International Mammalian Genome Society

B3 The Mouse Locus Catalog (MLC): a Database of Phenotypes and Alleles

Allan Peter Davis, Cathleen M. Lutz, Richard M. Baldarelli, Judith A. Blake, Janan T. Eppig, and Staff of Mouse Genome Informatics. The Jackson Laboratory, 600 Main Street, Bar Harbor, Maine 04609 USA

The Mouse Genome Database (MGD) has been available on the WWW since 1994 and represents a comprehensive resource using official standardized nomenclature to integrate biological information relevant to mouse genetics, including mutant phenotypes, molecular probes and segments, mammalian homology, genetic maps, gene expression patterns (GXD), inbred strain characteristics, tumor biology (MTB), and rat genome data. MGD is searchable, employing quick, user-friendly query screens with numerous search parameters to access data curated from over 55,000 publications, electronic submissions, and bulk data downloads.

One feature of MGD is the online Mouse Locus Catalog (MLC) which archives

detailed, concise phenotypic descriptions of mouse mutations. Expanding upon the work pioneered by Dr. Margaret Green in Genetic Variants and Strains of the Laboratory Mouse, the MLC is currently accessed under the "Phenotype (MLC)" heading on the marker detail page for a gene in MGD. Information is retrievable by gene name, gene symbol, allele, or key phenotype search terms in the "Genes, Markers, and Phenotypes" query form.

MLC reports have been restructured to present data in an improved format, including five category divisions, links to other databases, and literature references for users to examine additional and original sources:

1. Gene Family/Protein Domains: gene family descriptors with protein domain classifications (linked to Pfam).
2. Mouse Model/Disease: human ortholog and disease modeled in the mouse (linked to OMIM).
3. Gene/Gene Product Information: gene structure and protein function.
4. Expression: transcript size and adult expression sites (linked to GXD).
5. Phenotypes/Alleles and Variants: official allele nomenclature, inheritance, history of mutation, phenotype, and molecular resolution.

To keep the database current and accurate, we strongly encourage researchers to contact us to contribute phenotypic descriptions of their favorite mouse mutations or gene families. The templates are easy to use and require minimal writing effort for short, effective phenotypic descriptions of any mouse mutation. If interested, please contact MGD through our user help email: mgi-help@informatics.jax.org and it will be forwarded to an MLC scientific curator to initiate the simple process.

Since 1931 with the first Committee on Mouse Genetics Nomenclature, the scientific community has stressed the importance of standardizing genetic names. This allows different researchers to describe and share data with accuracy and clarity. With the exponential rise in gene targeted mutations, precise nomenclature is even more invaluable for a global scientific community. Towards that end, it is imperative that allele names follow a systematic guideline to distinguish one mutation from another. For those created by gene targeting, alleles should have a superscript designator using a personal LabCode (typically, a three-letter abbreviation of the principle investigator's name) issued by the Institute for Laboratory Animal Research (ILAR). Currently, the scientific curators at MGD propose and solicit a LabCode for a communicating author if one does not already exist. Members of the scientific community, however, are encouraged to apply for their own LabCode at the ILAR website (http://www2.nas.edu/labcode/) and to use them in their publications of targeted alleles. With the cooperative spirit that has defined the mouse genetics community through history, laboratories implementing this practice will help alleviate confusion when associating phenotypes with reported alleles.

MGD is publicly accessible at www.informatics.jax.org and is supported by NIH grant HG00330.