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PolySearch2: a significantly improved text-mining system for discovering associations between human diseases, genes, drugs, metabolites, toxins and more.

Liu Y, Liang Y, Wishart D - Nucleic Acids Res. (2015)

Bottom Line: PolySearch2 also searches 14 widely used, text-rich biological databases such as UniProt, DrugBank and Human Metabolome Database to improve its accuracy and coverage.PolySearch2 maintains an extensive thesaurus of biological terms and exploits the latest search engine technology to rapidly retrieve relevant articles and databases records.PolySearch2 also generates, ranks and annotates associative candidates and present results with relevancy statistics and highlighted key sentences to facilitate user interpretation.

View Article: PubMed Central - PubMed

Affiliation: Department of Computing Science, University of Alberta, Edmonton, T6G 2E8 Canada.

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A screenshot montage of PolySearch2's query interface and result display showing (A) the PolySearch2 query submission form, (B) the advanced option page for further query refinement, (C) the PolySearch2 result overview table and (D) the detailed result page showing the supporting evidence for a single association.
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Figure 1: A screenshot montage of PolySearch2's query interface and result display showing (A) the PolySearch2 query submission form, (B) the advanced option page for further query refinement, (C) the PolySearch2 result overview table and (D) the detailed result page showing the supporting evidence for a single association.

Mentions: PolySearch2 (http://polysearch.ca) features a completely re-designed web interface. Figure 1 shows a screenshot montage of various pages from PolySearch2's new web interface. Figure 1A shows the query submission page where users can initialize a search query. As with the original PolySearch, PolySearch2 still supports a ‘Given X, find all associated Y's’ type of query. Users can initialize a search by selecting the desired type of X (query term) and Y (target term) from pull-down menus and enter a search query keyword. At this point, user can submit a ‘Quick Search’ request or further configure the search using ‘Advanced Options’ (Figure 1B). Both of these features are new to PolySearch2. The Quick Search option will direct PolySearch2 to search previously computed cache results or to mine associations from the top 2000 relevant articles or database records across all text collections and databases. In the Quick Search, PolySearch2 automatically generates a synonym list (from the PolySearch2 thesauri) and proceeds with its regular searching, sorting, scoring, annotation and display (described in detail in (7)). ‘Advanced Options’ (Figure 1B) offers a greater degree of customizability to the search. For instance, users can edit the automatically generated synonym list (from the PolySearch2 thesaurus), edit custom filter words for identifying association patterns, provide custom negation words for filtering out sentences with negative associations, provide custom target terms to search, select or de-select source text collections and databases, indicate the number of documents to search, permit the inclusion or exclusion of hits with zero Z-scores (for higher recall) and/or provide an E-mail address for notifications.


PolySearch2: a significantly improved text-mining system for discovering associations between human diseases, genes, drugs, metabolites, toxins and more.

Liu Y, Liang Y, Wishart D - Nucleic Acids Res. (2015)

A screenshot montage of PolySearch2's query interface and result display showing (A) the PolySearch2 query submission form, (B) the advanced option page for further query refinement, (C) the PolySearch2 result overview table and (D) the detailed result page showing the supporting evidence for a single association.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4489268&req=5

Figure 1: A screenshot montage of PolySearch2's query interface and result display showing (A) the PolySearch2 query submission form, (B) the advanced option page for further query refinement, (C) the PolySearch2 result overview table and (D) the detailed result page showing the supporting evidence for a single association.
Mentions: PolySearch2 (http://polysearch.ca) features a completely re-designed web interface. Figure 1 shows a screenshot montage of various pages from PolySearch2's new web interface. Figure 1A shows the query submission page where users can initialize a search query. As with the original PolySearch, PolySearch2 still supports a ‘Given X, find all associated Y's’ type of query. Users can initialize a search by selecting the desired type of X (query term) and Y (target term) from pull-down menus and enter a search query keyword. At this point, user can submit a ‘Quick Search’ request or further configure the search using ‘Advanced Options’ (Figure 1B). Both of these features are new to PolySearch2. The Quick Search option will direct PolySearch2 to search previously computed cache results or to mine associations from the top 2000 relevant articles or database records across all text collections and databases. In the Quick Search, PolySearch2 automatically generates a synonym list (from the PolySearch2 thesauri) and proceeds with its regular searching, sorting, scoring, annotation and display (described in detail in (7)). ‘Advanced Options’ (Figure 1B) offers a greater degree of customizability to the search. For instance, users can edit the automatically generated synonym list (from the PolySearch2 thesaurus), edit custom filter words for identifying association patterns, provide custom negation words for filtering out sentences with negative associations, provide custom target terms to search, select or de-select source text collections and databases, indicate the number of documents to search, permit the inclusion or exclusion of hits with zero Z-scores (for higher recall) and/or provide an E-mail address for notifications.

Bottom Line: PolySearch2 also searches 14 widely used, text-rich biological databases such as UniProt, DrugBank and Human Metabolome Database to improve its accuracy and coverage.PolySearch2 maintains an extensive thesaurus of biological terms and exploits the latest search engine technology to rapidly retrieve relevant articles and databases records.PolySearch2 also generates, ranks and annotates associative candidates and present results with relevancy statistics and highlighted key sentences to facilitate user interpretation.

View Article: PubMed Central - PubMed

Affiliation: Department of Computing Science, University of Alberta, Edmonton, T6G 2E8 Canada.

Show MeSH
Related in: MedlinePlus