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Bioinformatics Advance Access originally published online on June 14, 2005
Bioinformatics 2005 21(16):3416-3421; doi:10.1093/bioinformatics/bti538
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Published by Oxford University Press 2005

A semantic analysis of the annotations of the human genome

Purvesh Khatri , Bogdan Done , Archana Rao , Arina Done and Sorin Draghici *

Department of Computer Science, Wayne State University 431 State Hall, Detroit, MI, 48202, USA

*To whom correspondence should be addressed.

The correct interpretation of any biological experiment depends in an essential way on the accuracy and consistency of the existing annotation databases. Such databases are ubiquitous and used by all life scientists in most experiments. However, it is well known that such databases are incomplete and many annotations may also be incorrect. In this paper we describe a technique that can be used to analyze the semantic content of such annotation databases. Our approach is able to extract implicit semantic relationships between genes and functions. This ability allows us to discover novel functions for known genes. This approach is able to identify missing and inaccurate annotations in existing annotation databases, and thus help improve their accuracy. We used our technique to analyze the current annotations of the human genome. From this body of annotations, we were able to predict 212 additional gene–function assignments. A subsequent literature search found that 138 of these gene–functions assignments are supported by existing peer-reviewed papers. An additional 23 assignments have been confirmed in the meantime by the addition of the respective annotations in later releases of the Gene Ontology database. Overall, the 161 confirmed assignments represent 75.95% of the proposed gene–function assignments. Only one of our predictions (0.4%) was contradicted by the existing literature. We could not find any relevant articles for 50 of our predictions (23.58%). The method is independent of the organism and can be used to analyze and improve the quality of the data of any public or private annotation database.

Availability: http://vortex.cs.wayne.edu/papers/semantic_analysis_bioinfo.pdf

Contact: sod{at}cs.wayne.edu

Received on April 19, 2005; revised on June 6, 2005; accepted on June 8, 2005

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