Zahedan Journal of Research in Medical Sciences

Published by: Neoscriber Demo Publisher

A Novel Measure for Semantic Similarity Computation of Gene Ontology Terms Using Weighted Aggregation of Information Contents

Amir Lakizadeh 1 , * and Saeed Jalili 2
Authors Information
1 Department of Computer Science, University of Qom, Qom, Iran
2 Department of Computer Engineering, Tarbiat Modares University Tehran, Iran
Article information
  • Hepatitis Monthly: August 2017, 19 (8); e12041
  • Published Online: August 31, 2017
  • Article Type: Research Article
  • Received: April 24, 2017
  • Revised: June 3, 2017
  • Accepted: July 1, 2017
  • DOI: 10.5812/zjrms.12041

To Cite: Lakizadeh A, Jalili S. A Novel Measure for Semantic Similarity Computation of Gene Ontology Terms Using Weighted Aggregation of Information Contents, Zahedan J Res Med Sci. 2017 ; 19(8):e12041. doi: 10.5812/zjrms.12041.

Abstract
Copyright © 2017, Kowsar Corp. This is an open-access article distributed under the terms of the Creative Commons Attribution-NonCommercial 4.0 International License (http://creativecommons.org/licenses/by-nc/4.0/) which permits copy and redistribute the material just in noncommercial usages, provided the original work is properly cited.
1. Background
2. Methods
3. Results
4. Discussion
Acknowledgements
Footnotes
References
  • 1. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, et al. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet. 2000; 25(1): 25-9[DOI][PubMed]
  • 2. Pesquita C, Faria D, Falcao AO, Lord P, Couto FM. Semantic similarity in biomedical ontologies. PLoS Comput Biol. 2009; 5(7)[DOI][PubMed]
  • 3. Xu Y, Guo M, Shi W, Liu X, Wang C. A novel insight into Gene Ontology semantic similarity. Genomics. 2013; 101(6): 368-75[DOI][PubMed]
  • 4. Harispe S, Sanchez D, Ranwez S, Janaqi S, Montmain J. A framework for unifying ontology-based semantic similarity measures: a study in the biomedical domain. J Biomed Inform. 2014; 48: 38-53[DOI][PubMed]
  • 5. Song X, Li L, Srimani PK, Yu PS, Wang JZ. Measure the Semantic Similarity of GO Terms Using Aggregate Information Content. IEEE/ACM Trans Comput Biol Bioinform. 2014; 11(3): 468-76[DOI][PubMed]
  • 6. Li B, Wang JZ, Feltus FA, Zhou J, Luo F. Effectively integrating information content and structural relationship to improve the GO-based similarity measure between proteins. 2010;
  • 7. Sevilla JL, Segura V, Podhorski A, Guruceaga E, Mato JM, Martinez-Cruz LA, et al. Correlation between gene expression and GO semantic similarity. IEEE/ACM Trans Comput Biol Bioinform. 2005; 2(4): 330-8[DOI][PubMed]
  • 8. Wang JZ, Du Z, Payattakool R, Yu PS, Chen CF. A new method to measure the semantic similarity of GO terms. Bioinformatics. 2007; 23(10): 1274-81[DOI][PubMed]
  • 9. Cheng J, Cline M, Martin J, Finkelstein D, Awad T, Kulp D, et al. A knowledge-based clustering algorithm driven by Gene Ontology. J Biopharm Stat. 2004; 14(3): 687-700[DOI][PubMed]
  • 10. Resnik P. Semantic similarity in a taxonomy: An information-based measure and its application to problems of ambiguity in natural language. J Artif Intell Res. 1999; 11: 95-130
  • 11. An information-theoretic definition of similarity. Proceedings of the 15th international conference on Machine Learning.
  • 12. Jiang JJ, Conrath DW. Semantic similarity based on corpus statistics and lexical taxonomy. 1997;
  • 13. Miller GA, Beckwith R, Fellbaum C, Gross D, Miller KJ. Introduction to wordnet: An on-line lexical database*. Int J Lexicogr. 1990; 3(4): 235-44[DOI]
  • 14. Semantic similarity over the gene ontology: family correlation and selecting disjunctive ancestors. Proceedings of the 14th ACM international conference on Information and knowledge management. : 343
  • 15. Couto FM, Silva MJ, Coutinho PM. Implementation of a functional semantic similarity measure between gene-products. 2003;
  • 16. Yuhua L, Bandar ZA, McLean D. An approach for measuring semantic similarity between words using multiple information sources. IEEE Trans Knowl Data Eng. 2003; 15(4): 871-82[DOI]
  • 17. Othman RM, Deris S, Illias RM. A genetic similarity algorithm for searching the Gene Ontology terms and annotating anonymous protein sequences. J Biomed Inform. 2008; 41(1): 65-81[DOI][PubMed]
  • 18. Lord PW, Stevens RD, Brass A, Goble CA. Investigating semantic similarity measures across the Gene Ontology: the relationship between sequence and annotation. Bioinformatics. 2003; 19(10): 1275-83[PubMed]
  • 19. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997; 25(17): 3389-402[DOI][PubMed]
  • 20. Joshi T, Xu D. Quantitative assessment of relationship between sequence similarity and function similarity. BMC Genomics. 2007; 8: 222[DOI][PubMed]
  • 21. Falcon S, Gentleman R. Using GOstats to test gene lists for GO term association. Bioinformatics. 2007; 23(2): 257-8[DOI][PubMed]
  • 22. Evaluating GO-based semantic similarity measures. Proc 10th Annual Bio-Ontologies Meeting.
  • 23. Couto FM, Silva MJ. Disjunctive shared information between ontology concepts: application to Gene Ontology. J Biomed Semantics. 2011; 2: 5[DOI][PubMed]
  • 24. Gene functional similarity analysis by definition-based semantic similarity measurement of GO terms. Canadian Conference on Artificial Intelligence. : 203-14
  • 25. Yang H, Nepusz T, Paccanaro A. Improving GO semantic similarity measures by exploring the ontology beneath the terms and modelling uncertainty. Bioinformatics. 2012; 28(10): 1383-9[DOI][PubMed]
  • 26. Gene expression correlation and gene ontology-based similarity: an assessment of quantitative relationships. 2004 CIBCB'04 Proceedings of the 2004 IEEE. : 25-31
  • 27. Jain S, Bader GD. An improved method for scoring protein-protein interactions using semantic similarity within the gene ontology. BMC Bioinformatics. 2010; 11: 562[DOI][PubMed]
  • 28. Warde-Farley D, Donaldson SL, Comes O, Zuberi K, Badrawi R, Chao P, et al. The GeneMANIA prediction server: biological network integration for gene prioritization and predicting gene function. Nucleic Acids Res. 2010; 38-20[DOI][PubMed]
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