iHOPerator: user-scripting a personalized bioinformatics Web, starting with the iHOP website

Abstract

Background: User-scripts are programs stored in Web browsers that can manipulate the content of websites prior to display in the browser. They provide a novel mechanism by which users can conveniently gain increased control over the content and the display of the information presented to them on the Web. As the Web is the primary medium by which scientists retrieve biological information, any improvements in the mechanisms that govern the utility or accessibility of this information may have profound effects. GreaseMonkey is a Mozilla Firefox extension that facilitates the development and deployment of user-scripts for the Firefox web-browser. We utilize this to enhance the content and the presentation of the iHOP (information Hyperlinked Over Proteins) website.

Results: The iHOPerator is a GreaseMonkey user-script that augments the gene-centred pages on iHOP by providing a compact, configurable visualization of the defining information for each gene and by enabling additional data, such as biochemical pathway diagrams, to be collected automatically from third party resources and displayed in the same browsing context.

Conclusion: This open-source script provides an extension to the iHOP website, demonstrating how user-scripts can personalize and enhance the Web browsing experience in a relevant biological setting. The novel, user-driven controls over the content and the display of Web resources made possible by user-scripts, such as the iHOPerator, herald the beginning of a transition from a resource-centric to a user-centric Web experience. We believe that this transition is a necessary step in the development of Web technology that will eventually result in profound improvements in the way life scientists interact with information.

Figure 1

Default iHOP page displaying the defining information for VEGF. The default iHOP gene-focused Web page without the enhancements provided by the iHOPerator script. The page is displaying the defining information for the gene VEGF. The top of the page displays alternate names while the bottom (extending well past the area that can be displayed in the figure) provides extractions from the text of abstracts associated with the gene.

Figure 2

A tag cloud built from MESH terms associated with Brca1. This tag cloud was built automatically using the iHOPerator user-script. It is composed of MESH terms extracted from abstracts associated with the gene Brca1 (in mouse). Colour (redness) correlates with the impact factor of the journals where the term occurs. Size correlates with the number of times the term occurs in association with the gene – in this case Brca1.

Figure 3

A tag cloud built from genes related to Brca1. This tag cloud was built automatically using the iHOPerator user-script. It is composed of gene names extracted from abstracts associated with the gene Brca1 (in mouse). Colour (redness) correlates with the impact factor of the journals where the gene name occurs. Size correlates with the number of times the related gene name occurs in association with the gene in question – in this case Brca1.

Figure 4

The iHOP webpage enhanced by the iHOPerator user-script. The iHOP webpage after it has been enhanced with the iHOPerator user-script. Compare with Figure 1. The Web page now includes a tag cloud composed of MESH terms from abstracts associated with the gene Brca1 in mouse as well as a panel of controls for manipulating the new visualization. The number of terms used to build the cloud, the scale of the fonts used, the presence or absence of the cloud on the page, and the actions taken when the user clicks on an element of the cloud are all under the user's control.

Figure 5

The iHOP webpage for IRF-3, enhanced with a tag cloud and a pathway diagram using the iHOPerator user-script. The iHOPerator user-script is shown providing access to a KEGG pathway diagram containing the gene IRF-3 within the context of the iHOP website. The diagram was retrieved as a result of a mouse-click on 'IRF-3' in the tag cloud.