Database Commons

a catalog of biological databases

e.g., animal; RNA; Methylation; China

Database information

MGD (Mouse Genome Database)

General information

Description: The Mouse Genome Database (MGD; http://www.informatics.jax.org) is the primary community model organism database for the laboratory mouse and serves as the source for key biological reference data related to mouse genes, gene functions, phenotypes and disease models with a strong emphasis on the relationship of these data to human biology and disease.
Year founded: 1994
Last update: 2018-11-27
Version: v6.13
Accessibility:
Manual:
Accessible
Real time : Checking...
Country/Region: United States
Data type:
DNA
Data object:
Database category:
Major organism:
Keywords:

Contact information

University/Institution: The Jackson Laboratory
Address: 600 Main Street
City: Bar Harbor
Province/State: Maine
Country/Region: United States
Contact name (PI/Team): Judith A. Blake
Contact email (PI/Helpdesk): mgi-help@jax.org

Record metadata

Created on: 2015-06-20
Curated by:
Shoaib Saleem [2019-10-28]
Dong Zou [2019-01-04]
[2018-11-27]
Lina Ma [2018-05-28]
Dong Zou [2018-02-13]
Dong Zou [2018-02-07]
zhang yang [2018-01-28]
Dong Zou [2018-01-27]
Shixiang Sun [2017-02-17]
Lin Liu [2016-03-27]
Lin Liu [2016-01-29]
Lin Liu [2016-01-05]
Li Yang [2015-11-24]
Li Yang [2015-11-23]
Li Yang [2015-06-26]

Ranking

All databases:
94/4692 (98.018%)
Health and medicine:
17/959 (98.332%)
Gene genome and annotation:
44/1246 (96.549%)
94
Total Rank
2,131
Citations
92.652
z-index

Community reviews

Not Rated
Data quality & quantity:
Content organization & presentation
System accessibility & reliability:

Word cloud

Publications

30407599
Mouse Genome Database (MGD) 2019. [PMID: 30407599]
Bult CJ, Blake JA, Smith CL, Kadin JA, Richardson JE, Mouse Genome Database Group .

The Mouse Genome Database (MGD; http://www.informatics.jax.org) is the community model organism genetic and genome resource for the laboratory mouse. MGD is the authoritative source for biological reference data sets related to mouse genes, gene functions, phenotypes, and mouse models of human disease. MGD is the primary outlet for official gene, allele and mouse strain nomenclature based on the guidelines set by the International Committee on Standardized Nomenclature for Mice. In this report we describe significant enhancements to MGD, including two new graphical user interfaces: (i) the Multi Genome Viewer for exploring the genomes of multiple mouse strains and (ii) the Phenotype-Gene Expression matrix which was developed in collaboration with the Gene Expression Database (GXD) and allows researchers to compare gene expression and phenotype annotations for mouse genes. Other recent improvements include enhanced efficiency of our literature curation processes and the incorporation of Transcriptional Start Site (TSS) annotations from RIKEN's FANTOM 5 initiative.

Nucleic Acids Res. 2019:47(D1) | 42 Citations (from Europe PMC, 2020-09-12)
29092072
Mouse Genome Database (MGD)-2018: knowledgebase for the laboratory mouse. [PMID: 29092072]
Smith CL, Blake JA, Kadin JA, Richardson JE, Bult CJ, Mouse Genome Database Group.

The Mouse Genome Database (MGD; http://www.informatics.jax.org) is the key community mouse database which supports basic, translational and computational research by providing integrated data on the genetics, genomics, and biology of the laboratory mouse. MGD serves as the source for biological reference data sets related to mouse genes, gene functions, phenotypes and disease models with an increasing emphasis on the association of these data to human biology and disease. We report here on recent enhancements to this resource, including improved access to mouse disease model and human phenotype data and enhanced relationships of mouse models to human disease.

Nucleic Acids Res. 2018:46(D1) | 82 Citations (from Europe PMC, 2020-09-19)
29761459
Mouse Genome Informatics (MGI) Is the International Resource for Information on the Laboratory Mouse. [PMID: 29761459]
Law M, Shaw DR.

