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1. List of Contributors

Author

Ackert-Bicknell, C., primary, Alam, M., additional, Bayne, K., additional, Begley, D., additional, Benavides, F.J., additional, Berdanier, C.D., additional, Berndt, A., additional, Bleich, A., additional, Bolliger Provencher, A., additional, Bonhomme, F., additional, Braun, A., additional, Bürge, T., additional, Clifford, C.B., additional, Cox, G.A., additional, Davisson, M.T., additional, Dorsch, M.M., additional, Entman, M.L., additional, Eppig, J., additional, Ernst, H., additional, Everds, N., additional, Frangogiannis, N.G., additional, Fukuta, K., additional, Gossler, A., additional, Guénet, J.-L., additional, Hardy, P., additional, Hartley, C.J., additional, Hedrich, H.J., additional, Hirota, J., additional, Hoymann, H.-G., additional, Jensen, T.L., additional, King, L.E., additional, Kispert, A., additional, Komárek, V., additional, König, B., additional, Krinke, G.J., additional, Leopold, W.R., additional, Linder, C.C., additional, Lister, D., additional, Lutz, C.M., additional, MacArthur Clark, J.A., additional, Mähler, M., additional, McConville, P., additional, Michael, L.H., additional, Mikkelsen, L.F., additional, Muller, W., additional, Nicklas, W., additional, Orth, A., additional, Otto, K., additional, Potter, C.P., additional, von Thaden, A.-K., additional, Pritchett-Corning, K.R., additional, Reddy, A.K., additional, Reifenberg, K., additional, Ritskes-Hoitinga, M., additional, Rittinghausen, S., additional, Rülicke, T., additional, Schaudien, D., additional, Schofield, P.N., additional, Sher, R.B., additional, Shimizu, S., additional, Silva, K.A., additional, Steinlechner, S., additional, Sundberg, B.A., additional, Sundberg, J.P., additional, Taffet, G.E., additional, Tobin, G., additional, Weber, K., additional, Wedekind, D., additional, Weiss, T., additional, Würbel, H., additional, and Zurlo, J., additional

Published
2012
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3. Comparative Genome Organization of Vertebrates: The First International Workshop on Comparative Genome Organization

Author

Andersson, L., Archibald, A., Ashburner, M., Audun, S., Barendse, W., Bitgood, J., Bottema, C., Broad, T., Brown, S., Burt, D., Charlier, C., Copeland, N., Davis, S., Davisson, M., Edwards, J., Eggen, A., Elgar, G., Eppig, J. T., Franklin, I., Grewe, P., Gill, T., Graves, J. A. M., Hawken, R., Hetzel, J., Hilyard, A., Jacob, H., Jaswinska, L., Jenkins, N., Kunz, H., Levan, G., Lie, O., Lyons, L., Maccarone, P., Mellersh, C., Montgomery, G., Moore, S., Moran, C., Morizot, D., Neff, M., Nicholas, F., O’Brien, S., Parsons, Y., Peters, J., Postlethwait, J., Raymond, M., Rothschild, M., Schook, L., Sugimoto, Y., Szpirer, C., Tate, M., Taylor, J., VandeBerg, J., Wakefield, M., Wienberg, J., and Womack, J.

Published
1996
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9. Integration of Mouse Phenome Data Resources

Author

Hancock, J, Adams, N, Aidinis, V, Blake, A, Blake, J, Bogue, M, Brown, S, Chesler, E, Davidson, D, Duran, C, Eppig, J, Gailus−Durner, V, Gates, H, Gkoutos, G, Greenaway, S, de Angelis, M, Kollias, G, Leblanc, S, Lee, K, Lengger, C, Maier, H, Mallon, A, Masuya, H, Melvin, D, and Müller, W

Published
2016

10. Mouse Genome Database: Curation Strategies for Alleles and Phenotypes in the Mouse

Author

Smith, C.L., Blake, J.A., Richardson, J.E., Kadin, J.A., and Eppig, J. T.

