MGD: the Mouse Genome Database

Judith A. Blake 0 Joel E. Richardson 0 Carol J. Bult 0 Jim A. Kadin 0 Janan T. Eppigand The Mouse Genome Database Group 0 Current members of the Mouse Genome Database Group are R. M. Baldarelli 0 J. S. Beal 0 D. W. Bradt 0 D. L. Burkart 0 N. E. Butler 0 J. Campbell 0 T. Chu 0 L. E. Corbani 0 S. Cousins 0 H. J. Drabkin 0 D. Dahmen 0 K. Frazer 0 D. M. Garippa 0 C. W. Goldsmith 0 P. L. Grant 0 M. Lennon-Pierce 0 J. Lewis 0 I. Lu 0 C. M. Lutz 0 L. J. Maltais 0 P. Mani 0 L. M. McKenzie 0 L. Ni 0 J. E. Ormsby 0 A. Planchart 0 S. Ramachandran 0 D. J. Reed 0 D. R. Shaw 0 C. L. Smith 0 P. Szauter 0 P. Vanden Borre 0 L. Washburn 0 J. Winslow 0 0 The Jackson Laboratory , 600 Main Street, Bar Harbor, ME 04609, USA The Mouse Genome Database (MGD) (http://www. informatics.jax.org) one component of a community database resource for the laboratory mouse, a key model organism for interpreting the human genome and for understandinghuman biology. MGD strives to provide an extensively integrated information resource with experimental details annotated from both literature and on-line genomic data sources. MGD curates and presents the consensus representation of genotype (sequence) to phenotype information includinghihgly detailed information about genes and gene products. Primary foci of integration are through representations of relationships between genes, sequences and phenotypes. MGD collaborates with other bioinformatics groups to curate a definitive set of information about the laboratory mouse. Recent developments include a general implementation of database structures for controlled vocabularies and the integration of a phenotype classification system. - The Mouse Genome Database (MGD) provides an integrated view of genetic and genomic information for the laboratory mouse (1). MGD contains information on mouse genes, genetic markers and genomic features as well as information on molecular segments ( probes, primers, cDNA clones, BACs and YACs) mutant phenotypes, comparative mapping data, graphical displays of linkage, cytogenetic and physical maps, experimental mapping data, as well as strain distribution patterns for recombinant inbred strains (RIs) and cross haplotypes. MGD is updated daily (Table 1). Since it first became available on the WWW, MGD has continued to evolve, expanding its data coverage, improving data handling, and providing several new data manipulation and display tools. MGD data statistics Number of references Number of genes Number of markers (including genes) Number of genes with sequence data Number of markers mapped Number of mouse/human curator orthologies 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 and integrated in the MGI system (includes ESTs) MGD is one component of the Mouse Genome Informatics (MGI) database resource (http://www.informatics.jax.org) located at The Jackson Laboratory (http://www.jax.org). Other projects and resources that contribute to MGI include the Gene Expression Database (GXD) (2), the Mouse Genome Sequencing (MGS) (3) project and the Mouse Tumor Biology Database (MTB; http://www.informatics.jax.org/mtb) (4). The MGI consortium group participates actively in the development and implementation of the Gene Ontologies (GO) (www.geneontology.org) (5). MGI curators also collaborate extensively with SWISS-PROT (6) and with the LocusLink project at NCBI (7) to evaluate associations between genes and sequences for the mouse. IMPROVEMENTS DURING 2002 Implementation of phenotype classifications A broad, high-level set of phenotype terms have been developed and employed to classify phenotype data in MGD. This defined vocabulary of 105 terms can be used to search, group, compare and analyze phenotypes. These phenotype classification terms appear on the Alleles and Phenotypes Query Form (Fig. 1), and on the Genes and Marker Query Form. The complete list of terms and their accession IDs is also available by FTP. On each form, there is a link to the phenotype classification terms, complete with definitions and examples. Users of the MGI database can select one or more terms from the list to search for records associated with a particular phenotype, in combination with many other parameters on the forms. In addition, textbased searches for more specific phenotypic terms remain available. A more comprehensive phenotype vocabulary continues to be developed by MGD staff and currently (September, 2002) contains over 1800 concepts. These terms are used to annotate mouse mutant phenotypes. Although these controlled terms are used to annotate mouse mutant phenotypes and can be viewed on allele detail pages, there currently is limited access to the full phenotype vocabulary as a query or analysis tool. Improvements to the MGI : GO browser The MGI GO Browser (http://www.informatics.jax.org/searches/ GO_form.shtml) allows database users to access genes in MGI using functional annotation terms from the GO. This Browser was developed in conjunction with the GXD. A general database implementation within MGI for structured, controlled vocabularies enhances the search and recovery capabilities of this browser. The GO Browser can be accessed from gene detail or query pages as well as directly from the MGI menus. A GO Browser query returns a graph reflecting both parents and children of the query term and a link to all MGI associations with that term or any of the subterms. Availability of MGI : GO files in various formats MGI gene-to-GO annotations are updated daily. Various files for the MGI gene/markers with the GO associations are publicly available. These files are updated each time MGI submits a new gene association file to the GO web site (http:// www.geneontology.org) and can be accessed on the MGI FTP server (ftp://www.informatics.jax.org/pub/informatics/reports/ gene_association.mgi). A file of all the GO terms used by MGI in the annotation of genes and gene products is also available. MGI also provides a file to the GO database of MGI Gene : SWISS-PROT associations. This information is incorporated into the GO database and thus enables users to recover mouse sequence data as a result of a semantic search against the GO database (http://www.godatabase.org/cgi-bin/go.cgi). OTHER INFORMATION MGD encourages user input into its gene and allele annotation efforts. On each gene detail and allele detail page, a clickable button (Your Input Welcome) brings the user to a web-based form for submitting updates to the information being viewed. Mouse gene nomenclature The MGD gene annotation group assigns unique symbols and names to mouse genes under the guidelines set by the International Committee on Standardized Genetic Nomenclature for mouse (http://www.informatics.jax.org/mgihome/nomen/ index.shtml#mnrg) (8). Scientists can reserve symbols prior to publication using the electronic nomenclature submission for (...truncated)