Hosting of the International Mouse Strain Resource
The International Mouse Strain Resource (IMSR) (http://www.informatics.jax.org/imsr/
) has as its goal to provide and maintain a worldwide catalog of resources for mouse strains and stocks. The IMSR has developed a searchable database with a web front-end to assist researchers in locating and obtaining the mouse resources they need (Figure ).
Figure 1 The new IMSR is a searchable online database of mouse strains and stocks available worldwide, including inbred, mutant and genetically engineered mice. The goal of the IMSR is to assist the international scientific community in locating and obtaining (more ...)
An initial version of the IMSR was developed in 1999 (6
) as a collaborative effort with the Medical Research Council (MRC) Mammalian Genetics Unit (Harwell, UK) and contained a searchable resource for mouse stocks and strains held at The Jackson Laboratory (JAX) and at the MRC Harwell sites. While this proved to be a useful resource, it was severely limited in containing only information for these two major mouse laboratories.
With the establishment of multiple mutagenesis centers, gene trap centers, and the increasing use of genetic engineering technologies, the number of mouse stocks and strains and the specialization of genotype and their characterization has exploded. A number of new repositories and distribution centers have been established worldwide to cope with the exponential increase in specialized mouse stocks. The new pressing need for a central cataloging of stocks and strains prompted us to re-develop the IMSR in a more robust fashion, such that it could easily accommodate data from multiple sites, provide a better search interface for users, and enable links to phenotype searching and to specific stock data from each site that distributed mouse resources.
Users can search IMSR by strain, gene or allele designations, strain state(s) and strain classes. For each strain satisfying the search criteria, IMSR provides users with data on where a strain is available from, in what state(s) the strain exists (e.g. live, cryopreserved embryos or gametes, ES cell lines), the class of strain and mutant alleles carried by the strain. Hypertext links are provided (i) from each strain designation to its strain information page at the holding site, (ii) to an auto-generated email form to the holder's designated representative for obtaining additional information or ordering the mouse resource and (iii) from each mutant phenotypic allele carried by a strain to the detailed characterization of that allele in the MGI.
Additional links from the IMSR homepage provide instructions for participating in IMSR by listing one's mouse resources, for searching MGI for additional mouse genetic, genomic and biological information, and for checking the official mouse nomenclature guidelines from the International Committee on Genetic Nomenclature for Mice.
Current centers with mouse resources included in IMSR are as follows: The Jackson Laboratory (JAX), the Mouse Mutant Regional Resources Centers (MMRRC), the Center for Animal Resources and Development (CARD), the Oak Ridge National Laboratory (ORNL), the European Mouse Mutant Archive (EMMA) and the BayGenomics Gene Trap Resource. In progress is the incorporation of stocks from the MRC Genetics Unit, Harwell (Har), the Beta Cell Biology Consortium (BCBC), Neuromice (NMICE) and the Mouse Models of Human Cancer Consortium (MMHCC). Interest has been expressed by several other sites, including additional mouse mutagenesis centers, additional gene trap resources, and other distribution centers. IMSR also accepts stock listings from individuals. All strains and stocks listed in IMSR should be available to the research community and regular updating from sites is required to keep the IMSR current.
Enhanced orthology resources
MGD provides a curated set of mammalian orthologs for the research community. Although MGD supports orthology annotations to over 20 mammalian genomes, the priority effort focuses on the creation of orthology sets among mouse, human and rat. This set is constructed through an iterative process using both computational and manual approaches. This year, we worked with the HomoloGene resource at the NCBI (7
) to reciprocally incorporate some of the HomoloGene computational three-way reciprocal best-hit sets into the MGI system. HomoloGene incorporates MGD-curated mammalian orthology sets in their resources. In addition, we continue to work with the research community to carefully curate gene family sets, usually at the instigation of the research community (8
The Orthology Detail Page in MGD (Figure ) for the gene Wt1 illustrates the paradigm for orthology data. All assertions of orthology are supported by a statement of evidence and a citation. There are links to comparative mapping visualizations and links to genomics resources for the other species represented.
Figure 2 Mammalian Orthology Detail Page. The Mammalian Orthology Query Results page presents a table of results from MGI orthology curation. The table includes species, symbol, chromosome, external and internal accession IDs and criteria for the assertions. (more ...)
Electronic publication of classic books in mouse genetics
MGD has responded to user requests in making electronic copies of popular out-of-print books available online. Two such books have been developed as online versions, Mouse Genetics
by Lee Silver (Oxford University Press, 1995) at http://www.informatics.jax.org/silver/
and The Coat Colors of Mice
by Willys K. Silvers (Springer Verlag, 1979) at http://www.informatics.jax.org/wksilvers/
(Figure ). To develop these online books, publisher and author copyrights were obtained, text was re-developed and hypertext links placed within the text for cross-referencing and to provide direct access to MGI for enhanced gene and reference data. Photographs and graphics were scanned into electronic form or in some cases, redrawn. Both books have been welcomed by MGD users and permission to include additional out-of-print books is being sought.