Automatic clustering of gene ontology by genetic algorithm
Abstract—Nowadays, Gene Ontology has been used widely by many researchers for biological data mining and information retrieval, integration of biological databases, finding genes, and incorporating knowledge in the Gene Ontology for gene clustering. However, the increase in size of the Gene Ontology...
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| Format: | Article |
| Language: | en |
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2006
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| Online Access: | http://eprints.utm.my/1009/1/RazibMOthman2006_AutomaticClusteringofGeneOntology.pdf http://eprints.utm.my/1009/ |
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| author | Othman, Razib M. Deris, Safaai Zakaria, Zalmiyah Illias, Rosli M. Mohamad, Saberi M. |
| author_facet | Othman, Razib M. Deris, Safaai Zakaria, Zalmiyah Illias, Rosli M. Mohamad, Saberi M. |
| author_sort | Othman, Razib M. |
| building | UTM Library |
| collection | Institutional Repository |
| content_provider | Universiti Teknologi Malaysia |
| content_source | UTM Institutional Repository |
| continent | Asia |
| country | Malaysia |
| description | Abstract—Nowadays, Gene Ontology has been used widely by many researchers for biological data mining and information retrieval, integration of biological databases, finding genes, and incorporating knowledge in the Gene Ontology for gene clustering. However, the increase in size of the Gene Ontology has caused problems in maintaining and processing them. One way to obtain their accessibility is by clustering them into fragmented groups. Clustering the Gene Ontology is a difficult combinatorial problem and can be modeled as a graph partitioning problem. Additionally, deciding the number k of clusters to use is not easily perceived and is a hard algorithmic problem. Therefore, an approach for solving the automatic clustering of the Gene Ontology is proposed by incorporating cohesion-and-coupling metric into a hybrid algorithm consisting of a genetic algorithm and a split-and-merge algorithm. Experimental results and an example of modularized Gene Ontology in RDF/XML format are given to illustrate the effectiveness of the algorithm |
| format | Article |
| id | my.utm.eprints-1009 |
| institution | Universiti Teknologi Malaysia |
| language | en |
| publishDate | 2006 |
| record_format | eprints |
| spelling | my.utm.eprints-10092010-10-13T08:16:59Z http://eprints.utm.my/1009/ Automatic clustering of gene ontology by genetic algorithm Othman, Razib M. Deris, Safaai Zakaria, Zalmiyah Illias, Rosli M. Mohamad, Saberi M. QA Mathematics Abstract—Nowadays, Gene Ontology has been used widely by many researchers for biological data mining and information retrieval, integration of biological databases, finding genes, and incorporating knowledge in the Gene Ontology for gene clustering. However, the increase in size of the Gene Ontology has caused problems in maintaining and processing them. One way to obtain their accessibility is by clustering them into fragmented groups. Clustering the Gene Ontology is a difficult combinatorial problem and can be modeled as a graph partitioning problem. Additionally, deciding the number k of clusters to use is not easily perceived and is a hard algorithmic problem. Therefore, an approach for solving the automatic clustering of the Gene Ontology is proposed by incorporating cohesion-and-coupling metric into a hybrid algorithm consisting of a genetic algorithm and a split-and-merge algorithm. Experimental results and an example of modularized Gene Ontology in RDF/XML format are given to illustrate the effectiveness of the algorithm 2006 Article PeerReviewed application/pdf en http://eprints.utm.my/1009/1/RazibMOthman2006_AutomaticClusteringofGeneOntology.pdf Othman, Razib M. and Deris, Safaai and Zakaria, Zalmiyah and Illias, Rosli M. and Mohamad, Saberi M. (2006) Automatic clustering of gene ontology by genetic algorithm. International Journal of Information Technology, 3 (1). pp. 37-46. ISSN 2070-3961 |
| spellingShingle | QA Mathematics Othman, Razib M. Deris, Safaai Zakaria, Zalmiyah Illias, Rosli M. Mohamad, Saberi M. Automatic clustering of gene ontology by genetic algorithm |
| title | Automatic clustering of gene ontology by genetic algorithm |
| title_full | Automatic clustering of gene ontology by genetic algorithm |
| title_fullStr | Automatic clustering of gene ontology by genetic algorithm |
| title_full_unstemmed | Automatic clustering of gene ontology by genetic algorithm |
| title_short | Automatic clustering of gene ontology by genetic algorithm |
| title_sort | automatic clustering of gene ontology by genetic algorithm |
| topic | QA Mathematics |
| url | http://eprints.utm.my/1009/1/RazibMOthman2006_AutomaticClusteringofGeneOntology.pdf http://eprints.utm.my/1009/ |
| url_provider | http://eprints.utm.my/ |