Subjects
Human genetics -- Research, Human chromosome abnormalities -- Research, Genetic disorders -- Research, Mice -- Genetic aspects, Chromosome mapping, Databases -- Design and construction, Gene expression -- Research, Biological sciences
Published
2001

11. Gene Expression Database for the Laboratory Mouse

Author

Begley, D. A., Eppig, J. T., Hayamizu, T., Hill, D. P., Kadin, J., McCright, I. J., Richardson, J., Smith, C., and Ringwald, M.

Subjects
Gene expression -- Information management, Mice as laboratory animals -- Genetic aspects, Genetic research, Cellular control mechanisms -- Research, Biological sciences
Abstract

The Gene Expression Database (GXD) is a community resource of gene expression information for the laboratory mouse. GXD is designed to store and integrate data from many types of expression assays in different mouse strains and mutants and to make this data available in formats appropriate for thorough analysis. Expression patterns are described using a comprehensive anatomical dictionary of the developing mouse embryo established in collaboration with the 3D atlas project in Edinburgh, United Kingdom, and standardized annotations complemented with digitized images of the original expression data. GXD is fully integrated with the Mouse Genome Database (MGD) to enable a combined analysis of genotype, expression, and phenotype information. Participation in the Gene Ontology Project provides standardized search terms to identify genes involved with specific molecular functions, biological processes, and cellular components. The database is updated and new expression data are made available on a daily basis. GXD currently includes the Gene Expression Index, a searchable index of expression literature for mouse development; in situ hybridization, immunohistochemistry, RT-PCR, and Northern and Western blot data obtained from the literature; and mouse cDNA and EST data. We have developed the Gene Expression Notebook {GEN), an electronic notebook designed to organize expression data in the laboratory and to directly submit data to GXD. Increased electronic submissions will significantly enhance the utility of GXD as a community resource. GXD is freely available at http:// www.informatics.jax.org.

Published
2001

14. Briefing Paper: Legal Issues on Phenotype Data Accessibility A paper prepared following internal discussions of the International Mouse Phenotyping Consortium, Interphenome and CASIMIR

Author

Bedu, E, Blake, J, Brown, S., Bubela, T, Bult, C, Church, D, Einhorn, D, Eppig, J, Fletcher, C, Hancock, J, Kim, J, Mallon, A-M, Masuya, H, McKenzie, A, McKerlie, C, Moore, M, Nguyen, T, Ramirez-Solis, R, Schofield, P, Smedley, D, Suzuki, T, Tanaka, N, Wakana, S, and Yen, J

Subjects
Data sharing, data licensing
Abstract

A summary of a discussion of the terms under which phenotype data should be licensed by representatives of the mouse research community convened by Interphenome and CASIMIR and held at the 23rd International Mammalian Genome Conference in La Jolla, California, in November 2009. We compare two simple options of making data available to the public domain with three licensing options from Creative Commons (See Appendix B for the Legal Code that underlies each of these options), namely, cc0 or a waiver of copyright and database rights, cc‐By (attribution), and cc‐By‐SA (attribution and share‐alike). Creative Commons is a nonprofit corporation that facilitates sharing through standard‐form free licenses and other legal tools (creativecommons.org).

Published
2009
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15. P4-S The Mouse Genome Informatics Database: An Integrated Resource for Mouse Genetics and Genomics

Author

Bult, C. J., Blake, J., Kadin, J., Eppig, J., Ringwald, M., Richardson, J., and Group, M.

Subjects
Poster Abstracts: Bioinfomatics
Abstract

The Mouse Genome Informatics (MGI; http://www.informatics.jax.org/) database integrates genetic and genomic data with the primary mission of facilitating the use of the mouse as a model system for understanding human biology and disease processes. MGI is the authoritative source of official mouse genetic nomenclature, gene ontology annotations, mammalian phenotype annotations, and mouse anatomy terms. MGI staff enforce the use of standardized genetic nomenclature, ontologies, and controlled vocabularies to describe mouse sequence data, genes, strains, expression data, alleles, and phenotypes. Extensive links between gene-centric information in MGI and other informatics resources (e.g., OMIM, Ensembl, UCSC, NCBI, UniProt) are maintained and updated on a regular basis.

