{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,28]],"date-time":"2026-02-28T09:01:30Z","timestamp":1772269290722,"version":"3.50.1"},"reference-count":40,"publisher":"Oxford University Press (OUP)","issue":"1","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2012,1,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Protein\u2013protein interactions (PPIs) are pivotal for many biological processes and similarity in Gene Ontology (GO) annotation has been found to be one of the strongest indicators for PPI. Most GO-driven algorithms for PPI inference combine machine learning and semantic similarity techniques. We introduce the concept of inducers as a method to integrate both approaches more effectively, leading to superior prediction accuracies.<\/jats:p>\n               <jats:p>Results: An inducer (ULCA) in combination with a Random Forest classifier compares favorably to several sequence-based methods, semantic similarity measures and multi-kernel approaches. On a newly created set of high-quality interaction data, the proposed method achieves high cross-species prediction accuracies (Area under the ROC curve \u2264 0.88), rendering it a valuable companion to sequence-based methods.<\/jats:p>\n               <jats:p>Availability: Software and datasets are available at http:\/\/bioinformatics.org.au\/go2ppi\/<\/jats:p>\n               <jats:p>Contact: \u00a0m.ragan@uq.edu.au<\/jats:p>","DOI":"10.1093\/bioinformatics\/btr610","type":"journal-article","created":{"date-parts":[[2011,11,5]],"date-time":"2011-11-05T04:36:36Z","timestamp":1320467796000},"page":"69-75","source":"Crossref","is-referenced-by-count":77,"title":["Gene Ontology-driven inference of protein\u2013protein interactions using inducers"],"prefix":"10.1093","volume":"28","author":[{"given":"Stefan R.","family":"Maetschke","sequence":"first","affiliation":[{"name":"1 Institute for Molecular Bioscience, 2Australian Research Council Centre of Excellence in Bioinformatics, The University of Queensland, Brisbane QLD 4072, Australia, 3Bioinformatics Research Centre, Aarhus University, Aarhus 8000, Denmark and 4Queensland Facility for Advanced Bioinformatics, The University of Queensland, Brisbane QLD 4072, Australia"}]},{"given":"Martin","family":"Simonsen","sequence":"additional","affiliation":[{"name":"1 Institute for Molecular Bioscience, 2Australian Research Council Centre of Excellence in Bioinformatics, The University of Queensland, Brisbane QLD 4072, Australia, 3Bioinformatics Research Centre, Aarhus University, Aarhus 8000, Denmark and 4Queensland Facility for Advanced Bioinformatics, The University of Queensland, Brisbane QLD 4072, Australia"},{"name":"1 Institute for Molecular Bioscience, 2Australian Research Council Centre of Excellence in Bioinformatics, The University of Queensland, Brisbane QLD 4072, Australia, 3Bioinformatics Research Centre, Aarhus University, Aarhus 8000, Denmark and 4Queensland Facility for Advanced Bioinformatics, The University of Queensland, Brisbane QLD 4072, Australia"}]},{"given":"Melissa J.","family":"Davis","sequence":"additional","affiliation":[{"name":"1 Institute for Molecular Bioscience, 2Australian Research Council Centre of Excellence in Bioinformatics, The University of Queensland, Brisbane QLD 4072, Australia, 3Bioinformatics Research Centre, Aarhus University, Aarhus 8000, Denmark and 4Queensland Facility for Advanced Bioinformatics, The University of Queensland, Brisbane QLD 4072, Australia"},{"name":"1 Institute for Molecular Bioscience, 2Australian Research Council Centre of Excellence in Bioinformatics, The University of Queensland, Brisbane QLD 4072, Australia, 3Bioinformatics Research Centre, Aarhus University, Aarhus 8000, Denmark and 4Queensland Facility for Advanced Bioinformatics, The University of Queensland, Brisbane QLD 4072, Australia"}]},{"given":"Mark A.","family":"Ragan","sequence":"additional","affiliation":[{"name":"1 Institute for Molecular Bioscience, 2Australian Research Council Centre of Excellence in Bioinformatics, The University of Queensland, Brisbane QLD 4072, Australia, 3Bioinformatics Research Centre, Aarhus University, Aarhus 8000, Denmark and 4Queensland