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  Exact Score Distribution Computation for Similarity Searches in Ontologies.

Schulz, M. H., Köhler, S., Bauer, S., Vingron, M., & Robinson, P. N. (2009). Exact Score Distribution Computation for Similarity Searches in Ontologies. In S. L. Salzberg, & T. Warnow (Eds.), Algorithms in Bioinformatics (pp. 298-309). New York [et al]: Springer.

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Item Permalink: http://hdl.handle.net/11858/00-001M-0000-0010-7D09-5 Version Permalink: http://hdl.handle.net/11858/00-001M-0000-0010-7D0A-3
Genre: Book Chapter

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 Creators:
Schulz, Marcel H.1, Author
Köhler, Sebastian, Author
Bauer, Sebastian, Author
Vingron, Martin2, Author              
Robinson, Peter N.3, Author              
Affiliations:
1Max Planck Society, ou_persistent13              
2Gene regulation (Martin Vingron), Dept. of Computational Molecular Biology (Head: Martin Vingron), Max Planck Institute for Molecular Genetics, Max Planck Society, ou_1479639              
3Research Group Development & Disease (Head: Stefan Mundlos), Max Planck Institute for Molecular Genetics, Max Planck Society, ou_1433557              

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Free keywords: Computer science
 Abstract: Semantic similarity searches in ontologies are an important component of many bioinformatic algorithms, e.g., protein function prediction with the Gene Ontology. In this paper we consider the exact computation of score distributions for similarity searches in ontologies, and introduce a simple null hypothesis which can be used to compute a P-value for the statistical significance of similarity scores. We concentrate on measures based on Resnik’s definition of ontological similarity. A new algorithm is proposed that collapses subgraphs of the ontology graph and thereby allows fast score distribution computation. The new algorithm is several orders of magnitude faster than the naive approach, as we demonstrate by computing score distributions for similarity searches in the Human Phenotype Ontology.

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Language(s): eng - English
 Dates: 2009-09-19
 Publication Status: Published in print
 Pages: -
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 Table of Contents: -
 Rev. Method: -
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Source 1

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Title: Algorithms in Bioinformatics
Source Genre: Book
 Creator(s):
Salzberg, Steven L., Editor
Warnow, Tandy, Editor
Affiliations:
-
Publ. Info: New York [et al] : Springer
Pages: 430 Volume / Issue: - Sequence Number: - Start / End Page: 298 - 309 Identifier: ISBN: 978-3-642-04240-9

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Title: Lecture Notes in Computer Science
Source Genre: Series
 Creator(s):
Hofmann, Alfred, Editor
Affiliations:
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Publ. Info: -
Pages: - Volume / Issue: 5724 Sequence Number: - Start / End Page: - Identifier: -