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Bioinformatics Advance Access originally published online on March 25, 2004
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Bioinformatics 20(12) © Oxford University Press 2004; all rights reserved.

Applications Note

A tool for gene expression based PubMed search through combining data sources

Maksym Korotkiy 1, Rutger Middelburg 2, Henk Dekker 2, Frank van Harmelen 1 and Jan Lankelma 2,3,*

1 Division of Computer Science, 2 Department of Medical Oncology, VU University Medical Center and 3 Tumor Cell Biology Group, Faculty of Earth and Life Sciences, Vrije Universiteit, De Boelelaan 1087, 1081 HV Amsterdam, The Netherlands

Received on August 28, 2003; revised on March 4, 2004; accepted on March 10, 2004
Advance Access Publication March 25, 2004

Summary: We present a new tool for the semi-automated querying of PubMed using a batch of tens to thousands of GenBank accession numbers or UniGene cluster ids. By combining information from UniGene and SWISS-PROT, microGENIE obtains information on the biological relevance of expressed genes, as identified by micro-array experiments, with minimal user intervention and time investment.

Availability: microGENIE is freely available from http://www.cs.vu.nl/microgenie

Supplementary information: The web site above supplies examples of input and output files.

Contact: jan.lankelma{at}falw.vu.nl

* To whom correspondence should be addressed.


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