EuroPhenome and EMPReSS: online mouse phenotyping resource

Abstract

EuroPhenome (http://www.europhenome.org) and EMPReSS (http://empress.har.mrc.ac.uk/) form an integrated resource to provide access to data and procedures for mouse phenotyping. EMPReSS describes 96 Standard Operating Procedures for mouse phenotyping. EuroPhenome contains data resulting from carrying out EMPReSS protocols on four inbred laboratory mouse strains. As well as web interfaces, both resources support web services to enable integration with other mouse phenotyping and functional genetics resources, and are committed to initiatives to improve integration of mouse phenotype databases. EuroPhenome will be the repository for a recently initiated effort to carry out large-scale phenotyping on a large number of knockout mouse lines (EUMODIC).

Figure 1.

View of the summary data display for EuroPhenome. The left-hand panel contains the tree-like browser that allows users to search for data derived from individual SOPs in a structured manner. The main panel contains a table displaying Parameter Name, Parameter Measurement Unit, Mean, Median, SD, Standard Error, Minimum and Maximum values, and number of mice measured. Links are also provided to the EMPReSS SOP, download the data in Excel format, and link to the corresponding MPD dataset. Clicking on the name of an individual SOP in the left-hand panel takes the user to a more detailed view (Figure 2). The example shown is for the SOP ‘Clinical chemistry parameters’.

Figure 2.

View of the detailed data display for an individual parameter in EuroPhenome. The graphical display at the top of the main panel illustrates mean values of the parameter for each mouse strain tested, separated into male and female. Error bars represent SDs. The table below gives Mean, SD, Standard Error and mouse numbers for each strain subdivided into sex and, where appropriate, age groups. Clicking on the link ‘To see this data split across centres click here’ expands this table to show results obtained in the different Eumorphia laboratories that carried out the test. The pull-down menu at the top right allows navigation between the different parameters measured by a given SOP, where appropriate.

Figure 3.

View of the SOP display in the EMPReSS browser. The tree-like display in the left-hand panel provides for easy navigation to individual SOPs, which are classified under the body system they investigate. The right hand panel displays the SOP itself. The SOP document is subdivided into 11 sections as described previously (9) plus an additional section providing a link to EuroPhenome. The view also provides status information about the SOP including a unique document ID, revision number (previous versions of SOPs are retained as appendices to the current version; a new version is only recorded is there has been a substantive change), review status and the validation level of the SOP [see (9) for details].