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Bioinformatics Advance Access originally published online on June 29, 2006
Bioinformatics 2006 22(16):2055-2057; doi:10.1093/bioinformatics/btl342
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© 2006 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commerical use, distribution, and reproduction in any medium, provided the original work is properly cited.

PDQ Wizard: automated prioritization and characterization of gene and protein lists using biomedical literature

G. R. Grimes 1,*, T. Q. Wen 2, M. Mewissen 1, R. M. Baxter 3, S. Moodie 1, J. S. Beattie 1 and P. Ghazal 1

1 The Scottish Centre for Genomic Technology and Informatics, University of Edinburgh 49 Little France Crescent, Edinburgh EH16 4SB, UK
2 eDIKT Programme, National E-Science Centre 15 South College Street, Edinburgh EH8 9AA, UK
3 Edinburgh Parallel Computing Centre, The University of Edinburgh, James Clerk Maxwell Building, King’s Buildings Edinburgh EH9 3JZ, UK

*To whom correspondence should be addressed.


  Abstract

Summary: PDQ Wizard automates the process of interrogating biomedical references using large lists of genes, proteins or free text. Using the principle of linkage through co-citation biologists can mine PubMed with these proteins or genes to identify relationships within a biological field of interest. In addition, PDQ Wizard provides novel features to define more specific relationships, highlight key publications describing those activities and relationships, and enhance protein queries. PDQ Wizard also outputs a metric that can be used for prioritization of genes and proteins for further research.

Availability: PDQ Wizard is freely available from http://www.gti.ed.ac.uk/pdqwizard/

Contact: Graeme.Grimes{at}ed.ac.uk

Supplementary Information: Supplementary Data are available http://www.gti.ed.ac.uk/pdqwizard/

Associate Editor: Thomas Lengauer

Received on March 16, 2006; revised on May 10, 2006; accepted on June 20, 2006

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