Journal of Biomedical Informatics
Taxonomy-based partitioning of the Gene Ontology
Journal of Biomedical Informatics
In situ migration of handcrafted ontologies to reason-able forms
Data & Knowledge Engineering
Metamodeling integration architecture for open biomedical ontologies: the GO extensions' case study
ER '07 Tutorials, posters, panels and industrial contributions at the 26th international conference on Conceptual modeling - Volume 83
Applied Ontology - Towards a Metaontology for the Biomedical Domain
Using ontology visualization to facilitate access to knowledge about human disease genes
Applied Ontology - Biomedical Ontology in Action
Semantic enrichment of journal articles using chemical named entity recognition
ACL '07 Proceedings of the 45th Annual Meeting of the ACL on Interactive Poster and Demonstration Sessions
Proceedings of the 2008 conference on Formal Ontology in Information Systems: Proceedings of the Fifth International Conference (FOIS 2008)
Against Idiosyncrasy in Ontology Development
Proceedings of the 2006 conference on Formal Ontology in Information Systems: Proceedings of the Fourth International Conference (FOIS 2006)
BioNLP '09 Proceedings of the Workshop on Current Trends in Biomedical Natural Language Processing
Experiences Using Logic Programming in Bioinformatics
ICLP '09 Proceedings of the 25th International Conference on Logic Programming
Aligning medical domain ontologies for clinical query extraction
EACL '09 Proceedings of the 12th Conference of the European Chapter of the Association for Computational Linguistics: Student Research Workshop
Foundational Process Relations in Bio-Ontologies
Proceedings of the 2010 conference on Formal Ontology in Information Systems: Proceedings of the Sixth International Conference (FOIS 2010)
Ontology modularization to improve semantic medical image annotation
Journal of Biomedical Informatics
Cross-product extensions of the Gene Ontology
Journal of Biomedical Informatics
Semantic systems biology: enabling integrative biology via semantic web technologies
Proceedings of the International Conference on Web Intelligence, Mining and Semantics
Applied Ontology - Towards a Metaontology for the Biomedical Domain
BioNLP '12 Proceedings of the 2012 Workshop on Biomedical Natural Language Processing
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Ontologies are intended to capture and formalize a domain of knowledge. The ontologies comprising the Open Biological Ontologies (OBO) project, which includes the Gene Ontology (GO), are formalizations of various domains of biological knowledge. Ontologies within OBO typically lack computable definitions that serve to differentiate a term from other similar terms. The computer is unable to determine the meaning of a term, which presents problems for tools such as automated reasoners. Reasoners can be of enormous benefit in managing a complex ontology. OBO term names frequently implicitly encode the kind of definitions that can be used by computational tools, such as automated reasoners. The definitions encoded in the names are not easily amenable to computation, because the names are ostensibly natural language phrases designed for human users. These names are highly regular in their grammar, and can thus be treated as valid sentences in some formal or computable language. With a description of the rules underlying this formal language, term names can be parsed to derive computable definitions, which can then be reasoned over. This paper describes the effort to elucidate that language, called Obol, and the attempts to reason over the resulting definitions. The current implementation finds unique non-trivial definitions for around half of the terms in the GO, and has been used to find 223 missing relationships, which have since been added to the ontology. Obol has utility as an ontology maintenance tool, and as a means of generating computable definitions for a whole ontology.The software is available under an open-source license from: . Supplementary material for this article can be found at: Copyright © 2004 John Wiley & Sons, Ltd.