Mouse Genome Informatics (MGI, http://www.informatics.jax.org/ ) web resources provide free access to meticulously curated information about the laboratory mouse. MGI's primary goal is to help researchers investigate the genetic foundations of human diseases by translating information from mouse phenotypes and disease models studies to human systems. MGI provides comprehensive phenotypes for over 50,000 mutant alleles in mice and provides experimental model descriptions for over 1500 human diseases. Curated data from scientific publications are integrated with those from high-throughput phenotyping and gene expression centers. Data are standardized using defined, hierarchical vocabularies such as the Mammalian Phenotype (MP) Ontology, Mouse Developmental Anatomy and the Gene Ontologies (GO). This chapter introduces you to Gene and Allele Detail pages and provides step-by-step instructions for simple searches and those that take advantage of the breadth of MGI data integration.

Methods Mol Biol. 2018:1757() | 3 Citations (from Europe PMC, 2020-09-12)
27899570
Mouse Genome Database (MGD)-2017: community knowledge resource for the laboratory mouse. [PMID: 27899570]
Blake JA, Eppig JT, Kadin JA, Richardson JE, Smith CL, Bult CJ, the Mouse Genome Database Group.

The Mouse Genome Database (MGD: http://www.informatics.jax.org) is the primary community data resource for the laboratory mouse. It provides a highly integrated and highly curated system offering a comprehensive view of current knowledge about mouse genes, genetic markers and genomic features as well as the associations of those features with sequence, phenotypes, functional and comparative information, and their relationships to human diseases. MGD continues to enhance access to these data, to extend the scope of data content and visualizations, and to provide infrastructure and user support that ensures effective and efficient use of MGD in the advancement of scientific knowledge. Here, we report on recent enhancements made to the resource and new features. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Nucleic Acids Res. 2017:45(D1) | 127 Citations (from Europe PMC, 2020-09-19)
26578600
Mouse genome database 2016. [PMID: 26578600]
Bult CJ, Eppig JT, Blake JA, Kadin JA, Richardson JE, Mouse Genome Database Group.

The Mouse Genome Database (MGD; http://www.informatics.jax.org) is the primary community model organism database for the laboratory mouse and serves as the source for key biological reference data related to mouse genes, gene functions, phenotypes and disease models with a strong emphasis on the relationship of these data to human biology and disease. As the cost of genome-scale sequencing continues to decrease and new technologies for genome editing become widely adopted, the laboratory mouse is more important than ever as a model system for understanding the biological significance of human genetic variation and for advancing the basic research needed to support the emergence of genome-guided precision medicine. Recent enhancements to MGD include new graphical summaries of biological annotations for mouse genes, support for mobile access to the database, tools to support the annotation and analysis of sets of genes, and expanded support for comparative biology through the expansion of homology data. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

Nucleic Acids Res. 2016:44(D1) | 46 Citations (from Europe PMC, 2020-09-19)
25348401
The Mouse Genome Database (MGD): facilitating mouse as a model for human biology and disease. [PMID: 25348401]
Eppig JT, Blake JA, Bult CJ, Kadin JA, Richardson JE, Mouse Genome Database Group.

The Mouse Genome Database (MGD, http://www.informatics.jax.org) serves the international biomedical research community as the central resource for integrated genomic, genetic and biological data on the laboratory mouse. To facilitate use of mouse as a model in translational studies, MGD maintains a core of high-quality curated data and integrates experimentally and computationally generated data sets. MGD maintains a unified catalog of genes and genome features, including functional RNAs, QTL and phenotypic loci. MGD curates and provides functional and phenotype annotations for mouse genes using the Gene Ontology and Mammalian Phenotype Ontology. MGD integrates phenotype data and associates mouse genotypes to human diseases, providing critical mouse-human relationships and access to repositories holding mouse models. MGD is the authoritative source of nomenclature for genes, genome features, alleles and strains following guidelines of the International Committee on Standardized Genetic Nomenclature for Mice. A new addition to MGD, the Human-Mouse: Disease Connection, allows users to explore gene-phenotype-disease relationships between human and mouse. MGD has also updated search paradigms for phenotypic allele attributes, incorporated incidental mutation data, added a module for display and exploration of genes and microRNA interactions and adopted the JBrowse genome browser. MGD resources are freely available to the scientific community. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

Nucleic Acids Res. 2015:43(Database issue) | 216 Citations (from Europe PMC, 2020-09-19)
24285300
The Mouse Genome Database: integration of and access to knowledge about the laboratory mouse. [PMID: 24285300]
Blake JA, Bult CJ, Eppig JT, Kadin JA, Richardson JE, Mouse Genome Database Group.

