ERA

Download the full-sized PDF of PolySearch: A web-based text mining system for extracting relationships between human diseases, genes, mutations, drugs and metabolitesDownload the full-sized PDF

Analytics

Share

Permanent link (DOI): https://doi.org/10.7939/R3ZG6G93X

Download

Export to: EndNote  |  Zotero  |  Mendeley

Communities

This file is in the following communities:

Biological Sciences, Department of

Collections

This file is in the following collections:

Journal Articles (Biological Sciences)

PolySearch: A web-based text mining system for extracting relationships between human diseases, genes, mutations, drugs and metabolites Open Access

Descriptions

Author or creator
Cheng, D.
Knox, C.
Young, N.
Stothard, P.
Damaraju, S.
Wishart, D.S.
Additional contributors
Subject/Keyword
protein-protein interactions
updates
information
databases
discovering patterns
resources
Type of item
Journal Article (Published)
Language
English
Place
Time
Description
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

Date created
2008
DOI
doi:10.7939/R3ZG6G93X
License information
Rights
© 2008 The Author(s)
Citation for previous publication
D Cheng, C Knox, N Young, P Stothard, S Damaraju and DS Wishart. "PolySearch: A web-based text mining system for extracting relationships between human diseases, genes, mutations, drugs and metabolites." Nucleic Acids Research 36 (Web Server issue) (2008): W399-405. DOI: 10.1093/nar/gkn296
Source
Link to related item

File Details

Date Uploaded
Date Modified
2014-04-24T22:26:26.477+00:00
Audit Status
Audits have not yet been run on this file.
Characterization
File format: pdf (Portable Document Format)
Mime type: application/pdf
File size: 4348522
Last modified: 2015:10:12 16:26:29-06:00
Filename: Nucleic_Acids_Research_36_2008_W399.pdf
Original checksum: 41056a88464b7f39883dfc2b6d3dee55
Well formed: true
Valid: true
File title: gkn296 399..405
Page count: 7
Activity of users you follow
User Activity Date