- Mouse phenome database. [PMID: 24243846]
Stephen C Grubb, Carol J Bult, Molly A Bogue
Nucleic acids research 2014:42(Database issue)
26 Citations (Google Scholar as of 2016-02-28)
Abstract: The Mouse Phenome Database (MPD; phenome.jax.org) was launched in 2001 as the data coordination center for the international Mouse Phenome Project. MPD integrates quantitative phenotype, gene expression and genotype data into a common annotated framework to facilitate query and analysis. MPD contains >3500 phenotype measurements or traits relevant to human health, including cancer, aging, cardiovascular disorders, obesity, infectious disease susceptibility, blood disorders, neurosensory disorders, drug addiction and toxicity. Since our 2012 NAR report, we have added >70 new data sets, including data from Collaborative Cross lines and Diversity Outbred mice. During this time we have completely revamped our homepage, improved search and navigational aspects of the MPD application, developed several web-enabled data analysis and visualization tools, annotated phenotype data to public ontologies, developed an ontology browser and released new single nucleotide polymorphism query functionality with much higher density coverage than before. Here, we summarize recent data acquisitions and describe our latest improvements.
- Mouse Phenome Database (MPD). [PMID: 22102583]
Terry P Maddatu, Stephen C Grubb, Carol J Bult, Molly A Bogue
Nucleic acids research 2012:40(Database issue)
45 Citations (Google Scholar as of 2016-02-28)
Abstract: The Mouse Phenome Project was launched a decade ago to complement mouse genome sequencing efforts by promoting new phenotyping initiatives under standardized conditions and collecting the data in a central public database, the Mouse Phenome Database (MPD; http://phenome.jax.org). MPD houses a wealth of strain characteristics data to facilitate the use of the laboratory mouse in translational research for human health and disease, helping alleviate problems involving experimentation in humans that cannot be done practically or ethically. Data sets are voluntarily contributed by researchers from a variety of institutions and settings, or in some cases, retrieved by MPD staff from public sources. MPD maintains a growing collection of standardized reference data that assists investigators in selecting mouse strains for research applications; houses treatment/control data for drug studies and other interventions; offers a standardized platform for discovering genotype-phenotype relationships; and provides tools for hypothesis testing. MPD improvements and updates since our last NAR report are presented, including the addition of new tools and features to facilitate navigation and data mining as well as the acquisition of new data (phenotypic, genotypic and gene expression).
- Mouse phenome database. [PMID: 18987003]
Stephen C Grubb, Terry P Maddatu, Carol J Bult, Molly A Bogue
Nucleic acids research 2009:37(Database issue)
79 Citations (Google Scholar as of 2016-02-28)
Abstract: The Mouse Phenome Database (MPD; http://www.jax.org/phenome) is an open source, web-based repository of phenotypic and genotypic data on commonly used and genetically diverse inbred strains of mice and their derivatives. MPD is also a facility for query, analysis and in silico hypothesis testing. Currently MPD contains about 1400 phenotypic measurements contributed by research teams worldwide, including phenotypes relevant to human health such as cancer susceptibility, aging, obesity, susceptibility to infectious diseases, atherosclerosis, blood disorders and neurosensory disorders. Electronic access to centralized strain data enables investigators to select optimal strains for many systems-based research applications, including physiological studies, drug and toxicology testing, modeling disease processes and complex trait analysis. The ability to select strains for specific research applications by accessing existing phenotype data can bypass the need to (re)characterize strains, precluding major investments of time and resources. This functionality, in turn, accelerates research and leverages existing community resources. Since our last NAR reporting in 2007, MPD has added more community-contributed data covering more phenotypic domains and implemented several new tools and features, including a new interactive Tool Demo available through the MPD homepage (quick link: http://phenome.jax.org/phenome/trytools).
- Integration of mouse phenome data resources [PMID: 17436037]
null null, John M Hancock, Niels C Adams, Vassilis Aidinis, Andrew Blake, Molly Bogue, Steve D M Brown, Elissa J Chesler, Duncan Davidson, Christopher Duran, Janan T Eppig, Valérie Gailus-Durner, Hilary Gates, Georgios V Gkoutos, Simon Greenaway, Martin Hrabé de Angelis, George Kollias, Sophie Leblanc, Kirsty Lee, Christoph Lengger, Holger Maier, Ann-Marie Mallon, Hiroshi Masuya, David G Melvin, Werner Müller, Helen Parkinson, Glenn Proctor, Eli Reuveni, Paul Schofield, Aadya Shukla, Cynthia Smith, Tetsuro Toyoda, Laurent Vasseur, Shigeharu Wakana, Alison Walling, Jacqui White, Joe Wood, Michalis Zouberakis
Mammalian genome : official journal of the International Mammalian Genome Society 2007:18(3)
51 Citations (Google Scholar as of 2016-02-29)
Abstract: Understanding the functions encoded in the mouse genome will be central to an understanding of the genetic basis of human disease. To achieve this it will be essential to be able to characterize the phenotypic consequences of variation and alterations in individual genes. Data on the phenotypes of mouse strains are currently held in a number of different forms (detailed descriptions of mouse lines, first-line phenotyping data on novel mutations, data on the normal features of inbred lines) at many sites worldwide. For the most efficient use of these data sets, we have initiated a process to develop standards for the description of phenotypes (using ontologies) and file formats for the description of phenotyping protocols and phenotype data sets. This process is ongoing and needs to be supported by the wider mouse genetics and phenotyping communities to succeed. We invite interested parties to contact us as we develop this process further.