International Mammalian Genome Society

17th International Mouse Genome Conference

9-12 November 2003, Braunschweig, Germany


Schofield P N
University of Cambridge

Co-Authors: 2) Rozell B, 3) Bard J B L, 4)Sundberg J, 5) Ward J, 6) Hoefler H, 6) Goessner W, 6) Quintanilla-Fend L, 1) Gruenberg M, 7) Delvenne P, 7) Boniver J, 1) Orpin J, 8) Covelli V, 8) Mancuso M T, 9) Ward A, 10) Engstrom W, 11) Sariola H, 12) Ellender M, 13) Hopewell J
Institutions: 2) Karolinska Institute Stockholm 3) University of Edinburgh, 4) The Jackson Laboratory, 5) National Cancer Institute, Frederick, 6) GSF - Forschungszentrum für Umwelt und Gesundheit Instituet fur Pathologie Neuherberg 7) Dept of Pathology, University Hospital of Liege, 8) ENEA, Casaccia, Italy, 9) University of Bath, 10) Biocentrum, University of Uppsala, 11) University of Helsinki, 12) National Radiological Protection Board UK, 13) Churchill Hospital Oxford

The flood of descriptive phenotypic data currently emerging from gene and phenotype driven post-genomic analysis of gene function is now considerable and is expected to rise dramatically in the next few years. Consequently there is a need to archive primary phenotype data in a way in which it is searchable and usable in the most flexible and least hypothesis-dependent manner possible. Pathbase ( addresses this problem for mouse histopathology, a key aspect of phenotype analysis.

The database is designed with images as the data objects, each provided with a wide range of meta-data describing the experimental manipulation, the genes and alleles involved, the anatomical site of the lesion and its pathogenesis amongst other aspects. The new release of Pathbase will be described in which key meta-data are provided through use of a series of orthogonal ontologies shared with other databases, for example GO, EMAGE and GXD, allowing for full database interoperability. The new release of the database contains over 1000 images of mouse lesions and normal histology, which are actively curated and searchable by any combination of attributes.

The Pathbase consortium has now completed a Mouse Pathology Ontology (MPATH) designed to be used for describing images of mouse lesions, which is fully defined and available on MPATH is in the form of a GO compliant DAG, constructed as a five level hierarchy based on familiar pathological concepts. The aims behind the structure of this ontology and its applicability will be discussed.

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