The role of ontologies in biological and biomedical research: a functional perspective.

Robert Hoehndorf,P N Schofield,G V Gkoutos

doi:10.1093/bib/bbv011

Abstract

Ontologies are widely used in biological and biomedical research. Their success lies in their combination of four main features present in almost all ontologies: provision of standard identifiers for classes and relations that represent the phenomena within a domain; provision of a vocabulary for a domain; provision of metadata that describes the intended meaning of the classes and relations in ontologies; and the provision of machine-readable axioms and definitions that enable computational access to some aspects of the meaning of classes and relations. While each of these features enables applications that facilitate data integration, data access and analysis, a great potential lies in the possibility of combining these four features to support integrative analysis and interpretation of multimodal data. Here, we provide a functional perspective on ontologies in biology and biomedicine, focusing on what ontologies can do and describing how they can be used in support of integrative research. We also outline perspectives for using ontologies in data-driven science, in particular their application in structured data mining and machine learning applications.

Highlights

The past 15 years have seen a revolution in the volume and complexity of data created in the life sciences, and with the increase in available data, the need for data management, integration and analysis has become an increasingly important challenge
We provide a functional perspective on ontologies in biology and biomedicine, focusing on what ontologies can do and describing how they can be used in support of integrative research
The use of ontologies began in the biological sciences around 1998 with the development of the Gene Ontology (GO) [1]

Summary

Introduction

The past 15 years have seen a revolution in the volume and complexity of data created in the life sciences, and with the increase in available data, the need for data management, integration and analysis has become an increasingly important challenge. Through labels associated with classes and relations, ontologies provide a domain vocabulary that can be exploited for applications ranging from natural language processing, creation of user interfaces, etc. These statements are the axioms, which form the features of ontologies that provide domain knowledge and fill the classes and relations with meaning.

Results

Conclusion