Bioinformatics Advance Access originally published online on January 18, 2005
Bioinformatics 2005 21(9):2049-2058; doi:10.1093/bioinformatics/bti268
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Co-occurrence based meta-analysis of scientific texts: retrieving biological relationships between genes
1Department of Medical Informatics, Erasmus MC—University Medical Center Rotterdam, The Netherlands
2Department of Urology, Erasmus MC—University Medical Center Rotterdam, The Netherlands
3Department of Pathology, Erasmus MC—University Medical Center Rotterdam, The Netherlands
*To whom correspondence should be addressed at Department of Medical Informatics, Erasmus MC—University Medical Center Rotterdam, PO Box 1738, 3000 DR Rotterdam, The Netherlands.
Motivation: The advent of high-throughput experiments in molecular biology creates a need for methods to efficiently extract and use information for large numbers of genes. Recently, the associative concept space (ACS) has been developed for the representation of information extracted from biomedical literature. The ACS is a Euclidean space in which thesaurus concepts are positioned and the distances between concepts indicates their relatedness. The ACS uses co-occurrence of concepts as a source of information. In this paper we evaluate how well the system can retrieve functionally related genes and we compare its performance with a simple gene co-occurrence method.
Results: To assess the performance of the ACS we composed a test set of five groups of functionally related genes. With the ACS good scores were obtained for four of the five groups. When compared to the gene co-occurrence method, the ACS is capable of revealing more functional biological relations and can achieve results with less literature available per gene. Hierarchical clustering was performed on the ACS output, as a potential aid to users, and was found to provide useful clusters. Our results suggest that the algorithm can be of value for researchers studying large numbers of genes.
Availability: The ACS program is available upon request from the authors.
Contact: r.jelier{at}erasmusmc.nl
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