The Mouse Genome Database (MGD): comprehensive resource for genetics and genomics of the laboratory mouse.

Abstract

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.

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The Mouse Genome Database (MGD):
comprehensive resource for genetics and
genomics of the laboratory mouse
Janan T. Eppig*, Judith A. Blake, Carol J. Bult, James A. Kadin, Joel E. Richardson
and the Mouse Genome Database Groupy
The Jackson Laboratory, Bar Harbor, ME 04609, USA
Received September 15, 2011; Accepted October 16, 2011
ABSTRACT
The Mouse Genome Database (MGD, http://www
.informatics.jax.org) is the international community
resourceforintegrated
biological data about the laboratory mouse. Data
in MGD are obtained through loads from major
data providers and experimental consortia, elec-
tronic submissions from laboratories and from the
biomedical literature. MGD maintains a compre-
hensive, unified, non-redundant catalog of mouse
genomefeaturesgenerated
predictions from NCBI, Ensembl and VEGA. MGD
serves as the authoritative source for the nomencla-
ture 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)
usingtermsfromthe
Ontology and disease names from the Online
Mendelian Inheritance in Man (OMIM) resource.
MGDisfreelyaccessible
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.
genetic,genomicand
by distillinggene
Mammalian Phenotype
onlinethroughour
INTRODUCTION
The Mouse Genome Database (MGD) (1–3) serves as a
primary resource for mammalian biologists, delivering a
spectrum of genetic, genomic and biological data support-
ing the use of mouse as a model for understanding human
biology and disease. Central to its data offerings are
the canonical mouse gene catalog, nucleotide
protein sequence associations, gene-to-function assign-
ments based on the Gene Ontology (GO) (4), a compre-
hensive catalog of mutant alleles, associations of mutant
genotypes to their phenotype through the Mammalian
Phenotype (MP) Ontology (5) and to the human diseases
for which they are a model through curated associations
to human diseases in Online Mendelian Inheritance in
Man database (OMIM) (6). In addition, MGD provides
a comprehensive genetic map, a genome browser (Mouse
GBrowse) forgenomeviewing,
Polymorphisms (SNPs) and other polymorphisms and
mammalian orthology data. A summary of the current
contents of MGD is given in Table 1.
Integrated with MGD are other components of the
Mouse Genome Informatics (MGI) database resource
(http://www.informatics.jax.org). These include the Gene
Expression Database (7), the Mouse Tumor Biology
Database (8) and the MouseCyc database of metabolic
pathways (9). Two additional resources tied to the main
MGI resource are the International Mouse Strain
Resource (IMSR) (10) and the Recombinase (cre)
Portal (1).
Data in MGD are obtained through data loads from
major resource providers [e.g. sequence data from
GenBank, gene models from NCBI, Ensembl, VEGA,
mutant allelesfrom
(ENU)-mutagenesis groups and International Knockout
Mouse Consortium (IKMC)], from electronic submissions
from investigator laboratories, and from the biomedical
and
SingleNucleotide
N-ethyl-N-nitrosourea
*To whom correspondence should be addressed. Tel: +1 207 288 6422; Fax: +1 207 288 6132; Email: janan.eppig@jax.org
yThe members of the Mouse Genome Database Group are provided in the Acknowledgements Section
Published online 10 November 2011Nucleic Acids Research, 2012, Vol. 40, Database issueD881–D886
doi:10.1093/nar/gkr974
? The Author(s) 2011. Published by Oxford University Press.
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/
by-nc/3.0), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

