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

Good BM, Kawas EA, Kuo BY, Wilkinson MD - BMC Bioinformatics (2006)

Bottom Line: 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.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.

View Article: PubMed Central - HTML - PubMed

Affiliation: The James Hogg iCAPTURE Centre for Cardiovascular and Pulmonary Research, Providence Health Care/University of British Columbia, St, Paul's Hospital, Rm, 166, 1081 Burrard St, Vancouver, British Columbia, V6Z 1Y6, Canada. goodb@interchange.ubc.ca

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.

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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.
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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.

Mentions: The iHOPerator script produces tag clouds based either on MESH keywords from the abstracts associated with a gene or from other genes that iHOP identifies as interacting with a gene. For example, (Figure 2) shows a tag cloud generated using MESH terms gathered from abstracts associated with the gene Brca1 and (Figure 3) shows a tag cloud composed of genes related to Brca1. In both clouds, the size of each tag is used to display the frequency of occurrence of that tag (gene or keyword) in the context of abstracts associated with Brca1 and colour is used to highlight the impact factor of the journals in which the tags appear. From the user's perspective, these tag clouds appear to be embedded directly within the iHOP Web page (Figure 4).


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

Good BM, Kawas EA, Kuo BY, Wilkinson MD - BMC Bioinformatics (2006)

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.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC1764905&req=5

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.
Mentions: The iHOPerator script produces tag clouds based either on MESH keywords from the abstracts associated with a gene or from other genes that iHOP identifies as interacting with a gene. For example, (Figure 2) shows a tag cloud generated using MESH terms gathered from abstracts associated with the gene Brca1 and (Figure 3) shows a tag cloud composed of genes related to Brca1. In both clouds, the size of each tag is used to display the frequency of occurrence of that tag (gene or keyword) in the context of abstracts associated with Brca1 and colour is used to highlight the impact factor of the journals in which the tags appear. From the user's perspective, these tag clouds appear to be embedded directly within the iHOP Web page (Figure 4).

Bottom Line: 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.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.

View Article: PubMed Central - HTML - PubMed

Affiliation: The James Hogg iCAPTURE Centre for Cardiovascular and Pulmonary Research, Providence Health Care/University of British Columbia, St, Paul's Hospital, Rm, 166, 1081 Burrard St, Vancouver, British Columbia, V6Z 1Y6, Canada. goodb@interchange.ubc.ca

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.

Show MeSH