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Bioinformatics Advance Access published online on June 29, 2006
Bioinformatics, doi:10.1093/bioinformatics/btl342
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© 2006 The Author(s)
Received March 16, 2006
Revised May 10, 2006
Accepted June 20, 2006

Article

PDQ Wizard: automated prioritisation and characterisation 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, The University of Edinburgh, The Chancellor's Building, College of Medicine, 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.
G. R. Grimes, E-mail: Graeme.Grimes{at}ed.ac.uk


  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 prioritisation of genes and proteins for further research.

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

Associate Editor: Thomas Lengauer
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