The Mouse Genome Database (MGD) (http://www.informatics.jax.org) is the community model organism database resource for the laboratory mouse, a premier animal model for the study of genetic and genomic systems relevant to human biology and disease. MGD maintains a comprehensive catalog of genes, functional RNAs and other genome features as well as heritable phenotypes and quantitative trait loci. The genome feature catalog is generated by the integration of computational and manual genome annotations generated by NCBI, Ensembl and Vega/HAVANA. MGD curates and maintains the comprehensive listing of functional annotations for mouse genes using the Gene Ontology, and MGD curates and integrates comprehensive phenotype annotations including associations of mouse models with human diseases. Recent improvements include integration of the latest mouse genome build (GRCm38), improved access to comparative and functional annotations for mouse genes with expanded representation of comparative vertebrate genomes and new loads of phenotype data from high-throughput phenotyping projects. All MGD resources are freely available to the research community.

Nucleic Acids Res. 2014:42(Database issue) | 136 Citations (from Europe PMC, 2020-09-19)
23175610
The mouse genome database: genotypes, phenotypes, and models of human disease. [PMID: 23175610]
Bult CJ, Eppig JT, Blake JA, Kadin JA, Richardson JE, Mouse Genome Database Group.

The laboratory mouse is the premier animal model for studying human biology because all life stages can be accessed experimentally, a completely sequenced reference genome is publicly available and there exists a myriad of genomic tools for comparative and experimental research. In the current era of genome scale, data-driven biomedical research, the integration of genetic, genomic and biological data are essential for realizing the full potential of the mouse as an experimental model. The Mouse Genome Database (MGD; http://www.informatics.jax.org), the community model organism database for the laboratory mouse, is designed to facilitate the use of the laboratory mouse as a model system for understanding human biology and disease. To achieve this goal, MGD integrates genetic and genomic data related to the functional and phenotypic characterization of mouse genes and alleles and serves as a comprehensive catalog for mouse models of human disease. Recent enhancements to MGD include the addition of human ortholog details to mouse Gene Detail pages, the inclusion of microRNA knockouts to MGD's catalog of alleles and phenotypes, the addition of video clips to phenotype images, providing access to genotype and phenotype data associated with quantitative trait loci (QTL) and improvements to the layout and display of Gene Ontology annotations.

Nucleic Acids Res. 2013:41(Database issue) | 44 Citations (from Europe PMC, 2020-09-19)
22075990
The Mouse Genome Database (MGD): comprehensive resource for genetics and genomics of the laboratory mouse. [PMID: 22075990]
Eppig JT, Blake JA, Bult CJ, Kadin JA, Richardson JE, Mouse Genome Database Group.

The Mouse Genome Database (MGD, http://www.informatics.jax.org) is the international community resource for integrated genetic, genomic and biological data about the laboratory mouse. Data in MGD are obtained through loads from major data providers and experimental consortia, electronic submissions from laboratories and from the biomedical literature. MGD maintains a comprehensive, unified, non-redundant catalog of mouse genome features generated by distilling gene predictions from NCBI, Ensembl and VEGA. MGD serves as the authoritative source for the nomenclature of mouse genes, mutations, alleles and strains. MGD is the primary source for evidence-supported functional annotations for mouse genes and gene products using the Gene Ontology (GO). MGD provides full annotation of phenotypes and human disease associations for mouse models (genotypes) using terms from the Mammalian Phenotype Ontology and disease names from the Online Mendelian Inheritance in Man (OMIM) resource. MGD is freely accessible online through our website, where users can browse and search interactively, access data in bulk using Batch Query or BioMart, download data files or use our web services Application Programming Interface (API). Improvements to MGD include expanded genome feature classifications, inclusion of new mutant allele sets and phenotype associations and extensions of GO to include new relationships and a new stream of annotations via phylogenetic-based approaches.

Nucleic Acids Res. 2012:40(Database issue) | 182 Citations (from Europe PMC, 2020-09-19)
23110975
Manual Gene Ontology annotation workflow at the Mouse Genome Informatics Database. [PMID: 23110975]
Drabkin HJ, Blake JA, Mouse Genome Informatics Database.