Published
2007

16. GXD: a gene expression database for the laboratory mouse. The Gene Expression Database Group

Author

Ringwald, M, Mangan, M E, Eppig, J T, Kadin, J A, and Richardson, J E

Subjects
Expressed Sequence Tags, Internet, Mice, Phenotype, Databases, Factual, Genes, Genotype, Terminology as Topic, Animals, Gene Expression, Information Storage and Retrieval, Mice, Inbred Strains, Research Article
Abstract

The Gene Expression Database (GXD) is a community resource that stores and integrates expression information for the laboratory mouse, with a particular emphasis on mouse development, and makes these data freely available in formats appropriate for comprehensive analysis. GXD is implemented as a relational database and integrated with the Mouse Genome Database (MGD) to enable global analysis of genotype, expression and phenotype information. Interconnections with sequence databases and with databases from other species further extend GXD's utility for the analysis of gene expression data. GXD is available through the Mouse Genome Informatics Web Site at http://www.informatics.jax.org/

Published
1999

17. Finding and sharing: new approaches to registries of databases and services for the biomedical sciences

Author

Luxembourg Centre for Systems Biomedicine (LCSB): Experimental Neurobiology (Balling Group) [research center], Smedley, D., Schofield, P., Chen, C. K., Aidinis, V., Ainali, C., Bard, J., Balling, Rudi, Birney, E., Blake, Andrew, Bongcam-Rudloff, E., Brookes, A. J., Cesareni, G., Chandras, C., Eppig, J., Flicek, P., Gkoutos, G., Greenaway, S., Gruenberger, M., Heriche, J. K., Lyall, A., Mallon, A. M., Muddyman, D., Reisinger, F., Ringwald, M., Rosenthal, N., Schughart, K., Swertz, M., Thorisson, G. A., Zouberakis, M., Hancock, J. M., Luxembourg Centre for Systems Biomedicine (LCSB): Experimental Neurobiology (Balling Group) [research center], Smedley, D., Schofield, P., Chen, C. K., Aidinis, V., Ainali, C., Bard, J., Balling, Rudi, Birney, E., Blake, Andrew, Bongcam-Rudloff, E., Brookes, A. J., Cesareni, G., Chandras, C., Eppig, J., Flicek, P., Gkoutos, G., Greenaway, S., Gruenberger, M., Heriche, J. K., Lyall, A., Mallon, A. M., Muddyman, D., Reisinger, F., Ringwald, M., Rosenthal, N., Schughart, K., Swertz, M., Thorisson, G. A., Zouberakis, M., and Hancock, J. M.

Abstract

The recent explosion of biological data and the concomitant proliferation of distributed databases make it challenging for biologists and bioinformaticians to discover the best data resources for their needs, and the most efficient way to access and use them. Despite a rapid acceleration in uptake of syntactic and semantic standards for interoperability, it is still difficult for users to find which databases support the standards and interfaces that they need. To solve these problems, several groups are developing registries of databases that capture key metadata describing the biological scope, utility, accessibility, ease-of-use and existence of web services allowing interoperability between resources. Here, we describe some of these initiatives including a novel formalism, the Database Description Framework, for describing database operations and functionality and encouraging good database practise. We expect such approaches will result in improved discovery, uptake and utilization of data resources. Database URL: http://www.casimir.org.uk/casimir_ddf.

Published
2010

20. Guidelines for human gene nomenclature (1997). HUGO Nomenclature Committee

Author

White, J. A., McAlpine, P. J., Antonarakis, Stylianos, Cann, H., Eppig, J. T., Frazer, K., Frezal, J., Lancet, D., Nahmias, J., Pearson, P., Peters, J., Scott, A., Scott, Hamish Steele, Spurr, N., Talbot, C., Jr., and Povey, S.

