Email updates

Keep up to date with the latest news and content from Genome Biology and BioMed Central.

Open Access Method

Novel metrics for evaluating the functional coherence of protein groups via protein semantic network

Bin Zheng12 and Xinghua Lu1*

Author Affiliations

1 Department of Biostatistics, Bioinformatics and Epidemiology, 135 Cannon Street, Charleston, South Carolina 29425, USA

2 Laboratory for Functional Neurogenomics, Center for Neurologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Landsdowne Street, Cambridge, Massachusetts 02139, USA

For all author emails, please log on.

Genome Biology 2007, 8:R153  doi:10.1186/gb-2007-8-7-r153

Published: 31 July 2007

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.