Facility for Advanced Bioinformatics, The University of Queensland, Brisbane QLD 4072, Australia"},{"name":"1 Institute for Molecular Bioscience, 2Australian Research Council Centre of Excellence in Bioinformatics, The University of Queensland, Brisbane QLD 4072, Australia, 3Bioinformatics Research Centre, Aarhus University, Aarhus 8000, Denmark and 4Queensland Facility for Advanced Bioinformatics, The University of Queensland, Brisbane QLD 4072, Australia"}]}],"member":"286","published-online":{"date-parts":[[2011,11,4]]},"reference":[{"key":"2023061011552526700_B1","doi-asserted-by":"crossref","first-page":"25","DOI":"10.1038\/75556","article-title":"Gene ontology: tool for the unification of biology. The Gene Ontology Consortium","volume":"21","author":"Ashburner","year":"2000","journal-title":"Nat. Genet."},{"key":"2023061011552526700_B2","doi-asserted-by":"crossref","first-page":"D154","DOI":"10.1093\/nar\/gki070","article-title":"The Universal Protein Resource (UniProt)","volume":"33","author":"Bairoch","year":"2005","journal-title":"Nucleic Acids Res."},{"key":"2023061011552526700_B3","doi-asserted-by":"crossref","first-page":"i38","DOI":"10.1093\/bioinformatics\/bti1016","article-title":"Kernel methods for predicting protein-protein interactions","volume":"21","author":"Ben-Hur","year":"2005","journal-title":"Bioinformatics"},{"issue":"Suppl. 1","key":"2023061011552526700_B4","doi-asserted-by":"crossref","first-page":"S2","DOI":"10.1186\/1471-2105-7-S1-S2","article-title":"Choosing negative examples for the prediction of protein-protein interactions","volume":"7","author":"Ben-Hur","year":"2006","journal-title":"BMC Bioinformatics"},{"key":"2023061011552526700_B5","doi-asserted-by":"crossref","first-page":"5","DOI":"10.1023\/A:1010933404324","article-title":"Random Forests","volume":"45","author":"Breiman","year":"2001","journal-title":"Mach. Learn."},{"key":"2023061011552526700_B6","doi-asserted-by":"crossref","first-page":"288","DOI":"10.1186\/1471-2164-10-288","article-title":"Predicting protein-protein interactions in Arabidopsis thaliana through integration of orthology, gene ontology and co-expression","volume":"10","author":"De Bodt","year":"2009","journal-title":"BMC Genomics"},{"key":"2023061011552526700_B7","doi-asserted-by":"crossref","first-page":"823","DOI":"10.1038\/35015694","article-title":"Protein function in the post-genomic era","volume":"405","author":"Eisenberg","year":"2000","journal-title":"Nature"},{"key":"2023061011552526700_B8","first-page":"302","article-title":"A 3-approximation for the minimum tree spanning k vertices","volume-title":"Proceedings of the IEEE Foundations of Computer Science","author":"Garg","year":"1996"},{"key":"2023061011552526700_B9","doi-asserted-by":"crossref","first-page":"3420","DOI":"10.1093\/nar\/gkn176","article-title":"High-throughput functional annotation and data mining with the Blast2GO suite","volume":"36","author":"G\u00f6tz","year":"2008","journal-title":"Nucleic Acids Res."},{"key":"2023061011552526700_B10","doi-asserted-by":"crossref","first-page":"3025","DOI":"10.1093\/nar\/gkn159","article-title":"Using support vector machine combined with auto covariance to predict protein-protein interactions from protein sequences","volume":"36","author":"Guo","year":"2008","journal-title":"Nucleic Acids Res."},{"key":"2023061011552526700_B11","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":"2023061011552526700_B12","doi-asserted-by":"crossref","first-page":"e4554","DOI":"10.1371\/journal.pone.0004554","article-title":"PPI Finder: a mining tool for human protein-protein interactions","volume":"2","author":"He","year":"2009","journal-title":"PLoS ONE"},{"key":"2023061011552526700_B13","doi-asserted-by":"crossref","first-page":"562","DOI":"10.1186\/1471-2105-11-562","article-title":"An improved method for scoring protein-protein interactions using semantic similarity within the gene ontology","volume":"11","author":"Jain","year":"2010","journal-title":"BMC Bioinformatics"},{"key":"2023061011552526700_B14","doi-asserted-by":"crossref","first-page":"449","DOI":"10.1126\/science.1087361","article-title":"A Bayesian networks approach for predicting protein-protein interactions from genomic data","volume":"302","author":"Jansen","year":"2003","journal-title":"Science"},{"key":"2023061011552526700_B15","doi-asserted-by":"crossref","first-page":"D412","DOI":"10.1093\/nar\/gkn760","article-title":"STRING 8 \u2014 A global view on proteins and their functional interactions in 630 organisms","volume":"37","author":"Jensen","year":"2009","journal-title":"Nucleic Acids Res."