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literature. All data are attributed to the original source
with access to references provided via PubMed where
available. For data loads, quality control reports are
generatedthatenumerate
anomalies and prioritize errors that need attention by
curators. Standards for gene, allele and strain nomencla-
ture, and for functional, phenotypic and human disease
annotations using vocabularies and ontologies enable con-
sistent annotations and robust data retrieval.
MGD data can be accessed in many ways. A Quick
Search box appears on all web pages and provides a
ubiquitous, fast and simple entry for broad keyword or
ID searches. More specialized query forms, accessible
via the Search pull down on the navigation bar, allow
multiparameter advanced searches, and the data content
area icons on the homepage lead users to specific accesses
to that data area. A vocabulary browser supports access
to MGD content through ontology terms. A variety of
regularly updated database reports can be accessed on
the File Transfer Protocol (FTP) site. Programmatic
access is provided through web services and through
direct SQL access.
format and/or content
KEY UPDATES AND CHANGES IN 2011
Expanded classification terms for genome features
New to MGD are feature type classifications as attributes
of genome features. The feature types allow users to refine
searches to include only specific classes of genome features
(protein-coding genes,
Quantitative Trait Loci (QTL), transgenes, pseudogenes,
etc.). Most of the classification terms and definitions are
derived from the Sequence Ontology (SO) (11). We have
also added new subclassification terms for genome
features formerly grouped as pseudogenes. The overarch-
ing term for these genome features is now pseudogenic
region (SO: 0000462), defined as a non-functional
feature descended from a gene or other functional
feature. In MGD, three subcomponents: pseudogene (a
sequence that closely resembles a known functional gene,
at another locus within a genome, which is non-functional
asa consequenceofmutations
mircoRNAs, lincRNAs,
that prevent its
transcription or translation); pseudogenic gene segment
(arecombinational unit
incorporated by somatic recombination in the final gene
transcript result in a non-functional product); and poly-
morphic pseudogene (a pseudogene lacking function
owing to a SNP or deletion/insertion, but in other indi-
viduals/haplotypes/strains the gene is translated) are cur-
rently in use. Where MGD, VEGA, Ensembl and
National Center for Biotechnology Information (NCBI)
disagree on the pseudogene subclassification type, a
biotype conflict note is presented to the user on the
MGD locus detail page. Where a genome feature is a
non-functional pseudogene in some mouse strains, but
functional in other mouse strains, a strain-specific note
is presented on the detail page (Figure 1).
ofagene whichwhen
Nomenclature harmonization: T-cell receptor and
immunoglobulin gene segments
Working with the Immunogenetics Information System,
IMGT/Gene-DB (12), MGD has expanded the number
of defined T-cell receptor and immunoglobulin gene
segments (a gene component region which acts as a
recombinational unit of a gene whose functional form is
generated throughsomatic
670 and harmonized nomenclature for these important
immunological gene segments.
recombination)to over
Mutant allele sets added
The number of mutant alleles in MGD has increased by
over 23640 this year. This largely reflects ongoing devel-
opment of genetically engineered and ENU-induced
mutations by major mutagenesis programs, with signifi-
cant contributions by individual investigators. Among
the major additions of new mutant alleles to MGD
were: 8364 new targeted mutations added from the
IKMC (13), 870 new transgenes added from the Gene
Expression Nervous System Atlas project (14), 492 new
targeted and gene trap mutations from a Genentech/
Lexicon collaboration (15) and over 200 new ENU muta-
tions from Dr Bruce Beutler’s Mutagenetix program (16).
Over 3000 new mutant alleles were developed from
investigator-initiated experiments and added to MGD
from biomedical literature curation or via investigator
data submissions to MGD. The remaining approximately
10000 new alleles are gene traps added via a data load
from NCBI’s Genome Survey Sequences Database (GSS)
(17), most of which were generated by the IKMC. Of the
current more than 596000 mutant alleles for mice, most
were generated and only exist in Embryonic Stem (ES) cell
lines, with approximately 30400 of these being either
created or developed into living mice.
The Quick Search tool now includes mutant alleles
To take advantage of the large number of new mutant
allele resources, MGD has improved the characteristics
its Quick Search tool, so it now returns the alleles, as
well as other genome features, most closely associated
with a query. (The previous implementation of the
Quick Search returned genome features at the level of
the gene.) This change helps users more easily locate
Table 1. Summary of MGD data content (14 September 2011)
Genes with nucleotide sequence data
Genes with protein sequence data
Genes with mutant alleles in mice
Genes with one of more mutant allelesa
Total mutant allelesa
Number of cre-containing transgenes and knock-ins
Genes with mouse experiment-based functional
(GO) annotations
Mouse/human orthologs
Mouse/rat orthologs
Human diseases with one or more mouse models
QTLs
Number of references
Number of reference SNPs
28803
25070
15145
20397
738414
1511
13524
17847
16686
1121
4670
169700
10089892
aMutant alleles include those occurring in mice and those existing only
in mouse ES cell lines. Of the 738414 total mutant alleles, 682745 are
gene traps in ES cell lines.
D882Nucleic AcidsResearch, 2012, Vol.40,Database issue

