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Bioinformatics Advance Access published online on July 29, 2004
Bioinformatics, doi:10.1093/bioinformatics/bth404
Bioinformatics © Oxford University Press 2004; all rights reserved
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Received May 11, 2004
Revised June 21, 2004
Accepted July 4, 2004

Applications note

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

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

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

* To whom correspondence should be addressed. E-mail: Lin00025{at}mc.duke.edu.


  Abstract

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 ten 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.


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