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Open Access Research article

Text mining and manual curation of chemical-gene-disease networks for the Comparative Toxicogenomics Database (CTD)

Thomas C Wiegers1*, Allan Peter Davis1, K Bretonnel Cohen23, Lynette Hirschman3 and Carolyn J Mattingly1

Author Affiliations

1 Department of Bioinformatics, The Mount Desert Island Biological Laboratory, Salisbury Cove, ME, USA

2 Center for Computational Pharmacology, University of Colorado School of Medicine, Aurora, CO, USA

3 Information Technology Center, The MITRE Corporation, 202 Burlington Road, Bedford, MA, USA

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BMC Bioinformatics 2009, 10:326  doi:10.1186/1471-2105-10-326

Published: 8 October 2009

Abstract

Background

The Comparative Toxicogenomics Database (CTD) is a publicly available resource that promotes understanding about the etiology of environmental diseases. It provides manually curated chemical-gene/protein interactions and chemical- and gene-disease relationships from the peer-reviewed, published literature. The goals of the research reported here were to establish a baseline analysis of current CTD curation, develop a text-mining prototype from readily available open source components, and evaluate its potential value in augmenting curation efficiency and increasing data coverage.

Results

Prototype text-mining applications were developed and evaluated using a CTD data set consisting of manually curated molecular interactions and relationships from 1,600 documents. Preliminary results indicated that the prototype found 80% of the gene, chemical, and disease terms appearing in curated interactions. These terms were used to re-rank documents for curation, resulting in increases in mean average precision (63% for the baseline vs. 73% for a rule-based re-ranking), and in the correlation coefficient of rank vs. number of curatable interactions per document (baseline 0.14 vs. 0.38 for the rule-based re-ranking).

Conclusion

This text-mining project is unique in its integration of existing tools into a single workflow with direct application to CTD. We performed a baseline assessment of the inter-curator consistency and coverage in CTD, which allowed us to measure the potential of these integrated tools to improve prioritization of journal articles for manual curation. Our study presents a feasible and cost-effective approach for developing a text mining solution to enhance manual curation throughput and efficiency.