Abstract
Ontologies, which are structured, hierarchical vocabularies, are widely used in molecular biology to annotate sequence and structure data. One such ontology, the GeneOntology, contains some 18000 terms on biological processes, molecular function, and cellular components. GeneOntology is available as flat file, in web formats such as XML and RDF, and as database. Using these formats we compare three different reasoners to query the GeneOntology. Prolog is the classical logic programming approach to reason over the ontology, Prova is a rule-based Java scripting language, and Xcerpt a query language for XML and RDF. We conclude by discussing the strengths and weaknesses of the three approaches.

URL:
http://rewerse.net/publications/rewerse-publications.html#REWERSE-RP-2005-41

BibTeX:

@inproceedings{REWERSE-RP-2005-41,
	author = {Andreas Doms and Tim Furche and Albert Burger and Michael Schroeder},
	title = {How to Query the GeneOntology},
	booktitle = {Proceedings of Symposium on Knowledge Representation in Bioinformatics, Espoo, Finland (17th June 2005)},
	year = {2005},
	url = {http://rewerse.net/publications/rewerse-publications.html#REWERSE-RP-2005-41}
}