Skip to main page content
Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
, 9 (6), R102

GMODWeb: A Web Framework for the Generic Model Organism Database


GMODWeb: A Web Framework for the Generic Model Organism Database

Brian D O'Connor et al. Genome Biol.


The Generic Model Organism Database (GMOD) initiative provides species-agnostic data models and software tools for representing curated model organism data. Here we describe GMODWeb, a GMOD project designed to speed the development of model organism database (MOD) websites. Sites created with GMODWeb provide integration with other GMOD tools and allow users to browse and search through a variety of data types. GMODWeb was built using the open source Turnkey web framework and is available from


Figure 1
Figure 1
Relationship between GMODWeb and Turnkey. GMODWeb is the result of customizations to a Turnkey website built with the Chado schema. The GMODWeb skin was the product of modifications mainly to the view layer. This included changes to the template view layer, including overriding default templates and CSS changes. Enhancements were also performed with layout changes through controller XML file modifications.
Figure 2
Figure 2
Turnkey::Generate and Turnkey::Render processes. (a) The process of creating a Turnkey-based website via Turnkey::Generate is shown. A SQL schema file is processed using SQL::Translator to create a directed graph representation of the relationships between tables. These are used by Turnkey::Generate to create an MVC-based web application. (b) The rendering of a Turnkey page by Turnkey::Render is shown. When a client request is received an XML document describing the relationships between objects is consulted. Model objects are created and combined with templates by the atom controller layer to produce a rendered page. This is returned to the client.
Figure 3
Figure 3
GMODWeb-built ParameciumDB website. An example gene feature rendered with the customized ParameciumDB skin.

Similar articles

See all similar articles

Cited by 16 PubMed Central articles

See all "Cited by" articles


    1. Grumbling G, Strelets V. FlyBase: anatomical data, images and queries. Nucleic Acids Res. 2006;34:D484–488. doi: 10.1093/nar/gkj068. - DOI - PMC - PubMed
    1. Flybase
    1. Schwarz E, Antoshechkin I, Bastiani C, Bieri T, Blasiar D, Canaran P, Chan J, Chen N, Chen W, Davis P, Fiedler T, Girard L, Harris T, Kenny E, Kishore R, Lawson D, Lee R, Mueller H, Nakamura C, Ozersky P, Petcherski A, Rogers A, Spooner W, Tuli M, Van Auken K, Wang D, Durbin R, Spieth J, Stein L, Sternberg P. WormBase: better software, richer content. Nucleic Acids Res. 2006;34:D475–D478. doi: 10.1093/nar/gkj061. - DOI - PMC - PubMed
    1. Wormbase
    1. Blake J, Eppig J, Bult C, Kadin J, Richardson J. The Mouse Genome Database (MGD): updates and enhancements. Nucleic Acids Res. 2006;34:D562–D567. doi: 10.1093/nar/gkj085. - DOI - PMC - PubMed

Publication types

LinkOut - more resources