A particular challenge in biomedical text mining is to find ways of handling 
'comprehensive' or 'associative' queries such as 'Find all genes associated with 
breast cancer'. Given that many queries in genomics, proteomics or metabolomics 
involve these kind of comprehensive searches we believe that a web-based tool 
that could support these searches would be quite useful. In response to this 
need, we have developed the PolySearch web server. PolySearch supports >50 
different classes of queries against nearly a dozen different types of text, 
scientific abstract or bioinformatic databases. The typical query supported by 
PolySearch is 'Given X, find all Y's' where X or Y can be diseases, tissues, 
cell compartments, gene/protein names, SNPs, mutations, drugs and metabolites. 
PolySearch also exploits a variety of techniques in text mining and information 
retrieval to identify, highlight and rank informative abstracts, paragraphs or 
sentences. PolySearch's performance has been assessed in tasks such as gene 
synonym identification, protein-protein interaction identification and disease 
gene identification using a variety of manually assembled 'gold standard' text 
corpuses. Its f-measure on these tasks is 88, 81 and 79%, respectively. These 
values are between 5 and 50% better than other published tools. The server is 
freely available at http://wishart.biology.ualberta.ca/polysearch.