{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,12]],"date-time":"2026-03-12T00:49:34Z","timestamp":1773276574001,"version":"3.50.1"},"reference-count":45,"publisher":"Springer Science and Business Media LLC","issue":"S3","license":[{"start":{"date-parts":[[2013,2,1]],"date-time":"2013-02-01T00:00:00Z","timestamp":1359676800000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/2.0"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2013,2]]},"DOI":"10.1186\/1471-2105-14-s3-s10","type":"journal-article","created":{"date-parts":[[2019,1,22]],"date-time":"2019-01-22T04:44:41Z","timestamp":1548132281000},"source":"Crossref","is-referenced-by-count":33,"title":["Combining heterogeneous data sources for accurate functional annotation of proteins"],"prefix":"10.1186","volume":"14","author":[{"given":"Artem","family":"Sokolov","sequence":"first","affiliation":[]},{"given":"Christopher","family":"Funk","sequence":"additional","affiliation":[]},{"given":"Kiley","family":"Graim","sequence":"additional","affiliation":[]},{"given":"Karin","family":"Verspoor","sequence":"additional","affiliation":[]},{"given":"Asa","family":"Ben-Hur","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2013,2,28]]},"reference":[{"issue":"2","key":"5699_CR1","doi-asserted-by":"publisher","first-page":"357","DOI":"10.1142\/S0219720010004744","volume":"8","author":"A Sokolov","year":"2010","unstructured":"Sokolov A, Ben-Hur A: Hierarchical classification of Gene Ontology terms using the GOstruct method. Journal of Bioinformatics and Compuational Biology. 2010, 8 (2): 357-376. 10.1142\/S0219720010004744.","journal-title":"Journal of Bioinformatics and Compuational Biology"},{"key":"5699_CR2","first-page":"100","volume-title":"Proceedings of the eleventh annual conference on Computational learning theory","author":"A Blum","year":"1998","unstructured":"Blum A, Mitchell T: Combining labeled and unlabeled data with co-training. Proceedings of the eleventh annual conference on Computational learning theory. 1998, ACM, 100-"},{"key":"5699_CR3","volume-title":"ACM Conference on Bioinformatics, Computational Biology and Biomedicine","author":"A Sokolov","year":"2011","unstructured":"Sokolov A, Ben-Hur A: Multi-view prediction of protein function. ACM Conference on Bioinformatics, Computational Biology and Biomedicine. 2011"},{"key":"5699_CR4","doi-asserted-by":"crossref","unstructured":"Gene Ontology Consortium: Gene ontology: tool for the unification of biology. Nat Genet. 2000, 25-9. 25","DOI":"10.1038\/75556"},{"issue":"7","key":"5699_CR5","doi-asserted-by":"publisher","first-page":"830","DOI":"10.1093\/bioinformatics\/btk048","volume":"22","author":"Z Barutcuoglu","year":"2006","unstructured":"Barutcuoglu Z, Schapire R, Troyanskaya O: Hierarchical multi-label prediction of gene function. Bioinformatics. 2006, 22 (7): 830-10.1093\/bioinformatics\/btk048.","journal-title":"Bioinformatics"},{"issue":"2","key":"5699_CR6","doi-asserted-by":"publisher","first-page":"207","DOI":"10.1186\/gb-2009-10-2-207","volume":"10","author":"Y Loewenstein","year":"2009","unstructured":"Loewenstein Y, Raimondo D, Redfern O, Watson J, Frishman D, Linial M, Orengo C, Thornton J, Tramontano A: Protein function annotation by homology-based inference. Genome Biology. 2009, 10 (2): 207-10.1186\/gb-2009-10-2-207. [ http:\/\/genomebiology.com\/2009\/10\/2\/207 ]","journal-title":"Genome Biology"},{"key":"5699_CR7","doi-asserted-by":"publisher","first-page":"313","DOI":"10.1038\/ng0498-313","volume":"18","author":"P Bork","year":"1998","unstructured":"Bork P, Koonin EV: Predicting functions from protein sequences - where are the bottlenecks?. Nature Genetics. 1998, 18: 313-318. 