Genome Biology
Volume 8
Issue 7 |
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 MethodNovel metrics for evaluating the functional coherence of protein groups via protein semantic networkBin Zheng1,2  and Xinghua Lu1  1Department of Biostatistics, Bioinformatics and Epidemiology, 135 Cannon Street, Charleston, South Carolina 29425, USA 2Laboratory for Functional Neurogenomics, Center for Neurologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Landsdowne Street, Cambridge, Massachusetts 02139, USA  author email corresponding author email
Genome Biology 2007,
8:R153doi:10.1186/gb-2007-8-7-r153
Subject areas: Bioinformatics, Genome studies Abstract
We present the metrics for assessing overall functional coherence of a group of proteins based on associated biomedical literature. A probabilistic topic model is applied to extract biologic concepts from a corpus of protein-related biomedical literature. Bipartite protein semantic networks are constructed, so that the functional coherence of a protein group can be evaluated with metrics that measure the closeness and strength of connectivity of the proteins in the network. | 
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