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BioGPS: an extensible and customizable portal for querying and organizing gene annotation resources.

Wu C, Orozco C, Boyer J, Leglise M, Goodale J, Batalov S, Hodge CL, Haase J, Janes J, Huss JW, Su AI - Genome Biol. (2009)

Bottom Line: Online gene annotation resources are indispensable for analysis of genomics data.However, the landscape of these online resources is highly fragmented, and scientists often visit dozens of these sites for each gene in a candidate gene list.Moreover, BioGPS embraces the principle of community intelligence, enabling any user to easily and directly contribute to the BioGPS platform.

View Article: PubMed Central - HTML - PubMed

Affiliation: Genomics Institute of the Novartis Research Foundation, 10675 John Jay Hopkins Dr, San Diego, CA 92121, USA. cwu@gnf.org

ABSTRACT
Online gene annotation resources are indispensable for analysis of genomics data. However, the landscape of these online resources is highly fragmented, and scientists often visit dozens of these sites for each gene in a candidate gene list. Here, we introduce BioGPS http://biogps.gnf.org, a centralized gene portal for aggregating distributed gene annotation resources. Moreover, BioGPS embraces the principle of community intelligence, enabling any user to easily and directly contribute to the BioGPS platform.

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Schematic representation of BioGPS. In step 1, the user loads the BioGPS site in a web browser and inputs a query (here, 'CDK2'). In step 2, the web browser transmits the query to the BioGPS server. In step 3, BioGPS resolves the query into a gene entity, and returns fully formed URLs for plugins in the plugin library. In step 4, the user's web browser retrieves content from the plugin providers for the gene of interest and renders it within the customizable BioGPS layout.
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Figure 1: Schematic representation of BioGPS. In step 1, the user loads the BioGPS site in a web browser and inputs a query (here, 'CDK2'). In step 2, the web browser transmits the query to the BioGPS server. In step 3, BioGPS resolves the query into a gene entity, and returns fully formed URLs for plugins in the plugin library. In step 4, the user's web browser retrieves content from the plugin providers for the gene of interest and renders it within the customizable BioGPS layout.

Mentions: Using simple HTML interfaces, BioGPS interacts with users and third-party plugin providers according to the outline in Figure 1. BioGPS maintains a plugin library that stores a 'Uniform Resource Locator (URL) template' for each registered plugin. This URL template indicates the basic syntax by which the external plugin server can be accessed and the type of gene identifier (for example, Entrez Gene, Ensembl, RefSeq) the plugin server will accept. When a user then queries BioGPS for a particular gene of interest, BioGPS resolves the user query to a canonical gene entity, translates that gene into all possible external identifiers, and then converts each plugin URL template into an actual website address. Those web site addresses are then passed back to be rendered in the user's browser as detailed in the next section. This design mirrors a traditional star schema in database warehouse design, where BioGPS serves as the fact table and where the dimension tables are distributed across many third-party servers [19]. This simple HTML-based data sharing mechanism allows most existing online tools to be easily integrated as BioGPS plugins, and it also allows new resources to be packaged as BioGPS plugins with minimal additional effort.


BioGPS: an extensible and customizable portal for querying and organizing gene annotation resources.

Wu C, Orozco C, Boyer J, Leglise M, Goodale J, Batalov S, Hodge CL, Haase J, Janes J, Huss JW, Su AI - Genome Biol. (2009)

Schematic representation of BioGPS. In step 1, the user loads the BioGPS site in a web browser and inputs a query (here, 'CDK2'). In step 2, the web browser transmits the query to the BioGPS server. In step 3, BioGPS resolves the query into a gene entity, and returns fully formed URLs for plugins in the plugin library. In step 4, the user's web browser retrieves content from the plugin providers for the gene of interest and renders it within the customizable BioGPS layout.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3091323&req=5

Figure 1: Schematic representation of BioGPS. In step 1, the user loads the BioGPS site in a web browser and inputs a query (here, 'CDK2'). In step 2, the web browser transmits the query to the BioGPS server. In step 3, BioGPS resolves the query into a gene entity, and returns fully formed URLs for plugins in the plugin library. In step 4, the user's web browser retrieves content from the plugin providers for the gene of interest and renders it within the customizable BioGPS layout.
Mentions: Using simple HTML interfaces, BioGPS interacts with users and third-party plugin providers according to the outline in Figure 1. BioGPS maintains a plugin library that stores a 'Uniform Resource Locator (URL) template' for each registered plugin. This URL template indicates the basic syntax by which the external plugin server can be accessed and the type of gene identifier (for example, Entrez Gene, Ensembl, RefSeq) the plugin server will accept. When a user then queries BioGPS for a particular gene of interest, BioGPS resolves the user query to a canonical gene entity, translates that gene into all possible external identifiers, and then converts each plugin URL template into an actual website address. Those web site addresses are then passed back to be rendered in the user's browser as detailed in the next section. This design mirrors a traditional star schema in database warehouse design, where BioGPS serves as the fact table and where the dimension tables are distributed across many third-party servers [19]. This simple HTML-based data sharing mechanism allows most existing online tools to be easily integrated as BioGPS plugins, and it also allows new resources to be packaged as BioGPS plugins with minimal additional effort.

Bottom Line: Online gene annotation resources are indispensable for analysis of genomics data.However, the landscape of these online resources is highly fragmented, and scientists often visit dozens of these sites for each gene in a candidate gene list.Moreover, BioGPS embraces the principle of community intelligence, enabling any user to easily and directly contribute to the BioGPS platform.

View Article: PubMed Central - HTML - PubMed

Affiliation: Genomics Institute of the Novartis Research Foundation, 10675 John Jay Hopkins Dr, San Diego, CA 92121, USA. cwu@gnf.org

ABSTRACT
Online gene annotation resources are indispensable for analysis of genomics data. However, the landscape of these online resources is highly fragmented, and scientists often visit dozens of these sites for each gene in a candidate gene list. Here, we introduce BioGPS http://biogps.gnf.org, a centralized gene portal for aggregating distributed gene annotation resources. Moreover, BioGPS embraces the principle of community intelligence, enabling any user to easily and directly contribute to the BioGPS platform.

Show MeSH