title: Semantic integration of physiology phenotypes with an application to the Cellular Phenotype Ontology.
abstract: BACKGROUND
  The systematic observation of phenotypes has become a crucial tool of functional genomics, and several large international projects are currently underway to identify and characterize the phenotypes that are associated with genotypes in several species. To integrate phenotype descriptions within and across species, phenotype ontologies have been developed. Applying ontologies to unify phenotype descriptions in the domain of physiology has been a particular challenge due to the high complexity of the underlying domain.
  
  
  RESULTS
  In this study, we present the outline of a theory and its implementation for an ontology of physiology-related phenotypes. We provide a formal description of process attributes and relate them to the attributes of their temporal parts and participants. We apply our theory to create the Cellular Phenotype Ontology (CPO). The CPO is an ontology of morphological and physiological phenotypic characteristics of cells, cell components and cellular processes. Its prime application is to provide terms and uniform definition patterns for the annotation of cellular phenotypes. The CPO can be used for the annotation of observed abnormalities in domains, such as systems microscopy, in which cellular abnormalities are observed and for which no phenotype ontology has been created.
  
  
  METHODS
  The CPO and the source code we generated to create the CPO are freely available on http://cell-phenotype.googlecode.com.
authors.affiliation: Department of Genetics, University of Cambridge, Downing Street, Cambridge, Cambridge CB2 3EH, UK. rh497@cam.ac.uk
authors.forename: Robert
authors.initials: R
authors.lastname: Hoehndorf
authors.forename: Midori A
authors.initials: MA
authors.lastname: Harris
authors.forename: Heinrich
authors.initials: H
authors.lastname: Herre
authors.forename: Gabriella
authors.initials: G
authors.lastname: Rustici
authors.forename: Georgios V
authors.initials: GV
authors.lastname: Gkoutos
mesh_terms: D002468:Cell Physiological Phenomena; D010641:Phenotype; D012660:Semantics; D018875:Vocabulary, Controlled