},{"key":"2023061011552526700_B16","first-page":"19","article-title":"Semantic similarity based on corpus statistics and lexical taxonomy","volume-title":"Proceedings of 10th International Conference on Research in Computational Linguistics","author":"Jiang","year":"1997"},{"key":"2023061011552526700_B17","doi-asserted-by":"crossref","first-page":"170","DOI":"10.1186\/1471-2105-8-170","article-title":"Estimating the annotation error rate of curated GO database sequence annotations","volume":"8","author":"Jones","year":"2007","journal-title":"BMC Bioinformatics"},{"key":"2023061011552526700_B18","first-page":"296","article-title":"An information-theoretic definition of similarity","volume-title":"Proceedings of the 15th International Conference on Machine Learning.","author":"Lin","year":"1998"},{"key":"2023061011552526700_B19","doi-asserted-by":"crossref","first-page":"154","DOI":"10.1186\/1471-2105-5-154","article-title":"Information assessment on predicting protein-protein interactions","volume":"5","author":"Lin","year":"2004","journal-title":"BMC Bioinformatics"},{"key":"2023061011552526700_B20","doi-asserted-by":"crossref","first-page":"945","DOI":"10.1101\/gr.3610305","article-title":"Assessing the limits of genomic data integration for predicting protein networks","volume":"15","author":"Lu","year":"2005","journal-title":"Genome Res."},{"key":"2023061011552526700_B21","doi-asserted-by":"crossref","first-page":"218","DOI":"10.1093\/bioinformatics\/bth483","article-title":"Predicting protein-protein interactions using signature products","volume":"21","author":"Martin","year":"2005","journal-title":"Bioinformatics"},{"key":"2023061011552526700_B22","doi-asserted-by":"crossref","first-page":"12123","DOI":"10.1073\/pnas.0505482102","article-title":"Large-scale identification of yeast integral membrane protein interactions","volume":"102","author":"Miller","year":"2005","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"2023061011552526700_B23","doi-asserted-by":"crossref","first-page":"419","DOI":"10.1186\/1471-2105-10-419","article-title":"Critical assessment of sequence-based protein-protein interaction prediction methods that do not require homologous protein sequences","volume":"10","author":"Park","year":"2009","journal-title":"BMC Bioinformatics"},{"key":"2023061011552526700_B24","doi-asserted-by":"crossref","first-page":"100","DOI":"10.1186\/1471-2105-6-100","article-title":"Filtering high-throughput protein-protein interaction data using a combination of genomic features","volume":"6","author":"Patil","year":"2005","journal-title":"BMC Bioinformatics"},{"issue":"Suppl. 5","key":"2023061011552526700_B25","doi-asserted-by":"crossref","first-page":"S4","DOI":"10.1186\/1471-2105-9-S5-S4","article-title":"Metrics for GO based protein semantic similarity: a systematic evaluation","volume":"9","author":"Pesquita","year":"2008","journal-title":"BMC Bioinformatics"},{"key":"2023061011552526700_B26","doi-asserted-by":"crossref","first-page":"e1000443","DOI":"10.1371\/journal.pcbi.1000443","article-title":"Semantic similarity in biomedical ontologies","volume":"5","author":"Pesquita","year":"2009","journal-title":"PLoS Comput. Biol."},{"key":"2023061011552526700_B27","doi-asserted-by":"crossref","first-page":"365","DOI":"10.1186\/1471-2105-7-365","article-title":"PIPE: a protein-protein interaction prediction engine based on the re-occurring short polypeptide sequences between known interacting protein pairs","volume":"7","author":"Pitre","year":"2006","journal-title":"BMC Bioinformatics"},{"key":"2023061011552526700_B28","doi-asserted-by":"crossref","first-page":"490","DOI":"10.1002\/prot.20865","article-title":"Evaluation of different biological data and computational methods for use in protein interaction prediction","volume":"63","author":"Qi","year":"2006","journal-title":"Proteins"},{"key":"2023061011552526700_B29","doi-asserted-by":"crossref","first-page":"e1000054","DOI":"10.1371\/journal.pcbi.1000054","article-title":"Predicting co-complexed protein pairs from heterogeneous data","volume":"4","author":"Qiu","year":"2008","journal-title":"PLoS Comput. Biol."