Mapping microarray chip feature IDs to Gene IDs for microarray platforms in NCBI GEO

Date

2008-06

Authors

Burkhardt, Cory
Robbins, Kay A.

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Publisher

UTSA Department of Computer Science

Abstract

The Gene Expression Omnibus or NCBI GEO (http://www.ncbi.nlm.nih.gov/projects/geo/) is one of the most comprehensive public repositories of microarray data. The data in NCBI GEO is organized into samples, series, datasets and platforms. Platform files specify the characteristics of a particular type of microarray chip, including a mapping of chip features to genetic features. These mappings are not standardized. This technical note describes a program GPLGeneMap that reads a platform specification in XML format and produces a mapping of chip features to NCBI Gene IDs. The mapping strategy is based on a user specification given in an XML file. The program produces a mapping file and a list of chip features that it was unable to map.

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Department

Computer Science