Text similarity: an alternative way to search MEDLINE
- PMID: 16926219
- DOI: 10.1093/bioinformatics/btl388
Text similarity: an alternative way to search MEDLINE
Abstract
Motivation: The most widely used literature search techniques, such as those offered by NCBI's PubMed system, require significant effort on the part of the searcher, and inexperienced searchers do not use these systems as effectively as experienced users. Improved literature search engines can save researchers time and effort by making it easier to locate the most important and relevant literature.
Results: We have created and optimized a new, hybrid search system for Medline that takes natural text as input and then delivers results with high precision and recall. The combination of a fast, low-sensitivity weighted keyword-based first pass algorithm to cast a wide net to gather an initial set of literature, followed by a unique sentence-alignment based similarity algorithm to rank order those results was developed that is sensitive, fast and easy to use. Several text similarity search algorithms, both standard and novel, were implemented and tested in order to determine which obtained the best results in information retrieval exercises.
Availability: Literature searching algorithms are implemented in a system called eTBLAST, freely accessible over the web at http://invention.swmed.edu. A variety of other derivative systems and visualization tools provides the user with an enhanced experience and additional capabilities.
Contact: Harold.Garner@UTSouthwestern.edu.
Similar articles
-
Discovering patterns to extract protein-protein interactions from the literature: Part II.Bioinformatics. 2005 Aug 1;21(15):3294-300. doi: 10.1093/bioinformatics/bti493. Epub 2005 May 12. Bioinformatics. 2005. PMID: 15890744
-
Ranking the whole MEDLINE database according to a large training set using text indexing.BMC Bioinformatics. 2005 Mar 24;6:75. doi: 10.1186/1471-2105-6-75. BMC Bioinformatics. 2005. PMID: 15790421 Free PMC article.
-
Protein annotation by EBIMed.Nat Biotechnol. 2006 Aug;24(8):902-3. doi: 10.1038/nbt0806-902. Nat Biotechnol. 2006. PMID: 16900125 No abstract available.
-
Status of text-mining techniques applied to biomedical text.Drug Discov Today. 2006 Apr;11(7-8):315-25. doi: 10.1016/j.drudis.2006.02.011. Drug Discov Today. 2006. PMID: 16580973 Review.
-
A survey of current work in biomedical text mining.Brief Bioinform. 2005 Mar;6(1):57-71. doi: 10.1093/bib/6.1.57. Brief Bioinform. 2005. PMID: 15826357 Review.
Cited by
-
Text mining for identification of biological entities related to antibiotic resistant organisms.PeerJ. 2022 May 5;10:e13351. doi: 10.7717/peerj.13351. eCollection 2022. PeerJ. 2022. PMID: 35539017 Free PMC article.
-
Duplicate publications: A sample of redundancy in the Journal of Urology.Can Urol Assoc J. 2012 Jun;6(3):177-80. doi: 10.5489/cuaj.11265. Can Urol Assoc J. 2012. PMID: 22664627 Free PMC article.
-
Leveraging user query sessions to improve searching of medical literature.AMIA Annu Symp Proc. 2013 Nov 16;2013:214-23. eCollection 2013. AMIA Annu Symp Proc. 2013. PMID: 24551332 Free PMC article.
-
Caipirini: using gene sets to rank literature.BioData Min. 2012 Feb 1;5(1):1. doi: 10.1186/1756-0381-5-1. BioData Min. 2012. PMID: 22297131 Free PMC article.
-
eTBLAST: a web server to identify expert reviewers, appropriate journals and similar publications.Nucleic Acids Res. 2007 Jul;35(Web Server issue):W12-5. doi: 10.1093/nar/gkm221. Epub 2007 Apr 22. Nucleic Acids Res. 2007. PMID: 17452348 Free PMC article.
Publication types
MeSH terms
LinkOut - more resources
Full Text Sources
Miscellaneous
