The anatomy of phenotype ontologies: principles, properties and applications

Georgios V. Gkoutos, Paul N Schofield, Robert Hoehndorf

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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
Pages (from-to)1008-1021
Number of pages14
JournalBriefings in Bioinformatics
Issue number5
Early online date06 Apr 2017
Publication statusPublished - 28 Sept 2018


  • phenotype
  • ontology
  • PATO
  • data integration
  • Semantic Web
  • Gene Ontology/statistics & numerical data
  • Humans
  • Biological Ontologies/statistics & numerical data
  • Ecology
  • Biodiversity
  • Computational Biology/methods
  • Animals, Domestic
  • Biological Evolution
  • Phenotype
  • Animals


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