The Mouse Genome Database, the Gene Expression Database and the Mouse Tumor Biology database are integrated components of the Mouse Genome Informatics (MGI) resource (http://www.informatics.jax.org). The MGI system presents both a consensus view and an experimental view of the knowledge concerning the genetics and genomics of the laboratory mouse. From genotype to phenotype, this information resource integrates information about genes, sequences, maps, expression analyses, alleles, strains and mutant phenotypes. Comparative mammalian data are also presented particularly in regards to the use of the mouse as a model for the investigation of molecular and genetic components of human diseases. These data are collected from literature curation as well as downloads of large datasets (SwissProt, LocusLink, etc.). MGI is one of the founding members of the Gene Ontology (GO) and uses the GO for functional annotation of genes. Here, we discuss the workflow associated with manual GO annotation at MGI, from literature collection to display of the annotations. Peer-reviewed literature is collected mostly from a set of journals available electronically. Selected articles are entered into a master bibliography and indexed to one of eight areas of interest such as 'GO' or 'homology' or 'phenotype'. Each article is then either indexed to a gene already contained in the database or funneled through a separate nomenclature database to add genes. The master bibliography and associated indexing provide information for various curator-reports such as 'papers selected for GO that refer to genes with NO GO annotation'. Once indexed, curators who have expertise in appropriate disciplines enter pertinent information. MGI makes use of several controlled vocabularies that ensure uniform data encoding, enable robust analysis and support the construction of complex queries. These vocabularies range from pick-lists to structured vocabularies such as the GO. All data associations are supported with statements of evidence as well as access to source publications.

Database (Oxford). 2012:2012() | 7 Citations (from Europe PMC, 2020-09-19)
21051359
The Mouse Genome Database (MGD): premier model organism resource for mammalian genomics and genetics. [PMID: 21051359]
Blake JA, Bult CJ, Kadin JA, Richardson JE, Eppig JT, Mouse Genome Database Group.

The Mouse Genome Database (MGD) is the community model organism database for the laboratory mouse and the authoritative source for phenotype and functional annotations of mouse genes. MGD includes a complete catalog of mouse genes and genome features with integrated access to genetic, genomic and phenotypic information, all serving to further the use of the mouse as a model system for studying human biology and disease. MGD is a major component of the Mouse Genome Informatics (MGI, http://www.informatics.jax.org/) resource. MGD contains standardized descriptions of mouse phenotypes, associations between mouse models and human genetic diseases, extensive integration of DNA and protein sequence data, normalized representation of genome and genome variant information. Data are obtained and integrated via manual curation of the biomedical literature, direct contributions from individual investigators and downloads from major informatics resource centers. MGD collaborates with the bioinformatics community on the development and use of biomedical ontologies such as the Gene Ontology (GO) and the Mammalian Phenotype (MP) Ontology. Major improvements to the Mouse Genome Database include comprehensive update of genetic maps, implementation of new classification terms for genome features, development of a recombinase (cre) portal and inclusion of all alleles generated by the International Knockout Mouse Consortium (IKMC).

Nucleic Acids Res. 2011:39(Database issue) | 163 Citations (from Europe PMC, 2020-09-19)
19864252
The Mouse Genome Database: enhancements and updates. [PMID: 19864252]
Bult CJ, Kadin JA, Richardson JE, Blake JA, Eppig JT, Mouse Genome Database Group.

The Mouse Genome Database (MGD) is a major component of the Mouse Genome Informatics (MGI, http://www.informatics.jax.org/) database resource and serves as the primary community model organism database for the laboratory mouse. MGD is the authoritative source for mouse gene, allele and strain nomenclature and for phenotype and functional annotations of mouse genes. MGD contains comprehensive data and information related to mouse 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 for MGD are obtained from diverse sources including manual curation of the biomedical literature and 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 and use of biomedical ontologies such as the Gene Ontology and the Mammalian Phenotype Ontology. Recent improvements in MGD described here includes integration of mouse gene trap allele and sequence data, integration of gene targeting information from the International Knockout Mouse Consortium, deployment of an MGI Biomart, and enhancements to our batch query capability for customized data access and retrieval.

