"},{"key":"430_CR27","volume-title":"Procof AAAI Conf on Artificial Intelligence (AAAI)","author":"YY Sun","year":"2010","unstructured":"Sun YY, Zhang Y, Zhou ZH. Multi-label learning with weak label. In: Procof AAAI Conf on Artificial Intelligence (AAAI). Atlanta, Georgia, USA: AAAI Press: 2010. p. 293\u2013598."},{"key":"430_CR28","volume-title":"Proc of Int Joint Conf on Artificial Intelligence (IJCAI)","author":"SJ Yang","year":"2013","unstructured":"Yang SJ, Jiang Y, Zhou ZH. Multi-instance multi-label learning with weak label. In: Proc of Int Joint Conf on Artificial Intelligence (IJCAI). Beijing, China: AAAI Press: 2013. p. 1862\u20131868."},{"issue":"3","key":"430_CR29","doi-asserted-by":"publisher","first-page":"579","DOI":"10.1109\/TCBB.2013.142","volume":"11","author":"G Yu","year":"2014","unstructured":"Yu G, Rangwala H, Domeniconi C, Zhang G, Yu Z. Protein Function Prediction with Incomplete Annotations. IEEE\/ACM Trans Comput Bi. 2014; 11(3):579\u2013591.","journal-title":"IEEE\/ACM Trans Comput Bi"},{"key":"430_CR30","volume-title":"Proc of IEEE Conf on Computer Vision and Pattern Recognition (CVPR)","author":"SS Bucak","year":"2011","unstructured":"Bucak SS, Jin R, Jain AK. Multi-label learning with incomplete class assignments. In: Proc of IEEE Conf on Computer Vision and Pattern Recognition (CVPR). Colorado Springs, Colorado, USA: IEEE: 2011. p. 2801\u20132808."},{"key":"430_CR31","volume-title":"Proc of European Conf on Machine Learning and Knowledge Discovery in Databases (ECML\/PKDD)","author":"G Yu","year":"2013","unstructured":"Yu G, Domeniconi C, Rangwala H, Zhang G. Protein Function Prediction Using Dependence Maximization. In: Proc of European Conf on Machine Learning and Knowledge Discovery in Databases (ECML\/PKDD). Prague, Czech Republic: Springer: 2013. p. 574\u2013589."},{"issue":"18","key":"430_CR32","doi-asserted-by":"publisher","first-page":"5539","DOI":"10.1093\/nar\/gkh894","volume":"32","author":"A Ruepp","year":"2004","unstructured":"Ruepp A, Zollner A, Maier D, Albermann K, Hani J, Mokrejs M, Tetko I, et al. The FunCat, a functional annotation scheme for systematic classification of proteins from whole genomes. Nucleic Acids Res. 2004; 32(18):5539\u20135545.","journal-title":"Nucleic Acids Res"},{"key":"430_CR33","doi-asserted-by":"publisher","first-page":"25","DOI":"10.1038\/75556","volume":"25","author":"M Ashburner","year":"2000","unstructured":"Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, et al. Gene Ontology: tool for the unification of biology. Nat Genet. 2000; 25:25\u201329.","journal-title":"Nat Genet"},{"issue":"13","key":"430_CR34","doi-asserted-by":"publisher","first-page":"i529","DOI":"10.1093\/bioinformatics\/btm195","volume":"23","author":"Y Tao","year":"2007","unstructured":"Tao Y, Sam L, Li J, Friedman C, Lussier YA. Information theory applied to the sparse gene ontology annotation network to predict novel gene function. Bioinformatics. 2007; 23(13):i529\u2013i538.","journal-title":"Bioinformatics"},{"key":"430_CR35","doi-asserted-by":"publisher","first-page":"350","DOI":"10.1186\/1471-2105-9-350","volume":"9","author":"X Jiang","year":"2008","unstructured":"Jiang X, Nariai N, Steffen M, Kolaczyk ED. Integration of relational and hierarchical network information for protein function prediction. BMC Bioinformatics. 2008; 9:350.","journal-title":"BMC Bioinformatics"},{"key":"430_CR36","doi-asserted-by":"publisher","first-page":"2","DOI":"10.1186\/1471-2105-11-2","volume":"11","author":"L Schietgat","year":"2010","unstructured":"Schietgat L, Vens C, Struyf J, Blockeel H, Kocev D, Dz\u0302eroski S. Predicting gene function using hierarchical multi-label decision tree ensembles. BMC Bioinformatics. 