A literature-based similarity metric for biological processes

doi:10.1186/1471-2105-7-363

BMC Bioinformatics

Volume 7

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Chagoyen M
Carmona-Saez P
Gil C
Carazo JM
Pascual-Montano A

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Methodology article

A literature-based similarity metric for biological processes

Monica Chagoyen¹^,2 , Pedro Carmona-Saez¹ , Concha Gil³^,4 , Jose M Carazo¹ and Alberto Pascual-Montano²

¹Biocomputing Unit. Centro Nacional de Biotecnologia – CSIC, Madrid, Spain

²Dpto. Arquitectura de Computadores y Automatica. Universidad Complutense de Madrid, Madrid, Spain

³Dpto. Microbiologia II. Facultad de Farmacia. Universidad Complutense de Madrid, Madrid, Spain

⁴Unidad de Proteomica UCM – Parque Cientifico de Madrid, Madrid, Spain

author email corresponding author email

BMC Bioinformatics 2006, 7:363doi:10.1186/1471-2105-7-363


Published:	26 July 2006

Additional files

Additional file 1:

Histograms. This file contains three histograms corresponding to the pair-wise similarities among biological processes in the 282 subset used for validation, as obtained by literature analysis, the GO ontology structure (using Lin and Czekanowski-Dice formulae) and S. cerevisiae genome annotation.

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Additional file 2:

Comparison of ontology-based similarities. This file contains the boxplot of Lin similarity along different intervals of Czekanowski-Dice similarity.

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Additional file 3:

Correlation with shared genes/references. This file contains plots of the literature-based similarity against (a) the number of genes shared by any two biological processes (note than no more than 3 genes are shared by any two processes); (b) the normalised number references shared by any two biological processes.

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Additional file 4:

Correlation among similarity metrics. This file contains the correlation coefficients (using Pearson, Spearman, Kendall and uncentered dot product methods) among the four similarity metrics used for the evaluation set.

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Additional file 5:

Similar biological processes according to the literature. This file contains the 49 biological process pairs which are similar according to literature and similar less than average according to both ontology-based metrics. The first 10 pairs correspond to Table 1 in the full text article.

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