Nucleic Acids Res. 2010:38(Database issue) | 48 Citations (from Europe PMC, 2020-09-19)
18981050
The Mouse Genome Database genotypes::phenotypes. [PMID: 18981050]
Blake JA, Bult CJ, Eppig JT, Kadin JA, Richardson JE, Mouse Genome Database Group.

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. Information in MGD is obtained from diverse sources, including the scientific literature and external databases, such as EntrezGene, UniProt and GenBank. In addition to its extensive collection of phenotypic allele information for mouse genes that is curated from the published biomedical literature and researcher submission, MGI includes a comprehensive representation of mouse genes including sequence, functional (GO) and comparative information. MGD provides a data mining platform that enables the development of translational research hypotheses based on comparative genotype, phenotype and functional analyses. MGI can be accessed by a variety of methods including web-based search forms, a genome sequence browser and downloadable database reports. Programmatic access is available using web services. Recent improvements in MGD described here include the unified mouse gene catalog for NCBI Build 37 of the reference genome assembly, and improved representation of mouse mutants and phenotypes.

Nucleic Acids Res. 2009:37(Database issue) | 74 Citations (from Europe PMC, 2020-09-19)
18158299
The Mouse Genome Database (MGD): mouse biology and model systems. [PMID: 18158299]
Bult CJ, Eppig JT, Kadin JA, Richardson JE, Blake JA, Mouse Genome Database Group.

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.

Nucleic Acids Res. 2008:36(Database issue) | 255 Citations (from Europe PMC, 2020-09-19)
17135206
The mouse genome database (MGD): new features facilitating a model system. [PMID: 17135206]
Eppig JT, Blake JA, Bult CJ, Kadin JA, Richardson JE, Mouse Genome Database Group.

The mouse genome database (MGD, http://www.informatics.jax.org/), the international community database for mouse, provides access to extensive integrated data on the genetics, genomics and biology of the laboratory mouse. The mouse is an excellent and unique animal surrogate for studying normal development and disease processes in humans. Thus, MGD's primary goals are to facilitate the use of mouse models for studying human disease and enable the development of translational research hypotheses based on comparative genotype, phenotype and functional analyses. Core MGD data content includes gene characterization and functions, phenotype and disease model descriptions, DNA and protein sequence data, polymorphisms, gene mapping data and genome coordinates, and comparative gene data focused on mammals. Data are integrated from diverse sources, ranging from major resource centers to individual investigator laboratories and the scientific literature, using a combination of automated processes and expert human curation. MGD collaborates with the bioinformatics community on the development of data and semantic standards, and it incorporates key ontologies into the MGD annotation system, including the Gene Ontology (GO), the Mammalian Phenotype Ontology, and the Anatomical Dictionary for Mouse Development and the Adult Anatomy. MGD is the authoritative source for mouse nomenclature for genes, alleles, and mouse strains, and for GO annotations to mouse genes. MGD provides a unique platform for data mining and hypothesis generation where one can express complex queries simultaneously addressing phenotypic effects, biochemical function and process, sub-cellular location, expression, sequence, polymorphism and mapping data. Both web-based querying and computational access to data are provided. Recent improvements in MGD described here include the incorporation of single nucleotide polymorphism data and search tools, the addition of PIR gene superfamily classifications, phenotype data for NIH-acquired knockout mice, images for mouse phenotypic genotypes, new functional graph displays of GO annotations, and new orthology displays including sequence information and graphic displays.

Nucleic Acids Res. 2007:35(Database issue) | 68 Citations (from Europe PMC, 2020-09-19)
17135195
Mouse Tumor Biology Database (MTB): status update and future directions. [PMID: 17135195]
Begley DA, Krupke DM, Vincent MJ, Sundberg JP, Bult CJ, Eppig JT.

The Mouse Tumor Biology (MTB) database provides access to data about endogenously arising tumors (both spontaneous and induced) in genetically defined mice (inbred, hybrid, mutant and genetically engineered mice). Data include information on the frequency and latency of mouse tumors, pathology reports and images, genomic changes occurring in the tumors, genetic (strain) background and literature or contributor citations. Data are curated from the primary literature or submitted directly from researchers. MTB is accessed via the Mouse Genome Informatics web site (http://www.informatics.jax.org). Integrated searches of MTB are enabled through use of multiple controlled vocabularies and by adherence to standardized nomenclature, when available. Recently MTB has been redesigned and its database infrastructure replaced with a robust relational database management system (RDMS). Web interface improvements include a new advanced query form and enhancements to already existing search capabilities. The Tumor Frequency Grid has been revised to enhance interactivity, providing an overview of reported tumor incidence across mouse strains and an entrée into the database. A new pathology data submission tool allows users to submit, edit and release data to the MTB system.

