Bio-ontologies: current trends and future directions

Abstract

In recent years, as a knowledge-based discipline, bioinformatics has been made more computationally amenable. After its beginnings as a technology advocated by computer scientists to overcome problems of heterogeneity, ontology has been taken up by biologists themselves as a means to consistently annotate features from genotype to phenotype. In medical informatics, artifacts called ontologies have been used for a longer period of time to produce controlled lexicons for coding schemes. In this article, we review the current position in ontologies and how they have become institutionalized within biomedicine. As the field has matured, the much older philosophical aspects of ontology have come into play. With this and the institutionalization of ontology has come greater formality. We review this trend and what benefits it might bring to ontologies and their use within biomedicine.

Figure 1

Bio-ontology timeline.

Figure 2

Representation of the molecular function ‘hexokinase activity’ in the Gene Ontology.

Figure 3

Example of gene products in rat, mouse and fruit fly annotated with the Gene Ontology term ‘hexokinase activity’.

Figure 4

The OBO ontologies arranged on a spectrum of genotype to phenotype, according to their main topic.

Figure 5

The history of the major players in medical ontologies.

Figure 6

The gross subject areas of ontology-like artifacts in medicine arranged in a space from the phenome to the prescriptome.

Figure 7

Growth of ontology papers in PubMed/ Medline.

Figure 8

Representation of the Gene Ontology term ‘‘glycerol catabolism’’ in the OBO format.

Figure 9

A complete definition of ReceptorProteinTyrosinePhosphatase.