GENOTEXT

GENOTEXT (GENOmics conTEXT) is an automated sytem that determines the experimental context of samples and data sets in the NCBI Gene Expression Omnibus. It extracts the contextual identifiers and annotations of samples and models these annotations using the largest available compendium of biomedical vocabularies, the Unified Medical Language System (UMLS).

The program and its results are pending publication.

The following software is available from this project. These programs are not meant to be downloaded and run; each will need modifications for ones own computer system and database structure.

• A program in Perl that iterates through GSE .soft files in a directory, extracts seven free-text annotations of each sample and series, and stores these in a MySQL database.
• A program in Java that iterates through the annotations in the MySQL database and uses MetaMap to map the text into UMLS concepts. This program requires the MetaMap Transfer libraries.
• A program in Java that iterates through the mappings and removes many (but not all!) that were manually determined to be incorrect.
• A program in R and its data file that together can create a dendrogram figure, clustering GEO data sets by the concepts mapped from their annotations. See the gallery for an example of this dendrogram.

Funding for this work was provided in part by:

• The National Center for Biomedical Computing "Informatics for Integrating Biology and the Bedside" funded by the National Library of Medicine, U54 LM008748
• "Career Development in Diabetes for Pediatric Endocrinologists" funded by the National Institute of Diabetes and Digestive and Kidney Diseases, K12 DK63696
• "Gene Expression in Prediabetes" funded by the National Institute of Diabetes and Digestive and Kidney Diseases, R01 DK62948
• The Diabetes Genome Anatomy Project funded by the National Institute of Diabetes and Digestive and Kidney Diseases, R01 DK62948
• Endocrine Fellows Foundation
• Genentech Center for Clinical Research and Education
• Lawson Wilkins Pediatric Endocrinology Society
• Merck-Massachusetts Institute of Technology partnership
• "Genomics of Cardiovascular Development, Adaptation, and Remodeling" (CardioGenomics) funded by the National Heart Lung and Blood Institute's Program in Genomic Applications, U01 HL066582
• "Harvard-MIT-NEMC Research Training in Health Informatics" funded by the National Library of Medicine, 5T15 LM07092
  

Updated January 10, 2006