Nucleic Acids Res. 2007:35(Database issue) | 7 Citations (from Europe PMC, 2020-09-19)
16381933
The Mouse Genome Database (MGD): updates and enhancements. [PMID: 16381933]
Blake JA, Eppig JT, Bult CJ, Kadin JA, Richardson JE, Mouse Genome Database Group.

The Mouse Genome Database (MGD) integrates genetic and genomic data for the mouse in order to facilitate the use of the mouse as a model system for understanding human biology and disease processes. A core component of the MGD effort is the acquisition and integration of genomic, genetic, functional and phenotypic information about mouse genes and gene products. MGD works within the broader bioinformatics community to define referential and semantic standards to facilitate data exchange between resources including the incorporation of information from the biomedical literature. MGD is also a platform for computational assessment of integrated biological data with the goal of identifying candidate genes associated with complex phenotypes. MGD is web accessible at http://www.informatics.jax.org. Recent improvements in MGD described here include the incorporation of an interactive genome browser, the enhancement of phenotype resources and the further development of functional annotation resources.

Nucleic Acids Res. 2006:34(Database issue) | 50 Citations (from Europe PMC, 2020-09-19)
15608240
The Mouse Genome Database (MGD): from genes to mice--a community resource for mouse biology. [PMID: 15608240]
Eppig JT, Bult CJ, Kadin JA, Richardson JE, Blake JA, Anagnostopoulos A, Baldarelli RM, Baya M, Beal JS, Bello SM, Boddy WJ, Bradt DW, Burkart DL, Butler NE, Campbell J, Cassell MA, Corbani LE, Cousins SL, Dahmen DJ, Dene H, Diehl AD, Drabkin HJ, Frazer KS, Frost P, Glass LH, Goldsmith CW, Grant PL, Lennon-Pierce M, Lewis J, Lu I, Maltais LJ, McAndrews-Hill M, McClellan L, Miers DB, Miller LA, Ni L, Ormsby JE, Qi D, Reddy TB, Reed DJ, Richards-Smith B, Shaw DR, Sinclair R, Smith CL, Szauter P, Walker MB, Walton DO, Washburn LL, Witham IT, Zhu Y, Mouse Genome Database Group.

The Mouse Genome Database (MGD) forms the core of the Mouse Genome Informatics (MGI) system (http://www.informatics.jax.org), a model organism database resource for the laboratory mouse. MGD provides essential integration of experimental knowledge for the mouse system with information annotated from both literature and online sources. MGD curates and presents consensus and experimental data representations of genotype (sequence) through phenotype information, including highly detailed reports about genes and gene products. Primary foci of integration are through representations of relationships among genes, sequences and phenotypes. MGD collaborates with other bioinformatics groups to curate a definitive set of information about the laboratory mouse and to build and implement the data and semantic standards that are essential for comparative genome analysis. Recent improvements in MGD discussed here include the enhancement of phenotype resources, the re-development of the International Mouse Strain Resource, IMSR, the update of mammalian orthology datasets and the electronic publication of classic books in mouse genetics.

Nucleic Acids Res. 2005:33(Database issue) | 153 Citations (from Europe PMC, 2020-09-19)
14681461
The Mouse Genome Database (MGD): integrating biology with the genome. [PMID: 14681461]
Bult CJ, Blake JA, Richardson JE, Kadin JA, Eppig JT, Baldarelli RM, Barsanti K, Baya M, Beal JS, Boddy WJ, Bradt DW, Burkart DL, Butler NE, Campbell J, Corey R, Corbani LE, Cousins S, Dene H, Drabkin HJ, Frazer K, Garippa DM, Glass LH, Goldsmith CW, Grant PL, King BL, Lennon-Pierce M, Lewis J, Lu I, Lutz CM, Maltais LJ, McKenzie LM, Miers D, Modrusan D, Ni L, Ormsby JE, Qi D, Ramachandran S, Reddy TB, Reed DJ, Sinclair R, Shaw DR, Smith CL, Szauter P, Taylor B, Vanden Borre P, Walker M, Washburn L, Witham I, Winslow J, Zhu Y, Mouse Genome Database Group.

