The Mouse Genome Database (MGD): from genes to mice—a community resource for mouse biology (original) (raw)
Journal Article
,
The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
* To whom correspondence should be addressed. Tel: +1 207 288 6248; Fax: +1 207 288 6132; Email: jblake@informatics.jax.org The Mouse Genome Database Group: A. Anagnostopoulos, R. M. Baldarelli, M. Baya, J. S. Beal, S. M. Bello, W. J. Boddy, D. W. Bradt, D. L. Burkart, N. E. Butler, J. Campbell, M. A. Cassell, L. E. Corbani, S. L. Cousins, D. J. Dahmen, H. Dene, A. D. Diehl, H. J. Drabkin, K. S. Frazer, P. Frost, L. H. Glass, C. W. Goldsmith, P. L. Grant, M. Lennon-Pierce, J. Lewis, I. Lu, L. J. Maltais, M. McAndrews-Hill, L. McClellan, D. B. Miers, L. A. Miller, L. Ni, J. E. Ormsby, D. Qi, T. B. K. Reddy, D. J. Reed, B. Richards-Smith, D. R. Shaw, R. Sinclair, C. L. Smith, P. Szauter, M. B. Walker, D. O. Walton, L. L. Washburn, I. T. Witham and Y. Zhu
Search for other works by this author on:
,
The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
Search for other works by this author on:
,
The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
Search for other works by this author on:
,
The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
Search for other works by this author on:
the Mouse Genome Database Group
The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
Search for other works by this author on:
Published:
01 January 2005
Cite
Janan T. Eppig, Carol J. Bult, James A. Kadin, Joel E. Richardson, Judith A. Blake, the Mouse Genome Database Group, The Mouse Genome Database (MGD): from genes to mice—a community resource for mouse biology, Nucleic Acids Research, Volume 33, Issue suppl_1, 1 January 2005, Pages D471–D475, https://doi.org/10.1093/nar/gki113
Close
Navbar Search Filter Mobile Enter search term Search
Abstract
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.
Received October 12, 2004; Revised and Accepted October 20, 2004
INTRODUCTION
The Mouse Genome Database (MGD) provides a comprehensive and integrated view of genetic, genomic and biological information for the laboratory mouse ( 1 , 2 ). MGD contains information on mouse genes, genetic markers and genomic features as well as the associations of these features with sequence sets, reagents, alleles and mutant phenotypes. MGD integrates sequence with biology through the curated association of genome, transcript and protein sequence sets with mouse genes—work done in collaboration with other large genome informatics resources.
MGD is updated daily and there are weekly data exchanges with other major genomics resources such as NCBI and Swiss-Prot. A recent snapshot of MGD content is listed in Table 1 . Since the first release of this database in 1994, MGD has continued to evolve, expanding its data coverage, improving data access and providing new data query, analysis and display tools.
Table 1.
Snapshot of data content in MGD: October 7, 2004
MGD data statistics | October 7, 2004 |
---|---|
Number of genes with sequence data | 28 287 |
Number of genes (including unmapped mutants) | 33 207 |
Number of markers (including genes) | 57 521 |
Number of markers mapped | 53 082 |
Number of genes with links to Swiss-Prot | 7769 |
Number of genes with GO annotations | 15 309 |
Number of mouse/human curated orthologies | 14 893 |
Number of mouse/rat curated orthologies | 12 679 |
Number of genes with one or more phenotypic alleles | 4996 |
Number of cataloged phenotypic alleles | 10 949 |
Number of references | 87 527 |
Number of mouse nucleotide sequences integrated into the MGI system (includes ESTs) | >7 600 000 |
MGD data statistics | October 7, 2004 |
---|---|
Number of genes with sequence data | 28 287 |
Number of genes (including unmapped mutants) | 33 207 |
Number of markers (including genes) | 57 521 |
Number of markers mapped | 53 082 |
Number of genes with links to Swiss-Prot | 7769 |
Number of genes with GO annotations | 15 309 |
Number of mouse/human curated orthologies | 14 893 |
Number of mouse/rat curated orthologies | 12 679 |
Number of genes with one or more phenotypic alleles | 4996 |
Number of cataloged phenotypic alleles | 10 949 |
Number of references | 87 527 |
Number of mouse nucleotide sequences integrated into the MGI system (includes ESTs) | >7 600 000 |
Table 1.
