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. 2019 Aug 28;10:1050.
doi: 10.3389/fpls.2019.01050. eCollection 2019.

MaizeDIG: Maize Database of Images and Genomes

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Free PMC article

MaizeDIG: Maize Database of Images and Genomes

Kyoung Tak Cho et al. Front Plant Sci. .
Free PMC article

Abstract

Background: An organism can be described by its observable features (phenotypes) and the genes and genomic information (genotypes) that cause these phenotypes. For many decades, researchers have tried to find relationships between genotypes and phenotypes, and great strides have been made. However, improved methods and tools for discovering and visualizing these phenotypic relationships are still needed. The maize genetics and genomics database (MaizeGDB, www.maizegdb.org) provides an array of useful resources for diverse data types including thousands of images related to mutant phenotypes in Zea mays ssp. mays (maize). To integrate mutant phenotype images with genomics information, we implemented and enhanced the web-based software package BioDIG (Biological Database of Images and Genomes). Findings: We developed a genotype-phenotype database for maize called MaizeDIG. MaizeDIG has several enhancements over the original BioDIG package. MaizeDIG, which supports multiple reference genome assemblies, is seamlessly integrated with genome browsers to accommodate custom tracks showing tagged mutant phenotypes images in their genomic context and allows for custom tagging of images to highlight the phenotype. This is accomplished through an updated interface allowing users to create image-to-gene links and is accessible via the image search tool. Conclusions: We have created a user-friendly and extensible web-based resource called MaizeDIG. MaizeDIG is preloaded with 2,396 images that are available on genome browsers for 10 different maize reference genomes. Approximately 90 images of classically defined maize genes have been manually annotated. MaizeDIG is available at http://maizedig.maizegdb.org/. The code is free and open source and can be found at https://github.com/Maize-Genetics-and-Genomics-Database/maizedig.

Keywords: BioDIG; MaizeDIG; MaizeGDB; QTL; gene model; genes; phenotype.

Figures

Figure 1
Figure 1
Structure of MaizeDIG. MaizeDIG’s structure is divided into four major components: data handling, image curation, image search, and genome browser integration.
Figure 2
Figure 2
Database structure of MaizeDIG. This image shows the database schema for the five major database tables used in MaizeDIG.
Figure 3
Figure 3
Maize curators workbench. A screenshot of the MaizeDIG Curators Workbench is shown with and image displaying the bronze2 (bz2) kernel phenotype segregating on a maize ear. Tools for image tagging, curation, and linking to the MaizeGDB Genome Browser can be accessed on the toolbar directly above the image. Mousing over each of the five tools activates a pull-down menu with a variety of options. The “Tagging Tools” pop-up that allows a user to add a tag to an existing tag group is shown. The collapsible vertical tool bar to the left of the image allows MaizeGDB curators to review their search history and recently viewed images as well their tags and tag groups. In the upper right-hand corner is a search box that allows curators to search over 2,300 images by Image Description (ID), Image Notes (IN), Gene Name (GN), Gene Symbol (GS), and Gene ID (GI). To the right of the image is the preloaded image description, Gene ID, Symbol, and Name as well as the Image ID. The phenotypic description as it will appear on the genome browser pop-up (minus the curator attribution) appears in the Notes section. The Gene Links information appears at the bottom once a successful gene link has been made between an image tag on the workbench and the genome browser.
Figure 4
Figure 4
MaizeDIG on the MaizeGDB Genome Browser. A screenshot of the MaizeDIG curated bronze2 (bz2) image and how it presents in the context of the MaizeGDB Genome Browser is shown. Mousing over any of the MaizeDIG images activates an image pop-up, while clicking on the image takes you to a webpage with a full screen image and phenotypic description. The majority of images in MaizeDIG are high-resolution and present well as a full screen image. Manually curated images have a red banner and are automatically sorted to the top of the image stock, while unannotated images have a green banner and are shown below. Note the multiple images shown for bz2. Some phenotypes may only have one image, while other phenotypes may have ten or more.

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