The anatomy of phenotype ontologies: principles, properties and applications

Georgios V Gkoutos, Paul N Schofield, Robert Hoehndorf

Research output: Contribution to journalArticlepeer-review

51 Scopus citations


The past decade has seen an explosion in the collection of genotype data in domains as diverse as medicine, ecology, livestock and plant breeding. Along with this comes the challenge of dealing with the related phenotype data, which is not only large but also highly multidimensional. Computational analysis of phenotypes has therefore become critical for our ability to understand the biological meaning of genomic data in the biological sciences. At the heart of computational phenotype analysis are the phenotype ontologies. A large number of these ontologies have been developed across many domains, and we are now at a point where the knowledge captured in the structure of these ontologies can be used for the integration and analysis of large interrelated data sets. The Phenotype And Trait Ontology framework provides a method for formal definitions of phenotypes and associated data sets and has proved to be key to our ability to develop methods for the integration and analysis of phenotype data. Here, we describe the development and products of the ontological approach to phenotype capture, the formal content of phenotype ontologies and how their content can be used computationally.
Original languageEnglish (US)
Pages (from-to)1008-1021
Number of pages14
JournalBriefings in Bioinformatics
Issue number5
StatePublished - Apr 6 2017

Bibliographical note

KAUST Repository Item: Exported on 2020-10-01
Acknowledgements: The National Science Foundation (IOS:1340112 to G.V.G.), the European Commission H2020 (grant agreement number 731075) to G.V.G. and the King Abdullah University of Science and Technology (to R.H.).


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