2010; 11:2.","journal-title":"BMC Bioinformatics"},{"issue":"12","key":"430_CR37","doi-asserted-by":"publisher","first-page":"1257","DOI":"10.1038\/82360","volume":"18","author":"B Schwikowski","year":"2000","unstructured":"Schwikowski B, Uetz P, Fields S. A network of protein\u2013protein interactions in yeast. Nat Biotechnol. 2000; 18(12):1257\u20131261.","journal-title":"Nat Biotechnol"},{"issue":"9","key":"430_CR38","doi-asserted-by":"publisher","first-page":"1600","DOI":"10.1109\/TPAMI.2008.216","volume":"31","author":"J Wang","year":"2009","unstructured":"Wang J, Wang F, Zhang C, Shen HC, Quan L. Linear neighborhood propagation and its applications. IEEE Trans Pattern Anal. 2009; 31(9):1600\u20131615.","journal-title":"IEEE Trans Pattern Anal"},{"key":"430_CR39","doi-asserted-by":"crossref","unstructured":"Sharan R, Ulitsky I, Shamir R. Network-based prediction of protein function. Mol SysT Biol. 2007;3(1). doi:10.1038\/msb4100129.","DOI":"10.1038\/msb4100129"},{"issue":"S1","key":"430_CR40","doi-asserted-by":"publisher","first-page":"i302","DOI":"10.1093\/bioinformatics\/bti1054","volume":"21","author":"E Nabieva","year":"2005","unstructured":"Nabieva E, Jim K, Agarwal A, Chazelle B, Singh M. Whole-proteome prediction of protein function via graph-theoretic analysis of interaction maps. Bioinformatics. 2005; 21(S1):i302\u2013i310.","journal-title":"Bioinformatics"},{"issue":"13","key":"430_CR41","doi-asserted-by":"publisher","first-page":"1623","DOI":"10.1093\/bioinformatics\/btl145","volume":"22","author":"HN Chua","year":"2006","unstructured":"Chua HN, Sung WK, Wong L. Exploiting indirect neighbours and topological weight to predict protein function from protein\u2013protein interactions. Bioinformatics. 2006; 22(13):1623\u20131630.","journal-title":"Bioinformatics"},{"issue":"10","key":"430_CR42","doi-asserted-by":"publisher","first-page":"e109130","DOI":"10.1371\/journal.pone.0109130","volume":"9","author":"G Pandey","year":"2014","unstructured":"Pandey G, Arora S, Manocha S, Whalen S. Enhancing the Functional Content of Eukaryotic Protein Interaction Networks. PLoS ONE. 2014; 9(10):e109130.","journal-title":"PLoS ONE"},{"issue":"6","key":"430_CR43","doi-asserted-by":"publisher","first-page":"368","DOI":"10.1016\/j.ygeno.2013.04.010","volume":"101","author":"Y Xu","year":"2013","unstructured":"Xu Y, Guo M, Shi W, Liu X, Wang C. A novel insight into Gene Ontology semantic similarity. Genomics. 2013; 101(6):368\u2013375.","journal-title":"Genomics"},{"key":"430_CR44","doi-asserted-by":"crossref","unstructured":"Yu G, Zhu H, Domeniconi C. Supplementary files for \u2018predicting protein functions using incomplete hierarchical labels\u2019. 2014. [ https:\/\/sites.google.com\/site\/guoxian85\/home\/pill ]","DOI":"10.1186\/s12859-014-0430-y"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/article\/10.1186\/s12859-014-0430-y\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-014-0430-y.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-014-0430-y","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-014-0430-y.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,8,19]],"date-time":"2019-08-19T15:11:17Z","timestamp":1566227477000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/s12859-014-0430-y"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2015,1,16]]},"references-count":44,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2015,12]]}},"alternative-id":["430"],"URL":"https:\/\/doi.org\/10.1186\/s12859-014-0430-y","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2015,1,16]]},"assertion":[{"value":"24 July 2014","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"11 December 2014","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"16 January 2015","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"1"}}