10.1038\/ng0498-313.","journal-title":"Nature Genetics"},{"key":"5699_CR8","first-page":"98","volume":"41","author":"D Devos","year":"2000","unstructured":"Devos D, Valencia A: Practical limits of function prediction. PROTEINS-NEW YORK. 2000, 41: 98-107.","journal-title":"PROTEINS-NEW YORK"},{"key":"5699_CR9","first-page":"55","volume":"1","author":"MY Galperin","year":"1998","unstructured":"Galperin MY, Koonin EV: Sources of systematic error in functional annotation of genomes: domain rearrangement, non-orthologous gene displacement, and operon disruption. In Silico Biology. 1998, 1: 55-67.","journal-title":"In Silico Biology"},{"issue":"12","key":"5699_CR10","doi-asserted-by":"publisher","first-page":"2637","DOI":"10.1007\/s00018-003-3114-8","volume":"60","author":"B Rost","year":"2003","unstructured":"Rost B, Liu J, Nair R, Wrzeszczynski K, Ofran Y: Automatic prediction of protein function. Cellular and Molecular Life Sciences. 2003, 60 (12): 2637-2650. 10.1007\/s00018-003-3114-8.","journal-title":"Cellular and Molecular Life Sciences"},{"key":"5699_CR11","doi-asserted-by":"publisher","first-page":"365","DOI":"10.1093\/nar\/gkg095","volume":"31","author":"B Boeckmann","year":"2003","unstructured":"Boeckmann B, Bairoch A, Apweiler R, Blatter M, Estreicher A, Gasteiger E, Martin M, Michoud K, O'Donovan C, Phan I: The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003. Nucleic acids research. 2003, 31: 365-10.1093\/nar\/gkg095.","journal-title":"Nucleic acids research"},{"key":"5699_CR12","volume-title":"Automatic Function Prediction special interest group meeting at ISMB","author":"T Hamp","year":"2011","unstructured":"Hamp T, Kassner R, Seemayer S, Vicedo E: Nearest-Neighbor Approaches to Predict Protein Function by Homology Inference Alone. Automatic Function Prediction special interest group meeting at ISMB. 2011"},{"issue":"13","key":"5699_CR13","doi-asserted-by":"publisher","first-page":"3712","DOI":"10.1093\/nar\/gkg582","volume":"31","author":"S Hennig","year":"2003","unstructured":"Hennig S, Groth D, Lehrach H: Automated Gene Ontology annotation for anonymous sequence data. Nucleic Acids Research. 2003, 31 (13): 3712-10.1093\/nar\/gkg582.","journal-title":"Nucleic Acids Research"},{"key":"5699_CR14","doi-asserted-by":"publisher","first-page":"178","DOI":"10.1186\/1471-2105-5-178","volume":"5","author":"D Martin","year":"2004","unstructured":"Martin D, Berriman M, Barton G: GOtcha: a new method for prediction of protein function assessed by the annotation of seven genomes. BMC bioinformatics. 2004, 5: 178-10.1186\/1471-2105-5-178.","journal-title":"BMC bioinformatics"},{"issue":"13","key":"5699_CR15","doi-asserted-by":"publisher","first-page":"3799","DOI":"10.1093\/nar\/gkg555","volume":"31","author":"G Zehetner","year":"2003","unstructured":"Zehetner G: OntoBlast function: From sequence similarities directly to potential functional annotations by ontology terms. Nucleic acids research. 2003, 31 (13): 3799-10.1093\/nar\/gkg555.","journal-title":"Nucleic acids research"},{"issue":"Suppl 1","key":"5699_CR16","doi-asserted-by":"publisher","first-page":"S4","DOI":"10.1186\/gb-2008-9-s1-s4","volume":"9","author":"S Mostafavi","year":"2008","unstructured":"Mostafavi S, Ray D, Warde-Farley D, Grouios C, Morris Q: GeneMANIA: a real-time multiple associationnetwork integration algorithm for predicting gene function. Genome Biology. 2008, 9 (Suppl 1): S4-10.1186\/gb-2008-9-s1-s4.","journal-title":"Genome Biology"},{"issue":"Suppl 1","key":"5699_CR17","doi-asserted-by":"publisher","first-page":"S3","DOI":"10.1186\/gb-2008-9-s1-s3","volume":"9","author":"Y Guan","year":"2008","unstructured":"Guan Y, Myers C, Hess D, Barutcuoglu Z, Caudy A, Troyanskaya O: Predicting gene function in a hierarchical context with an ensemble of classifiers. Genome Biology. 