title: The cellular microscopy phenotype ontology.
abstract: BACKGROUND
  Phenotypic data derived from high content screening is currently annotated using free-text, thus preventing the integration of independent datasets, including those generated in different biological domains, such as cell lines, mouse and human tissues.
  
  
  METHODS
  We present the Cellular Microscopy Phenotype Ontology (CMPO), a species neutral ontology for describing phenotypic observations relating to the whole cell, cellular components, cellular processes and cell populations. CMPO is compatible with related ontology efforts, allowing for future cross-species integration of phenotypic data. CMPO was developed following a curator-driven approach where phenotype data were annotated by expert biologists following the Entity-Quality (EQ) pattern. These EQs were subsequently transformed into new CMPO terms following an established post composition process.
  
  
  CONCLUSIONS
  CMPO is currently being utilized to annotate phenotypes associated with high content screening datasets stored in several image repositories including the Image Data Repository (IDR), MitoSys project database and the Cellular Phenotype Database to facilitate data browsing and discoverability.
authors.affiliation: European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Trust Genome Campus, Hinxton Cambridge, CB10 1SD UK.
authors.forename: Simon
authors.initials: S
authors.lastname: Jupp
authors.affiliation: European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Trust Genome Campus, Hinxton Cambridge, CB10 1SD UK.
authors.forename: James
authors.initials: J
authors.lastname: Malone
authors.affiliation: European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Trust Genome Campus, Hinxton Cambridge, CB10 1SD UK.
authors.forename: Tony
authors.initials: T
authors.lastname: Burdett
authors.affiliation: European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany.
authors.forename: Jean-Karim
authors.initials: JK
authors.lastname: Heriche
authors.affiliation: Centre for Gene Regulation and Expression, University of Dundee, Dundee, DD1 5EH UK.
authors.forename: Eleanor
authors.initials: E
authors.lastname: Williams
authors.affiliation: European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany.
authors.forename: Jan
authors.initials: J
authors.lastname: Ellenberg
authors.affiliation: European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Trust Genome Campus, Hinxton Cambridge, CB10 1SD UK.
authors.forename: Helen
authors.initials: H
authors.lastname: Parkinson
authors.affiliation: European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Trust Genome Campus, Hinxton Cambridge, CB10 1SD UK.
authors.forename: Gabriella
authors.initials: G
authors.lastname: Rustici
mesh_terms: D064229:Biological Ontologies; D002477:Cells / Q000166:cytology*; D008853:Microscopy; D010641:Phenotype; D059010:Single-Cell Analysis
keywords: Cellular phenotype; Imaging; OWL; Ontology