},{"key":"2023061011552526700_B30","first-page":"448","article-title":"Using information content to evaluate semantic similarity in a taxonomy","author":"Resnik","year":"1995","journal-title":"Proceedings of the 14th International Joint Conference on Artificial Intelligence"},{"key":"2023061011552526700_B31","doi-asserted-by":"crossref","first-page":"951","DOI":"10.1038\/nbt1103","article-title":"Probabilistic model of the human protein-protein interaction network","volume":"23","author":"Rhodes","year":"2005","journal-title":"Nat. Biotechnol."},{"key":"2023061011552526700_B32","doi-asserted-by":"crossref","first-page":"1173","DOI":"10.1093\/bioinformatics\/btp122","article-title":"The use of gene ontology evidence codes in preventing classifier assessment bias","volume":"25","author":"Rogers","year":"2009","journal-title":"BMC Bioinformatics"},{"key":"2023061011552526700_B33","doi-asserted-by":"crossref","first-page":"302","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":"Schlicker","year":"2006","journal-title":"BMC Bioinformatics"},{"key":"2023061011552526700_B34","doi-asserted-by":"crossref","first-page":"28","DOI":"10.1186\/1752-0509-3-28","article-title":"Protein-protein interaction as a predictor of subcellular location","volume":"3","author":"Shin","year":"2009","journal-title":"BMC Syst. Biol."},{"key":"2023061011552526700_B35","doi-asserted-by":"crossref","first-page":"4337","DOI":"10.1073\/pnas.0607879104","article-title":"Predicting protein-protein interactions based only on sequences information","volume":"104","author":"Shin","year":"2007","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"2023061011552526700_B36","doi-asserted-by":"crossref","first-page":"D540","DOI":"10.1093\/nar\/gkp1026","article-title":"The Negatome database: a reference set of non-interacting protein pairs","volume":"38","author":"Smialowski","year":"2010","journal-title":"Nucleic Acids Res."},{"key":"2023061011552526700_B37","doi-asserted-by":"crossref","first-page":"1251","DOI":"10.1038\/nbt1346","article-title":"The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration","volume":"25","author":"Smith","year":"2007","journal-title":"Nat. Biotechnol."},{"key":"2023061011552526700_B38","doi-asserted-by":"crossref","first-page":"399","DOI":"10.1038\/nature750","article-title":"Comparative assessment of large-scale datasets of protein-protein interactions","volume":"417","author":"von Mering","year":"2002","journal-title":"Nature"},{"key":"2023061011552526700_B39","doi-asserted-by":"crossref","first-page":"D433","DOI":"10.1093\/nar\/gki005","article-title":"STRING: known and predicted protein-protein associations, integrated and transferred across organisms","volume":"33","author":"von Mering","year":"2005","journal-title":"Nucleic Acids Res."},{"key":"2023061011552526700_B40","doi-asserted-by":"crossref","first-page":"2137","DOI":"10.1093\/nar\/gkl219","article-title":"Prediction of yeast protein-protein interaction network: insights from the Gene Ontology and annotations","volume":"34","author":"Wu","year":"2006","journal-title":"Nucleic Acids Res."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/28\/1\/69\/50568535\/bioinformatics_28_1_69.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/28\/1\/69\/50568535\/bioinformatics_28_1_69.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,6,10]],"date-time":"2023-06-10T11:55:57Z","timestamp":1686398157000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/28\/1\/69\/220214"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2011,11,4]]},"references-count":40,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2012,1,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btr610","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2012,1,1]]},"published":{"date-parts":[[2011,11,4]]}}}