2008, 9 (Suppl 1): S3-10.1186\/gb-2008-9-s1-s3.","journal-title":"Genome Biology"},{"issue":"Suppl 1","key":"5699_CR18","doi-asserted-by":"publisher","first-page":"S6","DOI":"10.1186\/gb-2008-9-s1-s6","volume":"9","author":"G Obozinski","year":"2008","unstructured":"Obozinski G, Lanckriet G, Grant C, Jordan M, Noble W: Consistent probabilistic outputs for proteinfunction prediction. Genome Biology. 2008, 9 (Suppl 1): S6-10.1186\/gb-2008-9-s1-s6.","journal-title":"Genome Biology"},{"issue":"suppl 1","key":"5699_CR19","doi-asserted-by":"publisher","first-page":"i169","DOI":"10.1093\/bioinformatics\/bth921","volume":"20","author":"C Joslyn","year":"2004","unstructured":"Joslyn C, Mniszewski S, Fulmer A, Heaton G: The gene ontology categorizer. Bioinformatics. 2004, 20 (suppl 1): i169-10.1093\/bioinformatics\/bth921.","journal-title":"Bioinformatics"},{"key":"5699_CR20","volume-title":"Conference on Uncertainty in Artificial Intelligence","author":"S Mostafavi","year":"2009","unstructured":"Mostafavi S, Morris Q: Using the Gene Ontology hierarchy when predicting gene function. Conference on Uncertainty in Artificial Intelligence. 2009"},{"issue":"Suppl 1","key":"5699_CR21","doi-asserted-by":"publisher","first-page":"S2","DOI":"10.1186\/gb-2008-9-s1-s2","volume":"9","author":"L Pe\u00f1a-Castillo","year":"2008","unstructured":"Pe\u00f1a-Castillo L, Tasan M, Myers C, Lee H, Joshi T, Zhang C, Guan Y, Leone M, Pagnani A, Kim W: A criticalassessment of Mus musculus gene function prediction using integrated genomic evidence. Genome Biology. 2008, 9 (Suppl 1): S2-10.1186\/gb-2008-9-s1-s2.","journal-title":"Genome Biology"},{"issue":"suppl 1","key":"5699_CR22","doi-asserted-by":"publisher","first-page":"S16","DOI":"10.1186\/1471-2105-6-S1-S16","volume":"6","author":"C Blaschke","year":"2005","unstructured":"Blaschke C, Leon E, Krallinger M, Valencia A: Evaluation of BioCreAtIvE assessment of task 2. BMC Bioinformatics. 2005, 6 (suppl 1): S16-10.1186\/1471-2105-6-S1-S16.","journal-title":"BMC Bioinformatics"},{"issue":"Suppl 1","key":"5699_CR23","doi-asserted-by":"publisher","first-page":"S18","DOI":"10.1186\/1471-2105-6-S1-S18","volume":"6","author":"S Ray","year":"2005","unstructured":"Ray S, Craven M: Learning Statistical Models for Annotating Proteins with Function Informationusing Biomedical Text. BMC Bioinformatics. 2005, 6 (Suppl 1): S18-10.1186\/1471-2105-6-S1-S18.","journal-title":"BMC Bioinformatics"},{"issue":"Suppl 1","key":"5699_CR24","doi-asserted-by":"publisher","first-page":"S22","DOI":"10.1186\/1471-2105-6-S1-S22","volume":"6","author":"S Rice","year":"2005","unstructured":"Rice S, Nenadic G, Stapley B: Mining protein function from text using term-based support vectormachines. BMC Bioinformatics. 2005, 6 (Suppl 1): S22-10.1186\/1471-2105-6-S1-S22.","journal-title":"BMC Bioinformatics"},{"key":"5699_CR25","volume-title":"Automatic Function Prediction special interest group meeting at ISMB","author":"A Wong","year":"2011","unstructured":"Wong A, Shatkay H: Predicting Protein Function using Text Data from the Biomedical Literature. Automatic Function Prediction special interest group meeting at ISMB. 2011"},{"key":"5699_CR26","doi-asserted-by":"crossref","DOI":"10.7551\/mitpress\/7443.001.0001","volume-title":"Predicting structured data","author":"G Bakir","year":"2007","unstructured":"Bakir G, Hofmann T, Sch\u00f6lkopf B: Predicting structured data. 2007, The MIT Press"},{"issue":"2","key":"5699_CR27","first-page":"453","volume":"6","author":"I Tsochantaridis","year":"2006","unstructured":"Tsochantaridis I, Joachims T, Hofmann T, Altun Y: Large margin methods for structured and interdependent output variables. Journal of Machine Learning Research. 