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relevant mouse model data from queries for phenotypes or
disease. Given that there are Quick Search accounts for
>90% of the interactive MGD searches, we expect this
change to have significant beneficial impact (Figure 2).
Extensions to GO annotations
GO annotations are being extended via phylogenetic-
based approaches. Through identification of phylogenet-
ically related orthologous, homologous and paralogous
genes across species, the GO consortium is promoting
coordinate annotations of these genes across organisms.
MGD is actively participating in these gene annotations to
enrich functional information about a highly curated
set of phylogenetically related genes among species and
to enable propagation of functional annotations between
organisms (18,19).
Retooling MGD infrastructure: a plan for the future
MGD is in the process of a significant infrastructure
migration project to move from the Sybase relational
database management system to a more technically attract-
ive open source database technology (PostgreSQL). Phase
I of this project is to move and rewrite software on our
public servers, specifically those components supporting
the web interface and direct SQL accounts. As well,
we are retooling the web interface software to use Solr
and Lucene to handle most querying, Java Spring
Model-View-Controller (MVC) for web page generation
and YAHOO User Interface (YUI) for on-page interactiv-
ity. Beyond the user benefits visible in the initial release,
this technology migration will position us well for future
developments. Phase II, to migrate and retool the software
residing on our back end servers (where the data loading
and curation occur) is also underway.
New direct access methods for MGD
MGD has always provided direct SQL access to a public
Sybase server. As part of the migration described in the
previous paragraph, the Sybase server has been retired,
and a public PostgreSQL server is now available.
In addition, for users who want MGD at their local
sites, we now provide complete database dumps for both
PostgreSQL and MySQL. The public SQL server and
the database dumps are updated on a weekly basis.
Dump files are available from our FTP site at ftp://ftp
.informatics.jax.org/pub/database_backups/. Instructions
can be found at http://www.informatics.jax.org/software.
shtml.Contact MGIUser
informatics.jax.org) to request a PostgreSQL account or
for assistance in using the database dumps. Individuals
interested in programmatic and bulk access may also
want to join the MGI-Technical listserve (http://www
.informatics.jax.org/mgihome/lists/lists.shtml) to receive
technical updates about the database.
Support (mgi-help@
Figure 1. Screenshots of the upper portion of two locus detail pages. (A) The BioType Conflict indicator (upper right), when opened, displays the
different biotype annotations for Psme2b-ps. In this case, MGI and NCBI assign this marker as a pseudogene, where VEGA and Ensembl have
assigned the status as protein coding gene. Links are provided to the underlying evidence that support the biotype assignments by different
annotation groups. (B) The strain-specific marker indicator (upper right), when opened, displays information about strains in which the gene
(in this case Ren2) is found or, not found, in the genome, with supporting reference links.
Nucleic Acids Research, 2012,Vol.40, Database issue D883

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OTHER INFORMATION
Mouse gene, allele and strain nomenclature
MGD
symbols and names for mouse genes, alleles and strains.
MGD follows and implements the guidelines set by
the International Committee on Standardized Genetic
Nomenclature for Mice (http://www.informatics.jax.org/
nomen). This official nomenclature is widely disseminated
through regular data exchange and curation of shared
links between MGI and other bioinformatics resources.
MGD staff members work with editors of journal publi-
cations and consortium projects to promote adherence
to mouse nomenclature standards in publications and
online data resources.
To support consistency of nomenclature across species,
MGD coordinates names and symbols for genes and
genome features with nomenclature experts from the
Human Gene Nomenclature Committee (HGNC) (20)
(http://www.genenames.org/)
Database (RGD) (21) http://rgd.mcw.edu). The MGD
nomenclature coordinator can be contacted by email
(nomen@informatics.jax.org).
istheinternationalauthoritative sourceof
and the RatGenome
Programmatic and bulk data access
Portions of the database are accessible programmatically
using web services and BioMart. The MGI web service
accepts SOAP 1.1 and 1.2 requests. For details, see
http://www.informatics.jax.org/mgihome/other/web_
service.shtml. The MGD BioMart is accessible at http://
biomart.informatics.jax.org.
about MartServices can be found at http://www.biomart
.org/martservice.html.
MGI also provides bulk data sets through regularly
updated FTP reports (ftp://ftp.informatics.jax.org/pub/
reports/index.html) and via the MGI Batch Query tool
(http://www.informatics.jax.org/javawi2/servlet/WIFetch?
page=batchQF) where users can develop a customized
bulk data set.
Additionalinformation
Electronic data submission
MGD accepts contributed data sets from individuals and
organizations for any type of data maintained by the
database. The most frequent types of contributed data
are mutant and phenotypic allele information originating
with the large mouse mutagenesis centers and strain
data from repositories that contribute to the IMSR
(http://www.findmice.org) (10). Each electronic submis-
sion receives a permanent database accession ID. All
data sets are associated with their source, either a publi-
cation or an electronic submission reference. Details about
data submission procedures can be found at http://www
.informatics.jax.org/submit.shtml.
Figure 2. Screenshot of the results of querying for ‘wavy’ using the MGI Quick Search box. Note that heritable phenotypic markers that identify
mutants whose underlying gene is not yet identified, such as Wf and Wtgr are retrieved, as well as genes (e.g. Pax1, with synonym of wavy tail),
and other types of mutant alleles in defined genes (e.g. Pax1un-ex, undulated extensive mutation of the Pax1 gene).
D884 Nucleic AcidsResearch, 2012, Vol.40,Database issue

