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Bioinformatics Advance Access originally published online on July 29, 2004
Bioinformatics 2004 20(18):3659-3661; doi:10.1093/bioinformatics/bth404
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Bioinformatics vol. 20 issue 18 © Oxford University Press 2004; all rights reserved.

Applications Note

MedlineR: an open source library in R for Medline literature data mining

Simon M. Lin 1,2,*, Patrick McConnell 1, Kimberly F. Johnson 1 and Jennifer Shoemaker 1,2

1 Duke Comprehensive Cancer Center and 2 Department of Biostatistics and Bioinformatics, Duke University Medical Center, Durham, NC 27710, USA

Received on May 11, 2004; revised on June 21, 2004; accepted on July 4, 2004
Advance Access Publication July 9, 2004

Summary: We describe an open source library written in the R programming language for Medline literature data mining. This MedlineR library includes programs to query Medline through the NCBI PubMed database; to construct the co-occurrence matrix; and to visualize the network topology of query terms. The open source nature of this library allows users to extend it freely in the statistical programming language of R. To demonstrate its utility, we have built an application to analyze term-association by using only 10 lines of code. We provide MedlineR as a library foundation for bioinformaticians and statisticians to build more sophisticated literature data mining applications.

Availability: The library is available from http://dbsr.duke.edu/pub/MedlineR.

Contact: Lin00025{at}mc.duke.edu

* To whom correspondence should be addressed.


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