2006, 6 (2): 453-","journal-title":"Journal of Machine Learning Research"},{"key":"5699_CR28","first-page":"1601","volume":"7","author":"J Rousu","year":"2006","unstructured":"Rousu J, Saunders C, Szedmak S, Shawe-Taylor J: Kernel-based learning of hierarchical multilabel classification models. The Journal of Machine Learning Research. 2006, 7: 1601-1626.","journal-title":"The Journal of Machine Learning Research"},{"key":"5699_CR29","volume-title":"Twenty Second International Conference on Machine Learning (ICML05)","author":"B Taskar","year":"2005","unstructured":"Taskar B, Chatalbashev V, Koller D, Guestrin C: Learning Structured Prediction Models: A Large Margin Approach. Twenty Second International Conference on Machine Learning (ICML05). 2005"},{"key":"5699_CR30","first-page":"S2","volume-title":"BMC proceedings","author":"K Astikainen","year":"2008","unstructured":"Astikainen K, Holm L, Pitkanen E, Szedmak S, Rousu J: Towards structured output prediction of enzyme. BMC proceedings. 2008, BioMed Central Ltd, 2: S2-"},{"issue":"7","key":"5699_CR31","doi-asserted-by":"publisher","first-page":"2086","DOI":"10.1002\/prot.23029","volume":"79","author":"W Clark","year":"2011","unstructured":"Clark W, Radivojac P: Analysis of protein function and its prediction from amino acid sequence. Proteins: Structure, Function, and Bioinformatics. 2011, 79 (7): 2086-2096. 10.1002\/prot.23029.","journal-title":"Proteins: Structure, Function, and Bioinformatics"},{"key":"5699_CR32","volume-title":"PhD thesis","author":"A Sokolov","year":"2011","unstructured":"Sokolov A: Accurate prediction of protein function using GOstruct. PhD thesis. 2011, Colorado State University"},{"issue":"9","key":"5699_CR33","doi-asserted-by":"publisher","first-page":"1173","DOI":"10.1093\/bioinformatics\/btp122","volume":"25","author":"M Rogers","year":"2009","unstructured":"Rogers M, Ben-Hur A: The use of Gene Ontology evidence codes in preventing classifier assessmentbias. Bioinformatics. 2009, 25 (9): 1173-10.1093\/bioinformatics\/btp122.","journal-title":"Bioinformatics"},{"issue":"3","key":"5699_CR34","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. J Mol Biol. 1990, 215 (3): 403-410.","journal-title":"J Mol Biol"},{"key":"5699_CR35","first-page":"48","volume-title":"Proceedings of the 4th annual Asia Pacific bioinformatics conference APBC06, Taipei, Taiwan","author":"P Horton","year":"2006","unstructured":"Horton P, Park K, Obayashi T, Nakai K: Protein subcellular localization prediction with WoLF PSORT. Proceedings of the 4th annual Asia Pacific bioinformatics conference APBC06, Taipei, Taiwan. 2006, Citeseer, 39: 48-"},{"issue":"3","key":"5699_CR36","doi-asserted-by":"publisher","first-page":"567","DOI":"10.1006\/jmbi.2000.4315","volume":"305","author":"A Krogh","year":"2001","unstructured":"Krogh A, Larsson B, Von Heijne G, Sonnhammer E: Predicting transmembrane protein topology with ahidden markov model: application to complete genomes1. Journal of molecular biology. 2001, 305 (3): 567-580. 10.1006\/jmbi.2000.4315.","journal-title":"Journal of molecular biology"},{"issue":"4","key":"5699_CR37","doi-asserted-by":"publisher","first-page":"996","DOI":"10.1002\/prot.20903","volume":"63","author":"I Bahir","year":"2006","unstructured":"Bahir I, Linial M: Functional grouping based on signatures in protein termini. Proteins: Structure, Function, and Bioinformatics. 2006, 63 (4): 996-1004. 10.1002\/prot.20903.","journal-title":"Proteins: Structure, Function, and Bioinformatics"},{"key":"5699_CR38","doi-asserted-by":"publisher","first-page":"43","DOI":"10.1186\/1752-0509-4-43","volume":"4","author":"A Coletta","year":"2010","unstructured":"Coletta A, Pinney J, Sol\u00eds D, Marsh J, Pettifer S, Attwood T: Low-complexity regions within protein sequences have position-dependent roles. BMC systems biology. 