A critical task in biomedical text mining is to discover potential associations between various types of biomedical entities. PolySearch 2.0 (polysearch.ca) is an online text-mining system for identifying relationships between human diseases, genes, proteins, drugs, metabolites, toxins, metabolic pathways, organs, tissues, subcellular organelles, positive health effects, negative health effects, drug actions, Gene Ontology terms, MeSH terms, ICD-10 medical codes, biological taxonomies and chemical taxonomies. PolySearch 2.0 supports a generalized 'Given X, find all associated Ys' query, where X and Y can be selected from the aforementioned biomedical entities. For example, 'Find all associated diseases with Bisphenol A'. PolySearch 2.0 searches for associations against comprehensive collections of free-text corpora, including local versions of MEDLINE abstracts, PubMed Central full-text articles, Wikipedia full-text articles, and US Patent application abstracts. PolySearch 2.0 also searches 14 widely used, text-rich biological databases such as UniProt, DrugBank and HMDB to improve its accuracy and coverage. PolySearch 2.0 maintains an extensive thesaurus of biological terms and exploits the latest search engine technology to rapidly retrieve relevant articles and databases records. PolySearch 2.0 also generates, ranks, and annotates associative candidates and present results with relevancy statistics and highlighted key sentences to facilitate user interpretation.View sample results on query "Given Toxin Bisphenol A Find associated Diseases"
Liu Y., Liang Y., Wishart D.S. (2015) PolySearch 2.0: A significantly improved text-mining system for discovering associations between human diseases, genes, drugs, metabolites, toxins, and more. Nucleic Acids Res. 2015 (Web Server Issue) Manuscript submitted.
This project is supported by the Canadian Institutes of Health Research (award #111062), Alberta Innovates - Health Solutions, and by The Metabolomics Innovation Centre (TMIC), a nationally-funded research and core facility that supports a wide range of cutting-edge metabolomic studies. TMIC is funded by Genome Alberta, Genome British Columbia, and Genome Canada, a not-for-profit organization that is leading Canada's national genomics strategy with $900 million in funding from the federal government.