Subjects
ddc:616, Genome, Human, Genetic Diseases, Inborn, Proteins, Genetic Diseases, Inborn/genetics, DNA, DNA/genetics, Enzymes, Species Specificity, Multigene Family, Terminology as Topic, Proteins/genetics, Animals, Humans, Enzymes/genetics, Alleles
Published
1997

21. The Mouse Genome Database (MGD). A comprehensive public resource of genetic, phenotypic and genomic data. The Mouse Genome Informatics Group

Author

Blake, J A, Richardson, J E, Davisson, M T, and Eppig, J T

Subjects
Mice, Genome, Databases, Factual, Animals, Private Sector, Maine, Research Article
Abstract

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.

Published
1997

25. The Mouse Tumor Biology Database (MTB)

Author

Begley, D. A., primary, Krupke, D. M., additional, Neuhauser, S. B., additional, Richardson, J. E., additional, Bult, C. J., additional, Eppig, J. T., additional, and Sundberg, J. P., additional

Published
2011
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27. The IKMC web portal: a central point of entry to data and resources from the International Knockout Mouse Consortium

Author

Ringwald, M., primary, Iyer, V., additional, Mason, J. C., additional, Stone, K. R., additional, Tadepally, H. D., additional, Kadin, J. A., additional, Bult, C. J., additional, Eppig, J. T., additional, Oakley, D. J., additional, Briois, S., additional, Stupka, E., additional, Maselli, V., additional, Smedley, D., additional, Liu, S., additional, Hansen, J., additional, Baldock, R., additional, Hicks, G. G., additional, and Skarnes, W. C., additional

Published
2010
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28. Finding and sharing: new approaches to registries of databases and services for the biomedical sciences

Author

Smedley, D., primary, Schofield, P., additional, Chen, C.-K., additional, Aidinis, V., additional, Ainali, C., additional, Bard, J., additional, Balling, R., additional, Birney, E., additional, Blake, A., additional, Bongcam-Rudloff, E., additional, Brookes, A. J., additional, Cesareni, G., additional, Chandras, C., additional, Eppig, J., additional, Flicek, P., additional, Gkoutos, G., additional, Greenaway, S., additional, Gruenberger, M., additional, Heriche, J.-K., additional, Lyall, A., additional, Mallon, A.-M., additional, Muddyman, D., additional, Reisinger, F., additional, Ringwald, M., additional, Rosenthal, N., additional, Schughart, K., additional, Swertz, M., additional, Thorisson, G. A., additional, Zouberakis, M., additional, and Hancock, J. M., additional

Published
2010
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29. Sequence interpretation. Functional annotation of mouse genome sequences.

Author

Nadeau, J. H., Balling, Rudi, Barsh, G., Beier, D., Brown, S. D., Bucan, M., Camper, S., Carlson, G., Copeland, N., Eppig, J., Fletcher, C., Frankel, W. N., Ganten, D., Goldowitz, D., Goodnow, C., Guenet, J. L., Hicks, G., Hrabe de Angelis, M., Jackson, I., Jacob, H. J., Jenkins, N., Johnson, D., Justice, M., Kay, S., Kingsley, D., Lehrach, H., Magnuson, T., Meisler, M., Poustka, A., Rinchik, E. M., Rossant, J., Russell, L. B., Schimenti, J., Shiroishi, T., Skarnes, W. C., Soriano, P., Stanford, W., Takahashi, J. S., Wurst, W., Zimmer, Andreas David, Nadeau, J. H., Balling, Rudi, Barsh, G., Beier, D., Brown, S. D., Bucan, M., Camper, S., Carlson, G., Copeland, N., Eppig, J., Fletcher, C., Frankel, W. N., Ganten, D., Goldowitz, D., Goodnow, C., Guenet, J. L., Hicks, G., Hrabe de Angelis, M., Jackson, I., Jacob, H. J., Jenkins, N., Johnson, D., Justice, M., Kay, S., Kingsley, D., Lehrach, H., Magnuson, T., Meisler, M., Poustka, A., Rinchik, E. M., Rossant, J., Russell, L. B., Schimenti, J., Shiroishi, T., Skarnes, W. C., Soriano, P., Stanford, W., Takahashi, J. S., Wurst, W., and Zimmer, Andreas David

