The Mouse Genome Database (MGD): the model organism database for the laboratory mouse

Judith A. Blake 0 1 Joel E. Richardson 0 1 Carol J. Bult 0 1 Jim A. Kadin 0 1 Janan T. Eppig 0 1 The Mouse Genome Database Group 0 1 0 Current members of the Mouse Genome Database Group are: R. M. Baldarelli , M. Baya, J. S. Beal, W. J. Boddy, D. W. Bradt, D. J. Burkart, N. E. Butler, J. Campbell, T. Chu, L. E. Corbani, S. Cousins, H. J. Drabkin, D. M. Garippa, C. W. Goldsmith, P. L. Grant, M. Lennon-Pierce, I. Lu, C. M. Lutz, L. J. Maltais, P. Mani, L. M. McKenzie, J. E. Ormsby, A. J. Planchart, S. Ramachandran, D. J. Reed, D. R. Shaw, C. Smith, P. Szauter, L. A. Trombley and T. C. Wiegers 1 The Jackson Laboratory , 600 Main Street, Bar Harbor, ME 04609, USA The Mouse Genome Database (MGD) is the community database resource for the laboratory mouse, a key model organism for interpreting the human genome and for understanding human biology and disease (http://www.informatics.jax.org). MGD strives to provide a highly curated, highly integrated information resource that not only includes the consensus view of current knowledge about the mouse, but also provides comparative genomic information particularly for human and rat genomes. MGD includes extensive information about mouse genes, supporting all gene attribute assertions with experimental data, statements of evidence and citation. Detailed information about alleles and mouse mutants includes genotype, molecular variant and phenotype descriptions. Extensive collaboration with other data providers such as NCBI, RIKEN and SWISS-PROT provides standardization of gene:sequence associations and robust interconnections between large information systems based on shared sequence curation. Recent integration of large datasets of mouse full-length cDNAs and radiation-hybrid mapped ESTs, the continued development and use of extensive structured vocabularies and the expansion of the representation of phenotypes highlight this year's developments. - The Mouse Genome Database (MGD; http://www.informatics. jax.org) is the public community resource representing the genetics, genomics and phenotypes of the laboratory mouse. MGD focuses on an integrated representation of genotype (sequence) to phenotype information including highly curated information about genes and gene products (1) (Table 1). Primary foci of integration are through representations of relationships between genes, sequences and phenotypes. The annotation pipeline includes extensive curation of the scientific literature. All annotations in MGD are supported with experimental evidence and citations. MGD provides official nomenclature for mouse genes and works closely with human and rat genome annotation groups to curate relationships between these genomes and to standardize the representation of genes and gene families. MGD provides information about alleles and targeted mutations, homology data for mammalian orthologs and detailed mapping data at both the gene and genomic levels. Extensive curation of sequence to gene associations provides the fundamental dataset against which computational annotation systems are calibrated and tested. MGD provides graphical views of the comparative genomic data from the gene, chromosomal region, genome or species perspective. Extensive experimental mapping data including genetic and physical maps are available, including data that conflicts with current consensus map positions. MGD is part of the Mouse Genome Informatics (MGI) project effort based at The Jackson Laboratory (http:// www.jax.org) and collaborates closely with the Gene Expression Database (GXD) (2), the Mouse Genome Sequencing (MGS) project and the Mouse Tumor Biology (MTB) database (3) to provide an integrated information resource for the laboratory mouse. MGD is a founding member of the Gene Ontology (GO) consortium (4) and contributes particularly to the development of mammalian components of the GO vocabularies. MGD curators collaborate extensively with SWISS-PROT (5) and with the LocusLink project at NCBI (6) to evaluate and update mouse gene:sequence associations. IMPROVEMENTS DURING 2001 Expanded allele and mutant phenotype data For each allele or mutant, MGD provides data describing the type of allele (e.g. ENU-induced, transgene targeted), the mouse strain on which it arose, the phenotypic characteristics of homozygous and heterozygous carriers and its relationship with human genes and disease. New data available include molecular details of the allelic change, ES cell lines and cell line strain (for targeted alleles), promoter details (where relevant) and expanded citations. In addition, phenotypic alleles are linked to GXD whenever expression data are available for mice carrying the allele. Controlled vocabularies for phenotypes MGD continues to develop and implement controlled and structured vocabularies to standardize the annotation of Number of markers (including genes) Number of genes with sequence data Number of markers mapped Number of mouse/human curated orthology reports Number of genes with links to SWISS-PROT Number of genes with GO annotations Number of genes with annotated alleles Number of annotated alleles Number of mouse nucleotide sequences curated in MGI system (includes ESTs) aSee text for caveats on this number. information for mouse genes and genomic features. A recent effort to develop and use standard vocabularies for describing mouse normal and mutant phenotypes will improve searching, classifying and analyzing phenotype data. The current structured vocabulary consists of several thousand terms, each associated with precise definitions and a citation as a source of the information. Terms are organized hierarchically, from general to specific, allowing annotation to reflect the state of knowledge about particular mutants (e.g. a newly discovered mutation may be observed to have a hearing defect; a better studied mutation may assign the hearing defect to degeneration of the organ of Corti). Phenotype vocabulary terms are being used to annotate the phenotypes of mice carrying heterozygous or homozygous mutant alleles on particular genetic backgrounds and these data are presented as part of the MGD allele and mutant phenotype reports. PhenoSlim. A particular subset of the phenotype vocabularies consisting of the broadest, high-level terms of the full phenotype vocabulary, referred to as PhenoSlim, includes approximately 100 terms and is being used to develop the initial phenotype query capability in MGD. Curated orthology assertions and gene family summaries MGD provides gene family pages that summarize information about mouse, human and rat orthologs. Each summary report includes official gene symbols, a representative sequence for each gene in each species and links to MGD gene reports, human LocusLink records and, in the near future, links to the Rat Genome Database (7) gene detail pages. An example of the claudin gene family pages can be viewed at http://www.informatics.jax.org/ mgihome/nomen/genefamilies/claudin.shtml. These c (...truncated)