CoPub Mapper mining MEDLINE based on search term co-publication.docVIP

BMC Bioinformatics BioMedCentral Software Open Access CoPub Mapper: mining MEDLINE based on search term co-publication Blaise TF Alako1, Antoine Veldhoven2, Sjozef van Baal3, Rob Jelier4, Stefan Verhoeven1, Ton Rullmann1, Jan Polman1 and Guido Jenster*2 Address: 1Department of Molecular Design Informatics, Organon NV, P.O. Box 20, 5340 BH Oss, The Netherlands, 2Department of Urology, Erasmus MC, P.O. Box 1738, 3000 DR Rotterdam, The Netherlands, 3Department of Genetics, Erasmus MC, Rotterdam, The Netherlands and 4Department of Medical Informatics, Erasmus MC, Rotterdam, The Netherlands Email: Blaise TF Alako - blaise.alako@wur.nl; Antoine Veldhoven - a.veldhoven@erasmusmc.nl; Sjozef van Baal - j.vanbaal@erasmusmc.nl; Rob Jelier - r.jelier@erasmusmc.nl; Stefan Verhoeven - stefan.verhoeven@; Ton Rullmann - ton.rullmann@; Jan Polman - jan.polman@; Guido Jenster* - g.jenster@erasmusmc.nl * Corresponding author Published: 11 March 2005 Received: 21 December 2004 Accepted: 11 March 2005 BMC Bioinformatics 2005, 6:51 doi:10.1186/1471-2105-6-51 This article is available from: /1471-2105/6/51 ? 2005 Alako et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Abstract Background: High throughput microarray analyses result in many differentially expressed genes that are potentially responsible for the biological process of interest. In order to identify biological similarities between genes, publications from MEDLINE were identified in which pairs of gene names and combinations of gene name with specific keywords were co-mentioned. Results: MEDLINE search strings for 15,621 known genes and 3,731 keywords were generated and validated. PubMed IDs were retrieved from MEDLINE and relative probability of