Snapshot of data content in MGD: October 7, 2004
MGD data statistics | October 7, 2004 |
---|---|
Number of genes with sequence data | 28 287 |
Number of genes (including unmapped mutants) | 33 207 |
Number of markers (including genes) | 57 521 |
Number of markers mapped | 53 082 |
Number of genes with links to Swiss-Prot | 7769 |
Number of genes with GO annotations | 15 309 |
Number of mouse/human curated orthologies | 14 893 |
Number of mouse/rat curated orthologies | 12 679 |
Number of genes with one or more phenotypic alleles | 4996 |
Number of cataloged phenotypic alleles | 10 949 |
Number of references | 87 527 |
Number of mouse nucleotide sequences integrated into the MGI system (includes ESTs) | >7 600 000 |
MGD data statistics | October 7, 2004 |
---|---|
Number of genes with sequence data | 28 287 |
Number of genes (including unmapped mutants) | 33 207 |
Number of markers (including genes) | 57 521 |
Number of markers mapped | 53 082 |
Number of genes with links to Swiss-Prot | 7769 |
Number of genes with GO annotations | 15 309 |
Number of mouse/human curated orthologies | 14 893 |
Number of mouse/rat curated orthologies | 12 679 |
Number of genes with one or more phenotypic alleles | 4996 |
Number of cataloged phenotypic alleles | 10 949 |
Number of references | 87 527 |
Number of mouse nucleotide sequences integrated into the MGI system (includes ESTs) | >7 600 000 |
MGD is the core component of the Mouse Genome Informatics (MGI) database resource ( http://www.informatics.jax.org ) hosted at The Jackson Laboratory ( http://www.jax.org ). Other projects and resources that are part of the MGI system include the Gene Expression Database (GXD) ( 3 ) and the Mouse Tumor Biology Database (MTB) ( 4 ) ( http://tumor.informatics.jax.org ). All MGI component groups participate actively in the development and application of the Gene Ontology (GO) ( 5 ) ( http://www.geneontology.org ).
IMPROVEMENTS DURING 2004
Hosting of the International Mouse Strain Resource
The International Mouse Strain Resource (IMSR) ( http://www.informatics.jax.org/imsr/ ) has as its goal to provide and maintain a worldwide catalog of resources for mouse strains and stocks. The IMSR has developed a searchable database with a web front-end to assist researchers in locating and obtaining the mouse resources they need ( Figure 1 ).
Figure 1.
The new IMSR is a searchable online database of mouse strains and stocks available worldwide, including inbred, mutant and genetically engineered mice. The goal of the IMSR is to assist the international scientific community in locating and obtaining mouse resources for research. The data content found in the IMSR is as it was supplied by data provider sites.
An initial version of the IMSR was developed in 1999 ( 6 ) as a collaborative effort with the Medical Research Council (MRC) Mammalian Genetics Unit (Harwell, UK) and contained a searchable resource for mouse stocks and strains held at The Jackson Laboratory (JAX) and at the MRC Harwell sites. While this proved to be a useful resource, it was severely limited in containing only information for these two major mouse laboratories.
With the establishment of multiple mutagenesis centers, gene trap centers, and the increasing use of genetic engineering technologies, the number of mouse stocks and strains and the specialization of genotype and their characterization has exploded. A number of new repositories and distribution centers have been established worldwide to cope with the exponential increase in specialized mouse stocks. The new pressing need for a central cataloging of stocks and strains prompted us to re-develop the IMSR in a more robust fashion, such that it could easily accommodate data from multiple sites, provide a better search interface for users, and enable links to phenotype searching and to specific stock data from each site that distributed mouse resources.
Users can search IMSR by strain, gene or allele designations, strain state(s) and strain classes. For each strain satisfying the search criteria, IMSR provides users with data on where a strain is available from, in what state(s) the strain exists (e.g. live, cryopreserved embryos or gametes, ES cell lines), the class of strain and mutant alleles carried by the strain. Hypertext links are provided (i) from each strain designation to its strain information page at the holding site, (ii) to an auto-generated email form to the holder's designated representative for obtaining additional information or ordering the mouse resource and (iii) from each mutant phenotypic allele carried by a strain to the detailed characterization of that allele in the MGI.
