Bayesian ontology querying for accurate and noise-tolerant semantic searches

Bioinformatics. 2012 Oct 1;28(19):2502-8. doi: 10.1093/bioinformatics/bts471. Epub 2012 Jul 26.


Motivation: Ontologies provide a structured representation of the concepts of a domain of knowledge as well as the relations between them. Attribute ontologies are used to describe the characteristics of the items of a domain, such as the functions of proteins or the signs and symptoms of disease, which opens the possibility of searching a database of items for the best match to a list of observed or desired attributes. However, naive search methods do not perform well on realistic data because of noise in the data, imprecision in typical queries and because individual items may not display all attributes of the category they belong to.

Results: We present a method for combining ontological analysis with Bayesian networks to deal with noise, imprecision and attribute frequencies and demonstrate an application of our method as a differential diagnostic support system for human genetics.

Availability: We provide an implementation for the algorithm and the benchmark at

Contact: or

Supplementary information: Supplementary Material for this article is available at Bioinformatics online.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms*
  • Bayes Theorem*
  • Computational Biology / methods*
  • Decision Support Techniques
  • Diagnosis, Differential
  • Humans
  • Models, Statistical
  • Semantics