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Gene-L’EXPO: a Tool to Extract Knowledge From Transcriptomes and Find ‘Literature-Sparse’ Relationships Between Genes and Tissues

By Teruyoshi Hishiki, Issei Tamada and Kousaku Okubo

Abstract

The increasing volume and diversity of transcriptome data in the public domain offer an opportunity to advance new questions and hypotheses. We anticipate that tools that can visualize the gap in the distribution of information between the scientific literature and actual data would prompt such questions. We focused on the roles played by various genes in tissues, and have developed a database that contrasts information on gene expression in tissues with PubMed text and transcriptome data. Data pairs of tissues and the genes that might be expressed there were automatically extracted from text with vocabularies for the genes and tissues. The anatomical categories of various expressed sequence tag (EST) libraries were also automatically determined. These types of information were linked using the hierarchical structure of the Metathesaurus in UMLS. The database, named Gene-L’EXPO, is accessible at http://www.genelexpo.jp

Topics: Articles
Publisher: American Medical Informatics Association
OAI identifier: oai:pubmedcentral.nih.gov:2656066
Provided by: PubMed Central
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