EuroPhenome: a repository for high-throughput mouse phenotyping data

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.

[1]  John M. Hancock,et al.  The functional annotation of mammalian genomes: the challenge of phenotyping. , 2009, Annual review of genetics.

[2]  J. M. Hancock,et al.  Post-publication sharing of data and tools , 2009, Nature.

[3]  John M. Hancock,et al.  Mouse, man, and meaning: bridging the semantics of mouse phenotype and human disease , 2009, Mammalian Genome.

[4]  John M. Hancock,et al.  Practical application of ontologies to annotate and analyse large scale raw mouse phenotype data , 2009, BMC Bioinformatics.

[5]  M. Hanazono,et al.  Assignment of the ARAF1 to porcine Chromosome Xpll.2-p13 by fluorescence in situ hybridization , 1997, Mammalian Genome.

[6]  Nigel W. Hardy,et al.  Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project , 2008, Nature Biotechnology.

[7]  John M. Hancock,et al.  EuroPhenome and EMPReSS: online mouse phenotyping resource , 2008 .

[8]  W. Wurst,et al.  EUCOMM--the European conditional mouse mutagenesis program. , 2007, Briefings in functional genomics & proteomics.

[9]  Steve D. M. Brown,et al.  The mouse ascending: perspectives for human-disease models , 2007, Nature Cell Biology.

[10]  Wolfgang Wurst,et al.  A Mouse for All Reasons , 2007, Cell.

[11]  John M. Hancock,et al.  Understanding Mammalian Genetic Systems: The Challenge of Phenotyping in the Mouse , 2006, PLoS genetics.

[12]  M. H. Angelis,et al.  EUMORPHIA and the European Mouse Phenotyping Resource for Standardized Screens (EMPReSS) , 2006 .

[13]  Martin Hrabé de Angelis,et al.  Standards of mouse model phenotyping , 2006 .

[14]  P Chambon,et al.  EMPReSS: standardized phenotype screens for functional annotation of the mouse genome , 2005, Nature Genetics.

[15]  John M. Hancock,et al.  BIOINFORMATICS APPLICATIONS NOTE Databases and ontologies EMPReSS: European Mouse Phenotyping Resource for Standardized Screens , 2005 .

[16]  John M. Hancock,et al.  Using ontologies to describe mouse phenotypes , 2004, Genome Biology.

[17]  Cynthia L. Smith,et al.  The Mammalian Phenotype Ontology as a tool for annotating, analyzing and comparing phenotypic information , 2004, Genome Biology.