by Sidahmed Benabderrahmane, Marie-Dominique Devignes, M Smail-Tabbone, O Poch, A Napoli
Abstract:
Motivation: Gene Ontology (GO) has become a widely used knowledge source in bioinformatics for measuring semantic similarity, with the purpose of gene functional clustering. Several approaches have been proposed that exploit features such as the GO hierarchy, information-content and the ontology structure. In this paper, we present a new synthetic measure, called IntelliGO, that explicits the integration of these features in novel framework which, moreover, considers meta data of annotations quality. The proposed measure can be used thereafter with the gene functional clustering. Results:We have validated our IntelliGO semantic similarity measure following a protocol that includes two steps. First, by comparing our measure with several popular measures. Secondly, by calculating the average similarity measure within a set of pre-selected pathways. The results are very promising.
Reference:
IntelliGO: Towards a New Synthetic Semantic Similarity Measure by Considering Metadata of Gene Functional Annotations Quality (Sidahmed Benabderrahmane, Marie-Dominique Devignes, M Smail-Tabbone, O Poch, A Napoli), Technical report, Université Henri Poincaré - Nancy I, 2010.
Bibtex Entry:
@techreport{Benabderrahmane2010a,
abstract = {Motivation: Gene Ontology (GO) has become a widely used knowledge source in bioinformatics for measuring semantic similarity, with the purpose of gene functional clustering. Several approaches have been proposed that exploit features such as the GO hierarchy, information-content and the ontology structure. In this paper, we present a new synthetic measure, called IntelliGO, that explicits the integration of these features in novel framework which, moreover, considers meta data of annotations quality. The proposed measure can be used thereafter with the gene functional clustering. Results:We have validated our IntelliGO semantic similarity measure following a protocol that includes two steps. First, by comparing our measure with several popular measures. Secondly, by calculating the average similarity measure within a set of pre-selected pathways. The results are very promising.},
author = {Benabderrahmane, Sidahmed and Devignes, Marie-Dominique and Smail-Tabbone, M and Poch, O and Napoli, A},
institution = {Universit\'{e} Henri Poincar\'{e} - Nancy I},
keywords = {SML-LIB-BIBLIO,lang:ENG},
mendeley-tags = {SML-LIB-BIBLIO,lang:ENG},
pages = {1--6},
title = {{IntelliGO: Towards a New Synthetic Semantic Similarity Measure by Considering Metadata of Gene Functional Annotations Quality}},
url = {http://ftp.heanet.ie/mirrors/sourceforge/i/project/in/intelligo/ISMB10\_v1.pdf},
year = {2010}
}