EuroPhenome: a repository for high-throughput mouse phenotyping data

Hugh Morgan, Tim Beck, Andrew Blake, Hilary Gates, Niels Adams, Guillaume Debouzy, Sophie Leblanc, Christoph Lengger, Holger Maier, David Melvin, Hamid Meziane, Dave Richardson, Sara Wells, Jacqui White, Joe Wood, EUMODIC Consortium, Martin Hrabé de Angelis, Steve D M Brown, John M Hancock, Ann-Marie MallonAndreas Lengeling

Research output: Contribution to journalArticlepeer-review

Abstract

The broad aim of biomedical science in the postgenomic era is to link genomic and phenotype information to allow deeper understanding of the processes leading from genomic changes to altered phenotype and disease. The EuroPhenome project (http://www.EuroPhenome.org) is a comprehensive resource for raw and annotated high-throughput phenotyping data arising from projects such as EUMODIC. EUMODIC is gathering data from the EMPReSSslim pipeline (http://www.empress.har.mrc.ac.uk/) which is performed on inbred mouse strains and knock-out lines arising from the EUCOMM project. The EuroPhenome interface allows the user to access the data via the phenotype or genotype. It also allows the user to access the data in a variety of ways, including graphical display, statistical analysis and access to the raw data via web services. The raw phenotyping data captured in EuroPhenome is annotated by an annotation pipeline which automatically identifies statistically different mutants from the appropriate baseline and assigns ontology terms for that specific test. Mutant phenotypes can be quickly identified using two EuroPhenome tools: PhenoMap, a graphical representation of statistically relevant phenotypes, and mining for a mutant using ontology terms. To assist with data definition and cross-database comparisons, phenotype data is annotated using combinations of terms from biological ontologies.
Original languageEnglish
Pages (from-to)D577-D585
Number of pages9
JournalNucleic Acids Research
Volume38
Issue numberDatabase issue
Early online date23 Nov 2009
DOIs
Publication statusPublished - 1 Jan 2010

Keywords

  • Animals
  • Computational Biology
  • Databases, Genetic
  • Databases, Protein
  • Information Storage and Retrieval
  • Internet
  • Mice
  • Mice, Inbred C57BL
  • Mice, Inbred Strains
  • Mice, Knockout
  • Phenotype
  • Programming Languages
  • Protein Structure, Tertiary
  • Software

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