Bioinformatics Advance Access originally published online on June 20, 2006
Bioinformatics 2006 22(16):2020-2027; doi:10.1093/bioinformatics/btl334
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© 2006 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-commerical use, distribution, and reproduction in any medium, provided the original work is properly cited.
Additional Gene Ontology structure for improved biological reasoning
1 Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology NO-7489 Trondheim, Norway
2 Department of Computer and Information Science, Norwegian University of Science and Technology NO-7491 Trondheim, Norway
3 SAS Institute AS Norway, Pb 2666 Solli NO-0203 Oslo, Norway
*To whom correspondence should be addressed.
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Abstract |
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Motivation: The Gene Ontology (GO) is a widely used terminology for gene product characterization in, for example, interpretation of biology underlying microarray experiments. The current GO defines term relationships within each of the independent subontologies: molecular function, biological process and cellular component. However, it is evident that there also exist biological relationships between terms of different subontologies. Our aim was to connect the three subontologies to enable GO to cover more biological knowledge, enable a more consistent use of GO and provide new opportunities for biological reasoning.
Results: We propose a new structure, the Second Gene Ontology Layer, capturing biological relations not directly reflected in the present ontology structure. Given molecular functions, these paths identify biological processes where the molecular functions are involved and cellular components where they are active. The current Second Layer contains 6271 validated paths, covering 54% of the molecular functions of GO and can be used to render existing gene annotation sets more complete and consistent. Applying Second Layer paths to a set of 4223 human genes, increased biological process annotations by 24% compared to publicly available annotations and reproduced 30% of them.
Availability: The Second GO is publicly available through the GO Annotation Toolbox (GOAT.no): http://www.goat.no
Contact: astrid.lagreid{at}ntnu.no
The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors.
Associate Editor: Jonathan Wren
Received on April 7, 2006; revised on May 30, 2006; accepted on June 12, 2006
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