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Bioinformatics Advance Access originally published online on September 6, 2007
Bioinformatics 2007 23(18):2477-2484; doi:10.1093/bioinformatics/btm375
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© 2007 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Medline search engine for finding genetic markers with biological significance

Weijian Xuan , Pinglang Wang , Stanley J. Watson and Fan Meng *

Molecular and Behavioral Neuroscience Institute and Department of Psychiatry, University of Michigan, Ann Arbor, Michigan 48109, USA

*To whom correspondence should be addressed.


  Abstract

Motivation: Genome-wide high density SNP association studies are expected to identify various SNP alleles associated with different complex disorders. Understanding the biological significance of these SNP alleles in the context of existing literature is a major challenge since existing search engines are not designed to search literature for SNPs or other genetic markers. The literature mining of gene and protein functions has received significant attention and effort while similar work on genetic markers and their related diseases is still in its infancy. Our goal is to develop a web-based tool that facilitates the mining of Medline literature related to genetic studies and gene/protein function studies. Our solution consists of four main function modules for (1) identification of different types of genetic markers or genetic variations in Medline records (2) distinguishing positive versus negative linkage or association between genetic markers and diseases (3) integrating marker genomic location data from different databases to enable the retrieval of Medline records related to markers in the same linkage disequilibrium region (4) and a web interface called MarkerInfoFinder to search, display, sort and download Medline citation results. Tests using published data suggest MarkerInfoFinder can significantly increase the efficiency of finding genetic disorders and their underlying molecular mechanisms. The functions we developed will also be used to build a knowledge base for genetic markers and diseases.

Availability: The MarkerInfoFinder is publicly available at: http://brainarray.mbni.med.umich.edu/brainarray/datamining/MarkerInfoFinder

Contact: mengf{at}umich.edu

Associate Editor: Alfonso Valencia

Received on August 25, 2006; revised on July 10, 2007; accepted on July 15, 2007

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