PubMatrix: a tool for multiplex literature mining

Software
http://pubmatrix.grc.nia.nih.gov/

PubMatrix: a tool for multiplex literature mining in PubMed
Kevin G Becker1 , Douglas A Hosack3 , Glynn Dennis Jr3 , Richard A Lempicki3 , Tiffani J Bright1 , Chris Cheadle1 and Jim Engel2
1Gene Expression and Genomics Unit, National Institutes of Health, Baltimore, MD, USA
2NCTS, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
3Laboratory of Immunopathogenesis and Bioinformatics, SAIC-Frederick, Inc., Frederick MD, USA

BMC Bioinformatics 2003, 4:61

The electronic version of this article is the complete one and can be found online at: http://www.biomedcentral.com/1471-2105/4/61

Received 29 July 2003
Accepted 10 December 2003
Published 10 December 2003

© 2003 Becker et al; licensee BioMed Central Ltd. This is an Open Access article: verbatim copying and redistribution of this article are permitted in all media for any purpose, provided this notice is preserved along with the article's original URL. Keywords: Literature mining, microarray, Proteomic, PubMed

Outline Abstract

Abstract
Background
Results
Conclusions
Availability and requirements
Authors' contributions
Acknowledgements
References


Background

Molecular experiments using multiplex strategies such as cDNA microarrays or proteomic approaches generate large datasets requiring biological interpretation. Text based data mining tools have recently been developed to query large biological datasets of this type of data. PubMatrix is a web-based tool that allows simple text based mining of the NCBI literature search service PubMed using any two lists of keywords terms, resulting in a frequency matrix of term co-occurrence.

Results

For example, a simple term selection procedure allows automatic pair-wise comparisons of approximately 1–100 search terms versus approximately 1–10 modifier terms, resulting in up to 1,000 pair wise comparisons. The matrix table of pair-wise comparisons can then be surveyed, queried individually, and archived. Lists of keywords can include any terms currently capable of being searched in PubMed. In the context of cDNA microarray studies, this may be used for the annotation of gene lists from clusters of genes that are expressed coordinately. An associated PubMatrix public archive provides previous searches using common useful lists of keyword terms.

Conclusions

In this way, lists of terms, such as gene names, or functional assignments can be assigned genetic, biological, or clinical relevance in a rapid flexible systematic fashion.
http://pubmatrix.grc.nia.nih.gov/