Published
2001
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36. Large-scale cDNA analysis reveals phased gene expression patterns during preimplantation mouse development

Author

Ko, M.S., primary, Kitchen, J.R., additional, Wang, X., additional, Threat, T.A., additional, Hasegawa, A., additional, Sun, T., additional, Grahovac, M.J., additional, Kargul, G.J., additional, Lim, M.K., additional, Cui, Y., additional, Sano, Y., additional, Tanaka, T., additional, Liang, Y., additional, Mason, S., additional, Paonessa, P.D., additional, Sauls, A.D., additional, DePalma, G.E., additional, Sharara, R., additional, Rowe, L.B., additional, Eppig, J., additional, Morrell, C., additional, and Doi, H., additional

Published
2000
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38. Genome-wide mapping of unselected transcripts from extraembryonic tissue of 7.5-day mouse embryos reveals enrichment in the t-complex and under-representation on the X chromosome

Author

Ko, M. S. H., primary, Threat, T. A., additional, Wang, X., additional, Horton, J. H., additional, Cui, Y., additional, Pryor, E., additional, Paris, J., additional, Wells-Smith, J., additional, Kitchen, J. R., additional, Rowe, L. B., additional, Eppig, J., additional, Satoh, T., additional, Brant, L., additional, Fujiwara, H., additional, Yotsumoto, S., additional, and Nakashima, H., additional

Published
1998
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39. The Mouse Gene Map

Author

Davisson, M. T., primary, Bradt, D. W., additional, Merriam, J. J., additional, Rockwood, S. F., additional, and Eppig, J. T., additional

Published
1998
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48. The Mouse Tumor Biology Database (MTB): A Central Electronic Resource for Locating and Integrating Mouse Tumor Pathology Data.

Author

Begley, D. A., Krupke, D. M., Neuhauser, S. B., Richardson, J. E., Bult, C. J., Eppig, J. T., and Sundberg, J. P.

Subjects
TUMORS, CANCER, MICE, PATHOLOGY, DATABASES
Abstract

This article offers information on Mouse Tumor Biology (MTB) Database. MTB was opened to the public in 1998, and it aims to provide a centralized electronic resource to collect and integrate data obtained from mouse cancer models in an easily searchable database. Incidence and latency of mouse tumors and pathology reports are among the data offered by the MTB. The article also explains MTB's data source and links as well as how pathology descriptions and images can be accessed in the database.

Published
2012
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49. Effect of in vitro maturation of mouse oocytes on the health and lifespan of adult offspring.

Author

Eppig, J J, O'Brien, M J, Wigglesworth, K, Nicholson, A, Zhang, W, and King, B A

Abstract

Background: In vitro maturation of oocytes can, in some circumstances, provide an alternative approach to gonadotrophin-induced maturation in clinical settings. However, the consequences of these protocols on the long-term health of offspring are unknown. Here, the long-term health status and lifespans of offspring produced by in vitro maturation of mouse oocytes was compared with that of oocytes induced to mature in vivo using gonadotrophin treatment.Methods: Mouse oocytes were matured in vitro using both an established optimized system and in the absence of amino acids to produce a suboptimal condition for maturation. Oocytes induced to mature in vivo with gonadotrophins constituted the control group. All metaphase II oocytes were fertilized in vitro and transferred at the 2-cell stage to the oviducts of pseudo-pregnant foster mothers for development to term. Offspring were subjected to a wide variety of physiological and behavioral tests for the first year of life and natural lifespan determined.Results: There was no difference among the groups in lifespan or in most of the physiological and behavioral analyses. However, the pulse rate and cardiac output were slightly, but significantly, reduced in the optimized in vitro matured group compared with the in vivo matured group (P = 0.0119 and P = 0.0197, respectively). Surprisingly, these decreases were largely abrogated in the in vitro group matured without amino acids.Conclusions: Evidence presented here using a mouse model suggests that the in vitro maturation of oocytes has minimal effects on the long-term health of offspring. However, a finding of slight reductions in pulse rate and cardiac output may focus future clinical attention. [ABSTRACT FROM AUTHOR]

Published
2009
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