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. 2011 Jan;39(Database issue):D1149-55.
doi: 10.1093/nar/gkq866. Epub 2010 Oct 8.

The Sol Genomics Network (solgenomics.net): Growing Tomatoes Using Perl

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Free PMC article

The Sol Genomics Network (solgenomics.net): Growing Tomatoes Using Perl

Aureliano Bombarely et al. Nucleic Acids Res. .
Free PMC article

Abstract

The Sol Genomics Network (SGN; http://solgenomics.net/) is a clade-oriented database (COD) containing biological data for species in the Solanaceae and their close relatives, with data types ranging from chromosomes and genes to phenotypes and accessions. SGN hosts several genome maps and sequences, including a pre-release of the tomato (Solanum lycopersicum cv Heinz 1706) reference genome. A new transcriptome component has been added to store RNA-seq and microarray data. SGN is also an open source software project, continuously developing and improving a complex system for storing, integrating and analyzing data. All code and development work is publicly visible on GitHub (http://github.com). The database architecture combines SGN-specific schemas and the community-developed Chado schema (http://gmod.org/wiki/Chado) for compatibility with other genome databases. The SGN curation model is community-driven, allowing researchers to add and edit information using simple web tools. Currently, over a hundred community annotators help curate the database. SGN can be accessed at http://solgenomics.net/.

Figures

Figure 1.
Figure 1.
The home page of the SGN. The home page is the main entry page, providing quick access to resources through graphical menus. Every SGN page consistently contains the same toolbar at the top with pull-down menus and links to login and help pages. On the lower part of the home page, the news and events sections keep the community informed and certain elements of the database are highlighted in different feature topics, such as a ‘locus of the week’. Links to other important resources are also provided.
Figure 2.
Figure 2.
SGN data type relationship diagram, in which the locus data type is a central node, from which most data on SGN data can be accessed with a few clicks. Other important data types include sequences and phenotypes.
Figure 3.
Figure 3.
SGN system architecture diagram. SGN is a three-tiered system, consisting of a front-end web interface, back-end code and a data store, which includes both files and a relational database. For example, the GEM component is composed of Javascript and Mason components to create the user-facing web interface, DBIx::Class-based Perl modules to manipulate and model the data and a relational database schema for storage.

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