The Mouse Genome Database (MGD): mouse biology and model systems

By Carol J. Bult, Janan T. Eppig, J. Kadin, J. Richardson, Judith A. Blake. Nucleic Acids Res., 2007

434 citations recorded by the source corpus.

The Mouse Genome Database, (MGD, http://www.informatics.jax.org/), integrates genetic, genomic and phenotypic information about the laboratory mouse, a primary animal model for studying human biology and disease. MGD data content includes comprehensive characterization of genes and their functions, standardized descriptions of mouse phenotypes, extensive integration of DNA and protein sequence data, normalized representation of genome and genome variant information including comparative data on mammalian genes. Data within MGD are obtained from diverse sources including manual curation of the biomedical literature, direct contributions from individual investigator's laboratories and major informatics resource centers such as Ensembl, UniProt and NCBI. MGD collaborates with the bioinformatics community on the development of data and semantic standards such as the Gene Ontology (GO) and the Mammalian Phenotype (MP) Ontology. MGD provides a data-mining platform that enables the development of translational research hypotheses based on comparative genotype, phenotype and functional analyses. Both web-based querying and computational access to data are provided. Recent improvements in MGD described here include the association of gene trap data with mouse genes and a new batch query capability for customized data access and retrieval.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/581ef3781c40fd17df2e01f9acfc6f609767ef0d

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Citations in the corpus

Annotation Error in Public Databases: Misannotation of Molecular Function in Enzyme Superfamilies (2009, background): “In addition, multidisciplinary efforts have focused on accurate annotation for the most important model organisms, including E. coli [35], yeast [36], mouse [37] and human [38].”
The UCSC genome browser and associated tools (2012, neutral): “Nomenclature Consortium (HGNC) [37], the Mouse Genome Database at Jackson Lab [38],”
Linking Human Diseases to Animal Models Using Ontology-Based Phenotype Annotation (2009, methodology): “9 mutations are not linked to SPH1 or EL1 in MGI, although they may make good models because they also exhibit spheroid erythrocytes and abnormal erythrocyte lysis (MGI:2447353).”
IUPHAR-DB: new receptors and tools for easy searching and visualization of pharmacological data (2010, methodology): “Each NHR in IUPHAR-DB is hyperlinked to the corresponding entries in other relevant databases, including several of the NCBI Entrez databases (5), the human, rat and mouse genome databases [HGNC (6), MGI (7) and RGD (8)] and NURSA.”
GeneCards Version 3: the human gene integrator (2010, background): “This section provides annotated information about gene function from UniProtKB (7) and Genatlas (21), animal model information from MGI (22), RNAi, primers and clones products from vendors, as well as molecular function ontologies visualized by the GO Consortium (18).”
Comparative Analysis of Proteome and Transcriptome Variation in Mouse (2011, neutral): “org/ [44].”
Functional Knowledge Transfer for High-accuracy Prediction of Under-studied Biological Processes (2013, methodology): “Phenotype and disease data from SGD [ 77 ] , MGI [ 78 ] , Wormbase [ 79 ] , Flybase [ 80 ] , GSEA [ 20 ] , Zfin [ 81 ] were incorporated into our functional networks by summing the co - occurrences of gene pairs in all phenotypes / diseases and normalizing by the size of the phenotype / disease .”
Genome-wide analysis of ETS-family DNA-binding in vitro and in vivo (2010, positive): “Subsequent analyses have identified a total of 27 and 26 ETS-family members in human and mouse genomes, respectively (Bult et al, 2008).”
Pathway Tools version 13.0: integrated software for pathway/genome informatics and systems biology (2010, background): “Development of organism-specific DBs Organism-specific DBs (also known as MODs) describe the genome and other information about an organism [8–19].”
BioGPS: an extensible and customizable portal for querying and organizing gene annotation resources (2009, methodology): “Other researchers may then consult the Mouse Genome Database (MGD) [3] and Rat Genome Database (RGD) [4] for annotation focused on these model organisms, including knockout phenotypes and quantitative trait loci.”
GREAT improves functional interpretation of cis-regulatory regions (2010, methodology): “Perhaps the strongest validation for the GREAT methodology comes from the MGI Expression: Detected ontology 38 .”