The Mouse Genome Database (MGD) is one component of the Mouse Genome Informatics (MGI) system (http://www.informatics.jax.org), a community database resource for the laboratory mouse. MGD strives to provide a comprehensive knowledgebase about the mouse with experiments and data annotated from both literature and online sources. MGD curates and presents consensus and experimental data representations of genetic, genotype (sequence) and phenotype information including highly detailed reports 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 and to build and implement the data and semantic standards that are essential for comparative genome analysis. Recent developments in MGD discussed here include an extensive integration of the mouse sequence data and substantial revisions in the presentation, query and visualization of sequence data.

Nucleic Acids Res. 2004:32(Database issue) | 39 Citations (from Europe PMC, 2020-09-19)
18428715
Searching the Mouse Genome Informatics (MGI) resources for information on mouse biology from genotype to phenotype. [PMID: 18428715]
Shaw D.

The Mouse Genome Informatics (MGI, http://www.informatics.jax.org/) resource provides the research community with access to information on the genetics, genomics, and biology of the laboratory mouse. Core data in MGI include gene characterization and function, phenotype and disease model descriptions, DNA and protein sequence data, gene expression data, mammalian orthologies, polymorphisms, mapping data, and links to other bioinformatics databases. Semantic integration is supported through the use of standardized nomenclature and controlled vocabularies such as the mouse Anatomical Dictionary and the Gene Ontologies. MouseBLAST offers a fast, sequence-based method for identifying genes and searching for similarity, and provides links from sequence to MGI biological data. MGI extracts and organizes data from primary literature. MGI data are shared with and widely displayed by other bioinformatics resources. The database is updated nightly with curated annotations and regularly adds new datasets and enhances user interface features. This unit provides a guide to using the MGI bioinformatics resource.

Curr Protoc Bioinformatics. 2004:Chapter 1() | 1 Citations (from Europe PMC, 2020-09-19)
12519980
MGD: the Mouse Genome Database. [PMID: 12519980]
Blake JA, Richardson JE, Bult CJ, Kadin JA, Eppig JT, Mouse Genome Database Group.

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 understanding human 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 including highly 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.

Nucleic Acids Res. 2003:31(1) | 140 Citations (from Europe PMC, 2020-09-19)
11752269
The Mouse Genome Database (MGD): the model organism database for the laboratory mouse. [PMID: 11752269]
Blake JA, Richardson JE, Bult CJ, Kadin JA, Eppig JT, Mouse Genome Database Group.

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.

Nucleic Acids Res. 2002:30(1) | 69 Citations (from Europe PMC, 2020-09-19)
11125058
The Mouse Genome Database (MGD): integration nexus for the laboratory mouse. [PMID: 11125058]
Blake JA, Eppig JT, Richardson JE, Bult CJ, Kadin JA.

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 provides standard nomenclature and consensus map positions for mouse genes and genetic markers; it provides a curated set of mammalian homology records, user-defined chromosomal maps, experimental data sets and the definitive mouse 'gene to sequence' reference set for the research community. The integration and standardization of these data sets facilitates the transition between mouse DNA sequence, gene and phenotype annotations. A recent focus on allele and phenotype representations enhances the ability of MGD to organize and present data for exploring the relationship between genotype and phenotype. This link between the genome and the biology of the mouse is especially important as phenotype information grows from large mutagenesis projects and genotype information grows from large-scale sequencing projects.

Nucleic Acids Res. 2001:29(1) | 40 Citations (from Europe PMC, 2020-09-19)
10592195
The Mouse Genome Database (MGD): expanding genetic and genomic resources for the laboratory mouse. The Mouse Genome Database Group. [PMID: 10592195]
Blake JA, Eppig JT, Richardson JE, Davisson MT.

