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. 2010 Jan;38(Database issue):D593-9.
doi: 10.1093/nar/gkp867. Epub 2009 Oct 23.

MouseBook: an integrated portal of mouse resources

Andrew Blake  1 , Karen Pickford, Simon Greenaway, Steve Thomas, Amanda Pickard, Christine M Williamson, Niels C Adams, Alison Walling, Tim Beck, Martin Fray, Jo Peters, Tom Weaver, Steve D M Brown, John M Hancock, Ann-Marie Mallon
Affiliations

MouseBook: an integrated portal of mouse resources

Andrew Blake et al. Nucleic Acids Res. 2010 Jan.

Abstract

The MouseBook (http://www.mousebook.org) databases and web portal provide access to information about mutant mouse lines held as live or cryopreserved stocks at MRC Harwell. The MouseBook portal integrates curated information from the MRC Harwell stock resource, and other Harwell databases, with information from external data resources to provide value-added information above and beyond what is available through other routes such as International Mouse Stain Resource (IMSR). MouseBook can be searched either using an intuitive Google style free text search or using the Mammalian Phenotype (MP) ontology tree structure. Text searches can be on gene, allele, strain identifier (e.g. MGI ID) or phenotype term and are assisted by automatic recognition of term types and autocompletion of gene and allele names covered by the database. Results are returned in a tabbed format providing categorized results identified from each of the catalogs in MouseBook. Individual result lines from each catalog include information on gene, allele, chromosomal location and phenotype, and provide a simple click-through link to further information as well as ordering the strain. The infrastructure underlying MouseBook has been designed to be extensible, allowing additional data sources to be added and enabling other sites to make their data directly available through MouseBook.

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Figures

Figure 1.
Figure 1.
Architecture overview showing how the MouseBook web portal interacts with MouseBook Data Sources. Internal sources (purple boxes) are interrogated using SQL queries. External data sources (orange boxes) are either interrogated using web services or, in the case of MGI data, imported into an internal MySQL database from reports on the MGI FTP site. OATH and the Stock Information Management System interact with the relevant databases to add functionality.
Figure 2.
Figure 2.
StockList Information Management System interface. This interface enables curators of the MRC Harwell Resource to directly enter new mutant strains or query and modify existing information. The screenshot shows the list of all strains on the left-hand side. Clicking on one stock, e.g. C3H;C-Chd7/H, shows all the current information about it. Each of the boxes can then be edited directly. Adding a new affected gene/allele launches a pop-up box enabling the user to select the MGI gene/allele they require. The interface also captures information such as whether the stock is in IMSR or EMMA. The bottom of the interface enables curators to store information which links to the Harwell internal animal husbandry LIMS system, Anonymus, which stores data about the physical samples.
Figure 3.
Figure 3.
The results of a MouseBook search for the free text ‘gnas’, a well-known imprinted gene. It shows hits within Harwell Mice, EMMA Mice, Imprinting Data and Publication catalogs having used both the free text ‘gnas’ (20) as well as the MGI identifier (MGI:95777), automatically ascertained by the search module, to query all MouseBook data sources. In case of the Harwell Mice search result’s tab, it shows the Strain Name, involved gene/allele symbols, the chromosome involved, phenotypic description and the ability to order material for all matched stocks.
Figure 4.
Figure 4.
The results of a MouseBook phenotype ontology term search using the high level ‘Behaviour/Neurological Phenotype’ term (MP:0005286). This hits annotations matching that MP term and any of its child terms. The results are shown displaying the Strain Name, the actual phenotype term that is annotated and the ability to order cryopreserved material.
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References

    1. Rosenthal N, Brown S. The mouse ascending: perspectives for human-disease models. Nat. Cell Biol. 2007;9:993–999. - PubMed
    1. Waterston RH, Lindblad-Toh K, Birney E, Rogers J, Abril JF, Agarwal P, Agarwala R, Ainscough R, Alexandersson M, An P, et al. Initial sequencing and comparative analysis of the mouse genome. Nature. 2002;420:520–562. - PubMed
    1. Brown SD, Hancock JM, Gates H. Understanding mammalian genetic systems: the challenge of phenotyping in the mouse. PLoS Genet. 2006;2:e118. - PMC - PubMed
    1. Hancock JM, Mallon AM. Phenobabelomics–mouse phenotype data resources. Brief. Funct. Genomic. Proteomic. 2007;6:292–301. - PubMed
    1. Mouse Phenotype Database Integration Consortium. Integration of mouse phenome data resources. Mamm. Genome. 2007;18:157–163. - PMC - PubMed

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