ABSTRACT
The International Mouse Phenotyping Consortium (IMPC) web portal (http://www.mousephenotype.org) provides the biomedical community with a unified point of access to mutant mice and rich collection of related emerging and existing mouse phenotype data. IMPC mouse clinics worldwide follow rigorous highly structured and standardized protocols for the experimentation, collection and dissemination of data. Dedicated 'data wranglers' work with each phenotyping center to collate data and perform quality control of data. An automated statistical analysis pipeline has been developed to identify knockout strains with a significant change in the phenotype parameters. Annotation with biomedical ontologies allows biologists and clinicians to easily find mouse strains with phenotypic traits relevant to their research. Data integration with other resources will provide insights into mammalian gene function and human disease. As phenotype data become available for every gene in the mouse, the IMPC web portal will become an invaluable tool for researchers studying the genetic contributions of genes to human diseases.
Subject(s)
Databases, Genetic , Mice, Knockout , Phenotype , Animals , Biological Ontologies , Internet , MiceABSTRACT
The International Knockout Mouse Consortium (IKMC) aims to mutate all protein-coding genes in the mouse using a combination of gene targeting and gene trapping in mouse embryonic stem (ES) cells and to make the generated resources readily available to the research community. The IKMC database and web portal (www.knockoutmouse.org) serves as the central public web site for IKMC data and facilitates the coordination and prioritization of work within the consortium. Researchers can access up-to-date information on IKMC knockout vectors, ES cells and mice for specific genes, and follow links to the respective repositories from which corresponding IKMC products can be ordered. Researchers can also use the web site to nominate genes for targeting, or to indicate that targeting of a gene should receive high priority. The IKMC database provides data to, and features extensive interconnections with, other community databases.
Subject(s)
Databases, Genetic , Mice, Knockout , Alleles , Animals , Gene Targeting , Genetic Vectors , Genomics , Internet , Mice , Molecular Sequence Annotation , User-Computer InterfaceABSTRACT
In this article, we describe the use of the BioMart data management system to provide integrated access to International Knockout Mouse Consortium (IKMC) data and other related mouse resources. The IKMC is currently mutating all mouse protein-coding genes in embryonic stem (ES) cells using gene targeting and gene trapping approaches. The BioMart portal allows researchers to identify and obtain IKMC knockout vectors, ES cells and mice for genes of interest. Gene annotation, expression, phenotype and disease data is also integrated from external BioMarts, allowing selection of IKMC products by a wide variety of criteria. These products are invaluable for researchers involved in the elucidation of gene function and the role of individual genes in human disease. Here, we describe these datasets in more detail and illustrate the functionality of the portal using several examples.
Subject(s)
Database Management Systems , Embryonic Stem Cells/physiology , Gene Knockout Techniques , Mice, Knockout/genetics , Animals , Biomedical Research , Databases, Genetic , Humans , International Cooperation , Internet , Mice , Molecular Sequence Annotation , Phenotype , Societies , User-Computer InterfaceABSTRACT
BioMart Central Portal is a first of its kind, community-driven effort to provide unified access to dozens of biological databases spanning genomics, proteomics, model organisms, cancer data, ontology information and more. Anybody can contribute an independently maintained resource to the Central Portal, allowing it to be exposed to and shared with the research community, and linking it with the other resources in the portal. Users can take advantage of the common interface to quickly utilize different sources without learning a new system for each. The system also simplifies cross-database searches that might otherwise require several complicated steps. Several integrated tools streamline common tasks, such as converting between ID formats and retrieving sequences. The combination of a wide variety of databases, an easy-to-use interface, robust programmatic access and the array of tools make Central Portal a one-stop shop for biological data querying. Here, we describe the structure of Central Portal and show example queries to demonstrate its capabilities.