Additional links from the IMSR homepage provide instructions for participating in IMSR by listing one's mouse resources, for searching MGI for additional mouse genetic, genomic and biological information, and for checking the official mouse nomenclature guidelines from the International Committee on Genetic Nomenclature for Mice.
Current centers with mouse resources included in IMSR are as follows: The Jackson Laboratory (JAX), the Mouse Mutant Regional Resources Centers (MMRRC), the Center for Animal Resources and Development (CARD), the Oak Ridge National Laboratory (ORNL), the European Mouse Mutant Archive (EMMA) and the BayGenomics Gene Trap Resource. In progress is the incorporation of stocks from the MRC Genetics Unit, Harwell (Har), the Beta Cell Biology Consortium (BCBC), Neuromice (NMICE) and the Mouse Models of Human Cancer Consortium (MMHCC). Interest has been expressed by several other sites, including additional mouse mutagenesis centers, additional gene trap resources, and other distribution centers. IMSR also accepts stock listings from individuals. All strains and stocks listed in IMSR should be available to the research community and regular updating from sites is required to keep the IMSR current.
Enhanced orthology resources
MGD provides a curated set of mammalian orthologs for the research community. Although MGD supports orthology annotations to over 20 mammalian genomes, the priority effort focuses on the creation of orthology sets among mouse, human and rat. This set is constructed through an iterative process using both computational and manual approaches. This year, we worked with the HomoloGene resource at the NCBI ( 7 ) to reciprocally incorporate some of the HomoloGene computational three-way reciprocal best-hit sets into the MGI system. HomoloGene incorporates MGD-curated mammalian orthology sets in their resources. In addition, we continue to work with the research community to carefully curate gene family sets, usually at the instigation of the research community ( 8 , 9 ).
The Orthology Detail Page in MGD ( Figure 2 ) for the gene Wt1 illustrates the paradigm for orthology data. All assertions of orthology are supported by a statement of evidence and a citation. There are links to comparative mapping visualizations and links to genomics resources for the other species represented.
Figure 2.
Mammalian Orthology Detail Page. The Mammalian Orthology Query Results page presents a table of results from MGI orthology curation. The table includes species, symbol, chromosome, external and internal accession IDs and criteria for the assertions. The criteria include both a statement of evidence and a citation. Hypertext links are incorporated as appropriate. Comparative chromosome map visualizations between any two of the species can be accessed from this page. These data are updated nightly.
Electronic publication of classic books in mouse genetics
MGD has responded to user requests in making electronic copies of popular out-of-print books available online. Two such books have been developed as online versions, Mouse Genetics by Lee Silver (Oxford University Press, 1995) at http://www.informatics.jax.org/silver/ and The Coat Colors of Mice by Willys K. Silvers (Springer Verlag, 1979) at http://www.informatics.jax.org/wksilvers/ ( Figure 3 ). To develop these online books, publisher and author copyrights were obtained, text was re-developed and hypertext links placed within the text for cross-referencing and to provide direct access to MGI for enhanced gene and reference data. Photographs and graphics were scanned into electronic form or in some cases, redrawn. Both books have been welcomed by MGD users and permission to include additional out-of-print books is being sought.
Figure 3.
Electronic publication of classic books in mouse genetics. MGI offers electronic versions of key out-of-print books in mouse genetics, Mouse Genetics by Lee M. Silver ( http://www.informatics.jax.org/silver/ ) and The Coat Colors of Mice by Willys K. Silvers ( http://www.informatics.jax.org/wksilvers/ ). Gene symbols in both books link to MGI gene detail pages where readers can access all the information MGI has assembled for that gene, including phenotypic alleles, nucleotide and protein sequence, mapping and expression data and GO annotations. References cited in the books are linked to PubMed or MGI reference detail pages, which, in turn are linked to additional curated information in MGI.
