Bioinformatics Advance Access originally published online on January 18, 2005
Bioinformatics 2005 21(9):2126-2127; doi:10.1093/bioinformatics/bti271
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IntegratedMap: a Web interface for integrating genetic map data
Center for Applied Genetic Technologies, University of Georgia 111 Riverbend Road, Athens, GA 30602, USA
*To whom correspondence should be addressed.
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Abstract |
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Summary: IntegratedMap is a Web application and database schema for storing and interactively displaying genetic map data. Its Web interface includes a menu for direct chromosome/linkage group selection, a search form for selection based on mapped object location and linkage group displays. An overview display provides convenient access to the full range of mapped and anchored object types with genetic locus details, such as numbers, types and names of mapped/anchored objects displayed in a compact scrollable list box that automatically updates based on selected map location and object type. Also, multilinkage group and localized map views are available along with links that can be configured for integration with other Web resources.
Availability: IntegratedMap is implemented in C#/ASP.NET and the package, including a MySQL schema creation script, is available from http://cggc.agtec.uga.edu/Data/download.asp
Contact: agingle{at}uga.edu
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INTRODUCTION |
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IntegratedMap was initially developed as a component of the CGGC resource for sorghum (http://cggc.agtec.uga.edu) and was motivated by the need for a Web interface that would provide both an overview of a high-density genetic map and serve as a portal to other Web resources for sorghum data. It was developed in an environment that benefited from collaboration with practical genetic mappers developing a high-density genetic map for sorghum (Bowers et al., 2003) where, e.g. a Centimorgan bin frequently contained >10 mapped or anchored objects. Therefore, we developed a dynamic image map based interface that provides the genetic map overview in a compact display with graphical user interface components, e.g. scrollable list boxes for mapped probes, polymorphisms and anchored BAC contigs. This approach has led to the development of a MySQL compatible Web application that provides a compact map overview and facilitates focused queries based on map location, mapped or anchored object and object type. Like its CGGC counterpart, the application can also be configured to serve as a portal to other Web resources with the configuration details described in the last section of the associated installation document (ftp://cggc.agtec.uga.edu/IntegratedMap/readme.pdf).
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DESCRIPTION |
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IntegratedMap is a Web application that dynamically presents genetic map data that is stored in a MySQL relational database (RDBMS) schema. In its design, we employed both top-down and bottom-up approaches for organizing and displaying genetic map data. The top-down approach involves assembling mapped objects into a compact single linkage group display ordered by map location to address user queries based on map location. The display provides information about mapped or anchored objects such as probes, BAC-contigs and polymorphism for the specified chromosome/linkage group. The focus of the bottom-up approach is on the attributes and characteristics of individual map objects and is designed to address user queries based on specified map objects as well as their association with particular chromosomes/linkage groups.
The application contains three display components: a single linkage group display (SLGD), a multiple linkage group display (MLGD) and a detailed regional map display (DRMD). In addition, it contains a menu for linkage group/chromosome selection and a search form that allows users to do fuzzy matching searches on partial object names.
The SLGD, an implementation of our top-down approach, provides the functionality for browsing a single chromosome/linkage group's mapped or associated objects based on map location. The resolution constraints of currently available display devices limit the amount of detailed information that can be displayed in a whole linkage group format. Our SLGD circumvents this through selective display of map objects by location. They are presented in a series of horizontal rows that contain links and summary statistical information for the associated map location bin (Fig. 1, SLGD). Selecting a particular row in the SLGD window launches a scrollable list of the associated objects with multiple hyperlinks, appearing as squares adjacent to the object names. These hyperlinks and their associated popups are user configurable via database updates that are described in the installation package documentation (ftp://cggc.agtec.uga.edu/IntegratedMap/readme.pdf). The MLGD component, an implementation of the bottom-up approach, provides visualization of multiple linkage groups to accommodate objects that are mapped to or associated with more than one linkage group (Fig. 1, MLGD). It highlights the object's multiple linkage group map locations in a single display frame and, thereby, provides a useful combination of object specificity and comparative information for the associated linkage groups. The DRMD facilitates the exploration of a specific map region in detail. Given a locus, the region centered at the locus, will be displayed in a zoomed frame (Fig. 1, DRMD). The number and the type of map objects in the region are shown as a series of horizontal rows in the frame. The object names, associated with configurable links, can be retrieved by mouse clicks on the row of interest.
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There are two ways in which a user can enter the application based on the focus of their research questions. A user who is interested in a particular linkage group will begin by selecting the linkage group of interest from the application's menu and navigate through the SLGD location bins; picking a region for exploration of mapped objects. However, a user who is interested in a particular object (e.g. probe or BAC-contig) and wants to study detailed regions in its associated linkage groups will begin with the application's search page where they can either type the object name or select it from a list.
IntegratedMap is an ASP.NET (Microsoft) Web application and is compatible with the Windows Internet Information Server (IIS). The genome map images are generated, on the fly, as bitmap objects using the .NET Framework's drawing classes and the interactive features of the interface are implemented using classic HTML image maps. It is a data-driven application and the downloadable version is compatible with a MySQL RDBMS back-end. The associated schema contains tables to accommodate map locations and information for anchored BAC-contigs, mapped probes and polymorphisms as well as for genome and map information. Detailed information is available in the installation package readme file.
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Acknowledgments |
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The authors wish to thank the collaborating labs for providing data and advice. We are grateful to the National Science Foundation, the United States Department of Agriculture, the Georgia Research Alliance, the National Grain Sorghum Producers and the University of Georgia Research Foundation for financial support.
Received on June 25, 2004; revised on December 15, 2004; accepted on January 10, 2005
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REFERENCE |
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TOPAbstractINTRODUCTIONDESCRIPTIONREFERENCE |
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Bowers, J.E., Abbey, C., Anderson, S., Chang, C., Draye, X., Hoppe, A.H., Jessup, R., Lemke, C., Lennington, J., Li, Z., et al. (2003) A high-density genetic recombination map of sequence-tagged sites for sorghum, as a framework for comparative structural and evolutionary genomics of tropical grains and grasses. Genetics, 165, 367–386
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