The Mouse Genome Database (MGD) is a comprehensive public database of mouse genomic, genetic and phenotypic information (http://www. informatics.jax.org). This community database provides information about genes, serves as a mapping resource of the mouse genome, details mammalian orthologs, integrates experimental data, represents standardized mouse nomenclature for genes and alleles, incorporates links to other genomic resources such as sequence data, and includes a variety of additional information about the laboratory mouse. MGD scientists and annotators work cooperatively with the research community to provide an integrated, consensus view of the mouse genome while also providing experimental data including data conflicting with the consensus representation. Recent improvements focus on the representation of phenotypic information and the enhancement of gene and allele descriptions.

Nucleic Acids Res. 2000:28(1) | 60 Citations (from Europe PMC, 2020-09-19)
10592196
Mouse tumor biology database (MTB): enhancements and current status. [PMID: 10592196]
Bult CJ, Krupke DM, Sundberg JP, Eppig JT.

The Mouse Tumor Biology Database (MTB) is a Web-based resource that provides access to information on tumor frequency and latency, genetics and pathology in genetically defined mice (transgenics, targeted mutations and inbred strains). MTB is designed to serve as an information resource for cancer genetics researchers who use the laboratory mouse as a model system for understanding human disease processes. Data in MTB are obtained from the primary scientific literature and direct submissions by the research community. MTB is accessible from the Mouse Genome Informatics Web site (http://www.informatics.jax.org). User support is available for MTB via Email at mgi-help@informatics.jax.org

Nucleic Acids Res. 2000:28(1) | 9 Citations (from Europe PMC, 2020-09-12)
9847150
The Mouse Genome Database (MGD): genetic and genomic information about the laboratory mouse. The Mouse Genome Database Group. [PMID: 9847150]
Blake JA, Richardson JE, Davisson MT, Eppig JT.

The Mouse Genome Database (MGD) focuses on the integration of mapping, homology, polymorphism and molecular data about the laboratory mouse. Detailed descriptions of genes including their chromosomal location, gene function, disease associations, mutant phenotypes, molecular polymorphisms and links to representative sequences including ESTs are integrated within MGD. The association of information from experiment to gene to genome requires careful coordination and implementation of standardized vocabularies, unique nomenclature constructions, and detailed information derived from multiple sources. This information is linked to other public databases that focus on additional information such as expression patterns, sequences, bibliographic details and large mapping panel data. Scientists participate in the curation of MGD data by generating the Chromosome Committee Reports, consulting on gene family nomenclature revisions, and providing descriptions of mouse strain characteristics and of new mutant phenotypes. MGD is accessible at http://www.informatics.jax.org

Nucleic Acids Res. 1999:27(1) | 29 Citations (from Europe PMC, 2020-09-19)
9399817
The Mouse Genome Database (MGD): a community resource. Status and enhancements. The Mouse Genome Informatics Group. [PMID: 9399817]
Blake JA, Eppig JT, Richardson JE, Davisson MT.

The Mouse Genome Database (MGD) is a comprehensive community database that integrates genetic, genomic and phenotypic information about the laboratory mouse. MGD provides detailed information about genes and genetic markers, elemental data from mapping experiments, descriptions of molecular segments including ESTs, probes, and cDNA clones, homology information between mouse and many other mammalian genomes, and phenotypic descriptions of gene mutations, gene function and mouse strains. All data are supported by citations. Interactive graphical displays of cytogenetic, genetic and physical maps are available. User support is provided through dedicated staff, bulletin boards, and user documentation. MGD can be accessed at http://www.informatics.jax.org

Nucleic Acids Res. 1998:26(1) | 14 Citations (from Europe PMC, 2020-09-19)
9045213
The Mouse Genome Database (MGD). A comprehensive public resource of genetic, phenotypic and genomic data. The Mouse Genome Informatics Group. [PMID: 9045213]
Blake JA, Richardson JE, Davisson MT, Eppig JT.

The Mouse Genome Database (MGD) is a comprehensive community resource of mouse genetic and biological information populated both with data from published literature and with data electronically submitted from the research community. MGD stores genetic, physical and comparative mapping data, clones/probes/PCR information, and phenotype descriptions for genes, mutations and mouse strains. Supporting software for importation, analysis, display and distribution of mouse genetic data have been developed. User support is provided through dedicated staff providing documentation, training, and response to individual user queries. MGD is accessible over the Internet at URL http://www.informatics.jax.org.

Nucleic Acids Res. 1997:25(1) | 27 Citations (from Europe PMC, 2020-09-19)