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Abstract
BackgroundBio-ontologies are key elements of knowledge management in bioinformatics. Rich and rigorous bio-ontologies should represent biological knowledge with high fidelity and robustness. The richness in bio-ontologies is a prior condition for diverse and efficient reasoning, and hence querying and hypothesis validation. Rigour allows a more consistent maintenance. Modelling such bio-ontologies is, however, a difficult task for bio-ontologists, because the necessary richness and rigour is difficult to achieve without extensive training.ResultsAnalogous to design patterns in software engineering, Ontology Design Patterns are solutions to typical modelling problems that bio-ontologists can use when building bio-ontologies. They offer a means of creating rich and rigorous bio-ontologies with reduced effort. The concept of Ontology Design Patterns is described and documentation and application methodologies for Ontology Design Patterns are presented. Some real-world use cases of Ontology Design Patterns are provided and tested in the Cell Cycle Ontology. Ontology Design Patterns, including those tested in the Cell Cycle Ontology, can be explored in the Ontology Design Patterns public catalogue that has been created based on the documentation system presented ().ConclusionsOntology Design Patterns provide a method for rich and rigorous modelling in bio-ontologies. They also offer advantages at different development levels (such as design, implementation and communication) enabling, if used, a more modular, well-founded and richer representation of the biological knowledge. This representation will produce a more efficient knowledge management in the long term.
Highlights
Bio-ontologies are key elements of knowledge management in bioinformatics
Ontology Design Patterns, including those tested in the Cell Cycle Ontology, can be explored in the Ontology Design Patterns public catalogue that has been created based on the documentation system presented
Many bio-ontologies are available through the Open Biomedical Ontologies (OBO) project [2], with the Gene Ontology (GO) [3] being the most important example
Summary
Bio-ontologies are key elements of knowledge management in bioinformatics. Rich and rigorous bio-ontologies should represent biological knowledge with high fidelity and robustness. Modelling such bio-ontologies is, a difficult task for bio-ontologists, because the necessary richness and rigour is difficult to achieve without extensive training. Ontologies are engineering artefacts that can formally represent the concepts and their relationships within a given knowledge domain. They can provide a computationally processable conceptual representation of our current understanding of reality, as described within the information we hold. Bio-ontologies are implemented in different Knowledge Representation (KR) languages, differing in properties that can be described along the following axes: Many bio-ontologies are available through the Open Biomedical Ontologies (OBO) project [2], with the Gene Ontology (GO) [3] being the most important example.
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