International Mammalian Genome Society

logo18th International Mouse Genome Conference

17-22 October 2004, Seattle, USA


POSTER 68 - SOPDB: A RESOURCE OF STANDARD OPERATING PROCEDURES FOR MOUSE PHENOTYPING

Green ECJ, Gkoutos GV, Weekes J, Mallon AM, Hancock JM

Mammalian Genetics Unit, Oxfordshire, United Kingdom

EUMORPHIA1 is an integrated research programme involving the development of new approaches in phenotyping, mutagenesis and informatics leading to improved characterisation of mouse models for the understanding of human physiology and disease.

The SOPdb resource is an XML database2 of Standard Operating Procedures (SOPs) that constitutes the European Comprehensive First-Line Phenotyping Protocol for mice (ECFLP)3 with a web interface.  The ECFLP is a precise, evolving, working manual of SOPs for primary pathophysiological analysis of mouse mutants, which will be used in all reference laboratories contributing to the EUMORPHIA project.  SOPdb allows storage, indexing, searching, retrieval and transformation of SOPs taking advantage of the XML technology.

A major challenge in modern biology is to link genome sequence information to gene function. In many organisms this is being done by characterising phenotypes that result from individual mutations. Efficiently expressing phenotypic information requires combinatorial use of ontologies.4 SOPs are vital for describing the phenotype they attempt to measure, the units and the manner of measurement as well as possible interpretations of observations.4 SOPdb will provide links to Assay ontologies to facilitate phenotypic descriptions generated according to our recently proposed schemal4.

References

1.EUMORPHIA: Understanding Human Disease Through Mouse Genetics. Available on line at: http://www.eumorphia.org/

2.eXist: Open Source XML Database. Available on line http://exist.sourceforge.net/

3.Coghill E.L., Lad H. and the EUMORPHIA Consortium, EUMORPHIA and the European Comprehensive First Line Phenotyping protocol, IMGC, 2004.

4.Gkoutos G.V., Green E.C.J., Mallon A.M., Hancock J.M., Davidson D. (2004). Building mouse phenotype ontologies. Pac Symp Biocomput., 2004, 178-89.

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