2010, 4: 43-10.1186\/1752-0509-4-43.","journal-title":"BMC systems biology"},{"issue":"suppl 1","key":"5699_CR39","doi-asserted-by":"publisher","first-page":"D412","DOI":"10.1093\/nar\/gkn760","volume":"37","author":"L Jensen","year":"2009","unstructured":"Jensen L, Kuhn M, Stark M, Charon S, Creevey C, Muller J, Doerks T, Julien P, Roth A, Simonovic M: STRING 8.a global view on proteins and their functional interactions in 630 organisms. Nucleic acids research. 2009, 37 (suppl 1): D412-","journal-title":"Nucleic acids research"},{"issue":"Web Server","key":"5699_CR40","doi-asserted-by":"publisher","first-page":"W368","DOI":"10.1093\/nar\/gkr440","volume":"39","author":"CS Greene","year":"2011","unstructured":"Greene CS, Troyanskaya OG: PILGRM: an interactive data-driven discovery platform for expert biologists. Nucleic acids research. 2011, 39 (Web Server): W368-W374. [ http:\/\/dx.doi.org\/10.1093\/nar\/gkr440 ]","journal-title":"Nucleic acids research"},{"key":"5699_CR41","unstructured":"Verspoor KM, Cohen KB, Lanfranchi A, Warner C, Johnson HL, Roeder C, Choi JD, Funk C, Malenkiy Y, Eckert M, Xue N, WAB, Bada M, Palmer M, Hunter LE: A corpus of full-text journal articles is a robust evaluation tool for revealing differences in performance of biomedical natural language processing tools. BMC Bioinformatics."},{"issue":"Suppl 8","key":"5699_CR42","doi-asserted-by":"publisher","first-page":"S2","DOI":"10.1186\/1471-2105-12-S8-S2","volume":"12","author":"Z Lu","year":"2011","unstructured":"Lu Z, Kao H, Wei C, Huang M, Liu J, Kuo C, Hsu C, Tsai R, Dai H, Okazaki N, Cho H, Gerner M, Solt I, Agarwal S, Liu F, Vishnyakova D, Ruch P, Romacker M, Rinaldi F, Bhattacharya S, Srinivasan P, Liu H, Torii M, Matos S, Campos D, Verspoor K, Livingston K, Wilbur W: The gene normalization task in BioCreativeIII. BMC Bioinformatics. 2011, 12 (Suppl 8): S2-10.1186\/1471-2105-12-S8-S2.","journal-title":"BMC Bioinformatics"},{"key":"5699_CR43","volume-title":"Proceedings of the SIGIR'03 Workshop on Text Analysis and Search for Bioinformatics","author":"C Verspoor","year":"2003","unstructured":"Verspoor C, Joslyn C, Papcun G: The Gene Ontology as a Source of Lexical Semantic Knowledge for a Biological Natural Language Processing Application. Proceedings of the SIGIR'03 Workshop on Text Analysis and Search for Bioinformatics. 2003"},{"issue":"suppl 1","key":"5699_CR44","doi-asserted-by":"publisher","first-page":"S21","DOI":"10.1186\/1471-2105-6-S1-S21","volume":"6","author":"F Couto","year":"2005","unstructured":"Couto F, Silva M, Coutinho P: Finding genomic ontology terms in text using evidence content. BMC Bioinformatics. 2005, 6 (suppl 1): S21-10.1186\/1471-2105-6-S1-S21.","journal-title":"BMC Bioinformatics"},{"key":"5699_CR45","first-page":"300-311","volume-title":"Proceedings of the Pacific Symposium on Biocomputing","author":"G Lanckriet","year":"2004","unstructured":"Lanckriet G, Deng M, Cristianini N, Jordan M, Noble W: Kernel-based data fusion and its application to. Proceedings of the Pacific Symposium on Biocomputing. 2004, World Scientific Singapore, 9: 300-311-"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-14-S3-S10.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1186\/1471-2105-14-S3-S10\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-14-S3-S10.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,11,14]],"date-time":"2019-11-14T18:11:45Z","timestamp":1573755105000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/1471-2105-14-S3-S10"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2013,2]]},"references-count":45,"journal-issue":{"issue":"S3","published-print":{"date-parts":[[2013,2]]}},"alternative-id":["5699"],"URL":"https:\/\/doi.org\/10.1186\/1471-2105-14-s3-s10","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2013,2]]},"article-number":"S10"}}