Ontologies in Biology: Design, Applications and Future Challenges

Citation: Jonathan B L Bard, Seung Y Rhee. Ontologies in Biology: Design, Applications and Future Challenges. In Nature Reviews: Genetics, 2004.
Link: Nature Reviews
Status: Incomplete

Summary

Until recently, the most important task of bioinformatics was thought to be the storage, retrieval and analysis of molecular data. However, as experimental technologies move from producing relatively simple data to more complex data, we need comparable advances in bioinformatics to manage and relate these data. There is also a great deal of sophisticated biological knowledge, often hierarchical in nature, that needs to be integrated with other data. One way to represent such biological knowledge is by using ontologies. The resulting biological ontologies are formal representations of areas of knowledge in which the essential terms are combined with structuring rules that describe the relationship between the terms. Knowledge that is structured within a biological ontology can then be linked to the molecular databases.

For any ontology to be of public value, it has to be widely disseminated and accepted by the field that it aims to summarize. Sociological factors are important in ontology production and acceptance, and a strong community involvement is also crucial.

Definitions

Phenotype: The observable traits or characteristics of an organism, for example hair color, weight, or the presence or absence of a disease. Phenotypic traits are not necessarily genetic.
Systematics: This is an umbrella term to describe the processes that describe species. There are three disciplines which are united under this broad locution: description of species (identification), the naming of names (taxonomy) and description of the relationships among and between taxa (phylogenetics).