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Bioinformatics Advance Access published online on April 9, 2008
Bioinformatics, doi:10.1093/bioinformatics/btn125
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© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

EPO-KB: A searchable knowledge base of biomarker to protein links

Jonathan L. Lustgarten 1,*, Chad Kimmel 1, Henrik Ryberg 2 and William Hogan 1,3

1Department of Biomedical Informatics, University of Pittsburgh, 220 Meyran Ave M-183 Parkvale, Pittsburgh, PA 15213.
2Department of Pathology, University of Pittsburgh, Pittsburgh, PA.
3University of Pittsburgh Medical Center, Pittsburgh, PA.

*To whom correspondence should be addressed. Jonathan L. Lustgarten, E-mail: JLL47{at}pitt.edu


  Abstract

Summary: The knowledge base EPO-KB (Empirical Proteomic Ontology Knowledge Base) is based on an OWL ontology that represents current knowledge linking Mass-To-Charge (m/z) ratios to proteins on multiple platforms including Matrix Assisted Laser/Desorption Ionization (MALDI) and Surface Enhanced Laser/Desorption Ionization (SELDI) - Time of Flight (TOF). At present, it contains information on m/z ratio to protein links that were extracted from 120 published research papers. It has a web interface that allows researchers to query and retrieve putative proteins that correspond to a user-specified m/z ratio. EPO-KB also allows automated entry of additional m/z ratio to protein links and is expandable to the addition of gene to protein and protein to disease links.

Availability: http://www.dbmi.pitt.edu/EPO-KB

Contact: JLL47{at}pitt.edu

Associate Editor: Prof. Alfonso Valencia

Received on December 24, 2007; revised on March 11, 2008; accepted on April 6, 2008

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