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

Overview

Journal AMIA Annu Symp Proc

Specialty Medical Informatics

Date 2008 Nov 13

PMID 18999036

Authors

Teruyoshi Hishiki

Issei Tamada

Kousaku Okubo

Affiliations

Soon will be listed here.

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.

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