OTHER INFORMATION
User input
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 ). Through curation of shared links between MGI and other bioinformatics resources, the official nomenclature for mouse genes is becoming widely disseminated. The MGI nomenclature group works closely with human ( http://www.gene.ucl.ac.uk/cgi-bin/nomenclature/searchgenes.pl ) and rat ( http://rgd.mcw.edu ) nomenclature specialists to provide consistent nomenclature for mammalian species. Scientists can reserve symbols prior to publication using the electronic nomenclature submission form ( http://www.informatics.jax.org/mgihome/nomen/nomen_submit_form.shtml ) or by contacting the MGD nomenclature coordinator by email ( nomen@informatics.jax.org ). The MGD nomenclature coordinator can also assist with other nomenclature issues, such as revision of gene family designations.
Electronic data submission
Any type of data that MGD maintains can be submitted as an electronic contribution. Over the last year, the most frequent submissions have been of mutant and phenotypic allele information originating from the large mouse mutagenesis centers. Other common types of submission include gene and strain nomenclature, mutant and QTL mapping data, polymorphisms and mammalian homologies. Each electronic submission receives a permanent database accession ID. All datasets are associated with either an electronic submission reference or a published paper. These reference pages provide links to associated datasets. Online information about data submission procedure is found at http://www.informatics.jax.org/mgihome/submissions/submissions_menu.shtml .
Community outreach and user support
MGD provides extensive user support through online documentation and easy email or phone access to User Support Staff. User Support WWW access: http://www.informatics.jax.org/mgihome/support/support.shtml
- Email access: mgi- help@informatics.jax.org
- Telephone access: +1 207 288 6445
- FAX access: +1 207 288 6132
Other outreach
MGI-LIST ( http://www.informatics.jax.org/mgihome/lists/lists.shtml ) is a moderated and active email bulletin board supported by the MGI User Support group. Other outreach includes Online Tutorials and answers to Frequently Asked Questions, available at http://www.informatics.jax.org/userdocs/helpdocs_menu.shtml .
IMPLEMENTATION
MGD is implemented in the Sybase relational database system, version 12.5. A large set of CGI scripts and Java Servlets mediate the user's interaction with the database. For computational users, direct SQL access can be requested through User Support. User-requested database reports and a number of widely used data files (generated daily) are available on the ftp site ( ftp://ftp.informatics.jax.org/pub/reports/index.html ).
CITING MGD
The following citation format is suggested when referring to datasets specific to the MGD component of MGI: Mouse Genome Database (MGD), Mouse Genome Informatics, The Jackson Laboratory, Bar Harbor, Maine ( http://www.informatics.jax.org ). [Type in date (month, year) when you retrieve the data cited.] For general citation of the MGI resource please cite this article.
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use permissions, please contact journals.permissions@oupjournals.org .
The Mouse Genome Database is supported by NIH/NHGRI grant HG00330.
REFERENCES
Bult,C.J., Blake,J.A., Richardson,J.E., Kadin,J.A., Eppig,J.T. and the Mouse Genome Database Group (
2004
) The Mouse Genome Database (MGD): integrating biology with the genome.
Nucleic Acids Res.
,
32
,
D476
–D481.
Blake,J.A., Richardson.J.E., Bult,C.J., Kadin,J.A., Eppig,J.T. and the Mouse Genome Database Group (
2003
) MGD: the Mouse Genome Database.
Nucleic Acids Res.
,
31
,
193
–195.
Hill,D.P., Begley,D.A., Finger,J.H., Hayamizu,T.F., McCright,I.J., Smith,C.M., Beal,J.S., Corbani,L.E., Blake,J.A., Eppig,J.T., Kadin,J.A., Richardson,J.E. and Ringwald,M. (
2004
) The Mouse Gene Expression Database (GXD): updates and enhancements.
Nucleic Acids Res.
,
32
,
D568
–D571.
Näf,D., Krupke,D.M., Sundberg,J.P., Eppig,J.T. and Bult,C.J. (
2002
) The mouse tumor biology database: a public resource for cancer genetics and pathology of the mouse.
Cancer Res.
,
62
,
1235
–1240.
The Gene Ontology Consortium (
2004
) The Gene Ontology (GO) Database and Informatics Resource.
Nucleic Acids Res.
,
32
,
D258
–D261.
Eppig,J.T. and Strivens,M. (
1999
) Finding a mouse: the International Mouse Strain Resource (IMSR).
Trends Genet.
,
15
,
81
–82.