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Additions and corrections to the representation of data
and information in MGD can be submitted using the
‘Your Input Welcome’ link that appears in the upper
right hand corner of gene and allele detail pages.
Community outreach and User Support
The MGD resource has full time staff members who
are dedicated to user support and training. Members of
the User Support team can be contacted via email, web
requests, phone or Fax.
. World
mgihome/support/support.shtml
. Email access: mgi-help@informatics.jax.org
. Telephone access: 1 207 288 6445
. Fax access: 1 207 288 6132
wideweb: http://www.informatics.jax.org/
MGD User Support staff are available for on-site training
on the use of MGD and other MGI data resources.
MGD’s traveling tutorial program (roadshow) includes
lectures, demos and hands-on tutorials, which can be
customized according to the research interests of the
audience.To inquireabout
roadshow, send email to mgi-help@informatics.jax.org.
On-line training materials for MGD and other MGI
data resources are available as FAQs and on-demand
help documents.
sponsoringaMGD
Other outreach
MGI-LIST
lists/lists.shtml) is a moderated and active email bulletin
board supported by the MGD User Support group. The
MGI listserve has over 2100 subscribers. On average, there
are three posts per day, every day. The MGI-Technical
listserve also has been instituted for technical information
for software developers and bioinformaticians accessing
MGI data, using APIs, and making links to MGI.
(http://www.informatics.jax.org/mgihome/
HIGH LEVEL OVERVIEW OF THE MAIN
COMPONENTS AND IMPLEMENTATION
The MGD production database comprises approximately
180 tables within which biological information is encoded.
As we are transitioning between database engines, we cur-
rently have instances in both Sybase and PostgreSQL.
BLAST-able databases,genome
sequence data and images are stored outside the relational
database. An editing interface and automated load
programs are used to input data into the MGD system.
Automated loads enter/update the bulk of data and
associations in MGD. A typical load will load ‘as much
as it can’(typically, the large majority) and report the rest
in various quality control reports. These are reviewed by
curators, who may resolve problem cases by editing MGD
and/or by communicating with data providers. The inter-
active graphical editing interface provides curators with
the ability to update the database, enter new data from
the literature, track curation status, etc.
Public data access to MGD is provided primarily
through the web interface where users can interactively
query and download our data through a web browser.
assemblyfilesfor
MouseBLAST allows users to do sequence similarity
searches against a variety of rodent sequence databases
that are updated weekly from selected sequence databases
from NCBI, UniProt and other providers. Mouse
GBrowse allows users to visualize mouse data sets
against the genome as a series of linear tracks. All
MGD files and programs are openly and freely available.
We continue to provide MGD BioMart with the
addition of new classification terms for genome features.
MGD BioMart supports chaining to several other
BioMarts including Ensembl,
Additional functionalities such as the ability to filter by
GO, MP Ontology and OMIM terms, and including
additional information about alleles, are planned for
future extensions. MGD BioMart is updated on a
weekly basis.
VEGA andRGD.
CITING MGD
For a general citation of the MGI resource please cite this
article. In addition, the following citation format is
suggested when referring to data sets specific to the
MGD component of MGI: MGD, MGI, The Jackson
Laboratory, Bar Harbor, Maine (URL: http://www
.informatics.jax.org). [Type in date (month, year) when
you retrieved the data cited.].
ACKNOWLEDGEMENTS
M. T. Airey, A. Anagnostopoulos, R. Babiuk, R. M.
Baldarelli, J. S. Beal, S. M. Bello, N. E. Butler,
J. Campbell, L. E. Corbani, S. L. Giannatto, H. Dene,
M. E. Dolan, H. R. Drabkin, K. L. Forthofer,
M. Knowlton, J.R. Lewis,
S. McClatchy, D. S. Miers, L. Ni, H. Onda, J. E.
Ormsby, J. M. Recla, D. J. Reed, B. Richards-Smith, D.
R. Shaw, R. Sinclair, D. Sitnikov, C. L. Smith, M.
Tomczuk, L. L. Washburn, Y. Zhu.
M.McAndrews-Hill,
FUNDING
National Institutes of Health/National Human Genome
Research Institute, The Mouse Genome Database (grant
HG000330). Funding for open access charge: National
Institutes of Health/ NHGRI (grant HG000330).
Conflict of interest statement. None declared.
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