International Mammalian Genome Society

The 13th International Mouse Genome Conference
October 31-November 3, 1999

Table of Contents * Structure * Bioinformatics * Sequence * Mapping * New Tools * Gene Discovery * Developmental * Mutagenesis * Functional Genomics

B4 The Language of Phenotypes: Bringing Sandard and Mutant Phenotype Vocabularies Into MGD

Janan T. Eppig, Judith A. Blake, Richard M. Baldarelli, Allan P. Davis, Cathy M. Lutz, and Joel E. Richardson. The Jackson Laboratory, Bar Harbor, ME 04609

The number of genes in mouse that have at least enough characterization to be given names now exceeds 10,000, about 10% of the estimated total gene number. Of these, several hundred were originally identified by Mendelian segregation of a recognizable phenotype. The number of spontaneously occurring alleles resulting in visible phenotypic effects is variable, with most genes having zero or one, to over 100 for the Kit gene. The number of available phenotypic mutant alleles is growing dramatically with our recent ability to create targeted mutations and the advent of systematic large-scale mutagenesis studies in mouse - new genes are being identified, new mutant alleles of known genes are being created, and additional heritable phenotypes of complex origin are being uncovered. There is a pressing need for associating meaningful annotation to phenotypes and to genes that will enhance our ability to search and compare identified genes and phentoypes.

Two efforts will be described that are actively being worked on by the Mouse Genome Database in collaboration with other groups. One, the Gene Ontology (GO) project, is a collaboration between the Saccharomyces Genome Database (SGD), FlyBase and the Mouse Genome Database (MGD), to develop three independently organized controlled vocabularies (gene ontologies) to describe functions, biological processes and cellular locations of gene products and to annotate genes in the respective databases against these vocabularies. The goal is to provide our users with a resource that allows queries using a standard set of terms within each species database and across species databases. The second effort is developing vocabularies to describe mouse/mammalian specific traits, phenotypes, and disease models and to apply these in MGD, among ENU mutagenesis centers, and among phenotyping groups to describe new mutants and strain characteristics. Structured vocabularies allow multiple terms to be associated with phenotypes and serve as descriptors to enhance searching, exploring multiple relationships, and analyzing pathways and disease mechanisms.

Supported by NIH grant HG00330.


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