Wheeler,D.L., Church,D.M., Edgar,R., Federhen,S., Helmberg,W., Madden,T.L., Pontius,J.U., Schuler,G.D., Schriml,L.M., Sequeira,E. et al . (
2004
) Database resources of the National Center for Biotechnology Information: update.
Nucleic Acids Res.
,
32
,
D35
–D40.
Mashek,D.G., Bornfeldt,K.E., Coleman,R.A., Berger,J., Bernlohr,D.A., Black,P., DiRusso,C.C., Farber,S.A., Guo,W., Hashimoto,N. et al . (
2004
) Revised nomenclature for the mammalian long-chain acyl-CoA synthetase gene family.
J. Lipid Res.
,
45
,
1958
–1961.
Nelson,D.R., Zeldin,D.C., Hoffman,S.M.G., Maltais,L.J., Wain,H.M. and Nebert,D.W. (
2004
) Comparison of cytochrome P450 (CYP ) genes from the mouse and human genomes, including nomenclature recommendations for genes, pseudogenes and alternative-splice variants.
Phamacogenetics
,
14
,
1
–18.
© 2005, the authors Nucleic Acids Research, Vol. 33, Database issue © Oxford University Press 2005; all rights reserved
I agree to the terms and conditions. You must accept the terms and conditions.
Submit a comment
Name
Affiliations
Comment title
Comment
You have entered an invalid code
Thank you for submitting a comment on this article. Your comment will be reviewed and published at the journal's discretion. Please check for further notifications by email.
Citations
Views
Altmetric
Metrics
Total Views 1,398
1,071 Pageviews
327 PDF Downloads
Since 12/1/2016
Month: | Total Views: |
---|---|
December 2016 | 1 |
January 2017 | 1 |
February 2017 | 8 |
March 2017 | 1 |
April 2017 | 4 |
June 2017 | 1 |
July 2017 | 3 |
August 2017 | 3 |
September 2017 | 2 |
October 2017 | 6 |
November 2017 | 7 |
December 2017 | 22 |
January 2018 | 8 |
February 2018 | 19 |
March 2018 | 25 |
April 2018 | 11 |
May 2018 | 14 |
June 2018 | 9 |
July 2018 | 31 |
August 2018 | 57 |
September 2018 | 7 |
October 2018 | 12 |
November 2018 | 10 |
December 2018 | 9 |
January 2019 | 10 |
February 2019 | 23 |
March 2019 | 18 |
April 2019 | 28 |
May 2019 | 28 |
June 2019 | 10 |
July 2019 | 18 |
August 2019 | 22 |
September 2019 | 27 |
October 2019 | 18 |
November 2019 | 14 |
December 2019 | 16 |
January 2020 | 16 |
February 2020 | 22 |
March 2020 | 7 |
April 2020 | 11 |
May 2020 | 9 |
June 2020 | 11 |
July 2020 | 26 |
August 2020 | 14 |
September 2020 | 13 |
October 2020 | 20 |
November 2020 | 16 |
December 2020 | 16 |
January 2021 | 23 |
February 2021 | 19 |
March 2021 | 17 |
April 2021 | 8 |
May 2021 | 9 |
June 2021 | 15 |
July 2021 | 5 |
August 2021 | 19 |
September 2021 | 13 |
October 2021 | 7 |
November 2021 | 10 |
December 2021 | 6 |
January 2022 | 12 |
February 2022 | 13 |
March 2022 | 17 |
April 2022 | 20 |
May 2022 | 15 |
June 2022 | 14 |
July 2022 | 17 |
August 2022 | 16 |
September 2022 | 15 |
October 2022 | 14 |
November 2022 | 9 |
December 2022 | 11 |
January 2023 | 15 |
February 2023 | 15 |
March 2023 | 7 |
April 2023 | 9 |
May 2023 | 8 |
June 2023 | 22 |
July 2023 | 14 |
August 2023 | 13 |
September 2023 | 20 |
October 2023 | 12 |
November 2023 | 23 |
December 2023 | 27 |
January 2024 | 29 |
February 2024 | 22 |
March 2024 | 23 |
April 2024 | 39 |
May 2024 | 20 |
June 2024 | 9 |
July 2024 | 16 |
August 2024 | 15 |
September 2024 | 14 |
October 2024 | 18 |
Citations
194 Web of Science
×
Email alerts
Citing articles via
More from Oxford Academic