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. 2008 Mar 26:9:169.
doi: 10.1186/1471-2105-9-169.

MausDB: an open source application for phenotype data and mouse colony management in large-scale mouse phenotyping projects

Holger Maier  1 , Christoph Lengger, Bruno Simic, Helmut Fuchs, Valérie Gailus-Durner, Martin Hrabé de Angelis
Affiliations

MausDB: an open source application for phenotype data and mouse colony management in large-scale mouse phenotyping projects

Holger Maier et al. BMC Bioinformatics. .

Abstract

Background: Large-scale, comprehensive and standardized high-throughput mouse phenotyping has been established as a tool of functional genome research by the German Mouse Clinic and others. In all these projects, vast amounts of data are continuously generated and need to be stored, prepared for data-mining procedures and eventually be made publicly available. Thus, central storage and integrated management of mouse phenotype data, genotype data, metadata and linked external data are highly important. Requirements most probably depend on the individual mouse housing unit or project and the demand for either very specific individual database solutions or very flexible solutions that can be easily adapted to local demands. Not every group has the resources and/or the know-how to develop software for this purpose. A database application has been developed for the German Mouse Clinic in order to meet all requirements mentioned above.

Results: We present MausDB, the German Mouse Clinic web-based database application that integrates standard mouse colony management, phenotyping workflow scheduling features and mouse phenotyping result data management. It links mouse phenotype data with genotype data, metadata and external data such as public web databases, which is a prerequisite for comprehensive data analysis and mining. We describe how this can be achieved with a lean and user-friendly system built on open standards.

Conclusion: MausDB is suited for large-scale, high-throughput phenotyping facilities but can also be used exclusively for mouse colony management within smaller units or projects. The system is successfully used as the primary mouse and data management tool of the German Mouse Clinic and other mouse facilities. We offer MausDB to the scientific community as open source software to provide a system for storage of data from functional genomics projects in a well-structured, easily accessible form.

