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This article is part of the supplement: Selected Proceedings of the First Summit on Translational Bioinformatics 2008

Open Access Proceedings

BioProspecting: novel marker discovery obtained by mining the bibleome

Peter L Elkin1*, Mark S Tuttle1, Brett E Trusko1 and Steven H Brown2

Author Affiliations

1 Center for Biomedical Informatics, Mount Sinai School of Medicine, New York, NY, USA

2 Department of Medicine, Vanderbilt University, Nashville, TN, USA

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BMC Bioinformatics 2009, 10(Suppl 2):S9  doi:10.1186/1471-2105-10-S2-S9

Published: 5 February 2009


BioProspecting is a novel approach that enabled our team to mine data related to genetic markers from the New England Journal of Medicine (NEJM) utilizing SNOMED CT and the Human Gene Onotology (HUGO). The Biomedical Informatics Research Collaborative was able to link genes and disorders using the Multi-threaded Clinical Vocabulary Server (MCVS) and natural language processing engine, whose output creates an ontology-network using the semantic encodings of the literature that is organized by these two terminologies. We identified relationships between (genes or proteins) and (diseases or drugs) as linked by metabolic functions and identified potentially novel functional relationships between, for example, genes and diseases (e.g. Article #1 ([Gene - IL27] = > {Enzyme - Dipeptidyl Carboxypeptidase 1}) and Article #2 ({Enzyme - Dipeptidyl Carboxypeptidase 1} < = [Disorder - Type II DM]) showing a metabolic link between IL27 and Type II DM). In this manuscript we describe our method for developing the database and its content as well as its potential to assist in the discovery of novel markers and drugs.