International Mammalian Genome Society

The 16th International Mouse Genome Conference (2002)


Oral Presentation

Sunday 17 November

16:45 - 17:00 HRS

PATHBASE: A MOUSE PATHOLOGY DATABASE AND REFERENCE SOURCE FOR IMAGES OF MUTANT MOUSE HISTOPATHOLOGY

PN Schofield
University of Cambridge

Co-Authors: 2) Bard A, 3) Rozell B, 4) Goessner W, 5) Delvenne P, 6) Sariola H, 7) Ellender M, 8) Ward A
Institutions: 1) Dept of Anatomy, University of Cambridge, UK 2) Dept.of Anatomy, University of Edinburgh,

3) Karolinska Institute, Stockholm, 4) GSF - Forschungszentrum für Umwelt und Gesundheit, Munich, 5) Dept. of Pathology, University Hospital of Liege, 6) Developmental Biology, Institute of Biomedicine, University of Helsinki, 7) National Radiological Protection Board, Harwell,  8)School of Biological Sciences, University of  Bath,

The primary aim of the Pathbase project is to generate a web-accessible database (http://www.pathbase.net) of histopathological images from transgenic and mutant mice, many of which are not publicly available elsewhere.Access to these images is via controlled vocabularies covering genetic manipulations, tissues and mouse strains, via standard gene nomenclature and via a new ontology of mouse pathology phenotypes. This ontology incorporates 425 known mouse pathologies hierarchically organised as "instances of" biological processes, and is intended to help standardise the very large and internationally variable diagnostic nomenclatures in a way compatible with efficient database searching as well as facilitating the formal description of mouse mutant phenotypes. The ontology will be publicly available on the Pathbase site and on the Global Open Biological Ontology site (http://www.geneontology.org). Image acquisition for the database proceeds either by curator driven requests, or by researchers uploading their own images onto the database, using a browser-based console that integrates the images with keywords, descriptions, comments, and cross-references to other databases and the literature. Pathbase assigns a unique PB identifier to each image and this facilitates reference to, and retrieval of, specific images by other databases. Pathbase will also incorporate a reference collection of pathology images for phenotype diagnosis, a teaching tool for mouse pathology and links to other mouse databases (e.g. GXD, the mouse gene-expression database http://www.informatics.jax.org/menus/expression_menu.shtml). Pathbase is funded under the European Commission's Fifth framework programme (QLRI-1999-00320)


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