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Figures

Figure 1
Figure 1
Workflow management. Upper left: a specific or custom workflow (a set of phenotyping assays in a distinct order) can be scheduled for a selection of mice. Lower right: a detailed schedule table (rows: phenotyping assays; columns: calendar weeks) is displayed as a final preview. Red boxes denote the calendar week in which the given assay is to be performed.
Figure 2
Figure 2
Phenotyping ordering system: reminder list. Upon login, a reminder list of ordered phenotyping tasks is displayed to every user. The list is sorted by calendar week and only contains phenotyping orders to be performed in the module to which a user is assigned. The name of the phenotyping task ("order list", left column) is composed of the mouse line, the assay to be measured and the due date. The rightmost column specifies the number of mice to be phenotyped in this order, whereas the 'parameterset' column denotes the assay to be performed. The order list link in the left column is clickable and leads to a more detailed view of the phenotyping order.
Figure 3
Figure 3
Phenotyping ordering system: phenotyping order list. A detailed view of every order list is available by following the link in the 'order list name' column of the reminder list (cf. Figure 2). The top table contains information on the order list, e.g. creation data, schedule date and a link to the parameter set (i.e. assay) to be measured. The scheduled date as well as the phenotyping order status can be modified using the respective controls. The bottom table is a list of all mice to be analyzed in the current phenotyping order along with important information,e.g. age, sex, genotype, line and current location.
Figure 4
Figure 4
Phenotyping records overview for a mouse. For every mouse, the phenotyping records overview summarizes available phenotyping data from every parameter set (i.e. assay). In the left column, the short names of the corresponding phenotyping parameter sets are specified, while the column 'description' explains the parameter sets in more detail. The 'record #' column shows the number of phenotyping records for every parameter set. The 'class' column names the classification of the parameter set (1: primary screen, 2: secondary screen). The 'project' column specifies the assigned project (i.e. phenotyping module) for a parameter set.
Figure 5
Figure 5
Phenotype data for a mouse from one parameter set (assay). The complete list of phenotyping data from a particular parameter set (assay) is accessible by following the link in the first column of the phenotyping record overview (cf. Figure 4). The table shows (from left to right) the short names and the descriptions of the parameters, their data type (integer, float, Boolean, or text), the individually measured values and their units, the date of measurement and the project assignment, which is relevant for access permission.
Figure 6
Figure 6
Detailed view of a single phenotype record. For every phenotyping record, a more detailed view is available by following the link in the 'value' column of the phenotyping data list (cf. Figure 5). This view additionally offers links to the corresponding order list and the parameter set description and shows the accessibility of the result ('is public'). In the 'probe taken' and 'measured' fields, date and time of sample taking and measurement, respectively, are shown. If the time is not given by the user, 00:00:00 is used instead. 'Measure user' names the screener who performed the measurement, while 'Responsible user' names the scientist who checked the results for validity before they were uploaded.
Figure 7
Figure 7
Table view of phenotype data for a set of mice. For a selection of mice from the cart, a customizable phenotype data table can be generated for selected parameters. Next to individual mouse metadata (grey columns), phenotype data values (white columns) are displayed. The table can be readily exported into a spreadsheet file, which can be downloaded from the MausDB server to the client computer by clicking the 'Export phenotyping data to Excel' button.
Figure 8
Figure 8
Cage history of a mouse. For any given mouse, the full history of cage placements, including time spent in the respective cage and cage mates during this time period, can be accessed. As cages keep their ID when moved between rooms and racks, the rightmost column informs about cage placement in rack(s).
Figure 9
Figure 9
Mouse "shopping cart". Mice can be placed together in a cart irrespective of their real rack or cage location; the cart can also contain dead mice. Table: For each mouse in the cart, the basic data (ID, ear mark, sex, date of birth, date of death, genotype, strain, line, room/rack/cage and comment) is displayed in a row. The background color of the mouse rows is sex-specific (blue: male; pink: female). Information about current location (room, rack and cage) is given for living mice. Individual mice can be selected via checkbox (second column) for further operations. The table can be sorted by clicking on the respective underlined header column. The cart can be emptied all at once, or individually selected mice can be removed or kept in the cart. Carts can be saved permanently with a custom name and reloaded later. Table information can be exported to Excel or another spreadsheet application. Bottom: Pressing one of the "buttons" at the bottom part of the cart view applies the respective operation to selected mice.
Figure 10
Figure 10
Search & find mask of MausDB. Mice can be searched for using different attributes as starting information, e.g. mouse ID, cage ID, date of birth or date of death, line, genotype or part of the mouse comment. As an option, searches can be restricted to mice currently in the cart, which allows complex search operations to be performed.
Figure 11
Figure 11
Cage card example. Front side (left part): the top row contains room (7109), rack (05) and cage (1894) information. The bar color can be freely assigned by the user and may visually encode the line or any other information in a user context. Mouse-specific rows contain the mouse ID together with ear mark, sex and date of birth (first row); line and strain/background (second row); genotype data (third row) and mouse comment (fourth row). Back side (right part): the top row contains room, rack and cage number as well as a bar code representation (Code39) of the cage number. Mouse-specific columns contain bar code representations (ITF) of the mouse ID as well as the mouse ID as text together with sex and ear mark in the left column. In the right column, the origin (orig) of a mouse is denoted as 'M' (mating) or 'I' (import), followed by the respective mating or import ID. When originating from a mating, father (fa) and mother (mo) IDs are printed. The mother ID is followed by '+' when more than one mother is assigned.
Figure 12
Figure 12
Rack view. Top table: the rack overview contains general information about rack capacity, cages in use, free cage slots and total mice in the rack. Bottom table: this table lists every cage currently in the rack. Cages can be viewed in expanded mode (cages 0002, 0109 and 0522 in this example) or in condensed mode, which is the default. In expanded mode, every mouse together with basic data (ID, ear mark, sex, date of birth, genotype, strain, line and comment) is displayed in a row. The background color of the mouse rows is sex-specific (blue: male; pink: female). Individual mice can be selected from all expanded cages via checkbox (second column) or moved to another cage (third column from the right). In condensed mode, only cage summary information (number of mice per sex, strain and line) is displayed. The whole cage can be moved to another rack (third column from the right), or a cage card can be printed. The background color of the cage rows is sex-specific (blue: male; pink: female; yellow: mixed cages).
Figure 13
Figure 13
Ancestor table. A pseudo-graphic, table-based view shows the ancestors of a given mouse (leftmost column). For every mouse, father and mother are displayed together with their ID and genotype.
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