Ontologies in biology: design, applications and future challenges

Key Points Bio-ontologies provide a means of formalizing biological knowledge — for example, about genes, anatomy and phenotypes — in complex hierarchies that are composed of terms and rules. Most bio-ontologies are stored at http://obo.sourceforge.net and are accepted by the community as authoritative. All bio-ontologies assign a unique identifier (ID) for each term and these allow the archiving, storing and accessing of data in databases. Ontology IDs provide a means of querying between databases (a function known as 'interoperability'). Complicated knowledge (such as that describing mutant phenotypes) can most easily be handled by composite annotations to multiple ontologies (anatomy, cell biology, pathology, traits, and so on). The review concludes by discussing some of the problems that the field is now facing. Biological knowledge is inherently complex and so cannot readily be integrated into existing databases of molecular (for example, sequence) data. An ontology is a formal way of representing knowledge in which concepts are described both by their meaning and their relationship to each other. Unique identifiers that are associated with each concept in biological ontologies (bio-ontologies) can be used for linking to and querying molecular databases. This article reviews the principal bio-ontologies and the current issues in their design and development: these include the ability to query across databases and the problems of constructing ontologies that describe complex knowledge, such as phenotypes.